Hugo_Symbol	Entrez_Gene_Id	Center	NCBI_Build	Chromosome	Start_position	End_position	Strand	Variant_Classification	Variant_Type	Reference_Allele	Tumor_Seq_Allele1	Tumor_Seq_Allele2	dbSNP_RS	dbSNP_Val_Status	Tumor_Sample_Barcode	Matched_Norm_Sample_Barcode	Match_Norm_Seq_Allele1	Match_Norm_Seq_Allele2	Tumor_Validation_Allele1	Tumor_Validation_Allele2	Match_Norm_Validation_Allele1	Match_Norm_Validation_Allele2	Verification_Status	Validation_Status	Mutation_Status	Sequencing_Phase	Sequence_Source	Validation_Method	Score	BAM_file	Sequencer	Tumor_Sample_UUID	Matched_Norm_Sample_UUID	Genome_Change	Annotation_Transcript	Transcript_Strand	Transcript_Exon	Transcript_Position	cDNA_Change	Codon_Change	Protein_Change	Other_Transcripts	Refseq_mRNA_Id	Refseq_prot_Id	SwissProt_acc_Id	SwissProt_entry_Id	Description	UniProt_AApos	UniProt_Region	UniProt_Site	UniProt_Natural_Variations	UniProt_Experimental_Info	GO_Biological_Process	GO_Cellular_Component	GO_Molecular_Function	COSMIC_overlapping_mutations	COSMIC_fusion_genes	COSMIC_tissue_types_affected	COSMIC_total_alterations_in_gene	Tumorscape_Amplification_Peaks	Tumorscape_Deletion_Peaks	TCGAscape_Amplification_Peaks	TCGAscape_Deletion_Peaks	DrugBank	ref_context	gc_content	CCLE_ONCOMAP_overlapping_mutations	CCLE_ONCOMAP_total_mutations_in_gene	CGC_Mutation_Type	CGC_Translocation_Partner	CGC_Tumor_Types_Somatic	CGC_Tumor_Types_Germline	CGC_Other_Diseases	DNARepairGenes_Role	FamilialCancerDatabase_Syndromes	MUTSIG_Published_Results	OREGANNO_ID	OREGANNO_Values	t_alt_count	t_ref_count	validation_status	validation_method	validation_tumor_sample	validation_alt_allele	filter
PRAMEF2	65122	broad.mit.edu	37	1	12920019	12920019	+	Silent	SNP	A	T	T			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr1:12920019A>T	uc001aum.1	+	3	846	c.759A>T	c.(757-759)GGA>GGT	p.G253G		NM_023014	NP_075390	O60811	PRAM2_HUMAN	PRAME family member 2	253											0	Ovarian(185;0.249)	Renal(390;0.000469)|Lung NSC(185;0.00143)|all_lung(284;0.00181)|Colorectal(325;0.00215)|Breast(348;0.00224)|Myeloproliferative disorder(586;0.0393)|Hepatocellular(190;0.0623)|Ovarian(437;0.0731)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00812)|Colorectal(212;2.4e-06)|Kidney(185;4.89e-05)|COAD - Colon adenocarcinoma(227;0.000152)|KIRC - Kidney renal clear cell carcinoma(229;0.000194)|BRCA - Breast invasive adenocarcinoma(304;0.000293)|STAD - Stomach adenocarcinoma(313;0.0072)|READ - Rectum adenocarcinoma(331;0.0649)		AACTCGAGGGATGGTTAGTCA	0.438													19	58	---	---	---	---	PASS
CASP9	842	broad.mit.edu	37	1	15844829	15844829	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr1:15844829C>A	uc001awn.2	-	2	289	c.194G>T	c.(193-195)CGA>CTA	p.R65L	CASP9_uc001awm.1_Missense_Mutation_p.R65L|CASP9_uc001awo.2_Missense_Mutation_p.R65L|CASP9_uc001awp.2_5'UTR|CASP9_uc009voi.2_5'UTR|CASP9_uc010obm.1_5'UTR|CASP9_uc001awq.2_5'UTR	NM_001229	NP_001220	P55211	CASP9_HUMAN	caspase 9 isoform alpha preproprotein	65	CARD.				activation of caspase activity by cytochrome c|induction of apoptosis by intracellular signals|nerve growth factor receptor signaling pathway|phosphatidylinositol-mediated signaling	cytosol	cysteine-type endopeptidase activity|enzyme activator activity|protein binding			central_nervous_system(1)|kidney(1)	2		Breast(348;0.000207)|all_lung(284;0.000211)|Colorectal(325;0.000259)|Lung NSC(340;0.000269)|Renal(390;0.000518)|Ovarian(437;0.0129)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;8.49e-07)|COAD - Colon adenocarcinoma(227;4.36e-05)|BRCA - Breast invasive adenocarcinoma(304;0.00013)|KIRC - Kidney renal clear cell carcinoma(229;0.00258)|STAD - Stomach adenocarcinoma(313;0.00763)|READ - Rectum adenocarcinoma(331;0.0655)		CTGACTCCCTCGAGTCTCCAG	0.527													4	83	---	---	---	---	PASS
SDC3	9672	broad.mit.edu	37	1	31349950	31349950	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr1:31349950C>A	uc001bse.2	-	3	366	c.319G>T	c.(319-321)GTG>TTG	p.V107L	SDC3_uc001bsd.2_Missense_Mutation_p.V49L	NM_014654	NP_055469	O75056	SDC3_HUMAN	syndecan 3	107	Extracellular (Potential).					integral to membrane	cytoskeletal protein binding			ovary(1)|central_nervous_system(1)	2		Myeloproliferative disorder(586;0.0393)|Colorectal(325;0.0466)|all_neural(195;0.0966)|Ovarian(437;0.127)|Medulloblastoma(700;0.151)		STAD - Stomach adenocarcinoma(196;0.0197)|READ - Rectum adenocarcinoma(331;0.0649)		GTGGTGGACACCGCCAGGGCT	0.647													5	11	---	---	---	---	PASS
BAI2	576	broad.mit.edu	37	1	32198745	32198745	+	Splice_Site	SNP	C	A	A			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr1:32198745C>A	uc001btn.2	-	26	3807	c.3453_splice	c.e26-1	p.M1151_splice	BAI2_uc001btm.2_Splice_Site_p.M145_splice|BAI2_uc001btp.1_Splice_Site_p.M145_splice|BAI2_uc010ogn.1_Splice_Site_p.G121_splice|BAI2_uc010ogo.1_Splice_Site_p.G760_splice|BAI2_uc010ogp.1_Splice_Site_p.M1084_splice|BAI2_uc010ogq.1_Splice_Site_p.G1118_splice|BAI2_uc001bto.2_Splice_Site_p.M1151_splice	NM_001703	NP_001694	O60241	BAI2_HUMAN	brain-specific angiogenesis inhibitor 2						negative regulation of angiogenesis|neuropeptide signaling pathway	integral to membrane|plasma membrane	G-protein coupled receptor activity			lung(5)|breast(4)|ovary(2)|central_nervous_system(1)|skin(1)	13		Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0606)|all_neural(195;0.0837)|Breast(348;0.174)		STAD - Stomach adenocarcinoma(196;0.0557)		GAGTGAGGCCCTGAGGGGACA	0.642													3	3	---	---	---	---	PASS
HIVEP3	59269	broad.mit.edu	37	1	42045717	42045717	+	Missense_Mutation	SNP	T	G	G			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr1:42045717T>G	uc001cgz.3	-	4	5965	c.4752A>C	c.(4750-4752)CAA>CAC	p.Q1584H	HIVEP3_uc001cha.3_Missense_Mutation_p.Q1584H|HIVEP3_uc001cgy.2_RNA	NM_024503	NP_078779	Q5T1R4	ZEP3_HUMAN	human immunodeficiency virus type I enhancer	1584					positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	zinc ion binding			ovary(4)|large_intestine(1)|central_nervous_system(1)	6	Ovarian(52;0.00769)|all_hematologic(146;0.109)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0367)				CCGTACCTTCTTGTGACTTGG	0.488													43	31	---	---	---	---	PASS
LEPRE1	64175	broad.mit.edu	37	1	43218306	43218306	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr1:43218306G>A	uc001chv.2	-	9	1488	c.1375C>T	c.(1375-1377)CTC>TTC	p.L459F	LEPRE1_uc001chw.2_Missense_Mutation_p.L459F|LEPRE1_uc001chx.3_Missense_Mutation_p.L459F	NM_022356	NP_071751	Q32P28	P3H1_HUMAN	leprecan 1 isoform 1	459					negative regulation of cell proliferation	endoplasmic reticulum|proteinaceous extracellular matrix	iron ion binding|L-ascorbic acid binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|procollagen-proline 3-dioxygenase activity			ovary(3)|lung(1)	4	Ovarian(52;0.00744)|all_hematologic(146;0.0977)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0505)			L-Proline(DB00172)|Succinic acid(DB00139)|Vitamin C(DB00126)	TTCATGGTGAGACTGATGCCT	0.507													19	30	---	---	---	---	PASS
HECTD3	79654	broad.mit.edu	37	1	45469399	45469399	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr1:45469399C>T	uc009vxk.2	-	20	2541	c.2443G>A	c.(2443-2445)GAC>AAC	p.D815N	HECTD3_uc001cmx.3_Missense_Mutation_p.D164N|HECTD3_uc001cmy.3_Missense_Mutation_p.D425N|HECTD3_uc010olh.1_Missense_Mutation_p.D531N	NM_024602	NP_078878	Q5T447	HECD3_HUMAN	HECT domain containing 3	815	HECT.				proteasomal ubiquitin-dependent protein catabolic process|protein ubiquitination involved in ubiquitin-dependent protein catabolic process	perinuclear region of cytoplasm	ubiquitin-protein ligase activity				0	Acute lymphoblastic leukemia(166;0.155)					GGCAGCGCGTCTGTGGTCTCG	0.612													11	32	---	---	---	---	PASS
PDZK1IP1	10158	broad.mit.edu	37	1	47653062	47653062	+	Silent	SNP	G	A	A			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr1:47653062G>A	uc001cqw.2	-	2	272	c.105C>T	c.(103-105)ATC>ATT	p.I35I		NM_005764	NP_005755	Q13113	PDZ1I_HUMAN	PDZK1 interacting protein 1	35	Helical; (Potential).					integral to membrane					0						CGGCCACCGCGATAAGGCCCT	0.632													9	22	---	---	---	---	PASS
RAB3B	5865	broad.mit.edu	37	1	52442657	52442657	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr1:52442657C>T	uc001cth.2	-	2	258	c.133G>A	c.(133-135)GAC>AAC	p.D45N		NM_002867	NP_002858	P20337	RAB3B_HUMAN	RAB3B, member RAS oncogene family	45					protein transport|small GTPase mediated signal transduction	plasma membrane	GTP binding|GTPase activity			ovary(1)	1						GTGAACGTGTCATCAGCATAG	0.502													23	64	---	---	---	---	PASS
ATG4C	84938	broad.mit.edu	37	1	63270862	63270862	+	Missense_Mutation	SNP	G	C	C			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr1:63270862G>C	uc001dat.2	+	3	258	c.96G>C	c.(94-96)AAG>AAC	p.K32N	ATG4C_uc001dau.2_Missense_Mutation_p.K32N	NM_178221	NP_835739	Q96DT6	ATG4C_HUMAN	APG4 autophagy 4 homolog C isoform 8	32					autophagic vacuole assembly|protein targeting to membrane|proteolysis	cytosol|extracellular region	cysteine-type endopeptidase activity			ovary(1)	1						TGAAAACAAAGACGTATTTTA	0.254													3	11	---	---	---	---	PASS
SLC35D1	23169	broad.mit.edu	37	1	67518532	67518532	+	Silent	SNP	G	T	T			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr1:67518532G>T	uc001ddk.2	-	3	630	c.246C>A	c.(244-246)GCC>GCA	p.A82A	SLC35D1_uc010oph.1_Silent_p.A3A	NM_015139	NP_055954	Q9NTN3	S35D1_HUMAN	solute carrier family 35 (UDP-glucuronic	82	Helical; (Potential).				chondroitin sulfate biosynthetic process|UDP-glucuronate biosynthetic process|xenobiotic metabolic process	integral to endoplasmic reticulum membrane	UDP-glucuronic acid transmembrane transporter activity|UDP-N-acetylgalactosamine transmembrane transporter activity				0					Lorazepam(DB00186)	CTGCCACTGTGGCCACCATCT	0.433													5	78	---	---	---	---	PASS
OLFM3	118427	broad.mit.edu	37	1	102270309	102270309	+	Nonsense_Mutation	SNP	G	A	A			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr1:102270309G>A	uc001duf.2	-	6	993	c.922C>T	c.(922-924)CAG>TAG	p.Q308*	OLFM3_uc001dug.2_Nonsense_Mutation_p.Q288*|OLFM3_uc001duh.2_RNA|OLFM3_uc001dui.2_RNA|OLFM3_uc001duj.2_Nonsense_Mutation_p.Q213*|OLFM3_uc001due.2_RNA	NM_058170	NP_477518	Q96PB7	NOE3_HUMAN	olfactomedin 3	308	Olfactomedin-like.					extracellular region				ovary(2)|skin(1)	3		all_epithelial(167;1.87e-06)|all_lung(203;8.12e-05)|Lung NSC(277;0.000189)		all cancers(265;0.0843)|Epithelial(280;0.0921)|COAD - Colon adenocarcinoma(174;0.145)		ATATTACTCTGATACTTGTTA	0.423													17	12	---	---	---	---	PASS
NOTCH2	4853	broad.mit.edu	37	1	120464395	120464395	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr1:120464395C>A	uc001eik.2	-	29	5507	c.5251G>T	c.(5251-5253)GGT>TGT	p.G1751C		NM_024408	NP_077719	Q04721	NOTC2_HUMAN	notch 2 preproprotein	1751	Cytoplasmic (Potential).				anti-apoptosis|bone remodeling|cell cycle arrest|cell fate determination|cell growth|hemopoiesis|induction of apoptosis|negative regulation of cell proliferation|nervous system development|Notch receptor processing|Notch signaling pathway|organ morphogenesis|positive regulation of Ras protein signal transduction|regulation of transcription, DNA-dependent|stem cell maintenance|transcription, DNA-dependent	cell surface|cytosol|endoplasmic reticulum lumen|extracellular region|Golgi lumen|integral to plasma membrane|nucleoplasm	calcium ion binding|ligand-regulated transcription factor activity|protein binding|receptor activity			lung(8)|haematopoietic_and_lymphoid_tissue(7)|ovary(4)|central_nervous_system(2)|skin(2)|kidney(2)|breast(1)|prostate(1)	27	all_neural(166;0.153)	all_lung(203;1.96e-06)|Lung NSC(69;1.47e-05)|all_epithelial(167;0.000809)		Lung(183;0.0242)|LUSC - Lung squamous cell carcinoma(189;0.133)		GTTCCAGTACCAATTAGGTTA	0.398			N|F|Mis		marginal zone lymphoma|DLBCL				Alagille_Syndrome				4	44	---	---	---	---	PASS
PDE4DIP	9659	broad.mit.edu	37	1	144921868	144921868	+	Silent	SNP	T	C	C			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr1:144921868T>C	uc001elw.3	-	9	1452	c.1161A>G	c.(1159-1161)GAA>GAG	p.E387E	NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Silent_p.E453E|PDE4DIP_uc001emc.1_Silent_p.E387E|PDE4DIP_uc001emd.1_Silent_p.E387E|PDE4DIP_uc001emb.1_Silent_p.E550E|PDE4DIP_uc001eme.1_5'UTR|PDE4DIP_uc001emf.1_Silent_p.E174E	NM_014644	NP_055459	Q5VU43	MYOME_HUMAN	phosphodiesterase 4D interacting protein isoform	387	Potential.				cellular protein complex assembly	centrosome|Golgi apparatus|myofibril|nucleus	enzyme binding			ovary(4)|haematopoietic_and_lymphoid_tissue(1)	5				Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126)		CTTTCTGCTGTTCACTCTCGT	0.438			T	PDGFRB	MPD								34	233	---	---	---	---	PASS
OTUD7B	56957	broad.mit.edu	37	1	149916189	149916189	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr1:149916189C>T	uc001etn.2	-	12	2455	c.2099G>A	c.(2098-2100)CGG>CAG	p.R700Q		NM_020205	NP_064590	Q6GQQ9	OTU7B_HUMAN	zinc finger protein Cezanne	700					negative regulation of I-kappaB kinase/NF-kappaB cascade	cytoplasm|microtubule cytoskeleton|nucleus	cysteine-type peptidase activity|DNA binding|protein binding|zinc ion binding			ovary(1)|breast(1)|skin(1)	3	Breast(34;0.0009)|Ovarian(49;0.0265)|all_hematologic(923;0.0597)|Hepatocellular(266;0.161)|Colorectal(459;0.171)		LUSC - Lung squamous cell carcinoma(543;0.171)|STAD - Stomach adenocarcinoma(528;0.247)			CCCAGACGGCCGAGGGATAGT	0.642													21	16	---	---	---	---	PASS
CGN	57530	broad.mit.edu	37	1	151508751	151508751	+	Missense_Mutation	SNP	A	T	T			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr1:151508751A>T	uc009wmw.2	+	19	3380	c.3236A>T	c.(3235-3237)GAG>GTG	p.E1079V	CGN_uc010pde.1_Missense_Mutation_p.E73V	NM_020770	NP_065821	Q9P2M7	CING_HUMAN	cingulin	1073	Potential.					myosin complex|tight junction	actin binding|motor activity			ovary(2)|pancreas(1)	3	Ovarian(49;0.0273)|Hepatocellular(266;0.0997)|all_hematologic(923;0.127)|Melanoma(130;0.185)		LUSC - Lung squamous cell carcinoma(543;0.181)			CGAAAACTGGAGCGGAAAGTT	0.483													23	69	---	---	---	---	PASS
LCE1C	353133	broad.mit.edu	37	1	152777718	152777718	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr1:152777718G>T	uc001fap.1	-	2	288	c.237C>A	c.(235-237)CAC>CAA	p.H79Q		NM_178351	NP_848128	Q5T751	LCE1C_HUMAN	late cornified envelope 1C	79	Gly-rich.				keratinization						0	Lung NSC(65;9.06e-30)|Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.171)			GGCGCCTGTGGTGGCTCAGGC	0.706													23	21	---	---	---	---	PASS
NUP210L	91181	broad.mit.edu	37	1	154026870	154026870	+	Missense_Mutation	SNP	C	G	G			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr1:154026870C>G	uc001fdw.2	-	25	3389	c.3317G>C	c.(3316-3318)GGT>GCT	p.G1106A	NUP210L_uc009woq.2_Missense_Mutation_p.G15A|NUP210L_uc010peh.1_Missense_Mutation_p.G1106A	NM_207308	NP_997191	Q5VU65	P210L_HUMAN	nucleoporin 210kDa-like isoform 1	1106						integral to membrane				skin(5)|ovary(4)|large_intestine(1)|central_nervous_system(1)	11	all_lung(78;9.35e-31)|Lung NSC(65;1.33e-28)|Hepatocellular(266;0.0877)|Melanoma(130;0.128)		LUSC - Lung squamous cell carcinoma(543;0.151)|Colorectal(543;0.198)			CTGGGGGCCACCTTCAGACAT	0.448													17	29	---	---	---	---	PASS
OR6N1	128372	broad.mit.edu	37	1	158736433	158736433	+	Missense_Mutation	SNP	T	C	C			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr1:158736433T>C	uc010piq.1	-	1	40	c.40A>G	c.(40-42)ATC>GTC	p.I14V		NM_001005185	NP_001005185	Q8NGY5	OR6N1_HUMAN	olfactory receptor, family 6, subfamily N,	14	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)	1	all_hematologic(112;0.0378)					AAGCCCAAGATGATGAATTCT	0.458													15	19	---	---	---	---	PASS
KCNJ10	3766	broad.mit.edu	37	1	160011200	160011200	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr1:160011200G>T	uc001fuw.1	-	2	1273	c.1123C>A	c.(1123-1125)CGC>AGC	p.R375S		NM_002241	NP_002232	P78508	IRK10_HUMAN	potassium inwardly-rectifying channel, subfamily	375	Cytoplasmic (By similarity).					integral to plasma membrane	ATP binding|ATP-activated inward rectifier potassium channel activity			ovary(1)	1	all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.111)			TTGCTGATGCGCACACTAAGG	0.532													9	5	---	---	---	---	PASS
LMX1A	4009	broad.mit.edu	37	1	165177302	165177302	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr1:165177302G>T	uc001gcy.1	-	6	1036	c.815C>A	c.(814-816)TCT>TAT	p.S272Y	LMX1A_uc001gcz.1_Missense_Mutation_p.S272Y|LMX1A_uc001gcw.1_Translation_Start_Site|LMX1A_uc001gcx.1_Missense_Mutation_p.S23Y	NM_177398	NP_796372	Q8TE12	LMX1A_HUMAN	LIM homeobox transcription factor 1, alpha	272	Gln-rich.					nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			central_nervous_system(3)|upper_aerodigestive_tract(1)|pancreas(1)	5	all_hematologic(923;0.248)					CAGCTTACCAGAGCTCAGCCT	0.552													7	17	---	---	---	---	PASS
LMX1A	4009	broad.mit.edu	37	1	165177303	165177303	+	Missense_Mutation	SNP	A	C	C			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr1:165177303A>C	uc001gcy.1	-	6	1035	c.814T>G	c.(814-816)TCT>GCT	p.S272A	LMX1A_uc001gcz.1_Missense_Mutation_p.S272A|LMX1A_uc001gcw.1_5'UTR|LMX1A_uc001gcx.1_Missense_Mutation_p.S23A	NM_177398	NP_796372	Q8TE12	LMX1A_HUMAN	LIM homeobox transcription factor 1, alpha	272	Gln-rich.					nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			central_nervous_system(3)|upper_aerodigestive_tract(1)|pancreas(1)	5	all_hematologic(923;0.248)					AGCTTACCAGAGCTCAGCCTC	0.552													7	17	---	---	---	---	PASS
PRRX1	5396	broad.mit.edu	37	1	170689004	170689004	+	Missense_Mutation	SNP	C	G	G			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr1:170689004C>G	uc001ghf.2	+	2	426	c.379C>G	c.(379-381)CTT>GTT	p.L127V	PRRX1_uc001ghe.2_Missense_Mutation_p.L127V	NM_022716	NP_073207	P54821	PRRX1_HUMAN	paired mesoderm homeobox 1 isoform pmx-1b	127	Homeobox.					nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription coactivator activity			ovary(1)	1	all_hematologic(923;0.0922)|Acute lymphoblastic leukemia(37;0.181)					GCGAGAAGACCTTGCCCGCCG	0.552													13	39	---	---	---	---	PASS
FMO4	2329	broad.mit.edu	37	1	171310617	171310617	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr1:171310617C>T	uc001gho.2	+	10	1533	c.1316C>T	c.(1315-1317)GCC>GTC	p.A439V		NM_002022	NP_002013	P31512	FMO4_HUMAN	flavin containing monooxygenase 4	439					xenobiotic metabolic process	integral to membrane|intrinsic to endoplasmic reticulum membrane|microsome	flavin adenine dinucleotide binding|flavin-containing monooxygenase activity|NADP binding			kidney(2)|skin(1)	3	all_cancers(6;3.9e-08)|all_hematologic(923;0.088)|Acute lymphoblastic leukemia(37;0.181)					GATATCGCTGCCTGCATAGGC	0.458													8	24	---	---	---	---	PASS
RFWD2	64326	broad.mit.edu	37	1	175958605	175958605	+	Silent	SNP	G	C	C			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr1:175958605G>C	uc001gku.1	-	16	1996	c.1740C>G	c.(1738-1740)GTC>GTG	p.V580V	RFWD2_uc001gkv.1_Silent_p.V556V|RFWD2_uc001gkw.1_Silent_p.V340V|RFWD2_uc009wwv.2_Silent_p.V379V|RFWD2_uc001gkt.1_Silent_p.V419V	NM_022457	NP_071902	Q8NHY2	RFWD2_HUMAN	ring finger and WD repeat domain 2 isoform a	580	WD 4.				DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest	centrosome|cytosol|focal adhesion|nuclear speck	protein binding|ubiquitin-protein ligase activity|zinc ion binding				0						CATAGTAGTGGACACAGTGAT	0.328													10	33	---	---	---	---	PASS
KIAA1614	57710	broad.mit.edu	37	1	180886140	180886140	+	Missense_Mutation	SNP	C	A	A	rs79485039	byFrequency	TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr1:180886140C>A	uc001gok.2	+	2	968	c.901C>A	c.(901-903)CGC>AGC	p.R301S		NM_020950	NP_066001	Q5VZ46	K1614_HUMAN	hypothetical protein LOC57710	301										ovary(3)|skin(1)	4						GGAGAGAAACCGCCTGTTGCT	0.642													12	25	---	---	---	---	PASS
NCF2	4688	broad.mit.edu	37	1	183532587	183532587	+	Missense_Mutation	SNP	A	C	C			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr1:183532587A>C	uc001gqj.3	-	12	1435	c.1160T>G	c.(1159-1161)CTG>CGG	p.L387R	NCF2_uc010pod.1_Missense_Mutation_p.L342R|NCF2_uc010poe.1_Missense_Mutation_p.L306R|NCF2_uc001gqk.3_Missense_Mutation_p.L387R	NM_000433	NP_000424	P19878	NCF2_HUMAN	neutrophil cytosolic factor 2	387	OPR.				cellular defense response|innate immune response|respiratory burst|superoxide anion generation	NADPH oxidase complex|nucleolus	electron carrier activity|protein C-terminus binding			ovary(3)	3						AGTGTGTTCCAGCCGGAGCTC	0.572													52	127	---	---	---	---	PASS
PRG4	10216	broad.mit.edu	37	1	186276229	186276229	+	Missense_Mutation	SNP	A	G	G			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr1:186276229A>G	uc001gru.3	+	7	1429	c.1378A>G	c.(1378-1380)ACA>GCA	p.T460A	PRG4_uc001grt.3_Missense_Mutation_p.T419A|PRG4_uc009wyl.2_Missense_Mutation_p.T367A|PRG4_uc009wym.2_Missense_Mutation_p.T326A|PRG4_uc010poo.1_Intron	NM_005807	NP_005798	Q92954	PRG4_HUMAN	proteoglycan 4 isoform A	460	15.|59 X 8 AA repeats of K-X-P-X-P-T-T-X.				cell proliferation|immune response	extracellular region	polysaccharide binding|protein binding|scavenger receptor activity			skin(1)	1						CAAGGAGCCTACACCCACCAC	0.657													4	79	---	---	---	---	PASS
FAM5C	339479	broad.mit.edu	37	1	190250825	190250825	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr1:190250825C>A	uc001gse.1	-	3	524	c.292G>T	c.(292-294)GGC>TGC	p.G98C	FAM5C_uc010pot.1_Intron	NM_199051	NP_950252	Q76B58	FAM5C_HUMAN	family with sequence similarity 5, member C	98						extracellular region				lung(2)|ovary(1)|kidney(1)|skin(1)	5	Prostate(682;0.198)					AGAGGAGAGCCAAGGAAATTT	0.398													9	27	---	---	---	---	PASS
CSRP1	1465	broad.mit.edu	37	1	201458112	201458112	+	Missense_Mutation	SNP	T	A	A			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr1:201458112T>A	uc001gws.2	-	4	473	c.282A>T	c.(280-282)GAA>GAT	p.E94D	CSRP1_uc001gwr.1_RNA|CSRP1_uc010ppr.1_Missense_Mutation_p.E94D|CSRP1_uc010pps.1_Missense_Mutation_p.E94D	NM_004078	NP_004069	P21291	CSRP1_HUMAN	cysteine and glycine-rich protein 1 isoform 1	94						nucleus	zinc ion binding			ovary(1)	1						GGCCAGGGGCTCTGCATGGAG	0.592													6	23	---	---	---	---	PASS
IL19	29949	broad.mit.edu	37	1	207013247	207013247	+	Missense_Mutation	SNP	G	C	C			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr1:207013247G>C	uc001hep.2	+	5	1202	c.263G>C	c.(262-264)AGG>ACG	p.R88T	IL19_uc001heo.2_Missense_Mutation_p.R126T|IL19_uc010prx.1_Missense_Mutation_p.R88T	NM_013371	NP_037503	Q9UHD0	IL19_HUMAN	interleukin 19 isoform 2 precursor	88					apoptosis|immune response|signal transduction	extracellular space	cytokine activity			ovary(1)|central_nervous_system(1)	2			BRCA - Breast invasive adenocarcinoma(75;0.211)			TACGTGGACAGGGTGTTCAAG	0.468													104	210	---	---	---	---	PASS
C1orf107	27042	broad.mit.edu	37	1	210024662	210024662	+	Missense_Mutation	SNP	C	T	T	rs140967197	byFrequency	TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr1:210024662C>T	uc001hhr.1	+	12	2217	c.2141C>T	c.(2140-2142)ACG>ATG	p.T714M	C1orf107_uc009xcu.1_Missense_Mutation_p.T429M	NM_014388	NP_055203	Q68CQ4	DIEXF_HUMAN	digestive-organ expansion factor homolog	714					multicellular organismal development	nucleus					0				OV - Ovarian serous cystadenocarcinoma(81;0.0367)		GAAGAGGCCACGTGGACCTGC	0.498													7	20	---	---	---	---	PASS
RYR2	6262	broad.mit.edu	37	1	237948022	237948022	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr1:237948022C>A	uc001hyl.1	+	90	13130	c.13010C>A	c.(13009-13011)CCC>CAC	p.P4337H	RYR2_uc010pya.1_Missense_Mutation_p.P752H	NM_001035	NP_001026	Q92736	RYR2_HUMAN	cardiac muscle ryanodine receptor	4337					cardiac muscle contraction|detection of calcium ion|induction of apoptosis by ionic changes|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum|response to caffeine|response to hypoxia|response to redox state	calcium channel complex|cytosol|plasma membrane|plasma membrane enriched fraction|sarcoplasmic reticulum membrane	calcium ion binding|calmodulin binding|identical protein binding|protein kinase A catalytic subunit binding|protein kinase A regulatory subunit binding|receptor activity|ryanodine-sensitive calcium-release channel activity|suramin binding			ovary(17)|large_intestine(6)|central_nervous_system(6)|pancreas(3)|breast(1)	33	Ovarian(103;0.103)	all_cancers(173;0.000368)|Melanoma(53;0.0179)|all_epithelial(177;0.0225)	OV - Ovarian serous cystadenocarcinoma(106;0.00606)			ATGCCAGACCCCACTCAGGAT	0.552													20	51	---	---	---	---	PASS
FMN2	56776	broad.mit.edu	37	1	240370853	240370853	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr1:240370853C>T	uc010pyd.1	+	5	2966	c.2741C>T	c.(2740-2742)CCT>CTT	p.P914L	FMN2_uc010pye.1_Missense_Mutation_p.P918L	NM_020066	NP_064450	Q9NZ56	FMN2_HUMAN	formin 2	914	Pro-rich.|FH1.				actin cytoskeleton organization|establishment of meiotic spindle localization|intracellular signal transduction|meiotic chromosome movement towards spindle pole|meiotic metaphase I|multicellular organismal development|oogenesis|polar body extrusion after meiotic divisions		actin binding			ovary(4)|pancreas(3)|skin(3)|large_intestine(1)|central_nervous_system(1)	12	Ovarian(103;0.127)	all_cancers(173;0.013)	OV - Ovarian serous cystadenocarcinoma(106;0.0106)			CCTCCCCCTCCTCTTCCCGGA	0.662													15	31	---	---	---	---	PASS
NLRP3	114548	broad.mit.edu	37	1	247587725	247587725	+	Missense_Mutation	SNP	G	C	C			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr1:247587725G>C	uc001icr.2	+	5	1118	c.980G>C	c.(979-981)CGG>CCG	p.R327P	NLRP3_uc001ics.2_Missense_Mutation_p.R327P|NLRP3_uc001icu.2_Missense_Mutation_p.R327P|NLRP3_uc001icw.2_Missense_Mutation_p.R327P|NLRP3_uc001icv.2_Missense_Mutation_p.R327P|NLRP3_uc010pyw.1_Missense_Mutation_p.R325P|NLRP3_uc001ict.1_Missense_Mutation_p.R325P	NM_001079821	NP_001073289	Q96P20	NALP3_HUMAN	NLR family, pyrin domain containing 3 isoform a	327	NACHT.				detection of biotic stimulus|induction of apoptosis|inflammatory response|negative regulation of NF-kappaB import into nucleus|negative regulation of NF-kappaB transcription factor activity|positive regulation of interleukin-1 beta secretion|protein oligomerization|signal transduction	cytoplasm	ATP binding|peptidoglycan binding|protein binding	p.R327G(1)		lung(8)|skin(8)|ovary(7)|upper_aerodigestive_tract(1)|breast(1)|pancreas(1)	26	all_cancers(71;9.66e-05)|all_epithelial(71;1.85e-05)|Breast(184;0.0226)|Ovarian(71;0.0377)|all_lung(81;0.0662)|Lung NSC(105;0.0724)	all_cancers(173;0.0172)	OV - Ovarian serous cystadenocarcinoma(106;0.0141)			AAGGCCGAGCGGGGAGACATT	0.587													19	37	---	---	---	---	PASS
OR14A16	284532	broad.mit.edu	37	1	247978715	247978715	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr1:247978715G>A	uc001idm.1	-	1	317	c.317C>T	c.(316-318)GCA>GTA	p.A106V		NM_001001966	NP_001001966	Q8NHC5	O14AG_HUMAN	olfactory receptor, family 14, subfamily A,	106	Helical; Name=3; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0						CTCTGCAGATGCTGAAGAAAG	0.473													36	76	---	---	---	---	PASS
GRHL1	29841	broad.mit.edu	37	2	10101464	10101464	+	Missense_Mutation	SNP	C	G	G	rs150933141		TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr2:10101464C>G	uc002raa.2	+	4	739	c.568C>G	c.(568-570)CTC>GTC	p.L190V	GRHL1_uc002rab.2_RNA|GRHL1_uc002rad.2_Missense_Mutation_p.I26M|GRHL1_uc010yjb.1_Missense_Mutation_p.L39V	NM_198182	NP_937825	Q9NZI5	GRHL1_HUMAN	grainyhead-like 1	190					cellular lipid metabolic process|multicellular organismal development|regulation of transcription, DNA-dependent|transcription, DNA-dependent	Golgi apparatus|nucleus	DNA binding			pancreas(1)|skin(1)	2	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)			Epithelial(75;0.172)|OV - Ovarian serous cystadenocarcinoma(76;0.246)		CGATCGGAATCTCAATACTGA	0.542													37	100	---	---	---	---	PASS
BIRC6	57448	broad.mit.edu	37	2	32692709	32692709	+	Missense_Mutation	SNP	G	C	C			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr2:32692709G>C	uc010ezu.2	+	27	5607	c.5473G>C	c.(5473-5475)GAG>CAG	p.E1825Q		NM_016252	NP_057336	Q9NR09	BIRC6_HUMAN	baculoviral IAP repeat-containing 6	1825					anti-apoptosis|apoptosis	intracellular	acid-amino acid ligase activity|cysteine-type endopeptidase inhibitor activity|protein binding			ovary(5)|skin(4)|lung(2)|central_nervous_system(1)|breast(1)|pancreas(1)	14	Acute lymphoblastic leukemia(172;0.155)					ATTAGGAGAAGAGGTGGATGG	0.438													16	61	---	---	---	---	PASS
MAP4K3	8491	broad.mit.edu	37	2	39552894	39552894	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr2:39552894G>T	uc002rro.2	-	11	875	c.784C>A	c.(784-786)CCT>ACT	p.P262T	MAP4K3_uc002rrp.2_Missense_Mutation_p.P262T|MAP4K3_uc010yns.1_5'UTR	NM_003618	NP_003609	Q8IVH8	M4K3_HUMAN	mitogen-activated protein kinase kinase kinase	262	Protein kinase.				JNK cascade		ATP binding|protein binding|protein serine/threonine kinase activity|small GTPase regulator activity			ovary(3)|lung(3)|stomach(1)|pancreas(1)	8		all_hematologic(82;0.211)				TCAGCAGTAGGTCTTTTTTTC	0.249													13	44	---	---	---	---	PASS
SLC8A1	6546	broad.mit.edu	37	2	40656873	40656873	+	Missense_Mutation	SNP	A	G	G			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr2:40656873A>G	uc002rrx.2	-	1	572	c.548T>C	c.(547-549)ATT>ACT	p.I183T	SLC8A1_uc002rry.2_Missense_Mutation_p.I183T|SLC8A1_uc002rrz.2_Missense_Mutation_p.I183T|SLC8A1_uc002rsa.2_Missense_Mutation_p.I183T|SLC8A1_uc002rsd.3_Missense_Mutation_p.I183T|SLC8A1_uc002rsb.1_Missense_Mutation_p.I183T|SLC8A1_uc010fan.1_Missense_Mutation_p.I183T|SLC8A1_uc002rsc.1_Missense_Mutation_p.I183T	NM_021097	NP_066920	P32418	NAC1_HUMAN	solute carrier family 8 (sodium/calcium	183	Helical; (Potential).				cell communication|muscle contraction|platelet activation	integral to plasma membrane	calcium:sodium antiporter activity|calmodulin binding|heat shock protein binding			ovary(1)|kidney(1)|central_nervous_system(1)|skin(1)	4					Alpha-Linolenic Acid(DB00132)|Icosapent(DB00159)	ACAGAGTGCAATAATGATGAA	0.473													9	21	---	---	---	---	PASS
UGP2	7360	broad.mit.edu	37	2	64109731	64109731	+	Silent	SNP	G	A	A			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr2:64109731G>A	uc002scm.2	+	4	693	c.387G>A	c.(385-387)CTG>CTA	p.L129L	UGP2_uc002scl.2_Silent_p.L118L|UGP2_uc010ypx.1_Silent_p.L138L	NM_006759	NP_006750	Q16851	UGPA_HUMAN	UDP-glucose pyrophosphorylase 2 isoform a	129					glycogen biosynthetic process|phosphorylation|UDP-glucose metabolic process|UDP-glucuronate biosynthetic process|xenobiotic metabolic process	cytosol	metal ion binding|protein binding|UTP:glucose-1-phosphate uridylyltransferase activity				0						CTAAAAGTCTGATTGGTGTGA	0.403													28	59	---	---	---	---	PASS
ALMS1	7840	broad.mit.edu	37	2	73717648	73717648	+	Silent	SNP	A	G	G			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr2:73717648A>G	uc002sje.1	+	12	8676	c.8565A>G	c.(8563-8565)CTA>CTG	p.L2855L	ALMS1_uc002sjf.1_Silent_p.L2811L|ALMS1_uc002sjg.2_Silent_p.L2241L|ALMS1_uc002sjh.1_Silent_p.L2241L	NM_015120	NP_055935	Q8TCU4	ALMS1_HUMAN	Alstrom syndrome 1	2853					G2/M transition of mitotic cell cycle	centrosome|cilium|cytosol|microtubule basal body|spindle pole				skin(3)|ovary(2)|breast(2)|pancreas(1)|lung(1)	9						GTTCCACCCTAGGAGTAAACA	0.408													30	33	---	---	---	---	PASS
C2orf78	388960	broad.mit.edu	37	2	74041054	74041054	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr2:74041054C>A	uc002sjr.1	+	2	669	c.548C>A	c.(547-549)GCC>GAC	p.A183D		NM_001080474	NP_001073943	A6NCI8	CB078_HUMAN	hypothetical protein LOC388960	183										ovary(2)	2						TCACTATCTGCCAGCCTTGTT	0.433													15	38	---	---	---	---	PASS
SNRNP200	23020	broad.mit.edu	37	2	96952118	96952118	+	Missense_Mutation	SNP	G	C	C			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr2:96952118G>C	uc002svu.2	-	29	4020	c.3934C>G	c.(3934-3936)CTG>GTG	p.L1312V	SNRNP200_uc002svt.2_5'Flank|SNRNP200_uc010yuj.1_5'Flank|SNRNP200_uc002svv.1_5'Flank|SNRNP200_uc002svw.1_Missense_Mutation_p.L384V	NM_014014	NP_054733	O75643	U520_HUMAN	activating signal cointegrator 1 complex subunit	1312						catalytic step 2 spliceosome|nucleoplasm|U5 snRNP	ATP binding|ATP-dependent helicase activity|nucleic acid binding|protein binding			ovary(5)|skin(4)|large_intestine(1)	10						CTGTTTCTCAGAGCAGACACG	0.532													32	90	---	---	---	---	PASS
NPHP1	4867	broad.mit.edu	37	2	110886762	110886762	+	Splice_Site	SNP	C	T	T			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr2:110886762C>T	uc002tfn.3	-	18	1975	c.1881_splice	c.e18+1	p.R627_splice	NPHP1_uc002tfm.3_Splice_Site_p.R572_splice|NPHP1_uc002tfl.3_Splice_Site_p.R628_splice|NPHP1_uc002tfo.3_Splice_Site_p.R509_splice|NPHP1_uc010ywx.1_Splice_Site_p.R571_splice|NPHP1_uc010fjv.1_Splice_Site_p.R571_splice	NM_207181	NP_997064	O15259	NPHP1_HUMAN	nephrocystin 1 isoform 2						actin cytoskeleton organization|cell projection organization|cell-cell adhesion|excretion|retina development in camera-type eye|signal transduction|spermatid differentiation|visual behavior	adherens junction|cell-cell junction|cilium axoneme|cytoplasm|cytoskeleton|motile cilium|photoreceptor connecting cilium	protein binding|structural molecule activity			ovary(2)	2						ATGCTACCCACCCTGAGAGCA	0.443													9	9	---	---	---	---	PASS
MERTK	10461	broad.mit.edu	37	2	112786239	112786239	+	Missense_Mutation	SNP	G	C	C			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr2:112786239G>C	uc002thk.1	+	19	2920	c.2798G>C	c.(2797-2799)GGG>GCG	p.G933A	MERTK_uc002thl.1_Missense_Mutation_p.G757A	NM_006343	NP_006334	Q12866	MERTK_HUMAN	MER receptor tyrosine kinase precursor	933	Cytoplasmic (Potential).				cell surface receptor linked signaling pathway|cell-cell signaling|leukocyte migration	integral to plasma membrane|soluble fraction	ATP binding|transmembrane receptor protein tyrosine kinase activity			lung(6)|upper_aerodigestive_tract(1)|stomach(1)|kidney(1)	9						ATCCTGAATGGGGGCAGTGAG	0.527													21	45	---	---	---	---	PASS
DDX18	8886	broad.mit.edu	37	2	118582248	118582248	+	Missense_Mutation	SNP	T	A	A			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr2:118582248T>A	uc002tlh.1	+	8	1269	c.1170T>A	c.(1168-1170)GAT>GAA	p.D390E		NM_006773	NP_006764	Q9NVP1	DDX18_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 18	390							ATP binding|ATP-dependent RNA helicase activity|RNA binding			breast(2)|ovary(1)|lung(1)	4						GCGTTGATGATGATAAAGCGA	0.393													30	89	---	---	---	---	PASS
CNTNAP5	129684	broad.mit.edu	37	2	125261958	125261958	+	Silent	SNP	C	A	A			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr2:125261958C>A	uc002tno.2	+	8	1513	c.1149C>A	c.(1147-1149)ACC>ACA	p.T383T	CNTNAP5_uc010flu.2_Silent_p.T384T	NM_130773	NP_570129	Q8WYK1	CNTP5_HUMAN	contactin associated protein-like 5 precursor	383	Laminin G-like 2.|Extracellular (Potential).				cell adhesion|signal transduction	integral to membrane	receptor binding			ovary(10)	10				BRCA - Breast invasive adenocarcinoma(221;0.248)		TGCCCGGCACCCCCCAAATTG	0.532													18	43	---	---	---	---	PASS
PKP4	8502	broad.mit.edu	37	2	159488331	159488331	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr2:159488331C>A	uc002tzv.2	+	8	1480	c.1220C>A	c.(1219-1221)CCC>CAC	p.P407H	PKP4_uc002tzt.1_Missense_Mutation_p.P259H|PKP4_uc002tzu.2_Missense_Mutation_p.P407H|PKP4_uc002tzw.2_Missense_Mutation_p.P407H|PKP4_uc002tzx.2_Missense_Mutation_p.P65H|PKP4_uc002tzy.1_Missense_Mutation_p.P65H|PKP4_uc002tzz.1_Missense_Mutation_p.P405H|PKP4_uc002uaa.2_Missense_Mutation_p.P259H	NM_003628	NP_003619	Q99569	PKP4_HUMAN	plakophilin 4 isoform a	407					cell adhesion	desmosome	protein binding			ovary(5)|skin(2)	7						GCCGTGTCTCCCGACTTGCAC	0.502										HNSCC(62;0.18)			6	100	---	---	---	---	PASS
BAZ2B	29994	broad.mit.edu	37	2	160304825	160304825	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr2:160304825C>A	uc002uao.2	-	5	782	c.430G>T	c.(430-432)GCC>TCC	p.A144S	BAZ2B_uc002uap.2_Missense_Mutation_p.A142S|BAZ2B_uc002uas.1_Missense_Mutation_p.A81S|BAZ2B_uc002uau.1_Missense_Mutation_p.A142S|BAZ2B_uc002uaq.1_Missense_Mutation_p.A72S|BAZ2B_uc002uat.3_Missense_Mutation_p.A81S|BAZ2B_uc010fop.1_Missense_Mutation_p.A142S	NM_013450	NP_038478	Q9UIF8	BAZ2B_HUMAN	bromodomain adjacent to zinc finger domain, 2B	144					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|protein binding|zinc ion binding			ovary(3)|skin(1)	4						TGATTCTGGGCTGGGGGAGCA	0.438													28	84	---	---	---	---	PASS
SCN2A	6326	broad.mit.edu	37	2	166231463	166231463	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr2:166231463C>T	uc002udc.2	+	22	4531	c.4241C>T	c.(4240-4242)TCT>TTT	p.S1414F	SCN2A_uc002udd.2_Missense_Mutation_p.S1414F|SCN2A_uc002ude.2_Missense_Mutation_p.S1414F	NM_001040142	NP_001035232	Q99250	SCN2A_HUMAN	sodium channel, voltage-gated, type II, alpha	1414	III.				myelination	node of Ranvier|voltage-gated sodium channel complex	voltage-gated sodium channel activity			ovary(6)|breast(1)|pancreas(1)	8					Lamotrigine(DB00555)	GGATATCTGTCTCTACTTCAA	0.299													8	24	---	---	---	---	PASS
PPIG	9360	broad.mit.edu	37	2	170493060	170493060	+	Missense_Mutation	SNP	C	G	G			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr2:170493060C>G	uc002uez.2	+	14	1512	c.1292C>G	c.(1291-1293)TCT>TGT	p.S431C	PPIG_uc010fpx.2_Missense_Mutation_p.S416C|PPIG_uc010fpy.2_Missense_Mutation_p.S424C|PPIG_uc002ufb.2_Missense_Mutation_p.S431C|PPIG_uc002ufd.2_Missense_Mutation_p.S428C	NM_004792	NP_004783	Q13427	PPIG_HUMAN	peptidylprolyl isomerase G	431					protein folding|RNA splicing	nuclear matrix|nuclear speck	cyclosporin A binding|peptidyl-prolyl cis-trans isomerase activity			ovary(2)|central_nervous_system(1)	3					L-Proline(DB00172)	GACCATAAATCTAACAGCAAA	0.333													8	35	---	---	---	---	PASS
HOXD11	3237	broad.mit.edu	37	2	176973689	176973689	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr2:176973689G>A	uc002uki.2	+	2	836	c.836G>A	c.(835-837)CGC>CAC	p.R279H	HOXD11_uc010fqx.2_RNA	NM_021192	NP_067015	P31277	HXD11_HUMAN	homeobox D11	279	Homeobox.					nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity				0			OV - Ovarian serous cystadenocarcinoma(117;0.0207)|Epithelial(96;0.18)	Colorectal(32;0.0521)|READ - Rectum adenocarcinoma(9;0.0678)		TACCAGATCCGCGAACTGGAA	0.522			T	NUP98	AML								34	70	---	---	---	---	PASS
OSBPL6	114880	broad.mit.edu	37	2	179236961	179236961	+	Splice_Site	SNP	G	T	T			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr2:179236961G>T	uc002ulx.2	+	14	1773	c.1395_splice	c.e14+1	p.E465_splice	OSBPL6_uc002ulw.2_Intron|OSBPL6_uc002uly.2_Splice_Site_p.E490_splice|OSBPL6_uc010zfe.1_Splice_Site_p.E434_splice|OSBPL6_uc002ulz.2_Intron|OSBPL6_uc002uma.2_Splice_Site_p.E469_splice	NM_032523	NP_115912	Q9BZF3	OSBL6_HUMAN	oxysterol-binding protein-like protein 6 isoform						lipid transport		lipid binding			pancreas(1)	1			OV - Ovarian serous cystadenocarcinoma(117;0.00578)|Epithelial(96;0.00847)|all cancers(119;0.0335)			CCCTGATGAGGTAAGACTCAT	0.323													19	13	---	---	---	---	PASS
TTN	7273	broad.mit.edu	37	2	179437048	179437048	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr2:179437048G>T	uc010zfg.1	-	275	66331	c.66107C>A	c.(66106-66108)CCT>CAT	p.P22036H	uc002umo.2_Intron|uc002ump.1_Intron|TTN_uc010zfh.1_Missense_Mutation_p.P15731H|TTN_uc010zfi.1_Missense_Mutation_p.P15664H|TTN_uc010zfj.1_Missense_Mutation_p.P15539H	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	22963							ATP binding|nucleic acid binding|protein serine/threonine kinase activity|protein tyrosine kinase activity			ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1)	153			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			GGTTTCAGCAGGCAGCCCAAT	0.453													12	31	---	---	---	---	PASS
TTN	7273	broad.mit.edu	37	2	179458090	179458090	+	Silent	SNP	C	A	A			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr2:179458090C>A	uc010zfg.1	-	248	51365	c.51141G>T	c.(51139-51141)CTG>CTT	p.L17047L	uc002umo.2_Intron|uc002ump.1_Intron|TTN_uc010zfh.1_Silent_p.L10742L|TTN_uc010zfi.1_Silent_p.L10675L|TTN_uc010zfj.1_Silent_p.L10550L	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	17974							ATP binding|nucleic acid binding|protein serine/threonine kinase activity|protein tyrosine kinase activity			ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1)	153			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			CTCTCTTTTCCAGGATGTAGT	0.403													5	84	---	---	---	---	PASS
TTN	7273	broad.mit.edu	37	2	179650444	179650444	+	Missense_Mutation	SNP	G	A	A	rs149061352	by1000genomes	TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr2:179650444G>A	uc010zfg.1	-	15	2620	c.2396C>T	c.(2395-2397)ACG>ATG	p.T799M	TTN_uc010zfh.1_Missense_Mutation_p.T753M|TTN_uc010zfi.1_Missense_Mutation_p.T753M|TTN_uc010zfj.1_Missense_Mutation_p.T753M|TTN_uc002unb.2_Missense_Mutation_p.T799M	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	799							ATP binding|nucleic acid binding|protein serine/threonine kinase activity|protein tyrosine kinase activity	p.T753M(1)		ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1)	153			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			TAATCTTTCCGTTGTTAGATC	0.418													22	58	---	---	---	---	PASS
COL5A2	1290	broad.mit.edu	37	2	189927941	189927941	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr2:189927941C>T	uc002uqk.2	-	27	2101	c.1826G>A	c.(1825-1827)GGG>GAG	p.G609E	COL5A2_uc010frx.2_Missense_Mutation_p.G185E	NM_000393	NP_000384	P05997	CO5A2_HUMAN	alpha 2 type V collagen preproprotein	609					axon guidance|collagen fibril organization|eye morphogenesis|skin development	collagen type V	extracellular matrix structural constituent			ovary(2)	2			OV - Ovarian serous cystadenocarcinoma(117;0.0106)|Epithelial(96;0.127)			CCCGGGCTGCCCTCTGATTCC	0.527													17	48	---	---	---	---	PASS
AOX1	316	broad.mit.edu	37	2	201501692	201501692	+	Missense_Mutation	SNP	G	A	A	rs113582006	by1000genomes	TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr2:201501692G>A	uc002uvx.2	+	22	2506	c.2405G>A	c.(2404-2406)CGT>CAT	p.R802H	AOX1_uc010zhf.1_Missense_Mutation_p.R358H|AOX1_uc010fsu.2_Missense_Mutation_p.R168H	NM_001159	NP_001150	Q06278	ADO_HUMAN	aldehyde oxidase 1	802					inflammatory response|reactive oxygen species metabolic process	cytoplasm	2 iron, 2 sulfur cluster binding|aldehyde oxidase activity|flavin adenine dinucleotide binding|iron ion binding|NAD binding|xanthine dehydrogenase activity			ovary(4)|pancreas(1)|skin(1)	6					Brimonidine(DB00484)|Chlorpromazine(DB00477)|Famciclovir(DB00426)|Menadione(DB00170)|Methotrexate(DB00563)|NADH(DB00157)|Palonosetron(DB00377)|Penciclovir(DB00299)|Raloxifene(DB00481)|Zaleplon(DB00962)|Zonisamide(DB00909)	CATGTAAGGCGTGTTGGTGGA	0.443													20	42	---	---	---	---	PASS
ALS2CR8	79800	broad.mit.edu	37	2	203820411	203820411	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr2:203820411C>T	uc002uzo.2	+	7	852	c.572C>T	c.(571-573)CCC>CTC	p.P191L	ALS2CR8_uc002uzn.2_Missense_Mutation_p.P89L|ALS2CR8_uc002uzm.2_Missense_Mutation_p.P191L|ALS2CR8_uc010zhy.1_Missense_Mutation_p.P191L|ALS2CR8_uc010zhz.1_RNA|ALS2CR8_uc010ftu.1_RNA|ALS2CR8_uc010zia.1_Missense_Mutation_p.P115L|ALS2CR8_uc010zib.1_Missense_Mutation_p.P115L|ALS2CR8_uc010zic.1_Missense_Mutation_p.P103L|ALS2CR8_uc002uzp.2_Missense_Mutation_p.P191L	NM_001104586	NP_001098056	Q8N187	AL2S8_HUMAN	amyotrophic lateral sclerosis 2 (juvenile)	191										large_intestine(1)|ovary(1)	2						CTGGAAGAACCCCTTCTGGGG	0.398													7	21	---	---	---	---	PASS
C2orf24	27013	broad.mit.edu	37	2	220037441	220037441	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr2:220037441C>A	uc002vju.3	-	8	1252	c.1100G>T	c.(1099-1101)TGG>TTG	p.W367L	NHEJ1_uc002vjq.3_5'Flank|SLC23A3_uc010zkr.1_5'Flank|SLC23A3_uc010zks.1_5'Flank|SLC23A3_uc010fwb.2_5'Flank|C2orf24_uc002vjv.2_Missense_Mutation_p.W367L	NM_015680	NP_056495	Q9BV87	CNPD1_HUMAN	hypothetical protein LOC27013	367	Pro-rich.				regulation of cyclin-dependent protein kinase activity	integral to membrane	protein kinase binding				0		Renal(207;0.0915)		Epithelial(149;8.92e-07)|all cancers(144;0.000151)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		GGTATGGTACCAGGGGCTGGA	0.602													7	29	---	---	---	---	PASS
ABCB6	10058	broad.mit.edu	37	2	220077986	220077986	+	Silent	SNP	G	A	A			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr2:220077986G>A	uc002vkc.1	-	12	2059	c.1782C>T	c.(1780-1782)AAC>AAT	p.N594N	ABCB6_uc010fwe.1_Silent_p.N548N	NM_005689	NP_005680	Q9NP58	ABCB6_HUMAN	ATP-binding cassette, sub-family B, member 6	594	ABC transporter.				cadmium ion transmembrane transport|cellular iron ion homeostasis|detoxification of cadmium ion|porphyrin biosynthetic process	ATP-binding cassette (ABC) transporter complex|Golgi apparatus|integral to mitochondrial outer membrane|plasma membrane|vacuolar membrane	ATP binding|efflux transmembrane transporter activity|heme binding|heme-transporting ATPase activity			breast(1)|central_nervous_system(1)	2		Renal(207;0.0474)		Epithelial(149;1.22e-06)|all cancers(144;0.000201)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		TGAAGTGCACGTTCTCAAACT	0.542													13	39	---	---	---	---	PASS
PTPRN	5798	broad.mit.edu	37	2	220161200	220161200	+	Silent	SNP	C	T	T			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr2:220161200C>T	uc002vkz.2	-	17	2438	c.2349G>A	c.(2347-2349)ACG>ACA	p.T783T	PTPRN_uc010zlc.1_Silent_p.T693T|PTPRN_uc002vla.2_Silent_p.T754T|uc010zld.1_5'Flank|MIR153-1_hsa-mir-153-1|MI0000463_5'Flank	NM_002846	NP_002837	Q16849	PTPRN_HUMAN	protein tyrosine phosphatase, receptor type, N	783	Cytoplasmic (Potential).|Tyrosine-protein phosphatase.				response to reactive oxygen species	integral to plasma membrane	transmembrane receptor protein tyrosine phosphatase activity			ovary(2)|lung(1)|skin(1)	4		Renal(207;0.0474)		Epithelial(149;4.22e-07)|all cancers(144;8.82e-05)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)|STAD - Stomach adenocarcinoma(1183;0.0875)		GCGGGCCCTGCGTGGCTATGT	0.602													16	42	---	---	---	---	PASS
NEU2	4759	broad.mit.edu	37	2	233899524	233899524	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr2:233899524C>A	uc010zmn.1	+	2	900	c.900C>A	c.(898-900)CAC>CAA	p.H300Q		NM_005383	NP_005374	Q9Y3R4	NEUR2_HUMAN	neuraminidase 2	300							exo-alpha-sialidase activity				0		Breast(86;0.00279)|Renal(207;0.00339)|all_hematologic(139;0.0116)|all_lung(227;0.0271)|Acute lymphoblastic leukemia(138;0.0326)|Lung NSC(271;0.0839)		Epithelial(121;7.17e-17)|BRCA - Breast invasive adenocarcinoma(100;0.000311)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(119;0.00942)|GBM - Glioblastoma multiforme(43;0.0488)		ACCCCACACACTCCTGGCAGA	0.711													6	19	---	---	---	---	PASS
COL6A3	1293	broad.mit.edu	37	2	238289580	238289580	+	Silent	SNP	C	T	T			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr2:238289580C>T	uc002vwl.2	-	5	2160	c.1875G>A	c.(1873-1875)AGG>AGA	p.R625R	COL6A3_uc002vwo.2_Silent_p.R419R|COL6A3_uc010znj.1_Silent_p.R218R|COL6A3_uc002vwq.2_Silent_p.R419R|COL6A3_uc002vwr.2_Silent_p.R218R|COL6A3_uc010znk.1_Silent_p.R625R	NM_004369	NP_004360	P12111	CO6A3_HUMAN	alpha 3 type VI collagen isoform 1 precursor	625	Nonhelical region.				axon guidance|cell adhesion|muscle organ development	collagen type VI|extracellular space	serine-type endopeptidase inhibitor activity			ovary(8)|central_nervous_system(6)|skin(2)|upper_aerodigestive_tract(1)|pancreas(1)	18		Breast(86;0.000301)|Renal(207;0.000966)|all_hematologic(139;0.067)|Ovarian(221;0.0694)|all_lung(227;0.0943)|Melanoma(123;0.203)		Epithelial(121;1.23e-21)|OV - Ovarian serous cystadenocarcinoma(60;1.34e-10)|Kidney(56;5.71e-09)|KIRC - Kidney renal clear cell carcinoma(57;1.51e-07)|BRCA - Breast invasive adenocarcinoma(100;0.00025)|Lung(119;0.0142)|LUSC - Lung squamous cell carcinoma(224;0.034)		CAGAGAGGGTCCTGAGAGGTG	0.552													6	17	---	---	---	---	PASS
OR6B2	389090	broad.mit.edu	37	2	240969639	240969639	+	Nonsense_Mutation	SNP	C	A	A			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr2:240969639C>A	uc002vyr.2	-	2	254	c.208G>T	c.(208-210)GAG>TAG	p.E70*	OR6B2_uc010zoc.1_Nonsense_Mutation_p.E70*	NM_001005853	NP_001005853	Q6IFH4	OR6B2_HUMAN	olfactory receptor, family 6, subfamily B,	70	Helical; Name=2; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0		all_epithelial(40;1.64e-11)|Breast(86;0.000327)|Renal(207;0.00571)|Ovarian(221;0.104)|all_hematologic(139;0.182)|all_lung(227;0.229)|Melanoma(123;0.238)		Epithelial(121;3.4e-29)|all cancers(36;2.08e-27)|OV - Ovarian serous cystadenocarcinoma(60;4.63e-14)|Kidney(56;2.99e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;1.56e-05)|Lung(119;0.00344)|LUSC - Lung squamous cell carcinoma(224;0.0148)		TACCAGATCTCCAGGAAAGAC	0.552													5	87	---	---	---	---	PASS
AQP12A	375318	broad.mit.edu	37	2	241631490	241631490	+	Splice_Site	SNP	G	C	C			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr2:241631490G>C	uc002vzu.2	+	2	193	c.124_splice	c.e2-1	p.M42_splice	AQP12A_uc002vzv.2_Intron	NM_198998	NP_945349	Q8IXF9	AQ12A_HUMAN	aquaporin 12A							integral to membrane	transporter activity				0		all_epithelial(40;7.49e-12)|Breast(86;0.000148)|Renal(207;0.00571)|Ovarian(221;0.104)|all_neural(83;0.107)|all_hematologic(139;0.182)|all_lung(227;0.186)|Melanoma(123;0.238)		Epithelial(32;2.2e-31)|all cancers(36;1.08e-28)|OV - Ovarian serous cystadenocarcinoma(60;2.13e-15)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;7.52e-06)|Lung(119;0.00163)|LUSC - Lung squamous cell carcinoma(224;0.008)|Colorectal(34;0.0124)|COAD - Colon adenocarcinoma(134;0.0757)		GCTGCCTGGAGATGAGGACGC	0.706													5	10	---	---	---	---	PASS
CELSR3	1951	broad.mit.edu	37	3	48670977	48670977	+	Nonsense_Mutation	SNP	C	A	A			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr3:48670977C>A	uc003cuf.1	-	37	10297	c.10297G>T	c.(10297-10299)GAG>TAG	p.E3433*	SLC26A6_uc003cug.2_Nonsense_Mutation_p.E18*|SLC26A6_uc003cuh.2_Nonsense_Mutation_p.E39*|SLC26A6_uc010hke.2_5'UTR|SLC26A6_uc003cuk.2_Nonsense_Mutation_p.E39*|SLC26A6_uc003cui.2_Nonsense_Mutation_p.E39*|SLC26A6_uc003cuj.2_Nonsense_Mutation_p.E39*|SLC26A6_uc011bbp.1_Nonsense_Mutation_p.E39*	NM_001407	NP_001398	Q9NYQ7	CELR3_HUMAN	cadherin EGF LAG seven-pass G-type receptor 3	Error:Variant_position_missing_in_Q9NYQ7_after_alignment					homophilic cell adhesion|multicellular organismal development|neuropeptide signaling pathway	integral to membrane|plasma membrane	calcium ion binding|G-protein coupled receptor activity|protein binding			ovary(5)|upper_aerodigestive_tract(2)|central_nervous_system(2)|skin(2)	11				BRCA - Breast invasive adenocarcinoma(193;0.000292)|KIRC - Kidney renal clear cell carcinoma(197;0.00549)|Kidney(197;0.00619)		TCCAAATGCTCCTGGTTCAGC	0.647													21	44	---	---	---	---	PASS
DNAH1	25981	broad.mit.edu	37	3	52430701	52430701	+	Missense_Mutation	SNP	A	C	C			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr3:52430701A>C	uc011bef.1	+	72	11759	c.11498A>C	c.(11497-11499)AAG>ACG	p.K3833T	DNAH1_uc003ddv.2_Missense_Mutation_p.K691T	NM_015512	NP_056327	Q9P2D7	DYH1_HUMAN	dynein, axonemal, heavy chain 1	3898	AAA 6 (By similarity).				ciliary or flagellar motility|microtubule-based movement|response to mechanical stimulus	axonemal dynein complex|cilium axoneme|cytoplasm|microtubule	ATP binding|ATPase activity|microtubule motor activity			large_intestine(3)	3				BRCA - Breast invasive adenocarcinoma(193;2.02e-05)|OV - Ovarian serous cystadenocarcinoma(275;0.000207)|Kidney(197;0.0022)|KIRC - Kidney renal clear cell carcinoma(197;0.00245)		GAGCGCCATAAGTTTGGGCCC	0.567													27	26	---	---	---	---	PASS
PBRM1	55193	broad.mit.edu	37	3	52623085	52623085	+	Splice_Site	SNP	C	G	G			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr3:52623085C>G	uc003des.2	-	18	2977	c.2965_splice	c.e18+1	p.G989_splice	PBRM1_uc003dex.2_Splice_Site|PBRM1_uc003deq.2_Splice_Site_p.G989_splice|PBRM1_uc003der.2_Splice_Site_p.G957_splice|PBRM1_uc003det.2_Splice_Site_p.G1004_splice|PBRM1_uc003deu.2_Splice_Site_p.G1004_splice|PBRM1_uc003dev.2_Splice_Site|PBRM1_uc003dew.2_Splice_Site_p.G989_splice|PBRM1_uc010hmk.1_Splice_Site_p.E989_splice|PBRM1_uc003dey.2_Splice_Site_p.E989_splice|PBRM1_uc003dez.1_Splice_Site_p.G988_splice|PBRM1_uc003dfb.1_Splice_Site_p.G901_splice|PBRM1_uc003dfa.1_Splice_Site_p.G335_splice	NM_181042	NP_060635	Q86U86	PB1_HUMAN	polybromo 1 isoform 4						chromatin remodeling|mitosis|negative regulation of cell proliferation|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nuclear chromosome	chromatin binding|DNA binding|protein binding			kidney(136)|breast(4)	140				BRCA - Breast invasive adenocarcinoma(193;1.8e-05)|Kidney(197;0.00105)|KIRC - Kidney renal clear cell carcinoma(197;0.00122)|OV - Ovarian serous cystadenocarcinoma(275;0.0613)		AACAAACTTACCAGCTGAATC	0.413			Mis|N|F|S|D|O		clear cell renal carcinoma|breast								26	38	---	---	---	---	PASS
CACNA1D	776	broad.mit.edu	37	3	53842704	53842704	+	Silent	SNP	G	A	A			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr3:53842704G>A	uc003dgv.3	+	46	5941	c.5778G>A	c.(5776-5778)GAG>GAA	p.E1926E	CACNA1D_uc003dgu.3_Silent_p.E1946E|CACNA1D_uc003dgy.3_Silent_p.E1902E|CACNA1D_uc003dgw.3_Silent_p.E1593E|CACNA1D_uc011bes.1_RNA	NM_001128840	NP_001122312	Q01668	CAC1D_HUMAN	calcium channel, voltage-dependent, L type,	1926	Cytoplasmic (Potential).				axon guidance|energy reserve metabolic process|regulation of insulin secretion	voltage-gated calcium channel complex	voltage-gated calcium channel activity			ovary(6)|upper_aerodigestive_tract(2)|liver(1)|central_nervous_system(1)|skin(1)	11				BRCA - Breast invasive adenocarcinoma(193;0.00029)|KIRC - Kidney renal clear cell carcinoma(284;0.0145)|Kidney(284;0.0175)|OV - Ovarian serous cystadenocarcinoma(275;0.0613)	Verapamil(DB00661)	TCAACTTTGAGTGCCTGCGCC	0.602													31	8	---	---	---	---	PASS
FAM116A	201627	broad.mit.edu	37	3	57657985	57657985	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr3:57657985G>A	uc003dja.2	-	3	388	c.317C>T	c.(316-318)TCA>TTA	p.S106L		NM_152678	NP_689891	Q8IWF6	F116A_HUMAN	hypothetical protein LOC201627	106										pancreas(1)	1				BRCA - Breast invasive adenocarcinoma(55;0.000621)|KIRC - Kidney renal clear cell carcinoma(284;0.0485)|Kidney(284;0.0607)		ACAGTTACCTGAATTTGAATC	0.259													13	10	---	---	---	---	PASS
PRICKLE2	166336	broad.mit.edu	37	3	64133179	64133179	+	Silent	SNP	G	T	T			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr3:64133179G>T	uc003dmf.2	-	7	1573	c.987C>A	c.(985-987)GCC>GCA	p.A329A		NM_198859	NP_942559	Q7Z3G6	PRIC2_HUMAN	prickle-like 2	329						cytoplasm|nuclear membrane	zinc ion binding			ovary(4)|skin(1)	5		Lung NSC(201;0.136)		BRCA - Breast invasive adenocarcinoma(55;0.000971)|KIRC - Kidney renal clear cell carcinoma(15;0.00443)|Kidney(15;0.00497)		CCTTGGCCCTGGCGTTCTGGA	0.587													5	80	---	---	---	---	PASS
LSAMP	4045	broad.mit.edu	37	3	116163861	116163861	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr3:116163861C>A	uc003ebt.2	-	1	518	c.18G>T	c.(16-18)CAG>CAT	p.Q6H	LSAMP_uc011bis.1_Missense_Mutation_p.Q6H|LSAMP_uc010hqq.1_RNA	NM_002338	NP_002329	Q13449	LSAMP_HUMAN	limbic system-associated membrane protein	6					cell adhesion|nervous system development	anchored to membrane|plasma membrane					0		all_cancers(1;0.00189)|all_epithelial(1;0.0366)|Myeloproliferative disorder(1037;0.17)|all_neural(597;0.208)|Lung NSC(201;0.215)		GBM - Glioblastoma multiforme(114;0.00117)|LUSC - Lung squamous cell carcinoma(41;0.0407)|Lung(219;0.152)		TCCGATCCGGCTGAACTCTCC	0.632													4	12	---	---	---	---	PASS
DTX3L	151636	broad.mit.edu	37	3	122288791	122288791	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr3:122288791G>A	uc003efk.2	+	3	1944	c.1855G>A	c.(1855-1857)GTT>ATT	p.V619I	DTX3L_uc010hrj.2_Intron	NM_138287	NP_612144	Q8TDB6	DTX3L_HUMAN	deltex 3-like	619					histone monoubiquitination|response to DNA damage stimulus	cytoplasm|nucleus	histone binding|ubiquitin-protein ligase activity|zinc ion binding			ovary(2)|lung(1)|breast(1)	4				GBM - Glioblastoma multiforme(114;0.0459)		GGTTTTCACTGTTTCAAGAGA	0.408													36	80	---	---	---	---	PASS
PARP14	54625	broad.mit.edu	37	3	122437429	122437429	+	Missense_Mutation	SNP	G	C	C			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr3:122437429G>C	uc003efq.3	+	14	4490	c.4431G>C	c.(4429-4431)GAG>GAC	p.E1477D	PARP14_uc010hrk.2_RNA|PARP14_uc003efr.2_Missense_Mutation_p.E1194D|PARP14_uc003efs.1_Missense_Mutation_p.E1194D	NM_017554	NP_060024	Q460N5	PAR14_HUMAN	poly (ADP-ribose) polymerase family, member 14	1477					regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus|plasma membrane	NAD+ ADP-ribosyltransferase activity			ovary(2)|breast(2)|lung(1)|pancreas(1)	6				GBM - Glioblastoma multiforme(114;0.0531)		AGTTGAATGAGCTGCAGAAGA	0.398													74	51	---	---	---	---	PASS
COPB2	9276	broad.mit.edu	37	3	139086994	139086994	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr3:139086994G>A	uc003etf.3	-	13	1668	c.1538C>T	c.(1537-1539)GCC>GTC	p.A513V	COPB2_uc011bmv.1_Missense_Mutation_p.A484V|COPB2_uc010hui.2_Missense_Mutation_p.A484V	NM_004766	NP_004757	P35606	COPB2_HUMAN	coatomer protein complex, subunit beta 2 (beta	513					COPI coating of Golgi vesicle|intra-Golgi vesicle-mediated transport|intracellular protein transport|retrograde vesicle-mediated transport, Golgi to ER	COPI vesicle coat|cytosol	protein binding|structural molecule activity			ovary(2)	2						TACCTCAAAGGCATCTTCAAT	0.348													20	36	---	---	---	---	PASS
CLSTN2	64084	broad.mit.edu	37	3	140251226	140251226	+	Missense_Mutation	SNP	T	C	C			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr3:140251226T>C	uc003etn.2	+	9	1595	c.1405T>C	c.(1405-1407)TAC>CAC	p.Y469H	CLSTN2_uc003etm.2_Missense_Mutation_p.Y469H	NM_022131	NP_071414	Q9H4D0	CSTN2_HUMAN	calsyntenin 2 precursor	469	Extracellular (Potential).				homophilic cell adhesion	endoplasmic reticulum membrane|Golgi membrane|integral to membrane|plasma membrane	calcium ion binding			skin(3)|large_intestine(2)|pancreas(1)|central_nervous_system(1)	7						GGTAACCTTATACATGGATGG	0.423										HNSCC(16;0.037)			62	7	---	---	---	---	PASS
HLTF	6596	broad.mit.edu	37	3	148789184	148789184	+	Nonsense_Mutation	SNP	C	T	T			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr3:148789184C>T	uc003ewq.1	-	7	967	c.749G>A	c.(748-750)TGG>TAG	p.W250*	HLTF_uc003ewr.1_Nonsense_Mutation_p.W250*|HLTF_uc003ews.1_Nonsense_Mutation_p.W250*|HLTF_uc010hve.1_Nonsense_Mutation_p.W250*	NM_139048	NP_620636	Q14527	HLTF_HUMAN	helicase-like transcription factor	250					chromatin modification|transcription, DNA-dependent	nucleus	ATP binding|DNA binding|helicase activity|ligase activity|zinc ion binding			ovary(1)	1			LUSC - Lung squamous cell carcinoma(72;0.0473)|Lung(72;0.0607)			TGACACCATCCAAGCTAGAGC	0.368													15	24	---	---	---	---	PASS
USP13	8975	broad.mit.edu	37	3	179399768	179399768	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr3:179399768C>T	uc003fkh.2	+	2	352	c.271C>T	c.(271-273)CAC>TAC	p.H91Y	USP13_uc003fkf.2_Missense_Mutation_p.H91Y	NM_003940	NP_003931	Q92995	UBP13_HUMAN	ubiquitin thiolesterase 13	91					ubiquitin-dependent protein catabolic process		cysteine-type endopeptidase activity|omega peptidase activity|protein binding|ubiquitin thiolesterase activity|ubiquitin-specific protease activity|zinc ion binding			ovary(1)	1	all_cancers(143;7.79e-15)|Ovarian(172;0.0338)|Breast(254;0.148)		OV - Ovarian serous cystadenocarcinoma(80;1e-25)|GBM - Glioblastoma multiforme(14;0.0169)			TGTATACATGCACCTGAAAAG	0.443													62	55	---	---	---	---	PASS
TFRC	7037	broad.mit.edu	37	3	195800873	195800873	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr3:195800873C>T	uc003fvz.3	-	4	645	c.362G>A	c.(361-363)CGC>CAC	p.R121H	TFRC_uc003fwa.3_Missense_Mutation_p.R121H|TFRC_uc010hzy.2_Missense_Mutation_p.R40H|TFRC_uc011btr.1_Intron	NM_003234	NP_003225	P02786	TFR1_HUMAN	transferrin receptor	121	Extracellular (Potential).				cellular iron ion homeostasis|endocytosis|interspecies interaction between organisms|proteolysis|transferrin transport|transmembrane transport	coated pit|endosome|integral to plasma membrane|melanosome	peptidase activity|transferrin receptor activity			ovary(3)	3	all_cancers(143;1.94e-08)|Ovarian(172;0.0634)|Breast(254;0.206)		Epithelial(36;1.36e-24)|all cancers(36;3.34e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.17e-18)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(46;0.00233)		CCAATATAAGCGACGTGCTGC	0.517			T	BCL6	NHL						OREG0016005	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	42	27	---	---	---	---	PASS
ARAP2	116984	broad.mit.edu	37	4	36115803	36115803	+	Missense_Mutation	SNP	T	C	C			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr4:36115803T>C	uc003gsq.1	-	26	4483	c.4145A>G	c.(4144-4146)AAT>AGT	p.N1382S		NM_015230	NP_056045	Q8WZ64	ARAP2_HUMAN	ArfGAP with RhoGAP domain, ankyrin repeat and PH	1382	Ras-associating.				regulation of ARF GTPase activity|small GTPase mediated signal transduction	cytosol	ARF GTPase activator activity|phosphatidylinositol-3,4,5-trisphosphate binding|zinc ion binding			ovary(1)|pancreas(1)|skin(1)	3						TAGCTCTTCATTTTCAATGAC	0.289													38	38	---	---	---	---	PASS
BEND4	389206	broad.mit.edu	37	4	42145670	42145670	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr4:42145670C>T	uc003gwn.2	-	3	1409	c.829G>A	c.(829-831)GCC>ACC	p.A277T	BEND4_uc003gwm.2_Missense_Mutation_p.A277T|BEND4_uc011byy.1_Missense_Mutation_p.A277T	NM_207406	NP_997289	Q6ZU67	BEND4_HUMAN	BEN domain containing 4 isoform a	277											0						TCCACGTCGGCCAGATGGCCA	0.517													16	13	---	---	---	---	PASS
GABRA4	2557	broad.mit.edu	37	4	46930488	46930488	+	Silent	SNP	A	G	G			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr4:46930488A>G	uc003gxg.2	-	9	1558	c.1419T>C	c.(1417-1419)GCT>GCC	p.A473A		NM_000809	NP_000800	P48169	GBRA4_HUMAN	gamma-aminobutyric acid A receptor, alpha 4	473	Cytoplasmic (Probable).				gamma-aminobutyric acid signaling pathway	cell junction|chloride channel complex|integral to plasma membrane|postsynaptic membrane	benzodiazepine receptor activity|chloride channel activity|extracellular ligand-gated ion channel activity|GABA-A receptor activity			ovary(2)|upper_aerodigestive_tract(1)|breast(1)	4					Alprazolam(DB00404)|Ethchlorvynol(DB00189)|Flunitrazepam(DB01544)|Flurazepam(DB00690)|Lorazepam(DB00186)|Meprobamate(DB00371)|Midazolam(DB00683)	GACGAGTAGAAGCAGATCCAA	0.478													15	24	---	---	---	---	PASS
HERC6	55008	broad.mit.edu	37	4	89363429	89363429	+	Missense_Mutation	SNP	G	C	C			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr4:89363429G>C	uc011cdi.1	+	23	3069	c.2886G>C	c.(2884-2886)CAG>CAC	p.Q962H	HERC6_uc011cdj.1_Missense_Mutation_p.Q926H|HERC6_uc011cdk.1_RNA|HERC6_uc011cdl.1_RNA	NM_017912	NP_060382	Q8IVU3	HERC6_HUMAN	hect domain and RLD 6 isoform 1	962	HECT.				protein ubiquitination involved in ubiquitin-dependent protein catabolic process	cytosol	ubiquitin-protein ligase activity			lung(3)|ovary(1)|kidney(1)	5		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;0.000222)		GAGGCATACAGAAAATGGAAA	0.343													8	9	---	---	---	---	PASS
TNIP3	79931	broad.mit.edu	37	4	122079902	122079902	+	Silent	SNP	C	A	A			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr4:122079902C>A	uc010ing.2	-	3	349	c.153G>T	c.(151-153)CTG>CTT	p.L51L	TNIP3_uc010inh.2_Silent_p.L51L|TNIP3_uc011cgj.1_Silent_p.L109L|TNIP3_uc010ini.2_Silent_p.L51L	NM_024873	NP_079149	Q96KP6	TNIP3_HUMAN	TNFAIP3 interacting protein 3	51	Potential.									ovary(1)	1						GGTTAACTTCCAGGAGCTGAA	0.323													20	9	---	---	---	---	PASS
CYP4V2	285440	broad.mit.edu	37	4	187118688	187118688	+	Missense_Mutation	SNP	A	T	T			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr4:187118688A>T	uc003iyw.3	+	5	910	c.606A>T	c.(604-606)GAA>GAT	p.E202D		NM_207352	NP_997235	Q6ZWL3	CP4V2_HUMAN	cytochrome P450, family 4, subfamily v,	202					response to stimulus|visual perception	endoplasmic reticulum membrane|integral to membrane	electron carrier activity|heme binding|monooxygenase activity|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen				0		all_cancers(14;4.27e-52)|all_epithelial(14;7.69e-39)|all_lung(41;1.34e-13)|Lung NSC(41;3.58e-13)|Melanoma(20;1.91e-06)|Colorectal(36;0.0066)|Hepatocellular(41;0.00886)|Renal(120;0.00988)|Prostate(90;0.00996)|all_hematologic(60;0.014)|all_neural(102;0.243)		OV - Ovarian serous cystadenocarcinoma(60;1.33e-10)|BRCA - Breast invasive adenocarcinoma(30;3.84e-05)|GBM - Glioblastoma multiforme(59;0.000132)|STAD - Stomach adenocarcinoma(60;0.000293)|LUSC - Lung squamous cell carcinoma(40;0.00242)|READ - Rectum adenocarcinoma(43;0.17)		ATTTTATAGAAACAGCTATGG	0.383													11	20	---	---	---	---	PASS
FAT1	2195	broad.mit.edu	37	4	187539652	187539652	+	Silent	SNP	C	T	T			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr4:187539652C>T	uc003izf.2	-	10	8276	c.8088G>A	c.(8086-8088)CCG>CCA	p.P2696P		NM_005245	NP_005236	Q14517	FAT1_HUMAN	FAT tumor suppressor 1 precursor	2696	Extracellular (Potential).|Cadherin 24.				actin filament organization|anatomical structure morphogenesis|cell migration|cell-cell signaling|establishment or maintenance of cell polarity|homophilic cell adhesion	cell-cell junction|integral to plasma membrane|nucleus|perinuclear region of cytoplasm	calcium ion binding|protein binding			ovary(10)|central_nervous_system(1)|pancreas(1)	12						GCTGCATTTCCGGTGGAAGGA	0.393										HNSCC(5;0.00058)			38	59	---	---	---	---	PASS
SLC6A19	340024	broad.mit.edu	37	5	1221346	1221346	+	Missense_Mutation	SNP	T	C	C			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr5:1221346T>C	uc003jbw.3	+	11	1675	c.1619T>C	c.(1618-1620)CTG>CCG	p.L540P		NM_001003841	NP_001003841	Q695T7	S6A19_HUMAN	solute carrier family 6, member 19	540	Helical; Name=11; (Potential).				cellular nitrogen compound metabolic process	integral to plasma membrane	amino acid transmembrane transporter activity|neurotransmitter:sodium symporter activity				0	all_cancers(3;3.55e-15)|Lung NSC(6;2.89e-14)|all_lung(6;2.2e-13)|all_epithelial(6;3.75e-10)		Epithelial(17;0.000356)|all cancers(22;0.00137)|OV - Ovarian serous cystadenocarcinoma(19;0.00239)|Lung(60;0.185)			GTCAGCCCCCTGCTCATGCTG	0.557													8	32	---	---	---	---	PASS
IRX1	79192	broad.mit.edu	37	5	3599450	3599450	+	Silent	SNP	C	A	A			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr5:3599450C>A	uc003jde.2	+	2	440	c.388C>A	c.(388-390)CGG>AGG	p.R130R		NM_024337	NP_077313	P78414	IRX1_HUMAN	iroquois homeobox protein 1	130	Homeobox; TALE-type.					nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			ovary(1)|pancreas(1)	2						GGACCCCGGGCGGCCCAAGAA	0.647													20	20	---	---	---	---	PASS
ADCY2	108	broad.mit.edu	37	5	7707871	7707871	+	Missense_Mutation	SNP	G	C	C			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr5:7707871G>C	uc003jdz.1	+	9	1388	c.1321G>C	c.(1321-1323)GTG>CTG	p.V441L	ADCY2_uc011cmo.1_Missense_Mutation_p.V261L	NM_020546	NP_065433	Q08462	ADCY2_HUMAN	adenylate cyclase 2	441	Cytoplasmic (Potential).				activation of adenylate cyclase activity by G-protein signaling pathway|activation of phospholipase C activity|activation of protein kinase A activity|cellular response to glucagon stimulus|energy reserve metabolic process|inhibition of adenylate cyclase activity by G-protein signaling pathway|nerve growth factor receptor signaling pathway|synaptic transmission|transmembrane transport|water transport	cytoplasm|dendrite|integral to membrane|plasma membrane	ATP binding|metal ion binding			ovary(5)|pancreas(1)|skin(1)	7						CGCTTATAAAGTGGAGGAGGG	0.408													22	75	---	---	---	---	PASS
DNAH5	1767	broad.mit.edu	37	5	13862706	13862706	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr5:13862706C>T	uc003jfd.2	-	29	4789	c.4747G>A	c.(4747-4749)GCC>ACC	p.A1583T		NM_001369	NP_001360	Q8TE73	DYH5_HUMAN	dynein, axonemal, heavy chain 5	1583	Stem (By similarity).				microtubule-based movement	cilium axoneme|cytoplasm|microtubule	ATP binding|ATPase activity|microtubule motor activity			ovary(14)|skin(13)|upper_aerodigestive_tract(1)|central_nervous_system(1)|breast(1)|pancreas(1)	31	Lung NSC(4;0.00476)					TCCATGTTGGCGATGATTTCC	0.453									Kartagener_syndrome				9	56	---	---	---	---	PASS
CDH12	1010	broad.mit.edu	37	5	21752268	21752268	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr5:21752268C>A	uc010iuc.2	-	12	2421	c.1963G>T	c.(1963-1965)GAC>TAC	p.D655Y	CDH12_uc011cno.1_Missense_Mutation_p.D615Y|CDH12_uc003jgk.2_Missense_Mutation_p.D655Y|uc003jgj.2_Intron	NM_004061	NP_004052	P55289	CAD12_HUMAN	cadherin 12, type 2 preproprotein	655	Cytoplasmic (Potential).				adherens junction organization|cell junction assembly|homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(2)	2						ATGACGTTGTCTCTGATGTCT	0.453										HNSCC(59;0.17)			35	43	---	---	---	---	PASS
PRDM9	56979	broad.mit.edu	37	5	23521148	23521148	+	Nonsense_Mutation	SNP	C	A	A			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr5:23521148C>A	uc003jgo.2	+	6	550	c.368C>A	c.(367-369)TCA>TAA	p.S123*		NM_020227	NP_064612	Q9NQV7	PRDM9_HUMAN	PR domain containing 9	123					meiosis|regulation of transcription, DNA-dependent|transcription, DNA-dependent	chromosome|nucleoplasm	histone-lysine N-methyltransferase activity|nucleic acid binding|zinc ion binding			ovary(3)|large_intestine(2)|pancreas(1)	6						CCCAAGGCGTCATTCAGTAAT	0.398										HNSCC(3;0.000094)			20	36	---	---	---	---	PASS
ADAMTS12	81792	broad.mit.edu	37	5	33624402	33624402	+	Missense_Mutation	SNP	C	G	G			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr5:33624402C>G	uc003jia.1	-	14	2240	c.2077G>C	c.(2077-2079)GTG>CTG	p.V693L	ADAMTS12_uc010iuq.1_Intron	NM_030955	NP_112217	P58397	ATS12_HUMAN	ADAM metallopeptidase with thrombospondin type 1	693	Cys-rich.				proteolysis	proteinaceous extracellular matrix	metalloendopeptidase activity|zinc ion binding			ovary(4)|skin(2)|upper_aerodigestive_tract(1)|lung(1)|kidney(1)	9						CCCAGGCACACACCGCAGCGA	0.517										HNSCC(64;0.19)			17	52	---	---	---	---	PASS
ELOVL7	79993	broad.mit.edu	37	5	60062459	60062459	+	Splice_Site	SNP	T	A	A			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr5:60062459T>A	uc003jsi.3	-	6	537	c.337_splice	c.e6-1	p.M113_splice	ELOVL7_uc011cqo.1_Splice_Site_p.M26_splice|ELOVL7_uc010iwk.2_Splice_Site_p.M113_splice|ELOVL7_uc003jsj.3_Splice_Site_p.M100_splice	NM_024930	NP_079206	A1L3X0	ELOV7_HUMAN	elongation of very long chain fatty acids-like						fatty acid elongation, polyunsaturated fatty acid|fatty acid elongation, saturated fatty acid|long-chain fatty-acyl-CoA biosynthetic process|triglyceride biosynthetic process|very long-chain fatty acid biosynthetic process	endoplasmic reticulum membrane|integral to membrane	fatty acid elongase activity|protein binding				0		Lung NSC(810;2.56e-06)|Prostate(74;0.0115)|Breast(144;0.0244)|Ovarian(174;0.0481)				ACGTGCCATCTGCAGAAGCAC	0.254													45	2	---	---	---	---	PASS
MAST4	375449	broad.mit.edu	37	5	66461703	66461703	+	Silent	SNP	C	T	T			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr5:66461703C>T	uc003jut.1	+	28	6197	c.6129C>T	c.(6127-6129)CTC>CTT	p.L2043L	MAST4_uc003juw.2_Silent_p.L1971L|MAST4_uc003jux.2_Intron	NM_015183	NP_055998	O15021	MAST4_HUMAN	microtubule associated serine/threonine kinase	2235						cytoplasm	ATP binding|magnesium ion binding|protein serine/threonine kinase activity			lung(6)|ovary(2)|kidney(2)|breast(2)|central_nervous_system(1)	13		Lung NSC(167;8.56e-06)|Prostate(74;0.00637)|Ovarian(174;0.0563)|Breast(144;0.0586)|Colorectal(97;0.245)		Lung(70;0.011)		CTCAGTCCCTCGGTGGCTCTA	0.617													13	19	---	---	---	---	PASS
PDE8B	8622	broad.mit.edu	37	5	76640754	76640754	+	Nonsense_Mutation	SNP	C	T	T	rs144671246		TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr5:76640754C>T	uc003kfa.2	+	7	919	c.874C>T	c.(874-876)CAG>TAG	p.Q292*	PDE8B_uc003kfb.2_Nonsense_Mutation_p.Q272*|PDE8B_uc003kfc.2_Nonsense_Mutation_p.Q292*|PDE8B_uc003kfd.2_Nonsense_Mutation_p.Q292*|PDE8B_uc003kfe.2_Nonsense_Mutation_p.Q292*	NM_003719	NP_003710	O95263	PDE8B_HUMAN	phosphodiesterase 8B isoform 1	292	PAS.				cyclic nucleotide metabolic process|regulation of transcription, DNA-dependent	cytosol	3',5'-cyclic-AMP phosphodiesterase activity|metal ion binding|two-component response regulator activity				0		all_lung(232;0.00043)|Lung NSC(167;0.00114)|Ovarian(174;0.0107)|Prostate(461;0.0605)		OV - Ovarian serous cystadenocarcinoma(54;2.21e-49)|Epithelial(54;5.82e-43)|all cancers(79;4.06e-38)		CCACGTGATTCAGGTATGGAA	0.363													20	23	---	---	---	---	PASS
HSPA9	3313	broad.mit.edu	37	5	137906809	137906809	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr5:137906809C>A	uc003ldf.2	-	4	358	c.250G>T	c.(250-252)GCC>TCC	p.A84S	HSPA9_uc011cyw.1_Missense_Mutation_p.A15S	NM_004134	NP_004125	P38646	GRP75_HUMAN	heat shock 70kDa protein 9 precursor	84					anti-apoptosis|protein folding	cell surface|mitochondrial nucleoid	ATP binding|unfolded protein binding				0			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00325)			GTGGTTCTGGCACCTTCGGCA	0.418													14	27	---	---	---	---	PASS
PURA	5813	broad.mit.edu	37	5	139494223	139494223	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr5:139494223C>T	uc003lfa.2	+	1	516	c.457C>T	c.(457-459)CGC>TGC	p.R153C		NM_005859	NP_005850	Q00577	PURA_HUMAN	purine-rich element binding protein A	153					DNA unwinding involved in replication|DNA-dependent DNA replication initiation	DNA replication factor A complex	double-stranded telomeric DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|single-stranded DNA binding|transcription factor binding				0			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GCGCGAGAACCGCAAGTACTA	0.706													4	14	---	---	---	---	PASS
PCDHB9	56127	broad.mit.edu	37	5	140568338	140568338	+	Missense_Mutation	SNP	A	C	C			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr5:140568338A>C	uc003liw.1	+	3	1447	c.1447A>C	c.(1447-1449)AAC>CAC	p.N483H		NM_019119	NP_061992	Q9Y5E1	PCDB9_HUMAN	protocadherin beta 9 precursor	483	Extracellular (Potential).|Cadherin 5.				calcium-dependent cell-cell adhesion|homophilic cell adhesion|synapse assembly|synaptic transmission	integral to membrane|plasma membrane	calcium ion binding				0			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			CTCAGGCACCAACGCCCAGGT	0.647													100	13	---	---	---	---	PASS
FCHSD1	89848	broad.mit.edu	37	5	141026213	141026213	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr5:141026213C>A	uc003llk.2	-	11	1052	c.1001G>T	c.(1000-1002)AGC>ATC	p.S334I	FCHSD1_uc010jgg.2_5'UTR|FCHSD1_uc003llj.2_RNA	NM_033449	NP_258260	Q86WN1	FCSD1_HUMAN	FCH and double SH3 domains 1	334									FCHSD1/BRAF(2)	skin(2)|ovary(1)|central_nervous_system(1)	4			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GGCAGCTCGGCTGGTCAAGCG	0.602													3	14	---	---	---	---	PASS
ADRB2	154	broad.mit.edu	37	5	148207577	148207577	+	Missense_Mutation	SNP	C	G	G			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr5:148207577C>G	uc003lpr.1	+	1	1422	c.1183C>G	c.(1183-1185)CCT>GCT	p.P395A	SH3TC2_uc003lpp.1_Intron	NM_000024	NP_000015	P07550	ADRB2_HUMAN	adrenergic, beta-2-, receptor, surface	395	Cytoplasmic.				activation of transmembrane receptor protein tyrosine kinase activity|desensitization of G-protein coupled receptor protein signaling pathway by arrestin|endosome to lysosome transport|positive regulation of MAPKKK cascade|receptor-mediated endocytosis	endosome|integral to plasma membrane|lysosome|receptor complex	beta2-adrenergic receptor activity|norepinephrine binding|potassium channel regulator activity|protein homodimerization activity			ovary(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)		Alprenolol(DB00866)|Arformoterol(DB01274)|Bambuterol(DB01408)|Bisoprolol(DB00612)|Bitolterol(DB00901)|Bretylium(DB01158)|Carteolol(DB00521)|Carvedilol(DB01136)|Clenbuterol(DB01407)|Desipramine(DB01151)|Epinephrine(DB00668)|Fenoterol(DB01288)|Formoterol(DB00983)|Isoproterenol(DB01064)|Labetalol(DB00598)|Levobunolol(DB01210)|Metipranolol(DB01214)|Nadolol(DB01203)|Norepinephrine(DB00368)|Orciprenaline(DB00816)|Oxprenolol(DB01580)|Penbutolol(DB01359)|Pindolol(DB00960)|Pirbuterol(DB01291)|Procaterol(DB01366)|Propranolol(DB00571)|Pseudoephedrine(DB00852)|Ritodrine(DB00867)|Salbutamol(DB01001)|Salmeterol(DB00938)|Terbutaline(DB00871)|Timolol(DB00373)	AGGTACTGTGCCTAGCGATAA	0.463													19	46	---	---	---	---	PASS
ARSI	340075	broad.mit.edu	37	5	149676856	149676856	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr5:149676856C>T	uc003lrv.2	-	2	2220	c.1631G>A	c.(1630-1632)CGC>CAC	p.R544H		NM_001012301	NP_001012301	Q5FYB1	ARSI_HUMAN	arylsulfatase family, member I precursor	544						endoplasmic reticulum|extracellular region	arylsulfatase activity|metal ion binding			ovary(1)|pancreas(1)	2			KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			TTTTTTCTTGCGACGACCCCG	0.537													64	35	---	---	---	---	PASS
RNF145	153830	broad.mit.edu	37	5	158621750	158621750	+	Silent	SNP	G	A	A			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr5:158621750G>A	uc003lxp.2	-	3	580	c.267C>T	c.(265-267)CTC>CTT	p.L89L	RNF145_uc011ddy.1_Silent_p.L103L|RNF145_uc003lxo.1_Silent_p.L117L|RNF145_uc011ddz.1_Silent_p.L106L|RNF145_uc010jiq.1_Silent_p.L119L|RNF145_uc011dea.1_Silent_p.L105L	NM_144726	NP_653327	Q96MT1	RN145_HUMAN	ring finger protein 145	89	Helical; (Potential).					integral to membrane	zinc ion binding			ovary(3)|lung(1)|skin(1)	5	Renal(175;0.00196)	Medulloblastoma(196;0.0523)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			CAGCATAGAGGAGCAGAGCAG	0.348													44	112	---	---	---	---	PASS
STK10	6793	broad.mit.edu	37	5	171488197	171488197	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr5:171488197C>T	uc003mbo.1	-	14	2458	c.2158G>A	c.(2158-2160)GAG>AAG	p.E720K		NM_005990	NP_005981	O94804	STK10_HUMAN	serine/threonine kinase 10	720	Potential.						ATP binding|protein serine/threonine kinase activity			ovary(3)|lung(2)|testis(1)|breast(1)|pancreas(1)	8	Renal(175;0.000159)|Lung NSC(126;0.0056)|all_lung(126;0.0094)	Medulloblastoma(196;0.00868)|all_neural(177;0.026)	Kidney(164;7.24e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000516)			TCACAGATCTCCCGCCTGTTG	0.617													42	56	---	---	---	---	PASS
DRD1	1812	broad.mit.edu	37	5	174869482	174869482	+	Silent	SNP	C	A	A			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr5:174869482C>A	uc003mcz.2	-	2	1566	c.621G>T	c.(619-621)GTG>GTT	p.V207V		NM_000794	NP_000785	P21728	DRD1_HUMAN	dopamine receptor D1	207	Helical; Name=5; (Potential).				activation of adenylate cyclase activity by dopamine receptor signaling pathway|activation of phospholipase C activity by dopamine receptor signaling pathway|adult walking behavior|cerebral cortex GABAergic interneuron migration|elevation of cytosolic calcium ion concentration involved in G-protein signaling coupled to IP3 second messenger|mating behavior|positive regulation of cAMP biosynthetic process|positive regulation of cell migration|positive regulation of potassium ion transport|positive regulation of release of sequestered calcium ion into cytosol|positive regulation of synaptic transmission, glutamatergic|prepulse inhibition|response to drug|synapse assembly|visual learning	endoplasmic reticulum membrane|membrane fraction	protein binding			ovary(2)|skin(1)	3	all_cancers(89;0.00895)|Renal(175;0.000159)|Lung NSC(126;0.00625)|all_lung(126;0.0104)	Medulloblastoma(196;0.0208)|all_neural(177;0.0277)|all_hematologic(541;0.214)	Kidney(164;3.85e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000183)		Acetophenazine(DB01063)|Amantadine(DB00915)|Apomorphine(DB00714)|Carphenazine(DB01038)|Chlorprothixene(DB01239)|Clozapine(DB00363)|Cocaine(DB00907)|Dopamine(DB00988)|Fenoldopam(DB00800)|Flupenthixol(DB00875)|Fluphenazine(DB00623)|Haloperidol(DB00502)|Levodopa(DB01235)|Lisuride(DB00589)|Loxapine(DB00408)|Methylergonovine(DB00353)|Minaprine(DB00805)|Olanzapine(DB00334)|Pegademase bovine(DB00061)|Pergolide(DB01186)|Perphenazine(DB00850)|Prochlorperazine(DB00433)|Promazine(DB00420)|Propiomazine(DB00777)|Quetiapine(DB01224)|Thiethylperazine(DB00372)|Thioridazine(DB00679)|Triflupromazine(DB00508)|Zuclopenthixol(DB01624)	TCATGATGGCCACAGGGATGT	0.502													64	10	---	---	---	---	PASS
FOXC1	2296	broad.mit.edu	37	6	1611183	1611183	+	Missense_Mutation	SNP	T	A	A			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr6:1611183T>A	uc003mtp.2	+	1	503	c.503T>A	c.(502-504)CTG>CAG	p.L168Q		NM_001453	NP_001444	Q12948	FOXC1_HUMAN	forkhead box C1	168	Fork-head.				anti-apoptosis|artery morphogenesis|blood vessel remodeling|brain development|camera-type eye development|cardiac muscle cell proliferation|collagen fibril organization|embryonic heart tube development|germ cell migration|glycosaminoglycan metabolic process|lacrimal gland development|lymphangiogenesis|metanephros development|negative regulation of mitotic cell cycle|neural crest cell fate commitment|Notch signaling pathway|odontogenesis of dentine-containing tooth|ossification|ovarian follicle development|paraxial mesodermal cell fate commitment|positive regulation of transcription from RNA polymerase II promoter|regulation of blood vessel size|regulation of organ growth|regulation of sequence-specific DNA binding transcription factor activity|somitogenesis|ureteric bud development|vascular endothelial growth factor receptor signaling pathway|vasculogenesis|ventricular cardiac muscle tissue morphogenesis	nuclear heterochromatin|transcription factor complex	chromatin DNA binding|DNA bending activity|double-stranded DNA binding|promoter binding|sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|specific RNA polymerase II transcription factor activity|specific transcriptional repressor activity|transcription activator activity|transcription factor binding|transcription regulatory region DNA binding			ovary(1)	1	Ovarian(93;0.0733)	all_cancers(2;4.45e-07)|all_epithelial(2;4.33e-05)|all_lung(73;0.0713)|all_hematologic(90;0.0895)		Epithelial(2;0.0904)|OV - Ovarian serous cystadenocarcinoma(45;0.095)|all cancers(2;0.168)		GGCAGCTTCCTGCGGCGGCGG	0.547													49	26	---	---	---	---	PASS
CAGE1	285782	broad.mit.edu	37	6	7373571	7373571	+	Missense_Mutation	SNP	A	C	C			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr6:7373571A>C	uc003mxi.2	-	4	1794	c.1073T>G	c.(1072-1074)CTT>CGT	p.L358R	CAGE1_uc003mxh.2_RNA|CAGE1_uc003mxj.2_Missense_Mutation_p.L249R|CAGE1_uc003mxk.1_Missense_Mutation_p.L249R	NM_205864	NP_995586	Q8TC20	CAGE1_HUMAN	cancer antigen 1	494	Potential.										0	Ovarian(93;0.0418)					TTCCTTTTCAAGTTTCTGGAA	0.383													8	29	---	---	---	---	PASS
CCDC90A	63933	broad.mit.edu	37	6	13802567	13802567	+	Nonsense_Mutation	SNP	G	A	A			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr6:13802567G>A	uc003nbd.2	-	3	675	c.547C>T	c.(547-549)CAA>TAA	p.Q183*	CCDC90A_uc010jpf.2_RNA	NM_001031713	NP_001026883	Q96AQ8	CC90A_HUMAN	coiled-coil domain containing 90A precursor	183						integral to membrane|mitochondrion					0	Breast(50;0.0027)|Ovarian(93;0.0964)	all_hematologic(90;0.117)				TCTGCTTGTTGAGTAGCAAAC	0.438													22	84	---	---	---	---	PASS
SCAND3	114821	broad.mit.edu	37	6	28543271	28543271	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr6:28543271G>T	uc003nlo.2	-	3	1829	c.1211C>A	c.(1210-1212)ACT>AAT	p.T404N		NM_052923	NP_443155	Q6R2W3	SCND3_HUMAN	SCAN domain containing 3	404	Integrase catalytic.				DNA integration|viral reproduction	nucleus	DNA binding|protein dimerization activity|sequence-specific DNA binding transcription factor activity			ovary(1)	1						CCGCAAAAAAGTTAACTTTGT	0.368													12	55	---	---	---	---	PASS
ZNF311	282890	broad.mit.edu	37	6	28963923	28963923	+	Missense_Mutation	SNP	T	C	C			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr6:28963923T>C	uc003nlu.2	-	7	1369	c.856A>G	c.(856-858)ACC>GCC	p.T286A	ZNF311_uc011dlk.1_Missense_Mutation_p.T194A|ZNF311_uc003nlv.2_Missense_Mutation_p.T194A	NM_001010877	NP_001010877	Q5JNZ3	ZN311_HUMAN	zinc finger protein 311	286	C2H2-type 2.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|protein binding|zinc ion binding				0						TGATTTCTGGTCTTGAATGCT	0.438													11	62	---	---	---	---	PASS
HLA-E	3133	broad.mit.edu	37	6	30459173	30459173	+	Silent	SNP	C	T	T			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr6:30459173C>T	uc003nqg.2	+	4	908	c.870C>T	c.(868-870)CCC>CCT	p.P290P	HLA-E_uc011dmg.1_RNA|HLA-E_uc011dmh.1_Silent_p.P331P	NM_005516	NP_005507	P13747	HLAE_HUMAN	major histocompatibility complex, class I, E	290	Ig-like C1-type.|Alpha-3.|Extracellular (Potential).				antigen processing and presentation of peptide antigen via MHC class I|interferon-gamma-mediated signaling pathway|regulation of immune response|type I interferon-mediated signaling pathway	integral to membrane|MHC class I protein complex	MHC class I receptor activity			central_nervous_system(4)|ovary(1)	5						TACCCGAGCCCGTCACCCTGA	0.617													12	74	---	---	---	---	PASS
FGD2	221472	broad.mit.edu	37	6	36976741	36976741	+	Missense_Mutation	SNP	C	G	G			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr6:36976741C>G	uc010jwp.1	+	2	371	c.200C>G	c.(199-201)ACA>AGA	p.T67R	FGD2_uc003onf.2_Missense_Mutation_p.T67R|FGD2_uc011dtu.1_Missense_Mutation_p.T67R|FGD2_uc003ong.2_5'UTR|FGD2_uc011dtv.1_5'UTR	NM_173558	NP_775829	Q7Z6J4	FGD2_HUMAN	FYVE, RhoGEF and PH domain containing 2	67					actin cytoskeleton organization|apoptosis|filopodium assembly|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Cdc42 GTPase activity|regulation of cell shape|small GTPase mediated signal transduction	cytoskeleton|cytosol|early endosome membrane|Golgi apparatus|lamellipodium|nucleus|ruffle membrane	metal ion binding|Rho guanyl-nucleotide exchange factor activity|small GTPase binding			upper_aerodigestive_tract(1)|lung(1)|pancreas(1)	3						GAGCCCAGGACAGTCAGCAGG	0.627													15	62	---	---	---	---	PASS
UBR2	23304	broad.mit.edu	37	6	42603239	42603239	+	Silent	SNP	A	G	G			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr6:42603239A>G	uc011dur.1	+	14	1629	c.1629A>G	c.(1627-1629)AAA>AAG	p.K543K	UBR2_uc011dus.1_Silent_p.K188K|UBR2_uc010jxv.1_Silent_p.K47K|UBR2_uc003osh.2_RNA	NM_015255	NP_056070	Q8IWV8	UBR2_HUMAN	ubiquitin protein ligase E3 component n-recognin	543					cellular response to leucine|chromatin silencing|histone H2A ubiquitination|negative regulation of TOR signaling cascade	nucleus|plasma membrane	leucine binding|zinc ion binding			ovary(3)|pancreas(1)	4	Colorectal(47;0.196)		Colorectal(64;0.00062)|COAD - Colon adenocarcinoma(64;0.00152)|all cancers(41;0.004)|KIRC - Kidney renal clear cell carcinoma(15;0.02)|Kidney(15;0.0388)|OV - Ovarian serous cystadenocarcinoma(102;0.196)			TACAAATGAAATTAACACATG	0.433													12	60	---	---	---	---	PASS
KIAA0240	23506	broad.mit.edu	37	6	42796618	42796618	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr6:42796618G>T	uc003osn.1	+	6	698	c.547G>T	c.(547-549)GGT>TGT	p.G183C	KIAA0240_uc003osm.1_Missense_Mutation_p.G183C|KIAA0240_uc011duw.1_Missense_Mutation_p.G183C|KIAA0240_uc003oso.1_Missense_Mutation_p.G183C|KIAA0240_uc003osp.1_Missense_Mutation_p.G183C	NM_015349	NP_056164	Q6AI39	K0240_HUMAN	hypothetical protein LOC23506	183										ovary(1)	1	Colorectal(47;0.196)		Colorectal(64;0.00237)|COAD - Colon adenocarcinoma(64;0.00473)|all cancers(41;0.00524)|KIRC - Kidney renal clear cell carcinoma(15;0.02)|Kidney(15;0.0388)|OV - Ovarian serous cystadenocarcinoma(102;0.104)			CAATACAGTGGGTGTACAACA	0.453													6	104	---	---	---	---	PASS
MEA1	4201	broad.mit.edu	37	6	42981026	42981026	+	Missense_Mutation	SNP	C	G	G			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr6:42981026C>G	uc003otk.2	-	2	197	c.130G>C	c.(130-132)GAA>CAA	p.E44Q	MEA1_uc010jyc.1_Missense_Mutation_p.E31Q|KLHDC3_uc003otl.2_5'Flank|KLHDC3_uc003otm.2_5'Flank|KLHDC3_uc010jyf.2_5'Flank|KLHDC3_uc003otn.2_5'Flank	NM_014623	NP_055438	Q16626	MEA1_HUMAN	male-enhanced antigen	44					cell differentiation|male gonad development|spermatogenesis		protein binding			central_nervous_system(1)|skin(1)	2			Colorectal(64;0.00237)|all cancers(41;0.00411)|COAD - Colon adenocarcinoma(64;0.00473)|OV - Ovarian serous cystadenocarcinoma(102;0.0664)|KIRC - Kidney renal clear cell carcinoma(15;0.133)|Kidney(15;0.188)			CCAGTGCCTTCTGAAGGGCCC	0.602													38	88	---	---	---	---	PASS
PKHD1	5314	broad.mit.edu	37	6	51900450	51900450	+	Missense_Mutation	SNP	G	C	C			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr6:51900450G>C	uc003pah.1	-	28	3443	c.3167C>G	c.(3166-3168)TCG>TGG	p.S1056W	PKHD1_uc003pai.2_Missense_Mutation_p.S1056W	NM_138694	NP_619639	P08F94	PKHD1_HUMAN	fibrocystin isoform 1	1056	IPT/TIG 5.|Extracellular (Potential).				cell-cell adhesion|cilium assembly|homeostatic process|kidney development|negative regulation of cellular component movement	anchored to external side of plasma membrane|apical plasma membrane|integral to membrane|microtubule basal body	protein binding|receptor activity			lung(15)|ovary(15)|large_intestine(5)|central_nervous_system(3)|skin(3)|breast(2)|upper_aerodigestive_tract(1)	44	Lung NSC(77;0.0605)					GATGGCACACGAGTAAGATCC	0.448													21	87	---	---	---	---	PASS
KLHL31	401265	broad.mit.edu	37	6	53517046	53517046	+	Missense_Mutation	SNP	C	G	G			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr6:53517046C>G	uc003pcb.3	-	3	1396	c.1255G>C	c.(1255-1257)GGG>CGG	p.G419R	uc003pcc.1_Silent_p.P146P	NM_001003760	NP_001003760	Q9H511	KLH31_HUMAN	kelch repeat and BTB (POZ) domain containing 1	419	Kelch 2.				regulation of transcription, DNA-dependent|transcription, DNA-dependent					ovary(1)	1	Lung NSC(77;0.0158)					TACACGAGCCCGTTGAACACG	0.612													19	62	---	---	---	---	PASS
COL12A1	1303	broad.mit.edu	37	6	75899527	75899527	+	Missense_Mutation	SNP	G	C	C			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr6:75899527G>C	uc003phs.2	-	6	565	c.399C>G	c.(397-399)TGC>TGG	p.C133W	COL12A1_uc003pht.2_Intron|COL12A1_uc003phu.1_5'Flank	NM_004370	NP_004361	Q99715	COCA1_HUMAN	collagen, type XII, alpha 1 long isoform	133					cell adhesion|collagen fibril organization|skeletal system development	collagen type XII|extracellular space	extracellular matrix structural constituent conferring tensile strength			ovary(6)|large_intestine(1)|breast(1)|skin(1)	9						CACTGACAGAGCATTCTGAAA	0.348													5	58	---	---	---	---	PASS
MDN1	23195	broad.mit.edu	37	6	90382276	90382276	+	Silent	SNP	T	C	C			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr6:90382276T>C	uc003pnn.1	-	81	13736	c.13620A>G	c.(13618-13620)CAA>CAG	p.Q4540Q		NM_014611	NP_055426	Q9NU22	MDN1_HUMAN	MDN1, midasin homolog	4540					protein complex assembly|regulation of protein complex assembly	nucleus	ATP binding|ATPase activity|unfolded protein binding			ovary(8)|skin(2)	10		all_cancers(76;1.47e-06)|Acute lymphoblastic leukemia(125;2.23e-10)|Prostate(29;5.55e-10)|all_hematologic(105;2.42e-06)|all_epithelial(107;0.00246)		BRCA - Breast invasive adenocarcinoma(108;0.0193)		CATAATCTTCTTGTGGGCTTG	0.373													3	49	---	---	---	---	PASS
RTN4IP1	84816	broad.mit.edu	37	6	107035607	107035607	+	Missense_Mutation	SNP	T	A	A			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr6:107035607T>A	uc003prj.2	-	7	1414	c.937A>T	c.(937-939)ATA>TTA	p.I313L	RTN4IP1_uc010kdd.2_Intron|RTN4IP1_uc003prk.2_Missense_Mutation_p.I213L	NM_032730	NP_116119	Q8WWV3	RT4I1_HUMAN	reticulon 4 interacting protein 1 precursor	313						mitochondrion	oxidoreductase activity|zinc ion binding				0	Breast(9;0.0107)|all_epithelial(6;0.14)	all_cancers(87;9.45e-05)|Acute lymphoblastic leukemia(125;2.13e-07)|all_hematologic(75;5.28e-06)|all_epithelial(87;0.0144)	Epithelial(6;0.000873)|all cancers(7;0.00363)|BRCA - Breast invasive adenocarcinoma(8;0.00721)|OV - Ovarian serous cystadenocarcinoma(5;0.0394)	all cancers(137;0.113)|BRCA - Breast invasive adenocarcinoma(108;0.127)|Epithelial(106;0.144)		CCATCTGCTATGCCCAATCGG	0.502													47	39	---	---	---	---	PASS
SLC35F1	222553	broad.mit.edu	37	6	118635213	118635213	+	Missense_Mutation	SNP	C	G	G			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr6:118635213C>G	uc003pxx.3	+	8	1226	c.1025C>G	c.(1024-1026)TCT>TGT	p.S342C	SLC35F1_uc003pxy.1_Missense_Mutation_p.S147C	NM_001029858	NP_001025029	Q5T1Q4	S35F1_HUMAN	solute carrier family 35, member F1	342	Helical; (Potential).				transport	integral to membrane				breast(1)	1				GBM - Glioblastoma multiforme(226;0.217)		TATCTCCTGTCTTTCTTCACC	0.473													22	44	---	---	---	---	PASS
TAAR2	9287	broad.mit.edu	37	6	132938493	132938493	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr6:132938493C>A	uc003qdl.1	-	2	852	c.852G>T	c.(850-852)TTG>TTT	p.L284F	TAAR2_uc010kfr.1_Missense_Mutation_p.L239F	NM_001033080	NP_001028252	Q9P1P5	TAAR2_HUMAN	trace amine associated receptor 2 isoform 1	284	Helical; Name=6; (Potential).					plasma membrane	G-protein coupled receptor activity			ovary(1)	1	Breast(56;0.135)			OV - Ovarian serous cystadenocarcinoma(155;0.00608)|GBM - Glioblastoma multiforme(226;0.0151)		AAAAGGGATCCAATAAAATTG	0.328													4	40	---	---	---	---	PASS
ARID1B	57492	broad.mit.edu	37	6	157527589	157527589	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr6:157527589G>A	uc003qqn.2	+	20	5412	c.5260G>A	c.(5260-5262)GCA>ACA	p.A1754T	ARID1B_uc003qqo.2_Missense_Mutation_p.A1714T|ARID1B_uc003qqp.2_Missense_Mutation_p.A1701T	NM_017519	NP_059989	Q8NFD5	ARI1B_HUMAN	AT rich interactive domain 1B (SWI1-like)	1759					chromatin-mediated maintenance of transcription|nervous system development|transcription, DNA-dependent	SWI/SNF complex	DNA binding|protein binding|transcription coactivator activity			ovary(1)|breast(1)	2		Breast(66;0.000162)|Ovarian(120;0.0265)		OV - Ovarian serous cystadenocarcinoma(65;3.19e-17)|BRCA - Breast invasive adenocarcinoma(81;1.01e-05)		GGACGCCGCTGCAGACCCAAA	0.507													20	47	---	---	---	---	PASS
SNX9	51429	broad.mit.edu	37	6	158357063	158357063	+	Silent	SNP	G	T	T			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr6:158357063G>T	uc003qqv.1	+	14	1607	c.1434G>T	c.(1432-1434)GTG>GTT	p.V478V		NM_016224	NP_057308	Q9Y5X1	SNX9_HUMAN	sorting nexin 9	478	BAR.				cell communication|intracellular protein transport|lipid tube assembly|positive regulation of GTPase activity|positive regulation of protein oligomerization|receptor-mediated endocytosis	clathrin-coated vesicle|cytoplasmic vesicle membrane|extrinsic to internal side of plasma membrane|ruffle|trans-Golgi network	1-phosphatidylinositol binding|protein homodimerization activity|ubiquitin protein ligase binding				0		Breast(66;0.000776)|Ovarian(120;0.0303)|Prostate(117;0.167)		OV - Ovarian serous cystadenocarcinoma(65;8.06e-18)|BRCA - Breast invasive adenocarcinoma(81;4.48e-05)		CCAGTCTCGTGGCAGAACAGG	0.348													7	25	---	---	---	---	PASS
RSPH3	83861	broad.mit.edu	37	6	159414882	159414882	+	Missense_Mutation	SNP	T	A	A			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr6:159414882T>A	uc003qrx.2	-	2	809	c.619A>T	c.(619-621)ACA>TCA	p.T207S	RSPH3_uc010kju.2_Missense_Mutation_p.T207S|RSPH3_uc003qry.1_Missense_Mutation_p.T207S	NM_031924	NP_114130	Q86UC2	RSPH3_HUMAN	radial spoke 3 homolog	207										ovary(1)|skin(1)	2		Breast(66;0.00519)|Ovarian(120;0.123)		OV - Ovarian serous cystadenocarcinoma(65;2.36e-16)|BRCA - Breast invasive adenocarcinoma(81;5.92e-06)		AGTGGCCCTGTCTGGAGTGCA	0.274													33	17	---	---	---	---	PASS
PARK2	5071	broad.mit.edu	37	6	161990421	161990421	+	Missense_Mutation	SNP	T	C	C			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr6:161990421T>C	uc003qtx.3	-	8	1033	c.899A>G	c.(898-900)GAG>GGG	p.E300G	PARK2_uc003qtv.3_Intron|PARK2_uc010kkd.2_Missense_Mutation_p.E109G|PARK2_uc003qtw.3_Missense_Mutation_p.E109G|PARK2_uc003qty.3_Missense_Mutation_p.E272G|PARK2_uc003qtz.3_Missense_Mutation_p.E151G|PARK2_uc010kke.1_Missense_Mutation_p.E319G|PARK2_uc011egf.1_5'UTR	NM_004562	NP_004553	O60260	PRKN2_HUMAN	parkin isoform 1	300					aggresome assembly|central nervous system development|mitochondrion degradation|negative regulation of actin filament bundle assembly|negative regulation of cell death|negative regulation of protein phosphorylation|negative regulation of release of cytochrome c from mitochondria|neuron death|positive regulation of I-kappaB kinase/NF-kappaB cascade|protein autoubiquitination|protein K48-linked ubiquitination|protein K63-linked ubiquitination|protein monoubiquitination|protein ubiquitination involved in ubiquitin-dependent protein catabolic process|regulation of autophagy|regulation of reactive oxygen species metabolic process	aggresome|cytosol|endoplasmic reticulum|Golgi apparatus|mitochondrion|nucleus|perinuclear region of cytoplasm	chaperone binding|PDZ domain binding|protein kinase binding|ubiquitin protein ligase binding|ubiquitin-protein ligase activity|zinc ion binding			upper_aerodigestive_tract(1)	1		all_cancers(1;8.13e-65)|all_epithelial(1;5.77e-64)|Colorectal(1;9.65e-15)|all_lung(1;1.66e-13)|Lung NSC(1;7.54e-11)|Melanoma(1;1.75e-09)|Breast(66;7.81e-05)|Ovarian(120;0.000981)|Prostate(117;0.0288)|Esophageal squamous(34;0.102)		UCEC - Uterine corpus endometrioid carcinoma (4;0.0663)|all cancers(1;1.9e-63)|Epithelial(1;1.5e-59)|Colorectal(1;2.16e-23)|OV - Ovarian serous cystadenocarcinoma(65;3.53e-20)|COAD - Colon adenocarcinoma(1;2.11e-15)|STAD - Stomach adenocarcinoma(1;4.64e-07)|BRCA - Breast invasive adenocarcinoma(81;1.49e-06)|READ - Rectum adenocarcinoma(1;2.95e-06)|GBM - Glioblastoma multiforme(2;7.23e-06)|Lung(1;0.00163)|KIRC - Kidney renal clear cell carcinoma(4;0.00371)|LUSC - Lung squamous cell carcinoma(1;0.00442)|Kidney(4;0.0046)		GTGATGGAGCTCTTTAATCAA	0.428													14	25	---	---	---	---	PASS
TMEM106B	54664	broad.mit.edu	37	7	12254526	12254526	+	Silent	SNP	G	T	T			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr7:12254526G>T	uc011jxk.1	+	3	490	c.90G>T	c.(88-90)CTG>CTT	p.L30L	TMEM106B_uc003ssh.2_Silent_p.L30L	NM_018374	NP_060844	Q9NUM4	T106B_HUMAN	transmembrane protein 106B	30						integral to membrane					0				UCEC - Uterine corpus endometrioid carcinoma (126;0.185)		GGAATGGACTGGTTAATAGTG	0.388													4	41	---	---	---	---	PASS
BBS9	27241	broad.mit.edu	37	7	33380528	33380528	+	Silent	SNP	G	A	A			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr7:33380528G>A	uc003tdn.1	+	11	1731	c.1218G>A	c.(1216-1218)GAG>GAA	p.E406E	BBS9_uc003tdo.1_Silent_p.E406E|BBS9_uc003tdp.1_Silent_p.E406E|BBS9_uc003tdq.1_Silent_p.E406E|BBS9_uc010kwn.1_RNA|BBS9_uc011kao.1_Silent_p.E284E	NM_198428	NP_940820	Q3SYG4	PTHB1_HUMAN	parathyroid hormone-responsive B1 isoform 2	406					fat cell differentiation|response to stimulus|visual perception	BBSome|cilium membrane|microtubule organizing center|nucleus	protein binding			ovary(3)|upper_aerodigestive_tract(1)|skin(1)	5			GBM - Glioblastoma multiforme(11;0.0894)			CCATGACTGAGAGAGAAGATG	0.313									Bardet-Biedl_syndrome				3	24	---	---	---	---	PASS
BBS9	27241	broad.mit.edu	37	7	33380529	33380529	+	Missense_Mutation	SNP	A	G	G			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr7:33380529A>G	uc003tdn.1	+	11	1732	c.1219A>G	c.(1219-1221)AGA>GGA	p.R407G	BBS9_uc003tdo.1_Missense_Mutation_p.R407G|BBS9_uc003tdp.1_Missense_Mutation_p.R407G|BBS9_uc003tdq.1_Missense_Mutation_p.R407G|BBS9_uc010kwn.1_RNA|BBS9_uc011kao.1_Missense_Mutation_p.R285G	NM_198428	NP_940820	Q3SYG4	PTHB1_HUMAN	parathyroid hormone-responsive B1 isoform 2	407					fat cell differentiation|response to stimulus|visual perception	BBSome|cilium membrane|microtubule organizing center|nucleus	protein binding			ovary(3)|upper_aerodigestive_tract(1)|skin(1)	5			GBM - Glioblastoma multiforme(11;0.0894)			CATGACTGAGAGAGAAGATGA	0.313									Bardet-Biedl_syndrome				3	24	---	---	---	---	PASS
HECW1	23072	broad.mit.edu	37	7	43485093	43485093	+	Silent	SNP	C	A	A			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr7:43485093C>A	uc003tid.1	+	11	2927	c.2322C>A	c.(2320-2322)GCC>GCA	p.A774A	HECW1_uc011kbi.1_Silent_p.A774A	NM_015052	NP_055867	Q76N89	HECW1_HUMAN	NEDD4-like ubiquitin-protein ligase 1	774					protein ubiquitination involved in ubiquitin-dependent protein catabolic process	cytoplasm|nucleus	ubiquitin-protein ligase activity			ovary(8)|lung(6)|breast(4)|skin(4)|pancreas(1)	23						ACGAGCTGGCCGCCCCTAGCG	0.632													6	3	---	---	---	---	PASS
DDC	1644	broad.mit.edu	37	7	50537776	50537776	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr7:50537776G>T	uc003tpf.3	-	12	1221	c.1135C>A	c.(1135-1137)CGC>AGC	p.R379S	DDC_uc010kza.2_Missense_Mutation_p.R294S|DDC_uc003tpg.3_Missense_Mutation_p.R379S	NM_000790	NP_000781	P20711	DDC_HUMAN	dopa decarboxylase (aromatic L-amino acid	379					cellular amino acid metabolic process|hormone biosynthetic process|neurotransmitter secretion	cytosol	aromatic-L-amino-acid decarboxylase activity|protein binding|pyridoxal phosphate binding			ovary(2)	2	Glioma(55;0.08)|all_neural(89;0.245)				Amantadine(DB00915)|Carbidopa(DB00190)|Flupenthixol(DB00875)|L-Tryptophan(DB00150)|Levodopa(DB01235)|Pimozide(DB01100)|Pyridoxal Phosphate(DB00114)|Remoxipride(DB00409)	GTCACCTTGCGGATATAAGCC	0.333													31	55	---	---	---	---	PASS
GRM3	2913	broad.mit.edu	37	7	86468590	86468590	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr7:86468590G>T	uc003uid.2	+	4	2859	c.1760G>T	c.(1759-1761)GGT>GTT	p.G587V	GRM3_uc010lef.2_Intron|GRM3_uc010leg.2_Missense_Mutation_p.G459V|GRM3_uc010leh.2_Missense_Mutation_p.G179V	NM_000840	NP_000831	Q14832	GRM3_HUMAN	glutamate receptor, metabotropic 3 precursor	587	Helical; Name=1; (Potential).				synaptic transmission	integral to plasma membrane				lung(4)|ovary(3)|central_nervous_system(2)|skin(2)|haematopoietic_and_lymphoid_tissue(1)|prostate(1)	13	Esophageal squamous(14;0.0058)|all_lung(186;0.132)|Lung NSC(181;0.142)				Acamprosate(DB00659)|Nicotine(DB00184)	GCCTGTCTGGGTTTTATGTGT	0.493													8	23	---	---	---	---	PASS
CTTNBP2	83992	broad.mit.edu	37	7	117431717	117431717	+	Silent	SNP	T	C	C			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr7:117431717T>C	uc003vjf.2	-	4	1625	c.1533A>G	c.(1531-1533)GGA>GGG	p.G511G		NM_033427	NP_219499	Q8WZ74	CTTB2_HUMAN	cortactin binding protein 2	511	Pro-rich.									ovary(4)|central_nervous_system(1)	5	Lung NSC(10;0.0018)|all_lung(10;0.002)			LUSC - Lung squamous cell carcinoma(290;0.133)		TTGGGGGCACTCCAGGCCTTG	0.537													32	35	---	---	---	---	PASS
PTPRZ1	5803	broad.mit.edu	37	7	121650911	121650911	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr7:121650911C>T	uc003vjy.2	+	12	2206	c.1811C>T	c.(1810-1812)TCC>TTC	p.S604F	PTPRZ1_uc003vjz.2_Missense_Mutation_p.S604F|PTPRZ1_uc011knt.1_Missense_Mutation_p.S54F	NM_002851	NP_002842	P23471	PTPRZ_HUMAN	protein tyrosine phosphatase, receptor-type,	604	Extracellular (Potential).				central nervous system development	integral to plasma membrane	protein binding|protein tyrosine/threonine phosphatase activity|transmembrane receptor protein tyrosine phosphatase activity			ovary(3)|large_intestine(2)|lung(2)|central_nervous_system(1)|kidney(1)	9						GAGAACATATCCCAAGGGTAT	0.413													21	3	---	---	---	---	PASS
PTPRZ1	5803	broad.mit.edu	37	7	121674395	121674395	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr7:121674395C>A	uc003vjy.2	+	17	5642	c.5247C>A	c.(5245-5247)GAC>GAA	p.D1749E	PTPRZ1_uc003vjz.2_Missense_Mutation_p.D882E|PTPRZ1_uc011knt.1_Missense_Mutation_p.D339E	NM_002851	NP_002842	P23471	PTPRZ_HUMAN	protein tyrosine phosphatase, receptor-type,	1749	Cytoplasmic (Potential).|Tyrosine-protein phosphatase 1.				central nervous system development	integral to plasma membrane	protein binding|protein tyrosine/threonine phosphatase activity|transmembrane receptor protein tyrosine phosphatase activity			ovary(3)|large_intestine(2)|lung(2)|central_nervous_system(1)|kidney(1)	9						ACCACCCAGACAACAAGCACA	0.353													18	5	---	---	---	---	PASS
BRAF	673	broad.mit.edu	37	7	140534646	140534646	+	Silent	SNP	T	C	C			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr7:140534646T>C	uc003vwc.3	-	3	328	c.267A>G	c.(265-267)CTA>CTG	p.L89L		NM_004333	NP_004324	P15056	BRAF_HUMAN	B-Raf	89					activation of MAPKK activity|anti-apoptosis|nerve growth factor receptor signaling pathway|organ morphogenesis|positive regulation of peptidyl-serine phosphorylation|small GTPase mediated signal transduction|synaptic transmission	cytosol|nucleus|plasma membrane	ATP binding|metal ion binding		KIAA1549/BRAF(229)|AKAP9_ENST00000356239/BRAF(10)|AGTRAP/BRAF(2)|FCHSD1/BRAF(2)|SLC45A3/BRAF(2)	thyroid(8166)|large_intestine(5052)|skin(3798)|NS(368)|central_nervous_system(284)|ovary(236)|lung(78)|eye(53)|prostate(44)|endometrium(30)|biliary_tract(28)|soft_tissue(27)|haematopoietic_and_lymphoid_tissue(22)|breast(18)|upper_aerodigestive_tract(13)|stomach(13)|pancreas(10)|small_intestine(10)|testis(7)|bone(6)|cervix(5)|genital_tract(4)|oesophagus(3)|urinary_tract(3)|adrenal_gland(3)|gastrointestinal_tract_(site_indeterminate)(2)|liver(2)|meninges(1)|kidney(1)|autonomic_ganglia(1)|pituitary(1)|salivary_gland(1)	18290	Melanoma(164;0.00956)				Sorafenib(DB00398)	GGAGTGCATCTAGCTTGCTGG	0.363		61	Mis|T|O	AKAP9|KIAA1549	melanoma|colorectal|papillary thyroid|borderline ov|Non small-cell lung cancer (NSCLC)|cholangiocarcinoma|pilocytic astrocytoma		Cardio-facio-cutaneous syndrome		Cardiofaciocutaneous_syndrome				38	8	---	---	---	---	PASS
EPHB6	2051	broad.mit.edu	37	7	142568305	142568305	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr7:142568305C>A	uc011kst.1	+	19	3611	c.2824C>A	c.(2824-2826)CCT>ACT	p.P942T	EPHB6_uc011ksu.1_Missense_Mutation_p.P942T|EPHB6_uc003wbs.2_Missense_Mutation_p.P650T|EPHB6_uc003wbt.2_Missense_Mutation_p.P416T|EPHB6_uc003wbu.2_Missense_Mutation_p.P650T|EPHB6_uc003wbv.2_Missense_Mutation_p.P326T	NM_004445	NP_004436	O15197	EPHB6_HUMAN	ephrin receptor EphB6 precursor	942	Cytoplasmic (Potential).					extracellular region|integral to plasma membrane	ATP binding|ephrin receptor activity			lung(8)|large_intestine(4)|central_nervous_system(3)|stomach(1)|skin(1)|ovary(1)|pancreas(1)	19	Melanoma(164;0.059)					CCTTCTGACCCCTGTGGCCCT	0.562													19	28	---	---	---	---	PASS
TPK1	27010	broad.mit.edu	37	7	144320288	144320288	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr7:144320288G>T	uc003weq.2	-	6	428	c.325C>A	c.(325-327)CAA>AAA	p.Q109K	TPK1_uc003weo.2_Missense_Mutation_p.Q104K|TPK1_uc003wep.2_RNA|TPK1_uc003wer.2_Missense_Mutation_p.Q109K|TPK1_uc003wes.2_RNA	NM_022445	NP_071890	Q9H3S4	TPK1_HUMAN	thiamin pyrophosphokinase 1 isoform a	109					thiamine diphosphate biosynthetic process	cytosol	ATP binding|kinase activity|thiamine diphosphokinase activity			ovary(2)	2					Thiamine(DB00152)	ATCTTCTTTTGGAGCATTTTA	0.318													5	86	---	---	---	---	PASS
NEIL2	252969	broad.mit.edu	37	8	11637323	11637323	+	Nonsense_Mutation	SNP	G	T	T			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr8:11637323G>T	uc003wug.2	+	3	1030	c.355G>T	c.(355-357)GAG>TAG	p.E119*	NEIL2_uc003wue.2_Nonsense_Mutation_p.E119*|NEIL2_uc003wuf.2_Nonsense_Mutation_p.E58*|NEIL2_uc011kxd.1_Intron	NM_145043	NP_659480	Q969S2	NEIL2_HUMAN	nei like 2 isoform a	119					base-excision repair|nucleotide-excision repair	nucleus	damaged DNA binding|DNA-(apurinic or apyrimidinic site) lyase activity|hydrolase activity, hydrolyzing N-glycosyl compounds|zinc ion binding				0	all_epithelial(15;0.103)		STAD - Stomach adenocarcinoma(15;0.00225)	COAD - Colon adenocarcinoma(149;0.166)		TGAGTATTTGGAGAGAGACGC	0.587								BER_DNA_glycosylases					4	32	---	---	---	---	PASS
PSD3	23362	broad.mit.edu	37	8	18725364	18725364	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr8:18725364C>T	uc003wza.2	-	4	1557	c.1454G>A	c.(1453-1455)CGC>CAC	p.R485H		NM_015310	NP_056125	Q9NYI0	PSD3_HUMAN	ADP-ribosylation factor guanine nucleotide	485					regulation of ARF protein signal transduction	cell junction|cytoplasm|postsynaptic density|postsynaptic membrane	ARF guanyl-nucleotide exchange factor activity			ovary(3)	3				Colorectal(111;0.0281)|READ - Rectum adenocarcinoma(644;0.183)		TTCTTTAATGCGCTGTTGTAT	0.463													37	51	---	---	---	---	PASS
PIWIL2	55124	broad.mit.edu	37	8	22212891	22212891	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr8:22212891G>T	uc003xbn.2	+	23	2943	c.2795G>T	c.(2794-2796)TGG>TTG	p.W932L	PIWIL2_uc011kzf.1_Missense_Mutation_p.W896L|PIWIL2_uc010ltv.2_Missense_Mutation_p.W932L|PIWIL2_uc003xbo.2_Missense_Mutation_p.W86L	NM_018068	NP_060538	Q8TC59	PIWL2_HUMAN	piwi-like 2	932	Piwi.				DNA methylation involved in gamete generation|gene silencing by RNA|germ-line stem cell maintenance|multicellular organismal development|oogenesis|piRNA metabolic process|positive regulation of translation|RNA 5'-end processing|spermatogenesis	chromatoid body|pi-body	piRNA binding			skin(1)	1				Colorectal(74;0.018)|COAD - Colon adenocarcinoma(73;0.0707)		CACATGTACTGGAATTGGCCT	0.463													4	26	---	---	---	---	PASS
DDHD2	23259	broad.mit.edu	37	8	38095096	38095096	+	Missense_Mutation	SNP	A	G	G			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr8:38095096A>G	uc003xlb.2	+	4	829	c.452A>G	c.(451-453)AAG>AGG	p.K151R	DDHD2_uc003xla.2_Missense_Mutation_p.K151R|DDHD2_uc003xlc.2_Missense_Mutation_p.K151R|DDHD2_uc011lbl.1_Silent_p.K3K	NM_015214	NP_056029	O94830	DDHD2_HUMAN	DDHD domain containing 2 isoform 1	151					lipid catabolic process	centrosome	hydrolase activity|metal ion binding			large_intestine(1)|ovary(1)	2	Colorectal(12;0.000442)	all_lung(54;0.0657)|Lung NSC(58;0.175)	BRCA - Breast invasive adenocarcinoma(5;3.76e-25)|COAD - Colon adenocarcinoma(9;0.0977)			GAATGGAAAAAGAAACTGGAA	0.323													6	8	---	---	---	---	PASS
PXDNL	137902	broad.mit.edu	37	8	52366225	52366225	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr8:52366225C>T	uc003xqu.3	-	10	1204	c.1103G>A	c.(1102-1104)GGA>GAA	p.G368E		NM_144651	NP_653252	A1KZ92	PXDNL_HUMAN	peroxidasin homolog-like precursor	368	Ig-like C2-type 2.				hydrogen peroxide catabolic process	extracellular space	heme binding|peroxidase activity			ovary(1)|pancreas(1)	2		all_cancers(86;0.107)|Lung NSC(129;0.00641)|all_epithelial(80;0.00716)|all_lung(136;0.015)				CAGCTCCAATCCATTGTCCCT	0.512													15	30	---	---	---	---	PASS
LYN	4067	broad.mit.edu	37	8	56879273	56879273	+	Splice_Site	SNP	G	T	T			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr8:56879273G>T	uc003xsk.3	+	9	1073	c.791_splice	c.e9-1	p.G264_splice	LYN_uc003xsl.3_Splice_Site_p.G243_splice	NM_002350	NP_002341	P07948	LYN_HUMAN	Yamaguchi sarcoma viral (v-yes-1) oncogene						erythrocyte differentiation|interspecies interaction between organisms|leukocyte migration|platelet activation|positive regulation of cellular component movement|positive regulation of stress-activated protein kinase signaling cascade|positive regulation of tyrosine phosphorylation of STAT protein|response to DNA damage stimulus|T cell costimulation	cytosol|Golgi apparatus|membrane raft|nucleus|perinuclear region of cytoplasm	ATP binding|ion channel binding|non-membrane spanning protein tyrosine kinase activity|receptor signaling protein tyrosine kinase activity			ovary(1)|breast(1)|central_nervous_system(1)	3		all_lung(136;0.0555)|Lung NSC(129;0.0726)|all_epithelial(80;0.0772)	Epithelial(17;0.000834)|all cancers(17;0.00598)			TTTCTTCCTAGGTTACTATAA	0.323													4	36	---	---	---	---	PASS
CHD7	55636	broad.mit.edu	37	8	61741222	61741222	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr8:61741222G>A	uc003xue.2	+	14	3856	c.3379G>A	c.(3379-3381)GAA>AAA	p.E1127K		NM_017780	NP_060250	Q9P2D1	CHD7_HUMAN	chromodomain helicase DNA binding protein 7	1127	Helicase ATP-binding.				central nervous system development|chromatin modification|cognition|cranial nerve development|face development|heart morphogenesis|in utero embryonic development|inner ear morphogenesis|nose development|palate development|regulation of growth hormone secretion|regulation of transcription, DNA-dependent|retina development in camera-type eye|skeletal system development|T cell differentiation|transcription, DNA-dependent	nucleus	ATP binding|chromatin binding|DNA binding|helicase activity			ovary(4)|large_intestine(1)|central_nervous_system(1)|lung(1)|breast(1)|pancreas(1)	9		all_cancers(86;0.2)|all_lung(136;0.0402)|Lung NSC(129;0.0459)|all_epithelial(80;0.0477)	BRCA - Breast invasive adenocarcinoma(89;0.143)			GTTACCTCAGGAACACAAAGT	0.448													9	18	---	---	---	---	PASS
GGH	8836	broad.mit.edu	37	8	63936743	63936743	+	Missense_Mutation	SNP	G	C	C			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr8:63936743G>C	uc003xuw.2	-	6	785	c.502C>G	c.(502-504)CAA>GAA	p.Q168E		NM_003878	NP_003869	Q92820	GGH_HUMAN	gamma-glutamyl hydrolase precursor	168	Gamma-glutamyl hydrolase.				glutamine metabolic process	extracellular space|lysosome|melanosome	gamma-glutamyl-peptidase activity				0	Breast(64;0.0716)	all_cancers(86;0.189)|Lung NSC(129;0.0324)|all_lung(136;0.0593)|all_epithelial(80;0.131)			Folic Acid(DB00158)|L-Glutamic Acid(DB00142)	CTGTGCAATTGACCTGAAATA	0.373													9	23	---	---	---	---	PASS
CNGB3	54714	broad.mit.edu	37	8	87755766	87755766	+	Silent	SNP	G	C	C			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr8:87755766G>C	uc003ydx.2	-	1	136	c.90C>G	c.(88-90)GGC>GGG	p.G30G		NM_019098	NP_061971	Q9NQW8	CNGB3_HUMAN	cyclic nucleotide gated channel beta 3	30	Cytoplasmic (Potential).				signal transduction|visual perception	integral to membrane	cGMP binding			ovary(2)|pancreas(1)	3						TTGGGTGAGAGCCTTCTTCAT	0.413													20	33	---	---	---	---	PASS
SLC26A7	115111	broad.mit.edu	37	8	92364054	92364054	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr8:92364054C>T	uc003yex.2	+	11	1435	c.1157C>T	c.(1156-1158)TCT>TTT	p.S386F	SLC26A7_uc003yey.2_RNA|SLC26A7_uc003yez.2_Missense_Mutation_p.S386F|SLC26A7_uc003yfa.2_Missense_Mutation_p.S386F	NM_052832	NP_439897	Q8TE54	S26A7_HUMAN	solute carrier family 26, member 7 isoform a	386	Helical; (Potential).					basolateral plasma membrane|integral to membrane|recycling endosome membrane	anion:anion antiporter activity|bicarbonate transmembrane transporter activity|chloride channel activity|oxalate transmembrane transporter activity|sulfate transmembrane transporter activity			ovary(2)	2			BRCA - Breast invasive adenocarcinoma(11;0.00802)			TGTCTAATATCTTGCATTTTC	0.363													15	47	---	---	---	---	PASS
VPS13B	157680	broad.mit.edu	37	8	100523350	100523350	+	Missense_Mutation	SNP	G	C	C			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr8:100523350G>C	uc003yiv.2	+	29	4429	c.4318G>C	c.(4318-4320)GAT>CAT	p.D1440H	VPS13B_uc003yiw.2_Missense_Mutation_p.D1415H|VPS13B_uc003yix.1_Missense_Mutation_p.D910H	NM_017890	NP_060360	Q7Z7G8	VP13B_HUMAN	vacuolar protein sorting 13B isoform 5	1440					protein transport					ovary(7)|skin(4)|lung(3)|central_nervous_system(2)|pancreas(2)|breast(1)|kidney(1)	20	Breast(36;3.73e-07)		OV - Ovarian serous cystadenocarcinoma(57;0.00636)			AAAACTTCTAGATGGCACTCA	0.348													51	5	---	---	---	---	PASS
UBR5	51366	broad.mit.edu	37	8	103297515	103297515	+	Missense_Mutation	SNP	T	C	C			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr8:103297515T>C	uc003ykr.1	-	40	5569	c.5536A>G	c.(5536-5538)ATG>GTG	p.M1846V	UBR5_uc003yks.1_Missense_Mutation_p.M1846V	NM_015902	NP_056986	O95071	UBR5_HUMAN	ubiquitin protein ligase E3 component n-recognin	1846					cell proliferation|positive regulation of canonical Wnt receptor signaling pathway|positive regulation of catenin import into nucleus|positive regulation of protein import into nucleus, translocation|progesterone receptor signaling pathway|protein polyubiquitination|protein ubiquitination involved in ubiquitin-dependent protein catabolic process|response to DNA damage stimulus	nucleus|soluble fraction	protein binding|RNA binding|ubiquitin-ubiquitin ligase activity|zinc ion binding			lung(16)|ovary(4)|large_intestine(3)|breast(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)|kidney(1)	28	all_cancers(14;8e-07)|all_epithelial(15;2.18e-08)|Lung NSC(17;2.55e-05)|all_lung(17;8.85e-05)		OV - Ovarian serous cystadenocarcinoma(57;0.000442)			GTAGAATCCATAATACTGACC	0.378													34	23	---	---	---	---	PASS
DCAF13	25879	broad.mit.edu	37	8	104427542	104427542	+	Silent	SNP	A	T	T			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr8:104427542A>T	uc003yln.2	+	1	601	c.324A>T	c.(322-324)CCA>CCT	p.P108P	SLC25A32_uc003yll.2_5'Flank|SLC25A32_uc011lhr.1_5'Flank|DCAF13_uc003ylm.1_5'UTR|DCAF13_uc003ylo.2_5'UTR	NM_015420	NP_056235	Q9NV06	DCA13_HUMAN	WD repeats and SOF1 domain containing	Error:Variant_position_missing_in_Q9NV06_after_alignment					rRNA processing	CUL4 RING ubiquitin ligase complex|nucleolus|ribonucleoprotein complex				breast(1)	1						CAGTTGAGCCAGCAGGCCGCC	0.637													15	25	---	---	---	---	PASS
TRPS1	7227	broad.mit.edu	37	8	116616594	116616594	+	Silent	SNP	C	A	A			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr8:116616594C>A	uc003ynz.2	-	3	2022	c.1563G>T	c.(1561-1563)ACG>ACT	p.T521T	TRPS1_uc011lhy.1_Silent_p.T525T|TRPS1_uc003yny.2_Silent_p.T534T|TRPS1_uc010mcy.2_Silent_p.T521T	NM_014112	NP_054831	Q9UHF7	TRPS1_HUMAN	zinc finger transcription factor TRPS1	521					negative regulation of transcription from RNA polymerase II promoter|NLS-bearing substrate import into nucleus|regulation of chondrocyte differentiation|skeletal system development|transcription from RNA polymerase II promoter	nucleus	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(2)|skin(2)|pancreas(1)|lung(1)|kidney(1)	7	all_cancers(13;5.44e-23)|all_epithelial(1;2.14e-27)|Lung NSC(37;2.55e-05)|Ovarian(258;0.0219)		Epithelial(1;9.78e-37)|all cancers(1;3.14e-31)|BRCA - Breast invasive adenocarcinoma(1;2.56e-12)			AATTATAGCTCGTTACCATAT	0.458									Langer-Giedion_syndrome				5	62	---	---	---	---	PASS
ZHX2	22882	broad.mit.edu	37	8	123964395	123964395	+	Silent	SNP	C	T	T			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr8:123964395C>T	uc003ypk.1	+	3	1212	c.645C>T	c.(643-645)ACC>ACT	p.T215T		NM_014943	NP_055758	Q9Y6X8	ZHX2_HUMAN	zinc fingers and homeoboxes 2	215	Required for homodimerization.					cytoplasm|nucleus|plasma membrane	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)|skin(1)	2	Lung NSC(37;2e-09)|Ovarian(258;0.0205)|Hepatocellular(40;0.105)		STAD - Stomach adenocarcinoma(47;0.00527)			TGGAAGGGACCGCCCGCCTGG	0.582													27	75	---	---	---	---	PASS
TG	7038	broad.mit.edu	37	8	134145777	134145777	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr8:134145777C>A	uc003ytw.2	+	47	8102	c.8061C>A	c.(8059-8061)GAC>GAA	p.D2687E	TG_uc010mdw.2_Missense_Mutation_p.D1446E|TG_uc011ljb.1_Missense_Mutation_p.D1056E|TG_uc011ljc.1_Missense_Mutation_p.D820E	NM_003235	NP_003226	P01266	THYG_HUMAN	thyroglobulin precursor	2687					hormone biosynthetic process|signal transduction|thyroid gland development|thyroid hormone generation	extracellular space	hormone activity			ovary(8)|breast(4)|pancreas(1)|central_nervous_system(1)|skin(1)	15	Ovarian(258;0.00438)|Acute lymphoblastic leukemia(118;0.155)	Myeloproliferative disorder(644;0.00878)|Acute lymphoblastic leukemia(644;0.0559)|Breast(495;0.0735)	BRCA - Breast invasive adenocarcinoma(115;0.000701)	KIRC - Kidney renal clear cell carcinoma(542;0.0546)		CCTGGCCTGACTTTGTACCCC	0.507													16	41	---	---	---	---	PASS
TG	7038	broad.mit.edu	37	8	134146939	134146939	+	Silent	SNP	G	A	A			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr8:134146939G>A	uc003ytw.2	+	48	8249	c.8208G>A	c.(8206-8208)CAG>CAA	p.Q2736Q	TG_uc010mdw.2_Silent_p.Q1495Q|TG_uc011ljb.1_Silent_p.Q1105Q|TG_uc011ljc.1_Silent_p.Q869Q	NM_003235	NP_003226	P01266	THYG_HUMAN	thyroglobulin precursor	2736					hormone biosynthetic process|signal transduction|thyroid gland development|thyroid hormone generation	extracellular space	hormone activity			ovary(8)|breast(4)|pancreas(1)|central_nervous_system(1)|skin(1)	15	Ovarian(258;0.00438)|Acute lymphoblastic leukemia(118;0.155)	Myeloproliferative disorder(644;0.00878)|Acute lymphoblastic leukemia(644;0.0559)|Breast(495;0.0735)	BRCA - Breast invasive adenocarcinoma(115;0.000701)	KIRC - Kidney renal clear cell carcinoma(542;0.0546)		AGGGCGGGCAGTCAGCAGAGA	0.537													40	22	---	---	---	---	PASS
RECQL4	9401	broad.mit.edu	37	8	145742508	145742508	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr8:145742508G>A	uc003zdj.2	-	4	312	c.280C>T	c.(280-282)CCA>TCA	p.P94S	LRRC14_uc003zdk.1_5'Flank|LRRC14_uc003zdl.1_5'Flank	NM_004260	NP_004251	O94761	RECQ4_HUMAN	RecQ protein-like 4	94					DNA duplex unwinding|DNA recombination|DNA repair	cytoplasm|nucleus	ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding			breast(2)|lung(1)|skin(1)	4	all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055)			CTCCGCCCTGGCGTAGACTGT	0.672			N|F|S			osteosarcoma|skin basal and sqamous cell		Genes_defective_in_diseases_associated_with_sensitivity_to_DNA_damaging_agents	RAPADILINO_syndrome|Rothmund-Thomson_syndrome|Baller-Gerold_syndrome				8	9	---	---	---	---	PASS
NDUFB6	4712	broad.mit.edu	37	9	32573013	32573013	+	Missense_Mutation	SNP	G	C	C			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr9:32573013G>C	uc003zre.1	-	1	170	c.46C>G	c.(46-48)CGA>GGA	p.R16G	NDUFB6_uc003zrf.1_Missense_Mutation_p.R16G	NM_002493	NP_002484	O95139	NDUB6_HUMAN	NADH dehydrogenase (ubiquinone) 1 beta	16					mitochondrial electron transport, NADH to ubiquinone|transport	integral to membrane|mitochondrial respiratory chain complex I	NADH dehydrogenase (ubiquinone) activity				0			LUSC - Lung squamous cell carcinoma(29;0.0181)	GBM - Glioblastoma multiforme(74;0.00199)	NADH(DB00157)	CTCAGCTCTCGCAGCTGCTGC	0.602											OREG0019131	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	4	17	---	---	---	---	PASS
C9orf131	138724	broad.mit.edu	37	9	35045209	35045209	+	Silent	SNP	C	A	A			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr9:35045209C>A	uc003zvw.2	+	2	2612	c.2583C>A	c.(2581-2583)TCC>TCA	p.S861S	C9orf131_uc003zvu.2_Silent_p.S813S|C9orf131_uc003zvv.2_Silent_p.S788S|C9orf131_uc003zvx.2_Silent_p.S826S	NM_203299	NP_976044	Q5VYM1	CI131_HUMAN	hypothetical protein LOC138724 isoform A	861											0	all_epithelial(49;0.22)		LUSC - Lung squamous cell carcinoma(32;0.00117)|Lung(28;0.00309)			TCCAGTCCTCCCACTGTCATC	0.552													8	234	---	---	---	---	PASS
DAPK1	1612	broad.mit.edu	37	9	90313662	90313662	+	Silent	SNP	G	A	A			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr9:90313662G>A	uc004apc.2	+	23	2841	c.2703G>A	c.(2701-2703)GAG>GAA	p.E901E	DAPK1_uc004apd.2_Silent_p.E901E|DAPK1_uc011ltg.1_Silent_p.E835E|DAPK1_uc011lth.1_Silent_p.E638E	NM_004938	NP_004929	P53355	DAPK1_HUMAN	death-associated protein kinase 1	901	ANK 9.				apoptosis|induction of apoptosis by extracellular signals|intracellular protein kinase cascade	actin cytoskeleton|cytoplasm	ATP binding|calmodulin binding|protein serine/threonine kinase activity			ovary(1)|breast(1)	2						CTGGAGGCGAGTTTGGATATG	0.562									Chronic_Lymphocytic_Leukemia_Familial_Clustering_of				16	24	---	---	---	---	PASS
TSTD2	158427	broad.mit.edu	37	9	100364999	100364999	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr9:100364999G>A	uc004axn.2	-	10	1791	c.1303C>T	c.(1303-1305)CCC>TCC	p.P435S	TSTD2_uc004axo.2_Missense_Mutation_p.P209S	NM_139246	NP_640339	Q5T7W7	TSTD2_HUMAN	thiosulfate sulfurtransferase (rhodanese)-like	435										ovary(2)	2						CGGCACTGGGGAGTAGAGCAG	0.507													15	36	---	---	---	---	PASS
KIAA1958	158405	broad.mit.edu	37	9	115337069	115337069	+	Nonsense_Mutation	SNP	A	T	T			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr9:115337069A>T	uc004bgf.1	+	2	884	c.709A>T	c.(709-711)AAG>TAG	p.K237*	KIAA1958_uc011lwx.1_Nonsense_Mutation_p.K237*	NM_133465	NP_597722	Q8N8K9	K1958_HUMAN	hypothetical protein LOC158405	237										skin(1)	1						GGCAAAACCCAAGCCTCAGAC	0.512													20	93	---	---	---	---	PASS
ZNF618	114991	broad.mit.edu	37	9	116811778	116811778	+	Silent	SNP	C	T	T			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr9:116811778C>T	uc004bid.2	+	15	2295	c.2196C>T	c.(2194-2196)CTC>CTT	p.L732L	ZNF618_uc004bic.2_Silent_p.L639L|ZNF618_uc011lxi.1_Silent_p.L699L|ZNF618_uc011lxj.1_Silent_p.L700L|ZNF618_uc010mvb.2_Silent_p.L322L	NM_133374	NP_588615	Q5T7W0	ZN618_HUMAN	zinc finger protein 618	732					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0						AGCACCTGCTCAGCAACCTGG	0.597													9	17	---	---	---	---	PASS
ZNF618	114991	broad.mit.edu	37	9	116811801	116811801	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr9:116811801C>T	uc004bid.2	+	15	2318	c.2219C>T	c.(2218-2220)ACG>ATG	p.T740M	ZNF618_uc004bic.2_Missense_Mutation_p.T647M|ZNF618_uc011lxi.1_Missense_Mutation_p.T707M|ZNF618_uc011lxj.1_Missense_Mutation_p.T708M|ZNF618_uc010mvb.2_Missense_Mutation_p.T330M	NM_133374	NP_588615	Q5T7W0	ZN618_HUMAN	zinc finger protein 618	740					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0						GCCATCCTGACGCCGGTGAAG	0.612													7	21	---	---	---	---	PASS
TNC	3371	broad.mit.edu	37	9	117808912	117808912	+	Missense_Mutation	SNP	G	C	C			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr9:117808912G>C	uc004bjj.3	-	17	5264	c.4902C>G	c.(4900-4902)GAC>GAG	p.D1634E	TNC_uc010mvf.2_Intron	NM_002160	NP_002151	P24821	TENA_HUMAN	tenascin C precursor	1634	Fibronectin type-III 12.				cell adhesion|response to wounding|signal transduction	extracellular space	receptor binding|syndecan binding			central_nervous_system(4)|upper_aerodigestive_tract(1)|ovary(1)|skin(1)	7						GACGGAAACCGTCTGGGGTGG	0.478													19	37	---	---	---	---	PASS
ABL1	25	broad.mit.edu	37	9	133760965	133760965	+	Silent	SNP	G	A	A			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr9:133760965G>A	uc004bzw.2	+	11	3291	c.3288G>A	c.(3286-3288)GAG>GAA	p.E1096E	ABL1_uc004bzv.2_Silent_p.E1115E	NM_005157	NP_005148	P00519	ABL1_HUMAN	c-abl oncogene 1, receptor tyrosine kinase	1096	Nuclear export signal (By similarity).|F-actin-binding.				actin cytoskeleton organization|axon guidance|blood coagulation|cell adhesion|DNA damage induced protein phosphorylation|DNA damage response, signal transduction resulting in induction of apoptosis|mismatch repair|muscle cell differentiation|negative regulation of protein serine/threonine kinase activity|peptidyl-tyrosine phosphorylation|positive regulation of muscle cell differentiation|positive regulation of oxidoreductase activity|regulation of transcription involved in S phase of mitotic cell cycle	cytoskeleton|cytosol|nuclear membrane|nucleolus|perinuclear region of cytoplasm	ATP binding|DNA binding|magnesium ion binding|manganese ion binding|mitogen-activated protein kinase binding|non-membrane spanning protein tyrosine kinase activity|proline-rich region binding|protein C-terminus binding|SH3 domain binding			haematopoietic_and_lymphoid_tissue(807)|lung(5)|stomach(2)|central_nervous_system(1)|breast(1)|skin(1)	817		all_hematologic(13;0.0361)|Acute lymphoblastic leukemia(5;0.0543)|Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;5.4e-05)	Adenosine triphosphate(DB00171)|Dasatinib(DB01254)|Imatinib(DB00619)	ATCTCCGGGAGCTTCAGATCT	0.527			T|Mis	BCR|ETV6|NUP214	CML|ALL|T-ALL								11	19	---	---	---	---	PASS
CACNA1B	774	broad.mit.edu	37	9	140907687	140907687	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr9:140907687C>A	uc004cog.2	+	18	2412	c.2267C>A	c.(2266-2268)GCC>GAC	p.A756D	CACNA1B_uc011mfd.1_Missense_Mutation_p.A287E	NM_000718	NP_000709	Q00975	CAC1B_HUMAN	calcium channel, voltage-dependent, N type,	756	Cytoplasmic (Potential).				membrane depolarization|synaptic transmission	voltage-gated calcium channel complex	ATP binding|protein C-terminus binding|voltage-gated calcium channel activity			breast(3)|large_intestine(2)|ovary(1)	6	all_cancers(76;0.166)			OV - Ovarian serous cystadenocarcinoma(145;1.16e-05)|Epithelial(140;0.000476)	Amlodipine(DB00381)|Gabapentin(DB00996)	TCCATCGCCGCGTAAGGCTCC	0.607													14	14	---	---	---	---	PASS
GPR158	57512	broad.mit.edu	37	10	25877958	25877958	+	Nonsense_Mutation	SNP	G	A	A			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr10:25877958G>A	uc001isj.2	+	8	1836	c.1776G>A	c.(1774-1776)TGG>TGA	p.W592*		NM_020752	NP_065803	Q5T848	GP158_HUMAN	G protein-coupled receptor 158 precursor	592	Helical; Name=5; (Potential).					integral to membrane|plasma membrane	G-protein coupled receptor activity			ovary(4)|large_intestine(2)|pancreas(1)|skin(1)	8						TCCTCTTGTGGGGTGTTTATC	0.393													7	15	---	---	---	---	PASS
SVIL	6840	broad.mit.edu	37	10	29754670	29754670	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr10:29754670C>T	uc001iut.1	-	34	6740	c.5987G>A	c.(5986-5988)AGT>AAT	p.S1996N	LOC387647_uc001iuo.1_Intron|LOC387647_uc001iup.2_Intron|LOC387647_uc001iuq.1_Intron|SVIL_uc010qdw.1_Missense_Mutation_p.S910N|SVIL_uc001iuu.1_Missense_Mutation_p.S1570N	NM_021738	NP_068506	O95425	SVIL_HUMAN	supervillin isoform 2	1996					cytoskeleton organization|skeletal muscle tissue development	cell junction|costamere|invadopodium|nucleus|podosome	actin filament binding			ovary(5)|upper_aerodigestive_tract(1)	6		Breast(68;0.103)				GAAGTTAAAACTTCCAGGATC	0.363													3	6	---	---	---	---	PASS
CDH23	64072	broad.mit.edu	37	10	73494018	73494018	+	Missense_Mutation	SNP	C	G	G			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr10:73494018C>G	uc001jrx.3	+	32	4503	c.4126C>G	c.(4126-4128)CTG>GTG	p.L1376V	C10orf105_uc001jsb.1_Intron|CDH23_uc001jsc.1_Missense_Mutation_p.L184V	NM_022124	NP_071407	Q9H251	CAD23_HUMAN	cadherin-like 23 isoform 1 precursor	1376	Cadherin 13.|Extracellular (Potential).				calcium ion transport|calcium-dependent cell-cell adhesion|cytosolic calcium ion homeostasis|equilibrioception|homophilic cell adhesion|photoreceptor cell maintenance|response to stimulus|sensory perception of sound	cytosol|integral to membrane|plasma membrane|stereocilium	calcium ion binding|protein binding			central_nervous_system(5)|large_intestine(4)|ovary(2)	11						AGTCCAGGGCCTGGTGGACCG	0.597													8	11	---	---	---	---	PASS
GSTO1	9446	broad.mit.edu	37	10	106022748	106022748	+	Missense_Mutation	SNP	G	C	C			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr10:106022748G>C	uc001kya.2	+	4	387	c.378G>C	c.(376-378)TTG>TTC	p.L126F		NM_004832	NP_004823	P78417	GSTO1_HUMAN	glutathione-S-transferase omega 1	126	GST C-terminal.				xenobiotic metabolic process	cytosol	glutathione transferase activity|monodehydroascorbate reductase (NADH) activity				0		Colorectal(252;0.102)|Breast(234;0.122)		Epithelial(162;8.07e-10)|all cancers(201;2.72e-08)|BRCA - Breast invasive adenocarcinoma(275;0.0147)	Glutathione(DB00143)	TGCCATCCTTGGTAGGAAGCT	0.373													15	13	---	---	---	---	PASS
SORCS1	114815	broad.mit.edu	37	10	108448089	108448089	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr10:108448089C>T	uc001kym.2	-	10	1429	c.1421G>A	c.(1420-1422)GGG>GAG	p.G474E	SORCS1_uc001kyl.2_Missense_Mutation_p.G474E|SORCS1_uc009xxs.2_Missense_Mutation_p.G474E|SORCS1_uc001kyn.1_Missense_Mutation_p.G474E|SORCS1_uc001kyo.2_Missense_Mutation_p.G474E	NM_052918	NP_443150	Q8WY21	SORC1_HUMAN	SORCS receptor 1 isoform a	474	Lumenal (Potential).					integral to membrane	neuropeptide receptor activity|protein binding			breast(1)|central_nervous_system(1)	2		Breast(234;0.0256)|Colorectal(252;0.09)|Lung NSC(174;0.168)		Epithelial(162;1.66e-05)|all cancers(201;0.000689)		TCCCTTTATCCCTGCTACCTG	0.398													5	14	---	---	---	---	PASS
C10orf96	374355	broad.mit.edu	37	10	118101585	118101585	+	Missense_Mutation	SNP	A	T	T			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr10:118101585A>T	uc001lck.2	+	5	571	c.320A>T	c.(319-321)AAA>ATA	p.K107I		NM_198515	NP_940917	P0C7W6	CJ096_HUMAN	hypothetical protein LOC374355	107										ovary(2)	2		Lung NSC(174;0.204)|all_lung(145;0.248)		all cancers(201;0.014)		GAGGAAGACAAATTTATTAAG	0.249													10	18	---	---	---	---	PASS
MUC2	4583	broad.mit.edu	37	11	1099773	1099773	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr11:1099773G>A	uc001lsx.1	+	43	14483	c.14456G>A	c.(14455-14457)GGA>GAA	p.G4819E		NM_002457	NP_002448	Q02817	MUC2_HUMAN	mucin 2 precursor	4819	VWFC 1.					inner mucus layer|outer mucus layer	protein binding			lung(1)|breast(1)	2		all_cancers(49;1.08e-07)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.191)		BRCA - Breast invasive adenocarcinoma(625;0.000207)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)	Pranlukast(DB01411)	GGCTGTGTGGGACCTGACAAT	0.572													31	61	---	---	---	---	PASS
MUC5B	727897	broad.mit.edu	37	11	1263589	1263589	+	Missense_Mutation	SNP	A	G	G			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr11:1263589A>G	uc009ycr.1	+	47	7684	c.7558A>G	c.(7558-7560)AGC>GGC	p.S2520G	MUC5B_uc001ltb.2_Missense_Mutation_p.S1830G	NM_017511	NP_059981	Q9HC84	MUC5B_HUMAN	SubName: Full=Mucin 5AC, oligomeric mucus/gel-forming;	1827	7 X Cys-rich subdomain repeats.|Thr-rich.|Cys-rich subdomain 3.				cell adhesion	extracellular region	extracellular matrix structural constituent|protein binding				0		all_cancers(49;6.97e-08)|all_epithelial(84;3.45e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.00141)|Lung(200;0.0853)|LUSC - Lung squamous cell carcinoma(625;0.1)		GGCACCAAAGAGCATAGAGTG	0.597													25	17	---	---	---	---	PASS
CHRNA10	57053	broad.mit.edu	37	11	3691059	3691059	+	Silent	SNP	G	A	A			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr11:3691059G>A	uc001lyf.2	-	2	246	c.174C>T	c.(172-174)ACC>ACT	p.T58T	CHRNA10_uc010qxt.1_5'UTR|CHRNA10_uc010qxu.1_5'UTR	NM_020402	NP_065135	Q9GZZ6	ACH10_HUMAN	cholinergic receptor, nicotinic, alpha 10	58	Extracellular (Potential).				elevation of cytosolic calcium ion concentration|regulation of cell proliferation|synaptic transmission, cholinergic	cell junction|postsynaptic membrane	calcium channel activity|receptor activity|receptor binding			ovary(1)	1		Medulloblastoma(188;0.0075)|Breast(177;0.0164)|all_neural(188;0.0577)		BRCA - Breast invasive adenocarcinoma(625;0.0344)|LUSC - Lung squamous cell carcinoma(625;0.192)	Chloroprocaine(DB01161)|Methadone(DB00333)|Nicotine(DB00184)|Pentolinium(DB01090)|Procaine(DB00721)|Trimethaphan(DB01116)	TCACCTCCAGGGTCACATTCA	0.552													15	48	---	---	---	---	PASS
OR52K2	119774	broad.mit.edu	37	11	4471324	4471324	+	Missense_Mutation	SNP	C	G	G			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr11:4471324C>G	uc001lyz.1	+	1	755	c.755C>G	c.(754-756)GCC>GGC	p.A252G		NM_001005172	NP_001005172	Q8NGK3	O52K2_HUMAN	olfactory receptor, family 52, subfamily K,	252	Helical; Name=6; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			skin(2)	2		Medulloblastoma(188;0.0075)|Breast(177;0.0461)|all_neural(188;0.0577)		Epithelial(150;1.48e-11)|BRCA - Breast invasive adenocarcinoma(625;0.0821)|LUSC - Lung squamous cell carcinoma(625;0.19)		GCCATCTTAGCCTTCTACACA	0.493													34	99	---	---	---	---	PASS
OR51T1	401665	broad.mit.edu	37	11	4903114	4903114	+	Silent	SNP	G	A	A			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr11:4903114G>A	uc010qyp.1	+	1	66	c.66G>A	c.(64-66)CAG>CAA	p.Q22Q		NM_001004759	NP_001004759	Q8NGJ9	O51T1_HUMAN	olfactory receptor, family 51, subfamily T,	Error:Variant_position_missing_in_Q8NGJ9_after_alignment					sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(2)|large_intestine(1)	3		Medulloblastoma(188;0.0075)|all_neural(188;0.0577)|Breast(177;0.086)		Epithelial(150;4.77e-12)|BRCA - Breast invasive adenocarcinoma(625;0.00435)|LUSC - Lung squamous cell carcinoma(625;0.19)		TCATAGTTCAGTGTCTTCAAC	0.308													24	18	---	---	---	---	PASS
NLRP10	338322	broad.mit.edu	37	11	7981729	7981729	+	Missense_Mutation	SNP	G	C	C	rs77351963		TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr11:7981729G>C	uc001mfv.1	-	2	1447	c.1430C>G	c.(1429-1431)TCT>TGT	p.S477C		NM_176821	NP_789791	Q86W26	NAL10_HUMAN	NLR family, pyrin domain containing 10	477	NACHT.						ATP binding			lung(4)|ovary(2)|pancreas(1)|kidney(1)|skin(1)	9				Epithelial(150;1.47e-07)|BRCA - Breast invasive adenocarcinoma(625;0.189)		CACCAGGTAAGACATGGCATG	0.517													30	62	---	---	---	---	PASS
SBF2	81846	broad.mit.edu	37	11	9875089	9875089	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr11:9875089G>T	uc001mib.2	-	20	2672	c.2534C>A	c.(2533-2535)CCA>CAA	p.P845Q	SBF2_uc001mif.3_Missense_Mutation_p.P601Q|uc001mig.2_Intron	NM_030962	NP_112224	Q86WG5	MTMRD_HUMAN	SET binding factor 2	845					myelination	cytoplasm|membrane	phosphatase activity|protein binding			upper_aerodigestive_tract(1)|ovary(1)|skin(1)	3				all cancers(16;2.88e-11)|Epithelial(150;3.61e-10)|BRCA - Breast invasive adenocarcinoma(625;0.00887)		GTGATTACCTGGTATCATGCA	0.388													4	47	---	---	---	---	PASS
USP47	55031	broad.mit.edu	37	11	11977671	11977671	+	Silent	SNP	A	G	G			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr11:11977671A>G	uc001mjs.2	+	28	4780	c.4017A>G	c.(4015-4017)GCA>GCG	p.A1339A	USP47_uc001mjr.2_Silent_p.A1271A|USP47_uc009ygi.2_Silent_p.A141A	NM_017944	NP_060414	Q96K76	UBP47_HUMAN	ubiquitin specific protease 47	1359					base-excision repair|cellular response to UV|monoubiquitinated protein deubiquitination|negative regulation of apoptosis|negative regulation of caspase activity|negative regulation of G2/M transition of mitotic cell cycle|negative regulation of transcription, DNA-dependent|positive regulation of cell growth|response to drug|ubiquitin-dependent protein catabolic process	cytoplasm|SCF ubiquitin ligase complex	ubiquitin thiolesterase activity|ubiquitin-specific protease activity|WD40-repeat domain binding			ovary(1)|skin(1)	2				Epithelial(150;0.000339)		AAGAGAAAGCACTAAAAATAT	0.383													30	51	---	---	---	---	PASS
NELL1	4745	broad.mit.edu	37	11	21596535	21596535	+	Silent	SNP	T	C	C			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr11:21596535T>C	uc001mqe.2	+	20	2553	c.2400T>C	c.(2398-2400)TGT>TGC	p.C800C	NELL1_uc001mqf.2_Silent_p.C753C|NELL1_uc009yid.2_Silent_p.C828C|NELL1_uc010rdo.1_Silent_p.C743C|NELL1_uc010rdp.1_Silent_p.C513C|NELL1_uc001mqh.2_Silent_p.C345C	NM_006157	NP_006148	Q92832	NELL1_HUMAN	nel-like 1 isoform 1 precursor	800	VWFC 5.				cell adhesion|nervous system development	extracellular region	calcium ion binding|structural molecule activity			ovary(2)|large_intestine(1)	3						GAGTCTGTTGTTCTGTGGATT	0.358													11	19	---	---	---	---	PASS
QSER1	79832	broad.mit.edu	37	11	32955081	32955081	+	Missense_Mutation	SNP	A	C	C			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr11:32955081A>C	uc001mty.2	+	4	2157	c.1890A>C	c.(1888-1890)AAA>AAC	p.K630N	QSER1_uc001mtz.1_Missense_Mutation_p.K391N|QSER1_uc001mua.2_Missense_Mutation_p.K135N	NM_001076786	NP_001070254	Q2KHR3	QSER1_HUMAN	glutamine and serine rich 1	630										ovary(3)|central_nervous_system(2)|skin(1)	6	Breast(20;0.158)					AAGCATCAAAAAAAGAAGAAA	0.373													17	43	---	---	---	---	PASS
C11orf41	25758	broad.mit.edu	37	11	33565884	33565884	+	Silent	SNP	T	A	A			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr11:33565884T>A	uc001mup.3	+	1	2008	c.1884T>A	c.(1882-1884)GGT>GGA	p.G628G	C11orf41_uc001mun.1_Silent_p.G628G	NM_012194	NP_036326	Q6ZVL6	CK041_HUMAN	hypothetical protein LOC25758	Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment						integral to membrane				ovary(2)	2						AATGGACAGGTGCAGCCACTA	0.507													14	20	---	---	---	---	PASS
RAG2	5897	broad.mit.edu	37	11	36615574	36615574	+	Missense_Mutation	SNP	C	G	G			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr11:36615574C>G	uc001mwv.3	-	2	333	c.145G>C	c.(145-147)GAT>CAT	p.D49H	C11orf74_uc010rfd.1_5'Flank|C11orf74_uc001mww.1_5'Flank|C11orf74_uc001mwx.1_5'Flank|C11orf74_uc001mwy.1_5'Flank|C11orf74_uc001mwz.1_5'Flank|C11orf74_uc010rfe.1_5'Flank	NM_000536	NP_000527	P55895	RAG2_HUMAN	recombination activating gene 2	49					chromatin modification|pre-B cell allelic exclusion|somatic diversification of immunoglobulins|T cell differentiation in thymus|V(D)J recombination	nucleus	chromatin binding|DNA binding|endonuclease activity|methylated histone residue binding|phosphatidylinositol-3,4,5-trisphosphate binding|phosphatidylinositol-3,4-bisphosphate binding|phosphatidylinositol-3,5-bisphosphate binding|phosphatidylinositol-4,5-bisphosphate binding|zinc ion binding			skin(3)|ovary(1)|pancreas(1)	5	all_lung(20;0.226)	all_hematologic(20;0.00756)				TGCTTTACATCCAGATGGAAA	0.458									Familial_Hemophagocytic_Lymphohistiocytosis				16	36	---	---	---	---	PASS
ACCS	84680	broad.mit.edu	37	11	44102744	44102744	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr11:44102744G>T	uc009yks.1	+	12	1129	c.985G>T	c.(985-987)GGG>TGG	p.G329W	EXT2_uc010rfo.1_Intron|ACCS_uc001mxx.2_Missense_Mutation_p.G329W	NM_001127219	NP_001120691	Q96QU6	1A1L1_HUMAN	1-aminocyclopropane-1-carboxylate synthase	329							1-aminocyclopropane-1-carboxylate synthase activity|protein homodimerization activity|pyridoxal phosphate binding|transferase activity, transferring nitrogenous groups			breast(2)|ovary(1)|lung(1)	4						CGGGATGTCTGGGCTCCGCTT	0.627													20	51	---	---	---	---	PASS
OR4S1	256148	broad.mit.edu	37	11	48328449	48328449	+	Silent	SNP	C	T	T			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr11:48328449C>T	uc010rhu.1	+	1	675	c.675C>T	c.(673-675)AGC>AGT	p.S225S		NM_001004725	NP_001004725	Q8NGB4	OR4S1_HUMAN	olfactory receptor, family 4, subfamily S,	225	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)	1						ACCTAAGAAGCCAGTCATCTG	0.458													66	30	---	---	---	---	PASS
OR4A16	81327	broad.mit.edu	37	11	55111277	55111277	+	Missense_Mutation	SNP	G	T	T	rs141072345		TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr11:55111277G>T	uc010rie.1	+	1	601	c.601G>T	c.(601-603)GGT>TGT	p.G201C		NM_001005274	NP_001005274	Q8NH70	O4A16_HUMAN	olfactory receptor, family 4, subfamily A,	201	Helical; Name=5; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			large_intestine(2)|pancreas(1)	3						GGTTGCCAATGGTGGAATAAT	0.428													19	81	---	---	---	---	PASS
OR4A16	81327	broad.mit.edu	37	11	55111278	55111278	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr11:55111278G>T	uc010rie.1	+	1	602	c.602G>T	c.(601-603)GGT>GTT	p.G201V		NM_001005274	NP_001005274	Q8NH70	O4A16_HUMAN	olfactory receptor, family 4, subfamily A,	201	Helical; Name=5; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			large_intestine(2)|pancreas(1)	3						GTTGCCAATGGTGGAATAATT	0.433													19	80	---	---	---	---	PASS
OR4C15	81309	broad.mit.edu	37	11	55322667	55322667	+	Silent	SNP	T	A	A			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr11:55322667T>A	uc010rig.1	+	1	885	c.885T>A	c.(883-885)TCT>TCA	p.S295S		NM_001001920	NP_001001920	Q8NGM1	OR4CF_HUMAN	olfactory receptor, family 4, subfamily C,	241	Helical; Name=6; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)|skin(1)	2						CCTGTGGATCTCACATTGCTG	0.428										HNSCC(20;0.049)			37	78	---	---	---	---	PASS
AHNAK	79026	broad.mit.edu	37	11	62259292	62259292	+	Silent	SNP	C	T	T			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr11:62259292C>T	uc001ntk.1	-	5	654	c.354G>A	c.(352-354)CAG>CAA	p.Q118Q		NM_024060	NP_076965	Q09666	AHNK_HUMAN	AHNAK nucleoprotein isoform 2	Error:Variant_position_missing_in_Q09666_after_alignment					nervous system development	nucleus	protein binding			ovary(10)|pancreas(4)|skin(4)|upper_aerodigestive_tract(1)	19		Melanoma(852;0.155)				GTGCTGATGGCTGTGGTGTGT	0.453													4	14	---	---	---	---	PASS
TUT1	64852	broad.mit.edu	37	11	62349016	62349016	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr11:62349016G>A	uc001nto.2	-	3	583	c.545C>T	c.(544-546)CCC>CTC	p.P182L		NM_022830	NP_073741	Q9H6E5	STPAP_HUMAN	terminal uridylyl transferase 1, U6	144					mRNA cleavage|mRNA polyadenylation|snRNA processing	nuclear speck|nucleolus	ATP binding|enzyme binding|mRNA 3'-UTR binding|polynucleotide adenylyltransferase activity|RNA uridylyltransferase activity|zinc ion binding			central_nervous_system(1)|skin(1)	2						GTGACTGTCGGGGGCCGCTCC	0.652													28	10	---	---	---	---	PASS
TUT1	64852	broad.mit.edu	37	11	62349017	62349017	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr11:62349017G>A	uc001nto.2	-	3	582	c.544C>T	c.(544-546)CCC>TCC	p.P182S		NM_022830	NP_073741	Q9H6E5	STPAP_HUMAN	terminal uridylyl transferase 1, U6	144					mRNA cleavage|mRNA polyadenylation|snRNA processing	nuclear speck|nucleolus	ATP binding|enzyme binding|mRNA 3'-UTR binding|polynucleotide adenylyltransferase activity|RNA uridylyltransferase activity|zinc ion binding			central_nervous_system(1)|skin(1)	2						TGACTGTCGGGGGCCGCTCCT	0.647													28	10	---	---	---	---	PASS
NXF1	10482	broad.mit.edu	37	11	62568576	62568576	+	Missense_Mutation	SNP	G	C	C			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr11:62568576G>C	uc001nvf.1	-	9	1032	c.896C>G	c.(895-897)TCT>TGT	p.S299C	NXF1_uc001nvg.1_Missense_Mutation_p.S299C|NXF1_uc009yog.1_Missense_Mutation_p.S342C|NXF1_uc010rmh.1_Missense_Mutation_p.S162C	NM_006362	NP_006353	Q9UBU9	NXF1_HUMAN	nuclear RNA export factor 1 isoform 1	299	LRR 2.|Interaction with THOC4.				gene expression|interspecies interaction between organisms	cytosol|nuclear speck	nucleotide binding|protein binding			skin(3)	3						TTCATTTCCAGAAAGGTTTAG	0.458													19	12	---	---	---	---	PASS
KCNK4	50801	broad.mit.edu	37	11	64064613	64064613	+	Silent	SNP	C	A	A			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr11:64064613C>A	uc001nzj.1	+	4	659	c.336C>A	c.(334-336)CGC>CGA	p.R112R	KCNK4_uc009ypl.1_Missense_Mutation_p.A85E|KCNK4_uc001nzk.1_Missense_Mutation_p.A46E|KCNK4_uc010rnk.1_5'UTR|KCNK4_uc001nzl.1_Missense_Mutation_p.A46E|KCNK4_uc001nzm.3_RNA|KCNK4_uc001nzn.1_Silent_p.R112R|KCNK4_uc001nzo.2_Silent_p.R112R|KCNK4_uc001nzp.1_5'UTR	NM_033310	NP_201567	Q9NYG8	KCNK4_HUMAN	TRAAK	112						integral to membrane	potassium channel activity|voltage-gated ion channel activity				0						TGGCCCTGCGCACAGATGCCG	0.652													15	11	---	---	---	---	PASS
FCHSD2	9873	broad.mit.edu	37	11	72598570	72598570	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr11:72598570C>A	uc009ytl.2	-	12	1312	c.1091G>T	c.(1090-1092)CGA>CTA	p.R364L	FCHSD2_uc010rrg.1_Missense_Mutation_p.R228L|FCHSD2_uc001oth.3_Missense_Mutation_p.R308L|FCHSD2_uc001oti.2_Missense_Mutation_p.R323L	NM_014824	NP_055639	O94868	FCSD2_HUMAN	FCH and double SH3 domains 2	364	Potential.						protein binding			ovary(1)	1			BRCA - Breast invasive adenocarcinoma(5;3.3e-05)			TAGCTCTGCTCGGCTTTGTTC	0.383													26	72	---	---	---	---	PASS
CCDC83	220047	broad.mit.edu	37	11	85576208	85576208	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr11:85576208C>A	uc001pbh.1	+	2	554	c.42C>A	c.(40-42)GAC>GAA	p.D14E	CCDC83_uc001pbg.1_Missense_Mutation_p.D14E	NM_173556	NP_775827	Q8IWF9	CCD83_HUMAN	coiled-coil domain containing 83	14										skin(1)	1		Acute lymphoblastic leukemia(157;4.88e-06)|all_hematologic(158;0.00572)				ATACACATGACGGGCCACCAA	0.368													50	160	---	---	---	---	PASS
GRM5	2915	broad.mit.edu	37	11	88780921	88780921	+	Silent	SNP	G	C	C			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr11:88780921G>C	uc001pcq.2	-	1	320	c.120C>G	c.(118-120)CTC>CTG	p.L40L	GRM5_uc009yvm.2_Silent_p.L40L|GRM5_uc009yvn.1_Silent_p.L40L	NM_001143831	NP_001137303	P41594	GRM5_HUMAN	glutamate receptor, metabotropic 5 isoform a	40	Extracellular (Potential).				activation of phospholipase C activity by metabotropic glutamate receptor signaling pathway|synaptic transmission	integral to plasma membrane	G-protein coupled receptor activity|glutamate receptor activity			central_nervous_system(4)|ovary(2)|lung(2)|breast(1)	9		Acute lymphoblastic leukemia(157;2.54e-05)|all_hematologic(158;0.00834)			Acamprosate(DB00659)	GAACAGAAAAGAGAGCTCCAA	0.517													11	20	---	---	---	---	PASS
FAT3	120114	broad.mit.edu	37	11	92087130	92087130	+	Nonsense_Mutation	SNP	G	T	T			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr11:92087130G>T	uc001pdj.3	+	1	1869	c.1852G>T	c.(1852-1854)GGA>TGA	p.G618*		NM_001008781	NP_001008781	Q8TDW7	FAT3_HUMAN	FAT tumor suppressor homolog 3	618	Cadherin 6.|Extracellular (Potential).				homophilic cell adhesion|multicellular organismal development	integral to membrane|plasma membrane	calcium ion binding			ovary(4)|pancreas(1)	5		Acute lymphoblastic leukemia(157;3.01e-05)|all_hematologic(158;0.00858)				AATCATTTCTGGAAATGAACT	0.363										TCGA Ovarian(4;0.039)			11	13	---	---	---	---	PASS
PANX1	24145	broad.mit.edu	37	11	93911564	93911564	+	Silent	SNP	G	A	A			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr11:93911564G>A	uc001per.2	+	3	736	c.351G>A	c.(349-351)GCG>GCA	p.A117A	PANX1_uc001peq.2_Silent_p.A117A	NM_015368	NP_056183	Q96RD7	PANX1_HUMAN	pannexin 1	117	Helical; (Potential).				positive regulation of interleukin-1 beta secretion|protein hexamerization|synaptic transmission	bleb|endoplasmic reticulum membrane|gap junction|integral to membrane	calcium channel activity|gap junction hemi-channel activity|leak channel activity|receptor binding				0		Acute lymphoblastic leukemia(157;2.31e-05)|all_hematologic(158;0.00824)				TGCTCTTTGCGATCCTCCTGT	0.473													27	14	---	---	---	---	PASS
AASDHPPT	60496	broad.mit.edu	37	11	105948587	105948587	+	Silent	SNP	G	A	A			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr11:105948587G>A	uc001pjc.1	+	1	296	c.150G>A	c.(148-150)CAG>CAA	p.Q50Q	KBTBD3_uc001pja.2_5'Flank|KBTBD3_uc001pjb.2_5'Flank|KBTBD3_uc009yxm.2_5'Flank|AASDHPPT_uc010rvn.1_RNA	NM_015423	NP_056238	Q9NRN7	ADPPT_HUMAN	aminoadipate-semialdehyde	50					macromolecule biosynthetic process|pantothenate metabolic process	cytosol	holo-[acyl-carrier-protein] synthase activity|magnesium ion binding|protein binding				0		Melanoma(852;0.000878)|Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.0017)|Breast(348;0.0321)		BRCA - Breast invasive adenocarcinoma(274;5.78e-05)|Epithelial(105;0.00622)|all cancers(92;0.041)		GCATTGGCCAGTTCGTCTTTG	0.607													12	24	---	---	---	---	PASS
CUL5	8065	broad.mit.edu	37	11	107959295	107959295	+	Missense_Mutation	SNP	T	A	A			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr11:107959295T>A	uc001pjv.2	+	12	1887	c.1220T>A	c.(1219-1221)CTG>CAG	p.L407Q	CUL5_uc001pju.2_RNA	NM_003478	NP_003469	Q93034	CUL5_HUMAN	Vasopressin-activated calcium-mobilizing	407					cell cycle arrest|cell proliferation|G1/S transition of mitotic cell cycle|induction of apoptosis by intracellular signals|interspecies interaction between organisms|negative regulation of cell proliferation|ubiquitin-dependent protein catabolic process|viral reproduction	cullin-RING ubiquitin ligase complex|cytosol	calcium channel activity|receptor activity|ubiquitin protein ligase binding			ovary(1)	1		all_cancers(61;7.09e-10)|all_epithelial(67;2.97e-06)|Acute lymphoblastic leukemia(157;3.95e-05)|Melanoma(852;4.48e-05)|all_hematologic(158;0.00014)|Breast(348;0.0258)|all_neural(303;0.072)		BRCA - Breast invasive adenocarcinoma(274;3.58e-05)|Epithelial(105;4.68e-05)|all cancers(92;0.00122)|OV - Ovarian serous cystadenocarcinoma(223;0.217)		TGCCCTGAGCTGCTTGCCAAT	0.333													13	38	---	---	---	---	PASS
RNF214	257160	broad.mit.edu	37	11	117150919	117150919	+	Silent	SNP	G	T	T			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr11:117150919G>T	uc001pqt.2	+	8	1134	c.1089G>T	c.(1087-1089)CTG>CTT	p.L363L	RNF214_uc001pqu.2_Silent_p.L363L|RNF214_uc010rxf.1_Silent_p.L208L	NM_207343	NP_997226	Q8ND24	RN214_HUMAN	ring finger protein 214	363	Potential.						zinc ion binding				0	all_hematologic(175;0.0487)	Breast(348;0.00908)|Medulloblastoma(222;0.0425)|all_hematologic(192;0.196)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;1.88e-05)|Epithelial(105;0.000397)|all cancers(92;0.00258)		AAGAGTTACTGGTACTGAAAC	0.358													7	156	---	---	---	---	PASS
IL10RA	3587	broad.mit.edu	37	11	117869931	117869931	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr11:117869931C>T	uc001prv.2	+	7	1389	c.1312C>T	c.(1312-1314)CCA>TCA	p.P438S	IL10RA_uc010rxl.1_Missense_Mutation_p.P418S|IL10RA_uc010rxm.1_Missense_Mutation_p.P418S|IL10RA_uc010rxn.1_Missense_Mutation_p.P289S|IL10RA_uc001prw.2_Missense_Mutation_p.P289S	NM_001558	NP_001549	Q13651	I10R1_HUMAN	interleukin 10 receptor, alpha precursor	438	Cytoplasmic (Potential).					integral to membrane|plasma membrane	interleukin-10 receptor activity			ovary(1)	1	all_hematologic(175;0.0487)	Medulloblastoma(222;0.0425)|all_hematologic(192;0.196)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;3.07e-05)|Epithelial(105;0.00108)		GGAAGAAGACCCAGCTGCTGT	0.607													21	42	---	---	---	---	PASS
BCL9L	283149	broad.mit.edu	37	11	118772641	118772641	+	Missense_Mutation	SNP	G	C	C			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr11:118772641G>C	uc001pug.2	-	6	2776	c.1811C>G	c.(1810-1812)CCA>CGA	p.P604R	BCL9L_uc009zal.2_Missense_Mutation_p.P599R	NM_182557	NP_872363	Q86UU0	BCL9L_HUMAN	B-cell CLL/lymphoma 9-like	604					negative regulation of transforming growth factor beta receptor signaling pathway|positive regulation of epithelial to mesenchymal transition|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent		transcription coactivator activity			ovary(1)|pancreas(1)	2	all_hematologic(175;0.0839)	Medulloblastoma(222;0.0425)|all_hematologic(192;0.103)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;7.66e-05)		CTGGTTGCCTGGGAAACGGGG	0.632													7	11	---	---	---	---	PASS
OR4D5	219875	broad.mit.edu	37	11	123810819	123810819	+	Missense_Mutation	SNP	C	G	G			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr11:123810819C>G	uc001pzk.1	+	1	496	c.496C>G	c.(496-498)CTG>GTG	p.L166V		NM_001001965	NP_001001965	Q8NGN0	OR4D5_HUMAN	olfactory receptor, family 4, subfamily D,	166	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)	1		Breast(109;0.00867)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.22)		BRCA - Breast invasive adenocarcinoma(274;4.88e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0399)		GACTATCCAGCTGCCATTCTG	0.478													13	27	---	---	---	---	PASS
OR8B2	26595	broad.mit.edu	37	11	124252313	124252313	+	Silent	SNP	C	T	T			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr11:124252313C>T	uc010sai.1	-	1	927	c.927G>A	c.(925-927)AGG>AGA	p.R309R		NM_001005468	NP_001005468	Q96RD0	OR8B2_HUMAN	olfactory receptor, family 8, subfamily B,	309	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0		Breast(109;0.0115)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;1.49e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0277)		ATATATTTCTCCTCTGAATTT	0.343													6	34	---	---	---	---	PASS
ENO2	2026	broad.mit.edu	37	12	7025668	7025668	+	Missense_Mutation	SNP	T	C	C			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr12:7025668T>C	uc001qru.1	+	3	395	c.173T>C	c.(172-174)TTA>TCA	p.L58S	ENO2_uc009zfi.1_Missense_Mutation_p.L58S|ENO2_uc010sfq.1_Missense_Mutation_p.L58S|ENO2_uc001qrv.1_Missense_Mutation_p.L58S	NM_001975	NP_001966	P09104	ENOG_HUMAN	enolase 2	58					gluconeogenesis|glycolysis	phosphopyruvate hydratase complex|plasma membrane	magnesium ion binding|phosphopyruvate hydratase activity				0						CAGCGTTACTTAGGCAAAGGT	0.572													11	20	---	---	---	---	PASS
A2ML1	144568	broad.mit.edu	37	12	9007400	9007400	+	Missense_Mutation	SNP	A	T	T			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr12:9007400A>T	uc001quz.3	+	22	2835	c.2737A>T	c.(2737-2739)ACA>TCA	p.T913S	A2ML1_uc001qva.1_Missense_Mutation_p.T493S|A2ML1_uc010sgm.1_Missense_Mutation_p.T413S	NM_144670	NP_653271	A8K2U0	A2ML1_HUMAN	alpha-2-macroglobulin-like 1 precursor	757						extracellular space	endopeptidase inhibitor activity			ovary(2)|skin(1)	3						GGTGGAGAAGACACACAGCTC	0.463													11	28	---	---	---	---	PASS
PHC1	1911	broad.mit.edu	37	12	9083501	9083501	+	Silent	SNP	C	G	G			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr12:9083501C>G	uc001qvd.2	+	7	1239	c.1083C>G	c.(1081-1083)CCC>CCG	p.P361P	PHC1_uc001qvc.1_Silent_p.P316P|PHC1_uc010sgn.1_Silent_p.P361P|PHC1_uc001qve.2_Silent_p.P361P	NM_004426	NP_004417	P78364	PHC1_HUMAN	polyhomeotic 1-like	361					multicellular organismal development	PcG protein complex	DNA binding|zinc ion binding			ovary(1)|breast(1)	2						CACCTGCGCCCAGCCAGACAC	0.423													4	11	---	---	---	---	PASS
A2M	2	broad.mit.edu	37	12	9227227	9227227	+	Missense_Mutation	SNP	T	A	A			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr12:9227227T>A	uc001qvk.1	-	29	3798	c.3685A>T	c.(3685-3687)ACC>TCC	p.T1229S	A2M_uc001qvj.1_Missense_Mutation_p.T271S|A2M_uc009zgk.1_Missense_Mutation_p.T1079S	NM_000014	NP_000005	P01023	A2MG_HUMAN	alpha-2-macroglobulin precursor	1229					blood coagulation, intrinsic pathway|negative regulation of complement activation, lectin pathway|platelet activation|platelet degranulation|regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol|extracellular space|platelet alpha granule lumen	enzyme binding|GTPase activator activity|interleukin-1 binding|interleukin-8 binding|serine-type endopeptidase inhibitor activity|tumor necrosis factor binding			central_nervous_system(4)|skin(1)	5					Bacitracin(DB00626)|Becaplermin(DB00102)	GTTGCAGAGGTCAGGTCCTCC	0.547													5	14	---	---	---	---	PASS
PZP	5858	broad.mit.edu	37	12	9309771	9309771	+	Missense_Mutation	SNP	C	G	G			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr12:9309771C>G	uc001qvl.2	-	28	3579	c.3550G>C	c.(3550-3552)GAC>CAC	p.D1184H	PZP_uc009zgl.2_Missense_Mutation_p.D970H	NM_002864	NP_002855			pregnancy-zone protein precursor											ovary(3)|upper_aerodigestive_tract(1)|large_intestine(1)	5						gtgCTCTCACCTTCTTTCACA	0.229													14	17	---	---	---	---	PASS
TMTC1	83857	broad.mit.edu	37	12	29709822	29709822	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr12:29709822G>T	uc001rjb.2	-	10	1794	c.1320C>A	c.(1318-1320)AAC>AAA	p.N440K	TMTC1_uc001riz.2_Missense_Mutation_p.N197K|TMTC1_uc001rja.2_Missense_Mutation_p.N284K|TMTC1_uc001rjc.1_Missense_Mutation_p.N502K	NM_175861	NP_787057	Q8IUR5	TMTC1_HUMAN	transmembrane and tetratricopeptide repeat	548	TPR 3.					integral to membrane	binding				0	Lung NSC(12;7.61e-10)|Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.032)					AAAGAGCCCGGTTATGCTGTG	0.502													20	50	---	---	---	---	PASS
ADAMTS20	80070	broad.mit.edu	37	12	43822241	43822241	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr12:43822241C>T	uc010skx.1	-	26	3748	c.3748G>A	c.(3748-3750)GTT>ATT	p.V1250I	ADAMTS20_uc001rno.1_Missense_Mutation_p.V368I|ADAMTS20_uc001rnp.1_Missense_Mutation_p.V404I	NM_025003	NP_079279	P59510	ATS20_HUMAN	a disintegrin-like and metalloprotease with	1250	TSP type-1 8.					proteinaceous extracellular matrix	zinc ion binding	p.P1250P(1)|p.P1250T(1)		central_nervous_system(5)|ovary(4)|lung(3)|large_intestine(2)|skin(2)|urinary_tract(1)|kidney(1)|pancreas(1)	19	all_cancers(12;2.6e-05)|Lung SC(27;0.184)	Lung NSC(34;0.0569)|all_lung(34;0.129)		GBM - Glioblastoma multiforme(48;0.0473)		AAAGGGCGAACTTCAGGATCA	0.478													9	43	---	---	---	---	PASS
TROAP	10024	broad.mit.edu	37	12	49724003	49724003	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr12:49724003G>A	uc001rtx.3	+	13	1542	c.1375G>A	c.(1375-1377)GGA>AGA	p.G459R	TROAP_uc009zlh.2_Missense_Mutation_p.G459R|TROAP_uc001rty.2_Missense_Mutation_p.G167R	NM_005480	NP_005471	Q12815	TROAP_HUMAN	tastin isoform 1	459					cell adhesion	cytoplasm				ovary(1)	1						CCCTCTTAATGGAGGCTCTTC	0.542													29	94	---	---	---	---	PASS
KCNH3	23416	broad.mit.edu	37	12	49936562	49936562	+	Silent	SNP	G	T	T			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr12:49936562G>T	uc001ruh.1	+	4	779	c.519G>T	c.(517-519)GTG>GTT	p.V173V	KCNH3_uc010smj.1_Silent_p.V113V	NM_012284	NP_036416	Q9ULD8	KCNH3_HUMAN	potassium voltage-gated channel, subfamily H	173	Cytoplasmic (Potential).				regulation of transcription, DNA-dependent	integral to membrane	two-component sensor activity|voltage-gated potassium channel activity				0						GCCGGGCCGTGCTCTACCACC	0.652													5	6	---	---	---	---	PASS
DIP2B	57609	broad.mit.edu	37	12	51090901	51090901	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr12:51090901C>A	uc001rwv.2	+	17	2147	c.1991C>A	c.(1990-1992)CCT>CAT	p.P664H	DIP2B_uc009zlt.2_Missense_Mutation_p.P94H	NM_173602	NP_775873	Q9P265	DIP2B_HUMAN	DIP2 disco-interacting protein 2 homolog B	664						nucleus	catalytic activity|transcription factor binding			ovary(4)|breast(1)|pancreas(1)	6						GGACTGAAGCCTGAGGCCATC	0.493													5	57	---	---	---	---	PASS
CD63	967	broad.mit.edu	37	12	56119959	56119959	+	Silent	SNP	A	G	G			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr12:56119959A>G	uc001shm.2	-	5	609	c.513T>C	c.(511-513)ATT>ATC	p.I171I	CD63_uc009znz.2_Silent_p.I148I|CD63_uc001shn.2_Silent_p.I171I|CD63_uc001sho.2_Silent_p.I171I|CD63_uc001shp.2_Silent_p.I171I	NM_001780	NP_001771	P08962	CD63_HUMAN	CD63 antigen isoform A	171	Extracellular (Potential).				platelet activation|platelet degranulation	integral to plasma membrane|late endosome membrane|lysosomal membrane|platelet dense granule membrane					0						CAGTAACATTAATGCAGCAGG	0.502													24	37	---	---	---	---	PASS
DTX3	196403	broad.mit.edu	37	12	58000741	58000741	+	Missense_Mutation	SNP	A	T	T			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr12:58000741A>T	uc001sow.1	+	5	432	c.95A>T	c.(94-96)GAG>GTG	p.E32V	DTX3_uc001sov.1_Missense_Mutation_p.E25V|DTX3_uc001sox.1_Missense_Mutation_p.E25V|DTX3_uc001soy.1_Missense_Mutation_p.E25V	NM_178502	NP_848597	Q8N9I9	DTX3_HUMAN	deltex homolog 3	32					Notch signaling pathway	cytoplasm	zinc ion binding			breast(1)|central_nervous_system(1)	2	Melanoma(17;0.122)					CTGAGCAAAGAGACCCCAGCC	0.592													61	85	---	---	---	---	PASS
TSPAN31	6302	broad.mit.edu	37	12	58140912	58140912	+	Nonsense_Mutation	SNP	G	T	T			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr12:58140912G>T	uc001spt.2	+	5	710	c.556G>T	c.(556-558)GAG>TAG	p.E186*	TSPAN31_uc009zqb.2_Nonsense_Mutation_p.E102*|TSPAN31_uc010ssa.1_Nonsense_Mutation_p.E108*	NM_005981	NP_005972	Q12999	TSN31_HUMAN	sarcoma amplified sequence	186	Helical; (Potential).				positive regulation of cell proliferation	integral to plasma membrane|membrane fraction					0	all_cancers(7;4.96e-69)|Lung NSC(6;5.5e-25)|all_lung(6;3.87e-23)|all_epithelial(6;1.66e-15)|Glioma(12;6.95e-05)|all_neural(12;0.00016)|Melanoma(17;0.122)		GBM - Glioblastoma multiforme(5;4.21e-120)|all cancers(5;3.75e-83)|BRCA - Breast invasive adenocarcinoma(9;0.0294)			TAGCTTTACAGAGGTAACATT	0.438													8	124	---	---	---	---	PASS
CPSF6	11052	broad.mit.edu	37	12	69650536	69650536	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr12:69650536C>A	uc001sut.3	+	4	544	c.434C>A	c.(433-435)CCT>CAT	p.P145H	CPSF6_uc001suu.3_Missense_Mutation_p.P145H|CPSF6_uc010stk.1_5'Flank	NM_007007	NP_008938	Q16630	CPSF6_HUMAN	cleavage and polyadenylation specific factor 6,	145	RRM.|Necessary for interaction with NUDT21/CPSF5.				mRNA polyadenylation|protein tetramerization	mRNA cleavage factor complex|paraspeckles|ribonucleoprotein complex	mRNA binding|nucleotide binding|protein binding				0	all_epithelial(5;2.47e-36)|Lung NSC(4;1.1e-32)|all_lung(4;6.26e-31)|Breast(13;1.59e-06)|Esophageal squamous(21;0.187)		Epithelial(6;4.89e-17)|BRCA - Breast invasive adenocarcinoma(5;8.5e-10)|Lung(24;6.04e-05)|LUAD - Lung adenocarcinoma(15;0.00107)|STAD - Stomach adenocarcinoma(21;0.0151)|LUSC - Lung squamous cell carcinoma(43;0.171)|Kidney(9;0.241)			GATCTGTTACCTAAAAGAGAA	0.383													6	96	---	---	---	---	PASS
TRHDE	29953	broad.mit.edu	37	12	72666957	72666957	+	Missense_Mutation	SNP	G	C	C			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr12:72666957G>C	uc001sxa.2	+	1	429	c.399G>C	c.(397-399)TGG>TGC	p.W133C	LOC283392_uc010stv.1_5'UTR	NM_013381	NP_037513	Q9UKU6	TRHDE_HUMAN	thyrotropin-releasing hormone degrading enzyme	133	Extracellular (Potential).				cell-cell signaling|proteolysis|signal transduction	integral to plasma membrane	aminopeptidase activity|metallopeptidase activity|zinc ion binding			ovary(2)|skin(1)	3						GGGAGCCGTGGGAGCCGTGGA	0.706													6	13	---	---	---	---	PASS
ACSS3	79611	broad.mit.edu	37	12	81472035	81472035	+	Missense_Mutation	SNP	C	T	T	rs12824208		TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr12:81472035C>T	uc001szl.1	+	1	227	c.136C>T	c.(136-138)CTC>TTC	p.L46F	ACSS3_uc001szm.1_Missense_Mutation_p.L46F	NM_024560	NP_078836	Q9H6R3	ACSS3_HUMAN	acyl-CoA synthetase short-chain family member 3	46						mitochondrion	acetate-CoA ligase activity|ATP binding			ovary(1)|lung(1)|central_nervous_system(1)|skin(1)	4						GCGGGGCGGTCTCGGGGGCCG	0.741													6	4	---	---	---	---	PASS
METAP2	10988	broad.mit.edu	37	12	95907481	95907481	+	Missense_Mutation	SNP	T	C	C			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr12:95907481T>C	uc001tec.2	+	11	1372	c.1238T>C	c.(1237-1239)CTT>CCT	p.L413P	METAP2_uc010suv.1_Missense_Mutation_p.L390P|METAP2_uc009ztd.2_Missense_Mutation_p.L377P|METAP2_uc001ted.2_Missense_Mutation_p.L412P|METAP2_uc001tef.2_Missense_Mutation_p.L390P|METAP2_uc001tee.2_RNA	NM_006838	NP_006829	P50579	AMPM2_HUMAN	methionyl aminopeptidase 2	413					N-terminal protein amino acid modification|peptidyl-methionine modification|protein processing|proteolysis	cytoplasm	aminopeptidase activity|metal ion binding|metalloexopeptidase activity				0					L-Methionine(DB00134)	TTTGGAACCCTTGCCTTCTGC	0.413													28	83	---	---	---	---	PASS
ALDH1L2	160428	broad.mit.edu	37	12	105459074	105459074	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr12:105459074G>T	uc001tlc.2	-	6	884	c.757C>A	c.(757-759)CCT>ACT	p.P253T	ALDH1L2_uc009zuo.2_5'UTR|ALDH1L2_uc009zup.2_RNA	NM_001034173	NP_001029345	Q3SY69	AL1L2_HUMAN	aldehyde dehydrogenase 1 family, member L2	253					10-formyltetrahydrofolate catabolic process|biosynthetic process	mitochondrion	acyl carrier activity|cofactor binding|formyltetrahydrofolate dehydrogenase activity|hydroxymethyl-, formyl- and related transferase activity|methyltransferase activity|phosphopantetheine binding			skin(1)	1						CAAGCTCCAGGGACTTTATCA	0.463													5	78	---	---	---	---	PASS
KDM2B	84678	broad.mit.edu	37	12	121877660	121877660	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr12:121877660C>T	uc001uat.2	-	22	3933	c.3829G>A	c.(3829-3831)GAC>AAC	p.D1277N	KDM2B_uc001uaq.2_Missense_Mutation_p.D717N|KDM2B_uc010szy.1_Missense_Mutation_p.D717N|KDM2B_uc001uar.2_Missense_Mutation_p.D868N|KDM2B_uc001uas.2_Missense_Mutation_p.D1208N|KDM2B_uc001uau.2_Intron|KDM2B_uc001uao.2_Missense_Mutation_p.D525N|KDM2B_uc010szx.1_Missense_Mutation_p.D525N|KDM2B_uc001uap.2_RNA	NM_032590	NP_115979	Q8NHM5	KDM2B_HUMAN	F-box and leucine-rich repeat protein 10 isoform	1277	LRR 5.				embryonic camera-type eye morphogenesis|fourth ventricle development|histone H2A monoubiquitination|initiation of neural tube closure|lateral ventricle development|midbrain development|midbrain-hindbrain boundary morphogenesis|negative regulation of neural precursor cell proliferation|negative regulation of neuron apoptosis|negative regulation of transcription from RNA polymerase II promoter|spermatogenesis|third ventricle development|transcription, DNA-dependent	nucleolus	DNA binding|histone demethylase activity (H3-K36 specific)|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|protein binding|rRNA binding|zinc ion binding			ovary(1)|skin(1)	2						CCTGACTCACCAGACAGGTTG	0.547													8	12	---	---	---	---	PASS
TMEM132D	121256	broad.mit.edu	37	12	129566492	129566492	+	Missense_Mutation	SNP	C	G	G			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr12:129566492C>G	uc009zyl.1	-	7	2063	c.1735G>C	c.(1735-1737)GTC>CTC	p.V579L	TMEM132D_uc001uia.2_Missense_Mutation_p.V117L	NM_133448	NP_597705	Q14C87	T132D_HUMAN	transmembrane protein 132D precursor	579	Extracellular (Potential).					integral to membrane				ovary(10)|pancreas(2)|upper_aerodigestive_tract(1)|skin(1)	14	all_neural(191;0.101)|Medulloblastoma(191;0.163)	all_epithelial(31;0.0934)|Breast(359;0.133)		OV - Ovarian serous cystadenocarcinoma(86;0.000288)|Epithelial(86;0.0116)|all cancers(50;0.0246)		TGCGTCAGGACCCGCACCATG	0.647													5	23	---	---	---	---	PASS
TMEM132D	121256	broad.mit.edu	37	12	129822210	129822210	+	Missense_Mutation	SNP	T	C	C			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr12:129822210T>C	uc009zyl.1	-	4	1596	c.1268A>G	c.(1267-1269)AAG>AGG	p.K423R		NM_133448	NP_597705	Q14C87	T132D_HUMAN	transmembrane protein 132D precursor	423	Extracellular (Potential).					integral to membrane				ovary(10)|pancreas(2)|upper_aerodigestive_tract(1)|skin(1)	14	all_neural(191;0.101)|Medulloblastoma(191;0.163)	all_epithelial(31;0.0934)|Breast(359;0.133)		OV - Ovarian serous cystadenocarcinoma(86;0.000288)|Epithelial(86;0.0116)|all cancers(50;0.0246)		AATCAAGTCCTTTGGGCTCAC	0.612													33	131	---	---	---	---	PASS
C13orf15	28984	broad.mit.edu	37	13	42032568	42032568	+	Missense_Mutation	SNP	C	G	G			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr13:42032568C>G	uc001uyi.2	+	2	499	c.197C>G	c.(196-198)GCC>GGC	p.A66G		NM_014059	NP_054778	Q9H4X1	RGC32_HUMAN	response gene to complement 32	66	Ser/Thr-rich.				cell cycle|regulation of cyclin-dependent protein kinase activity	microtubule organizing center|nucleus					0		Lung NSC(96;7.5e-06)|Prostate(109;0.0181)|Breast(139;0.0204)|Lung SC(185;0.0262)|Hepatocellular(98;0.114)		all cancers(112;8.62e-09)|Epithelial(112;8.99e-06)|OV - Ovarian serous cystadenocarcinoma(117;0.000504)|GBM - Glioblastoma multiforme(144;0.000909)|BRCA - Breast invasive adenocarcinoma(63;0.0679)		CGCAGCAGCGCCAGTGTCAGC	0.682													5	0	---	---	---	---	PASS
RB1	5925	broad.mit.edu	37	13	49030452	49030452	+	Nonsense_Mutation	SNP	A	T	T			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr13:49030452A>T	uc001vcb.2	+	19	2093	c.1927A>T	c.(1927-1929)AAA>TAA	p.K643*		NM_000321	NP_000312	P06400	RB_HUMAN	retinoblastoma 1	643	Pocket; binds T and E1A.|Domain B.				androgen receptor signaling pathway|cell cycle arrest|chromatin remodeling|G1 phase of mitotic cell cycle|interspecies interaction between organisms|maintenance of mitotic sister chromatid cohesion|mitotic cell cycle G1/S transition checkpoint|myoblast differentiation|negative regulation of cell growth|negative regulation of protein kinase activity|negative regulation of S phase of mitotic cell cycle|negative regulation of sequence-specific DNA binding transcription factor activity|positive regulation of mitotic metaphase/anaphase transition|protein localization to chromosome, centromeric region|Ras protein signal transduction|regulation of centromere complex assembly|regulation of cohesin localization to chromatin|regulation of lipid kinase activity|regulation of transcription involved in G1/S phase of mitotic cell cycle|S phase of mitotic cell cycle|sister chromatid biorientation	chromatin|PML body|Rb-E2F complex|SWI/SNF complex	androgen receptor binding|DNA binding|kinase binding|phosphoprotein binding|sequence-specific DNA binding transcription factor activity|transcription coactivator activity|transcription factor binding|ubiquitin protein ligase binding	p.?(6)		lung(94)|eye(89)|central_nervous_system(47)|bone(22)|breast(21)|urinary_tract(17)|haematopoietic_and_lymphoid_tissue(14)|ovary(10)|prostate(9)|soft_tissue(8)|skin(7)|endometrium(5)|cervix(3)|liver(3)|salivary_gland(2)|stomach(2)|oesophagus(1)|adrenal_gland(1)|kidney(1)|gastrointestinal_tract_(site_indeterminate)(1)|pituitary(1)	358		all_cancers(8;6.9e-71)|all_epithelial(8;4.61e-22)|Acute lymphoblastic leukemia(8;1.1e-21)|all_hematologic(8;2.3e-21)|all_lung(13;1.51e-09)|Lung NSC(96;7.03e-07)|Breast(56;1.53e-05)|Prostate(109;0.000493)|Myeloproliferative disorder(33;0.0179)|Hepatocellular(98;0.0207)|all_neural(104;0.0227)|Glioma(44;0.0286)|Lung SC(185;0.0301)		GBM - Glioblastoma multiforme(2;9.98e-18)|LUSC - Lung squamous cell carcinoma(3;0.013)	Insulin Glargine recombinant(DB00047)|Insulin Lyspro recombinant(DB00046)|Insulin recombinant(DB00030)|Insulin, porcine(DB00071)	GAAGCCATTGAAATCTACCTC	0.284		6	D|Mis|N|F|S		retinoblastoma|sarcoma|breast|small cell lung	retinoblastoma|sarcoma|breast|small cell lung			Hereditary_Retinoblastoma	TCGA GBM(7;6.82e-08)|TSP Lung(12;0.097)|TCGA Ovarian(6;0.080)			13	7	---	---	---	---	PASS
RCBTB2	1102	broad.mit.edu	37	13	49096059	49096059	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr13:49096059G>T	uc001vch.2	-	4	388	c.17C>A	c.(16-18)CCT>CAT	p.P6H	RCBTB2_uc010tgg.1_Intron|RCBTB2_uc001vci.2_Intron|RCBTB2_uc010tgh.1_Intron|RCBTB2_uc001vcj.2_Intron|RCBTB2_uc010acv.1_Intron|RCBTB2_uc010tgi.1_Intron	NM_001268	NP_001259	O95199	RCBT2_HUMAN	regulator of chromosome condensation and BTB	6							Ran guanyl-nucleotide exchange factor activity			ovary(2)|lung(2)|skin(1)	5		all_cancers(8;4.86e-71)|all_epithelial(8;2.11e-22)|Acute lymphoblastic leukemia(8;1.1e-21)|all_hematologic(8;2.3e-21)|all_lung(13;2.3e-10)|Lung NSC(96;1.07e-07)|Breast(56;1.53e-05)|Prostate(109;0.00174)|Hepatocellular(98;0.00826)|Myeloproliferative disorder(33;0.0179)|all_neural(104;0.0227)|Glioma(44;0.0286)|Lung SC(185;0.0301)		GBM - Glioblastoma multiforme(99;1.8e-09)|LUSC - Lung squamous cell carcinoma(3;0.116)		AGAGAAAAGAGGAAGTTCTTC	0.443													5	56	---	---	---	---	PASS
TDRD3	81550	broad.mit.edu	37	13	61083927	61083927	+	Nonsense_Mutation	SNP	G	T	T			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr13:61083927G>T	uc001via.2	+	9	1398	c.610G>T	c.(610-612)GAA>TAA	p.E204*	TDRD3_uc010aef.2_Nonsense_Mutation_p.E29*|TDRD3_uc001vhz.3_Nonsense_Mutation_p.E204*|TDRD3_uc010aeg.2_Nonsense_Mutation_p.E297*|TDRD3_uc001vib.3_Nonsense_Mutation_p.E203*	NM_030794	NP_110421	Q9H7E2	TDRD3_HUMAN	tudor domain containing 3 isoform 2	204	UBA.				chromatin modification	cytoplasm|nucleus	chromatin binding|methylated histone residue binding|nucleic acid binding|transcription coactivator activity			upper_aerodigestive_tract(1)|skin(1)	2		Prostate(109;0.173)|Breast(118;0.174)		GBM - Glioblastoma multiforme(99;0.000291)		GCACATAACGGAAATGGGCTT	0.413													37	12	---	---	---	---	PASS
UGGT2	55757	broad.mit.edu	37	13	96513122	96513122	+	Silent	SNP	C	T	T			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr13:96513122C>T	uc001vmt.2	-	32	3830	c.3660G>A	c.(3658-3660)TTG>TTA	p.L1220L		NM_020121	NP_064506	Q9NYU1	UGGG2_HUMAN	UDP-glucose ceramide glucosyltransferase-like 2	1220	Glucosyltransferase.				post-translational protein modification|protein folding|protein N-linked glycosylation via asparagine	endoplasmic reticulum lumen|ER-Golgi intermediate compartment	UDP-glucose:glycoprotein glucosyltransferase activity			ovary(2)|central_nervous_system(1)	3						TTTCTTTATGCAAGCTTACTG	0.264													4	6	---	---	---	---	PASS
SLC10A2	6555	broad.mit.edu	37	13	103703676	103703676	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr13:103703676G>T	uc001vpy.3	-	4	1289	c.692C>A	c.(691-693)ACA>AAA	p.T231K		NM_000452	NP_000443	Q12908	NTCP2_HUMAN	solute carrier family 10 (sodium/bile acid	231	Helical; (Potential).				bile acid metabolic process|organic anion transport	integral to plasma membrane	bile acid:sodium symporter activity			ovary(3)|skin(1)	4	all_neural(89;0.0662)|Medulloblastoma(90;0.163)|Lung SC(71;0.211)					AGGAAATATTGTTCCTATAAT	0.478													31	2	---	---	---	---	PASS
OR4N5	390437	broad.mit.edu	37	14	20612464	20612464	+	Silent	SNP	C	A	A			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr14:20612464C>A	uc010tla.1	+	1	570	c.570C>A	c.(568-570)ACC>ACA	p.T190T		NM_001004724	NP_001004724	Q8IXE1	OR4N5_HUMAN	olfactory receptor, family 4, subfamily N,	190	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)	1	all_cancers(95;0.00108)		Epithelial(56;7.58e-07)|all cancers(55;3.84e-06)	GBM - Glioblastoma multiforme(265;0.0143)		TGGCCTGCACCAATACCTTTG	0.532													15	25	---	---	---	---	PASS
CTSG	1511	broad.mit.edu	37	14	25042980	25042980	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr14:25042980C>T	uc001wpq.2	-	5	668	c.631G>A	c.(631-633)GCC>ACC	p.A211T		NM_001911	NP_001902	P08311	CATG_HUMAN	cathepsin G preproprotein	211	Peptidase S1.				immune response|proteolysis	cell surface|extracellular space|plasma membrane|stored secretory granule	heparin binding|serine-type endopeptidase activity			ovary(2)	2				GBM - Glioblastoma multiforme(265;0.0269)		ATGCCGTGGGCCACATTGTTA	0.572													22	32	---	---	---	---	PASS
BAZ1A	11177	broad.mit.edu	37	14	35264907	35264907	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr14:35264907G>T	uc001wsk.2	-	10	1761	c.1193C>A	c.(1192-1194)CCT>CAT	p.P398H	BAZ1A_uc001wsl.2_Missense_Mutation_p.P398H	NM_013448	NP_038476	Q9NRL2	BAZ1A_HUMAN	bromodomain adjacent to zinc finger domain, 1A	398					chromatin remodeling|regulation of transcription, DNA-dependent|transcription, DNA-dependent	ACF complex	zinc ion binding			lung(2)|central_nervous_system(2)|ovary(1)|breast(1)|skin(1)	7	Breast(36;0.0388)|Hepatocellular(127;0.158)		LUAD - Lung adenocarcinoma(48;7.23e-05)|Lung(238;0.00019)|Epithelial(34;0.0793)|all cancers(34;0.175)	GBM - Glioblastoma multiforme(112;0.0659)		ATCTTCTCTAGGTTTACTCCA	0.323													5	50	---	---	---	---	PASS
RPL10L	140801	broad.mit.edu	37	14	47120763	47120763	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr14:47120763C>A	uc001wwg.2	-	1	266	c.177G>T	c.(175-177)CAG>CAT	p.Q59H		NM_080746	NP_542784	Q96L21	RL10L_HUMAN	ribosomal protein L10-like protein	59					spermatogenesis|translation	cytosolic large ribosomal subunit|nucleus	structural constituent of ribosome			ovary(1)	1						CAGAAGACAGCTGCTCATATT	0.512													20	24	---	---	---	---	PASS
RTN1	6252	broad.mit.edu	37	14	60213061	60213061	+	Missense_Mutation	SNP	A	G	G			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr14:60213061A>G	uc001xen.1	-	2	589	c.380T>C	c.(379-381)CTT>CCT	p.L127P		NM_021136	NP_066959	Q16799	RTN1_HUMAN	reticulon 1 isoform A	127					neuron differentiation	integral to endoplasmic reticulum membrane	signal transducer activity			ovary(2)|central_nervous_system(2)	4				OV - Ovarian serous cystadenocarcinoma(108;0.0968)		TTCCTTCTGAAGAATTCCAGT	0.488													11	16	---	---	---	---	PASS
RTN1	6252	broad.mit.edu	37	14	60213190	60213190	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr14:60213190C>T	uc001xen.1	-	2	460	c.251G>A	c.(250-252)GGT>GAT	p.G84D		NM_021136	NP_066959	Q16799	RTN1_HUMAN	reticulon 1 isoform A	84					neuron differentiation	integral to endoplasmic reticulum membrane	signal transducer activity			ovary(2)|central_nervous_system(2)	4				OV - Ovarian serous cystadenocarcinoma(108;0.0968)		ACTGGAAACACCTGCCACACC	0.517													12	9	---	---	---	---	PASS
KCNH5	27133	broad.mit.edu	37	14	63416964	63416964	+	Missense_Mutation	SNP	T	C	C			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr14:63416964T>C	uc001xfx.2	-	7	1307	c.1256A>G	c.(1255-1257)TAC>TGC	p.Y419C	KCNH5_uc001xfy.2_Missense_Mutation_p.Y419C|KCNH5_uc001xfz.1_Missense_Mutation_p.Y361C|KCNH5_uc001xga.2_Missense_Mutation_p.Y361C	NM_139318	NP_647479	Q8NCM2	KCNH5_HUMAN	potassium voltage-gated channel, subfamily H,	419	Extracellular (Potential).				regulation of transcription, DNA-dependent	integral to membrane	calmodulin binding|two-component sensor activity|voltage-gated potassium channel activity			ovary(4)|skin(4)|central_nervous_system(1)	9				OV - Ovarian serous cystadenocarcinoma(108;0.00958)|BRCA - Breast invasive adenocarcinoma(234;0.168)		AGAGGACACGTACAATGAATC	0.478													11	23	---	---	---	---	PASS
RAD51L1	5890	broad.mit.edu	37	14	68292250	68292250	+	Missense_Mutation	SNP	C	G	G			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr14:68292250C>G	uc001xkf.1	+	3	218	c.154C>G	c.(154-156)CTT>GTT	p.L52V	RAD51L1_uc010aqq.2_Missense_Mutation_p.L52V|RAD51L1_uc001xkd.2_Missense_Mutation_p.L52V|RAD51L1_uc010aqr.2_5'UTR|RAD51L1_uc001xke.2_Missense_Mutation_p.L52V|RAD51L1_uc010aqs.1_Missense_Mutation_p.L52V|RAD51L1_uc001xkg.1_Missense_Mutation_p.L52V	NM_133509	NP_598193	O15315	RA51B_HUMAN	RAD51-like 1 isoform 3	52					blood coagulation|DNA repair|reciprocal meiotic recombination	nucleoplasm	ATP binding|DNA binding|DNA-dependent ATPase activity				0				UCEC - Uterine corpus endometrioid carcinoma (185;0.163)|all cancers(60;3.9e-06)|OV - Ovarian serous cystadenocarcinoma(108;0.000103)|BRCA - Breast invasive adenocarcinoma(234;0.000421)		TGTCCATGAACTTCTATGTAT	0.363			T	HMGA2	lipoma|uterine leiomyoma			Direct_reversal_of_damage|Homologous_recombination					18	23	---	---	---	---	PASS
PSEN1	5663	broad.mit.edu	37	14	73659572	73659572	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr14:73659572G>A	uc001xnr.2	+	7	1053	c.769G>A	c.(769-771)GAT>AAT	p.D257N	PSEN1_uc001xnv.2_Missense_Mutation_p.D253N|PSEN1_uc010ark.2_Missense_Mutation_p.D253N|PSEN1_uc001xnt.1_RNA|PSEN1_uc001xnu.2_RNA	NM_000021	NP_000012	P49768	PSN1_HUMAN	presenilin 1 isoform I-467	257	Helical; (Potential).	Probable.		D->E: Abolishes gamma-secretase activity. Reduces production of amyloid beta in APP processing. Accumulation of full-length PS1. Loss of binding of transition state analog gamma-secretase inhibitor.|D->A: Loss of endoproteolytic cleavage; reduces production of amyloid beta in APP processing and of NICD in NOTCH1 processing.	amyloid precursor protein catabolic process|anti-apoptosis|beta-amyloid metabolic process|cell-cell adhesion|induction of apoptosis by extracellular signals|membrane protein ectodomain proteolysis|membrane protein intracellular domain proteolysis|nerve growth factor receptor signaling pathway|Notch receptor processing|Notch signaling pathway|smooth endoplasmic reticulum calcium ion homeostasis	apical plasma membrane|axon|cell cortex|cell surface|centrosome|ciliary rootlet|dendritic shaft|endoplasmic reticulum membrane|gamma-secretase complex|Golgi membrane|growth cone|integral to plasma membrane|kinetochore|lysosomal membrane|membrane raft|mitochondrial inner membrane|neuromuscular junction|neuronal cell body|nuclear outer membrane|perinuclear region of cytoplasm|rough endoplasmic reticulum|smooth endoplasmic reticulum|Z disc	aspartic-type endopeptidase activity|beta-catenin binding|cadherin binding|calcium channel activity|PDZ domain binding			breast(1)|kidney(1)	2				BRCA - Breast invasive adenocarcinoma(234;0.00394)|OV - Ovarian serous cystadenocarcinoma(108;0.075)		TTCAGTATATGGTAAAACCCA	0.423													19	32	---	---	---	---	PASS
YLPM1	56252	broad.mit.edu	37	14	75264286	75264286	+	Missense_Mutation	SNP	T	G	G			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr14:75264286T>G	uc001xqj.3	+	5	2410	c.2286T>G	c.(2284-2286)TTT>TTG	p.F762L	YLPM1_uc001xql.3_RNA	NM_019589	NP_062535	P49750	YLPM1_HUMAN	YLP motif containing 1	567					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nuclear speck				ovary(2)|pancreas(1)	3			KIRC - Kidney renal clear cell carcinoma(43;0.238)	BRCA - Breast invasive adenocarcinoma(234;0.00162)		CTTGTAGATTTGATGGTCCTC	0.408													6	1	---	---	---	---	PASS
EML5	161436	broad.mit.edu	37	14	89087225	89087225	+	Missense_Mutation	SNP	A	G	G			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr14:89087225A>G	uc001xxg.2	-	39	5434	c.5248T>C	c.(5248-5250)TGT>CGT	p.C1750R	EML5_uc001xxf.2_Missense_Mutation_p.C537R|EML5_uc001xxd.2_5'Flank|EML5_uc001xxe.2_Missense_Mutation_p.C99R	NM_183387	NP_899243	Q05BV3	EMAL5_HUMAN	echinoderm microtubule associated protein like	1742	WD 26.					cytoplasm|microtubule				ovary(3)	3						GGGCTGTAACACACAGTACGA	0.343													9	11	---	---	---	---	PASS
SERPINA10	51156	broad.mit.edu	37	14	94752583	94752583	+	Silent	SNP	A	G	G			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr14:94752583A>G	uc001yct.2	-	4	1471	c.1005T>C	c.(1003-1005)GTT>GTC	p.V335V	SERPINA10_uc001ycu.3_Silent_p.V335V	NM_016186	NP_057270	Q9UK55	ZPI_HUMAN	serine (or cysteine) proteinase inhibitor, clade	335					regulation of proteolysis	extracellular region	serine-type endopeptidase inhibitor activity			ovary(2)|skin(1)	3		all_cancers(154;0.105)		Epithelial(152;0.135)|COAD - Colon adenocarcinoma(157;0.207)|all cancers(159;0.221)		TCGGAAAGAAAACTTCCATGT	0.408													10	21	---	---	---	---	PASS
SERPINA4	5267	broad.mit.edu	37	14	95030166	95030166	+	Missense_Mutation	SNP	A	C	C			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr14:95030166A>C	uc001ydk.2	+	2	413	c.347A>C	c.(346-348)GAT>GCT	p.D116A	SERPINA4_uc010avd.2_Missense_Mutation_p.D153A|SERPINA4_uc001ydl.2_Missense_Mutation_p.D116A	NM_006215	NP_006206	P29622	KAIN_HUMAN	serine (or cysteine) proteinase inhibitor, clade	116					regulation of proteolysis	extracellular space	serine-type endopeptidase inhibitor activity			ovary(3)|skin(1)	4				COAD - Colon adenocarcinoma(157;0.211)		TCTGAGTCCGATGTCCATAGG	0.637													8	28	---	---	---	---	PASS
C14orf73	91828	broad.mit.edu	37	14	103574849	103574849	+	Silent	SNP	C	T	T			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr14:103574849C>T	uc001ymk.2	+	10	2047	c.1971C>T	c.(1969-1971)GAC>GAT	p.D657D		NM_001077594	NP_001071062	Q17RC7	EX3L4_HUMAN	hypothetical protein LOC91828	657											0		Melanoma(154;0.155)	Epithelial(46;0.221)			GCTACCCCGACATCAGGTGTG	0.597													37	61	---	---	---	---	PASS
AHNAK2	113146	broad.mit.edu	37	14	105406088	105406088	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr14:105406088C>T	uc010axc.1	-	7	15820	c.15700G>A	c.(15700-15702)GAG>AAG	p.E5234K	AHNAK2_uc001ypx.2_Missense_Mutation_p.E5134K	NM_138420	NP_612429	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	5234						nucleus				ovary(1)	1		all_cancers(154;0.115)|Melanoma(154;0.155)|all_epithelial(191;0.183)	all cancers(16;0.000479)|OV - Ovarian serous cystadenocarcinoma(23;0.00659)|Epithelial(46;0.0151)|GBM - Glioblastoma multiforme(11;0.116)			ACAAGGAACTCTTTGACTTTA	0.552													19	217	---	---	---	---	PASS
AHNAK2	113146	broad.mit.edu	37	14	105410247	105410247	+	Missense_Mutation	SNP	C	G	G			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr14:105410247C>G	uc010axc.1	-	7	11661	c.11541G>C	c.(11539-11541)AAG>AAC	p.K3847N	AHNAK2_uc001ypx.2_Missense_Mutation_p.K3747N	NM_138420	NP_612429	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	3847						nucleus				ovary(1)	1		all_cancers(154;0.115)|Melanoma(154;0.155)|all_epithelial(191;0.183)	all cancers(16;0.000479)|OV - Ovarian serous cystadenocarcinoma(23;0.00659)|Epithelial(46;0.0151)|GBM - Glioblastoma multiforme(11;0.116)			GGTCAGTGGTCTTGAGGTCCC	0.637													7	151	---	---	---	---	PASS
TJP1	7082	broad.mit.edu	37	15	30024886	30024886	+	Nonsense_Mutation	SNP	G	A	A			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr15:30024886G>A	uc001zcr.2	-	14	2345	c.1870C>T	c.(1870-1872)CAG>TAG	p.Q624*	TJP1_uc010azl.2_Nonsense_Mutation_p.Q612*|TJP1_uc001zcq.2_Nonsense_Mutation_p.Q628*|TJP1_uc001zcs.2_Nonsense_Mutation_p.Q624*	NM_003257	NP_003248	Q07157	ZO1_HUMAN	tight junction protein 1 isoform a	624	Guanylate kinase-like.				cell-cell junction assembly|cellular component disassembly involved in apoptosis	basolateral plasma membrane|cell-cell adherens junction|Golgi apparatus|tight junction				ovary(4)|central_nervous_system(1)|pancreas(1)	6		all_lung(180;7.48e-11)|Breast(32;0.000153)		all cancers(64;3.29e-10)|Epithelial(43;5.34e-09)|BRCA - Breast invasive adenocarcinoma(123;0.0034)|GBM - Glioblastoma multiforme(186;0.0139)|Lung(196;0.186)		TGAACAGGCTGAGCGGACAAA	0.433													36	9	---	---	---	---	PASS
SPINT1	6692	broad.mit.edu	37	15	41145767	41145767	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr15:41145767C>A	uc001zna.2	+	4	888	c.684C>A	c.(682-684)GAC>GAA	p.D228E	SPINT1_uc001znb.2_Missense_Mutation_p.D228E|SPINT1_uc001znc.2_Missense_Mutation_p.D228E|SPINT1_uc010ucs.1_Missense_Mutation_p.D228E	NM_181642	NP_857593	O43278	SPIT1_HUMAN	serine peptidase inhibitor, Kunitz type 1	228						extracellular region|membrane fraction	protein binding|serine-type endopeptidase inhibitor activity			ovary(1)	1		all_cancers(109;1.35e-17)|all_epithelial(112;3.78e-15)|Lung NSC(122;9.68e-11)|all_lung(180;2.25e-09)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.0946)		GBM - Glioblastoma multiforme(113;2.91e-05)|COAD - Colon adenocarcinoma(120;0.153)|BRCA - Breast invasive adenocarcinoma(123;0.166)		CTAGCTCAGACCACCCAGAGG	0.592													11	10	---	---	---	---	PASS
TP53BP1	7158	broad.mit.edu	37	15	43769871	43769871	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr15:43769871C>A	uc001zrs.2	-	8	1008	c.860G>T	c.(859-861)AGT>ATT	p.S287I	TP53BP1_uc010udp.1_Missense_Mutation_p.S287I|TP53BP1_uc001zrq.3_Missense_Mutation_p.S292I|TP53BP1_uc001zrr.3_Missense_Mutation_p.S292I|TP53BP1_uc010udq.1_Missense_Mutation_p.S292I	NM_005657	NP_005648	Q12888	TP53B_HUMAN	tumor protein p53 binding protein 1 isoform 3	287					double-strand break repair via homologous recombination|positive regulation of transcription from RNA polymerase II promoter	condensed chromosome kinetochore|cytoplasm|nucleoplasm	p53 binding|RNA polymerase II activating transcription factor binding|RNA polymerase II transcription cofactor activity			ovary(2)|skin(2)|large_intestine(1)|pancreas(1)|kidney(1)	7		all_cancers(109;6.94e-11)|all_epithelial(112;2.69e-09)|Lung NSC(122;7.86e-07)|all_lung(180;7.84e-06)|Melanoma(134;0.0728)		GBM - Glioblastoma multiforme(94;1.59e-06)		CTGCAGTCCACTTTCCATAAG	0.438								Direct_reversal_of_damage|Other_conserved_DNA_damage_response_genes					28	28	---	---	---	---	PASS
SEMA7A	8482	broad.mit.edu	37	15	74704328	74704328	+	Silent	SNP	C	T	T			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr15:74704328C>T	uc002axv.2	-	11	1360	c.1320G>A	c.(1318-1320)GTG>GTA	p.V440V	SEMA7A_uc010ulk.1_Silent_p.V275V|SEMA7A_uc010ull.1_Silent_p.V426V	NM_003612	NP_003603	O75326	SEM7A_HUMAN	semaphorin 7A isoform 1 preproprotein	440	Sema.				axon guidance|immune response|inflammatory response|integrin-mediated signaling pathway|positive regulation of axon extension|positive regulation of ERK1 and ERK2 cascade|positive regulation of macrophage cytokine production|regulation of inflammatory response	anchored to membrane|external side of plasma membrane	receptor activity			breast(1)|central_nervous_system(1)	2						CCCCCGGTTCCACCACCTTGT	0.637													9	38	---	---	---	---	PASS
MAN2C1	4123	broad.mit.edu	37	15	75656914	75656914	+	Missense_Mutation	SNP	T	A	A			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr15:75656914T>A	uc002baf.2	-	5	532	c.515A>T	c.(514-516)CAG>CTG	p.Q172L	MAN2C1_uc002bag.2_Missense_Mutation_p.Q172L|MAN2C1_uc002bah.2_Missense_Mutation_p.Q172L|MAN2C1_uc010bkk.2_Missense_Mutation_p.Q172L|MAN2C1_uc010umi.1_Intron|MAN2C1_uc010umj.1_RNA|MAN2C1_uc010umk.1_RNA	NM_006715	NP_006706	Q9NTJ4	MA2C1_HUMAN	mannosidase, alpha, class 2C, member 1	172					mannose metabolic process		alpha-mannosidase activity|carbohydrate binding|protein binding|zinc ion binding				0						CCGGCTCAGCTGGAACATCTT	0.592													11	13	---	---	---	---	PASS
FBXO22	26263	broad.mit.edu	37	15	76205551	76205551	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr15:76205551G>A	uc002bbk.2	+	3	392	c.287G>A	c.(286-288)CGC>CAC	p.R96H	FBXO22_uc002bbj.1_Missense_Mutation_p.R96H|FBXO22_uc002bbl.2_5'UTR	NM_147188	NP_671717	Q8NEZ5	FBX22_HUMAN	F-box only protein 22 isoform a	96					ubiquitin-dependent protein catabolic process		ubiquitin-protein ligase activity				0						CAGAATGTTCGCATCTTACCA	0.338													14	40	---	---	---	---	PASS
TMED3	23423	broad.mit.edu	37	15	79606172	79606172	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr15:79606172C>T	uc002beu.2	+	2	343	c.242C>T	c.(241-243)ACG>ATG	p.T81M	TMED3_uc010unj.1_Missense_Mutation_p.T81M|TMED3_uc002bev.2_RNA	NM_007364	NP_031390	Q9Y3Q3	TMED3_HUMAN	transmembrane emp24 domain containing 3	81	Lumenal (Potential).|GOLD.				protein transport	ER-Golgi intermediate compartment membrane|Golgi apparatus|integral to membrane				ovary(1)|skin(1)	2						TACAGAGAAACGAAGAAGCAG	0.478													26	70	---	---	---	---	PASS
AKAP13	11214	broad.mit.edu	37	15	86198831	86198831	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr15:86198831G>A	uc002blv.1	+	11	4728	c.4558G>A	c.(4558-4560)GGT>AGT	p.G1520S	AKAP13_uc002blt.1_Missense_Mutation_p.G1520S|AKAP13_uc002blu.1_Missense_Mutation_p.G1520S|AKAP13_uc010bnf.1_Missense_Mutation_p.G160S|AKAP13_uc002blw.1_Missense_Mutation_p.G5S|AKAP13_uc010bne.1_Missense_Mutation_p.G173S	NM_007200	NP_009131	Q12802	AKP13_HUMAN	A-kinase anchor protein 13 isoform 2	1520					apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol|membrane|membrane fraction|nucleus	cAMP-dependent protein kinase activity|metal ion binding|protein binding|Rho guanyl-nucleotide exchange factor activity|signal transducer activity			central_nervous_system(3)|kidney(2)|urinary_tract(1)|liver(1)|skin(1)|ovary(1)	9						GGGAGCTGAGGGTCGAGAAAG	0.527													6	54	---	---	---	---	PASS
PCSK6	5046	broad.mit.edu	37	15	101872090	101872090	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr15:101872090C>T	uc002bwy.2	-	15	2319	c.2005G>A	c.(2005-2007)GTG>ATG	p.V669M	PCSK6_uc010bpd.2_Missense_Mutation_p.V465M|PCSK6_uc010bpe.2_Missense_Mutation_p.V669M|PCSK6_uc002bxa.2_Missense_Mutation_p.V669M|PCSK6_uc002bxb.2_Missense_Mutation_p.V669M	NM_002570	NP_002561	P29122	PCSK6_HUMAN	paired basic amino acid cleaving system 4	669					glycoprotein metabolic process|nerve growth factor processing|nerve growth factor production|nerve growth factor receptor signaling pathway|regulation of BMP signaling pathway|secretion by cell	cell surface|endomembrane system|endoplasmic reticulum|extracellular matrix|extracellular space|Golgi lumen|membrane|soluble fraction	eukaryotic cell surface binding|heparin binding|nerve growth factor binding|serine-type endopeptidase activity			pancreas(2)	2	Lung NSC(78;0.00102)|all_lung(78;0.00128)|Melanoma(26;0.00505)		OV - Ovarian serous cystadenocarcinoma(32;0.000803)|LUSC - Lung squamous cell carcinoma(107;0.187)|Lung(145;0.23)			GGAACTTCCACCTGGGAGGGT	0.572													5	18	---	---	---	---	PASS
GLIS2	84662	broad.mit.edu	37	16	4385313	4385313	+	Nonsense_Mutation	SNP	G	T	T			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr16:4385313G>T	uc002cwc.1	+	5	751	c.694G>T	c.(694-696)GAG>TAG	p.E232*		NM_032575	NP_115964	Q9BZE0	GLIS2_HUMAN	GLIS family zinc finger 2	232					cell differentiation|negative regulation of sequence-specific DNA binding transcription factor activity|negative regulation of transcription from RNA polymerase II promoter|nervous system development	cytoplasm|nuclear speck	RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription|transcription regulatory region DNA binding|zinc ion binding				0						ACACACCAACGAGAAGCCACA	0.642													3	31	---	---	---	---	PASS
PPL	5493	broad.mit.edu	37	16	4934563	4934563	+	Silent	SNP	G	T	T			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr16:4934563G>T	uc002cyd.1	-	22	4183	c.4093C>A	c.(4093-4095)CGG>AGG	p.R1365R		NM_002705	NP_002696	O60437	PEPL_HUMAN	periplakin	1365	Potential.				keratinization	cytoskeleton|desmosome|mitochondrion|nucleus	protein binding|structural constituent of cytoskeleton			ovary(4)|central_nervous_system(1)|skin(1)	6						GCCTCGGCCCGCAGGCCTGGC	0.672													6	120	---	---	---	---	PASS
ACSM2B	348158	broad.mit.edu	37	16	20565107	20565107	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr16:20565107C>T	uc002dhj.3	-	6	942	c.732G>A	c.(730-732)ATG>ATA	p.M244I	ACSM2B_uc002dhk.3_Missense_Mutation_p.M244I|ACSM2B_uc010bwf.1_Missense_Mutation_p.M244I	NM_182617	NP_872423	Q68CK6	ACS2B_HUMAN	acyl-CoA synthetase medium-chain family member	244					fatty acid metabolic process|xenobiotic metabolic process	mitochondrial matrix	ATP binding|butyrate-CoA ligase activity|CoA-ligase activity|metal ion binding			skin(3)|ovary(1)|central_nervous_system(1)	5						ACCCAGCATCCATCTTGGCCT	0.517													23	46	---	---	---	---	PASS
SRCAP	10847	broad.mit.edu	37	16	30735282	30735282	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr16:30735282C>A	uc002dze.1	+	25	4922	c.4537C>A	c.(4537-4539)CCA>ACA	p.P1513T	SRCAP_uc002dzf.2_RNA|SRCAP_uc002dzg.1_Missense_Mutation_p.P1308T|SRCAP_uc010bzz.1_Missense_Mutation_p.P1083T	NM_006662	NP_006653	Q6ZRS2	SRCAP_HUMAN	Snf2-related CBP activator protein	1513	Pro-rich.				interspecies interaction between organisms|regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	Golgi apparatus|nucleus|protein complex	ATP binding|DNA binding|helicase activity|histone acetyltransferase activity|transcription coactivator activity			ovary(3)|skin(1)	4			Colorectal(24;0.198)			GGCCACAGCTCCATCCCTGTC	0.582													14	42	---	---	---	---	PASS
SETD1A	9739	broad.mit.edu	37	16	30990990	30990990	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr16:30990990C>T	uc002ead.1	+	14	4569	c.3883C>T	c.(3883-3885)CAC>TAC	p.H1295Y		NM_014712	NP_055527	O15047	SET1A_HUMAN	SET domain containing 1A	1295					regulation of transcription, DNA-dependent|transcription, DNA-dependent	chromosome|nuclear speck|Set1C/COMPASS complex	histone-lysine N-methyltransferase activity|nucleotide binding|protein binding|RNA binding			ovary(2)|skin(1)	3						CCTGCTCAGCCACATCCTCCT	0.721													8	10	---	---	---	---	PASS
ITGAX	3687	broad.mit.edu	37	16	31382733	31382733	+	Silent	SNP	G	A	A			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr16:31382733G>A	uc002ebu.1	+	16	1987	c.1920G>A	c.(1918-1920)CGG>CGA	p.R640R	ITGAX_uc002ebt.2_Silent_p.R640R	NM_000887	NP_000878	P20702	ITAX_HUMAN	integrin alpha X precursor	640	Extracellular (Potential).				blood coagulation|cell adhesion|integrin-mediated signaling pathway|leukocyte migration|organ morphogenesis	integrin complex	protein binding|receptor activity			ovary(2)|central_nervous_system(1)|pancreas(1)	4						TTGAGTGTCGGGAGCAGGTGG	0.592													5	24	---	---	---	---	PASS
N4BP1	9683	broad.mit.edu	37	16	48594834	48594834	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr16:48594834C>A	uc002efp.2	-	2	1957	c.1720G>T	c.(1720-1722)GTT>TTT	p.V574F		NM_153029	NP_694574	O75113	N4BP1_HUMAN	Nedd4 binding protein 1	574					negative regulation of proteasomal ubiquitin-dependent protein catabolic process|negative regulation of protein ubiquitination	nucleolus|PML body					0		all_cancers(37;0.179)|all_lung(18;0.11)				GCATCAGTAACCGAAGGTAAC	0.453													74	51	---	---	---	---	PASS
SLC9A5	6553	broad.mit.edu	37	16	67293564	67293564	+	Missense_Mutation	SNP	T	G	G			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr16:67293564T>G	uc002esm.2	+	11	1778	c.1715T>G	c.(1714-1716)CTG>CGG	p.L572R	SLC9A5_uc010cee.2_Missense_Mutation_p.L277R|SLC9A5_uc010vji.1_Missense_Mutation_p.L76R|uc002esn.1_5'Flank	NM_004594	NP_004585	Q14940	SL9A5_HUMAN	solute carrier family 9 (sodium/hydrogen	572					regulation of pH	integral to membrane|plasma membrane	sodium:hydrogen antiporter activity			ovary(1)|pancreas(1)	2		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.00376)|Epithelial(162;0.0173)|all cancers(182;0.116)		ACCAACCTGCTGTGAGTCCTT	0.552													9	27	---	---	---	---	PASS
SMPD3	55512	broad.mit.edu	37	16	68405203	68405203	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr16:68405203G>T	uc002ewa.2	-	3	1304	c.882C>A	c.(880-882)AGC>AGA	p.S294R	SMPD3_uc010cfe.2_Missense_Mutation_p.S294R|SMPD3_uc010vlh.1_Missense_Mutation_p.S294R	NM_018667	NP_061137	Q9NY59	NSMA2_HUMAN	neutral sphingomyelin phosphodiesterase 3	294	Lumenal (Potential).				cell cycle|multicellular organismal development|sphingomyelin catabolic process	Golgi membrane|integral to membrane|plasma membrane	metal ion binding|sphingomyelin phosphodiesterase activity			skin(1)	1		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0184)|Epithelial(162;0.0785)	Phosphatidylserine(DB00144)	AGGCCGAGGGGCTGCCCAGGC	0.697													5	15	---	---	---	---	PASS
CDH13	1012	broad.mit.edu	37	16	83251007	83251007	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr16:83251007G>A	uc002fgx.2	+	5	661	c.541G>A	c.(541-543)GAT>AAT	p.D181N	CDH13_uc010vns.1_Missense_Mutation_p.D228N|CDH13_uc010vnt.1_5'UTR|CDH13_uc010vnu.1_Missense_Mutation_p.D142N	NM_001257	NP_001248	P55290	CAD13_HUMAN	cadherin 13 preproprotein	181	Cadherin 1.				adherens junction organization|calcium-dependent cell-cell adhesion|cell junction assembly|endothelial cell migration|homophilic cell adhesion|keratinocyte proliferation|lamellipodium assembly|localization within membrane|low-density lipoprotein particle mediated signaling|negative regulation of cell adhesion|negative regulation of cell proliferation|positive regulation of calcium-mediated signaling|positive regulation of cell migration|positive regulation of cell-matrix adhesion|positive regulation of endothelial cell proliferation|positive regulation of positive chemotaxis|positive regulation of smooth muscle cell proliferation|positive regulation of survival gene product expression|Rac protein signal transduction|regulation of endocytosis|regulation of epidermal growth factor receptor signaling pathway|Rho protein signal transduction|sprouting angiogenesis	anchored to membrane|caveola|extracellular space|integral to membrane|neuron projection	adiponectin binding|cadherin binding|calcium ion binding|low-density lipoprotein particle binding			large_intestine(1)	1		all_cancers(2;1.34e-11)|all_epithelial(2;4.3e-09)		COAD - Colon adenocarcinoma(5;0.0268)		AAAGGGAGTGGATCAAGAGCC	0.463													15	76	---	---	---	---	PASS
KCNG4	93107	broad.mit.edu	37	16	84256194	84256194	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr16:84256194C>T	uc010voc.1	-	3	1310	c.1189G>A	c.(1189-1191)GGG>AGG	p.G397R		NM_172347	NP_758857	Q8TDN1	KCNG4_HUMAN	potassium voltage-gated channel, subfamily G,	397						voltage-gated potassium channel complex	voltage-gated potassium channel activity			breast(3)	3						AGCACCCGCCCGGACTCCTTC	0.642													5	32	---	---	---	---	PASS
TM4SF5	9032	broad.mit.edu	37	17	4675353	4675353	+	Missense_Mutation	SNP	C	G	G			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr17:4675353C>G	uc002fyw.1	+	1	167	c.136C>G	c.(136-138)CAA>GAA	p.Q46E		NM_003963	NP_003954	O14894	T4S5_HUMAN	transmembrane 4 superfamily member 5	46	Extracellular (Potential).					integral to plasma membrane				ovary(1)	1						TCTCAGCTTGCAAGTCTGGCT	0.622													19	23	---	---	---	---	PASS
GP1BA	2811	broad.mit.edu	37	17	4836260	4836260	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr17:4836260C>A	uc010vsq.1	+	2	436	c.361C>A	c.(361-363)CTG>ATG	p.L121M	uc002fzn.1_RNA	NM_000173	NP_000164	P07359	GP1BA_HUMAN	platelet glycoprotein Ib alpha polypeptide	121											0						TCTCACCGTCCTGGACGTCTC	0.602													21	20	---	---	---	---	PASS
CHRNB1	1140	broad.mit.edu	37	17	7359243	7359243	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr17:7359243C>A	uc002ghb.2	+	10	1389	c.1348C>A	c.(1348-1350)CAG>AAG	p.Q450K	CHRNB1_uc010vty.1_Missense_Mutation_p.Q378K	NM_000747	NP_000738	P11230	ACHB_HUMAN	nicotinic acetylcholine receptor beta 1 subunit	450	Cytoplasmic (Potential).		Missing (in CMS-ACHRD; impairs AChR assembly by disrupting a specific interaction between beta and delta subunits).		behavioral response to nicotine|muscle contraction|muscle fiber development|neuromuscular synaptic transmission|postsynaptic membrane organization|regulation of membrane potential|synaptic transmission, cholinergic	cell junction|nicotinic acetylcholine-gated receptor-channel complex|postsynaptic membrane	acetylcholine binding|receptor activity			ovary(2)	2		Prostate(122;0.157)				GCTGCAGGAACAGGAGGACCA	0.612													3	22	---	---	---	---	PASS
TP53	7157	broad.mit.edu	37	17	7576853	7576853	+	Missense_Mutation	SNP	C	G	G	rs11575996		TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr17:7576853C>G	uc002gim.2	-	9	1187	c.993G>C	c.(991-993)CAG>CAC	p.Q331H	TP53_uc002gig.1_Intron|TP53_uc002gih.2_Missense_Mutation_p.Q331H|TP53_uc010cne.1_RNA|TP53_uc010cnf.1_Missense_Mutation_p.Q199H|TP53_uc010cng.1_Missense_Mutation_p.Q199H|TP53_uc002gii.1_Missense_Mutation_p.Q199H|TP53_uc010cnh.1_Missense_Mutation_p.Q331H|TP53_uc010cni.1_Missense_Mutation_p.Q331H|TP53_uc002gij.2_Missense_Mutation_p.Q331H	NM_001126112	NP_001119584	P04637	P53_HUMAN	tumor protein p53 isoform a	331	Oligomerization.|Interaction with HIPK1 (By similarity).|Interaction with CARM1.|Interaction with HIPK2.		Q -> R (in sporadic cancers; somatic mutation).|Q -> P (in sporadic cancers; somatic mutation).|Q -> H (in sporadic cancers; somatic mutation).		activation of caspase activity by cytochrome c|base-excision repair|blood coagulation|cell cycle arrest|cell differentiation|cell proliferation|cellular protein localization|cellular response to drug|cellular response to glucose starvation|cellular response to hypoxia|cellular response to ionizing radiation|cellular response to UV|determination of adult lifespan|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator|ER overload response|interspecies interaction between organisms|negative regulation of apoptosis|negative regulation of cell growth|negative regulation of cell proliferation|negative regulation of helicase activity|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transcription from RNA polymerase II promoter|nucleotide-excision repair|oxidative stress-induced premature senescence|positive regulation of histone deacetylation|positive regulation of neuron apoptosis|positive regulation of peptidyl-tyrosine phosphorylation|positive regulation of reactive oxygen species metabolic process|positive regulation of thymocyte apoptosis|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase II promoter|protein localization|protein tetramerization|Ras protein signal transduction|regulation of mitochondrial membrane permeability|replicative senescence|response to antibiotic|response to gamma radiation|response to X-ray	cytoplasm|cytosol|endoplasmic reticulum|insoluble fraction|mitochondrion|nuclear chromatin|nuclear matrix|nucleolus|nucleus|PML body|protein complex|replication fork	ATP binding|chaperone binding|chromatin binding|copper ion binding|damaged DNA binding|DNA strand annealing activity|histone acetyltransferase binding|p53 binding|protease binding|protein binding|protein heterodimerization activity|protein kinase binding|protein N-terminus binding|protein phosphatase 2A binding|RNA polymerase II transcription factor binding|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding|transcription regulatory region DNA binding|transcription repressor activity|ubiquitin protein ligase binding|zinc ion binding	p.Q331*(14)|p.0?(7)|p.Q331P(3)|p.Q331fs*6(1)|p.I332fs*49(1)|p.?(1)|p.Q331Q(1)|p.Q331R(1)|p.Q331H(1)|p.Q331fs*14(1)		large_intestine(4656)|breast(2429)|upper_aerodigestive_tract(2212)|lung(2028)|ovary(1592)|oesophagus(1462)|haematopoietic_and_lymphoid_tissue(1228)|stomach(1136)|urinary_tract(1114)|central_nervous_system(1085)|liver(805)|skin(694)|pancreas(375)|biliary_tract(247)|soft_tissue(209)|prostate(194)|endometrium(150)|bone(102)|vulva(79)|kidney(79)|cervix(68)|thyroid(54)|salivary_gland(43)|adrenal_gland(37)|peritoneum(33)|eye(24)|thymus(21)|genital_tract(16)|autonomic_ganglia(16)|small_intestine(14)|testis(11)|penis(10)|vagina(6)|meninges(5)|pituitary(4)|pleura(3)|gastrointestinal_tract_(site_indeterminate)(1)|NS(1)|Fallopian tube(1)|placenta(1)	22245		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)		GACTTAGTACCTGAAGGGTGA	0.453		111	Mis|N|F		breast|colorectal|lung|sarcoma|adrenocortical|glioma|multiple other tumour types	breast|sarcoma|adrenocortical carcinoma|glioma|multiple other tumour types		Other_conserved_DNA_damage_response_genes	Hereditary_Adrenocortical_Cancer|Endometrial_Cancer_Familial_Clustering_of|Hereditary_Breast-Ovarian_Cancer_non-BRCA1/2|Li-Fraumeni_syndrome|Osteosarcoma_Familial_Clustering_of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)			31	3	---	---	---	---	PASS
DHRS7C	201140	broad.mit.edu	37	17	9674965	9674965	+	Missense_Mutation	SNP	T	A	A			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr17:9674965T>A	uc010vvb.1	-	6	779	c.779A>T	c.(778-780)GAG>GTG	p.E260V	DHRS7C_uc010cof.2_Missense_Mutation_p.E259V	NM_001105571	NP_001099041	A6NNS2	DRS7C_HUMAN	dehydrogenase/reductase (SDR family) member 7C	260						extracellular region	binding|oxidoreductase activity				0						CATCACCTCCTCCGCCACCTC	0.627													13	0	---	---	---	---	PASS
LIG3	3980	broad.mit.edu	37	17	33326404	33326404	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr17:33326404G>A	uc002hik.1	+	15	2300	c.2192G>A	c.(2191-2193)GGA>GAA	p.G731E	LIG3_uc002hij.2_Missense_Mutation_p.G731E	NM_013975	NP_039269	P49916	DNLI3_HUMAN	ligase III, DNA, ATP-dependent isoform alpha	731					base-excision repair|cell division|DNA ligation involved in DNA repair|DNA replication|reciprocal meiotic recombination|spermatogenesis	nucleoplasm	ATP binding|DNA binding|DNA ligase (ATP) activity|protein binding|zinc ion binding			skin(3)|lung(2)|ovary(2)|large_intestine(1)|pancreas(1)	9		Ovarian(249;0.17)			Bleomycin(DB00290)	AAGTGTGCAGGAGGCCATGAT	0.577								Other_BER_factors					9	31	---	---	---	---	PASS
PIGW	284098	broad.mit.edu	37	17	34893620	34893620	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr17:34893620G>T	uc002hmy.1	+	2	713	c.670G>T	c.(670-672)GGC>TGC	p.G224C	MYO19_uc002hmw.2_5'Flank|MYO19_uc010cuu.2_5'Flank|MYO19_uc010wcy.1_5'Flank|MYO19_uc010wcz.1_5'Flank|MYO19_uc010wda.1_5'Flank|MYO19_uc002hmx.2_5'Flank|PIGW_uc002hmz.1_Missense_Mutation_p.G224C	NM_178517	NP_848612	Q7Z7B1	PIGW_HUMAN	phosphatidylinositol glycan, class W	224					C-terminal protein lipidation|preassembly of GPI anchor in ER membrane	endoplasmic reticulum membrane|integral to membrane	O-acyltransferase activity				0		Breast(25;0.00957)|Ovarian(249;0.17)	Kidney(155;0.104)	UCEC - Uterine corpus endometrioid carcinoma (308;0.0182)		AAAATCAATAGGCTATCAGGA	0.353													12	37	---	---	---	---	PASS
RAPGEFL1	51195	broad.mit.edu	37	17	38340578	38340578	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr17:38340578G>A	uc010cwu.1	+	3	584	c.94G>A	c.(94-96)GAG>AAG	p.E32K		NM_016339	NP_057423	Q9UHV5	RPGFL_HUMAN	Rap guanine nucleotide exchange factor	238					G-protein coupled receptor protein signaling pathway|nervous system development|small GTPase mediated signal transduction	intracellular|membrane fraction	guanyl-nucleotide exchange factor activity			ovary(1)|central_nervous_system(1)|skin(1)	3						TCAAGAGGAAGAGGGGGCCGG	0.597													22	45	---	---	---	---	PASS
TOP2A	7153	broad.mit.edu	37	17	38573130	38573130	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr17:38573130C>T	uc002huq.2	-	2	165	c.39G>A	c.(37-39)ATG>ATA	p.M13I		NM_001067	NP_001058	P11388	TOP2A_HUMAN	DNA topoisomerase II, alpha isozyme	13					apoptotic chromosome condensation|DNA ligation|DNA repair|DNA topological change|DNA-dependent DNA replication|mitotic cell cycle G2/M transition decatenation checkpoint|mitotic recombination|phosphatidylinositol-mediated signaling|positive regulation of apoptosis|positive regulation of retroviral genome replication|resolution of meiotic recombination intermediates|sister chromatid segregation	cytoplasm|DNA topoisomerase complex (ATP-hydrolyzing)|nucleolus|nucleoplasm|synaptonemal complex	ATP binding|chromatin binding|DNA topoisomerase (ATP-hydrolyzing) activity|DNA-dependent ATPase activity|drug binding|histone deacetylase binding|protein C-terminus binding|protein heterodimerization activity|protein homodimerization activity|protein kinase C binding|sequence-specific DNA binding transcription factor activity|ubiquitin binding			ovary(4)|large_intestine(1)|central_nervous_system(1)|skin(1)	7		Breast(137;0.00328)	STAD - Stomach adenocarcinoma(5;0.00183)		Amsacrine(DB00276)|Ciprofloxacin(DB00537)|Dexrazoxane(DB00380)|Doxorubicin(DB00997)|Enoxacin(DB00467)|Epirubicin(DB00445)|Etoposide(DB00773)|Fleroxacin(DB04576)|Gatifloxacin(DB01044)|Idarubicin(DB01177)|Levofloxacin(DB01137)|Lomefloxacin(DB00978)|Lucanthone(DB04967)|Mitoxantrone(DB01204)|Moxifloxacin(DB00218)|Norfloxacin(DB01059)|Ofloxacin(DB01165)|Pefloxacin(DB00487)|Podofilox(DB01179)|Sparfloxacin(DB01208)|Teniposide(DB00444)|Trovafloxacin(DB00685)|Valrubicin(DB00385)	TGTTGACTTGCATATTTTCAT	0.308													36	19	---	---	---	---	PASS
ATP6V0A1	535	broad.mit.edu	37	17	40635067	40635067	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr17:40635067C>T	uc002hzr.2	+	9	895	c.728C>T	c.(727-729)TCA>TTA	p.S243L	ATP6V0A1_uc002hzq.2_Missense_Mutation_p.S243L|ATP6V0A1_uc002hzs.2_Missense_Mutation_p.S250L|ATP6V0A1_uc010wgj.1_Missense_Mutation_p.S200L|ATP6V0A1_uc010wgk.1_Missense_Mutation_p.S200L|ATP6V0A1_uc010cyg.2_Intron|ATP6V0A1_uc010wgl.1_Missense_Mutation_p.S102L	NM_001130021	NP_001123493	Q93050	VPP1_HUMAN	ATPase, H+ transporting, lysosomal V0 subunit a1	243	Cytoplasmic (Potential).				ATP hydrolysis coupled proton transport|cellular iron ion homeostasis|insulin receptor signaling pathway|transferrin transport	cytoplasmic vesicle membrane|endosome membrane|Golgi apparatus|integral to membrane|melanosome|nucleus|plasma membrane|proton-transporting two-sector ATPase complex, proton-transporting domain	ATPase binding|hydrogen ion transmembrane transporter activity			pancreas(1)	1		all_cancers(22;1.18e-05)|Breast(137;0.000105)|all_epithelial(22;0.000254)		BRCA - Breast invasive adenocarcinoma(366;0.137)		TTCCGAGCCTCACTCTATCCC	0.418													9	28	---	---	---	---	PASS
ATP6V0A1	535	broad.mit.edu	37	17	40673107	40673107	+	Missense_Mutation	SNP	A	G	G			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr17:40673107A>G	uc002hzr.2	+	22	2650	c.2483A>G	c.(2482-2484)GAG>GGG	p.E828G	ATP6V0A1_uc002hzq.2_Missense_Mutation_p.E822G|ATP6V0A1_uc002hzs.2_Missense_Mutation_p.E829G|ATP6V0A1_uc010wgj.1_Missense_Mutation_p.E785G|ATP6V0A1_uc010wgk.1_Missense_Mutation_p.E779G|ATP6V0A1_uc010cyg.2_Missense_Mutation_p.E474G|ATP6V0A1_uc010wgl.1_Missense_Mutation_p.E687G|ATP6V0A1_uc002hzt.2_Missense_Mutation_p.E112G|ATP6V0A1_uc002hzu.2_Missense_Mutation_p.S113G	NM_001130021	NP_001123493	Q93050	VPP1_HUMAN	ATPase, H+ transporting, lysosomal V0 subunit a1	828	Cytoplasmic (Potential).				ATP hydrolysis coupled proton transport|cellular iron ion homeostasis|insulin receptor signaling pathway|transferrin transport	cytoplasmic vesicle membrane|endosome membrane|Golgi apparatus|integral to membrane|melanosome|nucleus|plasma membrane|proton-transporting two-sector ATPase complex, proton-transporting domain	ATPase binding|hydrogen ion transmembrane transporter activity			pancreas(1)	1		all_cancers(22;1.18e-05)|Breast(137;0.000105)|all_epithelial(22;0.000254)		BRCA - Breast invasive adenocarcinoma(366;0.137)		TTCTCCTTCGAGCATATTCGG	0.512													66	48	---	---	---	---	PASS
PSME3	10197	broad.mit.edu	37	17	40990190	40990190	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr17:40990190G>A	uc002ibr.2	+	6	599	c.373G>A	c.(373-375)GAG>AAG	p.E125K	PSME3_uc002ibp.2_Missense_Mutation_p.E64K|PSME3_uc002ibq.2_Missense_Mutation_p.E125K|PSME3_uc002ibs.2_Missense_Mutation_p.E136K|PSME3_uc010whd.1_Intron	NM_005789	NP_005780	P61289	PSME3_HUMAN	proteasome activator subunit 3 isoform 1	125					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|mRNA metabolic process|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|regulation of apoptosis|regulation of cellular amino acid metabolic process|regulation of proteasomal protein catabolic process|S phase of mitotic cell cycle|viral reproduction	cytoplasm|nucleus|proteasome activator complex	endopeptidase activator activity|identical protein binding|MDM2 binding|p53 binding				0		Breast(137;0.000143)		BRCA - Breast invasive adenocarcinoma(366;0.156)		AGTGAAACCTGAGATCCGGCT	0.512													17	41	---	---	---	---	PASS
AARSD1	80755	broad.mit.edu	37	17	41108544	41108544	+	Silent	SNP	C	T	T			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr17:41108544C>T	uc002icc.2	-	5	426	c.423G>A	c.(421-423)CTG>CTA	p.L141L	AARSD1_uc002icd.2_Silent_p.L254L|AARSD1_uc002ice.2_Silent_p.L224L|AARSD1_uc002icf.2_Silent_p.L315L|AARSD1_uc010whg.1_Silent_p.L315L|AARSD1_uc010cyu.1_Silent_p.L141L	NM_025267	NP_079543	Q9BTE6	AASD1_HUMAN	alanyl-tRNA synthetase domain containing 1	141					alanyl-tRNA aminoacylation	cytoplasm	alanine-tRNA ligase activity|ATP binding|metal ion binding|nucleic acid binding				0		Breast(137;0.00499)		BRCA - Breast invasive adenocarcinoma(366;0.161)		AGGGGGTGTCCAGCTCAATCG	0.393													9	32	---	---	---	---	PASS
PRAC	84366	broad.mit.edu	37	17	46799684	46799684	+	Missense_Mutation	SNP	T	C	C			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr17:46799684T>C	uc002iny.2	-	1	199	c.71A>G	c.(70-72)AAT>AGT	p.N24S	C17orf93_uc002inz.1_5'Flank	NM_032391	NP_115767	Q96KF2	PRAC_HUMAN	prostate cancer susceptibility candidate	24						nucleus					0						GTTTACCTTATTAGAGAGAAA	0.542													21	40	---	---	---	---	PASS
TEX14	56155	broad.mit.edu	37	17	56661932	56661932	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr17:56661932C>T	uc010dcz.1	-	19	3236	c.3118G>A	c.(3118-3120)GAG>AAG	p.E1040K	TEX14_uc002iwr.1_Missense_Mutation_p.E1034K|TEX14_uc002iws.1_Missense_Mutation_p.E1034K|TEX14_uc010dda.1_Missense_Mutation_p.E814K	NM_198393	NP_938207	Q8IWB6	TEX14_HUMAN	testis expressed sequence 14 isoform a	1040						cytoplasm	ATP binding|protein kinase activity			stomach(4)|lung(3)|breast(3)|ovary(3)|upper_aerodigestive_tract(1)|large_intestine(1)|skin(1)|pancreas(1)	17	Medulloblastoma(34;0.127)|all_neural(34;0.237)					TCTGGTTGCTCCTTTTGTCTG	0.433													16	34	---	---	---	---	PASS
KCNJ2	3759	broad.mit.edu	37	17	68171453	68171453	+	Silent	SNP	T	G	G			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr17:68171453T>G	uc010dfg.2	+	2	674	c.273T>G	c.(271-273)GCT>GCG	p.A91A	KCNJ2_uc002jir.2_Silent_p.A91A	NM_000891	NP_000882	P63252	IRK2_HUMAN	potassium inwardly-rectifying channel J2	91	Helical; Name=M1; (By similarity).				synaptic transmission	integral to plasma membrane	inward rectifier potassium channel activity|protein binding				0	Breast(10;1.64e-08)					TCTGCCTGGCTTTCGTCCTGT	0.532													15	58	---	---	---	---	PASS
KCNJ2	3759	broad.mit.edu	37	17	68171795	68171795	+	Missense_Mutation	SNP	C	G	G			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr17:68171795C>G	uc010dfg.2	+	2	1016	c.615C>G	c.(613-615)GAC>GAG	p.D205E	KCNJ2_uc002jir.2_Missense_Mutation_p.D205E	NM_000891	NP_000882	P63252	IRK2_HUMAN	potassium inwardly-rectifying channel J2	205	Cytoplasmic (By similarity).				synaptic transmission	integral to plasma membrane	inward rectifier potassium channel activity|protein binding				0	Breast(10;1.64e-08)					CCATGAGAGACGGCAAGCTGT	0.488													21	61	---	---	---	---	PASS
KIAA0195	9772	broad.mit.edu	37	17	73487781	73487781	+	Silent	SNP	C	A	A			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr17:73487781C>A	uc002jnz.3	+	14	1671	c.1396C>A	c.(1396-1398)CGA>AGA	p.R466R	KIAA0195_uc010wsa.1_Silent_p.R476R|KIAA0195_uc010wsb.1_Silent_p.R122R	NM_014738	NP_055553	Q12767	K0195_HUMAN	hypothetical protein LOC9772	466					ATP biosynthetic process|cation transport	integral to membrane	ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism			ovary(1)	1	all_cancers(13;3.15e-09)|all_epithelial(9;5.94e-10)|Breast(9;1.85e-09)|all_lung(278;0.246)		all cancers(21;5.01e-07)|Epithelial(20;5e-06)|Lung(188;0.0809)|LUSC - Lung squamous cell carcinoma(166;0.154)			GCCCCATGAACGAGACGCCCT	0.642													18	77	---	---	---	---	PASS
FASN	2194	broad.mit.edu	37	17	80039490	80039490	+	Silent	SNP	C	A	A			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr17:80039490C>A	uc002kdu.2	-	37	6510	c.6393G>T	c.(6391-6393)GTG>GTT	p.V2131V	FASN_uc002kdv.1_RNA	NM_004104	NP_004095	P49327	FAS_HUMAN	fatty acid synthase	2131	Acyl carrier.				energy reserve metabolic process|fatty acid biosynthetic process|long-chain fatty-acyl-CoA biosynthetic process|pantothenate metabolic process|positive regulation of cellular metabolic process|triglyceride biosynthetic process	cytosol|Golgi apparatus|melanosome|plasma membrane	3-hydroxypalmitoyl-[acyl-carrier-protein] dehydratase activity|3-oxoacyl-[acyl-carrier-protein] reductase (NADPH) activity|3-oxoacyl-[acyl-carrier-protein] synthase activity|[acyl-carrier-protein] S-acetyltransferase activity|[acyl-carrier-protein] S-malonyltransferase activity|acyl carrier activity|cofactor binding|enoyl-[acyl-carrier-protein] reductase (NADPH, B-specific) activity|myristoyl-[acyl-carrier-protein] hydrolase activity|oleoyl-[acyl-carrier-protein] hydrolase activity|palmitoyl-[acyl-carrier-protein] hydrolase activity|phosphopantetheine binding|protein binding|zinc ion binding			central_nervous_system(1)	1	all_neural(118;0.0878)|Ovarian(332;0.227)|all_lung(278;0.246)		OV - Ovarian serous cystadenocarcinoma(97;0.0211)|BRCA - Breast invasive adenocarcinoma(99;0.0237)		Cerulenin(DB01034)|Orlistat(DB01083)|Pyrazinamide(DB00339)	GGATGTGTGCCACGGCCTCCA	0.642													4	35	---	---	---	---	PASS
TEX19	400629	broad.mit.edu	37	17	80320050	80320050	+	Silent	SNP	G	A	A			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr17:80320050G>A	uc002keq.2	+	2	333	c.24G>A	c.(22-24)CGG>CGA	p.R8R		NM_207459	NP_997342	Q8NA77	TEX19_HUMAN	testis expressed 19	8						nucleus					0						TCAGCATGCGGTATGAGGAAG	0.582													79	37	---	---	---	---	PASS
THOC1	9984	broad.mit.edu	37	18	215489	215489	+	Missense_Mutation	SNP	T	C	C			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr18:215489T>C	uc002kkj.3	-	20	1658	c.1618A>G	c.(1618-1620)ATA>GTA	p.I540V	THOC1_uc002kkk.3_RNA|THOC1_uc002kkh.3_Missense_Mutation_p.I164V	NM_005131	NP_005122	Q96FV9	THOC1_HUMAN	THO complex 1	540					apoptosis|intronless viral mRNA export from host nucleus|mRNA processing|regulation of transcription elongation, DNA-dependent|RNA splicing|signal transduction|transcription, DNA-dependent	cytoplasm|nuclear matrix|nuclear speck|THO complex part of transcription export complex	DNA binding|protein binding|RNA binding			ovary(1)	1		all_cancers(4;0.0896)|Myeloproliferative disorder(11;0.0412)				CCTGTTTTTATTTCTTCAGAA	0.343													22	6	---	---	---	---	PASS
SMCHD1	23347	broad.mit.edu	37	18	2688397	2688397	+	Missense_Mutation	SNP	A	T	T			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr18:2688397A>T	uc002klm.3	+	6	833	c.644A>T	c.(643-645)CAT>CTT	p.H215L		NM_015295	NP_056110	A6NHR9	SMHD1_HUMAN	structural maintenance of chromosomes flexible	215					chromosome organization		ATP binding				0						TTTAGTGATCATTCAGGATAT	0.348													28	25	---	---	---	---	PASS
SMCHD1	23347	broad.mit.edu	37	18	2747616	2747616	+	Missense_Mutation	SNP	A	G	G			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr18:2747616A>G	uc002klm.3	+	30	4087	c.3898A>G	c.(3898-3900)ATA>GTA	p.I1300V	SMCHD1_uc002klk.3_RNA|SMCHD1_uc002kll.3_RNA	NM_015295	NP_056110	A6NHR9	SMHD1_HUMAN	structural maintenance of chromosomes flexible	1300					chromosome organization		ATP binding				0						ACATGTTAAAATAAGTCTTAC	0.323													3	16	---	---	---	---	PASS
KIAA0802	23255	broad.mit.edu	37	18	8783967	8783967	+	Missense_Mutation	SNP	A	C	C			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr18:8783967A>C	uc002knr.2	+	6	999	c.857A>C	c.(856-858)GAG>GCG	p.E286A	KIAA0802_uc002knq.2_Missense_Mutation_p.E286A|KIAA0802_uc010dkw.1_Missense_Mutation_p.E124A	NM_015210	NP_056025	Q9Y4B5	CC165_HUMAN	hypothetical protein LOC23255	637	Potential.										0						GAGGAAGCGGAGTTGCTCCGG	0.617													56	40	---	---	---	---	PASS
GNAL	2774	broad.mit.edu	37	18	11864603	11864603	+	Missense_Mutation	SNP	C	G	G			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr18:11864603C>G	uc010dkz.2	+	8	864	c.618C>G	c.(616-618)TTC>TTG	p.F206L	GNAL_uc002kqc.2_Missense_Mutation_p.F283L|GNAL_uc002kqd.2_Missense_Mutation_p.F206L|GNAL_uc010wzt.1_5'UTR	NM_001142339	NP_001135811	P38405	GNAL_HUMAN	guanine nucleotide binding protein (G protein),	206					activation of adenylate cyclase activity by dopamine receptor signaling pathway|inhibition of adenylate cyclase activity by G-protein signaling pathway|sensory perception of smell|synaptic transmission	heterotrimeric G-protein complex	adenylate cyclase activity|G-protein beta/gamma-subunit complex binding|G-protein-coupled receptor binding|GTP binding|GTPase activity|signal transducer activity			ovary(1)	1						AAGTAAACTTCCAGTGAGTAT	0.493													35	87	---	---	---	---	PASS
NEDD4L	23327	broad.mit.edu	37	18	56009014	56009014	+	Silent	SNP	A	G	G			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr18:56009014A>G	uc002lgy.2	+	15	1636	c.1362A>G	c.(1360-1362)TTA>TTG	p.L454L	NEDD4L_uc002lgz.2_Silent_p.L390L|NEDD4L_uc002lgx.2_Silent_p.L434L|NEDD4L_uc010xee.1_Silent_p.L333L|NEDD4L_uc002lhc.2_Silent_p.L446L|NEDD4L_uc002lhd.2_Silent_p.L333L|NEDD4L_uc002lhb.2_Silent_p.L313L|NEDD4L_uc002lhe.2_Silent_p.L426L|NEDD4L_uc002lhf.2_Silent_p.L313L|NEDD4L_uc002lhg.2_Silent_p.L333L|NEDD4L_uc002lhh.2_Intron|NEDD4L_uc010dpm.1_Intron	NM_001144967	NP_001138439	Q96PU5	NED4L_HUMAN	neural precursor cell expressed, developmentally	454					cellular sodium ion homeostasis|excretion|interspecies interaction between organisms|positive regulation of endocytosis|protein ubiquitination involved in ubiquitin-dependent protein catabolic process|regulation of protein catabolic process|response to metal ion|sodium ion transport|water homeostasis	cytoplasm	protein binding|sodium channel regulator activity|ubiquitin-protein ligase activity			lung(4)	4						CAGTAACTTTATCTGCCCCGC	0.527													14	13	---	---	---	---	PASS
CDH20	28316	broad.mit.edu	37	18	59217223	59217223	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr18:59217223G>A	uc010dps.1	+	10	1673	c.1661G>A	c.(1660-1662)CGG>CAG	p.R554Q	CDH20_uc002lif.2_Missense_Mutation_p.R548Q	NM_031891	NP_114097	Q9HBT6	CAD20_HUMAN	cadherin 20, type 2 preproprotein	554	Cadherin 5.|Extracellular (Potential).				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			breast(3)|ovary(1)|pancreas(1)	5		Colorectal(73;0.186)				AACACAGCACGGATTCTAACC	0.532													10	28	---	---	---	---	PASS
TMPRSS9	360200	broad.mit.edu	37	19	2422218	2422218	+	Nonsense_Mutation	SNP	G	T	T			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr19:2422218G>T	uc010xgx.1	+	13	2419	c.2419G>T	c.(2419-2421)GAG>TAG	p.E807*		NM_182973	NP_892018	Q7Z410	TMPS9_HUMAN	transmembrane protease, serine 9	807	Extracellular (Potential).				proteolysis	integral to plasma membrane	serine-type endopeptidase activity			ovary(1)|central_nervous_system(1)	2				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		AGACGCCCCGGAGGCCACCAC	0.632													21	71	---	---	---	---	PASS
MUC16	94025	broad.mit.edu	37	19	9058439	9058439	+	Silent	SNP	A	C	C			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr19:9058439A>C	uc002mkp.2	-	3	29211	c.29007T>G	c.(29005-29007)TCT>TCG	p.S9669S		NM_024690	NP_078966	Q8WXI7	MUC16_HUMAN	mucin 16	9671	Ser-rich.|Thr-rich.|Extracellular (Potential).				cell adhesion	extracellular space|extrinsic to membrane|integral to membrane|plasma membrane	protein binding			lung(30)|ovary(15)|breast(8)|large_intestine(1)|skin(1)|prostate(1)|pancreas(1)	57						ATGTAGCCAGAGAATAACCTG	0.478													26	23	---	---	---	---	PASS
KEAP1	9817	broad.mit.edu	37	19	10599944	10599944	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr19:10599944C>A	uc002moq.1	-	5	1788	c.1632G>T	c.(1630-1632)TGG>TGT	p.W544C	KEAP1_uc002mop.1_Intron|KEAP1_uc002mor.1_Missense_Mutation_p.W544C	NM_012289	NP_036421	Q14145	KEAP1_HUMAN	kelch-like ECH-associated protein 1	544	Kelch 5.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	centrosome|midbody|nucleus	protein binding			lung(12)|breast(3)|ovary(1)|pancreas(1)	17			OV - Ovarian serous cystadenocarcinoma(20;2.71e-09)|Epithelial(33;2.32e-06)|all cancers(31;1.42e-05)			CTACGAAAGTCCACGTCTCTG	0.602													33	4	---	---	---	---	PASS
OR7A17	26333	broad.mit.edu	37	19	14991871	14991871	+	Silent	SNP	G	T	T			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr19:14991871G>T	uc010xob.1	-	1	297	c.297C>A	c.(295-297)ACC>ACA	p.T99T		NM_030901	NP_112163	O14581	OR7AH_HUMAN	olfactory receptor, family 7, subfamily A,	99	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0	Ovarian(108;0.203)					AGCACATCTGGGTGATGCAGC	0.468													71	31	---	---	---	---	PASS
CPAMD8	27151	broad.mit.edu	37	19	17017851	17017851	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr19:17017851C>A	uc002nfb.2	-	30	4111	c.4079G>T	c.(4078-4080)TGT>TTT	p.C1360F		NM_015692	NP_056507	Q8IZJ3	CPMD8_HUMAN	C3 and PZP-like, alpha-2-macroglobulin domain	1313						extracellular space|plasma membrane	serine-type endopeptidase inhibitor activity			ovary(4)|breast(4)|large_intestine(3)|pancreas(1)|skin(1)	13						AGTCAGGGCACAGCTATAAGG	0.652													15	0	---	---	---	---	PASS
RYR1	6261	broad.mit.edu	37	19	38935234	38935234	+	Missense_Mutation	SNP	C	A	A	rs150038701		TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr19:38935234C>A	uc002oit.2	+	7	678	c.548C>A	c.(547-549)ACC>AAC	p.T183N	RYR1_uc002oiu.2_Missense_Mutation_p.T183N	NM_000540	NP_000531	P21817	RYR1_HUMAN	skeletal muscle ryanodine receptor isoform 1	183	Cytoplasmic.|MIR 2.				muscle contraction|release of sequestered calcium ion into cytosol|response to caffeine|response to hypoxia	cell cortex|cytosol|I band|integral to plasma membrane|junctional sarcoplasmic reticulum membrane|smooth endoplasmic reticulum|terminal cisterna	calcium ion binding|calmodulin binding|receptor activity|ryanodine-sensitive calcium-release channel activity			ovary(7)|pancreas(2)|breast(1)|central_nervous_system(1)|skin(1)	12	all_cancers(60;7.91e-06)		Lung(45;0.00172)|LUSC - Lung squamous cell carcinoma(53;0.00272)		Dantrolene(DB01219)	CACCTGTCGACCGCCAGTGGG	0.622													3	9	---	---	---	---	PASS
HNRNPL	3191	broad.mit.edu	37	19	39330801	39330801	+	Missense_Mutation	SNP	C	G	G	rs115791874	by1000genomes	TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr19:39330801C>G	uc010xul.1	-	8	1179	c.1168G>C	c.(1168-1170)GAT>CAT	p.D390H	HNRNPL_uc010ege.1_Missense_Mutation_p.D46H|HNRNPL_uc002ojj.1_Missense_Mutation_p.D46H|HNRNPL_uc002ojo.1_5'Flank|HNRNPL_uc002ojk.2_Missense_Mutation_p.D46H|HNRNPL_uc002ojl.2_Missense_Mutation_p.D46H|HNRNPL_uc010xum.1_Missense_Mutation_p.D257H|HNRNPL_uc002ojp.1_Missense_Mutation_p.D46H|HNRNPL_uc010xun.1_Missense_Mutation_p.W97C	NM_001533	NP_001524	P14866	HNRPL_HUMAN	heterogeneous nuclear ribonucleoprotein L	390	RRM 3.				nuclear mRNA splicing, via spliceosome	cytoplasm|heterogeneous nuclear ribonucleoprotein complex|nucleoplasm	nucleotide binding|protein binding|RNA binding|transcription regulatory region DNA binding				0	all_cancers(60;6.83e-06)|Ovarian(47;0.0454)		Lung(45;0.00342)|LUSC - Lung squamous cell carcinoma(53;0.00575)			TTAGATTGATCCAAGCCATAG	0.597													3	53	---	---	---	---	PASS
SUPT5H	6829	broad.mit.edu	37	19	39960853	39960853	+	Missense_Mutation	SNP	G	C	C			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr19:39960853G>C	uc002olo.3	+	17	1648	c.1469G>C	c.(1468-1470)GGC>GCC	p.G490A	SUPT5H_uc002olp.3_Missense_Mutation_p.G490A|SUPT5H_uc002olq.3_Missense_Mutation_p.G486A|SUPT5H_uc002oln.3_Missense_Mutation_p.G490A|SUPT5H_uc002olr.3_Missense_Mutation_p.G490A|SUPT5H_uc002ols.1_Missense_Mutation_p.G113A|SUPT5H_uc010egp.1_5'Flank	NM_001111020	NP_001104490	O00267	SPT5H_HUMAN	suppressor of Ty 5 homolog isoform a	490	KOW 3.				cell cycle|chromatin remodeling|mRNA capping|negative regulation of transcription elongation, DNA-dependent|negative regulation of transcription from RNA polymerase II promoter|positive regulation of transcription elongation from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase II promoter|positive regulation of viral transcription|response to organic substance|retroviral genome replication|transcription elongation from RNA polymerase II promoter	nucleoplasm	enzyme binding|protein heterodimerization activity			ovary(3)|pancreas(1)	4	all_cancers(60;6.69e-07)|all_lung(34;2.66e-08)|Lung NSC(34;3e-08)|all_epithelial(25;1.57e-06)|Ovarian(47;0.159)		Epithelial(26;3.9e-26)|all cancers(26;1.35e-23)|LUSC - Lung squamous cell carcinoma(53;0.000657)			GGCGACACAGGCCTCATTGTG	0.552													10	138	---	---	---	---	PASS
TIMM50	92609	broad.mit.edu	37	19	39978732	39978732	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr19:39978732G>T	uc002olu.1	+	9	1170	c.1037G>T	c.(1036-1038)CGA>CTA	p.R346L	TIMM50_uc002olt.1_RNA|TIMM50_uc002olv.1_Missense_Mutation_p.R45L	NM_001001563	NP_001001563	Q3ZCQ8	TIM50_HUMAN	translocase of inner mitochondrial membrane 50	243	Mitochondrial intermembrane (Potential).|FCP1 homology.				mitochondrial membrane organization|protein transport|release of cytochrome c from mitochondria|transmembrane transport	integral to membrane|mitochondrial inner membrane presequence translocase complex|nuclear speck	interleukin-2 receptor binding|protein serine/threonine phosphatase activity|protein tyrosine phosphatase activity|ribonucleoprotein binding|RNA binding			ovary(1)	1	all_cancers(60;4.04e-06)|all_lung(34;1.77e-07)|Lung NSC(34;2.09e-07)|all_epithelial(25;1.13e-05)|Ovarian(47;0.159)		Epithelial(26;5.89e-26)|all cancers(26;1.96e-23)|LUSC - Lung squamous cell carcinoma(53;0.000657)			GACCCAGCTCGAGTAGTAGTT	0.552													5	141	---	---	---	---	PASS
BCAM	4059	broad.mit.edu	37	19	45321844	45321844	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr19:45321844G>A	uc002ozu.2	+	9	1188	c.1144G>A	c.(1144-1146)GTG>ATG	p.V382M	BCAM_uc002ozt.1_Missense_Mutation_p.V382M	NM_005581	NP_005572	P50895	BCAM_HUMAN	basal cell adhesion molecule isoform 1	382	Extracellular (Potential).|Ig-like C2-type 2.				cell-matrix adhesion	integral to plasma membrane	laminin binding|laminin receptor activity			skin(1)	1	Lung NSC(12;0.000789)|all_lung(12;0.00218)	Ovarian(192;0.0728)|all_neural(266;0.112)				CAGTGCAGTCGTGAACTGCTC	0.642													15	3	---	---	---	---	PASS
PNMAL2	57469	broad.mit.edu	37	19	46998324	46998324	+	Silent	SNP	C	T	T			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr19:46998324C>T	uc002pes.2	-	1	846	c.399G>A	c.(397-399)TCG>TCA	p.S133S	uc002peu.1_Silent_p.S145S	NM_020709	NP_065760	Q9ULN7	PNML2_HUMAN	PNMA-like 2	133										central_nervous_system(1)	1		Ovarian(192;0.00965)|all_neural(266;0.0459)		OV - Ovarian serous cystadenocarcinoma(262;0.000322)|all cancers(93;0.00233)|GBM - Glioblastoma multiforme(486;0.0421)|Epithelial(262;0.0427)		CCTGCGTCTCCGAAGCGGGAG	0.701													22	26	---	---	---	---	PASS
EHD2	30846	broad.mit.edu	37	19	48221846	48221846	+	Missense_Mutation	SNP	A	T	T			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr19:48221846A>T	uc002phj.3	+	3	735	c.485A>T	c.(484-486)AAG>ATG	p.K162M	EHD2_uc010xyu.1_Missense_Mutation_p.K26M	NM_014601	NP_055416	Q9NZN4	EHD2_HUMAN	EH-domain containing 2	162					blood coagulation|endocytic recycling	nucleus|plasma membrane|recycling endosome membrane	ATP binding|calcium ion binding|GTP binding|GTPase activity|nucleic acid binding			ovary(1)|skin(1)	2		all_cancers(25;6.74e-07)|all_lung(116;2.02e-05)|Lung NSC(112;3.77e-05)|all_epithelial(76;4.89e-05)|all_neural(266;0.0332)|Ovarian(192;0.086)		OV - Ovarian serous cystadenocarcinoma(262;0.000336)|all cancers(93;0.000415)|Epithelial(262;0.0132)|GBM - Glioblastoma multiforme(486;0.0537)		TCGGGTGCCAAGCAGAGAGTG	0.383													15	0	---	---	---	---	PASS
GRIN2D	2906	broad.mit.edu	37	19	48922942	48922942	+	Silent	SNP	C	G	G			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr19:48922942C>G	uc002pjc.3	+	9	2050	c.1962C>G	c.(1960-1962)ACC>ACG	p.T654T	GRIN2D_uc010elx.2_5'UTR	NM_000836	NP_000827	O15399	NMDE4_HUMAN	N-methyl-D-aspartate receptor subunit 2D	654	Cytoplasmic (Potential).					cell junction|outer membrane-bounded periplasmic space|postsynaptic membrane	extracellular-glutamate-gated ion channel activity|protein binding			ovary(3)|breast(3)	6		all_epithelial(76;1.11e-06)|all_lung(116;5.79e-06)|Lung NSC(112;1.18e-05)|all_neural(266;0.0189)|Ovarian(192;0.0261)|Breast(70;0.203)		all cancers(93;0.00014)|OV - Ovarian serous cystadenocarcinoma(262;0.000233)|Epithelial(262;0.0112)|GBM - Glioblastoma multiforme(486;0.0161)	L-Glutamic Acid(DB00142)|Loperamide(DB00836)|Orphenadrine(DB01173)	GGGGAACCACCAGCAAAATCA	0.592													5	130	---	---	---	---	PASS
TEAD2	8463	broad.mit.edu	37	19	49845759	49845759	+	Missense_Mutation	SNP	T	G	G			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr19:49845759T>G	uc002pnj.2	-	11	1257	c.1166A>C	c.(1165-1167)AAG>ACG	p.K389T	uc002pnb.1_5'Flank|TEAD2_uc002png.2_Missense_Mutation_p.K392T|TEAD2_uc002pnh.2_Missense_Mutation_p.K393T|TEAD2_uc002pni.2_Missense_Mutation_p.K392T|TEAD2_uc010yao.1_Missense_Mutation_p.K261T|TEAD2_uc010emw.2_Missense_Mutation_p.K392T	NM_003598	NP_003589	Q15562	TEAD2_HUMAN	TEA domain family member 2	389	Transcriptional activation (Potential).				hippo signaling cascade		DNA binding|protein binding|sequence-specific DNA binding transcription factor activity			central_nervous_system(2)|ovary(1)	3		all_lung(116;7.65e-05)|Lung NSC(112;0.000132)|all_neural(266;0.0506)|Ovarian(192;0.15)		OV - Ovarian serous cystadenocarcinoma(262;0.00093)|GBM - Glioblastoma multiforme(486;0.0467)		CTGCCGCAACTTGTGCAAGAA	0.607													31	15	---	---	---	---	PASS
FPR3	2359	broad.mit.edu	37	19	52327627	52327627	+	Missense_Mutation	SNP	G	C	C			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr19:52327627G>C	uc002pxt.1	+	2	810	c.626G>C	c.(625-627)GGC>GCC	p.G209A		NM_002030	NP_002021	P25089	FPR3_HUMAN	formyl peptide receptor-like 2	209	Helical; Name=5; (Potential).				cellular component movement|chemotaxis	integral to membrane|plasma membrane	N-formyl peptide receptor activity			lung(4)|breast(1)|skin(1)	6						TTCATTATTGGCTTCAGCGTG	0.458													36	5	---	---	---	---	PASS
ZNF320	162967	broad.mit.edu	37	19	53384241	53384241	+	Missense_Mutation	SNP	T	G	G			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr19:53384241T>G	uc002qag.2	-	4	1329	c.1138A>C	c.(1138-1140)ACT>CCT	p.T380P	ZNF320_uc010eqh.1_5'Flank|ZNF320_uc010eqi.1_Intron|ZNF320_uc002qah.2_Missense_Mutation_p.T326P|ZNF320_uc002qai.2_Missense_Mutation_p.T380P	NM_207333	NP_997216	A2RRD8	ZN320_HUMAN	zinc finger protein 320	380					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0				GBM - Glioblastoma multiforme(134;0.0534)		CTCTCTCCAGTATGAACTCTC	0.403													29	41	---	---	---	---	PASS
LILRA5	353514	broad.mit.edu	37	19	54818729	54818729	+	Missense_Mutation	SNP	T	C	C			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr19:54818729T>C	uc002qfe.2	-	7	989	c.869A>G	c.(868-870)CAG>CGG	p.Q290R	LILRA5_uc002qff.2_Missense_Mutation_p.Q278R	NM_021250	NP_067073	A6NI73	LIRA5_HUMAN	leukocyte immunoglobulin-like receptor subfamily	290	Cytoplasmic (Potential).				innate immune response	extracellular region|integral to membrane	receptor activity			upper_aerodigestive_tract(1)	1	Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.105)		GGGGCTTCTCTGGCTGTGCCA	0.522													22	42	---	---	---	---	PASS
LILRB1	10859	broad.mit.edu	37	19	55144596	55144596	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr19:55144596C>A	uc002qgj.2	+	8	1428	c.1088C>A	c.(1087-1089)GCT>GAT	p.A363D	LILRB1_uc010erp.1_Intron|LILRB1_uc002qgl.2_Missense_Mutation_p.A363D|LILRB1_uc002qgk.2_Missense_Mutation_p.A363D|LILRB1_uc002qgm.2_Missense_Mutation_p.A363D|LILRB1_uc010erq.2_Missense_Mutation_p.A363D|LILRB1_uc010err.2_RNA	NM_006669	NP_006660	Q8NHL6	LIRB1_HUMAN	leukocyte immunoglobulin-like receptor,	363	Ig-like C2-type 4.|Extracellular (Potential).				regulation of immune response|response to virus	integral to membrane|plasma membrane	protein phosphatase 1 binding|receptor activity			large_intestine(1)|ovary(1)|skin(1)	3				GBM - Glioblastoma multiforme(193;0.0188)		GAGGGGGCAGCTGATGACCCA	0.577										HNSCC(37;0.09)			33	41	---	---	---	---	PASS
ZNF416	55659	broad.mit.edu	37	19	58087182	58087182	+	Silent	SNP	T	A	A			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr19:58087182T>A	uc002qpf.2	-	3	363	c.192A>T	c.(190-192)ATA>ATT	p.I64I	ZNF547_uc002qpm.3_Intron	NM_017879	NP_060349	Q9BWM5	ZN416_HUMAN	zinc finger protein 416	64	KRAB.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0		Colorectal(82;0.000256)|all_neural(62;0.0577)|Ovarian(87;0.156)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0259)		CCAGCGCAGTTATAAGTGCAA	0.557													71	39	---	---	---	---	PASS
ZSCAN22	342945	broad.mit.edu	37	19	58850392	58850392	+	Missense_Mutation	SNP	C	G	G			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr19:58850392C>G	uc002qsc.2	+	3	1323	c.1176C>G	c.(1174-1176)AGC>AGG	p.S392R	ZSCAN22_uc010yhz.1_3'UTR	NM_181846	NP_862829	P10073	ZSC22_HUMAN	zinc finger and SCAN domain containing 22	392	C2H2-type 5.				viral reproduction	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			pancreas(1)	1		all_cancers(17;3.11e-12)|all_epithelial(17;9.43e-09)|Colorectal(82;0.000256)|Lung NSC(17;0.000607)|all_lung(17;0.0024)|all_neural(62;0.0412)|Ovarian(87;0.156)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0289)		TCAGCCAGAGCACGCACCTGA	0.642													35	33	---	---	---	---	PASS
C20orf46	55321	broad.mit.edu	37	20	1161744	1161744	+	Silent	SNP	C	T	T			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr20:1161744C>T	uc010gaa.1	-	3	738	c.519G>A	c.(517-519)CTG>CTA	p.L173L	C20orf46_uc002weq.1_Silent_p.L173L	NM_018354	NP_060824	Q9NUR3	CT046_HUMAN	hypothetical protein LOC55321	173						integral to membrane	protein binding			ovary(1)	1						TGCACCTGTCCAGGTGGGAGC	0.642													9	15	---	---	---	---	PASS
CPXM1	56265	broad.mit.edu	37	20	2779185	2779185	+	Splice_Site	SNP	T	A	A			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr20:2779185T>A	uc002wgu.2	-	3	405	c.341_splice	c.e3-1	p.G114_splice	CPXM1_uc010gas.2_Splice_Site_p.G114_splice	NM_019609	NP_062555	Q96SM3	CPXM1_HUMAN	carboxypeptidase X, member 1 precursor						cell adhesion|proteolysis		metallocarboxypeptidase activity|zinc ion binding			ovary(2)|skin(2)	4						GAGGACAGCCTGGGGCGGGGA	0.622													11	22	---	---	---	---	PASS
PLCB1	23236	broad.mit.edu	37	20	8713943	8713943	+	Missense_Mutation	SNP	A	T	T			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr20:8713943A>T	uc002wnb.2	+	19	1950	c.1947A>T	c.(1945-1947)AGA>AGT	p.R649S	PLCB1_uc010zrb.1_Missense_Mutation_p.R548S|PLCB1_uc002wna.2_Missense_Mutation_p.R649S|PLCB1_uc002wnc.1_Missense_Mutation_p.R548S|PLCB1_uc002wnd.1_Missense_Mutation_p.R226S	NM_015192	NP_056007	Q9NQ66	PLCB1_HUMAN	phosphoinositide-specific phospholipase C beta 1	649	PI-PLC Y-box.				activation of meiosis involved in egg activation|CD24 biosynthetic process|cerebral cortex development|G1 phase|G2/M transition of mitotic cell cycle|glutamate signaling pathway|insulin-like growth factor receptor signaling pathway|interleukin-1-mediated signaling pathway|interleukin-12-mediated signaling pathway|interleukin-15-mediated signaling pathway|intracellular signal transduction|lipid catabolic process|memory|muscarinic acetylcholine receptor signaling pathway|negative regulation of monocyte extravasation|negative regulation of transcription, DNA-dependent|phosphatidylinositol metabolic process|positive regulation of acrosome reaction|positive regulation of developmental growth|positive regulation of embryonic development|positive regulation of interleukin-12 production|positive regulation of JNK cascade|positive regulation of myoblast differentiation|positive regulation of transcription, DNA-dependent|regulation of fertilization|regulation of G-protein coupled receptor protein signaling pathway|synaptic transmission	cytosol|nuclear chromatin|nuclear speck	calcium ion binding|calmodulin binding|enzyme binding|GTPase activator activity|phosphatidylinositol phospholipase C activity|phosphatidylinositol-4,5-bisphosphate binding|protein homodimerization activity|signal transducer activity			ovary(4)|breast(3)|upper_aerodigestive_tract(2)|skin(2)|lung(1)	12						GTGGCTACAGATTGAAGCCAG	0.408													27	38	---	---	---	---	PASS
C20orf26	26074	broad.mit.edu	37	20	20079442	20079442	+	Missense_Mutation	SNP	T	A	A			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr20:20079442T>A	uc002wru.2	+	8	919	c.843T>A	c.(841-843)AGT>AGA	p.S281R	C20orf26_uc010gcw.1_Missense_Mutation_p.S235R|C20orf26_uc010zse.1_Missense_Mutation_p.S281R|C20orf26_uc010zsf.1_Missense_Mutation_p.S281R	NM_015585	NP_056400	Q8NHU2	CT026_HUMAN	hypothetical protein LOC26074	281										ovary(3)|pancreas(1)	4				READ - Rectum adenocarcinoma(2;0.171)		AAGACCTAAGTGTCCGAAGAA	0.468													16	25	---	---	---	---	PASS
NFS1	9054	broad.mit.edu	37	20	34285673	34285673	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr20:34285673C>T	uc002xdw.1	-	3	321	c.257G>A	c.(256-258)GGG>GAG	p.G86E	NFS1_uc002xdt.1_Missense_Mutation_p.G26E|NFS1_uc002xdu.1_Missense_Mutation_p.G26E|NFS1_uc002xdv.1_RNA|NFS1_uc010zvk.1_5'UTR|NFS1_uc010zvl.1_Missense_Mutation_p.G86E|NFS1_uc002xdx.2_Missense_Mutation_p.G86E|ROMO1_uc002xdy.2_5'Flank|ROMO1_uc010gfm.2_5'Flank	NM_021100	NP_066923	Q9Y697	NFS1_HUMAN	NFS1 nitrogen fixation 1 precursor	86					cysteine metabolic process|iron incorporation into metallo-sulfur cluster|Mo-molybdopterin cofactor biosynthetic process|protein complex assembly|water-soluble vitamin metabolic process	cytosol|mitochondrial matrix|nucleus	cysteine desulfurase activity|protein homodimerization activity|pyridoxal phosphate binding			ovary(1)|skin(1)	2	Lung NSC(9;0.00608)|all_lung(11;0.00918)		BRCA - Breast invasive adenocarcinoma(18;0.0886)		L-Alanine(DB00160)|L-Cysteine(DB00151)|Pyridoxal Phosphate(DB00114)	GTGTGGGTTCCCATAGTAGTT	0.517													8	30	---	---	---	---	PASS
MYL9	10398	broad.mit.edu	37	20	35177601	35177601	+	Silent	SNP	C	T	T			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr20:35177601C>T	uc002xfl.1	+	4	562	c.468C>T	c.(466-468)TAC>TAT	p.Y156Y	uc002xfk.3_Intron|MYL9_uc002xfm.1_Silent_p.Y102Y	NM_006097	NP_006088	P24844	MYL9_HUMAN	myosin regulatory light chain 9 isoform a	156	EF-hand 3.				axon guidance|muscle contraction|regulation of muscle contraction	cytosol|muscle myosin complex	calcium ion binding|structural constituent of muscle				0	Breast(12;0.0192)	Myeloproliferative disorder(115;0.00878)				ACTTCAACTACGTGGAGTTCA	0.602													16	38	---	---	---	---	PASS
DHX35	60625	broad.mit.edu	37	20	37657130	37657130	+	Missense_Mutation	SNP	C	G	G			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr20:37657130C>G	uc002xjh.2	+	19	1882	c.1871C>G	c.(1870-1872)ACT>AGT	p.T624S	DHX35_uc010zwa.1_Missense_Mutation_p.T469S|DHX35_uc010zwb.1_Missense_Mutation_p.T469S|DHX35_uc010zwc.1_Missense_Mutation_p.T593S	NM_021931	NP_068750	Q9H5Z1	DHX35_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 35	624						catalytic step 2 spliceosome	ATP binding|ATP-dependent helicase activity|nucleic acid binding			lung(1)|kidney(1)|skin(1)	3		Myeloproliferative disorder(115;0.00878)				TTTCATTCTACTGGAGCTTAT	0.468													22	50	---	---	---	---	PASS
PLCG1	5335	broad.mit.edu	37	20	39802790	39802790	+	Silent	SNP	C	T	T			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr20:39802790C>T	uc002xjp.1	+	31	3790	c.3669C>T	c.(3667-3669)TTC>TTT	p.F1223F	PLCG1_uc002xjo.1_Silent_p.F1224F|PLCG1_uc010zwe.1_Silent_p.F889F	NM_182811	NP_877963	P19174	PLCG1_HUMAN	phospholipase C, gamma 1 isoform b	1223					activation of phospholipase C activity|axon guidance|blood coagulation|cellular response to epidermal growth factor stimulus|epidermal growth factor receptor signaling pathway|fibroblast growth factor receptor signaling pathway|interspecies interaction between organisms|intracellular signal transduction|leukocyte migration|nerve growth factor receptor signaling pathway|phospholipid catabolic process|positive regulation of angiogenesis|positive regulation of blood vessel endothelial cell migration|positive regulation of epithelial cell migration|T cell receptor signaling pathway	cytosol|lamellipodium|plasma membrane|ruffle	calcium ion binding|phosphatidylinositol phospholipase C activity|protein binding|receptor signaling protein activity			lung(3)|breast(3)|skin(2)	8		Myeloproliferative disorder(115;0.00878)				TCAGTCCCTTCAGTGGTACGT	0.607													37	29	---	---	---	---	PASS
ZBP1	81030	broad.mit.edu	37	20	56185336	56185336	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr20:56185336C>T	uc002xyo.2	-	7	1243	c.962G>A	c.(961-963)AGA>AAA	p.R321K	ZBP1_uc010gjm.2_Missense_Mutation_p.R320K|ZBP1_uc002xyp.2_Missense_Mutation_p.R246K	NM_030776	NP_110403	Q9H171	ZBP1_HUMAN	Z-DNA binding protein 1 isoform a	321						cytoplasm|nucleus	double-stranded RNA adenosine deaminase activity|left-handed Z-DNA binding|RNA binding			ovary(2)	2	Lung NSC(12;0.000545)|all_lung(29;0.00195)|Melanoma(10;0.242)		BRCA - Breast invasive adenocarcinoma(13;7.87e-13)|Epithelial(14;3.26e-09)|all cancers(14;3.62e-08)			CATGTGGATTCTCTGGGCGGC	0.582													108	78	---	---	---	---	PASS
GNAS	2778	broad.mit.edu	37	20	57415527	57415527	+	Missense_Mutation	SNP	G	C	C			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr20:57415527G>C	uc002xzt.2	+	1	733	c.366G>C	c.(364-366)GAG>GAC	p.E122D	GNASAS_uc002xzs.1_Intron|GNAS_uc002xzu.3_5'Flank|GNAS_uc010gjq.2_5'Flank	NM_016592	NP_057676	P63092	GNAS2_HUMAN	GNAS complex locus NESP55	Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment					activation of adenylate cyclase activity|cellular response to glucagon stimulus|energy reserve metabolic process|G-protein coupled receptor protein signaling pathway|intracellular transport|platelet activation|regulation of insulin secretion|sensory perception of smell|transmembrane transport|water transport	heterotrimeric G-protein complex|intrinsic to membrane|trans-Golgi network membrane	adenylate cyclase activity|GTP binding|GTPase activity|guanyl-nucleotide exchange factor activity|identical protein binding|signal transducer activity			pituitary(201)|thyroid(35)|ovary(15)|adrenal_gland(9)|liver(7)|large_intestine(5)|parathyroid(5)|kidney(5)|haematopoietic_and_lymphoid_tissue(3)|lung(2)|testis(1)|stomach(1)|small_intestine(1)|autonomic_ganglia(1)|pancreas(1)	292	all_lung(29;0.0104)		BRCA - Breast invasive adenocarcinoma(13;2.19e-08)|Colorectal(105;0.109)			TCGAGTCCGAGACCGACTTCG	0.637			Mis		pituitary adenoma		McCune-Albright syndrome; pseudohypoparathyroidism|type IA		3-Methylglutaconic_Aciduria_and_Myelodysplasia|McCune-Albright_syndrome|Mazabraud_syndrome	TSP Lung(22;0.16)			15	43	---	---	---	---	PASS
ERG	2078	broad.mit.edu	37	21	39795353	39795353	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr21:39795353G>A	uc010gnw.2	-	5	683	c.388C>T	c.(388-390)CGC>TGC	p.R130C	ERG_uc002yxa.2_Missense_Mutation_p.R123C|ERG_uc011aek.1_Missense_Mutation_p.R31C|ERG_uc010gnv.2_Missense_Mutation_p.R31C|ERG_uc010gnx.2_Missense_Mutation_p.R130C|ERG_uc011ael.1_Missense_Mutation_p.R130C|ERG_uc002yxb.2_Missense_Mutation_p.R130C|ERG_uc011aem.1_Missense_Mutation_p.R123C|ERG_uc002yxc.3_Missense_Mutation_p.R130C	NM_001136155	NP_001129627	P11308	ERG_HUMAN	ets-related isoform 4	130	PNT.				cell proliferation|multicellular organismal development|protein phosphorylation	cytoplasm|nucleus|ribonucleoprotein complex	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|signal transducer activity		TMPRSS2/ERG(2499)|FUS/ERG(163)|EWSR1/ERG(162)	prostate(2499)|bone(167)|haematopoietic_and_lymphoid_tissue(153)|soft_tissue(5)|lung(2)|skin(1)|ovary(1)	2828		Prostate(19;3.6e-06)				ATAACTCTGCGCTCGTTCGTG	0.602													9	17	---	---	---	---	PASS
DSCAM	1826	broad.mit.edu	37	21	41551009	41551009	+	Missense_Mutation	SNP	G	C	C			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr21:41551009G>C	uc002yyq.1	-	15	3244	c.2792C>G	c.(2791-2793)TCT>TGT	p.S931C	DSCAM_uc002yyr.1_RNA	NM_001389	NP_001380	O60469	DSCAM_HUMAN	Down syndrome cell adhesion molecule isoform	931	Extracellular (Potential).|Fibronectin type-III 1.				cell adhesion|dendrite self-avoidance|negative regulation of cell adhesion|positive regulation of axon extension involved in axon guidance|positive regulation of phosphorylation	axon|extracellular region|growth cone|integral to plasma membrane|membrane fraction	protein binding			ovary(6)|skin(4)|upper_aerodigestive_tract(1)	11		all_cancers(19;0.186)|Prostate(19;1.15e-05)|all_epithelial(19;0.0103)				TCTCTGAGCAGAATCCCAGGA	0.433													33	4	---	---	---	---	PASS
BACE2	25825	broad.mit.edu	37	21	42609440	42609440	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr21:42609440G>T	uc002yyw.2	+	3	865	c.402G>T	c.(400-402)AGG>AGT	p.R134S	BACE2_uc002yyx.2_Missense_Mutation_p.R134S|BACE2_uc002yyy.2_Missense_Mutation_p.R134S	NM_012105	NP_036237	Q9Y5Z0	BACE2_HUMAN	beta-site APP-cleaving enzyme 2 isoform A	134	Extracellular (Potential).				membrane protein ectodomain proteolysis|negative regulation of amyloid precursor protein biosynthetic process|peptide hormone processing	cell surface|endoplasmic reticulum|endosome|Golgi apparatus|integral to membrane	aspartic-type endopeptidase activity			ovary(2)	2		Prostate(19;1.57e-07)|all_epithelial(19;0.0251)				CTTTCTCCAGGTCTAGCACAT	0.328													18	2	---	---	---	---	PASS
COL6A1	1291	broad.mit.edu	37	21	47422159	47422159	+	Silent	SNP	G	C	C			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr21:47422159G>C	uc002zhu.1	+	32	2196	c.2094G>C	c.(2092-2094)GCG>GCC	p.A698A	COL6A1_uc010gqd.1_Silent_p.A29A|COL6A1_uc002zhv.1_Silent_p.A29A|COL6A1_uc002zhw.1_5'Flank	NM_001848	NP_001839	P12109	CO6A1_HUMAN	collagen, type VI, alpha 1 precursor	698	VWFA 2.|C-terminal globular domain.				axon guidance|cell adhesion|protein heterotrimerization	collagen type VI|protein complex	platelet-derived growth factor binding			ovary(1)	1	all_hematologic(128;0.24)			Colorectal(79;0.0265)|READ - Rectum adenocarcinoma(84;0.0649)	Palifermin(DB00039)	AGTGGATGGCGGGCGGCACCT	0.701													3	6	---	---	---	---	PASS
LOC96610	96610	broad.mit.edu	37	22	23055659	23055659	+	RNA	SNP	G	C	C			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr22:23055659G>C	uc011aim.1	+	153		c.9374G>C								Parts of antibodies, mostly variable regions.												0						TTACTGTCAGGTGTGGGATAG	0.582													17	14	---	---	---	---	PASS
SLC5A1	6523	broad.mit.edu	37	22	32487724	32487724	+	Nonsense_Mutation	SNP	G	T	T			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr22:32487724G>T	uc003amc.2	+	11	1487	c.1255G>T	c.(1255-1257)GAG>TAG	p.E419*	SLC5A1_uc011alz.1_Nonsense_Mutation_p.E292*	NM_000343	NP_000334	P13866	SC5A1_HUMAN	solute carrier family 5 (sodium/glucose	419	Cytoplasmic (Potential).				carbohydrate metabolic process	integral to plasma membrane	glucose:sodium symporter activity|protein binding			skin(1)	1						GAGAGCATCTGAGAAAGAGCT	0.532													33	28	---	---	---	---	PASS
UPK3A	7380	broad.mit.edu	37	22	45689169	45689169	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr22:45689169G>T	uc003bfy.2	+	5	685	c.679G>T	c.(679-681)GCT>TCT	p.A227S	UPK3A_uc010gzy.2_Missense_Mutation_p.A106S	NM_006953	NP_008884	O75631	UPK3A_HUMAN	uroplakin 3A precursor	227	Helical; (Potential).				epithelial cell differentiation	endoplasmic reticulum membrane|integral to membrane					0		Ovarian(80;0.00965)|all_neural(38;0.0416)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0178)		TGTGGGTTTTGCTGGCGCCAT	0.602													12	14	---	---	---	---	PASS
CELSR1	9620	broad.mit.edu	37	22	46785336	46785336	+	Missense_Mutation	SNP	T	A	A			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr22:46785336T>A	uc003bhw.1	-	18	6406	c.6406A>T	c.(6406-6408)AGG>TGG	p.R2136W	CELSR1_uc011arc.1_Missense_Mutation_p.R457W	NM_014246	NP_055061	Q9NYQ6	CELR1_HUMAN	cadherin EGF LAG seven-pass G-type receptor 1	2136	Extracellular (Potential).				central nervous system development|homophilic cell adhesion|neural tube closure|neuropeptide signaling pathway	integral to plasma membrane	calcium ion binding|G-protein coupled receptor activity|protein dimerization activity			lung(4)|breast(4)|pancreas(2)|skin(1)	11		Ovarian(80;0.00142)|Breast(42;0.00296)|all_neural(38;0.0416)|Colorectal(5;0.0766)		UCEC - Uterine corpus endometrioid carcinoma (28;0.00643)|BRCA - Breast invasive adenocarcinoma(115;0.171)		CGCAGCGCCCTCACCAGCTGC	0.632													4	15	---	---	---	---	PASS
TMEM27	57393	broad.mit.edu	37	X	15677138	15677138	+	Splice_Site	SNP	C	G	G			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chrX:15677138C>G	uc004cxc.1	-	3	459	c.203_splice	c.e3+1	p.E68_splice		NM_020665	NP_065716	Q9HBJ8	TMM27_HUMAN	transmembrane protein 27 precursor						proteolysis	integral to membrane	metallopeptidase activity|peptidyl-dipeptidase activity			ovary(1)	1	Hepatocellular(33;0.183)					TATTTGCTTACTCTGTTGCTT	0.318													6	8	---	---	---	---	PASS
FAM47A	158724	broad.mit.edu	37	X	34148516	34148516	+	Missense_Mutation	SNP	T	A	A			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chrX:34148516T>A	uc004ddg.2	-	1	1913	c.1880A>T	c.(1879-1881)AAT>ATT	p.N627I		NM_203408	NP_981953	Q5JRC9	FA47A_HUMAN	hypothetical protein LOC158724	627										ovary(4)|central_nervous_system(1)	5						GTCAAACAGATTCCTGATGGA	0.443													26	36	---	---	---	---	PASS
FAM47B	170062	broad.mit.edu	37	X	34962426	34962426	+	Missense_Mutation	SNP	A	C	C			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chrX:34962426A>C	uc004ddi.1	+	1	1496	c.1478A>C	c.(1477-1479)GAT>GCT	p.D493A		NM_152631	NP_689844	Q8NA70	FA47B_HUMAN	hypothetical protein LOC170062	493										ovary(3)|breast(1)	4						AGAACAACCGATCAAGACCAA	0.458													30	47	---	---	---	---	PASS
USP11	8237	broad.mit.edu	37	X	47102051	47102051	+	Silent	SNP	C	T	T			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chrX:47102051C>T	uc004dhp.2	+	12	1644	c.1644C>T	c.(1642-1644)CAC>CAT	p.H548H	USP11_uc004dhq.2_Silent_p.H275H	NM_004651	NP_004642	P51784	UBP11_HUMAN	ubiquitin specific peptidase 11	548					protein deubiquitination|ubiquitin-dependent protein catabolic process	cytoplasm|nucleus	cysteine-type endopeptidase activity|protein binding|ubiquitin thiolesterase activity|ubiquitin-specific protease activity			ovary(1)|lung(1)|central_nervous_system(1)	3						TCTTCAGTCACCGCTTCTATA	0.552													22	0	---	---	---	---	PASS
MIR223	407008	broad.mit.edu	37	X	65238772	65238772	+	RNA	SNP	G	A	A			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chrX:65238772G>A	hsa-mir-223|MI0000300	+			c.61G>A			uc004dwg.1_RNA|uc011mox.1_RNA																	0						CACTCCATGTGGTAGAGTGTC	0.537													5	6	---	---	---	---	PASS
STARD8	9754	broad.mit.edu	37	X	67938340	67938340	+	Silent	SNP	C	T	T			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chrX:67938340C>T	uc004dxa.2	+	5	1716	c.1344C>T	c.(1342-1344)TCC>TCT	p.S448S	STARD8_uc004dxb.2_Silent_p.S528S|STARD8_uc004dxc.3_Silent_p.S448S	NM_014725	NP_055540	Q92502	STAR8_HUMAN	StAR-related lipid transfer (START) domain	448					regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol|focal adhesion	GTPase activator activity			breast(3)|ovary(2)|pancreas(1)	6						TGGCCTCCTCCAGCGAACTTG	0.592													7	8	---	---	---	---	PASS
PCDH19	57526	broad.mit.edu	37	X	99551290	99551290	+	Silent	SNP	C	T	T			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chrX:99551290C>T	uc010nmz.2	-	6	5108	c.3432G>A	c.(3430-3432)AAG>AAA	p.K1144K	PCDH19_uc004efw.3_Silent_p.K1096K|PCDH19_uc004efx.3_Silent_p.K1097K	NM_020766	NP_001098713	Q8TAB3	PCD19_HUMAN	protocadherin 19 isoform b	1144	Cytoplasmic (Potential).				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(2)|breast(2)|upper_aerodigestive_tract(1)|urinary_tract(1)|skin(1)	7						GAACGATATCCTTCAGACGCT	0.493													48	2	---	---	---	---	PASS
CXorf57	55086	broad.mit.edu	37	X	105855370	105855370	+	Silent	SNP	G	T	T			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chrX:105855370G>T	uc004emi.3	+	1	211	c.60G>T	c.(58-60)CCG>CCT	p.P20P	CXorf57_uc004emj.3_Silent_p.P20P|CXorf57_uc004emh.2_Silent_p.P20P	NM_018015	NP_060485	Q6NSI4	CX057_HUMAN	hypothetical protein LOC55086	20										ovary(1)|lung(1)|breast(1)	3						TAGATTGGCCGAACCCTGAGA	0.572													27	3	---	---	---	---	PASS
TBC1D8B	54885	broad.mit.edu	37	X	106111678	106111678	+	Missense_Mutation	SNP	A	T	T			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chrX:106111678A>T	uc004emo.2	+	18	2949	c.2784A>T	c.(2782-2784)GAA>GAT	p.E928D	MORC4_uc004emp.3_Intron	NM_017752	NP_060222	Q0IIM8	TBC8B_HUMAN	TBC1 domain family, member 8B (with GRAM domain)	928						intracellular	calcium ion binding|Rab GTPase activator activity			ovary(2)|central_nervous_system(1)|skin(1)	4						TTTCCAAGGAAGAATTACTTT	0.323													4	1	---	---	---	---	PASS
GUCY2F	2986	broad.mit.edu	37	X	108684580	108684580	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chrX:108684580C>A	uc004eod.3	-	7	1977	c.1701G>T	c.(1699-1701)GAG>GAT	p.E567D	GUCY2F_uc011msq.1_RNA	NM_001522	NP_001513	P51841	GUC2F_HUMAN	guanylate cyclase 2F precursor	567	Protein kinase.|Cytoplasmic (Potential).				intracellular signal transduction|receptor guanylyl cyclase signaling pathway|visual perception	integral to plasma membrane|nuclear outer membrane	ATP binding|GTP binding|guanylate cyclase activity|protein kinase activity|receptor activity			lung(4)|breast(3)|central_nervous_system(1)	8						AATATCTTACCTCATAAATCG	0.403													5	73	---	---	---	---	PASS
AGTR2	186	broad.mit.edu	37	X	115304403	115304403	+	Silent	SNP	C	T	T			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chrX:115304403C>T	uc004eqh.3	+	3	1077	c.870C>T	c.(868-870)TGC>TGT	p.C290C		NM_000686	NP_000677	P50052	AGTR2_HUMAN	angiotensin II receptor, type 2	290	Extracellular (Potential).				behavior|blood vessel remodeling|brain development|G-protein signaling, coupled to cGMP nucleotide second messenger|intracellular protein kinase cascade|negative regulation of blood vessel endothelial cell migration|negative regulation of cell growth|negative regulation of heart rate|negative regulation of nerve growth factor receptor signaling pathway|nitric oxide mediated signal transduction|positive regulation of apoptosis|positive regulation of nitric-oxide synthase activity|positive regulation of phosphoprotein phosphatase activity|positive regulation of vasodilation|regulation of systemic arterial blood pressure by circulatory renin-angiotensin		angiotensin type II receptor activity|receptor antagonist activity			ovary(2)|lung(1)	3						TTAATAGCTGCGAAGTTATAG	0.483													38	50	---	---	---	---	PASS
MAGEA4	4103	broad.mit.edu	37	X	151092292	151092292	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chrX:151092292G>T	uc004fez.2	+	3	312	c.156G>T	c.(154-156)GAG>GAT	p.E52D	MAGEA4_uc004ffa.2_Missense_Mutation_p.E52D|MAGEA4_uc004ffb.2_Missense_Mutation_p.E52D|MAGEA4_uc004ffc.2_Missense_Mutation_p.E52D|MAGEA4_uc004ffd.2_Missense_Mutation_p.E52D	NM_002362	NP_002353	P43358	MAGA4_HUMAN	melanoma antigen family A, 4	52							protein binding			ovary(1)|breast(1)|central_nervous_system(1)	3	Acute lymphoblastic leukemia(192;6.56e-05)					GCACCCTGGAGGAAGTGCCTG	0.617													5	44	---	---	---	---	PASS
GABRA3	2556	broad.mit.edu	37	X	151358288	151358288	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chrX:151358288G>T	uc010ntk.1	-	9	1297	c.1057C>A	c.(1057-1059)CTG>ATG	p.L353M		NM_000808	NP_000799	P34903	GBRA3_HUMAN	gamma-aminobutyric acid A receptor, alpha 3	353	Helical; (Probable).				gamma-aminobutyric acid signaling pathway	cell junction|chloride channel complex|integral to plasma membrane|postsynaptic membrane	benzodiazepine receptor activity|chloride channel activity|extracellular ligand-gated ion channel activity|GABA-A receptor activity|protein binding			ovary(1)	1	Acute lymphoblastic leukemia(192;6.56e-05)				Alprazolam(DB00404)|Diazepam(DB00829)|Ethchlorvynol(DB00189)|Flunitrazepam(DB01544)|Flurazepam(DB00690)|Lorazepam(DB00186)|Meprobamate(DB00371)|Midazolam(DB00683)	AATTCAATCAGTGCAGAAAAT	0.478													19	27	---	---	---	---	PASS
FLNA	2316	broad.mit.edu	37	X	153581949	153581949	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chrX:153581949C>A	uc004fkk.2	-	36	6082	c.5833G>T	c.(5833-5835)GGC>TGC	p.G1945C	FLNA_uc004fki.2_Translation_Start_Site|FLNA_uc011mzn.1_Intron|FLNA_uc010nuu.1_Missense_Mutation_p.G1937C	NM_001110556	NP_001104026	P21333	FLNA_HUMAN	filamin A, alpha isoform 2	1945	Filamin 17.				actin crosslink formation|actin cytoskeleton reorganization|cell junction assembly|cytoplasmic sequestering of protein|establishment of protein localization|inhibition of adenylate cyclase activity by dopamine receptor signaling pathway|negative regulation of protein catabolic process|negative regulation of sequence-specific DNA binding transcription factor activity|platelet activation|platelet degranulation|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of transcription factor import into nucleus|protein localization at cell surface|protein stabilization|receptor clustering	cell cortex|cytosol|extracellular region|nucleus|plasma membrane	actin filament binding|Fc-gamma receptor I complex binding|glycoprotein binding|GTP-Ral binding|protein homodimerization activity|Rac GTPase binding|signal transducer activity|transcription factor binding			breast(6)	6	all_cancers(53;3.7e-16)|all_epithelial(53;2.97e-10)|all_lung(58;1.84e-07)|Lung NSC(58;5.84e-07)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)					AAGGGGCTGCCTGGGACGTGC	0.607													5	34	---	---	---	---	PASS
EPHA6	285220	broad.mit.edu	37	3	97356918	97356920	+	In_Frame_Del	DEL	ACA	-	-			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr3:97356918_97356920delACA	uc010how.1	+	14	2819_2821	c.2776_2778delACA	c.(2776-2778)ACAdel	p.T928del	EPHA6_uc011bgp.1_3'UTR|EPHA6_uc003drs.3_In_Frame_Del_p.T320del|EPHA6_uc003drr.3_In_Frame_Del_p.T320del|EPHA6_uc003drt.2_In_Frame_Del_p.T320del|EPHA6_uc010hox.1_RNA	NM_001080448	NP_001073917	Q9UF33	EPHA6_HUMAN	EPH receptor A6 isoform a	833	Protein kinase.|Cytoplasmic (Potential).					integral to plasma membrane	ATP binding|ephrin receptor activity			stomach(5)|lung(4)|central_nervous_system(3)|breast(1)|skin(1)|ovary(1)|kidney(1)	16						AGCTGCTTATACAACAACTGTAA	0.365													13	7	---	---	---	---	
GLUD1	2746	broad.mit.edu	37	10	88820739	88820739	+	Frame_Shift_Del	DEL	C	-	-			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr10:88820739delC	uc001keh.2	-	7	1089	c.992delG	c.(991-993)GGTfs	p.G331fs	GLUD1_uc001keg.2_Frame_Shift_Del_p.G164fs|GLUD1_uc010qmp.1_Frame_Shift_Del_p.G198fs	NM_005271	NP_005262	P00367	DHE3_HUMAN	glutamate dehydrogenase 1 precursor	331					glutamate biosynthetic process|glutamate catabolic process|positive regulation of insulin secretion	mitochondrial matrix	ADP binding|ATP binding|glutamate dehydrogenase|glutamate dehydrogenase activity|GTP binding|identical protein binding|leucine binding|NAD+ binding				0					L-Glutamic Acid(DB00142)|NADH(DB00157)	ATCAGACTCACCAACAGCAAT	0.363													58	40	---	---	---	---	
SFRS1	6426	broad.mit.edu	37	17	56082957	56082958	+	Frame_Shift_Del	DEL	TC	-	-			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr17:56082957_56082958delTC	uc002ivi.2	-	4	765_766	c.556_557delGA	c.(556-558)GAAfs	p.E186fs	SFRS1_uc002ivj.2_3'UTR	NM_006924	NP_008855	Q07955	SRSF1_HUMAN	splicing factor, arginine/serine-rich 1 isoform	186	RRM 2.			Missing: In MR-E; loss of ability to activate splicing.|Missing: In MR-B; strongly inhibits splicing.	mRNA 3'-end processing|mRNA export from nucleus|nuclear mRNA 5'-splice site recognition|termination of RNA polymerase II transcription	catalytic step 2 spliceosome|cytoplasm|nuclear speck	nucleotide binding|RNA binding				0		Colorectal(1115;0.0691)		LUAD - Lung adenocarcinoma(1115;0.247)		GTAGGCAGTTTCTCCCTATTGG	0.431													39	29	---	---	---	---	
LOC647946	647946	broad.mit.edu	37	18	36788075	36788075	+	RNA	DEL	A	-	-			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr18:36788075delA	uc002lak.1	-	4		c.1155delT			LOC647946_uc010xcj.1_RNA|LOC647946_uc002lal.1_RNA					Homo sapiens cDNA FLJ33284 fis, clone ASTRO2009458.												0						AAGTTGCCTTAAAAAAAAAAG	0.343													4	2	---	---	---	---	
STK11	6794	broad.mit.edu	37	19	1221314	1221314	+	Frame_Shift_Del	DEL	C	-	-	rs67873004		TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr19:1221314delC	uc002lrl.1	+	6	1952	c.837delC	c.(835-837)GGCfs	p.G279fs		NM_000455	NP_000446	Q15831	STK11_HUMAN	serine/threonine protein kinase 11	279	Protein kinase.				anoikis|cell cycle arrest|energy reserve metabolic process|insulin receptor signaling pathway|positive regulation of transforming growth factor beta receptor signaling pathway|regulation of fatty acid biosynthetic process|regulation of fatty acid oxidation	cytosol|nucleus	ATP binding|magnesium ion binding|protein serine/threonine kinase activity	p.0?(19)|p.P281fs*6(2)|p.?(2)|p.Y246fs*3(1)|p.G279F(1)		lung(174)|cervix(35)|skin(15)|large_intestine(12)|pancreas(6)|gastrointestinal_tract_(site_indeterminate)(5)|stomach(4)|ovary(4)|breast(2)|upper_aerodigestive_tract(1)|testis(1)|liver(1)|biliary_tract(1)|small_intestine(1)|urinary_tract(1)|oesophagus(1)|prostate(1)|kidney(1)	266		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;7.93e-06)|all_lung(49;1.25e-05)|Breast(49;0.000172)|Renal(1328;0.0183)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|Lung(535;0.00942)|STAD - Stomach adenocarcinoma(1328;0.18)		GCGACTGTGGCCCCCCGCTCT	0.607		14	D|Mis|N|F|S		NSCLC|pancreatic	jejunal harmartoma|ovarian|testicular|pancreatic			Peutz-Jeghers_syndrome	TSP Lung(3;<1E-08)			3	15	---	---	---	---	
IL12RB1	3594	broad.mit.edu	37	19	18180373	18180373	+	Frame_Shift_Del	DEL	G	-	-	rs140254802		TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr19:18180373delG	uc002nhw.1	-	10	1236	c.1172delC	c.(1171-1173)CCGfs	p.P391fs	IL12RB1_uc010xqb.1_Frame_Shift_Del_p.P391fs|IL12RB1_uc002nhx.1_Frame_Shift_Del_p.P431fs	NM_005535	NP_005526	P42701	I12R1_HUMAN	interleukin 12 receptor, beta 1 isoform 1	391	Extracellular (Potential).|Fibronectin type-III 4.				cellular response to interferon-gamma|interleukin-12-mediated signaling pathway|positive regulation of activated T cell proliferation|positive regulation of defense response to virus by host|positive regulation of interferon-gamma production|positive regulation of memory T cell differentiation|positive regulation of T cell mediated cytotoxicity|positive regulation of T-helper 1 type immune response|positive regulation of T-helper 17 cell lineage commitment|positive regulation of T-helper 17 type immune response	interleukin-12 receptor complex|interleukin-23 receptor complex	cytokine receptor activity			pancreas(1)	1						AGCCGGATCCGGGTCTTGCGG	0.637													1	30	---	---	---	---	
ZNF98	148198	broad.mit.edu	37	19	22575389	22575389	+	Frame_Shift_Del	DEL	C	-	-			TCGA-66-2754-01A-01D-0983-08	TCGA-66-2754-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	c34a64c8-3746-44f8-a7ee-77f502b6256c	de244b96-3214-45d1-bb11-a802818eafb4	g.chr19:22575389delC	uc002nqt.2	-	4	770	c.648delG	c.(646-648)GGGfs	p.G216fs		NM_001098626	NP_001092096	A6NK75	ZNF98_HUMAN	zinc finger protein 98	216	C2H2-type 2.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)|skin(1)	2		all_cancers(12;0.0536)|all_lung(12;0.00187)|Lung NSC(12;0.0019)|all_epithelial(12;0.00542)|Hepatocellular(1079;0.244)				TATAGGCTTTCCCACATTCTT	0.373													0	6	---	---	---	---