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
PLA2G2C	391013	broad.mit.edu	37	1	20501520	20501520	+	Silent	SNP	G	T	T			TCGA-18-4721-01A-01D-1441-08	TCGA-18-4721-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	d2ab2555-7288-47a4-a80c-bf62d65b67b8	f7b631ae-ee98-499b-9d26-dc945e7ac3b8	g.chr1:20501520G>T	uc009vpq.1	-	1	168	c.168C>A	c.(166-168)ATC>ATA	p.I56I		NM_001105572	NP_001099042			phospholipase A2, group IIC precursor												0		Colorectal(325;0.000147)|Renal(390;0.000469)|Lung NSC(340;0.00412)|all_lung(284;0.00419)|Breast(348;0.00526)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0427)		UCEC - Uterine corpus endometrioid carcinoma (279;0.018)|COAD - Colon adenocarcinoma(152;1.14e-05)|BRCA - Breast invasive adenocarcinoma(304;8.01e-05)|Kidney(64;0.000171)|GBM - Glioblastoma multiforme(114;0.000528)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.199)		CATCCACGGGGATCCCTTTAT	0.502													9	33	---	---	---	---	PASS
DEPDC1	55635	broad.mit.edu	37	1	68949739	68949739	+	Silent	SNP	A	G	G			TCGA-18-4721-01A-01D-1441-08	TCGA-18-4721-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	d2ab2555-7288-47a4-a80c-bf62d65b67b8	f7b631ae-ee98-499b-9d26-dc945e7ac3b8	g.chr1:68949739A>G	uc001dem.3	-	7	921	c.804T>C	c.(802-804)TAT>TAC	p.Y268Y	DEPDC1_uc001dej.3_5'Flank|DEPDC1_uc001dek.3_RNA|DEPDC1_uc001del.3_Silent_p.Y268Y	NM_001114120	NP_001107592	Q5TB30	DEP1A_HUMAN	DEP domain containing 1 isoform a	268					intracellular signal transduction|negative regulation of transcription, DNA-dependent|transcription, DNA-dependent	transcriptional repressor complex	GTPase activator activity|protein binding				0				OV - Ovarian serous cystadenocarcinoma(397;7.21e-36)		CAAATCCAACATAAGTTGGAT	0.279													25	64	---	---	---	---	PASS
CLCA1	1179	broad.mit.edu	37	1	86952423	86952423	+	Missense_Mutation	SNP	G	T	T			TCGA-18-4721-01A-01D-1441-08	TCGA-18-4721-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	d2ab2555-7288-47a4-a80c-bf62d65b67b8	f7b631ae-ee98-499b-9d26-dc945e7ac3b8	g.chr1:86952423G>T	uc001dlt.2	+	7	1298	c.1169G>T	c.(1168-1170)CGA>CTA	p.R390L	CLCA1_uc001dls.1_Missense_Mutation_p.R329L	NM_001285	NP_001276	A8K7I4	CLCA1_HUMAN	chloride channel accessory 1 precursor	390	VWFA.				calcium ion transport	extracellular space|integral to plasma membrane	chloride channel activity			ovary(1)	1		Lung NSC(277;0.239)		all cancers(265;0.0249)|Epithelial(280;0.0476)		AGCGGGCTTCGATCGGCATTT	0.438													34	75	---	---	---	---	PASS
AP4B1	10717	broad.mit.edu	37	1	114445388	114445388	+	Silent	SNP	C	A	A			TCGA-18-4721-01A-01D-1441-08	TCGA-18-4721-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	d2ab2555-7288-47a4-a80c-bf62d65b67b8	f7b631ae-ee98-499b-9d26-dc945e7ac3b8	g.chr1:114445388C>A	uc001eeb.2	-	2	353	c.210G>T	c.(208-210)CTG>CTT	p.L70L	AP4B1_uc001eec.2_Intron|AP4B1_uc001eed.2_Silent_p.L70L|AP4B1_uc010owp.1_Intron|AP4B1_uc001eea.1_5'Flank|AP4B1_uc010owq.1_Silent_p.L70L|DCLRE1B_uc001eeg.2_5'Flank|DCLRE1B_uc001eeh.2_5'Flank|DCLRE1B_uc001eei.2_5'Flank	NM_006594	NP_006585	Q9Y6B7	AP4B1_HUMAN	adaptor-related protein complex 4, beta 1	70					intracellular protein transport|vesicle-mediated transport	clathrin adaptor complex|soluble fraction|trans-Golgi network	protein binding|protein transporter activity			ovary(3)|central_nervous_system(1)	4	Lung SC(450;0.184)	all_cancers(81;4.5e-08)|all_epithelial(167;1.1e-07)|all_lung(203;1.53e-05)|Lung NSC(69;2.76e-05)		Lung(183;0.0234)|Colorectal(144;0.0686)|all cancers(265;0.0792)|Epithelial(280;0.0866)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)		TGCACATGTACAGATAAACCA	0.488													34	61	---	---	---	---	PASS
CD58	965	broad.mit.edu	37	1	117078706	117078706	+	Nonsense_Mutation	SNP	G	C	C			TCGA-18-4721-01A-01D-1441-08	TCGA-18-4721-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	d2ab2555-7288-47a4-a80c-bf62d65b67b8	f7b631ae-ee98-499b-9d26-dc945e7ac3b8	g.chr1:117078706G>C	uc001egm.2	-	3	630	c.509C>G	c.(508-510)TCA>TGA	p.S170*	CD58_uc001egn.2_RNA|CD58_uc010owy.1_Nonsense_Mutation_p.S170*|CD58_uc001ego.1_Intron|CD58_uc001egp.3_Nonsense_Mutation_p.S170*	NM_001779	NP_001770	P19256	LFA3_HUMAN	CD58 molecule isoform 1	170	Extracellular (Potential).|Ig-like C2-type.				blood coagulation|cell-cell adhesion|leukocyte migration	anchored to membrane|integral to plasma membrane	protein binding				0	Lung SC(450;0.225)	all_cancers(81;0.000363)|all_lung(203;0.000118)|all_epithelial(167;0.000149)|Lung NSC(69;0.000577)		Lung(183;0.0086)|LUSC - Lung squamous cell carcinoma(189;0.0528)|Colorectal(144;0.0775)|all cancers(265;0.109)|Epithelial(280;0.118)|COAD - Colon adenocarcinoma(174;0.121)		TATACTGGTTGAGTTACGTTT	0.343													18	63	---	---	---	---	PASS
PDE4DIP	9659	broad.mit.edu	37	1	144880779	144880779	+	Silent	SNP	G	A	A			TCGA-18-4721-01A-01D-1441-08	TCGA-18-4721-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	d2ab2555-7288-47a4-a80c-bf62d65b67b8	f7b631ae-ee98-499b-9d26-dc945e7ac3b8	g.chr1:144880779G>A	uc001elw.3	-	26	4140	c.3849C>T	c.(3847-3849)AGC>AGT	p.S1283S	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.S1239S|PDE4DIP_uc001elv.3_Silent_p.S290S	NM_014644	NP_055459	Q5VU43	MYOME_HUMAN	phosphodiesterase 4D interacting protein isoform	1283					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)		CCTCATTCTCGCTTCGGCCAC	0.572			T	PDGFRB	MPD								24	528	---	---	---	---	PASS
FLG	2312	broad.mit.edu	37	1	152285005	152285005	+	Missense_Mutation	SNP	C	A	A			TCGA-18-4721-01A-01D-1441-08	TCGA-18-4721-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	d2ab2555-7288-47a4-a80c-bf62d65b67b8	f7b631ae-ee98-499b-9d26-dc945e7ac3b8	g.chr1:152285005C>A	uc001ezu.1	-	3	2393	c.2357G>T	c.(2356-2358)AGG>ATG	p.R786M	uc001ezv.2_5'Flank	NM_002016	NP_002007	P20930	FILA_HUMAN	filaggrin	786	Ser-rich.				keratinocyte differentiation	cytoplasmic membrane-bounded vesicle|intermediate filament	calcium ion binding|structural molecule activity			ovary(9)|skin(4)|upper_aerodigestive_tract(3)	16	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			ACGTCGAGACCTTTCCCCTGA	0.557									Ichthyosis				44	457	---	---	---	---	PASS
KPRP	448834	broad.mit.edu	37	1	152732065	152732065	+	Missense_Mutation	SNP	A	G	G			TCGA-18-4721-01A-01D-1441-08	TCGA-18-4721-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	d2ab2555-7288-47a4-a80c-bf62d65b67b8	f7b631ae-ee98-499b-9d26-dc945e7ac3b8	g.chr1:152732065A>G	uc001fal.1	+	2	59	c.1A>G	c.(1-3)ATG>GTG	p.M1V		NM_001025231	NP_001020402	Q5T749	KPRP_HUMAN	keratinocyte proline-rich protein	1						cytoplasm				ovary(4)|pancreas(1)	5	Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.206)			CATCAGGACCATGTGTGACCA	0.607													19	38	---	---	---	---	PASS
LMX1A	4009	broad.mit.edu	37	1	165322491	165322491	+	Missense_Mutation	SNP	C	A	A			TCGA-18-4721-01A-01D-1441-08	TCGA-18-4721-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	d2ab2555-7288-47a4-a80c-bf62d65b67b8	f7b631ae-ee98-499b-9d26-dc945e7ac3b8	g.chr1:165322491C>A	uc001gcy.1	-	2	306	c.85G>T	c.(85-87)GTG>TTG	p.V29L	LMX1A_uc001gcz.1_Missense_Mutation_p.V29L	NM_177398	NP_796372	Q8TE12	LMX1A_HUMAN	LIM homeobox transcription factor 1, alpha	29						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)					TTGGGGCTCACCGCTCTGCCT	0.627													5	21	---	---	---	---	PASS
C1orf9	51430	broad.mit.edu	37	1	172520690	172520690	+	Nonsense_Mutation	SNP	C	G	G			TCGA-18-4721-01A-01D-1441-08	TCGA-18-4721-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	d2ab2555-7288-47a4-a80c-bf62d65b67b8	f7b631ae-ee98-499b-9d26-dc945e7ac3b8	g.chr1:172520690C>G	uc001giq.3	+	2	417	c.101C>G	c.(100-102)TCA>TGA	p.S34*	C1orf9_uc010pmm.1_Nonsense_Mutation_p.S34*|C1orf9_uc009wwd.2_Nonsense_Mutation_p.S34*|C1orf9_uc010pmn.1_Nonsense_Mutation_p.S34*|C1orf9_uc010pmo.1_RNA	NM_014283	NP_055098	Q9UBS9	OSPT_HUMAN	chromosome 1 open reading frame 9 protein	34					multicellular organismal development|ossification	integral to membrane|rough endoplasmic reticulum membrane				ovary(2)	2		Breast(1374;0.212)		Colorectal(1306;3.98e-05)|KIRC - Kidney renal clear cell carcinoma(1967;0.00544)		GAGAGTTCTTCAGCTTCAGCG	0.383													14	61	---	---	---	---	PASS
MRPS14	63931	broad.mit.edu	37	1	174987657	174987657	+	Missense_Mutation	SNP	A	G	G			TCGA-18-4721-01A-01D-1441-08	TCGA-18-4721-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	d2ab2555-7288-47a4-a80c-bf62d65b67b8	f7b631ae-ee98-499b-9d26-dc945e7ac3b8	g.chr1:174987657A>G	uc001gkk.2	-	2	118	c.101T>C	c.(100-102)ATG>ACG	p.M34T	MRPS14_uc009wwr.2_Missense_Mutation_p.M19T	NM_022100	NP_071383	O60783	RT14_HUMAN	mitochondrial ribosomal protein S14	34					translation	mitochondrial ribosome	protein binding|structural constituent of ribosome				0						ATCGCGCCACATTCTCCAGTC	0.438													20	152	---	---	---	---	PASS
NPL	80896	broad.mit.edu	37	1	182781313	182781313	+	Missense_Mutation	SNP	G	C	C	rs141892236	byFrequency	TCGA-18-4721-01A-01D-1441-08	TCGA-18-4721-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	d2ab2555-7288-47a4-a80c-bf62d65b67b8	f7b631ae-ee98-499b-9d26-dc945e7ac3b8	g.chr1:182781313G>C	uc009wyb.2	+	6	393	c.253G>C	c.(253-255)GTA>CTA	p.V85L	NPL_uc010pnx.1_Missense_Mutation_p.V66L|NPL_uc010pny.1_RNA|NPL_uc001gpo.1_Missense_Mutation_p.V66L|NPL_uc009wyc.2_Missense_Mutation_p.V85L|NPL_uc001gpp.3_Missense_Mutation_p.V85L|NPL_uc001gpq.1_Missense_Mutation_p.V85L	NM_030769	NP_110396	Q9BXD5	NPL_HUMAN	N-acetylneuraminate pyruvate lyase	85					carbohydrate metabolic process	cytoplasm	N-acetylneuraminate lyase activity			ovary(1)|central_nervous_system(1)|skin(1)	3						GATAATTCACGTAGGAGCACT	0.478													26	38	---	---	---	---	PASS
PRG4	10216	broad.mit.edu	37	1	186276765	186276765	+	Silent	SNP	G	A	A			TCGA-18-4721-01A-01D-1441-08	TCGA-18-4721-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	d2ab2555-7288-47a4-a80c-bf62d65b67b8	f7b631ae-ee98-499b-9d26-dc945e7ac3b8	g.chr1:186276765G>A	uc001gru.3	+	7	1965	c.1914G>A	c.(1912-1914)GAG>GAA	p.E638E	PRG4_uc001grt.3_Silent_p.E597E|PRG4_uc009wyl.2_Silent_p.E545E|PRG4_uc009wym.2_Silent_p.E504E|PRG4_uc010poo.1_Intron	NM_005807	NP_005798	Q92954	PRG4_HUMAN	proteoglycan 4 isoform A	638	59 X 8 AA repeats of K-X-P-X-P-T-T-X.|37; approximate.				cell proliferation|immune response	extracellular region	polysaccharide binding|protein binding|scavenger receptor activity			skin(1)	1						CCACCCCTGAGAAGCCCGCAC	0.682													7	24	---	---	---	---	PASS
LRRN2	10446	broad.mit.edu	37	1	204588134	204588134	+	Silent	SNP	G	A	A	rs114324888	by1000genomes	TCGA-18-4721-01A-01D-1441-08	TCGA-18-4721-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	d2ab2555-7288-47a4-a80c-bf62d65b67b8	f7b631ae-ee98-499b-9d26-dc945e7ac3b8	g.chr1:204588134G>A	uc001hbe.1	-	3	1375	c.987C>T	c.(985-987)CGC>CGT	p.R329R	MDM4_uc001hbd.1_Intron|LRRN2_uc001hbf.1_Silent_p.R329R|LRRN2_uc009xbf.1_Silent_p.R329R|MDM4_uc001hbc.2_Intron	NM_006338	NP_006329	O75325	LRRN2_HUMAN	leucine rich repeat neuronal 2 precursor	329	LRR 11.|Extracellular (Potential).				cell adhesion	integral to membrane	receptor activity			central_nervous_system(2)	2	all_cancers(21;0.0519)|Breast(84;0.112)|Prostate(682;0.19)		KIRC - Kidney renal clear cell carcinoma(13;0.0584)|Kidney(21;0.0934)|BRCA - Breast invasive adenocarcinoma(75;0.143)			GGTGGAAGGCGCGGGGGTGGA	0.607													23	25	---	---	---	---	PASS
USH2A	7399	broad.mit.edu	37	1	216424244	216424244	+	Splice_Site	SNP	C	G	G			TCGA-18-4721-01A-01D-1441-08	TCGA-18-4721-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	d2ab2555-7288-47a4-a80c-bf62d65b67b8	f7b631ae-ee98-499b-9d26-dc945e7ac3b8	g.chr1:216424244C>G	uc001hku.1	-	12	2554	c.2167_splice	c.e12+1	p.G723_splice	USH2A_uc001hkv.2_Splice_Site_p.G723_splice	NM_206933	NP_996816	O75445	USH2A_HUMAN	usherin isoform B						maintenance of organ identity|photoreceptor cell maintenance|response to stimulus|sensory perception of sound	basement membrane|cytoplasm|integral to membrane|stereocilium membrane	collagen binding			ovary(20)|upper_aerodigestive_tract(2)|skin(2)|kidney(1)|central_nervous_system(1)	26				OV - Ovarian serous cystadenocarcinoma(81;0.0547)|all cancers(67;0.0875)		GTTACACGTACCAATAACGTT	0.398										HNSCC(13;0.011)			12	19	---	---	---	---	PASS
COG2	22796	broad.mit.edu	37	1	230796514	230796514	+	Missense_Mutation	SNP	A	G	G			TCGA-18-4721-01A-01D-1441-08	TCGA-18-4721-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	d2ab2555-7288-47a4-a80c-bf62d65b67b8	f7b631ae-ee98-499b-9d26-dc945e7ac3b8	g.chr1:230796514A>G	uc001htw.2	+	3	396	c.245A>G	c.(244-246)GAC>GGC	p.D82G	COG2_uc001htx.2_Missense_Mutation_p.D82G|COG2_uc010pwc.1_5'UTR	NM_007357	NP_031383	Q14746	COG2_HUMAN	component of oligomeric golgi complex 2 isoform	82					Golgi organization|intra-Golgi vesicle-mediated transport|intracellular protein transport|oligosaccharide biosynthetic process|protein glycosylation	Golgi membrane|Golgi stack|Golgi transport complex	protein binding|protein transporter activity				0	Breast(184;0.0871)|Ovarian(103;0.183)	Prostate(94;0.178)				GTTGGCATGGACAAAGCCCTC	0.413													100	146	---	---	---	---	PASS
FMN2	56776	broad.mit.edu	37	1	240341284	240341284	+	Missense_Mutation	SNP	G	T	T			TCGA-18-4721-01A-01D-1441-08	TCGA-18-4721-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	d2ab2555-7288-47a4-a80c-bf62d65b67b8	f7b631ae-ee98-499b-9d26-dc945e7ac3b8	g.chr1:240341284G>T	uc010pyd.1	+	3	2071	c.1846G>T	c.(1846-1848)GGG>TGG	p.G616W	FMN2_uc010pye.1_Missense_Mutation_p.G616W	NM_020066	NP_064450	Q9NZ56	FMN2_HUMAN	formin 2	616					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)			CTATTCAGAAGGGCAGTTTCC	0.438													45	66	---	---	---	---	PASS
FMN2	56776	broad.mit.edu	37	1	240371038	240371038	+	Missense_Mutation	SNP	C	A	A			TCGA-18-4721-01A-01D-1441-08	TCGA-18-4721-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	d2ab2555-7288-47a4-a80c-bf62d65b67b8	f7b631ae-ee98-499b-9d26-dc945e7ac3b8	g.chr1:240371038C>A	uc010pyd.1	+	5	3151	c.2926C>A	c.(2926-2928)CCT>ACT	p.P976T	FMN2_uc010pye.1_Missense_Mutation_p.P980T	NM_020066	NP_064450	Q9NZ56	FMN2_HUMAN	formin 2	976	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)			AGCAGGAATACCTCCTCCACC	0.711													11	18	---	---	---	---	PASS
PXDN	7837	broad.mit.edu	37	2	1664699	1664699	+	Silent	SNP	C	A	A			TCGA-18-4721-01A-01D-1441-08	TCGA-18-4721-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	d2ab2555-7288-47a4-a80c-bf62d65b67b8	f7b631ae-ee98-499b-9d26-dc945e7ac3b8	g.chr2:1664699C>A	uc002qxa.2	-	14	1855	c.1791G>T	c.(1789-1791)CGG>CGT	p.R597R	PXDN_uc002qxb.1_Silent_p.R597R	NM_012293	NP_036425	Q92626	PXDN_HUMAN	peroxidasin precursor	597	Ig-like C2-type 4.				extracellular matrix organization|hydrogen peroxide catabolic process|immune response	endoplasmic reticulum|extracellular space|proteinaceous extracellular matrix	extracellular matrix structural constituent|heme binding|interleukin-1 receptor antagonist activity|peroxidase activity			pancreas(6)|ovary(2)	8	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.0797)	all_cancers(51;0.0845)|Lung NSC(108;0.00641)|all_epithelial(98;0.00716)		all cancers(51;0.0492)|OV - Ovarian serous cystadenocarcinoma(76;0.0973)|Epithelial(75;0.17)|GBM - Glioblastoma multiforme(21;0.228)		CAATGGTGTTCCGGGCCACAC	0.532													22	60	---	---	---	---	PASS
PXDN	7837	broad.mit.edu	37	2	1664700	1664700	+	Missense_Mutation	SNP	C	A	A			TCGA-18-4721-01A-01D-1441-08	TCGA-18-4721-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	d2ab2555-7288-47a4-a80c-bf62d65b67b8	f7b631ae-ee98-499b-9d26-dc945e7ac3b8	g.chr2:1664700C>A	uc002qxa.2	-	14	1854	c.1790G>T	c.(1789-1791)CGG>CTG	p.R597L	PXDN_uc002qxb.1_Missense_Mutation_p.R597L	NM_012293	NP_036425	Q92626	PXDN_HUMAN	peroxidasin precursor	597	Ig-like C2-type 4.				extracellular matrix organization|hydrogen peroxide catabolic process|immune response	endoplasmic reticulum|extracellular space|proteinaceous extracellular matrix	extracellular matrix structural constituent|heme binding|interleukin-1 receptor antagonist activity|peroxidase activity			pancreas(6)|ovary(2)	8	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.0797)	all_cancers(51;0.0845)|Lung NSC(108;0.00641)|all_epithelial(98;0.00716)		all cancers(51;0.0492)|OV - Ovarian serous cystadenocarcinoma(76;0.0973)|Epithelial(75;0.17)|GBM - Glioblastoma multiforme(21;0.228)		AATGGTGTTCCGGGCCACACA	0.532													22	61	---	---	---	---	PASS
ZNF512	84450	broad.mit.edu	37	2	27806571	27806571	+	Missense_Mutation	SNP	T	C	C			TCGA-18-4721-01A-01D-1441-08	TCGA-18-4721-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	d2ab2555-7288-47a4-a80c-bf62d65b67b8	f7b631ae-ee98-499b-9d26-dc945e7ac3b8	g.chr2:27806571T>C	uc002rla.2	+	2	164	c.77T>C	c.(76-78)GTG>GCG	p.V26A	ZNF512_uc010ylv.1_5'UTR|ZNF512_uc010ylw.1_Missense_Mutation_p.V26A|ZNF512_uc002rlb.2_Intron|ZNF512_uc010ylx.1_5'UTR|ZNF512_uc002rlc.2_Intron|ZNF512_uc010yly.1_Intron|ZNF512_uc010ylz.1_5'UTR	NM_032434	NP_115810	Q96ME7	ZN512_HUMAN	zinc finger protein 512	26					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1	Acute lymphoblastic leukemia(172;0.155)					ACGAGGATCGTGGGAGCTAAG	0.378													16	57	---	---	---	---	PASS
TTC27	55622	broad.mit.edu	37	2	33036187	33036187	+	Missense_Mutation	SNP	G	T	T			TCGA-18-4721-01A-01D-1441-08	TCGA-18-4721-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	d2ab2555-7288-47a4-a80c-bf62d65b67b8	f7b631ae-ee98-499b-9d26-dc945e7ac3b8	g.chr2:33036187G>T	uc002rom.2	+	17	2326	c.2095G>T	c.(2095-2097)GGC>TGC	p.G699C	TTC27_uc010ymx.1_Missense_Mutation_p.G649C|TTC27_uc002ron.2_RNA	NM_017735	NP_060205	Q6P3X3	TTC27_HUMAN	tetratricopeptide repeat domain 27	699	HAT 3.						protein binding			central_nervous_system(1)	1						GGAGTTATTTGGCAGAGTGAC	0.438													26	69	---	---	---	---	PASS
CEP68	23177	broad.mit.edu	37	2	65299172	65299172	+	Missense_Mutation	SNP	G	T	T			TCGA-18-4721-01A-01D-1441-08	TCGA-18-4721-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	d2ab2555-7288-47a4-a80c-bf62d65b67b8	f7b631ae-ee98-499b-9d26-dc945e7ac3b8	g.chr2:65299172G>T	uc002sdl.3	+	3	1156	c.942G>T	c.(940-942)CAG>CAT	p.Q314H	CEP68_uc002sdj.2_Missense_Mutation_p.Q314H|CEP68_uc010yqb.1_Missense_Mutation_p.Q314H|CEP68_uc002sdk.3_Missense_Mutation_p.Q314H|CEP68_uc010yqc.1_Missense_Mutation_p.Q314H|CEP68_uc010yqd.1_Missense_Mutation_p.Q314H	NM_015147	NP_055962	Q76N32	CEP68_HUMAN	centrosomal protein 68kDa	314					centrosome organization	centrosome				skin(1)	1						CCGGGCCTCAGCTCCCAAAGC	0.577													47	214	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	2	90193294	90193294	+	RNA	SNP	C	A	A			TCGA-18-4721-01A-01D-1441-08	TCGA-18-4721-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	d2ab2555-7288-47a4-a80c-bf62d65b67b8	f7b631ae-ee98-499b-9d26-dc945e7ac3b8	g.chr2:90193294C>A	uc010fhm.2	+	22		c.2884C>A								Parts of antibodies, mostly variable regions.																		TATGATGCCTCCAGTTTGGAA	0.522													6	102	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	2	90193295	90193295	+	RNA	SNP	C	G	G			TCGA-18-4721-01A-01D-1441-08	TCGA-18-4721-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	d2ab2555-7288-47a4-a80c-bf62d65b67b8	f7b631ae-ee98-499b-9d26-dc945e7ac3b8	g.chr2:90193295C>G	uc010fhm.2	+	22		c.2885C>G								Parts of antibodies, mostly variable regions.																		ATGATGCCTCCAGTTTGGAAA	0.517													6	100	---	---	---	---	PASS
ZC3H6	376940	broad.mit.edu	37	2	113069435	113069435	+	Missense_Mutation	SNP	A	G	G			TCGA-18-4721-01A-01D-1441-08	TCGA-18-4721-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	d2ab2555-7288-47a4-a80c-bf62d65b67b8	f7b631ae-ee98-499b-9d26-dc945e7ac3b8	g.chr2:113069435A>G	uc002thq.1	+	5	1062	c.668A>G	c.(667-669)AAG>AGG	p.K223R		NM_198581	NP_940983	P61129	ZC3H6_HUMAN	zinc finger CCCH-type domain containing 6	223							nucleic acid binding|zinc ion binding			ovary(3)|central_nervous_system(1)	4						GGCTTGCCGAAGAAAATCAAA	0.343													6	32	---	---	---	---	PASS
SCN2A	6326	broad.mit.edu	37	2	166164370	166164370	+	Missense_Mutation	SNP	G	T	T			TCGA-18-4721-01A-01D-1441-08	TCGA-18-4721-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	d2ab2555-7288-47a4-a80c-bf62d65b67b8	f7b631ae-ee98-499b-9d26-dc945e7ac3b8	g.chr2:166164370G>T	uc002udc.2	+	4	689	c.399G>T	c.(397-399)ATG>ATT	p.M133I	SCN2A_uc002udd.2_Missense_Mutation_p.M133I|SCN2A_uc002ude.2_Missense_Mutation_p.M133I	NM_001040142	NP_001035232	Q99250	SCN2A_HUMAN	sodium channel, voltage-gated, type II, alpha	133	I.|Helical; Name=S1 of repeat I; (Potential).				myelination	node of Ranvier|voltage-gated sodium channel complex	voltage-gated sodium channel activity			ovary(6)|breast(1)|pancreas(1)	8					Lamotrigine(DB00555)	TATTCAATATGCTCATTATGT	0.338													46	246	---	---	---	---	PASS
XIRP2	129446	broad.mit.edu	37	2	168102139	168102139	+	Missense_Mutation	SNP	A	G	G			TCGA-18-4721-01A-01D-1441-08	TCGA-18-4721-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	d2ab2555-7288-47a4-a80c-bf62d65b67b8	f7b631ae-ee98-499b-9d26-dc945e7ac3b8	g.chr2:168102139A>G	uc002udx.2	+	8	4255	c.4237A>G	c.(4237-4239)ATA>GTA	p.I1413V	XIRP2_uc010fpn.2_Intron|XIRP2_uc010fpo.2_Intron|XIRP2_uc010fpp.2_Intron|XIRP2_uc002udy.2_Missense_Mutation_p.I1238V|XIRP2_uc010fpq.2_Missense_Mutation_p.I1191V|XIRP2_uc010fpr.2_Intron|XIRP2_uc010fps.1_5'Flank	NM_152381	NP_689594	A4UGR9	XIRP2_HUMAN	xin actin-binding repeat containing 2 isoform 1	1238					actin cytoskeleton organization	cell junction	actin binding			skin(7)|ovary(6)|pancreas(1)	14						TATTGACCATATACAAGGTGG	0.333													22	84	---	---	---	---	PASS
ABCB11	8647	broad.mit.edu	37	2	169780261	169780261	+	Silent	SNP	G	A	A			TCGA-18-4721-01A-01D-1441-08	TCGA-18-4721-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	d2ab2555-7288-47a4-a80c-bf62d65b67b8	f7b631ae-ee98-499b-9d26-dc945e7ac3b8	g.chr2:169780261G>A	uc002ueo.1	-	28	3963	c.3837C>T	c.(3835-3837)ACC>ACT	p.T1279T	ABCB11_uc010zda.1_Silent_p.T697T|ABCB11_uc010zdb.1_Silent_p.T755T	NM_003742	NP_003733	O95342	ABCBB_HUMAN	ATP-binding cassette, sub-family B (MDR/TAP),	1279	Cytoplasmic (Potential).|ABC transporter 2.				bile acid biosynthetic process	apical plasma membrane|Golgi membrane|integral to plasma membrane|intercellular canaliculus|membrane fraction	ATP binding|bile acid-exporting ATPase activity|canalicular bile acid transmembrane transporter activity|sodium-exporting ATPase activity, phosphorylative mechanism			ovary(2)|large_intestine(2)|breast(1)	5					Adenosine triphosphate(DB00171)|Bosentan(DB00559)|Glibenclamide(DB01016)	CGTTCTGGATGGTGGACAAGC	0.512													26	109	---	---	---	---	PASS
CHRNA1	1134	broad.mit.edu	37	2	175618376	175618376	+	Silent	SNP	G	A	A			TCGA-18-4721-01A-01D-1441-08	TCGA-18-4721-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	d2ab2555-7288-47a4-a80c-bf62d65b67b8	f7b631ae-ee98-499b-9d26-dc945e7ac3b8	g.chr2:175618376G>A	uc002ujd.2	-	7	786	c.708C>T	c.(706-708)TCC>TCT	p.S236S	uc002uiw.2_Intron|CHRNA1_uc002uje.2_Silent_p.S211S|CHRNA1_uc002ujf.3_Silent_p.S211S	NM_001039523	NP_001034612	P02708	ACHA_HUMAN	nicotinic cholinergic receptor alpha 1 isoform a	236	Extracellular.				muscle cell homeostasis|neuromuscular junction development|neuromuscular process|neuromuscular synaptic transmission|neuron homeostasis|regulation of action potential in neuron|skeletal muscle contraction|skeletal muscle tissue growth	cell junction|cell surface|neuromuscular junction|nicotinic acetylcholine-gated receptor-channel complex|postsynaptic membrane	acetylcholine receptor activity|nicotinic acetylcholine-activated cation-selective channel activity			ovary(2)|central_nervous_system(1)|skin(1)	4						CGGGGCAGCAGGAATAGGTCA	0.592													34	91	---	---	---	---	PASS
NFE2L2	4780	broad.mit.edu	37	2	178098944	178098944	+	Missense_Mutation	SNP	C	T	T			TCGA-18-4721-01A-01D-1441-08	TCGA-18-4721-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	d2ab2555-7288-47a4-a80c-bf62d65b67b8	f7b631ae-ee98-499b-9d26-dc945e7ac3b8	g.chr2:178098944C>T	uc002ulh.3	-	2	656	c.101G>A	c.(100-102)CGA>CAA	p.R34Q	NFE2L2_uc002ulg.3_Missense_Mutation_p.R18Q|NFE2L2_uc010zfa.1_Missense_Mutation_p.R18Q|NFE2L2_uc002uli.3_Missense_Mutation_p.R18Q|NFE2L2_uc010fra.2_Missense_Mutation_p.R18Q|NFE2L2_uc010frb.2_Missense_Mutation_p.R18Q	NM_006164	NP_006155	Q16236	NF2L2_HUMAN	nuclear factor erythroid 2-like 2 isoform 1	34					transcription from RNA polymerase II promoter	centrosome|cytosol|nucleus|plasma membrane	protein dimerization activity|protein domain specific binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			central_nervous_system(1)	1			Epithelial(96;0.00442)|OV - Ovarian serous cystadenocarcinoma(117;0.00739)|all cancers(119;0.0195)|LUSC - Lung squamous cell carcinoma(2;0.036)|Lung(16;0.0935)			AAATACTTCTCGACTTACTCC	0.373			Mis		NSCLC|HNSCC					HNSCC(56;0.16)			40	55	---	---	---	---	PASS
TTN	7273	broad.mit.edu	37	2	179454485	179454485	+	Missense_Mutation	SNP	G	A	A			TCGA-18-4721-01A-01D-1441-08	TCGA-18-4721-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	d2ab2555-7288-47a4-a80c-bf62d65b67b8	f7b631ae-ee98-499b-9d26-dc945e7ac3b8	g.chr2:179454485G>A	uc010zfg.1	-	253	54487	c.54263C>T	c.(54262-54264)ACA>ATA	p.T18088I	uc002umo.2_Intron|uc002ump.1_Intron|TTN_uc010zfh.1_Missense_Mutation_p.T11783I|TTN_uc010zfi.1_Missense_Mutation_p.T11716I|TTN_uc010zfj.1_Missense_Mutation_p.T11591I	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	19015							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)			GGGAGTTTTTGTTTCGATGGT	0.403													61	244	---	---	---	---	PASS
FRZB	2487	broad.mit.edu	37	2	183730876	183730876	+	Silent	SNP	G	A	A			TCGA-18-4721-01A-01D-1441-08	TCGA-18-4721-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	d2ab2555-7288-47a4-a80c-bf62d65b67b8	f7b631ae-ee98-499b-9d26-dc945e7ac3b8	g.chr2:183730876G>A	uc002upa.1	-	1	623	c.405C>T	c.(403-405)GCC>GCT	p.A135A		NM_001463	NP_001454	Q92765	SFRP3_HUMAN	frizzled-related protein precursor	135	FZ.				brain development|cochlea morphogenesis|gonad development|mammary gland involution|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of cartilage development|negative regulation of cell growth|negative regulation of cell proliferation|negative regulation of hepatocyte differentiation|positive regulation of apoptosis|positive regulation of fat cell differentiation|skeletal system development|vasculature development|Wnt receptor signaling pathway	cytoplasm|extracellular space|membrane	PDZ domain binding|Wnt receptor activity|Wnt-protein binding			ovary(2)|lung(1)|central_nervous_system(1)	4			OV - Ovarian serous cystadenocarcinoma(117;0.109)|Epithelial(96;0.231)			GCTCCTCGCAGGCCAGGTTCT	0.637													7	17	---	---	---	---	PASS
ADAM23	8745	broad.mit.edu	37	2	207452057	207452057	+	Silent	SNP	A	T	T			TCGA-18-4721-01A-01D-1441-08	TCGA-18-4721-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	d2ab2555-7288-47a4-a80c-bf62d65b67b8	f7b631ae-ee98-499b-9d26-dc945e7ac3b8	g.chr2:207452057A>T	uc002vbq.2	+	19	1969	c.1746A>T	c.(1744-1746)CCA>CCT	p.P582P	ADAM23_uc010ziv.1_RNA	NM_003812	NP_003803	O75077	ADA23_HUMAN	ADAM metallopeptidase domain 23 preproprotein	582	Disintegrin.|Extracellular (Potential).				cell adhesion|central nervous system development|proteolysis	extracellular region|integral to plasma membrane	integrin binding|metalloendopeptidase activity|zinc ion binding			skin(2)|ovary(1)	3				LUSC - Lung squamous cell carcinoma(261;0.0961)|Lung(261;0.182)|Epithelial(149;0.205)		AGTGCCCACCAAATCTTCATA	0.313													29	102	---	---	---	---	PASS
TNS1	7145	broad.mit.edu	37	2	218713180	218713180	+	Missense_Mutation	SNP	T	A	A			TCGA-18-4721-01A-01D-1441-08	TCGA-18-4721-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	d2ab2555-7288-47a4-a80c-bf62d65b67b8	f7b631ae-ee98-499b-9d26-dc945e7ac3b8	g.chr2:218713180T>A	uc002vgt.2	-	17	2083	c.1685A>T	c.(1684-1686)GAG>GTG	p.E562V	TNS1_uc002vgr.2_Missense_Mutation_p.E562V|TNS1_uc002vgs.2_Missense_Mutation_p.E562V|TNS1_uc010zjv.1_Missense_Mutation_p.E562V|TNS1_uc010fvj.1_Missense_Mutation_p.E630V|TNS1_uc010fvk.1_Missense_Mutation_p.E687V|TNS1_uc010fvi.1_Missense_Mutation_p.E249V	NM_022648	NP_072174	Q9HBL0	TENS1_HUMAN	tensin	562						cytoplasm|cytoskeleton|focal adhesion	actin binding			ovary(3)|breast(1)	4		Renal(207;0.0483)|Lung NSC(271;0.213)		Epithelial(149;4.43e-06)|all cancers(144;0.000653)|LUSC - Lung squamous cell carcinoma(224;0.0091)|Lung(261;0.013)		GCTGGCAGACTCGTAGGGGTA	0.662													10	36	---	---	---	---	PASS
CUL3	8452	broad.mit.edu	37	2	225376242	225376242	+	Nonsense_Mutation	SNP	C	A	A			TCGA-18-4721-01A-01D-1441-08	TCGA-18-4721-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	d2ab2555-7288-47a4-a80c-bf62d65b67b8	f7b631ae-ee98-499b-9d26-dc945e7ac3b8	g.chr2:225376242C>A	uc002vny.2	-	6	1096	c.712G>T	c.(712-714)GAA>TAA	p.E238*	CUL3_uc010zls.1_Nonsense_Mutation_p.E172*|CUL3_uc010fwy.1_Nonsense_Mutation_p.E244*	NM_003590	NP_003581	Q13618	CUL3_HUMAN	cullin 3	238					cell cycle arrest|cell migration|cyclin catabolic process|cytokinesis|G1/S transition of mitotic cell cycle|induction of apoptosis by intracellular signals|mitotic anaphase|negative regulation of Rho protein signal transduction|positive regulation of cell proliferation|protein ubiquitination|stress fiber assembly	Cul3-RING ubiquitin ligase complex|Golgi apparatus|nucleus|polar microtubule	ubiquitin protein ligase binding			upper_aerodigestive_tract(1)|ovary(1)|liver(1)|kidney(1)	4		all_lung(227;0.00877)|Lung NSC(271;0.011)|Renal(207;0.0112)|all_hematologic(139;0.138)		Epithelial(121;1.58e-11)|all cancers(144;1.43e-08)|Lung(261;0.00863)|LUSC - Lung squamous cell carcinoma(224;0.00902)		ATTCTAGCTTCTACTTTCTTT	0.308													29	110	---	---	---	---	PASS
ATG7	10533	broad.mit.edu	37	3	11468389	11468389	+	Nonsense_Mutation	SNP	C	T	T			TCGA-18-4721-01A-01D-1441-08	TCGA-18-4721-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	d2ab2555-7288-47a4-a80c-bf62d65b67b8	f7b631ae-ee98-499b-9d26-dc945e7ac3b8	g.chr3:11468389C>T	uc003bwc.2	+	18	2185	c.2068C>T	c.(2068-2070)CAA>TAA	p.Q690*	ATG7_uc003bwd.2_Nonsense_Mutation_p.Q663*|ATG7_uc011aum.1_Intron	NM_006395	NP_006386	O95352	ATG7_HUMAN	APG7 autophagy 7-like isoform a	690					autophagy|cellular membrane fusion|positive regulation of protein modification process|protein lipidation|protein transport	cytoplasm	APG12 activating enzyme activity|protein homodimerization activity|ubiquitin activating enzyme activity			central_nervous_system(1)	1						TCAAGAAACCCAAGCTGCTGA	0.368													10	69	---	---	---	---	PASS
C3orf19	51244	broad.mit.edu	37	3	14706570	14706570	+	Missense_Mutation	SNP	G	A	A	rs138052160		TCGA-18-4721-01A-01D-1441-08	TCGA-18-4721-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	d2ab2555-7288-47a4-a80c-bf62d65b67b8	f7b631ae-ee98-499b-9d26-dc945e7ac3b8	g.chr3:14706570G>A	uc003byw.2	+	6	612	c.521G>A	c.(520-522)CGC>CAC	p.R174H	C3orf19_uc010hei.1_Missense_Mutation_p.R174H|C3orf19_uc010hej.2_Missense_Mutation_p.R79H	NM_016474	NP_057558	Q6PII3	CC019_HUMAN	hypothetical protein LOC51244	174											0						CGTTCCCGGCGCTGTATGAGA	0.473													26	168	---	---	---	---	PASS
LYZL4	131375	broad.mit.edu	37	3	42445550	42445550	+	Missense_Mutation	SNP	C	A	A			TCGA-18-4721-01A-01D-1441-08	TCGA-18-4721-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	d2ab2555-7288-47a4-a80c-bf62d65b67b8	f7b631ae-ee98-499b-9d26-dc945e7ac3b8	g.chr3:42445550C>A	uc003cle.2	-	4	608	c.359G>T	c.(358-360)GGG>GTG	p.G120V		NM_144634	NP_653235	Q96KX0	LYZL4_HUMAN	lysozyme-like 4 precursor	120					cell wall macromolecule catabolic process	extracellular region	lysozyme activity			central_nervous_system(1)	1				KIRC - Kidney renal clear cell carcinoma(284;0.222)		TGCTCCCATCCCTTCTTTTCC	0.383													15	60	---	---	---	---	PASS
CSPG5	10675	broad.mit.edu	37	3	47614277	47614277	+	Silent	SNP	G	T	T			TCGA-18-4721-01A-01D-1441-08	TCGA-18-4721-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	d2ab2555-7288-47a4-a80c-bf62d65b67b8	f7b631ae-ee98-499b-9d26-dc945e7ac3b8	g.chr3:47614277G>T	uc003crp.3	-	3	1457	c.1281C>A	c.(1279-1281)GGC>GGA	p.G427G	CSPG5_uc003crn.2_Silent_p.G289G|CSPG5_uc003cro.3_Silent_p.G427G|CSPG5_uc011bbb.1_Silent_p.G289G	NM_006574	NP_006565	O95196	CSPG5_HUMAN	chondroitin sulfate proteoglycan 5 (neuroglycan	427	Helical; (Potential).				cell differentiation|intracellular transport|nervous system development|regulation of growth	endoplasmic reticulum membrane|Golgi-associated vesicle membrane|integral to plasma membrane|membrane fraction	growth factor activity			ovary(1)|central_nervous_system(1)	2				BRCA - Breast invasive adenocarcinoma(193;0.000266)|KIRC - Kidney renal clear cell carcinoma(197;0.00551)|Kidney(197;0.00621)		GGGCAGCCGAGCCCACGGCCA	0.587													10	40	---	---	---	---	PASS
DNAH12	201625	broad.mit.edu	37	3	57489909	57489909	+	Missense_Mutation	SNP	G	A	A			TCGA-18-4721-01A-01D-1441-08	TCGA-18-4721-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	d2ab2555-7288-47a4-a80c-bf62d65b67b8	f7b631ae-ee98-499b-9d26-dc945e7ac3b8	g.chr3:57489909G>A	uc003dit.2	-	9	1101	c.920C>T	c.(919-921)ACT>ATT	p.T307I	DNAH12_uc003diu.2_Missense_Mutation_p.T307I	NM_178504	NP_848599	Q6ZR08	DYH12_HUMAN	dynein heavy chain domain 2 isoform 1	307	Stem (By similarity).				microtubule-based movement	cilium axoneme|cytoplasm|dynein complex|microtubule	ATP binding|ATPase activity|microtubule motor activity			pancreas(1)|skin(1)	2						TCCTTCTACAGTTCTCCTTAA	0.303													10	55	---	---	---	---	PASS
PDZRN3	23024	broad.mit.edu	37	3	73433255	73433255	+	Missense_Mutation	SNP	G	T	T			TCGA-18-4721-01A-01D-1441-08	TCGA-18-4721-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	d2ab2555-7288-47a4-a80c-bf62d65b67b8	f7b631ae-ee98-499b-9d26-dc945e7ac3b8	g.chr3:73433255G>T	uc003dpl.1	-	10	2558	c.2462C>A	c.(2461-2463)ACC>AAC	p.T821N	PDZRN3_uc011bgh.1_Missense_Mutation_p.T478N|PDZRN3_uc010hoe.1_Missense_Mutation_p.T519N|PDZRN3_uc011bgf.1_Missense_Mutation_p.T538N|PDZRN3_uc011bgg.1_Missense_Mutation_p.T541N	NM_015009	NP_055824	Q9UPQ7	PZRN3_HUMAN	PDZ domain containing ring finger 3	821							ubiquitin-protein ligase activity|zinc ion binding			pancreas(2)|ovary(2)|skin(2)|large_intestine(1)	7		Prostate(10;0.114)|Lung NSC(201;0.187)|Lung SC(41;0.236)		BRCA - Breast invasive adenocarcinoma(55;0.00041)|Epithelial(33;0.0023)|LUSC - Lung squamous cell carcinoma(21;0.0048)|Lung(16;0.0105)|KIRC - Kidney renal clear cell carcinoma(39;0.111)|Kidney(39;0.134)		CGGGCTATAGGTAGGGGTGCC	0.657													31	90	---	---	---	---	PASS
CNTN3	5067	broad.mit.edu	37	3	74419134	74419134	+	Missense_Mutation	SNP	C	A	A			TCGA-18-4721-01A-01D-1441-08	TCGA-18-4721-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	d2ab2555-7288-47a4-a80c-bf62d65b67b8	f7b631ae-ee98-499b-9d26-dc945e7ac3b8	g.chr3:74419134C>A	uc003dpm.1	-	6	747	c.667G>T	c.(667-669)GGT>TGT	p.G223C		NM_020872	NP_065923	Q9P232	CNTN3_HUMAN	contactin 3 precursor	223					cell adhesion	anchored to membrane|plasma membrane	protein binding			breast(3)|ovary(1)|skin(1)	5		Lung NSC(201;0.138)|Lung SC(41;0.21)		Epithelial(33;0.00212)|BRCA - Breast invasive adenocarcinoma(55;0.00258)|LUSC - Lung squamous cell carcinoma(21;0.00461)|Lung(16;0.01)		TCATATTCACCCATCACACCT	0.333													18	72	---	---	---	---	PASS
CNTN3	5067	broad.mit.edu	37	3	74419135	74419135	+	Missense_Mutation	SNP	C	T	T			TCGA-18-4721-01A-01D-1441-08	TCGA-18-4721-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	d2ab2555-7288-47a4-a80c-bf62d65b67b8	f7b631ae-ee98-499b-9d26-dc945e7ac3b8	g.chr3:74419135C>T	uc003dpm.1	-	6	746	c.666G>A	c.(664-666)ATG>ATA	p.M222I		NM_020872	NP_065923	Q9P232	CNTN3_HUMAN	contactin 3 precursor	222					cell adhesion	anchored to membrane|plasma membrane	protein binding			breast(3)|ovary(1)|skin(1)	5		Lung NSC(201;0.138)|Lung SC(41;0.21)		Epithelial(33;0.00212)|BRCA - Breast invasive adenocarcinoma(55;0.00258)|LUSC - Lung squamous cell carcinoma(21;0.00461)|Lung(16;0.01)		CATATTCACCCATCACACCTA	0.338													18	73	---	---	---	---	PASS
EPHA6	285220	broad.mit.edu	37	3	97454768	97454768	+	Splice_Site	SNP	G	T	T			TCGA-18-4721-01A-01D-1441-08	TCGA-18-4721-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	d2ab2555-7288-47a4-a80c-bf62d65b67b8	f7b631ae-ee98-499b-9d26-dc945e7ac3b8	g.chr3:97454768G>T	uc010how.1	+	16	2978	c.2935_splice	c.e16-1	p.V979_splice	EPHA6_uc003drt.2_Splice_Site_p.V371_splice|EPHA6_uc010hox.1_Splice_Site	NM_001080448	NP_001073917	Q9UF33	EPHA6_HUMAN	EPH receptor A6 isoform a							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						TTTGCATTTAGGTCATTCTGT	0.403													13	55	---	---	---	---	PASS
HHLA2	11148	broad.mit.edu	37	3	108077008	108077008	+	Missense_Mutation	SNP	G	A	A			TCGA-18-4721-01A-01D-1441-08	TCGA-18-4721-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	d2ab2555-7288-47a4-a80c-bf62d65b67b8	f7b631ae-ee98-499b-9d26-dc945e7ac3b8	g.chr3:108077008G>A	uc003dwy.3	+	6	1170	c.1003G>A	c.(1003-1005)GAA>AAA	p.E335K	HHLA2_uc011bhl.1_Missense_Mutation_p.E271K|HHLA2_uc010hpu.2_Missense_Mutation_p.E335K|HHLA2_uc003dwz.2_Missense_Mutation_p.E335K	NM_007072	NP_009003	Q9UM44	HHLA2_HUMAN	HERV-H LTR-associating 2 precursor	335						integral to membrane				ovary(1)	1						AGTGCATGTAGGTAAGTTGCA	0.338													13	49	---	---	---	---	PASS
MED12L	116931	broad.mit.edu	37	3	151085966	151085966	+	Silent	SNP	G	T	T			TCGA-18-4721-01A-01D-1441-08	TCGA-18-4721-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	d2ab2555-7288-47a4-a80c-bf62d65b67b8	f7b631ae-ee98-499b-9d26-dc945e7ac3b8	g.chr3:151085966G>T	uc003eyp.2	+	23	3410	c.3372G>T	c.(3370-3372)GGG>GGT	p.G1124G	MED12L_uc011bnz.1_Silent_p.G984G|P2RY12_uc011boa.1_Intron|P2RY12_uc003eyx.1_Intron|MED12L_uc003eyy.1_Silent_p.G287G	NM_053002	NP_443728	Q86YW9	MD12L_HUMAN	mediator of RNA polymerase II transcription,	1124					regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	mediator complex				ovary(4)|large_intestine(1)|central_nervous_system(1)|skin(1)	7			LUSC - Lung squamous cell carcinoma(72;0.0394)|Lung(72;0.0517)			CCGAGCCTGGGGCGAGAATGA	0.512													5	139	---	---	---	---	PASS
NAALADL2	254827	broad.mit.edu	37	3	174814846	174814846	+	Missense_Mutation	SNP	T	C	C			TCGA-18-4721-01A-01D-1441-08	TCGA-18-4721-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	d2ab2555-7288-47a4-a80c-bf62d65b67b8	f7b631ae-ee98-499b-9d26-dc945e7ac3b8	g.chr3:174814846T>C	uc003fit.2	+	2	397	c.310T>C	c.(310-312)TCT>CCT	p.S104P	NAALADL2_uc003fiu.1_Missense_Mutation_p.S97P	NM_207015	NP_996898	Q58DX5	NADL2_HUMAN	N-acetylated alpha-linked acidic dipeptidase 2	104	Cytoplasmic (Potential).				proteolysis	integral to membrane	peptidase activity			pancreas(1)	1	Ovarian(172;0.0102)	all_cancers(1;0.0272)|all_epithelial(1;0.0553)	OV - Ovarian serous cystadenocarcinoma(80;9.26e-28)	Colorectal(1;1.66e-10)|COAD - Colon adenocarcinoma(1;2.1e-07)|STAD - Stomach adenocarcinoma(1;0.00261)|READ - Rectum adenocarcinoma(3;0.0284)		TCAAGAAGAATCTGACTACAT	0.408													10	258	---	---	---	---	PASS
DCUN1D1	54165	broad.mit.edu	37	3	182681668	182681668	+	Splice_Site	SNP	C	G	G			TCGA-18-4721-01A-01D-1441-08	TCGA-18-4721-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	d2ab2555-7288-47a4-a80c-bf62d65b67b8	f7b631ae-ee98-499b-9d26-dc945e7ac3b8	g.chr3:182681668C>G	uc003fld.1	-	3	438	c.389_splice	c.e3+1	p.G130_splice	DCUN1D1_uc011bqn.1_Intron	NM_020640	NP_065691	Q96GG9	DCNL1_HUMAN	RP42 homolog							ubiquitin ligase complex	protein binding			ovary(1)	1	all_cancers(143;9.04e-15)|Ovarian(172;0.0355)		all cancers(12;2.54e-44)|Epithelial(37;4.71e-38)|LUSC - Lung squamous cell carcinoma(7;5.04e-25)|Lung(8;5.03e-23)|OV - Ovarian serous cystadenocarcinoma(80;7.41e-21)			TATATACTCACCCTAATTCTG	0.383													12	344	---	---	---	---	PASS
PDE6B	5158	broad.mit.edu	37	4	650791	650791	+	Missense_Mutation	SNP	A	C	C			TCGA-18-4721-01A-01D-1441-08	TCGA-18-4721-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	d2ab2555-7288-47a4-a80c-bf62d65b67b8	f7b631ae-ee98-499b-9d26-dc945e7ac3b8	g.chr4:650791A>C	uc003gap.2	+	9	1289	c.1236A>C	c.(1234-1236)GAA>GAC	p.E412D	PDE6B_uc003gao.3_Missense_Mutation_p.E412D|PDE6B_uc011buy.1_Missense_Mutation_p.E133D|uc003gaq.1_5'Flank	NM_000283	NP_000274	P35913	PDE6B_HUMAN	phosphodiesterase 6B isoform 1	412	GAF 2.				cytosolic calcium ion homeostasis|GMP metabolic process|phototransduction, visible light|platelet activation|visual perception	cytosol|membrane	3',5'-cyclic-GMP phosphodiesterase activity|metal ion binding				0						CCTTTGACGAACAGGACGAGG	0.597													21	61	---	---	---	---	PASS
DGKQ	1609	broad.mit.edu	37	4	955299	955299	+	Missense_Mutation	SNP	C	A	A	rs146830759		TCGA-18-4721-01A-01D-1441-08	TCGA-18-4721-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	d2ab2555-7288-47a4-a80c-bf62d65b67b8	f7b631ae-ee98-499b-9d26-dc945e7ac3b8	g.chr4:955299C>A	uc003gbw.2	-	21	2604	c.2530G>T	c.(2530-2532)GAC>TAC	p.D844Y	DGKQ_uc010ibn.2_Missense_Mutation_p.D831Y	NM_001347	NP_001338	P52824	DGKQ_HUMAN	diacylglycerol kinase, theta	844					activation of protein kinase C activity by G-protein coupled receptor protein signaling pathway|platelet activation|protein kinase C signaling cascade|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor|response to ATP|thrombin receptor signaling pathway	cytoskeleton|cytosol|nuclear speck|plasma membrane	activating transcription factor binding|ATP binding|diacylglycerol kinase activity|kinase binding|metal ion binding|phospholipase binding			kidney(1)	1			OV - Ovarian serous cystadenocarcinoma(23;0.0158)			AGCAGCCCGTCGTCCATGCGT	0.716													5	16	---	---	---	---	PASS
DRD5	1816	broad.mit.edu	37	4	9784721	9784721	+	Silent	SNP	C	T	T			TCGA-18-4721-01A-01D-1441-08	TCGA-18-4721-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	d2ab2555-7288-47a4-a80c-bf62d65b67b8	f7b631ae-ee98-499b-9d26-dc945e7ac3b8	g.chr4:9784721C>T	uc003gmb.3	+	1	1464	c.1068C>T	c.(1066-1068)CCC>CCT	p.P356P		NM_000798	NP_000789	P21918	DRD5_HUMAN	dopamine receptor D5	356	Helical; Name=7; (Potential).				activation of adenylate cyclase activity by dopamine receptor signaling pathway|activation of phospholipase C activity by dopamine receptor signaling pathway|cellular calcium ion homeostasis|negative regulation of NAD(P)H oxidase activity|reactive oxygen species metabolic process|synaptic transmission, dopaminergic	integral to plasma membrane				skin(1)	1					Apomorphine(DB00714)|Carphenazine(DB01038)|Fenoldopam(DB00800)|Zuclopenthixol(DB01624)	CACTCAACCCCGTCATCTATG	0.622													31	110	---	---	---	---	PASS
GABRB1	2560	broad.mit.edu	37	4	47163312	47163312	+	Missense_Mutation	SNP	G	T	T			TCGA-18-4721-01A-01D-1441-08	TCGA-18-4721-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	d2ab2555-7288-47a4-a80c-bf62d65b67b8	f7b631ae-ee98-499b-9d26-dc945e7ac3b8	g.chr4:47163312G>T	uc003gxh.2	+	4	661	c.287G>T	c.(286-288)AGG>ATG	p.R96M	GABRB1_uc011bze.1_Missense_Mutation_p.R26M	NM_000812	NP_000803	P18505	GBRB1_HUMAN	gamma-aminobutyric acid (GABA) A receptor, beta	96	Extracellular (Probable).				synaptic transmission	cell junction|chloride channel complex|integral to plasma membrane|postsynaptic membrane	chloride channel activity|extracellular ligand-gated ion channel activity|GABA-A receptor activity			ovary(2)	2					Ethchlorvynol(DB00189)|Flurazepam(DB00690)|Lorazepam(DB00186)|Midazolam(DB00683)	AAAGACAAAAGGCTTTCTTAT	0.368													12	313	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	4	69344689	69344689	+	Missense_Mutation	SNP	G	C	C			TCGA-18-4721-01A-01D-1441-08	TCGA-18-4721-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	d2ab2555-7288-47a4-a80c-bf62d65b67b8	f7b631ae-ee98-499b-9d26-dc945e7ac3b8	g.chr4:69344689G>C	uc003hdz.3	+	9	1154	c.1090G>C	c.(1090-1092)GGA>CGA	p.G364R		NM_014058	NP_054777			transmembrane protease, serine 11E																		CTCCTTAGAAGGAAAAACAGA	0.333													6	256	---	---	---	---	PASS
FAM13A	10144	broad.mit.edu	37	4	89671652	89671652	+	Silent	SNP	G	A	A			TCGA-18-4721-01A-01D-1441-08	TCGA-18-4721-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	d2ab2555-7288-47a4-a80c-bf62d65b67b8	f7b631ae-ee98-499b-9d26-dc945e7ac3b8	g.chr4:89671652G>A	uc003hse.1	-	15	2071	c.1863C>T	c.(1861-1863)TAC>TAT	p.Y621Y	FAM13A_uc003hsa.1_Silent_p.Y92Y|FAM13A_uc003hsb.1_Silent_p.Y295Y|FAM13A_uc003hsd.1_Silent_p.Y295Y|FAM13A_uc003hsc.1_Silent_p.Y281Y|FAM13A_uc011cdq.1_Silent_p.Y267Y|FAM13A_uc003hsf.1_Silent_p.Y207Y|FAM13A_uc003hsg.1_Silent_p.Y92Y|FAM13A_uc010ikr.1_Silent_p.Y117Y	NM_014883	NP_055698	O94988	FA13A_HUMAN	family with sequence similarity 13, member A1	621					regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol	GTPase activator activity			ovary(1)|liver(1)	2						GCCCATAAGCGTAGAACCGAG	0.557													23	92	---	---	---	---	PASS
PITX2	5308	broad.mit.edu	37	4	111539595	111539595	+	Missense_Mutation	SNP	G	T	T			TCGA-18-4721-01A-01D-1441-08	TCGA-18-4721-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	d2ab2555-7288-47a4-a80c-bf62d65b67b8	f7b631ae-ee98-499b-9d26-dc945e7ac3b8	g.chr4:111539595G>T	uc003iad.2	-	5	1222	c.640C>A	c.(640-642)CCC>ACC	p.P214T	PITX2_uc003iac.2_Missense_Mutation_p.P221T|PITX2_uc003iae.2_Missense_Mutation_p.P168T|PITX2_uc010iml.2_Missense_Mutation_p.P85T|PITX2_uc003iaf.2_Missense_Mutation_p.P214T	NM_153426	NP_700475	Q99697	PITX2_HUMAN	paired-like homeodomain transcription factor 2	214					determination of left/right symmetry|organ morphogenesis	transcription factor complex	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription factor binding|transcription factor binding				0		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;0.00222)		ATAGAGTTGGGTGGGGAAAAC	0.547													16	55	---	---	---	---	PASS
PCDH10	57575	broad.mit.edu	37	4	134072195	134072195	+	Silent	SNP	T	C	C			TCGA-18-4721-01A-01D-1441-08	TCGA-18-4721-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	d2ab2555-7288-47a4-a80c-bf62d65b67b8	f7b631ae-ee98-499b-9d26-dc945e7ac3b8	g.chr4:134072195T>C	uc003iha.2	+	1	1726	c.900T>C	c.(898-900)CTT>CTC	p.L300L	uc003igy.2_5'Flank|PCDH10_uc003igz.2_Silent_p.L300L	NM_032961	NP_116586	Q9P2E7	PCD10_HUMAN	protocadherin 10 isoform 1 precursor	300	Cadherin 3.|Extracellular (Potential).				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(2)	2				LUSC - Lung squamous cell carcinoma(193;0.227)		CGCGGGAGCTTTTCGGACTCT	0.622													26	61	---	---	---	---	PASS
SMARCA5	8467	broad.mit.edu	37	4	144468620	144468620	+	Silent	SNP	A	G	G			TCGA-18-4721-01A-01D-1441-08	TCGA-18-4721-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	d2ab2555-7288-47a4-a80c-bf62d65b67b8	f7b631ae-ee98-499b-9d26-dc945e7ac3b8	g.chr4:144468620A>G	uc003ijg.2	+	21	3198	c.2736A>G	c.(2734-2736)CAA>CAG	p.Q912Q		NM_003601	NP_003592	O60264	SMCA5_HUMAN	SWI/SNF-related matrix-associated	912					CenH3-containing nucleosome assembly at centromere|nucleosome positioning|regulation of transcription from RNA polymerase II promoter|transcription initiation, DNA-dependent	condensed chromosome|nucleolus|nucleoplasm|NURF complex|RSF complex	ATP binding|ATPase activity|DNA binding|helicase activity|nucleosome binding|protein binding			skin(1)	1	all_hematologic(180;0.158)					CGAGAATTCAAAGAAGAATAA	0.388													28	49	---	---	---	---	PASS
SMAD1	4086	broad.mit.edu	37	4	146479006	146479006	+	Missense_Mutation	SNP	C	G	G			TCGA-18-4721-01A-01D-1441-08	TCGA-18-4721-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	d2ab2555-7288-47a4-a80c-bf62d65b67b8	f7b631ae-ee98-499b-9d26-dc945e7ac3b8	g.chr4:146479006C>G	uc003ikc.2	+	7	1734	c.1318C>G	c.(1318-1320)CTG>GTG	p.L440V	SMAD1_uc003ikd.2_Missense_Mutation_p.L440V|SMAD1_uc010iov.2_Missense_Mutation_p.L440V|SMAD1_uc011cic.1_Missense_Mutation_p.L401V	NM_005900	NP_005891	Q15797	SMAD1_HUMAN	Sma- and Mad-related protein 1	440	MH2.				BMP signaling pathway|embryonic pattern specification|primary miRNA processing|SMAD protein complex assembly|transforming growth factor beta receptor signaling pathway	cytosol|integral to membrane|nuclear inner membrane	co-SMAD binding|I-SMAD binding|identical protein binding|protein kinase binding|sequence-specific DNA binding transcription factor activity|transforming growth factor beta receptor, pathway-specific cytoplasmic mediator activity			ovary(1)	1	all_hematologic(180;0.151)					TGAGATACATCTGCACGGCCC	0.478											OREG0016348	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	49	127	---	---	---	---	PASS
GALNTL6	442117	broad.mit.edu	37	4	173269787	173269787	+	Missense_Mutation	SNP	C	A	A			TCGA-18-4721-01A-01D-1441-08	TCGA-18-4721-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	d2ab2555-7288-47a4-a80c-bf62d65b67b8	f7b631ae-ee98-499b-9d26-dc945e7ac3b8	g.chr4:173269787C>A	uc003isv.2	+	5	1236	c.500C>A	c.(499-501)ACC>AAC	p.T167N		NM_001034845	NP_001030017	Q49A17	GLTL6_HUMAN	N-acetylgalactosaminyltransferase-like 6	167	Catalytic subdomain A.|Lumenal (Potential).					Golgi membrane|integral to membrane	metal ion binding|polypeptide N-acetylgalactosaminyltransferase activity|sugar binding			breast(2)|ovary(1)|skin(1)	4						ATTAACCGAACCCCAGGGAGT	0.408													19	161	---	---	---	---	PASS
ODZ3	55714	broad.mit.edu	37	4	183714169	183714169	+	Missense_Mutation	SNP	G	C	C			TCGA-18-4721-01A-01D-1441-08	TCGA-18-4721-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	d2ab2555-7288-47a4-a80c-bf62d65b67b8	f7b631ae-ee98-499b-9d26-dc945e7ac3b8	g.chr4:183714169G>C	uc003ivd.1	+	25	6381	c.6344G>C	c.(6343-6345)AGA>ACA	p.R2115T		NM_001080477	NP_001073946	Q9P273	TEN3_HUMAN	odz, odd Oz/ten-m homolog 3	2115	YD 17.|Extracellular (Potential).				signal transduction	integral to membrane					0		all_lung(41;2.69e-14)|Lung NSC(41;1.92e-11)|Melanoma(52;1.74e-05)|Colorectal(36;0.0062)|Breast(14;0.00748)|all_hematologic(60;0.0162)|Renal(120;0.0246)|Hepatocellular(41;0.0268)|Prostate(90;0.0283)|all_neural(102;0.155)|Medulloblastoma(177;0.184)		all cancers(43;1.42e-24)|Epithelial(43;6.86e-23)|OV - Ovarian serous cystadenocarcinoma(60;2.16e-11)|Colorectal(24;9.75e-06)|STAD - Stomach adenocarcinoma(60;2.96e-05)|COAD - Colon adenocarcinoma(29;0.00103)|GBM - Glioblastoma multiforme(59;0.00462)|LUSC - Lung squamous cell carcinoma(40;0.0391)|READ - Rectum adenocarcinoma(43;0.0487)		GTAACCAAGAGAGAGATTAAA	0.398													8	56	---	---	---	---	PASS
C4orf41	60684	broad.mit.edu	37	4	184626196	184626196	+	Nonsense_Mutation	SNP	G	T	T			TCGA-18-4721-01A-01D-1441-08	TCGA-18-4721-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	d2ab2555-7288-47a4-a80c-bf62d65b67b8	f7b631ae-ee98-499b-9d26-dc945e7ac3b8	g.chr4:184626196G>T	uc003ivx.2	+	27	3204	c.3028G>T	c.(3028-3030)GAG>TAG	p.E1010*	C4orf41_uc003ivw.2_Nonsense_Mutation_p.E1010*|C4orf41_uc010isc.2_Nonsense_Mutation_p.E354*|C4orf41_uc003ivy.2_Nonsense_Mutation_p.E616*	NM_021942	NP_068761	Q7Z392	CD041_HUMAN	hypothetical protein LOC60684 isoform a	1010											0		all_lung(41;4.4e-14)|Lung NSC(41;1.03e-13)|Colorectal(36;0.00139)|all_hematologic(60;0.00756)|Hepatocellular(41;0.00826)|Renal(120;0.00988)|Prostate(90;0.0235)|all_neural(102;0.202)		all cancers(43;1.39e-26)|Epithelial(43;2.42e-22)|OV - Ovarian serous cystadenocarcinoma(60;6.85e-10)|GBM - Glioblastoma multiforme(59;6.71e-06)|Colorectal(24;9.67e-06)|STAD - Stomach adenocarcinoma(60;2.36e-05)|COAD - Colon adenocarcinoma(29;7.07e-05)|LUSC - Lung squamous cell carcinoma(40;0.00984)|READ - Rectum adenocarcinoma(43;0.171)		CGTGATTGTGGAGAATATCCC	0.373													38	176	---	---	---	---	PASS
RNASEN	29102	broad.mit.edu	37	5	31409194	31409194	+	Nonsense_Mutation	SNP	C	A	A			TCGA-18-4721-01A-01D-1441-08	TCGA-18-4721-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	d2ab2555-7288-47a4-a80c-bf62d65b67b8	f7b631ae-ee98-499b-9d26-dc945e7ac3b8	g.chr5:31409194C>A	uc003jhg.2	-	32	4182	c.3823G>T	c.(3823-3825)GAA>TAA	p.E1275*	RNASEN_uc003jhh.2_Nonsense_Mutation_p.E1238*	NM_013235	NP_037367	Q9NRR4	RNC_HUMAN	ribonuclease III, nuclear isoform 1	1275	Necessary for interaction with DGCR8 and pri-miRNA processing activity.|DRBM.				gene silencing by RNA|ribosome biogenesis|RNA processing	nucleolus|nucleoplasm	double-stranded RNA binding|metal ion binding|protein binding|ribonuclease III activity				0						TCTTTTCCTTCTGTCCTAAGT	0.448													16	71	---	---	---	---	PASS
WDR70	55100	broad.mit.edu	37	5	37605177	37605177	+	Missense_Mutation	SNP	C	A	A	rs141732552	byFrequency	TCGA-18-4721-01A-01D-1441-08	TCGA-18-4721-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	d2ab2555-7288-47a4-a80c-bf62d65b67b8	f7b631ae-ee98-499b-9d26-dc945e7ac3b8	g.chr5:37605177C>A	uc003jkv.2	+	10	987	c.929C>A	c.(928-930)ACG>AAG	p.T310K	WDR70_uc010iva.1_Missense_Mutation_p.T310K	NM_018034	NP_060504	Q9NW82	WDR70_HUMAN	WD repeat domain 70	310	WD 3.									ovary(1)|central_nervous_system(1)	2	all_lung(31;0.000285)		COAD - Colon adenocarcinoma(61;0.14)|Colorectal(62;0.202)			ACTGTGAGGACGTGGGAAGTT	0.378													12	28	---	---	---	---	PASS
HEATR7B2	133558	broad.mit.edu	37	5	41000446	41000446	+	Missense_Mutation	SNP	C	A	A			TCGA-18-4721-01A-01D-1441-08	TCGA-18-4721-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	d2ab2555-7288-47a4-a80c-bf62d65b67b8	f7b631ae-ee98-499b-9d26-dc945e7ac3b8	g.chr5:41000446C>A	uc003jmj.3	-	39	4848	c.4358G>T	c.(4357-4359)CGT>CTT	p.R1453L	HEATR7B2_uc003jmi.3_Missense_Mutation_p.R1008L	NM_173489	NP_775760	Q7Z745	HTRB2_HUMAN	HEAT repeat family member 7B2	1453							binding			ovary(6)|central_nervous_system(2)	8						CAAGACATCACGGCAAGCCTG	0.483													10	49	---	---	---	---	PASS
RASGRF2	5924	broad.mit.edu	37	5	80363900	80363900	+	Missense_Mutation	SNP	C	T	T			TCGA-18-4721-01A-01D-1441-08	TCGA-18-4721-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	d2ab2555-7288-47a4-a80c-bf62d65b67b8	f7b631ae-ee98-499b-9d26-dc945e7ac3b8	g.chr5:80363900C>T	uc003kha.1	+	3	445	c.445C>T	c.(445-447)CAT>TAT	p.H149Y	RASGRF2_uc011ctn.1_RNA|RASGRF2_uc003khb.1_5'Flank	NM_006909	NP_008840	O14827	RGRF2_HUMAN	Ras protein-specific guanine	149					apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction|synaptic transmission	cytosol|endoplasmic reticulum membrane|plasma membrane	protein binding|Rho guanyl-nucleotide exchange factor activity			breast(5)|ovary(3)|large_intestine(2)|central_nervous_system(1)|skin(1)	12		Lung NSC(167;0.00498)|all_lung(232;0.00531)|Ovarian(174;0.0357)		OV - Ovarian serous cystadenocarcinoma(54;4.22e-42)|Epithelial(54;4.04e-35)|all cancers(79;2.52e-29)		GAAGTACATTCATCTAGTTCA	0.353													31	69	---	---	---	---	PASS
VCAN	1462	broad.mit.edu	37	5	82789510	82789510	+	Missense_Mutation	SNP	C	G	G	rs148875090	byFrequency	TCGA-18-4721-01A-01D-1441-08	TCGA-18-4721-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	d2ab2555-7288-47a4-a80c-bf62d65b67b8	f7b631ae-ee98-499b-9d26-dc945e7ac3b8	g.chr5:82789510C>G	uc003kii.3	+	4	947	c.591C>G	c.(589-591)GAC>GAG	p.D197E	VCAN_uc003kij.3_Missense_Mutation_p.D197E|VCAN_uc010jau.2_Missense_Mutation_p.D197E|VCAN_uc003kik.3_Missense_Mutation_p.D197E|VCAN_uc003kih.3_Missense_Mutation_p.D197E	NM_004385	NP_004376	P13611	CSPG2_HUMAN	versican isoform 1 precursor	197	Link 1.				cell adhesion|cell recognition|glial cell migration	extracellular space|proteinaceous extracellular matrix	calcium ion binding|hyaluronic acid binding|sugar binding			ovary(7)|skin(6)|lung(2)|central_nervous_system(1)	16		Lung NSC(167;0.0216)|all_lung(232;0.0251)|Ovarian(174;0.142)		OV - Ovarian serous cystadenocarcinoma(54;2.47e-41)|Epithelial(54;2.51e-34)|all cancers(79;5.19e-29)		AGCAGTGTGACGCAGGCTGGC	0.502													20	81	---	---	---	---	PASS
SPINK13	153218	broad.mit.edu	37	5	147661774	147661774	+	Nonsense_Mutation	SNP	T	A	A			TCGA-18-4721-01A-01D-1441-08	TCGA-18-4721-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	d2ab2555-7288-47a4-a80c-bf62d65b67b8	f7b631ae-ee98-499b-9d26-dc945e7ac3b8	g.chr5:147661774T>A	uc003lpc.2	+	4	278	c.216T>A	c.(214-216)TGT>TGA	p.C72*	uc003lpb.1_Intron|SPINK13_uc010jgt.2_RNA	NM_001040129	NP_001035218	Q1W4C9	ISK13_HUMAN	serine PI Kazal type 5-like 3 precursor	72	Kazal-like.					extracellular region	serine-type endopeptidase inhibitor activity				0						AGAATGAGTGTttcttttgtg	0.244													18	77	---	---	---	---	PASS
NSD1	64324	broad.mit.edu	37	5	176637416	176637416	+	Silent	SNP	A	T	T			TCGA-18-4721-01A-01D-1441-08	TCGA-18-4721-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	d2ab2555-7288-47a4-a80c-bf62d65b67b8	f7b631ae-ee98-499b-9d26-dc945e7ac3b8	g.chr5:176637416A>T	uc003mfr.3	+	5	2154	c.2016A>T	c.(2014-2016)ACA>ACT	p.T672T	NSD1_uc003mft.3_Silent_p.T403T|NSD1_uc003mfs.1_Silent_p.T569T|NSD1_uc011dfx.1_Silent_p.T320T	NM_022455	NP_071900	Q96L73	NSD1_HUMAN	nuclear receptor binding SET domain protein 1	672					negative regulation of transcription from RNA polymerase II promoter|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	chromosome|nucleus	androgen receptor binding|chromatin binding|estrogen receptor binding|histone methyltransferase activity (H3-K36 specific)|histone methyltransferase activity (H4-K20 specific)|ligand-dependent nuclear receptor binding|retinoid X receptor binding|thyroid hormone receptor binding|transcription corepressor activity|zinc ion binding			ovary(2)|kidney(1)	3	all_cancers(89;1.57e-05)|Renal(175;0.000269)|Lung NSC(126;0.00111)|all_lung(126;0.002)	all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)|Epithelial(233;0.198)	Kidney(146;0.235)		TCGATAGAACAGAGAACATGT	0.398			T	NUP98	AML		Sotos Syndrome		Beckwith-Wiedemann_syndrome|Sotos_syndrome|Weaver_syndrome	HNSCC(47;0.14)			23	88	---	---	---	---	PASS
RREB1	6239	broad.mit.edu	37	6	7247354	7247354	+	Silent	SNP	C	T	T			TCGA-18-4721-01A-01D-1441-08	TCGA-18-4721-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	d2ab2555-7288-47a4-a80c-bf62d65b67b8	f7b631ae-ee98-499b-9d26-dc945e7ac3b8	g.chr6:7247354C>T	uc003mxc.2	+	11	4896	c.4506C>T	c.(4504-4506)AGC>AGT	p.S1502S	RREB1_uc003mxb.2_Silent_p.S1557S|RREB1_uc010jnx.2_Intron	NM_001003698	NP_001003698	Q92766	RREB1_HUMAN	ras responsive element binding protein 1 isoform	1502					multicellular organismal development|positive regulation of transcription, DNA-dependent|Ras protein signal transduction|transcription from RNA polymerase II promoter	cytoplasm|nuclear speck	DNA binding|zinc ion binding			ovary(4)|large_intestine(2)|pancreas(2)|skin(2)|breast(1)	11	Ovarian(93;0.0398)	all_hematologic(90;0.0384)|Prostate(151;0.191)				CCCCCAAAAGCGTGGCCAGCA	0.612													18	27	---	---	---	---	PASS
HIVEP1	3096	broad.mit.edu	37	6	12122201	12122201	+	Missense_Mutation	SNP	G	A	A			TCGA-18-4721-01A-01D-1441-08	TCGA-18-4721-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	d2ab2555-7288-47a4-a80c-bf62d65b67b8	f7b631ae-ee98-499b-9d26-dc945e7ac3b8	g.chr6:12122201G>A	uc003nac.2	+	4	2352	c.2173G>A	c.(2173-2175)GGG>AGG	p.G725R	HIVEP1_uc011diq.1_RNA	NM_002114	NP_002105	P15822	ZEP1_HUMAN	human immunodeficiency virus type I enhancer	725					transcription, DNA-dependent	cytoplasm|nucleus	DNA binding|protein binding|zinc ion binding			ovary(3)|large_intestine(1)|central_nervous_system(1)|skin(1)	6	Breast(50;0.0639)|Ovarian(93;0.0816)	all_hematologic(90;0.117)				TTTGCCCACAGGGGAAAAGGC	0.507													22	47	---	---	---	---	PASS
HIST1H2BJ	8970	broad.mit.edu	37	6	27100317	27100317	+	Missense_Mutation	SNP	G	C	C			TCGA-18-4721-01A-01D-1441-08	TCGA-18-4721-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	d2ab2555-7288-47a4-a80c-bf62d65b67b8	f7b631ae-ee98-499b-9d26-dc945e7ac3b8	g.chr6:27100317G>C	uc003niv.2	-	1	259	c.213C>G	c.(211-213)TTC>TTG	p.F71L	HIST1H2BJ_uc003niu.1_RNA|HIST1H2AG_uc003niw.2_5'Flank	NM_021058	NP_066402	P06899	H2B1J_HUMAN	histone cluster 1, H2bj	71					defense response to bacterium|nucleosome assembly	nucleosome|nucleus	DNA binding				0						CGATGCGCTCGAAAATGTCGT	0.567													21	176	---	---	---	---	PASS
SCAND3	114821	broad.mit.edu	37	6	28542626	28542626	+	Missense_Mutation	SNP	C	T	T			TCGA-18-4721-01A-01D-1441-08	TCGA-18-4721-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	d2ab2555-7288-47a4-a80c-bf62d65b67b8	f7b631ae-ee98-499b-9d26-dc945e7ac3b8	g.chr6:28542626C>T	uc003nlo.2	-	3	2474	c.1856G>A	c.(1855-1857)TGT>TAT	p.C619Y		NM_052923	NP_443155	Q6R2W3	SCND3_HUMAN	SCAN domain containing 3	619					DNA integration|viral reproduction	nucleus	DNA binding|protein dimerization activity|sequence-specific DNA binding transcription factor activity			ovary(1)	1						ATTTCCATCACATGATATACA	0.428													12	45	---	---	---	---	PASS
SCAND3	114821	broad.mit.edu	37	6	28542795	28542795	+	Missense_Mutation	SNP	C	T	T			TCGA-18-4721-01A-01D-1441-08	TCGA-18-4721-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	d2ab2555-7288-47a4-a80c-bf62d65b67b8	f7b631ae-ee98-499b-9d26-dc945e7ac3b8	g.chr6:28542795C>T	uc003nlo.2	-	3	2305	c.1687G>A	c.(1687-1689)GCC>ACC	p.A563T		NM_052923	NP_443155	Q6R2W3	SCND3_HUMAN	SCAN domain containing 3	563	Potential.				DNA integration|viral reproduction	nucleus	DNA binding|protein dimerization activity|sequence-specific DNA binding transcription factor activity			ovary(1)	1						TCATACTGGGCTCTTAAAGTA	0.413													18	77	---	---	---	---	PASS
OR5V1	81696	broad.mit.edu	37	6	29323110	29323110	+	Missense_Mutation	SNP	A	G	G			TCGA-18-4721-01A-01D-1441-08	TCGA-18-4721-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	d2ab2555-7288-47a4-a80c-bf62d65b67b8	f7b631ae-ee98-499b-9d26-dc945e7ac3b8	g.chr6:29323110A>G	uc011dlo.1	-	1	945	c.863T>C	c.(862-864)ATA>ACA	p.I288T		NM_030876	NP_110503	Q9UGF6	OR5V1_HUMAN	olfactory receptor, family 5, subfamily V,	288	Helical; Name=7; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(3)|kidney(1)	4						TGTGTAAATTATAGGGTTTAG	0.393													53	123	---	---	---	---	PASS
TAPBP	6892	broad.mit.edu	37	6	33272838	33272838	+	Missense_Mutation	SNP	C	G	G			TCGA-18-4721-01A-01D-1441-08	TCGA-18-4721-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	d2ab2555-7288-47a4-a80c-bf62d65b67b8	f7b631ae-ee98-499b-9d26-dc945e7ac3b8	g.chr6:33272838C>G	uc003odx.1	-	4	967	c.796G>C	c.(796-798)GAG>CAG	p.E266Q	TAPBP_uc010jus.1_Missense_Mutation_p.E284Q|TAPBP_uc003ody.2_Missense_Mutation_p.E266Q|TAPBP_uc003odz.2_Missense_Mutation_p.E266Q|TAPBP_uc010jut.1_Missense_Mutation_p.E179Q|TAPBP_uc011drc.1_Missense_Mutation_p.E266Q	NM_003190	NP_003181	O15533	TPSN_HUMAN	tapasin isoform 1 precursor	266	Lumenal (Potential).				antigen processing and presentation of endogenous peptide antigen via MHC class I|immune response|peptide antigen stabilization|protein complex assembly|retrograde vesicle-mediated transport, Golgi to ER	Golgi membrane|MHC class I peptide loading complex|microsome	MHC class I protein binding|peptide antigen binding|peptide antigen-transporting ATPase activity|TAP1 binding|TAP2 binding|unfolded protein binding			ovary(1)	1						TAGGTGCCCTCCTGAAAGGGT	0.582													11	113	---	---	---	---	PASS
PRICKLE4	29964	broad.mit.edu	37	6	41754618	41754618	+	Silent	SNP	G	T	T			TCGA-18-4721-01A-01D-1441-08	TCGA-18-4721-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	d2ab2555-7288-47a4-a80c-bf62d65b67b8	f7b631ae-ee98-499b-9d26-dc945e7ac3b8	g.chr6:41754618G>T	uc011duf.1	+	8	1154	c.906G>T	c.(904-906)CTG>CTT	p.L302L	PRICKLE4_uc003ord.2_RNA|TOMM6_uc003org.2_RNA|TOMM6_uc011dug.1_5'Flank	NM_013397	NP_037529	Q2TBC4	PRIC4_HUMAN	over-expressed breast tumor protein	262						nucleus	zinc ion binding				0	Ovarian(28;0.0355)|Colorectal(47;0.121)		Epithelial(12;8.38e-05)|STAD - Stomach adenocarcinoma(11;0.000204)|Colorectal(64;0.00062)|COAD - Colon adenocarcinoma(64;0.00152)			AGAGGGGGCTGCCTGGATCCA	0.617											OREG0017435	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	38	110	---	---	---	---	PASS
UBR2	23304	broad.mit.edu	37	6	42643823	42643823	+	Missense_Mutation	SNP	G	T	T			TCGA-18-4721-01A-01D-1441-08	TCGA-18-4721-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	d2ab2555-7288-47a4-a80c-bf62d65b67b8	f7b631ae-ee98-499b-9d26-dc945e7ac3b8	g.chr6:42643823G>T	uc011dur.1	+	39	4281	c.4281G>T	c.(4279-4281)TTG>TTT	p.L1427F	UBR2_uc011dus.1_Missense_Mutation_p.L1072F|UBR2_uc003osh.2_Intron|UBR2_uc011dut.1_Missense_Mutation_p.L15F	NM_015255	NP_056070	Q8IWV8	UBR2_HUMAN	ubiquitin protein ligase E3 component n-recognin	1427					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)			TTCCTGCGTTGCAGTGTCAGG	0.458													13	156	---	---	---	---	PASS
EYS	346007	broad.mit.edu	37	6	66204975	66204975	+	Missense_Mutation	SNP	G	T	T			TCGA-18-4721-01A-01D-1441-08	TCGA-18-4721-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	d2ab2555-7288-47a4-a80c-bf62d65b67b8	f7b631ae-ee98-499b-9d26-dc945e7ac3b8	g.chr6:66204975G>T	uc011dxu.1	-	4	867	c.329C>A	c.(328-330)TCT>TAT	p.S110Y	EYS_uc003peq.2_Missense_Mutation_p.S110Y|EYS_uc003per.1_Missense_Mutation_p.S110Y|EYS_uc010kaj.1_RNA	NM_001142800	NP_001136272	Q5T1H1	EYS_HUMAN	eyes shut homolog isoform 1	110					response to stimulus|visual perception	extracellular region	calcium ion binding			lung(4)|ovary(1)|skin(1)	6						GCCAACGAAAGATGTTTCAGA	0.358													11	136	---	---	---	---	PASS
LCA5	167691	broad.mit.edu	37	6	80223047	80223047	+	Missense_Mutation	SNP	A	C	C			TCGA-18-4721-01A-01D-1441-08	TCGA-18-4721-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	d2ab2555-7288-47a4-a80c-bf62d65b67b8	f7b631ae-ee98-499b-9d26-dc945e7ac3b8	g.chr6:80223047A>C	uc003pix.2	-	3	1037	c.602T>G	c.(601-603)TTT>TGT	p.F201C	LCA5_uc003piy.2_Missense_Mutation_p.F201C|LCA5_uc011dyq.1_RNA|LCA5_uc011dyr.1_Missense_Mutation_p.F201C	NM_001122769	NP_001116241	Q86VQ0	LCA5_HUMAN	Leber congenital amaurosis 5	201	Potential.				protein transport	cilium axoneme|microtubule basal body	protein binding				0		all_cancers(76;3.32e-05)|Acute lymphoblastic leukemia(125;1.1e-05)|all_hematologic(105;0.00117)|all_epithelial(107;0.0176)		BRCA - Breast invasive adenocarcinoma(397;0.0657)		CTGTAAGGAAAATTTTGTCCT	0.368													43	138	---	---	---	---	PASS
NT5E	4907	broad.mit.edu	37	6	86201753	86201753	+	Silent	SNP	T	C	C			TCGA-18-4721-01A-01D-1441-08	TCGA-18-4721-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	d2ab2555-7288-47a4-a80c-bf62d65b67b8	f7b631ae-ee98-499b-9d26-dc945e7ac3b8	g.chr6:86201753T>C	uc003pko.3	+	8	1975	c.1419T>C	c.(1417-1419)GAT>GAC	p.D473D	NT5E_uc010kbr.2_Silent_p.D423D	NM_002526	NP_002517	P21589	5NTD_HUMAN	5' nucleotidase, ecto precursor	473					DNA metabolic process|purine base metabolic process|pyrimidine base metabolic process|pyrimidine nucleoside catabolic process	anchored to membrane|cytoplasm|membrane fraction|plasma membrane	5'-nucleotidase activity|nucleotide binding			ovary(3)|central_nervous_system(1)	4		all_cancers(76;0.000215)|Acute lymphoblastic leukemia(125;3.66e-08)|all_hematologic(105;8.61e-05)|all_epithelial(107;0.0427)		BRCA - Breast invasive adenocarcinoma(108;0.0417)	Pentoxifylline(DB00806)	TCAAATTAGATGTTCTTTGCA	0.443													51	226	---	---	---	---	PASS
GPR63	81491	broad.mit.edu	37	6	97246607	97246607	+	Missense_Mutation	SNP	C	T	T			TCGA-18-4721-01A-01D-1441-08	TCGA-18-4721-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	d2ab2555-7288-47a4-a80c-bf62d65b67b8	f7b631ae-ee98-499b-9d26-dc945e7ac3b8	g.chr6:97246607C>T	uc010kcl.2	-	3	1479	c.1001G>A	c.(1000-1002)AGC>AAC	p.S334N	GPR63_uc003pou.2_Missense_Mutation_p.S334N	NM_001143957	NP_001137429	Q9BZJ6	GPR63_HUMAN	G protein-coupled receptor 63	334	Helical; Name=6; (Potential).					integral to membrane|plasma membrane	G-protein coupled receptor activity|protein binding			upper_aerodigestive_tract(1)|ovary(1)	2		all_cancers(76;6.89e-05)|Acute lymphoblastic leukemia(125;7.02e-10)|all_hematologic(75;1.23e-06)|all_epithelial(107;0.0618)|Colorectal(196;0.0721)		BRCA - Breast invasive adenocarcinoma(108;0.0912)		TGCCACAAGGCTGTAAGTGGT	0.443													29	70	---	---	---	---	PASS
LAMA2	3908	broad.mit.edu	37	6	129475703	129475703	+	Missense_Mutation	SNP	A	G	G			TCGA-18-4721-01A-01D-1441-08	TCGA-18-4721-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	d2ab2555-7288-47a4-a80c-bf62d65b67b8	f7b631ae-ee98-499b-9d26-dc945e7ac3b8	g.chr6:129475703A>G	uc003qbn.2	+	8	1186	c.1081A>G	c.(1081-1083)AGA>GGA	p.R361G	LAMA2_uc003qbo.2_Missense_Mutation_p.R361G	NM_000426	NP_000417	P24043	LAMA2_HUMAN	laminin alpha 2 subunit isoform a precursor	361	Laminin EGF-like 2.				cell adhesion|muscle organ development|regulation of cell adhesion|regulation of cell migration|regulation of embryonic development	laminin-1 complex	receptor binding|structural molecule activity			ovary(8)|breast(1)|skin(1)	10				OV - Ovarian serous cystadenocarcinoma(136;0.178)|all cancers(137;0.245)		AAATGTTGCCAGAAGAAATCT	0.348													10	89	---	---	---	---	PASS
TMEM181	57583	broad.mit.edu	37	6	159044617	159044617	+	Missense_Mutation	SNP	G	A	A			TCGA-18-4721-01A-01D-1441-08	TCGA-18-4721-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	d2ab2555-7288-47a4-a80c-bf62d65b67b8	f7b631ae-ee98-499b-9d26-dc945e7ac3b8	g.chr6:159044617G>A	uc003qrm.3	+	11	1354	c.1343G>A	c.(1342-1344)CGA>CAA	p.R448Q	TMEM181_uc010kjr.1_Missense_Mutation_p.R279Q	NM_020823	NP_065874	Q9P2C4	TM181_HUMAN	G protein-coupled receptor 178	448					pathogenesis	integral to membrane	toxin binding			ovary(2)|central_nervous_system(1)	3		Breast(66;0.000776)|Ovarian(120;0.0303)		OV - Ovarian serous cystadenocarcinoma(65;8.15e-18)|BRCA - Breast invasive adenocarcinoma(81;1.38e-05)		TACCAGTATCGAGTTGATACC	0.259													3	48	---	---	---	---	PASS
PDE10A	10846	broad.mit.edu	37	6	165749635	165749635	+	Silent	SNP	C	A	A			TCGA-18-4721-01A-01D-1441-08	TCGA-18-4721-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	d2ab2555-7288-47a4-a80c-bf62d65b67b8	f7b631ae-ee98-499b-9d26-dc945e7ac3b8	g.chr6:165749635C>A	uc003qun.2	-	22	2455	c.2214G>T	c.(2212-2214)ACG>ACT	p.T738T	PDE10A_uc011egj.1_RNA|PDE10A_uc011egk.1_Silent_p.T668T|PDE10A_uc003quo.2_Silent_p.T748T	NM_006661	NP_006652	Q9Y233	PDE10_HUMAN	phosphodiesterase 10A isoform 2	738					platelet activation|signal transduction	cytosol	3',5'-cyclic-AMP phosphodiesterase activity|3',5'-cyclic-GMP phosphodiesterase activity|cAMP binding|cGMP binding|metal ion binding			ovary(3)|skin(2)	5		Breast(66;0.000425)|Prostate(117;0.104)|Ovarian(120;0.221)		OV - Ovarian serous cystadenocarcinoma(33;1.5e-17)|BRCA - Breast invasive adenocarcinoma(81;1.8e-06)|GBM - Glioblastoma multiforme(31;1.92e-05)	Dipyridamole(DB00975)	GAAGAGGCTCCGTGGGAGGGA	0.463													7	60	---	---	---	---	PASS
USP42	84132	broad.mit.edu	37	7	6183809	6183809	+	Silent	SNP	C	T	T	rs151011297	by1000genomes	TCGA-18-4721-01A-01D-1441-08	TCGA-18-4721-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	d2ab2555-7288-47a4-a80c-bf62d65b67b8	f7b631ae-ee98-499b-9d26-dc945e7ac3b8	g.chr7:6183809C>T	uc011jwo.1	+	9	1095	c.972C>T	c.(970-972)ACC>ACT	p.T324T	USP42_uc011jwn.1_Silent_p.T169T|USP42_uc010kth.1_Silent_p.T257T|USP42_uc011jwp.1_Silent_p.T324T|USP42_uc011jwq.1_Silent_p.T131T|USP42_uc011jwr.1_Silent_p.T169T	NM_032172	NP_115548	Q9H9J4	UBP42_HUMAN	ubiquitin specific peptidase 42	324					cell differentiation|protein deubiquitination|spermatogenesis|ubiquitin-dependent protein catabolic process		cysteine-type peptidase activity|ubiquitin thiolesterase activity			skin(2)|ovary(1)|pancreas(1)|breast(1)	5		Ovarian(82;0.0423)		UCEC - Uterine corpus endometrioid carcinoma (126;0.108)|OV - Ovarian serous cystadenocarcinoma(56;5.77e-14)		CAAATTTTACCGGTGGAAAAA	0.368													7	21	---	---	---	---	PASS
DGKB	1607	broad.mit.edu	37	7	14217688	14217688	+	Silent	SNP	C	A	A			TCGA-18-4721-01A-01D-1441-08	TCGA-18-4721-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	d2ab2555-7288-47a4-a80c-bf62d65b67b8	f7b631ae-ee98-499b-9d26-dc945e7ac3b8	g.chr7:14217688C>A	uc003ssz.2	-	23	2401	c.2214G>T	c.(2212-2214)CGG>CGT	p.R738R	DGKB_uc011jxt.1_Silent_p.R719R|DGKB_uc003sta.2_Silent_p.R738R|DGKB_uc011jxu.1_Silent_p.R737R	NM_004080	NP_004071	Q9Y6T7	DGKB_HUMAN	diacylglycerol kinase, beta isoform 1	738					activation of protein kinase C activity by G-protein coupled receptor protein signaling pathway|intracellular signal transduction|platelet activation	cytoplasm|plasma membrane	ATP binding|calcium ion binding|diacylglycerol kinase activity|protein binding			lung(5)|ovary(4)|breast(2)|skin(1)	12					Phosphatidylserine(DB00144)	GAGCCAGCCGCCGGCCAGCAC	0.507													19	94	---	---	---	---	PASS
STK31	56164	broad.mit.edu	37	7	23766889	23766889	+	Missense_Mutation	SNP	G	T	T			TCGA-18-4721-01A-01D-1441-08	TCGA-18-4721-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	d2ab2555-7288-47a4-a80c-bf62d65b67b8	f7b631ae-ee98-499b-9d26-dc945e7ac3b8	g.chr7:23766889G>T	uc003sws.3	+	5	346	c.279G>T	c.(277-279)CAG>CAT	p.Q93H	STK31_uc003swt.3_Missense_Mutation_p.Q70H|STK31_uc011jze.1_Missense_Mutation_p.Q93H|STK31_uc010kuq.2_Missense_Mutation_p.Q70H	NM_031414	NP_113602	Q9BXU1	STK31_HUMAN	serine/threonine kinase 31 isoform a	93	Tudor.						ATP binding|nucleic acid binding|protein serine/threonine kinase activity			skin(3)|lung(2)|ovary(2)|stomach(2)	9						CTGAAGATCAGTGTTGGTACA	0.303													16	89	---	---	---	---	PASS
HOXA3	3200	broad.mit.edu	37	7	27150111	27150111	+	Missense_Mutation	SNP	C	A	A			TCGA-18-4721-01A-01D-1441-08	TCGA-18-4721-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	d2ab2555-7288-47a4-a80c-bf62d65b67b8	f7b631ae-ee98-499b-9d26-dc945e7ac3b8	g.chr7:27150111C>A	uc011jzl.1	-	2	349	c.149G>T	c.(148-150)TGC>TTC	p.C50F	HOXA3_uc011jzk.1_Intron|HOXA3_uc003syk.2_Missense_Mutation_p.C50F	NM_030661	NP_109377	O43365	HXA3_HUMAN	homeobox A3 isoform a	50					angiogenesis	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			breast(2)	2						CTGGAGGGAGCAGGCGGGTCG	0.692													4	19	---	---	---	---	PASS
CALN1	83698	broad.mit.edu	37	7	71488694	71488694	+	Nonsense_Mutation	SNP	G	T	T			TCGA-18-4721-01A-01D-1441-08	TCGA-18-4721-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	d2ab2555-7288-47a4-a80c-bf62d65b67b8	f7b631ae-ee98-499b-9d26-dc945e7ac3b8	g.chr7:71488694G>T	uc003twa.3	-	4	850	c.323C>A	c.(322-324)TCA>TAA	p.S108*	CALN1_uc003twb.3_Nonsense_Mutation_p.S150*|CALN1_uc003twc.3_Nonsense_Mutation_p.S108*	NM_001017440	NP_001017440	Q9BXU9	CABP8_HUMAN	calneuron 1 isoform 2	108	Cytoplasmic (Potential).					Golgi apparatus|integral to membrane|perinuclear region of cytoplasm|plasma membrane	calcium ion binding			skin(1)	1		all_cancers(73;0.069)|Lung NSC(55;0.0658)|all_lung(88;0.0912)|all_epithelial(88;0.161)				GCGACCTTCTGAAGACACCAG	0.423													38	92	---	---	---	---	PASS
MAGI2	9863	broad.mit.edu	37	7	77764405	77764405	+	Missense_Mutation	SNP	G	T	T			TCGA-18-4721-01A-01D-1441-08	TCGA-18-4721-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	d2ab2555-7288-47a4-a80c-bf62d65b67b8	f7b631ae-ee98-499b-9d26-dc945e7ac3b8	g.chr7:77764405G>T	uc003ugx.2	-	17	3218	c.2964C>A	c.(2962-2964)CAC>CAA	p.H988Q	MAGI2_uc003ugy.2_Missense_Mutation_p.H974Q|MAGI2_uc010ldx.1_Missense_Mutation_p.H581Q	NM_012301	NP_036433	Q86UL8	MAGI2_HUMAN	membrane associated guanylate kinase, WW and PDZ	988	PDZ 5.					cell junction|synapse|synaptosome	phosphatase binding			ovary(5)|lung(4)|breast(1)|skin(1)	11		all_cancers(73;0.0064)|all_epithelial(88;0.087)|all_neural(109;0.0936)|Medulloblastoma(109;0.166)|Melanoma(862;0.236)				CGATGTCAGCGTGAGGCATGT	0.537													24	143	---	---	---	---	PASS
HGF	3082	broad.mit.edu	37	7	81386586	81386586	+	Missense_Mutation	SNP	C	T	T			TCGA-18-4721-01A-01D-1441-08	TCGA-18-4721-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	d2ab2555-7288-47a4-a80c-bf62d65b67b8	f7b631ae-ee98-499b-9d26-dc945e7ac3b8	g.chr7:81386586C>T	uc003uhl.2	-	4	566	c.401G>A	c.(400-402)CGC>CAC	p.R134H	HGF_uc003uhm.2_Missense_Mutation_p.R134H|HGF_uc003uhn.1_Missense_Mutation_p.R134H|HGF_uc003uho.1_Missense_Mutation_p.R134H|HGF_uc003uhp.2_Missense_Mutation_p.R134H	NM_000601	NP_000592	P14210	HGF_HUMAN	hepatocyte growth factor isoform 1	134	Kringle 1.				epithelial to mesenchymal transition|mitosis|platelet activation|platelet degranulation|proteolysis|regulation of branching involved in salivary gland morphogenesis by mesenchymal-epithelial signaling	platelet alpha granule lumen	growth factor activity|serine-type endopeptidase activity			ovary(2)|central_nervous_system(2)	4						CTTGTAGCTGCGTCCTTTACC	0.358													26	76	---	---	---	---	PASS
CPSF4	10898	broad.mit.edu	37	7	99048393	99048393	+	Missense_Mutation	SNP	G	C	C			TCGA-18-4721-01A-01D-1441-08	TCGA-18-4721-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	d2ab2555-7288-47a4-a80c-bf62d65b67b8	f7b631ae-ee98-499b-9d26-dc945e7ac3b8	g.chr7:99048393G>C	uc003uqj.2	+	5	615	c.472G>C	c.(472-474)GAG>CAG	p.E158Q	PTCD1_uc011kiw.1_Intron|CPSF4_uc003uqi.2_Missense_Mutation_p.E158Q|CPSF4_uc003uqk.2_Missense_Mutation_p.E158Q|CPSF4_uc011kix.1_Missense_Mutation_p.E105Q	NM_006693	NP_006684	O95639	CPSF4_HUMAN	cleavage and polyadenylation specific factor 4,	158	C3H1-type 5.				modification by virus of host mRNA processing|mRNA processing|viral infectious cycle	mRNA cleavage and polyadenylation specificity factor complex	RNA binding|zinc ion binding			central_nervous_system(1)	1	all_cancers(62;2.54e-08)|all_epithelial(64;2.55e-09)|Lung NSC(181;0.0053)|all_lung(186;0.00895)|Esophageal squamous(72;0.0166)					ATTCTGCCCGGAGGGGCCCTC	0.622													23	130	---	---	---	---	PASS
TAF6	6878	broad.mit.edu	37	7	99711547	99711547	+	Silent	SNP	G	T	T			TCGA-18-4721-01A-01D-1441-08	TCGA-18-4721-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	d2ab2555-7288-47a4-a80c-bf62d65b67b8	f7b631ae-ee98-499b-9d26-dc945e7ac3b8	g.chr7:99711547G>T	uc003uti.2	-	3	268	c.187C>A	c.(187-189)CGG>AGG	p.R63R	TAF6_uc003utg.2_Silent_p.R4R|TAF6_uc003uth.2_Silent_p.R120R|TAF6_uc003utk.2_Silent_p.R63R|TAF6_uc011kji.1_Silent_p.R100R|TAF6_uc003utj.2_Silent_p.R53R|TAF6_uc003utl.2_Silent_p.R63R|TAF6_uc003utm.2_Silent_p.R63R|TAF6_uc003utn.1_RNA	NM_139315	NP_647476	P49848	TAF6_HUMAN	TBP-associated factor 6 isoform alpha	63					negative regulation of cell cycle|negative regulation of cell proliferation|regulation of sequence-specific DNA binding transcription factor activity|transcription elongation from RNA polymerase II promoter|transcription initiation from RNA polymerase II promoter|viral reproduction	cytoplasm|MLL1 complex|transcription factor TFIID complex|transcription factor TFIID complex|transcription factor TFTC complex	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity			ovary(1)|central_nervous_system(1)	2	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)					AGCTTCTGCCGCTTCCCCATG	0.567													38	121	---	---	---	---	PASS
MUC17	140453	broad.mit.edu	37	7	100676743	100676743	+	Silent	SNP	T	G	G			TCGA-18-4721-01A-01D-1441-08	TCGA-18-4721-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	d2ab2555-7288-47a4-a80c-bf62d65b67b8	f7b631ae-ee98-499b-9d26-dc945e7ac3b8	g.chr7:100676743T>G	uc003uxp.1	+	3	2099	c.2046T>G	c.(2044-2046)ACT>ACG	p.T682T	MUC17_uc010lho.1_RNA	NM_001040105	NP_001035194	Q685J3	MUC17_HUMAN	mucin 17 precursor	682	Extracellular (Potential).|9.|59 X approximate tandem repeats.|Ser-rich.					extracellular region|integral to membrane|plasma membrane	extracellular matrix constituent, lubricant activity			ovary(14)|skin(8)|breast(3)|lung(2)	27	Lung NSC(181;0.136)|all_lung(186;0.182)					CAACCTCAACTTATACTGAAG	0.478													113	451	---	---	---	---	PASS
PIK3CG	5294	broad.mit.edu	37	7	106508508	106508508	+	Missense_Mutation	SNP	G	T	T			TCGA-18-4721-01A-01D-1441-08	TCGA-18-4721-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	d2ab2555-7288-47a4-a80c-bf62d65b67b8	f7b631ae-ee98-499b-9d26-dc945e7ac3b8	g.chr7:106508508G>T	uc003vdv.3	+	2	587	c.502G>T	c.(502-504)GTG>TTG	p.V168L	PIK3CG_uc003vdu.2_Missense_Mutation_p.V168L|PIK3CG_uc003vdw.2_Missense_Mutation_p.V168L	NM_002649	NP_002640	P48736	PK3CG_HUMAN	phosphoinositide-3-kinase, catalytic, gamma	168					G-protein coupled receptor protein signaling pathway|phosphatidylinositol-mediated signaling|platelet activation	phosphatidylinositol 3-kinase complex	1-phosphatidylinositol-3-kinase activity|ATP binding|phosphatidylinositol-4,5-bisphosphate 3-kinase activity|protein binding			lung(16)|central_nervous_system(8)|breast(5)|pancreas(3)|stomach(2)|ovary(2)|upper_aerodigestive_tract(1)|skin(1)	38						CGTCAGCAACGTGCACGACGA	0.672													12	43	---	---	---	---	PASS
WNT2	7472	broad.mit.edu	37	7	116955161	116955161	+	Silent	SNP	G	T	T	rs144337728		TCGA-18-4721-01A-01D-1441-08	TCGA-18-4721-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	d2ab2555-7288-47a4-a80c-bf62d65b67b8	f7b631ae-ee98-499b-9d26-dc945e7ac3b8	g.chr7:116955161G>T	uc003viz.2	-	3	852	c.552C>A	c.(550-552)GCC>GCA	p.A184A	WNT2_uc003vja.2_Silent_p.A88A	NM_003391	NP_003382	P09544	WNT2_HUMAN	wingless-type MMTV integration site family	184					atrial cardiac muscle tissue morphogenesis|canonical Wnt receptor signaling pathway|cardiac epithelial to mesenchymal transition|cellular response to retinoic acid|cellular response to transforming growth factor beta stimulus|dorsal/ventral axis specification|iris morphogenesis|labyrinthine layer blood vessel development|lens development in camera-type eye|lung induction|mammary gland epithelium development|neuron differentiation|positive regulation of canonical Wnt receptor signaling pathway|positive regulation of cardiac muscle cell proliferation|positive regulation of epithelial cell proliferation involved in lung morphogenesis|positive regulation of fibroblast proliferation|positive regulation of mesenchymal cell proliferation|positive regulation of sequence-specific DNA binding transcription factor activity|positive regulation of transcription from RNA polymerase II promoter|Wnt receptor signaling pathway, calcium modulating pathway	cytoplasm|extracellular space|proteinaceous extracellular matrix	cytokine activity|frizzled binding|frizzled-2 binding|signal transducer activity			breast(2)|central_nervous_system(2)|ovary(1)|lung(1)|skin(1)	7	all_epithelial(6;2.24e-06)|Lung NSC(10;0.000936)|all_lung(10;0.00109)		STAD - Stomach adenocarcinoma(10;0.000512)	LUSC - Lung squamous cell carcinoma(290;0.133)		GATTCATCAGGGCTCTGGCAt	0.423													28	150	---	---	---	---	PASS
TAS2R16	50833	broad.mit.edu	37	7	122635320	122635320	+	Silent	SNP	C	T	T			TCGA-18-4721-01A-01D-1441-08	TCGA-18-4721-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	d2ab2555-7288-47a4-a80c-bf62d65b67b8	f7b631ae-ee98-499b-9d26-dc945e7ac3b8	g.chr7:122635320C>T	uc003vkl.1	-	1	435	c.369G>A	c.(367-369)TTG>TTA	p.L123L		NM_016945	NP_058641	Q9NYV7	T2R16_HUMAN	taste receptor T2R16	123	Cytoplasmic (Potential).				detection of chemical stimulus involved in sensory perception of bitter taste	endoplasmic reticulum|external side of plasma membrane|trans-Golgi network	bitter taste receptor activity|protein binding			ovary(1)|skin(1)	2						GAAACAACCTCAAAATTCTCC	0.408													15	77	---	---	---	---	PASS
SSPO	23145	broad.mit.edu	37	7	149515739	149515739	+	Splice_Site	SNP	A	T	T			TCGA-18-4721-01A-01D-1441-08	TCGA-18-4721-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	d2ab2555-7288-47a4-a80c-bf62d65b67b8	f7b631ae-ee98-499b-9d26-dc945e7ac3b8	g.chr7:149515739A>T	uc010lpk.2	+	84	11642	c.11642_splice	c.e84-2	p.G3881_splice		NM_198455	NP_940857	A2VEC9	SSPO_HUMAN	SCO-spondin precursor						cell adhesion	extracellular space	peptidase inhibitor activity				0	Melanoma(164;0.165)|Ovarian(565;0.177)		OV - Ovarian serous cystadenocarcinoma(82;0.00625)			TCCCTCCCCCAGGTGGCTGGG	0.701													4	26	---	---	---	---	PASS
CSMD1	64478	broad.mit.edu	37	8	2966161	2966161	+	Missense_Mutation	SNP	A	C	C			TCGA-18-4721-01A-01D-1441-08	TCGA-18-4721-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	d2ab2555-7288-47a4-a80c-bf62d65b67b8	f7b631ae-ee98-499b-9d26-dc945e7ac3b8	g.chr8:2966161A>C	uc011kwk.1	-	44	7111	c.6721T>G	c.(6721-6723)TTT>GTT	p.F2241V	CSMD1_uc011kwj.1_Missense_Mutation_p.F1633V|CSMD1_uc010lrg.2_Missense_Mutation_p.F309V	NM_033225	NP_150094	Q96PZ7	CSMD1_HUMAN	CUB and Sushi multiple domains 1 precursor	2241	Extracellular (Potential).|CUB 13.					integral to membrane				breast(20)|large_intestine(5)	25		all_cancers(1;5.7e-41)|all_epithelial(1;2.54e-36)|Lung NSC(1;7.54e-11)|all_lung(1;3.2e-10)|Hepatocellular(1;3.78e-05)|Breast(1;0.000196)|Myeloproliferative disorder(4;0.000374)|Esophageal squamous(1;0.0157)|Ovarian(12;0.091)|Renal(68;0.144)|Colorectal(14;0.234)		all cancers(1;5.03e-41)|Epithelial(1;4.78e-31)|Lung(1;1.14e-14)|LUSC - Lung squamous cell carcinoma(1;2.34e-14)|GBM - Glioblastoma multiforme(1;4.49e-10)|Colorectal(4;1.18e-07)|OV - Ovarian serous cystadenocarcinoma(1;3.2e-07)|BRCA - Breast invasive adenocarcinoma(1;6.17e-07)|COAD - Colon adenocarcinoma(4;0.000539)|READ - Rectum adenocarcinoma(4;0.00896)|Kidney(5;0.00957)|KIRC - Kidney renal clear cell carcinoma(5;0.0689)		CCATTTGAAAAGTCGCTGTGG	0.488													6	23	---	---	---	---	PASS
DEFB1	1672	broad.mit.edu	37	8	6728282	6728282	+	Missense_Mutation	SNP	T	C	C			TCGA-18-4721-01A-01D-1441-08	TCGA-18-4721-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	d2ab2555-7288-47a4-a80c-bf62d65b67b8	f7b631ae-ee98-499b-9d26-dc945e7ac3b8	g.chr8:6728282T>C	uc003wqs.2	-	2	278	c.128A>G	c.(127-129)CAA>CGA	p.Q43R		NM_005218	NP_005209	P60022	DEFB1_HUMAN	defensin, beta 1 preproprotein	43					chemotaxis|defense response to bacterium|G-protein coupled receptor protein signaling pathway|innate immune response	extracellular region					0			STAD - Stomach adenocarcinoma(24;0.0984)	COAD - Colon adenocarcinoma(149;0.0162)|READ - Rectum adenocarcinoma(644;0.128)		ATAGAGACATTGCCCTCCACT	0.488													26	62	---	---	---	---	PASS
TNKS	8658	broad.mit.edu	37	8	9562186	9562186	+	Missense_Mutation	SNP	A	G	G			TCGA-18-4721-01A-01D-1441-08	TCGA-18-4721-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	d2ab2555-7288-47a4-a80c-bf62d65b67b8	f7b631ae-ee98-499b-9d26-dc945e7ac3b8	g.chr8:9562186A>G	uc003wss.2	+	6	1126	c.1121A>G	c.(1120-1122)CAT>CGT	p.H374R	TNKS_uc011kwv.1_Missense_Mutation_p.H374R|TNKS_uc011kww.1_Missense_Mutation_p.H137R	NM_003747	NP_003738	O95271	TNKS1_HUMAN	tankyrase, TRF1-interacting ankyrin-related	374	ANK 4.				mitotic spindle organization|mRNA transport|negative regulation of DNA binding|peptidyl-serine phosphorylation|peptidyl-threonine phosphorylation|positive regulation of canonical Wnt receptor signaling pathway|positive regulation of telomere maintenance via telomerase|protein auto-ADP-ribosylation|protein localization to chromosome, telomeric region|protein poly-ADP-ribosylation|protein polyubiquitination|protein transport|spindle assembly|transmembrane transport|Wnt receptor signaling pathway	chromosome, centromeric region|Golgi membrane|microsome|nuclear chromosome, telomeric region|nuclear membrane|nuclear pore|pericentriolar material	NAD+ ADP-ribosyltransferase activity|protein binding|zinc ion binding			lung(4)|ovary(2)|kidney(1)	7				COAD - Colon adenocarcinoma(149;0.0467)		ACTCCTTTACATCTAGCAGCG	0.383													33	100	---	---	---	---	PASS
CYP7A1	1581	broad.mit.edu	37	8	59404139	59404139	+	Silent	SNP	T	A	A			TCGA-18-4721-01A-01D-1441-08	TCGA-18-4721-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	d2ab2555-7288-47a4-a80c-bf62d65b67b8	f7b631ae-ee98-499b-9d26-dc945e7ac3b8	g.chr8:59404139T>A	uc003xtm.3	-	6	1473	c.1410A>T	c.(1408-1410)ATA>ATT	p.I470I		NM_000780	NP_000771	P22680	CP7A1_HUMAN	cytochrome P450, family 7, subfamily A,	470					bile acid biosynthetic process|cellular lipid metabolic process|cellular response to cholesterol|cellular response to glucose stimulus|cholesterol catabolic process|cholesterol homeostasis|regulation of bile acid biosynthetic process|xenobiotic metabolic process	endoplasmic reticulum membrane|microsome	cholesterol 7-alpha-monooxygenase activity|electron carrier activity|heme binding			ovary(1)	1		all_lung(136;0.0271)|Lung NSC(129;0.0351)|all_epithelial(80;0.0554)				CTTGGCCCTCTATAAGCTCCA	0.403									Neonatal_Giant_Cell_Hepatitis				25	66	---	---	---	---	PASS
NCOA2	10499	broad.mit.edu	37	8	71071794	71071794	+	Missense_Mutation	SNP	C	A	A			TCGA-18-4721-01A-01D-1441-08	TCGA-18-4721-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	d2ab2555-7288-47a4-a80c-bf62d65b67b8	f7b631ae-ee98-499b-9d26-dc945e7ac3b8	g.chr8:71071794C>A	uc003xyn.1	-	10	1232	c.1070G>T	c.(1069-1071)CGT>CTT	p.R357L		NM_006540	NP_006531	Q15596	NCOA2_HUMAN	nuclear receptor coactivator 2	357					cellular lipid metabolic process|transcription, DNA-dependent	nucleoplasm	histone acetyltransferase activity|ligand-dependent nuclear receptor binding|nuclear hormone receptor binding|signal transducer activity		PAX3/NCOA2(4)	lung(6)|soft_tissue(4)|breast(2)|skin(2)|ovary(1)|pancreas(1)	16	Breast(64;0.201)		Epithelial(68;0.0147)|OV - Ovarian serous cystadenocarcinoma(28;0.0455)|all cancers(69;0.0606)			AGTCTGAGAACGGATGAGTTT	0.398			T	RUNXBP2	AML								43	215	---	---	---	---	PASS
TRPA1	8989	broad.mit.edu	37	8	72964957	72964957	+	Missense_Mutation	SNP	G	T	T			TCGA-18-4721-01A-01D-1441-08	TCGA-18-4721-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	d2ab2555-7288-47a4-a80c-bf62d65b67b8	f7b631ae-ee98-499b-9d26-dc945e7ac3b8	g.chr8:72964957G>T	uc003xza.2	-	14	1863	c.1688C>A	c.(1687-1689)GCC>GAC	p.A563D	uc011lff.1_RNA|uc003xyy.2_RNA	NM_007332	NP_015628	O75762	TRPA1_HUMAN	ankyrin-like protein 1	563	Cytoplasmic (Potential).|ANK 14.					integral to plasma membrane				ovary(4)|lung(1)|kidney(1)	6			Epithelial(68;0.223)		Menthol(DB00825)	AAGCGCAACGGCTTTGGCGTG	0.463													27	111	---	---	---	---	PASS
KIAA1429	25962	broad.mit.edu	37	8	95531467	95531467	+	Missense_Mutation	SNP	A	C	C			TCGA-18-4721-01A-01D-1441-08	TCGA-18-4721-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	d2ab2555-7288-47a4-a80c-bf62d65b67b8	f7b631ae-ee98-499b-9d26-dc945e7ac3b8	g.chr8:95531467A>C	uc003ygo.1	-	9	2272	c.2259T>G	c.(2257-2259)ATT>ATG	p.I753M	KIAA1429_uc003ygp.2_Missense_Mutation_p.I753M|KIAA1429_uc010maz.1_RNA	NM_015496	NP_056311	Q69YN4	VIR_HUMAN	hypothetical protein LOC25962 isoform 1	753					mRNA processing|RNA splicing	nucleus				ovary(1)|skin(1)	2	Breast(36;3.29e-05)		BRCA - Breast invasive adenocarcinoma(8;0.00185)			ATGCATCATCAATAACACCAT	0.398													6	86	---	---	---	---	PASS
NIPAL2	79815	broad.mit.edu	37	8	99234724	99234724	+	Missense_Mutation	SNP	G	T	T			TCGA-18-4721-01A-01D-1441-08	TCGA-18-4721-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	d2ab2555-7288-47a4-a80c-bf62d65b67b8	f7b631ae-ee98-499b-9d26-dc945e7ac3b8	g.chr8:99234724G>T	uc003yil.1	-	5	797	c.541C>A	c.(541-543)CAG>AAG	p.Q181K	NIPAL2_uc011lgw.1_5'UTR|NIPAL2_uc003yim.1_Missense_Mutation_p.Q181K	NM_024759	NP_079035	Q9H841	NPAL2_HUMAN	NIPA-like domain containing 2	181	Helical; (Potential).					integral to membrane					0						ATCAGGAACTGCCATCCGACA	0.388													28	128	---	---	---	---	PASS
PKHD1L1	93035	broad.mit.edu	37	8	110424585	110424585	+	Missense_Mutation	SNP	C	A	A			TCGA-18-4721-01A-01D-1441-08	TCGA-18-4721-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	d2ab2555-7288-47a4-a80c-bf62d65b67b8	f7b631ae-ee98-499b-9d26-dc945e7ac3b8	g.chr8:110424585C>A	uc003yne.2	+	20	2281	c.2177C>A	c.(2176-2178)GCA>GAA	p.A726E		NM_177531	NP_803875	Q86WI1	PKHL1_HUMAN	fibrocystin L precursor	726	Extracellular (Potential).				immune response	cytosol|extracellular space|integral to membrane	receptor activity			ovary(9)|central_nervous_system(2)|large_intestine(1)|breast(1)|pancreas(1)	14			OV - Ovarian serous cystadenocarcinoma(57;9.88e-13)			TTTGACTCAGCAGATGTTAAA	0.373										HNSCC(38;0.096)			15	56	---	---	---	---	PASS
CSMD3	114788	broad.mit.edu	37	8	113418957	113418957	+	Splice_Site	SNP	C	A	A			TCGA-18-4721-01A-01D-1441-08	TCGA-18-4721-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	d2ab2555-7288-47a4-a80c-bf62d65b67b8	f7b631ae-ee98-499b-9d26-dc945e7ac3b8	g.chr8:113418957C>A	uc003ynu.2	-	35	5765	c.5606_splice	c.e35-1	p.A1869_splice	CSMD3_uc003yns.2_Splice_Site_p.A1071_splice|CSMD3_uc003ynt.2_Splice_Site_p.A1829_splice|CSMD3_uc011lhx.1_Splice_Site_p.A1765_splice	NM_198123	NP_937756	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3 isoform 1							integral to membrane|plasma membrane				ovary(21)|lung(11)|skin(11)|kidney(8)|large_intestine(6)|upper_aerodigestive_tract(2)|central_nervous_system(2)|urinary_tract(1)|breast(1)	63						CTAGGAACAGCTGTGTAGaaa	0.313										HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)			24	85	---	---	---	---	PASS
PLAA	9373	broad.mit.edu	37	9	26928209	26928209	+	Missense_Mutation	SNP	C	A	A			TCGA-18-4721-01A-01D-1441-08	TCGA-18-4721-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	d2ab2555-7288-47a4-a80c-bf62d65b67b8	f7b631ae-ee98-499b-9d26-dc945e7ac3b8	g.chr9:26928209C>A	uc003zqd.2	-	4	879	c.454G>T	c.(454-456)GCT>TCT	p.A152S	PLAA_uc003zqe.2_Missense_Mutation_p.A152S	NM_001031689	NP_001026859	Q9Y263	PLAP_HUMAN	phospholipase A2-activating protein	152	WD 4.				phospholipid metabolic process|signal transduction		phospholipase A2 activator activity				0		all_neural(3;3.53e-10)|Glioma(3;2.71e-09)		Lung(218;1.32e-05)|LUSC - Lung squamous cell carcinoma(38;0.00011)		CACACTGCAGCTGTATGACCC	0.403													30	97	---	---	---	---	PASS
GABBR2	9568	broad.mit.edu	37	9	101304211	101304211	+	Missense_Mutation	SNP	G	A	A			TCGA-18-4721-01A-01D-1441-08	TCGA-18-4721-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	d2ab2555-7288-47a4-a80c-bf62d65b67b8	f7b631ae-ee98-499b-9d26-dc945e7ac3b8	g.chr9:101304211G>A	uc004ays.2	-	3	730	c.574C>T	c.(574-576)CAC>TAC	p.H192Y		NM_005458	NP_005449	O75899	GABR2_HUMAN	G protein-coupled receptor 51 precursor	192	Extracellular (Potential).				negative regulation of adenylate cyclase activity|synaptic transmission	cell junction|integral to plasma membrane|postsynaptic membrane	G-protein coupled receptor activity|GABA-B receptor activity			ovary(2)|skin(2)	4		Acute lymphoblastic leukemia(62;0.0527)			Baclofen(DB00181)	CACTGGTAGTGCTTGAGCAAC	0.532													43	46	---	---	---	---	PASS
COL15A1	1306	broad.mit.edu	37	9	101797433	101797433	+	Missense_Mutation	SNP	C	G	G			TCGA-18-4721-01A-01D-1441-08	TCGA-18-4721-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	d2ab2555-7288-47a4-a80c-bf62d65b67b8	f7b631ae-ee98-499b-9d26-dc945e7ac3b8	g.chr9:101797433C>G	uc004azb.1	+	18	2423	c.2217C>G	c.(2215-2217)TTC>TTG	p.F739L		NM_001855	NP_001846	P39059	COFA1_HUMAN	alpha 1 type XV collagen precursor	739	Nonhelical region 3 (NC3).				angiogenesis|cell differentiation|signal transduction	collagen type XV|extracellular space|integral to membrane	binding			ovary(6)	6		Acute lymphoblastic leukemia(62;0.0562)				GACTTGGATTCGAGGTACTTT	0.512													5	226	---	---	---	---	PASS
IKBKAP	8518	broad.mit.edu	37	9	111656249	111656249	+	Missense_Mutation	SNP	T	C	C			TCGA-18-4721-01A-01D-1441-08	TCGA-18-4721-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	d2ab2555-7288-47a4-a80c-bf62d65b67b8	f7b631ae-ee98-499b-9d26-dc945e7ac3b8	g.chr9:111656249T>C	uc004bdm.3	-	26	3354	c.2834A>G	c.(2833-2835)AAA>AGA	p.K945R	IKBKAP_uc004bdl.2_Missense_Mutation_p.K596R|IKBKAP_uc011lwc.1_Missense_Mutation_p.K831R|IKBKAP_uc010mtq.2_Missense_Mutation_p.K596R|IKBKAP_uc004bdk.2_5'Flank|IKBKAP_uc010mtp.2_5'Flank	NM_003640	NP_003631	O95163	ELP1_HUMAN	inhibitor of kappa light polypeptide gene	945					immune response|protein complex assembly|regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	cytoplasm|DNA-directed RNA polymerase II, holoenzyme|nucleolus|transcription elongation factor complex	phosphorylase kinase regulator activity|protein binding|signal transducer activity			ovary(2)|skin(2)|upper_aerodigestive_tract(1)|breast(1)|kidney(1)	7						GCCAATGGCTTTTTCATATCG	0.274													41	59	---	---	---	---	PASS
KIAA1462	57608	broad.mit.edu	37	10	30318554	30318554	+	Missense_Mutation	SNP	T	C	C			TCGA-18-4721-01A-01D-1441-08	TCGA-18-4721-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	d2ab2555-7288-47a4-a80c-bf62d65b67b8	f7b631ae-ee98-499b-9d26-dc945e7ac3b8	g.chr10:30318554T>C	uc001iux.2	-	2	582	c.523A>G	c.(523-525)ATG>GTG	p.M175V	KIAA1462_uc001iuy.2_Intron|KIAA1462_uc001iuz.2_Missense_Mutation_p.M37V|KIAA1462_uc009xle.1_Missense_Mutation_p.M175V	NM_020848	NP_065899	Q9P266	K1462_HUMAN	hypothetical protein LOC57608	175										ovary(4)	4						GGACCTGACATTCGCAATTCT	0.542													61	195	---	---	---	---	PASS
LRIT1	26103	broad.mit.edu	37	10	85993952	85993952	+	Missense_Mutation	SNP	G	A	A			TCGA-18-4721-01A-01D-1441-08	TCGA-18-4721-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	d2ab2555-7288-47a4-a80c-bf62d65b67b8	f7b631ae-ee98-499b-9d26-dc945e7ac3b8	g.chr10:85993952G>A	uc001kcz.1	-	3	794	c.772C>T	c.(772-774)CCA>TCA	p.P258S		NM_015613	NP_056428	Q9P2V4	LRIT1_HUMAN	retina specific protein PAL	258	Lumenal (Potential).					integral to endoplasmic reticulum membrane					0						GCCACTCCTGGATGGAGCTCT	0.612													11	137	---	---	---	---	PASS
PDE6C	5146	broad.mit.edu	37	10	95380397	95380397	+	Silent	SNP	T	C	C	rs143708538		TCGA-18-4721-01A-01D-1441-08	TCGA-18-4721-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	d2ab2555-7288-47a4-a80c-bf62d65b67b8	f7b631ae-ee98-499b-9d26-dc945e7ac3b8	g.chr10:95380397T>C	uc001kiu.3	+	2	627	c.489T>C	c.(487-489)CAT>CAC	p.H163H		NM_006204	NP_006195	P51160	PDE6C_HUMAN	phosphodiesterase 6C	163	GAF 1.				visual perception	plasma membrane	3',5'-cyclic-GMP phosphodiesterase activity|cGMP binding|metal ion binding			ovary(2)|kidney(1)|skin(1)	4		Colorectal(252;0.123)				AGAACAGCCATTTTTCTGACT	0.443													6	111	---	---	---	---	PASS
OR51T1	401665	broad.mit.edu	37	11	4903941	4903941	+	Missense_Mutation	SNP	C	A	A			TCGA-18-4721-01A-01D-1441-08	TCGA-18-4721-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	d2ab2555-7288-47a4-a80c-bf62d65b67b8	f7b631ae-ee98-499b-9d26-dc945e7ac3b8	g.chr11:4903941C>A	uc010qyp.1	+	1	893	c.893C>A	c.(892-894)CCA>CAA	p.P298Q		NM_001004759	NP_001004759	Q8NGJ9	O51T1_HUMAN	olfactory receptor, family 51, subfamily T,	271	Extracellular (Potential).				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)		CACTCCACCCCAAGGGTGCTC	0.493													14	107	---	---	---	---	PASS
OR52A4	390053	broad.mit.edu	37	11	5142492	5142492	+	Nonsense_Mutation	SNP	C	T	T			TCGA-18-4721-01A-01D-1441-08	TCGA-18-4721-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	d2ab2555-7288-47a4-a80c-bf62d65b67b8	f7b631ae-ee98-499b-9d26-dc945e7ac3b8	g.chr11:5142492C>T	uc001lzz.1	-	1	317	c.317G>A	c.(316-318)TGG>TAG	p.W106*	OR52A4_uc001maa.2_RNA	NM_001005222	NP_001005222			olfactory receptor, family 52, subfamily A,											ovary(2)	2		Medulloblastoma(188;0.0049)|all_neural(188;0.0442)|Breast(177;0.0675)		Epithelial(150;1.7e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)|LUSC - Lung squamous cell carcinoma(625;0.2)		GTGGATGAGCCACATCTGAAA	0.453													12	50	---	---	---	---	PASS
EIF4G2	1982	broad.mit.edu	37	11	10821167	10821167	+	Silent	SNP	T	C	C			TCGA-18-4721-01A-01D-1441-08	TCGA-18-4721-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	d2ab2555-7288-47a4-a80c-bf62d65b67b8	f7b631ae-ee98-499b-9d26-dc945e7ac3b8	g.chr11:10821167T>C	uc001mjc.2	-	19	2673	c.2256A>G	c.(2254-2256)AAA>AAG	p.K752K	EIF4G2_uc001mjb.2_Silent_p.K546K|EIF4G2_uc009ygf.2_Silent_p.K546K|EIF4G2_uc001mjd.2_Silent_p.K714K	NM_001418	NP_001409	P78344	IF4G2_HUMAN	eukaryotic translation initiation factor 4	752	W2.				cell cycle arrest|cell death|regulation of translational initiation|RNA metabolic process	eukaryotic translation initiation factor 4F complex	protein binding|translation initiation factor activity			ovary(1)|central_nervous_system(1)	2				all cancers(16;2.8e-07)|Epithelial(150;4.18e-07)|BRCA - Breast invasive adenocarcinoma(625;0.111)		CTTTAATCCATTTATATATGG	0.368													43	121	---	---	---	---	PASS
ABCC8	6833	broad.mit.edu	37	11	17426064	17426064	+	Silent	SNP	C	T	T	rs144207158		TCGA-18-4721-01A-01D-1441-08	TCGA-18-4721-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	d2ab2555-7288-47a4-a80c-bf62d65b67b8	f7b631ae-ee98-499b-9d26-dc945e7ac3b8	g.chr11:17426064C>T	uc001mnc.2	-	28	3678	c.3552G>A	c.(3550-3552)GCG>GCA	p.A1184A		NM_000352	NP_000343	Q09428	ABCC8_HUMAN	ATP-binding cassette, sub-family C, member 8	1184	ABC transmembrane type-1 2.|Cytoplasmic (By similarity).				carbohydrate metabolic process|energy reserve metabolic process	integral to membrane	ATP binding|ATPase activity, coupled to transmembrane movement of substances|potassium ion transmembrane transporter activity|sulfonylurea receptor activity			ovary(1)	1				READ - Rectum adenocarcinoma(2;0.0325)|Colorectal(2;0.1)	Adenosine triphosphate(DB00171)|Glibenclamide(DB01016)|Gliclazide(DB01120)|Mitiglinide(DB01252)|Nateglinide(DB00731)|Repaglinide(DB00912)	ATCACCTGGACGCCACCCGGA	0.562													12	150	---	---	---	---	PASS
ANO5	203859	broad.mit.edu	37	11	22277035	22277035	+	Missense_Mutation	SNP	G	T	T			TCGA-18-4721-01A-01D-1441-08	TCGA-18-4721-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	d2ab2555-7288-47a4-a80c-bf62d65b67b8	f7b631ae-ee98-499b-9d26-dc945e7ac3b8	g.chr11:22277035G>T	uc001mqi.2	+	13	1616	c.1299G>T	c.(1297-1299)ATG>ATT	p.M433I	ANO5_uc001mqj.2_Missense_Mutation_p.M432I	NM_213599	NP_998764	Q75V66	ANO5_HUMAN	anoctamin 5 isoform a	433	Cytoplasmic (Potential).					chloride channel complex|endoplasmic reticulum membrane	chloride channel activity			central_nervous_system(3)|ovary(1)	4						TTGAAGCTATGTGTAAACACA	0.428													58	199	---	---	---	---	PASS
SLC17A6	57084	broad.mit.edu	37	11	22384297	22384297	+	Missense_Mutation	SNP	G	A	A			TCGA-18-4721-01A-01D-1441-08	TCGA-18-4721-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	d2ab2555-7288-47a4-a80c-bf62d65b67b8	f7b631ae-ee98-499b-9d26-dc945e7ac3b8	g.chr11:22384297G>A	uc001mqk.2	+	6	1087	c.674G>A	c.(673-675)GGA>GAA	p.G225E		NM_020346	NP_065079	Q9P2U8	VGLU2_HUMAN	solute carrier family 17 (sodium-dependent	225	Helical; (Potential).				sodium ion transport	cell junction|integral to membrane|synaptic vesicle membrane|synaptosome	L-glutamate transmembrane transporter activity|symporter activity			ovary(3)|breast(1)	4						TCCTATGCCGGAGCTGTGATT	0.398													28	90	---	---	---	---	PASS
OR4C16	219428	broad.mit.edu	37	11	55340171	55340171	+	Missense_Mutation	SNP	A	C	C			TCGA-18-4721-01A-01D-1441-08	TCGA-18-4721-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	d2ab2555-7288-47a4-a80c-bf62d65b67b8	f7b631ae-ee98-499b-9d26-dc945e7ac3b8	g.chr11:55340171A>C	uc010rih.1	+	1	568	c.568A>C	c.(568-570)ACC>CCC	p.T190P		NM_001004701	NP_001004701	Q8NGL9	OR4CG_HUMAN	olfactory receptor, family 4, subfamily C,	190	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)|skin(1)	2		all_epithelial(135;0.0748)				CTGTTCAGAAACCTATGTGGT	0.433													34	148	---	---	---	---	PASS
OR4P4	81300	broad.mit.edu	37	11	55406404	55406404	+	Missense_Mutation	SNP	C	A	A			TCGA-18-4721-01A-01D-1441-08	TCGA-18-4721-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	d2ab2555-7288-47a4-a80c-bf62d65b67b8	f7b631ae-ee98-499b-9d26-dc945e7ac3b8	g.chr11:55406404C>A	uc010rij.1	+	1	571	c.571C>A	c.(571-573)CAC>AAC	p.H191N		NM_001004124	NP_001004124	Q8NGL7	OR4P4_HUMAN	olfactory receptor, family 4, subfamily P,	191	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			central_nervous_system(1)	1						TTCTAATATACACATGATAGG	0.358													31	48	---	---	---	---	PASS
OR4S2	219431	broad.mit.edu	37	11	55418601	55418601	+	Silent	SNP	C	G	G			TCGA-18-4721-01A-01D-1441-08	TCGA-18-4721-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	d2ab2555-7288-47a4-a80c-bf62d65b67b8	f7b631ae-ee98-499b-9d26-dc945e7ac3b8	g.chr11:55418601C>G	uc001nhs.1	+	1	222	c.222C>G	c.(220-222)GTC>GTG	p.V74V		NM_001004059	NP_001004059	Q8NH73	OR4S2_HUMAN	olfactory receptor, family 4, subfamily S,	74	Helical; Name=2; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			skin(2)|ovary(1)	3		all_epithelial(135;0.0748)				ACTCTTCAGTCACAGCTCCCA	0.428													76	110	---	---	---	---	PASS
SPRYD5	84767	broad.mit.edu	37	11	55657502	55657502	+	Silent	SNP	C	A	A			TCGA-18-4721-01A-01D-1441-08	TCGA-18-4721-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	d2ab2555-7288-47a4-a80c-bf62d65b67b8	f7b631ae-ee98-499b-9d26-dc945e7ac3b8	g.chr11:55657502C>A	uc010rip.1	+	6	938	c.846C>A	c.(844-846)CTC>CTA	p.L282L	SPRYD5_uc010riq.1_Silent_p.L139L	NM_032681	NP_116070	Q9BSJ1	SPRY5_HUMAN	SPRY domain containing 5	282	B30.2/SPRY.					intracellular	zinc ion binding				0		all_epithelial(135;0.226)				TGGACAGCCTCAGTGGATTCA	0.493													16	70	---	---	---	---	PASS
OR5AS1	219447	broad.mit.edu	37	11	55798382	55798382	+	Missense_Mutation	SNP	C	T	T			TCGA-18-4721-01A-01D-1441-08	TCGA-18-4721-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	d2ab2555-7288-47a4-a80c-bf62d65b67b8	f7b631ae-ee98-499b-9d26-dc945e7ac3b8	g.chr11:55798382C>T	uc010riw.1	+	1	488	c.488C>T	c.(487-489)ACA>ATA	p.T163I		NM_001001921	NP_001001921	Q8N127	O5AS1_HUMAN	olfactory receptor, family 5, subfamily AS,	163	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(3)|liver(1)|skin(1)	5	Esophageal squamous(21;0.00693)					GTGTGCCTCACATTCAGGCTG	0.433													52	281	---	---	---	---	PASS
OR5B21	219968	broad.mit.edu	37	11	58275211	58275211	+	Missense_Mutation	SNP	G	A	A	rs148173637		TCGA-18-4721-01A-01D-1441-08	TCGA-18-4721-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	d2ab2555-7288-47a4-a80c-bf62d65b67b8	f7b631ae-ee98-499b-9d26-dc945e7ac3b8	g.chr11:58275211G>A	uc010rki.1	-	1	368	c.368C>T	c.(367-369)GCG>GTG	p.A123V		NM_001005218	NP_001005218	A6NL26	OR5BL_HUMAN	olfactory receptor, family 5, subfamily B,	123	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(3)	3	Esophageal squamous(5;0.0027)	Breast(21;0.0778)				CCTACATACCGCTGCATGGCG	0.527													12	54	---	---	---	---	PASS
CD5	921	broad.mit.edu	37	11	60885660	60885660	+	Silent	SNP	G	A	A	rs141935047		TCGA-18-4721-01A-01D-1441-08	TCGA-18-4721-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	d2ab2555-7288-47a4-a80c-bf62d65b67b8	f7b631ae-ee98-499b-9d26-dc945e7ac3b8	g.chr11:60885660G>A	uc009ynk.2	+	3	211	c.108G>A	c.(106-108)AGG>AGA	p.R36R		NM_014207	NP_055022	P06127	CD5_HUMAN	CD5 molecule precursor	36	Extracellular (Potential).|SRCR 1.				cell proliferation|cell recognition	integral to plasma membrane	scavenger receptor activity			ovary(1)	1		all_lung(304;5.94e-05)|Lung NSC(402;7.26e-05)		BRCA - Breast invasive adenocarcinoma(625;0.000946)|Lung(977;0.0086)|LUSC - Lung squamous cell carcinoma(625;0.0528)		TCCAGGCAAGGCTCACCCGTT	0.642													38	132	---	---	---	---	PASS
TUT1	64852	broad.mit.edu	37	11	62342847	62342847	+	Missense_Mutation	SNP	G	T	T			TCGA-18-4721-01A-01D-1441-08	TCGA-18-4721-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	d2ab2555-7288-47a4-a80c-bf62d65b67b8	f7b631ae-ee98-499b-9d26-dc945e7ac3b8	g.chr11:62342847G>T	uc001nto.2	-	9	2496	c.2458C>A	c.(2458-2460)CGT>AGT	p.R820S	EEF1G_uc001ntm.1_5'Flank|EEF1G_uc010rlw.1_5'Flank|EEF1G_uc001ntn.1_5'Flank|TUT1_uc001ntp.1_Missense_Mutation_p.R316S	NM_022830	NP_073741	Q9H6E5	STPAP_HUMAN	terminal uridylyl transferase 1, U6	782					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						AAGCGTCTACGGGCTCGCCGC	0.667													23	100	---	---	---	---	PASS
LGALS12	85329	broad.mit.edu	37	11	63277350	63277350	+	Missense_Mutation	SNP	T	C	C	rs80310877		TCGA-18-4721-01A-01D-1441-08	TCGA-18-4721-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	d2ab2555-7288-47a4-a80c-bf62d65b67b8	f7b631ae-ee98-499b-9d26-dc945e7ac3b8	g.chr11:63277350T>C	uc001nxa.2	+	4	880	c.539T>C	c.(538-540)GTT>GCT	p.V180A	LGALS12_uc001nxb.2_Missense_Mutation_p.V180A|LGALS12_uc001nxc.2_Missense_Mutation_p.V181A|LGALS12_uc001nxd.2_Missense_Mutation_p.V119A|LGALS12_uc001nxe.2_Missense_Mutation_p.V119A|LGALS12_uc009yot.2_Missense_Mutation_p.V140A	NM_033101	NP_149092	Q96DT0	LEG12_HUMAN	lectin, galactoside-binding, soluble, 12 isoform	180	Galectin 1.				apoptosis|induction of apoptosis by intracellular signals	nucleus	lactose binding			ovary(2)	2						GTAGAGGCTGTTGGATTCCTG	0.552													9	43	---	---	---	---	PASS
CDCA5	113130	broad.mit.edu	37	11	64846928	64846928	+	Missense_Mutation	SNP	G	C	C			TCGA-18-4721-01A-01D-1441-08	TCGA-18-4721-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	d2ab2555-7288-47a4-a80c-bf62d65b67b8	f7b631ae-ee98-499b-9d26-dc945e7ac3b8	g.chr11:64846928G>C	uc001ocp.2	-	5	740	c.575C>G	c.(574-576)CCC>CGC	p.P192R		NM_080668	NP_542399	Q96FF9	CDCA5_HUMAN	cell division cycle associated 5	192					cell division|double-strand break repair|G1/S transition of mitotic cell cycle|mitotic chromosome condensation|mitotic metaphase plate congression|mitotic sister chromatid cohesion|regulation of cohesin localization to chromatin	cytoplasm|nuclear chromatin|plasma membrane	chromatin binding|identical protein binding				0						ACAAACCCTGGGGACCTCGGT	0.597													23	90	---	---	---	---	PASS
RSF1	51773	broad.mit.edu	37	11	77412491	77412491	+	Missense_Mutation	SNP	A	G	G			TCGA-18-4721-01A-01D-1441-08	TCGA-18-4721-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	d2ab2555-7288-47a4-a80c-bf62d65b67b8	f7b631ae-ee98-499b-9d26-dc945e7ac3b8	g.chr11:77412491A>G	uc001oyn.2	-	6	1903	c.1783T>C	c.(1783-1785)TTT>CTT	p.F595L	RSF1_uc001oym.2_Missense_Mutation_p.F343L	NM_016578	NP_057662	Q96T23	RSF1_HUMAN	remodeling and spacing factor 1	595					CenH3-containing nucleosome assembly at centromere|negative regulation of DNA binding|negative regulation of transcription, DNA-dependent|nucleosome positioning|positive regulation of transcription, DNA-dependent|positive regulation of viral transcription|transcription initiation, DNA-dependent	RSF complex	histone binding|protein binding|zinc ion binding			ovary(2)|central_nervous_system(2)	4	all_cancers(14;1.54e-17)|all_epithelial(13;4.06e-20)|Ovarian(111;0.152)		Epithelial(5;3e-50)|all cancers(3;6.37e-47)|BRCA - Breast invasive adenocarcinoma(5;9.82e-31)			TTATCAAGAAAAGTCTTTTTG	0.428													54	204	---	---	---	---	PASS
FAT3	120114	broad.mit.edu	37	11	92086219	92086219	+	Missense_Mutation	SNP	T	C	C			TCGA-18-4721-01A-01D-1441-08	TCGA-18-4721-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	d2ab2555-7288-47a4-a80c-bf62d65b67b8	f7b631ae-ee98-499b-9d26-dc945e7ac3b8	g.chr11:92086219T>C	uc001pdj.3	+	1	958	c.941T>C	c.(940-942)CTG>CCG	p.L314P		NM_001008781	NP_001008781	Q8TDW7	FAT3_HUMAN	FAT tumor suppressor homolog 3	314	Cadherin 3.|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)				CAGTTCTTCCTGGCTAAGGAA	0.448										TCGA Ovarian(4;0.039)			12	35	---	---	---	---	PASS
FAT3	120114	broad.mit.edu	37	11	92533104	92533104	+	Missense_Mutation	SNP	G	T	T			TCGA-18-4721-01A-01D-1441-08	TCGA-18-4721-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	d2ab2555-7288-47a4-a80c-bf62d65b67b8	f7b631ae-ee98-499b-9d26-dc945e7ac3b8	g.chr11:92533104G>T	uc001pdj.3	+	9	6942	c.6925G>T	c.(6925-6927)GTT>TTT	p.V2309F		NM_001008781	NP_001008781	Q8TDW7	FAT3_HUMAN	FAT tumor suppressor homolog 3	2309	Cadherin 21.|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)				TGTTTTACAAGTTGTCTCTAT	0.363										TCGA Ovarian(4;0.039)			7	25	---	---	---	---	PASS
HTR3A	3359	broad.mit.edu	37	11	113860284	113860284	+	Silent	SNP	G	T	T			TCGA-18-4721-01A-01D-1441-08	TCGA-18-4721-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	d2ab2555-7288-47a4-a80c-bf62d65b67b8	f7b631ae-ee98-499b-9d26-dc945e7ac3b8	g.chr11:113860284G>T	uc010rxb.1	+	8	1583	c.1350G>T	c.(1348-1350)TCG>TCT	p.S450S	HTR3A_uc010rxa.1_Silent_p.S418S|HTR3A_uc009yyx.2_RNA|HTR3A_uc010rxc.1_Silent_p.S397S	NM_213621	NP_998786	P46098	5HT3A_HUMAN	5-hydroxytryptamine (serotonin) receptor 3A	412	Cytoplasmic (Potential).				digestion|synaptic transmission	cell junction|integral to plasma membrane|postsynaptic membrane	serotonin binding|serotonin receptor activity|serotonin-activated cation-selective channel activity				0		all_cancers(61;2.31e-17)|all_epithelial(67;2.1e-10)|all_hematologic(158;4.64e-05)|Melanoma(852;0.000312)|Acute lymphoblastic leukemia(157;0.000967)|Breast(348;0.0101)|all_neural(223;0.0281)|Prostate(24;0.0294)|Medulloblastoma(222;0.0425)		BRCA - Breast invasive adenocarcinoma(274;2.71e-06)|Epithelial(105;2.58e-05)|all cancers(92;0.000238)|OV - Ovarian serous cystadenocarcinoma(223;0.191)	Alosetron(DB00969)|Chloroprocaine(DB01161)|Cisapride(DB00604)|Dolasetron(DB00757)|Granisetron(DB00889)|Mirtazapine(DB00370)|Ondansetron(DB00904)|Palonosetron(DB00377)|Procaine(DB00721)|Tubocurarine(DB01199)	GGGAGGCCTCGCTGGCGGTGT	0.652													37	132	---	---	---	---	PASS
CRTAM	56253	broad.mit.edu	37	11	122720812	122720812	+	Missense_Mutation	SNP	T	A	A			TCGA-18-4721-01A-01D-1441-08	TCGA-18-4721-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	d2ab2555-7288-47a4-a80c-bf62d65b67b8	f7b631ae-ee98-499b-9d26-dc945e7ac3b8	g.chr11:122720812T>A	uc001pyj.2	+	2	83	c.83T>A	c.(82-84)GTG>GAG	p.V28E		NM_019604	NP_062550	O95727	CRTAM_HUMAN	class-I MHC-restricted T cell associated	28	Ig-like V-type.|Extracellular (Potential).				cell recognition|detection of tumor cell|positive regulation of cytokine secretion|positive regulation of natural killer cell mediated cytotoxicity directed against tumor cell target	integral to membrane|plasma membrane	receptor binding			ovary(1)	1		Breast(109;0.00249)|Lung NSC(97;0.0177)|all_lung(97;0.0179)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;5.28e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0308)		ACCATCACCGTGGAGGAAGGC	0.522													12	72	---	---	---	---	PASS
OR8G2	26492	broad.mit.edu	37	11	124095817	124095817	+	Nonsense_Mutation	SNP	C	A	A			TCGA-18-4721-01A-01D-1441-08	TCGA-18-4721-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	d2ab2555-7288-47a4-a80c-bf62d65b67b8	f7b631ae-ee98-499b-9d26-dc945e7ac3b8	g.chr11:124095817C>A	uc010saf.1	+	1	420	c.420C>A	c.(418-420)TGC>TGA	p.C140*		NM_001007249	NP_001007250	Q15614	OR8G2_HUMAN	olfactory receptor, family 8, subfamily G,	140						integral to membrane	olfactory receptor activity				0		Breast(109;0.0157)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.22)		BRCA - Breast invasive adenocarcinoma(274;4.91e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0528)		TTGCCATCTGCAGCCCCTTGC	0.463													64	255	---	---	---	---	PASS
PEX5	5830	broad.mit.edu	37	12	7362674	7362674	+	Missense_Mutation	SNP	C	T	T			TCGA-18-4721-01A-01D-1441-08	TCGA-18-4721-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	d2ab2555-7288-47a4-a80c-bf62d65b67b8	f7b631ae-ee98-499b-9d26-dc945e7ac3b8	g.chr12:7362674C>T	uc009zfu.1	+	17	2355	c.1775C>T	c.(1774-1776)CCC>CTC	p.P592L	PEX5_uc001qsw.2_Missense_Mutation_p.P592L|PEX5_uc010sgc.1_Missense_Mutation_p.P607L|PEX5_uc001qsu.2_Missense_Mutation_p.P555L|PEX5_uc010sgd.1_Missense_Mutation_p.P613L|PEX5_uc001qsv.2_Missense_Mutation_p.P584L	NM_001131026	NP_001124498	P50542	PEX5_HUMAN	peroxisomal biogenesis factor 5 isoform d	592					protein import into peroxisome matrix, translocation|protein targeting to peroxisome|protein tetramerization|protein transport	cytosol|peroxisomal matrix|peroxisomal membrane	peroxisome matrix targeting signal-1 binding|protein C-terminus binding|protein N-terminus binding			ovary(1)	1						AGCCGGGGCCCCCGGGGTGAA	0.572													13	84	---	---	---	---	PASS
PRB2	653247	broad.mit.edu	37	12	11546368	11546368	+	Missense_Mutation	SNP	G	A	A			TCGA-18-4721-01A-01D-1441-08	TCGA-18-4721-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	d2ab2555-7288-47a4-a80c-bf62d65b67b8	f7b631ae-ee98-499b-9d26-dc945e7ac3b8	g.chr12:11546368G>A	uc010shk.1	-	3	679	c.644C>T	c.(643-645)CCC>CTC	p.P215L		NM_006248	NP_006239			proline-rich protein BstNI subfamily 2												0		all_cancers(2;0.00558)|Acute lymphoblastic leukemia(2;3.94e-11)|all_hematologic(2;3.6e-09)	OV - Ovarian serous cystadenocarcinoma(49;0.185)			TGGAGGTGGGGGACCTTGAGG	0.612													57	369	---	---	---	---	PASS
BCL2L14	79370	broad.mit.edu	37	12	12232614	12232614	+	Silent	SNP	G	T	T			TCGA-18-4721-01A-01D-1441-08	TCGA-18-4721-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	d2ab2555-7288-47a4-a80c-bf62d65b67b8	f7b631ae-ee98-499b-9d26-dc945e7ac3b8	g.chr12:12232614G>T	uc001rac.2	+	2	576	c.375G>T	c.(373-375)TCG>TCT	p.S125S	ETV6_uc001raa.1_Intron|BCL2L14_uc001raf.1_RNA|BCL2L14_uc001rad.2_Silent_p.S125S|BCL2L14_uc001rae.2_Silent_p.S125S	NM_138723	NP_620049	Q9BZR8	B2L14_HUMAN	BCL2-like 14 isoform 1	125					apoptosis|regulation of apoptosis	cytosol|endomembrane system|intracellular organelle|membrane	protein binding			skin(1)	1		Prostate(47;0.0872)		BRCA - Breast invasive adenocarcinoma(232;0.154)		ACCAAGATTCGCACAGCCAGC	0.512													24	211	---	---	---	---	PASS
WBP11	51729	broad.mit.edu	37	12	14949741	14949741	+	Silent	SNP	C	T	T			TCGA-18-4721-01A-01D-1441-08	TCGA-18-4721-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	d2ab2555-7288-47a4-a80c-bf62d65b67b8	f7b631ae-ee98-499b-9d26-dc945e7ac3b8	g.chr12:14949741C>T	uc001rci.2	-	5	548	c.387G>A	c.(385-387)AAG>AAA	p.K129K		NM_016312	NP_057396	Q9Y2W2	WBP11_HUMAN	WW domain binding protein 11	129	Potential.				mRNA processing|RNA splicing|rRNA processing	cytoplasm	single-stranded DNA binding|WW domain binding			ovary(1)|lung(1)	2						CCTTGATTACCTTGACAGCAT	0.209													39	90	---	---	---	---	PASS
GALNT6	11226	broad.mit.edu	37	12	51759273	51759273	+	Missense_Mutation	SNP	G	A	A			TCGA-18-4721-01A-01D-1441-08	TCGA-18-4721-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	d2ab2555-7288-47a4-a80c-bf62d65b67b8	f7b631ae-ee98-499b-9d26-dc945e7ac3b8	g.chr12:51759273G>A	uc001ryk.2	-	4	980	c.755C>T	c.(754-756)GCC>GTC	p.A252V	GALNT6_uc009zma.1_RNA|GALNT6_uc001ryl.1_Missense_Mutation_p.A252V	NM_007210	NP_009141	Q8NCL4	GALT6_HUMAN	polypeptide N-acetylgalactosaminyltransferase 6	252	Catalytic subdomain A.|Lumenal (Potential).				protein O-linked glycosylation	Golgi membrane|integral to membrane|perinuclear region of cytoplasm	polypeptide N-acetylgalactosaminyltransferase activity|sugar binding			ovary(2)	2						CAGCAGCCGGGCGGTGATCAG	0.657													25	87	---	---	---	---	PASS
NR4A1	3164	broad.mit.edu	37	12	52452502	52452502	+	Missense_Mutation	SNP	T	G	G			TCGA-18-4721-01A-01D-1441-08	TCGA-18-4721-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	d2ab2555-7288-47a4-a80c-bf62d65b67b8	f7b631ae-ee98-499b-9d26-dc945e7ac3b8	g.chr12:52452502T>G	uc001rzs.2	+	8	1885	c.1571T>G	c.(1570-1572)GTG>GGG	p.V524G	NR4A1_uc010sno.1_Missense_Mutation_p.V537G|NR4A1_uc001rzt.2_Missense_Mutation_p.V524G|NR4A1_uc009zmc.2_Missense_Mutation_p.W138G	NM_002135	NP_002126	P22736	NR4A1_HUMAN	nuclear receptor subfamily 4, group A, member 1	524					nerve growth factor receptor signaling pathway|phosphatidylinositol-mediated signaling|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor		steroid hormone receptor activity|zinc ion binding				0				BRCA - Breast invasive adenocarcinoma(357;0.0967)		CCGCGGCGGGTGGAGGAGCTG	0.682													5	7	---	---	---	---	PASS
KRT2	3849	broad.mit.edu	37	12	53045439	53045439	+	Missense_Mutation	SNP	A	G	G			TCGA-18-4721-01A-01D-1441-08	TCGA-18-4721-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	d2ab2555-7288-47a4-a80c-bf62d65b67b8	f7b631ae-ee98-499b-9d26-dc945e7ac3b8	g.chr12:53045439A>G	uc001sat.2	-	1	521	c.488T>C	c.(487-489)CTC>CCC	p.L163P		NM_000423	NP_000414	P35908	K22E_HUMAN	keratin 2	163	Head.				keratinization|keratinocyte activation|keratinocyte migration|keratinocyte proliferation	Golgi apparatus|keratin filament	protein binding|structural constituent of cytoskeleton			ovary(2)	2				BRCA - Breast invasive adenocarcinoma(357;0.19)		TTTCACGTTGAGAGGCTGCAG	0.488													42	140	---	---	---	---	PASS
TARBP2	6895	broad.mit.edu	37	12	53899892	53899892	+	Missense_Mutation	SNP	G	A	A	rs140535249		TCGA-18-4721-01A-01D-1441-08	TCGA-18-4721-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	d2ab2555-7288-47a4-a80c-bf62d65b67b8	f7b631ae-ee98-499b-9d26-dc945e7ac3b8	g.chr12:53899892G>A	uc001sdo.2	+	9	1549	c.1061G>A	c.(1060-1062)CGT>CAT	p.R354H	TARBP2_uc001sdp.2_Missense_Mutation_p.R333H|TARBP2_uc001sdq.2_Missense_Mutation_p.R210H|TARBP2_uc001sdr.2_Missense_Mutation_p.R210H|TARBP2_uc001sds.2_3'UTR|TARBP2_uc001sdt.2_Missense_Mutation_p.R333H|TARBP2_uc001sdu.2_Missense_Mutation_p.R210H|TARBP2_uc001sdv.2_RNA	NM_134323	NP_599150	Q15633	TRBP2_HUMAN	TAR RNA binding protein 2 isoform a	354	Sufficient for interaction with DICER1.|DRBM 3.|Sufficient for interaction with PRKRA.				miRNA loading onto RISC involved in gene silencing by miRNA|negative regulation of defense response to virus by host|negative regulation of protein kinase activity|positive regulation of viral genome replication|pre-miRNA processing|production of siRNA involved in RNA interference|regulation of transcription from RNA polymerase II promoter|regulation of translation|regulation of viral transcription|targeting of mRNA for destruction involved in RNA interference	cytosol|nucleus|perinuclear region of cytoplasm|RNA-induced silencing complex	double-stranded RNA binding|protein homodimerization activity|siRNA binding			central_nervous_system(1)	1						GCTGCCCGCCGTGCCCTGCAG	0.632													8	34	---	---	---	---	PASS
WIF1	11197	broad.mit.edu	37	12	65449838	65449838	+	Missense_Mutation	SNP	C	A	A			TCGA-18-4721-01A-01D-1441-08	TCGA-18-4721-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	d2ab2555-7288-47a4-a80c-bf62d65b67b8	f7b631ae-ee98-499b-9d26-dc945e7ac3b8	g.chr12:65449838C>A	uc001ssk.2	-	8	1040	c.895G>T	c.(895-897)GGT>TGT	p.G299C		NM_007191	NP_009122	Q9Y5W5	WIF1_HUMAN	WNT inhibitory factor 1 precursor	299	EGF-like 4.				multicellular organismal development|Wnt receptor signaling pathway	extracellular region	protein tyrosine kinase activity			ovary(2)|lung(1)|skin(1)	4			LUAD - Lung adenocarcinoma(6;0.0234)|LUSC - Lung squamous cell carcinoma(43;0.0975)	GBM - Glioblastoma multiforme(28;0.0231)		CCCTGGTAACCTTTGGAACAC	0.438			T	HMGA2	pleomorphic salivary gland adenoma								18	101	---	---	---	---	PASS
SLC6A15	55117	broad.mit.edu	37	12	85285815	85285815	+	Missense_Mutation	SNP	C	T	T			TCGA-18-4721-01A-01D-1441-08	TCGA-18-4721-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	d2ab2555-7288-47a4-a80c-bf62d65b67b8	f7b631ae-ee98-499b-9d26-dc945e7ac3b8	g.chr12:85285815C>T	uc001szv.2	-	2	578	c.85G>A	c.(85-87)GCA>ACA	p.A29T	SLC6A15_uc010sul.1_Intron|SLC6A15_uc001szy.2_Missense_Mutation_p.A29T	NM_182767	NP_877499	Q9H2J7	S6A15_HUMAN	solute carrier family 6, member 15 isoform 1	29	Cytoplasmic (Potential).				cellular nitrogen compound metabolic process|leucine transport|proline transport	integral to plasma membrane	amino acid transmembrane transporter activity|neurotransmitter:sodium symporter activity			pancreas(2)|ovary(1)	3						TCATCAGCTGCGTCTTCATTG	0.398													83	238	---	---	---	---	PASS
MGAT4C	25834	broad.mit.edu	37	12	86374017	86374017	+	Missense_Mutation	SNP	G	T	T			TCGA-18-4721-01A-01D-1441-08	TCGA-18-4721-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	d2ab2555-7288-47a4-a80c-bf62d65b67b8	f7b631ae-ee98-499b-9d26-dc945e7ac3b8	g.chr12:86374017G>T	uc001tai.3	-	8	1737	c.487C>A	c.(487-489)CAT>AAT	p.H163N	MGAT4C_uc001tal.3_Missense_Mutation_p.H163N|MGAT4C_uc001taj.3_Missense_Mutation_p.H163N|MGAT4C_uc001tak.3_Missense_Mutation_p.H163N|MGAT4C_uc010sum.1_Missense_Mutation_p.H187N|MGAT4C_uc001tah.3_Missense_Mutation_p.H163N	NM_013244	NP_037376	Q9UBM8	MGT4C_HUMAN	alpha-1,3-mannosyl-glycoprotein	163	Lumenal (Potential).				post-translational protein modification|protein N-linked glycosylation via asparagine	Golgi membrane|integral to membrane	alpha-1,3-mannosylglycoprotein 4-beta-N-acetylglucosaminyltransferase activity|metal ion binding			ovary(3)	3						GCAATAATATGGTGCGCAAAT	0.403													41	219	---	---	---	---	PASS
MGAT4C	25834	broad.mit.edu	37	12	86374018	86374018	+	Missense_Mutation	SNP	G	T	T			TCGA-18-4721-01A-01D-1441-08	TCGA-18-4721-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	d2ab2555-7288-47a4-a80c-bf62d65b67b8	f7b631ae-ee98-499b-9d26-dc945e7ac3b8	g.chr12:86374018G>T	uc001tai.3	-	8	1736	c.486C>A	c.(484-486)CAC>CAA	p.H162Q	MGAT4C_uc001tal.3_Missense_Mutation_p.H162Q|MGAT4C_uc001taj.3_Missense_Mutation_p.H162Q|MGAT4C_uc001tak.3_Missense_Mutation_p.H162Q|MGAT4C_uc010sum.1_Missense_Mutation_p.H186Q|MGAT4C_uc001tah.3_Missense_Mutation_p.H162Q	NM_013244	NP_037376	Q9UBM8	MGT4C_HUMAN	alpha-1,3-mannosyl-glycoprotein	162	Lumenal (Potential).				post-translational protein modification|protein N-linked glycosylation via asparagine	Golgi membrane|integral to membrane	alpha-1,3-mannosylglycoprotein 4-beta-N-acetylglucosaminyltransferase activity|metal ion binding			ovary(3)	3						CAATAATATGGTGCGCAAATT	0.403													43	219	---	---	---	---	PASS
ARL1	400	broad.mit.edu	37	12	101794928	101794928	+	Nonsense_Mutation	SNP	G	C	C			TCGA-18-4721-01A-01D-1441-08	TCGA-18-4721-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	d2ab2555-7288-47a4-a80c-bf62d65b67b8	f7b631ae-ee98-499b-9d26-dc945e7ac3b8	g.chr12:101794928G>C	uc001tib.2	-	4	397	c.248C>G	c.(247-249)TCA>TGA	p.S83*	ARL1_uc010svn.1_Nonsense_Mutation_p.S37*|ARL1_uc010svo.1_RNA|ARL1_uc001tic.2_Nonsense_Mutation_p.S83*	NM_001177	NP_001168	P40616	ARL1_HUMAN	ADP-ribosylation factor-like 1	83					small GTPase mediated signal transduction	Golgi membrane	enzyme activator activity|GTP binding|GTPase activity|metal ion binding|protein binding			central_nervous_system(1)	1		Lung NSC(355;2.1e-05)|Breast(359;0.00015)|Myeloproliferative disorder(1001;0.163)		GBM - Glioblastoma multiforme(134;1.67e-09)|BRCA - Breast invasive adenocarcinoma(302;0.0125)		ATCTGTGTTTGAATAGTAACA	0.368													24	102	---	---	---	---	PASS
RPL6	6128	broad.mit.edu	37	12	112844596	112844596	+	Silent	SNP	G	A	A			TCGA-18-4721-01A-01D-1441-08	TCGA-18-4721-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	d2ab2555-7288-47a4-a80c-bf62d65b67b8	f7b631ae-ee98-499b-9d26-dc945e7ac3b8	g.chr12:112844596G>A	uc001ttu.2	-	4	664	c.435C>T	c.(433-435)ACC>ACT	p.T145T	RPL6_uc001ttv.2_Silent_p.T145T	NM_001024662	NP_001019833	Q02878	RL6_HUMAN	ribosomal protein L6	145					endocrine pancreas development|regulation of transcription, DNA-dependent|translational elongation|translational termination|viral transcription	cytosolic large ribosomal subunit	DNA binding|RNA binding|structural constituent of ribosome			large_intestine(1)	1						TGGTCCCGGGGGTAATGCTGG	0.562													11	59	---	---	---	---	PASS
CIT	11113	broad.mit.edu	37	12	120172134	120172134	+	Missense_Mutation	SNP	G	C	C			TCGA-18-4721-01A-01D-1441-08	TCGA-18-4721-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	d2ab2555-7288-47a4-a80c-bf62d65b67b8	f7b631ae-ee98-499b-9d26-dc945e7ac3b8	g.chr12:120172134G>C	uc001txi.1	-	25	3112	c.3059C>G	c.(3058-3060)ACC>AGC	p.T1020S	CIT_uc001txh.1_Missense_Mutation_p.T554S|CIT_uc001txj.1_Missense_Mutation_p.T1062S	NM_007174	NP_009105	O14578	CTRO_HUMAN	citron	1020	Potential.				intracellular signal transduction		ATP binding|metal ion binding|protein serine/threonine kinase activity|SH3 domain binding|small GTPase regulator activity			ovary(6)|urinary_tract(1)|lung(1)|breast(1)|skin(1)	10	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)	Myeloproliferative disorder(1001;0.0255)		BRCA - Breast invasive adenocarcinoma(302;0.211)		CTCCAGCATGGTGCACGTGGT	0.522													17	66	---	---	---	---	PASS
CHFR	55743	broad.mit.edu	37	12	133435751	133435751	+	Missense_Mutation	SNP	C	T	T			TCGA-18-4721-01A-01D-1441-08	TCGA-18-4721-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	d2ab2555-7288-47a4-a80c-bf62d65b67b8	f7b631ae-ee98-499b-9d26-dc945e7ac3b8	g.chr12:133435751C>T	uc001ulf.2	-	8	934	c.850G>A	c.(850-852)GTC>ATC	p.V284I	CHFR_uc001ulc.1_RNA|CHFR_uc001ule.2_Missense_Mutation_p.V272I|CHFR_uc010tbs.1_Missense_Mutation_p.V284I|CHFR_uc001uld.2_Missense_Mutation_p.V243I|CHFR_uc010tbt.1_Missense_Mutation_p.V192I	NM_001161344	NP_001154816	Q96EP1	CHFR_HUMAN	checkpoint with forkhead and ring finger domains	284					cell division|mitosis|mitotic cell cycle checkpoint|modification-dependent protein catabolic process|protein polyubiquitination	PML body	nucleotide binding|protein binding|ubiquitin-protein ligase activity|zinc ion binding			skin(1)	1	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_cancers(7;0.00552)|all_epithelial(31;0.226)		OV - Ovarian serous cystadenocarcinoma(86;2.59e-08)|Epithelial(86;6.38e-07)|all cancers(50;1.56e-05)		TCCTCGTGGACGGTTTGGGCA	0.567													10	95	---	---	---	---	PASS
MTUS2	23281	broad.mit.edu	37	13	29600302	29600302	+	Silent	SNP	T	C	C			TCGA-18-4721-01A-01D-1441-08	TCGA-18-4721-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	d2ab2555-7288-47a4-a80c-bf62d65b67b8	f7b631ae-ee98-499b-9d26-dc945e7ac3b8	g.chr13:29600302T>C	uc001usl.3	+	1	1555	c.1497T>C	c.(1495-1497)CCT>CCC	p.P499P		NM_001033602	NP_001028774	Q5JR59	MTUS2_HUMAN	hypothetical protein LOC23281 isoform a	489						cytoplasm|microtubule	microtubule binding|protein homodimerization activity				0						CCCTGGACCCTCAAAGTGGCC	0.498													3	76	---	---	---	---	PASS
LCP1	3936	broad.mit.edu	37	13	46730657	46730657	+	Missense_Mutation	SNP	T	C	C			TCGA-18-4721-01A-01D-1441-08	TCGA-18-4721-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	d2ab2555-7288-47a4-a80c-bf62d65b67b8	f7b631ae-ee98-499b-9d26-dc945e7ac3b8	g.chr13:46730657T>C	uc001vaz.3	-	5	533	c.407A>G	c.(406-408)AAT>AGT	p.N136S	LCP1_uc001vba.3_Missense_Mutation_p.N136S	NM_002298	NP_002289	P13796	PLSL_HUMAN	L-plastin	136	Actin-binding 1.|CH 1.				regulation of intracellular protein transport|T cell activation involved in immune response	cell junction|cytosol|ruffle membrane	calcium ion binding			lung(4)|ovary(3)	7		Lung NSC(96;1.27e-05)|Breast(56;8.04e-05)|Prostate(109;0.00217)|Hepatocellular(98;0.0207)|Lung SC(185;0.0262)	KIRC - Kidney renal clear cell carcinoma(16;0.234)	GBM - Glioblastoma multiforme(144;5.39e-05)		ATCAGGATCATTTTCCAGGGC	0.368			T	BCL6	NHL 								40	145	---	---	---	---	PASS
LECT1	11061	broad.mit.edu	37	13	53307423	53307423	+	Silent	SNP	C	T	T			TCGA-18-4721-01A-01D-1441-08	TCGA-18-4721-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	d2ab2555-7288-47a4-a80c-bf62d65b67b8	f7b631ae-ee98-499b-9d26-dc945e7ac3b8	g.chr13:53307423C>T	uc001vhf.2	-	3	396	c.285G>A	c.(283-285)GGG>GGA	p.G95G	LECT1_uc001vhg.2_Silent_p.G95G|LECT1_uc001vhh.2_Silent_p.G122G	NM_007015	NP_008946	O75829	LECT1_HUMAN	leukocyte cell derived chemotaxin 1 isoform 1	95					cartilage development|proteoglycan metabolic process	endomembrane system|extracellular region|integral to membrane				ovary(2)	2		Lung NSC(96;0.00212)|Breast(56;0.00235)|Hepatocellular(98;0.065)|Prostate(109;0.0771)|all_neural(104;0.173)		GBM - Glioblastoma multiforme(99;3.38e-08)		CCAAGTTGTTCCCAGCGTCTA	0.363													24	161	---	---	---	---	PASS
OR6S1	341799	broad.mit.edu	37	14	21109802	21109802	+	Missense_Mutation	SNP	C	G	G			TCGA-18-4721-01A-01D-1441-08	TCGA-18-4721-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	d2ab2555-7288-47a4-a80c-bf62d65b67b8	f7b631ae-ee98-499b-9d26-dc945e7ac3b8	g.chr14:21109802C>G	uc001vxv.1	-	1	49	c.49G>C	c.(49-51)GCA>CCA	p.A17P		NM_001001968	NP_001001968	Q8NH40	OR6S1_HUMAN	olfactory receptor, family 6, subfamily S,	17	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)|skin(1)	2	all_cancers(95;0.00304)		Epithelial(56;1.23e-06)|all cancers(55;1.01e-05)	GBM - Glioblastoma multiforme(265;0.0135)		GGGAGCCCTGCCAGGACGAAC	0.458													52	257	---	---	---	---	PASS
RPGRIP1	57096	broad.mit.edu	37	14	21794322	21794322	+	Missense_Mutation	SNP	A	T	T			TCGA-18-4721-01A-01D-1441-08	TCGA-18-4721-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	d2ab2555-7288-47a4-a80c-bf62d65b67b8	f7b631ae-ee98-499b-9d26-dc945e7ac3b8	g.chr14:21794322A>T	uc001wag.2	+	16	2700	c.2700A>T	c.(2698-2700)GAA>GAT	p.E900D	RPGRIP1_uc001wah.2_Missense_Mutation_p.E542D|RPGRIP1_uc001wai.2_Intron|RPGRIP1_uc001wak.2_Missense_Mutation_p.E375D|RPGRIP1_uc010aim.2_Missense_Mutation_p.E283D|RPGRIP1_uc001wal.2_Missense_Mutation_p.E259D|RPGRIP1_uc001wam.2_Missense_Mutation_p.E217D	NM_020366	NP_065099	Q96KN7	RPGR1_HUMAN	retinitis pigmentosa GTPase regulator	900					response to stimulus|visual perception	cilium				ovary(4)|breast(2)|pancreas(1)	7	all_cancers(95;0.0017)	all_cancers(140;0.0973)	Epithelial(56;6.24e-07)|all cancers(55;6.56e-06)	GBM - Glioblastoma multiforme(265;0.00888)		CAAAAAATGAATCTATCAAAG	0.453													8	30	---	---	---	---	PASS
CHD8	57680	broad.mit.edu	37	14	21859633	21859633	+	Nonsense_Mutation	SNP	G	A	A			TCGA-18-4721-01A-01D-1441-08	TCGA-18-4721-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	d2ab2555-7288-47a4-a80c-bf62d65b67b8	f7b631ae-ee98-499b-9d26-dc945e7ac3b8	g.chr14:21859633G>A	uc001was.1	-	36	6311	c.6217C>T	c.(6217-6219)CGA>TGA	p.R2073*	CHD8_uc001war.1_Nonsense_Mutation_p.R1969*	NM_020920	NP_065971	Q9HCK8	CHD8_HUMAN	chromodomain helicase DNA binding protein 8	2352					ATP-dependent chromatin remodeling|canonical Wnt receptor signaling pathway|negative regulation of transcription, DNA-dependent|negative regulation of Wnt receptor signaling pathway|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase III promoter|transcription, DNA-dependent	MLL1 complex	ATP binding|beta-catenin binding|DNA binding|DNA helicase activity|DNA-dependent ATPase activity|methylated histone residue binding|p53 binding			ovary(6)|upper_aerodigestive_tract(1)|large_intestine(1)|breast(1)|skin(1)	10	all_cancers(95;0.00121)		Epithelial(56;2.55e-06)|all cancers(55;1.73e-05)	GBM - Glioblastoma multiforme(265;0.00424)		GCTAGAAATCGGGGATCAACA	0.483													13	51	---	---	---	---	PASS
CMA1	1215	broad.mit.edu	37	14	24975388	24975388	+	Missense_Mutation	SNP	C	A	A			TCGA-18-4721-01A-01D-1441-08	TCGA-18-4721-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	d2ab2555-7288-47a4-a80c-bf62d65b67b8	f7b631ae-ee98-499b-9d26-dc945e7ac3b8	g.chr14:24975388C>A	uc001wpp.1	-	4	476	c.446G>T	c.(445-447)TGG>TTG	p.W149L	CMA1_uc010alx.1_Missense_Mutation_p.W38L	NM_001836	NP_001827	P23946	CMA1_HUMAN	chymase 1, mast cell preproprotein	149	Peptidase S1.				interleukin-1 beta biosynthetic process|proteolysis	extracellular region	serine-type endopeptidase activity				0				GBM - Glioblastoma multiforme(265;0.0271)		TGTTCTTCCCCAGCCAGCCAC	0.577													16	46	---	---	---	---	PASS
C14orf101	54916	broad.mit.edu	37	14	57092202	57092202	+	Nonsense_Mutation	SNP	G	T	T			TCGA-18-4721-01A-01D-1441-08	TCGA-18-4721-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	d2ab2555-7288-47a4-a80c-bf62d65b67b8	f7b631ae-ee98-499b-9d26-dc945e7ac3b8	g.chr14:57092202G>T	uc001xcm.2	+	12	1623	c.1501G>T	c.(1501-1503)GGA>TGA	p.G501*	C14orf101_uc001xcj.2_RNA|C14orf101_uc001xcl.1_RNA|C14orf101_uc001xcn.2_RNA|C14orf101_uc010trf.1_Nonsense_Mutation_p.G34*|C14orf101_uc001xco.2_Nonsense_Mutation_p.G34*	NM_017799	NP_060269	Q9NX78	CN101_HUMAN	hypothetical protein LOC54916	501						integral to membrane				breast(1)|central_nervous_system(1)	2				OV - Ovarian serous cystadenocarcinoma(311;0.226)		ATTACCTAGTGGAATGGTCAC	0.348													30	90	---	---	---	---	PASS
TSHR	7253	broad.mit.edu	37	14	81557425	81557425	+	Missense_Mutation	SNP	C	G	G			TCGA-18-4721-01A-01D-1441-08	TCGA-18-4721-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	d2ab2555-7288-47a4-a80c-bf62d65b67b8	f7b631ae-ee98-499b-9d26-dc945e7ac3b8	g.chr14:81557425C>G	uc001xvd.1	+	5	561	c.405C>G	c.(403-405)AAC>AAG	p.N135K	TSHR_uc001xvb.1_Missense_Mutation_p.N135K|TSHR_uc001xvc.2_Missense_Mutation_p.N135K|TSHR_uc010tvs.1_Missense_Mutation_p.N135K	NM_000369	NP_000360	P16473	TSHR_HUMAN	thyroid stimulating hormone receptor isoform 1	135	Extracellular (Potential).|LRR 2.				cell-cell signaling|positive regulation of cell proliferation	integral to plasma membrane	protein binding|thyroid-stimulating hormone receptor activity			thyroid(289)|ovary(5)|lung(3)|kidney(1)|skin(1)	299				BRCA - Breast invasive adenocarcinoma(234;0.0402)	Thyrotropin Alfa(DB00024)	GCATTTTCAACACTGGACTTA	0.274			Mis		toxic thyroid adenoma	thyroid  adenoma	Hereditary nonautoimmune hyperthyroidism; subclinical hypothyroidism 						16	154	---	---	---	---	PASS
EML5	161436	broad.mit.edu	37	14	89168804	89168804	+	Missense_Mutation	SNP	C	G	G			TCGA-18-4721-01A-01D-1441-08	TCGA-18-4721-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	d2ab2555-7288-47a4-a80c-bf62d65b67b8	f7b631ae-ee98-499b-9d26-dc945e7ac3b8	g.chr14:89168804C>G	uc001xxg.2	-	15	2410	c.2224G>C	c.(2224-2226)GTG>CTG	p.V742L	EML5_uc001xxh.1_5'UTR	NM_183387	NP_899243	Q05BV3	EMAL5_HUMAN	echinoderm microtubule associated protein like	742	WD 11.					cytoplasm|microtubule				ovary(3)	3						CCTGTTGCCACGTAGTCTTTC	0.368													4	94	---	---	---	---	PASS
CYFIP1	23191	broad.mit.edu	37	15	22969169	22969169	+	Missense_Mutation	SNP	G	A	A			TCGA-18-4721-01A-01D-1441-08	TCGA-18-4721-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	d2ab2555-7288-47a4-a80c-bf62d65b67b8	f7b631ae-ee98-499b-9d26-dc945e7ac3b8	g.chr15:22969169G>A	uc001yus.2	+	22	2499	c.2395G>A	c.(2395-2397)GAT>AAT	p.D799N	CYFIP1_uc001yut.2_Missense_Mutation_p.D799N|CYFIP1_uc010aya.1_Missense_Mutation_p.D827N|CYFIP1_uc001yuu.2_Missense_Mutation_p.D368N|CYFIP1_uc001yuv.2_5'UTR	NM_014608	NP_055423	Q7L576	CYFP1_HUMAN	cytoplasmic FMR1 interacting protein 1 isoform	799					axon extension|lamellipodium assembly|regulation of cell shape|ruffle organization	cell junction|lamellipodium|mRNA cap binding complex|perinuclear region of cytoplasm|ruffle|synapse|synaptosome	actin filament binding|Rac GTPase binding			ovary(4)|pancreas(3)|liver(1)|skin(1)	9		all_cancers(20;2.26e-25)|all_epithelial(15;2.1e-22)|Lung NSC(15;3.36e-17)|all_lung(15;1.04e-16)|Breast(32;0.000776)|Colorectal(260;0.0488)		all cancers(64;2.22e-06)|Epithelial(43;1.49e-05)|BRCA - Breast invasive adenocarcinoma(123;0.00101)		ACAGGAGCTGGATGGCCTGTT	0.632													5	44	---	---	---	---	PASS
GABRG3	2567	broad.mit.edu	37	15	27571980	27571980	+	Missense_Mutation	SNP	G	T	T			TCGA-18-4721-01A-01D-1441-08	TCGA-18-4721-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	d2ab2555-7288-47a4-a80c-bf62d65b67b8	f7b631ae-ee98-499b-9d26-dc945e7ac3b8	g.chr15:27571980G>T	uc001zbg.1	+	4	461	c.295G>T	c.(295-297)GCT>TCT	p.A99S	GABRG3_uc001zbf.2_Missense_Mutation_p.A99S	NM_033223	NP_150092	Q99928	GBRG3_HUMAN	gamma-aminobutyric acid (GABA) A receptor, gamma	99	Extracellular (Probable).				gamma-aminobutyric acid signaling pathway|synaptic transmission	cell junction|chloride channel complex|postsynaptic membrane	chloride channel activity|extracellular ligand-gated ion channel activity				0		all_lung(180;4.58e-12)|Breast(32;0.000625)|Colorectal(260;0.235)		all cancers(64;3.15e-07)|Epithelial(43;1.17e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0261)		CATATTTTTTGCTCAGACCTG	0.393													34	145	---	---	---	---	PASS
UBR1	197131	broad.mit.edu	37	15	43363018	43363018	+	Nonsense_Mutation	SNP	C	A	A			TCGA-18-4721-01A-01D-1441-08	TCGA-18-4721-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	d2ab2555-7288-47a4-a80c-bf62d65b67b8	f7b631ae-ee98-499b-9d26-dc945e7ac3b8	g.chr15:43363018C>A	uc001zqq.2	-	5	700	c.634G>T	c.(634-636)GAA>TAA	p.E212*	UBR1_uc010udk.1_Nonsense_Mutation_p.E212*	NM_174916	NP_777576	Q8IWV7	UBR1_HUMAN	ubiquitin protein ligase E3 component n-recognin	212					cellular response to leucine|negative regulation of TOR signaling cascade	cytosol	leucine binding|zinc ion binding			lung(1)	1		all_cancers(109;4.32e-15)|all_epithelial(112;4.05e-13)|Lung NSC(122;1.75e-08)|all_lung(180;2e-07)|Melanoma(134;0.0179)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;4.08e-07)|COAD - Colon adenocarcinoma(120;0.185)|Colorectal(105;0.214)		GGAGGCAGTTCTTTTTCCTCT	0.373													16	225	---	---	---	---	PASS
CCDC33	80125	broad.mit.edu	37	15	74627335	74627335	+	Missense_Mutation	SNP	G	T	T			TCGA-18-4721-01A-01D-1441-08	TCGA-18-4721-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	d2ab2555-7288-47a4-a80c-bf62d65b67b8	f7b631ae-ee98-499b-9d26-dc945e7ac3b8	g.chr15:74627335G>T	uc002axo.2	+	18	2439	c.2045G>T	c.(2044-2046)CGC>CTC	p.R682L	CCDC33_uc002axp.2_Missense_Mutation_p.R538L|CCDC33_uc002axq.2_Missense_Mutation_p.R309L|CCDC33_uc002axr.2_Missense_Mutation_p.R275L	NM_025055	NP_079331	Q8N5R6	CCD33_HUMAN	coiled-coil domain containing 33 isoform 1	885	Potential.						protein binding			ovary(3)|skin(2)	5						TCAGCTCGACGCTGGGGACGA	0.572													4	141	---	---	---	---	PASS
AKAP13	11214	broad.mit.edu	37	15	86270386	86270386	+	Silent	SNP	G	A	A			TCGA-18-4721-01A-01D-1441-08	TCGA-18-4721-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	d2ab2555-7288-47a4-a80c-bf62d65b67b8	f7b631ae-ee98-499b-9d26-dc945e7ac3b8	g.chr15:86270386G>A	uc002blv.1	+	28	7082	c.6912G>A	c.(6910-6912)GGG>GGA	p.G2304G	AKAP13_uc002blu.1_Silent_p.G2308G|AKAP13_uc010bnf.1_Silent_p.G925G|AKAP13_uc002blw.1_Silent_p.G769G|AKAP13_uc002blx.1_Silent_p.G549G	NM_007200	NP_009131	Q12802	AKP13_HUMAN	A-kinase anchor protein 13 isoform 2	2304	Interaction with ESR1.|PH.				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						TCAGCATGGGGATGACAGATC	0.448													33	103	---	---	---	---	PASS
NTRK3	4916	broad.mit.edu	37	15	88727478	88727478	+	Missense_Mutation	SNP	G	T	T			TCGA-18-4721-01A-01D-1441-08	TCGA-18-4721-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	d2ab2555-7288-47a4-a80c-bf62d65b67b8	f7b631ae-ee98-499b-9d26-dc945e7ac3b8	g.chr15:88727478G>T	uc002bme.1	-	3	463	c.301C>A	c.(301-303)CTC>ATC	p.L101I	NTRK3_uc002bmh.2_Missense_Mutation_p.L101I|NTRK3_uc002bmf.1_Missense_Mutation_p.L101I|NTRK3_uc010upl.1_Missense_Mutation_p.L3I|NTRK3_uc010bnh.1_Missense_Mutation_p.L101I|NTRK3_uc002bmg.2_Missense_Mutation_p.L101I	NM_001012338	NP_001012338	Q16288	NTRK3_HUMAN	neurotrophic tyrosine kinase, receptor, type 3	101	Extracellular (Potential).				transmembrane receptor protein tyrosine kinase signaling pathway	integral to plasma membrane	ATP binding|transmembrane receptor protein tyrosine kinase activity		ETV6/NTRK3(234)	soft_tissue(85)|kidney(66)|breast(56)|salivary_gland(26)|lung(22)|large_intestine(6)|ovary(6)|stomach(5)|central_nervous_system(3)|pancreas(3)|haematopoietic_and_lymphoid_tissue(2)|skin(1)	281			BRCA - Breast invasive adenocarcinoma(143;0.211)			CCGGTGTAGAGCTCCATGTCC	0.517			T	ETV6	congenital fibrosarcoma|Secretory breast 					TSP Lung(13;0.10)			13	67	---	---	---	---	PASS
SV2B	9899	broad.mit.edu	37	15	91795123	91795123	+	Silent	SNP	C	A	A			TCGA-18-4721-01A-01D-1441-08	TCGA-18-4721-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	d2ab2555-7288-47a4-a80c-bf62d65b67b8	f7b631ae-ee98-499b-9d26-dc945e7ac3b8	g.chr15:91795123C>A	uc002bqv.2	+	2	917	c.526C>A	c.(526-528)CGA>AGA	p.R176R	SV2B_uc002bqt.2_Silent_p.R176R|SV2B_uc010uqv.1_Silent_p.R25R|SV2B_uc002bqu.3_RNA	NM_014848	NP_055663	Q7L1I2	SV2B_HUMAN	synaptic vesicle protein 2B homolog	176	Cytoplasmic (Potential).				neurotransmitter transport	acrosomal vesicle|cell junction|integral to membrane|synaptic vesicle membrane	transmembrane transporter activity			ovary(3)|central_nervous_system(2)|skin(2)|upper_aerodigestive_tract(1)	8	Lung NSC(78;0.0987)|all_lung(78;0.172)		BRCA - Breast invasive adenocarcinoma(143;0.0895)			GGGAAGGAAGCGAGTCCTCAG	0.582													26	101	---	---	---	---	PASS
ADAMTS17	170691	broad.mit.edu	37	15	100533367	100533367	+	Silent	SNP	G	A	A			TCGA-18-4721-01A-01D-1441-08	TCGA-18-4721-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	d2ab2555-7288-47a4-a80c-bf62d65b67b8	f7b631ae-ee98-499b-9d26-dc945e7ac3b8	g.chr15:100533367G>A	uc002bvv.1	-	20	2914	c.2835C>T	c.(2833-2835)ACC>ACT	p.T945T		NM_139057	NP_620688	Q8TE56	ATS17_HUMAN	ADAM metallopeptidase with thrombospondin type 1	945	TSP type-1 4.				proteolysis	intracellular|proteinaceous extracellular matrix	metalloendopeptidase activity|zinc ion binding			ovary(2)|central_nervous_system(1)	3	Lung NSC(78;0.00299)|all_lung(78;0.00457)|Melanoma(26;0.00571)		OV - Ovarian serous cystadenocarcinoma(32;0.0013)|LUSC - Lung squamous cell carcinoma(107;0.132)|Lung(145;0.161)	COAD - Colon adenocarcinoma(1;0.111)|all cancers(203;0.219)		TGCACGCCACGGTCCGTTTCC	0.488													26	106	---	---	---	---	PASS
ALDOA	226	broad.mit.edu	37	16	30080176	30080176	+	Silent	SNP	G	A	A			TCGA-18-4721-01A-01D-1441-08	TCGA-18-4721-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	d2ab2555-7288-47a4-a80c-bf62d65b67b8	f7b631ae-ee98-499b-9d26-dc945e7ac3b8	g.chr16:30080176G>A	uc002dvw.2	+	8	1545	c.417G>A	c.(415-417)AAG>AAA	p.K139K	uc002dtf.2_Intron|BOLA2_uc010bzb.1_Intron|ALDOA_uc002dvx.2_Silent_p.K139K|ALDOA_uc002dvy.2_Silent_p.K139K|ALDOA_uc002dvz.2_Silent_p.K139K|ALDOA_uc002dwa.3_Silent_p.K139K|ALDOA_uc002dwb.1_Silent_p.K139K|ALDOA_uc002dwc.2_Silent_p.K139K|ALDOA_uc010veg.1_Silent_p.K193K|ALDOA_uc002dwd.2_Silent_p.K139K	NM_184043	NP_908932	P04075	ALDOA_HUMAN	fructose-bisphosphate aldolase A	139					actin filament organization|ATP biosynthetic process|fructose 1,6-bisphosphate metabolic process|gluconeogenesis|glycolysis|muscle cell homeostasis|platelet activation|platelet degranulation|protein homotetramerization|regulation of cell shape|striated muscle contraction	actin cytoskeleton|cytosol|extracellular vesicular exosome|I band|platelet alpha granule lumen	actin binding|fructose binding|fructose-bisphosphate aldolase activity|identical protein binding|tubulin binding			lung(1)	1						CCCAGTACAAGAAGGACGGAG	0.587											OREG0023729	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	28	137	---	---	---	---	PASS
SLC6A2	6530	broad.mit.edu	37	16	55734171	55734171	+	Missense_Mutation	SNP	A	T	T			TCGA-18-4721-01A-01D-1441-08	TCGA-18-4721-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	d2ab2555-7288-47a4-a80c-bf62d65b67b8	f7b631ae-ee98-499b-9d26-dc945e7ac3b8	g.chr16:55734171A>T	uc002eif.2	+	13	1822	c.1711A>T	c.(1711-1713)ATC>TTC	p.I571F	SLC6A2_uc010ccd.2_Intron|SLC6A2_uc002eig.2_Missense_Mutation_p.I571F|SLC6A2_uc002eih.2_Missense_Mutation_p.I571F|SLC6A2_uc002eii.2_Missense_Mutation_p.I466F|SLC6A2_uc002eij.2_Missense_Mutation_p.I285F	NM_001043	NP_001034	P23975	SC6A2_HUMAN	solute carrier family 6 member 2	571	Helical; Name=12; (Potential).				synaptic transmission	integral to plasma membrane|membrane fraction	norepinephrine:sodium symporter activity			lung(4)|ovary(2)|pancreas(2)	8				BRCA - Breast invasive adenocarcinoma(181;0.01)|Kidney(780;0.0267)	Amineptine(DB04836)|Amitriptyline(DB00321)|Amoxapine(DB00543)|Atomoxetine(DB00289)|Bethanidine(DB00217)|Bupropion(DB01156)|Clomipramine(DB01242)|Cocaine(DB00907)|Debrisoquin(DB04840)|Desipramine(DB01151)|Diethylpropion(DB00937)|Doxepin(DB01142)|Duloxetine(DB00476)|Ergotamine(DB00696)|Guanadrel Sulfate(DB00226)|Guanethidine(DB01170)|Imipramine(DB00458)|Maprotiline(DB00934)|Mazindol(DB00579)|Methylphenidate(DB00422)|Milnacipran(DB04896)|Nefazodone(DB01149)|Norepinephrine(DB00368)|Nortriptyline(DB00540)|Paroxetine(DB00715)|Phenmetrazine(DB00830)|Phentermine(DB00191)|Protriptyline(DB00344)|Reboxetine(DB00234)|Sibutramine(DB01105)|Tramadol(DB00193)|Trazodone(DB00656)|Trimipramine(DB00726)|Venlafaxine(DB00285)	CCTGGTGCCCATCTACGTCAT	0.617													48	109	---	---	---	---	PASS
FTSJD1	55783	broad.mit.edu	37	16	71319538	71319538	+	Missense_Mutation	SNP	C	T	T			TCGA-18-4721-01A-01D-1441-08	TCGA-18-4721-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	d2ab2555-7288-47a4-a80c-bf62d65b67b8	f7b631ae-ee98-499b-9d26-dc945e7ac3b8	g.chr16:71319538C>T	uc010cga.2	-	3	692	c.286G>A	c.(286-288)GGG>AGG	p.G96R	FTSJD1_uc002ezy.3_Missense_Mutation_p.G96R|FTSJD1_uc002ezz.3_Missense_Mutation_p.G96R	NM_001099642	NP_001093112	Q8IYT2	FTSJ1_HUMAN	FtsJ methyltransferase domain containing 1	96						integral to membrane	methyltransferase activity|nucleic acid binding			skin(1)	1						ATGATTTTCCCCGCTTTATTA	0.373													29	118	---	---	---	---	PASS
CDYL2	124359	broad.mit.edu	37	16	80718824	80718824	+	Missense_Mutation	SNP	T	G	G			TCGA-18-4721-01A-01D-1441-08	TCGA-18-4721-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	d2ab2555-7288-47a4-a80c-bf62d65b67b8	f7b631ae-ee98-499b-9d26-dc945e7ac3b8	g.chr16:80718824T>G	uc002ffs.2	-	2	332	c.227A>C	c.(226-228)AAG>ACG	p.K76T		NM_152342	NP_689555	Q8N8U2	CDYL2_HUMAN	chromodomain protein, Y-like 2	76						nucleus	catalytic activity|protein binding			central_nervous_system(1)	1						ACGCAGCAGCTTGGAGGTACT	0.517													34	110	---	---	---	---	PASS
JPH3	57338	broad.mit.edu	37	16	87723731	87723731	+	Silent	SNP	C	A	A			TCGA-18-4721-01A-01D-1441-08	TCGA-18-4721-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	d2ab2555-7288-47a4-a80c-bf62d65b67b8	f7b631ae-ee98-499b-9d26-dc945e7ac3b8	g.chr16:87723731C>A	uc002fkd.2	+	4	2019	c.1765C>A	c.(1765-1767)CGG>AGG	p.R589R	JPH3_uc010vou.1_RNA	NM_020655	NP_065706	Q8WXH2	JPH3_HUMAN	junctophilin 3	589	Cytoplasmic (Potential).				calcium ion transport into cytosol|regulation of ryanodine-sensitive calcium-release channel activity	integral to membrane|junctional sarcoplasmic reticulum membrane|plasma membrane	protein binding			ovary(1)|pancreas(1)	2				BRCA - Breast invasive adenocarcinoma(80;0.0287)		TTCCCACCACCGGGCCAGCAA	0.672													4	11	---	---	---	---	PASS
BANP	54971	broad.mit.edu	37	16	88052143	88052143	+	Silent	SNP	G	A	A			TCGA-18-4721-01A-01D-1441-08	TCGA-18-4721-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	d2ab2555-7288-47a4-a80c-bf62d65b67b8	f7b631ae-ee98-499b-9d26-dc945e7ac3b8	g.chr16:88052143G>A	uc002fkr.2	+	7	962	c.738G>A	c.(736-738)ACG>ACA	p.T246T	BANP_uc002fkp.2_Silent_p.T216T|BANP_uc002fkq.2_Silent_p.T216T|BANP_uc010vow.1_Silent_p.T254T|BANP_uc002fks.3_Silent_p.T215T|BANP_uc002fko.1_Silent_p.T152T|BANP_uc010vov.1_Silent_p.T221T	NM_079837	NP_524576	Q8N9N5	BANP_HUMAN	BTG3 associated nuclear protein isoform b	247	Interaction with CUX1 and HDAC1 (By similarity).|BEN.				cell cycle|chromatin modification|multicellular organismal development|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding				0				BRCA - Breast invasive adenocarcinoma(80;0.00551)		ACTGCCGCACGGCCGAGAAGA	0.647													12	58	---	---	---	---	PASS
FAM27L	284123	broad.mit.edu	37	17	21825561	21825561	+	RNA	SNP	C	T	T			TCGA-18-4721-01A-01D-1441-08	TCGA-18-4721-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	d2ab2555-7288-47a4-a80c-bf62d65b67b8	f7b631ae-ee98-499b-9d26-dc945e7ac3b8	g.chr17:21825561C>T	uc002gyz.2	+	1		c.192C>T				NR_028336				Homo sapiens family with sequence similarity 27-like, mRNA (cDNA clone MGC:35151 IMAGE:5169482), complete cds.												0				UCEC - Uterine corpus endometrioid carcinoma (53;0.11)|BRCA - Breast invasive adenocarcinoma(1;0.00463)		caggcctgcccggagggtgtt	0.000													18	121	---	---	---	---	PASS
NF1	4763	broad.mit.edu	37	17	29496972	29496972	+	Missense_Mutation	SNP	G	T	T			TCGA-18-4721-01A-01D-1441-08	TCGA-18-4721-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	d2ab2555-7288-47a4-a80c-bf62d65b67b8	f7b631ae-ee98-499b-9d26-dc945e7ac3b8	g.chr17:29496972G>T	uc002hgg.2	+	5	876	c.543G>T	c.(541-543)CAG>CAT	p.Q181H	NF1_uc002hge.1_Missense_Mutation_p.Q181H|NF1_uc002hgf.1_Missense_Mutation_p.Q181H|NF1_uc002hgh.2_Missense_Mutation_p.Q181H|NF1_uc010csn.1_Intron	NM_001042492	NP_001035957	P21359	NF1_HUMAN	neurofibromin isoform 1	181					actin cytoskeleton organization|adrenal gland development|artery morphogenesis|camera-type eye morphogenesis|cerebral cortex development|collagen fibril organization|forebrain astrocyte development|forebrain morphogenesis|heart development|liver development|MAPKKK cascade|metanephros development|myelination in peripheral nervous system|negative regulation of cell migration|negative regulation of endothelial cell proliferation|negative regulation of MAP kinase activity|negative regulation of MAPKKK cascade|negative regulation of neuroblast proliferation|negative regulation of oligodendrocyte differentiation|negative regulation of transcription factor import into nucleus|osteoblast differentiation|phosphatidylinositol 3-kinase cascade|pigmentation|positive regulation of adenylate cyclase activity|positive regulation of neuron apoptosis|Ras protein signal transduction|regulation of blood vessel endothelial cell migration|regulation of bone resorption|response to hypoxia|smooth muscle tissue development|spinal cord development|sympathetic nervous system development|visual learning|wound healing	axon|cytoplasm|dendrite|intrinsic to internal side of plasma membrane|nucleus	protein binding|Ras GTPase activator activity	p.E178_D186del(1)|p.Y182fs*8(1)		soft_tissue(159)|central_nervous_system(56)|lung(28)|large_intestine(27)|haematopoietic_and_lymphoid_tissue(18)|ovary(18)|autonomic_ganglia(12)|breast(3)|skin(3)|stomach(2)|thyroid(1)|prostate(1)|kidney(1)|pancreas(1)	330		all_cancers(10;1.29e-12)|all_epithelial(10;0.00347)|all_hematologic(16;0.00556)|Acute lymphoblastic leukemia(14;0.00593)|Breast(31;0.014)|Myeloproliferative disorder(56;0.0255)|all_lung(9;0.0321)|Lung NSC(157;0.0659)		UCEC - Uterine corpus endometrioid carcinoma (4;4.38e-05)|all cancers(4;1.64e-26)|Epithelial(4;9.15e-23)|OV - Ovarian serous cystadenocarcinoma(4;3.58e-21)|GBM - Glioblastoma multiforme(4;0.00146)		AATTGTTACAGTATATCAATG	0.274			D|Mis|N|F|S|O		neurofibroma|glioma	neurofibroma|glioma			Neurofibromatosis_type_1	TCGA GBM(6;<1E-08)|TSP Lung(7;0.0071)|TCGA Ovarian(3;0.0088)			14	67	---	---	---	---	PASS
NAGS	162417	broad.mit.edu	37	17	42085865	42085865	+	Missense_Mutation	SNP	T	C	C			TCGA-18-4721-01A-01D-1441-08	TCGA-18-4721-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	d2ab2555-7288-47a4-a80c-bf62d65b67b8	f7b631ae-ee98-499b-9d26-dc945e7ac3b8	g.chr17:42085865T>C	uc002ies.2	+	7	1501	c.1501T>C	c.(1501-1503)TTC>CTC	p.F501L	NAGS_uc010czn.2_Missense_Mutation_p.F509L|NAGS_uc002iet.2_Missense_Mutation_p.F125L	NM_153006	NP_694551	Q8N159	NAGS_HUMAN	N-acetylglutamate synthase	501	N-acetyltransferase.				arginine biosynthetic process|urea cycle	mitochondrial matrix	acetyl-CoA:L-glutamate N-acetyltransferase activity				0		Breast(137;0.00536)|Prostate(33;0.0724)		BRCA - Breast invasive adenocarcinoma(366;0.113)	L-Glutamic Acid(DB00142)	GTGGATCTTCTTCTGGTTTGG	0.532													5	316	---	---	---	---	PASS
CACNA1G	8913	broad.mit.edu	37	17	48655853	48655853	+	Silent	SNP	G	A	A			TCGA-18-4721-01A-01D-1441-08	TCGA-18-4721-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	d2ab2555-7288-47a4-a80c-bf62d65b67b8	f7b631ae-ee98-499b-9d26-dc945e7ac3b8	g.chr17:48655853G>A	uc002irk.1	+	9	2601	c.2229G>A	c.(2227-2229)AAG>AAA	p.K743K	CACNA1G_uc002iri.1_Silent_p.K743K|CACNA1G_uc002irj.1_Silent_p.K743K|CACNA1G_uc002irl.1_Silent_p.K743K|CACNA1G_uc002irm.1_Silent_p.K743K|CACNA1G_uc002irn.1_Silent_p.K743K|CACNA1G_uc002iro.1_Silent_p.K743K|CACNA1G_uc002irp.1_Silent_p.K743K|CACNA1G_uc002irq.1_Silent_p.K743K|CACNA1G_uc002irr.1_Silent_p.K743K|CACNA1G_uc002irs.1_Silent_p.K743K|CACNA1G_uc002irt.1_Silent_p.K743K|CACNA1G_uc002irv.1_Silent_p.K743K|CACNA1G_uc002irw.1_Silent_p.K743K|CACNA1G_uc002iru.1_Silent_p.K743K|CACNA1G_uc002irx.1_Silent_p.K656K|CACNA1G_uc002iry.1_Silent_p.K656K|CACNA1G_uc002irz.1_Silent_p.K656K|CACNA1G_uc002isa.1_Silent_p.K656K|CACNA1G_uc002isb.1_Silent_p.K656K|CACNA1G_uc002isc.1_Silent_p.K656K|CACNA1G_uc002isd.1_Silent_p.K656K|CACNA1G_uc002ise.1_Silent_p.K656K|CACNA1G_uc002isf.1_Silent_p.K656K|CACNA1G_uc002isg.1_Silent_p.K656K|CACNA1G_uc002ish.1_Silent_p.K656K|CACNA1G_uc002isi.1_Silent_p.K656K	NM_018896	NP_061496	O43497	CAC1G_HUMAN	voltage-dependent calcium channel alpha 1G	743	Cytoplasmic (Potential).|II.				axon guidance	voltage-gated calcium channel complex	low voltage-gated calcium channel activity			breast(1)	1	Breast(11;6.7e-17)		BRCA - Breast invasive adenocarcinoma(22;7.52e-09)		Ethosuximide(DB00593)|Flunarizine(DB04841)|Levetiracetam(DB01202)|Mibefradil(DB01388)|Pimozide(DB01100)|Trimethadione(DB00347)|Verapamil(DB00661)|Zonisamide(DB00909)	TGGACAGCAAGTACTTTGGCC	0.597													25	60	---	---	---	---	PASS
BTBD17	388419	broad.mit.edu	37	17	72352884	72352884	+	Missense_Mutation	SNP	C	T	T			TCGA-18-4721-01A-01D-1441-08	TCGA-18-4721-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	d2ab2555-7288-47a4-a80c-bf62d65b67b8	f7b631ae-ee98-499b-9d26-dc945e7ac3b8	g.chr17:72352884C>T	uc002jkn.2	-	3	1349	c.1349G>A	c.(1348-1350)CGC>CAC	p.R450H		NM_001080466	NP_001073935	A6NE02	BTBDH_HUMAN	BTB (POZ) domain containing 17 precursor	450						extracellular region					0						CTCGGAGTTGCGCCGCTGCAG	0.677													3	32	---	---	---	---	PASS
DLGAP1	9229	broad.mit.edu	37	18	3534195	3534195	+	Missense_Mutation	SNP	C	A	A			TCGA-18-4721-01A-01D-1441-08	TCGA-18-4721-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	d2ab2555-7288-47a4-a80c-bf62d65b67b8	f7b631ae-ee98-499b-9d26-dc945e7ac3b8	g.chr18:3534195C>A	uc002kmf.2	-	7	2543	c.2476G>T	c.(2476-2478)GAC>TAC	p.D826Y	DLGAP1_uc010wyz.1_Missense_Mutation_p.D826Y|DLGAP1_uc002kme.1_Missense_Mutation_p.D524Y|DLGAP1_uc010dkn.2_Missense_Mutation_p.D534Y|DLGAP1_uc010wyw.1_Missense_Mutation_p.D532Y|DLGAP1_uc010wyx.1_Missense_Mutation_p.D548Y|DLGAP1_uc010wyy.1_Missense_Mutation_p.D510Y|DLGAP1_uc002kmg.2_Missense_Mutation_p.D524Y	NM_004746	NP_004737	O14490	DLGP1_HUMAN	discs large homolog-associated protein 1 isoform	826					synaptic transmission	cell junction|postsynaptic density|postsynaptic membrane				ovary(2)|pancreas(1)|skin(1)	4		Colorectal(8;0.0257)				TACTTACTGTCTTCGGGCAGG	0.567													10	93	---	---	---	---	PASS
EPB41L3	23136	broad.mit.edu	37	18	5407707	5407707	+	Missense_Mutation	SNP	T	A	A			TCGA-18-4721-01A-01D-1441-08	TCGA-18-4721-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	d2ab2555-7288-47a4-a80c-bf62d65b67b8	f7b631ae-ee98-499b-9d26-dc945e7ac3b8	g.chr18:5407707T>A	uc002kmt.1	-	15	2236	c.2150A>T	c.(2149-2151)AAG>ATG	p.K717M	EPB41L3_uc010wzh.1_Missense_Mutation_p.K548M|EPB41L3_uc002kmu.1_Intron|EPB41L3_uc010dkq.1_Intron|EPB41L3_uc002kms.1_Intron|EPB41L3_uc010wze.1_Intron|EPB41L3_uc010wzf.1_Intron|EPB41L3_uc010wzg.1_Intron|EPB41L3_uc010dkr.2_Missense_Mutation_p.K109M	NM_012307	NP_036439	Q9Y2J2	E41L3_HUMAN	erythrocyte membrane protein band 4.1-like 3	717	Spectrin--actin-binding (Potential).				cortical actin cytoskeleton organization	cell-cell junction|cytoplasm|cytoskeleton|extrinsic to membrane	actin binding|structural molecule activity			ovary(5)	5						TACCTGTGCCTTGAGCTCTGC	0.383													12	119	---	---	---	---	PASS
EPB41L3	23136	broad.mit.edu	37	18	5428437	5428437	+	Missense_Mutation	SNP	C	T	T			TCGA-18-4721-01A-01D-1441-08	TCGA-18-4721-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	d2ab2555-7288-47a4-a80c-bf62d65b67b8	f7b631ae-ee98-499b-9d26-dc945e7ac3b8	g.chr18:5428437C>T	uc002kmt.1	-	9	1026	c.940G>A	c.(940-942)GGA>AGA	p.G314R	EPB41L3_uc010wzh.1_Missense_Mutation_p.G314R|EPB41L3_uc002kmu.1_Missense_Mutation_p.G314R|EPB41L3_uc010dkq.1_Missense_Mutation_p.G205R|EPB41L3_uc010dks.1_Missense_Mutation_p.G336R	NM_012307	NP_036439	Q9Y2J2	E41L3_HUMAN	erythrocyte membrane protein band 4.1-like 3	314	FERM.				cortical actin cytoskeleton organization	cell-cell junction|cytoplasm|cytoskeleton|extrinsic to membrane	actin binding|structural molecule activity			ovary(5)	5						GCACAAACTCCTAACATAATT	0.383													16	173	---	---	---	---	PASS
EPB41L3	23136	broad.mit.edu	37	18	5428438	5428438	+	Missense_Mutation	SNP	T	A	A			TCGA-18-4721-01A-01D-1441-08	TCGA-18-4721-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	d2ab2555-7288-47a4-a80c-bf62d65b67b8	f7b631ae-ee98-499b-9d26-dc945e7ac3b8	g.chr18:5428438T>A	uc002kmt.1	-	9	1025	c.939A>T	c.(937-939)TTA>TTT	p.L313F	EPB41L3_uc010wzh.1_Missense_Mutation_p.L313F|EPB41L3_uc002kmu.1_Missense_Mutation_p.L313F|EPB41L3_uc010dkq.1_Missense_Mutation_p.L204F|EPB41L3_uc010dks.1_Missense_Mutation_p.L335F	NM_012307	NP_036439	Q9Y2J2	E41L3_HUMAN	erythrocyte membrane protein band 4.1-like 3	313	FERM.				cortical actin cytoskeleton organization	cell-cell junction|cytoplasm|cytoskeleton|extrinsic to membrane	actin binding|structural molecule activity			ovary(5)	5						CACAAACTCCTAACATAATTT	0.388													16	169	---	---	---	---	PASS
PSMG2	56984	broad.mit.edu	37	18	12703145	12703145	+	Silent	SNP	C	A	A			TCGA-18-4721-01A-01D-1441-08	TCGA-18-4721-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	d2ab2555-7288-47a4-a80c-bf62d65b67b8	f7b631ae-ee98-499b-9d26-dc945e7ac3b8	g.chr18:12703145C>A	uc002krk.2	+	1	82	c.39C>A	c.(37-39)GCC>GCA	p.A13A	PSMG2_uc002krg.2_Intron|PSMG2_uc002krj.1_Silent_p.A13A|CEP76_uc002krh.3_5'Flank|CEP76_uc002kri.2_5'Flank|CEP76_uc010wzz.1_5'Flank|CEP76_uc010xaa.1_5'Flank|CEP76_uc010xab.1_5'Flank	NM_020232	NP_064617	Q969U7	PSMG2_HUMAN	proteasome (prosome, macropain) assembly	13					proteasome assembly	nucleus	protein binding				0						CCGACCTTGCCGGCTTCACCC	0.692													3	42	---	---	---	---	PASS
LAMA3	3909	broad.mit.edu	37	18	21451477	21451477	+	Missense_Mutation	SNP	G	A	A			TCGA-18-4721-01A-01D-1441-08	TCGA-18-4721-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	d2ab2555-7288-47a4-a80c-bf62d65b67b8	f7b631ae-ee98-499b-9d26-dc945e7ac3b8	g.chr18:21451477G>A	uc002kuq.2	+	38	4936	c.4850G>A	c.(4849-4851)CGC>CAC	p.R1617H	LAMA3_uc002kur.2_Missense_Mutation_p.R1617H|LAMA3_uc002kus.3_5'Flank|LAMA3_uc002kut.3_5'Flank	NM_198129	NP_937762	Q16787	LAMA3_HUMAN	laminin alpha 3 subunit isoform 1	1617	Laminin IV type A.				cell adhesion|epidermis development|hemidesmosome assembly|regulation of cell adhesion|regulation of cell migration|regulation of embryonic development	laminin-1 complex	receptor binding|structural molecule activity			ovary(8)|skin(2)|central_nervous_system(1)	11	all_cancers(21;7.81e-05)|all_epithelial(16;4.45e-07)|Lung NSC(20;0.00156)|all_lung(20;0.00508)|Colorectal(14;0.0202)|Ovarian(20;0.17)				Alteplase(DB00009)|Anistreplase(DB00029)|Reteplase(DB00015)|Tenecteplase(DB00031)	GCAGATGTGCGCATCCAAGGC	0.557													29	85	---	---	---	---	PASS
DSC3	1825	broad.mit.edu	37	18	28588002	28588002	+	Missense_Mutation	SNP	G	C	C			TCGA-18-4721-01A-01D-1441-08	TCGA-18-4721-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	d2ab2555-7288-47a4-a80c-bf62d65b67b8	f7b631ae-ee98-499b-9d26-dc945e7ac3b8	g.chr18:28588002G>C	uc002kwj.3	-	11	1798	c.1643C>G	c.(1642-1644)ACA>AGA	p.T548R	DSC3_uc002kwi.3_Missense_Mutation_p.T548R	NM_001941	NP_001932	Q14574	DSC3_HUMAN	desmocollin 3 isoform Dsc3a preproprotein	548	Cadherin 4.|Extracellular (Potential).				homophilic cell adhesion|protein stabilization	desmosome|integral to membrane|membrane fraction	calcium ion binding|gamma-catenin binding			ovary(2)|skin(2)	4			OV - Ovarian serous cystadenocarcinoma(10;0.125)			TGCCAGGACTGTAATATTATA	0.303													5	78	---	---	---	---	PASS
DSC2	1824	broad.mit.edu	37	18	28648028	28648028	+	Missense_Mutation	SNP	A	T	T			TCGA-18-4721-01A-01D-1441-08	TCGA-18-4721-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	d2ab2555-7288-47a4-a80c-bf62d65b67b8	f7b631ae-ee98-499b-9d26-dc945e7ac3b8	g.chr18:28648028A>T	uc002kwl.3	-	16	3113	c.2659T>A	c.(2659-2661)TTG>ATG	p.L887M	DSC2_uc002kwk.3_3'UTR	NM_024422	NP_077740	Q02487	DSC2_HUMAN	desmocollin 2 isoform Dsc2a preproprotein	887	Cytoplasmic (Potential).				homophilic cell adhesion	desmosome|integral to membrane	calcium ion binding			ovary(2)|skin(1)	3			OV - Ovarian serous cystadenocarcinoma(10;0.0241)			TTGGGCTCCAAATTATCCAAA	0.403													22	104	---	---	---	---	PASS
RIT2	6014	broad.mit.edu	37	18	40323576	40323576	+	Missense_Mutation	SNP	C	T	T			TCGA-18-4721-01A-01D-1441-08	TCGA-18-4721-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	d2ab2555-7288-47a4-a80c-bf62d65b67b8	f7b631ae-ee98-499b-9d26-dc945e7ac3b8	g.chr18:40323576C>T	uc002lav.2	-	5	709	c.536G>A	c.(535-537)AGG>AAG	p.R179K	RIT2_uc010dnf.2_3'UTR	NM_002930	NP_002921	Q99578	RIT2_HUMAN	Ras-like without CAAX 2	179					nerve growth factor receptor signaling pathway|small GTPase mediated signal transduction|synaptic transmission	intracellular|plasma membrane	calmodulin binding|GTP binding|GTPase activity			ovary(1)	1						GCGAATTTCCCTCACTAAGCC	0.423													38	142	---	---	---	---	PASS
MYO5B	4645	broad.mit.edu	37	18	47432926	47432926	+	Silent	SNP	C	T	T			TCGA-18-4721-01A-01D-1441-08	TCGA-18-4721-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	d2ab2555-7288-47a4-a80c-bf62d65b67b8	f7b631ae-ee98-499b-9d26-dc945e7ac3b8	g.chr18:47432926C>T	uc002leb.2	-	19	2565	c.2277G>A	c.(2275-2277)CTG>CTA	p.L759L		NM_001080467	NP_001073936	Q9ULV0	MYO5B_HUMAN	myosin VB	759	Myosin head-like.				protein transport	myosin complex	actin binding|ATP binding|calmodulin binding|motor activity			ovary(2)|skin(2)|central_nervous_system(1)	5				READ - Rectum adenocarcinoma(32;0.103)		TGTCAGCCCGCAGCTTCTCCA	0.557													16	71	---	---	---	---	PASS
SPPL2B	56928	broad.mit.edu	37	19	2334702	2334702	+	Silent	SNP	G	T	T			TCGA-18-4721-01A-01D-1441-08	TCGA-18-4721-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	d2ab2555-7288-47a4-a80c-bf62d65b67b8	f7b631ae-ee98-499b-9d26-dc945e7ac3b8	g.chr19:2334702G>T	uc002lvs.2	+	2	248	c.168G>T	c.(166-168)CCG>CCT	p.P56P	SPPL2B_uc010dsw.1_Silent_p.P28P|SPPL2B_uc010dsy.1_Silent_p.P28P|SPPL2B_uc010dsz.1_Silent_p.P56P|SPPL2B_uc002lvr.2_Silent_p.P56P	NM_152988	NP_694533	Q8TCT7	PSL1_HUMAN	signal peptide peptidase-like 2B isoform 2	56	Cytoplasmic (Potential).|PA.					Golgi membrane|integral to membrane	aspartic-type endopeptidase activity				0		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)|STAD - Stomach adenocarcinoma(1328;0.18)		CCCATCTTCCGCACGACCTCA	0.677													5	18	---	---	---	---	PASS
S1PR4	8698	broad.mit.edu	37	19	3179893	3179893	+	Missense_Mutation	SNP	G	C	C			TCGA-18-4721-01A-01D-1441-08	TCGA-18-4721-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	d2ab2555-7288-47a4-a80c-bf62d65b67b8	f7b631ae-ee98-499b-9d26-dc945e7ac3b8	g.chr19:3179893G>C	uc002lxg.2	+	1	1128	c.1103G>C	c.(1102-1104)AGC>ACC	p.S368T		NM_003775	NP_003766	O95977	S1PR4_HUMAN	sphingosine-1-phosphate receptor 4 precursor	368	Cytoplasmic (By similarity).				activation of phospholipase C activity|elevation of cytosolic calcium ion concentration|immune response	integral to plasma membrane	lipid binding|lysosphingolipid and lysophosphatidic acid receptor activity			lung(1)|skin(1)	2						CGCTCGCTCAGCTTTCGGATG	0.672													39	137	---	---	---	---	PASS
ZSWIM4	65249	broad.mit.edu	37	19	13941421	13941421	+	Missense_Mutation	SNP	G	A	A			TCGA-18-4721-01A-01D-1441-08	TCGA-18-4721-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	d2ab2555-7288-47a4-a80c-bf62d65b67b8	f7b631ae-ee98-499b-9d26-dc945e7ac3b8	g.chr19:13941421G>A	uc002mxh.1	+	13	2716	c.2527G>A	c.(2527-2529)GCC>ACC	p.A843T	ZSWIM4_uc010xng.1_Missense_Mutation_p.A766T	NM_023072	NP_075560	Q9H7M6	ZSWM4_HUMAN	zinc finger, SWIM-type containing 4	843							zinc ion binding			central_nervous_system(2)	2			OV - Ovarian serous cystadenocarcinoma(19;2.94e-23)|Epithelial(5;4.58e-19)			CAGCCACCCTGCCGTCAACGA	0.667													50	184	---	---	---	---	PASS
ZNF93	81931	broad.mit.edu	37	19	20044847	20044847	+	Silent	SNP	C	T	T			TCGA-18-4721-01A-01D-1441-08	TCGA-18-4721-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	d2ab2555-7288-47a4-a80c-bf62d65b67b8	f7b631ae-ee98-499b-9d26-dc945e7ac3b8	g.chr19:20044847C>T	uc002non.2	+	4	1194	c.1083C>T	c.(1081-1083)TTC>TTT	p.F361F		NM_031218	NP_112495	P35789	ZNF93_HUMAN	zinc finger protein 93	361	C2H2-type 8.					nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			pancreas(1)	1						GACATGAGTTCATTCATATGG	0.373													14	90	---	---	---	---	PASS
LRFN1	57622	broad.mit.edu	37	19	39798962	39798962	+	Missense_Mutation	SNP	C	T	T			TCGA-18-4721-01A-01D-1441-08	TCGA-18-4721-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	d2ab2555-7288-47a4-a80c-bf62d65b67b8	f7b631ae-ee98-499b-9d26-dc945e7ac3b8	g.chr19:39798962C>T	uc002okw.2	-	2	1627	c.1627G>A	c.(1627-1629)GTC>ATC	p.V543I		NM_020862	NP_065913	Q9P244	LRFN1_HUMAN	leucine rich repeat and fibronectin type III	543	Helical; (Potential).					cell junction|integral to membrane|postsynaptic density|postsynaptic membrane				ovary(2)	2	all_cancers(60;1.85e-07)|all_lung(34;4.03e-08)|Lung NSC(34;4.66e-08)|all_epithelial(25;6.4e-07)|Ovarian(47;0.0512)		Epithelial(26;1.96e-27)|all cancers(26;2.05e-24)|Lung(45;0.000278)|LUSC - Lung squamous cell carcinoma(53;0.000335)			GCGACGATGACGCCCCCGATG	0.652													8	20	---	---	---	---	PASS
CRX	1406	broad.mit.edu	37	19	48342762	48342762	+	Silent	SNP	G	A	A			TCGA-18-4721-01A-01D-1441-08	TCGA-18-4721-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	d2ab2555-7288-47a4-a80c-bf62d65b67b8	f7b631ae-ee98-499b-9d26-dc945e7ac3b8	g.chr19:48342762G>A	uc002phq.3	+	4	642	c.438G>A	c.(436-438)CTG>CTA	p.L146L		NM_000554	NP_000545	O43186	CRX_HUMAN	cone-rod homeobox protein	146			Missing (in LCA7).		organ morphogenesis|response to stimulus|visual perception		leucine zipper domain binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			breast(1)|central_nervous_system(1)	2		all_cancers(25;2.76e-09)|all_epithelial(76;7.01e-07)|all_lung(116;2.48e-06)|Lung NSC(112;5.15e-06)|Ovarian(192;0.0139)|all_neural(266;0.0146)|Breast(70;0.133)		OV - Ovarian serous cystadenocarcinoma(262;0.000266)|all cancers(93;0.000788)|Epithelial(262;0.0226)|GBM - Glioblastoma multiforme(486;0.0521)		GTCCCCCTCTGCCCGGCCCCT	0.672													40	114	---	---	---	---	PASS
BAX	581	broad.mit.edu	37	19	49459500	49459500	+	Missense_Mutation	SNP	C	G	G			TCGA-18-4721-01A-01D-1441-08	TCGA-18-4721-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	d2ab2555-7288-47a4-a80c-bf62d65b67b8	f7b631ae-ee98-499b-9d26-dc945e7ac3b8	g.chr19:49459500C>G	uc002plk.2	+	4	348	c.279C>G	c.(277-279)TTC>TTG	p.F93L	BAX_uc002plf.1_Missense_Mutation_p.F93L|BAX_uc002plg.1_Missense_Mutation_p.F56L|BAX_uc002plh.1_Missense_Mutation_p.F15L|BAX_uc010xzx.1_RNA|BAX_uc002plj.2_Missense_Mutation_p.F93L|BAX_uc002pll.2_Missense_Mutation_p.F44L|BAX_uc002plm.2_Missense_Mutation_p.F15L	NM_138761	NP_620116	Q07812	BAX_HUMAN	BCL2-associated X protein isoform alpha	93					activation of caspase activity by cytochrome c|activation of pro-apoptotic gene products|B cell apoptosis|cleavage of lamin|DNA fragmentation involved in apoptotic nuclear change|establishment or maintenance of transmembrane electrochemical gradient|induction of apoptosis by extracellular signals|induction of apoptosis by intracellular signals|induction of retinal programmed cell death|mitochondrial fragmentation involved in apoptosis|mitochondrial fusion|negative regulation of protein binding|negative regulation of survival gene product expression|nuclear fragmentation involved in apoptotic nuclear change|positive regulation of neuron apoptosis|protein homooligomerization|regulation of mitochondrial membrane potential|regulation of protein heterodimerization activity|regulation of protein homodimerization activity|release of cytochrome c from mitochondria|release of matrix enzymes from mitochondria|response to toxin|transformed cell apoptosis	cytosol|endoplasmic reticulum membrane|mitochondrial outer membrane|mitochondrial permeability transition pore complex|nucleus	BH3 domain binding|channel activity|lipid binding|protein heterodimerization activity|protein homodimerization activity			lung(1)|central_nervous_system(1)|skin(1)	3		all_epithelial(76;5.29e-07)|all_lung(116;1.7e-06)|Lung NSC(112;3.55e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)		OV - Ovarian serous cystadenocarcinoma(262;0.000159)|all cancers(93;0.00047)|GBM - Glioblastoma multiforme(486;0.018)|Epithelial(262;0.0279)		AGGTCTTTTTCCGAGTGGCAG	0.582													31	118	---	---	---	---	PASS
ENTPD6	955	broad.mit.edu	37	20	25201919	25201919	+	Missense_Mutation	SNP	G	T	T			TCGA-18-4721-01A-01D-1441-08	TCGA-18-4721-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	d2ab2555-7288-47a4-a80c-bf62d65b67b8	f7b631ae-ee98-499b-9d26-dc945e7ac3b8	g.chr20:25201919G>T	uc002wuj.2	+	11	1175	c.995G>T	c.(994-996)GGA>GTA	p.G332V	ENTPD6_uc010zsy.1_Missense_Mutation_p.G332V|ENTPD6_uc010gdj.1_Missense_Mutation_p.G304V|ENTPD6_uc010zsz.1_Missense_Mutation_p.G114V|ENTPD6_uc002wum.2_Missense_Mutation_p.G315V|ENTPD6_uc010zta.1_Missense_Mutation_p.G332V|ENTPD6_uc002wun.2_Intron|ENTPD6_uc002wuk.2_Missense_Mutation_p.G331V|ENTPD6_uc002wul.2_Missense_Mutation_p.G331V|ENTPD6_uc010ztb.1_Missense_Mutation_p.G304V|ENTPD6_uc010ztc.1_Missense_Mutation_p.G304V|ENTPD6_uc002wuo.2_Missense_Mutation_p.G84V|ENTPD6_uc010ztd.1_Intron|ENTPD6_uc010gdk.1_5'Flank|ENTPD6_uc010gdl.1_5'Flank	NM_001247	NP_001238	O75354	ENTP6_HUMAN	ectonucleoside triphosphate diphosphohydrolase 6	332	Lumenal (Potential).					Golgi membrane|integral to membrane	nucleoside-diphosphatase activity				0						AGTTTCAAAGGAGAGTGGGAA	0.517													15	53	---	---	---	---	PASS
HIRA	7290	broad.mit.edu	37	22	19371175	19371175	+	Silent	SNP	G	T	T			TCGA-18-4721-01A-01D-1441-08	TCGA-18-4721-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	d2ab2555-7288-47a4-a80c-bf62d65b67b8	f7b631ae-ee98-499b-9d26-dc945e7ac3b8	g.chr22:19371175G>T	uc002zpf.1	-	13	1603	c.1383C>A	c.(1381-1383)ATC>ATA	p.I461I	HIRA_uc011agx.1_Silent_p.I327I|HIRA_uc010grn.1_Silent_p.I461I|HIRA_uc010gro.1_Silent_p.I417I|HIRA_uc010grp.2_RNA	NM_003325	NP_003316	P54198	HIRA_HUMAN	HIR histone cell cycle regulation defective	461	Interaction with CCNA1.|Interaction with ASF1A.|Required for repression of histone gene transcription.			Missing: Abrogates binding to ASF1A.|I->D: Abrogates binding to ASF1A.	chromatin modification|regulation of transcription from RNA polymerase II promoter	PML body	chromatin binding|protein binding|sequence-specific DNA binding transcription factor activity|transcription corepressor activity			ovary(1)	1	Colorectal(54;0.0993)					AGAGAGGCGTGATTCTTCTCC	0.458													23	209	---	---	---	---	PASS
BCR	613	broad.mit.edu	37	22	23596020	23596020	+	Silent	SNP	C	T	T			TCGA-18-4721-01A-01D-1441-08	TCGA-18-4721-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	d2ab2555-7288-47a4-a80c-bf62d65b67b8	f7b631ae-ee98-499b-9d26-dc945e7ac3b8	g.chr22:23596020C>T	uc002zww.2	+	2	1910	c.1314C>T	c.(1312-1314)TGC>TGT	p.C438C	BCR_uc002zwx.2_Silent_p.C438C|BCR_uc011aiy.1_Silent_p.C27C|BCR_uc010gtx.1_5'UTR	NM_004327	NP_004318	P11274	BCR_HUMAN	breakpoint cluster region isoform 1	438					regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol	ATP binding|GTPase activator activity|protein serine/threonine kinase activity|Rho guanyl-nucleotide exchange factor activity		BCR/JAK2(6)	haematopoietic_and_lymphoid_tissue(6)|central_nervous_system(3)|urinary_tract(1)|lung(1)|skin(1)	12						GATACGGCTGCGCTGCAGACC	0.602			T	ABL1| FGFR1|JAK2 	CML|ALL|AML								19	49	---	---	---	---	PASS
NHP2L1	4809	broad.mit.edu	37	22	42071111	42071111	+	Silent	SNP	C	T	T			TCGA-18-4721-01A-01D-1441-08	TCGA-18-4721-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	d2ab2555-7288-47a4-a80c-bf62d65b67b8	f7b631ae-ee98-499b-9d26-dc945e7ac3b8	g.chr22:42071111C>T	uc003bat.2	-	3	407	c.213G>A	c.(211-213)CTG>CTA	p.L71L	NHP2L1_uc003bau.2_Silent_p.L71L|NHP2L1_uc003bav.2_Silent_p.L71L|NHP2L1_uc003baw.2_Silent_p.L71L	NM_005008	NP_004999	P55769	NH2L1_HUMAN	NHP2 non-histone chromosome protein 2-like 1	71					nuclear mRNA splicing, via spliceosome|ribosome biogenesis	box C/D snoRNP complex|nucleoplasm|spliceosomal complex	protein binding|RNA binding				0						CTTCACACAGCAGCGGCAGGT	0.587													18	90	---	---	---	---	PASS
PRR5-ARHGAP8	553158	broad.mit.edu	37	22	45221390	45221390	+	Missense_Mutation	SNP	C	A	A			TCGA-18-4721-01A-01D-1441-08	TCGA-18-4721-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	d2ab2555-7288-47a4-a80c-bf62d65b67b8	f7b631ae-ee98-499b-9d26-dc945e7ac3b8	g.chr22:45221390C>A	uc003bfd.2	+	12	1415	c.1143C>A	c.(1141-1143)CAC>CAA	p.H381Q	PRR5-ARHGAP8_uc003bfc.2_Missense_Mutation_p.H302Q|PRR5-ARHGAP8_uc011aqi.1_Missense_Mutation_p.H293Q|PRR5-ARHGAP8_uc011aqj.1_Missense_Mutation_p.H207Q|ARHGAP8_uc003bfi.2_Missense_Mutation_p.H171Q|ARHGAP8_uc010gzv.2_Missense_Mutation_p.H171Q|ARHGAP8_uc003bfj.2_Missense_Mutation_p.H202Q|ARHGAP8_uc003bfk.2_Missense_Mutation_p.H171Q|ARHGAP8_uc003bfl.2_RNA	NM_181335	NP_851852			Rho GTPase activating protein 8 isoform 2											skin(2)	2						AGAGCCTGCACGAGGGCCGGA	0.662													12	28	---	---	---	---	PASS
RLIM	51132	broad.mit.edu	37	X	73811938	73811938	+	Silent	SNP	G	C	C	rs61754468	by1000genomes	TCGA-18-4721-01A-01D-1441-08	TCGA-18-4721-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	d2ab2555-7288-47a4-a80c-bf62d65b67b8	f7b631ae-ee98-499b-9d26-dc945e7ac3b8	g.chrX:73811938G>C	uc004ebu.2	-	5	1502	c.1212C>G	c.(1210-1212)ACC>ACG	p.T404T	RLIM_uc004ebw.2_Silent_p.T404T	NM_183353	NP_899196	Q9NVW2	RNF12_HUMAN	ring finger protein, LIM domain interacting	404					random inactivation of X chromosome|transcription, DNA-dependent|ubiquitin-dependent protein catabolic process	cytoplasm|transcriptional repressor complex	transcription corepressor activity|ubiquitin-protein ligase activity|zinc ion binding			ovary(2)	2						GCCTTAACATGGTCTGAATTG	0.413													4	110	---	---	---	---	PASS
HTR2C	3358	broad.mit.edu	37	X	114141480	114141480	+	Silent	SNP	G	A	A			TCGA-18-4721-01A-01D-1441-08	TCGA-18-4721-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	d2ab2555-7288-47a4-a80c-bf62d65b67b8	f7b631ae-ee98-499b-9d26-dc945e7ac3b8	g.chrX:114141480G>A	uc004epu.1	+	6	1607	c.879G>A	c.(877-879)GAG>GAA	p.E293E	HTR2C_uc010nqc.1_Silent_p.E293E|HTR2C_uc004epv.1_3'UTR	NM_000868	NP_000859	P28335	5HT2C_HUMAN	5-hydroxytryptamine (serotonin) receptor 2C	293	Cytoplasmic (By similarity).				cGMP biosynthetic process|ERK1 and ERK2 cascade|feeding behavior|phosphatidylinositol biosynthetic process|release of sequestered calcium ion into cytosol|response to drug|synaptic transmission	cytoplasm|integral to membrane|nucleus|plasma membrane	1-(4-iodo-2,5-dimethoxyphenyl)propan-2-amine binding|drug binding|phosphatidylinositol phospholipase C activity|protein binding|serotonin binding|serotonin receptor activity			ovary(3)	3					Chlorprothixene(DB01239)|Clozapine(DB00363)|Dexfenfluramine(DB01191)|Fenfluramine(DB00574)|Methysergide(DB00247)|Mianserin(DB06148)|Minaprine(DB00805)|Mirtazapine(DB00370)|Olanzapine(DB00334)|Promazine(DB00420)|Propiomazine(DB00777)|Quetiapine(DB01224)|Sertindole(DB06144)|Thiethylperazine(DB00372)|Tramadol(DB00193)|Ziprasidone(DB00246)	AGAAGAAGGAGAGACGTCCTA	0.483													62	68	---	---	---	---	PASS
KIAA1210	57481	broad.mit.edu	37	X	118215438	118215438	+	Missense_Mutation	SNP	C	A	A			TCGA-18-4721-01A-01D-1441-08	TCGA-18-4721-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	d2ab2555-7288-47a4-a80c-bf62d65b67b8	f7b631ae-ee98-499b-9d26-dc945e7ac3b8	g.chrX:118215438C>A	uc004era.3	-	14	4984	c.4984G>T	c.(4984-4986)GTT>TTT	p.V1662F		NM_020721	NP_065772	Q9ULL0	K1210_HUMAN	hypothetical protein LOC57481	1662										ovary(4)|skin(1)	5						ATGGCAGGAACTTGCAGTATC	0.458													26	56	---	---	---	---	PASS
VGLL1	51442	broad.mit.edu	37	X	135632948	135632948	+	Missense_Mutation	SNP	G	A	A	rs138345606	byFrequency	TCGA-18-4721-01A-01D-1441-08	TCGA-18-4721-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	d2ab2555-7288-47a4-a80c-bf62d65b67b8	f7b631ae-ee98-499b-9d26-dc945e7ac3b8	g.chrX:135632948G>A	uc004ezy.2	+	4	826	c.656G>A	c.(655-657)CGT>CAT	p.R219H	MIR934_hsa-mir-934|MI0005756_5'Flank	NM_016267	NP_057351	Q99990	VGLL1_HUMAN	vestigial like 1	219					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	transcription coactivator activity				0	Acute lymphoblastic leukemia(192;0.000127)					TATGTATCTCGTGGATCTGCC	0.423													25	37	---	---	---	---	PASS