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
PANK4	55229	broad.mit.edu	37	1	2442178	2442178	+	Missense_Mutation	SNP	C	G	G			TCGA-39-5024-01A-21D-1817-08	TCGA-39-5024-11A-01D-1817-08									Somatic	Phase_I	Capture				Illumina GAIIx	388478e9-8c1f-43f8-88c4-811bf3cc2500	829ea6e6-1737-4fc6-8732-65e2d7fb2582	g.chr1:2442178C>G	uc001ajm.1	-	16	1886	c.1877G>C	c.(1876-1878)GGA>GCA	p.G626A	PANK4_uc010nza.1_Missense_Mutation_p.G587A	NM_018216	NP_060686	Q9NVE7	PANK4_HUMAN	pantothenate kinase 4	626					coenzyme A biosynthetic process	cytoplasm	ATP binding|pantothenate kinase activity			upper_aerodigestive_tract(1)|large_intestine(1)|ovary(1)	3	all_cancers(77;0.000158)|all_epithelial(69;8.01e-05)|all_lung(157;0.0212)|Lung NSC(156;0.0376)|Ovarian(185;0.0634)	all_epithelial(116;3.18e-20)|all_lung(118;1.67e-08)|Lung NSC(185;2.69e-06)|Breast(487;0.00147)|Renal(390;0.00183)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Lung SC(97;0.0847)|Medulloblastoma(700;0.123)		Epithelial(90;1.54e-37)|OV - Ovarian serous cystadenocarcinoma(86;6.95e-23)|GBM - Glioblastoma multiforme(42;2.81e-08)|Colorectal(212;4.25e-05)|COAD - Colon adenocarcinoma(227;0.000196)|Kidney(185;0.000342)|BRCA - Breast invasive adenocarcinoma(365;0.00445)|KIRC - Kidney renal clear cell carcinoma(229;0.00549)|STAD - Stomach adenocarcinoma(132;0.00644)|Lung(427;0.201)		GATGTCTATTCCACTGTTATC	0.532													5	145	---	---	---	---	PASS
RSC1A1	6248	broad.mit.edu	37	1	15987907	15987907	+	Missense_Mutation	SNP	C	T	T			TCGA-39-5024-01A-21D-1817-08	TCGA-39-5024-11A-01D-1817-08									Somatic	Phase_I	Capture				Illumina GAIIx	388478e9-8c1f-43f8-88c4-811bf3cc2500	829ea6e6-1737-4fc6-8732-65e2d7fb2582	g.chr1:15987907C>T	uc010obn.1	+	1	1544	c.1544C>T	c.(1543-1545)TCA>TTA	p.S515L		NM_006511	NP_006502	Q92681	RSCA1_HUMAN	regulatory solute carrier protein, family 1,	515					negative regulation of transport|regulation of transcription, DNA-dependent|transcription, DNA-dependent|transport	cell junction|Golgi apparatus|nucleus	ion channel inhibitor activity			ovary(1)	1		Colorectal(325;0.00108)|Renal(390;0.00145)|Breast(348;0.00276)|Lung NSC(340;0.00566)|all_lung(284;0.00831)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0798)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;5.73e-07)|COAD - Colon adenocarcinoma(227;3.49e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000114)|KIRC - Kidney renal clear cell carcinoma(229;0.00244)|STAD - Stomach adenocarcinoma(313;0.0072)|READ - Rectum adenocarcinoma(331;0.0649)		AAGTCTTTGTCATCCAATTTC	0.418													17	37	---	---	---	---	PASS
CROCC	9696	broad.mit.edu	37	1	17272075	17272075	+	Missense_Mutation	SNP	G	A	A	rs2781608	by1000genomes	TCGA-39-5024-01A-21D-1817-08	TCGA-39-5024-11A-01D-1817-08									Somatic	Phase_I	Capture				Illumina GAIIx	388478e9-8c1f-43f8-88c4-811bf3cc2500	829ea6e6-1737-4fc6-8732-65e2d7fb2582	g.chr1:17272075G>A	uc001azt.2	+	15	2179	c.2110G>A	c.(2110-2112)GCC>ACC	p.A704T	CROCC_uc009voz.1_Missense_Mutation_p.A467T|CROCC_uc001azu.2_Missense_Mutation_p.A7T	NM_014675	NP_055490	Q5TZA2	CROCC_HUMAN	ciliary rootlet coiled-coil	704	Potential.				cell cycle|cell projection organization|centrosome organization|protein localization	actin cytoskeleton|centriole|ciliary rootlet|plasma membrane	kinesin binding|structural molecule activity			ovary(2)|breast(2)|central_nervous_system(1)	5		Colorectal(325;3.46e-05)|Breast(348;0.000162)|Lung NSC(340;0.000174)|all_lung(284;0.000234)|Renal(390;0.000518)|Ovarian(437;0.00669)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00459)|BRCA - Breast invasive adenocarcinoma(304;7.63e-06)|COAD - Colon adenocarcinoma(227;1.07e-05)|Kidney(64;0.000163)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.181)		GGCCGAGAAGGCCGAGGTGGC	0.657													3	17	---	---	---	---	PASS
ATP13A2	23400	broad.mit.edu	37	1	17313556	17313556	+	Missense_Mutation	SNP	G	A	A			TCGA-39-5024-01A-21D-1817-08	TCGA-39-5024-11A-01D-1817-08									Somatic	Phase_I	Capture				Illumina GAIIx	388478e9-8c1f-43f8-88c4-811bf3cc2500	829ea6e6-1737-4fc6-8732-65e2d7fb2582	g.chr1:17313556G>A	uc001baa.2	-	26	3258	c.3068C>T	c.(3067-3069)ACC>ATC	p.T1023I	ATP13A2_uc001azz.1_Missense_Mutation_p.T170I|ATP13A2_uc001bab.2_Missense_Mutation_p.T1018I|ATP13A2_uc001bac.2_Missense_Mutation_p.T979I	NM_022089	NP_071372	Q9NQ11	AT132_HUMAN	ATPase type 13A2 isoform 1	1023	Extracellular (Potential).				ATP biosynthetic process|cation transport	integral to membrane	ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|metal ion binding			skin(2)|ovary(1)|central_nervous_system(1)	4		Colorectal(325;0.000147)|Breast(348;0.00104)|Renal(390;0.00145)|Lung NSC(340;0.00566)|all_lung(284;0.00797)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0646)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00462)|COAD - Colon adenocarcinoma(227;1.11e-05)|BRCA - Breast invasive adenocarcinoma(304;1.99e-05)|Kidney(64;0.000171)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00645)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.182)		CTGGGCCAGGGTCAGGAAGTA	0.687													10	43	---	---	---	---	PASS
UBR4	23352	broad.mit.edu	37	1	19447774	19447774	+	Silent	SNP	G	A	A			TCGA-39-5024-01A-21D-1817-08	TCGA-39-5024-11A-01D-1817-08									Somatic	Phase_I	Capture				Illumina GAIIx	388478e9-8c1f-43f8-88c4-811bf3cc2500	829ea6e6-1737-4fc6-8732-65e2d7fb2582	g.chr1:19447774G>A	uc001bbi.2	-	68	10054	c.10050C>T	c.(10048-10050)GCC>GCT	p.A3350A	UBR4_uc001bbk.1_Silent_p.A997A	NM_020765	NP_065816	Q5T4S7	UBR4_HUMAN	retinoblastoma-associated factor 600	3350	Ser-rich.				interspecies interaction between organisms	cytoplasm|cytoskeleton|integral to membrane|nucleus	calmodulin binding|ubiquitin-protein ligase activity|zinc ion binding			kidney(10)|ovary(7)|breast(4)|pancreas(2)|skin(2)	25		Colorectal(325;3.46e-05)|Renal(390;0.000147)|all_lung(284;0.000328)|Lung NSC(340;0.000406)|Breast(348;0.000814)|Ovarian(437;0.00774)|Myeloproliferative disorder(586;0.0256)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00674)|BRCA - Breast invasive adenocarcinoma(304;5.43e-05)|Kidney(64;0.000337)|KIRC - Kidney renal clear cell carcinoma(64;0.00426)|STAD - Stomach adenocarcinoma(196;0.00715)|READ - Rectum adenocarcinoma(331;0.0816)		CAGCCACAGGGGCTGAGGAGG	0.537													13	88	---	---	---	---	PASS
ECE1	1889	broad.mit.edu	37	1	21564678	21564678	+	Silent	SNP	C	A	A	rs141888962	by1000genomes	TCGA-39-5024-01A-21D-1817-08	TCGA-39-5024-11A-01D-1817-08									Somatic	Phase_I	Capture				Illumina GAIIx	388478e9-8c1f-43f8-88c4-811bf3cc2500	829ea6e6-1737-4fc6-8732-65e2d7fb2582	g.chr1:21564678C>A	uc001bek.2	-	11	1413	c.1338G>T	c.(1336-1338)GCG>GCT	p.A446A	ECE1_uc001bem.2_Silent_p.A430A|ECE1_uc001bej.2_Silent_p.A434A|ECE1_uc001bei.2_Silent_p.A443A|ECE1_uc010odl.1_Silent_p.A446A|ECE1_uc009vqa.1_Silent_p.A446A	NM_001397	NP_001388	P42892	ECE1_HUMAN	endothelin converting enzyme 1 isoform 1	446	Extracellular (Potential).				bradykinin catabolic process|calcitonin catabolic process|ear development|embryonic digit morphogenesis|endothelin maturation|heart development|positive regulation of receptor recycling|substance P catabolic process	early endosome|external side of plasma membrane|integral to membrane|intrinsic to endosome membrane|membrane fraction|perinuclear region of cytoplasm|plasma membrane|Weibel-Palade body	metal ion binding|metalloendopeptidase activity|protein homodimerization activity			ovary(2)|skin(1)	3		Lung NSC(340;1.14e-05)|all_lung(284;1.23e-05)|Colorectal(325;3.46e-05)|Renal(390;9.67e-05)|Breast(348;0.00147)|Ovarian(437;0.00432)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0183)|OV - Ovarian serous cystadenocarcinoma(117;4.83e-27)|COAD - Colon adenocarcinoma(152;1.36e-06)|GBM - Glioblastoma multiforme(114;1.47e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000162)|STAD - Stomach adenocarcinoma(196;0.00326)|KIRC - Kidney renal clear cell carcinoma(1967;0.00755)|READ - Rectum adenocarcinoma(331;0.0678)|Lung(427;0.206)		TGGGGCCCAACGCAAAGCCCA	0.562													9	59	---	---	---	---	PASS
ZNF436	80818	broad.mit.edu	37	1	23689283	23689283	+	Missense_Mutation	SNP	C	T	T			TCGA-39-5024-01A-21D-1817-08	TCGA-39-5024-11A-01D-1817-08									Somatic	Phase_I	Capture				Illumina GAIIx	388478e9-8c1f-43f8-88c4-811bf3cc2500	829ea6e6-1737-4fc6-8732-65e2d7fb2582	g.chr1:23689283C>T	uc001bgt.2	-	3	973	c.592G>A	c.(592-594)GAG>AAG	p.E198K	ZNF436_uc001bgu.2_Missense_Mutation_p.E198K	NM_030634	NP_085137	Q9C0F3	ZN436_HUMAN	zinc finger protein 436	198	C2H2-type 3.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			breast(1)	1		Colorectal(325;3.46e-05)|Lung NSC(340;4.15e-05)|all_lung(284;6.64e-05)|Renal(390;0.000219)|Breast(348;0.00262)|Ovarian(437;0.00539)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0227)|OV - Ovarian serous cystadenocarcinoma(117;6.44e-26)|Colorectal(126;5.5e-08)|COAD - Colon adenocarcinoma(152;3.09e-06)|GBM - Glioblastoma multiforme(114;5.97e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000977)|KIRC - Kidney renal clear cell carcinoma(1967;0.00336)|STAD - Stomach adenocarcinoma(196;0.0127)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.0853)|LUSC - Lung squamous cell carcinoma(448;0.187)		TTCCCACACTCGTTACAGTCA	0.423													31	182	---	---	---	---	PASS
DLGAP3	58512	broad.mit.edu	37	1	35332772	35332772	+	Silent	SNP	C	T	T			TCGA-39-5024-01A-21D-1817-08	TCGA-39-5024-11A-01D-1817-08									Somatic	Phase_I	Capture				Illumina GAIIx	388478e9-8c1f-43f8-88c4-811bf3cc2500	829ea6e6-1737-4fc6-8732-65e2d7fb2582	g.chr1:35332772C>T	uc001byc.2	-	9	2598	c.2598G>A	c.(2596-2598)GTG>GTA	p.V866V		NM_001080418	NP_001073887	O95886	DLGP3_HUMAN	discs, large (Drosophila) homolog-associated	866					cell-cell signaling	cell junction|postsynaptic density|postsynaptic membrane				ovary(3)	3		Myeloproliferative disorder(586;0.0393)				GGAAGGTGGGCACAGGGAACG	0.562													9	84	---	---	---	---	PASS
MACF1	23499	broad.mit.edu	37	1	39801303	39801303	+	Missense_Mutation	SNP	A	G	G			TCGA-39-5024-01A-21D-1817-08	TCGA-39-5024-11A-01D-1817-08									Somatic	Phase_I	Capture				Illumina GAIIx	388478e9-8c1f-43f8-88c4-811bf3cc2500	829ea6e6-1737-4fc6-8732-65e2d7fb2582	g.chr1:39801303A>G	uc010oiu.1	+	1	4494	c.4363A>G	c.(4363-4365)AGC>GGC	p.S1455G	MACF1_uc010ois.1_Intron|MACF1_uc001cda.1_Intron|MACF1_uc001cdc.1_Intron|MACF1_uc001cdb.1_Intron	NM_033044	NP_149033	Q9UPN3	MACF1_HUMAN	microfilament and actin filament cross-linker	3020					cell cycle arrest|Golgi to plasma membrane protein transport|positive regulation of Wnt receptor signaling pathway|regulation of epithelial cell migration|regulation of focal adhesion assembly|regulation of microtubule-based process|Wnt receptor signaling pathway|wound healing	Golgi apparatus|microtubule|ruffle membrane	actin filament binding|ATPase activity|calcium ion binding|microtubule binding			ovary(8)|breast(3)|central_nervous_system(3)|skin(2)	16	Lung NSC(20;5.57e-06)|Ovarian(52;0.00769)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;7.78e-19)|Epithelial(16;1.73e-17)|all cancers(16;2.49e-16)|LUSC - Lung squamous cell carcinoma(16;0.00146)|Lung(16;0.00204)			CCATATAAAGAGCCAACCTAG	0.373													11	62	---	---	---	---	PASS
MACF1	23499	broad.mit.edu	37	1	39824465	39824465	+	Missense_Mutation	SNP	G	A	A			TCGA-39-5024-01A-21D-1817-08	TCGA-39-5024-11A-01D-1817-08									Somatic	Phase_I	Capture				Illumina GAIIx	388478e9-8c1f-43f8-88c4-811bf3cc2500	829ea6e6-1737-4fc6-8732-65e2d7fb2582	g.chr1:39824465G>A	uc010oiu.1	+	10	7491	c.7360G>A	c.(7360-7362)GAG>AAG	p.E2454K	MACF1_uc010ois.1_Missense_Mutation_p.E1952K|MACF1_uc001cda.1_Missense_Mutation_p.E1860K|MACF1_uc001cdc.1_Missense_Mutation_p.E1039K|MACF1_uc001cdb.1_Missense_Mutation_p.E1039K	NM_033044	NP_149033	Q9UPN3	MACF1_HUMAN	microfilament and actin filament cross-linker	4019	Spectrin 2.				cell cycle arrest|Golgi to plasma membrane protein transport|positive regulation of Wnt receptor signaling pathway|regulation of epithelial cell migration|regulation of focal adhesion assembly|regulation of microtubule-based process|Wnt receptor signaling pathway|wound healing	Golgi apparatus|microtubule|ruffle membrane	actin filament binding|ATPase activity|calcium ion binding|microtubule binding			ovary(8)|breast(3)|central_nervous_system(3)|skin(2)	16	Lung NSC(20;5.57e-06)|Ovarian(52;0.00769)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;7.78e-19)|Epithelial(16;1.73e-17)|all cancers(16;2.49e-16)|LUSC - Lung squamous cell carcinoma(16;0.00146)|Lung(16;0.00204)			GCAGGCTTGTGAGGCCAACGT	0.512													21	73	---	---	---	---	PASS
INADL	10207	broad.mit.edu	37	1	62293228	62293228	+	Silent	SNP	C	A	A			TCGA-39-5024-01A-21D-1817-08	TCGA-39-5024-11A-01D-1817-08									Somatic	Phase_I	Capture				Illumina GAIIx	388478e9-8c1f-43f8-88c4-811bf3cc2500	829ea6e6-1737-4fc6-8732-65e2d7fb2582	g.chr1:62293228C>A	uc001dab.2	+	16	2067	c.1953C>A	c.(1951-1953)CGC>CGA	p.R651R	INADL_uc009waf.1_Silent_p.R651R|INADL_uc001daa.2_Silent_p.R651R|INADL_uc001dad.3_Silent_p.R348R|INADL_uc001dac.2_RNA	NM_176877	NP_795352	Q8NI35	INADL_HUMAN	InaD-like	651					intracellular signal transduction|tight junction assembly	apical plasma membrane|perinuclear region of cytoplasm|tight junction	protein binding			ovary(3)|skin(1)	4						AACCAAGGCGCACTGAAACCT	0.458													19	155	---	---	---	---	PASS
SNX7	51375	broad.mit.edu	37	1	99157223	99157223	+	Missense_Mutation	SNP	G	T	T			TCGA-39-5024-01A-21D-1817-08	TCGA-39-5024-11A-01D-1817-08									Somatic	Phase_I	Capture				Illumina GAIIx	388478e9-8c1f-43f8-88c4-811bf3cc2500	829ea6e6-1737-4fc6-8732-65e2d7fb2582	g.chr1:99157223G>T	uc010ouc.1	+	4	659	c.607G>T	c.(607-609)GAC>TAC	p.D203Y	SNX7_uc001dsa.2_Missense_Mutation_p.D139Y|SNX7_uc010oud.1_Intron	NM_015976	NP_057060	Q9UNH6	SNX7_HUMAN	sorting nexin 7 isoform a	139	PX.				cell communication|protein transport	cytoplasmic vesicle membrane	phosphatidylinositol binding|protein binding			ovary(2)|haematopoietic_and_lymphoid_tissue(1)	3		all_epithelial(167;7.64e-07)|all_lung(203;0.0006)|Lung NSC(277;0.00137)		Epithelial(280;0.0521)|all cancers(265;0.0687)|COAD - Colon adenocarcinoma(174;0.15)|Lung(183;0.207)|Colorectal(170;0.234)		ATTTAATGAAGACTTCAAAAT	0.338													5	47	---	---	---	---	PASS
LPPR5	163404	broad.mit.edu	37	1	99380394	99380394	+	Missense_Mutation	SNP	A	G	G	rs143279943		TCGA-39-5024-01A-21D-1817-08	TCGA-39-5024-11A-01D-1817-08									Somatic	Phase_I	Capture				Illumina GAIIx	388478e9-8c1f-43f8-88c4-811bf3cc2500	829ea6e6-1737-4fc6-8732-65e2d7fb2582	g.chr1:99380394A>G	uc001dsb.2	-	5	1103	c.881T>C	c.(880-882)ATG>ACG	p.M294T	LPPR5_uc001dsc.2_Missense_Mutation_p.M294T	NM_001037317	NP_001032394	Q32ZL2	LPPR5_HUMAN	phosphatidic acid phosphatase type 2d isoform 1	294						integral to membrane	hydrolase activity				0						AATGCTGATCATTGGCATCTG	0.358													20	106	---	---	---	---	PASS
CELSR2	1952	broad.mit.edu	37	1	109806324	109806324	+	Silent	SNP	C	G	G			TCGA-39-5024-01A-21D-1817-08	TCGA-39-5024-11A-01D-1817-08									Somatic	Phase_I	Capture				Illumina GAIIx	388478e9-8c1f-43f8-88c4-811bf3cc2500	829ea6e6-1737-4fc6-8732-65e2d7fb2582	g.chr1:109806324C>G	uc001dxa.3	+	9	4987	c.4926C>G	c.(4924-4926)CTC>CTG	p.L1642L		NM_001408	NP_001399	Q9HCU4	CELR2_HUMAN	cadherin EGF LAG seven-pass G-type receptor 2	1642	Extracellular (Potential).|Laminin G-like 2.				dendrite morphogenesis|homophilic cell adhesion|neural plate anterior/posterior regionalization|neuropeptide signaling pathway|regulation of cell-cell adhesion|regulation of transcription, DNA-dependent|Wnt receptor signaling pathway	cytoplasm|integral to membrane|plasma membrane	calcium ion binding|G-protein coupled receptor activity|protein binding			ovary(4)|lung(3)|skin(1)	8		all_epithelial(167;0.000114)|all_lung(203;0.000321)|Lung NSC(277;0.000626)|Breast(1374;0.244)		Colorectal(144;0.0296)|Lung(183;0.067)|COAD - Colon adenocarcinoma(174;0.114)|Epithelial(280;0.193)|all cancers(265;0.219)		ACCTCAGCCTCATGTTCCGCA	0.662											OREG0013632	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	15	113	---	---	---	---	PASS
AMPD2	271	broad.mit.edu	37	1	110170496	110170496	+	Missense_Mutation	SNP	C	T	T			TCGA-39-5024-01A-21D-1817-08	TCGA-39-5024-11A-01D-1817-08									Somatic	Phase_I	Capture				Illumina GAIIx	388478e9-8c1f-43f8-88c4-811bf3cc2500	829ea6e6-1737-4fc6-8732-65e2d7fb2582	g.chr1:110170496C>T	uc009wfh.1	+	10	1755	c.1213C>T	c.(1213-1215)CCA>TCA	p.P405S	AMPD2_uc009wfg.1_RNA|AMPD2_uc001dyb.1_Missense_Mutation_p.P324S|AMPD2_uc001dyc.1_Missense_Mutation_p.P405S|AMPD2_uc010ovr.1_Missense_Mutation_p.P330S|AMPD2_uc010ovs.1_Missense_Mutation_p.P287S|AMPD2_uc001dyd.1_Missense_Mutation_p.P286S|AMPD2_uc001dye.1_5'Flank	NM_004037	NP_004028	Q01433	AMPD2_HUMAN	adenosine monophosphate deaminase 2 (isoform L)	405					purine base metabolic process|purine ribonucleoside monophosphate biosynthetic process|purine-containing compound salvage	cytosol	AMP deaminase activity|metal ion binding			ovary(2)|breast(1)	3		all_epithelial(167;2.5e-05)|all_lung(203;0.000135)|Lung NSC(277;0.000269)|Breast(1374;0.244)		Lung(183;0.0425)|all cancers(265;0.0884)|Colorectal(144;0.109)|Epithelial(280;0.111)|LUSC - Lung squamous cell carcinoma(189;0.228)		GAAGAAAGTGCCACACCGAGA	0.582													4	92	---	---	---	---	PASS
TMOD4	29765	broad.mit.edu	37	1	151146054	151146054	+	Silent	SNP	T	C	C			TCGA-39-5024-01A-21D-1817-08	TCGA-39-5024-11A-01D-1817-08									Somatic	Phase_I	Capture				Illumina GAIIx	388478e9-8c1f-43f8-88c4-811bf3cc2500	829ea6e6-1737-4fc6-8732-65e2d7fb2582	g.chr1:151146054T>C	uc001exc.3	-	4	508	c.318A>G	c.(316-318)GCA>GCG	p.A106A	TMOD4_uc001exb.2_5'Flank|TMOD4_uc001exd.2_RNA|TMOD4_uc010pct.1_Intron	NM_013353	NP_037485	Q9NZQ9	TMOD4_HUMAN	tropomodulin 4 (muscle)	106					muscle contraction	cytoplasm|cytoskeleton	actin binding|tropomyosin binding			ovary(1)	1	Lung SC(34;0.00471)|Ovarian(49;0.0147)|all_hematologic(923;0.0597)|Hepatocellular(266;0.0997)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.0486)|LUSC - Lung squamous cell carcinoma(543;0.211)			TCTGCTCCTCTGCTGGGATTT	0.547													20	150	---	---	---	---	PASS
CD244	51744	broad.mit.edu	37	1	160811111	160811111	+	Missense_Mutation	SNP	C	G	G			TCGA-39-5024-01A-21D-1817-08	TCGA-39-5024-11A-01D-1817-08									Somatic	Phase_I	Capture				Illumina GAIIx	388478e9-8c1f-43f8-88c4-811bf3cc2500	829ea6e6-1737-4fc6-8732-65e2d7fb2582	g.chr1:160811111C>G	uc009wtq.2	-	3	737	c.559G>C	c.(559-561)GAG>CAG	p.E187Q	CD244_uc001fxa.2_Missense_Mutation_p.E182Q|CD244_uc009wtp.2_RNA|CD244_uc009wtr.2_Intron|CD244_uc010pjt.1_RNA	NM_016382	NP_057466	Q9BZW8	CD244_HUMAN	CD244 natural killer cell receptor 2B4	187	Extracellular (Potential).|Ig-like 2.				blood coagulation|leukocyte migration	integral to membrane|plasma membrane	protein binding|receptor activity			ovary(1)	1	all_cancers(52;2.72e-17)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.00737)			TCAACCTCCTCGTCCAGGTAG	0.517													10	187	---	---	---	---	PASS
PBX1	5087	broad.mit.edu	37	1	164789349	164789349	+	Missense_Mutation	SNP	G	T	T			TCGA-39-5024-01A-21D-1817-08	TCGA-39-5024-11A-01D-1817-08									Somatic	Phase_I	Capture				Illumina GAIIx	388478e9-8c1f-43f8-88c4-811bf3cc2500	829ea6e6-1737-4fc6-8732-65e2d7fb2582	g.chr1:164789349G>T	uc001gct.2	+	7	1296	c.1038G>T	c.(1036-1038)TTG>TTT	p.L346F	PBX1_uc010pku.1_Missense_Mutation_p.L346F|PBX1_uc010pkv.1_Missense_Mutation_p.L263F|PBX1_uc001gcs.2_Intron|PBX1_uc010pkw.1_Missense_Mutation_p.L236F	NM_002585	NP_002576	P40424	PBX1_HUMAN	pre-B-cell leukemia homeobox 1	346					negative regulation of sequence-specific DNA binding transcription factor activity|sex differentiation|steroid biosynthetic process	cytoplasm|nucleus	sequence-specific DNA binding transcription factor activity|transcription factor binding		EWSR1/PBX1(3)	soft_tissue(3)|lung(1)|skin(1)	5						CTGGAGATTTGTTCATGAGCG	0.498			T	TCF3|EWSR1	pre B-ALL|myoepithelioma								7	86	---	---	---	---	PASS
ASTN1	460	broad.mit.edu	37	1	176915252	176915252	+	Missense_Mutation	SNP	T	G	G			TCGA-39-5024-01A-21D-1817-08	TCGA-39-5024-11A-01D-1817-08									Somatic	Phase_I	Capture				Illumina GAIIx	388478e9-8c1f-43f8-88c4-811bf3cc2500	829ea6e6-1737-4fc6-8732-65e2d7fb2582	g.chr1:176915252T>G	uc001glc.2	-	13	2271	c.2059A>C	c.(2059-2061)ATC>CTC	p.I687L	ASTN1_uc001glb.1_Missense_Mutation_p.I687L|ASTN1_uc001gld.1_Missense_Mutation_p.I687L|ASTN1_uc009wwx.1_Missense_Mutation_p.I687L	NM_004319	NP_004310	O14525	ASTN1_HUMAN	astrotactin isoform 1	695	EGF-like 3.				cell migration|neuron cell-cell adhesion	integral to membrane				ovary(6)|skin(5)|central_nervous_system(2)|large_intestine(1)|lung(1)	15						TAGTCCTCGATGCACCTAGCA	0.512													7	98	---	---	---	---	PASS
RASAL2	9462	broad.mit.edu	37	1	178433416	178433416	+	Missense_Mutation	SNP	C	G	G			TCGA-39-5024-01A-21D-1817-08	TCGA-39-5024-11A-01D-1817-08									Somatic	Phase_I	Capture				Illumina GAIIx	388478e9-8c1f-43f8-88c4-811bf3cc2500	829ea6e6-1737-4fc6-8732-65e2d7fb2582	g.chr1:178433416C>G	uc001glr.2	+	13	2958	c.2833C>G	c.(2833-2835)CAG>GAG	p.Q945E	RASAL2_uc001glq.2_Missense_Mutation_p.Q1086E|RASAL2_uc009wxc.2_Missense_Mutation_p.Q459E	NM_004841	NP_004832	Q9UJF2	NGAP_HUMAN	RAS protein activator like 2 isoform 1	945					negative regulation of Ras protein signal transduction|signal transduction	cytoplasm|intrinsic to internal side of plasma membrane	Ras GTPase activator activity			ovary(2)|breast(2)|large_intestine(1)	5						GATGCAGGTTCAGTCACCTGT	0.468													11	60	---	---	---	---	PASS
TOR1AIP2	163590	broad.mit.edu	37	1	179815858	179815858	+	Missense_Mutation	SNP	G	A	A			TCGA-39-5024-01A-21D-1817-08	TCGA-39-5024-11A-01D-1817-08									Somatic	Phase_I	Capture				Illumina GAIIx	388478e9-8c1f-43f8-88c4-811bf3cc2500	829ea6e6-1737-4fc6-8732-65e2d7fb2582	g.chr1:179815858G>A	uc001gnk.2	-	6	1149	c.761C>T	c.(760-762)GCC>GTC	p.A254V	TOR1AIP2_uc001gnl.2_Missense_Mutation_p.A254V	NM_145034	NP_659471	Q8NFQ8	TOIP2_HUMAN	torsin A interacting protein 2	254						endoplasmic reticulum membrane|integral to membrane	protein binding			ovary(1)	1						GGCCAAAAAGGCCTCCAAAGC	0.493													35	101	---	---	---	---	PASS
SMG7	9887	broad.mit.edu	37	1	183507541	183507541	+	Missense_Mutation	SNP	T	A	A			TCGA-39-5024-01A-21D-1817-08	TCGA-39-5024-11A-01D-1817-08									Somatic	Phase_I	Capture				Illumina GAIIx	388478e9-8c1f-43f8-88c4-811bf3cc2500	829ea6e6-1737-4fc6-8732-65e2d7fb2582	g.chr1:183507541T>A	uc001gqg.2	+	12	1383	c.1261T>A	c.(1261-1263)TTA>ATA	p.L421I	SMG7_uc010pob.1_Missense_Mutation_p.L450I|SMG7_uc001gqf.2_Missense_Mutation_p.L421I|SMG7_uc001gqh.2_Missense_Mutation_p.L421I|SMG7_uc001gqi.2_Missense_Mutation_p.L379I|SMG7_uc010poc.1_Missense_Mutation_p.L379I	NM_173156	NP_775179	Q92540	SMG7_HUMAN	SMG-7 homolog isoform 1	421					mRNA export from nucleus|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay|regulation of dephosphorylation	cytoplasm|intermediate filament cytoskeleton|nucleus	protein phosphatase 2A binding			upper_aerodigestive_tract(1)|central_nervous_system(1)|skin(1)	3						GGAGTTTGAATTACAAGGATT	0.343													39	164	---	---	---	---	PASS
PLEKHA6	22874	broad.mit.edu	37	1	204237406	204237406	+	Missense_Mutation	SNP	C	A	A			TCGA-39-5024-01A-21D-1817-08	TCGA-39-5024-11A-01D-1817-08									Somatic	Phase_I	Capture				Illumina GAIIx	388478e9-8c1f-43f8-88c4-811bf3cc2500	829ea6e6-1737-4fc6-8732-65e2d7fb2582	g.chr1:204237406C>A	uc001hau.2	-	4	454	c.137G>T	c.(136-138)GGC>GTC	p.G46V		NM_014935	NP_055750	Q9Y2H5	PKHA6_HUMAN	phosphoinositol 3-phosphate-binding protein-3	46										ovary(3)|pancreas(1)	4	all_cancers(21;0.0222)|Breast(84;0.179)		KIRC - Kidney renal clear cell carcinoma(13;0.0584)|BRCA - Breast invasive adenocarcinoma(75;0.0833)|Kidney(21;0.0934)|Epithelial(59;0.229)			TGAGCGCTTGCCAAAGGCGAC	0.607													7	59	---	---	---	---	PASS
DTL	51514	broad.mit.edu	37	1	212273994	212273994	+	Missense_Mutation	SNP	G	C	C			TCGA-39-5024-01A-21D-1817-08	TCGA-39-5024-11A-01D-1817-08									Somatic	Phase_I	Capture				Illumina GAIIx	388478e9-8c1f-43f8-88c4-811bf3cc2500	829ea6e6-1737-4fc6-8732-65e2d7fb2582	g.chr1:212273994G>C	uc009xdc.2	+	14	1976	c.1662G>C	c.(1660-1662)AGG>AGC	p.R554S	DTL_uc010ptb.1_Missense_Mutation_p.R512S|DTL_uc001hiz.3_Missense_Mutation_p.R283S	NM_016448	NP_057532	Q9NZJ0	DTL_HUMAN	denticleless homolog	554					DNA replication|G2/M transition DNA damage checkpoint|protein monoubiquitination|protein polyubiquitination|response to UV|translesion synthesis|ubiquitin-dependent protein catabolic process	centrosome|Cul4A-RING ubiquitin ligase complex|Cul4B-RING ubiquitin ligase complex|nuclear membrane	protein binding				0				OV - Ovarian serous cystadenocarcinoma(81;0.00796)|all cancers(67;0.0385)|Epithelial(68;0.102)		TAAAGAGGAGGCTAGACTCAA	0.448													12	111	---	---	---	---	PASS
RAB4A	5867	broad.mit.edu	37	1	229424565	229424565	+	Missense_Mutation	SNP	G	T	T			TCGA-39-5024-01A-21D-1817-08	TCGA-39-5024-11A-01D-1817-08									Somatic	Phase_I	Capture				Illumina GAIIx	388478e9-8c1f-43f8-88c4-811bf3cc2500	829ea6e6-1737-4fc6-8732-65e2d7fb2582	g.chr1:229424565G>T	uc001hth.2	+	3	410	c.202G>T	c.(202-204)GAT>TAT	p.D68Y	RAB4A_uc001hti.2_RNA|RAB4A_uc001htj.2_Intron	NM_004578	NP_004569	P20338	RAB4A_HUMAN	RAB4A, member RAS oncogene family	63	GTP.						GDP binding|GTP binding|GTPase activity			ovary(1)	1	Breast(184;0.0858)|Ovarian(103;0.103)	Prostate(94;0.178)				ACAAATATGGGATACAGCAGG	0.254													13	119	---	---	---	---	PASS
EXO1	9156	broad.mit.edu	37	1	242042620	242042620	+	Missense_Mutation	SNP	G	A	A			TCGA-39-5024-01A-21D-1817-08	TCGA-39-5024-11A-01D-1817-08									Somatic	Phase_I	Capture				Illumina GAIIx	388478e9-8c1f-43f8-88c4-811bf3cc2500	829ea6e6-1737-4fc6-8732-65e2d7fb2582	g.chr1:242042620G>A	uc001hzh.2	+	13	2624	c.2084G>A	c.(2083-2085)TGC>TAC	p.C695Y	EXO1_uc001hzi.2_Missense_Mutation_p.C695Y|EXO1_uc001hzj.2_Missense_Mutation_p.C695Y|EXO1_uc009xgq.2_Missense_Mutation_p.C694Y	NM_130398	NP_569082	Q9UQ84	EXO1_HUMAN	exonuclease 1 isoform b	695	Interaction with MSH2.				meiosis|mismatch repair	nucleus	double-stranded DNA specific 5'-3' exodeoxyribonuclease activity|flap endonuclease activity|metal ion binding|protein binding|protein binding|ribonuclease H activity|single-stranded DNA specific 5'-3' exodeoxyribonuclease activity			ovary(2)|lung(2)|skin(1)	5	Ovarian(103;0.103)	all_cancers(173;0.0555)	OV - Ovarian serous cystadenocarcinoma(106;0.0107)			CTTTCTCAGTGCTCTAGTAAG	0.393								Direct_reversal_of_damage|Editing_and_processing_nucleases					9	80	---	---	---	---	PASS
OR2M3	127062	broad.mit.edu	37	1	248366988	248366988	+	Missense_Mutation	SNP	A	C	C	rs142664129		TCGA-39-5024-01A-21D-1817-08	TCGA-39-5024-11A-01D-1817-08									Somatic	Phase_I	Capture				Illumina GAIIx	388478e9-8c1f-43f8-88c4-811bf3cc2500	829ea6e6-1737-4fc6-8732-65e2d7fb2582	g.chr1:248366988A>C	uc010pzg.1	+	1	619	c.619A>C	c.(619-621)ATT>CTT	p.I207L		NM_001004689	NP_001004689	Q8NG83	OR2M3_HUMAN	olfactory receptor, family 2, subfamily M,	207	Helical; Name=5; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)|skin(1)	2	all_cancers(71;0.000149)|all_epithelial(71;1.27e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0245)			TATAGTAATGATTGTTTTCCC	0.423													89	254	---	---	---	---	PASS
OR2M7	391196	broad.mit.edu	37	1	248487074	248487074	+	Missense_Mutation	SNP	T	G	G			TCGA-39-5024-01A-21D-1817-08	TCGA-39-5024-11A-01D-1817-08									Somatic	Phase_I	Capture				Illumina GAIIx	388478e9-8c1f-43f8-88c4-811bf3cc2500	829ea6e6-1737-4fc6-8732-65e2d7fb2582	g.chr1:248487074T>G	uc010pzk.1	-	1	797	c.797A>C	c.(796-798)CAT>CCT	p.H266P		NM_001004691	NP_001004691	Q8NG81	OR2M7_HUMAN	olfactory receptor, family 2, subfamily M,	266	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			skin(2)	2	all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0265)			CATAGGAGAATGATGAGATGT	0.473													18	150	---	---	---	---	PASS
APOB	338	broad.mit.edu	37	2	21230157	21230157	+	Missense_Mutation	SNP	C	G	G			TCGA-39-5024-01A-21D-1817-08	TCGA-39-5024-11A-01D-1817-08									Somatic	Phase_I	Capture				Illumina GAIIx	388478e9-8c1f-43f8-88c4-811bf3cc2500	829ea6e6-1737-4fc6-8732-65e2d7fb2582	g.chr2:21230157C>G	uc002red.2	-	26	9711	c.9583G>C	c.(9583-9585)GAG>CAG	p.E3195Q		NM_000384	NP_000375	P04114	APOB_HUMAN	apolipoprotein B precursor	3195	Heparin-binding.				cholesterol homeostasis|cholesterol metabolic process|leukocyte migration|low-density lipoprotein particle clearance|low-density lipoprotein particle remodeling|platelet activation|positive regulation of cholesterol storage|positive regulation of macrophage derived foam cell differentiation|receptor-mediated endocytosis|response to virus	chylomicron remnant|clathrin-coated endocytic vesicle membrane|endoplasmic reticulum lumen|endoplasmic reticulum membrane|endosome lumen|endosome membrane|intermediate-density lipoprotein particle|low-density lipoprotein particle|mature chylomicron|microsome|plasma membrane|very-low-density lipoprotein particle	cholesterol transporter activity|enzyme binding|heparin binding|low-density lipoprotein particle receptor binding|phospholipid binding|protein heterodimerization activity			ovary(11)|skin(9)|central_nervous_system(3)|large_intestine(2)|upper_aerodigestive_tract(1)|pancreas(1)	27	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)				Atorvastatin(DB01076)	CTGATAAACTCACAAAGCACA	0.328													17	54	---	---	---	---	PASS
CAPN13	92291	broad.mit.edu	37	2	31010096	31010096	+	Silent	SNP	G	T	T			TCGA-39-5024-01A-21D-1817-08	TCGA-39-5024-11A-01D-1817-08									Somatic	Phase_I	Capture				Illumina GAIIx	388478e9-8c1f-43f8-88c4-811bf3cc2500	829ea6e6-1737-4fc6-8732-65e2d7fb2582	g.chr2:31010096G>T	uc002rnn.2	-	2	272	c.96C>A	c.(94-96)GGC>GGA	p.G32G	CAPN13_uc002rnp.1_Silent_p.G32G	NM_144575	NP_653176	Q6MZZ7	CAN13_HUMAN	calpain 13	32					proteolysis	intracellular	calcium ion binding|calcium-dependent cysteine-type endopeptidase activity			large_intestine(1)|ovary(1)	2	all_hematologic(175;0.0487)|Acute lymphoblastic leukemia(172;0.155)					TAAACGTCCGGCCCATGCTCA	0.527													5	33	---	---	---	---	PASS
THUMPD2	80745	broad.mit.edu	37	2	39971520	39971520	+	Nonsense_Mutation	SNP	C	A	A			TCGA-39-5024-01A-21D-1817-08	TCGA-39-5024-11A-01D-1817-08									Somatic	Phase_I	Capture				Illumina GAIIx	388478e9-8c1f-43f8-88c4-811bf3cc2500	829ea6e6-1737-4fc6-8732-65e2d7fb2582	g.chr2:39971520C>A	uc002rru.2	-	9	1214	c.1177G>T	c.(1177-1179)GAA>TAA	p.E393*	THUMPD2_uc002rrv.2_RNA|THUMPD2_uc010ynt.1_Nonsense_Mutation_p.E284*	NM_025264	NP_079540	Q9BTF0	THUM2_HUMAN	THUMP domain containing 2	393							methyltransferase activity			skin(1)	1		all_hematologic(82;0.248)				CTTTCCATTTCTTGTAGAATG	0.313													4	40	---	---	---	---	PASS
STON1-GTF2A1L	286749	broad.mit.edu	37	2	48808750	48808750	+	Silent	SNP	A	T	T			TCGA-39-5024-01A-21D-1817-08	TCGA-39-5024-11A-01D-1817-08									Somatic	Phase_I	Capture				Illumina GAIIx	388478e9-8c1f-43f8-88c4-811bf3cc2500	829ea6e6-1737-4fc6-8732-65e2d7fb2582	g.chr2:48808750A>T	uc010yol.1	+	1	1025	c.978A>T	c.(976-978)CCA>CCT	p.P326P	STON1_uc002rwo.3_Silent_p.P326P|STON1_uc010fbm.2_Silent_p.P326P|STON1-GTF2A1L_uc002rwp.1_Silent_p.P326P|STON1_uc002rwr.2_RNA|STON1_uc002rwq.2_Silent_p.P326P	NM_006873	NP_006864	B7ZL16	B7ZL16_HUMAN	stonin 1	326					endocytosis|intracellular protein transport|transcription initiation from RNA polymerase II promoter	clathrin adaptor complex|transcription factor TFIIA complex				ovary(3)|pancreas(1)|skin(1)	5		all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.176)	Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151)			AGCTTGATCCATATTGTAGGC	0.368													16	144	---	---	---	---	PASS
XPO1	7514	broad.mit.edu	37	2	61706014	61706014	+	Missense_Mutation	SNP	G	C	C			TCGA-39-5024-01A-21D-1817-08	TCGA-39-5024-11A-01D-1817-08									Somatic	Phase_I	Capture				Illumina GAIIx	388478e9-8c1f-43f8-88c4-811bf3cc2500	829ea6e6-1737-4fc6-8732-65e2d7fb2582	g.chr2:61706014G>C	uc002sbj.2	-	25	3885	c.3157C>G	c.(3157-3159)CAA>GAA	p.Q1053E	XPO1_uc010fcl.2_Missense_Mutation_p.Q1049E|XPO1_uc010ypn.1_Missense_Mutation_p.Q1049E|XPO1_uc002sbk.2_Missense_Mutation_p.Q614E|XPO1_uc002sbg.2_Missense_Mutation_p.Q250E|XPO1_uc002sbh.2_Missense_Mutation_p.Q700E	NM_003400	NP_003391	O14980	XPO1_HUMAN	exportin 1	1053					intracellular protein transport|mitotic prometaphase|mRNA metabolic process|mRNA transport|viral genome transport in host cell|viral infectious cycle	annulate lamellae|Cajal body|cytosol|kinetochore|nuclear envelope|nucleolus|ribonucleoprotein complex	protein binding|protein transporter activity|RNA binding			ovary(1)|haematopoietic_and_lymphoid_tissue(1)|central_nervous_system(1)|skin(1)	4			LUSC - Lung squamous cell carcinoma(7;5.71e-05)|Epithelial(17;0.0662)|all cancers(80;0.226)			ACAGACATTTGACGTTTATGT	0.388													11	89	---	---	---	---	PASS
EGR4	1961	broad.mit.edu	37	2	73519557	73519557	+	Silent	SNP	A	G	G			TCGA-39-5024-01A-21D-1817-08	TCGA-39-5024-11A-01D-1817-08									Somatic	Phase_I	Capture				Illumina GAIIx	388478e9-8c1f-43f8-88c4-811bf3cc2500	829ea6e6-1737-4fc6-8732-65e2d7fb2582	g.chr2:73519557A>G	uc010yrj.1	-	2	873	c.798T>C	c.(796-798)CCT>CCC	p.P266P	EGR4_uc010yrk.1_Silent_p.P265P	NM_001965	NP_001956	Q05215	EGR4_HUMAN	early growth response 4	162						intracellular	nucleic acid binding|zinc ion binding				0						CACCCGCGCAAGGCGAGGCCT	0.726													8	16	---	---	---	---	PASS
VWA3B	200403	broad.mit.edu	37	2	98804508	98804508	+	Missense_Mutation	SNP	G	A	A			TCGA-39-5024-01A-21D-1817-08	TCGA-39-5024-11A-01D-1817-08									Somatic	Phase_I	Capture				Illumina GAIIx	388478e9-8c1f-43f8-88c4-811bf3cc2500	829ea6e6-1737-4fc6-8732-65e2d7fb2582	g.chr2:98804508G>A	uc002syo.2	+	10	1646	c.1382G>A	c.(1381-1383)AGC>AAC	p.S461N	VWA3B_uc010yvh.1_Missense_Mutation_p.S311N|VWA3B_uc002syj.2_RNA|VWA3B_uc002syk.1_Intron|VWA3B_uc002syl.1_Intron|VWA3B_uc002sym.2_Missense_Mutation_p.S461N|VWA3B_uc002syn.1_Intron|VWA3B_uc010yvi.1_Missense_Mutation_p.S118N	NM_144992	NP_659429	Q502W6	VWA3B_HUMAN	von Willebrand factor A domain containing 3B	461										ovary(3)|large_intestine(2)|skin(1)	6						AAGGATGGGAGCTTGGTCCAC	0.498													9	91	---	---	---	---	PASS
CNTNAP5	129684	broad.mit.edu	37	2	125627272	125627272	+	Silent	SNP	C	T	T			TCGA-39-5024-01A-21D-1817-08	TCGA-39-5024-11A-01D-1817-08									Somatic	Phase_I	Capture				Illumina GAIIx	388478e9-8c1f-43f8-88c4-811bf3cc2500	829ea6e6-1737-4fc6-8732-65e2d7fb2582	g.chr2:125627272C>T	uc002tno.2	+	21	3730	c.3366C>T	c.(3364-3366)CTC>CTT	p.L1122L	CNTNAP5_uc010flu.2_Silent_p.L1123L	NM_130773	NP_570129	Q8WYK1	CNTP5_HUMAN	contactin associated protein-like 5 precursor	1122	Extracellular (Potential).|Laminin G-like 4.				cell adhesion|signal transduction	integral to membrane	receptor binding			ovary(10)	10				BRCA - Breast invasive adenocarcinoma(221;0.248)		AACTTCGACTCAGTTATAACT	0.423													6	41	---	---	---	---	PASS
COBLL1	22837	broad.mit.edu	37	2	165542495	165542495	+	Silent	SNP	G	C	C			TCGA-39-5024-01A-21D-1817-08	TCGA-39-5024-11A-01D-1817-08									Somatic	Phase_I	Capture				Illumina GAIIx	388478e9-8c1f-43f8-88c4-811bf3cc2500	829ea6e6-1737-4fc6-8732-65e2d7fb2582	g.chr2:165542495G>C	uc010zcw.1	-	17	3787	c.3663C>G	c.(3661-3663)CTC>CTG	p.L1221L	COBLL1_uc002ucp.2_Silent_p.L1154L|COBLL1_uc002ucq.2_Silent_p.L1116L|COBLL1_uc010zcx.1_Silent_p.L1162L|COBLL1_uc002ucn.2_Silent_p.L582L|COBLL1_uc002uco.2_Silent_p.L885L	NM_014900	NP_055715	Q53SF7	COBL1_HUMAN	COBL-like 1	1192										ovary(2)|pancreas(1)	3						TGGAATGGCTGAGTCTTGACC	0.438													8	82	---	---	---	---	PASS
PPIG	9360	broad.mit.edu	37	2	170493071	170493071	+	Missense_Mutation	SNP	G	A	A			TCGA-39-5024-01A-21D-1817-08	TCGA-39-5024-11A-01D-1817-08									Somatic	Phase_I	Capture				Illumina GAIIx	388478e9-8c1f-43f8-88c4-811bf3cc2500	829ea6e6-1737-4fc6-8732-65e2d7fb2582	g.chr2:170493071G>A	uc002uez.2	+	14	1523	c.1303G>A	c.(1303-1305)GAG>AAG	p.E435K	PPIG_uc010fpx.2_Missense_Mutation_p.E420K|PPIG_uc010fpy.2_Missense_Mutation_p.E428K|PPIG_uc002ufb.2_Missense_Mutation_p.E435K|PPIG_uc002ufd.2_Missense_Mutation_p.E432K	NM_004792	NP_004783	Q13427	PPIG_HUMAN	peptidylprolyl isomerase G	435					protein folding|RNA splicing	nuclear matrix|nuclear speck	cyclosporin A binding|peptidyl-prolyl cis-trans isomerase activity			ovary(2)|central_nervous_system(1)	3					L-Proline(DB00172)	TAACAGCAAAGAGAGAGACAT	0.323													5	45	---	---	---	---	PASS
TTN	7273	broad.mit.edu	37	2	179494076	179494076	+	Missense_Mutation	SNP	G	C	C			TCGA-39-5024-01A-21D-1817-08	TCGA-39-5024-11A-01D-1817-08									Somatic	Phase_I	Capture				Illumina GAIIx	388478e9-8c1f-43f8-88c4-811bf3cc2500	829ea6e6-1737-4fc6-8732-65e2d7fb2582	g.chr2:179494076G>C	uc010zfg.1	-	189	36896	c.36672C>G	c.(36670-36672)ATC>ATG	p.I12224M	TTN_uc010zfh.1_Missense_Mutation_p.I5919M|TTN_uc010zfi.1_Missense_Mutation_p.I5852M|TTN_uc010zfj.1_Missense_Mutation_p.I5727M	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	13151							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)			ATTCCACTGGGATATCTTCGT	0.483													6	67	---	---	---	---	PASS
TTN	7273	broad.mit.edu	37	2	179593630	179593630	+	Missense_Mutation	SNP	G	T	T			TCGA-39-5024-01A-21D-1817-08	TCGA-39-5024-11A-01D-1817-08									Somatic	Phase_I	Capture				Illumina GAIIx	388478e9-8c1f-43f8-88c4-811bf3cc2500	829ea6e6-1737-4fc6-8732-65e2d7fb2582	g.chr2:179593630G>T	uc010zfg.1	-	62	15627	c.15403C>A	c.(15403-15405)CTT>ATT	p.L5135I	TTN_uc010zfh.1_Intron|TTN_uc010zfi.1_Intron|TTN_uc010zfj.1_Intron|TTN_uc002umz.1_Missense_Mutation_p.L1796I	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	6062							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)			TGTACTAAAAGGAAAGCATAA	0.393													9	47	---	---	---	---	PASS
TTN	7273	broad.mit.edu	37	2	179597601	179597601	+	Silent	SNP	G	T	T			TCGA-39-5024-01A-21D-1817-08	TCGA-39-5024-11A-01D-1817-08									Somatic	Phase_I	Capture				Illumina GAIIx	388478e9-8c1f-43f8-88c4-811bf3cc2500	829ea6e6-1737-4fc6-8732-65e2d7fb2582	g.chr2:179597601G>T	uc010zfg.1	-	52	12794	c.12570C>A	c.(12568-12570)TCC>TCA	p.S4190S	TTN_uc010zfh.1_Intron|TTN_uc010zfi.1_Intron|TTN_uc010zfj.1_Intron|TTN_uc002umz.1_Silent_p.S851S	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	5117							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)			TGCTTCCCACGGAATTTGTGG	0.423													10	55	---	---	---	---	PASS
FZD7	8324	broad.mit.edu	37	2	202900382	202900382	+	Missense_Mutation	SNP	A	G	G			TCGA-39-5024-01A-21D-1817-08	TCGA-39-5024-11A-01D-1817-08									Somatic	Phase_I	Capture				Illumina GAIIx	388478e9-8c1f-43f8-88c4-811bf3cc2500	829ea6e6-1737-4fc6-8732-65e2d7fb2582	g.chr2:202900382A>G	uc002uyw.1	+	1	1073	c.1012A>G	c.(1012-1014)ATC>GTC	p.I338V		NM_003507	NP_003498	O75084	FZD7_HUMAN	frizzled 7 precursor	338	Helical; Name=3; (Potential).				axonogenesis|brain development|canonical Wnt receptor signaling pathway|cellular response to retinoic acid|G-protein signaling, coupled to cGMP nucleotide second messenger|gonad development|mesenchymal to epithelial transition|negative regulation of cell-substrate adhesion|negative regulation of ectodermal cell fate specification|positive regulation of epithelial cell proliferation involved in wound healing|positive regulation of phosphorylation|positive regulation of transcription, DNA-dependent|regulation of catenin import into nucleus|vasculature development|Wnt receptor signaling pathway, calcium modulating pathway	apical part of cell|cytoplasm|integral to membrane|neuron projection membrane	G-protein coupled receptor activity|PDZ domain binding|Wnt receptor activity|Wnt-protein binding			skin(2)|ovary(1)|breast(1)	4						GGGCTGCACCATCCTCTTCAT	0.632											OREG0015146	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	16	61	---	---	---	---	PASS
VIL1	7429	broad.mit.edu	37	2	219295494	219295494	+	Missense_Mutation	SNP	T	G	G			TCGA-39-5024-01A-21D-1817-08	TCGA-39-5024-11A-01D-1817-08									Somatic	Phase_I	Capture				Illumina GAIIx	388478e9-8c1f-43f8-88c4-811bf3cc2500	829ea6e6-1737-4fc6-8732-65e2d7fb2582	g.chr2:219295494T>G	uc002via.2	+	10	1060	c.995T>G	c.(994-996)GTG>GGG	p.V332G	VIL1_uc010zke.1_Missense_Mutation_p.V21G|VIL1_uc002vib.2_Missense_Mutation_p.V332G|VIL1_uc002vic.1_Missense_Mutation_p.V332G	NM_007127	NP_009058	P09327	VILI_HUMAN	villin 1	332	Core.				actin filament capping|actin filament depolymerization|actin filament polymerization|actin filament severing|apoptosis|cellular response to epidermal growth factor stimulus|cytoplasmic actin-based contraction involved in cell motility|epidermal growth factor receptor signaling pathway|positive regulation of actin filament bundle assembly|positive regulation of epithelial cell migration|regulation of actin nucleation|regulation of cell shape|regulation of lamellipodium morphogenesis|regulation of wound healing|response to bacterium	actin filament bundle|cytoplasm|filopodium tip|intracellular membrane-bounded organelle|lamellipodium|microvillus|ruffle	actin filament binding|calcium ion binding|caspase inhibitor activity|lysophosphatidic acid binding|phosphatidylinositol-4,5-bisphosphate binding|protein homodimerization activity			ovary(1)	1		Renal(207;0.0474)		Epithelial(149;6.88e-07)|all cancers(144;0.00013)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		CAGGTGGAGGTGCAGAATGAT	0.582													4	66	---	---	---	---	PASS
PSMD1	5707	broad.mit.edu	37	2	231927224	231927224	+	Missense_Mutation	SNP	G	A	A			TCGA-39-5024-01A-21D-1817-08	TCGA-39-5024-11A-01D-1817-08									Somatic	Phase_I	Capture				Illumina GAIIx	388478e9-8c1f-43f8-88c4-811bf3cc2500	829ea6e6-1737-4fc6-8732-65e2d7fb2582	g.chr2:231927224G>A	uc002vrn.1	+	4	270	c.139G>A	c.(139-141)GTT>ATT	p.V47I	PSMD1_uc002vrm.1_Missense_Mutation_p.V47I|PSMD1_uc010fxu.1_Intron	NM_002807	NP_002798	Q99460	PSMD1_HUMAN	proteasome 26S non-ATPase subunit 1	47					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|mRNA metabolic process|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|regulation of apoptosis|regulation of cellular amino acid metabolic process|regulation of protein catabolic process|S phase of mitotic cell cycle|viral reproduction	proteasome regulatory particle	enzyme regulator activity|protein binding			ovary(1)|skin(1)	2		Ovarian(221;0.000626)|Medulloblastoma(418;0.0109)|Renal(207;0.0112)|Lung NSC(271;0.0538)|all_lung(227;0.0713)|all_hematologic(139;0.0748)|Acute lymphoblastic leukemia(138;0.167)		Epithelial(121;4e-26)|LUSC - Lung squamous cell carcinoma(224;0.0138)|Lung(119;0.0168)	Bortezomib(DB00188)	TTTCAGAGAGGTTTTATACGA	0.393													13	84	---	---	---	---	PASS
C2orf57	165100	broad.mit.edu	37	2	232458735	232458735	+	Missense_Mutation	SNP	C	G	G			TCGA-39-5024-01A-21D-1817-08	TCGA-39-5024-11A-01D-1817-08									Somatic	Phase_I	Capture				Illumina GAIIx	388478e9-8c1f-43f8-88c4-811bf3cc2500	829ea6e6-1737-4fc6-8732-65e2d7fb2582	g.chr2:232458735C>G	uc002vrz.2	+	1	1124	c.1073C>G	c.(1072-1074)ACC>AGC	p.T358S		NM_152614	NP_689827	Q53QW1	CB057_HUMAN	hypothetical protein LOC165100	358										ovary(1)	1		Renal(207;0.025)|all_hematologic(139;0.0735)|Acute lymphoblastic leukemia(138;0.164)		Epithelial(121;1.33e-11)|LUSC - Lung squamous cell carcinoma(224;0.0115)|Lung(119;0.014)		CGCACCATCACCCGTGTGCTG	0.687													9	70	---	---	---	---	PASS
DGKD	8527	broad.mit.edu	37	2	234366959	234366959	+	Missense_Mutation	SNP	G	T	T			TCGA-39-5024-01A-21D-1817-08	TCGA-39-5024-11A-01D-1817-08									Somatic	Phase_I	Capture				Illumina GAIIx	388478e9-8c1f-43f8-88c4-811bf3cc2500	829ea6e6-1737-4fc6-8732-65e2d7fb2582	g.chr2:234366959G>T	uc002vui.1	+	22	2622	c.2610G>T	c.(2608-2610)AAG>AAT	p.K870N	DGKD_uc002vuj.1_Missense_Mutation_p.K826N|DGKD_uc010fyi.1_RNA	NM_152879	NP_690618	Q16760	DGKD_HUMAN	diacylglycerol kinase, delta 130kDa isoform 2	870					activation of protein kinase C activity by G-protein coupled receptor protein signaling pathway|cell growth|diacylglycerol metabolic process|endocytosis|epidermal growth factor receptor signaling pathway|multicellular organismal development|platelet activation|protein homooligomerization|protein transport|response to organic substance|second-messenger-mediated signaling	cytoplasm|cytoplasmic membrane-bounded vesicle|plasma membrane|plasma membrane	ATP binding|diacylglycerol binding|diacylglycerol kinase activity|metal ion binding|protein heterodimerization activity|protein homodimerization activity			central_nervous_system(2)|pancreas(1)|lung(1)|skin(1)	5		Breast(86;0.0013)|Renal(207;0.00339)|all_hematologic(139;0.0116)|all_lung(227;0.0179)|Acute lymphoblastic leukemia(138;0.0326)|Lung NSC(271;0.0538)		Epithelial(121;1.31e-16)|BRCA - Breast invasive adenocarcinoma(100;0.000416)|Lung(119;0.00285)|LUSC - Lung squamous cell carcinoma(224;0.00655)	Phosphatidylserine(DB00144)	TCGATGACAAGATTCTGGAGG	0.592													8	40	---	---	---	---	PASS
CNTN6	27255	broad.mit.edu	37	3	1427380	1427380	+	Missense_Mutation	SNP	G	A	A			TCGA-39-5024-01A-21D-1817-08	TCGA-39-5024-11A-01D-1817-08									Somatic	Phase_I	Capture				Illumina GAIIx	388478e9-8c1f-43f8-88c4-811bf3cc2500	829ea6e6-1737-4fc6-8732-65e2d7fb2582	g.chr3:1427380G>A	uc003boz.2	+	20	2870	c.2603G>A	c.(2602-2604)GGG>GAG	p.G868E	CNTN6_uc011asj.1_Missense_Mutation_p.G796E|CNTN6_uc003bpa.2_Missense_Mutation_p.G868E	NM_014461	NP_055276	Q9UQ52	CNTN6_HUMAN	contactin 6 precursor	868	Fibronectin type-III 3.				axon guidance|cell adhesion|central nervous system development|Notch signaling pathway	anchored to membrane|plasma membrane				skin(3)|lung(2)|breast(2)|pancreas(1)	8		all_cancers(2;0.000164)|all_epithelial(2;0.107)		Epithelial(13;0.000233)|all cancers(10;0.0013)|OV - Ovarian serous cystadenocarcinoma(96;0.0139)		AACATCACGGGGCTGAAAGCT	0.428													28	124	---	---	---	---	PASS
KCNH8	131096	broad.mit.edu	37	3	19491639	19491639	+	Missense_Mutation	SNP	A	T	T			TCGA-39-5024-01A-21D-1817-08	TCGA-39-5024-11A-01D-1817-08									Somatic	Phase_I	Capture				Illumina GAIIx	388478e9-8c1f-43f8-88c4-811bf3cc2500	829ea6e6-1737-4fc6-8732-65e2d7fb2582	g.chr3:19491639A>T	uc003cbk.1	+	9	1612	c.1417A>T	c.(1417-1419)ATA>TTA	p.I473L	KCNH8_uc011awe.1_Missense_Mutation_p.I473L|KCNH8_uc010hex.1_5'UTR|KCNH8_uc011awf.1_Missense_Mutation_p.I132L	NM_144633	NP_653234	Q96L42	KCNH8_HUMAN	potassium voltage-gated channel, subfamily H,	473	Cytoplasmic (Potential).					integral to membrane	two-component sensor activity			lung(4)|ovary(1)	5						GACAGCAATCATACAGAGGAT	0.453													17	66	---	---	---	---	PASS
PBRM1	55193	broad.mit.edu	37	3	52682440	52682440	+	Missense_Mutation	SNP	T	A	A			TCGA-39-5024-01A-21D-1817-08	TCGA-39-5024-11A-01D-1817-08									Somatic	Phase_I	Capture				Illumina GAIIx	388478e9-8c1f-43f8-88c4-811bf3cc2500	829ea6e6-1737-4fc6-8732-65e2d7fb2582	g.chr3:52682440T>A	uc003des.2	-	7	745	c.733A>T	c.(733-735)ATT>TTT	p.I245F	PBRM1_uc003dex.2_RNA|PBRM1_uc003deq.2_Missense_Mutation_p.I245F|PBRM1_uc003der.2_Missense_Mutation_p.I245F|PBRM1_uc003det.2_Missense_Mutation_p.I245F|PBRM1_uc003deu.2_Missense_Mutation_p.I245F|PBRM1_uc003dev.2_RNA|PBRM1_uc003dew.2_Missense_Mutation_p.I245F|PBRM1_uc010hmk.1_Missense_Mutation_p.I245F|PBRM1_uc003dey.2_Missense_Mutation_p.I245F|PBRM1_uc003dez.1_Missense_Mutation_p.I245F|PBRM1_uc003dfb.1_Missense_Mutation_p.I143F	NM_181042	NP_060635	Q86U86	PB1_HUMAN	polybromo 1 isoform 4	245	Bromo 2.				chromatin remodeling|mitosis|negative regulation of cell proliferation|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nuclear chromosome	chromatin binding|DNA binding|protein binding			kidney(136)|breast(4)	140				BRCA - Breast invasive adenocarcinoma(193;1.8e-05)|Kidney(197;0.00105)|KIRC - Kidney renal clear cell carcinoma(197;0.00122)|OV - Ovarian serous cystadenocarcinoma(275;0.0613)		ATTGCATGAATACTTTTGTAG	0.313			Mis|N|F|S|D|O		clear cell renal carcinoma|breast								19	79	---	---	---	---	PASS
CBLB	868	broad.mit.edu	37	3	105421219	105421219	+	Missense_Mutation	SNP	C	T	T			TCGA-39-5024-01A-21D-1817-08	TCGA-39-5024-11A-01D-1817-08									Somatic	Phase_I	Capture				Illumina GAIIx	388478e9-8c1f-43f8-88c4-811bf3cc2500	829ea6e6-1737-4fc6-8732-65e2d7fb2582	g.chr3:105421219C>T	uc003dwc.2	-	12	2000	c.1678G>A	c.(1678-1680)GAA>AAA	p.E560K	CBLB_uc011bhi.1_Missense_Mutation_p.E582K|CBLB_uc003dwd.1_Missense_Mutation_p.E560K|CBLB_uc003dwe.1_Missense_Mutation_p.E560K	NM_170662	NP_733762	Q13191	CBLB_HUMAN	Cas-Br-M (murine) ecotropic retroviral	560	Interaction with VAV1.|Pro-rich.				cell surface receptor linked signaling pathway|NLS-bearing substrate import into nucleus	cytoplasm|nucleus	calcium ion binding|ligase activity|signal transducer activity|zinc ion binding			lung(4)|ovary(3)|breast(1)|skin(1)	9						GGAGGTCTTTCAGGTGGCGGT	0.483			Mis S		AML								10	84	---	---	---	---	PASS
KIAA1524	57650	broad.mit.edu	37	3	108288392	108288392	+	Missense_Mutation	SNP	C	T	T			TCGA-39-5024-01A-21D-1817-08	TCGA-39-5024-11A-01D-1817-08									Somatic	Phase_I	Capture				Illumina GAIIx	388478e9-8c1f-43f8-88c4-811bf3cc2500	829ea6e6-1737-4fc6-8732-65e2d7fb2582	g.chr3:108288392C>T	uc003dxb.3	-	9	1226	c.957G>A	c.(955-957)ATG>ATA	p.M319I	KIAA1524_uc010hpv.1_5'Flank|KIAA1524_uc003dxc.1_Missense_Mutation_p.M160I|KIAA1524_uc010hpw.1_Missense_Mutation_p.M160I	NM_020890	NP_065941	Q8TCG1	CIP2A_HUMAN	p90 autoantigen	319						cytoplasm|integral to membrane	protein binding			ovary(2)|central_nervous_system(1)	3						GTTCAAACATCATCTGAGTGA	0.443													4	53	---	---	---	---	PASS
KIAA2018	205717	broad.mit.edu	37	3	113376876	113376876	+	Missense_Mutation	SNP	C	T	T			TCGA-39-5024-01A-21D-1817-08	TCGA-39-5024-11A-01D-1817-08									Somatic	Phase_I	Capture				Illumina GAIIx	388478e9-8c1f-43f8-88c4-811bf3cc2500	829ea6e6-1737-4fc6-8732-65e2d7fb2582	g.chr3:113376876C>T	uc003eam.2	-	7	4064	c.3653G>A	c.(3652-3654)GGA>GAA	p.G1218E	KIAA2018_uc003eal.2_Missense_Mutation_p.G1162E	NM_001009899	NP_001009899	Q68DE3	K2018_HUMAN	hypothetical protein LOC205717	1218					regulation of transcription, DNA-dependent	membrane|nucleus	calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity			skin(2)|ovary(1)	3						TGTTTTAATTCCTAGAGAACA	0.418													15	96	---	---	---	---	PASS
GTF2E1	2960	broad.mit.edu	37	3	120489615	120489615	+	Missense_Mutation	SNP	G	C	C			TCGA-39-5024-01A-21D-1817-08	TCGA-39-5024-11A-01D-1817-08									Somatic	Phase_I	Capture				Illumina GAIIx	388478e9-8c1f-43f8-88c4-811bf3cc2500	829ea6e6-1737-4fc6-8732-65e2d7fb2582	g.chr3:120489615G>C	uc003edz.3	+	3	603	c.489G>C	c.(487-489)GAG>GAC	p.E163D		NM_005513	NP_005504	P29083	T2EA_HUMAN	general transcription factor IIE, polypeptide 1,	163					interspecies interaction between organisms|regulation of transcription, DNA-dependent|transcription elongation from RNA polymerase II promoter|transcription initiation from RNA polymerase II promoter|viral reproduction	nucleoplasm	protein binding|zinc ion binding			ovary(1)	1				GBM - Glioblastoma multiforme(114;0.159)		AGGTAGAAGAGGATGAATCAG	0.418													7	237	---	---	---	---	PASS
POLQ	10721	broad.mit.edu	37	3	121200502	121200502	+	Missense_Mutation	SNP	C	A	A			TCGA-39-5024-01A-21D-1817-08	TCGA-39-5024-11A-01D-1817-08									Somatic	Phase_I	Capture				Illumina GAIIx	388478e9-8c1f-43f8-88c4-811bf3cc2500	829ea6e6-1737-4fc6-8732-65e2d7fb2582	g.chr3:121200502C>A	uc003eee.3	-	19	6257	c.6128G>T	c.(6127-6129)CGA>CTA	p.R2043L	POLQ_uc003eed.2_Missense_Mutation_p.R1215L	NM_199420	NP_955452	O75417	DPOLQ_HUMAN	DNA polymerase theta	2043					DNA repair|DNA replication	nucleoplasm	ATP binding|ATP-dependent helicase activity|damaged DNA binding|DNA-directed DNA polymerase activity|single-stranded DNA-dependent ATPase activity	p.G2043S(1)		ovary(4)|breast(3)|lung(2)|upper_aerodigestive_tract(1)|skin(1)	11				GBM - Glioblastoma multiforme(114;0.0915)		TGCTCTGTATCGCCCAGAATG	0.463								DNA_polymerases_(catalytic_subunits)					16	91	---	---	---	---	PASS
KALRN	8997	broad.mit.edu	37	3	124132412	124132412	+	Silent	SNP	G	A	A			TCGA-39-5024-01A-21D-1817-08	TCGA-39-5024-11A-01D-1817-08									Somatic	Phase_I	Capture				Illumina GAIIx	388478e9-8c1f-43f8-88c4-811bf3cc2500	829ea6e6-1737-4fc6-8732-65e2d7fb2582	g.chr3:124132412G>A	uc003ehg.2	+	14	2563	c.2436G>A	c.(2434-2436)CAG>CAA	p.Q812Q	KALRN_uc010hrv.1_Silent_p.Q812Q|KALRN_uc003ehf.1_Silent_p.Q812Q|KALRN_uc011bjy.1_Silent_p.Q812Q|KALRN_uc003ehh.1_Silent_p.Q158Q	NM_001024660	NP_001019831	O60229	KALRN_HUMAN	kalirin, RhoGEF kinase isoform 1	812					apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|nervous system development|regulation of Rho protein signal transduction|small GTPase mediated signal transduction|vesicle-mediated transport	actin cytoskeleton|cytosol	ATP binding|GTPase activator activity|metal ion binding|protein binding|protein serine/threonine kinase activity|Rho guanyl-nucleotide exchange factor activity			large_intestine(2)|ovary(2)|central_nervous_system(1)|skin(1)	6						AGCGGCTGCAGCGCCACACAG	0.542													19	54	---	---	---	---	PASS
RUVBL1	8607	broad.mit.edu	37	3	127872540	127872540	+	Translation_Start_Site	SNP	C	A	A			TCGA-39-5024-01A-21D-1817-08	TCGA-39-5024-11A-01D-1817-08									Somatic	Phase_I	Capture				Illumina GAIIx	388478e9-8c1f-43f8-88c4-811bf3cc2500	829ea6e6-1737-4fc6-8732-65e2d7fb2582	g.chr3:127872540C>A	uc003ekf.2	-	1	218	c.-533G>T	c.(-535--531)CAGGC>CATGC		EEFSEC_uc003eki.2_Missense_Mutation_p.L64M|EEFSEC_uc003ekj.2_Missense_Mutation_p.L64M	NM_003707	NP_003698	Q9Y265	RUVB1_HUMAN	RuvB-like 1						cell division|CenH3-containing nucleosome assembly at centromere|DNA recombination|DNA repair|histone H2A acetylation|histone H4 acetylation|mitosis|regulation of growth|regulation of transcription from RNA polymerase II promoter|spermatogenesis|transcription, DNA-dependent	Golgi apparatus|Ino80 complex|membrane|microtubule organizing center|MLL1 complex|NuA4 histone acetyltransferase complex|nuclear matrix	ATP binding|DNA helicase activity|protein binding			skin(1)	1				GBM - Glioblastoma multiforme(114;0.181)		GCCCGCGCGCCTGCGGTCGTC	0.721													3	16	---	---	---	---	PASS
DNAJC13	23317	broad.mit.edu	37	3	132201158	132201158	+	Missense_Mutation	SNP	C	G	G			TCGA-39-5024-01A-21D-1817-08	TCGA-39-5024-11A-01D-1817-08									Somatic	Phase_I	Capture				Illumina GAIIx	388478e9-8c1f-43f8-88c4-811bf3cc2500	829ea6e6-1737-4fc6-8732-65e2d7fb2582	g.chr3:132201158C>G	uc003eor.2	+	27	3028	c.2963C>G	c.(2962-2964)CCG>CGG	p.P988R		NM_015268	NP_056083	O75165	DJC13_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 13	988							heat shock protein binding			ovary(1)|breast(1)	2						AGGAGTGGCCCGTATGGATTT	0.413													9	40	---	---	---	---	PASS
STAG1	10274	broad.mit.edu	37	3	136068192	136068192	+	Missense_Mutation	SNP	C	T	T			TCGA-39-5024-01A-21D-1817-08	TCGA-39-5024-11A-01D-1817-08									Somatic	Phase_I	Capture				Illumina GAIIx	388478e9-8c1f-43f8-88c4-811bf3cc2500	829ea6e6-1737-4fc6-8732-65e2d7fb2582	g.chr3:136068192C>T	uc003era.1	-	29	3371	c.3079G>A	c.(3079-3081)GAG>AAG	p.E1027K	STAG1_uc003erb.1_Missense_Mutation_p.E1027K	NM_005862	NP_005853	Q8WVM7	STAG1_HUMAN	stromal antigen 1	1027					cell division|chromosome segregation|mitotic metaphase/anaphase transition|mitotic prometaphase	cell junction|chromatin|chromosome, centromeric region|nucleoplasm	protein binding			ovary(2)	2						AGGAATTTCTCTAGGTATGAA	0.403													6	57	---	---	---	---	PASS
TM4SF4	7104	broad.mit.edu	37	3	149216522	149216522	+	Missense_Mutation	SNP	G	T	T			TCGA-39-5024-01A-21D-1817-08	TCGA-39-5024-11A-01D-1817-08									Somatic	Phase_I	Capture				Illumina GAIIx	388478e9-8c1f-43f8-88c4-811bf3cc2500	829ea6e6-1737-4fc6-8732-65e2d7fb2582	g.chr3:149216522G>T	uc003exd.1	+	4	646	c.415G>T	c.(415-417)GAT>TAT	p.D139Y		NM_004617	NP_004608	P48230	T4S4_HUMAN	transmembrane 4 superfamily member 4	139	Extracellular (Potential).					integral to membrane					0			LUSC - Lung squamous cell carcinoma(72;0.0378)|Lung(72;0.048)			TTATCTCAATGATGAGGCCTT	0.448													13	72	---	---	---	---	PASS
KCNAB1	7881	broad.mit.edu	37	3	156232996	156232996	+	Silent	SNP	C	A	A			TCGA-39-5024-01A-21D-1817-08	TCGA-39-5024-11A-01D-1817-08									Somatic	Phase_I	Capture				Illumina GAIIx	388478e9-8c1f-43f8-88c4-811bf3cc2500	829ea6e6-1737-4fc6-8732-65e2d7fb2582	g.chr3:156232996C>A	uc003far.2	+	10	916	c.852C>A	c.(850-852)CTC>CTA	p.L284L	KCNAB1_uc011bon.1_Silent_p.L255L|KCNAB1_uc003fas.2_Silent_p.L273L|KCNAB1_uc003fat.2_Silent_p.L266L|KCNAB1_uc010hvt.1_Silent_p.L237L|KCNAB1_uc011boo.1_Silent_p.L160L	NM_172160	NP_751892	Q14722	KCAB1_HUMAN	potassium voltage-gated channel, shaker-related	284						cytoplasm|integral to membrane	oxidoreductase activity|potassium channel regulator activity|voltage-gated potassium channel activity			ovary(3)|skin(1)	4			LUSC - Lung squamous cell carcinoma(72;0.0461)|Lung(72;0.0465)			TGCCAGAGCTCTACCACAAAA	0.383													10	84	---	---	---	---	PASS
CHRD	8646	broad.mit.edu	37	3	184104631	184104631	+	Splice_Site	SNP	A	G	G			TCGA-39-5024-01A-21D-1817-08	TCGA-39-5024-11A-01D-1817-08									Somatic	Phase_I	Capture				Illumina GAIIx	388478e9-8c1f-43f8-88c4-811bf3cc2500	829ea6e6-1737-4fc6-8732-65e2d7fb2582	g.chr3:184104631A>G	uc003fov.2	+	17	2443	c.2197_splice	c.e17-2	p.R733_splice	CHRD_uc003fow.2_Splice_Site_p.R363_splice|CHRD_uc003fox.2_Splice_Site_p.R733_splice|CHRD_uc003foy.2_Splice_Site_p.R363_splice|CHRD_uc010hyc.2_Splice_Site_p.R323_splice|CHRD_uc011brr.1_Splice_Site_p.R275_splice	NM_003741	NP_003732	Q9H2X0	CHRD_HUMAN	chordin precursor						BMP signaling pathway involved in spinal cord dorsal/ventral patterning|floor plate development|negative regulation of BMP signaling pathway|negative regulation of cell migration|positive regulation of cell adhesion|skeletal system development	extracellular space	cytokine binding			skin(2)|ovary(1)	3	all_cancers(143;6.33e-11)|Ovarian(172;0.0339)		Epithelial(37;4.96e-33)|OV - Ovarian serous cystadenocarcinoma(80;2.72e-22)			TCCTCTCTGCAGAGACGAACG	0.657													3	67	---	---	---	---	PASS
LIPH	200879	broad.mit.edu	37	3	185236980	185236980	+	Missense_Mutation	SNP	C	A	A			TCGA-39-5024-01A-21D-1817-08	TCGA-39-5024-11A-01D-1817-08									Somatic	Phase_I	Capture				Illumina GAIIx	388478e9-8c1f-43f8-88c4-811bf3cc2500	829ea6e6-1737-4fc6-8732-65e2d7fb2582	g.chr3:185236980C>A	uc003fpm.2	-	6	946	c.836G>T	c.(835-837)GGC>GTC	p.G279V	LIPH_uc010hyh.2_Missense_Mutation_p.G245V	NM_139248	NP_640341	Q8WWY8	LIPH_HUMAN	lipase, member H precursor	279					lipid catabolic process	extracellular space|plasma membrane	heparin binding|phospholipase activity			ovary(1)|pancreas(1)	2	all_cancers(143;8.87e-11)|Ovarian(172;0.0386)		OV - Ovarian serous cystadenocarcinoma(80;1.31e-21)			GACACACTTGCCATTCCTATA	0.488													34	276	---	---	---	---	PASS
EVC	2121	broad.mit.edu	37	4	5743447	5743447	+	Missense_Mutation	SNP	T	A	A			TCGA-39-5024-01A-21D-1817-08	TCGA-39-5024-11A-01D-1817-08									Somatic	Phase_I	Capture				Illumina GAIIx	388478e9-8c1f-43f8-88c4-811bf3cc2500	829ea6e6-1737-4fc6-8732-65e2d7fb2582	g.chr4:5743447T>A	uc003gil.1	+	6	891	c.707T>A	c.(706-708)TTT>TAT	p.F236Y	EVC_uc003gim.1_RNA	NM_153717	NP_714928	P57679	EVC_HUMAN	Ellis van Creveld syndrome protein	236					muscle organ development	integral to membrane				ovary(1)|skin(1)	2		Myeloproliferative disorder(84;0.117)				CAATAGATGTTTATTCAGATT	0.234													9	64	---	---	---	---	PASS
PACRGL	133015	broad.mit.edu	37	4	20711365	20711365	+	Nonsense_Mutation	SNP	C	G	G			TCGA-39-5024-01A-21D-1817-08	TCGA-39-5024-11A-01D-1817-08									Somatic	Phase_I	Capture				Illumina GAIIx	388478e9-8c1f-43f8-88c4-811bf3cc2500	829ea6e6-1737-4fc6-8732-65e2d7fb2582	g.chr4:20711365C>G	uc010iek.2	+	5	726	c.335C>G	c.(334-336)TCA>TGA	p.S112*	PACRGL_uc003gpu.2_RNA|PACRGL_uc010iei.1_Nonsense_Mutation_p.S160*|PACRGL_uc003gpz.2_Nonsense_Mutation_p.S112*|PACRGL_uc011bxm.1_Intron|PACRGL_uc003gqa.2_Intron|PACRGL_uc003gpx.3_RNA|PACRGL_uc003gpv.2_Nonsense_Mutation_p.S112*|PACRGL_uc003gpw.2_RNA|PACRGL_uc010iej.1_RNA|PACRGL_uc011bxn.1_Intron|PACRGL_uc003gpy.2_Intron	NM_145048	NP_659485	Q8N7B6	PACRL_HUMAN	PARK2 co-regulated-like isoform 1	112							binding				0						GAAAGTCTTTCATTTGATCCA	0.289													7	112	---	---	---	---	PASS
SLC34A2	10568	broad.mit.edu	37	4	25677891	25677891	+	Missense_Mutation	SNP	C	G	G			TCGA-39-5024-01A-21D-1817-08	TCGA-39-5024-11A-01D-1817-08									Somatic	Phase_I	Capture				Illumina GAIIx	388478e9-8c1f-43f8-88c4-811bf3cc2500	829ea6e6-1737-4fc6-8732-65e2d7fb2582	g.chr4:25677891C>G	uc003grr.2	+	13	1674	c.1593C>G	c.(1591-1593)TTC>TTG	p.F531L	SLC34A2_uc003grs.2_Missense_Mutation_p.F530L|SLC34A2_uc010iev.2_Missense_Mutation_p.F530L	NM_006424	NP_006415	O95436	NPT2B_HUMAN	solute carrier family 34 (sodium phosphate),	531	Helical; Name=M7; (Potential).				cellular phosphate ion homeostasis	apical plasma membrane|brush border membrane|integral to plasma membrane	phosphate binding|sodium ion binding|sodium-dependent phosphate transmembrane transporter activity|sodium:phosphate symporter activity			skin(3)|ovary(1)|kidney(1)	5		Breast(46;0.0503)				TCGCCGTCTTCTACCTGATCA	0.612													24	159	---	---	---	---	PASS
NFXL1	152518	broad.mit.edu	37	4	47877170	47877170	+	Missense_Mutation	SNP	C	G	G			TCGA-39-5024-01A-21D-1817-08	TCGA-39-5024-11A-01D-1817-08									Somatic	Phase_I	Capture				Illumina GAIIx	388478e9-8c1f-43f8-88c4-811bf3cc2500	829ea6e6-1737-4fc6-8732-65e2d7fb2582	g.chr4:47877170C>G	uc010igh.2	-	18	2397	c.2220G>C	c.(2218-2220)AAG>AAC	p.K740N	NFXL1_uc003gxo.2_Missense_Mutation_p.K65N|NFXL1_uc003gxp.2_Missense_Mutation_p.K740N|NFXL1_uc003gxq.3_RNA|NFXL1_uc010igi.2_Missense_Mutation_p.K740N	NM_152995	NP_694540	Q6ZNB6	NFXL1_HUMAN	nuclear transcription factor, X-box binding-like	740						integral to membrane|nucleus	sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)|lung(1)|skin(1)	3						GGCTTGTGATCTTACAGTGAC	0.363													9	63	---	---	---	---	PASS
FRYL	285527	broad.mit.edu	37	4	48581237	48581237	+	Missense_Mutation	SNP	T	C	C			TCGA-39-5024-01A-21D-1817-08	TCGA-39-5024-11A-01D-1817-08									Somatic	Phase_I	Capture				Illumina GAIIx	388478e9-8c1f-43f8-88c4-811bf3cc2500	829ea6e6-1737-4fc6-8732-65e2d7fb2582	g.chr4:48581237T>C	uc003gyh.1	-	23	2886	c.2281A>G	c.(2281-2283)AGC>GGC	p.S761G	FRYL_uc003gyk.2_Missense_Mutation_p.S761G	NM_015030	NP_055845	O94915	FRYL_HUMAN	furry-like	761					regulation of transcription, DNA-dependent|transcription, DNA-dependent		protein binding			skin(1)	1						TCTATCGAGCTAGGGCAATAG	0.318													6	53	---	---	---	---	PASS
TECRL	253017	broad.mit.edu	37	4	65175614	65175614	+	Missense_Mutation	SNP	C	G	G			TCGA-39-5024-01A-21D-1817-08	TCGA-39-5024-11A-01D-1817-08									Somatic	Phase_I	Capture				Illumina GAIIx	388478e9-8c1f-43f8-88c4-811bf3cc2500	829ea6e6-1737-4fc6-8732-65e2d7fb2582	g.chr4:65175614C>G	uc003hcv.2	-	6	696	c.587G>C	c.(586-588)CGA>CCA	p.R196P	TECRL_uc003hcw.2_Missense_Mutation_p.R196P	NM_001010874	NP_001010874	Q5HYJ1	TECRL_HUMAN	steroid 5 alpha-reductase 2-like 2	196					lipid metabolic process	cytoplasm|integral to membrane	oxidoreductase activity, acting on the CH-CH group of donors				0						CAAAAGGTATCGGATGTAGTG	0.343													26	120	---	---	---	---	PASS
UGT2B28	54490	broad.mit.edu	37	4	70156509	70156509	+	Silent	SNP	G	A	A			TCGA-39-5024-01A-21D-1817-08	TCGA-39-5024-11A-01D-1817-08									Somatic	Phase_I	Capture				Illumina GAIIx	388478e9-8c1f-43f8-88c4-811bf3cc2500	829ea6e6-1737-4fc6-8732-65e2d7fb2582	g.chr4:70156509G>A	uc003hej.2	+	5	1292	c.1290G>A	c.(1288-1290)AAG>AAA	p.K430K	UGT2B28_uc010ihr.2_Intron	NM_053039	NP_444267	Q9BY64	UDB28_HUMAN	UDP glucuronosyltransferase 2 family,	430					xenobiotic metabolic process	endoplasmic reticulum membrane|integral to membrane|microsome	glucuronosyltransferase activity			skin(1)	1					Flunitrazepam(DB01544)	ATGCACTGAAGACAGTAATTA	0.418													35	135	---	---	---	---	PASS
UGT2B4	7363	broad.mit.edu	37	4	70361034	70361034	+	Missense_Mutation	SNP	C	G	G			TCGA-39-5024-01A-21D-1817-08	TCGA-39-5024-11A-01D-1817-08									Somatic	Phase_I	Capture				Illumina GAIIx	388478e9-8c1f-43f8-88c4-811bf3cc2500	829ea6e6-1737-4fc6-8732-65e2d7fb2582	g.chr4:70361034C>G	uc003hek.3	-	1	593	c.546G>C	c.(544-546)AAG>AAC	p.K182N	UGT2B4_uc011cap.1_Missense_Mutation_p.K46N|UGT2B4_uc003hel.3_Missense_Mutation_p.K182N	NM_021139	NP_066962	P06133	UD2B4_HUMAN	UDP glucuronosyltransferase 2B4 precursor	182					estrogen catabolic process|xenobiotic metabolic process	endoplasmic reticulum membrane|integral to membrane|microsome	glucuronosyltransferase activity			skin(2)	2						CTCCACTATGCTTTTCAATTG	0.443													6	55	---	---	---	---	PASS
SEC31A	22872	broad.mit.edu	37	4	83778220	83778220	+	Missense_Mutation	SNP	C	G	G			TCGA-39-5024-01A-21D-1817-08	TCGA-39-5024-11A-01D-1817-08									Somatic	Phase_I	Capture				Illumina GAIIx	388478e9-8c1f-43f8-88c4-811bf3cc2500	829ea6e6-1737-4fc6-8732-65e2d7fb2582	g.chr4:83778220C>G	uc003hnf.2	-	16	1930	c.1766G>C	c.(1765-1767)TGT>TCT	p.C589S	SEC31A_uc003hne.2_Missense_Mutation_p.C322S|SEC31A_uc011ccl.1_Missense_Mutation_p.C550S|SEC31A_uc003hnl.2_Missense_Mutation_p.C550S|SEC31A_uc003hng.2_Missense_Mutation_p.C589S|SEC31A_uc003hnh.2_Missense_Mutation_p.C589S|SEC31A_uc003hni.2_Missense_Mutation_p.C589S|SEC31A_uc003hnj.2_Missense_Mutation_p.C550S|SEC31A_uc011ccm.1_Missense_Mutation_p.C584S|SEC31A_uc011ccn.1_Missense_Mutation_p.C589S|SEC31A_uc003hnk.2_Missense_Mutation_p.C550S|SEC31A_uc003hnm.2_Missense_Mutation_p.C589S|SEC31A_uc003hnn.1_Missense_Mutation_p.C589S	NM_001077207	NP_001070675	O94979	SC31A_HUMAN	SEC31 homolog A isoform 1	589					COPII vesicle coating|post-translational protein modification|protein N-linked glycosylation via asparagine|protein transport|response to calcium ion	COPII vesicle coat|cytosol|endoplasmic reticulum membrane|perinuclear region of cytoplasm	calcium-dependent protein binding		SEC31A/JAK2(4)|SEC31A/ALK(3)	haematopoietic_and_lymphoid_tissue(4)|soft_tissue(3)|breast(1)	8		Hepatocellular(203;0.114)				ATCATGTAAACAAAGGTCAAC	0.408													6	56	---	---	---	---	PASS
GRID2	2895	broad.mit.edu	37	4	94344073	94344073	+	Missense_Mutation	SNP	A	C	C			TCGA-39-5024-01A-21D-1817-08	TCGA-39-5024-11A-01D-1817-08									Somatic	Phase_I	Capture				Illumina GAIIx	388478e9-8c1f-43f8-88c4-811bf3cc2500	829ea6e6-1737-4fc6-8732-65e2d7fb2582	g.chr4:94344073A>C	uc011cdt.1	+	10	1757	c.1499A>C	c.(1498-1500)CAA>CCA	p.Q500P	GRID2_uc011cdu.1_Missense_Mutation_p.Q405P	NM_001510	NP_001501	O43424	GRID2_HUMAN	glutamate receptor, ionotropic, delta 2	500	Extracellular (Potential).				glutamate signaling pathway	cell junction|integral to plasma membrane|outer membrane-bounded periplasmic space|postsynaptic membrane	extracellular-glutamate-gated ion channel activity|ionotropic glutamate receptor activity			ovary(3)|skin(2)|large_intestine(1)	6		Hepatocellular(203;0.114)|all_hematologic(202;0.177)		OV - Ovarian serous cystadenocarcinoma(123;3.22e-06)|LUSC - Lung squamous cell carcinoma(81;0.185)|Lung(65;0.191)	L-Glutamic Acid(DB00142)	GGAAGCCCACAAGAAGATGGG	0.383													8	50	---	---	---	---	PASS
CENPE	1062	broad.mit.edu	37	4	104066284	104066284	+	Missense_Mutation	SNP	C	T	T			TCGA-39-5024-01A-21D-1817-08	TCGA-39-5024-11A-01D-1817-08									Somatic	Phase_I	Capture				Illumina GAIIx	388478e9-8c1f-43f8-88c4-811bf3cc2500	829ea6e6-1737-4fc6-8732-65e2d7fb2582	g.chr4:104066284C>T	uc003hxb.1	-	32	4870	c.4780G>A	c.(4780-4782)GAA>AAA	p.E1594K	CENPE_uc003hxc.1_Missense_Mutation_p.E1569K	NM_001813	NP_001804	Q02224	CENPE_HUMAN	centromere protein E	1594	Potential.				blood coagulation|cell division|kinetochore assembly|microtubule-based movement|mitotic chromosome movement towards spindle pole|mitotic metaphase|mitotic metaphase plate congression|mitotic prometaphase|multicellular organismal development|positive regulation of protein kinase activity	condensed chromosome kinetochore|cytosol|microtubule|nucleus|spindle	ATP binding|kinetochore binding|microtubule motor activity			ovary(5)|breast(4)	9				OV - Ovarian serous cystadenocarcinoma(123;2.95e-08)		CTTTTCATTTCCTCTTTTTCC	0.343													19	83	---	---	---	---	PASS
KIAA1109	84162	broad.mit.edu	37	4	123165066	123165066	+	Missense_Mutation	SNP	A	T	T			TCGA-39-5024-01A-21D-1817-08	TCGA-39-5024-11A-01D-1817-08									Somatic	Phase_I	Capture				Illumina GAIIx	388478e9-8c1f-43f8-88c4-811bf3cc2500	829ea6e6-1737-4fc6-8732-65e2d7fb2582	g.chr4:123165066A>T	uc003ieh.2	+	29	4845	c.4800A>T	c.(4798-4800)TTA>TTT	p.L1600F	KIAA1109_uc003iek.2_Missense_Mutation_p.L219F	NM_015312	NP_056127	Q2LD37	K1109_HUMAN	fragile site-associated protein	1600					regulation of cell growth|regulation of epithelial cell differentiation	integral to membrane|nucleus				ovary(8)|skin(2)|pancreas(1)|central_nervous_system(1)	12						ATGAAACATTAACAGAAGAGT	0.393													15	85	---	---	---	---	PASS
TBC1D9	23158	broad.mit.edu	37	4	141543624	141543624	+	Missense_Mutation	SNP	C	T	T			TCGA-39-5024-01A-21D-1817-08	TCGA-39-5024-11A-01D-1817-08									Somatic	Phase_I	Capture				Illumina GAIIx	388478e9-8c1f-43f8-88c4-811bf3cc2500	829ea6e6-1737-4fc6-8732-65e2d7fb2582	g.chr4:141543624C>T	uc010ioj.2	-	21	3798	c.3526G>A	c.(3526-3528)GAC>AAC	p.D1176N		NM_015130	NP_055945	Q6ZT07	TBCD9_HUMAN	TBC1 domain family, member 9 (with GRAM domain)	1176						intracellular	calcium ion binding|Rab GTPase activator activity			ovary(1)	1	all_hematologic(180;0.162)	Medulloblastoma(177;0.00498)				TGCAGCTTGTCCTCCTCGTGG	0.667													4	51	---	---	---	---	PASS
TLR2	7097	broad.mit.edu	37	4	154624935	154624935	+	Silent	SNP	T	C	C			TCGA-39-5024-01A-21D-1817-08	TCGA-39-5024-11A-01D-1817-08									Somatic	Phase_I	Capture				Illumina GAIIx	388478e9-8c1f-43f8-88c4-811bf3cc2500	829ea6e6-1737-4fc6-8732-65e2d7fb2582	g.chr4:154624935T>C	uc003inq.2	+	3	1095	c.876T>C	c.(874-876)GTT>GTC	p.V292V	TLR2_uc003inr.2_Silent_p.V292V|TLR2_uc003ins.2_Silent_p.V292V	NM_003264	NP_003255	O60603	TLR2_HUMAN	toll-like receptor 2 precursor	292	Extracellular (Potential).				cellular response to diacyl bacterial lipopeptide|cellular response to lipoteichoic acid|cellular response to triacyl bacterial lipopeptide|detection of diacyl bacterial lipopeptide|detection of triacyl bacterial lipopeptide|I-kappaB phosphorylation|induction of apoptosis|inflammatory response|innate immune response|MyD88-dependent toll-like receptor signaling pathway|positive regulation of chemokine production|positive regulation of interferon-beta production|positive regulation of interleukin-12 production|positive regulation of interleukin-18 production|positive regulation of interleukin-6 production|positive regulation of interleukin-8 production|positive regulation of NF-kappaB import into nucleus|positive regulation of NF-kappaB transcription factor activity|positive regulation of nitric-oxide synthase biosynthetic process|positive regulation of toll-like receptor signaling pathway|positive regulation of transcription from RNA polymerase II promoter|positive regulation of tumor necrosis factor production|positive regulation of Wnt receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway	cytoplasm|integral to plasma membrane|Toll-like receptor 1-Toll-like receptor 2 protein complex	Gram-positive bacterial cell surface binding|lipopolysaccharide receptor activity|peptidoglycan binding|protein heterodimerization activity|transmembrane receptor activity|triacyl lipopeptide binding			ovary(1)|lung(1)|breast(1)	3	all_hematologic(180;0.093)	Renal(120;0.117)				TTAATGGAGTTGGTAATTTTA	0.343													17	90	---	---	---	---	PASS
PLRG1	5356	broad.mit.edu	37	4	155467273	155467273	+	Splice_Site	SNP	A	T	T			TCGA-39-5024-01A-21D-1817-08	TCGA-39-5024-11A-01D-1817-08									Somatic	Phase_I	Capture				Illumina GAIIx	388478e9-8c1f-43f8-88c4-811bf3cc2500	829ea6e6-1737-4fc6-8732-65e2d7fb2582	g.chr4:155467273A>T	uc003iny.2	-	5	467	c.404_splice	c.e5+1	p.K135_splice	PLRG1_uc003inz.2_Splice_Site_p.K126_splice|PLRG1_uc011cil.1_Intron	NM_002669	NP_002660	O43660	PLRG1_HUMAN	pleiotropic regulator 1 (PRL1 homolog,							catalytic step 2 spliceosome|nuclear speck	protein binding|signal transducer activity|transcription corepressor activity				0	all_hematologic(180;0.215)	Renal(120;0.0854)				AATATTTCATACTTGGTCTGC	0.318													8	58	---	---	---	---	PASS
NPY5R	4889	broad.mit.edu	37	4	164271506	164271506	+	Silent	SNP	C	T	T			TCGA-39-5024-01A-21D-1817-08	TCGA-39-5024-11A-01D-1817-08									Somatic	Phase_I	Capture				Illumina GAIIx	388478e9-8c1f-43f8-88c4-811bf3cc2500	829ea6e6-1737-4fc6-8732-65e2d7fb2582	g.chr4:164271506C>T	uc003iqn.2	+	4	263	c.81C>T	c.(79-81)TTC>TTT	p.F27F		NM_006174	NP_006165	Q15761	NPY5R_HUMAN	neuropeptide Y receptor Y5	27	Extracellular (Potential).				cardiac left ventricle morphogenesis|outflow tract morphogenesis	integral to plasma membrane				lung(6)|skin(1)	7	all_hematologic(180;0.166)	Prostate(90;0.109)				ATTCTGATTTCCCAGTCTGGG	0.393													6	85	---	---	---	---	PASS
SLC9A3	6550	broad.mit.edu	37	5	484789	484789	+	Missense_Mutation	SNP	C	G	G			TCGA-39-5024-01A-21D-1817-08	TCGA-39-5024-11A-01D-1817-08									Somatic	Phase_I	Capture				Illumina GAIIx	388478e9-8c1f-43f8-88c4-811bf3cc2500	829ea6e6-1737-4fc6-8732-65e2d7fb2582	g.chr5:484789C>G	uc003jbe.2	-	5	890	c.778G>C	c.(778-780)GGG>CGG	p.G260R	SLC9A3_uc011clx.1_Missense_Mutation_p.G260R	NM_004174	NP_004165	P48764	SL9A3_HUMAN	solute carrier family 9 (sodium/hydrogen	260	Helical; Name=H/M6; (Potential).					cell surface|integral to membrane	sodium:hydrogen antiporter activity				0			Epithelial(17;0.000529)|OV - Ovarian serous cystadenocarcinoma(19;0.00153)|all cancers(22;0.00186)|Lung(60;0.0863)			AGCGTGCCCCCCAGGCTCACC	0.662													10	147	---	---	---	---	PASS
ZNF622	90441	broad.mit.edu	37	5	16465211	16465211	+	Silent	SNP	C	T	T			TCGA-39-5024-01A-21D-1817-08	TCGA-39-5024-11A-01D-1817-08									Somatic	Phase_I	Capture				Illumina GAIIx	388478e9-8c1f-43f8-88c4-811bf3cc2500	829ea6e6-1737-4fc6-8732-65e2d7fb2582	g.chr5:16465211C>T	uc003jfq.2	-	1	684	c.564G>A	c.(562-564)AAG>AAA	p.K188K		NM_033414	NP_219482	Q969S3	ZN622_HUMAN	zinc finger protein 622	188						cytoplasm|nucleus	nucleic acid binding|zinc ion binding			ovary(1)	1						TTGCCAACTTCTTCGCCTGCT	0.622													27	416	---	---	---	---	PASS
CDH18	1016	broad.mit.edu	37	5	19473700	19473700	+	Missense_Mutation	SNP	C	A	A			TCGA-39-5024-01A-21D-1817-08	TCGA-39-5024-11A-01D-1817-08									Somatic	Phase_I	Capture				Illumina GAIIx	388478e9-8c1f-43f8-88c4-811bf3cc2500	829ea6e6-1737-4fc6-8732-65e2d7fb2582	g.chr5:19473700C>A	uc003jgc.2	-	12	2385	c.2008G>T	c.(2008-2010)GCC>TCC	p.A670S	CDH18_uc003jgd.2_Missense_Mutation_p.A670S|CDH18_uc011cnm.1_3'UTR	NM_004934	NP_004925	Q13634	CAD18_HUMAN	cadherin 18, type 2 preproprotein	670	Cytoplasmic (Potential).				adherens junction organization|cell junction assembly|homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(5)|large_intestine(1)|skin(1)	7	Lung NSC(1;0.00734)|all_lung(1;0.0197)					ATGTCAAAGGCCTCTGTGTCT	0.522													202	165	---	---	---	---	PASS
CARD6	84674	broad.mit.edu	37	5	40841657	40841657	+	Missense_Mutation	SNP	G	C	C			TCGA-39-5024-01A-21D-1817-08	TCGA-39-5024-11A-01D-1817-08									Somatic	Phase_I	Capture				Illumina GAIIx	388478e9-8c1f-43f8-88c4-811bf3cc2500	829ea6e6-1737-4fc6-8732-65e2d7fb2582	g.chr5:40841657G>C	uc003jmg.2	+	1	248	c.173G>C	c.(172-174)CGG>CCG	p.R58P		NM_032587	NP_115976	Q9BX69	CARD6_HUMAN	caspase recruitment domain family, member 6	58	CARD.				apoptosis|regulation of apoptosis	intracellular				ovary(2)|skin(2)|lung(1)	5						AAGAAAAGTCGGAAGCTGTTA	0.428													20	190	---	---	---	---	PASS
C6	729	broad.mit.edu	37	5	41176712	41176712	+	Missense_Mutation	SNP	G	C	C			TCGA-39-5024-01A-21D-1817-08	TCGA-39-5024-11A-01D-1817-08									Somatic	Phase_I	Capture				Illumina GAIIx	388478e9-8c1f-43f8-88c4-811bf3cc2500	829ea6e6-1737-4fc6-8732-65e2d7fb2582	g.chr5:41176712G>C	uc003jmk.2	-	8	1243	c.1033C>G	c.(1033-1035)CTG>GTG	p.L345V	C6_uc003jml.1_Missense_Mutation_p.L345V	NM_000065	NP_000056	P13671	CO6_HUMAN	complement component 6 precursor	345	MACPF.				complement activation, classical pathway|cytolysis|innate immune response	membrane attack complex	protein binding			ovary(3)|central_nervous_system(2)|skin(2)	7		Breast(839;1.07e-05)|Ovarian(839;0.0228)|Lung SC(612;0.0548)|Lung NSC(810;0.128)|all_neural(839;0.157)				TCTAGAGGCAGATGGTTAAGT	0.408													13	127	---	---	---	---	PASS
BDP1	55814	broad.mit.edu	37	5	70757692	70757692	+	Missense_Mutation	SNP	G	C	C			TCGA-39-5024-01A-21D-1817-08	TCGA-39-5024-11A-01D-1817-08									Somatic	Phase_I	Capture				Illumina GAIIx	388478e9-8c1f-43f8-88c4-811bf3cc2500	829ea6e6-1737-4fc6-8732-65e2d7fb2582	g.chr5:70757692G>C	uc003kbp.1	+	3	801	c.538G>C	c.(538-540)GAT>CAT	p.D180H	BDP1_uc003kbn.1_Missense_Mutation_p.D180H|BDP1_uc003kbo.2_Missense_Mutation_p.D180H	NM_018429	NP_060899	A6H8Y1	BDP1_HUMAN	transcription factor-like nuclear regulator	180	Interaction with ZBTB43.				regulation of transcription, DNA-dependent|transcription from RNA polymerase III promoter	nucleoplasm	DNA binding			skin(2)	2		Lung NSC(167;0.000422)|Prostate(74;0.00815)|Ovarian(174;0.0176)|Breast(144;0.198)		OV - Ovarian serous cystadenocarcinoma(47;5.28e-56)|Epithelial(20;2.31e-50)		GAGGCCACCAGATCGTTCAAA	0.279													4	130	---	---	---	---	PASS
CARTPT	9607	broad.mit.edu	37	5	71015177	71015177	+	Missense_Mutation	SNP	G	T	T			TCGA-39-5024-01A-21D-1817-08	TCGA-39-5024-11A-01D-1817-08									Somatic	Phase_I	Capture				Illumina GAIIx	388478e9-8c1f-43f8-88c4-811bf3cc2500	829ea6e6-1737-4fc6-8732-65e2d7fb2582	g.chr5:71015177G>T	uc003kbv.1	+	1	184	c.57G>T	c.(55-57)ATG>ATT	p.M19I		NM_004291	NP_004282	Q16568	CART_HUMAN	cocaine- and amphetamine-regulated transcript	19					activation of MAPKK activity|adult feeding behavior|cellular glucose homeostasis|cellular response to starvation|circadian regulation of gene expression|negative regulation of appetite|negative regulation of bone resorption|negative regulation of osteoclast differentiation|neuropeptide signaling pathway|positive regulation of blood pressure|positive regulation of epinephrine secretion|positive regulation of transmission of nerve impulse|synaptic transmission	extracellular space				ovary(1)	1		Lung NSC(167;0.00153)|Ovarian(174;0.0175)|Prostate(74;0.11)|Breast(144;0.198)		OV - Ovarian serous cystadenocarcinoma(47;8.4e-56)	Amphetamine(DB00182)	TGCTGCTGATGCTACCTCTGT	0.667													4	72	---	---	---	---	PASS
APC	324	broad.mit.edu	37	5	112174552	112174552	+	Silent	SNP	C	T	T			TCGA-39-5024-01A-21D-1817-08	TCGA-39-5024-11A-01D-1817-08									Somatic	Phase_I	Capture				Illumina GAIIx	388478e9-8c1f-43f8-88c4-811bf3cc2500	829ea6e6-1737-4fc6-8732-65e2d7fb2582	g.chr5:112174552C>T	uc010jby.2	+	16	3641	c.3261C>T	c.(3259-3261)CTC>CTT	p.L1087L	APC_uc011cvt.1_Silent_p.L1069L|APC_uc003kpz.3_Silent_p.L1087L|APC_uc003kpy.3_Silent_p.L1087L|APC_uc010jbz.2_Silent_p.L804L|APC_uc010jca.2_Silent_p.L387L	NM_001127511	NP_001120983	P25054	APC_HUMAN	adenomatous polyposis coli	1087	Ser-rich.|Responsible for down-regulation through a process mediated by direct ubiquitination.				canonical Wnt receptor signaling pathway|cell adhesion|cell cycle arrest|cell migration|cellular component disassembly involved in apoptosis|cytokinesis after mitosis|mitotic cell cycle spindle assembly checkpoint|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of cyclin-dependent protein kinase activity|negative regulation of microtubule depolymerization|positive regulation of apoptosis|positive regulation of cell migration|positive regulation of pseudopodium assembly|protein complex assembly|regulation of attachment of spindle microtubules to kinetochore|response to DNA damage stimulus|tight junction assembly	adherens junction|APC-Axin-1-beta-catenin complex|Axin-APC-beta-catenin-GSK3B complex|beta-catenin destruction complex|centrosome|cytosol|kinetochore|lamellipodium|lateral plasma membrane|nucleus|ruffle membrane|tight junction	beta-catenin binding|gamma-catenin binding|microtubule plus-end binding|protein kinase binding|protein kinase regulator activity	p.?(1)		large_intestine(2123)|stomach(123)|soft_tissue(55)|small_intestine(34)|breast(26)|pancreas(25)|urinary_tract(20)|lung(19)|thyroid(18)|liver(13)|central_nervous_system(10)|ovary(9)|skin(7)|upper_aerodigestive_tract(6)|adrenal_gland(6)|bone(6)|NS(5)|prostate(4)|endometrium(3)|kidney(1)|oesophagus(1)|biliary_tract(1)	2515		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		ATAAACACCTCAAGTTCCAAC	0.388		12	D|Mis|N|F|S		colorectal|pancreatic|desmoid|hepatoblastoma|glioma|other CNS	colorectal|pancreatic|desmoid|hepatoblastoma|glioma|other CNS			Hereditary_Desmoid_Disease|Familial_Adenomatous_Polyposis|Turcot_syndrome	TSP Lung(16;0.13)			3	56	---	---	---	---	PASS
PCDHGA8	9708	broad.mit.edu	37	5	140773546	140773546	+	Missense_Mutation	SNP	A	T	T			TCGA-39-5024-01A-21D-1817-08	TCGA-39-5024-11A-01D-1817-08									Somatic	Phase_I	Capture				Illumina GAIIx	388478e9-8c1f-43f8-88c4-811bf3cc2500	829ea6e6-1737-4fc6-8732-65e2d7fb2582	g.chr5:140773546A>T	uc003lkd.1	+	1	2064	c.1166A>T	c.(1165-1167)AAT>ATT	p.N389I	PCDHGA1_uc003lji.1_Intron|PCDHGA2_uc003ljk.1_Intron|PCDHGA3_uc003ljm.1_Intron|PCDHGA3_uc010jfx.1_Intron|PCDHGB1_uc003ljo.1_Intron|PCDHGA4_uc003ljq.1_Intron|PCDHGB2_uc003ljs.1_Intron|PCDHGA5_uc003lju.1_Intron|PCDHGB3_uc003ljw.1_Intron|PCDHGA6_uc003ljy.1_Intron|PCDHGA7_uc003lka.1_Intron|PCDHGB4_uc003lkc.1_Intron|PCDHGA8_uc003lkb.3_Missense_Mutation_p.N389I	NM_032088	NP_114477	Q9Y5G5	PCDG8_HUMAN	protocadherin gamma subfamily A, 8 isoform 1	389	Cadherin 4.|Extracellular (Potential).				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding				0			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			ACACGTGATAATTTACCTTTT	0.353													6	38	---	---	---	---	PASS
GRIA1	2890	broad.mit.edu	37	5	152873579	152873579	+	Missense_Mutation	SNP	G	T	T			TCGA-39-5024-01A-21D-1817-08	TCGA-39-5024-11A-01D-1817-08									Somatic	Phase_I	Capture				Illumina GAIIx	388478e9-8c1f-43f8-88c4-811bf3cc2500	829ea6e6-1737-4fc6-8732-65e2d7fb2582	g.chr5:152873579G>T	uc003lva.3	+	2	539	c.174G>T	c.(172-174)CAG>CAT	p.Q58H	GRIA1_uc003luy.3_Missense_Mutation_p.Q58H|GRIA1_uc003luz.3_5'UTR|GRIA1_uc011dcv.1_Intron|GRIA1_uc011dcw.1_Missense_Mutation_p.Q58H|GRIA1_uc011dcx.1_5'UTR|GRIA1_uc011dcy.1_Missense_Mutation_p.Q68H|GRIA1_uc011dcz.1_Missense_Mutation_p.Q68H|GRIA1_uc010jia.1_Missense_Mutation_p.Q38H	NM_001114183	NP_001107655	P42261	GRIA1_HUMAN	glutamate receptor, ionotropic, AMPA 1 isoform	58	Extracellular (Potential).				synaptic transmission	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|dendritic spine|endocytic vesicle membrane|endoplasmic reticulum membrane|neuronal cell body|postsynaptic density|postsynaptic membrane	alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity|kainate selective glutamate receptor activity|PDZ domain binding			ovary(4)|skin(2)	6		Medulloblastoma(196;0.0391)|all_neural(177;0.16)|all_hematologic(541;0.21)	Kidney(363;0.000173)|KIRC - Kidney renal clear cell carcinoma(527;0.000785)		Desflurane(DB01189)|Enflurane(DB00228)|Halothane(DB01159)|Isoflurane(DB00753)|L-Glutamic Acid(DB00142)|Methoxyflurane(DB01028)|Sevoflurane(DB01236)	TGCTCCCCCAGATTGATATTG	0.443													22	116	---	---	---	---	PASS
C5orf4	10826	broad.mit.edu	37	5	154202038	154202038	+	Missense_Mutation	SNP	C	A	A			TCGA-39-5024-01A-21D-1817-08	TCGA-39-5024-11A-01D-1817-08									Somatic	Phase_I	Capture				Illumina GAIIx	388478e9-8c1f-43f8-88c4-811bf3cc2500	829ea6e6-1737-4fc6-8732-65e2d7fb2582	g.chr5:154202038C>A	uc003lvs.3	-	7	843	c.672G>T	c.(670-672)GAG>GAT	p.E224D	C5orf4_uc003lvq.2_5'Flank|C5orf4_uc003lvr.2_5'Flank|C5orf4_uc011dde.1_Missense_Mutation_p.E201D	NM_032385	NP_115761	Q96IV6	CE004_HUMAN	hypothetical protein LOC10826	224	Helical; (Potential).				fatty acid biosynthetic process	integral to membrane	iron ion binding|oxidoreductase activity			ovary(1)	1	Renal(175;0.00488)	Medulloblastoma(196;0.0354)|all_neural(177;0.0999)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)			TCACTGCATGCTCTATAGGGT	0.537													16	166	---	---	---	---	PASS
ATP10B	23120	broad.mit.edu	37	5	160047859	160047859	+	Silent	SNP	G	A	A			TCGA-39-5024-01A-21D-1817-08	TCGA-39-5024-11A-01D-1817-08									Somatic	Phase_I	Capture				Illumina GAIIx	388478e9-8c1f-43f8-88c4-811bf3cc2500	829ea6e6-1737-4fc6-8732-65e2d7fb2582	g.chr5:160047859G>A	uc003lym.1	-	15	2758	c.1911C>T	c.(1909-1911)TTC>TTT	p.F637F	ATP10B_uc010jit.1_5'UTR|ATP10B_uc003lyn.2_Silent_p.F195F	NM_025153	NP_079429	O94823	AT10B_HUMAN	ATPase, class V, type 10B	637	Cytoplasmic (Potential).				ATP biosynthetic process	integral to membrane	ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|magnesium ion binding|phospholipid-translocating ATPase activity			ovary(3)|central_nervous_system(1)|pancreas(1)	5	Renal(175;0.00196)	Medulloblastoma(196;0.0377)|all_neural(177;0.121)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			CAGTGGATGAGAATGACTGGC	0.552													21	179	---	---	---	---	PASS
WWC1	23286	broad.mit.edu	37	5	167850747	167850747	+	Nonsense_Mutation	SNP	C	G	G			TCGA-39-5024-01A-21D-1817-08	TCGA-39-5024-11A-01D-1817-08									Somatic	Phase_I	Capture				Illumina GAIIx	388478e9-8c1f-43f8-88c4-811bf3cc2500	829ea6e6-1737-4fc6-8732-65e2d7fb2582	g.chr5:167850747C>G	uc003lzu.2	+	11	1577	c.1484C>G	c.(1483-1485)TCA>TGA	p.S495*	WWC1_uc003lzv.2_Nonsense_Mutation_p.S495*|WWC1_uc011den.1_Nonsense_Mutation_p.S495*|WWC1_uc003lzw.2_Nonsense_Mutation_p.S294*	NM_015238	NP_056053	Q8IX03	KIBRA_HUMAN	WW and C2 domain containing 1 isoform 3	495					cell migration|positive regulation of MAPKKK cascade|regulation of hippo signaling cascade|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus|perinuclear region of cytoplasm|ruffle membrane	protein binding|transcription coactivator activity			ovary(2)|skin(2)|breast(1)	5	Renal(175;0.000212)|Lung NSC(126;0.0875)|all_lung(126;0.166)	Medulloblastoma(196;0.0399)|all_neural(177;0.0577)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	all cancers(165;0.0364)|Epithelial(171;0.0765)|OV - Ovarian serous cystadenocarcinoma(192;0.0918)		TTCCGGCCCTCAGGCTGCATC	0.632													13	70	---	---	---	---	PASS
HIST1H2AG	8969	broad.mit.edu	37	6	27100914	27100914	+	Missense_Mutation	SNP	G	C	C			TCGA-39-5024-01A-21D-1817-08	TCGA-39-5024-11A-01D-1817-08									Somatic	Phase_I	Capture				Illumina GAIIx	388478e9-8c1f-43f8-88c4-811bf3cc2500	829ea6e6-1737-4fc6-8732-65e2d7fb2582	g.chr6:27100914G>C	uc003niw.2	+	1	98	c.64G>C	c.(64-66)GCC>CCC	p.A22P	HIST1H2BJ_uc003niu.1_5'Flank|HIST1H2BJ_uc003niv.2_5'Flank	NM_021064	NP_066408	P0C0S8	H2A1_HUMAN	histone cluster 1, H2ag	22					nucleosome assembly	nucleosome|nucleus	DNA binding|enzyme binding				0						CTCTTCTAGGGCCGGTCTCCA	0.647													13	42	---	---	---	---	PASS
OR2B2	81697	broad.mit.edu	37	6	27879783	27879783	+	Silent	SNP	C	A	A			TCGA-39-5024-01A-21D-1817-08	TCGA-39-5024-11A-01D-1817-08									Somatic	Phase_I	Capture				Illumina GAIIx	388478e9-8c1f-43f8-88c4-811bf3cc2500	829ea6e6-1737-4fc6-8732-65e2d7fb2582	g.chr6:27879783C>A	uc011dkw.1	-	1	315	c.315G>T	c.(313-315)CTG>CTT	p.L105L		NM_033057	NP_149046	Q9GZK3	OR2B2_HUMAN	olfactory receptor, family 2, subfamily B,	105	Helical; Name=3; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0						AACCCAAGGCCAGGAAAATGA	0.453													5	75	---	---	---	---	PASS
HLA-A	3105	broad.mit.edu	37	6	29911061	29911061	+	Missense_Mutation	SNP	G	C	C	rs41550512		TCGA-39-5024-01A-21D-1817-08	TCGA-39-5024-11A-01D-1817-08									Somatic	Phase_I	Capture				Illumina GAIIx	388478e9-8c1f-43f8-88c4-811bf3cc2500	829ea6e6-1737-4fc6-8732-65e2d7fb2582	g.chr6:29911061G>C	uc003nol.2	+	3	360	c.360G>C	c.(358-360)CAG>CAC	p.Q120H	HLA-G_uc011dmb.1_Intron|HCG4P6_uc003nog.1_RNA|HLA-A_uc010jrq.2_5'UTR|HLA-A_uc003nok.2_5'UTR|HLA-A_uc003non.2_Missense_Mutation_p.Q120H|HLA-A_uc003noo.2_Missense_Mutation_p.Q120H|HLA-A_uc010jrr.2_Missense_Mutation_p.Q120H|HLA-A_uc003nom.2_5'UTR|HLA-A_uc010klp.2_Missense_Mutation_p.Q92H|HLA-A_uc011dmc.1_5'UTR|HLA-A_uc011dmd.1_5'Flank	NM_002116	NP_002107	P30443	1A01_HUMAN	major histocompatibility complex, class I, A	120	Extracellular (Potential).|Alpha-2.				antigen processing and presentation of peptide antigen via MHC class I|interferon-gamma-mediated signaling pathway|interspecies interaction between organisms|regulation of immune response|type I interferon-mediated signaling pathway	integral to plasma membrane|MHC class I protein complex	MHC class I receptor activity			upper_aerodigestive_tract(1)|ovary(1)	2						ACACCATCCAGATAATGTATG	0.662									Melanoma_Familial_Clustering_of|Lichen_Sclerosis_et_Atrophicus_Familial_Clustering_of|Osteosarcoma_Familial_Clustering_of|Naso-/Oropharyngeal/Laryngeal_Cancer_Familial_Clustering_of	Multiple Myeloma(9;0.094)			4	8	---	---	---	---	PASS
TNXB	7148	broad.mit.edu	37	6	32020577	32020577	+	Silent	SNP	C	T	T			TCGA-39-5024-01A-21D-1817-08	TCGA-39-5024-11A-01D-1817-08									Somatic	Phase_I	Capture				Illumina GAIIx	388478e9-8c1f-43f8-88c4-811bf3cc2500	829ea6e6-1737-4fc6-8732-65e2d7fb2582	g.chr6:32020577C>T	uc003nzl.2	-	26	9181	c.8979G>A	c.(8977-8979)GTG>GTA	p.V2993V		NM_019105	NP_061978	P22105	TENX_HUMAN	tenascin XB isoform 1 precursor	3040	Fibronectin type-III 22.				actin cytoskeleton organization|cell adhesion|collagen metabolic process|elastic fiber assembly|signal transduction	extracellular space|intracellular|proteinaceous extracellular matrix	heparin binding|integrin binding				0						TGACACGCACCACCTGGGGCC	0.677													7	59	---	---	---	---	PASS
CLPS	1208	broad.mit.edu	37	6	35765000	35765000	+	Silent	SNP	C	T	T			TCGA-39-5024-01A-21D-1817-08	TCGA-39-5024-11A-01D-1817-08									Somatic	Phase_I	Capture				Illumina GAIIx	388478e9-8c1f-43f8-88c4-811bf3cc2500	829ea6e6-1737-4fc6-8732-65e2d7fb2582	g.chr6:35765000C>T	uc003ole.1	-	1	103	c.66G>A	c.(64-66)CGG>CGA	p.R22R	CLPS_uc003olf.1_Silent_p.R22R	NM_001832	NP_001823	P04118	COL_HUMAN	colipase preproprotein	22					lipid catabolic process|lipid digestion|retinoid metabolic process|steroid metabolic process	extracellular region					0						TAATGATCCCCCGGGGGCCAG	0.592													5	106	---	---	---	---	PASS
DAAM2	23500	broad.mit.edu	37	6	39835470	39835470	+	Missense_Mutation	SNP	G	T	T			TCGA-39-5024-01A-21D-1817-08	TCGA-39-5024-11A-01D-1817-08									Somatic	Phase_I	Capture				Illumina GAIIx	388478e9-8c1f-43f8-88c4-811bf3cc2500	829ea6e6-1737-4fc6-8732-65e2d7fb2582	g.chr6:39835470G>T	uc003oow.2	+	6	769	c.613G>T	c.(613-615)GCC>TCC	p.A205S	DAAM2_uc010jxc.2_Missense_Mutation_p.A205S|DAAM2_uc003oox.2_Missense_Mutation_p.A205S	NM_015345	NP_056160	Q86T65	DAAM2_HUMAN	dishevelled associated activator of	205	GBD/FH3.				actin cytoskeleton organization		actin binding|Rho GTPase binding			ovary(2)|skin(1)	3	Ovarian(28;0.0355)|Colorectal(47;0.196)					TAGTACCATAGCCCAGAGCCT	0.582													5	71	---	---	---	---	PASS
BAI3	577	broad.mit.edu	37	6	69949088	69949088	+	Silent	SNP	A	T	T			TCGA-39-5024-01A-21D-1817-08	TCGA-39-5024-11A-01D-1817-08									Somatic	Phase_I	Capture				Illumina GAIIx	388478e9-8c1f-43f8-88c4-811bf3cc2500	829ea6e6-1737-4fc6-8732-65e2d7fb2582	g.chr6:69949088A>T	uc003pev.3	+	20	3232	c.2784A>T	c.(2782-2784)ATA>ATT	p.I928I	BAI3_uc010kak.2_Silent_p.I928I|BAI3_uc011dxx.1_Silent_p.I134I|BAI3_uc003pex.1_Silent_p.I58I	NM_001704	NP_001695	O60242	BAI3_HUMAN	brain-specific angiogenesis inhibitor 3	928	Helical; Name=2; (Potential).				negative regulation of angiogenesis|neuropeptide signaling pathway	integral to membrane|plasma membrane	G-protein coupled receptor activity			lung(27)|ovary(8)|skin(6)|pancreas(4)|central_nervous_system(3)|urinary_tract(1)|breast(1)	50		all_lung(197;0.212)				ATATCCTCATACTGGTTGGAC	0.348													31	152	---	---	---	---	PASS
DDX43	55510	broad.mit.edu	37	6	74124385	74124385	+	Missense_Mutation	SNP	G	A	A			TCGA-39-5024-01A-21D-1817-08	TCGA-39-5024-11A-01D-1817-08									Somatic	Phase_I	Capture				Illumina GAIIx	388478e9-8c1f-43f8-88c4-811bf3cc2500	829ea6e6-1737-4fc6-8732-65e2d7fb2582	g.chr6:74124385G>A	uc003pgw.2	+	14	2065	c.1721G>A	c.(1720-1722)CGA>CAA	p.R574Q		NM_018665	NP_061135	Q9NXZ2	DDX43_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 43	574	Helicase C-terminal.					intracellular	ATP binding|ATP-dependent RNA helicase activity|RNA binding			ovary(2)|upper_aerodigestive_tract(1)|skin(1)	4						TACGTACACCGAATAGGGCGC	0.433													8	67	---	---	---	---	PASS
TRAF3IP2	10758	broad.mit.edu	37	6	111901417	111901417	+	Silent	SNP	C	A	A	rs117922343	by1000genomes	TCGA-39-5024-01A-21D-1817-08	TCGA-39-5024-11A-01D-1817-08									Somatic	Phase_I	Capture				Illumina GAIIx	388478e9-8c1f-43f8-88c4-811bf3cc2500	829ea6e6-1737-4fc6-8732-65e2d7fb2582	g.chr6:111901417C>A	uc011ebc.1	-	4	1620	c.1005G>T	c.(1003-1005)CCG>CCT	p.P335P	TRAF3IP2_uc003pvg.2_Silent_p.P335P|TRAF3IP2_uc003pvf.2_Silent_p.P335P|TRAF3IP2_uc010kdw.2_Silent_p.P335P|TRAF3IP2_uc010kdx.2_Silent_p.P335P	NM_147686	NP_679211	O43734	CIKS_HUMAN	TRAF3 interacting protein 2 isoform 2	344					intracellular signal transduction|positive regulation of I-kappaB kinase/NF-kappaB cascade	intracellular				ovary(2)|central_nervous_system(1)	3		all_cancers(87;7.87e-06)|Acute lymphoblastic leukemia(125;3.61e-09)|all_hematologic(75;2.63e-07)|all_epithelial(87;0.0024)|Colorectal(196;0.021)		OV - Ovarian serous cystadenocarcinoma(136;0.033)|all cancers(137;0.0412)|Epithelial(106;0.0732)		TTGGAAGCCCCGGAAAGGAGC	0.512													3	36	---	---	---	---	PASS
GJA1	2697	broad.mit.edu	37	6	121768672	121768672	+	Nonsense_Mutation	SNP	G	T	T			TCGA-39-5024-01A-21D-1817-08	TCGA-39-5024-11A-01D-1817-08									Somatic	Phase_I	Capture				Illumina GAIIx	388478e9-8c1f-43f8-88c4-811bf3cc2500	829ea6e6-1737-4fc6-8732-65e2d7fb2582	g.chr6:121768672G>T	uc003pyr.2	+	2	929	c.679G>T	c.(679-681)GAA>TAA	p.E227*	GJA1_uc011ebo.1_Nonsense_Mutation_p.E128*|GJA1_uc011ebp.1_Nonsense_Mutation_p.E15*	NM_000165	NP_000156	P17302	CXA1_HUMAN	connexin 43	227	Helical; (Potential).				cell-cell signaling|cellular membrane organization|gap junction assembly|heart development|muscle contraction|positive regulation of I-kappaB kinase/NF-kappaB cascade	connexon complex|Golgi-associated vesicle membrane|integral to plasma membrane|membrane raft	ion transmembrane transporter activity|signal transducer activity			ovary(2)	2				GBM - Glioblastoma multiforme(226;0.00252)	Carvedilol(DB01136)	GAATATCATTGAACTCTTCTA	0.512													30	166	---	---	---	---	PASS
LAMA2	3908	broad.mit.edu	37	6	129513971	129513971	+	Silent	SNP	C	T	T			TCGA-39-5024-01A-21D-1817-08	TCGA-39-5024-11A-01D-1817-08									Somatic	Phase_I	Capture				Illumina GAIIx	388478e9-8c1f-43f8-88c4-811bf3cc2500	829ea6e6-1737-4fc6-8732-65e2d7fb2582	g.chr6:129513971C>T	uc003qbn.2	+	12	1860	c.1755C>T	c.(1753-1755)AGC>AGT	p.S585S	LAMA2_uc003qbo.2_Silent_p.S585S	NM_000426	NP_000417	P24043	LAMA2_HUMAN	laminin alpha 2 subunit isoform a precursor	585	Laminin IV type A 1.				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)		ACTACTGGAGCGCGCCGGCTC	0.552													7	46	---	---	---	---	PASS
BCLAF1	9774	broad.mit.edu	37	6	136597477	136597477	+	Missense_Mutation	SNP	C	A	A			TCGA-39-5024-01A-21D-1817-08	TCGA-39-5024-11A-01D-1817-08									Somatic	Phase_I	Capture				Illumina GAIIx	388478e9-8c1f-43f8-88c4-811bf3cc2500	829ea6e6-1737-4fc6-8732-65e2d7fb2582	g.chr6:136597477C>A	uc003qgx.1	-	5	1439	c.1186G>T	c.(1186-1188)GAT>TAT	p.D396Y	BCLAF1_uc003qgw.1_Intron|BCLAF1_uc003qgy.1_Missense_Mutation_p.D394Y|BCLAF1_uc011edc.1_Intron|BCLAF1_uc011edd.1_RNA|BCLAF1_uc011ede.1_Missense_Mutation_p.D394Y	NM_014739	NP_055554	Q9NYF8	BCLF1_HUMAN	BCL2-associated transcription factor 1 isoform	396					induction of apoptosis|negative regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleolus	DNA binding|protein binding			ovary(1)	1	Colorectal(23;0.24)			GBM - Glioblastoma multiforme(68;0.00226)|OV - Ovarian serous cystadenocarcinoma(155;0.00331)		CCTTCTGAATCATTAAACTTT	0.443													25	554	---	---	---	---	PASS
HECA	51696	broad.mit.edu	37	6	139487474	139487474	+	Missense_Mutation	SNP	G	C	C			TCGA-39-5024-01A-21D-1817-08	TCGA-39-5024-11A-01D-1817-08									Somatic	Phase_I	Capture				Illumina GAIIx	388478e9-8c1f-43f8-88c4-811bf3cc2500	829ea6e6-1737-4fc6-8732-65e2d7fb2582	g.chr6:139487474G>C	uc003qin.2	+	2	610	c.325G>C	c.(325-327)GAG>CAG	p.E109Q		NM_016217	NP_057301	Q9UBI9	HDC_HUMAN	headcase	109					respiratory tube development						0				GBM - Glioblastoma multiforme(68;0.000252)|OV - Ovarian serous cystadenocarcinoma(155;0.000387)		GGTGGACCTGGAGAAGGACGA	0.517													5	168	---	---	---	---	PASS
VTA1	51534	broad.mit.edu	37	6	142487437	142487437	+	Missense_Mutation	SNP	A	G	G			TCGA-39-5024-01A-21D-1817-08	TCGA-39-5024-11A-01D-1817-08									Somatic	Phase_I	Capture				Illumina GAIIx	388478e9-8c1f-43f8-88c4-811bf3cc2500	829ea6e6-1737-4fc6-8732-65e2d7fb2582	g.chr6:142487437A>G	uc003qiw.2	+	2	200	c.185A>G	c.(184-186)AAG>AGG	p.K62R	VTA1_uc011edt.1_RNA|VTA1_uc011edu.1_Intron	NM_016485	NP_057569	Q9NP79	VTA1_HUMAN	Vps20-associated 1 homolog	62	Interaction with CHMP5.|Interaction with IST1.				cellular membrane organization|endosome transport|protein transport	cytosol|endosome membrane	protein binding				0	Breast(32;0.155)			OV - Ovarian serous cystadenocarcinoma(155;1.34e-05)|GBM - Glioblastoma multiforme(68;0.00182)		TTTTTATCAAAGTTAATGGAT	0.323													23	65	---	---	---	---	PASS
C6orf97	80129	broad.mit.edu	37	6	151914290	151914290	+	Missense_Mutation	SNP	A	T	T			TCGA-39-5024-01A-21D-1817-08	TCGA-39-5024-11A-01D-1817-08									Somatic	Phase_I	Capture				Illumina GAIIx	388478e9-8c1f-43f8-88c4-811bf3cc2500	829ea6e6-1737-4fc6-8732-65e2d7fb2582	g.chr6:151914290A>T	uc003qol.2	+	8	1431	c.1342A>T	c.(1342-1344)ATG>TTG	p.M448L		NM_025059	NP_079335	Q8IYT3	CF097_HUMAN	hypothetical protein LOC80129	448											0		Ovarian(120;0.126)	BRCA - Breast invasive adenocarcinoma(37;0.111)	OV - Ovarian serous cystadenocarcinoma(155;1.48e-10)		GTTGGACCAGATGGCTGCCGA	0.433													24	48	---	---	---	---	PASS
SYNE1	23345	broad.mit.edu	37	6	152763321	152763321	+	Silent	SNP	C	T	T			TCGA-39-5024-01A-21D-1817-08	TCGA-39-5024-11A-01D-1817-08									Somatic	Phase_I	Capture				Illumina GAIIx	388478e9-8c1f-43f8-88c4-811bf3cc2500	829ea6e6-1737-4fc6-8732-65e2d7fb2582	g.chr6:152763321C>T	uc010kiw.2	-	31	4499	c.3897G>A	c.(3895-3897)GCG>GCA	p.A1299A	SYNE1_uc003qot.3_Silent_p.A1306A|SYNE1_uc003qou.3_Silent_p.A1299A|SYNE1_uc010kjb.1_Silent_p.A1282A|SYNE1_uc003qow.2_Silent_p.A594A|SYNE1_uc003qox.1_Silent_p.A815A	NM_182961	NP_892006	Q8NF91	SYNE1_HUMAN	spectrin repeat containing, nuclear envelope 1	1299	Potential.|Cytoplasmic (Potential).				cell death|cytoskeletal anchoring at nuclear membrane|Golgi organization|muscle cell differentiation|nuclear matrix anchoring at nuclear membrane	cytoskeleton|Golgi apparatus|integral to membrane|nuclear outer membrane|postsynaptic membrane|sarcomere|SUN-KASH complex	actin binding|lamin binding			central_nervous_system(15)|upper_aerodigestive_tract(9)|ovary(8)|skin(6)|large_intestine(5)|pancreas(2)	45		Ovarian(120;0.0955)	BRCA - Breast invasive adenocarcinoma(37;0.243)	OV - Ovarian serous cystadenocarcinoma(155;2.24e-10)		CTCCCTGCTGCGCCTGCGCGA	0.567										HNSCC(10;0.0054)			12	91	---	---	---	---	PASS
TFB1M	51106	broad.mit.edu	37	6	155632376	155632376	+	Missense_Mutation	SNP	G	C	C			TCGA-39-5024-01A-21D-1817-08	TCGA-39-5024-11A-01D-1817-08									Somatic	Phase_I	Capture				Illumina GAIIx	388478e9-8c1f-43f8-88c4-811bf3cc2500	829ea6e6-1737-4fc6-8732-65e2d7fb2582	g.chr6:155632376G>C	uc003qqj.3	-	2	295	c.231C>G	c.(229-231)GAC>GAG	p.D77E	TFB1M_uc003qqk.2_Intron	NM_016020	NP_057104	Q8WVM0	TFB1M_HUMAN	transcription factor B1, mitochondrial	77					regulation of transcription, DNA-dependent|transcription, DNA-dependent	mitochondrial nucleoid	DNA binding|protein binding|rRNA (adenine-N6,N6-)-dimethyltransferase activity			skin(1)	1		Ovarian(120;0.196)		OV - Ovarian serous cystadenocarcinoma(155;1.48e-12)|BRCA - Breast invasive adenocarcinoma(81;0.0131)		GTTCAGCGACGTCGGCATTAA	0.433													28	73	---	---	---	---	PASS
PDCD2	5134	broad.mit.edu	37	6	170892822	170892822	+	Missense_Mutation	SNP	T	G	G			TCGA-39-5024-01A-21D-1817-08	TCGA-39-5024-11A-01D-1817-08									Somatic	Phase_I	Capture				Illumina GAIIx	388478e9-8c1f-43f8-88c4-811bf3cc2500	829ea6e6-1737-4fc6-8732-65e2d7fb2582	g.chr6:170892822T>G	uc003qxw.2	-	2	376	c.297A>C	c.(295-297)CAA>CAC	p.Q99H	PDCD2_uc003qxv.2_Missense_Mutation_p.Q66H|PDCD2_uc003qxx.1_Missense_Mutation_p.Q99H|PDCD2_uc003qxy.2_Missense_Mutation_p.Q66H|PDCD2_uc003qxz.2_Missense_Mutation_p.Q99H|PDCD2_uc003qya.2_Missense_Mutation_p.Q66H|PDCD2_uc003qyb.1_Intron	NM_002598	NP_002589	Q16342	PDCD2_HUMAN	programmed cell death 2 isoform 1	99					apoptosis	cytoplasm|nucleus	DNA binding|protein binding|zinc ion binding				0		Breast(66;5.08e-05)|Ovarian(120;0.125)|Esophageal squamous(34;0.246)		OV - Ovarian serous cystadenocarcinoma(33;6.91e-23)|BRCA - Breast invasive adenocarcinoma(81;4.82e-06)|GBM - Glioblastoma multiforme(31;0.142)		TCCTGGGTAGTTGATTCCTAA	0.368													6	52	---	---	---	---	PASS
SDK1	221935	broad.mit.edu	37	7	4249744	4249744	+	Missense_Mutation	SNP	G	A	A			TCGA-39-5024-01A-21D-1817-08	TCGA-39-5024-11A-01D-1817-08									Somatic	Phase_I	Capture				Illumina GAIIx	388478e9-8c1f-43f8-88c4-811bf3cc2500	829ea6e6-1737-4fc6-8732-65e2d7fb2582	g.chr7:4249744G>A	uc003smx.2	+	38	5628	c.5489G>A	c.(5488-5490)GGC>GAC	p.G1830D	SDK1_uc010kso.2_Missense_Mutation_p.G1086D|SDK1_uc003smy.2_Missense_Mutation_p.G317D	NM_152744	NP_689957	Q7Z5N4	SDK1_HUMAN	sidekick 1 precursor	1830	Fibronectin type-III 12.				cell adhesion	integral to membrane				large_intestine(3)|ovary(2)|skin(1)	6		all_cancers(1;0.127)|Ovarian(82;0.0177)|Myeloproliferative disorder(862;0.194)		UCEC - Uterine corpus endometrioid carcinoma (126;0.121)|OV - Ovarian serous cystadenocarcinoma(56;9.65e-15)		GCGGCCAACGGCATCCTGCAG	0.652													8	94	---	---	---	---	PASS
DFNA5	1687	broad.mit.edu	37	7	24784198	24784198	+	Missense_Mutation	SNP	G	C	C			TCGA-39-5024-01A-21D-1817-08	TCGA-39-5024-11A-01D-1817-08									Somatic	Phase_I	Capture				Illumina GAIIx	388478e9-8c1f-43f8-88c4-811bf3cc2500	829ea6e6-1737-4fc6-8732-65e2d7fb2582	g.chr7:24784198G>C	uc010kus.1	-	3	475	c.387C>G	c.(385-387)ATC>ATG	p.I129M	DFNA5_uc003swz.2_Translation_Start_Site|DFNA5_uc003sxa.1_Missense_Mutation_p.I129M|DFNA5_uc010kut.1_Translation_Start_Site|DFNA5_uc003sxb.2_Missense_Mutation_p.I129M|DFNA5_uc003sxc.2_Missense_Mutation_p.I129M	NM_001127453	NP_001120925	O60443	DFNA5_HUMAN	deafness, autosomal dominant 5 protein isoform	129					sensory perception of sound					ovary(1)	1						CAGAGTCTCTGATGAGCTGCT	0.502													9	154	---	---	---	---	PASS
AVL9	23080	broad.mit.edu	37	7	32612988	32612988	+	Missense_Mutation	SNP	G	C	C			TCGA-39-5024-01A-21D-1817-08	TCGA-39-5024-11A-01D-1817-08									Somatic	Phase_I	Capture				Illumina GAIIx	388478e9-8c1f-43f8-88c4-811bf3cc2500	829ea6e6-1737-4fc6-8732-65e2d7fb2582	g.chr7:32612988G>C	uc003tcv.1	+	12	1674	c.1528G>C	c.(1528-1530)GCG>CCG	p.A510P	AVL9_uc011kai.1_Intron|AVL9_uc010kwj.1_Missense_Mutation_p.A351P	NM_015060	NP_055875	Q8NBF6	AVL9_HUMAN	AVL9 homolog (S. cerevisiase)	510						integral to membrane					0						GGCCCAGTTTGCGGTCTACAT	0.507													19	118	---	---	---	---	PASS
TBX20	57057	broad.mit.edu	37	7	35284591	35284591	+	Silent	SNP	G	A	A			TCGA-39-5024-01A-21D-1817-08	TCGA-39-5024-11A-01D-1817-08									Somatic	Phase_I	Capture				Illumina GAIIx	388478e9-8c1f-43f8-88c4-811bf3cc2500	829ea6e6-1737-4fc6-8732-65e2d7fb2582	g.chr7:35284591G>A	uc011kas.1	-	4	635	c.624C>T	c.(622-624)CTC>CTT	p.L208L		NM_001077653	NP_001071121	Q9UMR3	TBX20_HUMAN	T-box transcription factor TBX20	208	T-box.					nucleus	DNA binding			central_nervous_system(1)	1						CATTGTTGGTGAGTTTCACCT	0.443													6	50	---	---	---	---	PASS
ABCA13	154664	broad.mit.edu	37	7	48545964	48545964	+	Missense_Mutation	SNP	G	A	A			TCGA-39-5024-01A-21D-1817-08	TCGA-39-5024-11A-01D-1817-08									Somatic	Phase_I	Capture				Illumina GAIIx	388478e9-8c1f-43f8-88c4-811bf3cc2500	829ea6e6-1737-4fc6-8732-65e2d7fb2582	g.chr7:48545964G>A	uc003toq.2	+	49	13349	c.13324G>A	c.(13324-13326)GCC>ACC	p.A4442T	ABCA13_uc010kys.1_Missense_Mutation_p.A1517T|ABCA13_uc010kyt.1_RNA|ABCA13_uc010kyu.1_Missense_Mutation_p.A172T	NM_152701	NP_689914	Q86UQ4	ABCAD_HUMAN	ATP binding cassette, sub-family A (ABC1),	4442					transport	integral to membrane	ATP binding|ATPase activity			ovary(5)|central_nervous_system(4)|skin(1)	10						ATATGGAGGGGCCTTGCTGAA	0.468													42	69	---	---	---	---	PASS
TYW1	55253	broad.mit.edu	37	7	66548450	66548450	+	Silent	SNP	G	A	A			TCGA-39-5024-01A-21D-1817-08	TCGA-39-5024-11A-01D-1817-08									Somatic	Phase_I	Capture				Illumina GAIIx	388478e9-8c1f-43f8-88c4-811bf3cc2500	829ea6e6-1737-4fc6-8732-65e2d7fb2582	g.chr7:66548450G>A	uc003tvn.2	+	11	1457	c.1308G>A	c.(1306-1308)CGG>CGA	p.R436R	TYW1_uc010lai.2_RNA|TYW1_uc011kef.1_Silent_p.R50R	NM_018264	NP_060734	Q9NV66	TYW1_HUMAN	radical S-adenosyl methionine and flavodoxin	436					tRNA processing		4 iron, 4 sulfur cluster binding|FMN binding|iron ion binding|oxidoreductase activity			skin(1)	1		Lung NSC(55;0.0846)|all_lung(88;0.183)				CTGAGTGGCGGTGGAAGATGG	0.438													21	102	---	---	---	---	PASS
GRM3	2913	broad.mit.edu	37	7	86479854	86479854	+	Missense_Mutation	SNP	T	G	G			TCGA-39-5024-01A-21D-1817-08	TCGA-39-5024-11A-01D-1817-08									Somatic	Phase_I	Capture				Illumina GAIIx	388478e9-8c1f-43f8-88c4-811bf3cc2500	829ea6e6-1737-4fc6-8732-65e2d7fb2582	g.chr7:86479854T>G	uc003uid.2	+	5	3659	c.2560T>G	c.(2560-2562)TCT>GCT	p.S854A	GRM3_uc010lef.2_Missense_Mutation_p.L496R|GRM3_uc010leg.2_Missense_Mutation_p.S726A|GRM3_uc010leh.2_Missense_Mutation_p.S446A	NM_000840	NP_000831	Q14832	GRM3_HUMAN	glutamate receptor, metabotropic 3 precursor	854	Cytoplasmic (Potential).				synaptic transmission	integral to plasma membrane				lung(4)|ovary(3)|central_nervous_system(2)|skin(2)|haematopoietic_and_lymphoid_tissue(1)|prostate(1)	13	Esophageal squamous(14;0.0058)|all_lung(186;0.132)|Lung NSC(181;0.142)				Acamprosate(DB00659)|Nicotine(DB00184)	GACCACATACTCTCAGTGTAA	0.478													17	110	---	---	---	---	PASS
MLL5	55904	broad.mit.edu	37	7	104752933	104752933	+	Missense_Mutation	SNP	C	T	T			TCGA-39-5024-01A-21D-1817-08	TCGA-39-5024-11A-01D-1817-08									Somatic	Phase_I	Capture				Illumina GAIIx	388478e9-8c1f-43f8-88c4-811bf3cc2500	829ea6e6-1737-4fc6-8732-65e2d7fb2582	g.chr7:104752933C>T	uc003vcm.2	+	27	5264	c.4730C>T	c.(4729-4731)TCT>TTT	p.S1577F	MLL5_uc010ljc.2_Missense_Mutation_p.S1577F|MLL5_uc010ljf.1_Intron|MLL5_uc010ljg.2_Missense_Mutation_p.S311F	NM_182931	NP_891847	Q8IZD2	MLL5_HUMAN	myeloid/lymphoid or mixed-lineage leukemia 5	1577	Pro-rich.				cell cycle arrest|cellular response to retinoic acid|DNA methylation|erythrocyte differentiation|neutrophil activation|neutrophil mediated immunity|positive regulation of granulocyte differentiation|positive regulation of transcription, DNA-dependent|retinoic acid receptor signaling pathway|transcription, DNA-dependent	MLL5-L complex|nuclear speck	enzyme binding|histone methyltransferase activity (H3-K4 specific)|transcription coactivator activity|zinc ion binding			ovary(2)|pancreas(1)	3						GGTAGTCTTTCTCAACAAACT	0.478													15	98	---	---	---	---	PASS
MKLN1	4289	broad.mit.edu	37	7	131128447	131128447	+	Missense_Mutation	SNP	A	T	T			TCGA-39-5024-01A-21D-1817-08	TCGA-39-5024-11A-01D-1817-08									Somatic	Phase_I	Capture				Illumina GAIIx	388478e9-8c1f-43f8-88c4-811bf3cc2500	829ea6e6-1737-4fc6-8732-65e2d7fb2582	g.chr7:131128447A>T	uc011kpm.1	+	11	1445	c.1381A>T	c.(1381-1383)ATG>TTG	p.M461L	MKLN1_uc011kpl.1_Missense_Mutation_p.M438L|MKLN1_uc010lmh.2_Missense_Mutation_p.M461L|MKLN1_uc003vqs.2_Missense_Mutation_p.M254L	NM_013255	NP_037387	Q9UL63	MKLN1_HUMAN	muskelin 1, intracellular mediator containing	461					signal transduction	cytoplasm	protein binding			breast(1)	1	Melanoma(18;0.162)					AGGACACTGCATGTTATTCCA	0.398													20	62	---	---	---	---	PASS
NUP205	23165	broad.mit.edu	37	7	135258457	135258457	+	Missense_Mutation	SNP	C	A	A			TCGA-39-5024-01A-21D-1817-08	TCGA-39-5024-11A-01D-1817-08									Somatic	Phase_I	Capture				Illumina GAIIx	388478e9-8c1f-43f8-88c4-811bf3cc2500	829ea6e6-1737-4fc6-8732-65e2d7fb2582	g.chr7:135258457C>A	uc003vsw.2	+	3	258	c.227C>A	c.(226-228)GCC>GAC	p.A76D	NUP205_uc011kqa.1_RNA	NM_015135	NP_055950	Q92621	NU205_HUMAN	nucleoporin 205kDa	76					carbohydrate metabolic process|glucose transport|mRNA transport|protein import into nucleus, docking|regulation of glucose transport|transmembrane transport|viral reproduction	nuclear pore	protein binding			ovary(3)|breast(1)|central_nervous_system(1)|skin(1)	6						GAGGGAGTCGCCATTCAGGGT	0.403													3	49	---	---	---	---	PASS
CLCN1	1180	broad.mit.edu	37	7	143028687	143028687	+	Missense_Mutation	SNP	C	A	A			TCGA-39-5024-01A-21D-1817-08	TCGA-39-5024-11A-01D-1817-08									Somatic	Phase_I	Capture				Illumina GAIIx	388478e9-8c1f-43f8-88c4-811bf3cc2500	829ea6e6-1737-4fc6-8732-65e2d7fb2582	g.chr7:143028687C>A	uc003wcr.1	+	10	1195	c.1108C>A	c.(1108-1110)CGC>AGC	p.R370S	CLCN1_uc011ktc.1_Missense_Mutation_p.R32S	NM_000083	NP_000074	P35523	CLCN1_HUMAN	chloride channel 1, skeletal muscle	370	Helical; (By similarity).				muscle contraction	chloride channel complex|integral to plasma membrane	voltage-gated chloride channel activity			ovary(2)|breast(1)|central_nervous_system(1)|skin(1)	5	Melanoma(164;0.205)					GTATCTGCATCGCCAAGTCAT	0.478													4	79	---	---	---	---	PASS
VIPR2	7434	broad.mit.edu	37	7	158835748	158835748	+	Missense_Mutation	SNP	C	A	A			TCGA-39-5024-01A-21D-1817-08	TCGA-39-5024-11A-01D-1817-08									Somatic	Phase_I	Capture				Illumina GAIIx	388478e9-8c1f-43f8-88c4-811bf3cc2500	829ea6e6-1737-4fc6-8732-65e2d7fb2582	g.chr7:158835748C>A	uc003woh.2	-	6	761	c.575G>T	c.(574-576)TGC>TTC	p.C192F	VIPR2_uc010lqx.2_RNA|VIPR2_uc010lqy.2_RNA	NM_003382	NP_003373	P41587	VIPR2_HUMAN	vasoactive intestinal peptide receptor 2	192	Extracellular (Potential).				cell-cell signaling	integral to plasma membrane				lung(1)|central_nervous_system(1)	2	Ovarian(565;0.152)	all_cancers(7;1.13e-11)|all_epithelial(9;0.000545)|all_hematologic(28;0.00603)	OV - Ovarian serous cystadenocarcinoma(82;0.00231)	UCEC - Uterine corpus endometrioid carcinoma (81;0.2)|STAD - Stomach adenocarcinoma(7;0.18)		CTGGTCAGGGCAGTGCAACGT	0.552													6	29	---	---	---	---	PASS
SLC18A1	6570	broad.mit.edu	37	8	20007193	20007193	+	Silent	SNP	C	T	T			TCGA-39-5024-01A-21D-1817-08	TCGA-39-5024-11A-01D-1817-08									Somatic	Phase_I	Capture				Illumina GAIIx	388478e9-8c1f-43f8-88c4-811bf3cc2500	829ea6e6-1737-4fc6-8732-65e2d7fb2582	g.chr8:20007193C>T	uc011kyq.1	-	13	1611	c.1140G>A	c.(1138-1140)TTG>TTA	p.L380L	SLC18A1_uc003wzl.2_Silent_p.L167L|SLC18A1_uc003wzm.2_Silent_p.L380L|SLC18A1_uc011kyr.1_Silent_p.L380L|SLC18A1_uc003wzn.2_Silent_p.L348L|SLC18A1_uc010ltf.2_RNA|SLC18A1_uc003wzo.2_Silent_p.L348L	NM_001135691	NP_001129163	P54219	VMAT1_HUMAN	solute carrier family 18 (vesicular monoamine),	380	Helical; (Potential).				neurotransmitter transport	clathrin sculpted monoamine transport vesicle membrane|integral to membrane|membrane fraction	drug transmembrane transporter activity|monoamine transmembrane transporter activity			ovary(2)	2				Colorectal(74;0.0747)		TTACACAGAGCAAGCTGGTAC	0.363													6	33	---	---	---	---	PASS
RAB11FIP1	80223	broad.mit.edu	37	8	37728907	37728907	+	Missense_Mutation	SNP	C	G	G			TCGA-39-5024-01A-21D-1817-08	TCGA-39-5024-11A-01D-1817-08									Somatic	Phase_I	Capture				Illumina GAIIx	388478e9-8c1f-43f8-88c4-811bf3cc2500	829ea6e6-1737-4fc6-8732-65e2d7fb2582	g.chr8:37728907C>G	uc003xkm.1	-	4	3457	c.3413G>C	c.(3412-3414)AGA>ACA	p.R1138T	RAB11FIP1_uc010lvz.1_Intron|RAB11FIP1_uc003xkn.1_Intron|RAB11FIP1_uc003xkl.1_Missense_Mutation_p.R467T|RAB11FIP1_uc003xko.1_Missense_Mutation_p.R467T|RAB11FIP1_uc003xkp.1_Intron	NM_001002814	NP_001002814	Q6WKZ4	RFIP1_HUMAN	RAB11 family interacting protein 1 isoform 3	1138					protein transport	centrosome|phagocytic vesicle membrane|recycling endosome	protein binding			ovary(1)|central_nervous_system(1)|skin(1)	3		Lung NSC(58;0.118)|all_lung(54;0.195)	LUSC - Lung squamous cell carcinoma(8;3.62e-11)			ATTTTCAACTCTACCAGCGGA	0.552											OREG0018713	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	28	188	---	---	---	---	PASS
ZMAT4	79698	broad.mit.edu	37	8	40554884	40554884	+	Missense_Mutation	SNP	A	T	T			TCGA-39-5024-01A-21D-1817-08	TCGA-39-5024-11A-01D-1817-08									Somatic	Phase_I	Capture				Illumina GAIIx	388478e9-8c1f-43f8-88c4-811bf3cc2500	829ea6e6-1737-4fc6-8732-65e2d7fb2582	g.chr8:40554884A>T	uc003xnr.2	-	4	375	c.229T>A	c.(229-231)TGC>AGC	p.C77S	ZMAT4_uc003xns.2_Missense_Mutation_p.C77S	NM_024645	NP_078921	Q9H898	ZMAT4_HUMAN	zinc finger, matrin type 4 isoform a	77	Matrin-type 2.					nucleus	DNA binding|zinc ion binding			pancreas(1)|central_nervous_system(1)|skin(1)	3	Ovarian(28;0.00724)|Colorectal(14;0.0468)	all_cancers(7;0.00936)|all_epithelial(6;3.53e-06)|all_lung(54;0.0318)|Lung NSC(58;0.0919)|Esophageal squamous(32;0.15)|Hepatocellular(245;0.152)	LUSC - Lung squamous cell carcinoma(45;0.00722)			CAGAGTGTGCAGCACTTGTTC	0.478													13	93	---	---	---	---	PASS
PXDNL	137902	broad.mit.edu	37	8	52321164	52321164	+	Missense_Mutation	SNP	G	A	A			TCGA-39-5024-01A-21D-1817-08	TCGA-39-5024-11A-01D-1817-08									Somatic	Phase_I	Capture				Illumina GAIIx	388478e9-8c1f-43f8-88c4-811bf3cc2500	829ea6e6-1737-4fc6-8732-65e2d7fb2582	g.chr8:52321164G>A	uc003xqu.3	-	17	3121	c.3020C>T	c.(3019-3021)GCG>GTG	p.A1007V	PXDNL_uc003xqt.3_RNA	NM_144651	NP_653252	A1KZ92	PXDNL_HUMAN	peroxidasin homolog-like precursor	1007					hydrogen peroxide catabolic process	extracellular space	heme binding|peroxidase activity			ovary(1)|pancreas(1)	2		all_cancers(86;0.107)|Lung NSC(129;0.00641)|all_epithelial(80;0.00716)|all_lung(136;0.015)				CTGCAGCTCCGCGCCCACGAT	0.622													6	17	---	---	---	---	PASS
DPYS	1807	broad.mit.edu	37	8	105456559	105456559	+	Missense_Mutation	SNP	G	C	C			TCGA-39-5024-01A-21D-1817-08	TCGA-39-5024-11A-01D-1817-08									Somatic	Phase_I	Capture				Illumina GAIIx	388478e9-8c1f-43f8-88c4-811bf3cc2500	829ea6e6-1737-4fc6-8732-65e2d7fb2582	g.chr8:105456559G>C	uc003yly.3	-	4	839	c.710C>G	c.(709-711)GCC>GGC	p.A237G		NM_001385	NP_001376	Q14117	DPYS_HUMAN	dihydropyrimidinase	237					protein homotetramerization|pyrimidine nucleoside catabolic process|thymine catabolic process|uracil catabolic process	cytosol	dihydropyrimidinase activity|zinc ion binding			upper_aerodigestive_tract(1)|ovary(1)	2			OV - Ovarian serous cystadenocarcinoma(57;1.61e-06)|STAD - Stomach adenocarcinoma(118;0.229)			CACAGCGCTGGCTATGGTGAT	0.547													22	52	---	---	---	---	PASS
CSMD3	114788	broad.mit.edu	37	8	113564842	113564842	+	Missense_Mutation	SNP	C	T	T			TCGA-39-5024-01A-21D-1817-08	TCGA-39-5024-11A-01D-1817-08									Somatic	Phase_I	Capture				Illumina GAIIx	388478e9-8c1f-43f8-88c4-811bf3cc2500	829ea6e6-1737-4fc6-8732-65e2d7fb2582	g.chr8:113564842C>T	uc003ynu.2	-	26	4501	c.4342G>A	c.(4342-4344)GAT>AAT	p.D1448N	CSMD3_uc003yns.2_Missense_Mutation_p.D720N|CSMD3_uc003ynt.2_Missense_Mutation_p.D1408N|CSMD3_uc011lhx.1_Missense_Mutation_p.D1344N	NM_198123	NP_937756	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3 isoform 1	1448	Extracellular (Potential).|CUB 8.					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						TTTCCAGGATCTACCTCAATC	0.363										HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)			10	59	---	---	---	---	PASS
COL14A1	7373	broad.mit.edu	37	8	121256238	121256238	+	Missense_Mutation	SNP	G	A	A			TCGA-39-5024-01A-21D-1817-08	TCGA-39-5024-11A-01D-1817-08									Somatic	Phase_I	Capture				Illumina GAIIx	388478e9-8c1f-43f8-88c4-811bf3cc2500	829ea6e6-1737-4fc6-8732-65e2d7fb2582	g.chr8:121256238G>A	uc003yox.2	+	20	2735	c.2470G>A	c.(2470-2472)GGA>AGA	p.G824R	COL14A1_uc003yoy.2_Missense_Mutation_p.G502R	NM_021110	NP_066933	Q05707	COEA1_HUMAN	collagen, type XIV, alpha 1 precursor	824	Fibronectin type-III 6.				cell-cell adhesion|collagen fibril organization	collagen type XIV|extracellular space	collagen binding|extracellular matrix structural constituent|protein binding, bridging			ovary(4)|kidney(4)|skin(2)|pancreas(1)|central_nervous_system(1)	12	Lung NSC(37;6.52e-07)|Ovarian(258;0.00769)|Hepatocellular(40;0.161)		OV - Ovarian serous cystadenocarcinoma(1;6.47e-38)|STAD - Stomach adenocarcinoma(47;0.00503)			CTCCGCTCCTGGAAAAACCTG	0.448													22	159	---	---	---	---	PASS
RECQL4	9401	broad.mit.edu	37	8	145738752	145738752	+	Missense_Mutation	SNP	G	A	A			TCGA-39-5024-01A-21D-1817-08	TCGA-39-5024-11A-01D-1817-08									Somatic	Phase_I	Capture				Illumina GAIIx	388478e9-8c1f-43f8-88c4-811bf3cc2500	829ea6e6-1737-4fc6-8732-65e2d7fb2582	g.chr8:145738752G>A	uc003zdj.2	-	15	2344	c.2312C>T	c.(2311-2313)ACG>ATG	p.T771M		NM_004260	NP_004251	O94761	RECQ4_HUMAN	RecQ protein-like 4	771	Helicase C-terminal.				DNA duplex unwinding|DNA recombination|DNA repair	cytoplasm|nucleus	ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding			breast(2)|lung(1)|skin(1)	4	all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055)			AAAGGCCACCGTGGCCACCAC	0.697			N|F|S			osteosarcoma|skin basal and sqamous cell		Genes_defective_in_diseases_associated_with_sensitivity_to_DNA_damaging_agents	RAPADILINO_syndrome|Rothmund-Thomson_syndrome|Baller-Gerold_syndrome				3	40	---	---	---	---	PASS
RANBP6	26953	broad.mit.edu	37	9	6015178	6015178	+	Missense_Mutation	SNP	G	C	C			TCGA-39-5024-01A-21D-1817-08	TCGA-39-5024-11A-01D-1817-08									Somatic	Phase_I	Capture				Illumina GAIIx	388478e9-8c1f-43f8-88c4-811bf3cc2500	829ea6e6-1737-4fc6-8732-65e2d7fb2582	g.chr9:6015178G>C	uc003zjr.2	-	1	441	c.430C>G	c.(430-432)CTT>GTT	p.L144V	RANBP6_uc011lmf.1_Intron|RANBP6_uc003zjs.2_Intron	NM_012416	NP_036548	O60518	RNBP6_HUMAN	RAN binding protein 6	144					protein transport	cytoplasm|nucleus	binding			ovary(3)	3		Acute lymphoblastic leukemia(23;0.158)		GBM - Glioblastoma multiforme(50;0.00522)|Lung(218;0.101)		GAATCAATAAGAAACTTCAGA	0.438													8	53	---	---	---	---	PASS
NFIB	4781	broad.mit.edu	37	9	14307521	14307521	+	Splice_Site	SNP	T	C	C			TCGA-39-5024-01A-21D-1817-08	TCGA-39-5024-11A-01D-1817-08									Somatic	Phase_I	Capture				Illumina GAIIx	388478e9-8c1f-43f8-88c4-811bf3cc2500	829ea6e6-1737-4fc6-8732-65e2d7fb2582	g.chr9:14307521T>C	uc003zle.2	-	2	466	c.31_splice	c.e2-1	p.D11_splice	NFIB_uc003zlf.2_Splice_Site_p.D11_splice|NFIB_uc011lmo.1_Splice_Site_p.D11_splice	NM_005596	NP_005587	O00712	NFIB_HUMAN	nuclear factor I/B						anterior commissure morphogenesis|chondrocyte differentiation|Clara cell differentiation|commissural neuron axon guidance|DNA replication|glial cell differentiation|lung ciliated cell differentiation|negative regulation of DNA binding|negative regulation of epithelial cell proliferation involved in lung morphogenesis|negative regulation of mesenchymal cell proliferation involved in lung development|positive regulation of transcription from RNA polymerase II promoter|principal sensory nucleus of trigeminal nerve development|Type I pneumocyte differentiation|Type II pneumocyte differentiation	cerebellar mossy fiber|nucleolus|nucleus	RNA polymerase II transcription corepressor activity|sequence-specific DNA binding RNA polymerase II transcription factor activity				0				GBM - Glioblastoma multiforme(50;4.4e-08)|LUAD - Lung adenocarcinoma(58;0.119)|Lung(218;0.164)		AAATTCATCCTGTGGAAGACA	0.408			T	MYB|HGMA2	adenoid cystic carcinoma|lipoma								16	41	---	---	---	---	PASS
HAUS6	54801	broad.mit.edu	37	9	19063106	19063106	+	Nonsense_Mutation	SNP	G	C	C			TCGA-39-5024-01A-21D-1817-08	TCGA-39-5024-11A-01D-1817-08									Somatic	Phase_I	Capture				Illumina GAIIx	388478e9-8c1f-43f8-88c4-811bf3cc2500	829ea6e6-1737-4fc6-8732-65e2d7fb2582	g.chr9:19063106G>C	uc003znk.2	-	14	1782	c.1529C>G	c.(1528-1530)TCA>TGA	p.S510*	HAUS6_uc011lmz.1_Nonsense_Mutation_p.S230*|HAUS6_uc003znl.1_Nonsense_Mutation_p.S374*|HAUS6_uc003znm.1_Nonsense_Mutation_p.S265*	NM_017645	NP_060115	Q7Z4H7	HAUS6_HUMAN	HAUS augmin-like complex, subunit 6	510					cell division|centrosome organization|mitosis|spindle assembly	centrosome|HAUS complex|microtubule|nucleus|spindle				ovary(2)	2						TGCAACATCTGATAATGGAGA	0.363													10	98	---	---	---	---	PASS
SLC24A2	25769	broad.mit.edu	37	9	19786143	19786143	+	Missense_Mutation	SNP	T	C	C			TCGA-39-5024-01A-21D-1817-08	TCGA-39-5024-11A-01D-1817-08									Somatic	Phase_I	Capture				Illumina GAIIx	388478e9-8c1f-43f8-88c4-811bf3cc2500	829ea6e6-1737-4fc6-8732-65e2d7fb2582	g.chr9:19786143T>C	uc003zoa.1	-	1	784	c.722A>G	c.(721-723)GAT>GGT	p.D241G	SLC24A2_uc003zob.1_Missense_Mutation_p.D241G	NM_020344	NP_065077	Q9UI40	NCKX2_HUMAN	solute carrier family 24	241	Cytoplasmic (Potential).				visual perception	integral to membrane|plasma membrane	calcium, potassium:sodium antiporter activity|symporter activity			ovary(3)	3				GBM - Glioblastoma multiforme(1;1.67e-55)|Lung(42;0.0443)		GAAAGACACATCTCGAAAGAG	0.388													26	47	---	---	---	---	PASS
PRSS3	5646	broad.mit.edu	37	9	33796728	33796728	+	Missense_Mutation	SNP	C	G	G			TCGA-39-5024-01A-21D-1817-08	TCGA-39-5024-11A-01D-1817-08									Somatic	Phase_I	Capture				Illumina GAIIx	388478e9-8c1f-43f8-88c4-811bf3cc2500	829ea6e6-1737-4fc6-8732-65e2d7fb2582	g.chr9:33796728C>G	uc003ztj.3	+	2	299	c.299C>G	c.(298-300)TCT>TGT	p.S100C	uc003ztk.1_Intron|PRSS3_uc003zti.3_Missense_Mutation_p.S57C|PRSS3_uc003ztl.3_Missense_Mutation_p.S43C	NM_007343	NP_031369	P35030	TRY3_HUMAN	mesotrypsin isoform 1 preproprotein	100	Peptidase S1.				digestion|endothelial cell migration|zymogen activation	extracellular space	calcium ion binding|protein binding|serine-type endopeptidase activity|serine-type peptidase activity				0			LUSC - Lung squamous cell carcinoma(29;0.0176)			TCCCTGAATTCTGGCTCCCAC	0.547													8	307	---	---	---	---	PASS
TLN1	7094	broad.mit.edu	37	9	35710635	35710635	+	Missense_Mutation	SNP	C	T	T			TCGA-39-5024-01A-21D-1817-08	TCGA-39-5024-11A-01D-1817-08									Somatic	Phase_I	Capture				Illumina GAIIx	388478e9-8c1f-43f8-88c4-811bf3cc2500	829ea6e6-1737-4fc6-8732-65e2d7fb2582	g.chr9:35710635C>T	uc003zxt.2	-	33	4603	c.4249G>A	c.(4249-4251)GGA>AGA	p.G1417R		NM_006289	NP_006280	Q9Y490	TLN1_HUMAN	talin 1	1417	Interaction with SYNM.				axon guidance|cell adhesion|cell-cell junction assembly|cellular component movement|cytoskeletal anchoring at plasma membrane|muscle contraction|platelet activation|platelet degranulation	actin cytoskeleton|centrosome|cytosol|extracellular region|focal adhesion|intracellular membrane-bounded organelle|ruffle membrane	actin binding|insulin receptor binding|LIM domain binding|structural constituent of cytoskeleton|vinculin binding			lung(7)|breast(3)|ovary(2)|central_nervous_system(1)	13	all_epithelial(49;0.167)		Lung(28;0.00276)|LUSC - Lung squamous cell carcinoma(32;0.00418)|STAD - Stomach adenocarcinoma(86;0.194)			GGCAGGTTTCCGTTCTTGGCA	0.547													10	61	---	---	---	---	PASS
MAMDC4	158056	broad.mit.edu	37	9	139751491	139751491	+	Missense_Mutation	SNP	T	A	A			TCGA-39-5024-01A-21D-1817-08	TCGA-39-5024-11A-01D-1817-08									Somatic	Phase_I	Capture				Illumina GAIIx	388478e9-8c1f-43f8-88c4-811bf3cc2500	829ea6e6-1737-4fc6-8732-65e2d7fb2582	g.chr9:139751491T>A	uc004cjs.2	+	16	2020	c.1970T>A	c.(1969-1971)ATT>AAT	p.I657N	MAMDC4_uc011mej.1_Translation_Start_Site	NM_206920	NP_996803	Q6UXC1	AEGP_HUMAN	apical early endosomal glycoprotein precursor	736	MAM 4.|Extracellular (Potential).				protein transport	integral to membrane				breast(4)|upper_aerodigestive_tract(2)|central_nervous_system(1)	7	all_cancers(76;0.0763)|all_epithelial(76;0.198)	Myeloproliferative disorder(178;0.0511)		OV - Ovarian serous cystadenocarcinoma(145;1.52e-05)|Epithelial(140;0.000171)		GGGCCCCAGATTGGTGAGTGG	0.662													5	35	---	---	---	---	PASS
FAM166A	401565	broad.mit.edu	37	9	140139670	140139670	+	Missense_Mutation	SNP	G	C	C			TCGA-39-5024-01A-21D-1817-08	TCGA-39-5024-11A-01D-1817-08									Somatic	Phase_I	Capture				Illumina GAIIx	388478e9-8c1f-43f8-88c4-811bf3cc2500	829ea6e6-1737-4fc6-8732-65e2d7fb2582	g.chr9:140139670G>C	uc004cmi.1	-	4	578	c.523C>G	c.(523-525)CTG>GTG	p.L175V		NM_001001710	NP_001001710	Q6J272	F166A_HUMAN	hypothetical protein LOC401565	175										ovary(1)	1						CAGTGGTACAGCTGGAGCGGG	0.692													10	55	---	---	---	---	PASS
LARP4B	23185	broad.mit.edu	37	10	909706	909706	+	Missense_Mutation	SNP	G	C	C			TCGA-39-5024-01A-21D-1817-08	TCGA-39-5024-11A-01D-1817-08									Somatic	Phase_I	Capture				Illumina GAIIx	388478e9-8c1f-43f8-88c4-811bf3cc2500	829ea6e6-1737-4fc6-8732-65e2d7fb2582	g.chr10:909706G>C	uc001ifs.1	-	4	448	c.407C>G	c.(406-408)TCT>TGT	p.S136C		NM_015155	NP_055970	Q92615	LAR4B_HUMAN	La ribonucleoprotein domain family, member 4B	136							nucleotide binding|RNA binding			ovary(2)|central_nervous_system(1)	3						TTCAGGCAGAGAGTCATATTC	0.468													12	103	---	---	---	---	PASS
SLC16A9	220963	broad.mit.edu	37	10	61414243	61414243	+	Missense_Mutation	SNP	T	C	C			TCGA-39-5024-01A-21D-1817-08	TCGA-39-5024-11A-01D-1817-08									Somatic	Phase_I	Capture				Illumina GAIIx	388478e9-8c1f-43f8-88c4-811bf3cc2500	829ea6e6-1737-4fc6-8732-65e2d7fb2582	g.chr10:61414243T>C	uc010qig.1	-	5	990	c.541A>G	c.(541-543)ATA>GTA	p.I181V		NM_194298	NP_919274	Q7RTY1	MOT9_HUMAN	solute carrier family 16 (monocarboxylic acid	181	Helical; (Potential).				urate metabolic process	integral to membrane|plasma membrane	symporter activity			skin(2)|ovary(1)	3						CAGGCTAATATATTTAAAGCT	0.423													69	97	---	---	---	---	PASS
JMJD1C	221037	broad.mit.edu	37	10	64967767	64967767	+	Missense_Mutation	SNP	T	A	A			TCGA-39-5024-01A-21D-1817-08	TCGA-39-5024-11A-01D-1817-08									Somatic	Phase_I	Capture				Illumina GAIIx	388478e9-8c1f-43f8-88c4-811bf3cc2500	829ea6e6-1737-4fc6-8732-65e2d7fb2582	g.chr10:64967767T>A	uc001jmn.2	-	10	3962	c.3662A>T	c.(3661-3663)GAA>GTA	p.E1221V	JMJD1C_uc001jml.2_Missense_Mutation_p.E1002V|JMJD1C_uc001jmm.2_Missense_Mutation_p.E933V|JMJD1C_uc010qiq.1_Missense_Mutation_p.E1039V|JMJD1C_uc009xpi.2_Missense_Mutation_p.E1039V|JMJD1C_uc009xpj.1_RNA|JMJD1C_uc009xpk.1_Missense_Mutation_p.E258V	NM_032776	NP_116165	Q15652	JHD2C_HUMAN	jumonji domain containing 1C isoform a	1221					blood coagulation|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleoplasm	histone demethylase activity (H3-K9 specific)|metal ion binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|thyroid hormone receptor binding			ovary(4)|breast(1)|central_nervous_system(1)	6	Prostate(12;0.0119)|all_hematologic(501;0.191)					ATAGCTGCCTTCCTTTCTTTC	0.438													17	137	---	---	---	---	PASS
JMJD1C	221037	broad.mit.edu	37	10	64967768	64967768	+	Nonsense_Mutation	SNP	C	A	A			TCGA-39-5024-01A-21D-1817-08	TCGA-39-5024-11A-01D-1817-08									Somatic	Phase_I	Capture				Illumina GAIIx	388478e9-8c1f-43f8-88c4-811bf3cc2500	829ea6e6-1737-4fc6-8732-65e2d7fb2582	g.chr10:64967768C>A	uc001jmn.2	-	10	3961	c.3661G>T	c.(3661-3663)GAA>TAA	p.E1221*	JMJD1C_uc001jml.2_Nonsense_Mutation_p.E1002*|JMJD1C_uc001jmm.2_Nonsense_Mutation_p.E933*|JMJD1C_uc010qiq.1_Nonsense_Mutation_p.E1039*|JMJD1C_uc009xpi.2_Nonsense_Mutation_p.E1039*|JMJD1C_uc009xpj.1_RNA|JMJD1C_uc009xpk.1_Nonsense_Mutation_p.E258*	NM_032776	NP_116165	Q15652	JHD2C_HUMAN	jumonji domain containing 1C isoform a	1221					blood coagulation|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleoplasm	histone demethylase activity (H3-K9 specific)|metal ion binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|thyroid hormone receptor binding			ovary(4)|breast(1)|central_nervous_system(1)	6	Prostate(12;0.0119)|all_hematologic(501;0.191)					TAGCTGCCTTCCTTTCTTTCC	0.443													17	140	---	---	---	---	PASS
PTEN	5728	broad.mit.edu	37	10	89692902	89692902	+	Missense_Mutation	SNP	G	A	A	rs121909218		TCGA-39-5024-01A-21D-1817-08	TCGA-39-5024-11A-01D-1817-08									Somatic	Phase_I	Capture				Illumina GAIIx	388478e9-8c1f-43f8-88c4-811bf3cc2500	829ea6e6-1737-4fc6-8732-65e2d7fb2582	g.chr10:89692902G>A	uc001kfb.2	+	6	1417	c.386G>A	c.(385-387)GGA>GAA	p.G129E		NM_000314	NP_000305	P60484	PTEN_HUMAN	phosphatase and tensin homolog	129	Phosphatase tensin-type.		G -> E (in CD; no lipid phosphatase activity but retains protein phosphatase activity; retains ability to inhibit focal adhesion formation).|G -> R (in glioblastoma; severely reduced protein phosphatase activity; loss of phosphatase activity towards Ins(1,3,4,5)P4).		activation of mitotic anaphase-promoting complex activity|apoptosis|canonical Wnt receptor signaling pathway|cell proliferation|central nervous system development|induction of apoptosis|inositol phosphate dephosphorylation|negative regulation of cell migration|negative regulation of cyclin-dependent protein kinase activity involved in G1/S|negative regulation of focal adhesion assembly|negative regulation of G1/S transition of mitotic cell cycle|negative regulation of protein kinase B signaling cascade|negative regulation of protein phosphorylation|nerve growth factor receptor signaling pathway|phosphatidylinositol dephosphorylation|phosphatidylinositol-mediated signaling|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process|positive regulation of sequence-specific DNA binding transcription factor activity|protein stabilization|regulation of neuron projection development|T cell receptor signaling pathway	cytosol|internal side of plasma membrane|PML body	anaphase-promoting complex binding|enzyme binding|inositol-1,3,4,5-tetrakisphosphate 3-phosphatase activity|lipid binding|magnesium ion binding|PDZ domain binding|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity|phosphatidylinositol-3,4-bisphosphate 3-phosphatase activity|phosphatidylinositol-3-phosphatase activity|protein serine/threonine phosphatase activity|protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity	p.G129R(6)|p.R55fs*1(4)|p.G129*(3)|p.K128_R130del(3)|p.?(2)|p.Y27fs*1(2)|p.Y27_N212>Y(2)|p.G129V(1)|p.K128fs*47(1)|p.A121_F145del(1)|p.G129E(1)|p.G129fs*5(1)|p.G127fs*5(1)|p.G129fs*50(1)|p.F56fs*2(1)|p.G129fs*51(1)		endometrium(831)|central_nervous_system(657)|skin(121)|haematopoietic_and_lymphoid_tissue(101)|large_intestine(99)|prostate(97)|breast(73)|lung(65)|ovary(58)|thyroid(29)|stomach(29)|upper_aerodigestive_tract(25)|cervix(24)|liver(20)|vulva(17)|kidney(15)|NS(14)|soft_tissue(13)|urinary_tract(12)|eye(8)|pancreas(6)|salivary_gland(5)|bone(5)|biliary_tract(4)|autonomic_ganglia(2)|meninges(2)|testis(1)|oesophagus(1)	2334		all_cancers(4;3.61e-31)|all_epithelial(4;3.96e-23)|Prostate(4;8.12e-23)|Breast(4;0.000111)|Melanoma(5;0.00146)|all_hematologic(4;0.00227)|Colorectal(252;0.00494)|all_neural(4;0.00513)|Acute lymphoblastic leukemia(4;0.0116)|Glioma(4;0.0274)|all_lung(38;0.132)	KIRC - Kidney renal clear cell carcinoma(1;0.214)	UCEC - Uterine corpus endometrioid carcinoma (6;0.000228)|all cancers(1;4.16e-84)|GBM - Glioblastoma multiforme(1;7.77e-49)|Epithelial(1;7.67e-41)|OV - Ovarian serous cystadenocarcinoma(1;6.22e-15)|BRCA - Breast invasive adenocarcinoma(1;1.1e-06)|Lung(2;3.18e-06)|Colorectal(12;4.88e-06)|LUSC - Lung squamous cell carcinoma(2;4.97e-06)|COAD - Colon adenocarcinoma(12;1.13e-05)|Kidney(1;0.000288)|KIRC - Kidney renal clear cell carcinoma(1;0.00037)|STAD - Stomach adenocarcinoma(243;0.218)		GCTGGAAAGGGACGAACTGGT	0.413		31	D|Mis|N|F|S		glioma| prostate|endometrial	harmartoma|glioma| prostate|endometrial			Proteus_syndrome|Cowden_syndrome|Juvenile_Polyposis|Hereditary_Mixed_Polyposis_Syndrome_type_1|Bannayan-Riley-Ruvalcaba_syndrome	HNSCC(9;0.0022)|TCGA GBM(2;<1E-08)|TSP Lung(26;0.18)			43	90	---	---	---	---	PASS
PNPLA2	57104	broad.mit.edu	37	11	822471	822471	+	Silent	SNP	C	T	T			TCGA-39-5024-01A-21D-1817-08	TCGA-39-5024-11A-01D-1817-08									Somatic	Phase_I	Capture				Illumina GAIIx	388478e9-8c1f-43f8-88c4-811bf3cc2500	829ea6e6-1737-4fc6-8732-65e2d7fb2582	g.chr11:822471C>T	uc001lrt.2	+	5	763	c.561C>T	c.(559-561)TTC>TTT	p.F187F	PNPLA2_uc009ycl.2_5'Flank	NM_020376	NP_065109	Q96AD5	PLPL2_HUMAN	patatin-like phospholipase domain containing 2	187	Lumenal (Potential).				negative regulation of sequestering of triglyceride|positive regulation of triglyceride catabolic process	integral to membrane|lipid particle|plasma membrane	triglyceride lipase activity				0		all_cancers(49;4.75e-06)|all_epithelial(84;0.00204)|Breast(177;0.00234)|Ovarian(85;0.0228)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762)		all cancers(45;1.63e-25)|Epithelial(43;1.28e-24)|OV - Ovarian serous cystadenocarcinoma(40;7.09e-19)|BRCA - Breast invasive adenocarcinoma(625;4.23e-05)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)		TGTCCCCCTTCTCGGGCGAGA	0.572													11	141	---	---	---	---	PASS
OR52B2	255725	broad.mit.edu	37	11	6190816	6190816	+	Silent	SNP	G	A	A			TCGA-39-5024-01A-21D-1817-08	TCGA-39-5024-11A-01D-1817-08									Somatic	Phase_I	Capture				Illumina GAIIx	388478e9-8c1f-43f8-88c4-811bf3cc2500	829ea6e6-1737-4fc6-8732-65e2d7fb2582	g.chr11:6190816G>A	uc010qzy.1	-	1	741	c.741C>T	c.(739-741)CTC>CTT	p.L247L		NM_001004052	NP_001004052	Q96RD2	O52B2_HUMAN	olfactory receptor, family 52, subfamily B,	247	Helical; Name=6; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0		Medulloblastoma(188;0.00776)|all_neural(188;0.0652)|Breast(177;0.114)		Epithelial(150;3.69e-08)|BRCA - Breast invasive adenocarcinoma(625;0.135)		GGATGACACAGAGGTGGGAGC	0.488													7	60	---	---	---	---	PASS
MRGPRX1	259249	broad.mit.edu	37	11	18955526	18955526	+	Missense_Mutation	SNP	G	A	A			TCGA-39-5024-01A-21D-1817-08	TCGA-39-5024-11A-01D-1817-08									Somatic	Phase_I	Capture				Illumina GAIIx	388478e9-8c1f-43f8-88c4-811bf3cc2500	829ea6e6-1737-4fc6-8732-65e2d7fb2582	g.chr11:18955526G>A	uc001mpg.2	-	1	1024	c.806C>T	c.(805-807)CCC>CTC	p.P269L		NM_147199	NP_671732	Q96LB2	MRGX1_HUMAN	MAS-related GPR, member X1	269	Helical; Name=7; (Potential).				acute-phase response	integral to membrane|plasma membrane	G-protein coupled receptor activity			pancreas(2)|central_nervous_system(1)	3						GTAAATGATGGGGTTGGCACT	0.468													13	120	---	---	---	---	PASS
LGR4	55366	broad.mit.edu	37	11	27390301	27390301	+	Missense_Mutation	SNP	T	G	G			TCGA-39-5024-01A-21D-1817-08	TCGA-39-5024-11A-01D-1817-08									Somatic	Phase_I	Capture				Illumina GAIIx	388478e9-8c1f-43f8-88c4-811bf3cc2500	829ea6e6-1737-4fc6-8732-65e2d7fb2582	g.chr11:27390301T>G	uc001mrj.3	-	18	2454	c.1969A>C	c.(1969-1971)AAT>CAT	p.N657H	LGR4_uc001mrk.3_Missense_Mutation_p.N633H	NM_018490	NP_060960	Q9BXB1	LGR4_HUMAN	leucine-rich repeat-containing G protein-coupled	657	Cytoplasmic (Potential).					integral to membrane|plasma membrane	protein-hormone receptor activity			ovary(1)	1						TTGAGATGATTGCTCTTCCCA	0.413													13	53	---	---	---	---	PASS
API5	8539	broad.mit.edu	37	11	43350426	43350426	+	Silent	SNP	C	G	G			TCGA-39-5024-01A-21D-1817-08	TCGA-39-5024-11A-01D-1817-08									Somatic	Phase_I	Capture				Illumina GAIIx	388478e9-8c1f-43f8-88c4-811bf3cc2500	829ea6e6-1737-4fc6-8732-65e2d7fb2582	g.chr11:43350426C>G	uc010rfh.1	+	9	1283	c.1110C>G	c.(1108-1110)CTC>CTG	p.L370L	API5_uc010rfg.1_Silent_p.L359L|API5_uc001mxf.2_Silent_p.L370L|API5_uc010rfi.1_Silent_p.L316L|API5_uc001mxg.2_Silent_p.L244L	NM_001142930	NP_001136402	Q9BZZ5	API5_HUMAN	apoptosis inhibitor 5 isoform a	370	Leucine-zipper.				anti-apoptosis|apoptosis	cytoplasm|spliceosomal complex	fibroblast growth factor binding			large_intestine(1)|ovary(1)|central_nervous_system(1)	3						CAGAAAAGCTCAAAGATTTCA	0.398													13	58	---	---	---	---	PASS
ARFGAP2	84364	broad.mit.edu	37	11	47188328	47188328	+	Missense_Mutation	SNP	G	A	A			TCGA-39-5024-01A-21D-1817-08	TCGA-39-5024-11A-01D-1817-08									Somatic	Phase_I	Capture				Illumina GAIIx	388478e9-8c1f-43f8-88c4-811bf3cc2500	829ea6e6-1737-4fc6-8732-65e2d7fb2582	g.chr11:47188328G>A	uc001ndt.2	-	13	1330	c.1315C>T	c.(1315-1317)CGG>TGG	p.R439W	ARFGAP2_uc010rha.1_Missense_Mutation_p.R170W|ARFGAP2_uc010rhb.1_Missense_Mutation_p.R411W|ARFGAP2_uc001ndu.2_Missense_Mutation_p.R303W|ARFGAP2_uc010rhc.1_Missense_Mutation_p.R170W	NM_032389	NP_115765	Q8N6H7	ARFG2_HUMAN	ADP-ribosylation factor GTPase activating	439	Required for interaction with coatomer.				protein transport|regulation of ARF GTPase activity|vesicle-mediated transport	Golgi membrane|nucleolus|plasma membrane	ARF GTPase activator activity|zinc ion binding			ovary(1)	1						TCCACCTCCCGCCCAAAGAAC	0.597													12	169	---	---	---	---	PASS
OR8H2	390151	broad.mit.edu	37	11	55872908	55872908	+	Silent	SNP	A	G	G			TCGA-39-5024-01A-21D-1817-08	TCGA-39-5024-11A-01D-1817-08									Somatic	Phase_I	Capture				Illumina GAIIx	388478e9-8c1f-43f8-88c4-811bf3cc2500	829ea6e6-1737-4fc6-8732-65e2d7fb2582	g.chr11:55872908A>G	uc010riy.1	+	1	390	c.390A>G	c.(388-390)CTA>CTG	p.L130L		NM_001005200	NP_001005200	Q8N162	OR8H2_HUMAN	olfactory receptor, family 8, subfamily H,	130	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)|skin(1)	2	Esophageal squamous(21;0.00693)					GCAGTCCTCTACACTACACAG	0.468										HNSCC(53;0.14)			25	201	---	---	---	---	PASS
OR4D10	390197	broad.mit.edu	37	11	59245380	59245380	+	Missense_Mutation	SNP	A	G	G			TCGA-39-5024-01A-21D-1817-08	TCGA-39-5024-11A-01D-1817-08									Somatic	Phase_I	Capture				Illumina GAIIx	388478e9-8c1f-43f8-88c4-811bf3cc2500	829ea6e6-1737-4fc6-8732-65e2d7fb2582	g.chr11:59245380A>G	uc001nnz.1	+	1	478	c.478A>G	c.(478-480)ATT>GTT	p.I160V		NM_001004705	NP_001004705	Q8NGI6	OR4DA_HUMAN	olfactory receptor, family 4, subfamily D,	160	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(2)|skin(1)	3						CATCGTGCAGATTTCCCTGTT	0.532													22	125	---	---	---	---	PASS
MS4A6A	64231	broad.mit.edu	37	11	59939686	59939686	+	Missense_Mutation	SNP	C	T	T			TCGA-39-5024-01A-21D-1817-08	TCGA-39-5024-11A-01D-1817-08									Somatic	Phase_I	Capture				Illumina GAIIx	388478e9-8c1f-43f8-88c4-811bf3cc2500	829ea6e6-1737-4fc6-8732-65e2d7fb2582	g.chr11:59939686C>T	uc001nor.2	-	7	930	c.692G>A	c.(691-693)GGC>GAC	p.G231D	MS4A6A_uc001noq.2_3'UTR|MS4A6A_uc001nos.3_Missense_Mutation_p.G259D|MS4A6A_uc009ymv.2_Missense_Mutation_p.G231D	NM_152852	NP_690591	Q9H2W1	M4A6A_HUMAN	membrane-spanning 4-domains, subfamily A, member	231	Cytoplasmic (Potential).					integral to membrane	receptor activity				0						TGAGGACATGCCAGAATTACC	0.328													23	181	---	---	---	---	PASS
SF3B2	10992	broad.mit.edu	37	11	65835515	65835515	+	Missense_Mutation	SNP	C	T	T			TCGA-39-5024-01A-21D-1817-08	TCGA-39-5024-11A-01D-1817-08									Somatic	Phase_I	Capture				Illumina GAIIx	388478e9-8c1f-43f8-88c4-811bf3cc2500	829ea6e6-1737-4fc6-8732-65e2d7fb2582	g.chr11:65835515C>T	uc001ogy.1	+	20	2469	c.2429C>T	c.(2428-2430)ACG>ATG	p.T810M	PACS1_uc001ogz.1_5'Flank|PACS1_uc001oha.1_5'Flank	NM_006842	NP_006833	Q13435	SF3B2_HUMAN	splicing factor 3B subunit 2	810					interspecies interaction between organisms	catalytic step 2 spliceosome|nucleoplasm|U12-type spliceosomal complex	nucleic acid binding|protein binding			ovary(2)|breast(1)	3						GACATGTCCACGGTGAGTACT	0.512											OREG0021094	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	16	122	---	---	---	---	PASS
DYNC2H1	79659	broad.mit.edu	37	11	103091471	103091471	+	Missense_Mutation	SNP	G	C	C			TCGA-39-5024-01A-21D-1817-08	TCGA-39-5024-11A-01D-1817-08									Somatic	Phase_I	Capture				Illumina GAIIx	388478e9-8c1f-43f8-88c4-811bf3cc2500	829ea6e6-1737-4fc6-8732-65e2d7fb2582	g.chr11:103091471G>C	uc001pho.2	+	57	9210	c.9066G>C	c.(9064-9066)AGG>AGC	p.R3022S	DYNC2H1_uc001phn.1_Missense_Mutation_p.R3022S|DYNC2H1_uc009yxe.1_Intron	NM_001080463	NP_001073932	Q8NCM8	DYHC2_HUMAN	dynein, cytoplasmic 2, heavy chain 1	3022	Stalk (By similarity).				cell projection organization|Golgi organization|microtubule-based movement|multicellular organismal development	cilium axoneme|dynein complex|Golgi apparatus|microtubule|plasma membrane	ATP binding|ATPase activity|microtubule motor activity				0		Acute lymphoblastic leukemia(157;0.000966)|all_hematologic(158;0.00348)		BRCA - Breast invasive adenocarcinoma(274;0.000177)|Epithelial(105;0.0785)		GAGTTTTAAGGTTGATGGGTA	0.358													9	85	---	---	---	---	PASS
TTC36	143941	broad.mit.edu	37	11	118398237	118398237	+	Silent	SNP	C	T	T			TCGA-39-5024-01A-21D-1817-08	TCGA-39-5024-11A-01D-1817-08									Somatic	Phase_I	Capture				Illumina GAIIx	388478e9-8c1f-43f8-88c4-811bf3cc2500	829ea6e6-1737-4fc6-8732-65e2d7fb2582	g.chr11:118398237C>T	uc001ptg.1	+	1	28	c.28C>T	c.(28-30)CTG>TTG	p.L10L	TTC36_uc010ryb.1_RNA|TTC36_uc010ryc.1_5'UTR	NM_001080441	NP_001073910	A6NLP5	TTC36_HUMAN	tetratricopeptide repeat domain 36	10							binding				0						TCAGGCAGTGCTGCAGGCCAT	0.527													33	152	---	---	---	---	PASS
SCN3B	55800	broad.mit.edu	37	11	123524489	123524489	+	Missense_Mutation	SNP	C	A	A			TCGA-39-5024-01A-21D-1817-08	TCGA-39-5024-11A-01D-1817-08									Somatic	Phase_I	Capture				Illumina GAIIx	388478e9-8c1f-43f8-88c4-811bf3cc2500	829ea6e6-1737-4fc6-8732-65e2d7fb2582	g.chr11:123524489C>A	uc001pza.1	-	2	428	c.21G>T	c.(19-21)TTG>TTT	p.L7F	SCN3B_uc001pzb.1_Missense_Mutation_p.L7F	NM_001040151	NP_001035241	Q9NY72	SCN3B_HUMAN	voltage-gated sodium channel beta-3 subunit	7					axon guidance	integral to membrane|plasma membrane	voltage-gated sodium channel activity			large_intestine(2)|ovary(2)|central_nervous_system(1)|skin(1)	6		Breast(109;0.00204)|Lung NSC(97;0.0177)|all_lung(97;0.0179)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;5.37e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0227)		CCAGGGGAAACAATCTATTGA	0.512													32	198	---	---	---	---	PASS
KDM5A	5927	broad.mit.edu	37	12	495116	495116	+	Missense_Mutation	SNP	C	G	G			TCGA-39-5024-01A-21D-1817-08	TCGA-39-5024-11A-01D-1817-08									Somatic	Phase_I	Capture				Illumina GAIIx	388478e9-8c1f-43f8-88c4-811bf3cc2500	829ea6e6-1737-4fc6-8732-65e2d7fb2582	g.chr12:495116C>G	uc001qif.1	-	2	553	c.190G>C	c.(190-192)GAA>CAA	p.E64Q	KDM5A_uc001qie.1_Missense_Mutation_p.E64Q|KDM5A_uc010sdn.1_Missense_Mutation_p.E64Q|KDM5A_uc010sdo.1_Intron	NM_001042603	NP_001036068	P29375	KDM5A_HUMAN	retinoblastoma binding protein 2 isoform 1	64					chromatin modification|multicellular organismal development|positive regulation of transcription, DNA-dependent|transcription from RNA polymerase II promoter	cytoplasm|nucleolus	DNA binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|sequence-specific DNA binding transcription factor activity|zinc ion binding			skin(2)|ovary(1)	3						CTTTTTACTTCACAGGCAAAT	0.368			T 	NUP98	AML								16	79	---	---	---	---	PASS
C1S	716	broad.mit.edu	37	12	7172571	7172571	+	Missense_Mutation	SNP	G	A	A			TCGA-39-5024-01A-21D-1817-08	TCGA-39-5024-11A-01D-1817-08									Somatic	Phase_I	Capture				Illumina GAIIx	388478e9-8c1f-43f8-88c4-811bf3cc2500	829ea6e6-1737-4fc6-8732-65e2d7fb2582	g.chr12:7172571G>A	uc001qsj.2	+	9	1404	c.685G>A	c.(685-687)GAC>AAC	p.D229N	C1S_uc001qsk.2_Missense_Mutation_p.D229N|C1S_uc001qsl.2_Missense_Mutation_p.D229N|C1S_uc009zfr.2_Missense_Mutation_p.D62N|C1S_uc009zfs.2_RNA	NM_201442	NP_958850	P09871	C1S_HUMAN	complement component 1, s subcomponent	229	CUB 2.				complement activation, classical pathway|innate immune response|proteolysis	extracellular region	calcium ion binding|serine-type endopeptidase activity			skin(1)	1					Abciximab(DB00054)|Adalimumab(DB00051)|Basiliximab(DB00074)|Cetuximab(DB00002)|Etanercept(DB00005)|Gemtuzumab ozogamicin(DB00056)|Ibritumomab(DB00078)|Immune globulin(DB00028)|Muromonab(DB00075)|Rituximab(DB00073)|Trastuzumab(DB00072)	GGAAGCAGCTGACTCAGCGGG	0.463													18	192	---	---	---	---	PASS
PTPRO	5800	broad.mit.edu	37	12	15650234	15650234	+	Silent	SNP	A	C	C			TCGA-39-5024-01A-21D-1817-08	TCGA-39-5024-11A-01D-1817-08									Somatic	Phase_I	Capture				Illumina GAIIx	388478e9-8c1f-43f8-88c4-811bf3cc2500	829ea6e6-1737-4fc6-8732-65e2d7fb2582	g.chr12:15650234A>C	uc001rcv.1	+	3	579	c.405A>C	c.(403-405)ACA>ACC	p.T135T	PTPRO_uc001rcw.1_Silent_p.T135T|PTPRO_uc001rcu.1_Silent_p.T135T	NM_030667	NP_109592	Q16827	PTPRO_HUMAN	receptor-type protein tyrosine phosphatase O	135	Extracellular (Potential).					integral to plasma membrane	protein binding|transmembrane receptor protein tyrosine phosphatase activity			skin(5)|ovary(2)|upper_aerodigestive_tract(1)|lung(1)	9		Hepatocellular(102;0.244)				CTCCTGAAACAGGAGTCCTGT	0.373													26	190	---	---	---	---	PASS
C12orf35	55196	broad.mit.edu	37	12	32137042	32137042	+	Silent	SNP	A	T	T			TCGA-39-5024-01A-21D-1817-08	TCGA-39-5024-11A-01D-1817-08									Somatic	Phase_I	Capture				Illumina GAIIx	388478e9-8c1f-43f8-88c4-811bf3cc2500	829ea6e6-1737-4fc6-8732-65e2d7fb2582	g.chr12:32137042A>T	uc001rks.2	+	4	3567	c.3153A>T	c.(3151-3153)CTA>CTT	p.L1051L		NM_018169	NP_060639	Q9HCM1	CL035_HUMAN	hypothetical protein LOC55196	1051										ovary(1)|skin(1)	2	all_cancers(9;3.36e-11)|all_epithelial(9;2.56e-11)|all_lung(12;5.67e-10)|Acute lymphoblastic leukemia(23;0.0122)|Lung SC(12;0.0336)|all_hematologic(23;0.0429)|Esophageal squamous(101;0.204)		OV - Ovarian serous cystadenocarcinoma(6;0.0114)			TCTTATACCTACATGACCAGC	0.438													31	124	---	---	---	---	PASS
RACGAP1	29127	broad.mit.edu	37	12	50387974	50387974	+	Nonsense_Mutation	SNP	G	A	A			TCGA-39-5024-01A-21D-1817-08	TCGA-39-5024-11A-01D-1817-08									Somatic	Phase_I	Capture				Illumina GAIIx	388478e9-8c1f-43f8-88c4-811bf3cc2500	829ea6e6-1737-4fc6-8732-65e2d7fb2582	g.chr12:50387974G>A	uc001rvt.2	-	14	1589	c.1279C>T	c.(1279-1281)CGA>TGA	p.R427*	RACGAP1_uc009zlm.1_Nonsense_Mutation_p.R427*|RACGAP1_uc001rvs.2_Nonsense_Mutation_p.R427*|RACGAP1_uc001rvu.2_Nonsense_Mutation_p.R427*	NM_013277	NP_037409	Q9H0H5	RGAP1_HUMAN	Rac GTPase activating protein 1	427	Rho-GAP.				blood coagulation|cytokinesis, actomyosin contractile ring assembly|cytokinesis, initiation of separation|embryo development|microtubule-based movement|neuroblast proliferation|regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction|spermatogenesis|sulfate transport	acrosomal vesicle|cytosol|microtubule|midbody|nucleus|spindle	alpha-tubulin binding|beta-tubulin binding|gamma-tubulin binding|GTPase activator activity|metal ion binding			kidney(1)	1						TTGAGGTTTCGAAGAAAGTCT	0.378													21	121	---	---	---	---	PASS
HNRNPA1	3178	broad.mit.edu	37	12	54678102	54678102	+	Splice_Site	SNP	G	T	T			TCGA-39-5024-01A-21D-1817-08	TCGA-39-5024-11A-01D-1817-08									Somatic	Phase_I	Capture				Illumina GAIIx	388478e9-8c1f-43f8-88c4-811bf3cc2500	829ea6e6-1737-4fc6-8732-65e2d7fb2582	g.chr12:54678102G>T	uc001sfl.2	+	10	1227	c.1123_splice	c.e10+1		HNRNPA1_uc001sfm.2_Splice_Site|HNRNPA1_uc009zng.2_Intron|HNRNPA1_uc009znh.2_Splice_Site|HNRNPA1_uc009zni.2_Splice_Site|HNRNPA1_uc001sfn.2_Splice_Site|HNRNPA1_uc001sfo.3_Splice_Site|HNRNPA1_uc009znj.1_3'UTR	NM_031157	NP_112420	P09651	ROA1_HUMAN	heterogeneous nuclear ribonucleoprotein A1						interspecies interaction between organisms|mRNA transport|nuclear import	catalytic step 2 spliceosome|cytoplasm|heterogeneous nuclear ribonucleoprotein complex|nucleolus|nucleoplasm	nucleotide binding|protein binding|single-stranded DNA binding			skin(2)|ovary(1)	3						TTTTAATTAGGTAAGTAAGCA	0.368													7	56	---	---	---	---	PASS
OR6C76	390326	broad.mit.edu	37	12	55820491	55820491	+	Missense_Mutation	SNP	G	C	C			TCGA-39-5024-01A-21D-1817-08	TCGA-39-5024-11A-01D-1817-08									Somatic	Phase_I	Capture				Illumina GAIIx	388478e9-8c1f-43f8-88c4-811bf3cc2500	829ea6e6-1737-4fc6-8732-65e2d7fb2582	g.chr12:55820491G>C	uc010spm.1	+	1	454	c.454G>C	c.(454-456)GTA>CTA	p.V152L		NM_001005183	NP_001005183	A6NM76	O6C76_HUMAN	olfactory receptor, family 6, subfamily C,	152	Helical; Name=4; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0						TGGTTTCTTGGTAATTTTTCC	0.443													21	116	---	---	---	---	PASS
MBD6	114785	broad.mit.edu	37	12	57919593	57919593	+	Missense_Mutation	SNP	A	C	C			TCGA-39-5024-01A-21D-1817-08	TCGA-39-5024-11A-01D-1817-08									Somatic	Phase_I	Capture				Illumina GAIIx	388478e9-8c1f-43f8-88c4-811bf3cc2500	829ea6e6-1737-4fc6-8732-65e2d7fb2582	g.chr12:57919593A>C	uc001soj.1	+	6	1066	c.842A>C	c.(841-843)CAC>CCC	p.H281P	MBD6_uc001sok.1_Missense_Mutation_p.H148P|MBD6_uc001sol.1_5'Flank	NM_052897	NP_443129	Q96DN6	MBD6_HUMAN	methyl-CpG binding domain protein 6	281	Pro-rich.					chromosome|nucleus	chromatin binding|DNA binding			central_nervous_system(3)|ovary(1)	4						CTCCCCGCCCACCCTGGTCCT	0.662													10	68	---	---	---	---	PASS
DPY19L2	283417	broad.mit.edu	37	12	64011105	64011105	+	Silent	SNP	A	C	C			TCGA-39-5024-01A-21D-1817-08	TCGA-39-5024-11A-01D-1817-08									Somatic	Phase_I	Capture				Illumina GAIIx	388478e9-8c1f-43f8-88c4-811bf3cc2500	829ea6e6-1737-4fc6-8732-65e2d7fb2582	g.chr12:64011105A>C	uc001srp.1	-	11	1378	c.1197T>G	c.(1195-1197)TCT>TCG	p.S399S	DPY19L2_uc009zqk.1_RNA	NM_173812	NP_776173	Q6NUT2	D19L2_HUMAN	dpy-19-like 2	399					multicellular organismal development|spermatid development	integral to membrane				central_nervous_system(1)|skin(1)	2			GBM - Glioblastoma multiforme(1;2.77e-05)	GBM - Glioblastoma multiforme(28;0.044)		ACAAAGATGAAGAATAATAAG	0.279													6	34	---	---	---	---	PASS
TCTN1	79600	broad.mit.edu	37	12	111070361	111070361	+	Missense_Mutation	SNP	G	C	C			TCGA-39-5024-01A-21D-1817-08	TCGA-39-5024-11A-01D-1817-08									Somatic	Phase_I	Capture				Illumina GAIIx	388478e9-8c1f-43f8-88c4-811bf3cc2500	829ea6e6-1737-4fc6-8732-65e2d7fb2582	g.chr12:111070361G>C	uc009zvs.2	+	5	817	c.709G>C	c.(709-711)GCA>CCA	p.A237P	TCTN1_uc009zvr.1_RNA|TCTN1_uc001trl.2_RNA|TCTN1_uc001trm.2_Missense_Mutation_p.A177P|TCTN1_uc010syc.1_RNA|TCTN1_uc001tro.2_RNA|TCTN1_uc001trp.3_Missense_Mutation_p.A237P|TCTN1_uc001trn.3_Missense_Mutation_p.A237P|TCTN1_uc001trj.1_Missense_Mutation_p.A181P|TCTN1_uc001trk.3_RNA|HVCN1_uc001trq.1_Intron	NM_001082537	NP_001076006	Q2MV58	TECT1_HUMAN	tectonic family member 1 isoform 2	237					multicellular organismal development	extracellular region					0						TAATAACCCTGCAGGTAAGAA	0.313													28	113	---	---	---	---	PASS
CIT	11113	broad.mit.edu	37	12	120195326	120195326	+	Missense_Mutation	SNP	G	C	C			TCGA-39-5024-01A-21D-1817-08	TCGA-39-5024-11A-01D-1817-08									Somatic	Phase_I	Capture				Illumina GAIIx	388478e9-8c1f-43f8-88c4-811bf3cc2500	829ea6e6-1737-4fc6-8732-65e2d7fb2582	g.chr12:120195326G>C	uc001txi.1	-	21	2482	c.2429C>G	c.(2428-2430)TCT>TGT	p.S810C	CIT_uc001txh.1_Missense_Mutation_p.S344C|CIT_uc001txj.1_Missense_Mutation_p.S852C	NM_007174	NP_009105	O14578	CTRO_HUMAN	citron	810	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)		CCTGAGTTCAGAAATCATCTC	0.527													21	131	---	---	---	---	PASS
NBEA	26960	broad.mit.edu	37	13	35615106	35615106	+	Missense_Mutation	SNP	A	G	G			TCGA-39-5024-01A-21D-1817-08	TCGA-39-5024-11A-01D-1817-08									Somatic	Phase_I	Capture				Illumina GAIIx	388478e9-8c1f-43f8-88c4-811bf3cc2500	829ea6e6-1737-4fc6-8732-65e2d7fb2582	g.chr13:35615106A>G	uc001uvb.2	+	3	537	c.331A>G	c.(331-333)ATT>GTT	p.I111V		NM_015678	NP_056493	Q8NFP9	NBEA_HUMAN	neurobeachin	111						cytosol|endomembrane system|plasma membrane|trans-Golgi network	protein binding			ovary(9)|large_intestine(2)	11		Breast(139;0.0141)|Lung SC(185;0.0548)|Prostate(109;0.207)		all cancers(112;1.93e-08)|Epithelial(112;1.62e-07)|BRCA - Breast invasive adenocarcinoma(63;0.00033)|OV - Ovarian serous cystadenocarcinoma(117;0.00109)|KIRC - Kidney renal clear cell carcinoma(186;0.00575)|Kidney(163;0.00656)|GBM - Glioblastoma multiforme(144;0.191)|Lung(94;0.199)		GATGAACTTTATTATCCAGGA	0.383													18	195	---	---	---	---	PASS
EPSTI1	94240	broad.mit.edu	37	13	43462602	43462602	+	Silent	SNP	T	C	C			TCGA-39-5024-01A-21D-1817-08	TCGA-39-5024-11A-01D-1817-08									Somatic	Phase_I	Capture				Illumina GAIIx	388478e9-8c1f-43f8-88c4-811bf3cc2500	829ea6e6-1737-4fc6-8732-65e2d7fb2582	g.chr13:43462602T>C	uc001uyw.1	-	13	1093	c.1017A>G	c.(1015-1017)TCA>TCG	p.S339S	EPSTI1_uc001uyx.1_3'UTR	NM_001002264	NP_001002264	Q96J88	ESIP1_HUMAN	epithelial stromal interaction 1 isoform 1	Error:Variant_position_missing_in_Q96J88_after_alignment										ovary(1)	1		Lung NSC(96;3.6e-06)|Breast(139;0.00869)|Prostate(109;0.0181)|Lung SC(185;0.0262)|Hepatocellular(98;0.114)		GBM - Glioblastoma multiforme(144;0.000528)|BRCA - Breast invasive adenocarcinoma(63;0.0858)		GGTCAGTTGATGAAGGCCAGA	0.368													5	137	---	---	---	---	PASS
MYCBP2	23077	broad.mit.edu	37	13	77672487	77672487	+	Silent	SNP	T	C	C			TCGA-39-5024-01A-21D-1817-08	TCGA-39-5024-11A-01D-1817-08									Somatic	Phase_I	Capture				Illumina GAIIx	388478e9-8c1f-43f8-88c4-811bf3cc2500	829ea6e6-1737-4fc6-8732-65e2d7fb2582	g.chr13:77672487T>C	uc001vkf.2	-	57	8779	c.8688A>G	c.(8686-8688)GAA>GAG	p.E2896E	MYCBP2_uc010aev.2_Silent_p.E2300E|MYCBP2_uc001vkg.1_Silent_p.E419E|MYCBP2_uc010aew.2_Silent_p.E282E	NM_015057	NP_055872	O75592	MYCB2_HUMAN	MYC binding protein 2	2896					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	ligase activity|protein binding|zinc ion binding			ovary(4)|breast(4)|skin(3)|lung(2)|pancreas(1)	14		Breast(118;0.212)|Acute lymphoblastic leukemia(28;0.22)		GBM - Glioblastoma multiforme(99;0.109)		AGGTGCAGACTTCGACCACCT	0.433													9	127	---	---	---	---	PASS
MYCBP2	23077	broad.mit.edu	37	13	77900608	77900608	+	Splice_Site	SNP	C	T	T			TCGA-39-5024-01A-21D-1817-08	TCGA-39-5024-11A-01D-1817-08									Somatic	Phase_I	Capture				Illumina GAIIx	388478e9-8c1f-43f8-88c4-811bf3cc2500	829ea6e6-1737-4fc6-8732-65e2d7fb2582	g.chr13:77900608C>T	uc001vkf.2	-	2	279	c.188_splice	c.e2+1	p.R63_splice	MYCBP2_uc010aev.2_Intron	NM_015057	NP_055872	O75592	MYCB2_HUMAN	MYC binding protein 2						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	ligase activity|protein binding|zinc ion binding			ovary(4)|breast(4)|skin(3)|lung(2)|pancreas(1)	14		Breast(118;0.212)|Acute lymphoblastic leukemia(28;0.22)		GBM - Glioblastoma multiforme(99;0.109)		TGGGGACGCACCTGGAGGCTG	0.692													4	39	---	---	---	---	PASS
SLITRK1	114798	broad.mit.edu	37	13	84455087	84455087	+	Missense_Mutation	SNP	C	G	G			TCGA-39-5024-01A-21D-1817-08	TCGA-39-5024-11A-01D-1817-08									Somatic	Phase_I	Capture				Illumina GAIIx	388478e9-8c1f-43f8-88c4-811bf3cc2500	829ea6e6-1737-4fc6-8732-65e2d7fb2582	g.chr13:84455087C>G	uc001vlk.2	-	1	1442	c.556G>C	c.(556-558)GGT>CGT	p.G186R		NM_052910	NP_443142	Q96PX8	SLIK1_HUMAN	slit and trk like 1 protein precursor	186	Extracellular (Potential).|LRR 6.					integral to membrane				ovary(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)|skin(1)	5	Medulloblastoma(90;0.18)	Breast(118;0.212)		GBM - Glioblastoma multiforme(99;0.07)		AGCCTGTTACCCCGGAGGTCG	0.527													5	121	---	---	---	---	PASS
DZIP1	22873	broad.mit.edu	37	13	96293633	96293633	+	Silent	SNP	C	T	T			TCGA-39-5024-01A-21D-1817-08	TCGA-39-5024-11A-01D-1817-08									Somatic	Phase_I	Capture				Illumina GAIIx	388478e9-8c1f-43f8-88c4-811bf3cc2500	829ea6e6-1737-4fc6-8732-65e2d7fb2582	g.chr13:96293633C>T	uc001vmk.2	-	5	1365	c.513G>A	c.(511-513)AAG>AAA	p.K171K	DZIP1_uc001vml.2_Silent_p.K171K|DZIP1_uc001vmn.2_Silent_p.K160K	NM_198968	NP_945319	Q86YF9	DZIP1_HUMAN	DAZ interacting protein 1 isoform 2	171					germ cell development|multicellular organismal development|spermatogenesis	cytoplasm|nucleus	nucleic acid binding|protein binding|zinc ion binding			ovary(2)	2	all_neural(89;0.0878)|Breast(111;0.148)|Medulloblastoma(90;0.163)		BRCA - Breast invasive adenocarcinoma(86;0.141)			CCTTGAGCGTCTTGATCTCCC	0.602													4	41	---	---	---	---	PASS
MBNL2	10150	broad.mit.edu	37	13	97999141	97999141	+	Missense_Mutation	SNP	C	G	G			TCGA-39-5024-01A-21D-1817-08	TCGA-39-5024-11A-01D-1817-08									Somatic	Phase_I	Capture				Illumina GAIIx	388478e9-8c1f-43f8-88c4-811bf3cc2500	829ea6e6-1737-4fc6-8732-65e2d7fb2582	g.chr13:97999141C>G	uc010aft.2	+	5	1440	c.624C>G	c.(622-624)ATC>ATG	p.I208M	MBNL2_uc001vmz.2_Missense_Mutation_p.I208M|MBNL2_uc001vna.2_Missense_Mutation_p.I208M|MBNL2_uc001vnb.2_RNA|MBNL2_uc010tij.1_Intron|MBNL2_uc001vnc.2_5'Flank	NM_144778	NP_659002	Q5VZF2	MBNL2_HUMAN	muscleblind-like 2 isoform 1	208					mRNA processing|regulation of RNA splicing|RNA splicing	cytoplasm|nucleus	RNA binding|zinc ion binding				0	all_neural(89;0.0982)|Medulloblastoma(90;0.163)|Lung SC(71;0.184)		BRCA - Breast invasive adenocarcinoma(86;0.218)			GCACCATGATCGACACAAGTG	0.527													27	56	---	---	---	---	PASS
SLC7A8	23428	broad.mit.edu	37	14	23609702	23609702	+	Missense_Mutation	SNP	C	T	T			TCGA-39-5024-01A-21D-1817-08	TCGA-39-5024-11A-01D-1817-08									Somatic	Phase_I	Capture				Illumina GAIIx	388478e9-8c1f-43f8-88c4-811bf3cc2500	829ea6e6-1737-4fc6-8732-65e2d7fb2582	g.chr14:23609702C>T	uc001wiz.2	-	5	1492	c.766G>A	c.(766-768)GAG>AAG	p.E256K	SLC7A8_uc001wix.2_Missense_Mutation_p.E53K|SLC7A8_uc010tnk.1_Intron|SLC7A8_uc010tnl.1_Missense_Mutation_p.E151K|SLC7A8_uc001wiy.2_RNA|SLC7A8_uc010akj.2_Missense_Mutation_p.E256K	NM_012244	NP_036376	Q9UHI5	LAT2_HUMAN	solute carrier family 7 (cationic amino acid	256					blood coagulation|cellular amino acid metabolic process|leukocyte migration|metal ion homeostasis|response to toxin	basolateral plasma membrane|cytoplasm|integral to plasma membrane	neutral amino acid transmembrane transporter activity|organic cation transmembrane transporter activity|peptide antigen binding|protein binding|toxin transporter activity			ovary(1)	1	all_cancers(95;4.6e-05)			GBM - Glioblastoma multiforme(265;0.00809)	L-Alanine(DB00160)|L-Glutamine(DB00130)|L-Phenylalanine(DB00120)	ACAAGCTCCTCAGTCACGTAA	0.527													6	199	---	---	---	---	PASS
BAZ1A	11177	broad.mit.edu	37	14	35231112	35231112	+	Missense_Mutation	SNP	T	C	C			TCGA-39-5024-01A-21D-1817-08	TCGA-39-5024-11A-01D-1817-08									Somatic	Phase_I	Capture				Illumina GAIIx	388478e9-8c1f-43f8-88c4-811bf3cc2500	829ea6e6-1737-4fc6-8732-65e2d7fb2582	g.chr14:35231112T>C	uc001wsk.2	-	24	4662	c.4094A>G	c.(4093-4095)AAT>AGT	p.N1365S	BAZ1A_uc001wsl.2_Missense_Mutation_p.N1333S	NM_013448	NP_038476	Q9NRL2	BAZ1A_HUMAN	bromodomain adjacent to zinc finger domain, 1A	1365					chromatin remodeling|regulation of transcription, DNA-dependent|transcription, DNA-dependent	ACF complex	zinc ion binding			lung(2)|central_nervous_system(2)|ovary(1)|breast(1)|skin(1)	7	Breast(36;0.0388)|Hepatocellular(127;0.158)		LUAD - Lung adenocarcinoma(48;7.23e-05)|Lung(238;0.00019)|Epithelial(34;0.0793)|all cancers(34;0.175)	GBM - Glioblastoma multiforme(112;0.0659)		TGGTGTATTATTAGCACTTTT	0.428													49	125	---	---	---	---	PASS
FBXO34	55030	broad.mit.edu	37	14	55817179	55817179	+	Missense_Mutation	SNP	G	C	C			TCGA-39-5024-01A-21D-1817-08	TCGA-39-5024-11A-01D-1817-08									Somatic	Phase_I	Capture				Illumina GAIIx	388478e9-8c1f-43f8-88c4-811bf3cc2500	829ea6e6-1737-4fc6-8732-65e2d7fb2582	g.chr14:55817179G>C	uc001xbu.2	+	2	316	c.71G>C	c.(70-72)AGA>ACA	p.R24T	FBXO34_uc001xbv.2_5'Flank|FBXO34_uc010aoo.2_Missense_Mutation_p.R24T	NM_017943	NP_060413	Q9NWN3	FBX34_HUMAN	F-box only protein 34	24										ovary(2)|lung(2)|skin(1)	5						GAAACGCAGAGAACTCCTATG	0.453													29	58	---	---	---	---	PASS
ZFYVE26	23503	broad.mit.edu	37	14	68274248	68274248	+	Silent	SNP	C	G	G			TCGA-39-5024-01A-21D-1817-08	TCGA-39-5024-11A-01D-1817-08									Somatic	Phase_I	Capture				Illumina GAIIx	388478e9-8c1f-43f8-88c4-811bf3cc2500	829ea6e6-1737-4fc6-8732-65e2d7fb2582	g.chr14:68274248C>G	uc001xka.2	-	5	892	c.753G>C	c.(751-753)GGG>GGC	p.G251G	ZFYVE26_uc010tsz.1_RNA|ZFYVE26_uc001xkc.3_Silent_p.G251G|ZFYVE26_uc010tta.1_Silent_p.G251G	NM_015346	NP_056161	Q68DK2	ZFY26_HUMAN	zinc finger, FYVE domain containing 26	251					cell cycle|cell death|cytokinesis|double-strand break repair via homologous recombination	centrosome|midbody	metal ion binding|phosphatidylinositol-3-phosphate binding|protein binding			ovary(9)|breast(2)	11				all cancers(60;0.000763)|OV - Ovarian serous cystadenocarcinoma(108;0.0011)|BRCA - Breast invasive adenocarcinoma(234;0.0115)		GCAGGGGACTCCCCTCGGTCC	0.627													17	40	---	---	---	---	PASS
ATXN3	4287	broad.mit.edu	37	14	92563086	92563086	+	Missense_Mutation	SNP	C	G	G			TCGA-39-5024-01A-21D-1817-08	TCGA-39-5024-11A-01D-1817-08									Somatic	Phase_I	Capture				Illumina GAIIx	388478e9-8c1f-43f8-88c4-811bf3cc2500	829ea6e6-1737-4fc6-8732-65e2d7fb2582	g.chr14:92563086C>G	uc001yac.3	-	2	190	c.121G>C	c.(121-123)GAT>CAT	p.D41H	ATXN3_uc010aug.2_Missense_Mutation_p.D41H|ATXN3_uc001yad.3_Intron|ATXN3_uc010auh.2_Missense_Mutation_p.D41H|ATXN3_uc001yae.3_5'UTR|ATXN3_uc010twl.1_Intron	NM_004993	NP_004984	P54252	ATX3_HUMAN	ataxin 3 reference isoform	41	Josephin.				cell death|nervous system development|nucleotide-excision repair|regulation of transcription, DNA-dependent|synaptic transmission|transcription, DNA-dependent	cytoplasm|nuclear matrix|nucleoplasm	cysteine-type peptidase activity|protein binding				0		all_cancers(154;0.0768)		COAD - Colon adenocarcinoma(157;0.224)		TCCTCCTCATCCAGCTGATGT	0.398													9	119	---	---	---	---	PASS
DYNC1H1	1778	broad.mit.edu	37	14	102499791	102499791	+	Silent	SNP	C	T	T			TCGA-39-5024-01A-21D-1817-08	TCGA-39-5024-11A-01D-1817-08									Somatic	Phase_I	Capture				Illumina GAIIx	388478e9-8c1f-43f8-88c4-811bf3cc2500	829ea6e6-1737-4fc6-8732-65e2d7fb2582	g.chr14:102499791C>T	uc001yks.2	+	54	10547	c.10383C>T	c.(10381-10383)ATC>ATT	p.I3461I		NM_001376	NP_001367	Q14204	DYHC1_HUMAN	cytoplasmic dynein 1 heavy chain 1	3461	Stalk (By similarity).|Potential.				cytoplasmic mRNA processing body assembly|G2/M transition of mitotic cell cycle|microtubule-based movement|mitotic spindle organization|stress granule assembly|transport	centrosome|cytoplasmic dynein complex|cytosol|Golgi apparatus|microtubule	ATP binding|ATPase activity, coupled|microtubule motor activity|protein binding			ovary(7)|central_nervous_system(2)|pancreas(1)	10						CCCAGGCCATCAAGGCAGACC	0.537													15	41	---	---	---	---	PASS
MARK3	4140	broad.mit.edu	37	14	103946810	103946810	+	Silent	SNP	G	A	A			TCGA-39-5024-01A-21D-1817-08	TCGA-39-5024-11A-01D-1817-08									Somatic	Phase_I	Capture				Illumina GAIIx	388478e9-8c1f-43f8-88c4-811bf3cc2500	829ea6e6-1737-4fc6-8732-65e2d7fb2582	g.chr14:103946810G>A	uc001ymz.3	+	14	2235	c.1569G>A	c.(1567-1569)CAG>CAA	p.Q523Q	MARK3_uc001ymx.3_Silent_p.Q523Q|MARK3_uc001ymw.3_Silent_p.Q523Q|MARK3_uc001yna.3_Silent_p.Q507Q|MARK3_uc001ymy.3_Silent_p.Q444Q|MARK3_uc010awp.2_Silent_p.Q546Q|MARK3_uc010tyb.1_Silent_p.Q318Q|MARK3_uc010awq.2_Silent_p.Q53Q	NM_001128918	NP_001122390	P27448	MARK3_HUMAN	MAP/microtubule affinity-regulating kinase 3	523							ATP binding|protein binding|protein serine/threonine kinase activity			central_nervous_system(2)|ovary(1)|stomach(1)	4		Melanoma(154;0.155)	Epithelial(46;0.241)			CAGTGATTCAGAATGGCAAAG	0.373													44	103	---	---	---	---	PASS
INO80	54617	broad.mit.edu	37	15	41388466	41388466	+	Missense_Mutation	SNP	C	T	T			TCGA-39-5024-01A-21D-1817-08	TCGA-39-5024-11A-01D-1817-08									Somatic	Phase_I	Capture				Illumina GAIIx	388478e9-8c1f-43f8-88c4-811bf3cc2500	829ea6e6-1737-4fc6-8732-65e2d7fb2582	g.chr15:41388466C>T	uc001zni.2	-	2	256	c.43G>A	c.(43-45)GAG>AAG	p.E15K	INO80_uc010ucu.1_RNA	NM_017553	NP_060023	Q9ULG1	INO80_HUMAN	INO80 complex homolog 1	15	Assembles INO80 complex module with putative regulatory components INO80E, INO80F, UCHL5, NFRKB, MCRS1 and IN80D.				cell division|cellular response to ionizing radiation|cellular response to UV|chromatin remodeling|double-strand break repair via homologous recombination|mitotic sister chromatid segregation|positive regulation of cell growth|positive regulation of DNA replication involved in S phase|positive regulation of transcription from RNA polymerase II promoter|regulation of G1/S transition of mitotic cell cycle|spindle assembly|UV-damage excision repair	Ino80 complex|microtubule	actin binding|alpha-tubulin binding|ATP binding|ATPase activity|DNA binding|DNA helicase activity			ovary(2)|pancreas(1)|skin(1)	4						TTTGCCAGCTCAGTGCAGCCT	0.517													4	26	---	---	---	---	PASS
SPG11	80208	broad.mit.edu	37	15	44900797	44900797	+	Missense_Mutation	SNP	G	C	C			TCGA-39-5024-01A-21D-1817-08	TCGA-39-5024-11A-01D-1817-08									Somatic	Phase_I	Capture				Illumina GAIIx	388478e9-8c1f-43f8-88c4-811bf3cc2500	829ea6e6-1737-4fc6-8732-65e2d7fb2582	g.chr15:44900797G>C	uc001ztx.2	-	19	3329	c.3298C>G	c.(3298-3300)CAG>GAG	p.Q1100E	SPG11_uc010ueh.1_Missense_Mutation_p.Q1100E|SPG11_uc010uei.1_Missense_Mutation_p.Q1100E	NM_025137	NP_079413	Q96JI7	SPTCS_HUMAN	spatacsin isoform 1	1100	Extracellular (Potential).				cell death	cytosol|integral to membrane|nucleus	protein binding			ovary(4)|skin(1)	5		all_cancers(109;1.29e-14)|all_epithelial(112;1.26e-12)|Lung NSC(122;1.34e-07)|all_lung(180;1.21e-06)|Melanoma(134;0.0122)		all cancers(107;2.93e-22)|GBM - Glioblastoma multiforme(94;1.55e-06)|COAD - Colon adenocarcinoma(120;0.0432)|Colorectal(105;0.0484)|Lung(196;0.104)|LUSC - Lung squamous cell carcinoma(244;0.214)		TCTTCATTCTGAACAACCTAA	0.363													9	30	---	---	---	---	PASS
SLC27A2	11001	broad.mit.edu	37	15	50515285	50515285	+	Missense_Mutation	SNP	G	A	A			TCGA-39-5024-01A-21D-1817-08	TCGA-39-5024-11A-01D-1817-08									Somatic	Phase_I	Capture				Illumina GAIIx	388478e9-8c1f-43f8-88c4-811bf3cc2500	829ea6e6-1737-4fc6-8732-65e2d7fb2582	g.chr15:50515285G>A	uc001zxw.2	+	5	1328	c.1096G>A	c.(1096-1098)GAA>AAA	p.E366K	SLC27A2_uc010bes.2_Missense_Mutation_p.E313K|SLC27A2_uc001zxx.2_Missense_Mutation_p.E131K	NM_003645	NP_003636	O14975	S27A2_HUMAN	solute carrier family 27 (fatty acid	366	Cytoplasmic (Potential).				bile acid biosynthetic process|fatty acid alpha-oxidation	endoplasmic reticulum membrane|integral to membrane|peroxisomal matrix|peroxisomal membrane	ATP binding|long-chain fatty acid-CoA ligase activity|phytanate-CoA ligase activity|pristanate-CoA ligase activity			ovary(1)|skin(1)	2		all_lung(180;0.00177)		all cancers(107;1.16e-06)|GBM - Glioblastoma multiforme(94;0.000113)		TGCTGCCACTGAAGGCAATAT	0.408													8	86	---	---	---	---	PASS
C15orf60	283677	broad.mit.edu	37	15	73852096	73852096	+	Missense_Mutation	SNP	C	G	G			TCGA-39-5024-01A-21D-1817-08	TCGA-39-5024-11A-01D-1817-08									Somatic	Phase_I	Capture				Illumina GAIIx	388478e9-8c1f-43f8-88c4-811bf3cc2500	829ea6e6-1737-4fc6-8732-65e2d7fb2582	g.chr15:73852096C>G	uc002avq.2	+	6	668	c.640C>G	c.(640-642)CTT>GTT	p.L214V	C15orf60_uc010bjb.2_Missense_Mutation_p.L186V	NM_001042367	NP_001035826	Q7Z4M0	CO060_HUMAN	hypothetical protein LOC283677	214										pancreas(1)	1						CCTGCAGACTCTTCTGGCATC	0.453													9	80	---	---	---	---	PASS
TBC1D21	161514	broad.mit.edu	37	15	74173766	74173766	+	Missense_Mutation	SNP	G	C	C			TCGA-39-5024-01A-21D-1817-08	TCGA-39-5024-11A-01D-1817-08									Somatic	Phase_I	Capture				Illumina GAIIx	388478e9-8c1f-43f8-88c4-811bf3cc2500	829ea6e6-1737-4fc6-8732-65e2d7fb2582	g.chr15:74173766G>C	uc002avz.2	+	2	170	c.87G>C	c.(85-87)AAG>AAC	p.K29N	TBC1D21_uc010ulc.1_Intron	NM_153356	NP_699187	Q8IYX1	TBC21_HUMAN	TBC1 domain family, member 21	29						intracellular	Rab GTPase activator activity			ovary(2)	2						CCATTGACAAGACAGAATGGG	0.433													15	105	---	---	---	---	PASS
ACSBG1	23205	broad.mit.edu	37	15	78474488	78474488	+	Splice_Site	SNP	C	G	G			TCGA-39-5024-01A-21D-1817-08	TCGA-39-5024-11A-01D-1817-08									Somatic	Phase_I	Capture				Illumina GAIIx	388478e9-8c1f-43f8-88c4-811bf3cc2500	829ea6e6-1737-4fc6-8732-65e2d7fb2582	g.chr15:78474488C>G	uc002bdh.2	-	8	951	c.895_splice	c.e8-1	p.I299_splice	ACSBG1_uc010umw.1_Splice_Site_p.I295_splice|ACSBG1_uc010umx.1_Splice_Site_p.I57_splice|ACSBG1_uc010umy.1_Splice_Site_p.I192_splice	NM_015162	NP_055977	Q96GR2	ACBG1_HUMAN	lipidosin						long-chain fatty acid metabolic process|myelination|very long-chain fatty acid metabolic process	cytoplasmic membrane-bounded vesicle|endoplasmic reticulum|microsome	ATP binding|long-chain fatty acid-CoA ligase activity|very long-chain fatty acid-CoA ligase activity			ovary(1)	1						TCCACGTGATCTGGAGGACAA	0.652													5	36	---	---	---	---	PASS
CHD2	1106	broad.mit.edu	37	15	93547926	93547926	+	Missense_Mutation	SNP	C	G	G			TCGA-39-5024-01A-21D-1817-08	TCGA-39-5024-11A-01D-1817-08									Somatic	Phase_I	Capture				Illumina GAIIx	388478e9-8c1f-43f8-88c4-811bf3cc2500	829ea6e6-1737-4fc6-8732-65e2d7fb2582	g.chr15:93547926C>G	uc002bsp.2	+	34	4933	c.4358C>G	c.(4357-4359)CCT>CGT	p.P1453R	CHD2_uc002bso.1_Missense_Mutation_p.P1453R	NM_001271	NP_001262	O14647	CHD2_HUMAN	chromodomain helicase DNA binding protein 2	1453					regulation of transcription from RNA polymerase II promoter	nucleus	ATP binding|ATP-dependent DNA helicase activity|DNA binding			ovary(1)|skin(1)	2	Lung NSC(78;0.00976)|all_lung(78;0.016)		BRCA - Breast invasive adenocarcinoma(143;0.0282)|OV - Ovarian serous cystadenocarcinoma(32;0.0814)			GGAAGTGAACCTGTCCCCATT	0.473													4	155	---	---	---	---	PASS
TIGD7	91151	broad.mit.edu	37	16	3349552	3349552	+	Missense_Mutation	SNP	C	G	G			TCGA-39-5024-01A-21D-1817-08	TCGA-39-5024-11A-01D-1817-08									Somatic	Phase_I	Capture				Illumina GAIIx	388478e9-8c1f-43f8-88c4-811bf3cc2500	829ea6e6-1737-4fc6-8732-65e2d7fb2582	g.chr16:3349552C>G	uc002cus.2	-	1	1849	c.1063G>C	c.(1063-1065)GAA>CAA	p.E355Q	ZNF263_uc002cur.2_3'UTR	NM_033208	NP_149985	Q6NT04	TIGD7_HUMAN	tigger transposable element derived 7	355	DDE.				regulation of transcription, DNA-dependent	chromosome, centromeric region|nucleus	DNA binding				0						TCACTTTCTTCAAATATTACA	0.274													11	79	---	---	---	---	PASS
MYH11	4629	broad.mit.edu	37	16	15853504	15853504	+	Silent	SNP	G	A	A			TCGA-39-5024-01A-21D-1817-08	TCGA-39-5024-11A-01D-1817-08									Somatic	Phase_I	Capture				Illumina GAIIx	388478e9-8c1f-43f8-88c4-811bf3cc2500	829ea6e6-1737-4fc6-8732-65e2d7fb2582	g.chr16:15853504G>A	uc002ddy.2	-	12	1437	c.1330C>T	c.(1330-1332)CTG>TTG	p.L444L	MYH11_uc002ddv.2_Silent_p.L451L|MYH11_uc002ddw.2_Silent_p.L444L|MYH11_uc002ddx.2_Silent_p.L451L|MYH11_uc010bvg.2_Silent_p.L276L|MYH11_uc002dea.1_Silent_p.L150L	NM_002474	NP_002465	P35749	MYH11_HUMAN	smooth muscle myosin heavy chain 11 isoform	444	Myosin head-like.				axon guidance|cardiac muscle fiber development|elastic fiber assembly|skeletal muscle myosin thick filament assembly|smooth muscle contraction	cytosol|melanosome|muscle myosin complex|myosin filament	actin binding|ATP binding|calmodulin binding|motor activity|structural constituent of muscle			ovary(6)|skin(3)|lung(2)|breast(2)|upper_aerodigestive_tract(1)|pancreas(1)	15						GTCTTGTCCAGGGCTTTGTTC	0.552			T	CBFB	AML								24	111	---	---	---	---	PASS
C16orf62	57020	broad.mit.edu	37	16	19603129	19603129	+	Silent	SNP	A	G	G			TCGA-39-5024-01A-21D-1817-08	TCGA-39-5024-11A-01D-1817-08									Somatic	Phase_I	Capture				Illumina GAIIx	388478e9-8c1f-43f8-88c4-811bf3cc2500	829ea6e6-1737-4fc6-8732-65e2d7fb2582	g.chr16:19603129A>G	uc002dgn.1	+	8	669	c.657A>G	c.(655-657)TCA>TCG	p.S219S	C16orf62_uc002dgo.1_Silent_p.S219S|C16orf62_uc002dgp.1_Intron|C16orf62_uc010vas.1_Silent_p.S93S|C16orf62_uc002dgm.1_Silent_p.S219S	NM_020314	NP_064710	Q7Z3J2	CP062_HUMAN	hypothetical protein LOC57020	219						integral to membrane				ovary(1)	1						AGCTTCTTTCAGACACCAGTG	0.368													13	98	---	---	---	---	PASS
NFATC2IP	84901	broad.mit.edu	37	16	28967599	28967599	+	Nonsense_Mutation	SNP	C	T	T			TCGA-39-5024-01A-21D-1817-08	TCGA-39-5024-11A-01D-1817-08									Somatic	Phase_I	Capture				Illumina GAIIx	388478e9-8c1f-43f8-88c4-811bf3cc2500	829ea6e6-1737-4fc6-8732-65e2d7fb2582	g.chr16:28967599C>T	uc002dru.2	+	5	802	c.787C>T	c.(787-789)CGA>TGA	p.R263*	uc010vct.1_Intron|NFATC2IP_uc002drt.2_Intron|NFATC2IP_uc002drv.2_5'UTR|NFATC2IP_uc010vdh.1_5'Flank	NM_032815	NP_116204	Q8NCF5	NF2IP_HUMAN	nuclear factor of activated T-cells,	263						cytoplasm|nucleus				ovary(1)	1						AGAGACCCCCCGACTCTTCCC	0.622													5	42	---	---	---	---	PASS
ADCY7	113	broad.mit.edu	37	16	50346817	50346817	+	Missense_Mutation	SNP	C	T	T			TCGA-39-5024-01A-21D-1817-08	TCGA-39-5024-11A-01D-1817-08									Somatic	Phase_I	Capture				Illumina GAIIx	388478e9-8c1f-43f8-88c4-811bf3cc2500	829ea6e6-1737-4fc6-8732-65e2d7fb2582	g.chr16:50346817C>T	uc002egd.1	+	21	2889	c.2621C>T	c.(2620-2622)TCC>TTC	p.S874F		NM_001114	NP_001105	P51828	ADCY7_HUMAN	adenylate cyclase 7	874	Cytoplasmic (Potential).				activation of adenylate cyclase activity by G-protein signaling pathway|activation of phospholipase C activity|activation of protein kinase A activity|cellular response to ethanol|cellular response to glucagon stimulus|energy reserve metabolic process|inhibition of adenylate cyclase activity by G-protein signaling pathway|nerve growth factor receptor signaling pathway|positive regulation of cAMP biosynthetic process|synaptic transmission|transmembrane transport|water transport	integral to membrane|plasma membrane	adenylate cyclase activity|ATP binding|metal ion binding			skin(1)	1		all_cancers(37;0.0127)		GBM - Glioblastoma multiforme(240;0.195)	Bromocriptine(DB01200)	TACCATCAGTCCTATGACTGC	0.547													12	80	---	---	---	---	PASS
CAMTA2	23125	broad.mit.edu	37	17	4883886	4883886	+	Missense_Mutation	SNP	C	T	T			TCGA-39-5024-01A-21D-1817-08	TCGA-39-5024-11A-01D-1817-08									Somatic	Phase_I	Capture				Illumina GAIIx	388478e9-8c1f-43f8-88c4-811bf3cc2500	829ea6e6-1737-4fc6-8732-65e2d7fb2582	g.chr17:4883886C>T	uc002gah.1	-	9	839	c.731G>A	c.(730-732)AGC>AAC	p.S244N	CAMTA2_uc010cku.1_Missense_Mutation_p.S267N|CAMTA2_uc002gag.1_Missense_Mutation_p.S243N|CAMTA2_uc002gai.1_Missense_Mutation_p.S246N|CAMTA2_uc010ckv.1_5'UTR|CAMTA2_uc010vsu.1_Missense_Mutation_p.S57N	NM_015099	NP_055914	O94983	CMTA2_HUMAN	calmodulin binding transcription activator 2	244					cardiac muscle hypertrophy in response to stress|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	nucleus	calmodulin binding|chromatin binding|histone deacetylase binding|transcription factor binding			ovary(1)	1						GTGTTTCGTGCTGCTGCATTT	0.572											OREG0024111	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	25	101	---	---	---	---	PASS
C17orf74	201243	broad.mit.edu	37	17	7330607	7330607	+	Missense_Mutation	SNP	G	A	A			TCGA-39-5024-01A-21D-1817-08	TCGA-39-5024-11A-01D-1817-08									Somatic	Phase_I	Capture				Illumina GAIIx	388478e9-8c1f-43f8-88c4-811bf3cc2500	829ea6e6-1737-4fc6-8732-65e2d7fb2582	g.chr17:7330607G>A	uc002ggw.2	+	3	1370	c.1297G>A	c.(1297-1299)GTC>ATC	p.V433I	FGF11_uc010vtw.1_Intron	NM_175734	NP_783861	Q0P670	CQ074_HUMAN	hypothetical protein LOC201243	433						integral to membrane					0		Prostate(122;0.157)				CTGGCCCAAAGTCCAGGCTGC	0.642													6	40	---	---	---	---	PASS
TP53	7157	broad.mit.edu	37	17	7576928	7576928	+	Splice_Site	SNP	T	A	A			TCGA-39-5024-01A-21D-1817-08	TCGA-39-5024-11A-01D-1817-08									Somatic	Phase_I	Capture				Illumina GAIIx	388478e9-8c1f-43f8-88c4-811bf3cc2500	829ea6e6-1737-4fc6-8732-65e2d7fb2582	g.chr17:7576928T>A	uc002gim.2	-	9	1114	c.920_splice	c.e9-1	p.A307_splice	TP53_uc002gig.1_Intron|TP53_uc002gih.2_Splice_Site_p.A307_splice|TP53_uc010cne.1_Splice_Site|TP53_uc010cnf.1_Splice_Site_p.A175_splice|TP53_uc010cng.1_Splice_Site_p.A175_splice|TP53_uc002gii.1_Splice_Site_p.A175_splice|TP53_uc010cnh.1_Splice_Site_p.A307_splice|TP53_uc010cni.1_Splice_Site_p.A307_splice|TP53_uc002gij.2_Splice_Site_p.A307_splice	NM_001126112	NP_001119584	P04637	P53_HUMAN	tumor protein p53 isoform a						activation of caspase activity by cytochrome c|base-excision repair|blood coagulation|cell cycle arrest|cell differentiation|cell proliferation|cellular protein localization|cellular response to drug|cellular response to glucose starvation|cellular response to hypoxia|cellular response to ionizing radiation|cellular response to UV|determination of adult lifespan|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator|ER overload response|interspecies interaction between organisms|negative regulation of apoptosis|negative regulation of cell growth|negative regulation of cell proliferation|negative regulation of helicase activity|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transcription from RNA polymerase II promoter|nucleotide-excision repair|oxidative stress-induced premature senescence|positive regulation of histone deacetylation|positive regulation of neuron apoptosis|positive regulation of peptidyl-tyrosine phosphorylation|positive regulation of reactive oxygen species metabolic process|positive regulation of thymocyte apoptosis|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase II promoter|protein localization|protein tetramerization|Ras protein signal transduction|regulation of mitochondrial membrane permeability|replicative senescence|response to antibiotic|response to gamma radiation|response to X-ray	cytoplasm|cytosol|endoplasmic reticulum|insoluble fraction|mitochondrion|nuclear chromatin|nuclear matrix|nucleolus|nucleus|PML body|protein complex|replication fork	ATP binding|chaperone binding|chromatin binding|copper ion binding|damaged DNA binding|DNA strand annealing activity|histone acetyltransferase binding|p53 binding|protease binding|protein binding|protein heterodimerization activity|protein kinase binding|protein N-terminus binding|protein phosphatase 2A binding|RNA polymerase II transcription factor binding|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding|transcription regulatory region DNA binding|transcription repressor activity|ubiquitin protein ligase binding|zinc ion binding	p.?(14)|p.0?(7)|p.A307fs*34(1)|p.L308fs*31(1)		large_intestine(4656)|breast(2429)|upper_aerodigestive_tract(2212)|lung(2028)|ovary(1592)|oesophagus(1462)|haematopoietic_and_lymphoid_tissue(1228)|stomach(1136)|urinary_tract(1114)|central_nervous_system(1085)|liver(805)|skin(694)|pancreas(375)|biliary_tract(247)|soft_tissue(209)|prostate(194)|endometrium(150)|bone(102)|vulva(79)|kidney(79)|cervix(68)|thyroid(54)|salivary_gland(43)|adrenal_gland(37)|peritoneum(33)|eye(24)|thymus(21)|genital_tract(16)|autonomic_ganglia(16)|small_intestine(14)|testis(11)|penis(10)|vagina(6)|meninges(5)|pituitary(4)|pleura(3)|gastrointestinal_tract_(site_indeterminate)(1)|NS(1)|Fallopian tube(1)|placenta(1)	22245		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)		TGGGCAGTGCTAGGAAAGAGG	0.493		111	Mis|N|F		breast|colorectal|lung|sarcoma|adrenocortical|glioma|multiple other tumour types	breast|sarcoma|adrenocortical carcinoma|glioma|multiple other tumour types		Other_conserved_DNA_damage_response_genes	Hereditary_Adrenocortical_Cancer|Endometrial_Cancer_Familial_Clustering_of|Hereditary_Breast-Ovarian_Cancer_non-BRCA1/2|Li-Fraumeni_syndrome|Osteosarcoma_Familial_Clustering_of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)			17	48	---	---	---	---	PASS
ELAC2	60528	broad.mit.edu	37	17	12908318	12908318	+	Missense_Mutation	SNP	G	A	A			TCGA-39-5024-01A-21D-1817-08	TCGA-39-5024-11A-01D-1817-08									Somatic	Phase_I	Capture				Illumina GAIIx	388478e9-8c1f-43f8-88c4-811bf3cc2500	829ea6e6-1737-4fc6-8732-65e2d7fb2582	g.chr17:12908318G>A	uc002gnz.3	-	11	1066	c.971C>T	c.(970-972)GCC>GTC	p.A324V	ELAC2_uc002gnv.3_5'Flank|ELAC2_uc002gnw.3_5'UTR|ELAC2_uc002gnx.3_Missense_Mutation_p.A84V|ELAC2_uc010vvo.1_Missense_Mutation_p.A147V|ELAC2_uc010vvp.1_Missense_Mutation_p.A305V|ELAC2_uc010vvq.1_Missense_Mutation_p.A324V|ELAC2_uc010vvr.1_Missense_Mutation_p.A284V	NM_018127	NP_060597	Q9BQ52	RNZ2_HUMAN	elaC homolog 2 isoform 1	324					tRNA processing	nucleus	endonuclease activity|metal ion binding|protein binding				0						CTGAAAGGTGGCATTCTCACA	0.502									Hereditary_Prostate_Cancer				42	148	---	---	---	---	PASS
TEKT3	64518	broad.mit.edu	37	17	15234856	15234856	+	Missense_Mutation	SNP	C	T	T			TCGA-39-5024-01A-21D-1817-08	TCGA-39-5024-11A-01D-1817-08									Somatic	Phase_I	Capture				Illumina GAIIx	388478e9-8c1f-43f8-88c4-811bf3cc2500	829ea6e6-1737-4fc6-8732-65e2d7fb2582	g.chr17:15234856C>T	uc002gon.2	-	3	234	c.47G>A	c.(46-48)AGA>AAA	p.R16K		NM_031898	NP_114104	Q9BXF9	TEKT3_HUMAN	tektin 3	16					microtubule cytoskeleton organization	cilium axoneme|flagellar axoneme|microtubule				ovary(2)	2				UCEC - Uterine corpus endometrioid carcinoma (92;0.0877)		TGGTGTTGGTCTAGGGTGGGC	0.438													11	67	---	---	---	---	PASS
PIGS	94005	broad.mit.edu	37	17	26890464	26890464	+	Silent	SNP	G	A	A			TCGA-39-5024-01A-21D-1817-08	TCGA-39-5024-11A-01D-1817-08									Somatic	Phase_I	Capture				Illumina GAIIx	388478e9-8c1f-43f8-88c4-811bf3cc2500	829ea6e6-1737-4fc6-8732-65e2d7fb2582	g.chr17:26890464G>A	uc002hbo.2	-	5	826	c.453C>T	c.(451-453)TCC>TCT	p.S151S	PIGS_uc002hbn.2_Silent_p.S143S|PIGS_uc010wap.1_Silent_p.S90S	NM_033198	NP_149975	Q96S52	PIGS_HUMAN	phosphatidylinositol glycan anchor biosynthesis,	151	Lumenal (Potential).				attachment of GPI anchor to protein|C-terminal protein lipidation	GPI-anchor transamidase complex	protein binding			breast(2)|urinary_tract(1)|kidney(1)	4	Lung NSC(42;0.00431)					GAAGAAGTGAGGAGTGTTCAG	0.537													9	67	---	---	---	---	PASS
WNK4	65266	broad.mit.edu	37	17	40936150	40936150	+	Silent	SNP	C	T	T			TCGA-39-5024-01A-21D-1817-08	TCGA-39-5024-11A-01D-1817-08									Somatic	Phase_I	Capture				Illumina GAIIx	388478e9-8c1f-43f8-88c4-811bf3cc2500	829ea6e6-1737-4fc6-8732-65e2d7fb2582	g.chr17:40936150C>T	uc002ibj.2	+	3	1008	c.987C>T	c.(985-987)CGC>CGT	p.R329R	WNK4_uc010wgx.1_Missense_Mutation_p.A23V|WNK4_uc002ibk.1_Silent_p.R101R|WNK4_uc010wgy.1_5'Flank	NM_032387	NP_115763	Q96J92	WNK4_HUMAN	WNK lysine deficient protein kinase 4	329	Protein kinase.				intracellular protein kinase cascade	tight junction	ATP binding|protein serine/threonine kinase activity			ovary(3)|skin(3)|stomach(1)	7		Breast(137;0.000143)		BRCA - Breast invasive adenocarcinoma(366;0.0749)		CGCTCAAGCGCGCCTCCTTTG	0.602													20	113	---	---	---	---	PASS
TBX2	6909	broad.mit.edu	37	17	59483116	59483116	+	Silent	SNP	C	A	A			TCGA-39-5024-01A-21D-1817-08	TCGA-39-5024-11A-01D-1817-08									Somatic	Phase_I	Capture				Illumina GAIIx	388478e9-8c1f-43f8-88c4-811bf3cc2500	829ea6e6-1737-4fc6-8732-65e2d7fb2582	g.chr17:59483116C>A	uc010wox.1	+	6	1886	c.1605C>A	c.(1603-1605)GGC>GGA	p.G535G	TBX2_uc002ize.2_3'UTR|TBX2_uc002izg.2_Silent_p.G381G	NM_005994	NP_005985	Q13207	TBX2_HUMAN	T-box 2	535	Gly-rich.				cell aging|positive regulation of cell proliferation		sequence-specific DNA binding				0						TGGACGCAGGCGGGCTGGGTC	0.736													2	1	---	---	---	---	PASS
MARCH10	162333	broad.mit.edu	37	17	60837244	60837244	+	Missense_Mutation	SNP	T	C	C			TCGA-39-5024-01A-21D-1817-08	TCGA-39-5024-11A-01D-1817-08									Somatic	Phase_I	Capture				Illumina GAIIx	388478e9-8c1f-43f8-88c4-811bf3cc2500	829ea6e6-1737-4fc6-8732-65e2d7fb2582	g.chr17:60837244T>C	uc010ddr.2	-	4	572	c.334A>G	c.(334-336)ATG>GTG	p.M112V	MARCH10_uc002jag.3_Missense_Mutation_p.M112V|MARCH10_uc010dds.2_Missense_Mutation_p.M112V|MARCH10_uc002jah.2_Missense_Mutation_p.M112V	NM_001100875	NP_001094345	Q8NA82	MARHA_HUMAN	ring finger protein 190	112							ligase activity|zinc ion binding				0						CTTACAGTCATGGTACTTTTA	0.413													23	97	---	---	---	---	PASS
RIOK3	8780	broad.mit.edu	37	18	21059301	21059301	+	Silent	SNP	C	G	G			TCGA-39-5024-01A-21D-1817-08	TCGA-39-5024-11A-01D-1817-08									Somatic	Phase_I	Capture				Illumina GAIIx	388478e9-8c1f-43f8-88c4-811bf3cc2500	829ea6e6-1737-4fc6-8732-65e2d7fb2582	g.chr18:21059301C>G	uc002kui.3	+	12	1982	c.1365C>G	c.(1363-1365)GTC>GTG	p.V455V	RIOK3_uc010dls.2_Silent_p.V452V|RIOK3_uc010xas.1_Silent_p.V439V|RIOK3_uc010xat.1_Silent_p.V199V	NM_003831	NP_003822	O14730	RIOK3_HUMAN	sudD suppressor of bimD6 homolog	455	Protein kinase.				chromosome segregation		ATP binding|protein binding|protein serine/threonine kinase activity			ovary(2)|central_nervous_system(1)	3	all_cancers(21;0.000106)|all_epithelial(16;6.74e-07)|Lung NSC(20;0.00171)|all_lung(20;0.0055)|Colorectal(14;0.0202)|Ovarian(20;0.127)					AAGGAGGAGTCAAGGAAGCCC	0.368													8	44	---	---	---	---	PASS
SLC14A2	8170	broad.mit.edu	37	18	43204692	43204692	+	Silent	SNP	C	T	T	rs141644181	byFrequency	TCGA-39-5024-01A-21D-1817-08	TCGA-39-5024-11A-01D-1817-08									Somatic	Phase_I	Capture				Illumina GAIIx	388478e9-8c1f-43f8-88c4-811bf3cc2500	829ea6e6-1737-4fc6-8732-65e2d7fb2582	g.chr18:43204692C>T	uc010dnj.2	+	3	384	c.63C>T	c.(61-63)TAC>TAT	p.Y21Y	SLC14A2_uc002lbb.2_Silent_p.Y21Y|SLC14A2_uc002lbe.2_Silent_p.Y21Y	NM_007163	NP_009094	Q15849	UT2_HUMAN	solute carrier family 14 (urea transporter),	21						apical plasma membrane|integral to membrane|membrane fraction	protein binding|urea transmembrane transporter activity			upper_aerodigestive_tract(1)|ovary(1)|central_nervous_system(1)|skin(1)	4						ACAAACTCTACGAGGCAGAGT	0.562													6	84	---	---	---	---	PASS
DCC	1630	broad.mit.edu	37	18	50923735	50923735	+	Missense_Mutation	SNP	T	C	C			TCGA-39-5024-01A-21D-1817-08	TCGA-39-5024-11A-01D-1817-08									Somatic	Phase_I	Capture				Illumina GAIIx	388478e9-8c1f-43f8-88c4-811bf3cc2500	829ea6e6-1737-4fc6-8732-65e2d7fb2582	g.chr18:50923735T>C	uc002lfe.1	+	18	3333	c.2746T>C	c.(2746-2748)TAT>CAT	p.Y916H	DCC_uc010xdr.1_Missense_Mutation_p.Y744H|DCC_uc010dpf.1_Missense_Mutation_p.Y551H	NM_005215	NP_005206	P43146	DCC_HUMAN	netrin receptor DCC precursor	916	Extracellular (Potential).|Fibronectin type-III 5.				apoptosis|induction of apoptosis|negative regulation of collateral sprouting|negative regulation of dendrite development	cytosol|integral to membrane				skin(8)|ovary(6)|upper_aerodigestive_tract(1)|large_intestine(1)|central_nervous_system(1)	17		all_cancers(7;0.11)|all_epithelial(6;0.00126)		Colorectal(16;0.0251)|COAD - Colon adenocarcinoma(17;0.0942)		AAACACAATGTATGAATTCTC	0.393													14	67	---	---	---	---	PASS
CDH19	28513	broad.mit.edu	37	18	64235805	64235805	+	Missense_Mutation	SNP	T	A	A			TCGA-39-5024-01A-21D-1817-08	TCGA-39-5024-11A-01D-1817-08									Somatic	Phase_I	Capture				Illumina GAIIx	388478e9-8c1f-43f8-88c4-811bf3cc2500	829ea6e6-1737-4fc6-8732-65e2d7fb2582	g.chr18:64235805T>A	uc002lkc.1	-	3	476	c.338A>T	c.(337-339)TAC>TTC	p.Y113F	CDH19_uc010dql.1_RNA|CDH19_uc010xey.1_Missense_Mutation_p.Y113F|CDH19_uc002lkd.2_Missense_Mutation_p.Y113F	NM_021153	NP_066976	Q9H159	CAD19_HUMAN	cadherin 19, type 2 preproprotein	113	Cadherin 1.|Extracellular (Potential).				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(1)|skin(1)	2		Esophageal squamous(42;0.0132)				TCTTAAGATGTAGAGGGATCG	0.433													23	148	---	---	---	---	PASS
RTTN	25914	broad.mit.edu	37	18	67687945	67687945	+	Missense_Mutation	SNP	T	C	C			TCGA-39-5024-01A-21D-1817-08	TCGA-39-5024-11A-01D-1817-08									Somatic	Phase_I	Capture				Illumina GAIIx	388478e9-8c1f-43f8-88c4-811bf3cc2500	829ea6e6-1737-4fc6-8732-65e2d7fb2582	g.chr18:67687945T>C	uc002lkp.2	-	45	6127	c.6059A>G	c.(6058-6060)CAG>CGG	p.Q2020R	RTTN_uc002lko.2_RNA|RTTN_uc010xfb.1_Missense_Mutation_p.Q1108R|RTTN_uc002lkn.2_Missense_Mutation_p.Q10R|RTTN_uc010dqp.2_Missense_Mutation_p.Q272R	NM_173630	NP_775901	Q86VV8	RTTN_HUMAN	rotatin	2020							binding			ovary(3)|pancreas(2)|skin(1)|breast(1)|central_nervous_system(1)	8		Esophageal squamous(42;0.129)				CAGTGGCATCTGGGAAGCCAA	0.473													25	181	---	---	---	---	PASS
RTTN	25914	broad.mit.edu	37	18	67742704	67742704	+	Missense_Mutation	SNP	T	A	A			TCGA-39-5024-01A-21D-1817-08	TCGA-39-5024-11A-01D-1817-08									Somatic	Phase_I	Capture				Illumina GAIIx	388478e9-8c1f-43f8-88c4-811bf3cc2500	829ea6e6-1737-4fc6-8732-65e2d7fb2582	g.chr18:67742704T>A	uc002lkp.2	-	33	4516	c.4448A>T	c.(4447-4449)CAC>CTC	p.H1483L	RTTN_uc002lko.2_RNA|RTTN_uc010xfb.1_Missense_Mutation_p.H571L	NM_173630	NP_775901	Q86VV8	RTTN_HUMAN	rotatin	1483							binding			ovary(3)|pancreas(2)|skin(1)|breast(1)|central_nervous_system(1)	8		Esophageal squamous(42;0.129)				AAAATGGCAGTGATATAAAAG	0.408													27	139	---	---	---	---	PASS
TYK2	7297	broad.mit.edu	37	19	10476232	10476232	+	Missense_Mutation	SNP	G	C	C			TCGA-39-5024-01A-21D-1817-08	TCGA-39-5024-11A-01D-1817-08									Somatic	Phase_I	Capture				Illumina GAIIx	388478e9-8c1f-43f8-88c4-811bf3cc2500	829ea6e6-1737-4fc6-8732-65e2d7fb2582	g.chr19:10476232G>C	uc002moc.3	-	7	1350	c.972C>G	c.(970-972)ATC>ATG	p.I324M	TYK2_uc010dxe.2_Missense_Mutation_p.I139M|TYK2_uc002mod.2_Missense_Mutation_p.I324M	NM_003331	NP_003322	P29597	TYK2_HUMAN	tyrosine kinase 2	324	FERM.				intracellular protein kinase cascade|regulation of type I interferon-mediated signaling pathway|type I interferon-mediated signaling pathway	cytoskeleton|cytosol|membrane|nucleus	ATP binding|growth hormone receptor binding|non-membrane spanning protein tyrosine kinase activity			lung(5)|large_intestine(2)|ovary(1)|breast(1)	9			OV - Ovarian serous cystadenocarcinoma(20;1.77e-09)|Epithelial(33;3.92e-06)|all cancers(31;8.95e-06)			GCCACCACTGGATGCCACCAG	0.652													16	97	---	---	---	---	PASS
NWD1	284434	broad.mit.edu	37	19	16861050	16861050	+	Missense_Mutation	SNP	C	A	A			TCGA-39-5024-01A-21D-1817-08	TCGA-39-5024-11A-01D-1817-08									Somatic	Phase_I	Capture				Illumina GAIIx	388478e9-8c1f-43f8-88c4-811bf3cc2500	829ea6e6-1737-4fc6-8732-65e2d7fb2582	g.chr19:16861050C>A	uc002neu.3	+	6	2019	c.1597C>A	c.(1597-1599)CCA>ACA	p.P533T	NWD1_uc002net.3_Missense_Mutation_p.P398T|NWD1_uc002nev.3_Missense_Mutation_p.P327T			Q149M9	NWD1_HUMAN	RecName: Full=NACHT and WD repeat domain-containing protein 1;	533	NACHT.						ATP binding			skin(3)|ovary(2)|pancreas(2)	7						GTGTGGGAACCCAGGGCGGCT	0.642													3	36	---	---	---	---	PASS
CILP2	148113	broad.mit.edu	37	19	19655799	19655799	+	Silent	SNP	C	T	T			TCGA-39-5024-01A-21D-1817-08	TCGA-39-5024-11A-01D-1817-08									Somatic	Phase_I	Capture				Illumina GAIIx	388478e9-8c1f-43f8-88c4-811bf3cc2500	829ea6e6-1737-4fc6-8732-65e2d7fb2582	g.chr19:19655799C>T	uc002nmv.3	+	8	2530	c.2445C>T	c.(2443-2445)GGC>GGT	p.G815G	CILP2_uc002nmw.3_Silent_p.G821G	NM_153221	NP_694953	Q8IUL8	CILP2_HUMAN	cartilage intermediate layer protein 2	815						proteinaceous extracellular matrix	carbohydrate binding|carboxypeptidase activity			ovary(1)	1						CCCTGGGCGGCGAGGAGCTGG	0.746													4	14	---	---	---	---	PASS
ZNF566	84924	broad.mit.edu	37	19	36940338	36940338	+	Silent	SNP	A	G	G			TCGA-39-5024-01A-21D-1817-08	TCGA-39-5024-11A-01D-1817-08									Somatic	Phase_I	Capture				Illumina GAIIx	388478e9-8c1f-43f8-88c4-811bf3cc2500	829ea6e6-1737-4fc6-8732-65e2d7fb2582	g.chr19:36940338A>G	uc002oea.3	-	5	880	c.798T>C	c.(796-798)AGT>AGC	p.S266S	ZNF566_uc010xte.1_Silent_p.S266S|ZNF566_uc010xtf.1_Silent_p.S267S|ZNF566_uc002oeb.3_Silent_p.S266S|ZNF566_uc002oec.3_Silent_p.S162S|ZNF566_uc010xtg.1_Silent_p.S162S	NM_032838	NP_116227	Q969W8	ZN566_HUMAN	zinc finger protein 566 isoform 1	266	C2H2-type 4.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0	Esophageal squamous(110;0.162)					AGTTTGAACCACTACTAAAGG	0.423													6	88	---	---	---	---	PASS
ZNF529	57711	broad.mit.edu	37	19	37037943	37037943	+	Missense_Mutation	SNP	T	C	C			TCGA-39-5024-01A-21D-1817-08	TCGA-39-5024-11A-01D-1817-08									Somatic	Phase_I	Capture				Illumina GAIIx	388478e9-8c1f-43f8-88c4-811bf3cc2500	829ea6e6-1737-4fc6-8732-65e2d7fb2582	g.chr19:37037943T>C	uc002oeh.3	-	5	1719	c.1517A>G	c.(1516-1518)TAT>TGT	p.Y506C	ZNF529_uc010xth.1_Missense_Mutation_p.Y506C|ZNF529_uc010xti.1_Missense_Mutation_p.Y488C|ZNF529_uc002oeg.3_Missense_Mutation_p.Y401C	NM_020951	NP_066002	Q6P280	ZN529_HUMAN	zinc finger protein 529 isoform a	473	C2H2-type 11.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			breast(1)	1	Esophageal squamous(110;0.198)					CTTGCATTCATAGGGTTTTTC	0.408													15	64	---	---	---	---	PASS
ZNF567	163081	broad.mit.edu	37	19	37210578	37210578	+	Missense_Mutation	SNP	T	C	C			TCGA-39-5024-01A-21D-1817-08	TCGA-39-5024-11A-01D-1817-08									Somatic	Phase_I	Capture				Illumina GAIIx	388478e9-8c1f-43f8-88c4-811bf3cc2500	829ea6e6-1737-4fc6-8732-65e2d7fb2582	g.chr19:37210578T>C	uc010xtl.1	+	6	1174	c.952T>C	c.(952-954)TTC>CTC	p.F318L	ZNF567_uc002oeo.1_Missense_Mutation_p.F318L|ZNF567_uc010xtk.1_Missense_Mutation_p.F318L|ZNF567_uc002oep.3_Missense_Mutation_p.F287L|ZNF567_uc002oeq.1_Missense_Mutation_p.F287L	NM_152603	NP_689816	Q8N184	ZN567_HUMAN	zinc finger protein 567	318	C2H2-type 4.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0	Esophageal squamous(110;0.198)		COAD - Colon adenocarcinoma(19;0.0454)|Colorectal(19;0.065)			TGGTAAGTCCTTCCGCCTCAA	0.423													6	38	---	---	---	---	PASS
ZNF607	84775	broad.mit.edu	37	19	38189610	38189610	+	Missense_Mutation	SNP	C	G	G			TCGA-39-5024-01A-21D-1817-08	TCGA-39-5024-11A-01D-1817-08									Somatic	Phase_I	Capture				Illumina GAIIx	388478e9-8c1f-43f8-88c4-811bf3cc2500	829ea6e6-1737-4fc6-8732-65e2d7fb2582	g.chr19:38189610C>G	uc002ohc.1	-	5	2018	c.1422G>C	c.(1420-1422)GAG>GAC	p.E474D	ZNF607_uc002ohb.1_Missense_Mutation_p.E473D	NM_032689	NP_116078	Q96SK3	ZN607_HUMAN	zinc finger protein 607	474					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0			UCEC - Uterine corpus endometrioid carcinoma (49;0.0775)			CATAGGGTTTCTCTCCTGTAT	0.378													12	102	---	---	---	---	PASS
SIPA1L3	23094	broad.mit.edu	37	19	38692538	38692538	+	Missense_Mutation	SNP	C	T	T			TCGA-39-5024-01A-21D-1817-08	TCGA-39-5024-11A-01D-1817-08									Somatic	Phase_I	Capture				Illumina GAIIx	388478e9-8c1f-43f8-88c4-811bf3cc2500	829ea6e6-1737-4fc6-8732-65e2d7fb2582	g.chr19:38692538C>T	uc002ohk.2	+	20	5530	c.5021C>T	c.(5020-5022)CCG>CTG	p.P1674L		NM_015073	NP_055888	O60292	SI1L3_HUMAN	signal-induced proliferation-associated 1 like	1674					regulation of small GTPase mediated signal transduction	intracellular	GTPase activator activity			ovary(1)|central_nervous_system(1)	2			Lung(45;0.000246)|LUSC - Lung squamous cell carcinoma(53;0.000292)			CTGAACGACCCGGCCCTGAGC	0.667													6	84	---	---	---	---	PASS
B3GNT8	374907	broad.mit.edu	37	19	41932349	41932349	+	Missense_Mutation	SNP	G	T	T			TCGA-39-5024-01A-21D-1817-08	TCGA-39-5024-11A-01D-1817-08									Somatic	Phase_I	Capture				Illumina GAIIx	388478e9-8c1f-43f8-88c4-811bf3cc2500	829ea6e6-1737-4fc6-8732-65e2d7fb2582	g.chr19:41932349G>T	uc002oqs.2	-	3	789	c.335C>A	c.(334-336)CCC>CAC	p.P112H	CYP2F1_uc010xvw.1_Intron|B3GNT8_uc002oqt.1_Intron	NM_198540	NP_940942	Q7Z7M8	B3GN8_HUMAN	UDP-GlcNAc:betaGal	112	Lumenal (Potential).				poly-N-acetyllactosamine biosynthetic process|protein glycosylation	Golgi membrane|integral to membrane	galactosyltransferase activity|protein N-acetylglucosaminyltransferase activity				0						GAGGTCCTTGGGGTAGGAGGC	0.682													10	44	---	---	---	---	PASS
ZNF221	7638	broad.mit.edu	37	19	44470198	44470198	+	Missense_Mutation	SNP	G	A	A			TCGA-39-5024-01A-21D-1817-08	TCGA-39-5024-11A-01D-1817-08									Somatic	Phase_I	Capture				Illumina GAIIx	388478e9-8c1f-43f8-88c4-811bf3cc2500	829ea6e6-1737-4fc6-8732-65e2d7fb2582	g.chr19:44470198G>A	uc002oxx.2	+	6	872	c.544G>A	c.(544-546)GTT>ATT	p.V182I	ZNF221_uc010ejb.1_Missense_Mutation_p.V182I|ZNF221_uc010xws.1_Missense_Mutation_p.V182I	NM_013359	NP_037491	Q9UK13	ZN221_HUMAN	zinc finger protein 221	182	C2H2-type 1.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			skin(1)	1		Prostate(69;0.0352)				CTTCAGTGATGTTTCTGTCTT	0.423													22	121	---	---	---	---	PASS
RPS11	6205	broad.mit.edu	37	19	50000835	50000835	+	Missense_Mutation	SNP	G	C	C			TCGA-39-5024-01A-21D-1817-08	TCGA-39-5024-11A-01D-1817-08									Somatic	Phase_I	Capture				Illumina GAIIx	388478e9-8c1f-43f8-88c4-811bf3cc2500	829ea6e6-1737-4fc6-8732-65e2d7fb2582	g.chr19:50000835G>C	uc002pob.1	+	3	286	c.206G>C	c.(205-207)CGA>CCA	p.R69P	SNORD35B_uc002poc.2_5'Flank	NM_001015	NP_001006	P62280	RS11_HUMAN	ribosomal protein S11	69					endocrine pancreas development|translational elongation|translational termination|viral transcription	cytosolic small ribosomal subunit	protein binding|rRNA binding|structural constituent of ribosome				0		all_lung(116;1.62e-07)|Lung NSC(112;8.47e-07)|all_neural(266;0.0381)|Ovarian(192;0.0392)		OV - Ovarian serous cystadenocarcinoma(262;0.00206)|GBM - Glioblastoma multiforme(486;0.0245)		GTGTCCATTCGAGGGCGGATC	0.542													5	98	---	---	---	---	PASS
PRR12	57479	broad.mit.edu	37	19	50099808	50099808	+	Missense_Mutation	SNP	C	T	T			TCGA-39-5024-01A-21D-1817-08	TCGA-39-5024-11A-01D-1817-08									Somatic	Phase_I	Capture				Illumina GAIIx	388478e9-8c1f-43f8-88c4-811bf3cc2500	829ea6e6-1737-4fc6-8732-65e2d7fb2582	g.chr19:50099808C>T	uc002poo.3	+	4	2216	c.2216C>T	c.(2215-2217)CCC>CTC	p.P739L		NM_020719	NP_065770	Q9ULL5	PRR12_HUMAN	proline rich 12	Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment							DNA binding			central_nervous_system(1)|pancreas(1)	2		all_lung(116;2.45e-07)|Lung NSC(112;1.24e-06)|Ovarian(192;0.0728)|all_neural(266;0.0887)		OV - Ovarian serous cystadenocarcinoma(262;0.00319)|GBM - Glioblastoma multiforme(134;0.0132)		GGCGAGACCCCCGAGGGGCTG	0.687													3	21	---	---	---	---	PASS
PPP2R1A	5518	broad.mit.edu	37	19	52714609	52714609	+	Missense_Mutation	SNP	G	A	A			TCGA-39-5024-01A-21D-1817-08	TCGA-39-5024-11A-01D-1817-08									Somatic	Phase_I	Capture				Illumina GAIIx	388478e9-8c1f-43f8-88c4-811bf3cc2500	829ea6e6-1737-4fc6-8732-65e2d7fb2582	g.chr19:52714609G>A	uc002pyp.2	+	4	526	c.367G>A	c.(367-369)GAC>AAC	p.D123N	PPP2R1A_uc010ydk.1_Missense_Mutation_p.D68N|PPP2R1A_uc010epm.1_Missense_Mutation_p.D163N|PPP2R1A_uc002pyq.2_5'UTR	NM_014225	NP_055040	P30153	2AAA_HUMAN	alpha isoform of regulatory subunit A, protein	123	PP2A subunit B binding.|SV40 small T antigen binding.|HEAT 3.|Polyoma small and medium T antigens Binding.				ceramide metabolic process|chromosome segregation|G2/M transition of mitotic cell cycle|inactivation of MAPK activity|induction of apoptosis|negative regulation of cell growth|negative regulation of tyrosine phosphorylation of Stat3 protein|protein complex assembly|protein dephosphorylation|regulation of cell adhesion|regulation of cell differentiation|regulation of DNA replication|regulation of transcription, DNA-dependent|regulation of Wnt receptor signaling pathway|response to organic substance|RNA splicing|second-messenger-mediated signaling	chromosome, centromeric region|cytosol|membrane|microtubule cytoskeleton|mitochondrion|nucleus|protein phosphatase type 2A complex|soluble fraction	antigen binding|protein heterodimerization activity|protein phosphatase type 2A regulator activity			endometrium(31)|ovary(28)|lung(2)|breast(2)|skin(1)|kidney(1)|pancreas(1)	66				GBM - Glioblastoma multiforme(134;0.00456)|OV - Ovarian serous cystadenocarcinoma(262;0.015)		CTCGCCCTCTGACCTGGAGGC	0.667			Mis		clear cell ovarian carcinoma								7	53	---	---	---	---	PASS
NLRP8	126205	broad.mit.edu	37	19	56466026	56466026	+	Missense_Mutation	SNP	G	C	C			TCGA-39-5024-01A-21D-1817-08	TCGA-39-5024-11A-01D-1817-08									Somatic	Phase_I	Capture				Illumina GAIIx	388478e9-8c1f-43f8-88c4-811bf3cc2500	829ea6e6-1737-4fc6-8732-65e2d7fb2582	g.chr19:56466026G>C	uc002qmh.2	+	3	673	c.602G>C	c.(601-603)AGA>ACA	p.R201T	NLRP8_uc010etg.2_Missense_Mutation_p.R201T	NM_176811	NP_789781	Q86W28	NALP8_HUMAN	NLR family, pyrin domain containing 8	201						cytoplasm	ATP binding			ovary(4)|breast(3)|central_nervous_system(2)|skin(2)|large_intestine(1)|kidney(1)	13		Colorectal(82;0.000147)|Ovarian(87;0.17)		GBM - Glioblastoma multiforme(193;0.0695)		CCCCAGGGTAGACAGCCCAAG	0.532													17	77	---	---	---	---	PASS
PEG3	5178	broad.mit.edu	37	19	57325481	57325481	+	Silent	SNP	G	C	C			TCGA-39-5024-01A-21D-1817-08	TCGA-39-5024-11A-01D-1817-08									Somatic	Phase_I	Capture				Illumina GAIIx	388478e9-8c1f-43f8-88c4-811bf3cc2500	829ea6e6-1737-4fc6-8732-65e2d7fb2582	g.chr19:57325481G>C	uc002qnu.2	-	7	4680	c.4329C>G	c.(4327-4329)GCC>GCG	p.A1443A	ZIM2_uc010ygq.1_Intron|ZIM2_uc010ygr.1_Intron|ZIM2_uc002qnr.2_Intron|ZIM2_uc002qnq.2_Intron|ZIM2_uc010etp.2_Intron|ZIM2_uc010ygs.1_Intron|PEG3_uc002qnt.2_Silent_p.A1414A|PEG3_uc002qnv.2_Silent_p.A1443A|PEG3_uc002qnw.2_Silent_p.A1319A|PEG3_uc002qnx.2_Silent_p.A1317A|PEG3_uc010etr.2_Silent_p.A1443A	NM_001146186	NP_001139658	Q9GZU2	PEG3_HUMAN	paternally expressed 3 isoform 1	1443	Glu-rich.|4 X 5 AA repeat of P-X-G-E-A.|1-4.				apoptosis|viral reproduction	cytoplasm|nucleus	nucleic acid binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(7)|skin(2)|upper_aerodigestive_tract(1)|large_intestine(1)|pancreas(1)	12		Colorectal(82;0.000256)|all_neural(62;0.103)|Ovarian(87;0.243)		GBM - Glioblastoma multiforme(193;0.0269)		TTGGCTGCTCGGCCTCTCCAT	0.572													15	95	---	---	---	---	PASS
STK35	140901	broad.mit.edu	37	20	2083902	2083902	+	Silent	SNP	C	T	T			TCGA-39-5024-01A-21D-1817-08	TCGA-39-5024-11A-01D-1817-08									Somatic	Phase_I	Capture				Illumina GAIIx	388478e9-8c1f-43f8-88c4-811bf3cc2500	829ea6e6-1737-4fc6-8732-65e2d7fb2582	g.chr20:2083902C>T	uc010gak.2	+	2	783	c.783C>T	c.(781-783)GTC>GTT	p.V261V	STK35_uc010zpu.1_Silent_p.V128V|STK35_uc002wfw.3_Silent_p.V128V	NM_080836	NP_543026	Q8TDR2	STK35_HUMAN	serine/threonine kinase 35	261	Protein kinase.					cytoplasm|nucleolus	ATP binding|protein serine/threonine kinase activity			ovary(1)	1						ACCAGAACGTCGTGCAGTTTG	0.632													8	22	---	---	---	---	PASS
UBOX5	22888	broad.mit.edu	37	20	3095978	3095978	+	Missense_Mutation	SNP	T	C	C			TCGA-39-5024-01A-21D-1817-08	TCGA-39-5024-11A-01D-1817-08									Somatic	Phase_I	Capture				Illumina GAIIx	388478e9-8c1f-43f8-88c4-811bf3cc2500	829ea6e6-1737-4fc6-8732-65e2d7fb2582	g.chr20:3095978T>C	uc002whw.2	-	4	1560	c.1390A>G	c.(1390-1392)ACT>GCT	p.T464A	uc002whv.1_Intron|UBOX5_uc002whx.2_Intron|UBOX5_uc002why.1_Missense_Mutation_p.T464A	NM_014948	NP_055763	O94941	RNF37_HUMAN	U-box domain containing 5 isoform a	464						nucleus|ubiquitin ligase complex	ubiquitin-protein ligase activity|zinc ion binding			ovary(1)|skin(1)	2						CTCCAGGAAGTGTTGCTCCCT	0.612											OREG0025729	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	5	35	---	---	---	---	PASS
MYT1	4661	broad.mit.edu	37	20	62853285	62853285	+	Missense_Mutation	SNP	G	C	C			TCGA-39-5024-01A-21D-1817-08	TCGA-39-5024-11A-01D-1817-08									Somatic	Phase_I	Capture				Illumina GAIIx	388478e9-8c1f-43f8-88c4-811bf3cc2500	829ea6e6-1737-4fc6-8732-65e2d7fb2582	g.chr20:62853285G>C	uc002yii.2	+	14	2645	c.2281G>C	c.(2281-2283)GAT>CAT	p.D761H	MYT1_uc002yih.2_Missense_Mutation_p.D463H|MYT1_uc002yij.2_Missense_Mutation_p.D420H	NM_004535	NP_004526	Q01538	MYT1_HUMAN	myelin transcription factor 1	761					cell differentiation|nervous system development	nucleus	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(2)	2	all_cancers(38;1.82e-11)|all_epithelial(29;3.3e-13)|Lung NSC(23;5.21e-10)|all_lung(23;1.92e-09)					TTCTGAAGCAGATGACCAGGA	0.517													6	54	---	---	---	---	PASS
USP25	29761	broad.mit.edu	37	21	17214736	17214736	+	Silent	SNP	A	C	C			TCGA-39-5024-01A-21D-1817-08	TCGA-39-5024-11A-01D-1817-08									Somatic	Phase_I	Capture				Illumina GAIIx	388478e9-8c1f-43f8-88c4-811bf3cc2500	829ea6e6-1737-4fc6-8732-65e2d7fb2582	g.chr21:17214736A>C	uc002yjy.1	+	18	2431	c.2214A>C	c.(2212-2214)CCA>CCC	p.P738P	USP25_uc011aby.1_Silent_p.P738P|USP25_uc002yjz.1_Silent_p.P738P|USP25_uc010gla.1_Intron	NM_013396	NP_037528	Q9UHP3	UBP25_HUMAN	ubiquitin specific peptidase 25	738					protein modification process|ubiquitin-dependent protein catabolic process	cytoplasm|nucleus	ubiquitin thiolesterase activity|ubiquitin-specific protease activity			ovary(3)|liver(2)	5				Epithelial(23;7.55e-05)|all cancers(11;0.000429)|COAD - Colon adenocarcinoma(22;0.00543)|OV - Ovarian serous cystadenocarcinoma(11;0.00743)|Colorectal(24;0.0116)|Lung(58;0.0853)|LUSC - Lung squamous cell carcinoma(23;0.0889)		CAGGAGACCCAGAATATCTAG	0.323													19	69	---	---	---	---	PASS
C21orf34	388815	broad.mit.edu	37	21	17443570	17443570	+	RNA	SNP	T	C	C			TCGA-39-5024-01A-21D-1817-08	TCGA-39-5024-11A-01D-1817-08									Somatic	Phase_I	Capture				Illumina GAIIx	388478e9-8c1f-43f8-88c4-811bf3cc2500	829ea6e6-1737-4fc6-8732-65e2d7fb2582	g.chr21:17443570T>C	uc002ykb.2	+	2		c.164T>C			C21orf34_uc010glc.2_RNA	NR_027790				Homo sapiens C21ORF34 (C21orf34) mRNA, partial cds, alternatively spliced.												0		Breast(209;0.152)		Epithelial(23;8.3e-05)|all cancers(11;0.000383)|Colorectal(24;0.00387)|COAD - Colon adenocarcinoma(22;0.0113)|OV - Ovarian serous cystadenocarcinoma(11;0.0127)|LUSC - Lung squamous cell carcinoma(23;0.153)		ACAGCTGGGCTGAACAAGATT	0.547													7	137	---	---	---	---	PASS
KRTAP19-5	337972	broad.mit.edu	37	21	31874377	31874377	+	Missense_Mutation	SNP	A	C	C			TCGA-39-5024-01A-21D-1817-08	TCGA-39-5024-11A-01D-1817-08									Somatic	Phase_I	Capture				Illumina GAIIx	388478e9-8c1f-43f8-88c4-811bf3cc2500	829ea6e6-1737-4fc6-8732-65e2d7fb2582	g.chr21:31874377A>C	uc011ada.1	-	1	32	c.32T>G	c.(31-33)CTG>CGG	p.L11R		NM_181611	NP_853642	Q3LI72	KR195_HUMAN	keratin associated protein 19-5	11						intermediate filament	protein binding				0						GCCGTAGCCCAGGCCTCCATA	0.567													23	86	---	---	---	---	PASS
IFNAR2	3455	broad.mit.edu	37	21	34625014	34625014	+	Silent	SNP	C	T	T			TCGA-39-5024-01A-21D-1817-08	TCGA-39-5024-11A-01D-1817-08									Somatic	Phase_I	Capture				Illumina GAIIx	388478e9-8c1f-43f8-88c4-811bf3cc2500	829ea6e6-1737-4fc6-8732-65e2d7fb2582	g.chr21:34625014C>T	uc002yrd.2	+	7	916	c.588C>T	c.(586-588)ATC>ATT	p.I196I	IFNAR2_uc002yrb.2_Silent_p.I196I|IFNAR2_uc002yrc.2_Silent_p.I196I|IFNAR2_uc002yre.2_Silent_p.I196I|IFNAR2_uc002yrf.2_Silent_p.I196I|IFNAR2_uc002yrg.2_Silent_p.I65I|IL10RB_uc002yrh.1_Silent_p.I46I|IL10RB_uc002yri.1_5'UTR	NM_207585	NP_997468	P48551	INAR2_HUMAN	interferon alpha/beta receptor 2 isoform a	196	Extracellular (Potential).				JAK-STAT cascade|regulation of type I interferon-mediated signaling pathway|response to interferon-alpha|response to virus|type I interferon-mediated signaling pathway	extracellular region|extracellular space|integral to plasma membrane	protein kinase binding|type I interferon binding|type I interferon receptor activity				0					Interferon Alfa-2a, Recombinant(DB00034)|Interferon Alfa-2b, Recombinant(DB00105)|Interferon alfa-n1(DB00011)|Interferon alfa-n3(DB00018)|Interferon alfacon-1(DB00069)|Interferon beta-1b(DB00068)|Peginterferon alfa-2a(DB00008)|Peginterferon alfa-2b(DB00022)	TCACCTATATCATTGACAAGT	0.353													4	48	---	---	---	---	PASS
SETD4	54093	broad.mit.edu	37	21	37418233	37418233	+	Missense_Mutation	SNP	G	C	C			TCGA-39-5024-01A-21D-1817-08	TCGA-39-5024-11A-01D-1817-08									Somatic	Phase_I	Capture				Illumina GAIIx	388478e9-8c1f-43f8-88c4-811bf3cc2500	829ea6e6-1737-4fc6-8732-65e2d7fb2582	g.chr21:37418233G>C	uc002yuw.1	-	5	1746	c.373C>G	c.(373-375)CTT>GTT	p.L125V	SETD4_uc002yux.1_Missense_Mutation_p.L101V|SETD4_uc002yuu.2_RNA|SETD4_uc002yuv.2_Missense_Mutation_p.L125V|SETD4_uc002yuy.2_Missense_Mutation_p.L125V|SETD4_uc002yuz.2_Missense_Mutation_p.L101V|SETD4_uc002yva.2_Missense_Mutation_p.L101V	NM_017438	NP_059134	Q9NVD3	SETD4_HUMAN	SET domain containing 4 isoform a	125	SET.									large_intestine(1)|ovary(1)	2						GGCTTCCAAAGAGATCGGTGC	0.463													7	129	---	---	---	---	PASS
DOPEY2	9980	broad.mit.edu	37	21	37591765	37591765	+	Missense_Mutation	SNP	A	G	G			TCGA-39-5024-01A-21D-1817-08	TCGA-39-5024-11A-01D-1817-08									Somatic	Phase_I	Capture				Illumina GAIIx	388478e9-8c1f-43f8-88c4-811bf3cc2500	829ea6e6-1737-4fc6-8732-65e2d7fb2582	g.chr21:37591765A>G	uc002yvg.2	+	10	1304	c.1225A>G	c.(1225-1227)ACC>GCC	p.T409A	DOPEY2_uc011aeb.1_Missense_Mutation_p.T409A	NM_005128	NP_005119	Q9Y3R5	DOP2_HUMAN	pad-1-like	409					endoplasmic reticulum organization|Golgi to endosome transport|multicellular organismal development|protein transport	Golgi membrane				ovary(1)|central_nervous_system(1)	2						ACTTAGCTACACCCAGAGTGG	0.463													19	112	---	---	---	---	PASS
BRWD1	54014	broad.mit.edu	37	21	40570728	40570728	+	Missense_Mutation	SNP	C	G	G			TCGA-39-5024-01A-21D-1817-08	TCGA-39-5024-11A-01D-1817-08									Somatic	Phase_I	Capture				Illumina GAIIx	388478e9-8c1f-43f8-88c4-811bf3cc2500	829ea6e6-1737-4fc6-8732-65e2d7fb2582	g.chr21:40570728C>G	uc002yxk.1	-	40	5753	c.5614G>C	c.(5614-5616)GAT>CAT	p.D1872H	BRWD1_uc010goc.1_Missense_Mutation_p.D515H|BRWD1_uc002yxl.2_Missense_Mutation_p.D1872H	NM_018963	NP_061836	Q9NSI6	BRWD1_HUMAN	bromodomain and WD repeat domain containing 1	1872					regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus				skin(3)|ovary(1)	4		Prostate(19;8.44e-08)|all_epithelial(19;0.223)				TTGTCATCATCTGAATCTAAA	0.338													13	75	---	---	---	---	PASS
DSCAM	1826	broad.mit.edu	37	21	41385159	41385159	+	Silent	SNP	C	T	T			TCGA-39-5024-01A-21D-1817-08	TCGA-39-5024-11A-01D-1817-08									Somatic	Phase_I	Capture				Illumina GAIIx	388478e9-8c1f-43f8-88c4-811bf3cc2500	829ea6e6-1737-4fc6-8732-65e2d7fb2582	g.chr21:41385159C>T	uc002yyq.1	-	33	6293	c.5841G>A	c.(5839-5841)CCG>CCA	p.P1947P	DSCAM_uc002yyr.1_RNA	NM_001389	NP_001380	O60469	DSCAM_HUMAN	Down syndrome cell adhesion molecule isoform	1947	Cytoplasmic (Potential).			HRPGDLIHLPPYLRMDFLLNRGGPGTSRDLSLGQACLEPQK SRTLKRPTVLEPIPMEAASSASSTREGQSWQPGAVATLPQR EGAELGQAAKMSSSQESLLDSRGHLKGNNPYAKSYTLV -> IGQVTSYICLHTLEWTFC (in Ref. 1; AAC17966).	cell adhesion|dendrite self-avoidance|negative regulation of cell adhesion|positive regulation of axon extension involved in axon guidance|positive regulation of phosphorylation	axon|extracellular region|growth cone|integral to plasma membrane|membrane fraction	protein binding			ovary(6)|skin(4)|upper_aerodigestive_tract(1)	11		all_cancers(19;0.186)|Prostate(19;1.15e-05)|all_epithelial(19;0.0103)				CGGCTTCCATCGGGATGGGCT	0.657													6	52	---	---	---	---	PASS
MX2	4600	broad.mit.edu	37	21	42779983	42779983	+	Missense_Mutation	SNP	T	A	A			TCGA-39-5024-01A-21D-1817-08	TCGA-39-5024-11A-01D-1817-08									Somatic	Phase_I	Capture				Illumina GAIIx	388478e9-8c1f-43f8-88c4-811bf3cc2500	829ea6e6-1737-4fc6-8732-65e2d7fb2582	g.chr21:42779983T>A	uc002yzf.1	+	14	2075	c.1971T>A	c.(1969-1971)AAT>AAA	p.N657K	MX2_uc002yzg.1_Missense_Mutation_p.N380K|MX2_uc010gop.1_Missense_Mutation_p.N139K	NM_002463	NP_002454	P20592	MX2_HUMAN	myxovirus resistance protein 2	657	GED.				response to virus|type I interferon-mediated signaling pathway	cytoplasm|nucleus	GTP binding|GTPase activity			ovary(2)	2		Prostate(19;1.57e-07)|all_epithelial(19;0.0222)				TCCGAGAGAATGGTGACTCCT	0.463													15	97	---	---	---	---	PASS
AIRE	326	broad.mit.edu	37	21	45709879	45709879	+	Silent	SNP	T	C	C			TCGA-39-5024-01A-21D-1817-08	TCGA-39-5024-11A-01D-1817-08									Somatic	Phase_I	Capture				Illumina GAIIx	388478e9-8c1f-43f8-88c4-811bf3cc2500	829ea6e6-1737-4fc6-8732-65e2d7fb2582	g.chr21:45709879T>C	uc002zei.2	+	7	934	c.807T>C	c.(805-807)GGT>GGC	p.G269G	AIRE_uc010gpq.2_5'Flank|AIRE_uc002zej.2_5'Flank|AIRE_uc010gpr.2_5'Flank	NM_000383	NP_000374	O43918	AIRE_HUMAN	autoimmune regulator isoform 1	269	SAND.				positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	chromatin binding|histone binding|transcription regulatory region DNA binding|translation regulator activity|zinc ion binding			skin(1)	1				Colorectal(79;0.0806)		AGGGTGGAGGTGAGGCTAGGC	0.692									Autoimmune_PolyEndocrinopathy_Candidiasis_Ectodermal_Dystrophy				5	18	---	---	---	---	PASS
CECR2	27443	broad.mit.edu	37	22	18022478	18022478	+	Missense_Mutation	SNP	C	A	A			TCGA-39-5024-01A-21D-1817-08	TCGA-39-5024-11A-01D-1817-08									Somatic	Phase_I	Capture				Illumina GAIIx	388478e9-8c1f-43f8-88c4-811bf3cc2500	829ea6e6-1737-4fc6-8732-65e2d7fb2582	g.chr22:18022478C>A	uc010gqw.1	+	15	2706	c.2580C>A	c.(2578-2580)AGC>AGA	p.S860R	CECR2_uc010gqv.1_Missense_Mutation_p.S719R|CECR2_uc002zml.2_Missense_Mutation_p.S719R	NM_031413	NP_113601	Q9BXF3	CECR2_HUMAN	cat eye syndrome chromosome region, candidate 2	902					chromatin modification|cytokinesis|cytoskeleton organization|DNA fragmentation involved in apoptotic nuclear change|vesicle-mediated transport		protein binding			ovary(1)|skin(1)	2		all_epithelial(15;0.139)		Lung(27;0.146)		TGATGGACAGCCCAGAGATGA	0.632													14	66	---	---	---	---	PASS
ZNF280A	129025	broad.mit.edu	37	22	22869714	22869714	+	Nonsense_Mutation	SNP	G	A	A			TCGA-39-5024-01A-21D-1817-08	TCGA-39-5024-11A-01D-1817-08									Somatic	Phase_I	Capture				Illumina GAIIx	388478e9-8c1f-43f8-88c4-811bf3cc2500	829ea6e6-1737-4fc6-8732-65e2d7fb2582	g.chr22:22869714G>A	uc002zwe.2	-	2	494	c.241C>T	c.(241-243)CAA>TAA	p.Q81*	LOC96610_uc011aim.1_Intron	NM_080740	NP_542778	P59817	Z280A_HUMAN	zinc finger protein 280A	81					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1	all_hematologic(9;0.0135)|Acute lymphoblastic leukemia(84;0.17)	all_hematologic(6;1.74e-30)|Acute lymphoblastic leukemia(6;7.75e-22)		READ - Rectum adenocarcinoma(21;0.145)		GCAGGATATTGACGGAAGTGG	0.473													25	109	---	---	---	---	PASS
PISD	23761	broad.mit.edu	37	22	32015789	32015789	+	Missense_Mutation	SNP	C	T	T			TCGA-39-5024-01A-21D-1817-08	TCGA-39-5024-11A-01D-1817-08									Somatic	Phase_I	Capture				Illumina GAIIx	388478e9-8c1f-43f8-88c4-811bf3cc2500	829ea6e6-1737-4fc6-8732-65e2d7fb2582	g.chr22:32015789C>T	uc003alm.3	-	8	1046	c.1039G>A	c.(1039-1041)GGC>AGC	p.G347S	PISD_uc003alk.2_Missense_Mutation_p.G313S|PISD_uc003all.2_Missense_Mutation_p.G258E|PISD_uc011alr.1_Missense_Mutation_p.G312S|PISD_uc003aln.3_Missense_Mutation_p.G309S	NM_014338	NP_055153	Q9UG56	PISD_HUMAN	phosphatidylserine decarboxylase	347					phospholipid biosynthetic process	mitochondrion	phosphatidylserine decarboxylase activity			central_nervous_system(2)|ovary(1)	3					Phosphatidylserine(DB00144)	TTGTAGGAGCCCTTGCTGTGC	0.607													10	45	---	---	---	---	PASS
MGAT3	4248	broad.mit.edu	37	22	39884490	39884490	+	Missense_Mutation	SNP	C	T	T	rs149871838		TCGA-39-5024-01A-21D-1817-08	TCGA-39-5024-11A-01D-1817-08									Somatic	Phase_I	Capture				Illumina GAIIx	388478e9-8c1f-43f8-88c4-811bf3cc2500	829ea6e6-1737-4fc6-8732-65e2d7fb2582	g.chr22:39884490C>T	uc003axv.3	+	2	1377	c.1138C>T	c.(1138-1140)CGC>TGC	p.R380C	MGAT3_uc010gxy.2_Missense_Mutation_p.R380C	NM_002409	NP_002400	Q09327	MGAT3_HUMAN	mannosyl (beta-1,4-)-glycoprotein	380	Lumenal (Potential).				post-translational protein modification|protein N-linked glycosylation via asparagine	Golgi membrane|integral to membrane	beta-1,4-mannosylglycoprotein 4-beta-N-acetylglucosaminyltransferase activity				0	Melanoma(58;0.04)					GGACGGCATCCGCCTGCGCCG	0.647													8	71	---	---	---	---	PASS
TNRC6B	23112	broad.mit.edu	37	22	40706902	40706902	+	Missense_Mutation	SNP	G	T	T			TCGA-39-5024-01A-21D-1817-08	TCGA-39-5024-11A-01D-1817-08									Somatic	Phase_I	Capture				Illumina GAIIx	388478e9-8c1f-43f8-88c4-811bf3cc2500	829ea6e6-1737-4fc6-8732-65e2d7fb2582	g.chr22:40706902G>T	uc011aor.1	+	17	4551	c.4340G>T	c.(4339-4341)GGC>GTC	p.G1447V	TNRC6B_uc003aym.2_Missense_Mutation_p.G643V|TNRC6B_uc003ayn.3_Missense_Mutation_p.G1337V|TNRC6B_uc003ayo.2_Missense_Mutation_p.G1194V	NM_001162501	NP_001155973	Q9UPQ9	TNR6B_HUMAN	trinucleotide repeat containing 6B isoform 1	1447					gene silencing by RNA|regulation of translation	cytoplasmic mRNA processing body	nucleotide binding|RNA binding				0						ACACTGGGTGGCCATACGGGT	0.507													4	26	---	---	---	---	PASS
DMD	1756	broad.mit.edu	37	X	31497149	31497149	+	Silent	SNP	C	A	A			TCGA-39-5024-01A-21D-1817-08	TCGA-39-5024-11A-01D-1817-08									Somatic	Phase_I	Capture				Illumina GAIIx	388478e9-8c1f-43f8-88c4-811bf3cc2500	829ea6e6-1737-4fc6-8732-65e2d7fb2582	g.chrX:31497149C>A	uc004dda.1	-	58	8863	c.8619G>T	c.(8617-8619)CTG>CTT	p.L2873L	DMD_uc004dcq.1_Silent_p.L144L|DMD_uc004dcr.1_Silent_p.L413L|DMD_uc004dcs.1_Silent_p.L413L|DMD_uc004dct.1_Silent_p.L413L|DMD_uc004dcu.1_Silent_p.L413L|DMD_uc004dcv.1_Silent_p.L413L|DMD_uc004dcw.2_Silent_p.L1529L|DMD_uc004dcx.2_Silent_p.L1532L|DMD_uc004dcz.2_Silent_p.L2750L|DMD_uc004dcy.1_Silent_p.L2869L|DMD_uc004ddb.1_Silent_p.L2865L	NM_004006	NP_003997	P11532	DMD_HUMAN	dystrophin Dp427m isoform	2873	Spectrin 20.				muscle filament sliding|peptide biosynthetic process	cell surface|costamere|cytoskeleton|cytosol|dystrophin-associated glycoprotein complex|sarcolemma	actin binding|dystroglycan binding|nitric-oxide synthase binding|protein binding|structural constituent of cytoskeleton|structural constituent of muscle|zinc ion binding			ovary(3)|pancreas(2)|large_intestine(1)	6		all_cancers(2;1.22e-16)|Acute lymphoblastic leukemia(2;4.65e-06)|all_hematologic(2;0.00108)|all_epithelial(3;0.00626)|all_neural(2;0.0189)|all_lung(315;0.182)|Glioma(3;0.203)				GCTGCTCTGTCAGAAATATTC	0.393													7	61	---	---	---	---	PASS
USP9X	8239	broad.mit.edu	37	X	41078486	41078486	+	Splice_Site	SNP	T	A	A			TCGA-39-5024-01A-21D-1817-08	TCGA-39-5024-11A-01D-1817-08									Somatic	Phase_I	Capture				Illumina GAIIx	388478e9-8c1f-43f8-88c4-811bf3cc2500	829ea6e6-1737-4fc6-8732-65e2d7fb2582	g.chrX:41078486T>A	uc004dfb.2	+	38	7198	c.6565_splice	c.e38+2	p.G2189_splice	USP9X_uc004dfc.2_Splice_Site_p.G2189_splice	NM_001039590	NP_001034679	Q93008	USP9X_HUMAN	ubiquitin specific protease 9, X-linked isoform						BMP signaling pathway|cell division|chromosome segregation|female gamete generation|mitosis|protein deubiquitination|transforming growth factor beta receptor signaling pathway|ubiquitin-dependent protein catabolic process	cytoplasm	co-SMAD binding|cysteine-type endopeptidase activity|ubiquitin thiolesterase activity			lung(3)|breast(2)|ovary(1)	6						CCAATTTAGGTAAGAATTTAA	0.323													7	47	---	---	---	---	PASS
DGKK	139189	broad.mit.edu	37	X	50165475	50165475	+	Missense_Mutation	SNP	C	A	A			TCGA-39-5024-01A-21D-1817-08	TCGA-39-5024-11A-01D-1817-08									Somatic	Phase_I	Capture				Illumina GAIIx	388478e9-8c1f-43f8-88c4-811bf3cc2500	829ea6e6-1737-4fc6-8732-65e2d7fb2582	g.chrX:50165475C>A	uc010njr.1	-	3	866	c.806G>T	c.(805-807)AGC>ATC	p.S269I		NM_001013742	NP_001013764	Q5KSL6	DGKK_HUMAN	diacylglycerol kinase kappa	269	PH.				activation of protein kinase C activity by G-protein coupled receptor protein signaling pathway|diacylglycerol metabolic process|intracellular signal transduction|platelet activation|response to oxidative stress	cytoplasm|plasma membrane	ATP binding|diacylglycerol kinase activity|metal ion binding			ovary(1)|kidney(1)	2	Ovarian(276;0.236)					TCTACAGCTGCTTTCTGCCAC	0.463													6	100	---	---	---	---	PASS
GPR173	54328	broad.mit.edu	37	X	53106694	53106694	+	Silent	SNP	C	A	A			TCGA-39-5024-01A-21D-1817-08	TCGA-39-5024-11A-01D-1817-08									Somatic	Phase_I	Capture				Illumina GAIIx	388478e9-8c1f-43f8-88c4-811bf3cc2500	829ea6e6-1737-4fc6-8732-65e2d7fb2582	g.chrX:53106694C>A	uc004dru.2	+	2	1149	c.891C>A	c.(889-891)CTC>CTA	p.L297L		NM_018969	NP_061842	Q9NS66	GP173_HUMAN	G protein-coupled receptor 173	297	Helical; Name=6; (Potential).					integral to membrane|plasma membrane	G-protein coupled receptor activity			skin(1)	1						TCTTTCTGCTCCTCTGGTCAC	0.597													5	36	---	---	---	---	PASS
FGD1	2245	broad.mit.edu	37	X	54472818	54472818	+	Silent	SNP	G	A	A			TCGA-39-5024-01A-21D-1817-08	TCGA-39-5024-11A-01D-1817-08									Somatic	Phase_I	Capture				Illumina GAIIx	388478e9-8c1f-43f8-88c4-811bf3cc2500	829ea6e6-1737-4fc6-8732-65e2d7fb2582	g.chrX:54472818G>A	uc004dtg.2	-	18	3344	c.2610C>T	c.(2608-2610)CTC>CTT	p.L870L		NM_004463	NP_004454	P98174	FGD1_HUMAN	faciogenital dysplasia protein	870	PH 2.				actin cytoskeleton organization|apoptosis|filopodium assembly|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|organ morphogenesis|regulation of Cdc42 GTPase activity|regulation of cell shape|small GTPase mediated signal transduction	cytoskeleton|cytosol|Golgi apparatus|lamellipodium|nucleus|plasma membrane|ruffle	metal ion binding|Rho guanyl-nucleotide exchange factor activity|small GTPase binding			ovary(3)|skin(2)|central_nervous_system(1)	6						CGAAGCCAATGAGGGGCAGGC	0.647													5	32	---	---	---	---	PASS
MAGED2	10916	broad.mit.edu	37	X	54841172	54841172	+	Missense_Mutation	SNP	G	T	T			TCGA-39-5024-01A-21D-1817-08	TCGA-39-5024-11A-01D-1817-08									Somatic	Phase_I	Capture				Illumina GAIIx	388478e9-8c1f-43f8-88c4-811bf3cc2500	829ea6e6-1737-4fc6-8732-65e2d7fb2582	g.chrX:54841172G>T	uc004dtk.1	+	11	1444	c.1350G>T	c.(1348-1350)GAG>GAT	p.E450D	MAGED2_uc004dtl.1_Missense_Mutation_p.E450D|MAGED2_uc004dtm.1_Missense_Mutation_p.E365D|MAGED2_uc010nkc.1_Missense_Mutation_p.R415I|MAGED2_uc004dtn.1_Missense_Mutation_p.E450D|MAGED2_uc004dto.1_Missense_Mutation_p.E424D	NM_177433	NP_803182	Q9UNF1	MAGD2_HUMAN	melanoma antigen family D, 2	450	MAGE.									ovary(2)|breast(1)	3						CTTACTATGAGACCAGCAAGA	0.532													5	65	---	---	---	---	PASS
ZXDA	7789	broad.mit.edu	37	X	57935713	57935713	+	Missense_Mutation	SNP	C	A	A			TCGA-39-5024-01A-21D-1817-08	TCGA-39-5024-11A-01D-1817-08									Somatic	Phase_I	Capture				Illumina GAIIx	388478e9-8c1f-43f8-88c4-811bf3cc2500	829ea6e6-1737-4fc6-8732-65e2d7fb2582	g.chrX:57935713C>A	uc004dve.2	-	1	1355	c.1142G>T	c.(1141-1143)AGC>ATC	p.S381I		NM_007156	NP_009087	P98168	ZXDA_HUMAN	zinc finger, X-linked, duplicated A	381	C2H2-type 4.|Required for interaction with ZXDC.				positive regulation of transcription, DNA-dependent	nucleus	C2H2 zinc finger domain binding|identical protein binding|nucleic acid binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)	1						TTCGAAGTGGCTGCGCTGGTG	0.567													20	115	---	---	---	---	PASS
AR	367	broad.mit.edu	37	X	66766199	66766199	+	Missense_Mutation	SNP	C	T	T			TCGA-39-5024-01A-21D-1817-08	TCGA-39-5024-11A-01D-1817-08									Somatic	Phase_I	Capture				Illumina GAIIx	388478e9-8c1f-43f8-88c4-811bf3cc2500	829ea6e6-1737-4fc6-8732-65e2d7fb2582	g.chrX:66766199C>T	uc004dwu.1	+	1	2326	c.1211C>T	c.(1210-1212)GCG>GTG	p.A404V	AR_uc011mpd.1_Missense_Mutation_p.A404V|AR_uc011mpe.1_RNA|AR_uc011mpf.1_Missense_Mutation_p.A404V	NM_000044	NP_000035	P10275	ANDR_HUMAN	androgen receptor isoform 1	402	Modulating.|Poly-Ala.				cell death|cell growth|cell proliferation|cell-cell signaling|negative regulation of apoptosis|negative regulation of integrin biosynthetic process|positive regulation of cell proliferation|positive regulation of integrin biosynthetic process|positive regulation of NF-kappaB transcription factor activity|positive regulation of phosphorylation|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase III promoter|regulation of establishment of protein localization in plasma membrane|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor|transport	cytoplasm|nuclear chromatin|nucleoplasm	androgen binding|androgen receptor activity|beta-catenin binding|enzyme binding|ligand-regulated transcription factor activity|protein dimerization activity|sequence-specific DNA binding transcription factor activity|transcription factor binding|transcription regulatory region DNA binding|zinc ion binding			ovary(3)|lung(2)|breast(2)|central_nervous_system(1)	8	all_cancers(1;0.173)|Prostate(1;2.27e-16)|all_epithelial(1;0.102)	all_lung(315;1.3e-11)			Bicalutamide(DB01128)|Cyproterone(DB04839)|Dromostanolone(DB00858)|Finasteride(DB01216)|Fluoxymesterone(DB01185)|Flutamide(DB00499)|Nandrolone(DB00984)|Nilutamide(DB00665)|Oxandrolone(DB00621)|Testosterone(DB00624)	GCTGCGGCGGCGCAGTGCCGC	0.736									Androgen_Insensitivity_Syndrome				3	6	---	---	---	---	PASS
IL2RG	3561	broad.mit.edu	37	X	70328193	70328193	+	Silent	SNP	C	T	T	rs148001866		TCGA-39-5024-01A-21D-1817-08	TCGA-39-5024-11A-01D-1817-08									Somatic	Phase_I	Capture				Illumina GAIIx	388478e9-8c1f-43f8-88c4-811bf3cc2500	829ea6e6-1737-4fc6-8732-65e2d7fb2582	g.chrX:70328193C>T	uc004dyw.1	-	7	872	c.858G>A	c.(856-858)ACG>ACA	p.T286T	CXorf65_uc011mpo.1_5'Flank|CXorf65_uc011mpp.1_5'Flank|IL2RG_uc004dyv.1_Silent_p.T15T|IL2RG_uc004dyx.1_Silent_p.T96T	NM_000206	NP_000197	P31785	IL2RG_HUMAN	interleukin 2 receptor, gamma precursor	286	Box 1 motif.|Cytoplasmic (Potential).				immune response|interleukin-4-mediated signaling pathway|interspecies interaction between organisms	external side of plasma membrane|integral to plasma membrane	cytokine receptor activity|interleukin-2 binding			pancreas(1)	1	Renal(35;0.156)				Aldesleukin(DB00041)|Denileukin diftitox(DB00004)	TTCGGGGCATCGTCCTGACAG	0.463									Severe_Combined_Immunodeficiency_X-linked				5	87	---	---	---	---	PASS
TSIX	9383	broad.mit.edu	37	X	73043423	73043423	+	RNA	SNP	T	C	C			TCGA-39-5024-01A-21D-1817-08	TCGA-39-5024-11A-01D-1817-08									Somatic	Phase_I	Capture				Illumina GAIIx	388478e9-8c1f-43f8-88c4-811bf3cc2500	829ea6e6-1737-4fc6-8732-65e2d7fb2582	g.chrX:73043423T>C	uc004ebn.2	+	1		c.31384T>C			XIST_uc004ebm.1_RNA	NR_003255				Homo sapiens XIST antisense RNA (non-protein coding) (TSIX), non-coding RNA.												0						CCTTTACTTCTGTAGGCCAGG	0.274													15	102	---	---	---	---	PASS
MAGT1	84061	broad.mit.edu	37	X	77150848	77150848	+	Silent	SNP	G	T	T			TCGA-39-5024-01A-21D-1817-08	TCGA-39-5024-11A-01D-1817-08									Somatic	Phase_I	Capture				Illumina GAIIx	388478e9-8c1f-43f8-88c4-811bf3cc2500	829ea6e6-1737-4fc6-8732-65e2d7fb2582	g.chrX:77150848G>T	uc004fof.2	-	1	218	c.156C>A	c.(154-156)ATC>ATA	p.I52I	MAGT1_uc004fog.3_RNA|MAGT1_uc004ect.3_Silent_p.I52I	NM_032121	NP_115497	Q9H0U3	MAGT1_HUMAN	magnesium transporter 1	20					protein N-linked glycosylation via asparagine	integral to membrane|oligosaccharyltransferase complex				upper_aerodigestive_tract(1)	1						CGTCGCAAACGATGAGCAGCG	0.557													6	42	---	---	---	---	PASS
BRWD3	254065	broad.mit.edu	37	X	80064747	80064747	+	Nonsense_Mutation	SNP	G	A	A			TCGA-39-5024-01A-21D-1817-08	TCGA-39-5024-11A-01D-1817-08									Somatic	Phase_I	Capture				Illumina GAIIx	388478e9-8c1f-43f8-88c4-811bf3cc2500	829ea6e6-1737-4fc6-8732-65e2d7fb2582	g.chrX:80064747G>A	uc004edt.2	-	2	351	c.88C>T	c.(88-90)CAG>TAG	p.Q30*	BRWD3_uc004edo.2_5'Flank|BRWD3_uc004edp.2_5'Flank|BRWD3_uc004edq.2_5'Flank|BRWD3_uc010nmj.1_5'Flank|BRWD3_uc004edr.2_5'Flank|BRWD3_uc004eds.2_5'Flank|BRWD3_uc004edu.2_5'UTR|BRWD3_uc004edv.2_5'UTR|BRWD3_uc004edw.2_5'UTR|BRWD3_uc004edx.2_5'UTR|BRWD3_uc004edy.2_5'UTR|BRWD3_uc004edz.2_5'UTR|BRWD3_uc004eea.2_5'UTR|BRWD3_uc004eeb.2_5'UTR	NM_153252	NP_694984	Q6RI45	BRWD3_HUMAN	bromodomain and WD repeat domain containing 3	30										ovary(4)	4						CCCCTTACCTGAGCGGATTTG	0.557													4	14	---	---	---	---	PASS
TCEAL3	85012	broad.mit.edu	37	X	102864065	102864065	+	Missense_Mutation	SNP	G	A	A			TCGA-39-5024-01A-21D-1817-08	TCGA-39-5024-11A-01D-1817-08									Somatic	Phase_I	Capture				Illumina GAIIx	388478e9-8c1f-43f8-88c4-811bf3cc2500	829ea6e6-1737-4fc6-8732-65e2d7fb2582	g.chrX:102864065G>A	uc004ekq.2	+	3	335	c.73G>A	c.(73-75)GAT>AAT	p.D25N	TCEAL3_uc004ekr.2_Missense_Mutation_p.D25N	NM_001006933	NP_001006934	Q969E4	TCAL3_HUMAN	transcription elongation factor A (SII)-like 3	25	Glu-rich.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus					0						agtagagcctgatgatgaagg	0.144													10	30	---	---	---	---	PASS
GUCY2F	2986	broad.mit.edu	37	X	108719118	108719118	+	Silent	SNP	C	T	T			TCGA-39-5024-01A-21D-1817-08	TCGA-39-5024-11A-01D-1817-08									Somatic	Phase_I	Capture				Illumina GAIIx	388478e9-8c1f-43f8-88c4-811bf3cc2500	829ea6e6-1737-4fc6-8732-65e2d7fb2582	g.chrX:108719118C>T	uc004eod.3	-	2	324	c.48G>A	c.(46-48)GCG>GCA	p.A16A	GUCY2F_uc011msq.1_RNA	NM_001522	NP_001513	P51841	GUC2F_HUMAN	guanylate cyclase 2F precursor	16					intracellular signal transduction|receptor guanylyl cyclase signaling pathway|visual perception	integral to plasma membrane|nuclear outer membrane	ATP binding|GTP binding|guanylate cyclase activity|protein kinase activity|receptor activity			lung(4)|breast(3)|central_nervous_system(1)	8						TCCTGAAAGCCGCAAACCAGA	0.542											OREG0019905	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	16	87	---	---	---	---	PASS
CHRDL1	91851	broad.mit.edu	37	X	109937485	109937485	+	Silent	SNP	C	T	T			TCGA-39-5024-01A-21D-1817-08	TCGA-39-5024-11A-01D-1817-08									Somatic	Phase_I	Capture				Illumina GAIIx	388478e9-8c1f-43f8-88c4-811bf3cc2500	829ea6e6-1737-4fc6-8732-65e2d7fb2582	g.chrX:109937485C>T	uc004eou.3	-	8	1033	c.684G>A	c.(682-684)GGG>GGA	p.G228G	CHRDL1_uc004eov.2_Silent_p.G222G|CHRDL1_uc004eow.2_Silent_p.G227G|CHRDL1_uc010nps.2_Silent_p.G227G|CHRDL1_uc004eot.2_Silent_p.G148G|CHRDL1_uc011mss.1_Silent_p.G142G	NM_001143981	NP_001137453	Q9BU40	CRDL1_HUMAN	chordin-like 1 isoform 1 precursor	221					BMP signaling pathway|cell differentiation|nervous system development|ossification	extracellular region					0						GACTTCTGGCCCCAGGAAAGC	0.478													32	139	---	---	---	---	PASS
LHFPL1	340596	broad.mit.edu	37	X	111914294	111914294	+	Missense_Mutation	SNP	C	T	T			TCGA-39-5024-01A-21D-1817-08	TCGA-39-5024-11A-01D-1817-08									Somatic	Phase_I	Capture				Illumina GAIIx	388478e9-8c1f-43f8-88c4-811bf3cc2500	829ea6e6-1737-4fc6-8732-65e2d7fb2582	g.chrX:111914294C>T	uc004epq.2	-	2	658	c.325G>A	c.(325-327)GAG>AAG	p.E109K	LHFPL1_uc004epp.2_Missense_Mutation_p.E132K|LHFPL1_uc010nqa.2_Intron|LHFPL1_uc010nqb.2_Missense_Mutation_p.E109K	NM_178175	NP_835469	Q86WI0	LHPL1_HUMAN	lipoma HMGIC fusion partner-like 1 precursor	109						integral to membrane					0						ATGAGCTCCTCCATGCAGCAA	0.582													14	68	---	---	---	---	PASS
FAM70A	55026	broad.mit.edu	37	X	119410745	119410745	+	Missense_Mutation	SNP	C	T	T			TCGA-39-5024-01A-21D-1817-08	TCGA-39-5024-11A-01D-1817-08									Somatic	Phase_I	Capture				Illumina GAIIx	388478e9-8c1f-43f8-88c4-811bf3cc2500	829ea6e6-1737-4fc6-8732-65e2d7fb2582	g.chrX:119410745C>T	uc004eso.3	-	8	969	c.742G>A	c.(742-744)GAC>AAC	p.D248N	FAM70A_uc004esp.3_Missense_Mutation_p.D224N|FAM70A_uc010nqo.2_Intron	NM_017938	NP_060408	Q5JRV8	FA70A_HUMAN	hypothetical protein LOC55026 isoform 1	248						integral to membrane				lung(1)|breast(1)	2						CTTACCATGTCCTTAAAGCCT	0.502													9	95	---	---	---	---	PASS
ATP1B4	23439	broad.mit.edu	37	X	119504619	119504619	+	Silent	SNP	G	A	A			TCGA-39-5024-01A-21D-1817-08	TCGA-39-5024-11A-01D-1817-08									Somatic	Phase_I	Capture				Illumina GAIIx	388478e9-8c1f-43f8-88c4-811bf3cc2500	829ea6e6-1737-4fc6-8732-65e2d7fb2582	g.chrX:119504619G>A	uc004esr.2	+	3	462	c.378G>A	c.(376-378)GTG>GTA	p.V126V	ATP1B4_uc004esq.2_Silent_p.V122V|ATP1B4_uc011mtx.1_Silent_p.V91V|ATP1B4_uc011mty.1_Intron	NM_001142447	NP_001135919	Q9UN42	AT1B4_HUMAN	ATPase, (Na+)/K+ transporting, beta 4	126	Helical; Signal-anchor for type II membrane protein; (Potential).				ATP biosynthetic process|regulation of transcription, DNA-dependent|transcription, DNA-dependent	integral to plasma membrane|nuclear inner membrane	sodium:potassium-exchanging ATPase activity			ovary(1)|skin(1)	2						TGGCTGCTGTGATCACCCTCT	0.502													12	376	---	---	---	---	PASS
MAGEC3	139081	broad.mit.edu	37	X	140985257	140985257	+	Silent	SNP	G	T	T			TCGA-39-5024-01A-21D-1817-08	TCGA-39-5024-11A-01D-1817-08									Somatic	Phase_I	Capture				Illumina GAIIx	388478e9-8c1f-43f8-88c4-811bf3cc2500	829ea6e6-1737-4fc6-8732-65e2d7fb2582	g.chrX:140985257G>T	uc011mwp.1	+	7	1713	c.1713G>T	c.(1711-1713)GTG>GTT	p.V571V	MAGEC3_uc004fbs.2_Silent_p.V273V|MAGEC3_uc010nsj.2_Silent_p.V273V	NM_138702	NP_619647	Q8TD91	MAGC3_HUMAN	melanoma antigen family C, 3 isoform 1	571	MAGE 2.									skin(2)|central_nervous_system(1)	3	Acute lymphoblastic leukemia(192;6.56e-05)					TCTGGGAAGTGTTGAGTGCAA	0.493													23	184	---	---	---	---	PASS
RPL10	6134	broad.mit.edu	37	X	153628196	153628196	+	Silent	SNP	C	T	T			TCGA-39-5024-01A-21D-1817-08	TCGA-39-5024-11A-01D-1817-08									Somatic	Phase_I	Capture				Illumina GAIIx	388478e9-8c1f-43f8-88c4-811bf3cc2500	829ea6e6-1737-4fc6-8732-65e2d7fb2582	g.chrX:153628196C>T	uc004fkm.2	+	5	431	c.243C>T	c.(241-243)GGC>GGT	p.G81G	uc010nuv.1_5'Flank|RPL10_uc004fko.2_Silent_p.G81G|RPL10_uc004fkn.1_Silent_p.G81G|RPL10_uc004fkp.1_Silent_p.G81G|RPL10_uc004fkq.1_RNA|RPL10_uc004fkr.1_Silent_p.G6G|SNORA70_uc010nux.1_5'Flank	NM_006013	NP_006004	P27635	RL10_HUMAN	ribosomal protein L10	81					endocrine pancreas development|translational elongation|translational termination|viral transcription	cytosolic large ribosomal subunit|endoplasmic reticulum	structural constituent of ribosome				0	all_cancers(53;3.7e-16)|all_epithelial(53;2.97e-10)|all_lung(58;1.84e-07)|Lung NSC(58;5.84e-07)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)					AAAGTTGTGGCAAAGATGGCT	0.507													14	110	---	---	---	---	PASS