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	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
KIAA0562	9731	broad.mit.edu	37	1	3756192	3756192	+	Missense_Mutation	SNP	C	A	A			TCGA-43-6647-01	TCGA-43-6647-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:3756192C>A	uc001aky.2	-	7	1074	c.715G>T	c.(715-717)GCC>TCC	p.A239S	KIAA0562_uc010nzm.1_RNA|KIAA0562_uc001akz.2_Missense_Mutation_p.A239S	NM_014704	NP_055519	O60308	CE104_HUMAN	glycine-, glutamate-,	239	Potential.					centriole	binding				0	all_cancers(77;0.0395)|Ovarian(185;0.0634)|all_lung(157;0.222)|Lung NSC(156;0.227)	all_epithelial(116;3.96e-21)|all_lung(118;2.74e-08)|Lung NSC(185;6.4e-06)|Breast(487;0.00066)|Renal(390;0.00121)|Hepatocellular(190;0.00335)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.031)|Lung SC(97;0.0548)|Medulloblastoma(700;0.212)		Epithelial(90;6.85e-39)|OV - Ovarian serous cystadenocarcinoma(86;1.59e-22)|GBM - Glioblastoma multiforme(42;3.16e-16)|Colorectal(212;2.01e-05)|COAD - Colon adenocarcinoma(227;7.99e-05)|BRCA - Breast invasive adenocarcinoma(365;0.000389)|Kidney(185;0.000513)|STAD - Stomach adenocarcinoma(132;0.00709)|KIRC - Kidney renal clear cell carcinoma(229;0.00714)|Lung(427;0.137)		TCAGCAATGGCTTGTTTTAGT	0.353													23	125	---	---	---	---	PASS
VPS13D	55187	broad.mit.edu	37	1	12378287	12378287	+	Missense_Mutation	SNP	G	A	A			TCGA-43-6647-01	TCGA-43-6647-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:12378287G>A	uc001atv.2	+	31	7448	c.7307G>A	c.(7306-7308)AGC>AAC	p.S2436N	VPS13D_uc001atw.2_Missense_Mutation_p.S2436N|VPS13D_uc001atx.2_Missense_Mutation_p.S1624N|VPS13D_uc001aty.1_Missense_Mutation_p.S174N	NM_015378	NP_056193	Q5THJ4	VP13D_HUMAN	vacuolar protein sorting 13D isoform 1	2436					protein localization					ovary(4)|pancreas(1)	5	Ovarian(185;0.249)	Lung NSC(185;4.08e-05)|all_lung(284;4.55e-05)|Renal(390;0.000147)|Colorectal(325;0.00058)|Breast(348;0.00093)|Ovarian(437;0.00965)|Hepatocellular(190;0.0202)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0327)|Colorectal(212;4.63e-06)|BRCA - Breast invasive adenocarcinoma(304;0.000289)|COAD - Colon adenocarcinoma(227;0.000801)|Kidney(185;0.00216)|KIRC - Kidney renal clear cell carcinoma(229;0.00544)|STAD - Stomach adenocarcinoma(313;0.012)|READ - Rectum adenocarcinoma(331;0.0476)|Lung(427;0.209)		AACTCTAGCAGCGAATCTGCT	0.443													4	137	---	---	---	---	PASS
COL16A1	1307	broad.mit.edu	37	1	32148971	32148971	+	Splice_Site	SNP	C	T	T			TCGA-43-6647-01	TCGA-43-6647-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:32148971C>T	uc001btk.1	-	35	2745	c.2380_splice	c.e35-1	p.G794_splice	COL16A1_uc001btj.1_Splice_Site_p.G623_splice|COL16A1_uc001btl.3_Splice_Site_p.G794_splice	NM_001856	NP_001847	Q07092	COGA1_HUMAN	alpha 1 type XVI collagen precursor						cell adhesion|female pregnancy|integrin-mediated signaling pathway	collagen type XVI	integrin binding|structural molecule activity			ovary(8)	8		Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0423)|all_neural(195;0.0837)|Breast(348;0.116)		STAD - Stomach adenocarcinoma(196;0.059)		CAGGCTCCCCCTGCAAGTCAG	0.627													12	180	---	---	---	---	PASS
DLGAP3	58512	broad.mit.edu	37	1	35370415	35370415	+	Silent	SNP	C	A	A	rs35523603		TCGA-43-6647-01	TCGA-43-6647-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:35370415C>A	uc001byc.2	-	1	570	c.570G>T	c.(568-570)CCG>CCT	p.P190P		NM_001080418	NP_001073887	O95886	DLGP3_HUMAN	discs, large (Drosophila) homolog-associated	190					cell-cell signaling	cell junction|postsynaptic density|postsynaptic membrane				ovary(3)	3		Myeloproliferative disorder(586;0.0393)				CCCGCTTCCCCGGCGCCTCCA	0.642													11	45	---	---	---	---	PASS
ANKRD34A	284615	broad.mit.edu	37	1	145474029	145474029	+	Missense_Mutation	SNP	C	T	T			TCGA-43-6647-01	TCGA-43-6647-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:145474029C>T	uc001enq.1	+	4	1994	c.701C>T	c.(700-702)CCA>CTA	p.P234L	NBPF10_uc001emp.3_Intron	NM_001039888	NP_001034977	Q69YU3	AN34A_HUMAN	ankyrin repeat domain 34	234	Pro-rich.										0	all_hematologic(18;0.0187)|Acute lymphoblastic leukemia(18;0.0786)					CTCCCCAAACCACCACGCCAT	0.627													5	76	---	---	---	---	PASS
MTMR11	10903	broad.mit.edu	37	1	149903325	149903325	+	Intron	SNP	G	A	A			TCGA-43-6647-01	TCGA-43-6647-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:149903325G>A	uc001etl.3	-						MTMR11_uc001etm.1_Intron|MTMR11_uc010pbm.1_Intron|MTMR11_uc010pbn.1_Intron	NM_001145862	NP_001139334	A4FU01	MTMRB_HUMAN	myotubularin related protein 11 isoform a								phosphatase activity			central_nervous_system(1)	1	Breast(34;0.0009)|Ovarian(49;0.0377)|all_hematologic(923;0.0597)|Hepatocellular(266;0.161)|Colorectal(459;0.171)		LUSC - Lung squamous cell carcinoma(543;0.221)|STAD - Stomach adenocarcinoma(528;0.247)			CGCTCTGGGTGATAAAGAGGA	0.527													7	40	---	---	---	---	PASS
CA14	23632	broad.mit.edu	37	1	150232578	150232578	+	Intron	SNP	T	A	A			TCGA-43-6647-01	TCGA-43-6647-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:150232578T>A	uc001etx.2	+						CA14_uc009wln.2_Missense_Mutation_p.S30T	NM_012113	NP_036245	Q9ULX7	CAH14_HUMAN	carbonic anhydrase XIV precursor							integral to membrane	carbonate dehydratase activity|metal ion binding			ovary(1)	1	Lung NSC(24;7.29e-29)|Breast(34;0.00211)|Ovarian(49;0.0167)|all_hematologic(923;0.0597)|Hepatocellular(266;0.161)|Colorectal(459;0.171)		LUSC - Lung squamous cell carcinoma(543;0.171)			TGAGCAGATCTCAAGGCCTCC	0.587													8	44	---	---	---	---	PASS
LCE3E	353145	broad.mit.edu	37	1	152538557	152538557	+	Missense_Mutation	SNP	C	A	A			TCGA-43-6647-01	TCGA-43-6647-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:152538557C>A	uc001faa.2	-	2	184	c.128G>T	c.(127-129)GGC>GTC	p.G43V		NM_178435	NP_848522	Q5T5B0	LCE3E_HUMAN	late cornified envelope 3E	43					keratinization					ovary(1)	1	Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		Lung(1;0.000294)|LUAD - Lung adenocarcinoma(1;0.00527)|LUSC - Lung squamous cell carcinoma(543;0.206)	UCEC - Uterine corpus endometrioid carcinoma (5;0.153)		AGGGCCACAGCCCCCAGAGCT	0.657													7	66	---	---	---	---	PASS
CRABP2	1382	broad.mit.edu	37	1	156670390	156670390	+	Nonsense_Mutation	SNP	C	A	A			TCGA-43-6647-01	TCGA-43-6647-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:156670390C>A	uc001fpr.2	-	3	447	c.310G>T	c.(310-312)GAG>TAG	p.E104*		NM_001878	NP_001869	P29373	RABP2_HUMAN	cellular retinoic acid binding protein 2	104					epidermis development|regulation of transcription, DNA-dependent|signal transduction	cytoplasm|nucleus	retinal binding|retinol binding|transporter activity			upper_aerodigestive_tract(1)	1	all_hematologic(923;0.088)|Hepatocellular(266;0.158)				Alitretinoin(DB00523)	TTGGGGCCCTCTCCCTTCAGG	0.552													12	89	---	---	---	---	PASS
CD1A	909	broad.mit.edu	37	1	158226635	158226635	+	Missense_Mutation	SNP	G	C	C			TCGA-43-6647-01	TCGA-43-6647-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:158226635G>C	uc001frt.2	+	4	1197	c.664G>C	c.(664-666)GTG>CTG	p.V222L		NM_001763	NP_001754	P06126	CD1A_HUMAN	CD1A antigen precursor	222	Extracellular (Potential).|Ig-like.				antigen processing and presentation|immune response	endosome membrane|integral to plasma membrane|MHC class I protein complex				pancreas(2)|skin(1)	3	all_hematologic(112;0.0378)				Antithymocyte globulin(DB00098)	TCTGCAGCTTGTGTGCCATGT	0.582													13	87	---	---	---	---	PASS
SLAMF1	6504	broad.mit.edu	37	1	160607107	160607107	+	Nonsense_Mutation	SNP	T	A	A			TCGA-43-6647-01	TCGA-43-6647-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:160607107T>A	uc001fwl.3	-	2	635	c.289A>T	c.(289-291)AAG>TAG	p.K97*	SLAMF1_uc010pjk.1_RNA|SLAMF1_uc010pjl.1_RNA|SLAMF1_uc010pjm.1_RNA|SLAMF1_uc001fwm.2_Nonsense_Mutation_p.K97*	NM_003037	NP_003028	Q13291	SLAF1_HUMAN	signaling lymphocytic activation molecule family	97	Extracellular (Potential).				interspecies interaction between organisms|lymphocyte activation|positive regulation of cell proliferation	integral to membrane	antigen binding|transmembrane receptor activity			ovary(1)|breast(1)	2	all_cancers(52;4.94e-17)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.0175)			AGATAAAACTTGTAGCGATCT	0.478													19	110	---	---	---	---	PASS
SLC9A11	284525	broad.mit.edu	37	1	173495857	173495857	+	Intron	SNP	T	A	A			TCGA-43-6647-01	TCGA-43-6647-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:173495857T>A	uc001giz.2	-						SLC9A11_uc009wwe.2_Intron|SLC9A11_uc010pmq.1_Intron	NM_178527	NP_848622	Q5TAH2	S9A11_HUMAN	solute carrier family 9, member 11						sodium ion transport	integral to membrane	ion channel activity|solute:hydrogen antiporter activity			ovary(2)	2						ATAGTTTCTGTAAAAAATTAA	0.279													6	48	---	---	---	---	PASS
TNR	7143	broad.mit.edu	37	1	175362911	175362911	+	Intron	SNP	G	T	T			TCGA-43-6647-01	TCGA-43-6647-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:175362911G>T	uc001gkp.1	-						TNR_uc009wwu.1_Intron	NM_003285	NP_003276	Q92752	TENR_HUMAN	tenascin R precursor						axon guidance|cell adhesion|signal transduction	proteinaceous extracellular matrix				pancreas(5)|ovary(4)|central_nervous_system(1)|skin(1)	11	Renal(580;0.146)					ACAGGTGAGTGTTACCTTTGG	0.458													20	188	---	---	---	---	PASS
PAPPA2	60676	broad.mit.edu	37	1	176740282	176740282	+	Missense_Mutation	SNP	T	A	A			TCGA-43-6647-01	TCGA-43-6647-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:176740282T>A	uc001gkz.2	+	17	5845	c.4681T>A	c.(4681-4683)TAT>AAT	p.Y1561N	PAPPA2_uc009www.2_RNA	NM_020318	NP_064714	Q9BXP8	PAPP2_HUMAN	pappalysin 2 isoform 1	1561	Sushi 3.				cell differentiation|proteolysis|regulation of cell growth	extracellular region|intracellular|membrane	metalloendopeptidase activity|zinc ion binding			ovary(7)|central_nervous_system(5)|skin(2)|lung(1)|breast(1)	16						ACCAGGGTACTATGTGGCAGA	0.473													10	58	---	---	---	---	PASS
NCF2	4688	broad.mit.edu	37	1	183543638	183543638	+	Missense_Mutation	SNP	G	T	T			TCGA-43-6647-01	TCGA-43-6647-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:183543638G>T	uc001gqj.3	-	4	760	c.485C>A	c.(484-486)GCG>GAG	p.A162E	NCF2_uc010pod.1_Intron|NCF2_uc010poe.1_Intron|NCF2_uc001gqk.3_Missense_Mutation_p.A162E	NM_000433	NP_000424	P19878	NCF2_HUMAN	neutrophil cytosolic factor 2	162					cellular defense response|innate immune response|respiratory burst|superoxide anion generation	NADPH oxidase complex|nucleolus	electron carrier activity|protein C-terminus binding			ovary(3)	3						ACACTCCATCGCCTTGTCGAT	0.463													27	245	---	---	---	---	PASS
DENND1B	163486	broad.mit.edu	37	1	197704774	197704774	+	Intron	SNP	C	A	A			TCGA-43-6647-01	TCGA-43-6647-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:197704774C>A	uc001guf.3	-						DENND1B_uc010ppe.1_Intron|DENND1B_uc010ppf.1_Intron|DENND1B_uc001gue.3_5'UTR	NM_144977	NP_659414	Q6P3S1	DEN1B_HUMAN	DENN/MADD domain containing 1B isoform 2							clathrin-coated vesicle|cytosol	guanyl-nucleotide exchange factor activity				0						CCATGAAGGTCGAGCTATGCG	0.498													9	31	---	---	---	---	PASS
PPP1R12B	4660	broad.mit.edu	37	1	202317984	202317984	+	Missense_Mutation	SNP	C	T	T			TCGA-43-6647-01	TCGA-43-6647-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:202317984C>T	uc001gya.1	+	1	149	c.5C>T	c.(4-6)GCG>GTG	p.A2V	PPP1R12B_uc001gxy.2_Missense_Mutation_p.A2V|PPP1R12B_uc009xad.1_5'UTR|PPP1R12B_uc009xae.1_Missense_Mutation_p.A2V|PPP1R12B_uc001gxz.1_Missense_Mutation_p.A2V	NM_002481	NP_002472	O60237	MYPT2_HUMAN	protein phosphatase 1, regulatory (inhibitor)	2					regulation of muscle contraction|signal transduction	cytoplasm	enzyme activator activity			ovary(3)	3			BRCA - Breast invasive adenocarcinoma(75;0.166)			GGAGCAATGGCGGAACTGGAG	0.652													9	60	---	---	---	---	PASS
PLEKHA6	22874	broad.mit.edu	37	1	204218303	204218303	+	Intron	SNP	G	T	T			TCGA-43-6647-01	TCGA-43-6647-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:204218303G>T	uc001hau.2	-							NM_014935	NP_055750	Q9Y2H5	PKHA6_HUMAN	phosphoinositol 3-phosphate-binding protein-3											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)			GCCACCCCCAGCTTCTCACCT	0.582													12	88	---	---	---	---	PASS
RYR2	6262	broad.mit.edu	37	1	237872358	237872358	+	Missense_Mutation	SNP	G	T	T			TCGA-43-6647-01	TCGA-43-6647-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:237872358G>T	uc001hyl.1	+	69	10222	c.10102G>T	c.(10102-10104)GCC>TCC	p.A3368S	RYR2_uc010pxz.1_Missense_Mutation_p.A323S	NM_001035	NP_001026	Q92736	RYR2_HUMAN	cardiac muscle ryanodine receptor	3368					cardiac muscle contraction|detection of calcium ion|induction of apoptosis by ionic changes|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum|response to caffeine|response to hypoxia|response to redox state	calcium channel complex|cytosol|plasma membrane|plasma membrane enriched fraction|sarcoplasmic reticulum membrane	calcium ion binding|calmodulin binding|identical protein binding|protein kinase A catalytic subunit binding|protein kinase A regulatory subunit binding|receptor activity|ryanodine-sensitive calcium-release channel activity|suramin binding			ovary(17)|large_intestine(6)|central_nervous_system(6)|pancreas(3)|breast(1)	33	Ovarian(103;0.103)	all_cancers(173;0.000368)|Melanoma(53;0.0179)|all_epithelial(177;0.0225)	OV - Ovarian serous cystadenocarcinoma(106;0.00606)			AGATCTCTATGCCTTCTACCC	0.458													5	44	---	---	---	---	PASS
CPSF3	51692	broad.mit.edu	37	2	9582063	9582063	+	Silent	SNP	T	C	C			TCGA-43-6647-01	TCGA-43-6647-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:9582063T>C	uc002qzo.1	+	9	1088	c.1053T>C	c.(1051-1053)GGT>GGC	p.G351G	CPSF3_uc010ewx.1_Silent_p.G351G|CPSF3_uc002qzp.1_Silent_p.G314G	NM_016207	NP_057291	Q9UKF6	CPSF3_HUMAN	cleavage and polyadenylation specific factor 3,	351					histone mRNA 3'-end processing|mRNA cleavage|mRNA export from nucleus|mRNA polyadenylation|nuclear mRNA splicing, via spliceosome|termination of RNA polymerase II transcription	mRNA cleavage and polyadenylation specificity factor complex|ribonucleoprotein complex	5'-3' exonuclease activity|endoribonuclease activity|metal ion binding|protein binding|RNA binding			breast(2)	2	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)	all_cancers(51;2.39e-25)|all_epithelial(98;8.75e-19)|Lung NSC(108;2.38e-06)|Ovarian(717;0.0308)		all cancers(51;2.2e-40)|Epithelial(75;6.71e-35)|OV - Ovarian serous cystadenocarcinoma(76;4.35e-21)|STAD - Stomach adenocarcinoma(1183;0.00644)		AGAGGAATGGTGTCATTATAG	0.458													22	147	---	---	---	---	PASS
DDX1	1653	broad.mit.edu	37	2	15760423	15760423	+	Missense_Mutation	SNP	G	T	T			TCGA-43-6647-01	TCGA-43-6647-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:15760423G>T	uc002rce.2	+	17	1586	c.1298G>T	c.(1297-1299)GGA>GTA	p.G433V	DDX1_uc010yjq.1_Missense_Mutation_p.G341V	NM_004939	NP_004930	Q92499	DDX1_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 1	433	Necessary for interaction with RELA.				DNA duplex unwinding|double-strand break repair|multicellular organismal development|regulation of transcription, DNA-dependent|regulation of translational initiation|spliceosome assembly|transcription, DNA-dependent	cleavage body|stress granule|tRNA-splicing ligase complex	ATP binding|ATP-dependent helicase activity|chromatin binding|DNA binding|DNA/RNA helicase activity|exonuclease activity|poly(A) RNA binding|protein binding|RNA helicase activity|transcription cofactor activity			central_nervous_system(2)|upper_aerodigestive_tract(1)|ovary(1)	4	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.197)	all_epithelial(98;2.96e-07)|Acute lymphoblastic leukemia(84;4.24e-05)|Ovarian(717;0.0694)	GBM - Glioblastoma multiforme(3;0.00969)	Epithelial(75;4.35e-05)|OV - Ovarian serous cystadenocarcinoma(76;0.133)		GACTTAAAAGGAGAAGACTCT	0.413													21	82	---	---	---	---	PASS
OSR1	130497	broad.mit.edu	37	2	19552084	19552084	+	Silent	SNP	C	G	G			TCGA-43-6647-01	TCGA-43-6647-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:19552084C>G	uc002rdc.2	-	3	1056	c.753G>C	c.(751-753)ACG>ACC	p.T251T		NM_145260	NP_660303	Q8TAX0	OSR1_HUMAN	odd-skipped related 1	251	C2H2-type 3.				chondrocyte differentiation|embryonic digit morphogenesis|embryonic forelimb morphogenesis|embryonic hindlimb morphogenesis|embryonic leg joint morphogenesis|embryonic skeletal joint morphogenesis|heart development|mesangial cell development|mesonephric duct morphogenesis|metanephric cap mesenchymal cell proliferation involved in metanephros development|metanephric glomerulus vasculature development|metanephric interstitial cell development|metanephric mesenchymal cell differentiation|metanephric nephron tubule development|metanephric smooth muscle tissue development|middle ear morphogenesis|negative regulation of apoptosis|negative regulation of nephron tubule epithelial cell differentiation|negative regulation of transcription from RNA polymerase II promoter|odontogenesis|palate development|pattern specification involved in metanephros development|positive regulation of bone mineralization|positive regulation of epithelial cell proliferation|positive regulation of gastrulation|positive regulation of transcription from RNA polymerase II promoter|pronephros development|renal vesicle progenitor cell differentiation|specification of anterior mesonephric tubule identity|specification of posterior mesonephric tubule identity|stem cell differentiation|transcription, DNA-dependent|ureter urothelium development|ureteric bud development	nucleolus	nucleic acid binding|zinc ion binding			ovary(1)	1	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.197)	Acute lymphoblastic leukemia(84;0.221)				GTGAGTGTAGCGTCTTGTGGA	0.507													10	77	---	---	---	---	PASS
BIRC6	57448	broad.mit.edu	37	2	32842813	32842813	+	Missense_Mutation	SNP	G	A	A			TCGA-43-6647-01	TCGA-43-6647-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:32842813G>A	uc010ezu.2	+	74	14550	c.14416G>A	c.(14416-14418)GAA>AAA	p.E4806K		NM_016252	NP_057336	Q9NR09	BIRC6_HUMAN	baculoviral IAP repeat-containing 6	4806					anti-apoptosis|apoptosis	intracellular	acid-amino acid ligase activity|cysteine-type endopeptidase inhibitor activity|protein binding			ovary(5)|skin(4)|lung(2)|central_nervous_system(1)|breast(1)|pancreas(1)	14	Acute lymphoblastic leukemia(172;0.155)					TCAGCTCCGCGAAGAGTTGCT	0.502													7	42	---	---	---	---	PASS
MAP4K3	8491	broad.mit.edu	37	2	39509662	39509662	+	Missense_Mutation	SNP	T	C	C			TCGA-43-6647-01	TCGA-43-6647-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:39509662T>C	uc002rro.2	-	22	1712	c.1621A>G	c.(1621-1623)AAA>GAA	p.K541E	MAP4K3_uc002rrp.2_Missense_Mutation_p.K520E|MAP4K3_uc010yns.1_Missense_Mutation_p.K94E	NM_003618	NP_003609	Q8IVH8	M4K3_HUMAN	mitogen-activated protein kinase kinase kinase	541					JNK cascade		ATP binding|protein binding|protein serine/threonine kinase activity|small GTPase regulator activity			ovary(3)|lung(3)|stomach(1)|pancreas(1)	8		all_hematologic(82;0.211)				ACATGCACTTTAGGTGTTGGA	0.328													7	80	---	---	---	---	PASS
PAPOLG	64895	broad.mit.edu	37	2	61019336	61019336	+	Missense_Mutation	SNP	C	G	G	rs149643688		TCGA-43-6647-01	TCGA-43-6647-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:61019336C>G	uc002sai.2	+	17	1822	c.1591C>G	c.(1591-1593)CTG>GTG	p.L531V	PAPOLG_uc002saj.2_Missense_Mutation_p.L220V|PAPOLG_uc002sak.2_Missense_Mutation_p.L66V|PAPOLG_uc010fch.2_Missense_Mutation_p.L220V	NM_022894	NP_075045	Q9BWT3	PAPOG_HUMAN	poly(A) polymerase gamma	531					mRNA processing|RNA polyadenylation|transcription, DNA-dependent	nucleus	ATP binding|metal ion binding|polynucleotide adenylyltransferase activity|RNA binding			ovary(1)|central_nervous_system(1)	2	all_hematologic(2;0.0797)		LUSC - Lung squamous cell carcinoma(5;1.19e-07)|Lung(5;2.86e-06)|Epithelial(17;0.0768)			TAGCAGTTGTCTGGATAGCTC	0.433													30	121	---	---	---	---	PASS
PAPOLG	64895	broad.mit.edu	37	2	61019427	61019427	+	Intron	SNP	C	T	T			TCGA-43-6647-01	TCGA-43-6647-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:61019427C>T	uc002sai.2	+						PAPOLG_uc002saj.2_Intron|PAPOLG_uc002sak.2_Intron|PAPOLG_uc010fch.2_Intron	NM_022894	NP_075045	Q9BWT3	PAPOG_HUMAN	poly(A) polymerase gamma						mRNA processing|RNA polyadenylation|transcription, DNA-dependent	nucleus	ATP binding|metal ion binding|polynucleotide adenylyltransferase activity|RNA binding			ovary(1)|central_nervous_system(1)	2	all_hematologic(2;0.0797)		LUSC - Lung squamous cell carcinoma(5;1.19e-07)|Lung(5;2.86e-06)|Epithelial(17;0.0768)			ACAGAAAGGTCTGTCTTTATT	0.378													17	103	---	---	---	---	PASS
REL	5966	broad.mit.edu	37	2	61149294	61149294	+	Missense_Mutation	SNP	C	G	G			TCGA-43-6647-01	TCGA-43-6647-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:61149294C>G	uc002sam.1	+	11	1708	c.1484C>G	c.(1483-1485)TCT>TGT	p.S495C	REL_uc002san.1_Missense_Mutation_p.S463C	NM_002908	NP_002899	Q04864	REL_HUMAN	v-rel reticuloendotheliosis viral oncogene	495					positive regulation of I-kappaB kinase/NF-kappaB cascade	nucleus	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity			ovary(2)|breast(1)	3	all_hematologic(2;0.0797)	Ovarian(717;0.0728)	LUSC - Lung squamous cell carcinoma(5;6.2e-08)|Lung(5;1.65e-06)|Epithelial(17;0.064)|all cancers(80;0.221)			TCTAATTGTTCTGTGAATATG	0.408			A		Hodgkin Lymphoma								3	153	---	---	---	---	PASS
PDCL3	79031	broad.mit.edu	37	2	101188144	101188144	+	Missense_Mutation	SNP	G	T	T			TCGA-43-6647-01	TCGA-43-6647-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:101188144G>T	uc002tao.2	+	5	573	c.461G>T	c.(460-462)TGC>TTC	p.C154F		NM_024065	NP_076970	Q9H2J4	PDCL3_HUMAN	phosducin-like 3	154					apoptosis|interspecies interaction between organisms	cytoplasm	protein binding				0						TCAACAACCTGCATACCCAAT	0.433													35	148	---	---	---	---	PASS
DPP10	57628	broad.mit.edu	37	2	116572486	116572486	+	Missense_Mutation	SNP	C	G	G			TCGA-43-6647-01	TCGA-43-6647-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:116572486C>G	uc002tla.1	+	20	2275	c.1818C>G	c.(1816-1818)TTC>TTG	p.F606L	DPP10_uc002tlb.1_Missense_Mutation_p.F556L|DPP10_uc002tlc.1_Missense_Mutation_p.F602L|DPP10_uc002tle.2_Missense_Mutation_p.F610L|DPP10_uc002tlf.1_Missense_Mutation_p.F599L	NM_020868	NP_065919	Q8N608	DPP10_HUMAN	dipeptidyl peptidase 10 isoform long	606	Extracellular (Potential).				proteolysis	integral to membrane|membrane fraction	serine-type peptidase activity			ovary(5)|large_intestine(2)|skin(2)|breast(1)	10						GAAGTGGATTCCAGGGTCTGA	0.403													11	94	---	---	---	---	PASS
TSN	7247	broad.mit.edu	37	2	122520626	122520626	+	Missense_Mutation	SNP	A	G	G			TCGA-43-6647-01	TCGA-43-6647-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:122520626A>G	uc002tnl.2	+	5	654	c.419A>G	c.(418-420)TAT>TGT	p.Y140C	TSN_uc002tnm.2_Missense_Mutation_p.Y93C|TSN_uc010yze.1_Intron|TSN_uc010flt.2_RNA	NM_004622	NP_004613	Q15631	TSN_HUMAN	translin	140					DNA recombination	cytoplasm|nucleus	sequence-specific DNA binding			breast(2)|large_intestine(1)	3		Ovarian(717;0.0563)|Prostate(154;0.116)				GTAGAAGATTATCTCTCAGGA	0.368													4	45	---	---	---	---	PASS
THSD7B	80731	broad.mit.edu	37	2	138414443	138414443	+	Missense_Mutation	SNP	G	T	T			TCGA-43-6647-01	TCGA-43-6647-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:138414443G>T	uc002tva.1	+	22	4096	c.4096G>T	c.(4096-4098)GTG>TTG	p.V1366L	THSD7B_uc010zbj.1_Intron	NM_001080427	NP_001073896			thrombospondin, type I, domain containing 7B											ovary(4)|central_nervous_system(2)|pancreas(1)	7				BRCA - Breast invasive adenocarcinoma(221;0.19)		CTTTGAGACTGTGGGCCGCCA	0.473													11	82	---	---	---	---	PASS
LRP1B	53353	broad.mit.edu	37	2	142567923	142567923	+	Missense_Mutation	SNP	T	C	C			TCGA-43-6647-01	TCGA-43-6647-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:142567923T>C	uc002tvj.1	-	2	1102	c.130A>G	c.(130-132)ACT>GCT	p.T44A	LRP1B_uc010fnl.1_Missense_Mutation_p.T81A	NM_018557	NP_061027	Q9NZR2	LRP1B_HUMAN	low density lipoprotein-related protein 1B	44	Extracellular (Potential).|LDL-receptor class A 1.				protein transport|receptor-mediated endocytosis	integral to membrane	calcium ion binding			lung(17)|skin(12)|ovary(12)|pancreas(3)|upper_aerodigestive_tract(2)|central_nervous_system(2)|liver(1)|kidney(1)	50		all_cancers(3;1.1e-60)|all_epithelial(3;1.94e-59)|all_lung(3;1.09e-24)|Lung NSC(3;5.65e-24)|Esophageal squamous(3;5.41e-13)|Renal(3;0.000147)|Breast(3;0.000527)|Hepatocellular(3;0.011)|all_neural(3;0.014)|Colorectal(150;0.101)		UCEC - Uterine corpus endometrioid carcinoma (2;0.00139)|Epithelial(1;1.25e-24)|all cancers(1;8.86e-24)|OV - Ovarian serous cystadenocarcinoma(1;2.45e-12)|LUSC - Lung squamous cell carcinoma(1;2.97e-10)|Lung(1;6.05e-09)|BRCA - Breast invasive adenocarcinoma(221;0.0103)		GAGACACAAGTCACGTGATCG	0.443										TSP Lung(27;0.18)			6	48	---	---	---	---	PASS
SCN3A	6328	broad.mit.edu	37	2	165947222	165947222	+	Missense_Mutation	SNP	G	T	T			TCGA-43-6647-01	TCGA-43-6647-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:165947222G>T	uc002ucx.2	-	28	5933	c.5441C>A	c.(5440-5442)TCT>TAT	p.S1814Y	SCN3A_uc010zcy.1_Missense_Mutation_p.S297Y|SCN3A_uc002ucy.2_Missense_Mutation_p.S1765Y|SCN3A_uc002ucz.2_Missense_Mutation_p.S1765Y	NM_006922	NP_008853	Q9NY46	SCN3A_HUMAN	sodium channel, voltage-gated, type III, alpha	1814						voltage-gated sodium channel complex	voltage-gated sodium channel activity			ovary(4)|breast(3)|skin(2)|central_nervous_system(1)	10					Lamotrigine(DB00555)	TGCAAAATCAGAGAGTTTAGA	0.483													27	132	---	---	---	---	PASS
SCN9A	6335	broad.mit.edu	37	2	167133750	167133750	+	Silent	SNP	A	G	G			TCGA-43-6647-01	TCGA-43-6647-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:167133750A>G	uc010fpl.2	-	16	2925	c.2584T>C	c.(2584-2586)TTG>CTG	p.L862L	uc002udp.2_RNA	NM_002977	NP_002968	Q15858	SCN9A_HUMAN	sodium channel, voltage-gated, type IX, alpha	873	II.|Helical; Name=S5 of repeat II; (Potential).					voltage-gated sodium channel complex	voltage-gated sodium channel activity			ovary(6)|central_nervous_system(5)|skin(2)	13					Lamotrigine(DB00555)|Lidocaine(DB00281)	ATGATGGCCAACACTAAGGTG	0.463													31	154	---	---	---	---	PASS
RBM45	129831	broad.mit.edu	37	2	178990747	178990747	+	Silent	SNP	A	G	G			TCGA-43-6647-01	TCGA-43-6647-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:178990747A>G	uc002ulv.2	+	9	1361	c.1269A>G	c.(1267-1269)TCA>TCG	p.S423S		NM_152945	NP_694453	Q8IUH3	RBM45_HUMAN	RNA binding motif protein 45	425	RRM 3.				cell differentiation|nervous system development	cytoplasm|nucleus	nucleotide binding|RNA binding				0			OV - Ovarian serous cystadenocarcinoma(117;0.00854)|Epithelial(96;0.00957)|all cancers(119;0.037)			ACCTTGTGTCAGGAAAAAATG	0.328													15	70	---	---	---	---	PASS
TTN	7273	broad.mit.edu	37	2	179640666	179640666	+	Missense_Mutation	SNP	T	G	G			TCGA-43-6647-01	TCGA-43-6647-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179640666T>G	uc010zfg.1	-	28	6149	c.5925A>C	c.(5923-5925)GAA>GAC	p.E1975D	TTN_uc010zfh.1_Missense_Mutation_p.E1929D|TTN_uc010zfi.1_Missense_Mutation_p.E1929D|TTN_uc010zfj.1_Missense_Mutation_p.E1929D|TTN_uc002unb.2_Missense_Mutation_p.E1975D|uc002unc.1_5'Flank	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	1975							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)			ACTTCACAACTTCTTTGGTTT	0.448													31	193	---	---	---	---	PASS
PTPRN	5798	broad.mit.edu	37	2	220162155	220162155	+	Missense_Mutation	SNP	C	A	A			TCGA-43-6647-01	TCGA-43-6647-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:220162155C>A	uc002vkz.2	-	14	1977	c.1888G>T	c.(1888-1890)GAC>TAC	p.D630Y	PTPRN_uc010zlc.1_Missense_Mutation_p.D540Y|PTPRN_uc002vla.2_Missense_Mutation_p.D601Y	NM_002846	NP_002837	Q16849	PTPRN_HUMAN	protein tyrosine phosphatase, receptor type, N	630	Cytoplasmic (Potential).				response to reactive oxygen species	integral to plasma membrane	transmembrane receptor protein tyrosine phosphatase activity			ovary(2)|lung(1)|skin(1)	4		Renal(207;0.0474)		Epithelial(149;4.22e-07)|all cancers(144;8.82e-05)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)|STAD - Stomach adenocarcinoma(1183;0.0875)		CGGCACAGGTCCTGTGGAGGA	0.582													4	66	---	---	---	---	PASS
EPM2AIP1	9852	broad.mit.edu	37	3	37033218	37033218	+	Missense_Mutation	SNP	C	G	G			TCGA-43-6647-01	TCGA-43-6647-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:37033218C>G	uc003cgk.2	-	1	1578	c.1351G>C	c.(1351-1353)GAT>CAT	p.D451H	MLH1_uc011aye.1_5'Flank|MLH1_uc003cgl.2_5'Flank|MLH1_uc011ayb.1_5'Flank|MLH1_uc010hge.2_5'Flank|MLH1_uc003cgn.3_5'Flank|MLH1_uc011ayc.1_5'Flank|MLH1_uc011ayd.1_5'Flank|MLH1_uc003cgo.2_5'Flank	NM_014805	NP_055620	Q7L775	EPMIP_HUMAN	EPM2A interacting protein 1	451						endoplasmic reticulum					0						ATTTTTTCATCTTCCTTATTT	0.333													3	52	---	---	---	---	PASS
COL7A1	1294	broad.mit.edu	37	3	48621171	48621171	+	Missense_Mutation	SNP	G	A	A			TCGA-43-6647-01	TCGA-43-6647-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:48621171G>A	uc003ctz.2	-	39	4322	c.4321C>T	c.(4321-4323)CCT>TCT	p.P1441S		NM_000094	NP_000085	Q02388	CO7A1_HUMAN	alpha 1 type VII collagen precursor	1441	Triple-helical region.|Interrupted collagenous region.				cell adhesion|epidermis development	basement membrane|collagen type VII	protein binding|serine-type endopeptidase inhibitor activity			ovary(4)|breast(3)|skin(3)|central_nervous_system(1)	11				BRCA - Breast invasive adenocarcinoma(193;0.000293)|KIRC - Kidney renal clear cell carcinoma(197;0.00558)|Kidney(197;0.00632)		TTCTTTCCAGGGGGGCCAACG	0.577													9	73	---	---	---	---	PASS
COL7A1	1294	broad.mit.edu	37	3	48621172	48621172	+	Silent	SNP	G	A	A			TCGA-43-6647-01	TCGA-43-6647-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:48621172G>A	uc003ctz.2	-	39	4321	c.4320C>T	c.(4318-4320)CCC>CCT	p.P1440P		NM_000094	NP_000085	Q02388	CO7A1_HUMAN	alpha 1 type VII collagen precursor	1440	Triple-helical region.|Interrupted collagenous region.				cell adhesion|epidermis development	basement membrane|collagen type VII	protein binding|serine-type endopeptidase inhibitor activity			ovary(4)|breast(3)|skin(3)|central_nervous_system(1)	11				BRCA - Breast invasive adenocarcinoma(193;0.000293)|KIRC - Kidney renal clear cell carcinoma(197;0.00558)|Kidney(197;0.00632)		TCTTTCCAGGGGGGCCAACGG	0.572													9	74	---	---	---	---	PASS
ADAMTS9	56999	broad.mit.edu	37	3	64617583	64617583	+	Missense_Mutation	SNP	C	G	G			TCGA-43-6647-01	TCGA-43-6647-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:64617583C>G	uc003dmg.2	-	15	2226	c.2194G>C	c.(2194-2196)GTT>CTT	p.V732L	ADAMTS9_uc011bfo.1_Missense_Mutation_p.V704L|ADAMTS9_uc003dmh.1_Missense_Mutation_p.V561L|ADAMTS9_uc003dmk.1_Missense_Mutation_p.V732L	NM_182920	NP_891550	Q9P2N4	ATS9_HUMAN	ADAM metallopeptidase with thrombospondin type 1	732	Cys-rich.				glycoprotein catabolic process|multicellular organismal development|proteolysis	proteinaceous extracellular matrix	metalloendopeptidase activity|zinc ion binding			ovary(2)|urinary_tract(1)|skin(1)	4		Lung NSC(201;0.00682)		BRCA - Breast invasive adenocarcinoma(55;0.00142)|Kidney(15;0.00202)|KIRC - Kidney renal clear cell carcinoma(15;0.00221)		GAGTTTAAAACATGATCGCAT	0.333													12	61	---	---	---	---	PASS
EPHA6	285220	broad.mit.edu	37	3	97454854	97454854	+	Nonsense_Mutation	SNP	G	A	A			TCGA-43-6647-01	TCGA-43-6647-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:97454854G>A	uc010how.1	+	16	3063	c.3020G>A	c.(3019-3021)TGG>TAG	p.W1007*	EPHA6_uc003drt.2_Nonsense_Mutation_p.W399*|EPHA6_uc010hox.1_RNA	NM_001080448	NP_001073917	Q9UF33	EPHA6_HUMAN	EPH receptor A6 isoform a	912	Protein kinase.|Cytoplasmic (Potential).					integral to plasma membrane	ATP binding|ephrin receptor activity			stomach(5)|lung(4)|central_nervous_system(3)|breast(1)|skin(1)|ovary(1)|kidney(1)	16						CTCCACTGCTGGCAGAAGGAG	0.488													6	62	---	---	---	---	PASS
OR5H1	26341	broad.mit.edu	37	3	97852280	97852280	+	Missense_Mutation	SNP	T	A	A			TCGA-43-6647-01	TCGA-43-6647-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:97852280T>A	uc011bgt.1	+	1	739	c.739T>A	c.(739-741)TCT>ACT	p.S247T		NM_001005338	NP_001005338	A6NKK0	OR5H1_HUMAN	olfactory receptor, family 5, subfamily H,	247	Helical; Name=6; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)|breast(1)	2						CCATCTCTTCTCTGTCTCTTT	0.408													8	160	---	---	---	---	PASS
MYLK	4638	broad.mit.edu	37	3	123367836	123367836	+	Missense_Mutation	SNP	A	G	G			TCGA-43-6647-01	TCGA-43-6647-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:123367836A>G	uc003ego.2	-	26	4679	c.4397T>C	c.(4396-4398)ATT>ACT	p.I1466T	MYLK_uc010hrr.2_5'UTR|MYLK_uc011bjv.1_Missense_Mutation_p.I266T|MYLK_uc011bjw.1_Missense_Mutation_p.I1466T|MYLK_uc003egp.2_Missense_Mutation_p.I1397T|MYLK_uc003egq.2_Missense_Mutation_p.I1466T|MYLK_uc003egr.2_Missense_Mutation_p.I1397T|MYLK_uc003egs.2_Missense_Mutation_p.I1290T	NM_053025	NP_444253	Q15746	MYLK_HUMAN	myosin light chain kinase isoform 1	1466	Protein kinase.				aorta smooth muscle tissue morphogenesis|muscle contraction	cytosol	actin binding|ATP binding|calmodulin binding|metal ion binding|myosin light chain kinase activity			ovary(6)|skin(2)|stomach(1)	9		Lung NSC(201;0.0496)		GBM - Glioblastoma multiforme(114;0.0736)		TCTCTCCTCAATGTCGTAGAA	0.517													14	112	---	---	---	---	PASS
CCDC14	64770	broad.mit.edu	37	3	123634171	123634171	+	Missense_Mutation	SNP	T	C	C			TCGA-43-6647-01	TCGA-43-6647-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:123634171T>C	uc011bjx.1	-	13	2408	c.2317A>G	c.(2317-2319)AAT>GAT	p.N773D	CCDC14_uc003egv.3_Missense_Mutation_p.N414D|CCDC14_uc003egx.3_Missense_Mutation_p.N573D|CCDC14_uc010hrt.2_Missense_Mutation_p.N732D|CCDC14_uc003egy.3_Missense_Mutation_p.N573D|CCDC14_uc003egz.2_Intron	NM_022757	NP_073594	Q49A88	CCD14_HUMAN	coiled-coil domain containing 14	773						centrosome					0		Lung NSC(201;0.0371)|Prostate(884;0.0405)|Myeloproliferative disorder(1037;0.205)		Lung(219;0.00942)|GBM - Glioblastoma multiforme(114;0.159)		TTATCCAAATTATGCTCATCT	0.403													33	179	---	---	---	---	PASS
SLC41A3	54946	broad.mit.edu	37	3	125725882	125725882	+	Intron	SNP	C	T	T			TCGA-43-6647-01	TCGA-43-6647-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:125725882C>T	uc003eij.2	-						SLC41A3_uc003eii.2_Missense_Mutation_p.E455K|SLC41A3_uc003eil.2_Missense_Mutation_p.E481K|SLC41A3_uc003eik.2_Intron|SLC41A3_uc011bkh.1_Missense_Mutation_p.E364K	NM_001008485	NP_001008485	Q96GZ6	S41A3_HUMAN	solute carrier family 41, member 3 isoform 1							integral to membrane|plasma membrane	cation transmembrane transporter activity				0				GBM - Glioblastoma multiforme(114;0.167)		GATGCCAGTTCTGAGATGCCA	0.547													14	78	---	---	---	---	PASS
SLITRK3	22865	broad.mit.edu	37	3	164906083	164906083	+	Missense_Mutation	SNP	C	G	G			TCGA-43-6647-01	TCGA-43-6647-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:164906083C>G	uc003fej.3	-	2	2980	c.2536G>C	c.(2536-2538)GTT>CTT	p.V846L	SLITRK3_uc003fek.2_Missense_Mutation_p.V846L	NM_014926	NP_055741	O94933	SLIK3_HUMAN	slit and trk like 3 protein precursor	846	Cytoplasmic (Potential).					integral to membrane				ovary(6)|skin(3)|pancreas(1)	10						ACTCCTGAAACCCCACCAACT	0.577										HNSCC(40;0.11)			3	129	---	---	---	---	PASS
CRMP1	1400	broad.mit.edu	37	4	5853199	5853199	+	Intron	SNP	G	A	A			TCGA-43-6647-01	TCGA-43-6647-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:5853199G>A	uc003gip.2	-						CRMP1_uc003gin.1_Intron|CRMP1_uc003giq.2_Intron|CRMP1_uc003gir.2_Intron|CRMP1_uc003gis.2_Intron	NM_001313	NP_001304	Q14194	DPYL1_HUMAN	collapsin response mediator protein 1 isoform 2						axon guidance|pyrimidine base catabolic process	cytosol|microtubule organizing center|spindle	dihydropyrimidinase activity|protein binding			ovary(2)	2				Colorectal(103;0.0721)		ATTGACGCCTGTTTCAAGATA	0.433													30	167	---	---	---	---	PASS
TLR1	7096	broad.mit.edu	37	4	38798666	38798666	+	Missense_Mutation	SNP	G	A	A			TCGA-43-6647-01	TCGA-43-6647-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:38798666G>A	uc003gtl.2	-	4	2061	c.1787C>T	c.(1786-1788)ACT>ATT	p.T596I		NM_003263	NP_003254	Q15399	TLR1_HUMAN	toll-like receptor 1 precursor	596	Helical; (Potential).				cellular response to triacyl bacterial lipopeptide|detection of triacyl bacterial lipopeptide|inflammatory response|innate immune response|macrophage activation|positive regulation of interleukin-6 biosynthetic process|positive regulation of tumor necrosis factor biosynthetic process	integral to plasma membrane|phagocytic vesicle membrane|Toll-like receptor 1-Toll-like receptor 2 protein complex	protein heterodimerization activity|transmembrane receptor activity			lung(2)|skin(2)|prostate(1)	5						GGAGGTCACAGTCACAGCCAA	0.532													13	82	---	---	---	---	PASS
MEPE	56955	broad.mit.edu	37	4	88766515	88766515	+	Silent	SNP	G	T	T			TCGA-43-6647-01	TCGA-43-6647-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:88766515G>T	uc003hqy.2	+	4	534	c.495G>T	c.(493-495)GGG>GGT	p.G165G	MEPE_uc010ikn.2_Silent_p.G52G	NM_020203	NP_064588	Q9NQ76	MEPE_HUMAN	matrix, extracellular phosphoglycoprotein with	165					skeletal system development	proteinaceous extracellular matrix	extracellular matrix structural constituent|protein binding			ovary(1)|lung(1)|skin(1)	3		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;0.000432)		AACTCCTGGGGGAAGAAAACA	0.403													10	60	---	---	---	---	PASS
CENPE	1062	broad.mit.edu	37	4	104030059	104030059	+	Missense_Mutation	SNP	C	G	G			TCGA-43-6647-01	TCGA-43-6647-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:104030059C>G	uc003hxb.1	-	48	8002	c.7912G>C	c.(7912-7914)GAA>CAA	p.E2638Q	CENPE_uc003hxc.1_Missense_Mutation_p.E2517Q	NM_001813	NP_001804	Q02224	CENPE_HUMAN	centromere protein E	2638	Globular autoinhibitory domain (By similarity).				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)		TTTGGTGATTCCTTTGGCACA	0.393													13	120	---	---	---	---	PASS
CENPE	1062	broad.mit.edu	37	4	104068579	104068579	+	Silent	SNP	C	A	A			TCGA-43-6647-01	TCGA-43-6647-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:104068579C>A	uc003hxb.1	-	29	4158	c.4068G>T	c.(4066-4068)ACG>ACT	p.T1356T	CENPE_uc003hxc.1_Silent_p.T1331T	NM_001813	NP_001804	Q02224	CENPE_HUMAN	centromere protein E	1356	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)		CTTCTTTTATCGTTTTAAGGT	0.343													15	108	---	---	---	---	PASS
QRFPR	84109	broad.mit.edu	37	4	122254094	122254094	+	Missense_Mutation	SNP	G	C	C			TCGA-43-6647-01	TCGA-43-6647-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:122254094G>C	uc010inj.1	-	4	1058	c.679C>G	c.(679-681)CTT>GTT	p.L227V	QRFPR_uc010ink.1_RNA|QRFPR_uc003ids.2_Missense_Mutation_p.L227V	NM_198179	NP_937822	Q96P65	QRFPR_HUMAN	G protein-coupled receptor 103	227	Helical; Name=5; (Potential).			VILFLLPLMVMLILYSKIGYELWIKKRVGDGSVLRTIHGKE MSKIAR -> SSSSSCLLW (in Ref. 1; AAL26488).		plasma membrane	neuropeptide Y receptor activity				0						ATCACCATAAGAGGCAGGAGG	0.423													10	91	---	---	---	---	PASS
FAT4	79633	broad.mit.edu	37	4	126372108	126372108	+	Missense_Mutation	SNP	A	G	G			TCGA-43-6647-01	TCGA-43-6647-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:126372108A>G	uc003ifj.3	+	9	9937	c.9937A>G	c.(9937-9939)AAA>GAA	p.K3313E	FAT4_uc011cgp.1_Missense_Mutation_p.K1611E|FAT4_uc003ifi.1_Missense_Mutation_p.K791E	NM_024582	NP_078858	Q6V0I7	FAT4_HUMAN	FAT tumor suppressor homolog 4 precursor	3313	Cadherin 32.|Extracellular (Potential).				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(9)|skin(5)|upper_aerodigestive_tract(2)|pancreas(2)	18						AGCAGCTCCTAAAGGTACTAT	0.383													14	84	---	---	---	---	PASS
CLGN	1047	broad.mit.edu	37	4	141320055	141320055	+	Nonsense_Mutation	SNP	C	T	T			TCGA-43-6647-01	TCGA-43-6647-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:141320055C>T	uc011chi.1	-	9	1052	c.834G>A	c.(832-834)TGG>TGA	p.W278*	CLGN_uc003iii.2_Nonsense_Mutation_p.W278*	NM_001130675	NP_001124147	O14967	CLGN_HUMAN	calmegin precursor	278	Lumenal (Potential).|1-1.				protein folding	endoplasmic reticulum membrane|integral to membrane	calcium ion binding|unfolded protein binding			ovary(2)|skin(1)	3	all_hematologic(180;0.162)					CTCTTTCATCCCATTCCTCAG	0.363													10	258	---	---	---	---	PASS
ARHGAP10	79658	broad.mit.edu	37	4	148876465	148876465	+	Splice_Site	SNP	A	G	G			TCGA-43-6647-01	TCGA-43-6647-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:148876465A>G	uc003ilf.2	+	16	1392	c.1392_splice	c.e16-2	p.R464_splice	ARHGAP10_uc003ilg.2_Splice_Site_p.R113_splice|ARHGAP10_uc003ilh.2_Splice_Site_p.R45_splice	NM_024605	NP_078881	A1A4S6	RHG10_HUMAN	Rho GTPase activating protein 10						apoptosis|filopodium assembly|regulation of apoptosis|small GTPase mediated signal transduction	cytosol|perinuclear region of cytoplasm|plasma membrane	cytoskeletal adaptor activity|SH3 domain binding			skin(2)|pancreas(1)|lung(1)	4	all_hematologic(180;0.151)	Renal(17;0.0166)		GBM - Glioblastoma multiforme(119;0.0423)		CTTTTCACACAGGAGTCTTCC	0.328													21	411	---	---	---	---	PASS
OXCT1	5019	broad.mit.edu	37	5	41739487	41739487	+	Intron	SNP	C	A	A			TCGA-43-6647-01	TCGA-43-6647-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:41739487C>A	uc003jmn.2	-						OXCT1_uc011cpo.1_Intron|OXCT1_uc011cpp.1_Intron	NM_000436	NP_000427	P55809	SCOT1_HUMAN	3-oxoacid CoA transferase 1 precursor						cellular lipid metabolic process|ketone body catabolic process	mitochondrial matrix	3-oxoacid CoA-transferase activity|protein homodimerization activity			ovary(2)|large_intestine(1)	3					Succinic acid(DB00139)	CACAGAAATACTTACTGCAAA	0.398													9	113	---	---	---	---	PASS
PDE4D	5144	broad.mit.edu	37	5	58285714	58285714	+	Silent	SNP	T	A	A			TCGA-43-6647-01	TCGA-43-6647-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:58285714T>A	uc003jsa.2	-	10	1492	c.1320A>T	c.(1318-1320)CCA>CCT	p.P440P	PDE4D_uc003jrx.2_Silent_p.P304P|PDE4D_uc003jry.2_Silent_p.P138P|PDE4D_uc003jrz.2_Silent_p.P376P|PDE4D_uc003jsb.2_Silent_p.P379P|PDE4D_uc003jrt.2_Silent_p.P138P|PDE4D_uc003jru.2_Silent_p.P216P|PDE4D_uc003jrv.2_Silent_p.P310P|PDE4D_uc003jrw.2_Silent_p.P318P|PDE4D_uc003jrs.2_Silent_p.P149P	NM_001104631	NP_001098101	Q08499	PDE4D_HUMAN	phosphodiesterase 4D isoform 1	440					signal transduction	cytosol|insoluble fraction|membrane|microtubule organizing center|soluble fraction	3',5'-cyclic-AMP phosphodiesterase activity|metal ion binding			breast(1)|central_nervous_system(1)	2		all_cancers(5;6.5e-58)|all_epithelial(5;1.75e-57)|all_lung(5;6.84e-18)|Lung NSC(5;1.29e-17)|Melanoma(5;0.00168)|Prostate(74;0.00234)|Colorectal(97;0.00629)|Ovarian(174;0.00832)|Breast(144;0.00996)|all_hematologic(6;0.0344)|Hepatocellular(6;0.0742)|Esophageal squamous(6;0.0954)		Epithelial(2;2.6e-55)|all cancers(2;2.66e-49)|OV - Ovarian serous cystadenocarcinoma(10;1.48e-39)|Colorectal(2;8.29e-08)|Lung(2;4.47e-07)|STAD - Stomach adenocarcinoma(2;1.11e-05)|COAD - Colon adenocarcinoma(2;0.00012)|LUSC - Lung squamous cell carcinoma(2;0.000775)|LUAD - Lung adenocarcinoma(3;0.0173)|READ - Rectum adenocarcinoma(2;0.0276)	Adenosine monophosphate(DB00131)|Dyphylline(DB00651)	AAGTATCTACTGGAATTTTAA	0.318													10	61	---	---	---	---	PASS
F2R	2149	broad.mit.edu	37	5	76012388	76012388	+	Intron	SNP	G	C	C			TCGA-43-6647-01	TCGA-43-6647-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:76012388G>C	uc003ken.3	+							NM_001992	NP_001983	P25116	PAR1_HUMAN	coagulation factor II receptor precursor						activation of caspase activity|anatomical structure morphogenesis|connective tissue replacement involved in inflammatory response wound healing|negative regulation of cell proliferation|platelet activation|positive regulation of blood coagulation|positive regulation of cell migration|positive regulation of collagen biosynthetic process|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of JAK-STAT cascade|positive regulation of MAPKKK cascade|positive regulation of release of sequestered calcium ion into cytosol|positive regulation of transcription, DNA-dependent|STAT protein import into nucleus|tyrosine phosphorylation of STAT protein	caveola|extracellular region|Golgi apparatus|integral to plasma membrane|platelet dense tubular network	receptor binding|thrombin receptor activity			ovary(3)	3		all_lung(232;0.000414)|Lung NSC(167;0.0011)|Prostate(461;0.00955)|Ovarian(174;0.0129)		all cancers(79;4.43e-43)	Streptokinase(DB00086)	GGTGGGGCGTGCCACCCCCTT	0.612													2	4	---	---	---	---	PASS
TGFBI	7045	broad.mit.edu	37	5	135390435	135390435	+	Missense_Mutation	SNP	G	C	C			TCGA-43-6647-01	TCGA-43-6647-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:135390435G>C	uc003lbf.3	+	10	1456	c.1295G>C	c.(1294-1296)AGG>ACG	p.R432T	TGFBI_uc003lbg.3_Missense_Mutation_p.R165T|TGFBI_uc003lbh.3_Missense_Mutation_p.R258T|TGFBI_uc011cyb.1_Missense_Mutation_p.R258T|TGFBI_uc010jed.2_Missense_Mutation_p.R165T	NM_000358	NP_000349	Q15582	BGH3_HUMAN	transforming growth factor, beta-induced, 68kDa	432	FAS1 3.				angiogenesis|cell adhesion|cell proliferation|negative regulation of cell adhesion|response to stimulus|visual perception	extracellular space|proteinaceous extracellular matrix	integrin binding			breast(3)|ovary(1)	4			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)			GCCCATACAAGGAATTTGCTT	0.458													46	314	---	---	---	---	PASS
PCDHA8	56140	broad.mit.edu	37	5	140221414	140221414	+	Missense_Mutation	SNP	T	G	G			TCGA-43-6647-01	TCGA-43-6647-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140221414T>G	uc003lhs.2	+	1	508	c.508T>G	c.(508-510)TAC>GAC	p.Y170D	PCDHA1_uc003lha.2_Intron|PCDHA1_uc003lhb.2_Intron|PCDHA2_uc003lhd.2_Intron|PCDHA3_uc003lhf.2_Intron|PCDHA4_uc003lhi.2_Intron|PCDHA4_uc003lhh.1_Intron|PCDHA5_uc003lhk.1_Intron|PCDHA5_uc003lhl.2_Intron|PCDHA6_uc003lhn.2_Intron|PCDHA6_uc003lho.2_Intron|PCDHA7_uc003lhq.2_Intron|PCDHA8_uc003lhr.1_Missense_Mutation_p.Y170D	NM_018911	NP_061734	Q9Y5H6	PCDA8_HUMAN	protocadherin alpha 8 isoform 1 precursor	170	Cadherin 2.|Extracellular (Potential).				homophilic cell adhesion|nervous system development	integral to plasma membrane	calcium ion binding|protein binding			upper_aerodigestive_tract(1)|ovary(1)	2			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CGTGTTAACCTACAGGCTTAG	0.443													8	99	---	---	---	---	PASS
DOCK2	1794	broad.mit.edu	37	5	169507178	169507178	+	Silent	SNP	G	A	A			TCGA-43-6647-01	TCGA-43-6647-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:169507178G>A	uc003maf.2	+	50	5258	c.5178G>A	c.(5176-5178)AAG>AAA	p.K1726K	DOCK2_uc011der.1_RNA|DOCK2_uc010jjm.2_Silent_p.K1218K|DOCK2_uc003mah.2_Silent_p.K282K	NM_004946	NP_004937	Q92608	DOCK2_HUMAN	dedicator of cytokinesis 2	1726					actin cytoskeleton organization|regulation of defense response to virus by virus|viral reproduction	cytoskeleton|cytosol|endomembrane system|membrane	electron carrier activity|GTP binding|GTPase binding|heme binding|Rac guanyl-nucleotide exchange factor activity|T cell receptor binding			ovary(5)|pancreas(2)	7	Renal(175;0.000159)|Lung NSC(126;0.0221)|all_lung(126;0.0337)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			TTTCCAGGAAGCATGAGTTCA	0.527													4	65	---	---	---	---	PASS
BTNL8	79908	broad.mit.edu	37	5	180376262	180376262	+	Missense_Mutation	SNP	G	A	A			TCGA-43-6647-01	TCGA-43-6647-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:180376262G>A	uc003mmp.2	+	7	1093	c.859G>A	c.(859-861)GCA>ACA	p.A287T	BTNL8_uc003mmq.2_Missense_Mutation_p.R330H|BTNL8_uc011dhg.1_Missense_Mutation_p.A162T|BTNL8_uc010jll.2_Missense_Mutation_p.R323H|BTNL8_uc010jlm.2_Missense_Mutation_p.A171T|BTNL8_uc011dhh.1_Missense_Mutation_p.A103T	NM_001040462	NP_001035552	Q6UX41	BTNL8_HUMAN	butyrophilin-like 8 isoform 2 precursor	287	B30.2/SPRY.|Cytoplasmic (Potential).					integral to membrane				upper_aerodigestive_tract(1)|skin(1)	2	all_cancers(89;3.37e-05)|all_epithelial(37;3.77e-06)|Renal(175;0.000159)|Lung NSC(126;0.00211)|all_lung(126;0.00371)|Breast(19;0.114)	all_cancers(40;0.0801)|Medulloblastoma(196;0.0392)|all_neural(177;0.0529)|all_hematologic(541;0.191)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			CCGGAAACACGCAGGTACCAA	0.557													10	31	---	---	---	---	PASS
BTN1A1	696	broad.mit.edu	37	6	26505289	26505289	+	Silent	SNP	A	T	T			TCGA-43-6647-01	TCGA-43-6647-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:26505289A>T	uc003nif.3	+	3	584	c.564A>T	c.(562-564)ACA>ACT	p.T188T		NM_001732	NP_001723	Q13410	BT1A1_HUMAN	butyrophilin, subfamily 1, member A1 precursor	188	Extracellular (Potential).|Ig-like V-type 2.					extracellular region|integral to plasma membrane	receptor activity			ovary(1)|skin(1)	2						TTCCATCTACATCAGAGTCCA	0.488													6	75	---	---	---	---	PASS
MUC21	394263	broad.mit.edu	37	6	30955950	30955950	+	Silent	SNP	C	T	T			TCGA-43-6647-01	TCGA-43-6647-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:30955950C>T	uc003nsh.2	+	3	1931	c.1680C>T	c.(1678-1680)AGC>AGT	p.S560S	MUC21_uc003nsi.1_RNA	NM_001010909	NP_001010909	Q5SSG8	MUC21_HUMAN	mucin 21 precursor	560	Cytoplasmic (Potential).|Cytoplasmic tail.					integral to membrane|plasma membrane				ovary(1)|skin(1)	2						TGGAGATGAGCGGGAGGAACA	0.597													6	39	---	---	---	---	PASS
SKIV2L	6499	broad.mit.edu	37	6	31937189	31937189	+	Missense_Mutation	SNP	C	T	T			TCGA-43-6647-01	TCGA-43-6647-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:31937189C>T	uc003nyn.1	+	27	3921	c.3532C>T	c.(3532-3534)CGG>TGG	p.R1178W	SKIV2L_uc011dou.1_Missense_Mutation_p.R1020W|SKIV2L_uc011dov.1_Missense_Mutation_p.R985W|STK19_uc003nyt.2_5'Flank|STK19_uc011dow.1_5'Flank|STK19_uc011dox.1_5'Flank|STK19_uc003nyv.2_5'Flank|STK19_uc003nyw.2_5'Flank|STK19_uc010jtn.1_5'Flank	NM_006929	NP_008860	Q15477	SKIV2_HUMAN	superkiller viralicidic activity 2-like homolog	1178						nucleus	ATP binding|ATP-dependent RNA helicase activity|protein binding|RNA binding			ovary(1)|large_intestine(1)|breast(1)|central_nervous_system(1)	4						TGAGTGGGCCCGGGGCATGGT	0.577													3	47	---	---	---	---	PASS
DNAH8	1769	broad.mit.edu	37	6	38690769	38690769	+	5'UTR	SNP	C	A	A			TCGA-43-6647-01	TCGA-43-6647-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:38690769C>A	uc003ooe.1	+	1					DNAH8_uc003ood.1_Silent_p.R62R	NM_001371	NP_001362			dynein, axonemal, heavy polypeptide 8											skin(8)|ovary(7)|lung(2)|large_intestine(1)|central_nervous_system(1)|kidney(1)|pancreas(1)	21						GGTGGATTATCGGGATCTCAT	0.537													6	49	---	---	---	---	PASS
PGK2	5232	broad.mit.edu	37	6	49754268	49754268	+	Silent	SNP	T	A	A			TCGA-43-6647-01	TCGA-43-6647-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:49754268T>A	uc003ozu.2	-	1	740	c.633A>T	c.(631-633)ATA>ATT	p.I211I		NM_138733	NP_620061	P07205	PGK2_HUMAN	phosphoglycerate kinase 2	211					glycolysis	cytosol	ATP binding|phosphoglycerate kinase activity			ovary(1)	1	Lung NSC(77;0.0402)					CTCCACCAAGTATAGCCAGAA	0.428													12	159	---	---	---	---	PASS
CASP8AP2	9994	broad.mit.edu	37	6	90571877	90571877	+	Missense_Mutation	SNP	A	G	G			TCGA-43-6647-01	TCGA-43-6647-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:90571877A>G	uc003pnr.2	+	7	645	c.449A>G	c.(448-450)CAT>CGT	p.H150R	CASP8AP2_uc003pns.2_Intron|CASP8AP2_uc003pnt.2_Missense_Mutation_p.H150R|CASP8AP2_uc011dzz.1_Missense_Mutation_p.H150R	NM_001137667	NP_001131139	Q9UKL3	C8AP2_HUMAN	caspase 8 associated protein 2	150					cell cycle|cellular response to mechanical stimulus|induction of apoptosis via death domain receptors|regulation of transcription, DNA-dependent|signal transduction|transcription, DNA-dependent	cytoplasm|nucleus	caspase activator activity|death receptor binding|transcription corepressor activity			ovary(2)	2		all_cancers(76;3.64e-09)|Prostate(29;1.16e-10)|Acute lymphoblastic leukemia(125;1.45e-10)|all_hematologic(105;7.74e-07)|all_epithelial(107;4.69e-05)|Lung NSC(302;0.238)		BRCA - Breast invasive adenocarcinoma(108;0.0953)		CGAAATAATCATAAAACTGCA	0.269													6	42	---	---	---	---	PASS
FRK	2444	broad.mit.edu	37	6	116289818	116289818	+	Nonsense_Mutation	SNP	G	T	T			TCGA-43-6647-01	TCGA-43-6647-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:116289818G>T	uc003pwi.1	-	3	998	c.551C>A	c.(550-552)TCA>TAA	p.S184*		NM_002031	NP_002022	P42685	FRK_HUMAN	fyn-related kinase	184	SH2.				negative regulation of cell proliferation	cytoplasm|nucleus	ATP binding|non-membrane spanning protein tyrosine kinase activity|protein binding			ovary(3)|lung(3)	6		all_cancers(87;0.00559)|all_epithelial(87;0.00738)|Colorectal(196;0.0465)		all cancers(137;0.0128)|OV - Ovarian serous cystadenocarcinoma(136;0.0209)|GBM - Glioblastoma multiforme(226;0.0459)|Epithelial(106;0.0625)		GTTCAGTGTTGAAAAGATTCT	0.413													27	151	---	---	---	---	PASS
SAMD3	154075	broad.mit.edu	37	6	130530728	130530728	+	Missense_Mutation	SNP	G	C	C			TCGA-43-6647-01	TCGA-43-6647-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:130530728G>C	uc003qbv.2	-	6	621	c.295C>G	c.(295-297)CCA>GCA	p.P99A	SAMD3_uc003qbx.2_Missense_Mutation_p.P99A|SAMD3_uc003qbw.2_Missense_Mutation_p.P99A|SAMD3_uc010kfg.1_Missense_Mutation_p.P99A|SAMD3_uc003qby.2_Missense_Mutation_p.P99A|SAMD3_uc003qbz.1_Missense_Mutation_p.P58A	NM_001017373	NP_001017373	Q8N6K7	SAMD3_HUMAN	sterile alpha motif domain containing 3 isoform	99										ovary(1)	1				GBM - Glioblastoma multiforme(226;0.00594)|OV - Ovarian serous cystadenocarcinoma(155;0.128)		TGCCTGGCTGGACTGGAGGAC	0.468													12	69	---	---	---	---	PASS
GRM1	2911	broad.mit.edu	37	6	146625878	146625878	+	Missense_Mutation	SNP	C	G	G			TCGA-43-6647-01	TCGA-43-6647-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:146625878C>G	uc010khw.1	+	4	1552	c.1082C>G	c.(1081-1083)ACT>AGT	p.T361S	GRM1_uc010khv.1_Missense_Mutation_p.T361S|GRM1_uc003qll.2_Missense_Mutation_p.T361S|GRM1_uc011edz.1_Missense_Mutation_p.T361S|GRM1_uc011eea.1_Missense_Mutation_p.T361S	NM_000838	NP_000829	Q13255	GRM1_HUMAN	glutamate receptor, metabotropic 1 isoform alpha	361	Extracellular (Potential).				synaptic transmission	integral to plasma membrane	G-protein coupled receptor activity|glutamate receptor activity			lung(8)|ovary(4)|central_nervous_system(3)|large_intestine(2)|breast(2)	19		Ovarian(120;0.0387)		OV - Ovarian serous cystadenocarcinoma(155;5.35e-08)|GBM - Glioblastoma multiforme(68;0.00762)	Acamprosate(DB00659)|L-Glutamic Acid(DB00142)	AGGCTGGACACTAACACGAGG	0.498													13	85	---	---	---	---	PASS
C6orf118	168090	broad.mit.edu	37	6	165711504	165711504	+	Silent	SNP	G	A	A			TCGA-43-6647-01	TCGA-43-6647-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:165711504G>A	uc003qum.3	-	5	1059	c.1023C>T	c.(1021-1023)CTC>CTT	p.L341L	C6orf118_uc011egi.1_RNA	NM_144980	NP_659417	Q5T5N4	CF118_HUMAN	hypothetical protein LOC168090	341											0		Breast(66;6.27e-05)|Ovarian(120;0.0228)|Prostate(117;0.0906)|all_neural(5;0.157)		OV - Ovarian serous cystadenocarcinoma(33;3.23e-18)|BRCA - Breast invasive adenocarcinoma(81;3.11e-06)|GBM - Glioblastoma multiforme(31;0.000313)		TGGCTGTCACGAGCATCCTCA	0.562													19	127	---	---	---	---	PASS
PMS2	5395	broad.mit.edu	37	7	6038907	6038907	+	Splice_Site	SNP	C	A	A			TCGA-43-6647-01	TCGA-43-6647-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:6038907C>A	uc003spl.2	-	6	625	c.538_splice	c.e6-1	p.E180_splice	PMS2_uc003spj.2_Splice_Site_p.E74_splice|PMS2_uc003spk.2_Splice_Site_p.E45_splice|PMS2_uc011jwl.1_Splice_Site_p.E45_splice|PMS2_uc010ktg.2_Intron|PMS2_uc010kte.2_Splice_Site_p.E180_splice|PMS2_uc010ktf.1_Splice_Site_p.E180_splice	NM_000535	NP_000526	P54278	PMS2_HUMAN	PMS2 postmeiotic segregation increased 2 isoform						mismatch repair|reciprocal meiotic recombination|somatic hypermutation of immunoglobulin genes	MutLalpha complex	ATP binding|ATPase activity|endonuclease activity|protein binding|single base insertion or deletion binding			lung(1)|central_nervous_system(1)	2		Ovarian(82;0.0694)		UCEC - Uterine corpus endometrioid carcinoma (126;0.101)|OV - Ovarian serous cystadenocarcinoma(56;4.39e-15)		TGGCATACTCCTGTTTAAAAA	0.393			Mis|N|F			colorectal|endometrial|ovarian|medulloblastoma|glioma		Direct_reversal_of_damage|MMR	Lynch_syndrome|Turcot_syndrome|Constitutional_Mismatch_Repair_Deficiency_Syndrome				5	61	---	---	---	---	PASS
ABCA13	154664	broad.mit.edu	37	7	48550793	48550793	+	Missense_Mutation	SNP	C	A	A			TCGA-43-6647-01	TCGA-43-6647-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:48550793C>A	uc003toq.2	+	51	13663	c.13638C>A	c.(13636-13638)TTC>TTA	p.F4546L	ABCA13_uc010kys.1_Missense_Mutation_p.F1621L|ABCA13_uc010kyt.1_RNA|ABCA13_uc010kyu.1_Missense_Mutation_p.F276L	NM_152701	NP_689914	Q86UQ4	ABCAD_HUMAN	ATP binding cassette, sub-family A (ABC1),	4546	Helical; (Potential).				transport	integral to membrane	ATP binding|ATPase activity			ovary(5)|central_nervous_system(4)|skin(1)	10						TGTCACTTTTCGGGTATGTGA	0.483													3	67	---	---	---	---	PASS
LANCL2	55915	broad.mit.edu	37	7	55493059	55493059	+	Missense_Mutation	SNP	G	A	A			TCGA-43-6647-01	TCGA-43-6647-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:55493059G>A	uc003tqp.2	+	7	1699	c.1121G>A	c.(1120-1122)GGC>GAC	p.G374D		NM_018697	NP_061167	Q9NS86	LANC2_HUMAN	LanC lantibiotic synthetase component C-like 2	374					negative regulation of transcription, DNA-dependent|positive regulation of abscisic acid mediated signaling pathway	cortical actin cytoskeleton|cytosol|nucleus|plasma membrane	ATP binding|catalytic activity|GTP binding|phosphatidylinositol-3-phosphate binding|phosphatidylinositol-4-phosphate binding|phosphatidylinositol-5-phosphate binding			ovary(1)|skin(1)	2	Breast(14;0.0379)		Lung(13;4.65e-05)|LUSC - Lung squamous cell carcinoma(13;0.000168)|STAD - Stomach adenocarcinoma(5;0.00128)|Epithelial(13;0.0706)			GCTGGCAACGGCTATTCCTTC	0.532													4	117	---	---	---	---	PASS
POM121C	100101267	broad.mit.edu	37	7	75051114	75051114	+	Silent	SNP	G	A	A			TCGA-43-6647-01	TCGA-43-6647-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:75051114G>A	uc003udk.3	-	13	3306	c.2421C>T	c.(2419-2421)ACC>ACT	p.T807T		NM_001099415	NP_001092885	A8CG34	P121C_HUMAN	POM121 membrane glycoprotein (rat)-like	1049	Pore side (Potential).				mRNA transport|protein transport|transmembrane transport	endoplasmic reticulum membrane|nuclear membrane|nuclear pore	protein binding				0						AGCCGGAGCTGGTGGCTGCAC	0.647													6	87	---	---	---	---	PASS
CACNA2D1	781	broad.mit.edu	37	7	81714198	81714198	+	Missense_Mutation	SNP	T	G	G			TCGA-43-6647-01	TCGA-43-6647-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:81714198T>G	uc003uhr.1	-	7	801	c.545A>C	c.(544-546)GAA>GCA	p.E182A		NM_000722	NP_000713	P54289	CA2D1_HUMAN	calcium channel, voltage-dependent, alpha	182	Extracellular (Potential).					voltage-gated calcium channel complex	metal ion binding			ovary(5)|pancreas(1)	6					Felodipine(DB01023)|Gabapentin(DB00996)|Ibutilide(DB00308)|Isradipine(DB00270)|Magnesium Sulfate(DB00653)|Nifedipine(DB01115)	CCAGTTGAGTTCATTTAACAC	0.328													9	74	---	---	---	---	PASS
GRM3	2913	broad.mit.edu	37	7	86415818	86415818	+	Missense_Mutation	SNP	G	C	C			TCGA-43-6647-01	TCGA-43-6647-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:86415818G>C	uc003uid.2	+	3	1809	c.710G>C	c.(709-711)CGC>CCC	p.R237P	GRM3_uc010lef.2_Missense_Mutation_p.R235P|GRM3_uc010leg.2_Missense_Mutation_p.R109P|GRM3_uc010leh.2_Intron	NM_000840	NP_000831	Q14832	GRM3_HUMAN	glutamate receptor, metabotropic 3 precursor	237	Extracellular (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)	GCCCGCCTGCGCAACATCTGC	0.607													8	61	---	---	---	---	PASS
ABCB4	5244	broad.mit.edu	37	7	87072693	87072693	+	Missense_Mutation	SNP	C	T	T			TCGA-43-6647-01	TCGA-43-6647-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:87072693C>T	uc003uiv.1	-	12	1374	c.1298G>A	c.(1297-1299)TGT>TAT	p.C433Y	ABCB4_uc003uiw.1_Missense_Mutation_p.C433Y|ABCB4_uc003uix.1_Missense_Mutation_p.C433Y	NM_018849	NP_061337	P21439	MDR3_HUMAN	ATP-binding cassette, subfamily B, member 4	433	ABC transporter 1.|Cytoplasmic (By similarity).|ATP 1 (By similarity).				cellular lipid metabolic process	apical plasma membrane|Golgi membrane|integral to plasma membrane|intercellular canaliculus|membrane fraction	ATP binding|xenobiotic-transporting ATPase activity			ovary(4)|skin(1)|pancreas(1)	6	Esophageal squamous(14;0.0058)|all_lung(186;0.201)|Lung NSC(181;0.203)					GCTCTTCCCACAGCCACTACT	0.517													43	183	---	---	---	---	PASS
SLC25A40	55972	broad.mit.edu	37	7	87476448	87476448	+	Intron	SNP	C	A	A			TCGA-43-6647-01	TCGA-43-6647-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:87476448C>A	uc003uje.2	-							NM_018843	NP_061331	Q8TBP6	S2540_HUMAN	mitochondrial carrier family protein						transmembrane transport	integral to membrane|mitochondrial inner membrane	binding			haematopoietic_and_lymphoid_tissue(1)	1	Esophageal squamous(14;0.00202)					CTAATACAAACAAGTTAAAAA	0.294													18	135	---	---	---	---	PASS
BET1	10282	broad.mit.edu	37	7	93623548	93623548	+	Silent	SNP	C	A	A			TCGA-43-6647-01	TCGA-43-6647-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:93623548C>A	uc003unf.1	-	4	513	c.351G>T	c.(349-351)CTG>CTT	p.L117L	BET1_uc003une.3_Intron	NM_005868	NP_005859	O15155	BET1_HUMAN	blocked early in transport 1	117	Vesicular (Potential).				ER to Golgi vesicle-mediated transport|protein transport	endoplasmic reticulum membrane|Golgi membrane|integral to membrane	protein binding				0	all_cancers(62;2.22e-10)|all_epithelial(64;1.38e-09)|Lung NSC(181;0.218)	Breast(660;0.000162)|Ovarian(593;0.000626)	STAD - Stomach adenocarcinoma(171;0.000967)			TGCATCACCTCAGTTTAATAA	0.328													7	37	---	---	---	---	PASS
CUX1	1523	broad.mit.edu	37	7	101882815	101882815	+	Missense_Mutation	SNP	C	A	A			TCGA-43-6647-01	TCGA-43-6647-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:101882815C>A	uc003uyx.3	+	23	3876	c.3838C>A	c.(3838-3840)CAG>AAG	p.Q1280K	CUX1_uc003uys.3_Missense_Mutation_p.Q1291K|CUX1_uc003uyt.2_Intron|CUX1_uc011kkn.1_Intron|CUX1_uc003uyw.2_Intron|CUX1_uc003uyv.2_Intron|CUX1_uc003uyu.2_Intron	NM_181552	NP_853530	P39880	CUX1_HUMAN	cut-like homeobox 1 isoform a	1280	Homeobox.				negative regulation of transcription from RNA polymerase II promoter	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			ovary(5)|pancreas(1)|central_nervous_system(1)|skin(1)	8						CCTCGCCACCCAGCTCAACCT	0.612													14	59	---	---	---	---	PASS
LAMB4	22798	broad.mit.edu	37	7	107692543	107692543	+	Silent	SNP	C	T	T			TCGA-43-6647-01	TCGA-43-6647-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:107692543C>T	uc010ljo.1	-	26	3999	c.3915G>A	c.(3913-3915)GCG>GCA	p.A1305A	LAMB4_uc003vey.2_Silent_p.A1305A|LAMB4_uc010ljp.1_Silent_p.A274A	NM_007356	NP_031382	A4D0S4	LAMB4_HUMAN	laminin, beta 4 precursor	1305	Domain II.				cell adhesion	basement membrane				ovary(4)|breast(2)|large_intestine(1)|skin(1)	8						TTCCCTTACCCGCAATGCTTG	0.408													25	123	---	---	---	---	PASS
SLC13A1	6561	broad.mit.edu	37	7	122759214	122759214	+	Missense_Mutation	SNP	G	C	C			TCGA-43-6647-01	TCGA-43-6647-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:122759214G>C	uc003vkm.2	-	13	1458	c.1433C>G	c.(1432-1434)TCT>TGT	p.S478C	SLC13A1_uc010lks.2_Missense_Mutation_p.S354C	NM_022444	NP_071889	Q9BZW2	S13A1_HUMAN	solute carrier family 13 (sodium/sulfate	478	Helical; (Potential).					integral to membrane|plasma membrane	sodium:sulfate symporter activity			ovary(2)	2					Succinic acid(DB00139)	CACCATCAAAGAAGATATCAG	0.373													18	75	---	---	---	---	PASS
CASP2	835	broad.mit.edu	37	7	142985626	142985626	+	Intron	SNP	A	T	T			TCGA-43-6647-01	TCGA-43-6647-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:142985626A>T	uc003wco.2	+						CASP2_uc003wcp.2_Intron|CASP2_uc011kta.1_Intron|CASP2_uc003wcq.2_5'Flank	NM_032982	NP_116764	P42575	CASP2_HUMAN	caspase 2 isoform 1 preproprotein						apoptosis|cellular response to mechanical stimulus|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|protein maturation by peptide bond cleavage	cytosol	cysteine-type endopeptidase activity|enzyme binding|protein binding|protein domain specific binding			lung(2)|ovary(1)	3	Melanoma(164;0.059)					GACGCAGGTAAGTAGGGAACG	0.692													6	36	---	---	---	---	PASS
DUSP4	1846	broad.mit.edu	37	8	29194783	29194783	+	Missense_Mutation	SNP	G	T	T			TCGA-43-6647-01	TCGA-43-6647-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:29194783G>T	uc003xhm.2	-	4	1335	c.945C>A	c.(943-945)AGC>AGA	p.S315R	DUSP4_uc003xhl.2_Missense_Mutation_p.S224R	NM_001394	NP_001385	Q13115	DUS4_HUMAN	dual specificity phosphatase 4 isoform 1	315	Tyrosine-protein phosphatase.				endoderm formation|inactivation of MAPK activity|innate immune response|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|nerve growth factor receptor signaling pathway|stress-activated MAPK cascade|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway	nucleoplasm	MAP kinase tyrosine/serine/threonine phosphatase activity|protein tyrosine phosphatase activity|protein tyrosine/threonine phosphatase activity	p.S315S(1)		lung(1)	1				KIRC - Kidney renal clear cell carcinoma(542;0.094)|Kidney(114;0.113)		GCGAGATGATGCTGCGGCGCT	0.637													3	63	---	---	---	---	PASS
ZBTB10	65986	broad.mit.edu	37	8	81412419	81412419	+	Missense_Mutation	SNP	A	G	G			TCGA-43-6647-01	TCGA-43-6647-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:81412419A>G	uc003ybx.3	+	2	2261	c.1663A>G	c.(1663-1665)ACA>GCA	p.T555A	ZBTB10_uc003ybv.3_Missense_Mutation_p.T263A|ZBTB10_uc003ybw.3_Missense_Mutation_p.T555A|ZBTB10_uc010lzt.2_Missense_Mutation_p.T555A	NM_001105539	NP_001099009	Q96DT7	ZBT10_HUMAN	zinc finger and BTB domain containing 10 isoform	555					transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			lung(1)	1	all_cancers(3;1.68e-09)|all_epithelial(4;5.13e-11)|Lung NSC(7;1.75e-07)|all_lung(9;7.38e-07)|Breast(3;2.96e-06)		BRCA - Breast invasive adenocarcinoma(6;0.000434)|Epithelial(68;0.00486)|all cancers(69;0.0296)			TGAAGGTCAAACAAAAGTGTT	0.368													3	29	---	---	---	---	PASS
ZFPM2	23414	broad.mit.edu	37	8	106815541	106815541	+	Silent	SNP	G	T	T			TCGA-43-6647-01	TCGA-43-6647-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:106815541G>T	uc003ymd.2	+	8	3254	c.3231G>T	c.(3229-3231)TCG>TCT	p.S1077S	ZFPM2_uc011lhs.1_Silent_p.S808S	NM_012082	NP_036214	Q8WW38	FOG2_HUMAN	zinc finger protein, multitype 2	1077					blood coagulation|negative regulation of fat cell differentiation|outflow tract septum morphogenesis|right ventricular cardiac muscle tissue morphogenesis|ventricular septum morphogenesis	nucleoplasm	DNA binding|RNA polymerase II transcription coactivator activity|transcription corepressor activity|transcription factor binding|zinc ion binding			ovary(4)|large_intestine(1)	5			OV - Ovarian serous cystadenocarcinoma(57;8.28e-08)			AATCTCCCTCGTGGATCTCTG	0.478													7	36	---	---	---	---	PASS
FER1L6	654463	broad.mit.edu	37	8	125052256	125052256	+	Intron	SNP	G	A	A			TCGA-43-6647-01	TCGA-43-6647-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:125052256G>A	uc003yqw.2	+						uc003yqx.1_Intron	NM_001039112	NP_001034201	Q2WGJ9	FR1L6_HUMAN	fer-1-like 6							integral to membrane				ovary(5)|skin(5)|central_nervous_system(1)	11	Lung NSC(37;4.1e-12)|Ovarian(258;0.00438)|all_neural(195;0.0741)		STAD - Stomach adenocarcinoma(47;0.00186)			AGGTAACCAGGGTAACCAAGA	0.517													14	70	---	---	---	---	PASS
LRRC14	9684	broad.mit.edu	37	8	145745252	145745252	+	Missense_Mutation	SNP	G	A	A			TCGA-43-6647-01	TCGA-43-6647-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:145745252G>A	uc003zdk.1	+	2	289	c.143G>A	c.(142-144)CGC>CAC	p.R48H	RECQL4_uc003zdj.2_5'Flank|LRRC14_uc003zdl.1_Missense_Mutation_p.R48H|LRRC14_uc003zdo.2_5'Flank	NM_014665	NP_055480	Q15048	LRC14_HUMAN	leucine rich repeat containing 14	48											0	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)			GTGGTACTGCGCGAGTTGGTA	0.637													14	97	---	---	---	---	PASS
OR13F1	138805	broad.mit.edu	37	9	107266678	107266678	+	Silent	SNP	G	T	T			TCGA-43-6647-01	TCGA-43-6647-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:107266678G>T	uc011lvm.1	+	1	135	c.135G>T	c.(133-135)CTG>CTT	p.L45L		NM_001004485	NP_001004485	Q8NGS4	O13F1_HUMAN	olfactory receptor, family 13, subfamily F,	45	Helical; Name=1; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			large_intestine(1)|ovary(1)|skin(1)	3						ACATTTTTCTGATCTCCATCA	0.468													22	132	---	---	---	---	PASS
OBP2B	29989	broad.mit.edu	37	9	136081733	136081733	+	Silent	SNP	C	T	T			TCGA-43-6647-01	TCGA-43-6647-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:136081733C>T	uc004ccz.2	-	5	501	c.459G>A	c.(457-459)TCG>TCA	p.S153S	OBP2B_uc010nad.2_RNA|OBP2B_uc011mcy.1_Silent_p.S85S	NM_014581	NP_055396	Q9NPH6	OBP2B_HUMAN	odorant binding protein 2B precursor	153					chemosensory behavior|sensory perception of smell	extracellular region	odorant binding|transporter activity				0				OV - Ovarian serous cystadenocarcinoma(145;3.41e-06)|Epithelial(140;1.88e-05)		TGTCCTCCTCCGAGAGTCCCT	0.582													7	90	---	---	---	---	PASS
DPP7	29952	broad.mit.edu	37	9	140006315	140006315	+	Intron	SNP	T	C	C			TCGA-43-6647-01	TCGA-43-6647-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:140006315T>C	uc004clh.2	-							NM_013379	NP_037511	Q9UHL4	DPP2_HUMAN	dipeptidyl peptidase 7 preproprotein							cytoplasmic membrane-bounded vesicle|extracellular region|lysosome	aminopeptidase activity|protein binding|serine-type peptidase activity				0	all_cancers(76;0.0926)		STAD - Stomach adenocarcinoma(284;0.0878)	OV - Ovarian serous cystadenocarcinoma(145;4.25e-05)|Epithelial(140;0.000633)		CCACCCCCCCTCAGCCTTACC	0.687													3	20	---	---	---	---	PASS
NDOR1	27158	broad.mit.edu	37	9	140110455	140110455	+	Missense_Mutation	SNP	T	C	C			TCGA-43-6647-01	TCGA-43-6647-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:140110455T>C	uc004clw.2	+	12	1651	c.1540T>C	c.(1540-1542)TTC>CTC	p.F514L	NDOR1_uc004clx.2_Missense_Mutation_p.F514L|NDOR1_uc011mes.1_Missense_Mutation_p.F507L|NDOR1_uc004cly.2_Missense_Mutation_p.F480L	NM_014434	NP_055249	Q9UHB4	NDOR1_HUMAN	NADPH dependent diflavin oxidoreductase 1	514					cell death	cytosol|intermediate filament cytoskeleton|nucleus|perinuclear region of cytoplasm	flavin adenine dinucleotide binding|FMN binding|iron ion binding|NADP binding|oxidoreductase activity|protein binding				0	all_cancers(76;0.0926)		STAD - Stomach adenocarcinoma(284;0.0698)	OV - Ovarian serous cystadenocarcinoma(145;6.37e-05)|Epithelial(140;0.00057)		CATCCCTGCCTTCTCCCGGGA	0.617													7	131	---	---	---	---	PASS
CALML5	51806	broad.mit.edu	37	10	5541037	5541037	+	Missense_Mutation	SNP	A	G	G			TCGA-43-6647-01	TCGA-43-6647-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:5541037A>G	uc001iic.2	-	1	497	c.365T>C	c.(364-366)ATG>ACG	p.M122T		NM_017422	NP_059118	Q9NZT1	CALL5_HUMAN	calmodulin-like 5	122	EF-hand 4.				epidermis development|signal transduction		calcium ion binding|protein binding				0						CTCGCGGATCATGGCGTCCAG	0.711													7	18	---	---	---	---	PASS
KIF5B	3799	broad.mit.edu	37	10	32320185	32320185	+	Missense_Mutation	SNP	T	C	C			TCGA-43-6647-01	TCGA-43-6647-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:32320185T>C	uc001iwe.3	-	14	1867	c.1397A>G	c.(1396-1398)GAT>GGT	p.D466G		NM_004521	NP_004512	P33176	KINH_HUMAN	kinesin family member 5B	466					stress granule disassembly|vesicle transport along microtubule	kinesin complex|microtubule|perinuclear region of cytoplasm|vesicle	ATP binding|microtubule binding|microtubule motor activity		KIF5B/ALK(4)	lung(4)|ovary(1)	5		Prostate(175;0.0137)				ATTGTCTTGATCCCTTCTGGT	0.383													3	37	---	---	---	---	PASS
PCDH15	65217	broad.mit.edu	37	10	55626456	55626456	+	Silent	SNP	T	C	C			TCGA-43-6647-01	TCGA-43-6647-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:55626456T>C	uc001jju.1	-	27	4058	c.3663A>G	c.(3661-3663)CAA>CAG	p.Q1221Q	PCDH15_uc010qhq.1_Silent_p.Q1226Q|PCDH15_uc010qhr.1_Silent_p.Q1221Q|PCDH15_uc010qhs.1_Silent_p.Q1233Q|PCDH15_uc010qht.1_Silent_p.Q1228Q|PCDH15_uc010qhu.1_Silent_p.Q1221Q|PCDH15_uc001jjv.1_Intron|PCDH15_uc010qhv.1_Silent_p.Q1221Q|PCDH15_uc010qhw.1_Silent_p.Q1184Q|PCDH15_uc010qhx.1_Silent_p.Q1150Q|PCDH15_uc010qhy.1_Silent_p.Q1226Q|PCDH15_uc010qhz.1_Silent_p.Q1221Q|PCDH15_uc010qia.1_Silent_p.Q1199Q|PCDH15_uc010qib.1_Silent_p.Q1199Q	NM_033056	NP_149045	Q96QU1	PCD15_HUMAN	protocadherin 15 isoform CD1-4 precursor	1221	Cadherin 11.|Extracellular (Potential).				equilibrioception|homophilic cell adhesion|photoreceptor cell maintenance|sensory perception of sound	extracellular region|extracellular space|integral to membrane|photoreceptor outer segment|plasma membrane|stereocilium|synapse	calcium ion binding			pancreas(5)|ovary(4)|upper_aerodigestive_tract(2)|skin(2)	13		Melanoma(3;0.117)|Lung SC(717;0.238)				TTGCAATAACTTGAAACTTGA	0.408										HNSCC(58;0.16)			3	66	---	---	---	---	PASS
C10orf35	219738	broad.mit.edu	37	10	71392747	71392747	+	Missense_Mutation	SNP	A	G	G			TCGA-43-6647-01	TCGA-43-6647-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:71392747A>G	uc001jpq.3	+	4	468	c.298A>G	c.(298-300)ATG>GTG	p.M100V		NM_145306	NP_660349	Q96D05	CJ035_HUMAN	hypothetical protein LOC219738	100	Helical; (Potential).					integral to membrane				ovary(1)|skin(1)	2						CCTGCTCATGATGCTTGGTGT	0.592													15	124	---	---	---	---	PASS
HTR7	3363	broad.mit.edu	37	10	92508999	92508999	+	Nonsense_Mutation	SNP	C	A	A			TCGA-43-6647-01	TCGA-43-6647-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:92508999C>A	uc001kha.2	-	2	1135	c.892G>T	c.(892-894)GAG>TAG	p.E298*	HTR7_uc001kgz.2_Nonsense_Mutation_p.E298*|HTR7_uc001khb.2_Nonsense_Mutation_p.E298*	NM_019859	NP_062873	P34969	5HT7R_HUMAN	5-hydroxytryptamine receptor 7 isoform d	298	Cytoplasmic (By similarity).				blood circulation|circadian rhythm	integral to plasma membrane	protein binding|serotonin receptor activity			ovary(1)	1					Eletriptan(DB00216)|Methysergide(DB00247)|Ziprasidone(DB00246)	TCTTCCACCTCCTTCTGGAGC	0.527													7	52	---	---	---	---	PASS
HTR7	3363	broad.mit.edu	37	10	92509000	92509000	+	Missense_Mutation	SNP	C	A	A			TCGA-43-6647-01	TCGA-43-6647-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:92509000C>A	uc001kha.2	-	2	1134	c.891G>T	c.(889-891)AAG>AAT	p.K297N	HTR7_uc001kgz.2_Missense_Mutation_p.K297N|HTR7_uc001khb.2_Missense_Mutation_p.K297N	NM_019859	NP_062873	P34969	5HT7R_HUMAN	5-hydroxytryptamine receptor 7 isoform d	297	Cytoplasmic (By similarity).				blood circulation|circadian rhythm	integral to plasma membrane	protein binding|serotonin receptor activity			ovary(1)	1					Eletriptan(DB00216)|Methysergide(DB00247)|Ziprasidone(DB00246)	CTTCCACCTCCTTCTGGAGCT	0.527													7	51	---	---	---	---	PASS
TNKS2	80351	broad.mit.edu	37	10	93600414	93600414	+	Missense_Mutation	SNP	G	T	T	rs143595087		TCGA-43-6647-01	TCGA-43-6647-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:93600414G>T	uc001khp.2	+	14	1921	c.1624G>T	c.(1624-1626)GTG>TTG	p.V542L		NM_025235	NP_079511	Q9H2K2	TNKS2_HUMAN	tankyrase, TRF1-interacting ankyrin-related	542	ANK 10.				positive regulation of canonical Wnt receptor signaling pathway|protein auto-ADP-ribosylation|protein localization to chromosome, telomeric region|protein polyubiquitination|Wnt receptor signaling pathway	Golgi membrane|microsome|nuclear envelope|pericentriolar material|perinuclear region of cytoplasm	NAD+ ADP-ribosyltransferase activity|protein binding			kidney(3)|skin(3)|ovary(1)|lung(1)	8		Colorectal(252;0.162)				AGTGTCCGTGGTGGAATATCT	0.433													21	101	---	---	---	---	PASS
TDRD1	56165	broad.mit.edu	37	10	115961240	115961240	+	Missense_Mutation	SNP	G	T	T			TCGA-43-6647-01	TCGA-43-6647-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:115961240G>T	uc001lbg.1	+	5	754	c.601G>T	c.(601-603)GCA>TCA	p.A201S	TDRD1_uc001lbf.2_Missense_Mutation_p.A192S|TDRD1_uc001lbh.1_Missense_Mutation_p.A192S|TDRD1_uc001lbi.1_Missense_Mutation_p.A192S|TDRD1_uc010qsc.1_5'Flank|TDRD1_uc001lbj.2_5'Flank	NM_198795	NP_942090	Q9BXT4	TDRD1_HUMAN	tudor domain containing 1	201	MYND-type.				DNA methylation involved in gamete generation|gene silencing by RNA|germ cell development|meiosis|multicellular organismal development|piRNA metabolic process|spermatogenesis	pi-body	nucleic acid binding|protein binding|zinc ion binding				0		Colorectal(252;0.172)|Breast(234;0.188)		Epithelial(162;0.0343)|all cancers(201;0.0754)		AGACTGGTCTGCACACAGCAT	0.428													12	116	---	---	---	---	PASS
DMBT1	1755	broad.mit.edu	37	10	124396774	124396774	+	Silent	SNP	G	C	C			TCGA-43-6647-01	TCGA-43-6647-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:124396774G>C	uc001lgk.1	+	51	6607	c.6501G>C	c.(6499-6501)ACG>ACC	p.T2167T	DMBT1_uc001lgl.1_Silent_p.T2157T|DMBT1_uc001lgm.1_Silent_p.T1539T|DMBT1_uc009xzz.1_Silent_p.T2166T|DMBT1_uc010qtx.1_Silent_p.T887T|DMBT1_uc009yab.1_Silent_p.T870T|DMBT1_uc009yac.1_Silent_p.T461T	NM_007329	NP_015568	Q9UGM3	DMBT1_HUMAN	deleted in malignant brain tumors 1 isoform b	2167	ZP.				epithelial cell differentiation|induction of bacterial agglutination|innate immune response|interspecies interaction between organisms|protein transport|response to virus	extrinsic to membrane|phagocytic vesicle membrane|zymogen granule membrane	calcium-dependent protein binding|Gram-negative bacterial cell surface binding|Gram-positive bacterial cell surface binding|pattern recognition receptor activity|scavenger receptor activity|zymogen binding			central_nervous_system(7)	7		all_neural(114;0.0765)|Lung NSC(174;0.132)|all_lung(145;0.163)|Breast(234;0.238)				CCCAGATAACGCCGAACCTGG	0.527													8	47	---	---	---	---	PASS
GPR123	84435	broad.mit.edu	37	10	134910554	134910554	+	Missense_Mutation	SNP	T	A	A			TCGA-43-6647-01	TCGA-43-6647-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:134910554T>A	uc001llx.3	+	3	516	c.80T>A	c.(79-81)GTC>GAC	p.V27D	GPR123_uc001llw.2_Missense_Mutation_p.V747D	NM_001083909	NP_001077378	Q86SQ6	GP123_HUMAN	G protein-coupled receptor 123	27	Helical; Name=1; (Potential).					integral to membrane|plasma membrane	G-protein coupled receptor activity				0		all_cancers(35;1.8e-10)|all_epithelial(44;8.95e-09)|Lung NSC(174;0.000845)|all_lung(145;0.00144)|all_neural(114;0.0299)|Colorectal(31;0.0585)|Melanoma(40;0.123)|Glioma(114;0.203)		OV - Ovarian serous cystadenocarcinoma(35;9.16e-06)|Epithelial(32;1.21e-05)|all cancers(32;1.63e-05)		TGCACGGCCGTCATGCTGCTC	0.622													8	56	---	---	---	---	PASS
ADAM8	101	broad.mit.edu	37	10	135086034	135086034	+	Missense_Mutation	SNP	C	G	G			TCGA-43-6647-01	TCGA-43-6647-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:135086034C>G	uc010qva.1	-	8	695	c.644G>C	c.(643-645)AGT>ACT	p.S215T	ADAM8_uc010quz.1_Missense_Mutation_p.S254T|ADAM8_uc009ybi.2_Missense_Mutation_p.S254T|ADAM8_uc010qvb.1_Missense_Mutation_p.S229T|ADAM8_uc009ybj.1_RNA			P78325	ADAM8_HUMAN	SubName: Full=cDNA FLJ50704, highly similar to ADAM 8 (EC 3.4.24.-) (A disintegrinand metalloproteinase domain 8);	215					integrin-mediated signaling pathway|proteolysis		metalloendopeptidase activity			large_intestine(2)|central_nervous_system(1)	3		all_cancers(35;1.14e-09)|all_epithelial(44;5.79e-08)|Lung NSC(174;0.00263)|all_lung(145;0.0039)|all_neural(114;0.0299)|Melanoma(40;0.123)|Colorectal(31;0.172)|Glioma(114;0.203)		all cancers(32;7.72e-06)|OV - Ovarian serous cystadenocarcinoma(35;8.23e-06)|Epithelial(32;1.02e-05)		CCTGTCCTGACTATTCCAAAT	0.607													6	69	---	---	---	---	PASS
OSBPL5	114879	broad.mit.edu	37	11	3114761	3114761	+	Nonsense_Mutation	SNP	C	A	A			TCGA-43-6647-01	TCGA-43-6647-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:3114761C>A	uc001lxk.2	-	17	2100	c.1942G>T	c.(1942-1944)GAG>TAG	p.E648*	OSBPL5_uc010qxq.1_Nonsense_Mutation_p.E559*|OSBPL5_uc009ydw.2_Nonsense_Mutation_p.E580*|OSBPL5_uc001lxl.2_Nonsense_Mutation_p.E580*|OSBPL5_uc009ydx.2_Nonsense_Mutation_p.E672*|OSBPL5_uc001lxj.2_Nonsense_Mutation_p.E102*	NM_020896	NP_065947	Q9H0X9	OSBL5_HUMAN	oxysterol-binding protein-like protein 5 isoform	648					cholesterol metabolic process|cholesterol transport|Golgi to plasma membrane transport	cytosol	oxysterol binding|protein binding			large_intestine(2)|central_nervous_system(1)	3		all_epithelial(84;0.000236)|Medulloblastoma(188;0.00106)|Breast(177;0.00328)|Ovarian(85;0.00556)|all_neural(188;0.00681)		BRCA - Breast invasive adenocarcinoma(625;0.00607)|LUSC - Lung squamous cell carcinoma(625;0.207)		CCTCACCTCTCGGACTCCAGC	0.667													15	93	---	---	---	---	PASS
OR51F1	256892	broad.mit.edu	37	11	4790235	4790235	+	Missense_Mutation	SNP	T	C	C			TCGA-43-6647-01	TCGA-43-6647-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:4790235T>C	uc010qyl.1	-	1	913	c.913A>G	c.(913-915)ATG>GTG	p.M305V		NM_001004752	NP_001004752	A6NLW9	A6NLW9_HUMAN	olfactory receptor, family 51, subfamily F,	305						integral to membrane	olfactory receptor activity			ovary(1)|skin(1)	2		Medulloblastoma(188;0.0075)|all_neural(188;0.0577)|Breast(177;0.0778)		Epithelial(150;5.87e-12)|BRCA - Breast invasive adenocarcinoma(625;0.0045)|LUSC - Lung squamous cell carcinoma(625;0.192)		AGACTGAGCATAGCCTTGCGG	0.418													10	66	---	---	---	---	PASS
OR51T1	401665	broad.mit.edu	37	11	4903293	4903293	+	Missense_Mutation	SNP	G	A	A			TCGA-43-6647-01	TCGA-43-6647-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:4903293G>A	uc010qyp.1	+	1	245	c.245G>A	c.(244-246)CGG>CAG	p.R82Q		NM_001004759	NP_001004759	Q8NGJ9	O51T1_HUMAN	olfactory receptor, family 51, subfamily T,	55	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(2)|large_intestine(1)	3		Medulloblastoma(188;0.0075)|all_neural(188;0.0577)|Breast(177;0.086)		Epithelial(150;4.77e-12)|BRCA - Breast invasive adenocarcinoma(625;0.00435)|LUSC - Lung squamous cell carcinoma(625;0.19)		ATTACTAAGCGGAGACTCCAC	0.473													11	136	---	---	---	---	PASS
MMP26	56547	broad.mit.edu	37	11	5009431	5009431	+	5'UTR	SNP	G	A	A			TCGA-43-6647-01	TCGA-43-6647-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:5009431G>A	uc001lzv.2	+	1						NM_021801	NP_068573	Q9NRE1	MMP26_HUMAN	matrix metalloproteinase 26 preproprotein						collagen catabolic process|proteolysis	proteinaceous extracellular matrix	metalloendopeptidase activity|zinc ion binding				0		Medulloblastoma(188;0.0025)|Breast(177;0.0204)|all_neural(188;0.0227)		Epithelial(150;1.33e-11)|BRCA - Breast invasive adenocarcinoma(625;0.0287)|LUSC - Lung squamous cell carcinoma(625;0.191)		TGGGACAAATGAGGGTTTGGC	0.502											OREG0003716	type=REGULATORY REGION|Gene=MMP26|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay	22	123	---	---	---	---	PASS
OR52E2	119678	broad.mit.edu	37	11	5080470	5080470	+	Missense_Mutation	SNP	T	C	C			TCGA-43-6647-01	TCGA-43-6647-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:5080470T>C	uc010qyw.1	-	1	388	c.388A>G	c.(388-390)AAT>GAT	p.N130D		NM_001005164	NP_001005164	Q8NGJ4	O52E2_HUMAN	olfactory receptor, family 52, subfamily E,	130	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(2)|skin(1)	3		Medulloblastoma(188;0.0061)|all_neural(188;0.0479)|Breast(177;0.086)		Epithelial(150;1.03e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)|LUSC - Lung squamous cell carcinoma(625;0.191)		TGGAGTGGATTGCAGATGGCC	0.453													5	38	---	---	---	---	PASS
NUCB2	4925	broad.mit.edu	37	11	17332477	17332477	+	Missense_Mutation	SNP	G	A	A			TCGA-43-6647-01	TCGA-43-6647-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:17332477G>A	uc001mmw.2	+	7	834	c.589G>A	c.(589-591)GAA>AAA	p.E197K	NUCB2_uc001mms.1_Missense_Mutation_p.E198K|NUCB2_uc001mmt.1_Missense_Mutation_p.E197K|NUCB2_uc001mmv.1_Missense_Mutation_p.E197K|NUCB2_uc009ygz.2_Missense_Mutation_p.E197K	NM_005013	NP_005004	P80303	NUCB2_HUMAN	nucleobindin 2 precursor	197	By similarity.					cytosol|ER-Golgi intermediate compartment|extracellular space|Golgi apparatus|plasma membrane	calcium ion binding|DNA binding				0						AACATTGAATGAAGAAAAGAG	0.303													18	139	---	---	---	---	PASS
UEVLD	55293	broad.mit.edu	37	11	18566213	18566213	+	Silent	SNP	T	A	A			TCGA-43-6647-01	TCGA-43-6647-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:18566213T>A	uc001mot.2	-	9	1097	c.1017A>T	c.(1015-1017)TCA>TCT	p.S339S	UEVLD_uc001mou.2_Silent_p.S339S|UEVLD_uc010rde.1_Silent_p.S209S|UEVLD_uc010rdf.1_Silent_p.S317S|UEVLD_uc010rdg.1_Silent_p.S209S|UEVLD_uc001mov.2_Silent_p.S317S	NM_001040697	NP_001035787	Q8IX04	UEVLD_HUMAN	ubiquitin-conjugating enzyme E2-like isoform a	339					cellular carbohydrate metabolic process|protein modification process|protein transport		binding|oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor				0						CTTCTTTGCCTGAAGTCTGTG	0.303													16	132	---	---	---	---	PASS
WT1	7490	broad.mit.edu	37	11	32439176	32439176	+	Silent	SNP	G	T	T			TCGA-43-6647-01	TCGA-43-6647-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:32439176G>T	uc001mtn.1	-	4	1093	c.897C>A	c.(895-897)TCC>TCA	p.S299S	WT1_uc001mtl.1_Silent_p.S87S|WT1_uc001mtm.1_Silent_p.S87S|WT1_uc001mto.1_Silent_p.S299S|WT1_uc001mtp.1_Silent_p.S299S|WT1_uc001mtq.1_Silent_p.S299S|WT1_uc009yjs.1_RNA	NM_024426	NP_077744	P19544	WT1_HUMAN	Wilms tumor 1 isoform D	231					adrenal cortex formation|branching involved in ureteric bud morphogenesis|camera-type eye development|cardiac muscle cell fate commitment|cellular response to cAMP|cellular response to gonadotropin stimulus|germ cell development|glomerular basement membrane development|glomerular visceral epithelial cell differentiation|induction of apoptosis|male genitalia development|male gonad development|mesenchymal to epithelial transition|metanephric epithelium development|metanephric S-shaped body morphogenesis|negative regulation of apoptosis|negative regulation of cell growth|negative regulation of female gonad development|negative regulation of metanephric glomerular mesangial cell proliferation|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transcription, DNA-dependent|negative regulation of translation|positive regulation of male gonad development|positive regulation of transcription, DNA-dependent|posterior mesonephric tubule development|regulation of organ formation|RNA splicing|sex determination|vasculogenesis|visceral serous pericardium development	cytoplasm|nuclear speck|nucleoplasm	C2H2 zinc finger domain binding|RNA binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding|zinc ion binding	p.D299Y(1)|p.D299fs*20(1)	EWSR1/WT1(231)	haematopoietic_and_lymphoid_tissue(318)|soft_tissue(231)|kidney(132)|pleura(2)|lung(2)|upper_aerodigestive_tract(1)|peritoneum(1)	687	Breast(20;0.247)		OV - Ovarian serous cystadenocarcinoma(30;0.128)			ATTCAAGCTGGGATGTCATTT	0.373			D|Mis|N|F|S	EWSR1	Wilms|desmoplastic small round cell tumor	Wilms			Denys-Drash_syndrome|Frasier_syndrome|Familial_Wilms_tumor|Wilms_tumor-Aniridia-ambiguous_Genitals-mental_Retardation				10	56	---	---	---	---	PASS
OR5M11	219487	broad.mit.edu	37	11	56310501	56310501	+	Missense_Mutation	SNP	G	T	T			TCGA-43-6647-01	TCGA-43-6647-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:56310501G>T	uc010rjl.1	-	1	233	c.233C>A	c.(232-234)ACC>AAC	p.T78N		NM_001005245	NP_001005245	Q96RB7	OR5MB_HUMAN	olfactory receptor, family 5, subfamily M,	78	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0						CATCTGCGGGGTTGCATTTGA	0.423													17	112	---	---	---	---	PASS
FTH1	2495	broad.mit.edu	37	11	61732988	61732988	+	Splice_Site	SNP	C	G	G			TCGA-43-6647-01	TCGA-43-6647-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:61732988C>G	uc001nsu.2	-	2	350	c.115_splice	c.e2-1	p.S39_splice		NM_002032	NP_002023	P02794	FRIH_HUMAN	ferritin, heavy polypeptide 1						cell proliferation|cellular membrane organization|immune response|intracellular sequestering of iron ion|iron ion transport|negative regulation of cell proliferation|post-Golgi vesicle-mediated transport	cytosol|intracellular ferritin complex	ferric iron binding|ferroxidase activity|protein binding			ovary(1)	1					Iron Dextran(DB00893)	AGTAGTAAGACTGAAAGGGGA	0.473													15	120	---	---	---	---	PASS
ATL3	25923	broad.mit.edu	37	11	63426637	63426637	+	Missense_Mutation	SNP	G	A	A			TCGA-43-6647-01	TCGA-43-6647-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:63426637G>A	uc001nxk.1	-	2	410	c.134C>T	c.(133-135)GCC>GTC	p.A45V	ATL3_uc010rms.1_Missense_Mutation_p.A27V|ATL3_uc001nxl.1_Missense_Mutation_p.A97V	NM_015459	NP_056274	Q6DD88	ATLA3_HUMAN	atlastin 3	45	Cytoplasmic.				endoplasmic reticulum organization|Golgi organization|protein homooligomerization	endoplasmic reticulum membrane|integral to membrane	GTP binding|GTPase activity|identical protein binding			pancreas(1)	1						GCTGGCCAAGGCTTTCTCATC	0.498													9	96	---	---	---	---	PASS
RCOR2	283248	broad.mit.edu	37	11	63681598	63681598	+	Missense_Mutation	SNP	T	C	C			TCGA-43-6647-01	TCGA-43-6647-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:63681598T>C	uc001nyc.2	-	8	1107	c.719A>G	c.(718-720)AAA>AGA	p.K240R		NM_173587	NP_775858	Q8IZ40	RCOR2_HUMAN	REST corepressor 2	240					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding			ovary(1)|skin(1)	2						GACCTCCTTTTTCCCAGGGCC	0.637													20	99	---	---	---	---	PASS
PPP1CA	5499	broad.mit.edu	37	11	67168706	67168706	+	Intron	SNP	G	A	A			TCGA-43-6647-01	TCGA-43-6647-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:67168706G>A	uc001okw.1	-						PPP1CA_uc009yro.1_Intron|PPP1CA_uc001okt.1_Missense_Mutation_p.S12L|PPP1CA_uc001oku.1_Intron|PPP1CA_uc001okv.1_Intron|PPP1CA_uc001okx.1_Intron|PPP1CA_uc001oky.2_Intron|TBC1D10C_uc001okz.2_5'Flank|TBC1D10C_uc001ola.2_5'Flank|TBC1D10C_uc001olb.2_5'Flank	NM_002708	NP_002699	P62136	PP1A_HUMAN	protein phosphatase 1, catalytic subunit, alpha						cell cycle|cell division|glycogen metabolic process|protein dephosphorylation|triglyceride catabolic process	cytosol|MLL5-L complex|nucleolus|PTW/PP1 phosphatase complex	metal ion binding|protein binding|protein phosphatase type 1 regulator activity|protein serine/threonine phosphatase activity			breast(1)|pancreas(1)	2			BRCA - Breast invasive adenocarcinoma(15;8.53e-07)			CCTGGACCCTGACAGGAGGAG	0.672													9	86	---	---	---	---	PASS
TRIM49	57093	broad.mit.edu	37	11	89531714	89531714	+	Missense_Mutation	SNP	G	T	T			TCGA-43-6647-01	TCGA-43-6647-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:89531714G>T	uc001pdb.2	-	8	1272	c.943C>A	c.(943-945)CAT>AAT	p.H315N		NM_020358	NP_065091	P0CI25	TRI49_HUMAN	ring finger protein 18	315	B30.2/SPRY.					intracellular	zinc ion binding				0		Acute lymphoblastic leukemia(157;2.31e-05)|all_hematologic(158;0.00556)				ACATCTTGATGGTCACATCCA	0.388													5	37	---	---	---	---	PASS
TRIM49	57093	broad.mit.edu	37	11	89531715	89531715	+	Missense_Mutation	SNP	G	T	T			TCGA-43-6647-01	TCGA-43-6647-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:89531715G>T	uc001pdb.2	-	8	1271	c.942C>A	c.(940-942)GAC>GAA	p.D314E		NM_020358	NP_065091	P0CI25	TRI49_HUMAN	ring finger protein 18	314	B30.2/SPRY.					intracellular	zinc ion binding				0		Acute lymphoblastic leukemia(157;2.31e-05)|all_hematologic(158;0.00556)				CATCTTGATGGTCACATCCAA	0.383													5	36	---	---	---	---	PASS
MMP1	4312	broad.mit.edu	37	11	102667499	102667499	+	Missense_Mutation	SNP	A	G	G			TCGA-43-6647-01	TCGA-43-6647-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:102667499A>G	uc001phi.2	-	4	664	c.521T>C	c.(520-522)TTT>TCT	p.F174S	uc001phh.1_Intron|MMP1_uc010ruv.1_Missense_Mutation_p.F108S	NM_002421	NP_002412	P03956	MMP1_HUMAN	matrix metalloproteinase 1 isoform 1	174	Metalloprotease.				blood coagulation|collagen catabolic process|interspecies interaction between organisms|leukocyte migration|proteolysis	proteinaceous extracellular matrix	calcium ion binding|metalloendopeptidase activity|zinc ion binding			skin(2)|ovary(1)|lung(1)	4	all_epithelial(12;0.0127)	all_neural(303;0.000318)|all_hematologic(158;0.00092)|Acute lymphoblastic leukemia(157;0.000967)	Epithelial(9;0.072)|Lung(13;0.0828)|LUSC - Lung squamous cell carcinoma(19;0.151)|all cancers(10;0.233)	OV - Ovarian serous cystadenocarcinoma(223;1.82e-07)|Epithelial(105;1.51e-06)|BRCA - Breast invasive adenocarcinoma(274;0.014)		AGGTCCATCAAAAGGAGAGTT	0.423													6	57	---	---	---	---	PASS
OR6M1	390261	broad.mit.edu	37	11	123676137	123676137	+	Silent	SNP	G	T	T			TCGA-43-6647-01	TCGA-43-6647-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:123676137G>T	uc010rzz.1	-	1	921	c.921C>A	c.(919-921)ACC>ACA	p.T307T		NM_001005325	NP_001005325	Q8NGM8	OR6M1_HUMAN	olfactory receptor, family 6, subfamily M,	307	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			skin(2)	2		Breast(109;0.0109)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;4.88e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.028)		TTTGTATCAAGGTCATGATTC	0.308													15	110	---	---	---	---	PASS
OR10G8	219869	broad.mit.edu	37	11	123900741	123900741	+	Missense_Mutation	SNP	C	T	T	rs149526223		TCGA-43-6647-01	TCGA-43-6647-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:123900741C>T	uc001pzp.1	+	1	412	c.412C>T	c.(412-414)CGC>TGC	p.R138C		NM_001004464	NP_001004464	Q8NGN5	O10G8_HUMAN	olfactory receptor, family 10, subfamily G,	138	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)|skin(1)	2		Breast(109;0.00867)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.22)		BRCA - Breast invasive adenocarcinoma(274;4.88e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0521)		GATGACTGGGCGCTCGTGTAC	0.562													21	135	---	---	---	---	PASS
HSN2	378465	broad.mit.edu	37	12	977837	977837	+	Missense_Mutation	SNP	G	T	T			TCGA-43-6647-01	TCGA-43-6647-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:977837G>T	uc001qiq.2	+	1	968	c.842G>T	c.(841-843)GGT>GTT	p.G281V	WNK1_uc001qio.3_Intron|WNK1_uc001qip.3_Intron|WNK1_uc001qir.3_Intron	NM_213655	NP_998820			hereditary sensory neuropathy, type II												0	all_cancers(10;0.0107)|all_epithelial(11;0.0151)|Ovarian(42;0.0512)|all_lung(10;0.0521)|Lung NSC(10;0.0987)		OV - Ovarian serous cystadenocarcinoma(31;0.000967)|BRCA - Breast invasive adenocarcinoma(9;0.0178)			GGAGAAGGAGGTGGAATTTTA	0.448													5	50	---	---	---	---	PASS
LRTM2	654429	broad.mit.edu	37	12	1943683	1943683	+	Silent	SNP	C	T	T			TCGA-43-6647-01	TCGA-43-6647-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:1943683C>T	uc001qjt.2	+	5	1715	c.909C>T	c.(907-909)AGC>AGT	p.S303S	CACNA2D4_uc001qjp.2_Intron|CACNA2D4_uc009zds.1_Intron|CACNA2D4_uc009zdt.1_Intron|CACNA2D4_uc009zdr.1_Intron|LRTM2_uc001qju.2_Silent_p.S303S|LRTM2_uc010sdx.1_Silent_p.S303S|LRTM2_uc001qjv.2_Silent_p.S65S	NM_001039029	NP_001034118	Q8N967	LRTM2_HUMAN	leucine-rich repeats and transmembrane domains 2	303	Extracellular (Potential).					integral to membrane				large_intestine(1)	1	Ovarian(42;0.107)		OV - Ovarian serous cystadenocarcinoma(31;0.000834)			GGCCGGCGAGCGTGAGGCGAG	0.677													12	57	---	---	---	---	PASS
CLECL1	160365	broad.mit.edu	37	12	9885651	9885651	+	Silent	SNP	G	A	A			TCGA-43-6647-01	TCGA-43-6647-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:9885651G>A	uc001qwj.2	-	1	210	c.210C>T	c.(208-210)GTC>GTT	p.V70V		NM_172004	NP_742001	Q8IZS7	CLCL1_HUMAN	type II transmembrane protein DCAL1	70	Helical; Signal-anchor for type II membrane protein; (Potential).					integral to membrane|plasma membrane	sugar binding				0						AGAGAGAGAAGACCACAAATG	0.438													17	84	---	---	---	---	PASS
STYK1	55359	broad.mit.edu	37	12	10780269	10780269	+	Missense_Mutation	SNP	G	C	C			TCGA-43-6647-01	TCGA-43-6647-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:10780269G>C	uc001qys.2	-	7	1209	c.688C>G	c.(688-690)CAC>GAC	p.H230D		NM_018423	NP_060893	Q6J9G0	STYK1_HUMAN	serine/threonine/tyrosine kinase 1	230	Protein kinase.					integral to membrane|plasma membrane	ATP binding|non-membrane spanning protein tyrosine kinase activity			central_nervous_system(3)|ovary(2)|lung(2)|breast(1)	8						TTTCCGATGTGATATACTTGT	0.403										HNSCC(73;0.22)			6	78	---	---	---	---	PASS
PDE3A	5139	broad.mit.edu	37	12	20769197	20769197	+	Silent	SNP	A	C	C			TCGA-43-6647-01	TCGA-43-6647-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:20769197A>C	uc001reh.1	+	4	1325	c.1303A>C	c.(1303-1305)AGA>CGA	p.R435R		NM_000921	NP_000912	Q14432	PDE3A_HUMAN	phosphodiesterase 3A	435					lipid metabolic process|platelet activation|signal transduction	cytosol|integral to membrane	3',5'-cyclic-AMP phosphodiesterase activity|3',5'-cyclic-GMP phosphodiesterase activity|cGMP-inhibited cyclic-nucleotide phosphodiesterase activity|metal ion binding			ovary(3)|upper_aerodigestive_tract(1)	4	Esophageal squamous(101;0.125)	Breast(259;0.134)			Aminophylline(DB01223)|Amrinone(DB01427)|Anagrelide(DB00261)|Cilostazol(DB01166)|Enoximone(DB04880)|Milrinone(DB00235)|Theophylline(DB00277)	TGGCTTGTTGAGACGAGTTTC	0.468													5	132	---	---	---	---	PASS
ADAMTS20	80070	broad.mit.edu	37	12	43925895	43925895	+	Missense_Mutation	SNP	T	C	C			TCGA-43-6647-01	TCGA-43-6647-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:43925895T>C	uc010skx.1	-	3	557	c.557A>G	c.(556-558)TAC>TGC	p.Y186C		NM_025003	NP_079279	P59510	ATS20_HUMAN	a disintegrin-like and metalloprotease with	186						proteinaceous extracellular matrix	zinc ion binding			central_nervous_system(5)|ovary(4)|lung(3)|large_intestine(2)|skin(2)|urinary_tract(1)|kidney(1)|pancreas(1)	19	all_cancers(12;2.6e-05)|Lung SC(27;0.184)	Lung NSC(34;0.0569)|all_lung(34;0.129)		GBM - Glioblastoma multiforme(48;0.0473)		GTCTTGTCTGTATATAAGATG	0.353													6	67	---	---	---	---	PASS
PLEKHA9	51054	broad.mit.edu	37	12	45567091	45567091	+	Missense_Mutation	SNP	G	A	A			TCGA-43-6647-01	TCGA-43-6647-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:45567091G>A	uc001rom.1	-	3	1595	c.1058C>T	c.(1057-1059)GCG>GTG	p.A353V	PLEKHA9_uc009zke.2_Missense_Mutation_p.A353V	NM_015899	NP_056983			pleckstrin homology domain containing, family A												0	Lung SC(27;0.192)|Renal(347;0.236)			GBM - Glioblastoma multiforme(48;0.173)		TACGGTTAACGCGGCCACAAA	0.502													5	86	---	---	---	---	PASS
USP15	9958	broad.mit.edu	37	12	62786902	62786902	+	Silent	SNP	A	T	T			TCGA-43-6647-01	TCGA-43-6647-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:62786902A>T	uc001src.1	+	19	2499	c.2490A>T	c.(2488-2490)GTA>GTT	p.V830V	USP15_uc001srb.1_Silent_p.V801V	NM_006313	NP_006304	Q9Y4E8	UBP15_HUMAN	ubiquitin specific peptidase 15	830					protein deubiquitination|ubiquitin-dependent protein catabolic process		cysteine-type endopeptidase activity|protein binding|ubiquitin thiolesterase activity|ubiquitin-specific protease activity			ovary(2)|lung(1)	3			GBM - Glioblastoma multiforme(1;0.000276)	GBM - Glioblastoma multiforme(28;0.0622)		TGCCTCCAGTACTTGTAGTAC	0.353													13	84	---	---	---	---	PASS
NAV3	89795	broad.mit.edu	37	12	78400700	78400700	+	Missense_Mutation	SNP	C	T	T			TCGA-43-6647-01	TCGA-43-6647-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:78400700C>T	uc001syp.2	+	8	1555	c.1382C>T	c.(1381-1383)TCT>TTT	p.S461F	NAV3_uc001syo.2_Missense_Mutation_p.S461F	NM_014903	NP_055718	Q8IVL0	NAV3_HUMAN	neuron navigator 3	461						nuclear outer membrane	ATP binding|nucleoside-triphosphatase activity			large_intestine(6)|ovary(5)|lung(2)|breast(1)|skin(1)|kidney(1)|pancreas(1)	17						AATAAAAAGTCTTTGCTACAG	0.413										HNSCC(70;0.22)			7	87	---	---	---	---	PASS
TPCN1	53373	broad.mit.edu	37	12	113706674	113706674	+	Missense_Mutation	SNP	G	A	A			TCGA-43-6647-01	TCGA-43-6647-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:113706674G>A	uc001tuw.2	+	6	953	c.656G>A	c.(655-657)CGG>CAG	p.R219Q	TPCN1_uc001tux.2_Missense_Mutation_p.R291Q|TPCN1_uc010syt.1_Missense_Mutation_p.R151Q	NM_017901	NP_060371	Q9ULQ1	TPC1_HUMAN	two pore segment channel 1 isoform 2	219	Helical; Name=S4 of repeat I; (Potential).					endosome membrane|integral to membrane|lysosomal membrane	NAADP-sensitive calcium-release channel activity|voltage-gated ion channel activity			skin(2)|ovary(1)	3						GGTGGCGTCCGGCGGTAAGGC	0.627													9	59	---	---	---	---	PASS
PLBD2	196463	broad.mit.edu	37	12	113826438	113826438	+	3'UTR	SNP	G	C	C			TCGA-43-6647-01	TCGA-43-6647-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:113826438G>C	uc001tve.2	+	12					PLBD2_uc001tvf.2_3'UTR	NM_173542	NP_775813	Q8NHP8	PLBL2_HUMAN	phospholipase B domain containing 2 isoform 1						lipid catabolic process	lysosomal lumen	hydrolase activity				0						CTGAAGTTCTGTCCCTGCTCT	0.632													5	25	---	---	---	---	PASS
FZD10	11211	broad.mit.edu	37	12	130648774	130648774	+	Silent	SNP	G	A	A			TCGA-43-6647-01	TCGA-43-6647-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:130648774G>A	uc001uii.2	+	1	1743	c.1287G>A	c.(1285-1287)ACG>ACA	p.T429T	uc001uig.1_5'Flank|uc001uih.1_5'Flank	NM_007197	NP_009128	Q9ULW2	FZD10_HUMAN	frizzled 10 precursor	429	Cytoplasmic (Potential).				brain development|canonical Wnt receptor signaling pathway|cellular response to retinoic acid|embryo development|gonad development|negative regulation of Rho GTPase activity|neuron differentiation|non-canonical Wnt receptor signaling pathway|positive regulation of JUN kinase activity|positive regulation of Rac GTPase activity|regulation of actin cytoskeleton organization|vasculature development	cell projection|cell surface|cytoplasm|integral to plasma membrane	G-protein coupled receptor activity|PDZ domain binding|Wnt receptor activity|Wnt-protein binding			lung(3)|breast(1)|central_nervous_system(1)	5	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;1.3e-06)|Epithelial(86;1.66e-05)|all cancers(50;5.18e-05)		TGATGAAGACGGGCGGCGAGA	0.612													6	61	---	---	---	---	PASS
POLE	5426	broad.mit.edu	37	12	133201572	133201572	+	Silent	SNP	C	G	G			TCGA-43-6647-01	TCGA-43-6647-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:133201572C>G	uc001uks.1	-	48	6710	c.6666G>C	c.(6664-6666)CTG>CTC	p.L2222L	POLE_uc001ukq.1_Silent_p.L432L|POLE_uc001ukr.1_Silent_p.L1026L|POLE_uc010tbq.1_RNA	NM_006231	NP_006222	Q07864	DPOE1_HUMAN	DNA-directed DNA polymerase epsilon	2222	C4-type (Potential).				base-excision repair, gap-filling|DNA synthesis involved in DNA repair|DNA-dependent DNA replication initiation|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|nucleotide-excision repair, DNA gap filling|S phase of mitotic cell cycle|telomere maintenance via recombination|telomere maintenance via semi-conservative replication|transcription-coupled nucleotide-excision repair	nucleoplasm	chromatin binding|DNA binding|DNA-directed DNA polymerase activity|nucleotide binding|protein binding|zinc ion binding			ovary(3)|skin(3)|lung(1)|central_nervous_system(1)	8	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_epithelial(31;0.0416)		OV - Ovarian serous cystadenocarcinoma(86;5.22e-08)|Epithelial(86;4.03e-07)|all cancers(50;1.18e-05)		CGCGGCACTTCAGGCAGACCT	0.657								DNA_polymerases_(catalytic_subunits)|Direct_reversal_of_damage					4	42	---	---	---	---	PASS
RNF17	56163	broad.mit.edu	37	13	25442751	25442751	+	Missense_Mutation	SNP	C	G	G			TCGA-43-6647-01	TCGA-43-6647-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:25442751C>G	uc001upr.2	+	31	4216	c.4175C>G	c.(4174-4176)GCT>GGT	p.A1392G	RNF17_uc010aab.2_RNA|RNF17_uc010tde.1_Missense_Mutation_p.A1388G|RNF17_uc001ups.2_Missense_Mutation_p.A1331G|RNF17_uc010aac.2_Missense_Mutation_p.A584G|RNF17_uc010aad.2_Missense_Mutation_p.A402G	NM_031277	NP_112567	Q9BXT8	RNF17_HUMAN	ring finger protein 17	1392					multicellular organismal development	cytoplasm|nucleus	hydrolase activity, acting on ester bonds|nucleic acid binding|zinc ion binding			ovary(1)|skin(1)	2		Lung SC(185;0.0225)|Breast(139;0.077)		all cancers(112;0.0114)|OV - Ovarian serous cystadenocarcinoma(117;0.0311)|Epithelial(112;0.0524)		TTGCTTTCGGCTGAAACAGAC	0.363													13	104	---	---	---	---	PASS
FAM123A	219287	broad.mit.edu	37	13	25745075	25745075	+	Missense_Mutation	SNP	C	A	A			TCGA-43-6647-01	TCGA-43-6647-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:25745075C>A	uc001uqb.2	-	1	783	c.683G>T	c.(682-684)GGC>GTC	p.G228V	FAM123A_uc001uqa.2_Missense_Mutation_p.G228V|FAM123A_uc001uqc.2_Missense_Mutation_p.G228V	NM_152704	NP_689917	Q8N7J2	F123A_HUMAN	hypothetical protein LOC219287 isoform 1	228										ovary(2)|large_intestine(1)|lung(1)	4		Lung SC(185;0.0225)|Breast(139;0.0602)		all cancers(112;0.0071)|Epithelial(112;0.0398)|OV - Ovarian serous cystadenocarcinoma(117;0.151)|GBM - Glioblastoma multiforme(144;0.222)|Lung(94;0.241)		GGTGAGCGAGCCGGGTAGGAT	0.597													3	8	---	---	---	---	PASS
ZIC5	85416	broad.mit.edu	37	13	100617671	100617671	+	Missense_Mutation	SNP	T	C	C			TCGA-43-6647-01	TCGA-43-6647-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:100617671T>C	uc001vom.1	-	2	2201	c.1952A>G	c.(1951-1953)GAA>GGA	p.E651G		NM_033132	NP_149123	Q96T25	ZIC5_HUMAN	zinc finger protein of the cerebellum 5	651					cell differentiation	nucleus	DNA binding|zinc ion binding				0	all_neural(89;0.0837)|Medulloblastoma(90;0.18)|Lung SC(71;0.184)					CCCGTAAATTTCCTCATCTTC	0.468													18	119	---	---	---	---	PASS
OR4K2	390431	broad.mit.edu	37	14	20345270	20345270	+	Missense_Mutation	SNP	C	A	A			TCGA-43-6647-01	TCGA-43-6647-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:20345270C>A	uc001vwh.1	+	1	844	c.844C>A	c.(844-846)CTG>ATG	p.L282M		NM_001005501	NP_001005501	Q8NGD2	OR4K2_HUMAN	olfactory receptor, family 4, subfamily K,	282	Helical; Name=7; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(2)|skin(2)	4	all_cancers(95;0.00108)		Epithelial(56;9.96e-07)|all cancers(55;2.95e-06)	GBM - Glioblastoma multiforme(265;0.00327)		TACTCCCACTCTGAACCCAAT	0.373													5	166	---	---	---	---	PASS
RNASE11	122651	broad.mit.edu	37	14	21052471	21052471	+	Missense_Mutation	SNP	G	A	A			TCGA-43-6647-01	TCGA-43-6647-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:21052471G>A	uc010ahv.2	-	2	348	c.163C>T	c.(163-165)CCG>TCG	p.P55S	RNASE11_uc010ahx.2_Missense_Mutation_p.P55S|RNASE11_uc010ahw.2_Missense_Mutation_p.P55S|RNASE11_uc001vxs.2_Missense_Mutation_p.P55S	NM_145250	NP_660293	Q8TAA1	RNS11_HUMAN	ribonuclease, RNase A family, 11 (non-active)	55						extracellular region	nucleic acid binding|pancreatic ribonuclease activity			ovary(3)	3	all_cancers(95;0.00238)	all_lung(585;0.235)	Epithelial(56;1.85e-06)|all cancers(55;1.46e-05)	GBM - Glioblastoma multiforme(265;0.0139)		AACAGGATCGGGTTCATTAAT	0.368													27	243	---	---	---	---	PASS
AKAP6	9472	broad.mit.edu	37	14	33291766	33291766	+	Missense_Mutation	SNP	T	C	C			TCGA-43-6647-01	TCGA-43-6647-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:33291766T>C	uc001wrq.2	+	13	4917	c.4747T>C	c.(4747-4749)TTT>CTT	p.F1583L		NM_004274	NP_004265	Q13023	AKAP6_HUMAN	A-kinase anchor protein 6	1583	Ser-rich.				protein targeting	calcium channel complex|nuclear membrane|sarcoplasmic reticulum	protein kinase A binding|receptor binding			breast(6)|ovary(5)|lung(4)|skin(3)|large_intestine(2)|pancreas(1)	21	Breast(36;0.0388)|Prostate(35;0.15)		LUAD - Lung adenocarcinoma(48;0.00107)|Lung(238;0.00677)|STAD - Stomach adenocarcinoma(7;0.116)	GBM - Glioblastoma multiforme(265;0.019)		ATTGGGCATCTTTAAAAATGG	0.428													21	127	---	---	---	---	PASS
DACT1	51339	broad.mit.edu	37	14	59113810	59113810	+	Silent	SNP	C	G	G			TCGA-43-6647-01	TCGA-43-6647-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:59113810C>G	uc001xdw.2	+	4	2633	c.2469C>G	c.(2467-2469)CTC>CTG	p.L823L	DACT1_uc010trv.1_Silent_p.L542L|DACT1_uc001xdx.2_Silent_p.L786L|DACT1_uc010trw.1_Silent_p.L542L	NM_016651	NP_057735	Q9NYF0	DACT1_HUMAN	dapper 1 isoform 1	823					multicellular organismal development|Wnt receptor signaling pathway	cytoplasm|nucleus				large_intestine(2)|lung(2)|ovary(1)	5						AGAAGATCCTCCGCTTTCGGT	0.453													28	175	---	---	---	---	PASS
RTN1	6252	broad.mit.edu	37	14	60212638	60212638	+	Missense_Mutation	SNP	G	A	A			TCGA-43-6647-01	TCGA-43-6647-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:60212638G>A	uc001xen.1	-	2	1012	c.803C>T	c.(802-804)TCT>TTT	p.S268F		NM_021136	NP_066959	Q16799	RTN1_HUMAN	reticulon 1 isoform A	268					neuron differentiation	integral to endoplasmic reticulum membrane	signal transducer activity			ovary(2)|central_nervous_system(2)	4				OV - Ovarian serous cystadenocarcinoma(108;0.0968)		CTGTTCTTCAGAGAGATCATC	0.473													9	155	---	---	---	---	PASS
PCNX	22990	broad.mit.edu	37	14	71575553	71575553	+	Silent	SNP	A	C	C			TCGA-43-6647-01	TCGA-43-6647-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:71575553A>C	uc001xmo.2	+	34	6980	c.6534A>C	c.(6532-6534)TCA>TCC	p.S2178S	PCNX_uc010are.1_Silent_p.S2067S|PCNX_uc010arf.1_Silent_p.S966S|PCNX_uc001xmp.2_Silent_p.S262S	NM_014982	NP_055797	Q96RV3	PCX1_HUMAN	pecanex-like 1	2178	Ser-rich.					integral to membrane				ovary(1)	1			KIRC - Kidney renal clear cell carcinoma(12;0.206)	all cancers(60;0.00835)|BRCA - Breast invasive adenocarcinoma(234;0.00951)|OV - Ovarian serous cystadenocarcinoma(108;0.0417)		TGGAACCCTCAGGTCAGAGCG	0.562													5	69	---	---	---	---	PASS
HEATR4	399671	broad.mit.edu	37	14	73989131	73989131	+	Missense_Mutation	SNP	G	T	T			TCGA-43-6647-01	TCGA-43-6647-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:73989131G>T	uc010tub.1	-	3	1048	c.726C>A	c.(724-726)GAC>GAA	p.D242E	HEATR4_uc010tua.1_Missense_Mutation_p.D195E	NM_203309	NP_976054			HEAT repeat containing 4											ovary(1)	1				BRCA - Breast invasive adenocarcinoma(234;0.00386)|OV - Ovarian serous cystadenocarcinoma(108;0.0719)		TGTGACTCCAGTCGTACTGCT	0.577													14	81	---	---	---	---	PASS
TTC7B	145567	broad.mit.edu	37	14	91252596	91252596	+	Silent	SNP	G	A	A			TCGA-43-6647-01	TCGA-43-6647-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:91252596G>A	uc001xyp.2	-	2	320	c.198C>T	c.(196-198)GCC>GCT	p.A66A		NM_001010854	NP_001010854	Q86TV6	TTC7B_HUMAN	tetratricopeptide repeat domain 7B	66							binding			ovary(2)	2		Melanoma(154;0.222)				CTCGGGGACTGGCCCCCTGCC	0.602													16	69	---	---	---	---	PASS
SERPINA6	866	broad.mit.edu	37	14	94780437	94780437	+	Silent	SNP	G	A	A			TCGA-43-6647-01	TCGA-43-6647-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:94780437G>A	uc001ycv.2	-	2	653	c.549C>T	c.(547-549)GTC>GTT	p.V183V	SERPINA6_uc010auv.2_RNA	NM_001756	NP_001747	P08185	CBG_HUMAN	corticosteroid binding globulin precursor	183					regulation of proteolysis|transport	extracellular space	serine-type endopeptidase inhibitor activity|steroid binding			skin(3)|ovary(1)|central_nervous_system(1)	5		all_cancers(154;0.0482)|all_epithelial(191;0.166)		COAD - Colon adenocarcinoma(157;0.211)	Alclometasone(DB00240)|Beclomethasone(DB00394)|Ciclesonide(DB01410)|Flumethasone Pivalate(DB00663)|Flunisolide(DB00180)|Fluocinolone Acetonide(DB00591)|Fluocinonide(DB01047)|Fluorometholone(DB00324)|Flurandrenolide(DB00846)|Fluticasone Propionate(DB00588)|Halobetasol Propionate(DB00596)|Medrysone(DB00253)|Mitotane(DB00648)|Paramethasone(DB01384)|Prednisolone(DB00860)|Rimexolone(DB00896)|Triamcinolone(DB00620)	AAAACAAGTCGACAATTTTCC	0.488													4	114	---	---	---	---	PASS
CLMN	79789	broad.mit.edu	37	14	95669821	95669821	+	Missense_Mutation	SNP	G	A	A			TCGA-43-6647-01	TCGA-43-6647-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:95669821G>A	uc001yef.2	-	9	1981	c.1865C>T	c.(1864-1866)CCT>CTT	p.P622L		NM_024734	NP_079010	Q96JQ2	CLMN_HUMAN	calmin	622						integral to membrane	actin binding				0				Epithelial(152;0.193)		CTTAACTTGAGGCTCTGGCGA	0.448													5	77	---	---	---	---	PASS
INF2	64423	broad.mit.edu	37	14	105175017	105175017	+	Missense_Mutation	SNP	C	A	A			TCGA-43-6647-01	TCGA-43-6647-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:105175017C>A	uc001ypb.2	+	10	2040	c.1897C>A	c.(1897-1899)CTC>ATC	p.L633I	INF2_uc010tyi.1_Missense_Mutation_p.L633I|INF2_uc001ypc.2_Missense_Mutation_p.L633I|INF2_uc010awz.1_RNA	NM_022489	NP_071934	Q27J81	INF2_HUMAN	inverted formin 2 isoform 1	633	FH2.				actin cytoskeleton organization	endoplasmic reticulum|nucleus|perinuclear region of cytoplasm	actin binding|Rho GTPase binding				0		all_cancers(154;0.0896)|Melanoma(154;0.155)|all_epithelial(191;0.172)	all cancers(16;0.00188)|OV - Ovarian serous cystadenocarcinoma(23;0.0191)|Epithelial(46;0.047)|GBM - Glioblastoma multiforme(11;0.116)	Epithelial(152;0.176)		GATCACTTTCCTCGATGCCAA	0.622											OREG0022959	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	9	173	---	---	---	---	PASS
ADAM6	8755	broad.mit.edu	37	14	106641689	106641689	+	RNA	SNP	A	C	C			TCGA-43-6647-01	TCGA-43-6647-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:106641689A>C	uc010tyt.1	-	1021		c.24312T>G								Parts of antibodies, mostly variable regions.												0						AGTTTGTGTTACCATTGTAAG	0.542													7	231	---	---	---	---	PASS
C15orf2	23742	broad.mit.edu	37	15	24921331	24921331	+	Missense_Mutation	SNP	C	T	T			TCGA-43-6647-01	TCGA-43-6647-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:24921331C>T	uc001ywo.2	+	1	791	c.317C>T	c.(316-318)CCG>CTG	p.P106L		NM_018958	NP_061831	Q9NZP6	CO002_HUMAN	hypothetical protein LOC23742	106					cell differentiation|multicellular organismal development|spermatogenesis					ovary(2)|large_intestine(2)|skin(2)|kidney(1)|central_nervous_system(1)	8		all_cancers(20;2.14e-21)|all_epithelial(15;4.77e-19)|Lung NSC(15;1.43e-14)|all_lung(15;9.57e-14)|Breast(32;0.00086)		all cancers(64;3.19e-24)|Epithelial(43;2.67e-17)|GBM - Glioblastoma multiforme(186;7.36e-07)|BRCA - Breast invasive adenocarcinoma(123;0.000273)|Lung(196;0.229)		CGGAACCCCCCGAGGTTTGGA	0.677													3	60	---	---	---	---	PASS
C15orf41	84529	broad.mit.edu	37	15	36989572	36989572	+	Missense_Mutation	SNP	G	T	T			TCGA-43-6647-01	TCGA-43-6647-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:36989572G>T	uc001zje.3	+	8	775	c.525G>T	c.(523-525)GAG>GAT	p.E175D	C15orf41_uc001zjd.2_Missense_Mutation_p.E175D|C15orf41_uc010bbb.1_Missense_Mutation_p.E77D|C15orf41_uc001zjf.2_Missense_Mutation_p.E77D|C15orf41_uc010uci.1_Missense_Mutation_p.E77D	NM_001130010	NP_001123482	Q9Y2V0	CO041_HUMAN	hypothetical protein LOC84529 isoform 1	175							protein binding			pancreas(1)	1		all_epithelial(112;3.06e-10)|Lung NSC(122;6.48e-08)|all_lung(180;8.31e-07)|Melanoma(134;0.222)		all cancers(64;1.76e-19)|GBM - Glioblastoma multiforme(113;5.03e-07)|BRCA - Breast invasive adenocarcinoma(123;0.11)		TGCTTCTAGAGAAAAACCTGT	0.408													10	162	---	---	---	---	PASS
TMOD3	29766	broad.mit.edu	37	15	52155121	52155121	+	Missense_Mutation	SNP	G	C	C			TCGA-43-6647-01	TCGA-43-6647-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:52155121G>C	uc002abm.2	+	2	259	c.40G>C	c.(40-42)GAC>CAC	p.D14H		NM_014547	NP_055362	Q9NYL9	TMOD3_HUMAN	tropomodulin 3 (ubiquitous)	14						cytoplasm|cytoskeleton	actin binding|tropomyosin binding			ovary(1)	1				all cancers(107;0.00194)		AAAGTACAAAGACCTTGATGA	0.443													6	76	---	---	---	---	PASS
CHRNA3	1136	broad.mit.edu	37	15	78894314	78894314	+	Missense_Mutation	SNP	A	C	C			TCGA-43-6647-01	TCGA-43-6647-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:78894314A>C	uc002bec.2	-	5	856	c.670T>G	c.(670-672)TGC>GGC	p.C224G	CHRNA3_uc002bea.2_RNA|CHRNA3_uc002beb.2_Missense_Mutation_p.C224G	NM_000743	NP_000734	P32297	ACHA3_HUMAN	cholinergic receptor, nicotinic, alpha 3	224	Extracellular (Potential).				activation of transmembrane receptor protein tyrosine kinase activity|behavioral response to nicotine|locomotory behavior|regulation of acetylcholine secretion|regulation of dendrite morphogenesis|regulation of excitatory postsynaptic membrane potential|regulation of smooth muscle contraction|synaptic transmission involved in micturition|synaptic transmission, cholinergic	cell junction|dendrite|neuronal cell body|nicotinic acetylcholine-gated receptor-channel complex|postsynaptic density|postsynaptic membrane	acetylcholine receptor activity|nicotinic acetylcholine-activated cation-selective channel activity			central_nervous_system(3)|ovary(1)	4						ATCTCCTCGCAGCAGTTGTAC	0.547													4	50	---	---	---	---	PASS
TMEM8A	58986	broad.mit.edu	37	16	424040	424040	+	Silent	SNP	G	A	A			TCGA-43-6647-01	TCGA-43-6647-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:424040G>A	uc002cgu.3	-	11	1996	c.1867C>T	c.(1867-1869)CTG>TTG	p.L623L	TMEM8A_uc002cgv.3_Silent_p.L430L	NM_021259	NP_067082	Q9HCN3	TMM8A_HUMAN	transmembrane protein 8 (five membrane-spanning	623	Helical; (Potential).				cell adhesion	integral to plasma membrane				central_nervous_system(2)|pancreas(1)	3						GCCATGCACAGGATGGTGACC	0.662											OREG0003702	type=REGULATORY REGION|Gene=TMEM8|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay	5	21	---	---	---	---	PASS
TSC2	7249	broad.mit.edu	37	16	2129610	2129610	+	Nonsense_Mutation	SNP	G	T	T			TCGA-43-6647-01	TCGA-43-6647-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:2129610G>T	uc002con.2	+	29	3443	c.3337G>T	c.(3337-3339)GAG>TAG	p.E1113*	TSC2_uc010bsd.2_Nonsense_Mutation_p.E1113*|TSC2_uc002coo.2_Nonsense_Mutation_p.E1069*|TSC2_uc010uvv.1_Nonsense_Mutation_p.E1033*|TSC2_uc010uvw.1_Nonsense_Mutation_p.E1021*|TSC2_uc002cop.2_Nonsense_Mutation_p.E869*	NM_000548	NP_000539	P49815	TSC2_HUMAN	tuberous sclerosis 2 isoform 1	1113					cell cycle arrest|endocytosis|heart development|insulin receptor signaling pathway|insulin-like growth factor receptor signaling pathway|negative regulation of cell size|negative regulation of phosphatidylinositol 3-kinase cascade|negative regulation of protein kinase B signaling cascade|negative regulation of TOR signaling cascade|negative regulation of Wnt receptor signaling pathway|nerve growth factor receptor signaling pathway|neural tube closure|phosphatidylinositol-mediated signaling|positive chemotaxis|protein import into nucleus|protein kinase B signaling cascade|regulation of endocytosis|regulation of insulin receptor signaling pathway|regulation of small GTPase mediated signal transduction	Golgi apparatus|nucleus|perinuclear region of cytoplasm|TSC1-TSC2 complex	GTPase activator activity|protein homodimerization activity			central_nervous_system(4)|lung(3)|ovary(2)|pancreas(1)	10		Hepatocellular(780;0.0202)				GGCCAAGCTGGAGTCCCAGGC	0.682			D|Mis|N|F|S			hamartoma|renal cell			Tuberous_Sclerosis				4	16	---	---	---	---	PASS
ADCY9	115	broad.mit.edu	37	16	4016686	4016686	+	Missense_Mutation	SNP	G	C	C			TCGA-43-6647-01	TCGA-43-6647-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:4016686G>C	uc002cvx.2	-	11	3691	c.3152C>G	c.(3151-3153)TCC>TGC	p.S1051C		NM_001116	NP_001107	O60503	ADCY9_HUMAN	adenylate cyclase 9	1051	Cytoplasmic (Potential).				activation of adenylate cyclase activity by G-protein signaling pathway|activation of phospholipase C activity|activation of protein kinase A activity|cellular response to glucagon stimulus|energy reserve metabolic process|inhibition of adenylate cyclase activity by G-protein signaling pathway|nerve growth factor receptor signaling pathway|synaptic transmission|transmembrane transport|water transport	integral to plasma membrane	adenylate cyclase activity|ATP binding|metal ion binding			ovary(4)|large_intestine(1)|central_nervous_system(1)	6						ATGGTTCTTGGAGTAGGTCTG	0.592													38	171	---	---	---	---	PASS
ZP2	7783	broad.mit.edu	37	16	21211169	21211169	+	Silent	SNP	G	C	C			TCGA-43-6647-01	TCGA-43-6647-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:21211169G>C	uc002dii.2	-	15	1725	c.1725C>G	c.(1723-1725)ACC>ACG	p.T575T	ZP2_uc010bwn.1_Silent_p.T605T	NM_003460	NP_003451	Q05996	ZP2_HUMAN	zona pellucida glycoprotein 2 preproprotein	575	Extracellular (Potential).|ZP.				binding of sperm to zona pellucida|intracellular protein transport	endoplasmic reticulum|Golgi apparatus|integral to membrane|multivesicular body|plasma membrane|proteinaceous extracellular matrix|stored secretory granule	acrosin binding|coreceptor activity			central_nervous_system(2)|ovary(1)	3				GBM - Glioblastoma multiforme(48;0.0573)		GATGGAAGGTGGTCTGGTAGT	0.498													8	111	---	---	---	---	PASS
IL21R	50615	broad.mit.edu	37	16	27448887	27448887	+	Silent	SNP	C	A	A			TCGA-43-6647-01	TCGA-43-6647-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:27448887C>A	uc002doq.1	+	4	464	c.231C>A	c.(229-231)GCC>GCA	p.A77A	IL21R_uc002dor.1_Silent_p.A77A|IL21R_uc002dos.1_Silent_p.A77A	NM_181078	NP_851564	Q9HBE5	IL21R_HUMAN	interleukin 21 receptor precursor	77	Extracellular (Potential).				natural killer cell activation	integral to membrane	interleukin-21 receptor activity			ovary(2)|lung(1)|breast(1)	4						CCACGCATGCCACCTACACCT	0.557			T	BCL6	NHL								8	58	---	---	---	---	PASS
C16orf86	388284	broad.mit.edu	37	16	67702132	67702132	+	Nonsense_Mutation	SNP	C	T	T			TCGA-43-6647-01	TCGA-43-6647-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:67702132C>T	uc002ety.2	+	4	740	c.583C>T	c.(583-585)CAG>TAG	p.Q195*	C16orf48_uc002etw.1_5'Flank|C16orf48_uc010cem.1_5'Flank|C16orf86_uc002etx.1_3'UTR|C16orf86_uc002etz.2_RNA	NM_001012984	NP_001013002	Q6ZW13	CP086_HUMAN	hypothetical protein LOC388284	195											0		Acute lymphoblastic leukemia(13;3.76e-06)|all_hematologic(13;0.000303)|Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0143)|Epithelial(162;0.047)|all cancers(182;0.228)		GCCGCTGTACCAGTACGTCAA	0.672											OREG0023886	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	3	19	---	---	---	---	PASS
HAS3	3038	broad.mit.edu	37	16	69143365	69143365	+	Missense_Mutation	SNP	G	T	T			TCGA-43-6647-01	TCGA-43-6647-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:69143365G>T	uc010cfh.2	+	2	291	c.67G>T	c.(67-69)GGT>TGT	p.G23C	HAS3_uc002ewk.2_Missense_Mutation_p.G23C|HAS3_uc010vlk.1_Missense_Mutation_p.G23C|HAS3_uc002ewl.2_Missense_Mutation_p.G23C	NM_005329	NP_005320	O00219	HAS3_HUMAN	hyaluronan synthase 3 isoform a	23	Helical; Name=1; (Potential).				carbohydrate metabolic process	integral to plasma membrane	hyaluronan synthase activity				0		Ovarian(137;0.101)		OV - Ovarian serous cystadenocarcinoma(108;0.0694)		GGCAGTGCTGGGTGGCATCCT	0.632													4	47	---	---	---	---	PASS
CPNE7	27132	broad.mit.edu	37	16	89661838	89661838	+	Missense_Mutation	SNP	G	A	A			TCGA-43-6647-01	TCGA-43-6647-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:89661838G>A	uc002fnp.2	+	16	1721	c.1591G>A	c.(1591-1593)GCC>ACC	p.A531T	CPNE7_uc002fnq.2_Missense_Mutation_p.A456T	NM_014427	NP_055242	Q9UBL6	CPNE7_HUMAN	copine 7 isoform b	531	VWFA.				lipid metabolic process		transporter activity				0		all_hematologic(23;0.0748)		all cancers(4;3.63e-08)|OV - Ovarian serous cystadenocarcinoma(4;1.7e-06)|BRCA - Breast invasive adenocarcinoma(80;0.0147)		CACACGGGAGGCCATTGTGCG	0.627													4	42	---	---	---	---	PASS
POLR2A	5430	broad.mit.edu	37	17	7402446	7402446	+	Missense_Mutation	SNP	G	A	A			TCGA-43-6647-01	TCGA-43-6647-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:7402446G>A	uc002ghf.3	+	9	1658	c.1424G>A	c.(1423-1425)CGC>CAC	p.R475H	POLR2A_uc002ghe.2_Missense_Mutation_p.R475H	NM_000937	NP_000928	P24928	RPB1_HUMAN	DNA-directed RNA polymerase II A	475					mRNA capping|nuclear mRNA splicing, via spliceosome|positive regulation of viral transcription|protein phosphorylation|regulation of transcription, DNA-dependent|transcription elongation from RNA polymerase II promoter|transcription initiation from RNA polymerase II promoter|transcription-coupled nucleotide-excision repair|viral reproduction	DNA-directed RNA polymerase II, core complex	DNA binding|DNA-directed RNA polymerase activity|metal ion binding|RNA-directed RNA polymerase activity|ubiquitin protein ligase binding			pancreas(1)	1		Prostate(122;0.173)				CATCGGGTCCGCATTCTCCCA	0.562													4	139	---	---	---	---	PASS
PER1	5187	broad.mit.edu	37	17	8047094	8047094	+	Silent	SNP	G	A	A			TCGA-43-6647-01	TCGA-43-6647-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:8047094G>A	uc002gkd.2	-	19	2800	c.2562C>T	c.(2560-2562)TGC>TGT	p.C854C	PER1_uc010cns.2_5'Flank|PER1_uc010vuq.1_Intron	NM_002616	NP_002607	O15534	PER1_HUMAN	period 1	854	Pro-rich.				circadian rhythm|entrainment of circadian clock|negative regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	signal transducer activity			lung(2)|breast(2)|skin(2)|large_intestine(1)|ovary(1)|kidney(1)	9						GTGAGACATAGCAGGGCGCTT	0.697			T	ETV6	AML|CMML			Other_conserved_DNA_damage_response_genes					6	38	---	---	---	---	PASS
MYH4	4622	broad.mit.edu	37	17	10351379	10351379	+	Missense_Mutation	SNP	G	A	A			TCGA-43-6647-01	TCGA-43-6647-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:10351379G>A	uc002gmn.2	-	34	4832	c.4721C>T	c.(4720-4722)TCT>TTT	p.S1574F	uc002gml.1_Intron	NM_017533	NP_060003	Q9Y623	MYH4_HUMAN	myosin, heavy polypeptide 4, skeletal muscle	1574	Potential.				muscle filament sliding	muscle myosin complex|myosin filament|sarcomere	actin binding|ATP binding|calmodulin binding|microfilament motor activity|structural constituent of muscle			ovary(10)|skin(2)|central_nervous_system(1)	13						GTCAATCTCAGATTTCACCTG	0.383													18	80	---	---	---	---	PASS
PIGL	9487	broad.mit.edu	37	17	16137283	16137283	+	Splice_Site	SNP	A	T	T			TCGA-43-6647-01	TCGA-43-6647-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:16137283A>T	uc002gpv.2	+	2	268	c.236_splice	c.e2-2	p.G79_splice	PIGL_uc010vwd.1_Splice_Site_p.G79_splice	NM_004278	NP_004269	Q9Y2B2	PIGL_HUMAN	phosphatidylinositol glycan anchor biosynthesis,						C-terminal protein lipidation|preassembly of GPI anchor in ER membrane	endoplasmic reticulum membrane|integral to membrane	N-acetylglucosaminylphosphatidylinositol deacetylase activity				0				UCEC - Uterine corpus endometrioid carcinoma (92;0.0934)		TGTTACCCTCAGGAAATTACT	0.348													5	46	---	---	---	---	PASS
TAOK1	57551	broad.mit.edu	37	17	27805292	27805292	+	Missense_Mutation	SNP	G	A	A			TCGA-43-6647-01	TCGA-43-6647-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:27805292G>A	uc002hdz.1	+	6	570	c.376G>A	c.(376-378)GTG>ATG	p.V126M	TAOK1_uc010wbe.1_Missense_Mutation_p.V126M|TAOK1_uc010wbf.1_Missense_Mutation_p.V126M|TAOK1_uc002heb.1_5'Flank	NM_020791	NP_065842	Q7L7X3	TAOK1_HUMAN	TAO kinase 1	126	Protein kinase.				mitotic prometaphase	cytosol|intracellular membrane-bounded organelle	ATP binding|protein serine/threonine kinase activity			upper_aerodigestive_tract(1)|lung(1)|central_nervous_system(1)|skin(1)	4			Colorectal(6;0.198)			ATTACAAGAAGTGGAAATAGC	0.289													13	95	---	---	---	---	PASS
KRT35	3886	broad.mit.edu	37	17	39635146	39635146	+	Nonsense_Mutation	SNP	G	T	T			TCGA-43-6647-01	TCGA-43-6647-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:39635146G>T	uc002hws.2	-	4	856	c.813C>A	c.(811-813)TGC>TGA	p.C271*		NM_002280	NP_002271	Q92764	KRT35_HUMAN	keratin 35	271	Rod.|Coil 2.				anatomical structure morphogenesis	intermediate filament	protein binding|structural molecule activity			ovary(1)|skin(1)	2		Breast(137;0.000286)				TTTCATACTGGCACCTCATCT	0.557													4	94	---	---	---	---	PASS
DBF4B	80174	broad.mit.edu	37	17	42800348	42800348	+	Missense_Mutation	SNP	G	T	T			TCGA-43-6647-01	TCGA-43-6647-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:42800348G>T	uc002ihf.2	+	3	396	c.183G>T	c.(181-183)AAG>AAT	p.K61N	DBF4B_uc002ihd.1_Missense_Mutation_p.K61N|DBF4B_uc010wjb.1_RNA|DBF4B_uc002ihe.2_5'UTR|DBF4B_uc010wjc.1_Missense_Mutation_p.K45N|DBF4B_uc002ihg.2_Missense_Mutation_p.K45N	NM_145663	NP_663696	Q8NFT6	DBF4B_HUMAN	DBF4 homolog B isoform 1	61	BRCT.				cell cycle	nucleus	nucleic acid binding|zinc ion binding				0		Prostate(33;0.0322)				CTGCTGGCAAGAATCTCCAGT	0.527													15	82	---	---	---	---	PASS
ITGB4	3691	broad.mit.edu	37	17	73753277	73753277	+	Intron	SNP	C	T	T			TCGA-43-6647-01	TCGA-43-6647-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:73753277C>T	uc002jpg.2	+						ITGB4_uc002jph.2_Intron|ITGB4_uc002jpi.3_Intron|ITGB4_uc002jpj.2_Intron|GALK1_uc010wsi.1_Intron	NM_000213	NP_000204	P16144	ITB4_HUMAN	integrin beta 4 isoform 1 precursor						cell communication|cell motility|cell-matrix adhesion|hemidesmosome assembly|integrin-mediated signaling pathway|multicellular organismal development|response to wounding	cell leading edge|cell surface|hemidesmosome|integrin complex	protein binding|receptor activity			lung(4)	4	all_cancers(13;1.5e-07)		all cancers(21;8.32e-07)|Epithelial(20;1.92e-06)|BRCA - Breast invasive adenocarcinoma(9;0.00194)|Lung(188;0.132)|LUSC - Lung squamous cell carcinoma(166;0.154)			TCTGCCCACCCCAGGACCCTT	0.672													8	74	---	---	---	---	PASS
MGAT5B	146664	broad.mit.edu	37	17	74934111	74934111	+	Missense_Mutation	SNP	G	C	C			TCGA-43-6647-01	TCGA-43-6647-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:74934111G>C	uc002jti.2	+	11	1600	c.1497G>C	c.(1495-1497)GAG>GAC	p.E499D	MGAT5B_uc002jth.2_Missense_Mutation_p.E488D	NM_198955	NP_945193	Q3V5L5	MGT5B_HUMAN	N-acetylglucosaminyltranferase VB isoform 2	490	Lumenal (Potential).					Golgi membrane|integral to membrane	alpha-1,6-mannosyl-glycoprotein 6-beta-N-acetylglucosaminyltransferase activity|metal ion binding			ovary(2)|skin(1)	3						AATACATGGAGATCCATGGCA	0.552													5	71	---	---	---	---	PASS
SMAD4	4089	broad.mit.edu	37	18	48581307	48581307	+	Missense_Mutation	SNP	C	A	A			TCGA-43-6647-01	TCGA-43-6647-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:48581307C>A	uc010xdp.1	+	5	1149	c.611C>A	c.(610-612)TCT>TAT	p.S204Y	SMAD4_uc010xdo.1_RNA|SMAD4_uc002lfb.3_Missense_Mutation_p.S49Y	NM_005359	NP_005350	Q13485	SMAD4_HUMAN	mothers against decapentaplegic homolog 4	204					BMP signaling pathway|negative regulation of cell growth|negative regulation of protein catabolic process|negative regulation of transcription, DNA-dependent|palate development|positive regulation of epithelial to mesenchymal transition|positive regulation of pathway-restricted SMAD protein phosphorylation|positive regulation of SMAD protein import into nucleus|positive regulation of transforming growth factor beta receptor signaling pathway|regulation of transforming growth factor-beta2 production|response to hypoxia|response to transforming growth factor beta stimulus|SMAD protein complex assembly|SMAD protein signal transduction|transforming growth factor beta receptor signaling pathway	activin responsive factor complex|centrosome|cytosol	I-SMAD binding|protein homodimerization activity|R-SMAD binding|transcription regulatory region DNA binding|transforming growth factor beta receptor, common-partner cytoplasmic mediator activity	p.0?(35)|p.?(3)		pancreas(170)|large_intestine(108)|thyroid(19)|lung(11)|small_intestine(9)|upper_aerodigestive_tract(8)|biliary_tract(8)|ovary(7)|breast(6)|stomach(5)|oesophagus(3)|testis(2)|central_nervous_system(2)|haematopoietic_and_lymphoid_tissue(2)|gastrointestinal_tract_(site_indeterminate)(2)|liver(2)|kidney(1)|urinary_tract(1)|vulva(1)|skin(1)|NS(1)	369		all_cancers(7;0.203)|Colorectal(6;0.003)|all_epithelial(6;0.00336)		Colorectal(16;0.0032)|COAD - Colon adenocarcinoma(17;0.0708)|READ - Rectum adenocarcinoma(32;0.155)		TTAGCCCCATCTGAGTCTAAT	0.468									Juvenile_Polyposis|Hereditary_Hemorrhagic_Telangiectasia				10	116	---	---	---	---	PASS
STK11	6794	broad.mit.edu	37	19	1218443	1218443	+	Silent	SNP	G	A	A			TCGA-43-6647-01	TCGA-43-6647-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:1218443G>A	uc002lrl.1	+	2	1433	c.318G>A	c.(316-318)CGG>CGA	p.R106R		NM_000455	NP_000446	Q15831	STK11_HUMAN	serine/threonine protein kinase 11	106	Protein kinase.				anoikis|cell cycle arrest|energy reserve metabolic process|insulin receptor signaling pathway|positive regulation of transforming growth factor beta receptor signaling pathway|regulation of fatty acid biosynthetic process|regulation of fatty acid oxidation	cytosol|nucleus	ATP binding|magnesium ion binding|protein serine/threonine kinase activity	p.0?(19)|p.?(3)|p.E98_G155del(3)|p.R106R(1)|p.G52_P179del(1)		lung(174)|cervix(35)|skin(15)|large_intestine(12)|pancreas(6)|gastrointestinal_tract_(site_indeterminate)(5)|stomach(4)|ovary(4)|breast(2)|upper_aerodigestive_tract(1)|testis(1)|liver(1)|biliary_tract(1)|small_intestine(1)|urinary_tract(1)|oesophagus(1)|prostate(1)|kidney(1)	266		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;7.93e-06)|all_lung(49;1.25e-05)|Breast(49;0.000172)|Renal(1328;0.0183)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|Lung(535;0.00942)|STAD - Stomach adenocarcinoma(1328;0.18)		GGAGGTTACGGCACAAAAATG	0.552		14	D|Mis|N|F|S		NSCLC|pancreatic	jejunal harmartoma|ovarian|testicular|pancreatic			Peutz-Jeghers_syndrome	TSP Lung(3;<1E-08)			4	189	---	---	---	---	PASS
ZNF77	58492	broad.mit.edu	37	19	2936662	2936662	+	Missense_Mutation	SNP	C	A	A			TCGA-43-6647-01	TCGA-43-6647-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:2936662C>A	uc002lws.3	-	3	302	c.171G>T	c.(169-171)CAG>CAT	p.Q57H		NM_021217	NP_067040	Q15935	ZNF77_HUMAN	zinc finger protein 77	57	KRAB.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleolus	DNA binding|zinc ion binding			ovary(1)	1				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|GBM - Glioblastoma multiforme(1328;2.11e-07)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|Lung(535;0.174)|STAD - Stomach adenocarcinoma(1328;0.18)		AAACGTCCCTCTGAGAACTTG	0.348													10	67	---	---	---	---	PASS
FUT3	2525	broad.mit.edu	37	19	5844073	5844073	+	Missense_Mutation	SNP	G	T	T			TCGA-43-6647-01	TCGA-43-6647-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:5844073G>T	uc002mdk.2	-	2	875	c.778C>A	c.(778-780)CTG>ATG	p.L260M	FUT3_uc002mdm.2_Missense_Mutation_p.L260M|FUT3_uc002mdj.2_Missense_Mutation_p.L260M|FUT3_uc002mdl.2_Missense_Mutation_p.L260M	NM_001097641	NP_001091110	P21217	FUT3_HUMAN	fucosyltransferase 3	260	Lumenal (Potential).				protein glycosylation	Golgi cisterna membrane|integral to membrane|membrane fraction	3-galactosyl-N-acetylglucosaminide 4-alpha-L-fucosyltransferase activity				0						TTCCTCCACAGCTTCTCGGTG	0.632													20	119	---	---	---	---	PASS
MUC16	94025	broad.mit.edu	37	19	8993440	8993440	+	Silent	SNP	G	A	A			TCGA-43-6647-01	TCGA-43-6647-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:8993440G>A	uc002mkp.2	-	66	41853	c.41649C>T	c.(41647-41649)AGC>AGT	p.S13883S	MUC16_uc010dwi.2_RNA|MUC16_uc010dwj.2_Silent_p.S700S|MUC16_uc010xki.1_RNA	NM_024690	NP_078966	Q8WXI7	MUC16_HUMAN	mucin 16	13886	Extracellular (Potential).|SEA 12.			Missing (in Ref. 3; AAK74120).	cell adhesion	extracellular space|extrinsic to membrane|integral to membrane|plasma membrane	protein binding			lung(30)|ovary(15)|breast(8)|large_intestine(1)|skin(1)|prostate(1)|pancreas(1)	57						GGGTCAGCTGGCTCAGCTCCA	0.592													8	146	---	---	---	---	PASS
ICAM5	7087	broad.mit.edu	37	19	10403724	10403724	+	Missense_Mutation	SNP	G	A	A			TCGA-43-6647-01	TCGA-43-6647-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:10403724G>A	uc002mnu.3	+	6	1332	c.1267G>A	c.(1267-1269)GAG>AAG	p.E423K	ICAM5_uc002mnv.3_Missense_Mutation_p.E298K	NM_003259	NP_003250	Q9UMF0	ICAM5_HUMAN	intercellular adhesion molecule 5 precursor	423	Extracellular (Potential).|Ig-like C2-type 5.				cell-cell adhesion	integral to plasma membrane				breast(3)	3			OV - Ovarian serous cystadenocarcinoma(20;2.64e-09)|Epithelial(33;4.31e-06)|all cancers(31;9.75e-06)			GACGTGGCCCGAGGGCCCAGA	0.692													9	67	---	---	---	---	PASS
TMEM205	374882	broad.mit.edu	37	19	11453492	11453492	+	Nonstop_Mutation	SNP	T	A	A			TCGA-43-6647-01	TCGA-43-6647-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:11453492T>A	uc002mrb.2	-	4	757	c.569A>T	c.(568-570)TAG>TTG	p.*190L	TMEM205_uc002mra.2_Nonstop_Mutation_p.*190L|TMEM205_uc002mqz.2_Nonstop_Mutation_p.*190L|TMEM205_uc002mrc.2_Nonstop_Mutation_p.*190L	NM_001145416	NP_001138888	Q6UW68	TM205_HUMAN	transmembrane protein 205	190						integral to membrane					0						GGGCCCATGCTAGAGGCTCCT	0.542													23	157	---	---	---	---	PASS
ZNF536	9745	broad.mit.edu	37	19	31039443	31039443	+	Missense_Mutation	SNP	T	A	A			TCGA-43-6647-01	TCGA-43-6647-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:31039443T>A	uc002nsu.1	+	4	3055	c.2917T>A	c.(2917-2919)TAT>AAT	p.Y973N	ZNF536_uc010edd.1_Missense_Mutation_p.Y973N	NM_014717	NP_055532	O15090	ZN536_HUMAN	zinc finger protein 536	973					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	zinc ion binding			ovary(7)|large_intestine(2)|skin(2)	11	Esophageal squamous(110;0.0834)					GAAATCTCAGTATGAACCCCT	0.592													21	121	---	---	---	---	PASS
ZNF536	9745	broad.mit.edu	37	19	31039656	31039656	+	Nonsense_Mutation	SNP	C	T	T			TCGA-43-6647-01	TCGA-43-6647-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:31039656C>T	uc002nsu.1	+	4	3268	c.3130C>T	c.(3130-3132)CAA>TAA	p.Q1044*	ZNF536_uc010edd.1_Nonsense_Mutation_p.Q1044*	NM_014717	NP_055532	O15090	ZN536_HUMAN	zinc finger protein 536	1044					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	zinc ion binding			ovary(7)|large_intestine(2)|skin(2)	11	Esophageal squamous(110;0.0834)					CTGCAAAGACCAAGCCCGGGA	0.542													5	66	---	---	---	---	PASS
LIN37	55957	broad.mit.edu	37	19	36245292	36245292	+	Splice_Site	SNP	A	T	T			TCGA-43-6647-01	TCGA-43-6647-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:36245292A>T	uc002obm.2	+	10	774	c.660_splice	c.e10-2	p.R220_splice	uc002obl.2_5'Flank	NM_019104	NP_061977	Q96GY3	LIN37_HUMAN	lin-37 homolog								protein binding				0	all_lung(56;3.33e-07)|Lung NSC(56;5.02e-07)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0515)			CTGCCTCCCCAGGTGGAAGGA	0.597													21	55	---	---	---	---	PASS
NPHS1	4868	broad.mit.edu	37	19	36339628	36339628	+	Missense_Mutation	SNP	A	T	T			TCGA-43-6647-01	TCGA-43-6647-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:36339628A>T	uc002oby.2	-	9	1081	c.1081T>A	c.(1081-1083)TGT>AGT	p.C361S		NM_004646	NP_004637	O60500	NPHN_HUMAN	nephrin precursor	361	Ig-like C2-type 4.|Extracellular (Potential).				cell adhesion|excretion|muscle organ development	integral to plasma membrane				ovary(4)|skin(1)	5	all_lung(56;7.14e-07)|Lung NSC(56;1.12e-06)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0515)			TTGCTGACACAGGAGAGTGTC	0.577													9	92	---	---	---	---	PASS
KIRREL2	84063	broad.mit.edu	37	19	36350435	36350435	+	Missense_Mutation	SNP	C	A	A			TCGA-43-6647-01	TCGA-43-6647-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:36350435C>A	uc002ocb.3	+	5	787	c.575C>A	c.(574-576)ACC>AAC	p.T192N	KIRREL2_uc002obz.3_Missense_Mutation_p.T192N|KIRREL2_uc002oca.3_Missense_Mutation_p.T142N|KIRREL2_uc002occ.3_Missense_Mutation_p.T139N|KIRREL2_uc002ocd.3_Missense_Mutation_p.T189N	NM_199180	NP_954649	Q6UWL6	KIRR2_HUMAN	kin of IRRE-like 2 isoform c	192	Ig-like C2-type 2.|Extracellular (Potential).				cell adhesion	integral to membrane|plasma membrane				ovary(1)|central_nervous_system(1)|skin(1)	3	all_lung(56;7.14e-07)|Lung NSC(56;1.12e-06)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0515)			TTAACCCTGACCCCTTTCAGC	0.542													12	112	---	---	---	---	PASS
ZNF226	7769	broad.mit.edu	37	19	44680803	44680803	+	Missense_Mutation	SNP	A	G	G			TCGA-43-6647-01	TCGA-43-6647-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:44680803A>G	uc002oyp.2	+	6	1532	c.1388A>G	c.(1387-1389)CAG>CGG	p.Q463R	ZNF226_uc002oyq.2_Missense_Mutation_p.Q346R|ZNF226_uc002oyr.2_Missense_Mutation_p.Q346R|ZNF226_uc010ejg.2_3'UTR|ZNF226_uc002oys.2_Missense_Mutation_p.Q463R|ZNF226_uc002oyt.2_Missense_Mutation_p.Q463R	NM_001032373	NP_001027545	Q9NYT6	ZN226_HUMAN	zinc finger protein 226 isoform a	463	C2H2-type 8.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0		Prostate(69;0.0352)|all_neural(266;0.202)				TCAAGTCTTCAGGCCCATCAG	0.433													3	89	---	---	---	---	PASS
KLK12	43849	broad.mit.edu	37	19	51535168	51535168	+	Missense_Mutation	SNP	G	T	T			TCGA-43-6647-01	TCGA-43-6647-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:51535168G>T	uc002pvg.1	-	3	541	c.421C>A	c.(421-423)CAC>AAC	p.H141N	KLK12_uc010ycp.1_RNA|KLK12_uc010ycq.1_Intron|KLK12_uc010ycr.1_Intron|KLK12_uc010ycs.1_Intron|KLK12_uc002pvh.1_Missense_Mutation_p.H141N|KLK12_uc002pvi.1_Missense_Mutation_p.H141N|KLK12_uc002pvj.1_Intron	NM_145894	NP_665901	Q9UKR0	KLK12_HUMAN	kallikrein 12 isoform 2	141	Peptidase S1.				proteolysis	extracellular region|soluble fraction	serine-type endopeptidase activity			ovary(1)	1		all_neural(266;0.026)		OV - Ovarian serous cystadenocarcinoma(262;0.00328)|GBM - Glioblastoma multiforme(134;0.00399)		CCTGAGACGTGGCACTCGGTG	0.677													18	136	---	---	---	---	PASS
ZNF816A	125893	broad.mit.edu	37	19	53454512	53454512	+	Silent	SNP	A	G	G			TCGA-43-6647-01	TCGA-43-6647-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:53454512A>G	uc002qal.1	-	5	817	c.516T>C	c.(514-516)ACT>ACC	p.T172T	ZNF321_uc010eqj.2_Intron|ZNF321_uc002qak.1_Intron|ZNF816A_uc002qam.1_Silent_p.T156T	NM_001031665	NP_001026835	Q0VGE8	ZN816_HUMAN	zinc finger protein 816A	172					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0				GBM - Glioblastoma multiforme(134;0.0313)		TTTTCCCTTTAGTCTGAAACA	0.403													23	167	---	---	---	---	PASS
SIRPG	55423	broad.mit.edu	37	20	1616921	1616921	+	Missense_Mutation	SNP	G	A	A			TCGA-43-6647-01	TCGA-43-6647-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:1616921G>A	uc002wfm.1	-	3	726	c.661C>T	c.(661-663)CGC>TGC	p.R221C	SIRPG_uc002wfn.1_Missense_Mutation_p.R221C|SIRPG_uc002wfo.1_Intron|uc002wfp.1_Intron	NM_018556	NP_061026	Q9P1W8	SIRPG_HUMAN	signal-regulatory protein gamma isoform 1	221	Extracellular (Potential).|Ig-like C1-type 1.				blood coagulation|cell adhesion|cell junction assembly|cell-cell signaling|intracellular signal transduction|leukocyte migration|negative regulation of cell proliferation|positive regulation of cell proliferation|positive regulation of cell-cell adhesion|positive regulation of T cell activation	integral to membrane|intracellular|plasma membrane	protein binding			ovary(1)	1						ACCTGAGAGCGAACGTCCCAG	0.617													4	114	---	---	---	---	PASS
BFSP1	631	broad.mit.edu	37	20	17495386	17495386	+	Missense_Mutation	SNP	C	A	A			TCGA-43-6647-01	TCGA-43-6647-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:17495386C>A	uc002wpo.2	-	3	553	c.514G>T	c.(514-516)GCA>TCA	p.A172S	BFSP1_uc002wpp.2_Missense_Mutation_p.A47S|BFSP1_uc010zrn.1_Missense_Mutation_p.A33S|BFSP1_uc010zro.1_Missense_Mutation_p.A33S	NM_001195	NP_001186	Q12934	BFSP1_HUMAN	filensin isoform 1	172	Rod.|Coil 1B.					cytoplasm|intermediate filament|membrane	structural constituent of cytoskeleton|structural constituent of eye lens			central_nervous_system(1)	1						CTGTCCTTTGCCGCACTGATA	0.502													11	240	---	---	---	---	PASS
BCL2L1	598	broad.mit.edu	37	20	30253775	30253775	+	Missense_Mutation	SNP	C	A	A			TCGA-43-6647-01	TCGA-43-6647-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:30253775C>A	uc002wwl.2	-	3	1045	c.679G>T	c.(679-681)GGC>TGC	p.G227C	BCL2L1_uc002wwk.2_RNA|BCL2L1_uc002wwm.2_Missense_Mutation_p.G164C|BCL2L1_uc002wwn.2_Missense_Mutation_p.G227C	NM_138578	NP_612815	Q07817	B2CL1_HUMAN	BCL2-like 1 isoform 1	227					induction of apoptosis by intracellular signals|negative regulation of establishment of protein localization in plasma membrane|negative regulation of survival gene product expression|regulation of mitochondrial membrane permeability|regulation of mitochondrial membrane potential|release of cytochrome c from mitochondria|response to cytokine stimulus	integral to membrane|mitochondrial outer membrane|nuclear membrane	BH3 domain binding|identical protein binding			lung(1)|central_nervous_system(1)	2	all_cancers(5;3.47e-06)|all_epithelial(3;1.83e-06)|Lung NSC(7;2.08e-06)|all_lung(7;3.63e-06)|all_hematologic(12;0.158)|Ovarian(7;0.198)		Epithelial(4;2.97e-06)|all cancers(5;3.21e-05)|OV - Ovarian serous cystadenocarcinoma(3;0.00052)|Colorectal(19;0.0055)|COAD - Colon adenocarcinoma(19;0.0264)			AAGAGTGAGCCCAGCAGAACC	0.602													11	70	---	---	---	---	PASS
BCL2L1	598	broad.mit.edu	37	20	30253776	30253776	+	Silent	SNP	C	G	G			TCGA-43-6647-01	TCGA-43-6647-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:30253776C>G	uc002wwl.2	-	3	1044	c.678G>C	c.(676-678)CTG>CTC	p.L226L	BCL2L1_uc002wwk.2_RNA|BCL2L1_uc002wwm.2_Silent_p.L163L|BCL2L1_uc002wwn.2_Silent_p.L226L	NM_138578	NP_612815	Q07817	B2CL1_HUMAN	BCL2-like 1 isoform 1	226	Helical; (Potential).				induction of apoptosis by intracellular signals|negative regulation of establishment of protein localization in plasma membrane|negative regulation of survival gene product expression|regulation of mitochondrial membrane permeability|regulation of mitochondrial membrane potential|release of cytochrome c from mitochondria|response to cytokine stimulus	integral to membrane|mitochondrial outer membrane|nuclear membrane	BH3 domain binding|identical protein binding			lung(1)|central_nervous_system(1)	2	all_cancers(5;3.47e-06)|all_epithelial(3;1.83e-06)|Lung NSC(7;2.08e-06)|all_lung(7;3.63e-06)|all_hematologic(12;0.158)|Ovarian(7;0.198)		Epithelial(4;2.97e-06)|all cancers(5;3.21e-05)|OV - Ovarian serous cystadenocarcinoma(3;0.00052)|Colorectal(19;0.0055)|COAD - Colon adenocarcinoma(19;0.0264)			AGAGTGAGCCCAGCAGAACCA	0.602													10	71	---	---	---	---	PASS
SEMG2	6407	broad.mit.edu	37	20	43850507	43850507	+	Nonsense_Mutation	SNP	G	A	A			TCGA-43-6647-01	TCGA-43-6647-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:43850507G>A	uc010ggz.2	+	2	291	c.234G>A	c.(232-234)TGG>TGA	p.W78*	SEMG2_uc002xnk.2_Nonsense_Mutation_p.W78*|SEMG2_uc002xnl.2_Nonsense_Mutation_p.W78*	NM_003008	NP_002999	Q02383	SEMG2_HUMAN	semenogelin II precursor	78	Repeat-rich region.|3-1.				sexual reproduction	extracellular space|stored secretory granule	structural molecule activity			skin(1)	1		Myeloproliferative disorder(115;0.0122)				ATCATGACTGGACCCGAAAAA	0.373													6	75	---	---	---	---	PASS
TPD52L2	7165	broad.mit.edu	37	20	62517372	62517372	+	Intron	SNP	T	C	C			TCGA-43-6647-01	TCGA-43-6647-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:62517372T>C	uc002yhc.2	+						TPD52L2_uc002ygy.2_Silent_p.A160A|TPD52L2_uc002ygz.2_Intron|TPD52L2_uc002yha.2_Silent_p.A140A|TPD52L2_uc002yhb.2_Intron|TPD52L2_uc002yhd.2_Intron|TPD52L2_uc011abk.1_Intron|TPD52L2_uc011abl.1_Intron|TPD52L2_uc002yhe.2_Intron	NM_003288	NP_003279	O43399	TPD54_HUMAN	tumor protein D52-like 2 isoform e						regulation of cell proliferation	perinuclear region of cytoplasm	protein binding|protein homodimerization activity			ovary(1)|skin(1)	2	all_cancers(38;1.3e-12)|all_epithelial(29;2.23e-14)|Lung NSC(23;5.92e-10)|all_lung(23;2.08e-09)					CTTCCAGGGCTCATCCATTTT	0.602													7	116	---	---	---	---	PASS
LOC96610	96610	broad.mit.edu	37	22	22712462	22712462	+	RNA	SNP	T	C	C			TCGA-43-6647-01	TCGA-43-6647-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:22712462T>C	uc011aim.1	+	41		c.4250T>C								Parts of antibodies, mostly variable regions.												0						ACTCCTCATCTATAGTAATAA	0.562													4	188	---	---	---	---	PASS
LOC96610	96610	broad.mit.edu	37	22	22712501	22712501	+	RNA	SNP	T	G	G			TCGA-43-6647-01	TCGA-43-6647-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:22712501T>G	uc011aim.1	+	41		c.4289T>G								Parts of antibodies, mostly variable regions.												0						CCCTGACCGATTCTCTGGCTC	0.557													6	202	---	---	---	---	PASS
MTMR3	8897	broad.mit.edu	37	22	30415501	30415501	+	Missense_Mutation	SNP	C	A	A			TCGA-43-6647-01	TCGA-43-6647-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:30415501C>A	uc003agv.3	+	17	2181	c.1853C>A	c.(1852-1854)ACC>AAC	p.T618N	MTMR3_uc003agu.3_Missense_Mutation_p.T618N|MTMR3_uc003agw.3_Missense_Mutation_p.T618N	NM_021090	NP_066576	Q13615	MTMR3_HUMAN	myotubularin-related protein 3 isoform c	618					phosphatidylinositol dephosphorylation	cytoplasm|membrane|membrane fraction|nucleus	metal ion binding|phosphatidylinositol-3-phosphatase activity|protein serine/threonine phosphatase activity|protein tyrosine phosphatase activity			breast(3)|ovary(1)|skin(1)	5			OV - Ovarian serous cystadenocarcinoma(5;0.00204)|Epithelial(10;0.06)|all cancers(5;0.107)			GACAATCTGACCACAGCCTGT	0.532													3	86	---	---	---	---	PASS
CSF2RB	1439	broad.mit.edu	37	22	37333578	37333578	+	Silent	SNP	C	T	T			TCGA-43-6647-01	TCGA-43-6647-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:37333578C>T	uc003aqa.3	+	14	1945	c.1728C>T	c.(1726-1728)GCC>GCT	p.A576A	CSF2RB_uc003aqc.3_Silent_p.A582A	NM_000395	NP_000386	P32927	IL3RB_HUMAN	colony stimulating factor 2 receptor, beta	576	Cytoplasmic (Potential).				respiratory gaseous exchange	granulocyte macrophage colony-stimulating factor receptor complex	cytokine receptor activity			skin(2)|pancreas(1)	3					Sargramostim(DB00020)	CGCCTGCCGCCTCCCACACAC	0.657													4	26	---	---	---	---	PASS
KLHDC7B	113730	broad.mit.edu	37	22	50988132	50988132	+	Missense_Mutation	SNP	A	G	G	rs137863644		TCGA-43-6647-01	TCGA-43-6647-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:50988132A>G	uc003bmi.2	+	1	1671	c.1537A>G	c.(1537-1539)ACA>GCA	p.T513A		NM_138433	NP_612442	Q96G42	KLD7B_HUMAN	kelch domain containing 7B	513	Kelch 5.									central_nervous_system(1)	1		all_cancers(38;1.53e-10)|all_epithelial(38;1.82e-09)|Breast(42;0.000448)|all_lung(38;0.000665)|Lung NSC(38;0.0104)|Ovarian(80;0.104)|Lung SC(80;0.162)|Hepatocellular(38;0.178)		OV - Ovarian serous cystadenocarcinoma(4;7.49e-69)|all cancers(3;9.79e-66)|Epithelial(4;1.3e-63)|GBM - Glioblastoma multiforme(4;0.000399)|Lung(4;0.125)|BRCA - Breast invasive adenocarcinoma(115;0.205)|LUAD - Lung adenocarcinoma(64;0.247)		GCGCTACAACACAGTGACCGG	0.697													3	57	---	---	---	---	PASS
CSF2RA	1438	broad.mit.edu	37	X	1422916	1422916	+	Intron	SNP	A	G	G			TCGA-43-6647-01	TCGA-43-6647-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:1422916A>G	uc010nct.2	+						CSF2RA_uc011mhb.1_Intron|CSF2RA_uc004cpq.2_Intron|CSF2RA_uc004cpn.2_Intron|CSF2RA_uc004cpo.2_Intron|CSF2RA_uc010ncu.2_Intron|CSF2RA_uc011mhc.1_Intron|CSF2RA_uc004cpp.2_Intron|CSF2RA_uc010ncv.2_Intron|CSF2RA_uc004cpr.2_Intron	NM_001161529	NP_001155001	P15509	CSF2R_HUMAN	colony stimulating factor 2 receptor alpha chain							extracellular region|integral to plasma membrane	cytokine receptor activity			ovary(2)	2		all_cancers(21;4.28e-07)|all_epithelial(21;2.07e-08)|all_lung(23;2.81e-05)|Lung NSC(23;0.000693)|Lung SC(21;0.122)			Sargramostim(DB00020)	TTAAAAGGTAACCTGTGAAAC	0.527													9	291	---	---	---	---	PASS
SHROOM2	357	broad.mit.edu	37	X	9863737	9863737	+	Missense_Mutation	SNP	C	G	G			TCGA-43-6647-01	TCGA-43-6647-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:9863737C>G	uc004csu.1	+	4	1879	c.1789C>G	c.(1789-1791)CGG>GGG	p.R597G		NM_001649	NP_001640	Q13796	SHRM2_HUMAN	apical protein of Xenopus-like	597					apical protein localization|brain development|cell migration|cell morphogenesis|cellular pigment accumulation|ear development|establishment of melanosome localization|eye pigment granule organization|lens morphogenesis in camera-type eye|melanosome organization	apical plasma membrane|cell-cell adherens junction|microtubule|tight junction	actin filament binding|beta-catenin binding|ligand-gated sodium channel activity			ovary(3)|skin(3)|upper_aerodigestive_tract(1)|breast(1)	8		Hepatocellular(5;0.000888)				GGGGAAGCGCCGGCCTGAGAG	0.682													2	9	---	---	---	---	PASS
DCAF8L1	139425	broad.mit.edu	37	X	27999274	27999274	+	Missense_Mutation	SNP	G	T	T	rs139451923	byFrequency	TCGA-43-6647-01	TCGA-43-6647-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:27999274G>T	uc004dbx.1	-	1	293	c.178C>A	c.(178-180)CTG>ATG	p.L60M		NM_001017930	NP_001017930	A6NGE4	DC8L1_HUMAN	DDB1 and CUL4 associated factor 8-like 1	60										ovary(3)|skin(1)	4						GCATCGTTCAGGAAACCACCA	0.507													12	105	---	---	---	---	PASS
DMD	1756	broad.mit.edu	37	X	32360339	32360339	+	Missense_Mutation	SNP	C	G	G			TCGA-43-6647-01	TCGA-43-6647-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:32360339C>G	uc004dda.1	-	41	6044	c.5800G>C	c.(5800-5802)GAG>CAG	p.E1934Q	DMD_uc004dcw.2_Missense_Mutation_p.E590Q|DMD_uc004dcx.2_Missense_Mutation_p.E593Q|DMD_uc004dcz.2_Missense_Mutation_p.E1811Q|DMD_uc004dcy.1_Missense_Mutation_p.E1930Q|DMD_uc004ddb.1_Missense_Mutation_p.E1926Q|DMD_uc010ngo.1_Intron	NM_004006	NP_003997	P11532	DMD_HUMAN	dystrophin Dp427m isoform	1934	Spectrin 13.				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)				GACAAGCCCTCAGCTTGCCTA	0.522													12	59	---	---	---	---	PASS
SSX5	6758	broad.mit.edu	37	X	48047126	48047126	+	Missense_Mutation	SNP	C	G	G			TCGA-43-6647-01	TCGA-43-6647-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:48047126C>G	uc004dja.1	-	7	561	c.508G>C	c.(508-510)GAG>CAG	p.E170Q	SSX5_uc004diz.1_Missense_Mutation_p.E211Q	NM_175723	NP_783729	O60225	SSX5_HUMAN	synovial sarcoma, X breakpoint 5 isoform b	170					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	nucleic acid binding				0						TGCTTTCTCTCACGCACTCTG	0.498													29	468	---	---	---	---	PASS
KCND1	3750	broad.mit.edu	37	X	48825921	48825921	+	Missense_Mutation	SNP	G	T	T			TCGA-43-6647-01	TCGA-43-6647-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:48825921G>T	uc004dlx.1	-	1	2331	c.758C>A	c.(757-759)GCC>GAC	p.A253D	KCND1_uc004dlw.1_5'Flank	NM_004979	NP_004970	Q9NSA2	KCND1_HUMAN	potassium voltage-gated channel, Shal-related	253	Cytoplasmic (Potential).					voltage-gated potassium channel complex	metal ion binding|voltage-gated potassium channel activity			ovary(2)|lung(1)	3						ACGGCTGGGGGCGGCAAACAG	0.582													4	37	---	---	---	---	PASS
CCNB3	85417	broad.mit.edu	37	X	50053412	50053412	+	Missense_Mutation	SNP	C	T	T			TCGA-43-6647-01	TCGA-43-6647-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:50053412C>T	uc004dox.3	+	6	2541	c.2243C>T	c.(2242-2244)TCT>TTT	p.S748F	CCNB3_uc004doy.2_Missense_Mutation_p.S748F|CCNB3_uc004doz.2_Intron|CCNB3_uc010njq.2_Intron	NM_033031	NP_149020	Q8WWL7	CCNB3_HUMAN	cyclin B3 isoform 3	748					cell division|meiosis|regulation of cyclin-dependent protein kinase activity|regulation of G2/M transition of mitotic cell cycle	nucleus	protein kinase binding			ovary(4)|lung(3)|large_intestine(1)|pancreas(1)	9	Ovarian(276;0.236)					ACACAATTATCTTTAAAGAAG	0.418													4	29	---	---	---	---	PASS
DGKK	139189	broad.mit.edu	37	X	50133404	50133404	+	Missense_Mutation	SNP	C	A	A			TCGA-43-6647-01	TCGA-43-6647-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:50133404C>A	uc010njr.1	-	12	1908	c.1848G>T	c.(1846-1848)TGG>TGT	p.W616C		NM_001013742	NP_001013764	Q5KSL6	DGKK_HUMAN	diacylglycerol kinase kappa	616	DAGKc.				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)					TCATCACACTCCATCTGAAAT	0.388													27	176	---	---	---	---	PASS
DGKK	139189	broad.mit.edu	37	X	50133405	50133405	+	Missense_Mutation	SNP	C	G	G			TCGA-43-6647-01	TCGA-43-6647-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:50133405C>G	uc010njr.1	-	12	1907	c.1847G>C	c.(1846-1848)TGG>TCG	p.W616S		NM_001013742	NP_001013764	Q5KSL6	DGKK_HUMAN	diacylglycerol kinase kappa	616	DAGKc.				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)					CATCACACTCCATCTGAAATG	0.393													26	175	---	---	---	---	PASS
SHROOM4	57477	broad.mit.edu	37	X	50376730	50376730	+	Missense_Mutation	SNP	G	T	T			TCGA-43-6647-01	TCGA-43-6647-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:50376730G>T	uc004dpe.2	-	4	2369	c.2343C>A	c.(2341-2343)AGC>AGA	p.S781R	SHROOM4_uc004dpd.3_RNA|SHROOM4_uc004dpf.1_Missense_Mutation_p.S665R	NM_020717	NP_065768	Q9ULL8	SHRM4_HUMAN	shroom family member 4	781					actin filament organization|brain development|cell morphogenesis|cognition	apical plasma membrane|basal plasma membrane|internal side of plasma membrane|nucleus	actin filament binding			upper_aerodigestive_tract(1)	1	Ovarian(276;0.236)					ATAAGGATTTGCTACTCTCTT	0.433													17	135	---	---	---	---	PASS
MAGED2	10916	broad.mit.edu	37	X	54838617	54838617	+	Missense_Mutation	SNP	G	T	T			TCGA-43-6647-01	TCGA-43-6647-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:54838617G>T	uc004dtk.1	+	7	1112	c.1018G>T	c.(1018-1020)GAT>TAT	p.D340Y	MAGED2_uc004dtl.1_Missense_Mutation_p.D340Y|MAGED2_uc004dtm.1_Missense_Mutation_p.D255Y|MAGED2_uc010nkc.1_Missense_Mutation_p.D340Y|MAGED2_uc004dtn.1_Missense_Mutation_p.D340Y|MAGED2_uc004dto.1_Missense_Mutation_p.D314Y|SNORA11_uc004dtp.1_5'Flank	NM_177433	NP_803182	Q9UNF1	MAGD2_HUMAN	melanoma antigen family D, 2	340	MAGE.									ovary(2)|breast(1)	3						GAAGGAAATTGATAAGAATGA	0.498													6	70	---	---	---	---	PASS
FOXR2	139628	broad.mit.edu	37	X	55650240	55650240	+	Silent	SNP	G	A	A			TCGA-43-6647-01	TCGA-43-6647-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:55650240G>A	uc004duo.2	+	1	408	c.96G>A	c.(94-96)CTG>CTA	p.L32L		NM_198451	NP_940853	Q6PJQ5	FOXR2_HUMAN	forkhead box R2	32					embryo development|organ development|pattern specification process|regulation of sequence-specific DNA binding transcription factor activity|tissue development	transcription factor complex	DNA bending activity|double-stranded DNA binding|promoter binding|sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|specific RNA polymerase II transcription factor activity|specific transcriptional repressor activity|transcription activator activity|transcription factor binding			lung(2)|central_nervous_system(1)	3						AGTTATTTCTGCCTTGTACCA	0.468													13	100	---	---	---	---	PASS
FAM123B	139285	broad.mit.edu	37	X	63411933	63411933	+	Missense_Mutation	SNP	T	G	G			TCGA-43-6647-01	TCGA-43-6647-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:63411933T>G	uc004dvo.2	-	2	1507	c.1234A>C	c.(1234-1236)ACT>CCT	p.T412P		NM_152424	NP_689637	Q5JTC6	F123B_HUMAN	family with sequence similarity 123B	412					Wnt receptor signaling pathway	cytoplasm|nucleus|plasma membrane		p.0?(40)		kidney(99)|large_intestine(6)|ovary(3)|lung(2)|breast(1)|liver(1)	112						ATTTGGGCAGTTTCCCACAGA	0.333													6	118	---	---	---	---	PASS
AR	367	broad.mit.edu	37	X	66765851	66765851	+	Missense_Mutation	SNP	C	A	A			TCGA-43-6647-01	TCGA-43-6647-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:66765851C>A	uc004dwu.1	+	1	1978	c.863C>A	c.(862-864)GCC>GAC	p.A288D	AR_uc011mpd.1_Missense_Mutation_p.A288D|AR_uc011mpe.1_RNA|AR_uc011mpf.1_Missense_Mutation_p.A288D	NM_000044	NP_000035	P10275	ANDR_HUMAN	androgen receptor isoform 1	286	Modulating.				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)	GCCCCATTGGCCGAATGCAAA	0.557									Androgen_Insensitivity_Syndrome				6	57	---	---	---	---	PASS
KIAA2022	340533	broad.mit.edu	37	X	73963303	73963303	+	Silent	SNP	T	C	C			TCGA-43-6647-01	TCGA-43-6647-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:73963303T>C	uc004eby.2	-	3	1706	c.1089A>G	c.(1087-1089)CAA>CAG	p.Q363Q		NM_001008537	NP_001008537	Q5QGS0	K2022_HUMAN	hypothetical protein LOC340533	363					base-excision repair, gap-filling|DNA replication proofreading|DNA replication, removal of RNA primer|nucleotide-excision repair, DNA gap filling|regulation of mitotic cell cycle|S phase of mitotic cell cycle	delta DNA polymerase complex	3'-5'-exodeoxyribonuclease activity|DNA-directed DNA polymerase activity			ovary(7)|large_intestine(4)|skin(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)	15						GGACCTTGAATTGGGAAAAAT	0.478													18	83	---	---	---	---	PASS
BRWD3	254065	broad.mit.edu	37	X	79946652	79946652	+	Missense_Mutation	SNP	C	T	T			TCGA-43-6647-01	TCGA-43-6647-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:79946652C>T	uc004edt.2	-	31	3765	c.3502G>A	c.(3502-3504)GTT>ATT	p.V1168I	BRWD3_uc010nmi.1_RNA|BRWD3_uc004edo.2_Missense_Mutation_p.V764I|BRWD3_uc004edp.2_Missense_Mutation_p.V997I|BRWD3_uc004edq.2_Missense_Mutation_p.V764I|BRWD3_uc010nmj.1_Missense_Mutation_p.V764I|BRWD3_uc004edr.2_Missense_Mutation_p.V838I|BRWD3_uc004eds.2_Missense_Mutation_p.V764I|BRWD3_uc004edu.2_Missense_Mutation_p.V838I|BRWD3_uc004edv.2_Missense_Mutation_p.V764I|BRWD3_uc004edw.2_Missense_Mutation_p.V764I|BRWD3_uc004edx.2_Missense_Mutation_p.V764I|BRWD3_uc004edy.2_Missense_Mutation_p.V764I|BRWD3_uc004edz.2_Missense_Mutation_p.V838I|BRWD3_uc004eea.2_Missense_Mutation_p.V838I|BRWD3_uc004eeb.2_Missense_Mutation_p.V764I	NM_153252	NP_694984	Q6RI45	BRWD3_HUMAN	bromodomain and WD repeat domain containing 3	1168	Bromo 1.									ovary(4)	4						TCCACTGGAACAGCAAAAGGG	0.368													10	59	---	---	---	---	PASS
HDX	139324	broad.mit.edu	37	X	83724491	83724491	+	Silent	SNP	G	A	A			TCGA-43-6647-01	TCGA-43-6647-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:83724491G>A	uc004eek.1	-	3	349	c.240C>T	c.(238-240)ATC>ATT	p.I80I	HDX_uc011mqv.1_Silent_p.I80I|HDX_uc004eel.1_Silent_p.I22I	NM_144657	NP_653258	Q7Z353	HDX_HUMAN	highly divergent homeobox	80						nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			upper_aerodigestive_tract(1)|ovary(1)	2						TTCTGACTGTGATGTCTGGAG	0.438													14	56	---	---	---	---	PASS
BHLHB9	80823	broad.mit.edu	37	X	102004380	102004380	+	Missense_Mutation	SNP	C	G	G			TCGA-43-6647-01	TCGA-43-6647-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:102004380C>G	uc010nog.2	+	4	1028	c.457C>G	c.(457-459)CCT>GCT	p.P153A	BHLHB9_uc011mrq.1_Missense_Mutation_p.P153A|BHLHB9_uc011mrr.1_Missense_Mutation_p.P153A|BHLHB9_uc011mrs.1_Missense_Mutation_p.P153A|BHLHB9_uc011mrt.1_Missense_Mutation_p.P153A|BHLHB9_uc004ejo.2_Missense_Mutation_p.P153A|BHLHB9_uc011mru.1_Missense_Mutation_p.P153A|BHLHB9_uc011mrv.1_Missense_Mutation_p.P153A	NM_001142526	NP_001135998	Q6PI77	BHLH9_HUMAN	basic helix-loop-helix domain containing, class	153						cytoplasm|nucleus	binding			ovary(2)	2						GGAGTTGGAACCTGCGGCTGG	0.488													34	181	---	---	---	---	PASS
CXorf57	55086	broad.mit.edu	37	X	105876353	105876353	+	Intron	SNP	C	A	A			TCGA-43-6647-01	TCGA-43-6647-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:105876353C>A	uc004emi.3	+						CXorf57_uc004emj.3_Intron|CXorf57_uc004emh.2_Intron	NM_018015	NP_060485	Q6NSI4	CX057_HUMAN	hypothetical protein LOC55086											ovary(1)|lung(1)|breast(1)	3						ATATTCTATCCATATAGAAAA	0.299													22	103	---	---	---	---	PASS
STAG2	10735	broad.mit.edu	37	X	123205067	123205067	+	Missense_Mutation	SNP	G	T	T			TCGA-43-6647-01	TCGA-43-6647-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:123205067G>T	uc004etz.3	+	24	2766	c.2427G>T	c.(2425-2427)ATG>ATT	p.M809I	STAG2_uc004eua.2_Missense_Mutation_p.M809I|STAG2_uc004eub.2_Missense_Mutation_p.M809I|STAG2_uc004euc.2_Missense_Mutation_p.M809I|STAG2_uc004eud.2_Missense_Mutation_p.M809I|STAG2_uc004eue.2_Missense_Mutation_p.M809I	NM_006603	NP_006594	Q8N3U4	STAG2_HUMAN	stromal antigen 2 isoform b	809					cell division|meiosis|mitotic metaphase/anaphase transition|mitotic prometaphase|negative regulation of DNA endoreduplication|sister chromatid cohesion	chromatin|chromosome, centromeric region|nucleoplasm	protein binding			ovary(4)|skin(1)	5						GGCGTGACATGTTAGAGCCAT	0.363													29	235	---	---	---	---	PASS
DCAF12L2	340578	broad.mit.edu	37	X	125299535	125299535	+	Missense_Mutation	SNP	C	G	G			TCGA-43-6647-01	TCGA-43-6647-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:125299535C>G	uc004euk.1	-	1	400	c.373G>C	c.(373-375)GTG>CTG	p.V125L		NM_001013628	NP_001013650	Q5VW00	DC122_HUMAN	DDB1 and CUL4 associated factor 12-like 2	125										lung(2)|skin(2)|large_intestine(1)|pancreas(1)|ovary(1)	7						CCTGACTGCACGTCCACCACA	0.642													21	87	---	---	---	---	PASS
SMARCA1	6594	broad.mit.edu	37	X	128649887	128649887	+	Missense_Mutation	SNP	A	T	T			TCGA-43-6647-01	TCGA-43-6647-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:128649887A>T	uc004eun.3	-	4	626	c.513T>A	c.(511-513)TTT>TTA	p.F171L	SMARCA1_uc004eup.3_Missense_Mutation_p.F171L|SMARCA1_uc011muk.1_Missense_Mutation_p.F171L|SMARCA1_uc011mul.1_Missense_Mutation_p.F171L	NM_003069	NP_003060	P28370	SMCA1_HUMAN	SWI/SNF-related matrix-associated	171					ATP-dependent chromatin remodeling|brain development|neuron differentiation|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	NURF complex	ATP binding|DNA binding|helicase activity|nucleosome binding|protein binding			ovary(3)|skin(1)	4						GTGACACCTCAAATCTAATAC	0.348													13	83	---	---	---	---	PASS
ENOX2	10495	broad.mit.edu	37	X	129799638	129799638	+	Missense_Mutation	SNP	G	T	T			TCGA-43-6647-01	TCGA-43-6647-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:129799638G>T	uc004evw.2	-	10	1498	c.1080C>A	c.(1078-1080)AGC>AGA	p.S360R	ENOX2_uc004evx.2_Missense_Mutation_p.S331R|ENOX2_uc004evy.2_Missense_Mutation_p.S331R|ENOX2_uc004evv.2_Missense_Mutation_p.S187R	NM_182314	NP_872114	Q16206	ENOX2_HUMAN	ecto-NOX disulfide-thiol exchanger 2 isoform b	360					cell growth|electron transport chain|regulation of growth|transport|ultradian rhythm	cytosol|external side of plasma membrane|extracellular space	nucleic acid binding|nucleotide binding|protein disulfide oxidoreductase activity			ovary(1)	1						TGCACCACACGCTGATGTTCT	0.483													5	33	---	---	---	---	PASS
ARHGAP36	158763	broad.mit.edu	37	X	130217853	130217853	+	Silent	SNP	G	T	T			TCGA-43-6647-01	TCGA-43-6647-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:130217853G>T	uc004evz.2	+	4	810	c.465G>T	c.(463-465)GTG>GTT	p.V155V	ARHGAP36_uc004ewa.2_Silent_p.V143V|ARHGAP36_uc004ewb.2_Silent_p.V124V|ARHGAP36_uc004ewc.2_Silent_p.V19V	NM_144967	NP_659404	Q6ZRI8	RHG36_HUMAN	hypothetical protein LOC158763 precursor	155	Arg-rich.				regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol	GTPase activator activity			ovary(3)	3						GAAACGTGGTGCGAAGGGTGT	0.612													26	97	---	---	---	---	PASS
MIR513C	100302114	broad.mit.edu	37	X	146271247	146271247	+	RNA	SNP	G	T	T			TCGA-43-6647-01	TCGA-43-6647-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:146271247G>T	hsa-mir-513c|MI0006649	-			c.59G>T																				0						ttctcagaaaggtgaaattta	0.184													6	68	---	---	---	---	PASS
MAGEA1	4100	broad.mit.edu	37	X	152482623	152482623	+	Missense_Mutation	SNP	C	T	T			TCGA-43-6647-01	TCGA-43-6647-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:152482623C>T	uc004fhf.2	-	3	608	c.388G>A	c.(388-390)GAG>AAG	p.E130K		NM_004988	NP_004979	P43355	MAGA1_HUMAN	melanoma antigen family A, 1	130	MAGE.					cytoplasm|plasma membrane				central_nervous_system(7)|ovary(1)|lung(1)|breast(1)	10	all_hematologic(71;4.25e-06)|Acute lymphoblastic leukemia(192;6.56e-05)					ATGACACTCTCCAGCATTTCT	0.473													31	207	---	---	---	---	PASS
FLNA	2316	broad.mit.edu	37	X	153582286	153582286	+	Nonsense_Mutation	SNP	C	A	A			TCGA-43-6647-01	TCGA-43-6647-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:153582286C>A	uc004fkk.2	-	35	5932	c.5683G>T	c.(5683-5685)GAG>TAG	p.E1895*	FLNA_uc004fki.2_5'UTR|FLNA_uc011mzn.1_Nonsense_Mutation_p.E86*|FLNA_uc010nuu.1_Nonsense_Mutation_p.E1887*	NM_001110556	NP_001104026	P21333	FLNA_HUMAN	filamin A, alpha isoform 2	1895	Filamin 17.				actin crosslink formation|actin cytoskeleton reorganization|cell junction assembly|cytoplasmic sequestering of protein|establishment of protein localization|inhibition of adenylate cyclase activity by dopamine receptor signaling pathway|negative regulation of protein catabolic process|negative regulation of sequence-specific DNA binding transcription factor activity|platelet activation|platelet degranulation|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of transcription factor import into nucleus|protein localization at cell surface|protein stabilization|receptor clustering	cell cortex|cytosol|extracellular region|nucleus|plasma membrane	actin filament binding|Fc-gamma receptor I complex binding|glycoprotein binding|GTP-Ral binding|protein homodimerization activity|Rac GTPase binding|signal transducer activity|transcription factor binding			breast(6)	6	all_cancers(53;3.7e-16)|all_epithelial(53;2.97e-10)|all_lung(58;1.84e-07)|Lung NSC(58;5.84e-07)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)					TGCTCACCCTCTCCTGCATCC	0.587											OREG0003596	type=REGULATORY REGION|Gene=BC028089|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay	8	88	---	---	---	---	PASS
PLXNA3	55558	broad.mit.edu	37	X	153695768	153695768	+	Missense_Mutation	SNP	C	T	T			TCGA-43-6647-01	TCGA-43-6647-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:153695768C>T	uc004flm.2	+	19	3568	c.3395C>T	c.(3394-3396)CCC>CTC	p.P1132L		NM_017514	NP_059984	P51805	PLXA3_HUMAN	plexin A3 precursor	1132	IPT/TIG 4.|Extracellular (Potential).				axon guidance	integral to membrane|intracellular|plasma membrane	transmembrane receptor activity			upper_aerodigestive_tract(1)|ovary(1)|central_nervous_system(1)	3	all_cancers(53;5.05e-16)|all_epithelial(53;1.87e-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)					CCGCTGGGGCCCTCTGGCGTG	0.662													17	30	---	---	---	---	PASS
VBP1	7411	broad.mit.edu	37	X	154448554	154448554	+	Missense_Mutation	SNP	T	C	C			TCGA-43-6647-01	TCGA-43-6647-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:154448554T>C	uc004fnc.2	+	2	247	c.188T>C	c.(187-189)ATG>ACG	p.M63T	VBP1_uc004fnd.2_Missense_Mutation_p.M26T	NM_003372	NP_003363	P61758	PFD3_HUMAN	von Hippel-Lindau binding protein 1	63					'de novo' posttranslational protein folding	nucleus|prefoldin complex	unfolded protein binding				0	all_cancers(53;1.86e-17)|all_epithelial(53;2.71e-11)|all_lung(58;1.84e-07)|Lung NSC(58;5.62e-07)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)|Renal(33;0.214)					TATAAGTTTATGGAACTCAAC	0.299													18	47	---	---	---	---	PASS
TMLHE	55217	broad.mit.edu	37	X	154741382	154741382	+	Missense_Mutation	SNP	A	T	T			TCGA-43-6647-01	TCGA-43-6647-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:154741382A>T	uc004fnn.2	-	5	876	c.710T>A	c.(709-711)CTA>CAA	p.L237Q	TMLHE_uc004fno.2_Missense_Mutation_p.L237Q|TMLHE_uc004fnp.3_Missense_Mutation_p.L237Q	NM_018196	NP_060666	Q9NVH6	TMLH_HUMAN	trimethyllysine hydroxylase, epsilon	237					carnitine biosynthetic process	mitochondrial matrix	iron ion binding|L-ascorbic acid binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|trimethyllysine dioxygenase activity			ovary(1)	1	all_cancers(53;1.86e-17)|all_epithelial(53;2.71e-11)|all_lung(58;1.84e-07)|Lung NSC(58;5.62e-07)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)|Renal(33;0.214)				Succinic acid(DB00139)|Vitamin C(DB00126)	ATCCAGAGCTAGCTTGGTGTA	0.418													34	138	---	---	---	---	PASS
TUFT1	7286	broad.mit.edu	37	1	151530466	151530466	+	Intron	DEL	A	-	-			TCGA-43-6647-01	TCGA-43-6647-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:151530466delA	uc001eyl.2	+						TUFT1_uc001eym.2_Intron|TUFT1_uc010pdf.1_Intron|TUFT1_uc010pdg.1_Intron	NM_020127	NP_064512	Q9NNX1	TUFT1_HUMAN	tuftelin 1 isoform 1						bone mineralization|odontogenesis	cytoplasm|extracellular region	structural constituent of tooth enamel				0	Ovarian(49;0.0273)|Hepatocellular(266;0.0997)|all_hematologic(923;0.127)|Melanoma(130;0.185)		LUSC - Lung squamous cell carcinoma(543;0.181)			AAAAAAACTTAAAAAAAAAAA	0.184													6	3	---	---	---	---	
SOAT1	6646	broad.mit.edu	37	1	179310672	179310672	+	Intron	DEL	T	-	-			TCGA-43-6647-01	TCGA-43-6647-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:179310672delT	uc001gml.2	+						SOAT1_uc010pni.1_Intron|SOAT1_uc001gmm.2_Intron|SOAT1_uc010pnj.1_Intron|SOAT1_uc010pnk.1_Intron	NM_003101	NP_003092	P35610	SOAT1_HUMAN	sterol O-acyltransferase 1						cholesterol efflux|cholesterol esterification|cholesterol homeostasis|cholesterol metabolic process|cholesterol storage|macrophage derived foam cell differentiation|positive regulation of amyloid precursor protein biosynthetic process|very-low-density lipoprotein particle assembly	endoplasmic reticulum membrane|integral to membrane|microsome	cholesterol binding|cholesterol O-acyltransferase activity|fatty-acyl-CoA binding			central_nervous_system(1)|skin(1)	2					Ezetimibe(DB00973)|Hesperetin(DB01094)	TACGTTGAACttttttttttt	0.149													4	2	---	---	---	---	
ITSN2	50618	broad.mit.edu	37	2	24435349	24435350	+	Intron	DEL	CA	-	-			TCGA-43-6647-01	TCGA-43-6647-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:24435349_24435350delCA	uc002rfe.2	-						ITSN2_uc002rff.2_Intron	NM_006277	NP_006268	Q9NZM3	ITSN2_HUMAN	intersectin 2 isoform 1						endocytosis|regulation of Rho protein signal transduction	cytoplasm	calcium ion binding|Rho guanyl-nucleotide exchange factor activity|SH3/SH2 adaptor activity			kidney(2)|ovary(1)|central_nervous_system(1)	4	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					TGTTTCTGTGCACACACACACA	0.545													6	3	---	---	---	---	
ITSN2	50618	broad.mit.edu	37	2	24553641	24553641	+	Intron	DEL	T	-	-			TCGA-43-6647-01	TCGA-43-6647-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:24553641delT	uc002rfe.2	-						ITSN2_uc002rff.2_Intron|ITSN2_uc002rfg.2_Intron|ITSN2_uc010eyd.2_Intron	NM_006277	NP_006268	Q9NZM3	ITSN2_HUMAN	intersectin 2 isoform 1						endocytosis|regulation of Rho protein signal transduction	cytoplasm	calcium ion binding|Rho guanyl-nucleotide exchange factor activity|SH3/SH2 adaptor activity			kidney(2)|ovary(1)|central_nervous_system(1)	4	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					TTCAttttacttttttttttt	0.119													4	2	---	---	---	---	
ORC4L	5000	broad.mit.edu	37	2	148712820	148712820	+	Intron	DEL	T	-	-			TCGA-43-6647-01	TCGA-43-6647-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:148712820delT	uc002twi.2	-						ORC4L_uc002twj.2_Intron|ORC4L_uc010zbo.1_Intron|ORC4L_uc010zbp.1_Intron|ORC4L_uc010fnr.2_Intron|ORC4L_uc010zbq.1_Intron|ORC4L_uc002twk.2_Intron|ORC4L_uc010zbr.1_Intron	NM_181741	NP_859525	O43929	ORC4_HUMAN	origin recognition complex subunit 4						cell cycle checkpoint|DNA-dependent DNA replication initiation|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|S phase of mitotic cell cycle	nuclear origin of replication recognition complex|nucleoplasm	ATP binding|DNA replication origin binding|nucleoside-triphosphatase activity|protein binding				0				BRCA - Breast invasive adenocarcinoma(221;0.0963)|COAD - Colon adenocarcinoma(177;0.203)		ttatgagagcttttttttttg	0.070													4	2	---	---	---	---	
DNAH7	56171	broad.mit.edu	37	2	196640386	196640388	+	Intron	DEL	AAC	-	-	rs66697816		TCGA-43-6647-01	TCGA-43-6647-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:196640386_196640388delAAC	uc002utj.3	-						DNAH7_uc002uti.3_Intron	NM_018897	NP_061720	Q8WXX0	DYH7_HUMAN	dynein, axonemal, heavy chain 7						ciliary or flagellar motility|microtubule-based movement	axonemal dynein complex|cilium axoneme|cytoplasm|microtubule	ATP binding|microtubule motor activity			skin(10)|ovary(2)	12						AAAAAAAAAAAACACACGTTCAG	0.158													4	2	---	---	---	---	
DES	1674	broad.mit.edu	37	2	220286391	220286392	+	Intron	INS	-	T	T			TCGA-43-6647-01	TCGA-43-6647-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:220286391_220286392insT	uc002vll.2	+							NM_001927	NP_001918	P17661	DESM_HUMAN	desmin						cytoskeleton organization|muscle filament sliding|regulation of heart contraction	cytosol|Z disc	protein binding|structural constituent of cytoskeleton			central_nervous_system(2)	2		Renal(207;0.0183)		Epithelial(149;5.25e-07)|all cancers(144;0.000103)|Lung(261;0.00533)|LUSC - Lung squamous cell carcinoma(224;0.008)		CCTGGAAACAAttttttttttt	0.292													4	4	---	---	---	---	
DNAJB11	51726	broad.mit.edu	37	3	186302424	186302425	+	Intron	INS	-	TG	TG	rs112885079	by1000genomes	TCGA-43-6647-01	TCGA-43-6647-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:186302424_186302425insTG	uc003fqi.2	+							NM_016306	NP_057390	Q9UBS4	DJB11_HUMAN	DnaJ (Hsp40) homolog, subfamily B, member 11						protein folding	endoplasmic reticulum lumen	heat shock protein binding			ovary(1)|lung(1)	2	all_cancers(143;2.84e-12)|Ovarian(172;0.0339)		OV - Ovarian serous cystadenocarcinoma(80;1.44e-20)	GBM - Glioblastoma multiforme(93;0.0476)		gtgtgtgtgtatgtgtgtgtgt	0.287													5	4	---	---	---	---	
MARVELD2	153562	broad.mit.edu	37	5	68716482	68716482	+	Intron	DEL	T	-	-			TCGA-43-6647-01	TCGA-43-6647-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:68716482delT	uc003jwq.2	+						MARVELD2_uc010ixf.2_Intron|MARVELD2_uc003jwr.1_Intron|MARVELD2_uc003jws.1_Intron	NM_001038603	NP_001033692	Q8N4S9	MALD2_HUMAN	MARVEL domain containing 2 isoform 1						sensory perception of sound	integral to membrane|tight junction					0		Lung NSC(167;0.000937)|Prostate(74;0.0187)|Ovarian(174;0.16)		OV - Ovarian serous cystadenocarcinoma(47;7.31e-57)|Epithelial(20;1.05e-52)|all cancers(19;2.63e-48)|Lung(70;0.0183)		TCTTTCTTCCTTTTTTTTTTT	0.338													4	3	---	---	---	---	
COL23A1	91522	broad.mit.edu	37	5	177772456	177772457	+	Intron	INS	-	T	T	rs78634385		TCGA-43-6647-01	TCGA-43-6647-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:177772456_177772457insT	uc003mje.2	-							NM_173465	NP_775736	Q86Y22	CONA1_HUMAN	collagen, type XXIII, alpha 1							collagen|integral to membrane|plasma membrane	protein binding			central_nervous_system(1)|skin(1)	2	all_cancers(89;0.00188)|Renal(175;0.000159)|Lung NSC(126;0.00814)|all_lung(126;0.0129)	all_neural(177;0.00802)|Medulloblastoma(196;0.0145)|all_hematologic(541;0.248)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	OV - Ovarian serous cystadenocarcinoma(192;0.153)|all cancers(165;0.172)		TGTATCATCTCTTTTTTTTTTC	0.292													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	180699087	180699087	+	RNA	DEL	A	-	-	rs33935828		TCGA-43-6647-01	TCGA-43-6647-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:180699087delA	uc003mnq.2	+	3		c.451delA								Homo sapiens cDNA clone IMAGE:3910094, partial cds.																		TTTCCATCAGAAAAAAAAAAA	0.408													4	2	---	---	---	---	
ORC3L	23595	broad.mit.edu	37	6	88330898	88330899	+	Intron	INS	-	A	A	rs146557982	by1000genomes	TCGA-43-6647-01	TCGA-43-6647-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:88330898_88330899insA	uc003pmh.2	+						ORC3L_uc011dzl.1_Intron|ORC3L_uc011dzm.1_Intron|ORC3L_uc011dzn.1_Intron|ORC3L_uc003pmg.2_Intron|ORC3L_uc003pmi.2_Intron|ORC3L_uc011dzo.1_Intron|ORC3L_uc011dzp.1_Intron	NM_012381	NP_036513	Q9UBD5	ORC3_HUMAN	origin recognition complex, subunit 3 isoform 2						cell cycle checkpoint|DNA replication|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|S phase of mitotic cell cycle	nuclear origin of replication recognition complex|nucleoplasm	DNA replication origin binding|protein binding				0		all_cancers(76;9.05e-09)|Acute lymphoblastic leukemia(125;2.15e-10)|Prostate(29;5.29e-10)|all_hematologic(105;1.08e-06)|all_epithelial(107;0.000114)		BRCA - Breast invasive adenocarcinoma(108;0.0469)		CTTAAAATATGGAGTTATATAG	0.282													3	4	---	---	---	---	
RAET1L	154064	broad.mit.edu	37	6	150342943	150342944	+	Intron	INS	-	T	T			TCGA-43-6647-01	TCGA-43-6647-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:150342943_150342944insT	uc011eei.1	-							NM_130900	NP_570970	Q5VY80	RET1L_HUMAN	retinoic acid early transcript 1L precursor						antigen processing and presentation|immune response	anchored to membrane|MHC class I protein complex					0		Ovarian(120;0.028)	BRCA - Breast invasive adenocarcinoma(37;0.193)	OV - Ovarian serous cystadenocarcinoma(155;2.4e-12)		gttggtcaggcggtctcgaatt	0.030													5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	167342833	167342834	+	IGR	INS	-	A	A	rs10694728		TCGA-43-6647-01	TCGA-43-6647-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:167342833_167342834insA								RPS6KA2 (67062 upstream) : RNASET2 (174 downstream)																							GTTTAATAGAGAAAAAAAAAAA	0.480													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	61968770	61968770	+	IGR	DEL	G	-	-	rs61713499		TCGA-43-6647-01	TCGA-43-6647-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:61968770delG								None (None upstream) : LOC643955 (782902 downstream)																							ttgaaacactgtttttgcgga	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	4985366	4985367	+	IGR	INS	-	T	T			TCGA-43-6647-01	TCGA-43-6647-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:4985366_4985367insT								CSMD1 (133038 upstream) : None (None downstream)																							tctgacgcttcttttttttttt	0.223													4	3	---	---	---	---	
LY96	23643	broad.mit.edu	37	8	74939175	74939176	+	Intron	INS	-	T	T	rs11379988		TCGA-43-6647-01	TCGA-43-6647-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:74939175_74939176insT	uc003yad.2	+							NM_015364	NP_056179	Q9Y6Y9	LY96_HUMAN	MD-2 protein precursor						cellular defense response|detection of lipopolysaccharide|I-kappaB kinase/NF-kappaB cascade|inflammatory response|innate immune response|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway	extracellular space|lipopolysaccharide receptor complex|plasma membrane	coreceptor activity|lipopolysaccharide receptor activity|protein binding				0	Breast(64;0.0311)		Epithelial(68;0.0208)|BRCA - Breast invasive adenocarcinoma(89;0.0499)|all cancers(69;0.0619)			ctttttctttcttttttttttt	0.129													4	2	---	---	---	---	
CNTNAP3	79937	broad.mit.edu	37	9	39287925	39287925	+	Intron	DEL	C	-	-			TCGA-43-6647-01	TCGA-43-6647-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:39287925delC	uc004abi.2	-						CNTNAP3_uc004abj.2_Intron|CNTNAP3_uc011lqr.1_Intron|CNTNAP3_uc004abk.1_Intron|CNTNAP3_uc011lqs.1_Intron	NM_033655	NP_387504	Q9BZ76	CNTP3_HUMAN	cell recognition molecule CASPR3 precursor						cell adhesion|cell recognition|signal transduction	extracellular region|integral to membrane|plasma membrane	receptor binding			ovary(1)	1				GBM - Glioblastoma multiforme(29;0.02)|Lung(182;0.0681)		AAAAAAAAAACAAAGTTTTCC	0.403													5	4	---	---	---	---	
LDHA	3939	broad.mit.edu	37	11	18428564	18428564	+	Intron	DEL	A	-	-	rs79367445		TCGA-43-6647-01	TCGA-43-6647-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:18428564delA	uc001mok.3	+						LDHA_uc010rdc.1_Intron|LDHA_uc009yhn.2_Intron|LDHA_uc009yho.2_Intron|LDHA_uc001mol.3_Intron|LDHA_uc010rdd.1_Intron	NM_005566	NP_005557	P00338	LDHA_HUMAN	lactate dehydrogenase A isoform 1						glycolysis|pyruvate metabolic process	cytosol	L-lactate dehydrogenase activity|protein binding			central_nervous_system(3)	3					NADH(DB00157)	aaaaaaaattaaaaaaaaaaa	0.144													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	30932783	30932783	+	Intron	DEL	T	-	-	rs72110565		TCGA-43-6647-01	TCGA-43-6647-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:30932783delT	uc001mss.1	-						uc009yjk.1_Intron					Homo sapiens mRNA for KIAA1493 protein, partial cds.																		TCTATGACAGTTTTTTTTTTT	0.274													3	3	---	---	---	---	
ANKRD33	341405	broad.mit.edu	37	12	52285209	52285210	+	3'UTR	INS	-	TA	TA	rs147140141	by1000genomes	TCGA-43-6647-01	TCGA-43-6647-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:52285209_52285210insTA	uc001rzf.3	+	6					ANKRD33_uc001rzh.3_3'UTR|ANKRD33_uc001rzd.2_3'UTR|ANKRD33_uc001rze.2_3'UTR|ANKRD33_uc001rzg.3_3'UTR|ANKRD33_uc001rzi.3_3'UTR	NM_001130015	NP_001123487	Q7Z3H0	ANR33_HUMAN	ankyrin repeat domain 33 isoform 1												0				BRCA - Breast invasive adenocarcinoma(357;0.0969)		TGCTCTCAACCTatatatatac	0.302													4	2	---	---	---	---	
KSR2	283455	broad.mit.edu	37	12	117965094	117965107	+	Intron	DEL	ACACACACACACAG	-	-	rs59836858		TCGA-43-6647-01	TCGA-43-6647-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:117965094_117965107delACACACACACACAG	uc001two.2	-							NM_173598	NP_775869	Q6VAB6	KSR2_HUMAN	kinase suppressor of ras 2						intracellular signal transduction	cytoplasm|membrane	ATP binding|metal ion binding|protein serine/threonine kinase activity			lung(10)|central_nervous_system(2)|stomach(1)|large_intestine(1)|breast(1)	15	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)					CGacacacacacacacacacacagacacacacac	0.234													4	3	---	---	---	---	
INTS6	26512	broad.mit.edu	37	13	51936274	51936274	+	3'UTR	DEL	T	-	-			TCGA-43-6647-01	TCGA-43-6647-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:51936274delT	uc001vfk.2	-	18					SERPINE3_uc010tgp.1_Intron|INTS6_uc001vfi.2_3'UTR|INTS6_uc001vfj.2_3'UTR|INTS6_uc001vfl.2_3'UTR	NM_012141	NP_036273	Q9UL03	INT6_HUMAN	integrator complex subunit 6 isoform a						snRNA processing	actin cytoskeleton|integrator complex	protein binding|transmembrane receptor activity			ovary(1)|lung(1)	2		Breast(56;0.000286)|Lung NSC(96;0.00145)|Prostate(109;0.00403)|Hepatocellular(98;0.065)|Myeloproliferative disorder(33;0.163)|all_neural(104;0.19)		GBM - Glioblastoma multiforme(99;7.7e-08)		TTAATGTAGATTTTTTTTTTT	0.313													4	2	---	---	---	---	
COMMD6	170622	broad.mit.edu	37	13	76112127	76112127	+	5'Flank	DEL	A	-	-			TCGA-43-6647-01	TCGA-43-6647-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:76112127delA	uc001vjo.1	-						COMMD6_uc001vjn.1_5'Flank|COMMD6_uc010aet.1_5'Flank|COMMD6_uc001vjp.1_Intron	NM_203495	NP_987091	Q7Z4G1	COMD6_HUMAN	COMM domain containing 6 isoform b							cytoplasm|nucleus	protein binding				0		Breast(118;0.0979)|Prostate(6;0.122)		GBM - Glioblastoma multiforme(99;0.0104)		ACATTGAGCTAAAAGAAAATT	0.383													7	5	---	---	---	---	
C13orf16	121793	broad.mit.edu	37	13	111995413	111995413	+	Intron	DEL	A	-	-			TCGA-43-6647-01	TCGA-43-6647-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:111995413delA	uc001vsa.2	+							NM_152324	NP_689537	Q8N6K0	CM016_HUMAN	hypothetical protein LOC121793							integral to membrane					0	all_lung(23;3.96e-05)|Lung NSC(43;0.00156)|Lung SC(71;0.0753)|all_neural(89;0.0804)|Medulloblastoma(90;0.163)		all cancers(43;0.113)|GBM - Glioblastoma multiforme(44;0.174)|BRCA - Breast invasive adenocarcinoma(86;0.188)			CAGTTTGTTCAAAATTGTAAT	0.522													6	3	---	---	---	---	
SNX6	58533	broad.mit.edu	37	14	35037350	35037351	+	Intron	INS	-	T	T			TCGA-43-6647-01	TCGA-43-6647-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:35037350_35037351insT	uc001wsf.1	-						SNX6_uc001wse.1_Intron|SNX6_uc010tpm.1_Intron|SNX6_uc010amm.1_Intron	NM_152233	NP_689419	Q9UNH7	SNX6_HUMAN	sorting nexin 6 isoform b						cell communication|intracellular protein transport|negative regulation of epidermal growth factor receptor activity|negative regulation of transcription, DNA-dependent|negative regulation of transforming growth factor beta receptor signaling pathway|retrograde transport, endosome to Golgi	cytoplasmic vesicle membrane|early endosome membrane|nucleus	phosphatidylinositol binding|protein homodimerization activity				0	Breast(36;0.0473)|Hepatocellular(127;0.158)		LUAD - Lung adenocarcinoma(48;0.00169)|Lung(238;0.00199)|Epithelial(34;0.187)	GBM - Glioblastoma multiforme(112;0.0245)		AGTTACTCCAAttttttttttt	0.233													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	52754676	52754676	+	IGR	DEL	A	-	-	rs71444753		TCGA-43-6647-01	TCGA-43-6647-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:52754676delA								PTGDR (11235 upstream) : PTGER2 (26340 downstream)																							ATGTTAAGCCaaaaaaaaaaa	0.303													4	2	---	---	---	---	
PCNX	22990	broad.mit.edu	37	14	71493712	71493712	+	Intron	DEL	A	-	-			TCGA-43-6647-01	TCGA-43-6647-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:71493712delA	uc001xmo.2	+						PCNX_uc010are.1_Intron|PCNX_uc010arf.1_Intron	NM_014982	NP_055797	Q96RV3	PCX1_HUMAN	pecanex-like 1							integral to membrane				ovary(1)	1			KIRC - Kidney renal clear cell carcinoma(12;0.206)	all cancers(60;0.00835)|BRCA - Breast invasive adenocarcinoma(234;0.00951)|OV - Ovarian serous cystadenocarcinoma(108;0.0417)		TTGAAATTAGAAAAAAAAAAG	0.284													4	2	---	---	---	---	
SPTLC2	9517	broad.mit.edu	37	14	78036584	78036584	+	Intron	DEL	G	-	-			TCGA-43-6647-01	TCGA-43-6647-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:78036584delG	uc001xub.2	-							NM_004863	NP_004854	O15270	SPTC2_HUMAN	serine palmitoyltransferase, long chain base							integral to membrane|serine C-palmitoyltransferase complex	pyridoxal phosphate binding|serine C-palmitoyltransferase activity|transferase activity, transferring nitrogenous groups			upper_aerodigestive_tract(1)|ovary(1)	2			Kidney(204;0.164)	BRCA - Breast invasive adenocarcinoma(234;0.0346)	L-Serine(DB00133)|Pyridoxal Phosphate(DB00114)	aaaaaaaaaagaaaaaCAATT	0.149													6	3	---	---	---	---	
SQRDL	58472	broad.mit.edu	37	15	45980714	45980714	+	Intron	DEL	T	-	-			TCGA-43-6647-01	TCGA-43-6647-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:45980714delT	uc001zvt.2	+						SQRDL_uc001zvu.2_Intron|SQRDL_uc001zvv.2_Intron	NM_021199	NP_067022	Q9Y6N5	SQRD_HUMAN	sulfide dehydrogenase like precursor								oxidoreductase activity			ovary(1)	1		Lung NSC(122;0.000117)|all_lung(180;0.000737)|Melanoma(134;0.0417)		all cancers(107;5.89e-18)|GBM - Glioblastoma multiforme(94;1.21e-06)|COAD - Colon adenocarcinoma(120;0.17)|Colorectal(133;0.188)		tctgtttttcttttttttttt	0.139													6	3	---	---	---	---	
SECISBP2L	9728	broad.mit.edu	37	15	49319807	49319807	+	Intron	DEL	A	-	-	rs7177172	by1000genomes	TCGA-43-6647-01	TCGA-43-6647-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:49319807delA	uc001zxe.1	-						SECISBP2L_uc001zxd.1_Intron|SECISBP2L_uc010bep.1_Intron|SECISBP2L_uc010beq.1_Intron	NM_014701	NP_055516	Q93073	SBP2L_HUMAN	SECIS binding protein 2-like											breast(1)|skin(1)	2						AAACCTTATTAtttttttttt	0.129													4	2	---	---	---	---	
LOC595101	595101	broad.mit.edu	37	16	30347982	30347983	+	5'Flank	INS	-	T	T	rs148333845		TCGA-43-6647-01	TCGA-43-6647-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:30347982_30347983insT	uc002dxp.1	-							NR_002453				Homo sapiens cDNA FLJ39663 fis, clone SMINT2007187.												0						CTCTGtttctattttttttttt	0.233													6	4	---	---	---	---	
TRPV1	7442	broad.mit.edu	37	17	3494199	3494200	+	Intron	INS	-	C	C	rs140971657	by1000genomes	TCGA-43-6647-01	TCGA-43-6647-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:3494199_3494200insC	uc010vrr.1	-						TRPV1_uc010vro.1_Intron|TRPV1_uc010vrp.1_Intron|TRPV1_uc010vrq.1_Intron|TRPV1_uc010vrs.1_Intron|TRPV1_uc010vrt.1_Intron|TRPV1_uc010vru.1_Intron	NM_080706	NP_542437	Q8NER1	TRPV1_HUMAN	transient receptor potential cation channel,						cell surface receptor linked signaling pathway|chemosensory behavior|thermoception	cell junction|dendritic spine membrane|integral to plasma membrane|postsynaptic membrane	ATP binding|calcium channel activity|calmodulin binding			ovary(1)	1				Lung(1;0.055)|COAD - Colon adenocarcinoma(5;0.0896)|LUAD - Lung adenocarcinoma(1115;0.131)	Alpha-Linolenic Acid(DB00132)|Aspartame(DB00168)|Icosapent(DB00159)	GGACAACCATGCCCCCCTGCTT	0.649													4	3	---	---	---	---	
USP32	84669	broad.mit.edu	37	17	58332410	58332410	+	Intron	DEL	T	-	-	rs35284371		TCGA-43-6647-01	TCGA-43-6647-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:58332410delT	uc002iyo.1	-						USP32_uc002iyn.1_Intron|USP32_uc010wov.1_Intron	NM_032582	NP_115971	Q8NFA0	UBP32_HUMAN	ubiquitin specific protease 32						protein deubiquitination|ubiquitin-dependent protein catabolic process	Golgi apparatus|membrane	calcium ion binding|cysteine-type peptidase activity|ubiquitin thiolesterase activity			lung(2)|breast(2)|large_intestine(1)	5	all_neural(34;0.0878)|Medulloblastoma(34;0.0922)		Epithelial(12;2.02e-11)|all cancers(12;5.23e-10)|Colorectal(3;0.198)			AATGTAGTTCttttttttttt	0.353													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	62932555	62932556	+	IGR	DEL	GT	-	-	rs35142297		TCGA-43-6647-01	TCGA-43-6647-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:62932555_62932556delGT								LRRC37A3 (16969 upstream) : AMZ2P1 (30112 downstream)																							gtgtgtgttcgtgtgtgtgtgt	0.238													4	3	---	---	---	---	
SMARCA4	6597	broad.mit.edu	37	19	11168782	11168783	+	Intron	INS	-	A	A			TCGA-43-6647-01	TCGA-43-6647-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:11168782_11168783insA	uc002mqf.3	+						SMARCA4_uc010dxp.2_Intron|SMARCA4_uc010dxo.2_Intron|SMARCA4_uc010dxq.2_Intron|SMARCA4_uc010dxr.2_Intron|SMARCA4_uc002mqj.3_Intron|SMARCA4_uc010dxs.2_Intron|SMARCA4_uc002mqh.3_Intron	NM_003072	NP_003063	P51532	SMCA4_HUMAN	SWI/SNF-related matrix-associated						chromatin remodeling|negative regulation of androgen receptor signaling pathway|negative regulation of cell growth|negative regulation of S phase of mitotic cell cycle|negative regulation of transcription from RNA polymerase II promoter|nervous system development|positive regulation of sequence-specific DNA binding transcription factor activity|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	nBAF complex|npBAF complex|nuclear chromatin|SWI/SNF complex|WINAC complex	androgen receptor binding|ATP binding|DNA binding|DNA-dependent ATPase activity|helicase activity|histone acetyl-lysine binding|identical protein binding|p53 binding|protein N-terminus binding|transcription corepressor activity			lung(29)|ovary(8)|pancreas(7)|large_intestine(5)|central_nervous_system(5)|skin(3)|prostate(3)|breast(2)|adrenal_gland(1)|stomach(1)|liver(1)|autonomic_ganglia(1)|kidney(1)	67		all_lung(6;0.0512)|Lung NSC(9;0.0568)				aactccgtctcaaaaaaaaaaa	0.228			F|N|Mis		NSCLC				Rhabdoid_Predisposition_syndrome				4	3	---	---	---	---	
ETV2	2116	broad.mit.edu	37	19	36133983	36133983	+	Intron	DEL	G	-	-	rs74172755		TCGA-43-6647-01	TCGA-43-6647-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:36133983delG	uc002oas.2	+						ETV2_uc002oar.2_Intron|ETV2_uc002oat.2_Intron|ETV2_uc002oau.2_Intron	NM_014209	NP_055024	O00321	ETV2_HUMAN	ets variant gene 2								sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity				0	all_lung(56;2.22e-07)|Lung NSC(56;3.47e-07)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0515)			GGTGGGGACTGGGGTCCCGAG	0.652													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	53703995	53703995	+	IGR	DEL	T	-	-	rs113703393		TCGA-43-6647-01	TCGA-43-6647-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:53703995delT								ZNF665 (7376 upstream) : ZNF677 (34643 downstream)																							TGTTTCCCCCttttttttttt	0.229													6	3	---	---	---	---	
C22orf43	51233	broad.mit.edu	37	22	23973867	23973868	+	Intron	INS	-	C	C	rs141675360	by1000genomes	TCGA-43-6647-01	TCGA-43-6647-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:23973867_23973868insC	uc002zxf.2	-							NM_016449	NP_057533	Q6PGQ1	CV043_HUMAN	hypothetical protein LOC51233											skin(1)	1						TGTCCCCCATGCCCAGACCTGG	0.535													3	3	---	---	---	---	
MOV10L1	54456	broad.mit.edu	37	22	50582279	50582280	+	Intron	DEL	CT	-	-	rs5845922		TCGA-43-6647-01	TCGA-43-6647-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:50582279_50582280delCT	uc003bjj.2	+						MOV10L1_uc003bjk.3_Intron|MOV10L1_uc011arp.1_Intron	NM_018995	NP_061868	Q9BXT6	M10L1_HUMAN	MOV10-like 1 isoform 1						germ cell development|multicellular organismal development|spermatogenesis		ATP binding|ATP-dependent RNA helicase activity|magnesium ion binding|RNA binding			ovary(2)|skin(1)	3		all_cancers(38;3.31e-11)|all_epithelial(38;5.69e-10)|all_lung(38;3.73e-05)|Breast(42;0.000525)|Lung NSC(38;0.000954)|Ovarian(80;0.0367)|Lung SC(80;0.114)		LUAD - Lung adenocarcinoma(64;0.0215)|BRCA - Breast invasive adenocarcinoma(115;0.24)		atgaatctgactctgtttctgc	0.228													1	5	---	---	---	---	
