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
GPR153	387509	broad.mit.edu	37	1	6314124	6314124	+	Missense_Mutation	SNP	A	G	G			TCGA-C5-A1ME-01A-11D-A13W-08	TCGA-C5-A1ME-10A-01D-A13W-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:6314124A>G	uc001amp.1	-	3	700	c.440T>C	c.(439-441)GTT>GCT	p.V147A		NM_207370	NP_997253	Q6NV75	GP153_HUMAN	G protein-coupled receptor 153	147	Helical; Name=4; (Potential).					integral to membrane|plasma membrane	G-protein coupled receptor activity				0	Ovarian(185;0.0634)	all_cancers(23;8.07e-33)|all_epithelial(116;4.45e-18)|all_lung(118;1.09e-06)|all_neural(13;3.68e-06)|Lung NSC(185;1.52e-05)|all_hematologic(16;2.39e-05)|Acute lymphoblastic leukemia(12;0.000372)|Glioma(11;0.00127)|Renal(390;0.00188)|Colorectal(325;0.00342)|Breast(487;0.00475)|Hepatocellular(190;0.0218)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.15)		Epithelial(90;1.91e-37)|GBM - Glioblastoma multiforme(13;4.87e-29)|OV - Ovarian serous cystadenocarcinoma(86;3.03e-19)|Colorectal(212;1.33e-07)|COAD - Colon adenocarcinoma(227;1.36e-05)|Kidney(185;4.89e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.000911)|BRCA - Breast invasive adenocarcinoma(365;0.00109)|STAD - Stomach adenocarcinoma(132;0.00313)|READ - Rectum adenocarcinoma(331;0.0642)|Lung(427;0.246)		GTGCCAGCCAACGGCAGGCAG	0.622													4	80	---	---	---	---	PASS
CLCN6	1185	broad.mit.edu	37	1	11897157	11897157	+	Silent	SNP	C	T	T			TCGA-C5-A1ME-01A-11D-A13W-08	TCGA-C5-A1ME-10A-01D-A13W-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:11897157C>T	uc001ate.3	+	19	2195	c.2082C>T	c.(2080-2082)ATC>ATT	p.I694I	CLCN6_uc010oat.1_Silent_p.I410I|CLCN6_uc010oau.1_Silent_p.I672I	NM_001286	NP_001277	P51797	CLCN6_HUMAN	chloride channel 6 isoform ClC-6a	694	Cytoplasmic (By similarity).				cell volume homeostasis|signal transduction	endosome membrane|integral to membrane	antiporter activity|ATP binding|voltage-gated chloride channel activity				0	Ovarian(185;0.249)	Lung NSC(185;8.69e-05)|all_lung(284;9.87e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Ovarian(437;0.00965)|Hepatocellular(190;0.0202)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;6.13e-06)|COAD - Colon adenocarcinoma(227;0.000274)|BRCA - Breast invasive adenocarcinoma(304;0.000311)|Kidney(185;0.000816)|KIRC - Kidney renal clear cell carcinoma(229;0.00268)|STAD - Stomach adenocarcinoma(313;0.00743)|READ - Rectum adenocarcinoma(331;0.0649)		ATGAGCACATCGCCTCTGAGG	0.632													6	20	---	---	---	---	PASS
PAX7	5081	broad.mit.edu	37	1	19027177	19027177	+	Missense_Mutation	SNP	C	T	T			TCGA-C5-A1ME-01A-11D-A13W-08	TCGA-C5-A1ME-10A-01D-A13W-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:19027177C>T	uc001bay.2	+	6	1415	c.817C>T	c.(817-819)CGT>TGT	p.R273C	PAX7_uc001baz.2_Missense_Mutation_p.R271C|PAX7_uc010oct.1_Missense_Mutation_p.R273C	NM_002584	NP_002575	P23759	PAX7_HUMAN	paired box 7 isoform 1	273	Homeobox.				anti-apoptosis	nucleus	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity		PAX7/FOXO1(197)	soft_tissue(197)|lung(3)|prostate(1)|ovary(1)|breast(1)	203		Colorectal(325;3.46e-05)|all_lung(284;0.000439)|Renal(390;0.000518)|Lung NSC(340;0.000543)|Breast(348;0.00093)|Ovarian(437;0.00768)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00609)|BRCA - Breast invasive adenocarcinoma(304;4.71e-05)|Kidney(64;0.000279)|KIRC - Kidney renal clear cell carcinoma(64;0.00371)|STAD - Stomach adenocarcinoma(196;0.00658)|READ - Rectum adenocarcinoma(331;0.0576)		CGCCCGTTGGCGTAAGCAGGC	0.652			T	FOXO1A	alveolar rhabdomyosarcoma								8	45	---	---	---	---	PASS
WDTC1	23038	broad.mit.edu	37	1	27627932	27627932	+	Missense_Mutation	SNP	T	A	A			TCGA-C5-A1ME-01A-11D-A13W-08	TCGA-C5-A1ME-10A-01D-A13W-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:27627932T>A	uc009vst.2	+	13	1983	c.1448T>A	c.(1447-1449)CTC>CAC	p.L483H	WDTC1_uc001bno.2_Missense_Mutation_p.L482H|WDTC1_uc001bnp.1_RNA|WDTC1_uc001bnq.2_Missense_Mutation_p.L161H	NM_015023	NP_055838	Q8N5D0	WDTC1_HUMAN	WD and tetratricopeptide repeats 1	483							protein binding			ovary(1)|central_nervous_system(1)	2		all_cancers(24;3.12e-19)|all_epithelial(13;4.18e-18)|Colorectal(325;0.000147)|all_lung(284;0.000366)|Lung NSC(340;0.000548)|Renal(390;0.00211)|Breast(348;0.00257)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0707)|all_neural(195;0.0966)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0443)|OV - Ovarian serous cystadenocarcinoma(117;1.09e-27)|Colorectal(126;8.83e-09)|COAD - Colon adenocarcinoma(152;1.02e-06)|BRCA - Breast invasive adenocarcinoma(304;0.000544)|KIRC - Kidney renal clear cell carcinoma(1967;0.00201)|STAD - Stomach adenocarcinoma(196;0.00321)|READ - Rectum adenocarcinoma(331;0.0476)		ACAGCTGCCCTCTTCTCTAAA	0.453													4	31	---	---	---	---	PASS
CSMD2	114784	broad.mit.edu	37	1	34208936	34208936	+	Silent	SNP	G	T	T			TCGA-C5-A1ME-01A-11D-A13W-08	TCGA-C5-A1ME-10A-01D-A13W-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:34208936G>T	uc001bxn.1	-	14	2027	c.1998C>A	c.(1996-1998)CTC>CTA	p.L666L	CSMD2_uc001bxm.1_Silent_p.L706L	NM_052896	NP_443128	Q7Z408	CSMD2_HUMAN	CUB and Sushi multiple domains 2	666	Extracellular (Potential).|CUB 4.					integral to membrane|plasma membrane	protein binding			ovary(6)|skin(5)|pancreas(1)	12		Myeloproliferative disorder(586;0.0294)|all_neural(195;0.249)				TCTGGAACTCGAGACGGGCCA	0.602													5	35	---	---	---	---	PASS
TGFBR3	7049	broad.mit.edu	37	1	92195435	92195435	+	Missense_Mutation	SNP	C	A	A			TCGA-C5-A1ME-01A-11D-A13W-08	TCGA-C5-A1ME-10A-01D-A13W-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:92195435C>A	uc001doh.2	-	6	1130	c.664G>T	c.(664-666)GTG>TTG	p.V222L	TGFBR3_uc009wde.2_5'UTR|TGFBR3_uc010osy.1_Missense_Mutation_p.V180L|TGFBR3_uc001doi.2_Missense_Mutation_p.V222L|TGFBR3_uc001doj.2_Missense_Mutation_p.V222L	NM_003243	NP_003234	Q03167	TGBR3_HUMAN	transforming growth factor, beta receptor III	222	Extracellular (Potential).				BMP signaling pathway|cardiac epithelial to mesenchymal transition|cardiac muscle cell proliferation|cell growth|cell migration|definitive erythrocyte differentiation|heart trabecula formation|immune response|intracellular protein kinase cascade|liver development|negative regulation of cellular component movement|negative regulation of epithelial cell proliferation|palate development|pathway-restricted SMAD protein phosphorylation|response to follicle-stimulating hormone stimulus|response to luteinizing hormone stimulus|response to prostaglandin E stimulus|transforming growth factor beta receptor signaling pathway|ventricular cardiac muscle tissue morphogenesis	external side of plasma membrane|extracellular space|inhibin-betaglycan-ActRII complex|integral to plasma membrane|intracellular membrane-bounded organelle	coreceptor activity|heparin binding|PDZ domain binding|SMAD binding|transforming growth factor beta binding|transforming growth factor beta receptor activity, type III|type II transforming growth factor beta receptor binding			ovary(3)	3		all_lung(203;0.00719)|Lung NSC(277;0.0268)		all cancers(265;0.0108)|Epithelial(280;0.0825)		CTGGACATCACACACCCTTCT	0.473													4	99	---	---	---	---	PASS
AHCYL1	10768	broad.mit.edu	37	1	110561084	110561084	+	Missense_Mutation	SNP	G	A	A			TCGA-C5-A1ME-01A-11D-A13W-08	TCGA-C5-A1ME-10A-01D-A13W-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:110561084G>A	uc001dyx.2	+	12	1580	c.1213G>A	c.(1213-1215)GAT>AAT	p.D405N	AHCYL1_uc010ovw.1_Missense_Mutation_p.D358N|AHCYL1_uc001dyy.2_Missense_Mutation_p.D358N|AHCYL1_uc010ovx.1_Missense_Mutation_p.D358N	NM_006621	NP_006612	O43865	SAHH2_HUMAN	S-adenosylhomocysteine hydrolase-like 1	405	NAD binding (By similarity).				one-carbon metabolic process	endoplasmic reticulum	adenosylhomocysteinase activity			ovary(1)	1		all_epithelial(167;3.58e-05)|all_lung(203;0.000116)|Lung NSC(277;0.000233)		Lung(183;0.0259)|Colorectal(144;0.123)|all cancers(265;0.134)|Epithelial(280;0.141)|LUSC - Lung squamous cell carcinoma(189;0.143)		CACAGAAATCGATGTGGTAAG	0.413													9	39	---	---	---	---	PASS
DENND2C	163259	broad.mit.edu	37	1	115168296	115168296	+	Missense_Mutation	SNP	C	T	T			TCGA-C5-A1ME-01A-11D-A13W-08	TCGA-C5-A1ME-10A-01D-A13W-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:115168296C>T	uc001efd.1	-	4	1012	c.310G>A	c.(310-312)GAT>AAT	p.D104N	DENND2C_uc001eez.2_RNA|DENND2C_uc001efc.1_Missense_Mutation_p.D104N	NM_198459	NP_940861	Q68D51	DEN2C_HUMAN	DENN/MADD domain containing 2C	104										skin(3)	3	all_epithelial(7;9.54e-05)|all_lung(7;0.000179)|Lung NSC(6;0.00195)|Lung SC(450;0.211)	all_cancers(81;4.64e-07)|all_epithelial(167;4.2e-07)|all_lung(203;9.97e-06)|Lung NSC(69;1.74e-05)		Lung(183;0.0234)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|all cancers(265;0.112)|Epithelial(280;0.124)|LUSC - Lung squamous cell carcinoma(189;0.133)		AAGTGTGTATCGTCATATTCA	0.353													16	103	---	---	---	---	PASS
SPAG17	200162	broad.mit.edu	37	1	118623724	118623724	+	Nonsense_Mutation	SNP	C	A	A			TCGA-C5-A1ME-01A-11D-A13W-08	TCGA-C5-A1ME-10A-01D-A13W-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:118623724C>A	uc001ehk.2	-	15	2277	c.2209G>T	c.(2209-2211)GAG>TAG	p.E737*		NM_206996	NP_996879	Q6Q759	SPG17_HUMAN	sperm associated antigen 17	737						cilium|flagellar axoneme|microtubule				upper_aerodigestive_tract(2)|ovary(2)|large_intestine(1)|skin(1)	6	Esophageal squamous(2;0.0106)	all_cancers(81;0.0204)|all_lung(203;9.46e-05)|Lung NSC(69;0.000675)|all_epithelial(167;0.01)		Lung(183;0.0858)		TTTAACTTACCCAGAGACTCA	0.303													7	90	---	---	---	---	PASS
ANXA9	8416	broad.mit.edu	37	1	150958852	150958852	+	Silent	SNP	C	A	A			TCGA-C5-A1ME-01A-11D-A13W-08	TCGA-C5-A1ME-10A-01D-A13W-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:150958852C>A	uc001ewa.2	+	8	983	c.513C>A	c.(511-513)ACC>ACA	p.T171T		NM_003568	NP_003559	O76027	ANXA9_HUMAN	annexin A9	171	Annexin 2.				cell-cell adhesion	cell surface|cytosol	acetylcholine receptor activity|calcium ion binding|calcium-dependent phospholipid binding|phosphatidylserine binding|protein homodimerization activity				0	all_lung(15;1.09e-34)|Lung NSC(24;1.1e-30)|Lung SC(34;0.00202)|Ovarian(49;0.0167)|all_hematologic(923;0.0597)|Hepatocellular(266;0.0997)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.0486)|LUSC - Lung squamous cell carcinoma(543;0.211)			CATCTGAGACCAGTGGCATCT	0.562													8	31	---	---	---	---	PASS
NPR1	4881	broad.mit.edu	37	1	153660099	153660099	+	Intron	SNP	C	G	G			TCGA-C5-A1ME-01A-11D-A13W-08	TCGA-C5-A1ME-10A-01D-A13W-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:153660099C>G	uc001fcs.3	+						NPR1_uc010pdz.1_Intron|NPR1_uc010pea.1_Intron	NM_000906	NP_000897	P16066	ANPRA_HUMAN	natriuretic peptide receptor 1 precursor						body fluid secretion|intracellular signal transduction|negative regulation of angiogenesis|negative regulation of cell growth|positive regulation of renal sodium excretion|positive regulation of urine volume|receptor guanylyl cyclase signaling pathway|regulation of blood pressure|regulation of blood vessel size|regulation of vascular permeability|regulation of vasodilation		ATP binding|GTP binding|guanylate cyclase activity|natriuretic peptide receptor activity|peptide receptor activity, G-protein coupled|protein kinase activity			ovary(3)|lung(2)|stomach(1)|breast(1)	7	all_lung(78;3.75e-32)|Lung NSC(65;1.37e-30)|Hepatocellular(266;0.0877)|Melanoma(130;0.199)		LUSC - Lung squamous cell carcinoma(543;0.151)		Erythrityl Tetranitrate(DB01613)|Isosorbide Dinitrate(DB00883)|Isosorbide Mononitrate(DB01020)|Nesiritide(DB04899)|Nitric Oxide(DB00435)|Nitroglycerin(DB00727)|Nitroprusside(DB00325)	CTACCGACCTCTGACCCACAG	0.547													8	160	---	---	---	---	PASS
CREB3L4	148327	broad.mit.edu	37	1	153941905	153941905	+	Missense_Mutation	SNP	G	A	A			TCGA-C5-A1ME-01A-11D-A13W-08	TCGA-C5-A1ME-10A-01D-A13W-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:153941905G>A	uc001fdn.3	+	4	783	c.517G>A	c.(517-519)GTA>ATA	p.V173I	SLC39A1_uc001fdl.2_5'Flank|CREB3L4_uc010pef.1_Missense_Mutation_p.V26I|CREB3L4_uc001fdo.3_Missense_Mutation_p.V153I|CREB3L4_uc001fdm.1_Missense_Mutation_p.V173I|CREB3L4_uc001fdp.1_Missense_Mutation_p.V153I|CREB3L4_uc010peg.1_3'UTR|CREB3L4_uc001fdr.2_Missense_Mutation_p.V173I|CREB3L4_uc001fdq.2_Missense_Mutation_p.V153I	NM_130898	NP_570968	Q8TEY5	CR3L4_HUMAN	cAMP responsive element binding protein 3-like	173	Cytoplasmic (Potential).				response to unfolded protein	endoplasmic reticulum membrane|Golgi membrane|integral to membrane|nucleus	protein dimerization activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			ovary(1)	1	all_lung(78;3.05e-32)|Lung NSC(65;3.74e-30)|Hepatocellular(266;0.0877)|Melanoma(130;0.199)		LUSC - Lung squamous cell carcinoma(543;0.151)			AGCAGGCACCGTAGCCCCAGT	0.532													11	64	---	---	---	---	PASS
LGR6	59352	broad.mit.edu	37	1	202279443	202279443	+	Missense_Mutation	SNP	A	G	G			TCGA-C5-A1ME-01A-11D-A13W-08	TCGA-C5-A1ME-10A-01D-A13W-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:202279443A>G	uc001gxu.2	+	16	1525	c.1525A>G	c.(1525-1527)AAA>GAA	p.K509E	LGR6_uc001gxv.2_Missense_Mutation_p.K457E|LGR6_uc009xab.2_RNA|LGR6_uc001gxw.2_Missense_Mutation_p.K370E	NM_001017403	NP_001017403	Q9HBX8	LGR6_HUMAN	leucine-rich repeat-containing G protein-coupled	509	Extracellular (Potential).					integral to membrane|plasma membrane	protein-hormone receptor activity			large_intestine(4)|ovary(3)|skin(2)|pancreas(1)	10						GGAGTCTTCAAAAAGGCCCCT	0.577													4	53	---	---	---	---	PASS
LBR	3930	broad.mit.edu	37	1	225599076	225599076	+	Missense_Mutation	SNP	T	C	C			TCGA-C5-A1ME-01A-11D-A13W-08	TCGA-C5-A1ME-10A-01D-A13W-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:225599076T>C	uc001hoy.2	-	9	1294	c.1151A>G	c.(1150-1152)AAA>AGA	p.K384R	LBR_uc001hoz.2_Missense_Mutation_p.K384R|LBR_uc001hpa.1_Missense_Mutation_p.K384R	NM_002296	NP_002287	Q14739	LBR_HUMAN	lamin B receptor	384					cholesterol biosynthetic process	integral to nuclear inner membrane	chromo shadow domain binding|delta14-sterol reductase activity|DNA binding|lamin binding|receptor activity			ovary(1)|skin(1)	2	Breast(184;0.165)			GBM - Glioblastoma multiforme(131;0.117)		ACAAAAGTATTTGAGATCAAA	0.358													3	102	---	---	---	---	PASS
TRIM58	25893	broad.mit.edu	37	1	248039396	248039396	+	Missense_Mutation	SNP	G	T	T			TCGA-C5-A1ME-01A-11D-A13W-08	TCGA-C5-A1ME-10A-01D-A13W-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:248039396G>T	uc001ido.2	+	6	1114	c.1066G>T	c.(1066-1068)GCA>TCA	p.A356S	OR2W3_uc001idp.1_Intron	NM_015431	NP_056246	Q8NG06	TRI58_HUMAN	tripartite motif-containing 58	356	B30.2/SPRY.					intracellular	zinc ion binding			skin(3)|ovary(1)|pancreas(1)|lung(1)|central_nervous_system(1)	7	all_cancers(71;0.000139)|all_epithelial(71;1.58e-05)|Breast(184;0.0117)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)	all_cancers(173;0.0286)	OV - Ovarian serous cystadenocarcinoma(106;0.0319)			GGGAGAAGGAGCAGAGTGGGG	0.572													12	43	---	---	---	---	PASS
FAM49A	81553	broad.mit.edu	37	2	16746927	16746927	+	Missense_Mutation	SNP	G	C	C			TCGA-C5-A1ME-01A-11D-A13W-08	TCGA-C5-A1ME-10A-01D-A13W-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:16746927G>C	uc010exm.1	-	3	327	c.179C>G	c.(178-180)CCA>CGA	p.P60R	FAM49A_uc002rck.1_Missense_Mutation_p.P60R	NM_030797	NP_110424	Q9H0Q0	FA49A_HUMAN	family with sequence similarity 49, member A	60						intracellular					0	Acute lymphoblastic leukemia(172;0.0734)|all_hematologic(175;0.088)		GBM - Glioblastoma multiforme(3;0.00969)			TCGGATCTCTGGGCCTGCGCC	0.517													5	121	---	---	---	---	PASS
ZNF638	27332	broad.mit.edu	37	2	71660368	71660368	+	Silent	SNP	A	G	G			TCGA-C5-A1ME-01A-11D-A13W-08	TCGA-C5-A1ME-10A-01D-A13W-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:71660368A>G	uc002shx.2	+	27	6145	c.5826A>G	c.(5824-5826)GCA>GCG	p.A1942A	ZNF638_uc002shy.2_Silent_p.A1942A|ZNF638_uc002shz.2_Silent_p.A1921A|ZNF638_uc002sia.2_Silent_p.A1942A|ZNF638_uc010fed.2_RNA|ZNF638_uc002sic.2_Silent_p.A1039A|ZNF638_uc002sid.2_Silent_p.A311A	NM_014497	NP_055312	Q14966	ZN638_HUMAN	zinc finger protein 638	1942	Matrin-type.				RNA splicing	cytoplasm|nuclear speck	double-stranded DNA binding|nucleotide binding|RNA binding|zinc ion binding			pancreas(2)|ovary(1)|skin(1)	4						GTGAAAAAGCAATGACAAATC	0.343													5	195	---	---	---	---	PASS
EDAR	10913	broad.mit.edu	37	2	109545671	109545671	+	Nonsense_Mutation	SNP	A	T	T			TCGA-C5-A1ME-01A-11D-A13W-08	TCGA-C5-A1ME-10A-01D-A13W-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:109545671A>T	uc002teq.3	-	4	770	c.339T>A	c.(337-339)TGT>TGA	p.C113*	EDAR_uc010fjn.2_Nonsense_Mutation_p.C113*|EDAR_uc010yws.1_Nonsense_Mutation_p.C113*	NM_022336	NP_071731	Q9UNE0	EDAR_HUMAN	ectodysplasin A receptor precursor	113	TNFR-Cys 2.|Extracellular (Potential).				apoptosis|cell differentiation	integral to membrane	protein binding|transmembrane receptor activity			skin(1)	1						GGCAAGGGCCACACTCAGCGT	0.602													3	34	---	---	---	---	PASS
TMEM163	81615	broad.mit.edu	37	2	135223716	135223716	+	Missense_Mutation	SNP	C	A	A			TCGA-C5-A1ME-01A-11D-A13W-08	TCGA-C5-A1ME-10A-01D-A13W-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:135223716C>A	uc002ttx.2	-	6	702	c.636G>T	c.(634-636)AAG>AAT	p.K212N	TMEM163_uc002tty.2_RNA	NM_030923	NP_112185	Q8TC26	TM163_HUMAN	transmembrane protein 163	212						integral to membrane					0				BRCA - Breast invasive adenocarcinoma(221;0.154)		TGGTCAGAACCTTCCCCAGCA	0.507													3	17	---	---	---	---	PASS
MBD5	55777	broad.mit.edu	37	2	149247488	149247488	+	Silent	SNP	G	A	A			TCGA-C5-A1ME-01A-11D-A13W-08	TCGA-C5-A1ME-10A-01D-A13W-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:149247488G>A	uc002twm.3	+	12	4576	c.3588G>A	c.(3586-3588)CAG>CAA	p.Q1196Q	MBD5_uc010zbs.1_Intron|MBD5_uc010fns.2_Silent_p.Q1196Q|MBD5_uc002two.2_Silent_p.Q454Q|MBD5_uc002twp.2_Silent_p.Q246Q	NM_018328	NP_060798	Q9P267	MBD5_HUMAN	methyl-CpG binding domain protein 5	1196						chromosome|nucleus	chromatin binding|DNA binding			skin(3)|ovary(2)	5				BRCA - Breast invasive adenocarcinoma(221;0.0569)		CCAAAAAACAGTGGGACGGGG	0.483													61	69	---	---	---	---	PASS
CCDC148	130940	broad.mit.edu	37	2	159170296	159170296	+	Missense_Mutation	SNP	T	C	C			TCGA-C5-A1ME-01A-11D-A13W-08	TCGA-C5-A1ME-10A-01D-A13W-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:159170296T>C	uc002tzq.2	-	8	1138	c.875A>G	c.(874-876)TAT>TGT	p.Y292C	CCDC148_uc002tzr.2_Missense_Mutation_p.Y140C|CCDC148_uc010foh.2_Missense_Mutation_p.Y5C|CCDC148_uc010foi.1_Missense_Mutation_p.Y239C|CCDC148_uc010foj.1_Missense_Mutation_p.Y140C|CCDC148_uc010fok.1_Missense_Mutation_p.Y206C	NM_138803	NP_620158	Q8NFR7	CC148_HUMAN	coiled-coil domain containing 148	292										ovary(2)	2						GTGAGGAAAATATCTTTGTAA	0.378													13	77	---	---	---	---	PASS
LY75	4065	broad.mit.edu	37	2	160729002	160729002	+	Missense_Mutation	SNP	C	T	T			TCGA-C5-A1ME-01A-11D-A13W-08	TCGA-C5-A1ME-10A-01D-A13W-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:160729002C>T	uc002ubc.3	-	13	2146	c.2077G>A	c.(2077-2079)GAA>AAA	p.E693K	LY75_uc002ubb.3_Missense_Mutation_p.E693K|LY75_uc010fos.2_Missense_Mutation_p.E693K|LY75_uc010fot.1_Missense_Mutation_p.E693K	NM_002349	NP_002340	O60449	LY75_HUMAN	lymphocyte antigen 75 precursor	693	Extracellular (Potential).|C-type lectin 4.				endocytosis|immune response|inflammatory response	integral to plasma membrane	receptor activity|sugar binding				0				COAD - Colon adenocarcinoma(177;0.132)		TCCTTTATTTCATCCACATGG	0.378													9	85	---	---	---	---	PASS
TTN	7273	broad.mit.edu	37	2	179483070	179483070	+	Silent	SNP	A	T	T			TCGA-C5-A1ME-01A-11D-A13W-08	TCGA-C5-A1ME-10A-01D-A13W-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179483070A>T	uc010zfg.1	-	201	39635	c.39411T>A	c.(39409-39411)GTT>GTA	p.V13137V	TTN_uc010zfh.1_Silent_p.V6832V|TTN_uc010zfi.1_Silent_p.V6765V|TTN_uc010zfj.1_Silent_p.V6640V	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	14064							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)			CTGTGGCCAGAACCCAGGTCT	0.458													19	77	---	---	---	---	PASS
ABCB6	10058	broad.mit.edu	37	2	220074986	220074986	+	Missense_Mutation	SNP	C	T	T			TCGA-C5-A1ME-01A-11D-A13W-08	TCGA-C5-A1ME-10A-01D-A13W-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:220074986C>T	uc002vkc.1	-	18	2663	c.2386G>A	c.(2386-2388)GTC>ATC	p.V796I	ABCB6_uc010fwe.1_Missense_Mutation_p.V750I	NM_005689	NP_005680	Q9NP58	ABCB6_HUMAN	ATP-binding cassette, sub-family B, member 6	796	ABC transporter.				cadmium ion transmembrane transport|cellular iron ion homeostasis|detoxification of cadmium ion|porphyrin biosynthetic process	ATP-binding cassette (ABC) transporter complex|Golgi apparatus|integral to mitochondrial outer membrane|plasma membrane|vacuolar membrane	ATP binding|efflux transmembrane transporter activity|heme binding|heme-transporting ATPase activity			breast(1)|central_nervous_system(1)	2		Renal(207;0.0474)		Epithelial(149;1.22e-06)|all cancers(144;0.000201)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		TCCTTGATGACGAGGATCTGG	0.552													8	69	---	---	---	---	PASS
CHRNG	1146	broad.mit.edu	37	2	233406222	233406222	+	Missense_Mutation	SNP	C	A	A			TCGA-C5-A1ME-01A-11D-A13W-08	TCGA-C5-A1ME-10A-01D-A13W-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:233406222C>A	uc002vsx.1	+	5	510	c.489C>A	c.(487-489)AAC>AAA	p.N163K	CHRNG_uc010fyd.2_Missense_Mutation_p.N163K|CHRNG_uc010fye.1_Intron	NM_005199	NP_005190	P07510	ACHG_HUMAN	cholinergic receptor, nicotinic, gamma	163	Extracellular (Potential).				muscle contraction	cell junction|postsynaptic membrane	acetylcholine receptor activity				0		all_hematologic(139;0.00793)|Renal(207;0.0112)|Acute lymphoblastic leukemia(138;0.0182)|all_lung(227;0.0449)|Lung NSC(271;0.132)		Epithelial(121;6.39e-16)|BRCA - Breast invasive adenocarcinoma(100;0.00079)|LUSC - Lung squamous cell carcinoma(224;0.00757)|Lung(119;0.0086)		ACTGGCAGAACTGCTCCCTTA	0.582													23	83	---	---	---	---	PASS
DGKD	8527	broad.mit.edu	37	2	234356724	234356724	+	Intron	SNP	T	C	C			TCGA-C5-A1ME-01A-11D-A13W-08	TCGA-C5-A1ME-10A-01D-A13W-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:234356724T>C	uc002vui.1	+						DGKD_uc002vuj.1_Intron|DGKD_uc010fyh.1_Intron|DGKD_uc010fyi.1_Intron	NM_152879	NP_690618	Q16760	DGKD_HUMAN	diacylglycerol kinase, delta 130kDa isoform 2						activation of protein kinase C activity by G-protein coupled receptor protein signaling pathway|cell growth|diacylglycerol metabolic process|endocytosis|epidermal growth factor receptor signaling pathway|multicellular organismal development|platelet activation|protein homooligomerization|protein transport|response to organic substance|second-messenger-mediated signaling	cytoplasm|cytoplasmic membrane-bounded vesicle|plasma membrane|plasma membrane	ATP binding|diacylglycerol binding|diacylglycerol kinase activity|metal ion binding|protein heterodimerization activity|protein homodimerization activity			central_nervous_system(2)|pancreas(1)|lung(1)|skin(1)	5		Breast(86;0.0013)|Renal(207;0.00339)|all_hematologic(139;0.0116)|all_lung(227;0.0179)|Acute lymphoblastic leukemia(138;0.0326)|Lung NSC(271;0.0538)		Epithelial(121;1.31e-16)|BRCA - Breast invasive adenocarcinoma(100;0.000416)|Lung(119;0.00285)|LUSC - Lung squamous cell carcinoma(224;0.00655)	Phosphatidylserine(DB00144)	CCATTTGGGGTGATTGCAGGT	0.537													3	62	---	---	---	---	PASS
MST1R	4486	broad.mit.edu	37	3	49934783	49934783	+	Missense_Mutation	SNP	C	G	G			TCGA-C5-A1ME-01A-11D-A13W-08	TCGA-C5-A1ME-10A-01D-A13W-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:49934783C>G	uc003cxy.3	-	7	2377	c.2113G>C	c.(2113-2115)GAA>CAA	p.E705Q	MST1R_uc011bdd.1_Missense_Mutation_p.E705Q|MST1R_uc011bdc.1_5'Flank	NM_002447	NP_002438	Q04912	RON_HUMAN	macrophage stimulating 1 receptor precursor	705	IPT/TIG 2.|Extracellular (Potential).				cellular component movement|defense response|multicellular organismal development|positive regulation of cell proliferation|single fertilization|transmembrane receptor protein tyrosine kinase signaling pathway	integral to plasma membrane	ATP binding|macrophage colony-stimulating factor receptor activity|protein binding			ovary(5)|lung(1)	6				BRCA - Breast invasive adenocarcinoma(193;4.65e-05)|KIRC - Kidney renal clear cell carcinoma(197;0.00553)|Kidney(197;0.00625)		CTCTGGCCTTCAAGAGTGAGA	0.597													6	45	---	---	---	---	PASS
GNAI2	2771	broad.mit.edu	37	3	50293634	50293634	+	Missense_Mutation	SNP	G	A	A			TCGA-C5-A1ME-01A-11D-A13W-08	TCGA-C5-A1ME-10A-01D-A13W-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:50293634G>A	uc003cyq.1	+	5	596	c.475G>A	c.(475-477)GAC>AAC	p.D159N	GNAI2_uc003cyo.1_Missense_Mutation_p.D143N|GNAI2_uc003cyp.1_Missense_Mutation_p.D143N|GNAI2_uc010hlg.1_Missense_Mutation_p.D78N|GNAI2_uc011bdn.1_Missense_Mutation_p.D122N|GNAI2_uc003cyr.1_Missense_Mutation_p.D78N	NM_002070	NP_002061	P04899	GNAI2_HUMAN	guanine nucleotide binding protein (G protein),	159					adenosine receptor signaling pathway|cell cycle|cell division|gamma-aminobutyric acid signaling pathway|inhibition of adenylate cyclase activity by G-protein signaling pathway|negative regulation of calcium ion transport via voltage-gated calcium channel activity|platelet activation|response to nutrient|synaptic transmission	centrosome|heterotrimeric G-protein complex|midbody	G-protein beta/gamma-subunit complex binding|G-protein-coupled receptor binding|GTP binding|GTPase activity|signal transducer activity			ovary(1)|central_nervous_system(1)|skin(1)	3				BRCA - Breast invasive adenocarcinoma(193;0.000288)|KIRC - Kidney renal clear cell carcinoma(197;0.00571)|Kidney(197;0.00651)		CTACCTGAACGACCTGGAGCG	0.617													5	17	---	---	---	---	PASS
RASSF1	11186	broad.mit.edu	37	3	50374657	50374657	+	Intron	SNP	C	T	T			TCGA-C5-A1ME-01A-11D-A13W-08	TCGA-C5-A1ME-10A-01D-A13W-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:50374657C>T	uc003dad.1	-						RASSF1_uc003dab.1_Missense_Mutation_p.E32K|RASSF1_uc003dac.2_Intron|RASSF1_uc003dae.1_Intron|RASSF1_uc010hlk.1_Intron|RASSF1_uc003daf.1_Intron|RASSF1_uc011bdq.1_3'UTR	NM_170714	NP_733832	Q9NS23	RASF1_HUMAN	Ras association domain family 1 isoform D						cell cycle arrest|negative regulation of cell cycle arrest|positive regulation of protein ubiquitination|protein stabilization|Ras protein signal transduction|response to DNA damage stimulus	microtubule|microtubule cytoskeleton|microtubule organizing center|nucleus|spindle pole	identical protein binding|protein binding|protein N-terminus binding|zinc ion binding			ovary(1)|skin(1)	2				BRCA - Breast invasive adenocarcinoma(193;0.000278)|OV - Ovarian serous cystadenocarcinoma(275;0.0015)|KIRC - Kidney renal clear cell carcinoma(197;0.00551)|Kidney(197;0.00621)		AAGTACTGCTCGAGCTCCGAG	0.687													8	24	---	---	---	---	PASS
IQCF2	389123	broad.mit.edu	37	3	51897275	51897275	+	Silent	SNP	C	T	T			TCGA-C5-A1ME-01A-11D-A13W-08	TCGA-C5-A1ME-10A-01D-A13W-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:51897275C>T	uc003dbt.1	+	3	422	c.384C>T	c.(382-384)ATC>ATT	p.I128I	IQCF1_uc003dbq.3_Intron|IQCF2_uc003dbu.1_RNA	NM_203424	NP_982248	Q8IXL9	IQCF2_HUMAN	IQ motif containing F2	128	IQ 2.										0				BRCA - Breast invasive adenocarcinoma(193;8.01e-05)|Kidney(197;0.000537)|KIRC - Kidney renal clear cell carcinoma(197;0.000716)		CCATCTACATCATCCAGGGCC	0.577													17	78	---	---	---	---	PASS
MAGI1	9223	broad.mit.edu	37	3	65425603	65425603	+	Silent	SNP	T	C	C	rs62642828	byFrequency	TCGA-C5-A1ME-01A-11D-A13W-08	TCGA-C5-A1ME-10A-01D-A13W-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:65425603T>C	uc003dmn.2	-	9	1747	c.1221A>G	c.(1219-1221)CAA>CAG	p.Q407Q	MAGI1_uc003dmm.2_Silent_p.Q407Q|MAGI1_uc003dmo.2_Silent_p.Q407Q|MAGI1_uc003dmp.2_Silent_p.Q407Q|MAGI1_uc010hny.2_Silent_p.Q292Q	NM_001033057	NP_001028229	Q96QZ7	MAGI1_HUMAN	membrane associated guanylate kinase, WW and PDZ	407	Poly-Gln.				cell adhesion|cell surface receptor linked signaling pathway|protein complex assembly	tight junction	ATP binding|protein C-terminus binding			lung(2)|skin(1)|breast(1)|kidney(1)|pancreas(1)	6		Lung NSC(201;0.0016)		BRCA - Breast invasive adenocarcinoma(55;0.00138)|KIRC - Kidney renal clear cell carcinoma(15;0.0988)|Kidney(15;0.133)		gctgctgctgttgctgctgct	0.338											OREG0015658	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	3	58	---	---	---	---	PASS
SLC2A9	56606	broad.mit.edu	37	4	9982212	9982212	+	Intron	SNP	T	G	G			TCGA-C5-A1ME-01A-11D-A13W-08	TCGA-C5-A1ME-10A-01D-A13W-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:9982212T>G	uc003gmc.2	-						SLC2A9_uc003gmd.2_Intron	NM_020041	NP_064425	Q9NRM0	GTR9_HUMAN	solute carrier family 2, member 9 protein						glucose transport|urate metabolic process	integral to membrane|plasma membrane	sugar:hydrogen symporter activity			ovary(3)	3						GGAGCCACACTCACCTTTCCC	0.552													6	30	---	---	---	---	PASS
ANKRD17	26057	broad.mit.edu	37	4	73943173	73943173	+	Nonsense_Mutation	SNP	G	A	A			TCGA-C5-A1ME-01A-11D-A13W-08	TCGA-C5-A1ME-10A-01D-A13W-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:73943173G>A	uc003hgp.2	-	32	7603	c.7486C>T	c.(7486-7488)CAA>TAA	p.Q2496*	ANKRD17_uc003hgo.2_Nonsense_Mutation_p.Q2383*|ANKRD17_uc003hgq.2_Nonsense_Mutation_p.Q2245*|ANKRD17_uc003hgr.2_Nonsense_Mutation_p.Q2495*	NM_032217	NP_115593	O75179	ANR17_HUMAN	ankyrin repeat domain protein 17 isoform a	2496					interspecies interaction between organisms	cytoplasm|nucleus	RNA binding			ovary(5)|skin(3)|upper_aerodigestive_tract(1)|lung(1)	10	Breast(15;0.000295)		Epithelial(6;8.86e-07)|OV - Ovarian serous cystadenocarcinoma(6;6.22e-06)|all cancers(17;1.51e-05)|Lung(101;0.103)|LUSC - Lung squamous cell carcinoma(112;0.154)			GCTTGATGTTGTGAAAATACT	0.458													4	136	---	---	---	---	PASS
TRPC3	7222	broad.mit.edu	37	4	122828641	122828641	+	Missense_Mutation	SNP	C	T	T			TCGA-C5-A1ME-01A-11D-A13W-08	TCGA-C5-A1ME-10A-01D-A13W-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:122828641C>T	uc003ieg.2	-	7	1948	c.1874G>A	c.(1873-1875)CGG>CAG	p.R625Q	TRPC3_uc010inr.2_Missense_Mutation_p.R497Q|TRPC3_uc003ief.2_Missense_Mutation_p.R552Q|TRPC3_uc011cgl.1_Missense_Mutation_p.R289Q	NM_001130698	NP_001124170	Q13507	TRPC3_HUMAN	transient receptor potential cation channel,	540	Helical; (Potential).				axon guidance|phototransduction|platelet activation	integral to plasma membrane	protein binding|store-operated calcium channel activity			ovary(2)	2						GTACGCAATCCGAGAGAAGCT	0.448													22	113	---	---	---	---	PASS
KIAA1109	84162	broad.mit.edu	37	4	123227038	123227038	+	Missense_Mutation	SNP	G	A	A			TCGA-C5-A1ME-01A-11D-A13W-08	TCGA-C5-A1ME-10A-01D-A13W-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:123227038G>A	uc003ieh.2	+	55	9724	c.9679G>A	c.(9679-9681)GAG>AAG	p.E3227K	KIAA1109_uc003iel.1_Missense_Mutation_p.E1162K	NM_015312	NP_056127	Q2LD37	K1109_HUMAN	fragile site-associated protein	3227					regulation of cell growth|regulation of epithelial cell differentiation	integral to membrane|nucleus				ovary(8)|skin(2)|pancreas(1)|central_nervous_system(1)	12						TTAGGTTTATGAGGAAGCTGG	0.289													7	27	---	---	---	---	PASS
FBXO38	81545	broad.mit.edu	37	5	147785921	147785921	+	Missense_Mutation	SNP	C	G	G			TCGA-C5-A1ME-01A-11D-A13W-08	TCGA-C5-A1ME-10A-01D-A13W-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:147785921C>G	uc003lpf.1	+	7	952	c.832C>G	c.(832-834)CTT>GTT	p.L278V	FBXO38_uc003lpg.1_Missense_Mutation_p.L278V|FBXO38_uc003lph.2_Missense_Mutation_p.L278V	NM_205836	NP_995308	Q6PIJ6	FBX38_HUMAN	F-box protein 38 isoform b	278						cytoplasm|nucleus				ovary(4)|skin(2)	6			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CCTTGGAGGTCTTATCCAACA	0.338													4	76	---	---	---	---	PASS
SSR1	6745	broad.mit.edu	37	6	7310258	7310258	+	Silent	SNP	C	T	T			TCGA-C5-A1ME-01A-11D-A13W-08	TCGA-C5-A1ME-10A-01D-A13W-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:7310258C>T	uc003mxf.3	-	2	272	c.84G>A	c.(82-84)TTG>TTA	p.L28L	SSR1_uc003mxg.3_Silent_p.L28L|SSR1_uc010jny.2_Silent_p.L28L	NM_003144	NP_003135	P43307	SSRA_HUMAN	signal sequence receptor, alpha precursor	28	Lumenal (Potential).				cotranslational protein targeting to membrane|positive regulation of cell proliferation	endoplasmic reticulum membrane|integral to membrane	signal sequence binding				0	Ovarian(93;0.0398)					CCACTGCTAACAAGCCTAATG	0.358													4	66	---	---	---	---	PASS
HIST1H4C	8364	broad.mit.edu	37	6	26104206	26104206	+	Missense_Mutation	SNP	T	A	A			TCGA-C5-A1ME-01A-11D-A13W-08	TCGA-C5-A1ME-10A-01D-A13W-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:26104206T>A	uc003ngi.2	+	1	31	c.31T>A	c.(31-33)TTG>ATG	p.L11M		NM_003542	NP_003533	P62805	H4_HUMAN	histone cluster 1, H4c	11					CenH3-containing nucleosome assembly at centromere|negative regulation of megakaryocyte differentiation|phosphatidylinositol-mediated signaling|telomere maintenance	nucleoplasm|nucleosome	DNA binding|protein binding				0						CGGAAAAGGCTTGGGGAAGGG	0.532													7	54	---	---	---	---	PASS
ZNF193	7746	broad.mit.edu	37	6	28194897	28194897	+	Missense_Mutation	SNP	G	A	A			TCGA-C5-A1ME-01A-11D-A13W-08	TCGA-C5-A1ME-10A-01D-A13W-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:28194897G>A	uc003nkq.1	+	2	150	c.35G>A	c.(34-36)GGT>GAT	p.G12D	ZNF193_uc003nkr.1_Missense_Mutation_p.G12D|ZNF193_uc010jqz.1_Missense_Mutation_p.G12D	NM_006299	NP_006290	O15535	ZN193_HUMAN	zinc finger protein 193	12					viral reproduction	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding				0						TTATCCCTGGGTGTTCAAGTT	0.453													11	35	---	---	---	---	PASS
HLA-E	3133	broad.mit.edu	37	6	30459060	30459060	+	Missense_Mutation	SNP	G	A	A			TCGA-C5-A1ME-01A-11D-A13W-08	TCGA-C5-A1ME-10A-01D-A13W-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:30459060G>A	uc003nqg.2	+	4	795	c.757G>A	c.(757-759)GAG>AAG	p.E253K	HLA-E_uc011dmg.1_RNA|HLA-E_uc011dmh.1_Missense_Mutation_p.E294K	NM_005516	NP_005507	P13747	HLAE_HUMAN	major histocompatibility complex, class I, E	253	Ig-like C1-type.|Alpha-3.|Extracellular (Potential).				antigen processing and presentation of peptide antigen via MHC class I|interferon-gamma-mediated signaling pathway|regulation of immune response|type I interferon-mediated signaling pathway	integral to membrane|MHC class I protein complex	MHC class I receptor activity			central_nervous_system(4)|ovary(1)	5						GGAGCTCGTGGAGACCAGGCC	0.637													14	70	---	---	---	---	PASS
SKIV2L	6499	broad.mit.edu	37	6	31928481	31928481	+	Missense_Mutation	SNP	C	T	T	rs150758406		TCGA-C5-A1ME-01A-11D-A13W-08	TCGA-C5-A1ME-10A-01D-A13W-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:31928481C>T	uc003nyn.1	+	6	897	c.508C>T	c.(508-510)CGG>TGG	p.R170W	RDBP_uc003nyk.2_5'Flank|RDBP_uc011dot.1_5'Flank|RDBP_uc003nyl.1_5'Flank|RDBP_uc003nym.1_5'Flank|SKIV2L_uc011dou.1_Missense_Mutation_p.R12W|SKIV2L_uc011dov.1_Intron	NM_006929	NP_008860	Q15477	SKIV2_HUMAN	superkiller viralicidic activity 2-like homolog	170						nucleus	ATP binding|ATP-dependent RNA helicase activity|protein binding|RNA binding			ovary(1)|large_intestine(1)|breast(1)|central_nervous_system(1)	4						TCTGAACACACGGGAGGAGGC	0.507													9	115	---	---	---	---	PASS
COL11A2	1302	broad.mit.edu	37	6	33147578	33147578	+	Missense_Mutation	SNP	C	T	T			TCGA-C5-A1ME-01A-11D-A13W-08	TCGA-C5-A1ME-10A-01D-A13W-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:33147578C>T	uc003ocx.1	-	13	1592	c.1364G>A	c.(1363-1365)CGG>CAG	p.R455Q	COL11A2_uc010jul.1_5'Flank|COL11A2_uc003ocy.1_Missense_Mutation_p.R369Q|COL11A2_uc003ocz.1_Missense_Mutation_p.R348Q	NM_080680	NP_542411	P13942	COBA2_HUMAN	collagen, type XI, alpha 2 isoform 1	455	Nonhelical region.				cartilage development|cell adhesion|collagen fibril organization|sensory perception of sound|soft palate development	collagen type XI	extracellular matrix structural constituent conferring tensile strength|protein binding, bridging			ovary(3)|skin(2)	5						ACTGCCAAACCGGAACTGAGG	0.642													4	39	---	---	---	---	PASS
GPR111	222611	broad.mit.edu	37	6	47646846	47646846	+	Silent	SNP	T	C	C			TCGA-C5-A1ME-01A-11D-A13W-08	TCGA-C5-A1ME-10A-01D-A13W-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:47646846T>C	uc010jzj.1	+	4	448	c.447T>C	c.(445-447)ACT>ACC	p.T149T	GPR111_uc010jzk.1_Silent_p.T81T|GPR111_uc003oyy.2_RNA	NM_153839	NP_722581	Q8IZF7	GP111_HUMAN	G-protein coupled receptor 111	149	Extracellular (Potential).				neuropeptide signaling pathway	integral to membrane|plasma membrane	G-protein coupled receptor activity			skin(1)	1						CCTGCCAGACTCTTAATGCCC	0.458													15	52	---	---	---	---	PASS
ZNF292	23036	broad.mit.edu	37	6	87925715	87925715	+	Missense_Mutation	SNP	C	A	A			TCGA-C5-A1ME-01A-11D-A13W-08	TCGA-C5-A1ME-10A-01D-A13W-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:87925715C>A	uc003plm.3	+	2	304	c.263C>A	c.(262-264)GCC>GAC	p.A88D	ZNF292_uc003pll.1_Missense_Mutation_p.A88D	NM_015021	NP_055836	O60281	ZN292_HUMAN	zinc finger protein 292	88					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(4)	4		all_cancers(76;3.82e-09)|Prostate(29;1.34e-10)|Acute lymphoblastic leukemia(125;2.17e-10)|all_hematologic(105;1.08e-06)|all_epithelial(107;5.31e-05)		BRCA - Breast invasive adenocarcinoma(108;0.0199)		TATGTTAAAGCCCGACCTTAT	0.378													3	61	---	---	---	---	PASS
GPR126	57211	broad.mit.edu	37	6	142758605	142758605	+	Silent	SNP	G	A	A			TCGA-C5-A1ME-01A-11D-A13W-08	TCGA-C5-A1ME-10A-01D-A13W-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:142758605G>A	uc010khc.2	+	23	3765	c.3354G>A	c.(3352-3354)AAG>AAA	p.K1118K	GPR126_uc010khd.2_Silent_p.K1090K|GPR126_uc010khe.2_Silent_p.K1118K|GPR126_uc010khf.2_Silent_p.K1090K|GPR126_uc011edv.1_Silent_p.K178K	NM_020455	NP_065188	Q86SQ4	GP126_HUMAN	G protein-coupled receptor 126 alpha 1	1118	Cytoplasmic (Potential).				neuropeptide signaling pathway	integral to membrane|plasma membrane	G-protein coupled receptor activity			ovary(1)	1	Breast(32;0.176)			OV - Ovarian serous cystadenocarcinoma(155;9.33e-06)|GBM - Glioblastoma multiforme(68;0.00121)		GTGCTATGAAGGAGAATGTTC	0.338													10	43	---	---	---	---	PASS
INTS1	26173	broad.mit.edu	37	7	1517492	1517492	+	Missense_Mutation	SNP	C	T	T			TCGA-C5-A1ME-01A-11D-A13W-08	TCGA-C5-A1ME-10A-01D-A13W-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:1517492C>T	uc003skn.2	-	34	4812	c.4711G>A	c.(4711-4713)GCC>ACC	p.A1571T	INTS1_uc003skm.1_5'Flank	NM_001080453	NP_001073922	Q8N201	INT1_HUMAN	integrator complex subunit 1	1571					snRNA processing	integral to membrane|integrator complex|nuclear membrane					0		Ovarian(82;0.0253)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0181)|OV - Ovarian serous cystadenocarcinoma(56;6.99e-15)		AACGGGGAGGCAGCATCCGCA	0.657													10	27	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	7	100549927	100549927	+	5'Flank	SNP	G	A	A			TCGA-C5-A1ME-01A-11D-A13W-08	TCGA-C5-A1ME-10A-01D-A13W-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:100549927G>A	uc003uxk.1	+						uc003uxl.1_5'Flank					Homo sapiens MUC3B mRNA for intestinal mucin, partial cds.																		AGTGACCACCGTCACCAGTAC	0.547													5	27	---	---	---	---	PASS
ZNF277	11179	broad.mit.edu	37	7	111846857	111846857	+	Missense_Mutation	SNP	A	G	G			TCGA-C5-A1ME-01A-11D-A13W-08	TCGA-C5-A1ME-10A-01D-A13W-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:111846857A>G	uc003vge.2	+	1	215	c.86A>G	c.(85-87)TAT>TGT	p.Y29C	DOCK4_uc003vfx.2_5'Flank|DOCK4_uc003vfy.2_5'Flank|DOCK4_uc003vga.1_5'Flank|DOCK4_uc010ljt.1_5'Flank|ZNF277_uc003vgd.2_Missense_Mutation_p.Y29C|ZNF277_uc003vgf.2_5'UTR|ZNF277_uc003vgc.2_Missense_Mutation_p.Y29C	NM_021994	NP_068834	Q9NRM2	ZN277_HUMAN	zinc finger protein (C2H2 type) 277	29						nucleus	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(2)|breast(2)	4						GGTGTAGGTTATGGGGGTGAG	0.612													8	30	---	---	---	---	PASS
MGAM	8972	broad.mit.edu	37	7	141802440	141802440	+	Silent	SNP	G	C	C			TCGA-C5-A1ME-01A-11D-A13W-08	TCGA-C5-A1ME-10A-01D-A13W-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:141802440G>C	uc003vwy.2	+	46	5340	c.5286G>C	c.(5284-5286)GGG>GGC	p.G1762G		NM_004668	NP_004659	O43451	MGA_HUMAN	maltase-glucoamylase	1762	Glucoamylase.|Lumenal (Potential).				polysaccharide digestion|starch catabolic process	apical plasma membrane|integral to membrane	carbohydrate binding|glucan 1,4-alpha-glucosidase activity|maltose alpha-glucosidase activity			ovary(2)	2	Melanoma(164;0.0272)				Acarbose(DB00284)|Miglitol(DB00491)|Voglibose(DB04878)	ATACCTATGGGAAAGGACTCT	0.418													3	19	---	---	---	---	PASS
EIF2C2	27161	broad.mit.edu	37	8	141566113	141566113	+	Missense_Mutation	SNP	C	T	T			TCGA-C5-A1ME-01A-11D-A13W-08	TCGA-C5-A1ME-10A-01D-A13W-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:141566113C>T	uc003yvn.2	-	10	1191	c.1151G>A	c.(1150-1152)CGA>CAA	p.R384Q	EIF2C2_uc010men.2_Missense_Mutation_p.R307Q|EIF2C2_uc010meo.2_Missense_Mutation_p.R384Q	NM_012154	NP_036286	Q9UKV8	AGO2_HUMAN	argonaute 2 isoform 1	384					mRNA cleavage involved in gene silencing by miRNA|negative regulation of translation involved in gene silencing by miRNA|negative regulation of translational initiation|pre-miRNA processing|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasmic mRNA processing body|cytosol|micro-ribonucleoprotein complex|mRNA cap binding complex|nucleus|polysome|RNA-induced silencing complex	endoribonuclease activity, cleaving siRNA-paired mRNA|metal ion binding|protein binding|RNA 7-methylguanosine cap binding|siRNA binding|translation initiation factor activity				0	all_cancers(97;2.54e-14)|all_epithelial(106;5.99e-13)|Lung NSC(106;1.45e-05)|all_lung(105;2.07e-05)|Ovarian(258;0.0154)|Acute lymphoblastic leukemia(118;0.155)	Breast(495;0.159)	BRCA - Breast invasive adenocarcinoma(115;0.158)			ACTTGCACTTCGCATCTGGCA	0.542													4	65	---	---	---	---	PASS
TESK1	7016	broad.mit.edu	37	9	35608000	35608000	+	Missense_Mutation	SNP	C	T	T			TCGA-C5-A1ME-01A-11D-A13W-08	TCGA-C5-A1ME-10A-01D-A13W-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:35608000C>T	uc003zxa.2	+	7	1123	c.787C>T	c.(787-789)CGC>TGC	p.R263C	TESK1_uc003zwz.1_RNA|TESK1_uc010mks.2_Missense_Mutation_p.R103C	NM_006285	NP_006276	Q15569	TESK1_HUMAN	testis-specific protein kinase 1	263	Protein kinase.				cell junction assembly|spermatogenesis	cytosol	ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity|protein tyrosine kinase activity			stomach(2)|breast(2)|lung(1)|ovary(1)|skin(1)	7			Lung(28;0.00276)|LUSC - Lung squamous cell carcinoma(32;0.00418)|STAD - Stomach adenocarcinoma(86;0.194)			CTACCTACCACGCACTGAGGT	0.512													7	38	---	---	---	---	PASS
TSC1	7248	broad.mit.edu	37	9	135801105	135801105	+	Missense_Mutation	SNP	C	T	T			TCGA-C5-A1ME-01A-11D-A13W-08	TCGA-C5-A1ME-10A-01D-A13W-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:135801105C>T	uc004cca.2	-	5	466	c.232G>A	c.(232-234)GAA>AAA	p.E78K	TSC1_uc004ccb.3_Missense_Mutation_p.E78K|TSC1_uc011mcq.1_Intron|TSC1_uc011mcr.1_5'UTR|TSC1_uc011mcs.1_5'UTR|TSC1_uc004ccc.1_Missense_Mutation_p.E78K|TSC1_uc004ccd.2_Missense_Mutation_p.E78K|TSC1_uc004cce.1_Missense_Mutation_p.E78K	NM_000368	NP_000359	Q92574	TSC1_HUMAN	tuberous sclerosis 1 protein isoform 1	78					activation of Rho GTPase activity|cell cycle arrest|cell-matrix adhesion|insulin receptor signaling pathway|negative regulation of cell proliferation|negative regulation of protein ubiquitination|negative regulation of TOR signaling cascade|negative regulation of translation|positive regulation of focal adhesion assembly|regulation of phosphoprotein phosphatase activity|regulation of stress fiber assembly|rRNA export from nucleus	cell cortex|lamellipodium|membrane|TSC1-TSC2 complex	chaperone binding|protein N-terminus binding			lung(4)|central_nervous_system(3)|breast(2)|haematopoietic_and_lymphoid_tissue(1)|urinary_tract(1)|skin(1)|ovary(1)|bone(1)	14				OV - Ovarian serous cystadenocarcinoma(145;4.32e-08)|Epithelial(140;2.72e-06)		CCCACATATTCGTTAATCCTG	0.443			D|Mis|N|F|S			hamartoma|renal cell			Tuberous_Sclerosis				10	31	---	---	---	---	PASS
FAM107B	83641	broad.mit.edu	37	10	14816480	14816480	+	Silent	SNP	G	A	A			TCGA-C5-A1ME-01A-11D-A13W-08	TCGA-C5-A1ME-10A-01D-A13W-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:14816480G>A	uc001ina.1	-	1	417	c.183C>T	c.(181-183)GGC>GGT	p.G61G	FAM107B_uc010qbu.1_RNA	NM_031453	NP_113641	Q9H098	F107B_HUMAN	hypothetical protein LOC83641	Error:Variant_position_missing_in_Q9H098_after_alignment										breast(4)	4						TTGGCTGTCTGCCTGCTTTGG	0.547													53	56	---	---	---	---	PASS
EPC1	80314	broad.mit.edu	37	10	32560653	32560653	+	Missense_Mutation	SNP	C	T	T			TCGA-C5-A1ME-01A-11D-A13W-08	TCGA-C5-A1ME-10A-01D-A13W-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:32560653C>T	uc001iwg.1	-	14	2537	c.2267G>A	c.(2266-2268)CGA>CAA	p.R756Q	EPC1_uc001iwi.3_Missense_Mutation_p.R683Q|EPC1_uc001iwh.1_Missense_Mutation_p.R733Q	NM_025209	NP_079485	Q9H2F5	EPC1_HUMAN	enhancer of polycomb 1	756					histone H2A acetylation|histone H4 acetylation|negative regulation of gene expression, epigenetic|negative regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase II promoter|regulation of growth|transcription, DNA-dependent	NuA4 histone acetyltransferase complex|nuclear membrane|Piccolo NuA4 histone acetyltransferase complex				ovary(3)|central_nervous_system(1)	4		Prostate(175;0.0199)				TACAGTTAATCGAATGTTGTT	0.413													8	205	---	---	---	---	PASS
PARD3	56288	broad.mit.edu	37	10	34739377	34739377	+	Splice_Site	SNP	C	G	G			TCGA-C5-A1ME-01A-11D-A13W-08	TCGA-C5-A1ME-10A-01D-A13W-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:34739377C>G	uc010qej.1	-	5	583	c.583_splice	c.e5-1	p.K195_splice	PARD3_uc010qek.1_Splice_Site_p.K195_splice|PARD3_uc010qel.1_Splice_Site_p.K195_splice|PARD3_uc010qem.1_Splice_Site_p.K195_splice|PARD3_uc010qen.1_Splice_Site_p.K195_splice|PARD3_uc010qeo.1_Splice_Site_p.K195_splice|PARD3_uc010qep.1_Intron|PARD3_uc010qeq.1_Intron|PARD3_uc001ixp.1_Splice_Site_p.K60_splice|PARD3_uc001ixq.1_Splice_Site_p.K195_splice|PARD3_uc001ixr.1_Splice_Site_p.K195_splice|PARD3_uc001ixt.1_Intron|PARD3_uc001ixu.1_Intron	NM_019619	NP_062565	Q8TEW0	PARD3_HUMAN	partitioning-defective protein 3 homolog						activation of protein kinase C activity by G-protein coupled receptor protein signaling pathway|asymmetric cell division|axonogenesis|cell cycle|establishment of epithelial cell polarity|protein complex assembly|protein targeting to membrane|tight junction assembly	cell cortex|cytoskeleton|cytosol|endomembrane system|tight junction	phosphatidylinositol-3,4,5-trisphosphate binding|phosphatidylinositol-3-phosphate binding|phosphatidylinositol-4,5-bisphosphate binding|protein binding			ovary(1)	1		Breast(68;0.0707)				TTTCATCTTTCTATTCAAAAA	0.398													6	46	---	---	---	---	PASS
MGEA5	10724	broad.mit.edu	37	10	103557892	103557892	+	Missense_Mutation	SNP	C	A	A			TCGA-C5-A1ME-01A-11D-A13W-08	TCGA-C5-A1ME-10A-01D-A13W-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:103557892C>A	uc001ktv.2	-	10	2272	c.1829G>T	c.(1828-1830)CGA>CTA	p.R610L	MGEA5_uc001ktu.2_RNA|MGEA5_uc010qqe.1_Missense_Mutation_p.R557L|MGEA5_uc009xws.2_Missense_Mutation_p.R557L|MGEA5_uc001ktw.2_Missense_Mutation_p.R610L	NM_012215	NP_036347	O60502	NCOAT_HUMAN	meningioma expressed antigen 5 (hyaluronidase)	610	Histone acetyltransferase activity (By similarity).				glycoprotein catabolic process	cytoplasm|nucleus	histone acetyltransferase activity|hyalurononglucosaminidase activity			ovary(2)|skin(1)	3		Colorectal(252;0.207)		Epithelial(162;4.67e-09)|all cancers(201;2.54e-07)		CTTGGCTGCTCGTGACCGCCA	0.388													18	62	---	---	---	---	PASS
XPNPEP1	7511	broad.mit.edu	37	10	111647914	111647914	+	Missense_Mutation	SNP	G	A	A			TCGA-C5-A1ME-01A-11D-A13W-08	TCGA-C5-A1ME-10A-01D-A13W-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:111647914G>A	uc001kyp.1	-	7	556	c.416C>T	c.(415-417)GCC>GTC	p.A139V	XPNPEP1_uc009xxt.1_Missense_Mutation_p.A182V|XPNPEP1_uc001kyq.1_Missense_Mutation_p.A68V|XPNPEP1_uc010qrb.1_Missense_Mutation_p.A182V	NM_020383	NP_065116	Q9NQW7	XPP1_HUMAN	X-prolyl aminopeptidase (aminopeptidase P) 1,	139					bradykinin catabolic process|proteolysis		manganese ion binding|metalloaminopeptidase activity|protein homodimerization activity			ovary(3)|pancreas(1)	4		Breast(234;0.174)		Epithelial(162;1.64e-05)|all cancers(201;0.000564)|BRCA - Breast invasive adenocarcinoma(275;0.0721)		GTGATGGCCGGCACTTCTCAG	0.557													5	14	---	---	---	---	PASS
C10orf120	399814	broad.mit.edu	37	10	124459221	124459221	+	Missense_Mutation	SNP	T	C	C			TCGA-C5-A1ME-01A-11D-A13W-08	TCGA-C5-A1ME-10A-01D-A13W-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:124459221T>C	uc001lgn.2	-	1	118	c.86A>G	c.(85-87)AAG>AGG	p.K29R		NM_001010912	NP_001010912	Q5SQS8	CJ120_HUMAN	hypothetical protein LOC399814	29										kidney(1)	1		all_neural(114;0.169)|Glioma(114;0.222)				TCTAACTGGCTTTTCATTCTT	0.443													7	83	---	---	---	---	PASS
ADAM12	8038	broad.mit.edu	37	10	127737897	127737897	+	Silent	SNP	C	G	G			TCGA-C5-A1ME-01A-11D-A13W-08	TCGA-C5-A1ME-10A-01D-A13W-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:127737897C>G	uc001ljk.2	-	16	2264	c.1851G>C	c.(1849-1851)GGG>GGC	p.G617G	ADAM12_uc010qul.1_Silent_p.G568G|ADAM12_uc001ljm.2_Silent_p.G617G|ADAM12_uc001ljn.2_Silent_p.G614G|ADAM12_uc001ljl.3_Silent_p.G614G	NM_003474	NP_003465	O43184	ADA12_HUMAN	ADAM metallopeptidase domain 12 isoform 1	617	Extracellular (Potential).|Cys-rich.				cell adhesion|epidermal growth factor receptor signaling pathway|myoblast fusion|proteolysis	extracellular region|integral to membrane|plasma membrane	metalloendopeptidase activity|protein binding|SH3 domain binding|zinc ion binding			breast(4)|ovary(2)|central_nervous_system(2)|upper_aerodigestive_tract(1)	9		all_epithelial(44;7.06e-05)|all_lung(145;0.00563)|Lung NSC(174;0.00834)|Colorectal(57;0.102)|all_neural(114;0.107)|Breast(234;0.22)		COAD - Colon adenocarcinoma(40;0.141)|Colorectal(40;0.216)		ACACGTGGGTCCCCCGGCACA	0.552													5	243	---	---	---	---	PASS
CARS	833	broad.mit.edu	37	11	3059277	3059277	+	Intron	SNP	C	T	T			TCGA-C5-A1ME-01A-11D-A13W-08	TCGA-C5-A1ME-10A-01D-A13W-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:3059277C>T	uc001lxh.2	-						CARS_uc001lxe.2_Intron|CARS_uc001lxf.2_Intron|CARS_uc001lxg.2_Intron|CARS_uc010qxo.1_Intron|CARS_uc010qxp.1_Intron|uc001lxi.1_Intron	NM_001751	NP_001742	P49589	SYCC_HUMAN	cysteinyl-tRNA synthetase isoform b						cysteinyl-tRNA aminoacylation	cytoplasm|cytosol	ATP binding|cysteine-tRNA ligase activity|metal ion binding|protein homodimerization activity|protein homodimerization activity|tRNA binding|tRNA binding		CARS/ALK(5)	soft_tissue(5)|ovary(2)	7		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;0.00317)|LUSC - Lung squamous cell carcinoma(625;0.218)	L-Cysteine(DB00151)	TGTGAAGCCTCACCTCCACAC	0.547			T	ALK	ALCL						OREG0020690	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	14	71	---	---	---	---	PASS
ENDOD1	23052	broad.mit.edu	37	11	94861718	94861718	+	Missense_Mutation	SNP	C	G	G			TCGA-C5-A1ME-01A-11D-A13W-08	TCGA-C5-A1ME-10A-01D-A13W-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:94861718C>G	uc001pfh.2	+	2	553	c.478C>G	c.(478-480)CTC>GTC	p.L160V		NM_015036	NP_055851	O94919	ENDD1_HUMAN	endonuclease domain containing 1 precursor	160						extracellular region	endonuclease activity|metal ion binding|nucleic acid binding				0		Acute lymphoblastic leukemia(157;2.33e-05)|all_hematologic(158;0.00824)				CACATTTACTCTCACAAATTC	0.493													3	39	---	---	---	---	PASS
MIRLET7A2	406882	broad.mit.edu	37	11	122017232	122017232	+	RNA	SNP	G	A	A			TCGA-C5-A1ME-01A-11D-A13W-08	TCGA-C5-A1ME-10A-01D-A13W-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:122017232G>A	hsa-let-7a-2|MI0000061	-			c.70G>A			LOC399959_uc009zba.2_Intron|uc001pyg.2_RNA																	0						AAGACCCAAGGAAAGCTAGGA	0.423													4	50	---	---	---	---	PASS
HSN2	378465	broad.mit.edu	37	12	978057	978057	+	Silent	SNP	A	G	G			TCGA-C5-A1ME-01A-11D-A13W-08	TCGA-C5-A1ME-10A-01D-A13W-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:978057A>G	uc001qiq.2	+	1	1188	c.1062A>G	c.(1060-1062)CAA>CAG	p.Q354Q	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)			ATTCCTCACAAATCACTTCTT	0.498													102	190	---	---	---	---	PASS
CLEC4A	50856	broad.mit.edu	37	12	8281849	8281849	+	Intron	SNP	C	T	T			TCGA-C5-A1ME-01A-11D-A13W-08	TCGA-C5-A1ME-10A-01D-A13W-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:8281849C>T	uc001qtz.1	+						CLEC4A_uc009zga.1_Intron|CLEC4A_uc001qub.1_Intron|CLEC4A_uc001quc.1_Intron|CLEC4A_uc009zgb.1_Intron	NM_016184	NP_057268	Q9UMR7	CLC4A_HUMAN	C-type lectin domain family 4, member A isoform						cell adhesion|cell surface receptor linked signaling pathway|innate immune response	integral to plasma membrane	sugar binding|transmembrane receptor activity				0				Kidney(36;0.0915)		GGTCTTTATTCTCTTTTCCAG	0.303													4	25	---	---	---	---	PASS
STRAP	11171	broad.mit.edu	37	12	16042950	16042950	+	Intron	SNP	G	C	C			TCGA-C5-A1ME-01A-11D-A13W-08	TCGA-C5-A1ME-10A-01D-A13W-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:16042950G>C	uc001rdc.3	+						STRAP_uc010shw.1_Intron|STRAP_uc001rdd.3_Intron	NM_007178	NP_009109	Q9Y3F4	STRAP_HUMAN	serine/threonine kinase receptor associated						mRNA processing|RNA splicing	cell junction|mitochondrion|spliceosomal complex	identical protein binding			skin(1)	1		Hepatocellular(102;0.121)				GCAGGTATCAGAAAATGGAAT	0.363													9	70	---	---	---	---	PASS
STRAP	11171	broad.mit.edu	37	12	16043597	16043597	+	Missense_Mutation	SNP	G	A	A			TCGA-C5-A1ME-01A-11D-A13W-08	TCGA-C5-A1ME-10A-01D-A13W-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:16043597G>A	uc001rdc.3	+	4	751	c.397G>A	c.(397-399)GAA>AAA	p.E133K	STRAP_uc010shw.1_Missense_Mutation_p.E146K|STRAP_uc001rdd.3_Missense_Mutation_p.E39K	NM_007178	NP_009109	Q9Y3F4	STRAP_HUMAN	serine/threonine kinase receptor associated	133	WD 3.				mRNA processing|RNA splicing	cell junction|mitochondrion|spliceosomal complex	identical protein binding			skin(1)	1		Hepatocellular(102;0.121)				GAACAAACCTGAAGCAGGTAA	0.294													9	114	---	---	---	---	PASS
KRAS	3845	broad.mit.edu	37	12	25398284	25398284	+	Missense_Mutation	SNP	C	T	T	rs121913529		TCGA-C5-A1ME-01A-11D-A13W-08	TCGA-C5-A1ME-10A-01D-A13W-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:25398284C>T	uc001rgp.1	-	2	216	c.35G>A	c.(34-36)GGT>GAT	p.G12D	KRAS_uc001rgq.1_Missense_Mutation_p.G12D|KRAS_uc001rgr.2_RNA	NM_033360	NP_203524	P01116	RASK_HUMAN	c-K-ras2 protein isoform a precursor	12	GTP.		G -> D (in pancreatic carcinoma, GASC and lung carcinoma; somatic mutation).|G -> R (in lung cancer and bladder cancer; somatic mutation).|G -> S (in lung carcinoma and GASC; somatic mutation).|G -> A (in a colorectal cancer sample; somatic mutation).|G -> C (in lung carcinoma; somatic mutation).|G -> V (in lung carcinoma, pancreatic carcinoma, colon cancer and GASC; somatic mutation).		activation of MAPKK activity|axon guidance|blood coagulation|epidermal growth factor receptor signaling pathway|insulin receptor signaling pathway|leukocyte migration|nerve growth factor receptor signaling pathway|Ras protein signal transduction	plasma membrane	GTP binding|GTPase activity|protein binding	p.G12D(7175)|p.G12V(4780)|p.G12C(2482)|p.G12A(1180)|p.G12S(1119)|p.G12R(691)|p.G12?(50)|p.G12F(34)|p.G12N(6)|p.G12G(6)|p.G12L(5)|p.G12I(4)|p.G12_G13insG(4)|p.G12E(3)|p.G12W(3)|p.A11_G12insGA(2)|p.G12Y(2)|p.G12fs*3(1)		large_intestine(12391)|pancreas(3285)|lung(2847)|biliary_tract(521)|ovary(443)|endometrium(339)|haematopoietic_and_lymphoid_tissue(318)|stomach(203)|thyroid(149)|prostate(85)|soft_tissue(77)|small_intestine(62)|upper_aerodigestive_tract(59)|cervix(49)|urinary_tract(48)|skin(38)|liver(31)|breast(28)|testis(17)|oesophagus(15)|central_nervous_system(9)|peritoneum(6)|salivary_gland(6)|kidney(5)|gastrointestinal_tract_(site_indeterminate)(5)|thymus(5)|eye(4)|autonomic_ganglia(2)|bone(2)|genital_tract(1)|penis(1)|adrenal_gland(1)	21052	all_cancers(2;1e-35)|all_epithelial(2;1.97e-38)|all_lung(3;2.1e-23)|Lung NSC(3;1.16e-22)|Acute lymphoblastic leukemia(6;0.00231)|all_hematologic(7;0.00259)|Melanoma(3;0.0301)|Colorectal(261;0.11)|Ovarian(17;0.12)		OV - Ovarian serous cystadenocarcinoma(3;1.23e-21)|Epithelial(3;1.31e-20)|all cancers(3;5.45e-18)|STAD - Stomach adenocarcinoma(2;2.68e-05)			GCCTACGCCACCAGCTCCAAC	0.348	G12D(HPAC_PANCREAS)|G12V(SW403_LARGE_INTESTINE)|G12D(HPAFII_PANCREAS)|G12D(PANC0403_PANCREAS)|G12D(KOPN8_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(KMS28BM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12V(NCIH441_LUNG)|G12D(SU8686_PANCREAS)|G12D(SUIT2_PANCREAS)|G12D(PK1_PANCREAS)|G12V(KP3_PANCREAS)|G12D(PANC0813_PANCREAS)|G12A(SW1116_LARGE_INTESTINE)|G12D(LS180_LARGE_INTESTINE)|G12V(NCIH727_LUNG)|G12V(PATU8988S_PANCREAS)|G12V(CAPAN2_PANCREAS)|G12D(KP4_PANCREAS)|G12D(LS513_LARGE_INTESTINE)|G12D(SNUC2A_LARGE_INTESTINE)|G12V(SW480_LARGE_INTESTINE)|G12V(COLO668_LUNG)|G12D(COLO678_LARGE_INTESTINE)|G12V(RERFLCAD2_LUNG)|G12D(PANC0203_PANCREAS)|G12V(CFPAC1_PANCREAS)|G12V(SW900_LUNG)|G12V(LCLC97TM1_LUNG)|G12V(SW620_LARGE_INTESTINE)|G12A(MM1S_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12V(SH10TC_STOMACH)|G12V(A498_KIDNEY)|G12D(PK59_PANCREAS)|G12D(HEC1A_ENDOMETRIUM)|G12D(PANC0504_PANCREAS)|G12V(SNGM_ENDOMETRIUM)|G12A(RERFLCAD1_LUNG)|G12A(KPNSI9S_AUTONOMIC_GANGLIA)|G12D(ASPC1_PANCREAS)|G12A(RPMI8226_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12V(RCM1_LARGE_INTESTINE)|G12V(CORL23_LUNG)|G12D(SW1990_PANCREAS)|G12D(HEYA8_OVARY)|G12A(NCIH1573_LUNG)|G12A(NCIH2009_LUNG)|G12V(HUPT4_PANCREAS)|G12D(KARPAS620_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12D(HEC50B_ENDOMETRIUM)|G12V(YAPC_PANCREAS)|G12V(NCIH2444_LUNG)|G12V(HCC56_LARGE_INTESTINE)|G12D(MCAS_OVARY)|G12V(DANG_PANCREAS)|G12V(SHP77_LUNG)|G12D(AGS_STOMACH)|G12D(SKLU1_LUNG)|G12V(QGP1_PANCREAS)|G12D(L33_PANCREAS)|G12V(PANC0327_PANCREAS)|G12D(PANC1_PANCREAS)|G12V(RKN_OVARY)|G12V(PATU8902_PANCREAS)	119	Mis		pancreatic|colorectal|lung|thyroid|AML|others				Cardiofaciocutaneous_syndrome|Noonan_syndrome	TSP Lung(1;<1E-08)|Multiple Myeloma(2;<1E-6)			18	19	---	---	---	---	PASS
SLC4A8	9498	broad.mit.edu	37	12	51856147	51856147	+	Silent	SNP	G	A	A			TCGA-C5-A1ME-01A-11D-A13W-08	TCGA-C5-A1ME-10A-01D-A13W-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:51856147G>A	uc001rys.1	+	10	1333	c.1155G>A	c.(1153-1155)GGG>GGA	p.G385G	SLC4A8_uc010sni.1_Silent_p.G332G|SLC4A8_uc001rym.2_Silent_p.G332G|SLC4A8_uc001ryn.2_Silent_p.G332G|SLC4A8_uc001ryo.2_Silent_p.G332G|SLC4A8_uc001ryp.1_3'UTR|SLC4A8_uc010snj.1_Silent_p.G412G|SLC4A8_uc001ryq.3_Silent_p.G385G|SLC4A8_uc001ryr.2_Silent_p.G385G|SLC4A8_uc010snk.1_Silent_p.G332G	NM_001039960	NP_001035049	Q2Y0W8	S4A8_HUMAN	solute carrier family 4, sodium bicarbonate	385	Extracellular (Potential).				bicarbonate transport|sodium ion transport	integral to membrane|plasma membrane	inorganic anion exchanger activity			ovary(3)|pancreas(1)|skin(1)	5				BRCA - Breast invasive adenocarcinoma(357;0.15)		TCCTGGCGGGGATTGATGAGT	0.458													4	127	---	---	---	---	PASS
KRT2	3849	broad.mit.edu	37	12	53039041	53039041	+	Missense_Mutation	SNP	C	A	A			TCGA-C5-A1ME-01A-11D-A13W-08	TCGA-C5-A1ME-10A-01D-A13W-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:53039041C>A	uc001sat.2	-	9	1715	c.1682G>T	c.(1681-1683)GGA>GTA	p.G561V		NM_000423	NP_000414	P35908	K22E_HUMAN	keratin 2	561	Tail.				keratinization|keratinocyte activation|keratinocyte migration|keratinocyte proliferation	Golgi apparatus|keratin filament	protein binding|structural constituent of cytoskeleton			ovary(2)	2				BRCA - Breast invasive adenocarcinoma(357;0.19)		GCCATATCCTCCTCCAGAGAT	0.582													8	255	---	---	---	---	PASS
XPOT	11260	broad.mit.edu	37	12	64818397	64818397	+	Missense_Mutation	SNP	T	G	G			TCGA-C5-A1ME-01A-11D-A13W-08	TCGA-C5-A1ME-10A-01D-A13W-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:64818397T>G	uc001ssb.2	+	12	1627	c.1201T>G	c.(1201-1203)TTT>GTT	p.F401V		NM_007235	NP_009166	O43592	XPOT_HUMAN	tRNA exportin	401					intracellular protein transport|tRNA export from nucleus	cytoplasm|nucleoplasm	protein transporter activity|tRNA binding			ovary(2)	2				GBM - Glioblastoma multiforme(28;0.0404)		TGAAGCCATGTTTGTAGAATA	0.294													3	105	---	---	---	---	PASS
RAB3IP	117177	broad.mit.edu	37	12	70178523	70178523	+	Missense_Mutation	SNP	A	C	C			TCGA-C5-A1ME-01A-11D-A13W-08	TCGA-C5-A1ME-10A-01D-A13W-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:70178523A>C	uc001svp.2	+	4	1029	c.582A>C	c.(580-582)GAA>GAC	p.E194D	RAB3IP_uc001svl.1_Missense_Mutation_p.E178D|RAB3IP_uc001svm.2_Missense_Mutation_p.E178D|RAB3IP_uc001svn.2_Missense_Mutation_p.E178D|RAB3IP_uc001svo.2_RNA|RAB3IP_uc001svq.2_Missense_Mutation_p.E194D|RAB3IP_uc001svr.2_RNA|RAB3IP_uc001svs.2_RNA|RAB3IP_uc001svt.2_5'UTR	NM_175623	NP_783322	Q96QF0	RAB3I_HUMAN	RAB3A interacting protein isoform alpha 2	194	Potential.				cilium assembly|Golgi to plasma membrane transport|protein localization to organelle|protein transport	actin cortical patch|centrosome|cytosol|lamellipodium|microtubule basal body|nucleus	guanyl-nucleotide exchange factor activity|protein binding			ovary(1)	1	Esophageal squamous(21;0.187)		Lung(24;0.000381)|OV - Ovarian serous cystadenocarcinoma(12;0.00168)|STAD - Stomach adenocarcinoma(21;0.00694)			AAGATGAAGAATGTGAGAGGC	0.348													10	56	---	---	---	---	PASS
NTN4	59277	broad.mit.edu	37	12	96063914	96063914	+	Nonsense_Mutation	SNP	C	A	A			TCGA-C5-A1ME-01A-11D-A13W-08	TCGA-C5-A1ME-10A-01D-A13W-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:96063914C>A	uc001tei.2	-	8	1968	c.1519G>T	c.(1519-1521)GAA>TAA	p.E507*	NTN4_uc009ztf.2_Intron|NTN4_uc009ztg.2_Nonsense_Mutation_p.E470*	NM_021229	NP_067052	Q9HB63	NET4_HUMAN	netrin 4 precursor	507	NTR.				axon guidance	basement membrane|plasma membrane				upper_aerodigestive_tract(1)|ovary(1)	2						TCCTTACATTCGCATTTACCT	0.338													10	23	---	---	---	---	PASS
RFX4	5992	broad.mit.edu	37	12	107114545	107114545	+	Silent	SNP	C	A	A			TCGA-C5-A1ME-01A-11D-A13W-08	TCGA-C5-A1ME-10A-01D-A13W-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:107114545C>A	uc001tlr.2	+	13	1308	c.1242C>A	c.(1240-1242)GCC>GCA	p.A414A	RFX4_uc001tls.2_Silent_p.A423A|RFX4_uc001tlt.2_Silent_p.A423A|RFX4_uc001tlv.2_Silent_p.A320A	NM_213594	NP_998759	Q33E94	RFX4_HUMAN	regulatory factor X4 isoform c	414	Necessary for dimerization.				transcription, DNA-dependent	nucleus	DNA binding			upper_aerodigestive_tract(1)	1						AGGTGGCTGCCAAGAGACAAG	0.428													3	47	---	---	---	---	PASS
SLAIN1	122060	broad.mit.edu	37	13	78320890	78320890	+	Silent	SNP	C	T	T			TCGA-C5-A1ME-01A-11D-A13W-08	TCGA-C5-A1ME-10A-01D-A13W-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:78320890C>T	uc010thy.1	+	4	709	c.666C>T	c.(664-666)AGC>AGT	p.S222S	SLAIN1_uc001vkk.1_Silent_p.S145S|SLAIN1_uc001vkl.1_Silent_p.S101S|SLAIN1_uc010thz.1_Silent_p.S100S|SLAIN1_uc010aex.1_Intron|SLAIN1_uc010aey.1_Intron|SLAIN1_uc001vkm.2_Silent_p.S101S	NM_144595	NP_653196	Q8ND83	SLAI1_HUMAN	SLAIN motif family, member 1 B	364										ovary(1)|skin(1)	2		Acute lymphoblastic leukemia(28;0.0279)|Breast(118;0.037)		GBM - Glioblastoma multiforme(99;0.0853)		GTAGGAGGAGCCCCAGTTCCC	0.473													6	77	---	---	---	---	PASS
DZIP1	22873	broad.mit.edu	37	13	96293802	96293802	+	Missense_Mutation	SNP	G	A	A			TCGA-C5-A1ME-01A-11D-A13W-08	TCGA-C5-A1ME-10A-01D-A13W-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:96293802G>A	uc001vmk.2	-	5	1196	c.344C>T	c.(343-345)CCG>CTG	p.P115L	DZIP1_uc001vml.2_Missense_Mutation_p.P115L|DZIP1_uc001vmn.2_Missense_Mutation_p.P104L	NM_198968	NP_945319	Q86YF9	DZIP1_HUMAN	DAZ interacting protein 1 isoform 2	115					germ cell development|multicellular organismal development|spermatogenesis	cytoplasm|nucleus	nucleic acid binding|protein binding|zinc ion binding			ovary(2)	2	all_neural(89;0.0878)|Breast(111;0.148)|Medulloblastoma(90;0.163)		BRCA - Breast invasive adenocarcinoma(86;0.141)			CAGCAGCACCGGGTCCACCCC	0.602													6	87	---	---	---	---	PASS
RTN1	6252	broad.mit.edu	37	14	60212650	60212650	+	Missense_Mutation	SNP	A	G	G			TCGA-C5-A1ME-01A-11D-A13W-08	TCGA-C5-A1ME-10A-01D-A13W-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:60212650A>G	uc001xen.1	-	2	1000	c.791T>C	c.(790-792)ATA>ACA	p.I264T		NM_021136	NP_066959	Q16799	RTN1_HUMAN	reticulon 1 isoform A	264					neuron differentiation	integral to endoplasmic reticulum membrane	signal transducer activity			ovary(2)|central_nervous_system(2)	4				OV - Ovarian serous cystadenocarcinoma(108;0.0968)		GAGATCATCTATGTATGGAGC	0.453													5	128	---	---	---	---	PASS
C14orf39	317761	broad.mit.edu	37	14	60933701	60933701	+	Missense_Mutation	SNP	G	A	A			TCGA-C5-A1ME-01A-11D-A13W-08	TCGA-C5-A1ME-10A-01D-A13W-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:60933701G>A	uc001xez.3	-	10	939	c.829C>T	c.(829-831)CTT>TTT	p.L277F	C14orf39_uc010apo.2_5'UTR	NM_174978	NP_777638	Q08AQ4	Q08AQ4_HUMAN	hypothetical protein LOC317761	277										ovary(2)|haematopoietic_and_lymphoid_tissue(1)|skin(1)	4				OV - Ovarian serous cystadenocarcinoma(108;0.0448)		TCATAAGGAAGAAATAATTGA	0.279													3	23	---	---	---	---	PASS
SLC8A3	6547	broad.mit.edu	37	14	70512940	70512940	+	Silent	SNP	G	A	A			TCGA-C5-A1ME-01A-11D-A13W-08	TCGA-C5-A1ME-10A-01D-A13W-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:70512940G>A	uc001xly.2	-	8	3262	c.2508C>T	c.(2506-2508)ATC>ATT	p.I836I	SLC8A3_uc001xlu.2_Silent_p.I193I|SLC8A3_uc001xlv.2_Silent_p.I207I|SLC8A3_uc001xlw.2_Silent_p.I833I|SLC8A3_uc001xlx.2_Silent_p.I834I|SLC8A3_uc001xlz.2_Silent_p.I830I|SLC8A3_uc010ara.2_RNA|SLC8A3_uc001xma.2_3'UTR	NM_183002	NP_892114	P57103	NAC3_HUMAN	solute carrier family 8 (sodium/calcium	836	Helical; (Potential).				cell communication|platelet activation	integral to membrane|plasma membrane	calcium:sodium antiporter activity|calmodulin binding			skin(3)|ovary(2)|breast(2)	7				BRCA - Breast invasive adenocarcinoma(234;0.0079)|all cancers(60;0.0102)|OV - Ovarian serous cystadenocarcinoma(108;0.0555)		AGGCCAGGCCGATGCCCAGGA	0.617											OREG0022773	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	3	11	---	---	---	---	PASS
CATSPER2	117155	broad.mit.edu	37	15	43939482	43939482	+	Intron	SNP	G	A	A			TCGA-C5-A1ME-01A-11D-A13W-08	TCGA-C5-A1ME-10A-01D-A13W-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:43939482G>A	uc001zsh.2	-						CATSPER2_uc010bdm.2_Intron|CATSPER2_uc001zsi.2_Intron|CATSPER2_uc001zsj.2_Intron|CATSPER2_uc001zsk.2_Intron	NM_172095	NP_742093	Q96P56	CTSR2_HUMAN	sperm-associated cation channel 2 isoform 2						cell differentiation|multicellular organismal development|spermatogenesis	cilium|flagellar membrane|integral to membrane	calcium channel activity|protein binding|voltage-gated ion channel activity			ovary(1)	1		all_cancers(109;3.26e-15)|all_epithelial(112;1.48e-12)|Lung NSC(122;2.76e-08)|all_lung(180;3.1e-07)|Melanoma(134;0.027)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;3.56e-07)		TGAGTGACATGAAAGGATACA	0.463													4	27	---	---	---	---	PASS
KIAA1370	56204	broad.mit.edu	37	15	52877015	52877015	+	Missense_Mutation	SNP	C	T	T			TCGA-C5-A1ME-01A-11D-A13W-08	TCGA-C5-A1ME-10A-01D-A13W-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:52877015C>T	uc002acg.3	-	12	3157	c.3004G>A	c.(3004-3006)GTG>ATG	p.V1002M	KIAA1370_uc002ach.3_RNA|KIAA1370_uc010bfg.1_Missense_Mutation_p.V914M|KIAA1370_uc002acf.3_Missense_Mutation_p.V32M|KIAA1370_uc010ugf.1_Missense_Mutation_p.V1009M	NM_019600	NP_062546	Q32MH5	K1370_HUMAN	hypothetical protein LOC56204	1002											0				all cancers(107;0.0803)		CTTCTCTTCACTTCTTGTTTA	0.358													6	26	---	---	---	---	PASS
IRX6	79190	broad.mit.edu	37	16	55362886	55362886	+	Silent	SNP	G	A	A			TCGA-C5-A1ME-01A-11D-A13W-08	TCGA-C5-A1ME-10A-01D-A13W-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:55362886G>A	uc002ehy.2	+	5	1529	c.996G>A	c.(994-996)GCG>GCA	p.A332A	IRX6_uc002ehx.2_Silent_p.A332A	NM_024335	NP_077311	P78412	IRX6_HUMAN	iroquois homeobox protein 6	332						nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			central_nervous_system(5)|ovary(1)	6						TCCTCTCGGCGGAGACAGGCA	0.632													4	46	---	---	---	---	PASS
CDH11	1009	broad.mit.edu	37	16	65022100	65022100	+	Missense_Mutation	SNP	G	A	A			TCGA-C5-A1ME-01A-11D-A13W-08	TCGA-C5-A1ME-10A-01D-A13W-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:65022100G>A	uc002eoi.2	-	7	1393	c.959C>T	c.(958-960)ACG>ATG	p.T320M	CDH11_uc010cdn.2_Intron|CDH11_uc002eoj.2_Missense_Mutation_p.T320M|CDH11_uc010vin.1_Missense_Mutation_p.T194M	NM_001797	NP_001788	P55287	CAD11_HUMAN	cadherin 11, type 2 preproprotein	320	Cadherin 3.|Extracellular (Potential).				adherens junction organization|cell junction assembly|homophilic cell adhesion|ossification|skeletal system development	integral to membrane|plasma membrane	calcium ion binding|protein binding			lung(10)|ovary(3)|skin(1)	14		Ovarian(137;0.0973)		OV - Ovarian serous cystadenocarcinoma(108;0.205)		TTCATAGTCCGTTGTGATTTC	0.438			T	USP6	aneurysmal bone cysts					TSP Lung(24;0.17)			49	145	---	---	---	---	PASS
ATP6V0D1	9114	broad.mit.edu	37	16	67514899	67514899	+	Missense_Mutation	SNP	C	T	T			TCGA-C5-A1ME-01A-11D-A13W-08	TCGA-C5-A1ME-10A-01D-A13W-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:67514899C>T	uc002ete.1	-	1	191	c.91G>A	c.(91-93)GCC>ACC	p.A31T	ATP6V0D1_uc010vjo.1_Missense_Mutation_p.A31T	NM_004691	NP_004682	P61421	VA0D1_HUMAN	ATPase, H+ transporting, lysosomal, V0 subunit	31					ATP hydrolysis coupled proton transport|cellular iron ion homeostasis|insulin receptor signaling pathway|transferrin transport	endosome membrane|proton-transporting V-type ATPase, V0 domain|vacuolar proton-transporting V-type ATPase complex					0		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0439)|Epithelial(162;0.101)		AGGTAGTCGGCCTGGCTGAGC	0.642													7	31	---	---	---	---	PASS
FA2H	79152	broad.mit.edu	37	16	74752969	74752969	+	Missense_Mutation	SNP	G	A	A			TCGA-C5-A1ME-01A-11D-A13W-08	TCGA-C5-A1ME-10A-01D-A13W-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:74752969G>A	uc002fde.1	-	5	771	c.703C>T	c.(703-705)CGC>TGC	p.R235C	FA2H_uc002fdd.1_5'Flank|FA2H_uc010vmy.1_RNA	NM_024306	NP_077282	Q7L5A8	FA2H_HUMAN	fatty acid 2-hydroxylase	235			R -> C (in SPG35; significantly reduced enzymatic function).		cell death|electron transport chain|fatty acid biosynthetic process|sphingolipid metabolic process|transport	endoplasmic reticulum membrane|integral to membrane|microsome	heme binding|oxidoreductase activity				0						AACAGGAAGCGGTGGATGAGG	0.607													15	27	---	---	---	---	PASS
PLD2	5338	broad.mit.edu	37	17	4720323	4720323	+	Silent	SNP	C	T	T			TCGA-C5-A1ME-01A-11D-A13W-08	TCGA-C5-A1ME-10A-01D-A13W-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:4720323C>T	uc002fzc.2	+	16	1775	c.1674C>T	c.(1672-1674)CAC>CAT	p.H558H	PLD2_uc010vsj.1_Silent_p.H415H|PLD2_uc002fzd.2_Silent_p.H558H	NM_002663	NP_002654	O14939	PLD2_HUMAN	phospholipase D2	558	Catalytic.				cell communication|cytoskeleton organization|small GTPase mediated signal transduction		NAPE-specific phospholipase D activity|phosphatidylinositol binding|phospholipase D activity			breast(2)|upper_aerodigestive_tract(1)|ovary(1)|central_nervous_system(1)	5					Choline(DB00122)	TTGCCCGGCACTTCATCCAGC	0.632													10	51	---	---	---	---	PASS
NLE1	54475	broad.mit.edu	37	17	33467052	33467052	+	Missense_Mutation	SNP	C	T	T	rs144542845	byFrequency	TCGA-C5-A1ME-01A-11D-A13W-08	TCGA-C5-A1ME-10A-01D-A13W-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:33467052C>T	uc002hiy.1	-	3	224	c.196G>A	c.(196-198)GAT>AAT	p.D66N	NLE1_uc010ctn.1_5'UTR|NLE1_uc002hiz.1_5'UTR	NM_018096	NP_060566	Q9NVX2	NLE1_HUMAN	Notchless gene homolog isoform a	66						nucleolus				breast(3)|ovary(1)	4		Ovarian(249;0.17)				ATCTCAGCATCGTGGACAAAG	0.552													6	19	---	---	---	---	PASS
KRT31	3881	broad.mit.edu	37	17	39553231	39553231	+	Missense_Mutation	SNP	G	A	A			TCGA-C5-A1ME-01A-11D-A13W-08	TCGA-C5-A1ME-10A-01D-A13W-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:39553231G>A	uc002hwn.2	-	2	418	c.365C>T	c.(364-366)TCT>TTT	p.S122F	KRT31_uc010cxn.2_Missense_Mutation_p.S122F	NM_002277	NP_002268	Q15323	K1H1_HUMAN	keratin 31	122	Rod.|Coil 1B.				epidermis development	intermediate filament	protein binding|structural constituent of cytoskeleton				0		Breast(137;0.000496)				GGCATTCTCAGACTTGGTACA	0.428													11	46	---	---	---	---	PASS
WNK4	65266	broad.mit.edu	37	17	40934779	40934779	+	Silent	SNP	C	A	A			TCGA-C5-A1ME-01A-11D-A13W-08	TCGA-C5-A1ME-10A-01D-A13W-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:40934779C>A	uc002ibj.2	+	2	643	c.622C>A	c.(622-624)CGG>AGG	p.R208R	WNK4_uc010wgx.1_5'UTR|WNK4_uc002ibk.1_5'Flank|WNK4_uc010wgy.1_5'Flank	NM_032387	NP_115763	Q96J92	WNK4_HUMAN	WNK lysine deficient protein kinase 4	208	Protein kinase.				intracellular protein kinase cascade	tight junction	ATP binding|protein serine/threonine kinase activity			ovary(3)|skin(3)|stomach(1)	7		Breast(137;0.000143)		BRCA - Breast invasive adenocarcinoma(366;0.0749)		CCCACAGACTCGGAAACTGTC	0.597													3	29	---	---	---	---	PASS
SLC4A1	6521	broad.mit.edu	37	17	42336551	42336551	+	Missense_Mutation	SNP	C	A	A			TCGA-C5-A1ME-01A-11D-A13W-08	TCGA-C5-A1ME-10A-01D-A13W-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:42336551C>A	uc002igf.3	-	9	1005	c.856G>T	c.(856-858)GCC>TCC	p.A286S	SLC4A1_uc002igg.3_Missense_Mutation_p.A286S	NM_000342	NP_000333	P02730	B3AT_HUMAN	solute carrier family 4, anion exchanger, member	286	Cytoplasmic.				bicarbonate transport|cellular ion homeostasis	basolateral plasma membrane|cortical cytoskeleton|integral to plasma membrane|Z disc	ankyrin binding|chloride transmembrane transporter activity|inorganic anion exchanger activity|protein anchor|protein homodimerization activity			ovary(1)|central_nervous_system(1)|skin(1)	3		Breast(137;0.014)|Prostate(33;0.0181)		BRCA - Breast invasive adenocarcinoma(366;0.115)		ATGAGGGTGGCAGCAGCCCGG	0.647													6	37	---	---	---	---	PASS
ABCC3	8714	broad.mit.edu	37	17	48750921	48750921	+	Missense_Mutation	SNP	C	T	T			TCGA-C5-A1ME-01A-11D-A13W-08	TCGA-C5-A1ME-10A-01D-A13W-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:48750921C>T	uc002isl.2	+	19	2581	c.2501C>T	c.(2500-2502)CCG>CTG	p.P834L		NM_003786	NP_003777	O15438	MRP3_HUMAN	ATP-binding cassette, sub-family C, member 3	834	ABC transporter 1.|Cytoplasmic (By similarity).				bile acid metabolic process	integral to plasma membrane|membrane fraction	ATP binding|bile acid-exporting ATPase activity|organic anion transmembrane transporter activity			skin(3)|central_nervous_system(1)	4			BRCA - Breast invasive adenocarcinoma(22;3.05e-09)		Glibenclamide(DB01016)	GAGATGGGCCCGTACCCAGCC	0.602													8	46	---	---	---	---	PASS
CBX4	8535	broad.mit.edu	37	17	77808441	77808441	+	Missense_Mutation	SNP	C	T	T			TCGA-C5-A1ME-01A-11D-A13W-08	TCGA-C5-A1ME-10A-01D-A13W-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:77808441C>T	uc002jxe.2	-	5	1163	c.1000G>A	c.(1000-1002)GGG>AGG	p.G334R		NM_003655	NP_003646	O00257	CBX4_HUMAN	chromobox homolog 4	334	Interaction with BMI1.				anti-apoptosis|chromatin modification|negative regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	Golgi apparatus|PcG protein complex	enzyme binding|transcription corepressor activity			skin(2)	2			OV - Ovarian serous cystadenocarcinoma(97;0.0102)|BRCA - Breast invasive adenocarcinoma(99;0.0224)			TCGCTAACCCCGGACACCTCC	0.672											OREG0024799	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	6	14	---	---	---	---	PASS
PIAS2	9063	broad.mit.edu	37	18	44407992	44407992	+	Missense_Mutation	SNP	C	T	T			TCGA-C5-A1ME-01A-11D-A13W-08	TCGA-C5-A1ME-10A-01D-A13W-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:44407992C>T	uc002lck.2	-	11	1596	c.1438G>A	c.(1438-1440)GAA>AAA	p.E480K	PIAS2_uc010dnp.2_Missense_Mutation_p.E178K|PIAS2_uc002lcl.2_Missense_Mutation_p.E480K|PIAS2_uc010xda.1_Missense_Mutation_p.E178K|PIAS2_uc002lcm.2_Missense_Mutation_p.E480K	NM_004671	NP_004662	O75928	PIAS2_HUMAN	protein inhibitor of activated STAT X isoform	480					androgen receptor signaling pathway|negative regulation of androgen receptor signaling pathway|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	nuclear speck|PML body	androgen receptor binding|DNA binding|protein binding|SUMO ligase activity|transcription coactivator activity|zinc ion binding			ovary(2)|breast(1)|skin(1)	4						TCTTCCTCTTCGTCAGAAGAG	0.408													18	73	---	---	---	---	PASS
ASNA1	439	broad.mit.edu	37	19	12858250	12858250	+	Silent	SNP	G	A	A			TCGA-C5-A1ME-01A-11D-A13W-08	TCGA-C5-A1ME-10A-01D-A13W-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:12858250G>A	uc002muv.2	+	6	773	c.759G>A	c.(757-759)CTG>CTA	p.L253L	ASNA1_uc002muw.2_Silent_p.L252L	NM_004317	NP_004308	O43681	ASNA_HUMAN	arsA arsenite transporter, ATP-binding, homolog	253					response to arsenic-containing substance	endoplasmic reticulum|nucleolus|soluble fraction	arsenite-transporting ATPase activity|ATP binding|metal ion binding			ovary(2)	2					Adenosine triphosphate(DB00171)	CTGAGTTCCTGTCCCTGTATG	0.567													8	28	---	---	---	---	PASS
PHLDB3	653583	broad.mit.edu	37	19	43982280	43982280	+	Missense_Mutation	SNP	C	A	A			TCGA-C5-A1ME-01A-11D-A13W-08	TCGA-C5-A1ME-10A-01D-A13W-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:43982280C>A	uc002own.3	-	15	1966	c.1707G>T	c.(1705-1707)AAG>AAT	p.K569N	PHLDB3_uc010eit.2_Missense_Mutation_p.K239N	NM_198850	NP_942147	Q6NSJ2	PHLB3_HUMAN	pleckstrin homology-like domain, family B,	569	PH.										0		Prostate(69;0.0153)				TGGTCTCTTCCTTGTCTGGTA	0.498													3	39	---	---	---	---	PASS
CD3EAP	10849	broad.mit.edu	37	19	45912703	45912703	+	Missense_Mutation	SNP	G	A	A			TCGA-C5-A1ME-01A-11D-A13W-08	TCGA-C5-A1ME-10A-01D-A13W-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:45912703G>A	uc002pbq.1	+	3	1965	c.1477G>A	c.(1477-1479)GAG>AAG	p.E493K	CD3EAP_uc002pbr.1_Missense_Mutation_p.E495K	NM_012099	NP_036231	O15446	RPA34_HUMAN	CD3E antigen, epsilon polypeptide associated	493					rRNA transcription|transmembrane receptor protein tyrosine kinase signaling pathway	chromosome|RNA polymerase I transcription factor complex	DNA-directed RNA polymerase activity			large_intestine(2)|ovary(2)	4		all_neural(266;0.224)|Ovarian(192;0.231)		OV - Ovarian serous cystadenocarcinoma(262;0.0251)		GTCTGGGGAGGAGGCTCCCAC	0.592													12	13	---	---	---	---	PASS
ZNF329	79673	broad.mit.edu	37	19	58640193	58640193	+	Silent	SNP	G	A	A	rs116840582	byFrequency	TCGA-C5-A1ME-01A-11D-A13W-08	TCGA-C5-A1ME-10A-01D-A13W-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:58640193G>A	uc002qrn.2	-	4	915	c.678C>T	c.(676-678)ACC>ACT	p.T226T	ZNF329_uc010euk.1_RNA|ZNF329_uc002qro.1_RNA|ZNF329_uc002qrp.1_RNA	NM_024620	NP_078896	Q86UD4	ZN329_HUMAN	zinc finger protein 329	226					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			skin(1)	1		Colorectal(82;5.46e-05)|all_neural(62;0.0182)|Breast(46;0.029)|Ovarian(87;0.0443)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.017)|Lung(386;0.216)		GCTTCTCTCCGGTGTGAGTTC	0.433													29	192	---	---	---	---	PASS
PABPC1L	80336	broad.mit.edu	37	20	43559250	43559250	+	Silent	SNP	G	A	A			TCGA-C5-A1ME-01A-11D-A13W-08	TCGA-C5-A1ME-10A-01D-A13W-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:43559250G>A	uc010ggv.1	+	8	1204	c.1122G>A	c.(1120-1122)CGG>CGA	p.R374R	PABPC1L_uc010zwq.1_RNA|PABPC1L_uc002xmv.2_RNA|PABPC1L_uc002xmw.2_5'Flank|PABPC1L_uc002xmx.2_5'Flank	NM_001124756	NP_001118228	Q4VXU2	PAP1L_HUMAN	poly(A)-binding protein, cytoplasmic 1-like	374							nucleotide binding|RNA binding			ovary(1)	1						AAGAGGAGCGGAAGGCCATCT	0.627													7	246	---	---	---	---	PASS
NCOA3	8202	broad.mit.edu	37	20	46255736	46255736	+	Intron	SNP	C	T	T			TCGA-C5-A1ME-01A-11D-A13W-08	TCGA-C5-A1ME-10A-01D-A13W-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:46255736C>T	uc002xtk.2	+						NCOA3_uc010ght.1_Intron|NCOA3_uc002xtl.2_Intron|NCOA3_uc002xtm.2_Intron|NCOA3_uc002xtn.2_Intron|NCOA3_uc010zyc.1_5'Flank	NM_181659	NP_858045	Q9Y6Q9	NCOA3_HUMAN	nuclear receptor coactivator 3 isoform a						androgen receptor signaling pathway|cellular lipid metabolic process|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	nucleoplasm	androgen receptor binding|histone acetyltransferase activity|ligand-dependent nuclear receptor binding|protein N-terminus binding|signal transducer activity|thyroid hormone receptor binding			ovary(3)|lung(1)|skin(1)	5						ATTAACATATCCTATTTTAGG	0.209													5	85	---	---	---	---	PASS
NCAM2	4685	broad.mit.edu	37	21	22710836	22710836	+	Silent	SNP	G	A	A			TCGA-C5-A1ME-01A-11D-A13W-08	TCGA-C5-A1ME-10A-01D-A13W-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:22710836G>A	uc002yld.1	+	8	1275	c.1026G>A	c.(1024-1026)ACG>ACA	p.T342T	NCAM2_uc011acb.1_Silent_p.T200T|NCAM2_uc011acc.1_Silent_p.T367T	NM_004540	NP_004531	O15394	NCAM2_HUMAN	neural cell adhesion molecule 2 precursor	342	Ig-like C2-type 4.|Extracellular (Potential).				neuron cell-cell adhesion	integral to membrane|plasma membrane				ovary(4)	4		Lung NSC(9;0.195)		all cancers(11;0.00102)|OV - Ovarian serous cystadenocarcinoma(11;0.00121)|Epithelial(23;0.00147)|Colorectal(24;0.174)		ATGGCTTCACGTTCACTGAAG	0.388													10	24	---	---	---	---	PASS
CSF2RB	1439	broad.mit.edu	37	22	37334311	37334311	+	Missense_Mutation	SNP	G	A	A	rs146598061		TCGA-C5-A1ME-01A-11D-A13W-08	TCGA-C5-A1ME-10A-01D-A13W-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:37334311G>A	uc003aqa.3	+	14	2678	c.2461G>A	c.(2461-2463)GAC>AAC	p.D821N	CSF2RB_uc003aqc.3_Missense_Mutation_p.D827N	NM_000395	NP_000386	P32927	IL3RB_HUMAN	colony stimulating factor 2 receptor, beta	821	Cytoplasmic (Potential).				respiratory gaseous exchange	granulocyte macrophage colony-stimulating factor receptor complex	cytokine receptor activity			skin(2)|pancreas(1)	3					Sargramostim(DB00020)	GCAAGTGGGCGACTATTGCTT	0.647													38	108	---	---	---	---	PASS
RANGAP1	5905	broad.mit.edu	37	22	41652800	41652800	+	Missense_Mutation	SNP	A	C	C			TCGA-C5-A1ME-01A-11D-A13W-08	TCGA-C5-A1ME-10A-01D-A13W-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:41652800A>C	uc003azs.2	-	7	2273	c.803T>G	c.(802-804)GTG>GGG	p.V268G	RANGAP1_uc003azt.2_Missense_Mutation_p.V268G|RANGAP1_uc003azu.2_Missense_Mutation_p.V268G|RANGAP1_uc011aoz.1_Missense_Mutation_p.V213G	NM_002883	NP_002874	P46060	RAGP1_HUMAN	Ran GTPase activating protein 1	268					mitotic prometaphase|signal transduction	condensed chromosome kinetochore|cytosol|nuclear membrane|nuclear pore|soluble fraction|spindle pole	protein binding|Ran GTPase activator activity				0						AAAATTAATCACCTCCACCTG	0.637													6	4	---	---	---	---	PASS
SAMM50	25813	broad.mit.edu	37	22	44359204	44359204	+	Silent	SNP	A	G	G			TCGA-C5-A1ME-01A-11D-A13W-08	TCGA-C5-A1ME-10A-01D-A13W-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:44359204A>G	uc003bej.2	+	2	257	c.60A>G	c.(58-60)GGA>GGG	p.G20G	PNPLA3_uc010gzm.1_RNA|SAMM50_uc011aqd.1_5'UTR	NM_015380	NP_056195	Q9Y512	SAM50_HUMAN	sorting and assembly machinery component 50	20					protein import into mitochondrial outer membrane	integral to membrane|integral to membrane of membrane fraction|mitochondrial sorting and assembly machinery complex	protein binding			skin(1)	1		all_neural(38;0.0966)|Ovarian(80;0.105)|Glioma(61;0.222)				CTGATTTTGGAGGATTAGGAG	0.403													3	123	---	---	---	---	PASS
AWAT1	158833	broad.mit.edu	37	X	69460048	69460048	+	Missense_Mutation	SNP	C	T	T			TCGA-C5-A1ME-01A-11D-A13W-08	TCGA-C5-A1ME-10A-01D-A13W-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:69460048C>T	uc004dxy.2	+	7	936	c.895C>T	c.(895-897)CAT>TAT	p.H299Y		NM_001013579	NP_001013597	Q58HT5	AWAT1_HUMAN	wax synthase 1	299					lipid biosynthetic process	endoplasmic reticulum membrane|integral to membrane	long-chain-alcohol O-fatty-acyltransferase activity			ovary(3)	3						GGACAAATACCATGCACTTTA	0.478													4	29	---	---	---	---	PASS
ZMAT1	84460	broad.mit.edu	37	X	101159271	101159271	+	Missense_Mutation	SNP	G	A	A			TCGA-C5-A1ME-01A-11D-A13W-08	TCGA-C5-A1ME-10A-01D-A13W-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:101159271G>A	uc011mrl.1	-	3	465	c.154C>T	c.(154-156)CTT>TTT	p.L52F	ZMAT1_uc004ein.2_5'UTR|ZMAT1_uc011mrm.1_5'UTR	NM_001011657	NP_001011657	Q5H9K5	ZMAT1_HUMAN	zinc finger, matrin type 1 isoform 1	Error:Variant_position_missing_in_A7MD47_after_alignment						nucleus	zinc ion binding			ovary(1)	1						TCTGTAAAAAGTTCAGCCTTT	0.318													4	54	---	---	---	---	PASS
DOCK11	139818	broad.mit.edu	37	X	117676692	117676692	+	Missense_Mutation	SNP	A	G	G			TCGA-C5-A1ME-01A-11D-A13W-08	TCGA-C5-A1ME-10A-01D-A13W-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:117676692A>G	uc004eqp.2	+	2	170	c.107A>G	c.(106-108)AAG>AGG	p.K36R		NM_144658	NP_653259	Q5JSL3	DOC11_HUMAN	dedicator of cytokinesis 11	36					blood coagulation	cytosol	GTP binding			ovary(3)	3						ATAAAGGAAAAGGCCAAAGTT	0.378													3	138	---	---	---	---	PASS
OCRL	4952	broad.mit.edu	37	X	128699816	128699816	+	Missense_Mutation	SNP	C	T	T			TCGA-C5-A1ME-01A-11D-A13W-08	TCGA-C5-A1ME-10A-01D-A13W-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:128699816C>T	uc004euq.2	+	13	1477	c.1312C>T	c.(1312-1314)CTT>TTT	p.L438F	OCRL_uc004eur.2_Missense_Mutation_p.L438F	NM_000276	NP_000267	Q01968	OCRL_HUMAN	phosphatidylinositol polyphosphate 5-phosphatase	438					regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	clathrin-coated vesicle|cytosol|early endosome|Golgi stack|Golgi-associated vesicle	GTPase activator activity|phosphatidylinositol-4,5-bisphosphate 5-phosphatase activity|protein binding			lung(2)|ovary(1)|kidney(1)	4						GGTGAAAAGTCTTATTAATAA	0.353													5	193	---	---	---	---	PASS
ARHGAP4	393	broad.mit.edu	37	X	153184347	153184347	+	Missense_Mutation	SNP	A	G	G			TCGA-C5-A1ME-01A-11D-A13W-08	TCGA-C5-A1ME-10A-01D-A13W-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:153184347A>G	uc004fjk.1	-	7	1013	c.971T>C	c.(970-972)GTG>GCG	p.V324A	ARHGAP4_uc011mzf.1_Missense_Mutation_p.V301A|ARHGAP4_uc004fjl.1_Missense_Mutation_p.V364A|ARHGAP4_uc010nup.1_RNA	NM_001666	NP_001657	P98171	RHG04_HUMAN	Rho GTPase activating protein 4 isoform 2	324					apoptosis|cytoskeleton organization|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|Rho protein signal transduction	cytosol|focal adhesion|nucleus	Rho GTPase activator activity|Rho guanyl-nucleotide exchange factor activity|SH3/SH2 adaptor activity			central_nervous_system(1)	1	all_cancers(53;6.72e-15)|all_epithelial(53;3.19e-09)|all_lung(58;3.39e-06)|all_hematologic(71;4.25e-06)|Lung NSC(58;4.7e-06)|Acute lymphoblastic leukemia(192;6.56e-05)					GGTAGCATGCACCTCGAGAAC	0.637													9	105	---	---	---	---	PASS
CCDC18	343099	broad.mit.edu	37	1	93692082	93692083	+	Intron	DEL	AT	-	-	rs71875718		TCGA-C5-A1ME-01A-11D-A13W-08	TCGA-C5-A1ME-10A-01D-A13W-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:93692082_93692083delAT	uc001dpq.2	+						CCDC18_uc009wdl.1_Intron	NM_206886	NP_996769	Q5T9S5	CCD18_HUMAN	sarcoma antigen NY-SAR-41											ovary(2)|breast(2)|pancreas(1)	5		all_lung(203;0.00196)|Lung NSC(277;0.00903)|Melanoma(281;0.099)|all_neural(321;0.185)|Glioma(108;0.203)		all cancers(265;0.00166)|GBM - Glioblastoma multiforme(16;0.00551)|Epithelial(280;0.0967)		GTAGGACAAAatatatatatat	0.124													4	2	---	---	---	---	
FCRL1	115350	broad.mit.edu	37	1	157774037	157774037	+	Intron	DEL	C	-	-	rs71658497		TCGA-C5-A1ME-01A-11D-A13W-08	TCGA-C5-A1ME-10A-01D-A13W-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:157774037delC	uc001frg.2	-						FCRL1_uc001frf.2_5'Flank|FCRL1_uc001frh.2_Intron|FCRL1_uc001fri.2_Intron|FCRL1_uc001frj.2_Intron	NM_052938	NP_443170	Q96LA6	FCRL1_HUMAN	Fc receptor-like 1 isoform 1 precursor							integral to membrane|plasma membrane	receptor activity			skin(4)|ovary(3)	7	all_hematologic(112;0.0378)		LUSC - Lung squamous cell carcinoma(543;0.24)			CATGTCTCCACCCCCCCCCCA	0.527													6	3	---	---	---	---	
RASGEF1C	255426	broad.mit.edu	37	5	179528352	179528352	+	3'UTR	DEL	G	-	-			TCGA-C5-A1ME-01A-11D-A13W-08	TCGA-C5-A1ME-10A-01D-A13W-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:179528352delG	uc003mlq.2	-	13					RASGEF1C_uc003mlr.2_3'UTR|RASGEF1C_uc003mlp.3_3'UTR	NM_175062	NP_778232	Q8N431	RGF1C_HUMAN	RasGEF domain family, member 1C						regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	intracellular	guanyl-nucleotide exchange factor activity			ovary(1)	1	all_cancers(89;3.44e-05)|all_epithelial(37;1.22e-05)|Renal(175;0.000269)|Lung NSC(126;0.00199)|all_lung(126;0.00351)|Breast(19;0.137)	all_cancers(40;0.0242)|Medulloblastoma(196;0.00498)|all_neural(177;0.0137)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			TGGCCACTGTGGGGGGGGGGG	0.672													4	8	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	180722144	180722144	+	IGR	DEL	T	-	-			TCGA-C5-A1ME-01A-11D-A13W-08	TCGA-C5-A1ME-10A-01D-A13W-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:180722144delT								TRIM52 (34025 upstream) : None (None downstream)																							CCCAAAGGAAttttttttttt	0.219													3	3	---	---	---	---	
PAK1IP1	55003	broad.mit.edu	37	6	10702474	10702474	+	Intron	DEL	A	-	-			TCGA-C5-A1ME-01A-11D-A13W-08	TCGA-C5-A1ME-10A-01D-A13W-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:10702474delA	uc003mzg.2	+							NM_017906	NP_060376	Q9NWT1	PK1IP_HUMAN	PAK1 interacting protein 1						negative regulation of signal transduction	nucleolus|plasma membrane					0	Ovarian(93;0.107)|Breast(50;0.137)	all_hematologic(90;0.117)				accctgcctcaaaaaaaaaaa	0.109													4	3	---	---	---	---	
SYCP2L	221711	broad.mit.edu	37	6	10908125	10908126	+	Intron	INS	-	T	T	rs145403835		TCGA-C5-A1ME-01A-11D-A13W-08	TCGA-C5-A1ME-10A-01D-A13W-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:10908125_10908126insT	uc003mzo.2	+						SYCP2L_uc011din.1_Intron|SYCP2L_uc010jow.2_Intron	NM_001040274	NP_001035364	Q5T4T6	SYC2L_HUMAN	synaptonemal complex protein 2-like							nucleus				ovary(1)|skin(1)	2	Breast(50;0.0838)|Ovarian(93;0.107)	all_hematologic(90;0.135)	Epithelial(50;0.239)			ATACAGATAGGttttttttttt	0.178													5	4	---	---	---	---	
CGA	1081	broad.mit.edu	37	6	87797954	87797956	+	Intron	DEL	AAC	-	-	rs67709858		TCGA-C5-A1ME-01A-11D-A13W-08	TCGA-C5-A1ME-10A-01D-A13W-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:87797954_87797956delAAC	uc003plj.1	-							NM_000735	NP_000726	P01215	GLHA_HUMAN	glycoprotein hormones, alpha polypeptide						hormone biosynthetic process|peptide hormone processing|signal transduction	extracellular region|soluble fraction	hormone activity			ovary(1)	1		all_cancers(76;5.98e-09)|Acute lymphoblastic leukemia(125;2.15e-10)|Prostate(29;5.29e-10)|all_hematologic(105;1.08e-06)|all_epithelial(107;0.000102)		BRCA - Breast invasive adenocarcinoma(108;0.0484)		AAAAAAAAAAAACAAAAAACAGT	0.369													4	2	---	---	---	---	
TRDN	10345	broad.mit.edu	37	6	123786155	123786155	+	Intron	DEL	A	-	-			TCGA-C5-A1ME-01A-11D-A13W-08	TCGA-C5-A1ME-10A-01D-A13W-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:123786155delA	uc003pzj.1	-						TRDN_uc003pzk.1_Intron|TRDN_uc003pzl.1_Intron|TRDN_uc010ken.2_Intron|uc003pzm.1_Intron	NM_006073	NP_006064	Q13061	TRDN_HUMAN	triadin						muscle contraction	integral to membrane|plasma membrane|sarcoplasmic reticulum membrane	receptor binding			ovary(1)	1				GBM - Glioblastoma multiforme(226;0.184)		TAGGAATTGGAAAAAAAAAAG	0.398													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	57929445	57929445	+	IGR	DEL	A	-	-			TCGA-C5-A1ME-01A-11D-A13W-08	TCGA-C5-A1ME-10A-01D-A13W-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:57929445delA								ZNF716 (396180 upstream) : None (None downstream)																							ACAAGAGACTAGGGGGATAAG	0.403													4	2	---	---	---	---	
RAB5B	5869	broad.mit.edu	37	12	56384192	56384192	+	Intron	DEL	A	-	-			TCGA-C5-A1ME-01A-11D-A13W-08	TCGA-C5-A1ME-10A-01D-A13W-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:56384192delA	uc001siv.2	+						RAB5B_uc001siw.2_Intron|RAB5B_uc009zog.2_Intron|RAB5B_uc010spz.1_Intron	NM_002868	NP_002859	P61020	RAB5B_HUMAN	RAB5B, member RAS oncogene family						protein transport|small GTPase mediated signal transduction	early endosome membrane|melanosome|membrane fraction|plasma membrane	GTP binding|GTP-dependent protein binding|GTPase activity				0			UCEC - Uterine corpus endometrioid carcinoma (6;0.0471)|OV - Ovarian serous cystadenocarcinoma(18;0.235)			actccgcctcaaaaaaaaaag	0.189													4	2	---	---	---	---	
SEMA6D	80031	broad.mit.edu	37	15	48054097	48054099	+	Intron	DEL	AAG	-	-	rs149404019		TCGA-C5-A1ME-01A-11D-A13W-08	TCGA-C5-A1ME-10A-01D-A13W-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:48054097_48054099delAAG	uc010bek.2	+						SEMA6D_uc001zvw.2_Intron|SEMA6D_uc001zvx.1_Intron|SEMA6D_uc001zvy.2_Intron|SEMA6D_uc001zvz.2_Intron|SEMA6D_uc001zwa.2_Intron|SEMA6D_uc001zwb.2_Intron|SEMA6D_uc001zwc.2_Intron	NM_153618	NP_705871	Q8NFY4	SEM6D_HUMAN	semaphorin 6D isoform 4 precursor						axon guidance	cytoplasm|integral to membrane|plasma membrane	receptor activity			skin(3)|breast(1)	4		all_lung(180;0.000635)|Myeloproliferative disorder(241;0.116)|Melanoma(134;0.18)		all cancers(107;1.2e-11)|GBM - Glioblastoma multiforme(94;1.2e-06)		TTTCCAAAAAAAGAAGAAATTAA	0.291													4	2	---	---	---	---	
POLG	5428	broad.mit.edu	37	15	89876828	89876833	+	In_Frame_Del	DEL	TGCTGC	-	-			TCGA-C5-A1ME-01A-11D-A13W-08	TCGA-C5-A1ME-10A-01D-A13W-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:89876828_89876833delTGCTGC	uc002bns.3	-	2	435_440	c.153_158delGCAGCA	c.(151-159)CAGCAGCAA>CAA	p.51_53QQQ>Q	POLG_uc002bnr.3_In_Frame_Del_p.51_53QQQ>Q	NM_002693	NP_002684	P54098	DPOG1_HUMAN	DNA-directed DNA polymerase gamma	51_53	Poly-Gln.				base-excision repair, gap-filling|cell death|DNA-dependent DNA replication	mitochondrial nucleoid	DNA binding|DNA-directed DNA polymerase activity|protease binding			ovary(1)|lung(1)	2	Lung NSC(78;0.0472)|all_lung(78;0.089)		STAD - Stomach adenocarcinoma(125;0.165)			aggctgctgttgctgctgctgctgct	0.466								DNA_polymerases_(catalytic_subunits)					5	4	---	---	---	---	
TPSAB1	7177	broad.mit.edu	37	16	1291717	1291718	+	Intron	INS	-	G	G			TCGA-C5-A1ME-01A-11D-A13W-08	TCGA-C5-A1ME-10A-01D-A13W-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:1291717_1291718insG	uc002ckz.2	+						TPSAB1_uc010uux.1_Intron	NM_003294	NP_003285	Q15661	TRYB1_HUMAN	tryptase alpha/beta 1 precursor						defense response|proteolysis	extracellular space	protein binding|serine-type endopeptidase activity				0		Hepatocellular(780;0.00369)				CTGGGGACAGTGGAGGTGGGGC	0.703													3	3	---	---	---	---	
APOB48R	55911	broad.mit.edu	37	16	28507398	28507424	+	Splice_Site	DEL	GGGACAGCCTCAGGAGGGGAGGAGGCC	-	-	rs62034314		TCGA-C5-A1ME-01A-11D-A13W-08	TCGA-C5-A1ME-10A-01D-A13W-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:28507398_28507424delGGGACAGCCTCAGGAGGGGAGGAGGCC	uc002dqb.1	+	2	1053	c.1043_splice	c.e2+1	p.A348_splice	uc010vct.1_Intron|APOB48R_uc010byg.1_5'UTR	NM_018690	NP_061160	Q0VD83	APOBR_HUMAN	apolipoprotein B48 receptor						cholesterol metabolic process|lipid transport	chylomicron|low-density lipoprotein particle|plasma membrane|very-low-density lipoprotein particle					0						CGGGGAGGCTGGGACAGCCTCAGGAGGGGAGGAGGCCGGGACAGCCT	0.705													11	9	---	---	---	---	
UBA2	10054	broad.mit.edu	37	19	34949488	34949498	+	Intron	DEL	AAAAAAAAAAG	-	-	rs60349858		TCGA-C5-A1ME-01A-11D-A13W-08	TCGA-C5-A1ME-10A-01D-A13W-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:34949488_34949498delAAAAAAAAAAG	uc002nvk.2	+						UBA2_uc010xrx.1_Intron|UBA2_uc002nvl.2_Intron	NM_005499	NP_005490	Q9UBT2	SAE2_HUMAN	SUMO-1 activating enzyme subunit 2						protein sumoylation	nucleus	ATP binding|enzyme activator activity|ligase activity|metal ion binding|protein heterodimerization activity|SUMO activating enzyme activity			ovary(1)	1	Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.211)			aaaaaaaaaaaaaaaaaaaaGAAGGTTGAAA	0.171													4	2	---	---	---	---	
STS	412	broad.mit.edu	37	X	7175843	7175844	+	Intron	DEL	TG	-	-			TCGA-C5-A1ME-01A-11D-A13W-08	TCGA-C5-A1ME-10A-01D-A13W-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:7175843_7175844delTG	uc004cry.3	+							NM_000351	NP_000342	P08842	STS_HUMAN	steryl-sulfatase precursor						female pregnancy|steroid catabolic process	endoplasmic reticulum membrane|endosome|Golgi apparatus|integral to membrane|lysosome|microsome|plasma membrane	metal ion binding|steryl-sulfatase activity			central_nervous_system(1)	1		Colorectal(8;0.0136)|Medulloblastoma(8;0.184)			Estrone(DB00655)	AATGTATAGAtgtgtgtgtgtg	0.228									Ichthyosis				4	2	---	---	---	---	
DKC1	1736	broad.mit.edu	37	X	153994771	153994771	+	Intron	DEL	A	-	-			TCGA-C5-A1ME-01A-11D-A13W-08	TCGA-C5-A1ME-10A-01D-A13W-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:153994771delA	uc004fmm.2	+						DKC1_uc010nvf.2_Intron|SNORA36A_uc004fmn.2_5'Flank	NM_001363	NP_001354	O60832	DKC1_HUMAN	dyskerin isoform 1						cell proliferation|pseudouridine synthesis|rRNA processing|telomere maintenance via telomerase	Cajal body|nucleolus|telomerase holoenzyme complex	protein binding|pseudouridine synthase activity|RNA binding|telomerase activity				0	all_cancers(53;8.15e-17)|all_epithelial(53;1.1e-10)|all_lung(58;6.63e-07)|Lung NSC(58;2.08e-06)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)|Renal(33;0.214)					CTTCATTAAGAAAAAAAAAAA	0.418									Congenital_Dyskeratosis				4	2	---	---	---	---	
