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	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	i_TCGAscape_Amplification_Peaks	i_TCGAscape_Deletion_Peaks	DrugBank	i_ACHILLES_Top_Genes	i_CCLE_ONCOMAP_overlapping_mutations	i_CCLE_ONCOMAP_total_mutations_in_gene	i_CCLE_SEQ_overlapping_mutations	i_CCLE_SEQ_total_mutations_in_gene	MUTSIG_Significant_Genes	OREGANNO_ID	OREGANNO_Values	i_tumor_f	i_init_t_lod	i_t_lod_fstar	i_t_alt_count	i_t_ref_count	i_normal_best_gt	i_failure_reasons	i_judgement	validation_status	validation_method	validation_tumor_sample	validation_alt_allele	dataset	TCGAscape_Amplification_Peaks	TCGAscape_Deletion_Peaks	type	classification	start	end	gene	chr	ref_allele	tum_allele1	tum_allele2	context_orig	context65	gene_name	newbase	categ	categ_ignoring_null_categ
ANK3	288	broad.mit.edu	36	10	61506052	61506052	+	Silent	SNP	C	T	T			TCGA-27-1830-01	TCGA-27-1830-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr10:61506052C>T	uc001jky.1	-	c.4593G>A	c.(4591-4593)ACG>ACA	p.T1531T	ANK3_uc001jkz.2_Intron|ANK3_uc001jkv.1_Intron|ANK3_uc001jkw.1_Intron|ANK3_uc009xpa.1_Intron|ANK3_uc001jkx.1_Intron|ANK3_uc009xpb.1_Intron	NM_020987	NP_066267	Q12955	ANK3_HUMAN	ankyrin 3 isoform 1	1531	Ser-rich.				establishment of protein localization|signal transduction	basolateral plasma membrane|cytoplasm|cytoskeleton	protein binding			ovary(6)|pancreas(2)|central_nervous_system(1)|skin(1)	10														0.491667	185.028971	185.035956	59	61	CC		KEEP	---	---	---	---	capture			Silent	SNP	61506052	61506052	625	10	C	T	T	27	27	ANK3	T	1	1
TLL2	7093	broad.mit.edu	36	10	98146999	98146999	+	Missense_Mutation	SNP	G	A	A			TCGA-27-1830-01	TCGA-27-1830-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr10:98146999G>A	uc001kml.1	-	c.1318C>T	c.(1318-1320)CGG>TGG	p.R440W	TLL2_uc009xvf.1_Missense_Mutation_p.R418W	NM_012465	NP_036597	Q9Y6L7	TLL2_HUMAN	tolloid-like 2	440	CUB 1.				cell differentiation|multicellular organismal development|proteolysis	extracellular region	calcium ion binding|metalloendopeptidase activity|zinc ion binding			ovary(1)|pancreas(1)	2		Colorectal(252;0.0846)												0.402985	81.339808	81.881898	27	40	GG		KEEP	---	---	---	---	capture		Epithelial(162;1.51e-07)|all cancers(201;7.59e-06)	Missense_Mutation	SNP	98146999	98146999	16476	10	G	A	A	39	39	TLL2	A	1	1
SIPA1	6494	broad.mit.edu	36	11	65165054	65165054	+	Missense_Mutation	SNP	G	C	C			TCGA-27-1830-01	TCGA-27-1830-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr11:65165054G>C	uc001ofb.1	+	c.86G>C	c.(85-87)CGC>CCC	p.R29P	SIPA1_uc009yqo.1_Missense_Mutation_p.R29P|SIPA1_uc009yqp.1_Missense_Mutation_p.R29P|SIPA1_uc001ofd.1_Missense_Mutation_p.R29P|SIPA1_uc009yqq.1_Missense_Mutation_p.R29P	NM_153253	NP_694985	Q96FS4	SIPA1_HUMAN	signal-induced proliferation-associated protein	29					cell proliferation|cytoskeleton organization|intracellular signal transduction|negative regulation of cell adhesion|negative regulation of cell cycle|negative regulation of cell growth	cytosol|endomembrane system|membrane|nucleus|perinuclear region of cytoplasm	Rap GTPase activator activity				0														0.4	8.719299	8.827754	4	6	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	65165054	65165054	14823	11	G	C	C	38	38	SIPA1	C	3	3
SBNO1	55206	broad.mit.edu	36	12	122360274	122360274	+	Silent	SNP	C	T	T			TCGA-27-1830-01	TCGA-27-1830-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr12:122360274C>T	uc009zxw.1	-	c.3378G>A	c.(3376-3378)GCG>GCA	p.A1126A	SBNO1_uc009zxv.1_Non-coding_Transcript|SBNO1_uc001uer.1_Silent_p.A1125A|SBNO1_uc009zxx.1_Silent_p.A77A|SBNO1_uc001ues.1_Silent_p.A77A	NM_018183	NP_060653	A3KN83	SBNO1_HUMAN	sno, strawberry notch homolog 1	1126							ATP binding|DNA binding|hydrolase activity			breast(5)|ovary(1)|kidney(1)	7	all_neural(191;0.101)|Medulloblastoma(191;0.163)													0.261745	215.224532	230.523455	78	220	CC		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(86;0.000701)|Epithelial(86;0.00197)	Silent	SNP	122360274	122360274	14343	12	C	T	T	23	23	SBNO1	T	1	1
KRT8	3856	broad.mit.edu	36	12	51580672	51580672	+	Silent	SNP	G	A	A			TCGA-27-1830-01	TCGA-27-1830-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr12:51580672G>A	uc009zmk.1	-	c.741C>T	c.(739-741)GAC>GAT	p.D247D	KRT8_uc001sbd.1_Silent_p.D219D|KRT8_uc009zmj.1_Silent_p.D219D|KRT8_uc009zml.1_Silent_p.D219D|KRT8_uc009zmm.1_Silent_p.D219D	NM_002273	NP_002264	P05787	K2C8_HUMAN	keratin 8	219	Coil 1B.|Rod.				cytoskeleton organization|interspecies interaction between organisms	cytoplasm|keratin filament|nuclear matrix|nucleoplasm	protein binding|structural molecule activity			ovary(1)	1					Alteplase(DB00009)|Anistreplase(DB00029)|Reteplase(DB00015)|Tenecteplase(DB00031)									0.257732	63.634869	68.791331	25	72	GG		KEEP	---	---	---	---	capture		BRCA - Breast invasive adenocarcinoma(357;0.108)	Silent	SNP	51580672	51580672	8808	12	G	A	A	40	40	KRT8	A	1	1
VWF	7450	broad.mit.edu	36	12	5998149	5998149	+	Nonsense_Mutation	SNP	G	A	A	rs61750112	unknown	TCGA-27-1830-01	TCGA-27-1830-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr12:5998149G>A	uc001qnn.1	-	c.4696C>T	c.(4696-4698)CGA>TGA	p.R1566*		NM_000552	NP_000543	P04275	VWF_HUMAN	von Willebrand factor preproprotein	1566	VWFA 2.				blood coagulation, intrinsic pathway|cell-substrate adhesion|platelet activation|platelet degranulation|protein homooligomerization	endoplasmic reticulum|platelet alpha granule lumen|proteinaceous extracellular matrix|Weibel-Palade body	chaperone binding|collagen binding|glycoprotein binding|immunoglobulin binding|integrin binding|protease binding|protein homodimerization activity|protein N-terminus binding			ovary(3)|pancreas(2)|breast(1)|central_nervous_system(1)	7					Antihemophilic Factor(DB00025)									0.178571	47.893402	61.508987	25	115	GG		KEEP	---	---	---	---	capture			Nonsense_Mutation	SNP	5998149	5998149	17818	12	G	A	A	38	38	VWF	A	5	1
IRAK3	11213	broad.mit.edu	36	12	64883779	64883779	+	Nonsense_Mutation	SNP	G	A	A			TCGA-27-1830-01	TCGA-27-1830-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr12:64883779G>A	uc001sth.1	+	c.155G>A	c.(154-156)TGG>TAG	p.W52*		NM_007199	NP_009130	Q9Y616	IRAK3_HUMAN	interleukin-1 receptor-associated kinase 3	52	Death.				interleukin-1-mediated signaling pathway|MyD88-dependent toll-like receptor signaling pathway|negative regulation of cytokine-mediated signaling pathway|negative regulation of innate immune response|negative regulation of interleukin-12 production|negative regulation of interleukin-6 production|negative regulation of macrophage cytokine production|negative regulation of MAP kinase activity|negative regulation of NF-kappaB transcription factor activity|negative regulation of protein catabolic process|negative regulation of protein complex disassembly|negative regulation of toll-like receptor signaling pathway|negative regulation of tumor necrosis factor production|positive regulation of macrophage tolerance induction|positive regulation of NF-kappaB transcription factor activity|response to exogenous dsRNA|response to lipopolysaccharide|response to peptidoglycan|response to virus	cytoplasm|nucleus	ATP binding|magnesium ion binding|protein heterodimerization activity|protein homodimerization activity|protein serine/threonine kinase activity			ovary(2)|lung(1)|central_nervous_system(1)	4										206				0.365385	109.918581	111.577576	38	66	GG		KEEP	---	---	---	---	capture		GBM - Glioblastoma multiforme(28;0.0203)	Nonsense_Mutation	SNP	64883779	64883779	8127	12	G	A	A	47	47	IRAK3	A	5	2
CD163L1	283316	broad.mit.edu	36	12	7419562	7419562	+	Splice_Site_SNP	SNP	C	T	T			TCGA-27-1830-01	TCGA-27-1830-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr12:7419562C>T	uc001qsy.1	-	c.2686_splice	c.e10+1	p.R896_splice		NM_174941	NP_777601			scavenger receptor cysteine-rich type 1							extracellular region|integral to membrane|plasma membrane	scavenger receptor activity			ovary(8)|central_nervous_system(1)	9														0.282209	116.380134	123.328059	46	117	CC		KEEP	---	---	---	---	capture			Splice_Site_SNP	SNP	7419562	7419562	3095	12	C	T	T	19	19	CD163L1	T	5	1
LTB4R2	56413	broad.mit.edu	36	14	23850387	23850387	+	Missense_Mutation	SNP	T	G	G			TCGA-27-1830-01	TCGA-27-1830-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr14:23850387T>G	uc001woq.1	+	c.770T>G	c.(769-771)GTG>GGG	p.V257G	LTB4R_uc001wos.1_5'Flank|LTB4R_uc001wot.1_5'Flank|CIDEB_uc001woo.1_5'UTR|CIDEB_uc001wop.1_5'UTR|LTB4R2_uc010alo.1_Missense_Mutation_p.V226G|LTB4R2_uc001wor.1_Missense_Mutation_p.V226G	NM_019839	NP_062813	Q9NPC1	LT4R2_HUMAN	leukotriene B4 receptor 2	257	Helical; Name=6; (Potential).				chemotaxis|negative regulation of adenylate cyclase activity	integral to plasma membrane					0														0.304348	6.782422	7.722331	7	16	TT		KEEP	---	---	---	---	capture		GBM - Glioblastoma multiforme(265;0.018)	Missense_Mutation	SNP	23850387	23850387	9448	14	T	G	G	59	59	LTB4R2	G	4	4
HEATR5A	25938	broad.mit.edu	36	14	30876522	30876522	+	Missense_Mutation	SNP	C	A	A			TCGA-27-1830-01	TCGA-27-1830-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr14:30876522C>A	uc001wrf.2	-	c.2399G>T	c.(2398-2400)TGC>TTC	p.C800F	HEATR5A_uc010ami.1_Missense_Mutation_p.C698F|HEATR5A_uc001wrg.1_Missense_Mutation_p.C682F	NM_015473	NP_056288			HEAT repeat containing 5A											ovary(1)	1	Hepatocellular(127;0.0877)|Breast(36;0.137)													0.25	6.885747	7.801123	4	12	CC		KEEP	---	---	---	---	capture	LUAD - Lung adenocarcinoma(48;0.00292)|Lung(238;0.0164)|BRCA - Breast invasive adenocarcinoma(188;0.0797)|STAD - Stomach adenocarcinoma(7;0.173)	GBM - Glioblastoma multiforme(265;0.0059)	Missense_Mutation	SNP	30876522	30876522	7314	14	C	A	A	25	25	HEATR5A	A	3	3
MEGF11	84465	broad.mit.edu	36	15	63993169	63993169	+	Silent	SNP	T	G	G			TCGA-27-1830-01	TCGA-27-1830-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr15:63993169T>G	uc002apm.2	-	c.2670A>C	c.(2668-2670)ACA>ACC	p.T890T	MEGF11_uc010bhn.1_Silent_p.T815T|MEGF11_uc002apl.2_Silent_p.T815T|MEGF11_uc002apn.1_Silent_p.T890T	NM_032445	NP_115821	A6BM72	MEG11_HUMAN	multiple EGF-like-domains 11	890						basolateral plasma membrane|integral to membrane				pancreas(1)	1														0.28	7.008663	8.181041	7	18	TT		KEEP	---	---	---	---	capture			Silent	SNP	63993169	63993169	9850	15	T	G	G	59	59	MEGF11	G	4	4
CLCN7	1186	broad.mit.edu	36	16	1438998	1438998	+	Silent	SNP	G	A	A			TCGA-27-1830-01	TCGA-27-1830-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr16:1438998G>A	uc002clv.2	-	c.1767C>T	c.(1765-1767)ACC>ACT	p.T589T	CLCN7_uc002clw.2_Silent_p.T565T|CLCN7_uc010brq.1_5'Flank|CLCN7_uc002clu.2_Silent_p.T37T	NM_001287	NP_001278	P51798	CLCN7_HUMAN	chloride channel 7 isoform a	589	Helical; (By similarity).					integral to membrane|lysosomal membrane	antiporter activity|ATP binding|voltage-gated chloride channel activity			ovary(1)	1		Hepatocellular(780;0.0893)												0.352113	72.455845	73.824412	25	46	GG		KEEP	---	---	---	---	capture			Silent	SNP	1438998	1438998	3604	16	G	A	A	39	39	CLCN7	A	1	1
ZNF19	7567	broad.mit.edu	36	16	70067177	70067177	+	Silent	SNP	G	A	A			TCGA-27-1830-01	TCGA-27-1830-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr16:70067177G>A	uc010cgc.1	-	c.774C>T	c.(772-774)TCC>TCT	p.S258S	ZNF23_uc002fai.2_Intron|ZNF19_uc002fak.1_Silent_p.S246S|ZNF19_uc002fal.1_Silent_p.S246S|ZNF19_uc002fam.1_Silent_p.S258S	NM_006961	NP_008892	P17023	ZNF19_HUMAN	zinc finger protein 19	258	C2H2-type 4.				regulation of transcription, DNA-dependent	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding				0		Ovarian(137;0.00965)												0.168919	54.288402	69.641706	25	123	GG		KEEP	---	---	---	---	capture		BRCA - Breast invasive adenocarcinoma(221;0.0161)|Kidney(780;0.0598)	Silent	SNP	70067177	70067177	18346	16	G	A	A	39	39	ZNF19	A	1	1
IFI35	3430	broad.mit.edu	36	17	38419792	38419792	+	Missense_Mutation	SNP	G	A	A			TCGA-27-1830-01	TCGA-27-1830-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr17:38419792G>A	uc010cyv.1	+	c.817G>A	c.(817-819)GTA>ATA	p.V273I		NM_005533	NP_005524	P80217	IN35_HUMAN	interferon-induced protein 35	271				EVEALTVVPQGQQGLAVFTSESG -> GRGPDSRTPRTAGP SSLHL (in Ref. 1; no nucleotide entry).	response to virus|type I interferon-mediated signaling pathway	nucleus	protein binding			ovary(1)	1		Breast(137;0.00499)												0.60396	183.584128	184.538939	61	40	GG		KEEP	---	---	---	---	capture		BRCA - Breast invasive adenocarcinoma(366;0.157)	Missense_Mutation	SNP	38419792	38419792	7817	17	G	A	A	40	40	IFI35	A	1	1
DSG3	1830	broad.mit.edu	36	18	27308115	27308115	+	Missense_Mutation	SNP	C	T	T			TCGA-27-1830-01	TCGA-27-1830-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr18:27308115C>T	uc002kws.1	+	c.2135C>T	c.(2134-2136)GCG>GTG	p.A712V	DSG3_uc002kwt.1_5'UTR	NM_001944	NP_001935	P32926	DSG3_HUMAN	desmoglein 3 preproprotein	712	Cytoplasmic (Potential).				cellular component disassembly involved in apoptosis|homophilic cell adhesion	cytosol|desmosome|integral to membrane	calcium ion binding			ovary(3)|lung(1)|central_nervous_system(1)	5														0.210526	57.718057	68.042064	28	105	CC		KEEP	---	---	---	---	capture	OV - Ovarian serous cystadenocarcinoma(10;0.00504)		Missense_Mutation	SNP	27308115	27308115	4962	18	C	T	T	27	27	DSG3	T	1	1
LPIN2	9663	broad.mit.edu	36	18	2912055	2912055	+	Missense_Mutation	SNP	C	G	G			TCGA-27-1830-01	TCGA-27-1830-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr18:2912055C>G	uc002klo.1	-	c.2317G>C	c.(2317-2319)GCC>CCC	p.A773P		NM_014646	NP_055461	Q92539	LPIN2_HUMAN	lipin 2	773	C-LIP.				fatty acid metabolic process|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent|triglyceride biosynthetic process	cytosol|endoplasmic reticulum membrane|nucleus	phosphatidate phosphatase activity|transcription coactivator activity			ovary(1)|skin(1)	2														0.368421	8.904278	9.196044	7	12	CC		KEEP	---	---	---	---	capture		READ - Rectum adenocarcinoma(2;0.0419)|Colorectal(6;0.156)	Missense_Mutation	SNP	2912055	2912055	9292	18	C	G	G	27	27	LPIN2	G	3	3
FBXW9	84261	broad.mit.edu	36	19	12663246	12663246	+	Missense_Mutation	SNP	G	C	C			TCGA-27-1830-01	TCGA-27-1830-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr19:12663246G>C	uc010dyx.1	-	c.671C>G	c.(670-672)GCG>GGG	p.A224G	FBXW9_uc002mum.1_Missense_Mutation_p.A234G|FBXW9_uc002mun.1_Missense_Mutation_p.A71G	NM_032301	NP_115677	Q5XUX1	FBXW9_HUMAN	F-box and WD-40 domain protein 9	234	WD 2.						protein binding			ovary(1)	1														0.555556	9.553531	9.564835	5	4	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	12663246	12663246	6008	19	G	C	C	38	38	FBXW9	C	3	3
ZNF429	353088	broad.mit.edu	36	19	21504413	21504413	+	Missense_Mutation	SNP	C	A	A			TCGA-27-1830-01	TCGA-27-1830-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr19:21504413C>A	uc002nqd.1	+	c.117C>A	c.(115-117)AAC>AAA	p.N39K	ZNF429_uc010ecu.1_Missense_Mutation_p.N39K	NM_001001415	NP_001001415	Q86V71	ZN429_HUMAN	zinc finger protein 429	39	KRAB.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(2)	2														0.186603	83.297738	102.53259	39	170	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	21504413	21504413	18495	19	C	A	A	20	20	ZNF429	A	3	3
OAZ1	4946	broad.mit.edu	36	19	2222460	2222460	+	Missense_Mutation	SNP	C	T	T			TCGA-27-1830-01	TCGA-27-1830-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr19:2222460C>T	uc002lvk.1	+	c.223C>T	c.(223-225)CCT>TCT	p.P75S	SPPL2B_uc010dsw.1_Intron|OAZ1_uc002lvl.1_Non-coding_Transcript|OAZ1_uc002lvm.1_Non-coding_Transcript	NM_004152	NP_004143	P54368	OAZ1_HUMAN	ornithine decarboxylase antizyme 1	75					polyamine biosynthetic process|regulation of cellular amino acid metabolic process	cytosol	ornithine decarboxylase inhibitor activity				0		Hepatocellular(1079;0.137)			L-Ornithine(DB00129)									0.318182	36.541077	37.830521	14	30	CC		KEEP	---	---	---	---	capture		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)	Missense_Mutation	SNP	2222460	2222460	11209	19	C	T	T	22	22	OAZ1	T	2	2
TMEM149	79713	broad.mit.edu	36	19	40922509	40922509	+	Silent	SNP	G	A	A			TCGA-27-1830-01	TCGA-27-1830-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr19:40922509G>A	uc010eej.1	-	c.903C>T	c.(901-903)GGC>GGT	p.G301G	TMEM149_uc002obb.1_Intron|TMEM149_uc002obc.1_Silent_p.G221G|TMEM149_uc002obd.2_Silent_p.G221G	NM_024660	NP_078936	Q9H665	IGFR1_HUMAN	transmembrane protein 149	221	Cytoplasmic (Potential).					integral to membrane|plasma membrane					0	all_lung(56;3.33e-07)|Lung NSC(56;5.02e-07)|Esophageal squamous(110;0.162)													0.303571	224.074288	233.713219	85	195	GG		KEEP	---	---	---	---	capture	LUSC - Lung squamous cell carcinoma(66;0.0515)		Silent	SNP	40922509	40922509	16594	19	G	A	A	38	38	TMEM149	A	1	1
SYCP1	6847	broad.mit.edu	36	1	115289077	115289077	+	Missense_Mutation	SNP	G	A	A			TCGA-27-1830-01	TCGA-27-1830-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:115289077G>A	uc001efr.1	+	c.2105G>A	c.(2104-2106)CGA>CAA	p.R702Q	SYCP1_uc001efq.1_Missense_Mutation_p.R702Q|SYCP1_uc009wgw.1_Missense_Mutation_p.R702Q	NM_003176	NP_003167	Q15431	SYCP1_HUMAN	synaptonemal complex protein 1	702	Potential.				cell division|reciprocal meiotic recombination|spermatogenesis|synaptonemal complex assembly		DNA binding				0	Lung SC(450;0.211)	all_cancers(81;8.65e-08)|all_epithelial(167;3.32e-07)|all_lung(203;6.55e-06)|Lung NSC(69;1.11e-05)|Acute lymphoblastic leukemia(138;0.221)												0.344828	29.341114	29.957836	10	19	GG		KEEP	---	---	---	---	capture		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)	Missense_Mutation	SNP	115289077	115289077	15952	1	G	A	A	37	37	SYCP1	A	1	1
PTGFRN	5738	broad.mit.edu	36	1	117286166	117286166	+	Missense_Mutation	SNP	G	T	T			TCGA-27-1830-01	TCGA-27-1830-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:117286166G>T	uc001egv.1	+	c.356G>T	c.(355-357)TGT>TTT	p.C119F		NM_020440	NP_065173	Q9P2B2	FPRP_HUMAN	prostaglandin F2 receptor negative regulator	119	Extracellular (Potential).|Ig-like C2-type 1.					endoplasmic reticulum membrane|Golgi apparatus|integral to membrane	protein binding			liver(1)	1	Lung SC(450;0.225)	all_cancers(81;0.00104)|all_lung(203;8.97e-05)|all_epithelial(167;0.000139)|Lung NSC(69;0.000446)												0.315385	111.320034	115.266076	41	89	GG		KEEP	---	---	---	---	capture		Lung(183;0.0704)|LUSC - Lung squamous cell carcinoma(189;0.227)|Colorectal(144;0.248)	Missense_Mutation	SNP	117286166	117286166	13205	1	G	T	T	48	48	PTGFRN	T	3	3
PTGFRN	5738	broad.mit.edu	36	1	117288861	117288861	+	Silent	SNP	G	C	C			TCGA-27-1830-01	TCGA-27-1830-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:117288861G>C	uc001egv.1	+	c.456G>C	c.(454-456)CGG>CGC	p.R152R		NM_020440	NP_065173	Q9P2B2	FPRP_HUMAN	prostaglandin F2 receptor negative regulator	152	Ig-like C2-type 2.|Extracellular (Potential).					endoplasmic reticulum membrane|Golgi apparatus|integral to membrane	protein binding			liver(1)	1	Lung SC(450;0.225)	all_cancers(81;0.00104)|all_lung(203;8.97e-05)|all_epithelial(167;0.000139)|Lung NSC(69;0.000446)												0.4	7.553368	7.62209	4	6	GG		KEEP	---	---	---	---	capture		Lung(183;0.0704)|LUSC - Lung squamous cell carcinoma(189;0.227)|Colorectal(144;0.248)	Silent	SNP	117288861	117288861	13205	1	G	C	C	42	42	PTGFRN	C	3	3
CR2	1380	broad.mit.edu	36	1	205716222	205716222	+	Missense_Mutation	SNP	C	T	T			TCGA-27-1830-01	TCGA-27-1830-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr1:205716222C>T	uc001hfv.1	+	c.2737C>T	c.(2737-2739)CCG>TCG	p.P913S	CR2_uc001hfw.1_Missense_Mutation_p.P854S|CR2_uc009xch.1_Intron	NM_001006658	NP_001006659	P20023	CR2_HUMAN	complement component (3d/Epstein Barr virus)	854	Sushi 14.|Extracellular (Potential).				complement activation, classical pathway|innate immune response	integral to membrane|plasma membrane	complement receptor activity|protein homodimerization activity			upper_aerodigestive_tract(1)|urinary_tract(1)|ovary(1)	3														0.264286	96.209257	103.242846	37	103	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	205716222	205716222	3981	1	C	T	T	30	30	CR2	T	2	2
ARTN	9048	broad.mit.edu	36	1	44174821	44174821	+	Missense_Mutation	SNP	T	C	C			TCGA-27-1830-01	TCGA-27-1830-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr1:44174821T>C	uc001ckw.1	+	c.511T>C	c.(511-513)TGC>CGC	p.C171R	ARTN_uc001cks.1_Missense_Mutation_p.C154R|ARTN_uc001ckt.1_Missense_Mutation_p.C162R|ARTN_uc001cku.1_Missense_Mutation_p.C154R|ARTN_uc001ckv.1_Missense_Mutation_p.C162R	NM_057160	NP_476501	Q5T4W7	ARTN_HUMAN	neurotrophic factor artemin isoform 2	154					axon guidance|neuroblast proliferation|signal transduction	extracellular region	growth factor activity				0	Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0511)												0.75	7.717446	7.937965	3	1	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	44174821	44174821	1019	1	T	C	C	55	55	ARTN	C	4	4
MSH4	4438	broad.mit.edu	36	1	76121955	76121955	+	Missense_Mutation	SNP	A	T	T			TCGA-27-1830-01	TCGA-27-1830-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr1:76121955A>T	uc001dhd.1	+	c.1968A>T	c.(1966-1968)AAA>AAT	p.K656N		NM_002440	NP_002431	O15457	MSH4_HUMAN	mutS homolog 4	656					chiasma assembly|homologous chromosome segregation|meiotic mismatch repair|reciprocal meiotic recombination	mismatch repair complex|synaptonemal complex	ATP binding|damaged DNA binding|DNA-dependent ATPase activity|mismatched DNA binding			ovary(1)|lung(1)	2														0.360656	123.362155	125.449144	44	78	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	76121955	76121955	10265	1	A	T	T	1	1	MSH4	T	4	4
XKR7	343702	broad.mit.edu	36	20	30048134	30048134	+	Missense_Mutation	SNP	C	T	T			TCGA-27-1830-01	TCGA-27-1830-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr20:30048134C>T	uc002wxe.1	+	c.953C>T	c.(952-954)GCG>GTG	p.A318V		NM_001011718	NP_001011718	Q5GH72	XKR7_HUMAN	XK, Kell blood group complex subunit-related	318	Helical; (Potential).					integral to membrane				ovary(1)|breast(1)	2														0.285714	65.223353	68.966962	26	65	CC		KEEP	---	---	---	---	capture	Colorectal(19;0.00306)|COAD - Colon adenocarcinoma(19;0.0347)		Missense_Mutation	SNP	30048134	30048134	18017	20	C	T	T	27	27	XKR7	T	1	1
PXMP4	11264	broad.mit.edu	36	20	31771667	31771667	+	Missense_Mutation	SNP	G	C	C			TCGA-27-1830-01	TCGA-27-1830-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr20:31771667G>C	uc002wzv.1	-	c.8C>G	c.(7-9)GCC>GGC	p.A3G	PXMP4_uc002wzw.1_Missense_Mutation_p.A3G	NM_007238	NP_009169	Q9Y6I8	PXMP4_HUMAN	peroxisomal membrane protein 4 isoform a	3						integral to membrane|membrane fraction|peroxisomal membrane					0														0.259259	7.197857	8.646606	7	20	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	31771667	31771667	13309	20	G	C	C	42	42	PXMP4	C	3	3
JPH2	57158	broad.mit.edu	36	20	42221844	42221844	+	Missense_Mutation	SNP	C	T	T			TCGA-27-1830-01	TCGA-27-1830-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr20:42221844C>T	uc002xli.1	-	c.997G>A	c.(997-999)GAC>AAC	p.D333N		NM_020433	NP_065166	Q9BR39	JPH2_HUMAN	junctophilin 2 isoform 1	333	MORN 8.|Cytoplasmic (Potential).				calcium ion transport into cytosol|regulation of ryanodine-sensitive calcium-release channel activity	integral to membrane|junctional sarcoplasmic reticulum membrane|plasma membrane					0		Myeloproliferative disorder(115;0.0122)												0.275862	19.789382	21.100021	8	21	CC		KEEP	---	---	---	---	capture	COAD - Colon adenocarcinoma(18;0.00189)		Missense_Mutation	SNP	42221844	42221844	8265	20	C	T	T	31	31	JPH2	T	1	1
DSCAM	1826	broad.mit.edu	36	21	40387535	40387535	+	Missense_Mutation	SNP	A	C	C			TCGA-27-1830-01	TCGA-27-1830-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr21:40387535A>C	uc002yyq.1	-	c.3833T>G	c.(3832-3834)GTC>GGC	p.V1278G	DSCAM_uc002yyr.1_Non-coding_Transcript	NM_001389	NP_001380	O60469	DSCAM_HUMAN	Down syndrome cell adhesion molecule isoform	1278	Fibronectin type-III 4.|Extracellular (Potential).				cell adhesion|dendrite self-avoidance|negative regulation of cell adhesion|positive regulation of axon extension involved in axon guidance|positive regulation of phosphorylation	axon|extracellular region|growth cone|integral to plasma membrane|membrane fraction	protein binding			ovary(6)	6		all_cancers(19;0.186)|Prostate(19;1.15e-05)|all_epithelial(19;0.0103)				Melanoma(134;970 1778 1785 21664 32388)								0.3125	13.86943	14.370048	5	11	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	40387535	40387535	4952	21	A	C	C	10	10	DSCAM	C	4	4
PCBP3	54039	broad.mit.edu	36	21	46174336	46174336	+	Silent	SNP	C	A	A			TCGA-27-1830-01	TCGA-27-1830-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr21:46174336C>A	uc010gqb.1	+	c.795C>A	c.(793-795)CCC>CCA	p.P265P	PCBP3_uc002zhp.1_Silent_p.P265P|PCBP3_uc002zhq.1_Silent_p.P233P|PCBP3_uc002zhr.1_Silent_p.P264P|PCBP3_uc002zhs.1_Silent_p.P239P|PCBP3_uc002zht.1_Silent_p.P255P	NM_020528	NP_065389	P57721	PCBP3_HUMAN	poly(rC) binding protein 3 isoform 1	265					mRNA metabolic process	cytosol|mitochondrion|nucleus|ribonucleoprotein complex	DNA binding|RNA binding				0	all_hematologic(128;0.24)													0.218935	92.801312	105.08899	37	132	CC		KEEP	---	---	---	---	capture		Colorectal(79;0.0411)|READ - Rectum adenocarcinoma(84;0.0649)	Silent	SNP	46174336	46174336	11922	21	C	A	A	23	23	PCBP3	A	3	3
TTN	7273	broad.mit.edu	36	2	179170981	179170981	+	Missense_Mutation	SNP	T	A	A			TCGA-27-1830-01	TCGA-27-1830-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr2:179170981T>A	uc002umr.1	-	c.49457A>T	c.(49456-49458)AAG>ATG	p.K16486M	TTN_uc002ums.1_Missense_Mutation_p.K10181M|TTN_uc010frc.1_Missense_Mutation_p.K10114M|TTN_uc010frd.1_Missense_Mutation_p.K9989M	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	17413										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										8722				0.102236	26.354363	75.730178	32	281	TT		KEEP	---	---	---	---	capture	OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)		Missense_Mutation	SNP	179170981	179170981	17290	2	T	A	A	56	56	TTN	A	4	4
SOS1	6654	broad.mit.edu	36	2	39115952	39115952	+	Missense_Mutation	SNP	T	C	C			TCGA-27-1830-01	TCGA-27-1830-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr2:39115952T>C	uc002rrk.2	-	c.979A>G	c.(979-981)ATA>GTA	p.I327V	SOS1_uc002rrj.2_5'UTR|SOS1_uc002rrl.1_Missense_Mutation_p.I59V	NM_005633	NP_005624	Q07889	SOS1_HUMAN	son of sevenless homolog 1	327	DH.				apoptosis|axon guidance|blood coagulation|epidermal growth factor receptor signaling pathway|fibroblast growth factor receptor signaling pathway|induction of apoptosis by extracellular signals|insulin receptor signaling pathway|leukocyte migration|nerve growth factor receptor signaling pathway|Ras protein signal transduction	cytosol	DNA binding|protein binding|Rho GTPase activator activity|Rho guanyl-nucleotide exchange factor activity			ovary(4)|lung(1)|central_nervous_system(1)	6		all_hematologic(82;0.21)								444				0.268657	51.021786	54.257518	18	49	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	39115952	39115952	15436	2	T	C	C	52	52	SOS1	C	4	4
SLC4A5	57835	broad.mit.edu	36	2	74315765	74315765	+	Missense_Mutation	SNP	G	C	C			TCGA-27-1830-01	TCGA-27-1830-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr2:74315765G>C	uc002sko.1	-	c.2404C>G	c.(2404-2406)CCC>GCC	p.P802A	SLC4A5_uc002skl.2_Non-coding_Transcript|SLC4A5_uc002skn.1_Missense_Mutation_p.P802A|SLC4A5_uc010ffc.1_Missense_Mutation_p.P802A|SLC4A5_uc002skp.1_Intron|SLC4A5_uc002sks.1_Intron	NM_021196	NP_067019	Q9BY07	S4A5_HUMAN	sodium bicarbonate transporter 4 isoform a	802	Cytoplasmic (Potential).					apical plasma membrane|integral to membrane	inorganic anion exchanger activity|sodium:bicarbonate symporter activity			ovary(5)|central_nervous_system(1)|skin(1)	7														0.125	14.325298	24.215447	9	63	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	74315765	74315765	15154	2	G	C	C	41	41	SLC4A5	C	3	3
MYLK	4638	broad.mit.edu	36	3	124940487	124940487	+	Nonsense_Mutation	SNP	G	A	A			TCGA-27-1830-01	TCGA-27-1830-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr3:124940487G>A	uc003ego.1	-	c.535C>T	c.(535-537)CGA>TGA	p.R179*	MYLK_uc003egp.1_Nonsense_Mutation_p.R179*|MYLK_uc003egq.1_Nonsense_Mutation_p.R179*|MYLK_uc003egr.1_Nonsense_Mutation_p.R179*|MYLK_uc003egs.1_Nonsense_Mutation_p.R3*|MYLK_uc010hrs.1_Nonsense_Mutation_p.R179*	NM_053025	NP_444253	Q15746	MYLK_HUMAN	myosin light chain kinase isoform 1	179	Ig-like C2-type 2.				aorta smooth muscle tissue morphogenesis|muscle contraction|protein phosphorylation	cytosol	actin binding|ATP binding|calmodulin binding|metal ion binding|myosin light chain kinase activity			ovary(6)	6		Lung NSC(201;0.0496)								766				0.350877	54.582991	55.700784	20	37	GG		KEEP	---	---	---	---	capture		GBM - Glioblastoma multiforme(114;0.0736)	Nonsense_Mutation	SNP	124940487	124940487	10451	3	G	A	A	40	40	MYLK	A	5	1
ST3GAL6	10402	broad.mit.edu	36	3	99989620	99989620	+	Missense_Mutation	SNP	C	T	T			TCGA-27-1830-01	TCGA-27-1830-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr3:99989620C>T	uc010hpd.1	+	c.641C>T	c.(640-642)ACA>ATA	p.T214I	ST3GAL6_uc003dsy.1_Missense_Mutation_p.T75I|ST3GAL6_uc003dsz.1_Missense_Mutation_p.T161I|ST3GAL6_uc003dta.1_Missense_Mutation_p.T43I|ST3GAL6_uc003dtb.1_Missense_Mutation_p.T17I|ST3GAL6_uc003dtc.1_Missense_Mutation_p.T161I	NM_006100	NP_006091	Q9Y274	SIA10_HUMAN	alpha2,3-sialyltransferase VI	161	Lumenal (Potential).				amino sugar metabolic process|glycolipid metabolic process|protein glycosylation|protein lipoylation	integral to Golgi membrane	sialyltransferase activity			ovary(1)	1														0.296875	97.495217	102.220834	38	90	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	99989620	99989620	15737	3	C	T	T	17	17	ST3GAL6	T	2	2
TACR3	6870	broad.mit.edu	36	4	104730412	104730412	+	Missense_Mutation	SNP	C	T	T			TCGA-27-1830-01	TCGA-27-1830-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr4:104730412C>T	uc003hxe.1	-	c.1274G>A	c.(1273-1275)CGG>CAG	p.R425Q		NM_001059	NP_001050	P29371	NK3R_HUMAN	tachykinin receptor 3	425	Cytoplasmic (Potential).					integral to plasma membrane	tachykinin receptor activity			ovary(2)|skin(1)	3		Hepatocellular(203;0.217)												0.324885	421.945469	433.744839	141	293	CC		KEEP	---	---	---	---	capture		UCEC - Uterine corpus endometrioid carcinoma (10;0.22)|OV - Ovarian serous cystadenocarcinoma(123;3.4e-08)	Missense_Mutation	SNP	104730412	104730412	16028	4	C	T	T	23	23	TACR3	T	1	1
GUF1	60558	broad.mit.edu	36	4	44375448	44375448	+	Missense_Mutation	SNP	C	G	G			TCGA-27-1830-01	TCGA-27-1830-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr4:44375448C>G	uc003gww.2	+	c.52C>G	c.(52-54)CGA>GGA	p.R18G	GUF1_uc010ifz.1_Non-coding_Transcript	NM_021927	NP_068746	Q8N442	GUF1_HUMAN	GUF1 GTPase homolog	18					translation	mitochondrial inner membrane	GTP binding|GTPase activity				0														0.16	6.987512	9.736989	4	21	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	44375448	44375448	7179	4	C	G	G	19	19	GUF1	G	3	3
DCUN1D4	23142	broad.mit.edu	36	4	52460255	52460255	+	Missense_Mutation	SNP	C	G	G			TCGA-27-1830-01	TCGA-27-1830-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr4:52460255C>G	uc003gze.1	+	c.569C>G	c.(568-570)TCT>TGT	p.S190C	DCUN1D4_uc003gzf.1_Missense_Mutation_p.S190C|DCUN1D4_uc003gzg.1_Non-coding_Transcript|DCUN1D4_uc003gzh.1_Non-coding_Transcript	NM_001040402	NP_001035492	Q92564	DCNL4_HUMAN	DCN1, defective in cullin neddylation 1, domain	190	DCUN1.									ovary(2)	2														0.129032	12.453365	20.766273	8	54	CC		KEEP	---	---	---	---	capture	GBM - Glioblastoma multiforme(4;1.93e-11)|LUSC - Lung squamous cell carcinoma(32;0.00654)		Missense_Mutation	SNP	52460255	52460255	4487	4	C	G	G	32	32	DCUN1D4	G	3	3
LPHN3	23284	broad.mit.edu	36	4	62441246	62441246	+	Missense_Mutation	SNP	G	C	C			TCGA-27-1830-01	TCGA-27-1830-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr4:62441246G>C	uc010ihh.1	+	c.1554G>C	c.(1552-1554)AAG>AAC	p.K518N	LPHN3_uc003hcq.2_Missense_Mutation_p.K518N|LPHN3_uc003hcs.1_Missense_Mutation_p.K347N	NM_015236	NP_056051	Q9HAR2	LPHN3_HUMAN	latrophilin 3 precursor	518	Extracellular (Potential).				neuropeptide signaling pathway	integral to membrane|plasma membrane	G-protein coupled receptor activity|sugar binding			ovary(1)|central_nervous_system(1)|pancreas(1)	3														0.318182	10.406871	11.059915	7	15	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	62441246	62441246	9290	4	G	C	C	34	34	LPHN3	C	3	3
EPHA5	2044	broad.mit.edu	36	4	65915703	65915703	+	Missense_Mutation	SNP	C	T	T			TCGA-27-1830-01	TCGA-27-1830-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr4:65915703C>T	uc003hcy.1	-	c.1891G>A	c.(1891-1893)GAA>AAA	p.E631K	EPHA5_uc003hcx.1_Missense_Mutation_p.E563K|EPHA5_uc003hcz.1_Missense_Mutation_p.E609K|EPHA5_uc003hda.1_Missense_Mutation_p.E632K	NM_004439	NP_004430	P54756	EPHA5_HUMAN	ephrin receptor EphA5 isoform a precursor	631	Cytoplasmic (Potential).				cAMP-mediated signaling|ephrin receptor signaling pathway|neuron development|protein phosphorylation	dendrite|external side of plasma membrane|integral to plasma membrane|neuronal cell body|perinuclear region of cytoplasm|rough endoplasmic reticulum	ATP binding|transmembrane-ephrin receptor activity			lung(12)|ovary(2)|central_nervous_system(1)	15										537	TSP Lung(17;0.13)			0.177778	33.243197	42.044289	16	74	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	65915703	65915703	5363	4	C	T	T	32	32	EPHA5	T	2	2
C4orf35	85438	broad.mit.edu	36	4	71235595	71235595	+	Missense_Mutation	SNP	G	A	A			TCGA-27-1830-01	TCGA-27-1830-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr4:71235595G>A	uc003hff.1	+	c.250G>A	c.(250-252)GAC>AAC	p.D84N	C4orf35_uc010ihx.1_Missense_Mutation_p.D84N	NM_033122	NP_149113	Q96KC9	CABS1_HUMAN	testis development protein NYD-SP26	84						flagellum	calcium ion binding				0		all_hematologic(202;0.196)												0.293706	111.892009	117.340441	42	101	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	71235595	71235595	2360	4	G	A	A	37	37	C4orf35	A	1	1
DNAH5	1767	broad.mit.edu	36	5	13894162	13894162	+	Missense_Mutation	SNP	T	A	A			TCGA-27-1830-01	TCGA-27-1830-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr5:13894162T>A	uc003jfd.2	-	c.5562A>T	c.(5560-5562)AAA>AAT	p.K1854N		NM_001369	NP_001360	Q8TE73	DYH5_HUMAN	dynein, axonemal, heavy chain 5	1854	Stem (By similarity).				microtubule-based movement	cilium axoneme|cytoplasm|microtubule	ATP binding|ATPase activity|microtubule motor activity			ovary(14)|breast(1)|central_nervous_system(1)|pancreas(1)	17	Lung NSC(4;0.00476)													0.335484	137.243476	140.959605	52	103	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	13894162	13894162	4787	5	T	A	A	64	64	DNAH5	A	4	4
PCDHGA11	56105	broad.mit.edu	36	5	140780994	140780994	+	Missense_Mutation	SNP	C	A	A			TCGA-27-1830-01	TCGA-27-1830-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr5:140780994C>A	uc003lkq.1	+	c.16C>A	c.(16-18)CAG>AAG	p.Q6K	PCDHGA1_uc003lji.1_Intron|PCDHGA2_uc003ljk.1_Intron|PCDHGA3_uc010jfx.1_Intron|PCDHGA3_uc003ljm.1_Intron|PCDHGB1_uc003ljo.1_Intron|PCDHGA4_uc003ljq.1_Intron|PCDHGB2_uc003ljs.1_Intron|PCDHGA5_uc003lju.1_Intron|PCDHGB3_uc003ljw.1_Intron|PCDHGA6_uc003ljy.1_Intron|PCDHGA7_uc003lka.1_Intron|PCDHGB4_uc003lkc.1_Intron|PCDHGA8_uc003lkd.1_Intron|PCDHGB5_uc003lkf.1_Intron|PCDHGA9_uc003lkh.1_Intron|PCDHGB6_uc003lkj.1_Intron|PCDHGA10_uc003lkl.1_Intron|PCDHGB7_uc003lkn.1_Intron|PCDHGA11_uc003lko.1_Missense_Mutation_p.Q6K|PCDHGA11_uc003lkp.1_Missense_Mutation_p.Q6K	NM_018914	NP_061737	Q9Y5H2	PCDGB_HUMAN	protocadherin gamma subfamily A, 11 isoform 1	6					homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding				0														0.266667	6.585248	7.33323	4	11	CC		KEEP	---	---	---	---	capture	KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)		Missense_Mutation	SNP	140780994	140780994	11972	5	C	A	A	17	17	PCDHGA11	A	3	3
HEATR7B2	133558	broad.mit.edu	36	5	41034516	41034516	+	Missense_Mutation	SNP	T	G	G			TCGA-27-1830-01	TCGA-27-1830-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr5:41034516T>G	uc003jmj.2	-	c.4606A>C	c.(4606-4608)ACC>CCC	p.T1536P	HEATR7B2_uc003jmi.2_Missense_Mutation_p.T1091P	NM_173489	NP_775760	Q7Z745	HTRB2_HUMAN	HEAT repeat family member 7B2	1536							binding			ovary(6)|central_nervous_system(2)	8														0.6	8.016684	8.058847	3	2	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	41034516	41034516	7318	5	T	G	G	58	58	HEATR7B2	G	4	4
SESN1	27244	broad.mit.edu	36	6	109426458	109426458	+	Missense_Mutation	SNP	C	T	T			TCGA-27-1830-01	TCGA-27-1830-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr6:109426458C>T	uc003psu.1	-	c.923G>A	c.(922-924)GGC>GAC	p.G308D	SESN1_uc003pst.2_Missense_Mutation_p.G249D	NM_014454	NP_055269	Q9Y6P5	SESN1_HUMAN	sestrin 1	249					cell cycle arrest|negative regulation of cell proliferation|response to DNA damage stimulus	nucleus				ovary(1)	1		all_cancers(87;6.45e-05)|Acute lymphoblastic leukemia(125;3.55e-10)|all_hematologic(75;1.68e-07)|all_epithelial(87;0.0106)|Colorectal(196;0.0637)												0.100457	16.335274	51.201153	22	197	CC		KEEP	---	---	---	---	capture		Epithelial(106;0.0014)|BRCA - Breast invasive adenocarcinoma(108;0.00146)|all cancers(137;0.0031)|OV - Ovarian serous cystadenocarcinoma(136;0.0117)	Missense_Mutation	SNP	109426458	109426458	14612	6	C	T	T	26	26	SESN1	T	2	2
PKHD1	5314	broad.mit.edu	36	6	52049080	52049080	+	Missense_Mutation	SNP	G	A	A			TCGA-27-1830-01	TCGA-27-1830-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr6:52049080G>A	uc003pah.1	-	c.401C>T	c.(400-402)GCG>GTG	p.A134V	PKHD1_uc003pai.1_Missense_Mutation_p.A134V	NM_138694	NP_619639	P08F94	PKHD1_HUMAN	fibrocystin isoform 1	134	Extracellular (Potential).				cell-cell adhesion|cilium assembly|homeostatic process|kidney development|negative regulation of cellular component movement	anchored to external side of plasma membrane|apical plasma membrane|integral to membrane|microtubule basal body	protein binding|receptor activity			ovary(12)|large_intestine(5)|central_nervous_system(3)	20	Lung NSC(77;0.0605)									1537				0.309278	79.315322	82.458619	30	67	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	52049080	52049080	12396	6	G	A	A	38	38	PKHD1	A	1	1
IBTK	25998	broad.mit.edu	36	6	82980785	82980785	+	Silent	SNP	A	C	C			TCGA-27-1830-01	TCGA-27-1830-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr6:82980785A>C	uc003pjl.1	-	c.2082T>G	c.(2080-2082)GTT>GTG	p.V694V	IBTK_uc010kbi.1_Silent_p.V388V|IBTK_uc003pjm.1_Silent_p.V694V	NM_015525	NP_056340	Q9P2D0	IBTK_HUMAN	inhibitor of Bruton's tyrosine kinase	694					negative regulation of protein phosphorylation|release of sequestered calcium ion into cytosol	cytoplasm|membrane|nucleus	protein kinase binding|protein tyrosine kinase inhibitor activity			ovary(2)|central_nervous_system(2)	4		all_cancers(76;3.38e-06)|Acute lymphoblastic leukemia(125;3.41e-06)|all_hematologic(105;0.000865)|all_epithelial(107;0.0037)												0.306977	207.079999	214.215807	66	149	AA		KEEP	---	---	---	---	capture		BRCA - Breast invasive adenocarcinoma(397;0.0901)	Silent	SNP	82980785	82980785	7776	6	A	C	C	13	13	IBTK	C	4	4
PLXNA4	91584	broad.mit.edu	36	7	131516696	131516696	+	Missense_Mutation	SNP	G	A	A			TCGA-27-1830-01	TCGA-27-1830-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr7:131516696G>A	uc003vra.2	-	c.3476C>T	c.(3475-3477)ACG>ATG	p.T1159M		NM_020911	NP_065962	Q9HCM2	PLXA4_HUMAN	plexin A4 isoform 1	1159	IPT/TIG 4.|Extracellular (Potential).					integral to membrane|intracellular|plasma membrane				ovary(1)	1														0.1875	182.376036	226.269764	90	390	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	131516696	131516696	12548	7	G	A	A	40	40	PLXNA4	A	1	1
GIMAP8	155038	broad.mit.edu	36	7	149802262	149802262	+	Silent	SNP	G	A	A			TCGA-27-1830-01	TCGA-27-1830-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr7:149802262G>A	uc003whj.1	+	c.912G>A	c.(910-912)CCG>CCA	p.P304P		NM_175571	NP_783161	Q8ND71	GIMA8_HUMAN	GTPase, IMAP family member 8	304						endoplasmic reticulum|Golgi apparatus|mitochondrion	GTP binding			ovary(1)|breast(1)|central_nervous_system(1)	3														0.189076	101.104797	122.576786	45	193	GG		KEEP	---	---	---	---	capture	OV - Ovarian serous cystadenocarcinoma(82;0.0218)	UCEC - Uterine corpus endometrioid carcinoma (81;0.17)	Silent	SNP	149802262	149802262	6653	7	G	A	A	39	39	GIMAP8	A	1	1
OC90	729330	broad.mit.edu	36	8	133113333	133113333	+	Silent	SNP	G	C	C			TCGA-27-1830-01	TCGA-27-1830-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr8:133113333G>C	uc003ytg.1	-	c.1008C>G	c.(1006-1008)GGC>GGG	p.G336G		NM_001080399	NP_001073868	Q02509	OC90_HUMAN	otoconin 90	352	Phospholipase A2-like 2.				lipid catabolic process|phospholipid metabolic process		calcium ion binding|phospholipase A2 activity			ovary(2)|skin(1)	3	Esophageal squamous(12;0.00693)|Ovarian(258;0.00769)|Acute lymphoblastic leukemia(118;0.155)													0.204082	7.559256	11.653645	10	39	GG		KEEP	---	---	---	---	capture	BRCA - Breast invasive adenocarcinoma(115;0.000805)		Silent	SNP	133113333	133113333	11219	8	G	C	C	38	38	OC90	C	3	3
TEX15	56154	broad.mit.edu	36	8	30822403	30822403	+	Missense_Mutation	SNP	C	T	T			TCGA-27-1830-01	TCGA-27-1830-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr8:30822403C>T	uc003xil.1	-	c.3673G>A	c.(3673-3675)GCT>ACT	p.A1225T		NM_031271	NP_112561	Q9BXT5	TEX15_HUMAN	testis expressed 15	1225										ovary(3)	3														0.324324	67.378166	69.403089	24	50	CC		KEEP	---	---	---	---	capture		KIRC - Kidney renal clear cell carcinoma(542;0.0918)|Kidney(114;0.111)	Missense_Mutation	SNP	30822403	30822403	16306	8	C	T	T	27	27	TEX15	T	1	1
WRN	7486	broad.mit.edu	36	8	31045321	31045321	+	Silent	SNP	T	G	G			TCGA-27-1830-01	TCGA-27-1830-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr8:31045321T>G	uc003xio.2	+	c.660T>G	c.(658-660)GGT>GGG	p.G220G		NM_000553	NP_000544	Q14191	WRN_HUMAN	Werner syndrome protein	220	Interaction with WRNIP1 (By similarity).|3'-5' exonuclease.				base-excision repair|cellular response to starvation|DNA recombination|DNA synthesis involved in DNA repair|multicellular organismal aging|nucleolus to nucleoplasm transport|positive regulation of hydrolase activity|regulation of apoptosis|replication fork processing|response to oxidative stress|response to UV-C|telomere maintenance	centrosome|nucleolus|nucleoplasm	3'-5' exonuclease activity|ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|four-way junction helicase activity|G-quadruplex DNA binding|magnesium ion binding|manganese ion binding|protein complex binding|protein homodimerization activity|Y-form DNA binding			ovary(2)|kidney(2)|large_intestine(1)	5		Breast(100;0.195)				Ovarian(18;161 598 2706 14834 27543)				832				0.363636	8.720251	9.189026	8	14	TT		KEEP	---	---	---	---	capture		KIRC - Kidney renal clear cell carcinoma(542;0.147)|Kidney(114;0.176)|Colorectal(111;0.192)	Silent	SNP	31045321	31045321	17976	8	T	G	G	60	60	WRN	G	4	4
ZCCHC5	203430	broad.mit.edu	36	X	77799684	77799684	+	Missense_Mutation	SNP	A	G	G			TCGA-27-1830-01	TCGA-27-1830-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chrX:77799684A>G	uc004edc.1	-	c.890T>C	c.(889-891)ATC>ACC	p.I297T	ZCCHC5_uc010nmd.1_Missense_Mutation_p.I297T	NM_152694	NP_689907	Q8N8U3	ZCHC5_HUMAN	zinc finger, CCHC domain containing 5	297							nucleic acid binding|zinc ion binding			ovary(1)	1														0.809524	58.124255	59.979006	17	4	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	77799684	77799684	18179	23	A	G	G	12	12	ZCCHC5	G	4	4
KIAA1751	85452	broad.mit.edu	36	1	1876616	1876617	+	Frame_Shift_Ins	INS	-	CTGGTGCGCGT	CTGGTGCGCGT			TCGA-27-1830-01	TCGA-27-1830-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:1876616_1876617insCTGGTGCGCGT	uc009vkz.1	-	c.2382_2383insACGCGCACCAG	c.(2380-2385)CAGCGGfs	p.Q794fs	KIAA1751_uc001aim.1_3'UTR	NM_001080484	NP_001073953	Q9C0B2	K1751_HUMAN	hypothetical protein LOC85452	Error:Variant_position_missing_in_Q9C0B2_after_alignment										pancreas(1)	1	all_cancers(77;0.000708)|all_epithelial(69;0.000943)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;6.04e-15)|all_lung(118;9.67e-07)|Lung NSC(185;5.59e-05)|Renal(390;0.00571)|Breast(487;0.0183)|Hepatocellular(190;0.0268)|Myeloproliferative disorder(586;0.028)|Ovarian(437;0.127)|Medulloblastoma(700;0.151)|Lung SC(97;0.217)		Epithelial(90;8.79e-39)|OV - Ovarian serous cystadenocarcinoma(86;9.61e-25)|GBM - Glioblastoma multiforme(42;1.2e-07)|Colorectal(212;4.84e-05)|COAD - Colon adenocarcinoma(227;0.000214)|Kidney(185;0.00254)|BRCA - Breast invasive adenocarcinoma(365;0.00461)|STAD - Stomach adenocarcinoma(132;0.00645)|KIRC - Kidney renal clear cell carcinoma(229;0.037)|Lung(427;0.205)										0.50			3	3				---	---	---	---	capture_indel			Frame_Shift_Ins	INS	1876616	1876617	8567	1	-	CTGGTGCGCGT	CTGGTGCGCGT	38	38	KIAA1751	CTGGTGCGCGT	5	5
