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	TCGAscape_Amplification_Peaks	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_judgement	validation_status	validation_method	validation_tumor_sample	validation_alt_allele	dataset	Oncotatorv0393GAF20hg19Feb2011dbSNPbuild132UniProtRelease2011_6	type	classification	start	end	gene	chr	ref_allele	tum_allele1	tum_allele2	newbase	context_orig	context65	gene_name	categ	categ_ignoring_null_categ
PAX2	5076	broad.mit.edu	37	10	102568895	102568895	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z017-01	TCGA-17-Z017-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:102568895C>A	uc001krk.3	+	c.890C>A	c.(889-891)ACC>AAC	p.T297N	PAX2_uc001krl.3_Missense_Mutation_p.T274N|PAX2_uc001krm.3_Missense_Mutation_p.T297N|PAX2_uc001kro.3_Missense_Mutation_p.T274N|PAX2_uc001krn.3_Missense_Mutation_p.T274N|PAX2_uc010qps.1_Missense_Mutation_p.T273N|PAX2_uc001krp.1_Missense_Mutation_p.T270N	NM_003990	NP_003981	Q02962	PAX2_HUMAN	paired box protein 2 isoform e	297					anti-apoptosis|axonogenesis|brain morphogenesis|branching involved in ureteric bud morphogenesis|cell fate determination|cellular response to glucose stimulus|cellular response to hydrogen peroxide|cellular response to retinoic acid|cochlea development|glial cell differentiation|inner ear morphogenesis|mesenchymal to epithelial transition involved in metanephros morphogenesis|mesodermal cell fate specification|mesonephros development|metanephric collecting duct development|metanephric distal convoluted tubule development|metanephric mesenchymal cell differentiation|metanephric nephron tubule formation|negative regulation of caspase activity|negative regulation of cytolysis|negative regulation of mesenchymal stem cell apoptosis involved in metanephric nephron morphogenesis|negative regulation of reactive oxygen species metabolic process|negative regulation of transcription, DNA-dependent|nephric duct formation|neural tube closure|optic chiasma development|optic cup morphogenesis involved in camera-type eye development|optic nerve formation|optic nerve structural organization|positive regulation of branching involved in ureteric bud morphogenesis|positive regulation of epithelial cell proliferation|positive regulation of gene-specific transcription from RNA polymerase II promoter|positive regulation of mesenchymal to epithelial transition involved in metanephros morphogenesis|pronephric field specification|protein kinase B signaling cascade|reactive oxygen species metabolic process|regulation of metanephric nephron tubule epithelial cell differentiation|regulation of metanephros size|retinal pigment epithelium development|stem cell differentiation|transcription from RNA polymerase II promoter|ureter development|vestibulocochlear nerve formation|visual perception	centriolar satellite|nucleus|protein complex|protein-DNA complex	core promoter proximal region sequence-specific DNA binding|promoter binding|superoxide-generating NADPH oxidase activity|transcription activator activity|transcription repressor activity				0		Colorectal(252;0.234)		Epithelial(162;1.32e-08)|all cancers(201;7.32e-07)										0.264151	35.423677	38.090741	14	39	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	102568895	102568895	11899	10	C	A	A	A	234	18	PAX2	2	2
PDZD7	79955	broad.mit.edu	37	10	102783311	102783311	+	Nonsense_Mutation	SNP	C	A	A			TCGA-17-Z017-01	TCGA-17-Z017-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:102783311C>A	uc001ksn.2	-	c.424G>T	c.(424-426)GAG>TAG	p.E142*	PDZD7_uc001kso.1_Nonsense_Mutation_p.E142*	NM_024895	NP_079171	Q9H5P4	PDZD7_HUMAN	PDZ domain containing 7	142	PDZ 1.				response to stimulus|visual perception	cilium|nucleus	protein binding			breast(1)|central_nervous_system(1)	2				Epithelial(162;6.98e-09)|all cancers(201;3.55e-07)										0.210526	15.98901	18.92864	8	30	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	102783311	102783311	12125	10	C	A	A	A	390	30	PDZD7	5	2
ADD3	120	broad.mit.edu	37	10	111890202	111890202	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z017-01	TCGA-17-Z017-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:111890202G>A	uc001kyt.3	+	c.1690G>A	c.(1690-1692)GAG>AAG	p.E564K	ADD3_uc001kys.3_Missense_Mutation_p.E564K|ADD3_uc001kyu.2_Missense_Mutation_p.E564K|ADD3_uc001kyv.2_Missense_Mutation_p.E564K|ADD3_uc001kyw.2_Missense_Mutation_p.E564K|ADD3_uc001kyx.2_Missense_Mutation_p.E137K	NM_016824	NP_058432	Q9UEY8	ADDG_HUMAN	adducin 3 (gamma) isoform a	564						cytoskeleton	actin binding|calmodulin binding|metal ion binding|structural constituent of cytoskeleton			ovary(2)|large_intestine(1)	3		Breast(234;0.052)|Lung NSC(174;0.223)		Epithelial(162;4.15e-05)|all cancers(201;0.000587)|BRCA - Breast invasive adenocarcinoma(275;0.0742)										0.141844	34.803959	52.247265	20	121	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	111890202	111890202	307	10	G	A	A	A	429	33	ADD3	2	2
SHOC2	8036	broad.mit.edu	37	10	112724437	112724437	+	Missense_Mutation	SNP	A	T	T			TCGA-17-Z017-01	TCGA-17-Z017-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:112724437A>T	uc001kzl.3	+	c.321A>T	c.(319-321)TTA>TTT	p.L107F	SHOC2_uc009xxx.2_Missense_Mutation_p.L107F|SHOC2_uc010qrg.1_Intron|SHOC2_uc001kzn.2_Missense_Mutation_p.L107F	NM_007373	NP_031399	Q9UQ13	SHOC2_HUMAN	soc-2 suppressor of clear homolog	107	LRR 1.				fibroblast growth factor receptor signaling pathway|positive regulation of Ras protein signal transduction|Ras protein signal transduction	nucleus|protein phosphatase type 1 complex	protein phosphatase binding|protein phosphatase regulator activity			ovary(1)	1				Epithelial(162;0.000796)|all cancers(201;0.011)|BRCA - Breast invasive adenocarcinoma(275;0.126)										0.132653	43.319306	68.996586	26	170	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	112724437	112724437	14782	10	A	T	T	T	206	16	SHOC2	3	3
PTPRE	5791	broad.mit.edu	37	10	129868648	129868648	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z017-01	TCGA-17-Z017-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:129868648G>T	uc009yat.2	+	c.1260G>T	c.(1258-1260)AAG>AAT	p.K420N	PTPRE_uc001lkb.2_Missense_Mutation_p.K409N|PTPRE_uc009yau.2_Missense_Mutation_p.K409N|PTPRE_uc001lkd.2_Missense_Mutation_p.K351N|PTPRE_uc010quq.1_Missense_Mutation_p.K310N	NM_006504	NP_006495	P23469	PTPRE_HUMAN	protein tyrosine phosphatase, receptor type, E	409	Cytoplasmic (Potential).				negative regulation of insulin receptor signaling pathway|protein phosphorylation	cytoplasm|integral to membrane|intermediate filament cytoskeleton|nucleus|plasma membrane	transmembrane receptor protein tyrosine phosphatase activity			ovary(1)	1		all_epithelial(44;1.66e-05)|all_lung(145;0.00456)|Lung NSC(174;0.0066)|all_neural(114;0.0936)|Colorectal(57;0.141)|Breast(234;0.166)|Melanoma(40;0.203)				Colon(52;977 1184 20575 41685)								0.12766	14.429467	27.150622	12	82	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	129868648	129868648	13257	10	G	T	T	T	438	34	PTPRE	2	2
ACBD5	91452	broad.mit.edu	37	10	27508756	27508756	+	Missense_Mutation	SNP	T	A	A			TCGA-17-Z017-01	TCGA-17-Z017-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:27508756T>A	uc010qdp.1	-	c.521A>T	c.(520-522)AAC>ATC	p.N174I	ACBD5_uc010qdm.1_Missense_Mutation_p.N172I|ACBD5_uc010qdn.1_Missense_Mutation_p.N65I|ACBD5_uc010qdo.1_Missense_Mutation_p.N65I|ACBD5_uc001ito.2_Missense_Mutation_p.N139I|ACBD5_uc001itp.2_Missense_Mutation_p.N65I|ACBD5_uc001itq.2_Missense_Mutation_p.N65I|ACBD5_uc001itr.1_5'UTR	NM_145698	NP_663736	Q5T8D3	ACBD5_HUMAN	acyl-Coenzyme A binding domain containing 5	183					transport	integral to membrane	fatty-acyl-CoA binding				0														0.291667	37.631492	39.497005	14	34	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	27508756	27508756	126	10	T	A	A	A	780	60	ACBD5	3	3
C10orf71	118461	broad.mit.edu	37	10	50531470	50531470	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z017-01	TCGA-17-Z017-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:50531470G>T	uc010qgp.1	+	c.880G>T	c.(880-882)GCT>TCT	p.A294S		NM_199459	NP_955629	Q711Q0	CJ071_HUMAN	hypothetical protein LOC118461 isoform 2	294											0														0.288732	100.688193	106.39122	41	101	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	50531470	50531470	1651	10	G	T	T	T	442	34	C10orf71	2	2
SLC18A3	6572	broad.mit.edu	37	10	50819611	50819611	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z017-01	TCGA-17-Z017-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:50819611C>A	uc001jhw.2	+	c.825C>A	c.(823-825)AAC>AAA	p.N275K	CHAT_uc001jhv.1_Intron|CHAT_uc001jhx.1_5'Flank|CHAT_uc001jhy.1_5'Flank|CHAT_uc001jia.2_5'Flank|CHAT_uc001jhz.2_5'Flank|CHAT_uc010qgs.1_5'Flank	NM_003055	NP_003046	Q16572	VACHT_HUMAN	vesicular acetylcholine transporter	275	Cytoplasmic (Potential).				neurotransmitter secretion	clathrin sculpted acetylcholine transport vesicle membrane|integral to plasma membrane|membrane fraction	acetylcholine transmembrane transporter activity			ovary(1)	1														0.233333	16.012618	17.963637	7	23	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	50819611	50819611	14923	10	C	A	A	A	233	18	SLC18A3	2	2
NET1	10276	broad.mit.edu	37	10	5498644	5498644	+	Missense_Mutation	SNP	T	G	G			TCGA-17-Z017-01	TCGA-17-Z017-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:5498644T>G	uc001iia.2	+	c.1478T>G	c.(1477-1479)TTC>TGC	p.F493C	NET1_uc010qar.1_Missense_Mutation_p.F312C|NET1_uc001iib.2_Missense_Mutation_p.F439C|NET1_uc010qas.1_Missense_Mutation_p.F312C	NM_001047160	NP_001040625	Q7Z628	ARHG8_HUMAN	neuroepithelial cell transforming gene 1 isoform	493	PH.				apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of cell growth|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol|nucleus	Rho guanyl-nucleotide exchange factor activity			breast(1)	1														0.197531	33.65889	40.560257	16	65	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	5498644	5498644	10737	10	T	G	G	G	806	62	NET1	4	4
ATM	472	broad.mit.edu	37	11	108175416	108175416	+	Missense_Mutation	SNP	T	G	G			TCGA-17-Z017-01	TCGA-17-Z017-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:108175416T>G	uc001pkb.1	+	c.5511T>G	c.(5509-5511)TTT>TTG	p.F1837L	ATM_uc009yxr.1_Missense_Mutation_p.F1837L|ATM_uc001pke.1_Missense_Mutation_p.F489L|ATM_uc001pkg.1_Missense_Mutation_p.F194L|ATM_uc009yxt.1_5'UTR	NM_000051	NP_000042	Q13315	ATM_HUMAN	ataxia telangiectasia mutated isoform 1	1837					cell cycle arrest|cellular response to gamma radiation|DNA damage induced protein phosphorylation|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|double-strand break repair via homologous recombination|G2/M transition DNA damage checkpoint|histone mRNA catabolic process|mitotic cell cycle spindle assembly checkpoint|negative regulation of B cell proliferation|peptidyl-serine phosphorylation|positive regulation of DNA damage response, signal transduction by p53 class mediator|pre-B cell allelic exclusion|protein autophosphorylation|reciprocal meiotic recombination|replicative senescence	cytoplasmic membrane-bounded vesicle|nucleoplasm	1-phosphatidylinositol-3-kinase activity|ATP binding|DNA binding|DNA-dependent protein kinase activity|identical protein binding|protein complex binding|protein dimerization activity|protein N-terminus binding			haematopoietic_and_lymphoid_tissue(174)|lung(24)|breast(14)|large_intestine(9)|ovary(5)|kidney(5)|central_nervous_system(4)|upper_aerodigestive_tract(1)|stomach(1)|NS(1)	238		all_cancers(61;9.64e-12)|all_epithelial(67;9.97e-08)|Melanoma(852;2.55e-06)|Acute lymphoblastic leukemia(157;3.95e-05)|all_hematologic(158;0.00014)|Breast(348;0.0258)|all_neural(303;0.072)		Epithelial(105;9.05e-06)|BRCA - Breast invasive adenocarcinoma(274;1.06e-05)|all cancers(92;0.000208)|Colorectal(284;0.116)|OV - Ovarian serous cystadenocarcinoma(223;0.147)						1073	TSP Lung(14;0.12)			0.215686	30.597887	34.400944	11	40	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	108175416	108175416	1128	11	T	G	G	G	829	64	ATM	4	4
CBL	867	broad.mit.edu	37	11	119145632	119145632	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z017-01	TCGA-17-Z017-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:119145632C>T	uc001pwe.2	+	c.838C>T	c.(838-840)CGG>TGG	p.R280W		NM_005188	NP_005179	P22681	CBL_HUMAN	Cas-Br-M (murine) ecotropic retroviral	280	Cbl-PTB.|SH2-like.				epidermal growth factor receptor signaling pathway|negative regulation of apoptosis|negative regulation of epidermal growth factor receptor signaling pathway|positive regulation of receptor-mediated endocytosis	cytosol|nucleus	calcium ion binding|sequence-specific DNA binding transcription factor activity|SH3 domain binding|signal transducer activity|ubiquitin-protein ligase activity|zinc ion binding			haematopoietic_and_lymphoid_tissue(133)|lung(9)|central_nervous_system(2)|ovary(1)	145		Medulloblastoma(222;0.0425)|Breast(348;0.052)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;4.92e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.000784)						309				0.140845	15.007993	23.847776	10	61	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	119145632	119145632	2819	11	C	T	T	T	399	31	CBL	1	1
NELL1	4745	broad.mit.edu	37	11	20805255	20805255	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z017-01	TCGA-17-Z017-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:20805255C>A	uc009yid.2	+	c.298C>A	c.(298-300)CAT>AAT	p.H100N	NELL1_uc001mqe.2_Missense_Mutation_p.H72N|NELL1_uc001mqf.2_Missense_Mutation_p.H72N|NELL1_uc010rdo.1_Missense_Mutation_p.H72N|NELL1_uc010rdp.1_5'UTR	NM_006157	NP_006148	Q92832	NELL1_HUMAN	nel-like 1 isoform 1 precursor	72					cell adhesion|nervous system development	extracellular region	calcium ion binding|structural molecule activity			ovary(2)|large_intestine(1)	3														0.168539	28.465732	37.729125	15	74	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	20805255	20805255	10732	11	C	A	A	A	377	29	NELL1	2	2
MAPK8IP1	9479	broad.mit.edu	37	11	45924191	45924191	+	Silent	SNP	C	T	T			TCGA-17-Z017-01	TCGA-17-Z017-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:45924191C>T	uc001nbr.2	+	c.873C>T	c.(871-873)GAC>GAT	p.D291D		NM_005456	NP_005447	Q9UQF2	JIP1_HUMAN	mitogen-activated protein kinase 8 interacting	291					vesicle-mediated transport	nucleus|perinuclear region of cytoplasm	kinesin binding|MAP-kinase scaffold activity|protein kinase inhibitor activity			ovary(1)	1				GBM - Glioblastoma multiforme(35;0.231)										0.318182	18.419049	19.064552	7	15	KEEP	---	---	---	---	capture		Silent	SNP	45924191	45924191	9667	11	C	T	T	T	246	19	MAPK8IP1	1	1
OR51B5	282763	broad.mit.edu	37	11	5364598	5364598	+	Missense_Mutation	SNP	G	C	C			TCGA-17-Z017-01	TCGA-17-Z017-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:5364598G>C	uc001map.1	-	c.157C>G	c.(157-159)CTT>GTT	p.L53V	HBG2_uc001mak.1_Intron|HBE1_uc001mam.1_Intron|OR51B5_uc001maq.1_Missense_Mutation_p.L53V	NM_001005567	NP_001005567	Q9H339	O51B5_HUMAN	olfactory receptor, family 51, subfamily B,	53	Helical; Name=2; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0		Medulloblastoma(188;0.0075)|all_neural(188;0.0572)|Breast(177;0.0675)		Epithelial(150;3.05e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)										0.229358	67.131903	74.44325	25	84	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	5364598	5364598	11501	11	G	C	C	C	429	33	OR51B5	3	3
OR5I1	10798	broad.mit.edu	37	11	55703852	55703852	+	Missense_Mutation	SNP	T	A	A			TCGA-17-Z017-01	TCGA-17-Z017-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:55703852T>A	uc010ris.1	-	c.25A>T	c.(25-27)ACG>TCG	p.T9S		NM_006637	NP_006628	Q13606	OR5I1_HUMAN	olfactory receptor, family 5, subfamily I,	9	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)	1														0.166667	22.682162	29.637145	11	55	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	55703852	55703852	11574	11	T	A	A	A	767	59	OR5I1	3	3
OR5R1	219479	broad.mit.edu	37	11	56185534	56185534	+	Missense_Mutation	SNP	T	A	A			TCGA-17-Z017-01	TCGA-17-Z017-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:56185534T>A	uc010rji.1	-	c.175A>T	c.(175-177)ATG>TTG	p.M59L		NM_001004744	NP_001004744	Q8NH85	OR5R1_HUMAN	olfactory receptor, family 5, subfamily R,	59	Helical; Name=2; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(2)	2	Esophageal squamous(21;0.00448)													0.209302	63.666844	73.747939	27	102	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	56185534	56185534	11590	11	T	A	A	A	637	49	OR5R1	3	3
TCN1	6947	broad.mit.edu	37	11	59620776	59620776	+	Silent	SNP	G	T	T			TCGA-17-Z017-01	TCGA-17-Z017-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:59620776G>T	uc001noj.2	-	c.1140C>A	c.(1138-1140)CGC>CGA	p.R380R		NM_001062	NP_001053	P20061	TCO1_HUMAN	transcobalamin I precursor	380					cobalamin metabolic process|cobalamin transport|cobalt ion transport	extracellular region	cobalamin binding			ovary(1)	1		all_epithelial(135;0.198)			Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)									0.24359	46.787696	51.460879	19	59	KEEP	---	---	---	---	capture		Silent	SNP	59620776	59620776	16232	11	G	T	T	T	431	34	TCN1	2	2
DCHS1	8642	broad.mit.edu	37	11	6647186	6647186	+	Silent	SNP	T	A	A			TCGA-17-Z017-01	TCGA-17-Z017-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:6647186T>A	uc001mem.1	-	c.6696A>T	c.(6694-6696)ACA>ACT	p.T2232T		NM_003737	NP_003728	Q96JQ0	PCD16_HUMAN	dachsous 1 precursor	2232	Extracellular (Potential).|Cadherin 21.				calcium-dependent cell-cell adhesion|homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(3)|large_intestine(1)|pancreas(1)	5		Medulloblastoma(188;0.00263)|all_neural(188;0.026)		Epithelial(150;6.35e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)										0.272727	24.860749	26.396861	9	24	KEEP	---	---	---	---	capture		Silent	SNP	6647186	6647186	4458	11	T	A	A	A	704	55	DCHS1	3	3
OR5P2	120065	broad.mit.edu	37	11	7818426	7818426	+	Missense_Mutation	SNP	C	G	G			TCGA-17-Z017-01	TCGA-17-Z017-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:7818426C>G	uc001mfp.1	-	c.64G>C	c.(64-66)GAT>CAT	p.D22H		NM_153444	NP_703145	Q8WZ92	OR5P2_HUMAN	olfactory receptor, family 5, subfamily P,	22	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(2)|central_nervous_system(1)	3				Epithelial(150;8.62e-08)|BRCA - Breast invasive adenocarcinoma(625;0.189)										0.337349	87.973907	89.916257	28	55	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	7818426	7818426	11588	11	C	G	G	G	416	32	OR5P2	3	3
STYK1	55359	broad.mit.edu	37	12	10772762	10772762	+	Missense_Mutation	SNP	T	C	C			TCGA-17-Z017-01	TCGA-17-Z017-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:10772762T>C	uc001qys.2	-	c.1250A>G	c.(1249-1251)TAC>TGC	p.Y417C		NM_018423	NP_060893	Q6J9G0	STYK1_HUMAN	serine/threonine/tyrosine kinase 1	417					protein phosphorylation	integral to membrane|plasma membrane	ATP binding|non-membrane spanning protein tyrosine kinase activity	p.Y417C(1)		central_nervous_system(3)|ovary(2)|lung(1)	6										211				0.436464	253.176194	253.815591	79	102	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	10772762	10772762	15879	12	T	C	C	C	741	57	STYK1	4	4
GRIN2B	2904	broad.mit.edu	37	12	14018911	14018911	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z017-01	TCGA-17-Z017-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:14018911G>A	uc001rbt.2	-	c.232C>T	c.(232-234)CCA>TCA	p.P78S		NM_000834	NP_000825	Q13224	NMDE2_HUMAN	N-methyl-D-aspartate receptor subunit 2B	78	Extracellular (Potential).				response to ethanol	cell junction|N-methyl-D-aspartate selective glutamate receptor complex|outer membrane-bounded periplasmic space|postsynaptic membrane	glycine binding|N-methyl-D-aspartate selective glutamate receptor activity|zinc ion binding			central_nervous_system(4)|ovary(3)|lung(2)|skin(1)	10					Felbamate(DB00949)|Haloperidol(DB00502)|L-Glutamic Acid(DB00142)|Loperamide(DB00836)|Memantine(DB01043)					371				0.431034	233.304463	234.02448	75	99	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	14018911	14018911	7059	12	G	A	A	A	559	43	GRIN2B	2	2
KRAS	3845	broad.mit.edu	37	12	25398282	25398282	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z017-01	TCGA-17-Z017-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:25398282C>A	uc001rgp.1	-	c.37G>T	c.(37-39)GGC>TGC	p.G13C	KRAS_uc001rgq.1_Missense_Mutation_p.G13C|KRAS_uc001rgr.2_Non-coding_Transcript	NM_033360	NP_203524	P01116	RASK_HUMAN	c-K-ras2 protein isoform a precursor	13	GTP.		G -> R (in pylocytic astrocytoma; somatic mutation; increase activation of the Ras pathway).|G -> D (in a breast carcinoma cell line 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.G13C(174)|p.G13S(58)|p.G13R(41)|p.G13D(31)|p.G12_G13insG(4)|p.G13N(3)|p.G13E(1)|p.G13I(1)		large_intestine(11742)|pancreas(3256)|lung(2694)|biliary_tract(514)|ovary(437)|endometrium(339)|haematopoietic_and_lymphoid_tissue(303)|stomach(179)|thyroid(145)|prostate(85)|soft_tissue(75)|small_intestine(62)|upper_aerodigestive_tract(59)|cervix(49)|urinary_tract(48)|skin(38)|breast(27)|liver(21)|testis(17)|oesophagus(15)|central_nervous_system(8)|peritoneum(5)|kidney(5)|salivary_gland(5)|thymus(5)|eye(4)|gastrointestinal_tract_(site_indeterminate)(4)|autonomic_ganglia(2)|bone(2)|genital_tract(1)|penis(1)|adrenal_gland(1)	20148	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)			Pancreas(8;6 143 191 305 2070 2426 4376 10944 11745 26467 38091 50869)	G13C(TOV21G_OVARY)|G13C(MORCPR_LUNG)|G13C(NCIH1355_LUNG)|G13C(NCIH1734_LUNG)	119	p.G13C(NCIH1734-Tumor)|p.G13C(NCIH1355-Tumor)|p.G13C(MORCPR-Tumor)|p.G13C(TOV21G-Tumor)	262	TSP Lung(1;<1E-8)|Multiple Myeloma(2;<1E-6)			0.466667	22.424219	22.438681	7	8	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	25398282	25398282	8753	12	C	A	A	A	273	21	KRAS	2	2
KRT4	3851	broad.mit.edu	37	12	53205732	53205732	+	Silent	SNP	G	T	T			TCGA-17-Z017-01	TCGA-17-Z017-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:53205732G>T	uc001saz.2	-	c.714C>A	c.(712-714)GTC>GTA	p.V238V		NM_002272	NP_002263	P19013	K2C4_HUMAN	keratin 4	178	Coil 1A.|Rod.				cytoskeleton organization|epithelial cell differentiation|negative regulation of epithelial cell proliferation	keratin filament	structural molecule activity			ovary(4)	4						Pancreas(190;284 2995 41444 45903)								0.333333	26.443798	27.179921	10	20	KEEP	---	---	---	---	capture		Silent	SNP	53205732	53205732	8792	12	G	T	T	T	522	41	KRT4	2	2
CD163L1	283316	broad.mit.edu	37	12	7586213	7586213	+	Missense_Mutation	SNP	G	C	C			TCGA-17-Z017-01	TCGA-17-Z017-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:7586213G>C	uc010sge.1	-	c.202C>G	c.(202-204)CAG>GAG	p.Q68E	CD163L1_uc001qsy.2_Missense_Mutation_p.Q68E	NM_174941	NP_777601	Q9NR16	C163B_HUMAN	scavenger receptor cysteine-rich type 1	68	SRCR 1.|Extracellular (Potential).					extracellular region|integral to membrane|plasma membrane	scavenger receptor activity			ovary(8)|central_nervous_system(1)	9														0.216312	160.663057	181.570619	61	221	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	7586213	7586213	3095	12	G	C	C	C	624	48	CD163L1	3	3
CLEC4A	50856	broad.mit.edu	37	12	8288251	8288251	+	Silent	SNP	A	G	G			TCGA-17-Z017-01	TCGA-17-Z017-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:8288251A>G	uc001qtz.1	+	c.369A>G	c.(367-369)GAA>GAG	p.E123E	CLEC4A_uc009zga.1_Silent_p.E84E|CLEC4A_uc001qub.1_Silent_p.E90E|CLEC4A_uc001quc.1_Silent_p.E51E|CLEC4A_uc009zgb.1_Intron	NM_016184	NP_057268	Q9UMR7	CLC4A_HUMAN	C-type lectin domain family 4, member A isoform	123	Extracellular (Potential).|C-type lectin.				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)										0.371134	116.979335	118.392976	36	61	KEEP	---	---	---	---	capture		Silent	SNP	8288251	8288251	3650	12	A	G	G	G	50	4	CLEC4A	4	4
MTMR6	9107	broad.mit.edu	37	13	25835922	25835922	+	Missense_Mutation	SNP	T	A	A			TCGA-17-Z017-01	TCGA-17-Z017-01										Phase_I	Unspecified				Illumina GAIIx	g.chr13:25835922T>A	uc001uqf.3	-	c.610A>T	c.(610-612)AGT>TGT	p.S204C	MTMR6_uc001uqe.1_Missense_Mutation_p.S204C	NM_004685	NP_004676	Q9Y217	MTMR6_HUMAN	myotubularin related protein 6	204	Myotubularin phosphatase.					cytoplasm|nuclear envelope	calcium-activated potassium channel activity|protein serine/threonine phosphatase activity|protein tyrosine phosphatase activity			ovary(2)	2		Lung SC(185;0.0225)|Breast(139;0.0351)		all cancers(112;0.00927)|Epithelial(112;0.0474)|OV - Ovarian serous cystadenocarcinoma(117;0.164)										0.428571	27.778805	27.870492	9	12	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	25835922	25835922	10340	13	T	A	A	A	689	53	MTMR6	3	3
B3GALTL	145173	broad.mit.edu	37	13	31848718	31848718	+	Missense_Mutation	SNP	G	T	T	rs34830061		TCGA-17-Z017-01	TCGA-17-Z017-01										Phase_I	Unspecified				Illumina GAIIx	g.chr13:31848718G>T	uc010aaz.2	+	c.733G>T	c.(733-735)GTG>TTG	p.V245L	B3GALTL_uc001utn.3_Non-coding_Transcript	NM_194318	NP_919299	Q6Y288	B3GLT_HUMAN	beta 1,3-galactosyltransferase-like	245	Lumenal (Potential).				fucose metabolic process	endoplasmic reticulum membrane|integral to membrane	transferase activity, transferring glycosyl groups			ovary(1)	1		Lung SC(185;0.0257)		all cancers(112;0.00436)|Epithelial(112;0.0285)|OV - Ovarian serous cystadenocarcinoma(117;0.0512)|GBM - Glioblastoma multiforme(144;0.184)										0.2	20.278532	23.625321	8	32	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	31848718	31848718	1273	13	G	T	T	T	520	40	B3GALTL	1	1
BRCA2	675	broad.mit.edu	37	13	32906434	32906434	+	Silent	SNP	A	T	T			TCGA-17-Z017-01	TCGA-17-Z017-01										Phase_I	Unspecified				Illumina GAIIx	g.chr13:32906434A>T	uc001uub.1	+	c.819A>T	c.(817-819)TCA>TCT	p.S273S	BRCA2_uc001uua.1_Silent_p.S150S	NM_000059	NP_000050	P51587	BRCA2_HUMAN	breast cancer 2, early onset	273					cell cycle cytokinesis|centrosome duplication|double-strand break repair via homologous recombination|negative regulation of mammary gland epithelial cell proliferation|nucleotide-excision repair|positive regulation of transcription, DNA-dependent|regulation of S phase of mitotic cell cycle	BRCA2-MAGE-D1 complex|centrosome|nucleoplasm|stored secretory granule	gamma-tubulin binding|H3 histone acetyltransferase activity|H4 histone acetyltransferase activity|protease binding|single-stranded DNA binding|transcription activator activity			ovary(19)|endometrium(8)|breast(7)|oesophagus(5)|large_intestine(4)|central_nervous_system(3)|lung(3)|pancreas(3)|cervix(1)|salivary_gland(1)|liver(1)|skin(1)|kidney(1)	57		Lung SC(185;0.0262)		all cancers(112;7.13e-07)|Epithelial(112;1.59e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.000732)|BRCA - Breast invasive adenocarcinoma(63;0.0291)|GBM - Glioblastoma multiforme(144;0.0704)		Esophageal Squamous(138;838 1285 7957 30353 30468 36915 49332)				677	TCGA Ovarian(8;0.087)			0.233333	18.609589	20.562203	7	23	KEEP	---	---	---	---	capture		Silent	SNP	32906434	32906434	1530	13	A	T	T	T	93	8	BRCA2	3	3
DYNC1H1	1778	broad.mit.edu	37	14	102505474	102505474	+	Silent	SNP	C	T	T			TCGA-17-Z017-01	TCGA-17-Z017-01										Phase_I	Unspecified				Illumina GAIIx	g.chr14:102505474C>T	uc001yks.2	+	c.11343C>T	c.(11341-11343)ACC>ACT	p.T3781T		NM_001376	NP_001367	Q14204	DYHC1_HUMAN	cytoplasmic dynein 1 heavy chain 1	3781	Potential.|AAA 5 (By similarity).				cytoplasmic mRNA processing body assembly|G2/M transition of mitotic cell cycle|microtubule-based movement|mitotic spindle organization|stress granule assembly|transport	cytoplasmic dynein complex|cytosol|Golgi apparatus|microtubule	ATP binding|ATPase activity, coupled|microtubule motor activity|protein binding			ovary(7)|central_nervous_system(2)|pancreas(1)	10														0.341463	38.835942	39.747324	14	27	KEEP	---	---	---	---	capture		Silent	SNP	102505474	102505474	5027	14	C	T	T	T	262	21	DYNC1H1	2	2
OR4N5	390437	broad.mit.edu	37	14	20611982	20611982	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z017-01	TCGA-17-Z017-01										Phase_I	Unspecified				Illumina GAIIx	g.chr14:20611982C>A	uc010tla.1	+	c.88C>A	c.(88-90)CTA>ATA	p.L30I		NM_001004724	NP_001004724	Q8IXE1	OR4N5_HUMAN	olfactory receptor, family 4, subfamily N,	30	Helical; Name=1; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)	1	all_cancers(95;0.00108)		Epithelial(56;7.58e-07)|all cancers(55;3.84e-06)	GBM - Glioblastoma multiforme(265;0.0143)										0.241379	183.995813	203.478478	77	242	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	20611982	20611982	11489	14	C	A	A	A	363	28	OR4N5	2	2
MYH6	4624	broad.mit.edu	37	14	23863473	23863473	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z017-01	TCGA-17-Z017-01										Phase_I	Unspecified				Illumina GAIIx	g.chr14:23863473G>T	uc001wjv.2	-	c.2489C>A	c.(2488-2490)CCC>CAC	p.P830H		NM_002471	NP_002462	P13533	MYH6_HUMAN	myosin heavy chain 6	830			P -> L (in CMD1EE).		adult heart development|atrial cardiac muscle tissue morphogenesis|cardiac muscle fiber development|in utero embryonic development|muscle filament sliding|regulation of ATPase activity|regulation of blood pressure|regulation of heart rate|regulation of the force of heart contraction|sarcomere organization|striated muscle contraction|ventricular cardiac muscle tissue morphogenesis|visceral muscle development	cytosol|focal adhesion|muscle myosin complex|myosin filament|nucleus|sarcomere	actin binding|actin-dependent ATPase activity|ATP binding|calmodulin binding|microfilament motor activity|protein kinase binding|structural constituent of muscle			pancreas(2)|ovary(1)	3	all_cancers(95;2.54e-05)			GBM - Glioblastoma multiforme(265;0.00764)|READ - Rectum adenocarcinoma(4;0.0289)|Colorectal(4;0.0441)										0.261538	42.950743	46.292309	17	48	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	23863473	23863473	10433	14	G	T	T	T	559	43	MYH6	2	2
NFATC4	4776	broad.mit.edu	37	14	24839231	24839231	+	Silent	SNP	T	C	C			TCGA-17-Z017-01	TCGA-17-Z017-01										Phase_I	Unspecified				Illumina GAIIx	g.chr14:24839231T>C	uc010tol.1	+	c.816T>C	c.(814-816)TTT>TTC	p.F272F	NFATC4_uc010tok.1_Silent_p.F272F|NFATC4_uc010alr.2_Silent_p.F272F|NFATC4_uc010als.2_Silent_p.F222F|NFATC4_uc010tom.1_Silent_p.F222F|NFATC4_uc010ton.1_Silent_p.F222F|NFATC4_uc010too.1_Silent_p.F222F|NFATC4_uc010alt.2_Silent_p.F241F|NFATC4_uc010top.1_Silent_p.F241F|NFATC4_uc010toq.1_Silent_p.F241F|NFATC4_uc010alu.2_Intron|NFATC4_uc001wpc.2_Silent_p.F209F|NFATC4_uc010tor.1_Silent_p.F209F|NFATC4_uc010tos.1_Silent_p.F139F|NFATC4_uc010tot.1_Silent_p.F197F|NFATC4_uc010tou.1_Silent_p.F139F|NFATC4_uc010tov.1_Silent_p.F197F|NFATC4_uc010tow.1_Silent_p.F139F|NFATC4_uc010alv.2_Silent_p.F197F|NFATC4_uc010tox.1_Silent_p.F139F|NFATC4_uc001wpd.2_5'Flank|NFATC4_uc010toy.1_5'Flank|NFATC4_uc010toz.1_5'Flank	NM_004554	NP_004545	Q14934	NFAC4_HUMAN	nuclear factor of activated T-cells,	209	Pro-rich.				cell differentiation|inflammatory response|regulation of transcription, DNA-dependent|transcription from RNA polymerase II promoter	cytoplasm|intermediate filament cytoskeleton|nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|transcription coactivator activity			ovary(1)|central_nervous_system(1)	2				GBM - Glioblastoma multiforme(265;0.018)										0.347826	21.392334	21.862745	8	15	KEEP	---	---	---	---	capture		Silent	SNP	24839231	24839231	10765	14	T	C	C	C	816	63	NFATC4	4	4
AKAP6	9472	broad.mit.edu	37	14	33290934	33290934	+	Silent	SNP	G	T	T			TCGA-17-Z017-01	TCGA-17-Z017-01										Phase_I	Unspecified				Illumina GAIIx	g.chr14:33290934G>T	uc001wrq.2	+	c.3915G>T	c.(3913-3915)CTG>CTT	p.L1305L		NM_004274	NP_004265	Q13023	AKAP6_HUMAN	A-kinase anchor protein 6	1305					protein targeting	calcium channel complex|nuclear membrane|sarcoplasmic reticulum	protein kinase A binding|receptor binding			breast(6)|ovary(5)|large_intestine(2)|lung(2)|pancreas(1)	16	Breast(36;0.0388)|Prostate(35;0.15)		LUAD - Lung adenocarcinoma(48;0.00107)|Lung(238;0.00677)|STAD - Stomach adenocarcinoma(7;0.116)	GBM - Glioblastoma multiforme(265;0.019)		Melanoma(49;821 1200 7288 13647 42351)				483				0.222222	49.171239	55.545914	20	70	KEEP	---	---	---	---	capture		Silent	SNP	33290934	33290934	458	14	G	T	T	T	574	45	AKAP6	2	2
LRFN5	145581	broad.mit.edu	37	14	42360493	42360493	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z017-01	TCGA-17-Z017-01										Phase_I	Unspecified				Illumina GAIIx	g.chr14:42360493C>A	uc001wvm.2	+	c.1426C>A	c.(1426-1428)CTG>ATG	p.L476M	LRFN5_uc010ana.2_Intron	NM_152447	NP_689660	Q96NI6	LRFN5_HUMAN	leucine rich repeat and fibronectin type III	476	Extracellular (Potential).|Fibronectin type-III.					integral to membrane				ovary(5)|pancreas(2)|central_nervous_system(1)	8			LUAD - Lung adenocarcinoma(50;0.0223)|Lung(238;0.0728)	GBM - Glioblastoma multiforme(112;0.00847)										0.147727	21.616046	32.103528	13	75	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	42360493	42360493	9314	14	C	A	A	A	415	32	LRFN5	2	2
C14orf101	54916	broad.mit.edu	37	14	57078984	57078984	+	Missense_Mutation	SNP	A	G	G			TCGA-17-Z017-01	TCGA-17-Z017-01										Phase_I	Unspecified				Illumina GAIIx	g.chr14:57078984A>G	uc001xcm.2	+	c.838A>G	c.(838-840)AGT>GGT	p.S280G	C14orf101_uc001xcj.2_Non-coding_Transcript|C14orf101_uc001xck.2_Missense_Mutation_p.S280G|C14orf101_uc010aot.1_Missense_Mutation_p.S280G|C14orf101_uc001xcl.1_Non-coding_Transcript|C14orf101_uc001xcn.2_Non-coding_Transcript|C14orf101_uc010trf.1_5'UTR	NM_017799	NP_060269	Q9NX78	CN101_HUMAN	hypothetical protein LOC54916	280						integral to membrane				breast(1)	1				OV - Ovarian serous cystadenocarcinoma(311;0.226)										0.304348	39.129657	40.702611	14	32	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	57078984	57078984	1782	14	A	G	G	G	91	7	C14orf101	4	4
SPTB	6710	broad.mit.edu	37	14	65239517	65239517	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z017-01	TCGA-17-Z017-01										Phase_I	Unspecified				Illumina GAIIx	g.chr14:65239517C>A	uc001xhr.2	-	c.5334G>T	c.(5332-5334)ATG>ATT	p.M1778I	SPTB_uc001xhs.2_Missense_Mutation_p.M1778I|SPTB_uc001xht.2_Missense_Mutation_p.M1778I|SPTB_uc001xhu.2_Missense_Mutation_p.M1778I|SPTB_uc010aqi.2_Missense_Mutation_p.M439I	NM_001024858	NP_001020029	P11277	SPTB1_HUMAN	spectrin beta isoform a	1778	Spectrin 15.				actin filament capping|axon guidance	cell surface|cytosol|intrinsic to internal side of plasma membrane|protein complex|spectrin|spectrin-associated cytoskeleton	actin filament binding|structural constituent of cytoskeleton			ovary(7)|lung(1)|central_nervous_system(1)	9		all_lung(585;4.15e-09)		all cancers(60;4.33e-34)|OV - Ovarian serous cystadenocarcinoma(108;8.32e-20)|BRCA - Breast invasive adenocarcinoma(234;0.0628)										0.18	17.086251	21.872734	9	41	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	65239517	65239517	15632	14	C	A	A	A	221	17	SPTB	2	2
NRXN3	9369	broad.mit.edu	37	14	79423671	79423671	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z017-01	TCGA-17-Z017-01										Phase_I	Unspecified				Illumina GAIIx	g.chr14:79423671C>T	uc001xun.2	+	c.1243C>T	c.(1243-1245)CTT>TTT	p.L415F	NRXN3_uc001xum.1_Non-coding_Transcript|NRXN3_uc010asv.1_Missense_Mutation_p.L540F	NM_004796	NP_004787	Q9Y4C0	NRX3A_HUMAN	neurexin 3 isoform 1 precursor	788	Laminin G-like 4.|Extracellular (Potential).				axon guidance|cell adhesion	integral to plasma membrane	metal ion binding|receptor activity			ovary(3)|pancreas(2)|breast(1)|central_nervous_system(1)	7		Renal(4;0.00876)		BRCA - Breast invasive adenocarcinoma(234;0.00544)|Kidney(3;0.029)|KIRC - Kidney renal clear cell carcinoma(182;0.223)										0.25641	53.961022	58.159095	20	58	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	79423671	79423671	11072	14	C	T	T	T	312	24	NRXN3	2	2
CLMN	79789	broad.mit.edu	37	14	95682072	95682072	+	Splice_Site_SNP	SNP	T	A	A			TCGA-17-Z017-01	TCGA-17-Z017-01										Phase_I	Unspecified				Illumina GAIIx	g.chr14:95682072T>A	uc001yef.2	-	c.325_splice	c.e5-1	p.V109_splice		NM_024734	NP_079010			calmin							integral to membrane	actin binding				0				Epithelial(152;0.193)										0.3	18.242581	18.95707	6	14	KEEP	---	---	---	---	capture		Splice_Site_SNP	SNP	95682072	95682072	3680	14	T	A	A	A	715	55	CLMN	5	3
ATG2B	55102	broad.mit.edu	37	14	96761865	96761865	+	Silent	SNP	T	A	A			TCGA-17-Z017-01	TCGA-17-Z017-01										Phase_I	Unspecified				Illumina GAIIx	g.chr14:96761865T>A	uc001yfi.2	-	c.5172A>T	c.(5170-5172)ACA>ACT	p.T1724T		NM_018036	NP_060506	Q96BY7	ATG2B_HUMAN	ATG2 autophagy related 2 homolog B	1724										ovary(1)|kidney(1)	2		all_cancers(154;0.0462)|all_epithelial(191;0.123)|Melanoma(154;0.155)		Epithelial(152;0.21)|COAD - Colon adenocarcinoma(157;0.244)										0.242424	44.167645	48.159597	16	50	KEEP	---	---	---	---	capture		Silent	SNP	96761865	96761865	1113	14	T	A	A	A	808	63	ATG2B	3	3
OR4N4	283694	broad.mit.edu	37	15	22382663	22382663	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z017-01	TCGA-17-Z017-01										Phase_I	Unspecified				Illumina GAIIx	g.chr15:22382663G>T	uc001yuc.1	+	c.191G>T	c.(190-192)GGC>GTC	p.G64V	LOC727924_uc001yub.1_Non-coding_Transcript|OR4N4_uc010tzv.1_Missense_Mutation_p.G64V	NM_001005241	NP_001005241	Q8N0Y3	OR4N4_HUMAN	olfactory receptor, family 4, subfamily N,	64	Helical; Name=2; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(4)	4		all_cancers(20;1.94e-20)|all_epithelial(15;3.94e-18)|Lung NSC(15;8.53e-15)|all_lung(15;2.87e-14)|Breast(32;0.00519)|Colorectal(260;0.101)	GBM - Glioblastoma multiforme(6;0.124)	all cancers(64;1.64e-11)|Epithelial(43;5.81e-10)|BRCA - Breast invasive adenocarcinoma(123;0.000255)|Kidney(6;0.00736)|KIRC - Kidney renal clear cell carcinoma(6;0.0135)|GBM - Glioblastoma multiforme(186;0.0963)										0.076364	-8.450894	42.153608	21	254	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	22382663	22382663	11488	15	G	T	T	T	546	42	OR4N4	2	2
AQR	9716	broad.mit.edu	37	15	35210473	35210473	+	Missense_Mutation	SNP	T	A	A			TCGA-17-Z017-01	TCGA-17-Z017-01										Phase_I	Unspecified				Illumina GAIIx	g.chr15:35210473T>A	uc001ziv.2	-	c.1328A>T	c.(1327-1329)TAC>TTC	p.Y443F		NM_014691	NP_055506	O60306	AQR_HUMAN	aquarius	443					nuclear mRNA splicing, via spliceosome	catalytic step 2 spliceosome	RNA binding			large_intestine(1)	1		Lung NSC(122;8.7e-10)|all_lung(180;1.47e-08)		all cancers(64;4.34e-18)|GBM - Glioblastoma multiforme(113;4.59e-07)|BRCA - Breast invasive adenocarcinoma(123;0.0283)										0.285714	15.04073	15.906603	6	15	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	35210473	35210473	846	15	T	A	A	A	741	57	AQR	3	3
AP4E1	23431	broad.mit.edu	37	15	51293309	51293309	+	Missense_Mutation	SNP	C	G	G			TCGA-17-Z017-01	TCGA-17-Z017-01										Phase_I	Unspecified				Illumina GAIIx	g.chr15:51293309C>G	uc001zyx.1	+	c.3182C>G	c.(3181-3183)TCT>TGT	p.S1061C	AP4E1_uc010bex.1_Non-coding_Transcript	NM_007347	NP_031373	Q9UPM8	AP4E1_HUMAN	adaptor-related protein complex 4, epsilon 1	1061					intracellular protein transport|vesicle-mediated transport	COPI vesicle coat	binding|structural molecule activity				0				all cancers(107;0.000893)|GBM - Glioblastoma multiforme(94;0.00364)										0.371134	113.77439	115.189947	36	61	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	51293309	51293309	762	15	C	G	G	G	416	32	AP4E1	3	3
GCOM1	145781	broad.mit.edu	37	15	58006742	58006742	+	Missense_Mutation	SNP	A	T	T			TCGA-17-Z017-01	TCGA-17-Z017-01										Phase_I	Unspecified				Illumina GAIIx	g.chr15:58006742A>T	uc002aem.2	+	c.1518A>T	c.(1516-1518)CAA>CAT	p.Q506H	GCOM1_uc002aeq.2_Non-coding_Transcript|GCOM1_uc002aen.2_Non-coding_Transcript|GCOM1_uc010bfy.2_Non-coding_Transcript|GCOM1_uc002aeo.2_Missense_Mutation_p.K438M|GCOM1_uc002aep.2_Non-coding_Transcript|GCOM1_uc010bfx.2_Non-coding_Transcript|GRINL1A_uc002aes.2_Missense_Mutation_p.Q93H|GRINL1A_uc010ugu.1_Non-coding_Transcript|GRINL1A_uc002aet.3_Missense_Mutation_p.Q324H|GRINL1A_uc002aeu.3_Missense_Mutation_p.Q167H	NM_001018090	NP_001018100	P0CAP1	GCOM1_HUMAN	GRINL1A combined protein isoform 1	343	Potential.									ovary(1)	1														0.316092	152.360794	157.595953	55	119	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	58006742	58006742	6571	15	A	T	T	T	39	3	GCOM1	3	3
STRA6	64220	broad.mit.edu	37	15	74473151	74473151	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z017-01	TCGA-17-Z017-01										Phase_I	Unspecified				Illumina GAIIx	g.chr15:74473151G>T	uc002axj.2	-	c.1929C>A	c.(1927-1929)GAC>GAA	p.D643E	STRA6_uc002axi.2_Missense_Mutation_p.D413E|STRA6_uc010ulh.1_Missense_Mutation_p.D642E|STRA6_uc002axk.2_Missense_Mutation_p.D604E|STRA6_uc010bji.2_Missense_Mutation_p.D604E|STRA6_uc002axl.2_Missense_Mutation_p.D536E|STRA6_uc002axm.2_Missense_Mutation_p.D604E|STRA6_uc002axn.2_Missense_Mutation_p.D595E|STRA6_uc010uli.1_Missense_Mutation_p.D641E	NM_022369	NP_071764	Q9BX79	STRA6_HUMAN	stimulated by retinoic acid gene 6 homolog	604	Cytoplasmic (Potential).				transport	integral to membrane|plasma membrane|protein complex	receptor activity			central_nervous_system(1)	1														0.236842	22.700312	25.075424	9	29	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	74473151	74473151	15842	15	G	T	T	T	620	48	STRA6	2	2
BNC1	646	broad.mit.edu	37	15	83926700	83926700	+	Missense_Mutation	SNP	T	C	C			TCGA-17-Z017-01	TCGA-17-Z017-01										Phase_I	Unspecified				Illumina GAIIx	g.chr15:83926700T>C	uc002bjt.1	-	c.2479A>G	c.(2479-2481)ATG>GTG	p.M827V	BNC1_uc010uos.1_Missense_Mutation_p.M815V	NM_001717	NP_001708	Q01954	BNC1_HUMAN	basonuclin 1	827					epidermis development|positive regulation of cell proliferation|regulation of transcription, DNA-dependent	cytoplasm|nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(3)	3														0.230769	64.548923	71.454674	24	80	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	83926700	83926700	1499	15	T	C	C	C	676	52	BNC1	4	4
ACAN	176	broad.mit.edu	37	15	89398511	89398511	+	Missense_Mutation	SNP	C	G	G			TCGA-17-Z017-01	TCGA-17-Z017-01										Phase_I	Unspecified				Illumina GAIIx	g.chr15:89398511C>G	uc010upo.1	+	c.2695C>G	c.(2695-2697)CTG>GTG	p.L899V	ACAN_uc010upp.1_Missense_Mutation_p.L899V|ACAN_uc002bna.2_Non-coding_Transcript	NM_013227	NP_037359			aggrecan isoform 2 precursor											ovary(2)|central_nervous_system(1)	3	Lung NSC(78;0.0392)|all_lung(78;0.077)		BRCA - Breast invasive adenocarcinoma(143;0.146)											0.333333	17.144358	17.58699	6	12	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	89398511	89398511	118	15	C	G	G	G	311	24	ACAN	3	3
SV2B	9899	broad.mit.edu	37	15	91832761	91832761	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z017-01	TCGA-17-Z017-01										Phase_I	Unspecified				Illumina GAIIx	g.chr15:91832761G>T	uc002bqv.2	+	c.1719G>T	c.(1717-1719)ATG>ATT	p.M573I	SV2B_uc010uqv.1_Missense_Mutation_p.M422I|SV2B_uc002bqu.3_Non-coding_Transcript	NM_014848	NP_055663	Q7L1I2	SV2B_HUMAN	synaptic vesicle protein 2B homolog	573	Helical; (Potential).				neurotransmitter transport|transmembrane transport	acrosomal vesicle|cell junction|integral to membrane|synaptic vesicle membrane	transporter activity			ovary(3)|central_nervous_system(2)	5	Lung NSC(78;0.0987)|all_lung(78;0.172)		BRCA - Breast invasive adenocarcinoma(143;0.0895)											0.185841	42.298046	52.767291	21	92	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	91832761	91832761	15938	15	G	T	T	T	598	46	SV2B	2	2
TMC5	79838	broad.mit.edu	37	16	19501836	19501836	+	Missense_Mutation	SNP	A	G	G			TCGA-17-Z017-01	TCGA-17-Z017-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:19501836A>G	uc002dgc.3	+	c.2693A>G	c.(2692-2694)TAT>TGT	p.Y898C	TMC5_uc010vaq.1_Missense_Mutation_p.Y846C|TMC5_uc002dgb.3_Intron|TMC5_uc010var.1_Missense_Mutation_p.Y898C|TMC5_uc002dgd.1_Missense_Mutation_p.Y652C|TMC5_uc002dge.3_Missense_Mutation_p.Y652C|TMC5_uc002dgf.3_Missense_Mutation_p.Y581C|TMC5_uc002dgg.3_Missense_Mutation_p.Y539C	NM_001105248	NP_001098718	Q6UXY8	TMC5_HUMAN	transmembrane channel-like 5 isoform a	898	Cytoplasmic (Potential).					integral to membrane					0														0.241245	172.884844	188.538364	62	195	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	19501836	19501836	16518	16	A	G	G	G	208	16	TMC5	4	4
DCUN1D3	123879	broad.mit.edu	37	16	20873760	20873760	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z017-01	TCGA-17-Z017-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:20873760G>A	uc002dhz.2	-	c.101C>T	c.(100-102)GCA>GTA	p.A34V	ERI2_uc002dht.3_Intron	NM_173475	NP_775746	Q8IWE4	DCNL3_HUMAN	DCN1, defective in cullin neddylation 1, domain	34					negative regulation of cell growth|negative regulation of S phase of mitotic cell cycle|positive regulation of apoptosis|response to gamma radiation|response to UV-C	perinuclear region of cytoplasm				ovary(2)	2				GBM - Glioblastoma multiforme(48;0.249)										0.227941	126.646472	145.107643	62	210	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	20873760	20873760	4486	16	G	A	A	A	598	46	DCUN1D3	2	2
HBM	3042	broad.mit.edu	37	16	216613	216613	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z017-01	TCGA-17-Z017-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:216613C>T	uc002cfu.1	+	c.332C>T	c.(331-333)TCC>TTC	p.S111F		NM_001003938	NP_001003938	Q6B0K9	HBM_HUMAN	hemoglobin mu chain	111						hemoglobin complex	heme binding|oxygen binding|oxygen transporter activity				0		all_cancers(16;1.62e-06)|all_epithelial(16;4.01e-06)|Hepatocellular(16;0.000325)|Lung NSC(18;0.0104)|all_lung(18;0.0239)												0.107143	2.505644	6.792897	3	25	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	216613	216613	7266	16	C	T	T	T	390	30	HBM	2	2
KIAA0556	23247	broad.mit.edu	37	16	27788315	27788315	+	Missense_Mutation	SNP	G	C	C			TCGA-17-Z017-01	TCGA-17-Z017-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:27788315G>C	uc002dow.2	+	c.4516G>C	c.(4516-4518)GCG>CCG	p.A1506P	KIAA0556_uc010vco.1_Missense_Mutation_p.A8P	NM_015202	NP_056017	O60303	K0556_HUMAN	hypothetical protein LOC23247	1506										ovary(4)|large_intestine(2)	6														0.194175	49.33842	58.326464	20	83	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	27788315	27788315	8490	16	G	C	C	C	598	46	KIAA0556	3	3
SALL1	6299	broad.mit.edu	37	16	51174345	51174345	+	Silent	SNP	C	G	G			TCGA-17-Z017-01	TCGA-17-Z017-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:51174345C>G	uc010vgs.1	-	c.1788G>C	c.(1786-1788)GGG>GGC	p.G596G	SALL1_uc010vgr.1_Silent_p.G499G|SALL1_uc010cbv.2_Intron	NM_002968	NP_002959	Q9NSC2	SALL1_HUMAN	sal-like 1 isoform a	596					adrenal gland development|branching involved in ureteric bud morphogenesis|embryonic digestive tract development|embryonic digit morphogenesis|gonad development|histone deacetylation|inductive cell-cell signaling|mesenchymal to epithelial transition involved in metanephros morphogenesis|negative regulation of transcription from RNA polymerase II promoter|olfactory bulb interneuron differentiation|olfactory bulb mitral cell layer development|olfactory nerve development|outer ear morphogenesis|pituitary gland development|positive regulation of transcription from RNA polymerase II promoter|positive regulation of Wnt receptor signaling pathway|ureteric bud invasion|ventricular septum development	chromocenter|cytoplasm|heterochromatin|nucleus	beta-catenin binding|DNA binding|sequence-specific DNA binding transcription factor activity|transcription activator activity|transcription repressor activity|zinc ion binding			ovary(3)	3		all_cancers(37;0.0322)	COAD - Colon adenocarcinoma(2;0.24)			GBM(103;1352 1446 1855 4775 8890)								0.241379	16.119099	17.88352	7	22	KEEP	---	---	---	---	capture		Silent	SNP	51174345	51174345	14290	16	C	G	G	G	275	22	SALL1	3	3
AP1G1	164	broad.mit.edu	37	16	71787790	71787790	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z017-01	TCGA-17-Z017-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:71787790C>A	uc002fbb.2	-	c.1299G>T	c.(1297-1299)AAG>AAT	p.K433N	AP1G1_uc002fba.2_Missense_Mutation_p.K413N|AP1G1_uc010cgg.2_Missense_Mutation_p.K410N	NM_001128	NP_001119	O43747	AP1G1_HUMAN	adaptor-related protein complex 1, gamma 1	410					endocytosis|intracellular protein transport|post-Golgi vesicle-mediated transport|regulation of defense response to virus by virus|viral reproduction	clathrin adaptor complex|clathrin coated vesicle membrane|cytosol|Golgi membrane|lysosomal membrane|recycling endosome	kinesin binding|protein transporter activity			ovary(2)	2		Ovarian(137;0.125)												0.248322	93.19351	101.654069	37	112	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	71787790	71787790	742	16	C	A	A	A	233	18	AP1G1	2	2
MYH4	4622	broad.mit.edu	37	17	10368833	10368833	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z017-01	TCGA-17-Z017-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:10368833C>T	uc002gmn.2	-	c.431G>A	c.(430-432)CGA>CAA	p.R144Q		NM_017533	NP_060003	Q9Y623	MYH4_HUMAN	myosin, heavy polypeptide 4, skeletal muscle	144	Myosin head-like.				muscle filament sliding	muscle myosin complex|myosin filament|sarcomere	actin binding|ATP binding|calmodulin binding|microfilament motor activity|structural constituent of muscle			ovary(10)|central_nervous_system(1)	11														0.333333	104.966127	107.682771	37	74	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	10368833	10368833	10432	17	C	T	T	T	403	31	MYH4	1	1
SSH2	85464	broad.mit.edu	37	17	28004720	28004720	+	Silent	SNP	G	A	A			TCGA-17-Z017-01	TCGA-17-Z017-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:28004720G>A	uc010wbh.1	-	c.519C>T	c.(517-519)AGC>AGT	p.S173S	SSH2_uc002heo.1_Silent_p.S146S|SSH2_uc002hep.1_Silent_p.S146S|SSH2_uc002heq.2_Silent_p.S153S|SSH2_uc002her.2_Silent_p.S146S|SSH2_uc010csc.1_Silent_p.S146S	NM_033389	NP_203747	Q76I76	SSH2_HUMAN	slingshot 2	146					actin cytoskeleton organization|regulation of actin polymerization or depolymerization|regulation of axonogenesis|regulation of lamellipodium assembly	cytoplasm|cytoskeleton	actin binding|protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity				0														0.213675	58.162871	66.985557	25	92	KEEP	---	---	---	---	capture		Silent	SNP	28004720	28004720	15701	17	G	A	A	A	490	38	SSH2	1	1
LIG3	3980	broad.mit.edu	37	17	33326409	33326409	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z017-01	TCGA-17-Z017-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:33326409C>T	uc002hik.1	+	c.2197C>T	c.(2197-2199)CAT>TAT	p.H733Y	LIG3_uc002hij.2_Missense_Mutation_p.H733Y	NM_013975	NP_039269	P49916	DNLI3_HUMAN	ligase III, DNA, ATP-dependent isoform alpha	733					base-excision repair|cell division|DNA ligation involved in DNA repair|DNA replication|reciprocal meiotic recombination|spermatogenesis	nucleoplasm	ATP binding|DNA binding|DNA ligase (ATP) activity|protein binding|zinc ion binding			ovary(2)|large_intestine(1)|pancreas(1)	4		Ovarian(249;0.17)			Bleomycin(DB00290)									0.326087	41.424174	42.65077	15	31	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	33326409	33326409	9108	17	C	T	T	T	273	21	LIG3	2	2
PSMD3	5709	broad.mit.edu	37	17	38153787	38153787	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z017-01	TCGA-17-Z017-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:38153787G>A	uc002htn.1	+	c.1558G>A	c.(1558-1560)GAG>AAG	p.E520K	PSMD3_uc010wen.1_Non-coding_Transcript|PSMD3_uc010weo.1_Missense_Mutation_p.E421K	NM_002809	NP_002800	O43242	PSMD3_HUMAN	proteasome 26S non-ATPase subunit 3	520					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|mRNA metabolic process|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|regulation of apoptosis|regulation of cellular amino acid metabolic process|regulation of protein catabolic process|S phase of mitotic cell cycle|viral reproduction	proteasome complex	enzyme regulator activity|protein binding			ovary(1)|pancreas(1)	2	Colorectal(19;0.000442)					Ovarian(186;531 2051 6385 19668 48409)								0.25	30.975925	33.703514	12	36	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	38153787	38153787	13152	17	G	A	A	A	533	41	PSMD3	2	2
CD300LG	146894	broad.mit.edu	37	17	41926251	41926251	+	Silent	SNP	C	T	T			TCGA-17-Z017-01	TCGA-17-Z017-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:41926251C>T	uc002iem.2	+	c.369C>T	c.(367-369)TTC>TTT	p.F123F	CD300LG_uc002iek.1_Silent_p.F123F|CD300LG_uc002iel.1_Silent_p.F123F|CD300LG_uc010czk.2_Silent_p.F123F|CD300LG_uc010wil.1_Silent_p.F123F|CD300LG_uc010czl.2_Silent_p.F123F	NM_145273	NP_660316	Q6UXG3	CLM9_HUMAN	CD300 molecule-like family member g precursor	123	Extracellular (Potential).					apical plasma membrane|basolateral plasma membrane|integral to membrane|multivesicular body membrane	receptor activity				0		Breast(137;0.0199)		BRCA - Breast invasive adenocarcinoma(366;0.115)										0.212121	16.811329	19.335973	7	26	KEEP	---	---	---	---	capture		Silent	SNP	41926251	41926251	3130	17	C	T	T	T	402	31	CD300LG	1	1
HOXB1	3211	broad.mit.edu	37	17	46606949	46606949	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z017-01	TCGA-17-Z017-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:46606949C>A	uc002ink.1	-	c.866G>T	c.(865-867)TGC>TTC	p.C289F		NM_002144	NP_002135	P14653	HXB1_HUMAN	homeobox B1	289						nucleus	protein domain specific binding|sequence-specific DNA binding transcription factor activity|transcription regulator activity			ovary(1)	1														0.283019	38.81299	40.989258	15	38	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	46606949	46606949	7591	17	C	A	A	A	325	25	HOXB1	2	2
BPTF	2186	broad.mit.edu	37	17	65907022	65907022	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z017-01	TCGA-17-Z017-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:65907022G>A	uc002jgf.2	+	c.3022G>A	c.(3022-3024)GAT>AAT	p.D1008N	BPTF_uc002jge.2_Missense_Mutation_p.D1134N	NM_182641	NP_872579	Q12830	BPTF_HUMAN	bromodomain PHD finger transcription factor	1134					brain development|chromatin remodeling|negative regulation of transcription from RNA polymerase II promoter|positive regulation of gene-specific transcription|transcription, DNA-dependent	cytoplasm|NURF complex	sequence-specific DNA binding|transcription factor binding|transcription regulator activity|zinc ion binding			ovary(2)	2	all_cancers(12;6e-11)		BRCA - Breast invasive adenocarcinoma(8;7.48e-08)|Colorectal(3;0.0984)|LUSC - Lung squamous cell carcinoma(166;0.24)											0.166667	13.005782	17.424905	7	35	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	65907022	65907022	1523	17	G	A	A	A	585	45	BPTF	2	2
TP53	7157	broad.mit.edu	37	17	7577518	7577518	+	Missense_Mutation	SNP	T	A	A			TCGA-17-Z017-01	TCGA-17-Z017-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:7577518T>A	uc002gim.2	-	c.763A>T	c.(763-765)ATC>TTC	p.I255F	TP53_uc002gig.1_Missense_Mutation_p.I255F|TP53_uc002gih.2_Missense_Mutation_p.I255F|TP53_uc010cne.1_5'Flank|TP53_uc010cnf.1_Missense_Mutation_p.I123F|TP53_uc010cng.1_Missense_Mutation_p.I123F|TP53_uc002gii.1_Missense_Mutation_p.I123F|TP53_uc010cnh.1_Missense_Mutation_p.I255F|TP53_uc010cni.1_Missense_Mutation_p.I255F|TP53_uc002gij.2_Missense_Mutation_p.I255F|TP53_uc010cnj.1_Non-coding_Transcript|TP53_uc002gin.2_Missense_Mutation_p.I162F|TP53_uc002gio.2_Missense_Mutation_p.I123F	NM_001126112	NP_001119584	P04637	P53_HUMAN	tumor protein p53 isoform a	255	|Interaction with HIPK1 (By similarity).|Interaction with AXIN1 (By similarity).		I -> T (in sporadic cancers; somatic mutation).|I -> S (in sporadic cancers; somatic mutation).|I -> M (in sporadic cancers; somatic mutation).|I -> V (in sporadic cancers; somatic mutation).|I -> N (in sporadic cancers; somatic mutation).|I -> F (in sporadic cancers; somatic mutation).		activation of caspase activity by cytochrome c|base-excision repair|blood coagulation|cell cycle arrest|cell differentiation|cell proliferation|cellular protein localization|cellular response to drug|cellular response to glucose starvation|cellular response to hypoxia|cellular response to ionizing radiation|cellular response to UV|determination of adult lifespan|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator|ER overload response|interspecies interaction between organisms|negative regulation of apoptosis|negative regulation of cell growth|negative regulation of cell proliferation|negative regulation of gene-specific transcription from RNA polymerase II promoter|negative regulation of helicase activity|negative regulation of transcription from RNA polymerase II promoter|nucleotide-excision repair|oxidative stress-induced premature senescence|positive regulation of gene-specific transcription from RNA polymerase II promoter|positive regulation of histone deacetylation|positive regulation of neuron apoptosis|positive regulation of peptidyl-tyrosine phosphorylation|positive regulation of reactive oxygen species metabolic process|positive regulation of thymocyte apoptosis|positive regulation of transcription from RNA polymerase II promoter|protein localization|protein tetramerization|Ras protein signal transduction|regulation of mitochondrial membrane permeability|replicative senescence|response to antibiotic|response to gamma radiation|response to X-ray	chromatin|cytoplasm|cytosol|endoplasmic reticulum|insoluble fraction|mitochondrion|nuclear matrix|nucleolus|nucleus|PML body|protein complex|replication fork	ATP binding|chaperone binding|chromatin binding|copper ion binding|damaged DNA binding|DNA strand annealing activity|histone acetyltransferase binding|p53 binding|promoter binding|promoter binding|protease binding|protein heterodimerization activity|protein kinase binding|protein N-terminus binding|protein phosphatase 2A binding|sequence-specific DNA binding transcription factor activity|specific transcriptional repressor activity|transcription activator activity|transcription factor binding|ubiquitin protein ligase binding|zinc ion binding	p.I255F(16)|p.I255del(7)|p.0?(6)|p.I255fs*9(3)|p.I255V(3)|p.I255fs*8(1)|p.?(1)|p.I254fs*7(1)|p.R249_T256delRPILTIIT(1)|p.I255fs*90(1)		large_intestine(4614)|breast(2344)|upper_aerodigestive_tract(2150)|lung(1958)|ovary(1559)|oesophagus(1462)|haematopoietic_and_lymphoid_tissue(1212)|stomach(1127)|urinary_tract(1113)|central_nervous_system(1072)|liver(805)|skin(693)|pancreas(370)|biliary_tract(247)|soft_tissue(209)|prostate(192)|endometrium(150)|bone(102)|vulva(79)|kidney(79)|cervix(68)|thyroid(54)|salivary_gland(41)|adrenal_gland(37)|peritoneum(33)|eye(24)|thymus(21)|genital_tract(16)|autonomic_ganglia(16)|small_intestine(14)|testis(11)|penis(10)|vagina(6)|meninges(5)|pituitary(4)|pleura(3)|gastrointestinal_tract_(site_indeterminate)(1)|NS(1)|Fallopian tube(1)|placenta(1)	21904		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)		Pancreas(47;798 1329 9957 10801)		111		690	TCGA GBM(1;<1E-8)|TSP Lung(2;<1E-8)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)			0.254545	35.223963	38.2314	14	41	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	7577518	7577518	16923	17	T	A	A	A	663	51	TP53	3	3
GUCY2D	3000	broad.mit.edu	37	17	7918200	7918200	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z017-01	TCGA-17-Z017-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:7918200C>A	uc002gjt.2	+	c.2600C>A	c.(2599-2601)ACG>AAG	p.T867K		NM_000180	NP_000171	Q02846	GUC2D_HUMAN	guanylate cyclase 2D, membrane (retina-specific)	867	Cytoplasmic (Potential).				intracellular signal transduction|protein phosphorylation|receptor guanylyl cyclase signaling pathway|visual perception	integral to plasma membrane|nuclear outer membrane	ATP binding|GTP binding|guanylate cyclase activity|protein kinase activity|receptor activity			skin(1)	1		Prostate(122;0.157)								285				0.322581	29.147413	30.009538	10	21	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	7918200	7918200	7177	17	C	A	A	A	247	19	GUCY2D	1	1
C18orf1	753	broad.mit.edu	37	18	13645521	13645521	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z017-01	TCGA-17-Z017-01										Phase_I	Unspecified				Illumina GAIIx	g.chr18:13645521C>A	uc002ksa.2	+	c.786C>A	c.(784-786)CAC>CAA	p.H262Q	C18orf1_uc002ksb.2_Missense_Mutation_p.H244Q|C18orf1_uc002kse.2_Missense_Mutation_p.H225Q|C18orf1_uc002ksf.2_Missense_Mutation_p.H207Q|C18orf1_uc002ksg.1_Missense_Mutation_p.H185Q|C18orf1_uc002ksh.1_Missense_Mutation_p.H204Q|C18orf1_uc002ksi.1_Missense_Mutation_p.H186Q	NM_181481	NP_852146	O15165	CR001_HUMAN	hypothetical protein LOC753 isoform alpha 1	262	Cytoplasmic (Potential).					integral to membrane|plasma membrane				ovary(2)|skin(1)	3				READ - Rectum adenocarcinoma(73;0.0642)										0.342105	37.264285	38.10096	13	25	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	13645521	13645521	1955	18	C	A	A	A	233	18	C18orf1	2	2
SNRPD1	6632	broad.mit.edu	37	18	19203777	19203777	+	Nonsense_Mutation	SNP	C	T	T			TCGA-17-Z017-01	TCGA-17-Z017-01										Phase_I	Unspecified				Illumina GAIIx	g.chr18:19203777C>T	uc002ktj.1	+	c.160C>T	c.(160-162)CAG>TAG	p.Q54*		NM_006938	NP_008869	P62314	SMD1_HUMAN	small nuclear ribonucleoprotein D1 polypeptide	54					ncRNA metabolic process|spliceosomal snRNP assembly|spliceosome assembly	catalytic step 2 spliceosome|cytosol|nucleoplasm|small nuclear ribonucleoprotein complex|U12-type spliceosomal complex	protein binding|RNA binding				0														0.15942	17.776409	25.406875	11	58	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	19203777	19203777	15364	18	C	T	T	T	221	17	SNRPD1	5	2
DSC3	1825	broad.mit.edu	37	18	28602406	28602406	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z017-01	TCGA-17-Z017-01										Phase_I	Unspecified				Illumina GAIIx	g.chr18:28602406G>T	uc002kwj.3	-	c.838C>A	c.(838-840)CTG>ATG	p.L280M	DSC3_uc002kwi.3_Missense_Mutation_p.L280M	NM_001941	NP_001932	Q14574	DSC3_HUMAN	desmocollin 3 isoform Dsc3a preproprotein	280	Extracellular (Potential).|Cadherin 2.				homophilic cell adhesion|protein stabilization	desmosome|integral to membrane|membrane fraction	calcium ion binding|gamma-catenin binding			ovary(2)	2			OV - Ovarian serous cystadenocarcinoma(10;0.125)											0.264957	82.372075	88.214121	31	86	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	28602406	28602406	4951	18	G	T	T	T	451	35	DSC3	2	2
DSG3	1830	broad.mit.edu	37	18	29036401	29036401	+	Splice_Site_SNP	SNP	A	T	T			TCGA-17-Z017-01	TCGA-17-Z017-01										Phase_I	Unspecified				Illumina GAIIx	g.chr18:29036401A>T	uc002kws.2	+	c.49_splice	c.e2-2	p.V17_splice		NM_001944	NP_001935			desmoglein 3 preproprotein						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			OV - Ovarian serous cystadenocarcinoma(10;0.00504)											0.142857	15.260834	22.144156	8	48	KEEP	---	---	---	---	capture		Splice_Site_SNP	SNP	29036401	29036401	4962	18	A	T	T	T	91	7	DSG3	5	3
DLGAP1	9229	broad.mit.edu	37	18	3879466	3879466	+	Missense_Mutation	SNP	C	G	G			TCGA-17-Z017-01	TCGA-17-Z017-01										Phase_I	Unspecified				Illumina GAIIx	g.chr18:3879466C>G	uc002kmf.2	-	c.603G>C	c.(601-603)TGG>TGC	p.W201C	DLGAP1_uc010wyz.1_Missense_Mutation_p.W201C|DLGAP1_uc002kmk.2_Missense_Mutation_p.W201C	NM_004746	NP_004737	O14490	DLGP1_HUMAN	discs large homolog-associated protein 1 isoform	201					synaptic transmission	cell junction|postsynaptic density|postsynaptic membrane				ovary(2)|pancreas(1)|skin(1)	4		Colorectal(8;0.0257)												0.186813	38.115494	46.493525	17	74	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	3879466	3879466	4739	18	C	G	G	G	234	18	DLGAP1	3	3
NETO1	81832	broad.mit.edu	37	18	70417732	70417732	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z017-01	TCGA-17-Z017-01										Phase_I	Unspecified				Illumina GAIIx	g.chr18:70417732C>A	uc002lkw.2	-	c.1106G>T	c.(1105-1107)CGT>CTT	p.R369L	NETO1_uc002lkx.1_Missense_Mutation_p.R368L|NETO1_uc002lky.1_Missense_Mutation_p.R369L	NM_138966	NP_620416	Q8TDF5	NETO1_HUMAN	neuropilin- and tolloid-like protein 1 isoform 3	369	Cytoplasmic (Potential).				memory|regulation of long-term neuronal synaptic plasticity|visual learning	cell junction|excitatory synapse|extracellular region|integral to membrane|postsynaptic density|postsynaptic membrane	receptor activity			ovary(2)	2		Esophageal squamous(42;0.129)		READ - Rectum adenocarcinoma(1;0.0487)										0.27027	115.15265	122.18689	40	108	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	70417732	70417732	10738	18	C	A	A	A	247	19	NETO1	1	1
KIAA0802	23255	broad.mit.edu	37	18	8824940	8824940	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z017-01	TCGA-17-Z017-01										Phase_I	Unspecified				Illumina GAIIx	g.chr18:8824940G>T	uc002knr.2	+	c.3432G>T	c.(3430-3432)GAG>GAT	p.E1144D	KIAA0802_uc002knq.2_Missense_Mutation_p.E1103D|KIAA0802_uc002kns.2_Missense_Mutation_p.E484D	NM_015210	NP_056025	Q9Y4B5	K0802_HUMAN	hypothetical protein LOC23255	1454										ovary(6)|central_nervous_system(1)	7										468				0.173077	16.445663	21.693802	9	43	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	8824940	8824940	8501	18	G	T	T	T	451	35	KIAA0802	2	2
ATP4A	495	broad.mit.edu	37	19	36050049	36050049	+	Silent	SNP	G	A	A			TCGA-17-Z017-01	TCGA-17-Z017-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:36050049G>A	uc002oal.1	-	c.1101C>T	c.(1099-1101)TGC>TGT	p.C367C	ATP4A_uc010eee.1_5'Flank	NM_000704	NP_000695	P20648	ATP4A_HUMAN	hydrogen/potassium-exchanging ATPase 4A	367	Cytoplasmic (Potential).				ATP biosynthetic process|ATP hydrolysis coupled proton transport	integral to plasma membrane	ATP binding|hydrogen:potassium-exchanging ATPase activity|magnesium ion binding				0	all_lung(56;1.05e-07)|Lung NSC(56;1.63e-07)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0724)		Esomeprazole(DB00736)|Lansoprazole(DB00448)|Omeprazole(DB00338)|Pantoprazole(DB00213)|Rabeprazole(DB01129)|Trifluoperazine(DB00831)									0.116118	71.602453	155.230432	67	510	KEEP	---	---	---	---	capture		Silent	SNP	36050049	36050049	1164	19	G	A	A	A	490	38	ATP4A	1	1
LGALS13	29124	broad.mit.edu	37	19	40095876	40095876	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z017-01	TCGA-17-Z017-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:40095876G>T	uc002omb.2	+	c.151G>T	c.(151-153)GCC>TCC	p.A51S		NM_013268	NP_037400	Q9UHV8	PP13_HUMAN	galectin-13	51	Galectin.				lipid catabolic process|phospholipid metabolic process		lysophospholipase activity|sugar binding			ovary(1)	1	all_cancers(60;1.77e-05)|all_lung(34;5.38e-08)|Lung NSC(34;6.37e-08)|Ovarian(47;0.116)		Epithelial(26;3.28e-26)|OV - Ovarian serous cystadenocarcinoma(5;7.31e-25)|all cancers(26;1.15e-23)|LUSC - Lung squamous cell carcinoma(53;0.00281)											0.195122	33.579973	40.667701	16	66	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	40095876	40095876	9065	19	G	T	T	T	598	46	LGALS13	2	2
PSG6	5675	broad.mit.edu	37	19	43421938	43421938	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z017-01	TCGA-17-Z017-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:43421938G>T	uc002ovj.1	-	c.7C>A	c.(7-9)CCC>ACC	p.P3T	PSG3_uc002ouf.2_Intron|PSG11_uc002ouw.2_Intron|PSG7_uc002ous.1_Intron|PSG7_uc002out.1_Intron|PSG10_uc002ouv.1_Intron|PSG6_uc002ovh.1_Intron|PSG6_uc002ovi.2_Intron|PSG6_uc010xwk.1_Intron|PSG11_uc002ovk.1_Intron|PSG6_uc002ovf.1_Missense_Mutation_p.P3T|PSG6_uc002ovg.1_Missense_Mutation_p.P3T	NM_002782	NP_002773	Q00889	PSG6_HUMAN	pregnancy specific beta-1-glycoprotein 6 isoform	3					female pregnancy	extracellular region				ovary(1)	1		Prostate(69;0.00899)												0.243243	67.62898	74.26349	27	84	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	43421938	43421938	13112	19	G	T	T	T	572	44	PSG6	2	2
CRX	1406	broad.mit.edu	37	19	48343114	48343114	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z017-01	TCGA-17-Z017-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:48343114G>T	uc002phq.3	+	c.790G>T	c.(790-792)GTG>TTG	p.V264L		NM_000554	NP_000545	O43186	CRX_HUMAN	cone-rod homeobox protein	264					organ morphogenesis|response to stimulus|visual perception		sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			breast(1)|central_nervous_system(1)	2		all_cancers(25;2.76e-09)|all_epithelial(76;7.01e-07)|all_lung(116;2.48e-06)|Lung NSC(112;5.15e-06)|Ovarian(192;0.0139)|all_neural(266;0.0146)|Breast(70;0.133)		OV - Ovarian serous cystadenocarcinoma(262;0.000266)|all cancers(93;0.000788)|Epithelial(262;0.0226)|GBM - Glioblastoma multiforme(486;0.0521)		Pancreas(57;461 1196 22201 40716 47188)								0.172566	83.323031	106.183542	39	187	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	48343114	48343114	4041	19	G	T	T	T	520	40	CRX	1	1
EMP3	2014	broad.mit.edu	37	19	48830831	48830831	+	Silent	SNP	G	T	T			TCGA-17-Z017-01	TCGA-17-Z017-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:48830831G>T	uc002piv.2	+	c.132G>T	c.(130-132)ACG>ACT	p.T44T		NM_001425	NP_001416	P54852	EMP3_HUMAN	epithelial membrane protein 3	44					cell growth|negative regulation of cell proliferation	integral to membrane					0		all_epithelial(76;6.08e-07)|all_lung(116;5.76e-06)|Lung NSC(112;1.18e-05)|all_neural(266;0.00989)|Prostate(7;0.0143)|Ovarian(192;0.0261)|Breast(70;0.203)		OV - Ovarian serous cystadenocarcinoma(262;0.000138)|all cancers(93;0.00017)|Epithelial(262;0.0138)|GBM - Glioblastoma multiforme(486;0.0146)										0.111111	3.50662	7.542319	3	24	KEEP	---	---	---	---	capture		Silent	SNP	48830831	48830831	5296	19	G	T	T	T	509	40	EMP3	1	1
SIGLEC10	89790	broad.mit.edu	37	19	51918646	51918646	+	Silent	SNP	G	T	T			TCGA-17-Z017-01	TCGA-17-Z017-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:51918646G>T	uc002pwo.2	-	c.1119C>A	c.(1117-1119)GGC>GGA	p.G373G	SIGLEC10_uc002pwp.2_Silent_p.G315G|SIGLEC10_uc002pwq.2_Silent_p.G315G|SIGLEC10_uc002pwr.2_Silent_p.G373G|SIGLEC10_uc010ycy.1_Silent_p.G283G|SIGLEC10_uc010ycz.1_Silent_p.G325G|SIGLEC10_uc010eow.2_Silent_p.G185G|SIGLEC10_uc002pws.1_Silent_p.G209G	NM_033130	NP_149121	Q96LC7	SIG10_HUMAN	sialic acid binding Ig-like lectin 10 precursor	373	Ig-like C2-type 3.|Extracellular (Potential).				cell adhesion	extracellular region|integral to membrane|plasma membrane	sugar binding				0		all_neural(266;0.0199)		GBM - Glioblastoma multiforme(134;0.000668)|OV - Ovarian serous cystadenocarcinoma(262;0.0101)										0.134615	8.891972	15.623923	7	45	KEEP	---	---	---	---	capture		Silent	SNP	51918646	51918646	14801	19	G	T	T	T	535	42	SIGLEC10	2	2
PRKCG	5582	broad.mit.edu	37	19	54401312	54401312	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z017-01	TCGA-17-Z017-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:54401312C>A	uc010yeg.1	+	c.1039C>A	c.(1039-1041)CAC>AAC	p.H347N	PRKCG_uc010yef.1_Nonsense_Mutation_p.C317*|PRKCG_uc002qcq.1_Missense_Mutation_p.H347N|PRKCG_uc010yeh.1_Missense_Mutation_p.H234N	NM_002739	NP_002730	P05129	KPCG_HUMAN	protein kinase C, gamma	347					activation of phospholipase C activity|cell death|intracellular signal transduction|negative regulation of protein catabolic process|negative regulation of protein ubiquitination|nerve growth factor receptor signaling pathway|platelet activation|positive regulation of mismatch repair|protein phosphorylation|synaptic transmission	cytosol	ATP binding|protein kinase C activity|zinc ion binding			lung(4)|ovary(2)|pancreas(2)|large_intestine(1)	9	all_cancers(19;0.0462)|all_epithelial(19;0.0258)|all_lung(19;0.185)|Ovarian(34;0.19)|Lung NSC(19;0.218)			GBM - Glioblastoma multiforme(134;0.0521)						505				0.137931	6.579336	10.256742	4	25	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	54401312	54401312	12955	19	C	A	A	A	325	25	PRKCG	2	2
LAIR1	3903	broad.mit.edu	37	19	54868136	54868136	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z017-01	TCGA-17-Z017-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:54868136G>A	uc002qfk.1	-	c.547C>T	c.(547-549)CTC>TTC	p.L183F	LAIR1_uc002qfl.1_Missense_Mutation_p.L166F|LAIR1_uc002qfm.1_Missense_Mutation_p.L182F|LAIR1_uc002qfn.1_Missense_Mutation_p.L165F|LAIR1_uc010yex.1_Missense_Mutation_p.L176F|LAIR1_uc002qfo.2_Missense_Mutation_p.L165F	NM_002287	NP_002278	Q6GTX8	LAIR1_HUMAN	leukocyte-associated immunoglobulin-like	183	Helical; (Potential).					integral to membrane|plasma membrane	protein binding|receptor activity			ovary(4)	4	Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.0573)										0.20339	29.663368	34.486257	12	47	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	54868136	54868136	8925	19	G	A	A	A	455	35	LAIR1	2	2
LILRA2	11027	broad.mit.edu	37	19	55085904	55085904	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z017-01	TCGA-17-Z017-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:55085904G>T	uc002qgg.3	+	c.207G>T	c.(205-207)TGG>TGT	p.W69C	LILRA2_uc010ern.2_Missense_Mutation_p.W69C|LILRA2_uc002qgf.2_Missense_Mutation_p.W69C|LILRA2_uc010yfe.1_Missense_Mutation_p.W69C|LILRA2_uc010yff.1_Missense_Mutation_p.W57C|LILRA2_uc010ero.2_Missense_Mutation_p.W57C|LILRA2_uc010yfg.1_Missense_Mutation_p.W69C	NM_001130917	NP_001124389	Q8N149	LIRA2_HUMAN	leukocyte immunoglobulin-like receptor,	69	Extracellular (Potential).|Ig-like C2-type 1.				defense response	integral to membrane	antigen binding|receptor activity			ovary(1)	1				GBM - Glioblastoma multiforme(193;0.0963)										0.184211	27.308804	34.41757	14	62	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	55085904	55085904	9111	19	G	T	T	T	559	43	LILRA2	2	2
ZSCAN5B	342933	broad.mit.edu	37	19	56701625	56701625	+	Silent	SNP	C	G	G			TCGA-17-Z017-01	TCGA-17-Z017-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:56701625C>G	uc010ygh.1	-	c.1059G>C	c.(1057-1059)CCG>CCC	p.P353P		NM_001080456	NP_001073925	A6NJL1	ZSA5B_HUMAN	zinc finger and SCAN domain containing 5B	353					regulation of transcription, DNA-dependent|viral reproduction	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)	1														0.156522	36.725442	49.634127	18	97	KEEP	---	---	---	---	capture		Silent	SNP	56701625	56701625	18843	19	C	G	G	G	340	27	ZSCAN5B	3	3
ZSCAN5B	342933	broad.mit.edu	37	19	56703226	56703226	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z017-01	TCGA-17-Z017-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:56703226C>A	uc010ygh.1	-	c.581G>T	c.(580-582)AGG>ATG	p.R194M		NM_001080456	NP_001073925	A6NJL1	ZSA5B_HUMAN	zinc finger and SCAN domain containing 5B	194					regulation of transcription, DNA-dependent|viral reproduction	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)	1														0.102041	0.400168	8.276127	5	44	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	56703226	56703226	18843	19	C	A	A	A	312	24	ZSCAN5B	2	2
ZSCAN1	284312	broad.mit.edu	37	19	58551817	58551817	+	Splice_Site_SNP	SNP	G	C	C			TCGA-17-Z017-01	TCGA-17-Z017-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:58551817G>C	uc002qrc.1	+	c.371_splice	c.e4-1	p.V124_splice		NM_182572	NP_872378			zinc finger and SCAN domain containing 1						regulation of transcription, DNA-dependent|viral reproduction	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)	1		Colorectal(82;5.46e-05)|all_neural(62;0.0182)|Breast(46;0.0389)|Ovarian(87;0.0443)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0152)										0.113636	6.441598	12.921751	5	39	KEEP	---	---	---	---	capture		Splice_Site_SNP	SNP	58551817	58551817	18830	19	G	C	C	C	468	36	ZSCAN1	5	3
TRAPPC5	126003	broad.mit.edu	37	19	7747434	7747434	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z017-01	TCGA-17-Z017-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:7747434G>T	uc002mhi.1	+	c.295G>T	c.(295-297)GGC>TGC	p.G99C	TRAPPC5_uc002mhj.1_Missense_Mutation_p.G99C|TRAPPC5_uc002mhk.1_Missense_Mutation_p.G99C	NM_001042462	NP_001035927	Q8IUR0	TPPC5_HUMAN	trafficking protein particle complex 5	99					vesicle-mediated transport	endoplasmic reticulum	guanylate cyclase activity|heme binding				0														0.346154	27.468991	28.011462	9	17	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	7747434	7747434	17006	19	G	T	T	T	507	39	TRAPPC5	1	1
KCNA2	3737	broad.mit.edu	37	1	111146839	111146839	+	Missense_Mutation	SNP	C	G	G			TCGA-17-Z017-01	TCGA-17-Z017-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:111146839C>G	uc001dzu.2	-	c.566G>C	c.(565-567)CGG>CCG	p.R189P	KCNA2_uc009wfv.1_Missense_Mutation_p.R189P|KCNA2_uc009wfw.2_Missense_Mutation_p.R189P	NM_004974	NP_004965	P16389	KCNA2_HUMAN	potassium voltage-gated channel, shaker-related	189						juxtaparanode region of axon|voltage-gated potassium channel complex	delayed rectifier potassium channel activity			ovary(1)	1		all_cancers(81;5.55e-06)|all_epithelial(167;1.87e-05)|all_lung(203;0.000199)|Lung NSC(277;0.000398)		Colorectal(144;0.00878)|Lung(183;0.0234)|all cancers(265;0.0492)|Epithelial(280;0.0529)|COAD - Colon adenocarcinoma(174;0.131)|LUSC - Lung squamous cell carcinoma(189;0.133)|READ - Rectum adenocarcinoma(129;0.191)		Pancreas(18;568 735 10587 23710 36357)								0.272727	57.675564	61.766629	24	64	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	111146839	111146839	8308	1	C	G	G	G	299	23	KCNA2	3	3
MAGI3	260425	broad.mit.edu	37	1	114226575	114226575	+	Nonsense_Mutation	SNP	G	A	A			TCGA-17-Z017-01	TCGA-17-Z017-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:114226575G>A	uc001edk.2	+	c.4385G>A	c.(4384-4386)TGG>TAG	p.W1462*	MAGI3_uc001edi.3_3'UTR|MAGI3_uc010owm.1_3'UTR|MAGI3_uc001edj.2_3'UTR|MAGI3_uc009wgo.2_Non-coding_Transcript	NM_001142782	NP_001136254	Q5TCQ9	MAGI3_HUMAN	membrane-associated guanylate kinase-related  3	1487					apoptosis|interspecies interaction between organisms|intracellular signal transduction	nucleus|tight junction	ATP binding|guanylate kinase activity|protein binding			ovary(2)|central_nervous_system(1)	3	Lung SC(450;0.184)	all_cancers(81;2.34e-09)|all_epithelial(167;7.41e-09)|all_lung(203;7.13e-06)|Lung NSC(69;1.2e-05)		Lung(183;0.0234)|Colorectal(144;0.0686)|all cancers(265;0.0792)|Epithelial(280;0.0866)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)										0.162791	13.396505	18.045437	7	36	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	114226575	114226575	9575	1	G	A	A	A	611	47	MAGI3	5	2
TRIM33	51592	broad.mit.edu	37	1	114952806	114952807	+	Missense_Mutation	DNP	CT	AA	AA			TCGA-17-Z017-01	TCGA-17-Z017-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:114952806_114952807CT>AA	uc001eew.2	-	c.2193_2194AG>TT	c.(2191-2196)TCAGGT>TCTTGT	p.G732C	TRIM33_uc010owr.1_Missense_Mutation_p.G346C|TRIM33_uc010ows.1_Missense_Mutation_p.G364C|TRIM33_uc001eex.2_Missense_Mutation_p.G732C	NM_015906	NP_056990	Q9UPN9	TRI33_HUMAN	tripartite motif-containing 33 protein isoform	732					negative regulation of BMP signaling pathway|negative regulation of transcription, DNA-dependent|protein ubiquitination|regulation of transforming growth factor beta receptor signaling pathway|transcription, DNA-dependent	nucleus	co-SMAD binding|DNA binding|ligase activity|R-SMAD binding|zinc ion binding			central_nervous_system(3)|lung(2)|large_intestine(1)|breast(1)|skin(1)|ovary(1)	9	all_epithelial(7;0.000132)|all_lung(7;0.00106)|Lung SC(450;0.184)	all_cancers(81;3.03e-08)|all_epithelial(167;3.24e-08)|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)						377				0.148148	27.239682	40.067002	16	92	KEEP	---	---	---	---	capture		Missense_Mutation	DNP	114952806	114952807	17051	1	CT	AA	AA	AA	312	24	TRIM33	2	2
NHLH2	4808	broad.mit.edu	37	1	116380682	116380682	+	Silent	SNP	C	A	A			TCGA-17-Z017-01	TCGA-17-Z017-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:116380682C>A	uc009wgz.2	-	c.312G>T	c.(310-312)CTG>CTT	p.L104L	NHLH2_uc001efy.2_Silent_p.L104L	NM_001111061	NP_001104531	Q02577	HEN2_HUMAN	nescient helix loop helix 2	104	Helix-loop-helix motif.				cell differentiation|central nervous system development|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|transcription regulator activity				0	Lung SC(450;0.184)	all_cancers(81;1.75e-06)|all_epithelial(167;1.16e-06)|all_lung(203;9.55e-06)|Lung NSC(69;5.83e-05)		Lung(183;0.0171)|Colorectal(144;0.0686)|LUSC - Lung squamous cell carcinoma(189;0.0903)|all cancers(265;0.108)|COAD - Colon adenocarcinoma(174;0.111)|Epithelial(280;0.12)										0.26087	15.438913	16.629767	6	17	KEEP	---	---	---	---	capture		Silent	SNP	116380682	116380682	10804	1	C	A	A	A	314	25	NHLH2	2	2
MAN1A2	10905	broad.mit.edu	37	1	118039517	118039517	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z017-01	TCGA-17-Z017-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:118039517G>A	uc001ehd.1	+	c.1417G>A	c.(1417-1419)GAT>AAT	p.D473N	MAN1A2_uc009whg.1_Missense_Mutation_p.D263N	NM_006699	NP_006690	O60476	MA1A2_HUMAN	mannosidase, alpha, class 1A, member 2	473	Lumenal (Potential).				N-glycan processing|post-translational protein modification|protein N-linked glycosylation via asparagine	Golgi membrane|integral to membrane|membrane fraction	calcium ion binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity				0	Lung SC(450;0.225)	all_cancers(81;7.9e-06)|all_epithelial(167;7.39e-07)|all_lung(203;2.84e-06)|Lung NSC(69;1.99e-05)		Lung(183;0.0688)|Kidney(133;0.114)|LUSC - Lung squamous cell carcinoma(189;0.223)|KIRC - Kidney renal clear cell carcinoma(1967;0.237)|Colorectal(144;0.243)		Ovarian(33;199 881 8228 13687 31538)								0.237705	71.999389	79.682099	29	93	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	118039517	118039517	9594	1	G	A	A	A	429	33	MAN1A2	2	2
SPAG17	200162	broad.mit.edu	37	1	118565977	118565977	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z017-01	TCGA-17-Z017-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:118565977G>T	uc001ehk.2	-	c.4019C>A	c.(4018-4020)TCT>TAT	p.S1340Y		NM_206996	NP_996879	Q6Q759	SPG17_HUMAN	sperm associated antigen 17	1340						cilium|flagellar axoneme|microtubule				ovary(2)|large_intestine(1)	3	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)										0.134615	19.77375	33.242172	14	90	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	118565977	118565977	15482	1	G	T	T	T	429	33	SPAG17	2	2
FLG	2312	broad.mit.edu	37	1	152285700	152285700	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z017-01	TCGA-17-Z017-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:152285700C>A	uc001ezu.1	-	c.1662G>T	c.(1660-1662)AGG>AGT	p.R554S		NM_002016	NP_002007	P20930	FILA_HUMAN	filaggrin	554	Ser-rich.				keratinocyte differentiation	cytoplasmic membrane-bounded vesicle|intermediate filament	calcium ion binding|structural molecule activity			ovary(9)	9	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)											0.202703	99.553836	117.782155	45	177	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	152285700	152285700	6160	1	C	A	A	A	233	18	FLG	2	2
IQGAP3	128239	broad.mit.edu	37	1	156503601	156503601	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z017-01	TCGA-17-Z017-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:156503601C>A	uc001fpf.2	-	c.3940G>T	c.(3940-3942)GAT>TAT	p.D1314Y		NM_178229	NP_839943	Q86VI3	IQGA3_HUMAN	IQ motif containing GTPase activating protein 3	1314					small GTPase mediated signal transduction	intracellular	calmodulin binding|Ras GTPase activator activity			ovary(5)	5	all_hematologic(923;0.088)|Hepatocellular(266;0.158)													0.125	6.113524	12.714336	6	42	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	156503601	156503601	8119	1	C	A	A	A	390	30	IQGAP3	2	2
OR6K2	81448	broad.mit.edu	37	1	158669686	158669686	+	Missense_Mutation	SNP	A	T	T			TCGA-17-Z017-01	TCGA-17-Z017-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:158669686A>T	uc001fsu.1	-	c.757T>A	c.(757-759)TTT>ATT	p.F253I		NM_001005279	NP_001005279	Q8NGY2	OR6K2_HUMAN	olfactory receptor, family 6, subfamily K,	253	Helical; Name=6; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			pancreas(1)	1	all_hematologic(112;0.0378)													0.154472	33.045912	47.083961	19	104	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	158669686	158669686	11612	1	A	T	T	T	39	3	OR6K2	3	3
F11R	50848	broad.mit.edu	37	1	160970066	160970066	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z017-01	TCGA-17-Z017-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:160970066G>A	uc010pjw.1	-	c.473C>T	c.(472-474)TCA>TTA	p.S158L	F11R_uc010pjv.1_Missense_Mutation_p.S105L|F11R_uc009wtt.2_Missense_Mutation_p.S154L|F11R_uc001fxe.3_Missense_Mutation_p.S154L|F11R_uc009wtu.2_Missense_Mutation_p.S154L|F11R_uc001fxf.3_Missense_Mutation_p.S154L	NM_016946	NP_058642	Q9Y624	JAM1_HUMAN	F11 receptor precursor	154	Ig-like V-type 2.|Extracellular (Potential).				blood coagulation|inflammatory response|interspecies interaction between organisms|leukocyte migration|tight junction assembly	integral to membrane|tight junction				ovary(2)	2	all_cancers(52;6.73e-18)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.00207)											0.136364	13.727126	22.180257	9	57	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	160970066	160970066	5532	1	G	A	A	A	585	45	F11R	2	2
DUSP27	92235	broad.mit.edu	37	1	167096156	167096156	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z017-01	TCGA-17-Z017-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:167096156C>A	uc001geb.1	+	c.1788C>A	c.(1786-1788)CAC>CAA	p.H596Q		NM_001080426	NP_001073895	Q5VZP5	DUS27_HUMAN	dual specificity phosphatase 27	596					protein dephosphorylation		protein tyrosine/serine/threonine phosphatase activity			ovary(3)	3														0.229167	26.702545	29.929556	11	37	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	167096156	167096156	5009	1	C	A	A	A	233	18	DUSP27	2	2
PAPPA2	60676	broad.mit.edu	37	1	176526298	176526298	+	Silent	SNP	T	A	A			TCGA-17-Z017-01	TCGA-17-Z017-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:176526298T>A	uc001gkz.2	+	c.840T>A	c.(838-840)GCT>GCA	p.A280A	PAPPA2_uc001gky.1_Silent_p.A280A|PAPPA2_uc009www.2_Non-coding_Transcript	NM_020318	NP_064714	Q9BXP8	PAPP2_HUMAN	pappalysin 2 isoform 1	280					cell differentiation|proteolysis|regulation of cell growth	extracellular region|intracellular|membrane	metalloendopeptidase activity|zinc ion binding			ovary(7)|central_nervous_system(5)|lung(1)|breast(1)	14														0.17284	31.416746	39.591267	14	67	KEEP	---	---	---	---	capture		Silent	SNP	176526298	176526298	11850	1	T	A	A	A	704	55	PAPPA2	3	3
TDRD5	163589	broad.mit.edu	37	1	179631373	179631373	+	Silent	SNP	C	T	T			TCGA-17-Z017-01	TCGA-17-Z017-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:179631373C>T	uc010pnp.1	+	c.2457C>T	c.(2455-2457)AGC>AGT	p.S819S	TDRD5_uc001gnf.1_Silent_p.S765S|TDRD5_uc001gnh.1_Silent_p.S320S	NM_173533	NP_775804	Q8NAT2	TDRD5_HUMAN	tudor domain containing 5	810					DNA methylation involved in gamete generation|P granule organization|spermatid development	chromatoid body|pi-body	nucleic acid binding			ovary(2)|central_nervous_system(1)|skin(1)	4														0.193548	25.862635	31.297846	12	50	KEEP	---	---	---	---	capture		Silent	SNP	179631373	179631373	16260	1	C	T	T	T	337	26	TDRD5	2	2
IGSF21	84966	broad.mit.edu	37	1	18692124	18692124	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z017-01	TCGA-17-Z017-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:18692124G>T	uc001bau.1	+	c.948G>T	c.(946-948)GAG>GAT	p.E316D	IGSF21_uc001bav.1_Missense_Mutation_p.E137D	NM_032880	NP_116269	Q96ID5	IGS21_HUMAN	immunoglobin superfamily, member 21 precursor	316						extracellular region				ovary(2)|large_intestine(1)	3		Colorectal(325;0.000147)|Renal(390;0.00145)|all_lung(284;0.00366)|Lung NSC(340;0.00376)|Breast(348;0.00387)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0439)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0121)|BRCA - Breast invasive adenocarcinoma(304;5.52e-05)|Kidney(64;0.00103)|KIRC - Kidney renal clear cell carcinoma(64;0.0102)|STAD - Stomach adenocarcinoma(196;0.0118)|READ - Rectum adenocarcinoma(331;0.157)										0.204918	55.604891	65.464019	25	97	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	18692124	18692124	7900	1	G	T	T	T	451	35	IGSF21	2	2
AKR7A2	8574	broad.mit.edu	37	1	19633560	19633560	+	Missense_Mutation	SNP	T	C	C			TCGA-17-Z017-01	TCGA-17-Z017-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:19633560T>C	uc001bbw.2	-	c.724A>G	c.(724-726)AAG>GAG	p.K242E	AKR7A2_uc001bbx.2_Missense_Mutation_p.K207E	NM_003689	NP_003680	O43488	ARK72_HUMAN	aldo-keto reductase family 7, member A2	242					carbohydrate metabolic process|cellular aldehyde metabolic process|oxidation-reduction process	Golgi apparatus	alditol:NADP+ 1-oxidoreductase activity|electron carrier activity			central_nervous_system(1)	1		Colorectal(325;3.46e-05)|Renal(390;0.000147)|all_lung(284;0.000321)|Lung NSC(340;0.000398)|Breast(348;0.00049)|Ovarian(437;0.00764)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00461)|BRCA - Breast invasive adenocarcinoma(304;1.83e-05)|Kidney(64;0.000167)|GBM - Glioblastoma multiforme(114;0.00115)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)										0.261538	36.043522	39.391855	17	48	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	19633560	19633560	478	1	T	C	C	C	819	63	AKR7A2	4	4
KIF21B	23046	broad.mit.edu	37	1	200956012	200956012	+	Missense_Mutation	SNP	G	T	T	rs79881792		TCGA-17-Z017-01	TCGA-17-Z017-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:200956012G>T	uc001gvs.1	-	c.3649C>A	c.(3649-3651)CTG>ATG	p.L1217M	KIF21B_uc001gvr.1_Missense_Mutation_p.L1217M|KIF21B_uc009wzl.1_Missense_Mutation_p.L1217M|KIF21B_uc010ppn.1_Missense_Mutation_p.L1217M	NM_017596	NP_060066	O75037	KI21B_HUMAN	kinesin family member 21B	1217					microtubule-based movement	cytoplasm|microtubule	ATP binding|microtubule motor activity			ovary(3)	3														0.157895	5.212388	7.333337	3	16	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	200956012	200956012	8600	1	G	T	T	T	438	34	KIF21B	2	2
TNNT2	7139	broad.mit.edu	37	1	201335967	201335967	+	Missense_Mutation	SNP	T	C	C			TCGA-17-Z017-01	TCGA-17-Z017-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:201335967T>C	uc001gwf.2	-	c.232A>G	c.(232-234)AGG>GGG	p.R78G	TNNT2_uc001gwg.2_Missense_Mutation_p.R68G|TNNT2_uc001gwh.2_Missense_Mutation_p.R63G|TNNT2_uc001gwi.2_Missense_Mutation_p.R77G|TNNT2_uc009wzr.2_Missense_Mutation_p.R9G|TNNT2_uc001gwj.1_5'Flank|TNNT2_uc009wzs.1_Missense_Mutation_p.R43G|TNNT2_uc001gwk.1_Missense_Mutation_p.R9G|TNNT2_uc009wzt.1_Missense_Mutation_p.R68G|TNNT2_uc001gwl.1_Non-coding_Transcript	NM_000364	NP_000355	P45379	TNNT2_HUMAN	troponin T type 2, cardiac isoform 1	78					ATP catabolic process|muscle filament sliding|negative regulation of ATPase activity|positive regulation of ATPase activity|regulation of heart contraction|response to calcium ion|response to calcium ion|ventricular cardiac muscle tissue morphogenesis	cytosol|troponin complex	actin binding|tropomyosin binding|troponin C binding|troponin I binding				0														0.144444	18.351116	29.27882	13	77	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	201335967	201335967	16872	1	T	C	C	C	713	55	TNNT2	4	4
MAPKAPK2	9261	broad.mit.edu	37	1	206906050	206906050	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z017-01	TCGA-17-Z017-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:206906050C>T	uc001hem.1	+	c.1190C>T	c.(1189-1191)GCT>GTT	p.A397V	MAPKAPK2_uc001hel.1_3'UTR	NM_032960	NP_116584	P49137	MAPK2_HUMAN	mitogen-activated protein kinase-activated	397					activation of MAPK activity|hormone biosynthetic process|innate immune response|leukotriene biosynthetic process|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|nerve growth factor receptor signaling pathway|prostanoid metabolic process|Ras protein signal transduction|stress-activated MAPK cascade|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway	cytosol|nucleoplasm	ATP binding|protein binding|protein serine/threonine kinase activity|signal transducer activity				0	Breast(84;0.183)		BRCA - Breast invasive adenocarcinoma(75;0.211)							114				0.283019	41.753761	43.964687	15	38	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	206906050	206906050	9672	1	C	T	T	T	364	28	MAPKAPK2	2	2
CD34	947	broad.mit.edu	37	1	208072370	208072370	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z017-01	TCGA-17-Z017-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:208072370G>A	uc001hgw.1	-	c.464C>T	c.(463-465)ACA>ATA	p.T155I	CD34_uc001hgx.1_Missense_Mutation_p.T155I|CD34_uc010psj.1_Intron	NM_001025109	NP_001020280	P28906	CD34_HUMAN	CD34 antigen isoform a	155	Extracellular (Potential).				cell-cell adhesion|leukocyte migration|regulation of immune response	external side of plasma membrane|integral to membrane	carbohydrate binding			ovary(1)	1														0.194332	98.648265	120.186348	48	199	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	208072370	208072370	3134	1	G	A	A	A	624	48	CD34	2	2
KCNH1	3756	broad.mit.edu	37	1	211263912	211263912	+	Nonsense_Mutation	SNP	G	T	T			TCGA-17-Z017-01	TCGA-17-Z017-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:211263912G>T	uc001hib.2	-	c.431C>A	c.(430-432)TCA>TAA	p.S144*	KCNH1_uc001hic.2_Nonsense_Mutation_p.S144*	NM_172362	NP_758872	O95259	KCNH1_HUMAN	potassium voltage-gated channel, subfamily H,	144	PAC.|Cytoplasmic (Potential).				myoblast fusion|regulation of transcription, DNA-dependent	voltage-gated potassium channel complex	calmodulin binding|delayed rectifier potassium channel activity|two-component sensor activity			ovary(4)|central_nervous_system(1)	5				OV - Ovarian serous cystadenocarcinoma(81;0.0109)|all cancers(67;0.141)|Epithelial(68;0.185)										0.181818	39.717962	50.203906	20	90	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	211263912	211263912	8336	1	G	T	T	T	585	45	KCNH1	5	2
USH2A	7399	broad.mit.edu	37	1	216256892	216256892	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z017-01	TCGA-17-Z017-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:216256892C>A	uc001hku.1	-	c.5204G>T	c.(5203-5205)GGA>GTA	p.G1735V		NM_206933	NP_996816	O75445	USH2A_HUMAN	usherin isoform B	1735	Laminin G-like 2.|Extracellular (Potential).				maintenance of organ identity|photoreceptor cell maintenance|response to stimulus|sensory perception of sound	basement membrane|cytoplasm|integral to membrane|stereocilium membrane	collagen binding			ovary(20)|kidney(1)|central_nervous_system(1)	22				OV - Ovarian serous cystadenocarcinoma(81;0.0547)|all cancers(67;0.0875)										0.204969	70.43433	83.39984	33	128	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	216256892	216256892	17598	1	C	A	A	A	390	30	USH2A	2	2
KIAA1383	54627	broad.mit.edu	37	1	232942878	232942878	+	Missense_Mutation	SNP	G	C	C			TCGA-17-Z017-01	TCGA-17-Z017-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:232942878G>C	uc001hvh.2	+	c.2109G>C	c.(2107-2109)AAG>AAC	p.K703N		NM_019090	NP_061963	Q9P2G4	K1383_HUMAN	hypothetical protein LOC54627	561										ovary(1)	1		all_cancers(173;0.00528)|Prostate(94;0.122)|all_epithelial(177;0.169)												0.461538	20.749179	20.765896	6	7	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	232942878	232942878	8537	1	G	C	C	C	464	36	KIAA1383	3	3
RYR2	6262	broad.mit.edu	37	1	237586495	237586495	+	Missense_Mutation	SNP	G	C	C			TCGA-17-Z017-01	TCGA-17-Z017-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:237586495G>C	uc001hyl.1	+	c.952G>C	c.(952-954)GAC>CAC	p.D318H		NM_001035	NP_001026	Q92736	RYR2_HUMAN	cardiac muscle ryanodine receptor	318	Cytoplasmic (By similarity).|MIR 4.				cardiac muscle contraction|detection of calcium ion|induction of apoptosis by ionic changes|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum|response to caffeine|response to hypoxia|response to redox state	calcium channel complex|plasma membrane|plasma membrane enriched fraction|sarcoplasmic reticulum membrane	calcium ion binding|calmodulin binding|identical protein binding|protein kinase A catalytic subunit binding|protein kinase A regulatory subunit binding|receptor activity|ryanodine-sensitive calcium-release channel activity|suramin binding			ovary(17)|large_intestine(6)|central_nervous_system(6)|pancreas(3)|breast(1)	33	Ovarian(103;0.103)	all_cancers(173;0.000368)|Melanoma(53;0.0179)|all_epithelial(177;0.0225)	OV - Ovarian serous cystadenocarcinoma(106;0.00606)											0.197531	39.060583	45.956718	16	65	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	237586495	237586495	14249	1	G	C	C	C	533	41	RYR2	3	3
CEP170	9859	broad.mit.edu	37	1	243362479	243362479	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z017-01	TCGA-17-Z017-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:243362479G>A	uc001hzs.2	-	c.514C>T	c.(514-516)CGT>TGT	p.R172C	CEP170_uc001hzt.2_Missense_Mutation_p.R172C|CEP170_uc001hzu.2_Missense_Mutation_p.R172C	NM_014812	NP_055627	Q5SW79	CE170_HUMAN	centrosomal protein 170kDa isoform alpha	172						centriole|microtubule|spindle				ovary(1)|haematopoietic_and_lymphoid_tissue(1)	2	all_neural(11;0.101)	all_cancers(173;0.003)	all cancers(7;5.81e-06)|GBM - Glioblastoma multiforme(7;0.000443)|OV - Ovarian serous cystadenocarcinoma(106;0.0101)											0.181818	13.865527	16.97642	6	27	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	243362479	243362479	3383	1	G	A	A	A	507	39	CEP170	1	1
OR2T3	343173	broad.mit.edu	37	1	248637525	248637525	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z017-01	TCGA-17-Z017-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:248637525C>A	uc001iel.1	+	c.874C>A	c.(874-876)CCC>ACC	p.P292T		NM_001005495	NP_001005495	Q8NH03	OR2T3_HUMAN	olfactory receptor, family 2, subfamily T,	292	Helical; Name=7; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0	all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0265)											0.112595	47.616242	125.300163	59	465	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	248637525	248637525	11429	1	C	A	A	A	286	22	OR2T3	2	2
SYF2	25949	broad.mit.edu	37	1	25554002	25554002	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z017-01	TCGA-17-Z017-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:25554002C>A	uc001bjt.1	-	c.398G>T	c.(397-399)CGC>CTC	p.R133L	SYF2_uc001bju.1_Missense_Mutation_p.R91L|SYF2_uc010oeo.1_Missense_Mutation_p.R133L	NM_015484	NP_056299	O95926	SYF2_HUMAN	SYF2 homolog, RNA splicing factor isoform 1	133					nuclear mRNA splicing, via spliceosome	catalytic step 2 spliceosome					0		Colorectal(325;3.46e-05)|Lung NSC(340;0.000245)|all_lung(284;0.000335)|Renal(390;0.0007)|Ovarian(437;0.00473)|Breast(348;0.0101)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0936)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0416)|OV - Ovarian serous cystadenocarcinoma(117;1.5e-26)|Colorectal(126;2.54e-08)|COAD - Colon adenocarcinoma(152;9.31e-07)|BRCA - Breast invasive adenocarcinoma(304;0.000455)|STAD - Stomach adenocarcinoma(196;0.000766)|KIRC - Kidney renal clear cell carcinoma(1967;0.00145)|GBM - Glioblastoma multiforme(114;0.00443)|READ - Rectum adenocarcinoma(331;0.0936)|Lung(427;0.201)										0.161017	40.16181	53.053427	19	99	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	25554002	25554002	15958	1	C	A	A	A	351	27	SYF2	1	1
ZDHHC18	84243	broad.mit.edu	37	1	27176877	27176877	+	Silent	SNP	C	G	G			TCGA-17-Z017-01	TCGA-17-Z017-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:27176877C>G	uc001bnb.2	+	c.732C>G	c.(730-732)CTC>CTG	p.L244L	ZDHHC18_uc010ofh.1_Silent_p.L109L	NM_032283	NP_115659	Q9NUE0	ZDH18_HUMAN	zinc finger, DHHC-type containing 18	244	Helical; (Potential).					integral to membrane	zinc ion binding				0		all_cancers(24;5.82e-22)|all_epithelial(13;9.91e-20)|Colorectal(325;0.000147)|Breast(348;0.000706)|all_lung(284;0.00122)|Lung NSC(340;0.00128)|Renal(390;0.00211)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0707)|all_neural(195;0.0966)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|all cancers(4;5.71e-53)|Epithelial(14;4.73e-52)|OV - Ovarian serous cystadenocarcinoma(117;1.53e-29)|Colorectal(126;1.9e-09)|COAD - Colon adenocarcinoma(152;4.2e-07)|BRCA - Breast invasive adenocarcinoma(304;0.000548)|STAD - Stomach adenocarcinoma(196;0.00065)|KIRC - Kidney renal clear cell carcinoma(1967;0.000779)|GBM - Glioblastoma multiforme(114;0.0265)|READ - Rectum adenocarcinoma(331;0.0455)|Lung(427;0.163)|LUSC - Lung squamous cell carcinoma(448;0.237)										0.108108	5.573606	11.205364	4	33	KEEP	---	---	---	---	capture		Silent	SNP	27176877	27176877	18196	1	C	G	G	G	405	32	ZDHHC18	3	3
CSMD2	114784	broad.mit.edu	37	1	34383799	34383799	+	Silent	SNP	G	T	T			TCGA-17-Z017-01	TCGA-17-Z017-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:34383799G>T	uc001bxm.1	-	c.816C>A	c.(814-816)ATC>ATA	p.I272I	CSMD2_uc001bxn.1_Silent_p.I232I	NM_052896	NP_443128	Q7Z408	CSMD2_HUMAN	CUB and Sushi multiple domains 2	232	CUB 2.|Extracellular (Potential).					integral to membrane|plasma membrane	protein binding			ovary(5)|pancreas(1)	6		Myeloproliferative disorder(586;0.0294)|all_neural(195;0.249)												0.186441	22.288498	27.725221	11	48	KEEP	---	---	---	---	capture		Silent	SNP	34383799	34383799	4086	1	G	T	T	T	525	41	CSMD2	2	2
THRAP3	9967	broad.mit.edu	37	1	36754665	36754665	+	Missense_Mutation	SNP	C	G	G			TCGA-17-Z017-01	TCGA-17-Z017-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:36754665C>G	uc001cae.3	+	c.1045C>G	c.(1045-1047)CTA>GTA	p.L349V	THRAP3_uc001caf.3_Missense_Mutation_p.L349V|THRAP3_uc001cag.1_Missense_Mutation_p.L349V	NM_005119	NP_005110	Q9Y2W1	TR150_HUMAN	thyroid hormone receptor associated protein 3	349					androgen receptor signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription initiation from RNA polymerase II promoter	mediator complex	ATP binding|ligand-dependent nuclear receptor transcription coactivator activity|receptor activity|RNA polymerase II transcription mediator activity|thyroid hormone receptor binding|transcription activator activity|vitamin D receptor binding			ovary(5)|lung(1)	6		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.164)				Pancreas(129;785 1795 20938 23278 32581)				199				0.137931	21.743408	32.770499	12	75	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	36754665	36754665	16402	1	C	G	G	G	415	32	THRAP3	3	3
IPP	3652	broad.mit.edu	37	1	46179937	46179938	+	Nonsense_Mutation	DNP	TC	CA	CA			TCGA-17-Z017-01	TCGA-17-Z017-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:46179937_46179938TC>CA	uc001cou.2	-	c.1510_1511GA>TG	c.(1510-1512)GAA>TGA	p.E504*	IPP_uc001cos.3_Nonsense_Mutation_p.E504*	NM_005897	NP_005888	Q9Y573	IPP_HUMAN	intracisternal A particle-promoted polypeptide	504	Kelch 5.					actin cytoskeleton|cytoplasm	actin binding			ovary(1)	1	Acute lymphoblastic leukemia(166;0.155)													0.208955	38.420021	43.668114	14	53	KEEP	---	---	---	---	capture		Nonsense_Mutation	DNP	46179937	46179938	8101	1	TC	CA	CA	CA	806	62	IPP	5	4
IL12RB2	3595	broad.mit.edu	37	1	67792502	67792502	+	Missense_Mutation	SNP	A	G	G			TCGA-17-Z017-01	TCGA-17-Z017-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:67792502A>G	uc001ddu.2	+	c.449A>G	c.(448-450)GAC>GGC	p.D150G	IL12RB2_uc010oqi.1_Missense_Mutation_p.D150G|IL12RB2_uc010oqj.1_Missense_Mutation_p.D150G|IL12RB2_uc010oqk.1_Non-coding_Transcript|IL12RB2_uc010oql.1_Missense_Mutation_p.D150G|IL12RB2_uc010oqm.1_Missense_Mutation_p.D150G|IL12RB2_uc010oqn.1_Non-coding_Transcript	NM_001559	NP_001550	Q99665	I12R2_HUMAN	interleukin 12 receptor, beta 2 precursor	150	Extracellular (Potential).|Fibronectin type-III 1.				positive regulation of cell proliferation|positive regulation of interferon-gamma production	integral to plasma membrane	cytokine receptor activity			ovary(2)|central_nervous_system(1)	3														0.142857	9.755978	14.053428	5	30	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	67792502	67792502	7928	1	A	G	G	G	130	10	IL12RB2	4	4
LPHN2	23266	broad.mit.edu	37	1	82436122	82436122	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z017-01	TCGA-17-Z017-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:82436122G>T	uc001dit.3	+	c.2807G>T	c.(2806-2808)AGG>ATG	p.R936M	LPHN2_uc001dis.2_Intron|LPHN2_uc001diu.2_Missense_Mutation_p.R936M|LPHN2_uc001div.2_Missense_Mutation_p.R936M|LPHN2_uc009wcd.2_Missense_Mutation_p.R936M|LPHN2_uc001diw.2_Missense_Mutation_p.R520M|LPHN2_uc009wce.1_Missense_Mutation_p.R22M	NM_012302	NP_036434	O95490	LPHN2_HUMAN	latrophilin 2 precursor	949	Cytoplasmic (Potential).				neuropeptide signaling pathway	integral to membrane|plasma membrane	G-protein coupled receptor activity|latrotoxin receptor activity|sugar binding			ovary(2)|central_nervous_system(1)	3				all cancers(265;0.00142)|Epithelial(280;0.00829)|OV - Ovarian serous cystadenocarcinoma(397;0.077)|STAD - Stomach adenocarcinoma(256;0.248)										0.228571	19.391525	21.749935	8	27	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	82436122	82436122	9289	1	G	T	T	T	455	35	LPHN2	2	2
COL24A1	255631	broad.mit.edu	37	1	86304322	86304322	+	Splice_Site_SNP	SNP	C	T	T			TCGA-17-Z017-01	TCGA-17-Z017-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:86304322C>T	uc001dlj.2	-	c.3628_splice	c.e43-1	p.G1210_splice	COL24A1_uc001dli.2_Splice_Site_SNP_p.G346_splice|COL24A1_uc010osd.1_Splice_Site_SNP_p.G510_splice|COL24A1_uc001dlk.2_Splice_Site_SNP|COL24A1_uc010ose.1_Splice_Site_SNP|COL24A1_uc010osf.1_Splice_Site_SNP	NM_152890	NP_690850			collagen, type XXIV, alpha 1 precursor						cell adhesion	collagen	extracellular matrix structural constituent			ovary(3)|central_nervous_system(1)	4				all cancers(265;0.0627)|Epithelial(280;0.0689)										0.2	92.511839	108.83526	39	156	KEEP	---	---	---	---	capture		Splice_Site_SNP	SNP	86304322	86304322	3821	1	C	T	T	T	312	24	COL24A1	5	2
CLCA4	22802	broad.mit.edu	37	1	87041215	87041215	+	Missense_Mutation	SNP	T	A	A			TCGA-17-Z017-01	TCGA-17-Z017-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:87041215T>A	uc009wcs.2	+	c.1884T>A	c.(1882-1884)AAT>AAA	p.N628K	CLCA4_uc009wct.2_Missense_Mutation_p.N391K|CLCA4_uc009wcu.2_Missense_Mutation_p.N448K	NM_012128	NP_036260	Q14CN2	CLCA4_HUMAN	chloride channel accessory 4	628						apical plasma membrane|extracellular region|integral to plasma membrane	chloride channel activity			ovary(2)	2		Lung NSC(277;0.238)		all cancers(265;0.0202)|Epithelial(280;0.0404)										0.230088	70.094816	77.637722	26	87	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	87041215	87041215	3595	1	T	A	A	A	660	51	CLCA4	3	3
DNMT3B	1789	broad.mit.edu	37	20	31368194	31368194	+	Missense_Mutation	SNP	T	C	C			TCGA-17-Z017-01	TCGA-17-Z017-01										Phase_I	Unspecified				Illumina GAIIx	g.chr20:31368194T>C	uc002wyc.2	+	c.65T>C	c.(64-66)CTC>CCC	p.L22P	DNMT3B_uc010ztx.1_Non-coding_Transcript|DNMT3B_uc010zty.1_Non-coding_Transcript|DNMT3B_uc002wyd.2_Missense_Mutation_p.L22P|DNMT3B_uc002wye.2_Missense_Mutation_p.L22P|DNMT3B_uc010gee.2_Non-coding_Transcript|DNMT3B_uc010gef.2_Non-coding_Transcript|DNMT3B_uc010ztz.1_Missense_Mutation_p.L22P|DNMT3B_uc010zua.1_Missense_Mutation_p.L22P|DNMT3B_uc002wyf.2_Missense_Mutation_p.L34P	NM_006892	NP_008823	Q9UBC3	DNM3B_HUMAN	DNA cytosine-5 methyltransferase 3 beta isoform	22	Interaction with DNMT1 and DNMT3A.				negative regulation of histone H3-K9 methylation|positive regulation of gene expression|positive regulation of histone H3-K4 methylation		protein binding|transcription corepressor activity|zinc ion binding			ovary(2)|lung(1)	3										1211				0.352941	16.744552	17.068885	6	11	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	31368194	31368194	4860	20	T	C	C	C	702	54	DNMT3B	4	4
TP53TG5	27296	broad.mit.edu	37	20	44004176	44004176	+	Missense_Mutation	SNP	T	A	A			TCGA-17-Z017-01	TCGA-17-Z017-01										Phase_I	Unspecified				Illumina GAIIx	g.chr20:44004176T>A	uc002xny.2	-	c.271A>T	c.(271-273)AAT>TAT	p.N91Y	SYS1_uc002xnw.1_3'UTR|SYS1-DBNDD2_uc002xnx.2_Intron	NM_014477	NP_055292	Q9Y2B4	T53G5_HUMAN	TP53-target gene 5 protein	91					intracellular signal transduction|negative regulation of cell growth	cytoplasm|nucleus				central_nervous_system(1)	1														0.254902	35.655028	38.431694	13	38	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	44004176	44004176	16935	20	T	A	A	A	819	63	TP53TG5	3	3
RASSF2	9770	broad.mit.edu	37	20	4771116	4771116	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z017-01	TCGA-17-Z017-01										Phase_I	Unspecified				Illumina GAIIx	g.chr20:4771116C>A	uc002wld.2	-	c.518G>T	c.(517-519)GGC>GTC	p.G173V	RASSF2_uc002wlc.2_Non-coding_Transcript|RASSF2_uc002wle.2_Non-coding_Transcript|RASSF2_uc002wlf.2_Missense_Mutation_p.G173V	NM_170774	NP_739580	P50749	RASF2_HUMAN	Ras association domain family 2	173					cell cycle|signal transduction	nucleus	protein binding	p.G173V(1)		ovary(3)|lung(2)|large_intestine(1)	6						Melanoma(158;1891 3343 50738)								0.423077	31.2175	31.352316	11	15	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	4771116	4771116	13547	20	C	A	A	A	338	26	RASSF2	2	2
DIDO1	11083	broad.mit.edu	37	20	61513366	61513366	+	Silent	SNP	C	A	A			TCGA-17-Z017-01	TCGA-17-Z017-01										Phase_I	Unspecified				Illumina GAIIx	g.chr20:61513366C>A	uc002ydr.1	-	c.3942G>T	c.(3940-3942)CTG>CTT	p.L1314L	DIDO1_uc002yds.1_Silent_p.L1314L	NM_033081	NP_149072	Q9BTC0	DIDO1_HUMAN	death inducer-obliterator 1 isoform c	1314					apoptosis	cytoplasm|nucleus	zinc ion binding			ovary(3)	3	Breast(26;5.68e-08)					Melanoma(25;381 482 3385 5362 7955 17159 17174 40604 47095)								0.5	9.825045	9.825045	3	3	KEEP	---	---	---	---	capture		Silent	SNP	61513366	61513366	4701	20	C	A	A	A	262	21	DIDO1	2	2
KRTAP15-1	254950	broad.mit.edu	37	21	31812895	31812895	+	Missense_Mutation	SNP	T	A	A			TCGA-17-Z017-01	TCGA-17-Z017-01										Phase_I	Unspecified				Illumina GAIIx	g.chr21:31812895T>A	uc002yod.2	+	c.250T>A	c.(250-252)TGC>AGC	p.C84S		NM_181623	NP_853654	Q3LI76	KR151_HUMAN	keratin associated protein 15-1	84						intermediate filament					0														0.320225	162.449005	167.540763	57	121	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	31812895	31812895	8841	21	T	A	A	A	715	55	KRTAP15-1	3	3
GART	2618	broad.mit.edu	37	21	34877985	34877985	+	Missense_Mutation	SNP	T	A	A			TCGA-17-Z017-01	TCGA-17-Z017-01										Phase_I	Unspecified				Illumina GAIIx	g.chr21:34877985T>A	uc002yrx.2	-	c.2608A>T	c.(2608-2610)AAT>TAT	p.N870Y	GART_uc002yrz.2_Missense_Mutation_p.N870Y|GART_uc010gmd.2_Missense_Mutation_p.N532Y|GART_uc002yry.2_Missense_Mutation_p.N870Y	NM_000819	NP_000810	P22102	PUR2_HUMAN	phosphoribosylglycinamide formyltransferase,	870	GART.				'de novo' IMP biosynthetic process|purine base biosynthetic process	cytosol	ATP binding|metal ion binding|methyltransferase activity|phosphoribosylamine-glycine ligase activity|phosphoribosylformylglycinamidine cyclo-ligase activity|phosphoribosylglycinamide formyltransferase activity|protein binding			ovary(1)	1					Pemetrexed(DB00642)									0.263158	10.161391	11.130144	5	14	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	34877985	34877985	6507	21	T	A	A	A	832	64	GART	3	3
TRPM2	7226	broad.mit.edu	37	21	45784063	45784063	+	Silent	SNP	C	G	G			TCGA-17-Z017-01	TCGA-17-Z017-01										Phase_I	Unspecified				Illumina GAIIx	g.chr21:45784063C>G	uc010gpt.1	+	c.321C>G	c.(319-321)ACC>ACG	p.T107T	TRPM2_uc002zet.1_Silent_p.T107T|TRPM2_uc002zeu.1_Silent_p.T107T|TRPM2_uc002zew.1_Silent_p.T107T	NM_003307	NP_003298	O94759	TRPM2_HUMAN	transient receptor potential cation channel,	107	Cytoplasmic (Potential).					integral to plasma membrane	ADP-ribose diphosphatase activity|calcium channel activity|sodium channel activity			ovary(1)|central_nervous_system(1)|pancreas(1)	3														0.25	9.594408	10.502133	4	12	KEEP	---	---	---	---	capture		Silent	SNP	45784063	45784063	17137	21	C	G	G	G	301	24	TRPM2	3	3
NAGA	4668	broad.mit.edu	37	22	42464516	42464516	+	Missense_Mutation	SNP	G	C	C			TCGA-17-Z017-01	TCGA-17-Z017-01										Phase_I	Unspecified				Illumina GAIIx	g.chr22:42464516G>C	uc003bbx.2	-	c.79C>G	c.(79-81)CCC>GCC	p.P27A	NAGA_uc003bby.2_Missense_Mutation_p.P27A|NAGA_uc003bbw.3_Missense_Mutation_p.P27A	NM_000262	NP_000253	P17050	NAGAB_HUMAN	alpha-N-acetylgalactosaminidase precursor	27					glycoside catabolic process|glycosylceramide catabolic process|oligosaccharide metabolic process	lysosome	alpha-galactosidase activity|alpha-N-acetylgalactosaminidase activity|cation binding|protein homodimerization activity			central_nervous_system(1)	1														0.435897	55.370877	55.510286	17	22	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	42464516	42464516	10537	22	G	C	C	C	572	44	NAGA	3	3
PDCL3	79031	broad.mit.edu	37	2	101183005	101183005	+	Missense_Mutation	SNP	A	G	G			TCGA-17-Z017-01	TCGA-17-Z017-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:101183005A>G	uc002tao.2	+	c.47A>G	c.(46-48)AAA>AGA	p.K16R		NM_024065	NP_076970	Q9H2J4	PDCL3_HUMAN	phosducin-like 3	16					apoptosis|interspecies interaction between organisms	cytoplasm	protein binding				0														0.4375	46.645442	46.754373	14	18	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	101183005	101183005	12049	2	A	G	G	G	13	1	PDCL3	4	4
SCN3A	6328	broad.mit.edu	37	2	165971985	165971985	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z017-01	TCGA-17-Z017-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:165971985G>T	uc002ucx.2	-	c.3494C>A	c.(3493-3495)CCG>CAG	p.P1165Q	SCN3A_uc002ucy.2_Missense_Mutation_p.P1116Q|SCN3A_uc002ucz.2_Missense_Mutation_p.P1116Q|SCN3A_uc002uda.1_Missense_Mutation_p.P985Q|SCN3A_uc002udb.1_Missense_Mutation_p.P985Q	NM_006922	NP_008853	Q9NY46	SCN3A_HUMAN	sodium channel, voltage-gated, type III, alpha	1165						voltage-gated sodium channel complex	voltage-gated sodium channel activity			ovary(4)|breast(3)|central_nervous_system(1)	8					Lamotrigine(DB00555)									0.241935	40.709182	44.464344	15	47	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	165971985	165971985	14400	2	G	T	T	T	507	39	SCN3A	1	1
XIRP2	129446	broad.mit.edu	37	2	168103802	168103802	+	Missense_Mutation	SNP	T	C	C			TCGA-17-Z017-01	TCGA-17-Z017-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:168103802T>C	uc002udx.2	+	c.5900T>C	c.(5899-5901)GTT>GCT	p.V1967A	XIRP2_uc010fpn.2_Intron|XIRP2_uc010fpo.2_Intron|XIRP2_uc010fpp.2_Intron|XIRP2_uc002udy.2_Missense_Mutation_p.V1792A|XIRP2_uc010fpq.2_Missense_Mutation_p.V1745A|XIRP2_uc010fpr.2_Intron|XIRP2_uc010fps.1_5'Flank	NM_152381	NP_689594	A4UGR9	XIRP2_HUMAN	xin actin-binding repeat containing 2 isoform 1	1792					actin cytoskeleton organization	cell junction	actin binding			ovary(6)|pancreas(1)|skin(1)	8														0.243902	84.797142	92.142355	30	93	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	168103802	168103802	18011	2	T	C	C	C	780	60	XIRP2	4	4
FN1	2335	broad.mit.edu	37	2	216295507	216295507	+	Nonsense_Mutation	SNP	G	A	A			TCGA-17-Z017-01	TCGA-17-Z017-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:216295507G>A	uc002vfa.2	-	c.616C>T	c.(616-618)CAA>TAA	p.Q206*	FN1_uc002vfb.2_Nonsense_Mutation_p.Q206*|FN1_uc002vfc.2_Nonsense_Mutation_p.Q206*|FN1_uc002vfd.2_Nonsense_Mutation_p.Q206*|FN1_uc002vfe.2_Nonsense_Mutation_p.Q206*|FN1_uc002vff.2_Nonsense_Mutation_p.Q206*|FN1_uc002vfg.2_Nonsense_Mutation_p.Q206*|FN1_uc002vfh.2_Nonsense_Mutation_p.Q206*|FN1_uc002vfi.2_Nonsense_Mutation_p.Q206*|FN1_uc002vfj.2_Nonsense_Mutation_p.Q206*|FN1_uc002vfl.2_Nonsense_Mutation_p.Q206*	NM_212482	NP_997647	P02751	FINC_HUMAN	fibronectin 1 isoform 1 preproprotein	206	Fibrin- and heparin-binding 1.|Fibronectin type-I 4.				acute-phase response|angiogenesis|leukocyte migration|peptide cross-linking|platelet activation|platelet degranulation|regulation of cell shape|substrate adhesion-dependent cell spreading	ER-Golgi intermediate compartment|fibrinogen complex|platelet alpha granule lumen|proteinaceous extracellular matrix	collagen binding|extracellular matrix structural constituent|heparin binding			central_nervous_system(7)|large_intestine(2)|breast(2)|ovary(1)|pancreas(1)	13		Renal(323;0.127)		Epithelial(149;9.59e-07)|all cancers(144;0.000174)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00948)	Alteplase(DB00009)|Anistreplase(DB00029)|Reteplase(DB00015)|Tenecteplase(DB00031)					1374				0.214286	20.750062	23.917793	9	33	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	216295507	216295507	6204	2	G	A	A	A	611	47	FN1	5	2
CAPN10	11132	broad.mit.edu	37	2	241528836	241528836	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z017-01	TCGA-17-Z017-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:241528836G>A	uc002vzk.1	+	c.218G>A	c.(217-219)TGC>TAC	p.C73Y	CAPN10_uc010zoh.1_Missense_Mutation_p.C73Y|CAPN10_uc002vzl.1_Missense_Mutation_p.C73Y|CAPN10_uc002vzm.1_Intron|CAPN10_uc002vzn.1_5'UTR|CAPN10_uc002vzo.1_Non-coding_Transcript|CAPN10_uc010fzg.1_Non-coding_Transcript|CAPN10_uc002vzp.1_Non-coding_Transcript|CAPN10_uc002vzq.1_Missense_Mutation_p.C73Y	NM_023083	NP_075571	Q9HC96	CAN10_HUMAN	calpain 10 isoform a	73	Calpain catalytic.	By similarity.			actin cytoskeleton reorganization|cellular response to insulin stimulus|positive regulation of apoptosis|positive regulation of glucose import|positive regulation of insulin secretion|positive regulation of intracellular transport|proteolysis	cytosol|plasma membrane	calcium-dependent cysteine-type endopeptidase activity|cytoskeletal protein binding|SNARE binding			ovary(3)|large_intestine(2)|lung(1)	6		all_epithelial(40;1.72e-15)|Breast(86;2.14e-05)|Renal(207;0.00183)|Ovarian(221;0.0228)|all_lung(227;0.0294)|all_neural(83;0.0459)|Lung NSC(271;0.094)|all_hematologic(139;0.158)|Melanoma(123;0.16)|Hepatocellular(293;0.244)		Epithelial(32;1.13e-31)|all cancers(36;3.24e-29)|OV - Ovarian serous cystadenocarcinoma(60;2.82e-15)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;5.1e-06)|Lung(119;0.00168)|Colorectal(34;0.00495)|LUSC - Lung squamous cell carcinoma(224;0.00813)|COAD - Colon adenocarcinoma(134;0.032)										0.186047	14.571829	18.547391	8	35	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	241528836	241528836	2740	2	G	A	A	A	598	46	CAPN10	2	2
C2orf78	388960	broad.mit.edu	37	2	74043608	74043608	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z017-01	TCGA-17-Z017-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:74043608G>A	uc002sjr.1	+	c.2258G>A	c.(2257-2259)CGA>CAA	p.R753Q		NM_001080474	NP_001073943	A6NCI8	CB078_HUMAN	hypothetical protein LOC388960	753										ovary(2)	2														0.04	-25.778266	14.087885	7	168	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	74043608	74043608	2285	2	G	A	A	A	481	37	C2orf78	1	1
TMEM131	23505	broad.mit.edu	37	2	98475769	98475769	+	Missense_Mutation	SNP	T	C	C			TCGA-17-Z017-01	TCGA-17-Z017-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:98475769T>C	uc002syh.3	-	c.481A>G	c.(481-483)AGG>GGG	p.R161G	TMEM131_uc010yvg.1_Non-coding_Transcript	NM_015348	NP_056163	Q92545	TM131_HUMAN	RW1 protein	161						integral to membrane				ovary(4)|central_nervous_system(2)	6														0.46	159.643012	159.781942	46	54	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	98475769	98475769	16575	2	T	C	C	C	687	53	TMEM131	4	4
LOC401052	401052	broad.mit.edu	37	3	10049235	10049235	+	Nonsense_Mutation	SNP	G	T	T			TCGA-17-Z017-01	TCGA-17-Z017-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:10049235G>T	uc003bur.1	-	c.150C>A	c.(148-150)TAC>TAA	p.Y50*	CIDEC_uc003bto.2_Intron	NM_001008737	NP_001008737	B3KMQ7	B3KMQ7_HUMAN	hypothetical protein LOC401052	50											0														0.302326	74.017183	77.0177	26	60	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	10049235	10049235	9228	3	G	T	T	T	516	40	LOC401052	5	1
ABI3BP	25890	broad.mit.edu	37	3	100568898	100568898	+	Missense_Mutation	SNP	T	A	A			TCGA-17-Z017-01	TCGA-17-Z017-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:100568898T>A	uc003dun.2	-	c.1366A>T	c.(1366-1368)ACG>TCG	p.T456S	ABI3BP_uc003duo.2_Missense_Mutation_p.T498S	NM_015429	NP_056244	Q7Z7G0	TARSH_HUMAN	ABI gene family, member 3 (NESH) binding protein	456	Pro-rich.					extracellular space				ovary(2)|large_intestine(1)	3														0.1875	12.632351	15.557981	6	26	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	100568898	100568898	92	3	T	A	A	A	741	57	ABI3BP	3	3
DZIP3	9666	broad.mit.edu	37	3	108344739	108344739	+	Silent	SNP	C	A	A			TCGA-17-Z017-01	TCGA-17-Z017-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:108344739C>A	uc003dxd.2	+	c.504C>A	c.(502-504)ATC>ATA	p.I168I	DZIP3_uc003dxf.1_Silent_p.I168I|DZIP3_uc011bhm.1_Intron|DZIP3_uc003dxe.1_Silent_p.I168I	NM_014648	NP_055463	Q86Y13	DZIP3_HUMAN	DAZ interacting protein 3, zinc finger	168					protein polyubiquitination	cytoplasm	polyubiquitin binding|RNA binding|ubiquitin-protein ligase activity|zinc ion binding			ovary(1)|central_nervous_system(1)	2														0.223684	38.131693	43.468988	17	59	KEEP	---	---	---	---	capture		Silent	SNP	108344739	108344739	5051	3	C	A	A	A	382	30	DZIP3	2	2
TRAT1	50852	broad.mit.edu	37	3	108572676	108572676	+	Silent	SNP	C	T	T			TCGA-17-Z017-01	TCGA-17-Z017-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:108572676C>T	uc003dxi.1	+	c.513C>T	c.(511-513)CCC>CCT	p.P171P	TRAT1_uc010hpx.1_Silent_p.P134P	NM_016388	NP_057472	Q6PIZ9	TRAT1_HUMAN	T-cell receptor interacting molecule	171	Cytoplasmic (Potential).				cellular defense response|negative regulation of receptor recycling|negative regulation of transport|positive regulation of calcium-mediated signaling|positive regulation of T cell receptor signaling pathway|T cell receptor signaling pathway	integral to plasma membrane|T cell receptor complex	phosphatidylinositol-4,5-bisphosphate 3-kinase activity|transmembrane receptor protein tyrosine kinase adaptor activity				0														0.284404	88.478283	93.027443	31	78	KEEP	---	---	---	---	capture		Silent	SNP	108572676	108572676	17010	3	C	T	T	T	262	21	TRAT1	2	2
TRPC1	7220	broad.mit.edu	37	3	142499778	142499778	+	Silent	SNP	G	T	T			TCGA-17-Z017-01	TCGA-17-Z017-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:142499778G>T	uc003evc.2	+	c.867G>T	c.(865-867)ACG>ACT	p.T289T	TRPC1_uc003evb.2_Silent_p.T255T	NM_003304	NP_003295	P48995	TRPC1_HUMAN	transient receptor potential cation channel,	289	Cytoplasmic (Potential).				axon guidance|cytosolic calcium ion homeostasis|positive regulation of release of sequestered calcium ion into cytosol|response to calcium ion	integral to plasma membrane	protein binding|store-operated calcium channel activity			ovary(2)	2														0.180328	24.933513	30.759044	11	50	KEEP	---	---	---	---	capture		Silent	SNP	142499778	142499778	17129	3	G	T	T	T	509	40	TRPC1	1	1
CPA3	1359	broad.mit.edu	37	3	148597578	148597578	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z017-01	TCGA-17-Z017-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:148597578G>T	uc003ewm.2	+	c.478G>T	c.(478-480)GGG>TGG	p.G160W		NM_001870	NP_001861	P15088	CBPA3_HUMAN	carboxypeptidase A3 precursor	160					proteolysis	stored secretory granule|transport vesicle	metallocarboxypeptidase activity|zinc ion binding			breast(1)	1			LUSC - Lung squamous cell carcinoma(72;0.0934)|Lung(72;0.115)											0.192982	22.787962	27.808144	11	46	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	148597578	148597578	3929	3	G	T	T	T	611	47	CPA3	2	2
HLTF	6596	broad.mit.edu	37	3	148750077	148750077	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z017-01	TCGA-17-Z017-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:148750077G>A	uc003ewq.1	-	c.2960C>T	c.(2959-2961)ACT>ATT	p.T987I	HLTF_uc003ewr.1_Missense_Mutation_p.T987I|HLTF_uc003ews.1_Missense_Mutation_p.T986I|HLTF_uc010hve.1_Missense_Mutation_p.T986I	NM_139048	NP_620636	Q14527	HLTF_HUMAN	helicase-like transcription factor	987	Helicase C-terminal.|Interaction with SP1 and SP3.				chromatin modification|transcription, DNA-dependent	nucleus	ATP binding|DNA binding|helicase activity|ligase activity|zinc ion binding				0			LUSC - Lung squamous cell carcinoma(72;0.0473)|Lung(72;0.0607)											0.16129	7.938721	11.358482	5	26	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	148750077	148750077	7506	3	G	A	A	A	468	36	HLTF	2	2
RSRC1	51319	broad.mit.edu	37	3	157920997	157920997	+	Nonsense_Mutation	SNP	A	T	T			TCGA-17-Z017-01	TCGA-17-Z017-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:157920997A>T	uc003fbt.2	+	c.457A>T	c.(457-459)AAA>TAA	p.K153*	RSRC1_uc011bou.1_Intron|RSRC1_uc003fbu.1_Nonsense_Mutation_p.K153*|RSRC1_uc003fbv.2_Intron	NM_016625	NP_057709	Q96IZ7	RSRC1_HUMAN	arginine/serine-rich coiled-coil 1	153					nucleocytoplasmic transport	cytoplasm|nuclear speck	protein binding				0			Lung(72;0.00416)|LUSC - Lung squamous cell carcinoma(72;0.00575)											0.311111	36.332705	37.763082	14	31	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	157920997	157920997	14194	3	A	T	T	T	169	13	RSRC1	5	3
PLCL2	23228	broad.mit.edu	37	3	17056386	17056386	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z017-01	TCGA-17-Z017-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:17056386G>A	uc011awc.1	+	c.2977G>A	c.(2977-2979)GTA>ATA	p.V993I	PLCL2_uc011awd.1_Missense_Mutation_p.V875I	NM_001144382	NP_001137854	Q9UPR0	PLCL2_HUMAN	phospholipase C-like 2 isoform 1	1001					intracellular signal transduction|lipid metabolic process	cytoplasm	calcium ion binding|phosphatidylinositol phospholipase C activity|signal transducer activity			ovary(1)|lung(1)	2														0.061947	-8.821498	13.760935	7	106	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	17056386	17056386	12466	3	G	A	A	A	520	40	PLCL2	1	1
HRG	3273	broad.mit.edu	37	3	186395280	186395280	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z017-01	TCGA-17-Z017-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:186395280C>A	uc003fqq.2	+	c.1186C>A	c.(1186-1188)CCC>ACC	p.P396T		NM_000412	NP_000403	P04196	HRG_HUMAN	histidine-rich glycoprotein precursor	396	His/Pro-rich (HRR).				fibrinolysis|platelet activation|platelet degranulation	extracellular region|plasma membrane|platelet alpha granule lumen	cysteine-type endopeptidase inhibitor activity|heparin binding			ovary(1)|central_nervous_system(1)	2	all_cancers(143;6.64e-12)|Ovarian(172;0.0339)		OV - Ovarian serous cystadenocarcinoma(80;5.73e-20)	GBM - Glioblastoma multiforme(93;0.0683)										0.294118	24.736403	26.026591	10	24	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	186395280	186395280	7646	3	C	A	A	A	286	22	HRG	2	2
GOLGA4	2803	broad.mit.edu	37	3	37343688	37343688	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z017-01	TCGA-17-Z017-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:37343688G>A	uc003cgw.2	+	c.1165G>A	c.(1165-1167)GCA>ACA	p.A389T	GOLGA4_uc010hgr.1_Intron|GOLGA4_uc003cgv.2_Missense_Mutation_p.A367T|GOLGA4_uc010hgs.2_Intron|GOLGA4_uc003cgx.2_Missense_Mutation_p.A248T	NM_002078	NP_002069	Q13439	GOGA4_HUMAN	golgi autoantigen, golgin subfamily a, 4	367	Potential.|Glu-rich.				vesicle-mediated transport	Golgi membrane|trans-Golgi network				ovary(2)|breast(1)|central_nervous_system(1)	4														0.333333	32.588959	33.474103	12	24	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	37343688	37343688	6824	3	G	A	A	A	494	38	GOLGA4	1	1
FLNB	2317	broad.mit.edu	37	3	58095863	58095863	+	Missense_Mutation	SNP	G	C	C			TCGA-17-Z017-01	TCGA-17-Z017-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:58095863G>C	uc010hne.2	+	c.2450G>C	c.(2449-2451)GGG>GCG	p.G817A	FLNB_uc003djj.2_Missense_Mutation_p.G817A|FLNB_uc003djk.2_Missense_Mutation_p.G817A|FLNB_uc010hnf.2_Missense_Mutation_p.G817A|FLNB_uc003djl.2_Missense_Mutation_p.G648A|FLNB_uc003djm.2_Missense_Mutation_p.G648A	NM_001164317	NP_001157789	O75369	FLNB_HUMAN	filamin B isoform 1	817	Filamin 6.				actin cytoskeleton organization|cell differentiation|cytoskeletal anchoring at plasma membrane|signal transduction	cell cortex|integral to membrane|nucleus|sarcomere	actin binding			breast(6)|ovary(3)	9				BRCA - Breast invasive adenocarcinoma(55;0.000335)|KIRC - Kidney renal clear cell carcinoma(284;0.0726)|Kidney(284;0.0898)						676				0.296703	61.579063	64.950486	27	64	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	58095863	58095863	6176	3	G	C	C	C	559	43	FLNB	3	3
DDX60L	91351	broad.mit.edu	37	4	169377245	169377245	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z017-01	TCGA-17-Z017-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:169377245C>T	uc003irq.3	-	c.782G>A	c.(781-783)CGT>CAT	p.R261H	DDX60L_uc003irr.1_Missense_Mutation_p.R261H|DDX60L_uc003irs.1_De_novo_Start_OutOfFrame	NM_001012967	NP_001012985	Q5H9U9	DDX6L_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 60-like	261							ATP binding|ATP-dependent helicase activity|RNA binding			ovary(1)	1		Prostate(90;0.00876)|Renal(120;0.0183)|all_neural(102;0.0837)|Melanoma(52;0.132)		GBM - Glioblastoma multiforme(119;0.175)										0.166667	17.614387	23.937264	10	50	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	169377245	169377245	4550	4	C	T	T	T	247	19	DDX60L	1	1
UFSP2	55325	broad.mit.edu	37	4	186339797	186339797	+	Silent	SNP	G	T	T			TCGA-17-Z017-01	TCGA-17-Z017-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:186339797G>T	uc003ixo.2	-	c.210C>A	c.(208-210)ACC>ACA	p.T70T	UFSP2_uc003ixn.2_5'Flank|UFSP2_uc003ixq.2_5'UTR|UFSP2_uc003ixp.2_Non-coding_Transcript	NM_018359	NP_060829	Q9NUQ7	UFSP2_HUMAN	UFM1-specific peptidase 2	70						endoplasmic reticulum|nucleus	small conjugating protein-specific protease activity				0		all_lung(41;1.3e-11)|Lung NSC(41;2.25e-11)|Melanoma(20;0.00109)|Colorectal(36;0.0215)|Renal(120;0.0246)|Hepatocellular(41;0.0268)|Prostate(90;0.0283)|all_hematologic(60;0.0749)		all cancers(43;3.4e-25)|Epithelial(43;2.23e-22)|OV - Ovarian serous cystadenocarcinoma(60;1.54e-11)|BRCA - Breast invasive adenocarcinoma(30;8.1e-05)|GBM - Glioblastoma multiforme(59;0.000148)|STAD - Stomach adenocarcinoma(60;0.000782)|LUSC - Lung squamous cell carcinoma(40;0.00939)|COAD - Colon adenocarcinoma(29;0.0108)|READ - Rectum adenocarcinoma(43;0.166)										0.230769	56.213317	63.161818	24	80	KEEP	---	---	---	---	capture		Silent	SNP	186339797	186339797	17496	4	G	T	T	T	600	47	UFSP2	2	2
PPARGC1A	10891	broad.mit.edu	37	4	23815833	23815833	+	Missense_Mutation	SNP	A	T	T			TCGA-17-Z017-01	TCGA-17-Z017-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:23815833A>T	uc003gqs.2	-	c.1273T>A	c.(1273-1275)TCT>ACT	p.S425T	PPARGC1A_uc003gqt.2_Non-coding_Transcript|PPARGC1A_uc011bxp.1_Non-coding_Transcript|PPARGC1A_uc010ier.1_Non-coding_Transcript	NM_013261	NP_037393	Q9UBK2	PRGC1_HUMAN	peroxisome proliferator-activated receptor	425					androgen receptor signaling pathway|brown fat cell differentiation|cellular glucose homeostasis|digestion|fatty acid oxidation|gluconeogenesis|mitochondrion organization|mRNA processing|neuron death|positive regulation of fatty acid oxidation|positive regulation of gene-specific transcription from RNA polymerase II promoter|positive regulation of gluconeogenesis|positive regulation of histone acetylation|positive regulation of sequence-specific DNA binding transcription factor activity|protein complex assembly|protein stabilization|response to muscle activity|response to starvation|RNA splicing|temperature homeostasis|transcription initiation from RNA polymerase II promoter	DNA-directed RNA polymerase II, core complex	androgen receptor binding|DNA binding|ligand-dependent nuclear receptor binding|ligand-dependent nuclear receptor transcription coactivator activity|nucleotide binding|RNA binding|RNA polymerase II transcription mediator activity|transcription factor binding			ovary(2)|lung(2)|kidney(2)	6		Breast(46;0.0503)				Esophageal Squamous(29;694 744 13796 34866 44181)				410				0.240506	37.354667	42.249796	19	60	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	23815833	23815833	12730	4	A	T	T	T	117	9	PPARGC1A	3	3
GRK4	2868	broad.mit.edu	37	4	2990509	2990509	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z017-01	TCGA-17-Z017-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:2990509G>T	uc003ggn.1	+	c.204G>T	c.(202-204)AGG>AGT	p.R68S	GRK4_uc003ggo.1_Missense_Mutation_p.R68S|GRK4_uc003ggp.1_Missense_Mutation_p.R36S|GRK4_uc003ggq.1_Missense_Mutation_p.R36S	NM_182982	NP_892027	P32298	GRK4_HUMAN	G protein-coupled receptor kinase 4 isoform	68	RGS.|N-terminal.					cell cortex	ATP binding|G-protein coupled receptor kinase activity|signal transducer activity			lung(1)	1				UCEC - Uterine corpus endometrioid carcinoma (64;0.168)						1452				0.153846	18.205989	25.654349	10	55	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	2990509	2990509	7070	4	G	T	T	T	542	42	GRK4	2	2
RHOH	399	broad.mit.edu	37	4	40245314	40245314	+	Missense_Mutation	SNP	G	C	C			TCGA-17-Z017-01	TCGA-17-Z017-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:40245314G>C	uc003guz.2	+	c.308G>C	c.(307-309)AGG>ACG	p.R103T		NM_004310	NP_004301	Q15669	RHOH_HUMAN	ras homolog gene family, member H precursor	103					negative regulation of I-kappaB kinase/NF-kappaB cascade|regulation of small GTPase mediated signal transduction|regulation of transcription, DNA-dependent|small GTPase mediated signal transduction|T cell differentiation	cytosol|mitochondrion|plasma membrane	GTP binding|GTPase inhibitor activity|kinase inhibitor activity|Rho GTPase binding			ovary(1)	1										33				0.301587	43.318004	45.589088	19	44	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	40245314	40245314	13815	4	G	C	C	C	455	35	RHOH	3	3
YIPF7	285525	broad.mit.edu	37	4	44638008	44638008	+	Missense_Mutation	SNP	A	G	G			TCGA-17-Z017-01	TCGA-17-Z017-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:44638008A>G	uc010ifx.1	-	c.283T>C	c.(283-285)TCC>CCC	p.S95P	YIPF7_uc010ify.1_Missense_Mutation_p.S95P	NM_182592	NP_872398	Q8N8F6	YIPF7_HUMAN	Yip1 domain family, member 7	95						endoplasmic reticulum membrane|integral to membrane					0														0.223404	53.615165	60.243185	21	73	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	44638008	44638008	18066	4	A	G	G	G	156	12	YIPF7	4	4
KDR	3791	broad.mit.edu	37	4	55963852	55963852	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z017-01	TCGA-17-Z017-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:55963852G>T	uc003has.2	-	c.2591C>A	c.(2590-2592)ACA>AAA	p.T864K	KDR_uc003hat.1_Missense_Mutation_p.T864K	NM_002253	NP_002244	P35968	VGFR2_HUMAN	kinase insert domain receptor precursor	864	Protein kinase.|Cytoplasmic (Potential).				angiogenesis|cell differentiation|interspecies interaction between organisms|positive regulation of endothelial cell migration|positive regulation of endothelial cell proliferation|positive regulation of focal adhesion assembly|positive regulation of positive chemotaxis|protein phosphorylation|regulation of cell shape	integral to plasma membrane	ATP binding|growth factor binding|Hsp90 protein binding|integrin binding|receptor signaling protein tyrosine kinase activity|vascular endothelial growth factor receptor activity			lung(9)|soft_tissue(4)|central_nervous_system(4)|large_intestine(2)|ovary(2)|kidney(1)	22	all_cancers(7;0.0255)|all_lung(4;0.00175)|Lung NSC(11;0.00384)|all_epithelial(27;0.034)|Glioma(25;0.08)|all_neural(26;0.101)		Epithelial(7;0.189)		Sorafenib(DB00398)|Sunitinib(DB01268)					1022	TSP Lung(20;0.16)			0.175676	26.626398	33.968582	13	61	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	55963852	55963852	8445	4	G	T	T	T	624	48	KDR	2	2
TECRL	253017	broad.mit.edu	37	4	65274942	65274942	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z017-01	TCGA-17-Z017-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:65274942G>T	uc003hcv.2	-	c.128C>A	c.(127-129)GCG>GAG	p.A43E	TECRL_uc003hcw.2_Missense_Mutation_p.A43E	NM_001010874	NP_001010874	Q5HYJ1	TECRL_HUMAN	steroid 5 alpha-reductase 2-like 2	43					lipid metabolic process|oxidation-reduction process	cytoplasm|integral to membrane	oxidoreductase activity, acting on the CH-CH group of donors				0														0.261538	44.983956	48.304454	17	48	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	65274942	65274942	16273	4	G	T	T	T	494	38	TECRL	1	1
KIAA0232	9778	broad.mit.edu	37	4	6873323	6873323	+	Missense_Mutation	SNP	T	C	C			TCGA-17-Z017-01	TCGA-17-Z017-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:6873323T>C	uc003gjr.3	+	c.3824T>C	c.(3823-3825)ATA>ACA	p.I1275T	KIAA0232_uc003gjq.3_Missense_Mutation_p.I1275T	NM_014743	NP_055558	Q92628	K0232_HUMAN	hypothetical protein LOC9778	1275							ATP binding			ovary(2)	2														0.181034	51.909908	62.99721	21	95	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	6873323	6873323	8470	4	T	C	C	C	637	49	KIAA0232	4	4
SLC6A19	340024	broad.mit.edu	37	5	1216989	1216989	+	Missense_Mutation	SNP	A	C	C			TCGA-17-Z017-01	TCGA-17-Z017-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:1216989A>C	uc003jbw.3	+	c.1102A>C	c.(1102-1104)AAC>CAC	p.N368H		NM_001003841	NP_001003841	Q695T7	S6A19_HUMAN	solute carrier family 6, member 19	368	Extracellular (Potential).				cellular nitrogen compound metabolic process	integral to plasma membrane	amino acid transmembrane transporter activity|neurotransmitter:sodium symporter activity				0	all_cancers(3;3.55e-15)|Lung NSC(6;2.89e-14)|all_lung(6;2.2e-13)|all_epithelial(6;3.75e-10)		Epithelial(17;0.000356)|all cancers(22;0.00137)|OV - Ovarian serous cystadenocarcinoma(19;0.00239)|Lung(60;0.185)											0.116279	4.230131	10.509623	5	38	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	1216989	1216989	15179	5	A	C	C	C	65	5	SLC6A19	4	4
FBN2	2201	broad.mit.edu	37	5	127686693	127686693	+	Missense_Mutation	SNP	G	C	C			TCGA-17-Z017-01	TCGA-17-Z017-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:127686693G>C	uc003kuu.2	-	c.2679C>G	c.(2677-2679)AGC>AGG	p.S893R	FBN2_uc003kuv.2_Missense_Mutation_p.S860R	NM_001999	NP_001990	P35556	FBN2_HUMAN	fibrillin 2 precursor	893					bone trabecula formation|negative regulation of transforming growth factor beta receptor signaling pathway by extracellular sequestering of TGFbeta|positive regulation of bone mineralization|positive regulation of osteoblast differentiation	microfibril	calcium ion binding|extracellular matrix structural constituent			ovary(8)|large_intestine(4)|kidney(1)|pancreas(1)	14		all_cancers(142;0.0216)|Prostate(80;0.0551)	KIRC - Kidney renal clear cell carcinoma(527;0.0268)|Kidney(363;0.0488)	OV - Ovarian serous cystadenocarcinoma(64;0.0821)|Epithelial(69;0.146)						1552				0.24359	52.391484	57.061374	19	59	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	127686693	127686693	5939	5	G	C	C	C	542	42	FBN2	3	3
PCDHB7	56129	broad.mit.edu	37	5	140553933	140553933	+	Missense_Mutation	SNP	T	A	A			TCGA-17-Z017-01	TCGA-17-Z017-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:140553933T>A	uc003lit.2	+	c.1517T>A	c.(1516-1518)ATC>AAC	p.I506N		NM_018940	NP_061763	Q9Y5E2	PCDB7_HUMAN	protocadherin beta 7 precursor	506	Extracellular (Potential).|Cadherin 5.				calcium-dependent cell-cell adhesion|homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(3)|central_nervous_system(1)	4			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)											0.265306	34.057541	36.493787	13	36	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	140553933	140553933	11967	5	T	A	A	A	650	50	PCDHB7	3	3
PCDHB7	56129	broad.mit.edu	37	5	140554452	140554452	+	Missense_Mutation	SNP	A	T	T			TCGA-17-Z017-01	TCGA-17-Z017-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:140554452A>T	uc003lit.2	+	c.2036A>T	c.(2035-2037)GAC>GTC	p.D679V	PCDHB8_uc011dai.1_5'Flank	NM_018940	NP_061763	Q9Y5E2	PCDB7_HUMAN	protocadherin beta 7 precursor	679	Extracellular (Potential).				calcium-dependent cell-cell adhesion|homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(3)|central_nervous_system(1)	4			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)											0.055556	-19.153653	18.229009	10	170	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	140554452	140554452	11967	5	A	T	T	T	130	10	PCDHB7	3	3
PCDHB7	56129	broad.mit.edu	37	5	140554673	140554673	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z017-01	TCGA-17-Z017-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:140554673C>A	uc003lit.2	+	c.2257C>A	c.(2257-2259)CTG>ATG	p.L753M	PCDHB8_uc011dai.1_5'Flank	NM_018940	NP_061763	Q9Y5E2	PCDB7_HUMAN	protocadherin beta 7 precursor	753	Cytoplasmic (Potential).				calcium-dependent cell-cell adhesion|homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(3)|central_nervous_system(1)	4			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)											0.043137	-39.010148	18.34179	11	244	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	140554673	140554673	11967	5	C	A	A	A	311	24	PCDHB7	2	2
PCDHB11	56125	broad.mit.edu	37	5	140579470	140579470	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z017-01	TCGA-17-Z017-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:140579470C>A	uc003liy.2	+	c.123C>A	c.(121-123)AGC>AGA	p.S41R	PCDHB11_uc011daj.1_Intron	NM_018931	NP_061754	Q9Y5F2	PCDBB_HUMAN	protocadherin beta 11 precursor	41	Extracellular (Potential).|Cadherin 1.				calcium-dependent cell-cell adhesion|homophilic cell adhesion|synapse assembly|synaptic transmission	integral to plasma membrane	calcium ion binding			ovary(2)	2			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)											0.25	32.479221	35.204733	12	36	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	140579470	140579470	11956	5	C	A	A	A	350	27	PCDHB11	1	1
PCDHGA3	56112	broad.mit.edu	37	5	140723843	140723843	+	Missense_Mutation	SNP	C	G	G			TCGA-17-Z017-01	TCGA-17-Z017-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:140723843C>G	uc003ljm.1	+	c.243C>G	c.(241-243)AGC>AGG	p.S81R	PCDHGA1_uc003lji.1_Intron|PCDHGA2_uc003ljk.1_Intron|PCDHGA3_uc010jfx.1_5'UTR|PCDHGA3_uc011dap.1_Missense_Mutation_p.S81R	NM_018916	NP_061739	Q9Y5H0	PCDG3_HUMAN	protocadherin gamma subfamily A, 3 isoform 1	81	Cadherin 1.|Extracellular (Potential).				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			breast(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)											0.298507	60.881803	63.308364	20	47	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	140723843	140723843	11975	5	C	G	G	G	350	27	PCDHGA3	3	3
PCDHGB3	56102	broad.mit.edu	37	5	140751832	140751832	+	Missense_Mutation	SNP	G	C	C			TCGA-17-Z017-01	TCGA-17-Z017-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:140751832G>C	uc003ljw.1	+	c.1871G>C	c.(1870-1872)GGT>GCT	p.G624A	PCDHGA1_uc003lji.1_Intron|PCDHGA2_uc003ljk.1_Intron|PCDHGA3_uc003ljm.1_Intron|PCDHGA3_uc010jfx.1_Intron|PCDHGB1_uc003ljo.1_Intron|PCDHGA4_uc003ljq.1_Intron|PCDHGB2_uc003ljs.1_Intron|PCDHGA5_uc003lju.1_Intron|PCDHGA6_uc003ljy.1_5'Flank|PCDHGB3_uc011dat.1_Missense_Mutation_p.G624A|PCDHGA6_uc011dau.1_5'Flank	NM_018924	NP_061747	Q9Y5G1	PCDGF_HUMAN	protocadherin gamma subfamily B, 3 isoform 1	624	Extracellular (Potential).|Cadherin 6.				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding				0			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)											0.171429	13.628675	17.199846	6	29	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	140751832	140751832	11984	5	G	C	C	C	572	44	PCDHGB3	3	3
PCDHGA7	56108	broad.mit.edu	37	5	140764399	140764399	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z017-01	TCGA-17-Z017-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:140764399G>T	uc003lka.1	+	c.1933G>T	c.(1933-1935)GCC>TCC	p.A645S	PCDHGA1_uc003lji.1_Intron|PCDHGA2_uc003ljk.1_Intron|PCDHGA3_uc003ljm.1_Intron|PCDHGA3_uc010jfx.1_Intron|PCDHGB1_uc003ljo.1_Intron|PCDHGA4_uc003ljq.1_Intron|PCDHGB2_uc003ljs.1_Intron|PCDHGA5_uc003lju.1_Intron|PCDHGB3_uc003ljw.1_Intron|PCDHGA6_uc003ljy.1_Intron|PCDHGA7_uc003ljz.1_Missense_Mutation_p.A645S	NM_018920	NP_061743	Q9Y5G6	PCDG7_HUMAN	protocadherin gamma subfamily A, 7 isoform 1	645	Extracellular (Potential).|Cadherin 6.				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding				0			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)											0.263158	11.828124	12.753555	5	14	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	140764399	140764399	11979	5	G	T	T	T	546	42	PCDHGA7	2	2
ITK	3702	broad.mit.edu	37	5	156608054	156608054	+	Silent	SNP	T	C	C			TCGA-17-Z017-01	TCGA-17-Z017-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:156608054T>C	uc003lwo.1	+	c.66T>C	c.(64-66)TCT>TCC	p.S22S		NM_005546	NP_005537	Q08881	ITK_HUMAN	IL2-inducible T-cell kinase	22	PH.				cellular defense response|intracellular signal transduction|protein phosphorylation|T cell receptor signaling pathway	cytosol|plasma membrane	ATP binding|metal ion binding|non-membrane spanning protein tyrosine kinase activity|protein binding			ovary(8)|lung(4)|skin(3)|stomach(1)|central_nervous_system(1)	17	Renal(175;0.00212)	Medulloblastoma(196;0.0354)|all_neural(177;0.1)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)			Esophageal Squamous(70;1378 1469 8785 19883)				330				0.164557	26.223855	34.664706	13	66	KEEP	---	---	---	---	capture		Silent	SNP	156608054	156608054	8213	5	T	C	C	C	691	54	ITK	4	4
CCNG1	900	broad.mit.edu	37	5	162869132	162869132	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z017-01	TCGA-17-Z017-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:162869132C>T	uc003lzb.2	+	c.679C>T	c.(679-681)CTT>TTT	p.L227F	CCNG1_uc011dek.1_Missense_Mutation_p.L91F|CCNG1_uc011del.1_Missense_Mutation_p.L91F|CCNG1_uc003lzc.2_Non-coding_Transcript	NM_199246	NP_954854	P51959	CCNG1_HUMAN	cyclin G1	227					cell division|mitosis|regulation of cyclin-dependent protein kinase activity	nucleus		p.L227F(1)		lung(1)|kidney(1)	2	Renal(175;0.000281)	Medulloblastoma(196;0.00853)|all_neural(177;0.0408)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	all cancers(165;0.0597)|OV - Ovarian serous cystadenocarcinoma(192;0.107)|Epithelial(171;0.164)						99				0.170213	15.581031	20.424453	8	39	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	162869132	162869132	3050	5	C	T	T	T	416	32	CCNG1	2	2
HK3	3101	broad.mit.edu	37	5	176310847	176310847	+	Silent	SNP	G	A	A			TCGA-17-Z017-01	TCGA-17-Z017-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:176310847G>A	uc003mfa.2	-	c.1977C>T	c.(1975-1977)GCC>GCT	p.A659A	HK3_uc003mez.2_Silent_p.A215A	NM_002115	NP_002106	P52790	HXK3_HUMAN	hexokinase 3	659	Catalytic.				glucose transport|glycolysis|transmembrane transport	cytosol|membrane	ATP binding|glucokinase activity			ovary(3)|large_intestine(1)|breast(1)	5	all_cancers(89;0.000104)|Renal(175;0.000269)|Lung NSC(126;0.00696)|all_lung(126;0.0115)	Medulloblastoma(196;0.00498)|all_neural(177;0.0138)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)											0.346154	24.164453	24.708993	9	17	KEEP	---	---	---	---	capture		Silent	SNP	176310847	176310847	7483	5	G	A	A	A	600	47	HK3	2	2
FYB	2533	broad.mit.edu	37	5	39202804	39202804	+	Nonsense_Mutation	SNP	C	A	A			TCGA-17-Z017-01	TCGA-17-Z017-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:39202804C>A	uc011cpl.1	-	c.289G>T	c.(289-291)GGA>TGA	p.G97*	FYB_uc003jls.2_Nonsense_Mutation_p.G87*|FYB_uc003jlt.2_Nonsense_Mutation_p.G87*|FYB_uc003jlu.2_Nonsense_Mutation_p.G87*	NM_001465	NP_001456	O15117	FYB_HUMAN	FYN binding protein (FYB-120/130) isoform 1	87					cell junction assembly|immune response|intracellular protein kinase cascade|NLS-bearing substrate import into nucleus|protein phosphorylation|T cell receptor signaling pathway	cytosol|nucleus	protein binding			ovary(2)	2	all_lung(31;0.000343)		Epithelial(62;0.235)											0.147059	24.141371	36.389128	15	87	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	39202804	39202804	6375	5	C	A	A	A	273	21	FYB	5	2
HEATR7B2	133558	broad.mit.edu	37	5	41018009	41018009	+	Missense_Mutation	SNP	G	C	C			TCGA-17-Z017-01	TCGA-17-Z017-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:41018009G>C	uc003jmj.3	-	c.2827C>G	c.(2827-2829)CTG>GTG	p.L943V	HEATR7B2_uc003jmi.3_Missense_Mutation_p.L498V	NM_173489	NP_775760	Q7Z745	HTRB2_HUMAN	HEAT repeat family member 7B2	943							binding			ovary(6)|central_nervous_system(2)	8														0.216216	18.482984	21.229978	8	29	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	41018009	41018009	7318	5	G	C	C	C	451	35	HEATR7B2	3	3
ERBB2IP	55914	broad.mit.edu	37	5	65350250	65350250	+	Missense_Mutation	SNP	A	T	T			TCGA-17-Z017-01	TCGA-17-Z017-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:65350250A>T	uc011cqx.1	+	c.3104A>T	c.(3103-3105)AAT>ATT	p.N1035I	ERBB2IP_uc003jui.1_Missense_Mutation_p.N1035I|ERBB2IP_uc003juj.1_Missense_Mutation_p.N1035I|ERBB2IP_uc003juk.1_Missense_Mutation_p.N1035I|ERBB2IP_uc011cqy.1_Missense_Mutation_p.N1035I|ERBB2IP_uc011cqz.1_Intron|ERBB2IP_uc010iwx.1_Missense_Mutation_p.N1031I|ERBB2IP_uc003jul.1_Missense_Mutation_p.N1031I	NM_018695	NP_061165	Q96RT1	LAP2_HUMAN	ERBB2 interacting protein isoform 2	1035					basal protein localization|cell adhesion|cell cycle|cell growth|epidermal growth factor receptor signaling pathway|establishment or maintenance of epithelial cell apical/basal polarity|integrin-mediated signaling pathway|intermediate filament cytoskeleton organization	basement membrane|cytoplasm|hemidesmosome|nucleus	ErbB-2 class receptor binding|integrin binding|structural constituent of cytoskeleton			ovary(3)|lung(2)|central_nervous_system(1)	6		Lung NSC(167;9.45e-06)|Prostate(74;0.0139)|Ovarian(174;0.0547)|Breast(144;0.093)|Colorectal(97;0.234)		UCEC - Uterine corpus endometrioid carcinoma (4;0.0767)|Lung(70;0.00191)										0.277228	71.052407	75.566396	28	73	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	65350250	65350250	5400	5	A	T	T	T	52	4	ERBB2IP	3	3
BHMT2	23743	broad.mit.edu	37	5	78379105	78379105	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z017-01	TCGA-17-Z017-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:78379105G>T	uc003kft.2	+	c.689G>T	c.(688-690)GGG>GTG	p.G230V	BHMT2_uc011cth.1_Missense_Mutation_p.G166V	NM_017614	NP_060084	Q9H2M3	BHMT2_HUMAN	betaine-homocysteine methyltransferase 2	230	Hcy-binding.				methionine biosynthetic process	cytoplasm	betaine-homocysteine S-methyltransferase activity|homocysteine S-methyltransferase activity|zinc ion binding			ovary(1)	1		all_lung(232;0.00063)|Lung NSC(167;0.00171)|Ovarian(174;0.0261)|Prostate(461;0.191)		OV - Ovarian serous cystadenocarcinoma(54;2.09e-45)|Epithelial(54;9.3e-41)|all cancers(79;4.09e-36)	L-Methionine(DB00134)									0.294118	64.715218	67.897973	25	60	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	78379105	78379105	1451	5	G	T	T	T	559	43	BHMT2	2	2
ACOT12	134526	broad.mit.edu	37	5	80626271	80626271	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z017-01	TCGA-17-Z017-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:80626271G>T	uc003khl.3	-	c.1610C>A	c.(1609-1611)GCC>GAC	p.A537D	RNU5E_uc011cto.1_Intron	NM_130767	NP_570123	Q8WYK0	ACO12_HUMAN	acyl-CoA thioesterase 12	537	START.				acyl-CoA metabolic process|fatty acid metabolic process	cytosol	acetyl-CoA hydrolase activity|carboxylesterase activity			ovary(1)|kidney(1)	2		Lung NSC(167;0.0176)|all_lung(232;0.0205)|Ovarian(174;0.135)		OV - Ovarian serous cystadenocarcinoma(54;1.37e-45)|Epithelial(54;1.25e-39)|all cancers(79;5.01e-34)										0.416667	56.59096	56.881968	20	28	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	80626271	80626271	151	5	G	T	T	T	546	42	ACOT12	2	2
VCAN	1462	broad.mit.edu	37	5	82786291	82786291	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z017-01	TCGA-17-Z017-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:82786291G>T	uc003kii.3	+	c.445G>T	c.(445-447)GGG>TGG	p.G149W	VCAN_uc003kij.3_Missense_Mutation_p.G149W|VCAN_uc010jau.2_Missense_Mutation_p.G149W|VCAN_uc003kik.3_Missense_Mutation_p.G149W|VCAN_uc003kih.3_Missense_Mutation_p.G149W	NM_004385	NP_004376	P13611	CSPG2_HUMAN	versican isoform 1 precursor	149					cell adhesion|cell recognition|glial cell migration	extracellular space|proteinaceous extracellular matrix	calcium ion binding|hyaluronic acid binding|sugar binding			ovary(7)|skin(3)|lung(2)|central_nervous_system(1)	13		Lung NSC(167;0.0216)|all_lung(232;0.0251)|Ovarian(174;0.142)		OV - Ovarian serous cystadenocarcinoma(54;2.47e-41)|Epithelial(54;2.51e-34)|all cancers(79;5.19e-29)										0.271605	58.616951	62.425605	22	59	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	82786291	82786291	17703	5	G	T	T	T	611	47	VCAN	2	2
TAS2R1	50834	broad.mit.edu	37	5	9630051	9630051	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z017-01	TCGA-17-Z017-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:9630051C>A	uc003jem.1	-	c.94G>T	c.(94-96)GGC>TGC	p.G32C		NM_019599	NP_062545	Q9NYW7	TA2R1_HUMAN	taste receptor T2R1	32	Cytoplasmic (Potential).				chemosensory behavior|sensory perception of taste	integral to membrane	taste receptor activity			ovary(3)	3														0.160377	33.104808	44.745866	17	89	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	9630051	9630051	16087	5	C	A	A	A	273	21	TAS2R1	2	2
ETV7	51513	broad.mit.edu	37	6	36334711	36334711	+	Silent	SNP	C	G	G			TCGA-17-Z017-01	TCGA-17-Z017-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:36334711C>G	uc003omb.2	-	c.849G>C	c.(847-849)CTG>CTC	p.L283L	ETV7_uc003olz.1_Silent_p.L283L|ETV7_uc003oma.1_Silent_p.L228L|ETV7_uc010jwg.2_Non-coding_Transcript|ETV7_uc003omc.2_Silent_p.L228L|ETV7_uc010jwj.2_Silent_p.L224L|ETV7_uc010jwh.2_Silent_p.L202L|ETV7_uc010jwi.2_Silent_p.L206L|ETV7_uc011dtl.1_Silent_p.L132L	NM_016135	NP_057219	Q9Y603	ETV7_HUMAN	ets variant 7	283	ETS.				organ morphogenesis|regulation of transcription, DNA-dependent|transcription from RNA polymerase II promoter	nucleus	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|specific RNA polymerase II transcription factor activity			ovary(1)|skin(1)	2														0.485149	162.869735	162.88915	49	52	KEEP	---	---	---	---	capture		Silent	SNP	36334711	36334711	5477	6	C	G	G	G	314	25	ETV7	3	3
GTPBP2	54676	broad.mit.edu	37	6	43593175	43593175	+	Silent	SNP	G	A	A			TCGA-17-Z017-01	TCGA-17-Z017-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:43593175G>A	uc003ovt.1	-	c.630C>T	c.(628-630)CGC>CGT	p.R210R	GTPBP2_uc010jyv.2_Silent_p.R122R|GTPBP2_uc003ovs.2_Silent_p.R210R	NM_019096	NP_061969	Q9BX10	GTPB2_HUMAN	GTP binding protein 2	210							GTP binding|GTPase activity			liver(1)	1	all_cancers(18;9.36e-06)|Lung NSC(15;0.00161)|all_lung(25;0.004)		all cancers(41;0.000501)|Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|STAD - Stomach adenocarcinoma(11;0.0826)|OV - Ovarian serous cystadenocarcinoma(102;0.167)			GBM(116;405 1620 28302 32150 44768)								0.497076	246.976944	246.978002	85	86	KEEP	---	---	---	---	capture		Silent	SNP	43593175	43593175	7160	6	G	A	A	A	535	42	GTPBP2	2	2
C6orf138	442213	broad.mit.edu	37	6	47846929	47846929	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z017-01	TCGA-17-Z017-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:47846929C>A	uc011dwm.1	-	c.1600G>T	c.(1600-1602)GTG>TTG	p.V534L	C6orf138_uc011dwn.1_Missense_Mutation_p.V298L	NM_001013732	NP_001013754	Q6ZW05	CF138_HUMAN	hypothetical protein LOC442213	551						integral to membrane	hedgehog receptor activity			central_nervous_system(1)	1														0.5	55.848923	55.848923	18	18	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	47846929	47846929	2435	6	C	A	A	A	234	18	C6orf138	2	2
PKHD1	5314	broad.mit.edu	37	6	51524198	51524198	+	Missense_Mutation	SNP	A	T	T			TCGA-17-Z017-01	TCGA-17-Z017-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:51524198A>T	uc003pah.1	-	c.10726T>A	c.(10726-10728)TGG>AGG	p.W3576R		NM_138694	NP_619639	P08F94	PKHD1_HUMAN	fibrocystin isoform 1	3576	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				0.412281	149.005322	149.771133	47	67	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	51524198	51524198	12396	6	A	T	T	T	91	7	PKHD1	3	3
COL9A1	1297	broad.mit.edu	37	6	71003934	71003934	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z017-01	TCGA-17-Z017-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:71003934G>T	uc003pfg.3	-	c.632C>A	c.(631-633)CCA>CAA	p.P211Q		NM_001851	NP_001842	P20849	CO9A1_HUMAN	alpha 1 type IX collagen isoform 1 precursor	211	Nonhelical region (NC4).|TSP N-terminal.				axon guidance|cell adhesion|organ morphogenesis	collagen type IX	extracellular matrix structural constituent conferring tensile strength|metal ion binding			ovary(4)	4														0.439394	177.227449	177.650701	58	74	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	71003934	71003934	3845	6	G	T	T	T	611	47	COL9A1	2	2
EPHA7	2045	broad.mit.edu	37	6	93956625	93956625	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z017-01	TCGA-17-Z017-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:93956625C>T	uc003poe.2	-	c.2611G>A	c.(2611-2613)GAT>AAT	p.D871N	EPHA7_uc003pof.2_Missense_Mutation_p.D866N|EPHA7_uc011eac.1_Missense_Mutation_p.D867N	NM_004440	NP_004431	Q15375	EPHA7_HUMAN	ephrin receptor EphA7 precursor	871	Cytoplasmic (Potential).|Protein kinase.				protein phosphorylation|transmembrane receptor protein tyrosine kinase signaling pathway	integral to plasma membrane	ATP binding|ephrin receptor activity			ovary(7)|lung(6)|central_nervous_system(3)|large_intestine(2)|skin(2)|pancreas(1)	21		all_cancers(76;7.47e-10)|Acute lymphoblastic leukemia(125;1.88e-09)|all_hematologic(75;1.75e-07)|all_epithelial(107;3.6e-05)|Lung NSC(302;0.0368)|all_lung(197;0.0509)|Colorectal(196;0.142)		BRCA - Breast invasive adenocarcinoma(108;0.0847)						635				0.205128	35.168075	41.451421	16	62	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	93956625	93956625	5365	6	C	T	T	T	390	30	EPHA7	2	2
CPA1	1357	broad.mit.edu	37	7	130020972	130020972	+	Silent	SNP	G	A	A			TCGA-17-Z017-01	TCGA-17-Z017-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:130020972G>A	uc003vpx.2	+	c.99G>A	c.(97-99)GAG>GAA	p.E33E	CPA1_uc011kpf.1_5'UTR|CPA1_uc003vpw.2_Silent_p.E33E	NM_001868	NP_001859	P15085	CBPA1_HUMAN	carboxypeptidase A1 precursor	33					proteolysis	extracellular space	metallocarboxypeptidase activity|zinc ion binding			ovary(1)	1	Melanoma(18;0.0435)													0.25	17.241873	18.602906	6	18	KEEP	---	---	---	---	capture		Silent	SNP	130020972	130020972	3927	7	G	A	A	A	451	35	CPA1	2	2
TRYX3	136541	broad.mit.edu	37	7	141955425	141955425	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z017-01	TCGA-17-Z017-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:141955425C>A	uc003vxb.2	-	c.109G>T	c.(109-111)GAC>TAC	p.D37Y	TRYX3_uc003vxc.3_Missense_Mutation_p.D37Y	NM_001001317	NP_001001317	Q8IYP2	PRS58_HUMAN	trypsin X3 precursor	37	Peptidase S1.				proteolysis	extracellular region	serine-type endopeptidase activity				0	Melanoma(164;0.0272)													0.521127	226.345633	226.400345	74	68	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	141955425	141955425	17155	7	C	A	A	A	377	29	TRYX3	2	2
OR6V1	346517	broad.mit.edu	37	7	142749650	142749650	+	Silent	SNP	A	T	T			TCGA-17-Z017-01	TCGA-17-Z017-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:142749650A>T	uc011ksv.1	+	c.213A>T	c.(211-213)GTA>GTT	p.V71V		NM_001001667	NP_001001667	Q8N148	OR6V1_HUMAN	olfactory receptor, family 6, subfamily V,	71	Helical; Name=2; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)	1	Melanoma(164;0.059)													0.1875	145.89646	180.999702	72	312	KEEP	---	---	---	---	capture		Silent	SNP	142749650	142749650	11622	7	A	T	T	T	158	13	OR6V1	3	3
PDIA4	9601	broad.mit.edu	37	7	148702415	148702415	+	Missense_Mutation	SNP	T	A	A			TCGA-17-Z017-01	TCGA-17-Z017-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:148702415T>A	uc003wff.2	-	c.1340A>T	c.(1339-1341)GAG>GTG	p.E447V		NM_004911	NP_004902	P13667	PDIA4_HUMAN	protein disulfide isomerase A4 precursor	447					cell redox homeostasis|glycerol ether metabolic process|protein secretion	endoplasmic reticulum lumen|melanosome	electron carrier activity|protein binding|protein disulfide isomerase activity|protein disulfide oxidoreductase activity			ovary(1)	1	Melanoma(164;0.15)		OV - Ovarian serous cystadenocarcinoma(82;0.00385)									OREG0018420	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	0.493333	106.870869	106.873717	37	38	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	148702415	148702415	12091	7	T	A	A	A	702	54	PDIA4	3	3
ABCB5	340273	broad.mit.edu	37	7	20782578	20782578	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z017-01	TCGA-17-Z017-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:20782578G>T	uc010kuh.2	+	c.3103G>T	c.(3103-3105)GGC>TGC	p.G1035C	ABCB5_uc003suw.3_Missense_Mutation_p.G590C	NM_001163941	NP_001157413	Q2M3G0	ABCB5_HUMAN	ATP-binding cassette, sub-family B, member 5	590	Cytoplasmic (Potential).|ABC transporter 2.				regulation of membrane potential	apical plasma membrane|Golgi membrane|integral to plasma membrane|intercellular canaliculus	ATP binding|ATPase activity, coupled to transmembrane movement of substances|efflux transmembrane transporter activity			large_intestine(1)|ovary(1)|pancreas(1)	3														0.146154	31.507921	47.101392	19	111	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	20782578	20782578	45	7	G	T	T	T	611	47	ABCB5	2	2
AVL9	23080	broad.mit.edu	37	7	32609734	32609734	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z017-01	TCGA-17-Z017-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:32609734C>A	uc003tcv.1	+	c.1318C>A	c.(1318-1320)CAA>AAA	p.Q440K	AVL9_uc011kai.1_Intron|AVL9_uc010kwj.1_Missense_Mutation_p.Q281K	NM_015060	NP_055875	Q8NBF6	AVL9_HUMAN	AVL9 homolog (S. cerevisiase)	440						integral to membrane					0														0.149606	35.658166	50.59684	19	108	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	32609734	32609734	1249	7	C	A	A	A	221	17	AVL9	2	2
POM121L12	285877	broad.mit.edu	37	7	53103986	53103986	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z017-01	TCGA-17-Z017-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:53103986C>T	uc003tpz.2	+	c.622C>T	c.(622-624)CGG>TGG	p.R208W		NM_182595	NP_872401	Q8N7R1	P1L12_HUMAN	POM121 membrane glycoprotein-like 12	208											0														0.54386	91.337454	91.43569	31	26	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	53103986	53103986	12669	7	C	T	T	T	347	27	POM121L12	1	1
SEMA3A	10371	broad.mit.edu	37	7	83592525	83592525	+	Missense_Mutation	SNP	T	A	A			TCGA-17-Z017-01	TCGA-17-Z017-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:83592525T>A	uc003uhz.2	-	c.1856A>T	c.(1855-1857)GAA>GTA	p.E619V		NM_006080	NP_006071	Q14563	SEM3A_HUMAN	semaphorin 3A precursor	619	Ig-like C2-type.				axon guidance	extracellular region|membrane	receptor activity			ovary(2)|breast(1)|kidney(1)	4														0.243781	115.268119	127.301709	49	152	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	83592525	83592525	14510	7	T	A	A	A	806	62	SEMA3A	3	3
ZFPM2	23414	broad.mit.edu	37	8	106431376	106431376	+	Silent	SNP	G	T	T			TCGA-17-Z017-01	TCGA-17-Z017-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:106431376G>T	uc003ymd.2	+	c.45G>T	c.(43-45)CCG>CCT	p.P15P		NM_012082	NP_036214	Q8WW38	FOG2_HUMAN	zinc finger protein, multitype 2	15					blood coagulation|transcription, DNA-dependent	nucleoplasm	DNA binding|RNA polymerase II transcription factor activity|transcription corepressor activity|transcription repressor activity|zinc ion binding			ovary(4)|large_intestine(1)	5			OV - Ovarian serous cystadenocarcinoma(57;8.28e-08)											0.275	29.404211	31.23106	11	29	KEEP	---	---	---	---	capture		Silent	SNP	106431376	106431376	18248	8	G	T	T	T	483	38	ZFPM2	1	1
TG	7038	broad.mit.edu	37	8	133906050	133906050	+	Silent	SNP	G	A	A			TCGA-17-Z017-01	TCGA-17-Z017-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:133906050G>A	uc003ytw.2	+	c.2877G>A	c.(2875-2877)GTG>GTA	p.V959V		NM_003235	NP_003226	P01266	THYG_HUMAN	thyroglobulin precursor	959	Thyroglobulin type-1 8.				hormone biosynthetic process|regulation of synaptic transmission|signal transduction		carboxylesterase activity|hormone activity			ovary(8)|breast(4)|pancreas(1)	13	Ovarian(258;0.00438)|Acute lymphoblastic leukemia(118;0.155)	Myeloproliferative disorder(644;0.00878)|Acute lymphoblastic leukemia(644;0.0559)|Breast(495;0.0735)	BRCA - Breast invasive adenocarcinoma(115;0.000701)	KIRC - Kidney renal clear cell carcinoma(542;0.0546)						1778				0.360215	199.06989	202.271035	67	119	KEEP	---	---	---	---	capture		Silent	SNP	133906050	133906050	16341	8	G	A	A	A	600	47	TG	2	2
C8orf80	389643	broad.mit.edu	37	8	27925799	27925799	+	Silent	SNP	G	A	A			TCGA-17-Z017-01	TCGA-17-Z017-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:27925799G>A	uc003xgm.3	-	c.414C>T	c.(412-414)TGC>TGT	p.C138C		NM_001010906	NP_001010906	Q68CJ6	SLIP_HUMAN	speckled-like pattern in the germinal center	138						nucleus	GTP binding|GTPase activity			ovary(1)|central_nervous_system(1)	2		Ovarian(32;0.0218)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0228)|KIRC - Kidney renal clear cell carcinoma(542;0.126)|Kidney(114;0.15)|Colorectal(74;0.181)										0.1875	5.013742	6.479185	3	13	KEEP	---	---	---	---	capture		Silent	SNP	27925799	27925799	2551	8	G	A	A	A	594	46	C8orf80	2	2
CSMD1	64478	broad.mit.edu	37	8	3047572	3047572	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z017-01	TCGA-17-Z017-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:3047572C>A	uc011kwk.1	-	c.5263G>T	c.(5263-5265)GGT>TGT	p.G1755C	CSMD1_uc011kwj.1_Missense_Mutation_p.G1147C|CSMD1_uc003wqe.2_Missense_Mutation_p.G911C|CSMD1_uc010lrg.2_5'Flank	NM_033225	NP_150094	Q96PZ7	CSMD1_HUMAN	CUB and Sushi multiple domains 1 precursor	1755	Sushi 10.|Extracellular (Potential).					integral to membrane				breast(20)|large_intestine(5)	25		all_cancers(1;5.7e-41)|all_epithelial(1;2.54e-36)|Lung NSC(1;7.54e-11)|all_lung(1;3.2e-10)|Hepatocellular(1;3.78e-05)|Breast(1;0.000196)|Myeloproliferative disorder(4;0.000374)|Esophageal squamous(1;0.0157)|Ovarian(12;0.091)|Renal(68;0.144)|Colorectal(14;0.234)		all cancers(1;5.03e-41)|Epithelial(1;4.78e-31)|Lung(1;1.14e-14)|LUSC - Lung squamous cell carcinoma(1;2.34e-14)|GBM - Glioblastoma multiforme(1;4.49e-10)|Colorectal(4;1.18e-07)|OV - Ovarian serous cystadenocarcinoma(1;3.2e-07)|BRCA - Breast invasive adenocarcinoma(1;6.17e-07)|COAD - Colon adenocarcinoma(4;0.000539)|READ - Rectum adenocarcinoma(4;0.00896)|Kidney(5;0.00957)|KIRC - Kidney renal clear cell carcinoma(5;0.0689)										0.307692	10.092845	10.522874	4	9	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	3047572	3047572	4085	8	C	A	A	A	273	21	CSMD1	2	2
OR13C3	138803	broad.mit.edu	37	9	107298670	107298670	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z017-01	TCGA-17-Z017-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:107298670C>T	uc004bcb.1	-	c.425G>A	c.(424-426)TGT>TAT	p.C142Y		NM_001001961	NP_001001961	Q8NGS6	O13C3_HUMAN	olfactory receptor, family 13, subfamily C,	142	Helical; Name=3; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			pancreas(1)	1						GBM(86;1248 1274 14222 15028 46219)								0.261538	165.56769	178.957292	68	192	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	107298670	107298670	11341	9	C	T	T	T	221	17	OR13C3	2	2
OBP2A	29991	broad.mit.edu	37	9	138439035	138439035	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z017-01	TCGA-17-Z017-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:138439035G>T	uc004cgb.2	+	c.218G>T	c.(217-219)CGG>CTG	p.R73L	OBP2A_uc004cgc.2_Missense_Mutation_p.R73L|OBP2A_uc010nau.2_Non-coding_Transcript|OBP2A_uc010nav.2_Silent_p.S28S	NM_014582	NP_055397	Q9NY56	OBP2A_HUMAN	odorant binding protein 2A precursor	73					response to stimulus|sensory perception of smell	extracellular region	odorant binding|transporter activity				0				OV - Ovarian serous cystadenocarcinoma(145;3.39e-07)|Epithelial(140;1.11e-06)|all cancers(34;2.04e-05)										0.076923	0.77091	10.286762	4	48	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	138439035	138439035	11215	9	G	T	T	T	507	39	OBP2A	1	1
IFNA14	3448	broad.mit.edu	37	9	21239770	21239770	+	Missense_Mutation	SNP	G	C	C			TCGA-17-Z017-01	TCGA-17-Z017-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:21239770G>C	uc010mis.2	-	c.165C>G	c.(163-165)GAC>GAG	p.D55E	IFNA14_uc003zoo.1_Non-coding_Transcript	NM_002172	NP_002163	P01570	IFN14_HUMAN	interferon, alpha 14 precursor	55					blood coagulation|regulation of type I interferon-mediated signaling pathway|response to virus|type I interferon-mediated signaling pathway	extracellular space	cytokine activity|cytokine receptor binding				0				Lung(24;2.12e-22)|LUSC - Lung squamous cell carcinoma(38;1.4e-13)										0.230769	67.759452	74.657233	24	80	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	21239770	21239770	7835	9	G	C	C	C	620	48	IFNA14	3	3
KIAA0020	9933	broad.mit.edu	37	9	2820023	2820023	+	Missense_Mutation	SNP	T	C	C			TCGA-17-Z017-01	TCGA-17-Z017-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:2820023T>C	uc003zhp.1	-	c.1264A>G	c.(1264-1266)ATA>GTA	p.I422V	KIAA0020_uc010mhc.1_Missense_Mutation_p.I421V|KIAA0020_uc003zhq.1_Missense_Mutation_p.I421V	NM_014878	NP_055693	Q15397	K0020_HUMAN	KIAA0020 protein	422	Pumilio 5.|PUM-HD.					endoplasmic reticulum|nucleolus	RNA binding			ovary(1)	1				GBM - Glioblastoma multiforme(50;0.0319)										0.102564	7.041645	19.321455	8	70	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	2820023	2820023	8458	9	T	C	C	C	663	51	KIAA0020	4	4
TAF1L	138474	broad.mit.edu	37	9	32630458	32630458	+	Missense_Mutation	SNP	C	G	G			TCGA-17-Z017-01	TCGA-17-Z017-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:32630458C>G	uc003zrg.1	-	c.5120G>C	c.(5119-5121)GGC>GCC	p.G1707A		NM_153809	NP_722516	Q8IZX4	TAF1L_HUMAN	TBP-associated factor RNA polymerase 1-like	1707					male meiosis|regulation of transcription from RNA polymerase II promoter|transcription initiation, DNA-dependent	transcription factor TFIID complex	DNA binding|histone acetyltransferase activity|protein serine/threonine kinase activity|TBP-class protein binding|transcription activator activity			lung(8)|large_intestine(3)|central_nervous_system(3)|skin(2)|ovary(2)|breast(1)|pancreas(1)	20			LUSC - Lung squamous cell carcinoma(29;0.0181)	GBM - Glioblastoma multiforme(74;0.00301)						234				0.163522	54.599056	71.661843	26	133	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	32630458	32630458	16044	9	C	G	G	G	338	26	TAF1L	3	3
PTPRD	5789	broad.mit.edu	37	9	8528597	8528597	+	Silent	SNP	G	T	T			TCGA-17-Z017-01	TCGA-17-Z017-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:8528597G>T	uc003zkk.2	-	c.535C>A	c.(535-537)CGA>AGA	p.R179R	PTPRD_uc003zkp.2_Silent_p.R179R|PTPRD_uc003zkq.2_Silent_p.R179R|PTPRD_uc003zkr.2_Silent_p.R179R|PTPRD_uc003zks.2_Silent_p.R179R|PTPRD_uc003zkl.2_Silent_p.R179R|PTPRD_uc003zkm.2_Silent_p.R179R|PTPRD_uc003zkn.2_Silent_p.R179R|PTPRD_uc003zko.2_Silent_p.R179R|PTPRD_uc003zkt.1_Silent_p.R179R	NM_002839	NP_002830	P23468	PTPRD_HUMAN	protein tyrosine phosphatase, receptor type, D	179	Extracellular (Potential).|Ig-like C2-type 2.				transmembrane receptor protein tyrosine phosphatase signaling pathway	integral to plasma membrane	protein binding|transmembrane receptor protein tyrosine phosphatase activity			lung(10)|large_intestine(3)|ovary(2)|urinary_tract(1)	16		all_cancers(3;3.38e-95)|all_epithelial(3;2.84e-91)|all_lung(3;7.3e-56)|Lung NSC(3;1.82e-52)|Renal(3;3.42e-19)|all_hematologic(3;0.000134)|all_neural(3;0.00409)|Acute lymphoblastic leukemia(23;0.0069)|Melanoma(3;0.0121)|Myeloproliferative disorder(4;0.0122)|Medulloblastoma(3;0.0144)|Lung SC(3;0.0301)|Ovarian(56;0.0694)|Hepatocellular(3;0.0824)		all cancers(1;3.38e-12)|Epithelial(1;2.12e-09)|STAD - Stomach adenocarcinoma(1;1.29e-07)|KIRC - Kidney renal clear cell carcinoma(3;5.49e-07)|Kidney(3;6.36e-07)|GBM - Glioblastoma multiforme(50;9.05e-05)|Lung(1;0.000189)|BRCA - Breast invasive adenocarcinoma(1;0.00178)|LUSC - Lung squamous cell carcinoma(1;0.0115)|LUAD - Lung adenocarcinoma(58;0.119)						1253	TSP Lung(15;0.13)			0.166667	78.50899	100.61608	35	175	KEEP	---	---	---	---	capture		Silent	SNP	8528597	8528597	13256	9	G	T	T	T	519	40	PTPRD	1	1
ROR2	4920	broad.mit.edu	37	9	94486414	94486414	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z017-01	TCGA-17-Z017-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:94486414C>A	uc004arj.1	-	c.2362G>T	c.(2362-2364)GGG>TGG	p.G788W	ROR2_uc004ari.1_Intron	NM_004560	NP_004551	Q01974	ROR2_HUMAN	receptor tyrosine kinase-like orphan receptor 2	788	Cytoplasmic (Potential).|Pro-rich.				negative regulation of cell proliferation|positive regulation of cell migration|protein phosphorylation|transmembrane receptor protein tyrosine kinase signaling pathway	integral to plasma membrane	ATP binding|transmembrane receptor protein tyrosine kinase activity|Wnt-protein binding	p.G788W(1)		lung(6)|central_nervous_system(5)|ovary(3)|large_intestine(2)	16										461				0.327869	52.374922	53.979878	20	41	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	94486414	94486414	14006	9	C	A	A	A	286	22	ROR2	2	2
WWC3	55841	broad.mit.edu	37	X	10109476	10109476	+	Missense_Mutation	SNP	G	C	C			TCGA-17-Z017-01	TCGA-17-Z017-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:10109476G>C	uc004csx.3	+	c.3214G>C	c.(3214-3216)GAG>CAG	p.E1072Q	WWC3_uc010nds.2_Missense_Mutation_p.E736Q|WWC3_uc010ndt.2_Non-coding_Transcript	NM_015691	NP_056506	Q9ULE0	WWC3_HUMAN	WWC family member 3	1072										ovary(4)	4														0.142857	14.432192	22.188329	9	54	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	10109476	10109476	17987	23	G	C	C	C	533	41	WWC3	3	3
CLCN4	1183	broad.mit.edu	37	X	10188801	10188801	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z017-01	TCGA-17-Z017-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:10188801G>T	uc004csy.3	+	c.2076G>T	c.(2074-2076)AAG>AAT	p.K692N	CLCN4_uc011mid.1_Missense_Mutation_p.K598N	NM_001830	NP_001821	P51793	CLCN4_HUMAN	chloride channel 4	692	Cytoplasmic (By similarity).					early endosome membrane|integral to membrane|late endosome membrane	antiporter activity|ATP binding|voltage-gated chloride channel activity			ovary(2)|lung(2)	4						Melanoma(74;1050 1296 1576 30544 38374)								0.175676	98.16521	127.49992	52	244	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	10188801	10188801	3601	23	G	T	T	T	438	34	CLCN4	2	2
RIPPLY1	92129	broad.mit.edu	37	X	106145412	106145412	+	Silent	SNP	G	T	T			TCGA-17-Z017-01	TCGA-17-Z017-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:106145412G>T	uc004emr.1	-	c.189C>A	c.(187-189)TCC>TCA	p.S63S	MORC4_uc004emp.3_Intron|CLDN2_uc004emq.1_Intron|RIPPLY1_uc004ems.1_Intron	NM_138382	NP_612391	Q0D2K3	RIPP1_HUMAN	ripply1 homolog	63					negative regulation of transcription, DNA-dependent|somite rostral/caudal axis specification|somite specification|transcription, DNA-dependent	nucleus					0														0.310345	23.05954	23.991573	9	20	KEEP	---	---	---	---	capture		Silent	SNP	106145412	106145412	13861	23	G	T	T	T	600	47	RIPPLY1	2	2
MORC4	79710	broad.mit.edu	37	X	106219857	106219857	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z017-01	TCGA-17-Z017-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:106219857G>A	uc004emu.3	-	c.1114C>T	c.(1114-1116)CCT>TCT	p.P372S	MORC4_uc004emp.3_Intron|MORC4_uc004emv.3_Missense_Mutation_p.P372S|MORC4_uc004emw.3_Missense_Mutation_p.P120S	NM_024657	NP_078933	Q8TE76	MORC4_HUMAN	zinc finger, CW type with coiled-coil domain 2	372							ATP binding|zinc ion binding			ovary(1)	1														0.175	67.106183	87.033268	35	165	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	106219857	106219857	10095	23	G	A	A	A	572	44	MORC4	2	2
IL13RA2	3598	broad.mit.edu	37	X	114245312	114245312	+	Missense_Mutation	SNP	A	T	T			TCGA-17-Z017-01	TCGA-17-Z017-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:114245312A>T	uc004epx.2	-	c.601T>A	c.(601-603)TAT>AAT	p.Y201N	IL13RA2_uc010nqd.1_Missense_Mutation_p.Y201N	NM_000640	NP_000631	Q14627	I13R2_HUMAN	interleukin 13 receptor, alpha 2 precursor	201	Extracellular (Potential).|Fibronectin type-III 2.					extracellular space|integral to membrane|soluble fraction	cytokine receptor activity			ovary(1)|lung(1)	2														0.176471	30.580453	38.959825	15	70	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	114245312	114245312	7931	23	A	T	T	T	195	15	IL13RA2	3	3
KLHL13	90293	broad.mit.edu	37	X	117043455	117043455	+	Missense_Mutation	SNP	T	C	C			TCGA-17-Z017-01	TCGA-17-Z017-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:117043455T>C	uc011mtp.1	-	c.1181A>G	c.(1180-1182)TAT>TGT	p.Y394C	KLHL13_uc004eqk.2_Missense_Mutation_p.Y341C|KLHL13_uc004eql.2_Missense_Mutation_p.Y392C|KLHL13_uc011mtn.1_Missense_Mutation_p.Y232C|KLHL13_uc011mto.1_Missense_Mutation_p.Y386C|KLHL13_uc004eqm.2_Missense_Mutation_p.Y341C|KLHL13_uc011mtq.1_Missense_Mutation_p.Y376C	NM_033495	NP_277030	Q9P2N7	KLH13_HUMAN	kelch-like 13	392	Kelch 2.				cytokinesis|mitosis|protein ubiquitination	Cul3-RING ubiquitin ligase complex				kidney(1)	1														0.176471	41.390123	51.449836	18	84	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	117043455	117043455	8681	23	T	C	C	C	637	49	KLHL13	4	4
WDR44	54521	broad.mit.edu	37	X	117570673	117570673	+	Silent	SNP	T	C	C			TCGA-17-Z017-01	TCGA-17-Z017-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:117570673T>C	uc004eqn.2	+	c.1860T>C	c.(1858-1860)TTT>TTC	p.F620F	WDR44_uc004eqo.2_Silent_p.F620F|WDR44_uc011mtr.1_Silent_p.F595F|WDR44_uc010nqi.2_Silent_p.F330F	NM_019045	NP_061918	Q5JSH3	WDR44_HUMAN	WD repeat domain 44 protein	620	WD 2.					cytosol|endosome membrane|Golgi apparatus|perinuclear region of cytoplasm				lung(2)|ovary(1)|pancreas(1)	4														0.297297	33.411406	34.770111	11	26	KEEP	---	---	---	---	capture		Silent	SNP	117570673	117570673	17869	23	T	C	C	C	803	62	WDR44	4	4
THOC2	57187	broad.mit.edu	37	X	122757644	122757644	+	Missense_Mutation	SNP	G	C	C			TCGA-17-Z017-01	TCGA-17-Z017-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:122757644G>C	uc004etu.2	-	c.3497C>G	c.(3496-3498)GCT>GGT	p.A1166G	THOC2_uc010nqt.1_5'Flank|THOC2_uc004etw.1_5'Flank	NM_001081550	NP_001075019	Q8NI27	THOC2_HUMAN	THO complex 2	1166					intronless viral mRNA export from host nucleus|mRNA processing|RNA splicing	THO complex part of transcription export complex	protein binding|RNA binding			ovary(3)	3														0.243902	55.059101	59.959775	20	62	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	122757644	122757644	16393	23	G	C	C	C	442	34	THOC2	3	3
ACTRT1	139741	broad.mit.edu	37	X	127185705	127185705	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z017-01	TCGA-17-Z017-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:127185705C>A	uc004eum.2	-	c.481G>T	c.(481-483)GGG>TGG	p.G161W		NM_138289	NP_612146	Q8TDG2	ACTT1_HUMAN	actin-related protein T1	161						cytoplasm|cytoskeleton				ovary(2)|central_nervous_system(2)	4														0.265363	244.028607	261.873805	95	263	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	127185705	127185705	219	23	C	A	A	A	273	21	ACTRT1	2	2
IGSF1	3547	broad.mit.edu	37	X	130415733	130415733	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z017-01	TCGA-17-Z017-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:130415733C>T	uc004ewd.2	-	c.1432G>A	c.(1432-1434)GGC>AGC	p.G478S	IGSF1_uc004ewe.3_Missense_Mutation_p.G467S|IGSF1_uc004ewf.2_Missense_Mutation_p.G458S	NM_001555	NP_001546	Q8N6C5	IGSF1_HUMAN	immunoglobulin superfamily, member 1 isoform 1	478	Extracellular (Potential).|Ig-like C2-type 5.				regulation of transcription, DNA-dependent	extracellular region|integral to membrane	inhibin beta-A binding|inhibin beta-B binding			ovary(3)|lung(1)|central_nervous_system(1)	5														0.216216	61.642209	69.886314	24	87	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	130415733	130415733	7897	23	C	T	T	T	312	24	IGSF1	2	2
ARHGEF6	9459	broad.mit.edu	37	X	135770096	135770096	+	Missense_Mutation	SNP	G	C	C			TCGA-17-Z017-01	TCGA-17-Z017-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:135770096G>C	uc004fab.2	-	c.1240C>G	c.(1240-1242)CTC>GTC	p.L414V	ARHGEF6_uc011mwd.1_Missense_Mutation_p.L287V|ARHGEF6_uc011mwe.1_Missense_Mutation_p.L260V	NM_004840	NP_004831	Q15052	ARHG6_HUMAN	Rac/Cdc42 guanine nucleotide exchange factor 6	414	DH.				apoptosis|cell junction assembly|induction of apoptosis by extracellular signals|JNK cascade|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol	GTPase activator activity|Rho guanyl-nucleotide exchange factor activity				0	Acute lymphoblastic leukemia(192;0.000127)													0.218391	51.176529	57.535575	19	68	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	135770096	135770096	925	23	G	C	C	C	429	33	ARHGEF6	3	3
MAGEC1	9947	broad.mit.edu	37	X	140995522	140995522	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z017-01	TCGA-17-Z017-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:140995522C>A	uc004fbt.2	+	c.2332C>A	c.(2332-2334)CCT>ACT	p.P778T	MAGEC1_uc010nsl.1_Intron	NM_005462	NP_005453	O60732	MAGC1_HUMAN	melanoma antigen family C, 1	778							protein binding			ovary(1)|kidney(1)|central_nervous_system(1)	3	Acute lymphoblastic leukemia(192;6.56e-05)													0.24183	183.297739	201.900492	74	232	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	140995522	140995522	9561	23	C	A	A	A	234	18	MAGEC1	2	2
MAGEA6	4105	broad.mit.edu	37	X	151869625	151869626	+	Missense_Mutation	DNP	CC	AG	AG			TCGA-17-Z017-01	TCGA-17-Z017-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:151869625_151869626CC>AG	uc004ffq.1	+	c.315_316CC>AG	c.(313-318)TTCCAA>TTAGAA	p.105_106FQ>LE	MAGEA6_uc004ffr.1_Missense_Mutation_p.105_106FQ>LE|MAGEA2_uc010nto.2_Intron	NM_005363	NP_005354	P43360	MAGA6_HUMAN	melanoma antigen family A, 6	105_106							protein binding				0	Acute lymphoblastic leukemia(192;6.56e-05)													0.161765	41.68051	56.465641	22	114	KEEP	---	---	---	---	capture		Missense_Mutation	DNP	151869625	151869626	9549	23	CC	AG	AG	AG	389	30	MAGEA6	2	2
SLC6A8	6535	broad.mit.edu	37	X	152956967	152956967	+	Missense_Mutation	SNP	C	G	G			TCGA-17-Z017-01	TCGA-17-Z017-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:152956967C>G	uc004fib.3	+	c.603C>G	c.(601-603)GAC>GAG	p.D201E	SLC6A8_uc004fic.3_Missense_Mutation_p.D201E|SLC6A8_uc011myx.1_Missense_Mutation_p.D86E|SLC6A8_uc010nuj.2_5'Flank|SLC6A8_uc010nui.1_Missense_Mutation_p.D86E	NM_005629	NP_005620	P48029	SC6A8_HUMAN	solute carrier family 6 member 8 isoform 1	201	Extracellular (Potential).				creatine metabolic process|muscle contraction	integral to plasma membrane	creatine:sodium symporter activity|neurotransmitter:sodium symporter activity			pancreas(1)	1	all_hematologic(71;4.25e-06)|Acute lymphoblastic leukemia(192;6.56e-05)				Creatine(DB00148)					206				0.230769	25.663927	28.24767	9	30	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	152956967	152956967	15187	23	C	G	G	G	233	18	SLC6A8	3	3
SCML2	10389	broad.mit.edu	37	X	18264765	18264765	+	Missense_Mutation	SNP	A	T	T			TCGA-17-Z017-01	TCGA-17-Z017-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:18264765A>T	uc004cyl.2	-	c.1754T>A	c.(1753-1755)CTA>CAA	p.L585Q	SCML2_uc004cyk.3_Non-coding_Transcript|SCML2_uc010nfd.1_Missense_Mutation_p.L585Q|SCML2_uc011miz.1_Missense_Mutation_p.L519Q|SCML2_uc010nfc.2_Missense_Mutation_p.L321Q	NM_006089	NP_006080	Q9UQR0	SCML2_HUMAN	sex comb on midleg-like 2	585					anatomical structure morphogenesis|regulation of transcription, DNA-dependent	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity				0	Hepatocellular(33;0.183)					Esophageal Squamous(100;1252 1965 19021 35517)								0.198582	61.424098	73.345969	28	113	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	18264765	18264765	14392	23	A	T	T	T	195	15	SCML2	3	3
TAB3	257397	broad.mit.edu	37	X	30873050	30873050	+	Silent	SNP	A	G	G			TCGA-17-Z017-01	TCGA-17-Z017-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:30873050A>G	uc004dcj.2	-	c.732T>C	c.(730-732)ACT>ACC	p.T244T	TAB3_uc004dck.2_Silent_p.T244T|TAB3_uc010ngl.2_Silent_p.T244T	NM_152787	NP_690000	Q8N5C8	TAB3_HUMAN	mitogen-activated protein kinase kinase kinase 7	244	Pro-rich.				activation of MAPK activity|I-kappaB kinase/NF-kappaB cascade|innate immune response|JNK cascade|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|positive regulation of NF-kappaB transcription factor activity|stress-activated MAPK cascade|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway	cytosol|endosome membrane|plasma membrane	protein binding|zinc ion binding			ovary(1)	1						Pancreas(164;1598 1985 29022 43301 49529)								0.388889	23.421596	23.616094	7	11	KEEP	---	---	---	---	capture		Silent	SNP	30873050	30873050	16018	23	A	G	G	G	132	11	TAB3	4	4
FAM47A	158724	broad.mit.edu	37	X	34149363	34149363	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z017-01	TCGA-17-Z017-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:34149363G>T	uc004ddg.2	-	c.1033C>A	c.(1033-1035)CGT>AGT	p.R345S		NM_203408	NP_981953	Q5JRC9	FA47A_HUMAN	hypothetical protein LOC158724	345										ovary(4)|central_nervous_system(1)	5														0.238095	46.663429	51.923837	20	64	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	34149363	34149363	5790	23	G	T	T	T	481	37	FAM47A	1	1
FAM47A	158724	broad.mit.edu	37	X	34150181	34150181	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z017-01	TCGA-17-Z017-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:34150181C>A	uc004ddg.2	-	c.215G>T	c.(214-216)CGC>CTC	p.R72L		NM_203408	NP_981953	Q5JRC9	FA47A_HUMAN	hypothetical protein LOC158724	72								p.R72H(1)		ovary(4)|central_nervous_system(1)	5														0.255319	119.794535	129.954623	48	140	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	34150181	34150181	5790	23	C	A	A	A	351	27	FAM47A	1	1
TSPAN7	7102	broad.mit.edu	37	X	38533540	38533540	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z017-01	TCGA-17-Z017-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:38533540G>T	uc011mkk.1	+	c.462G>T	c.(460-462)AGG>AGT	p.R154S	TSPAN7_uc004deg.3_Missense_Mutation_p.R137S|TSPAN7_uc011mkj.1_Missense_Mutation_p.R163S|TSPAN7_uc004deh.2_Missense_Mutation_p.R45S	NM_004615	NP_004606	P41732	TSN7_HUMAN	tetraspanin 7	137	Extracellular (Potential).				interspecies interaction between organisms	integral to plasma membrane				ovary(1)	1														0.15	4.810811	7.160756	3	17	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	38533540	38533540	17203	23	G	T	T	T	529	41	TSPAN7	2	2
RBM10	8241	broad.mit.edu	37	X	47039331	47039331	+	Silent	SNP	G	T	T			TCGA-17-Z017-01	TCGA-17-Z017-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:47039331G>T	uc004dhi.2	+	c.1149G>T	c.(1147-1149)GGG>GGT	p.G383G	RBM10_uc004dhf.2_Silent_p.G318G|RBM10_uc004dhg.2_Silent_p.G241G|RBM10_uc004dhh.2_Silent_p.G318G|RBM10_uc010nhq.2_Silent_p.G241G	NM_005676	NP_005667	P98175	RBM10_HUMAN	RNA binding motif protein 10 isoform 1	318	RRM 2.				mRNA processing|RNA splicing	chromatin remodeling complex	nucleotide binding|RNA binding|zinc ion binding			large_intestine(1)|ovary(1)|pancreas(1)	3						Melanoma(171;120 2705 19495 39241)								0.4375	20.72267	20.777127	7	9	KEEP	---	---	---	---	capture		Silent	SNP	47039331	47039331	13572	23	G	T	T	T	548	43	RBM10	2	2
ELK1	2002	broad.mit.edu	37	X	47496438	47496438	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z017-01	TCGA-17-Z017-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:47496438G>A	uc004dik.3	-	c.1162C>T	c.(1162-1164)CGT>TGT	p.R388C	ELK1_uc010nhv.2_Missense_Mutation_p.R388C|ELK1_uc010nhw.2_Missense_Mutation_p.R278C|ELK1_uc004dil.3_Non-coding_Transcript	NM_001114123	NP_001107595	P19419	ELK1_HUMAN	ELK1 protein	388	Sufficient for interaction with MAD2L2.				innate immune response|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|nerve growth factor receptor signaling pathway|positive regulation of transcription from RNA polymerase II promoter|stress-activated MAPK cascade|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway	nucleus	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription activator activity			ovary(2)	2										33				0.2	7.034842	8.276614	3	12	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	47496438	47496438	5251	23	G	A	A	A	507	39	ELK1	1	1
PORCN	64840	broad.mit.edu	37	X	48374534	48374534	+	Missense_Mutation	SNP	G	C	C			TCGA-17-Z017-01	TCGA-17-Z017-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:48374534G>C	uc010nie.1	+	c.1173G>C	c.(1171-1173)TTG>TTC	p.L391F	PORCN_uc004djr.1_Missense_Mutation_p.L386F|PORCN_uc004djs.1_Missense_Mutation_p.L380F|PORCN_uc004djt.1_Missense_Mutation_p.L309F|PORCN_uc011mlx.1_Missense_Mutation_p.L309F|PORCN_uc004dju.1_Missense_Mutation_p.L249F|PORCN_uc004djv.1_Missense_Mutation_p.L391F|PORCN_uc004djw.1_Missense_Mutation_p.L385F	NM_203475	NP_982301	Q9H237	PORCN_HUMAN	porcupine isoform D	391	Extracellular (Potential).				Wnt receptor signaling pathway	endoplasmic reticulum membrane|integral to membrane	acyltransferase activity			ovary(2)|central_nervous_system(1)	3										97				0.233333	16.008674	17.962344	7	23	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	48374534	48374534	12687	23	G	C	C	C	607	47	PORCN	3	3
WNK3	65267	broad.mit.edu	37	X	54334456	54334456	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z017-01	TCGA-17-Z017-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:54334456C>T	uc004dtc.1	-	c.988G>A	c.(988-990)GAT>AAT	p.D330N	WNK3_uc004dtd.1_Missense_Mutation_p.D330N	NM_020922	NP_065973	Q9BYP7	WNK3_HUMAN	WNK lysine deficient protein kinase 3 isoform 1	330	Protein kinase.				intracellular protein kinase cascade|protein phosphorylation		ATP binding|protein binding|protein serine/threonine kinase activity			lung(4)|ovary(3)|kidney(2)|central_nervous_system(2)	11										290				0.186275	39.067139	48.47385	19	83	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	54334456	54334456	17953	23	C	T	T	T	416	32	WNK3	2	2
FGD1	2245	broad.mit.edu	37	X	54472781	54472781	+	Missense_Mutation	SNP	G	C	C			TCGA-17-Z017-01	TCGA-17-Z017-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:54472781G>C	uc004dtg.2	-	c.2647C>G	c.(2647-2649)CGG>GGG	p.R883G		NM_004463	NP_004454	P98174	FGD1_HUMAN	faciogenital dysplasia protein	883	PH 2.				actin cytoskeleton organization|apoptosis|filopodium assembly|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|organ morphogenesis|regulation of Cdc42 GTPase activity|regulation of cell shape|small GTPase mediated signal transduction	cytoskeleton|cytosol|Golgi apparatus|lamellipodium|nucleus|plasma membrane|ruffle	Rho guanyl-nucleotide exchange factor activity|small GTPase binding|zinc ion binding			ovary(3)|skin(2)|central_nervous_system(1)	6														0.391304	27.770322	28.008104	9	14	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	54472781	54472781	6069	23	G	C	C	C	493	38	FGD1	3	3
SPIN4	139886	broad.mit.edu	37	X	62570191	62570191	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z017-01	TCGA-17-Z017-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:62570191C>T	uc004dvf.2	-	c.508G>A	c.(508-510)GAC>AAC	p.D170N		NM_001012968	NP_001012986	Q56A73	SPIN4_HUMAN	spindlin family, member 4	170					gamete generation					ovary(1)|lung(1)	2														0.174157	60.111414	77.951925	31	147	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	62570191	62570191	15568	23	C	T	T	T	377	29	SPIN4	2	2
FAM155B	27112	broad.mit.edu	37	X	68749571	68749571	+	Silent	SNP	G	A	A			TCGA-17-Z017-01	TCGA-17-Z017-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:68749571G>A	uc004dxk.2	+	c.1191G>A	c.(1189-1191)CAG>CAA	p.Q397Q		NM_015686	NP_056501	O75949	F155B_HUMAN	transmembrane protein 28	398						integral to membrane				ovary(1)|breast(1)	2														0.172414	10.356075	13.296919	5	24	KEEP	---	---	---	---	capture		Silent	SNP	68749571	68749571	5664	23	G	A	A	A	464	36	FAM155B	2	2
ZCCHC5	203430	broad.mit.edu	37	X	77913900	77913900	+	Silent	SNP	T	A	A			TCGA-17-Z017-01	TCGA-17-Z017-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:77913900T>A	uc004edc.1	-	c.18A>T	c.(16-18)GCA>GCT	p.A6A		NM_152694	NP_689907	Q8N8U3	ZCHC5_HUMAN	zinc finger, CCHC domain containing 5	6							nucleic acid binding|zinc ion binding			ovary(1)	1														0.227273	24.832535	27.832665	10	34	KEEP	---	---	---	---	capture		Silent	SNP	77913900	77913900	18179	23	T	A	A	A	704	55	ZCCHC5	3	3
SATL1	340562	broad.mit.edu	37	X	84363384	84363384	+	Silent	SNP	G	A	A			TCGA-17-Z017-01	TCGA-17-Z017-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:84363384G>A	uc011mqx.1	-	c.591C>T	c.(589-591)GGC>GGT	p.G197G	SATL1_uc004een.2_Silent_p.G197G	NM_001163541	NP_001157013	Q86VE3	SATL1_HUMAN	spermidine/spermine N1-acetyl transferase-like 1	10	Gln-rich.						N-acetyltransferase activity			breast(2)	2														0.235294	53.751152	60.288637	24	78	KEEP	---	---	---	---	capture		Silent	SNP	84363384	84363384	14336	23	G	A	A	A	483	38	SATL1	1	1
PABPC5	140886	broad.mit.edu	37	X	90690938	90690938	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z017-01	TCGA-17-Z017-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:90690938C>A	uc004efg.2	+	c.362C>A	c.(361-363)GCC>GAC	p.A121D	PABPC5_uc004eff.1_Intron	NM_080832	NP_543022	Q96DU9	PABP5_HUMAN	poly(A) binding protein, cytoplasmic 5	121	RRM 2.					cytoplasm	nucleotide binding|RNA binding			ovary(1)|lung(1)|pancreas(1)	3														0.169811	32.130466	43.031662	18	88	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	90690938	90690938	11783	23	C	A	A	A	338	26	PABPC5	2	2
PCDH11X	27328	broad.mit.edu	37	X	91133015	91133015	+	Silent	SNP	C	A	A			TCGA-17-Z017-01	TCGA-17-Z017-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:91133015C>A	uc004efk.1	+	c.1776C>A	c.(1774-1776)ATC>ATA	p.I592I	PCDH11X_uc004efl.1_Silent_p.I592I|PCDH11X_uc004efo.1_Silent_p.I592I|PCDH11X_uc010nmv.1_Silent_p.I592I|PCDH11X_uc004efm.1_Silent_p.I592I|PCDH11X_uc004efn.1_Silent_p.I592I|PCDH11X_uc004efh.1_Silent_p.I592I|PCDH11X_uc004efj.1_Silent_p.I592I	NM_032968	NP_116750	Q9BZA7	PC11X_HUMAN	protocadherin 11 X-linked isoform c	592	Extracellular (Potential).|Cadherin 6.				homophilic cell adhesion	integral to plasma membrane	calcium ion binding			large_intestine(2)	2						NSCLC(38;925 1092 2571 38200 45895)								0.189873	30.972566	38.085121	15	64	KEEP	---	---	---	---	capture		Silent	SNP	91133015	91133015	11928	23	C	A	A	A	369	29	PCDH11X	2	2
PCDH11X	27328	broad.mit.edu	37	X	91873562	91873562	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z017-01	TCGA-17-Z017-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:91873562C>T	uc004efk.1	+	c.3667C>T	c.(3667-3669)CCT>TCT	p.P1223S	PCDH11X_uc004efl.1_Missense_Mutation_p.P1213S|PCDH11X_uc004efo.1_Missense_Mutation_p.P1186S|PCDH11X_uc010nmv.1_3'UTR|PCDH11X_uc004efm.1_Missense_Mutation_p.P1215S|PCDH11X_uc004efn.1_Missense_Mutation_p.P1205S	NM_032968	NP_116750	Q9BZA7	PC11X_HUMAN	protocadherin 11 X-linked isoform c	1223	Cytoplasmic (Potential).				homophilic cell adhesion	integral to plasma membrane	calcium ion binding			large_intestine(2)	2						NSCLC(38;925 1092 2571 38200 45895)								0.208661	118.140864	138.101274	53	201	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	91873562	91873562	11928	23	C	T	T	T	390	30	PCDH11X	2	2
PCDH11X	27328	broad.mit.edu	37	X	91873578	91873578	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z017-01	TCGA-17-Z017-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:91873578C>A	uc004efk.1	+	c.3683C>A	c.(3682-3684)GCT>GAT	p.A1228D	PCDH11X_uc004efl.1_Missense_Mutation_p.A1218D|PCDH11X_uc004efo.1_Missense_Mutation_p.A1191D|PCDH11X_uc010nmv.1_3'UTR|PCDH11X_uc004efm.1_Missense_Mutation_p.A1220D|PCDH11X_uc004efn.1_Missense_Mutation_p.A1210D	NM_032968	NP_116750	Q9BZA7	PC11X_HUMAN	protocadherin 11 X-linked isoform c	1228	Cytoplasmic (Potential).				homophilic cell adhesion	integral to plasma membrane	calcium ion binding			large_intestine(2)	2						NSCLC(38;925 1092 2571 38200 45895)								0.19305	104.801841	127.582156	50	209	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	91873578	91873578	11928	23	C	A	A	A	364	28	PCDH11X	2	2
PCDH19	57526	broad.mit.edu	37	X	99662938	99662938	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z017-01	TCGA-17-Z017-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:99662938C>A	uc010nmz.2	-	c.658G>T	c.(658-660)GGC>TGC	p.G220C	PCDH19_uc004efw.3_Missense_Mutation_p.G220C|PCDH19_uc004efx.3_Missense_Mutation_p.G220C	NM_020766	NP_001098713	Q8TAB3	PCD19_HUMAN	protocadherin 19 isoform b	220	Cadherin 2.|Extracellular (Potential).				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(2)|breast(2)|upper_aerodigestive_tract(1)|urinary_tract(1)|skin(1)	7														0.28	17.915776	19.002869	7	18	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	99662938	99662938	11934	23	C	A	A	A	286	22	PCDH19	2	2
KRTAP5-5	439915	broad.mit.edu	37	11	1651191	1651199	+	In_Frame_Del	DEL	GGCTGTGGA	-	-	rs35089393		TCGA-17-Z017-01	TCGA-17-Z017-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:1651191_1651199delGGCTGTGGA	uc001lty.2	+	c.121_129delGGCTGTGGA	c.(121-129)GGCTGTGGAdel	p.GCG47del		NM_001001480	NP_001001480	Q701N2	KRA55_HUMAN	keratin associated protein 5-5	47_49						keratin filament				lung(1)	1		all_epithelial(84;0.00018)|Ovarian(85;0.0014)|Breast(177;0.00147)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.000614)|Lung(200;0.0681)|LUSC - Lung squamous cell carcinoma(625;0.082)										0.48			13	14		---	---	---	---	capture_indel		In_Frame_Del	DEL	1651191	1651199	8886	11	GGCTGTGGA	-	-	-	507	39	KRTAP5-5	5	5
DPEP2	64174	broad.mit.edu	37	16	68026995	68026996	+	Frame_Shift_Ins	INS	-	G	G			TCGA-17-Z017-01	TCGA-17-Z017-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:68026995_68026996insG	uc002evd.3	-	c.120_121insC	c.(118-123)CCCAGAfs	p.P40fs	DPEP2_uc010cey.2_Frame_Shift_Ins_p.P40fs|DPEP2_uc002eve.2_Frame_Shift_Ins_p.P40fs|DPEP2_uc002evf.2_Non-coding_Transcript|DPEP2_uc002evg.2_Frame_Shift_Ins_p.P40fs	NM_022355	NP_071750	Q9H4A9	DPEP2_HUMAN	dipeptidase 2 precursor	40_41					hormone biosynthetic process|leukotriene biosynthetic process|prostanoid metabolic process|proteolysis	anchored to membrane|plasma membrane	dipeptidase activity|dipeptidyl-peptidase activity|metal ion binding|metalloexopeptidase activity			skin(1)	1		Ovarian(137;0.192)		OV - Ovarian serous cystadenocarcinoma(108;0.0119)|Epithelial(162;0.0489)|all cancers(182;0.239)										0.33			2	4		---	---	---	---	capture_indel		Frame_Shift_Ins	INS	68026995	68026996	4898	16	-	G	G	G	713	55	DPEP2	5	5
SMARCA4	6597	broad.mit.edu	37	19	11107209	11107209	+	Frame_Shift_Del	DEL	C	-	-			TCGA-17-Z017-01	TCGA-17-Z017-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:11107209_11107209delC	uc010dxo.2	+	c.1801_1801delC	c.(1801-1803)CCGfs	p.P601fs	SMARCA4_uc002mqf.3_Frame_Shift_Del_p.P601fs|SMARCA4_uc010dxp.2_Frame_Shift_Del_p.P601fs|SMARCA4_uc002mqg.1_Frame_Shift_Del_p.P601fs|SMARCA4_uc010dxq.2_Frame_Shift_Del_p.P601fs|SMARCA4_uc010dxr.2_Frame_Shift_Del_p.P601fs|SMARCA4_uc002mqj.3_Frame_Shift_Del_p.P601fs|SMARCA4_uc010dxs.2_Frame_Shift_Del_p.P601fs	NM_001128849	NP_001122321	P51532	SMCA4_HUMAN	SWI/SNF-related matrix-associated	601					chromatin remodeling|negative regulation of androgen receptor signaling pathway|negative regulation of gene-specific transcription from RNA polymerase II promoter|negative regulation of S phase of mitotic cell cycle|nervous system development|positive regulation of gene-specific transcription from RNA polymerase II promoter|positive regulation of sequence-specific DNA binding transcription factor activity|transcription, DNA-dependent	nBAF complex|npBAF complex|SWI/SNF complex|WINAC complex	androgen receptor binding|ATP binding|DNA binding|DNA-dependent ATPase activity|helicase activity|histone acetyl-lysine binding|identical protein binding|p53 binding|protein N-terminus binding|transcription activator activity|transcription corepressor activity	p.?(1)		lung(29)|ovary(7)|pancreas(7)|large_intestine(5)|prostate(3)|central_nervous_system(2)|breast(2)|adrenal_gland(1)|stomach(1)|liver(1)|skin(1)|autonomic_ganglia(1)|kidney(1)	61		all_lung(6;0.0512)|Lung NSC(9;0.0568)								582				0.33			45	91		---	---	---	---	capture_indel		Frame_Shift_Del	DEL	11107209	11107209	15268	19	C	-	-	-	338	26	SMARCA4	5	5
MSH3	4437	broad.mit.edu	37	5	79950724	79950725	+	In_Frame_Ins	INS	-	CCGCAGCGC	CCGCAGCGC	rs72432994		TCGA-17-Z017-01	TCGA-17-Z017-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:79950724_79950725insCCGCAGCGC	uc003kgz.2	+	c.178_179insCCGCAGCGC	c.(178-180)GCC>GCCGCAGCGCCC	p.63_64insAAP	DHFR_uc011ctl.1_5'Flank|DHFR_uc011ctm.1_5'Flank|DHFR_uc010jap.1_5'Flank|DHFR_uc003kgx.1_Intron|DHFR_uc003kgy.1_5'UTR	NM_002439	NP_002430	P20585	MSH3_HUMAN	mutS homolog 3	63_64			Missing.		maintenance of DNA repeat elements|meiotic mismatch repair|negative regulation of DNA recombination|positive regulation of helicase activity|reciprocal meiotic recombination|somatic recombination of immunoglobulin gene segments	MutSbeta complex|nuclear chromosome	ATP binding|DNA-dependent ATPase activity|double-strand/single-strand DNA junction binding|enzyme binding|loop DNA binding|Y-form DNA binding			ovary(1)	1		Lung NSC(167;0.00479)|all_lung(232;0.00507)|Ovarian(174;0.0261)|Breast(144;0.244)		OV - Ovarian serous cystadenocarcinoma(54;2.38e-45)|Epithelial(54;1.58e-38)|all cancers(79;4.93e-33)		Melanoma(88;1010 1399 13793 26548 36275)			p.A60A(G401-Tumor)|p.A60A(UMUC1-Tumor)|p.A60A(KM12-Tumor)|p.A60A(COLO818-Tumor)|p.A60A(IGR37-Tumor)|p.A60A(NCIH1648-Tumor)|p.A60A(CI1-Tumor)|p.A60A(NCIH23-Tumor)|p.A60A(CA46-Tumor)|p.A60A(MCAS-Tumor)|p.A60A(HEC59-Tumor)|p.A60A(HS604.T-Tumor)|p.A60A(EHEB-Tumor)|p.A60A(HCC2157-Tumor)|p.A60A(CORL279-Tumor)|p.A60A(697-Tumor)|p.A60A(CAOV4-Tumor)|p.A60A(CAPAN2-Tumor)|p.A60A(NCIH1915-Tumor)|p.A60A(MFE296-Tumor)|p.A60A(COLO829-Tumor)|p.A60A(SCABER-Tumor)|p.A60A(EFE184-Tumor)|p.A60A(SF295-Tumor)|p.A60A(EB2-Tumor)|p.A60A(IGR39-Tumor)|p.A60A(CAPAN1-Tumor)	1101				0.67			4	2		---	---	---	---	capture_indel		In_Frame_Ins	INS	79950724	79950725	10264	5	-	CCGCAGCGC	CCGCAGCGC	CCGCAGCGC	546	42	MSH3	5	5
