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
KAZALD1	81621	broad.mit.edu	37	10	102824352	102824352	+	Missense_Mutation	SNP	G	T	T	rs36116329	byFrequency	TCGA-17-Z051-01	TCGA-17-Z051-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:102824352G>T	uc001ksr.2	+	c.767G>T	c.(766-768)CGC>CTC	p.R256L	KAZALD1_uc001kss.3_Non-coding_Transcript	NM_030929	NP_112191	Q96I82	KAZD1_HUMAN	Kazal-type serine peptidase inhibitor domain 1	256	Ig-like C2-type.				cell differentiation|multicellular organismal development|ossification|regulation of cell growth		insulin-like growth factor binding				0				Epithelial(162;6.21e-09)|all cancers(201;3.14e-07)										0.390244	46.186481	46.620277	16	25	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	102824352	102824352	8293	10	G	T	T	T	494	38	KAZALD1	1	1
NRAP	4892	broad.mit.edu	37	10	115423195	115423195	+	Missense_Mutation	SNP	T	G	G			TCGA-17-Z051-01	TCGA-17-Z051-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:115423195T>G	uc001lal.3	-	c.83A>C	c.(82-84)AAA>ACA	p.K28T	NRAP_uc001laj.2_Missense_Mutation_p.K28T|NRAP_uc001lak.2_Missense_Mutation_p.K28T	NM_198060	NP_932326	Q86VF7	NRAP_HUMAN	nebulin-related anchoring protein isoform S	28	LIM zinc-binding.					fascia adherens|muscle tendon junction	actin binding|muscle alpha-actinin binding|zinc ion binding			ovary(6)|central_nervous_system(3)	9		Colorectal(252;0.0233)|Breast(234;0.188)		Epithelial(162;0.00392)|all cancers(201;0.00569)										0.196078	22.618665	27.012783	10	41	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	115423195	115423195	11043	10	T	G	G	G	832	64	NRAP	4	4
CUBN	8029	broad.mit.edu	37	10	16990535	16990535	+	Silent	SNP	G	T	T			TCGA-17-Z051-01	TCGA-17-Z051-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:16990535G>T	uc001ioo.2	-	c.5151C>A	c.(5149-5151)GTC>GTA	p.V1717V		NM_001081	NP_001072	O60494	CUBN_HUMAN	cubilin precursor	1717	CUB 11.				cholesterol metabolic process|cobalamin transport|hormone biosynthetic process|lipoprotein metabolic process|receptor-mediated endocytosis|tissue homeostasis|vitamin D metabolic process	brush border membrane|cytosol|endosome membrane|extrinsic to external side of plasma membrane|lysosomal lumen|lysosomal membrane	calcium ion binding|cobalamin binding|protein homodimerization activity|receptor activity|transporter activity			ovary(9)|breast(4)|pancreas(2)|large_intestine(1)|central_nervous_system(1)|kidney(1)	18					Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)					2704				0.101449	0.2561	11.247887	7	62	KEEP	---	---	---	---	capture		Silent	SNP	16990535	16990535	4211	10	G	T	T	T	418	33	CUBN	2	2
APBB1IP	54518	broad.mit.edu	37	10	26800771	26800771	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z051-01	TCGA-17-Z051-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:26800771G>T	uc001iss.2	+	c.627G>T	c.(625-627)GAG>GAT	p.E209D	APBB1IP_uc009xks.1_Missense_Mutation_p.E209D	NM_019043	NP_061916	Q7Z5R6	AB1IP_HUMAN	amyloid beta (A4) precursor protein-binding,	209	Ras-associating.				blood coagulation|signal transduction	cytoskeleton|cytosol|focal adhesion|lamellipodium				lung(4)|skin(2)|central_nervous_system(1)	7										307				0.226891	59.804234	67.924607	27	92	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	26800771	26800771	770	10	G	T	T	T	425	33	APBB1IP	2	2
RBP3	5949	broad.mit.edu	37	10	48383953	48383953	+	Silent	SNP	G	T	T			TCGA-17-Z051-01	TCGA-17-Z051-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:48383953G>T	uc001jez.2	-	c.3279C>A	c.(3277-3279)CCC>CCA	p.P1093P		NM_002900	NP_002891	P10745	RET3_HUMAN	retinol-binding protein 3 precursor	1093	4 X approximate tandem repeats.|4.				lipid metabolic process|proteolysis|transport|visual perception	interphotoreceptor matrix	retinal binding|serine-type peptidase activity			large_intestine(1)|central_nervous_system(1)	2					Vitamin A(DB00162)									0.206897	10.934437	13.246031	6	23	KEEP	---	---	---	---	capture		Silent	SNP	48383953	48383953	13626	10	G	T	T	T	600	47	RBP3	2	2
SLC18A3	6572	broad.mit.edu	37	10	50818821	50818821	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z051-01	TCGA-17-Z051-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:50818821C>A	uc001jhw.2	+	c.35C>A	c.(34-36)GCG>GAG	p.A12E	CHAT_uc001jhv.1_Intron|CHAT_uc001jhx.1_5'Flank|CHAT_uc001jhy.1_5'Flank	NM_003055	NP_003046	Q16572	VACHT_HUMAN	vesicular acetylcholine transporter	12	Cytoplasmic (Potential).				neurotransmitter secretion	clathrin sculpted acetylcholine transport vesicle membrane|integral to plasma membrane|membrane fraction	acetylcholine transmembrane transporter activity			ovary(1)	1														0.75	9.869507	10.057184	3	1	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	50818821	50818821	14923	10	C	A	A	A	351	27	SLC18A3	1	1
CHAT	1103	broad.mit.edu	37	10	50833700	50833700	+	Splice_Site_SNP	SNP	G	T	T			TCGA-17-Z051-01	TCGA-17-Z051-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:50833700G>T	uc001jhz.2	+	c.933_splice	c.e6+1	p.Q311_splice	CHAT_uc001jhv.1_Splice_Site_SNP_p.Q193_splice|CHAT_uc001jhx.1_Splice_Site_SNP_p.Q193_splice|CHAT_uc001jhy.1_Splice_Site_SNP_p.Q193_splice|CHAT_uc001jia.2_Splice_Site_SNP_p.Q193_splice|CHAT_uc010qgs.1_Splice_Site_SNP_p.Q193_splice	NM_020549	NP_065574			choline acetyltransferase isoform 2						neurotransmitter biosynthetic process|neurotransmitter secretion	cytosol|nucleus	choline O-acetyltransferase activity			central_nervous_system(3)	3		all_neural(218;0.107)		GBM - Glioblastoma multiforme(2;0.000585)	Choline(DB00122)									0.75	20.552351	21.006247	6	2	KEEP	---	---	---	---	capture		Splice_Site_SNP	SNP	50833700	50833700	3447	10	G	T	T	T	572	44	CHAT	5	2
ARID5B	84159	broad.mit.edu	37	10	63852047	63852047	+	Missense_Mutation	SNP	T	G	G			TCGA-17-Z051-01	TCGA-17-Z051-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:63852047T>G	uc001jlt.1	+	c.2825T>G	c.(2824-2826)GTC>GGC	p.V942G		NM_032199	NP_115575	Q14865	ARI5B_HUMAN	AT rich interactive domain 5B (MRF1-like)	942					negative regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|transcription repressor activity			ovary(2)|kidney(1)	3	Prostate(12;0.016)|all_hematologic(501;0.215)													0.19084	101.542524	124.970649	50	212	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	63852047	63852047	937	10	T	G	G	G	754	58	ARID5B	4	4
NUDT13	25961	broad.mit.edu	37	10	74879877	74879877	+	Nonsense_Mutation	SNP	C	G	G			TCGA-17-Z051-01	TCGA-17-Z051-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:74879877C>G	uc001jtj.2	+	c.185C>G	c.(184-186)TCA>TGA	p.S62*	NUDT13_uc010qkc.1_5'UTR|NUDT13_uc010qkd.1_5'UTR|NUDT13_uc009xqw.2_Non-coding_Transcript|NUDT13_uc001jtk.2_Nonsense_Mutation_p.S62*|NUDT13_uc010qke.1_5'UTR|NUDT13_uc001jtl.2_Nonsense_Mutation_p.S62*	NM_015901	NP_056985	Q86X67	NUD13_HUMAN	nudix-type motif 13	62							hydrolase activity|metal ion binding				0	Prostate(51;0.0119)													0.5	61.52108	61.52108	18	18	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	74879877	74879877	11134	10	C	G	G	G	377	29	NUDT13	5	3
MYOZ1	58529	broad.mit.edu	37	10	75394386	75394386	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z051-01	TCGA-17-Z051-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:75394386C>A	uc001jur.2	-	c.358G>T	c.(358-360)GGC>TGC	p.G120C		NM_021245	NP_067068	Q9NP98	MYOZ1_HUMAN	myozenin 1	120	Gly-rich.				myofibril assembly	nucleus|pseudopodium	FATZ binding			ovary(2)	2	Prostate(51;0.0112)													0.222222	24.480525	28.311441	12	42	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	75394386	75394386	10490	10	C	A	A	A	286	22	MYOZ1	2	2
ITIH2	3698	broad.mit.edu	37	10	7763666	7763666	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z051-01	TCGA-17-Z051-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:7763666C>T	uc001ijs.2	+	c.793C>T	c.(793-795)CGG>TGG	p.R265W		NM_002216	NP_002207	P19823	ITIH2_HUMAN	inter-alpha globulin inhibitor H2 polypeptide	265					hyaluronan metabolic process	extracellular region	serine-type endopeptidase inhibitor activity			ovary(1)|pancreas(1)	2														0.560976	152.259595	152.52551	46	36	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	7763666	7763666	8208	10	C	T	T	T	295	23	ITIH2	1	1
PAPSS2	9060	broad.mit.edu	37	10	89505590	89505590	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z051-01	TCGA-17-Z051-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:89505590C>T	uc001kew.2	+	c.1723C>T	c.(1723-1725)CAC>TAC	p.H575Y	PAPSS2_uc001kex.2_Missense_Mutation_p.H570Y	NM_001015880	NP_001015880	O95340	PAPS2_HUMAN	3'-phosphoadenosine 5'-phosphosulfate synthase 2	570	Adenylyl-sulfate kinase.				3'-phosphoadenosine 5'-phosphosulfate biosynthetic process|skeletal system development|sulfate assimilation|xenobiotic metabolic process	cytosol	adenylylsulfate kinase activity|ATP binding|protein binding|sulfate adenylyltransferase (ATP) activity			central_nervous_system(1)	1		Melanoma(5;0.019)|Colorectal(252;0.123)		UCEC - Uterine corpus endometrioid carcinoma (6;0.00164)|Colorectal(12;0.000323)|COAD - Colon adenocarcinoma(12;0.00124)										0.488889	59.734551	59.739722	22	23	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	89505590	89505590	11852	10	C	T	T	T	325	25	PAPSS2	2	2
TUBB8	347688	broad.mit.edu	37	10	93941	93941	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z051-01	TCGA-17-Z051-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:93941G>T	uc001ifi.2	-	c.391C>A	c.(391-393)CAG>AAG	p.Q131K	TUBB8_uc009xhe.2_Missense_Mutation_p.Q94K|TUBB8_uc010pzs.1_Missense_Mutation_p.Q59K	NM_177987	NP_817124	Q3ZCM7	TBB8_HUMAN	tubulin, beta 8 isoform 1	131					microtubule-based movement|protein polymerization	cytoplasm|microtubule	GTP binding|GTPase activity|structural molecule activity			ovary(1)	1		all_cancers(4;0.00131)|all_lung(4;0.000777)|Lung NSC(4;0.0043)|all_epithelial(10;0.0154)|Colorectal(49;0.235)		Epithelial(11;0.00341)|all cancers(11;0.00922)|OV - Ovarian serous cystadenocarcinoma(14;0.0508)|Lung(33;0.132)		Pancreas(192;2041 3010 9013 18103)								0.186047	16.899301	20.852472	8	35	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	93941	93941	17316	10	G	T	T	T	598	46	TUBB8	2	2
MUC6	4588	broad.mit.edu	37	11	1017909	1017909	+	Missense_Mutation	SNP	A	G	G			TCGA-17-Z051-01	TCGA-17-Z051-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:1017909A>G	uc001lsw.2	-	c.4892T>C	c.(4891-4893)GTC>GCC	p.V1631A		NM_005961	NP_005952	Q6W4X9	MUC6_HUMAN	mucin 6, gastric	1631	Pro-rich.|Thr-rich.|1; truncated.|Approximate repeats.				maintenance of gastrointestinal epithelium	extracellular region	extracellular matrix structural constituent			ovary(1)	1		all_cancers(49;3.3e-08)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		all cancers(45;1.24e-24)|BRCA - Breast invasive adenocarcinoma(625;0.00031)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)										0.058824	-5.279731	12.031807	5	80	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	1017909	1017909	10374	11	A	G	G	G	130	10	MUC6	4	4
DSCAML1	57453	broad.mit.edu	37	11	117303888	117303888	+	Silent	SNP	C	G	G			TCGA-17-Z051-01	TCGA-17-Z051-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:117303888C>G	uc001prh.1	-	c.5172G>C	c.(5170-5172)CTG>CTC	p.L1724L		NM_020693	NP_065744	Q8TD84	DSCL1_HUMAN	Down syndrome cell adhesion molecule like 1	1664	Cytoplasmic (Potential).				axonogenesis|brain development|cell fate determination|dorsal/ventral pattern formation|embryonic skeletal system morphogenesis|homophilic cell adhesion	cell surface|integral to membrane|plasma membrane	protein homodimerization activity			ovary(3)|large_intestine(2)	5	all_hematologic(175;0.0487)	Breast(348;0.0424)|Medulloblastoma(222;0.0523)|all_hematologic(192;0.232)		BRCA - Breast invasive adenocarcinoma(274;9.12e-06)|Epithelial(105;0.00172)										0.402174	118.081534	118.870801	37	55	KEEP	---	---	---	---	capture		Silent	SNP	117303888	117303888	4953	11	C	G	G	G	314	25	DSCAML1	3	3
OR6M1	390261	broad.mit.edu	37	11	123676277	123676277	+	Missense_Mutation	SNP	G	C	C			TCGA-17-Z051-01	TCGA-17-Z051-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:123676277G>C	uc010rzz.1	-	c.781C>G	c.(781-783)CAG>GAG	p.Q261E		NM_001005325	NP_001005325	Q8NGM8	OR6M1_HUMAN	olfactory receptor, family 6, subfamily M,	261	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0		Breast(109;0.0109)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;4.88e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.028)										0.38806	177.97547	179.444738	52	82	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	123676277	123676277	11615	11	G	C	C	C	585	45	OR6M1	3	3
PTH	5741	broad.mit.edu	37	11	13513995	13513995	+	Missense_Mutation	SNP	T	C	C			TCGA-17-Z051-01	TCGA-17-Z051-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:13513995T>C	uc001mlb.2	-	c.305A>G	c.(304-306)GAC>GGC	p.D102G		NM_000315	NP_000306	P01270	PTHY_HUMAN	parathyroid hormone preproprotein	102					bone resorption|cAMP metabolic process|cell-cell signaling|cellular calcium ion homeostasis|cellular macromolecule biosynthetic process|induction of apoptosis by hormones|positive regulation of cAMP biosynthetic process|positive regulation of gene-specific transcription from RNA polymerase II promoter|positive regulation of glucose import|positive regulation of glycogen biosynthetic process|skeletal system development		hormone activity|peptide hormone receptor binding			ovary(1)	1				BRCA - Breast invasive adenocarcinoma(625;0.00116)|Epithelial(150;0.0357)|LUSC - Lung squamous cell carcinoma(625;0.0836)										0.223881	41.499805	46.187502	15	52	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	13513995	13513995	13212	11	T	C	C	C	754	58	PTH	4	4
NAV2	89797	broad.mit.edu	37	11	19970595	19970595	+	Missense_Mutation	SNP	A	G	G			TCGA-17-Z051-01	TCGA-17-Z051-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:19970595A>G	uc001mpr.3	+	c.2614A>G	c.(2614-2616)AAG>GAG	p.K872E	NAV2_uc001mpp.2_Missense_Mutation_p.K808E|NAV2_uc010rdm.1_Missense_Mutation_p.K895E	NM_182964	NP_892009	Q8IVL1	NAV2_HUMAN	neuron navigator 2 isoform 1	895						nucleus	ATP binding|helicase activity			ovary(1)|pancreas(1)	2														0.507246	110.412104	110.415084	35	34	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	19970595	19970595	10580	11	A	G	G	G	65	5	NAV2	4	4
OR5L1	219437	broad.mit.edu	37	11	55579435	55579435	+	Missense_Mutation	SNP	A	G	G			TCGA-17-Z051-01	TCGA-17-Z051-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:55579435A>G	uc001nhw.1	+	c.493A>G	c.(493-495)AGG>GGG	p.R165G		NM_001004738	NP_001004738	Q8NGL2	OR5L1_HUMAN	olfactory receptor, family 5, subfamily L,	165	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(2)	2		all_epithelial(135;0.208)												0.441558	476.886696	477.797901	136	172	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	55579435	55579435	11580	11	A	G	G	G	192	15	OR5L1	4	4
OR56A4	120793	broad.mit.edu	37	11	6023456	6023456	+	Missense_Mutation	SNP	G	C	C			TCGA-17-Z051-01	TCGA-17-Z051-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:6023456G>C	uc010qzv.1	-	c.923C>G	c.(922-924)ACA>AGA	p.T308R		NM_001005179	NP_001005179	Q8NGH8	O56A4_HUMAN	olfactory receptor, family 56, subfamily A,	256	Helical; Name=6; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			central_nervous_system(1)	1		Medulloblastoma(188;0.00776)|all_neural(188;0.0652)|Breast(177;0.114)		Epithelial(150;7.01e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)										0.568966	123.68525	123.926026	33	25	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	6023456	6023456	11545	11	G	C	C	C	624	48	OR56A4	3	3
BATF2	116071	broad.mit.edu	37	11	64756651	64756651	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z051-01	TCGA-17-Z051-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:64756651G>A	uc001ocf.1	-	c.775C>T	c.(775-777)CAC>TAC	p.H259Y	BATF2_uc001oce.1_Missense_Mutation_p.H174Y	NM_138456	NP_612465	Q8N1L9	BATF2_HUMAN	basic leucine zipper transcription factor,	259					regulation of transcription, DNA-dependent	nucleus	protein dimerization activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			ovary(1)	1														0.168421	29.660597	39.538436	16	79	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	64756651	64756651	1347	11	G	A	A	A	585	45	BATF2	2	2
TBX10	347853	broad.mit.edu	37	11	67402588	67402588	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z051-01	TCGA-17-Z051-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:67402588G>A	uc001omp.2	-	c.154C>T	c.(154-156)CCC>TCC	p.P52S		NM_005995	NP_005986	O75333	TBX10_HUMAN	T-box 10	52					anatomical structure morphogenesis|regulation of transcription from RNA polymerase II promoter	nucleus	DNA binding|RNA polymerase II transcription factor activity|sequence-specific DNA binding transcription factor activity				0														0.448276	37.194556	37.257665	13	16	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	67402588	67402588	16177	11	G	A	A	A	546	42	TBX10	2	2
ARNTL2	56938	broad.mit.edu	37	12	27556474	27556474	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z051-01	TCGA-17-Z051-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:27556474G>A	uc001rht.1	+	c.1586G>A	c.(1585-1587)AGG>AAG	p.R529K	ARNTL2_uc001rhw.2_Missense_Mutation_p.R492K|ARNTL2_uc010sjp.1_Missense_Mutation_p.R492K|ARNTL2_uc001rhu.1_Missense_Mutation_p.R515K|ARNTL2_uc009zji.1_Missense_Mutation_p.R495K|ARNTL2_uc001rhv.1_Missense_Mutation_p.R481K	NM_020183	NP_064568	Q8WYA1	BMAL2_HUMAN	aryl hydrocarbon receptor nuclear	529					circadian rhythm|entrainment of circadian clock|regulation of transcription from RNA polymerase II promoter	nucleus	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity|signal transducer activity|transcription regulator activity			ovary(1)	1	Colorectal(261;0.0847)|Lung SC(9;0.184)													0.272727	53.422392	56.493884	18	48	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	27556474	27556474	986	12	G	A	A	A	455	35	ARNTL2	2	2
PRICKLE1	144165	broad.mit.edu	37	12	42854161	42854161	+	Missense_Mutation	SNP	T	A	A			TCGA-17-Z051-01	TCGA-17-Z051-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:42854161T>A	uc010skv.1	-	c.1946A>T	c.(1945-1947)CAG>CTG	p.Q649L	PRICKLE1_uc001rnl.2_Missense_Mutation_p.Q649L|PRICKLE1_uc010skw.1_Missense_Mutation_p.Q649L|PRICKLE1_uc001rnm.2_Missense_Mutation_p.Q649L|PRICKLE1_uc001rnk.1_5'Flank	NM_001144881	NP_001138353	Q96MT3	PRIC1_HUMAN	prickle homolog 1	649					negative regulation of canonical Wnt receptor signaling pathway|negative regulation of transcription, DNA-dependent|positive regulation of proteasomal ubiquitin-dependent protein catabolic process|positive regulation of protein ubiquitination	cytosol|nuclear membrane	zinc ion binding			ovary(3)	3	all_cancers(12;4.25e-05)|Breast(8;0.176)			GBM - Glioblastoma multiforme(48;0.2)										0.383721	95.150463	96.171047	33	53	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	42854161	42854161	12929	12	T	A	A	A	715	55	PRICKLE1	3	3
DBX2	440097	broad.mit.edu	37	12	45410235	45410235	+	Missense_Mutation	SNP	T	A	A			TCGA-17-Z051-01	TCGA-17-Z051-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:45410235T>A	uc001rok.1	-	c.854A>T	c.(853-855)CAG>CTG	p.Q285L		NM_001004329	NP_001004329	Q6ZNG2	DBX2_HUMAN	developing brain homeobox 2	285					regulation of transcription, DNA-dependent	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription regulator activity				0	Lung SC(27;0.192)	Lung NSC(34;0.142)		GBM - Glioblastoma multiforme(48;0.0515)										0.193798	110.208968	132.778535	50	208	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	45410235	45410235	4431	12	T	A	A	A	715	55	DBX2	3	3
NACA	4666	broad.mit.edu	37	12	57110315	57110315	+	Nonsense_Mutation	SNP	G	A	A			TCGA-17-Z051-01	TCGA-17-Z051-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:57110315G>A	uc009zoy.1	-	c.4999C>T	c.(4999-5001)CAA>TAA	p.Q1667*	NACA_uc001slz.2_Intron|NACA_uc001sly.2_Intron|NACA_uc001smc.2_Intron|NACA_uc001sma.2_Intron|NACA_uc001smb.2_Intron|NACA_uc010squ.1_Intron	NM_001113203	NP_001106674	Q13765	NACA_HUMAN	nascent polypeptide-associated complex alpha	Error:Variant_position_missing_in_Q13765_after_alignment					interspecies interaction between organisms|protein transport|transcription, DNA-dependent|translation	nascent polypeptide-associated complex|nucleus	DNA binding			ovary(1)	1										449				0.375	9.323615	9.433131	3	5	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	57110315	57110315	10528	12	G	A	A	A	585	45	NACA	5	2
RB1	5925	broad.mit.edu	37	13	48941648	48941648	+	Nonsense_Mutation	SNP	C	T	T			TCGA-17-Z051-01	TCGA-17-Z051-01										Phase_I	Unspecified				Illumina GAIIx	g.chr13:48941648C>T	uc001vcb.2	+	c.958C>T	c.(958-960)CGA>TGA	p.R320*	RB1_uc010act.1_Nonsense_Mutation_p.R21*	NM_000321	NP_000312	P06400	RB_HUMAN	retinoblastoma 1	320					androgen receptor signaling pathway|cell cycle arrest|chromatin remodeling|G1 phase of mitotic cell cycle|interspecies interaction between organisms|maintenance of mitotic sister chromatid cohesion|mitotic cell cycle G1/S transition checkpoint|myoblast differentiation|negative regulation of cell growth|negative regulation of protein kinase activity|negative regulation of S phase of mitotic cell cycle|negative regulation of sequence-specific DNA binding transcription factor activity|positive regulation of mitotic metaphase/anaphase transition|protein localization to chromosome, centromeric region|Ras protein signal transduction|regulation of centromere complex assembly|regulation of cohesin localization to chromatin|regulation of lipid kinase activity|regulation of transcription involved in G1/S phase of mitotic cell cycle|S phase of mitotic cell cycle|sister chromatid biorientation	chromatin|PML body|Rb-E2F complex|SWI/SNF complex	androgen receptor binding|DNA binding|kinase binding|phosphoprotein binding|sequence-specific DNA binding transcription factor activity|transcription coactivator activity|transcription factor binding|transcription repressor activity|ubiquitin protein ligase binding	p.R320*(9)		lung(93)|eye(89)|central_nervous_system(47)|bone(22)|breast(20)|urinary_tract(17)|haematopoietic_and_lymphoid_tissue(14)|ovary(10)|soft_tissue(8)|prostate(8)|skin(7)|endometrium(5)|cervix(3)|liver(3)|salivary_gland(2)|stomach(2)|oesophagus(1)|adrenal_gland(1)|kidney(1)|gastrointestinal_tract_(site_indeterminate)(1)|pituitary(1)	355		all_cancers(8;6.9e-71)|all_epithelial(8;4.61e-22)|Acute lymphoblastic leukemia(8;1.1e-21)|all_hematologic(8;2.3e-21)|all_lung(13;1.51e-09)|Lung NSC(96;7.03e-07)|Breast(56;1.53e-05)|Prostate(109;0.000493)|Myeloproliferative disorder(33;0.0179)|Hepatocellular(98;0.0207)|all_neural(104;0.0227)|Glioma(44;0.0286)|Lung SC(185;0.0301)		GBM - Glioblastoma multiforme(2;9.98e-18)|LUSC - Lung squamous cell carcinoma(3;0.013)	Insulin Glargine recombinant(DB00047)|Insulin Lyspro recombinant(DB00046)|Insulin recombinant(DB00030)|Insulin, porcine(DB00071)		R320*(ISHIKAWAHERAKLIO02ER_ENDOMETRIUM)|R320*(GMS10_CENTRAL_NERVOUS_SYSTEM)	6	p.R320*(GMS10-Tumor)|p.R320*(ISHIKAWAHERAKLIO02ER-Tumor)|p.R320*(FTC238-Tumor)	568	TCGA GBM(7;6.82e-08)|TSP Lung(12;0.097)|TCGA Ovarian(6;0.080)			0.72549	116.589304	118.922114	37	14	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	48941648	48941648	13559	13	C	T	T	T	243	19	RB1	5	1
PCDH9	5101	broad.mit.edu	37	13	67799571	67799571	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z051-01	TCGA-17-Z051-01										Phase_I	Unspecified				Illumina GAIIx	g.chr13:67799571C>A	uc001vik.2	-	c.3002G>T	c.(3001-3003)GGC>GTC	p.G1001V	PCDH9_uc001vil.2_Missense_Mutation_p.G1001V|PCDH9_uc010thl.1_Missense_Mutation_p.G1001V|PCDH9_uc001vin.3_Missense_Mutation_p.G1001V	NM_203487	NP_982354	Q9HC56	PCDH9_HUMAN	protocadherin 9 isoform 1 precursor	1001	Cytoplasmic (Potential).				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(4)|pancreas(1)	5		Hepatocellular(98;0.0906)|Breast(118;0.107)		GBM - Glioblastoma multiforme(99;0.00819)										0.754098	144.173485	147.761529	46	15	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	67799571	67799571	11938	13	C	A	A	A	338	26	PCDH9	2	2
AHNAK2	113146	broad.mit.edu	37	14	105414449	105414449	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z051-01	TCGA-17-Z051-01										Phase_I	Unspecified				Illumina GAIIx	g.chr14:105414449G>T	uc010axc.1	-	c.7339C>A	c.(7339-7341)CCC>ACC	p.P2447T	AHNAK2_uc001ypx.2_Missense_Mutation_p.P2347T	NM_138420	NP_612429	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	2447						nucleus				ovary(1)	1		all_cancers(154;0.115)|Melanoma(154;0.155)|all_epithelial(191;0.183)	all cancers(16;0.000479)|OV - Ovarian serous cystadenocarcinoma(23;0.00659)|Epithelial(46;0.0151)|GBM - Glioblastoma multiforme(11;0.116)											0.529412	51.349112	51.374721	18	16	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	105414449	105414449	418	14	G	T	T	T	546	42	AHNAK2	2	2
MMP14	4323	broad.mit.edu	37	14	23306131	23306131	+	Silent	SNP	C	T	T			TCGA-17-Z051-01	TCGA-17-Z051-01										Phase_I	Unspecified				Illumina GAIIx	g.chr14:23306131C>T	uc001whc.2	+	c.105C>T	c.(103-105)CCC>CCT	p.P35P		NM_004995	NP_004986	P50281	MMP14_HUMAN	matrix metalloproteinase 14 preproprotein	35						extracellular matrix|integral to plasma membrane|melanosome	calcium ion binding|metalloendopeptidase activity|zinc ion binding				0	all_cancers(95;9.47e-05)			GBM - Glioblastoma multiforme(265;0.00551)								OREG0022586	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	0.059701	-5.545667	8.036225	4	63	KEEP	---	---	---	---	capture		Silent	SNP	23306131	23306131	10043	14	C	T	T	T	288	23	MMP14	1	1
WDHD1	11169	broad.mit.edu	37	14	55493492	55493492	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z051-01	TCGA-17-Z051-01										Phase_I	Unspecified				Illumina GAIIx	g.chr14:55493492C>T	uc001xbm.1	-	c.14G>A	c.(13-15)CGG>CAG	p.R5Q	WDHD1_uc001xbn.1_Intron|SOCS4_uc001xbo.2_5'Flank|SOCS4_uc001xbp.2_5'Flank	NM_007086	NP_009017	O75717	WDHD1_HUMAN	WD repeat and HMG-box DNA binding protein 1	5						cytoplasm|nucleoplasm	DNA binding				0										606				0.05036	-14.575843	15.199989	7	132	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	55493492	55493492	17844	14	C	T	T	T	299	23	WDHD1	1	1
TUBGCP5	114791	broad.mit.edu	37	15	22848330	22848330	+	Missense_Mutation	SNP	A	T	T			TCGA-17-Z051-01	TCGA-17-Z051-01										Phase_I	Unspecified				Illumina GAIIx	g.chr15:22848330A>T	uc001yuq.2	+	c.920A>T	c.(919-921)CAT>CTT	p.H307L	TUBGCP5_uc001yur.3_Missense_Mutation_p.H307L|TUBGCP5_uc010axz.1_5'Flank	NM_001102610	NP_001096080	Q96RT8	GCP5_HUMAN	tubulin, gamma complex associated protein 5	307					G2/M transition of mitotic cell cycle|microtubule nucleation	cytosol|gamma-tubulin ring complex|microtubule|spindle pole	microtubule binding				0		all_cancers(20;2.26e-25)|all_epithelial(15;2.1e-22)|Lung NSC(15;3.36e-17)|all_lung(15;1.04e-16)|Breast(32;0.000776)|Colorectal(260;0.0488)		all cancers(64;2.86e-06)|Epithelial(43;2.63e-05)|BRCA - Breast invasive adenocarcinoma(123;0.000949)										0.434783	63.193762	63.364145	20	26	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	22848330	22848330	17324	15	A	T	T	T	104	8	TUBGCP5	3	3
GABRG3	2567	broad.mit.edu	37	15	27271912	27271912	+	Missense_Mutation	SNP	G	T	T	rs79497756		TCGA-17-Z051-01	TCGA-17-Z051-01										Phase_I	Unspecified				Illumina GAIIx	g.chr15:27271912G>T	uc001zbg.1	+	c.214G>T	c.(214-216)GTA>TTA	p.V72L	GABRG3_uc001zbf.2_Missense_Mutation_p.V72L	NM_033223	NP_150092	Q99928	GBRG3_HUMAN	gamma-aminobutyric acid (GABA) A receptor, gamma	72	Extracellular (Probable).				gamma-aminobutyric acid signaling pathway|synaptic transmission	cell junction|chloride channel complex|postsynaptic membrane	chloride channel activity|extracellular ligand-gated ion channel activity				0		all_lung(180;4.58e-12)|Breast(32;0.000625)|Colorectal(260;0.235)		all cancers(64;3.15e-07)|Epithelial(43;1.17e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0261)		NSCLC(114;800 1656 7410 37729 45293)								0.24	17.038856	18.580216	6	19	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	27271912	27271912	6424	15	G	T	T	T	520	40	GABRG3	1	1
APBA2	321	broad.mit.edu	37	15	29398932	29398932	+	Silent	SNP	G	T	T			TCGA-17-Z051-01	TCGA-17-Z051-01										Phase_I	Unspecified				Illumina GAIIx	g.chr15:29398932G>T	uc001zck.2	+	c.1827G>T	c.(1825-1827)TCG>TCT	p.S609S	APBA2_uc010azj.2_Silent_p.S597S|APBA2_uc010uat.1_Silent_p.S597S|APBA2_uc001zcl.2_Silent_p.S597S	NM_005503	NP_005494	Q99767	APBA2_HUMAN	amyloid beta A4 precursor protein-binding,	609	PDZ 1.				nervous system development|protein transport		protein binding				0		all_lung(180;1.73e-12)|Breast(32;2.89e-05)|Colorectal(260;0.234)		all cancers(64;7.44e-11)|Epithelial(43;5.74e-10)|GBM - Glioblastoma multiforme(186;0.026)|BRCA - Breast invasive adenocarcinoma(123;0.0286)|Lung(196;0.24)										0.210526	8.695091	10.164584	4	15	KEEP	---	---	---	---	capture		Silent	SNP	29398932	29398932	767	15	G	T	T	T	496	39	APBA2	1	1
POLG	5428	broad.mit.edu	37	15	89865208	89865209	+	Missense_Mutation	DNP	GG	AC	AC			TCGA-17-Z051-01	TCGA-17-Z051-01										Phase_I	Unspecified				Illumina GAIIx	g.chr15:89865208_89865209GG>AC	uc002bns.3	-	c.2464_2465CC>GT	c.(2464-2466)CCC>GTC	p.P822V	POLG_uc002bnr.3_Missense_Mutation_p.P822V	NM_002693	NP_002684	P54098	DPOG1_HUMAN	DNA-directed DNA polymerase gamma	822					base-excision repair, gap-filling|DNA-dependent DNA replication	mitochondrial nucleoid	DNA binding|DNA-directed DNA polymerase activity|protease binding			ovary(1)|lung(1)	2	Lung NSC(78;0.0472)|all_lung(78;0.089)		STAD - Stomach adenocarcinoma(125;0.165)			Colon(73;648 1203 11348 18386 27782)								0.464789	94.156779	94.234208	33	38	KEEP	---	---	---	---	capture		Missense_Mutation	DNP	89865208	89865209	12628	15	GG	AC	AC	AC	559	43	POLG	2	2
TBC1D24	57465	broad.mit.edu	37	16	2546726	2546726	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z051-01	TCGA-17-Z051-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:2546726G>A	uc002cql.2	+	c.577G>A	c.(577-579)GCG>ACG	p.A193T	TBC1D24_uc002cqk.2_Missense_Mutation_p.A193T|TBC1D24_uc002cqm.2_Missense_Mutation_p.A193T|TBC1D24_uc010bsm.2_5'Flank	NM_020705	NP_065756	Q9ULP9	TBC24_HUMAN	TBC1 domain family, member 24	193	Rab-GAP TBC.				neuron projection development	cytoplasm	protein binding|Rab GTPase activator activity				0														0.434783	26.728871	26.816741	10	13	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	2546726	2546726	16136	16	G	A	A	A	546	42	TBC1D24	2	2
ABCC12	94160	broad.mit.edu	37	16	48162431	48162431	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z051-01	TCGA-17-Z051-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:48162431G>A	uc002efc.1	-	c.1454C>T	c.(1453-1455)CCA>CTA	p.P485L	ABCC12_uc002eey.1_Non-coding_Transcript|ABCC12_uc002eez.1_Non-coding_Transcript|ABCC12_uc002efa.1_Non-coding_Transcript|ABCC12_uc002efb.1_Non-coding_Transcript|ABCC12_uc002efd.1_Non-coding_Transcript|ABCC12_uc002efe.1_Missense_Mutation_p.P485L	NM_033226	NP_150229	Q96J65	MRP9_HUMAN	ATP-binding cassette protein C12	485	ABC transporter 1.					integral to membrane	ATP binding|ATPase activity, coupled to transmembrane movement of substances			ovary(2)	2		all_cancers(37;0.0474)|all_lung(18;0.047)												0.078603	-1.42711	40.13039	18	211	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	48162431	48162431	53	16	G	A	A	A	611	47	ABCC12	2	2
ABCC11	85320	broad.mit.edu	37	16	48244989	48244989	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z051-01	TCGA-17-Z051-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:48244989C>T	uc002eff.1	-	c.1478G>A	c.(1477-1479)GGG>GAG	p.G493E	ABCC11_uc002efg.1_Missense_Mutation_p.G493E|ABCC11_uc002efh.1_Missense_Mutation_p.G493E|ABCC11_uc010vgk.1_Non-coding_Transcript	NM_033151	NP_149163	Q96J66	ABCCB_HUMAN	ATP-binding cassette, sub-family C, member 11	493	Cytoplasmic (Potential).					integral to membrane	ATP binding|ATPase activity, coupled to transmembrane movement of substances			ovary(3)|central_nervous_system(1)	4		all_cancers(37;0.127)|all_lung(18;0.132)|Breast(268;0.166)												0.169173	94.724701	122.272803	45	221	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	48244989	48244989	52	16	C	T	T	T	286	22	ABCC11	2	2
NUP93	9688	broad.mit.edu	37	16	56866268	56866268	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z051-01	TCGA-17-Z051-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:56866268C>T	uc002eka.2	+	c.1313C>T	c.(1312-1314)TCA>TTA	p.S438L	NUP93_uc002ekb.2_Missense_Mutation_p.S315L|NUP93_uc010vhi.1_Missense_Mutation_p.S315L	NM_014669	NP_055484	Q8N1F7	NUP93_HUMAN	nucleoporin 93kDa	438					carbohydrate metabolic process|glucose transport|mRNA transport|protein transport|regulation of glucose transport|transmembrane transport|viral reproduction	nuclear pore	protein binding			ovary(1)|lung(1)	2						Colon(33;610 796 1305 1705 38917)								0.05102	-22.525277	19.345001	10	186	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	56866268	56866268	11177	16	C	T	T	T	377	29	NUP93	2	2
RSPRY1	89970	broad.mit.edu	37	16	57261339	57261339	+	Missense_Mutation	SNP	C	G	G			TCGA-17-Z051-01	TCGA-17-Z051-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:57261339C>G	uc002elb.2	+	c.1247C>G	c.(1246-1248)CCT>CGT	p.P416R	RSPRY1_uc002elc.2_Missense_Mutation_p.P416R|RSPRY1_uc002eld.2_Missense_Mutation_p.P416R	NM_133368	NP_588609	Q96DX4	RSPRY_HUMAN	ring finger and SPRY domain containing 1	416	B30.2/SPRY.					extracellular region	zinc ion binding			ovary(1)	1														0.148936	9.669208	15.282624	7	40	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	57261339	57261339	14193	16	C	G	G	G	312	24	RSPRY1	3	3
MLKL	197259	broad.mit.edu	37	16	74729467	74729467	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z051-01	TCGA-17-Z051-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:74729467G>T	uc002fdb.2	-	c.189C>A	c.(187-189)AAC>AAA	p.N63K	MLKL_uc002fdc.2_Missense_Mutation_p.N63K	NM_152649	NP_689862	Q8NB16	MLKL_HUMAN	mixed lineage kinase domain-like isoform 1	63					protein phosphorylation		ATP binding|protein binding|protein kinase activity			stomach(2)	2										182				0.340909	84.315656	86.287665	30	58	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	74729467	74729467	10009	16	G	T	T	T	568	44	MLKL	2	2
MYOCD	93649	broad.mit.edu	37	17	12642628	12642628	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z051-01	TCGA-17-Z051-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:12642628G>A	uc002gno.2	+	c.700G>A	c.(700-702)GTG>ATG	p.V234M	MYOCD_uc002gnn.2_Missense_Mutation_p.V234M|MYOCD_uc002gnp.1_Missense_Mutation_p.V138M	NM_001146312	NP_001139784	Q8IZQ8	MYCD_HUMAN	myocardin isoform 1	234					cardiac cell differentiation|positive regulation of gene-specific transcription from RNA polymerase II promoter|positive regulation of smooth muscle contraction|regulation of smooth muscle cell differentiation|transcription, DNA-dependent	nucleus	nucleic acid binding|transcription factor binding			central_nervous_system(2)|ovary(1)	3				UCEC - Uterine corpus endometrioid carcinoma (92;0.0969)										0.085714	0.504472	6.588156	3	32	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	12642628	12642628	10482	17	G	A	A	A	520	40	MYOCD	1	1
AARSD1	80755	broad.mit.edu	37	17	41106915	41106915	+	Nonsense_Mutation	SNP	C	A	A			TCGA-17-Z051-01	TCGA-17-Z051-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:41106915C>A	uc002icf.2	-	c.1453G>T	c.(1453-1455)GGA>TGA	p.G485*	AARSD1_uc002icc.2_Nonsense_Mutation_p.G311*|AARSD1_uc002icd.2_Nonsense_Mutation_p.G424*|AARSD1_uc002ice.2_Nonsense_Mutation_p.G394*|AARSD1_uc010whg.1_Nonsense_Mutation_p.G485*	NM_025267	NP_079543	Q9BTE6	AASD1_HUMAN	alanyl-tRNA synthetase domain containing 1	311					alanyl-tRNA aminoacylation	cytoplasm	alanine-tRNA ligase activity|ATP binding|metal ion binding|nucleic acid binding				0		Breast(137;0.00499)		BRCA - Breast invasive adenocarcinoma(366;0.161)										0.330986	131.723163	135.294964	47	95	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	41106915	41106915	22	17	C	A	A	A	286	22	AARSD1	5	2
KIF2B	84643	broad.mit.edu	37	17	51901864	51901864	+	Silent	SNP	T	A	A			TCGA-17-Z051-01	TCGA-17-Z051-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:51901864T>A	uc002iua.2	+	c.1470T>A	c.(1468-1470)CCT>CCA	p.P490P		NM_032559	NP_115948	Q8N4N8	KIF2B_HUMAN	kinesin family member 2B	490					blood coagulation|cell division|microtubule depolymerization|microtubule-based movement|mitotic prometaphase|regulation of chromosome segregation	condensed chromosome kinetochore|cytosol|microtubule|microtubule organizing center|nucleolus|spindle	ATP binding|microtubule motor activity			ovary(5)	5														0.348624	105.584897	107.80338	38	71	KEEP	---	---	---	---	capture		Silent	SNP	51901864	51901864	8609	17	T	A	A	A	691	54	KIF2B	3	3
COLEC12	81035	broad.mit.edu	37	18	346516	346516	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z051-01	TCGA-17-Z051-01										Phase_I	Unspecified				Illumina GAIIx	g.chr18:346516G>T	uc002kkm.2	-	c.1106C>A	c.(1105-1107)ACC>AAC	p.T369N		NM_130386	NP_569057	Q5KU26	COL12_HUMAN	collectin sub-family member 12	369	Extracellular (Potential).				carbohydrate mediated signaling|innate immune response|phagocytosis, recognition|protein homooligomerization	collagen|integral to membrane	galactose binding|low-density lipoprotein particle binding|metal ion binding|pattern recognition receptor activity|scavenger receptor activity			ovary(1)|pancreas(1)	2		all_cancers(4;0.0442)|Myeloproliferative disorder(11;0.0426)												0.42268	122.154975	122.661601	41	56	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	346516	346516	3850	18	G	T	T	T	572	44	COLEC12	2	2
CYP4F12	66002	broad.mit.edu	37	19	15791312	15791312	+	Missense_Mutation	SNP	A	T	T			TCGA-17-Z051-01	TCGA-17-Z051-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:15791312A>T	uc002nbl.2	+	c.508A>T	c.(508-510)AGT>TGT	p.S170C	CYP4F12_uc010xoo.1_Missense_Mutation_p.S170C|CYP4F12_uc010xop.1_3'UTR	NM_023944	NP_076433	Q9HCS2	CP4FC_HUMAN	cytochrome P450, family 4, subfamily F,	170					oxidation-reduction process|xenobiotic metabolic process	endoplasmic reticulum membrane|integral to membrane|microsome	aromatase activity|electron carrier activity|heme binding|oxygen binding			ovary(2)|central_nervous_system(2)	4	Acute lymphoblastic leukemia(2;0.0367)													0.282051	28.008136	29.673018	11	28	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	15791312	15791312	4352	19	A	T	T	T	143	11	CYP4F12	3	3
ZNF681	148213	broad.mit.edu	37	19	23926607	23926607	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z051-01	TCGA-17-Z051-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:23926607C>T	uc002nrk.3	-	c.1745G>A	c.(1744-1746)AGA>AAA	p.R582K	ZNF681_uc002nrl.3_Missense_Mutation_p.R513K|ZNF681_uc002nrj.3_Missense_Mutation_p.R513K	NM_138286	NP_612143	Q96N22	ZN681_HUMAN	zinc finger protein 681	582	C2H2-type 15.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0		all_lung(12;0.11)|Lung NSC(12;0.163)|all_epithelial(12;0.206)												0.240741	33.645959	36.959268	13	41	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	23926607	23926607	18683	19	C	T	T	T	416	32	ZNF681	2	2
ZBTB32	27033	broad.mit.edu	37	19	36207448	36207448	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z051-01	TCGA-17-Z051-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:36207448C>A	uc002oay.2	+	c.1258C>A	c.(1258-1260)CTG>ATG	p.L420M	ZBTB32_uc002oaz.2_Non-coding_Transcript|MLL4_uc010eei.2_5'Flank	NM_014383	NP_055198	Q9Y2Y4	ZBT32_HUMAN	zinc finger and BTB domain containing 32	420	C2H2-type 2.				DNA repair|negative regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	nucleoplasm	DNA binding|protein binding|specific RNA polymerase II transcription factor activity|transcription corepressor activity|zinc ion binding			ovary(1)	1	all_lung(56;2.22e-07)|Lung NSC(56;3.47e-07)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0515)									OREG0025433	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	0.327731	100.478587	103.613328	39	80	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	36207448	36207448	18121	19	C	A	A	A	311	24	ZBTB32	2	2
SPTBN4	57731	broad.mit.edu	37	19	41019462	41019462	+	Splice_Site_SNP	SNP	G	T	T			TCGA-17-Z051-01	TCGA-17-Z051-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:41019462G>T	uc002ony.2	+	c.2765_splice	c.e14+1	p.R922_splice	SPTBN4_uc002onx.2_Splice_Site_SNP_p.R922_splice|SPTBN4_uc002onz.2_Splice_Site_SNP_p.R922_splice|SPTBN4_uc010egx.2_Splice_Site_SNP	NM_020971	NP_066022			spectrin, beta, non-erythrocytic 4 isoform						actin filament capping|axon guidance|cytoskeletal anchoring at plasma membrane|vesicle-mediated transport	cytosol|nuclear matrix|PML body|spectrin	actin binding|ankyrin binding|structural constituent of cytoskeleton			ovary(3)|central_nervous_system(1)	4			Lung(22;0.000114)|LUSC - Lung squamous cell carcinoma(20;0.000384)											0.4	25.697452	25.87192	8	12	KEEP	---	---	---	---	capture		Splice_Site_SNP	SNP	41019462	41019462	15635	19	G	T	T	T	572	44	SPTBN4	5	2
GIPR	2696	broad.mit.edu	37	19	46184989	46184989	+	Silent	SNP	G	T	T			TCGA-17-Z051-01	TCGA-17-Z051-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:46184989G>T	uc002pcu.1	+	c.1197G>T	c.(1195-1197)GTG>GTT	p.V399V	GIPR_uc002pct.1_3'UTR|GIPR_uc010xxp.1_Silent_p.V363V|GIPR_uc010xxq.1_Non-coding_Transcript	NM_000164	NP_000155	P48546	GIPR_HUMAN	gastric inhibitory polypeptide receptor	399	Cytoplasmic (Potential).				generation of precursor metabolites and energy|response to nutrient	integral to membrane|plasma membrane					0		Ovarian(192;0.051)|all_neural(266;0.112)		OV - Ovarian serous cystadenocarcinoma(262;0.0056)|GBM - Glioblastoma multiforme(486;0.0832)|Epithelial(262;0.199)										0.75	46.432153	47.56972	15	5	KEEP	---	---	---	---	capture		Silent	SNP	46184989	46184989	6663	19	G	T	T	T	587	46	GIPR	2	2
LRRC4B	94030	broad.mit.edu	37	19	51022505	51022505	+	Silent	SNP	C	T	T			TCGA-17-Z051-01	TCGA-17-Z051-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:51022505C>T	uc002pss.2	-	c.465G>A	c.(463-465)GAG>GAA	p.E155E		NM_001080457	NP_001073926	Q9NT99	LRC4B_HUMAN	leucine rich repeat containing 4B precursor	155	LRR 3.|Extracellular (Potential).					cell junction|integral to membrane|presynaptic membrane				central_nervous_system(1)	1		all_neural(266;0.131)		OV - Ovarian serous cystadenocarcinoma(262;0.00284)|GBM - Glioblastoma multiforme(134;0.0188)										0.305882	68.347583	71.188074	26	59	KEEP	---	---	---	---	capture		Silent	SNP	51022505	51022505	9382	19	C	T	T	T	259	20	LRRC4B	2	2
ZNF468	90333	broad.mit.edu	37	19	53344722	53344722	+	Silent	SNP	C	T	T			TCGA-17-Z051-01	TCGA-17-Z051-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:53344722C>T	uc002qaf.2	-	c.825G>A	c.(823-825)GAG>GAA	p.E275E	ZNF468_uc002qae.2_Silent_p.E222E	NM_001008801	NP_001008801	Q5VIY5	ZN468_HUMAN	zinc finger protein ZNF468 isoform 2	275	C2H2-type 3.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(2)	2				GBM - Glioblastoma multiforme(134;0.0358)										0.0875	8.581858	49.904753	21	219	KEEP	---	---	---	---	capture		Silent	SNP	53344722	53344722	18521	19	C	T	T	T	259	20	ZNF468	2	2
CACNG6	59285	broad.mit.edu	37	19	54496139	54496139	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z051-01	TCGA-17-Z051-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:54496139G>T	uc002qct.2	+	c.8G>T	c.(7-9)TGG>TTG	p.W3L	CACNG6_uc002qcu.2_Missense_Mutation_p.W3L|CACNG6_uc002qcv.2_Missense_Mutation_p.W3L	NM_145814	NP_665813	Q9BXT2	CCG6_HUMAN	voltage-dependent calcium channel gamma-6	3						voltage-gated calcium channel complex	voltage-gated calcium channel activity			ovary(2)	2	all_cancers(19;0.0128)|all_epithelial(19;0.00564)|all_lung(19;0.031)|Lung NSC(19;0.0358)|Ovarian(34;0.19)			GBM - Glioblastoma multiforme(134;0.168)										0.25	44.2809	48.611258	19	57	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	54496139	54496139	2677	19	G	T	T	T	611	47	CACNG6	2	2
ZNF667	63934	broad.mit.edu	37	19	56973727	56973727	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z051-01	TCGA-17-Z051-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:56973727G>A	uc002qnd.2	-	c.13C>T	c.(13-15)CGG>TGG	p.R5W	ZNF667_uc010etl.2_De_novo_Start_OutOfFrame|ZNF667_uc002qne.2_Missense_Mutation_p.R5W|ZNF667_uc010etm.2_De_novo_Start_InFrame	NM_022103	NP_071386	Q5HYK9	ZN667_HUMAN	zinc finger protein 667	5					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			pancreas(1)	1		Colorectal(82;0.000256)|Ovarian(87;0.243)		GBM - Glioblastoma multiforme(193;0.0615)										0.253071	253.033084	275.50509	103	304	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	56973727	56973727	18669	19	G	A	A	A	519	40	ZNF667	1	1
SPAG17	200162	broad.mit.edu	37	1	118579413	118579413	+	Missense_Mutation	SNP	C	G	G			TCGA-17-Z051-01	TCGA-17-Z051-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:118579413C>G	uc001ehk.2	-	c.3413G>C	c.(3412-3414)GGA>GCA	p.G1138A		NM_206996	NP_996879	Q6Q759	SPG17_HUMAN	sperm associated antigen 17	1138						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)										0.5	18.775282	18.775282	5	5	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	118579413	118579413	15482	1	C	G	G	G	390	30	SPAG17	3	3
MTMR11	10903	broad.mit.edu	37	1	149902342	149902342	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z051-01	TCGA-17-Z051-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:149902342C>T	uc001etl.3	-	c.1562G>A	c.(1561-1563)CGT>CAT	p.R521H	SF3B4_uc001etj.1_5'Flank|SF3B4_uc001etk.1_5'Flank|SF3B4_uc009wll.1_5'Flank|MTMR11_uc001etm.1_Missense_Mutation_p.R449H|MTMR11_uc010pbm.1_3'UTR	NM_001145862	NP_001139334	A4FU01	MTMRB_HUMAN	myotubularin related protein 11 isoform a	521	Myotubularin phosphatase.						phosphatase activity			central_nervous_system(1)	1	Breast(34;0.0009)|Ovarian(49;0.0377)|all_hematologic(923;0.0597)|Hepatocellular(266;0.161)|Colorectal(459;0.171)		LUSC - Lung squamous cell carcinoma(543;0.221)|STAD - Stomach adenocarcinoma(528;0.247)						p.R493H(HS839.T-Tumor)|p.R493H(HCC366-Tumor)|p.R493H(BICR31-Tumor)|p.R493H(MC116-Tumor)|p.R493H(42MGBA-Tumor)|p.R493H(UACC257-Tumor)|p.R493H(U2OS-Tumor)|p.R493H(K029AX-Tumor)	238				0.161359	133.924672	185.302761	76	395	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	149902342	149902342	10333	1	C	T	T	T	247	19	MTMR11	1	1
THEM5	284486	broad.mit.edu	37	1	151820329	151820329	+	Silent	SNP	G	T	T			TCGA-17-Z051-01	TCGA-17-Z051-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:151820329G>T	uc009wnd.2	-	c.585C>A	c.(583-585)CCC>CCA	p.P195P		NM_182578	NP_872384	Q8N1Q8	THEM5_HUMAN	thioesterase superfamily member 5	195							hydrolase activity			ovary(1)	1	Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.14)		LUSC - Lung squamous cell carcinoma(543;0.181)											0.268657	48.738305	51.96346	18	49	KEEP	---	---	---	---	capture		Silent	SNP	151820329	151820329	16387	1	G	T	T	T	496	39	THEM5	1	1
FLG	2312	broad.mit.edu	37	1	152286011	152286011	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z051-01	TCGA-17-Z051-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:152286011G>T	uc001ezu.1	-	c.1351C>A	c.(1351-1353)CAA>AAA	p.Q451K		NM_002016	NP_002007	P20930	FILA_HUMAN	filaggrin	451	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)											0.213018	77.195989	90.07458	36	133	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	152286011	152286011	6160	1	G	T	T	T	611	47	FLG	2	2
GBA	2629	broad.mit.edu	37	1	155208062	155208062	+	Silent	SNP	C	T	T			TCGA-17-Z051-01	TCGA-17-Z051-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:155208062C>T	uc001fjh.2	-	c.624G>A	c.(622-624)CAG>CAA	p.Q208Q	RAG1AP1_uc010pey.1_Intron|GBA_uc010pfw.1_Silent_p.Q95Q|GBA_uc010pfx.1_Silent_p.Q159Q|GBA_uc001fji.2_Silent_p.Q208Q|GBA_uc001fjj.2_Silent_p.Q208Q|GBA_uc001fjk.2_Silent_p.Q208Q|GBA_uc001fjl.2_Silent_p.Q208Q|GBA_uc010pfy.1_Silent_p.Q121Q|GBA_uc009wqk.1_Silent_p.Q121Q	NM_000157	NP_000148	P04062	GLCM_HUMAN	glucocerebrosidase precursor	208					carbohydrate metabolic process|cell death|lysosome organization|sphingolipid metabolic process	lysosomal membrane	cation binding|glucosylceramidase activity|protein binding			ovary(1)	1	all_lung(78;2.32e-23)|Hepatocellular(266;0.0877)|all_hematologic(923;0.088)		Epithelial(20;3.72e-10)|all cancers(21;1.19e-09)|BRCA - Breast invasive adenocarcinoma(34;0.000752)|LUSC - Lung squamous cell carcinoma(543;0.193)		Alglucerase(DB00088)|Imiglucerase(DB00053)									0.166667	19.143871	24.829818	9	45	KEEP	---	---	---	---	capture		Silent	SNP	155208062	155208062	6532	1	C	T	T	T	363	28	GBA	2	2
OR10J3	441911	broad.mit.edu	37	1	159283909	159283909	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z051-01	TCGA-17-Z051-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:159283909C>A	uc010piu.1	-	c.541G>T	c.(541-543)GAT>TAT	p.D181Y		NM_001004467	NP_001004467	Q5JRS4	O10J3_HUMAN	olfactory receptor, family 10, subfamily J,	181	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(2)	2	all_hematologic(112;0.0429)													0.509091	170.496551	170.504374	56	54	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	159283909	159283909	11317	1	C	A	A	A	377	29	OR10J3	2	2
DUSP27	92235	broad.mit.edu	37	1	167086710	167086710	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z051-01	TCGA-17-Z051-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:167086710C>A	uc001geb.1	+	c.351C>A	c.(349-351)GAC>GAA	p.D117E		NM_001080426	NP_001073895	Q5VZP5	DUS27_HUMAN	dual specificity phosphatase 27	117					protein dephosphorylation		protein tyrosine/serine/threonine phosphatase activity			ovary(3)	3														0.47619	28.836077	28.847062	10	11	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	167086710	167086710	5009	1	C	A	A	A	233	18	DUSP27	2	2
ARL8A	127829	broad.mit.edu	37	1	202103614	202103614	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z051-01	TCGA-17-Z051-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:202103614G>A	uc001gxk.1	-	c.542C>T	c.(541-543)TCG>TTG	p.S181L		NM_138795	NP_620150	Q96BM9	ARL8A_HUMAN	ADP-ribosylation factor-like 8A	181					cell division|chromosome segregation|mitosis|small GTPase mediated signal transduction	late endosome membrane|lysosomal membrane|midbody|spindle midzone	alpha-tubulin binding|beta-tubulin binding|GTP binding|GTPase activity			ovary(2)	2														0.258278	95.993611	103.964371	39	112	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	202103614	202103614	964	1	G	A	A	A	481	37	ARL8A	1	1
ZC3H11A	9877	broad.mit.edu	37	1	203798755	203798755	+	Missense_Mutation	SNP	G	C	C			TCGA-17-Z051-01	TCGA-17-Z051-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:203798755G>C	uc001hac.2	+	c.475G>C	c.(475-477)GCT>CCT	p.A159P	ZC3H11A_uc001had.2_Missense_Mutation_p.A159P|ZC3H11A_uc001hae.2_Missense_Mutation_p.A159P|ZC3H11A_uc001haf.2_Missense_Mutation_p.A159P|ZC3H11A_uc010pqm.1_Missense_Mutation_p.A105P|ZC3H11A_uc001hag.1_Missense_Mutation_p.A159P	NM_014827	NP_055642	O75152	ZC11A_HUMAN	zinc finger CCCH-type containing 11A	159							nucleic acid binding|protein binding|zinc ion binding			lung(1)|central_nervous_system(1)	2	all_cancers(21;0.0904)|all_epithelial(62;0.234)		BRCA - Breast invasive adenocarcinoma(75;0.109)											0.139623	73.92087	107.139779	37	228	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	203798755	203798755	18148	1	G	C	C	C	598	46	ZC3H11A	3	3
EYA3	2140	broad.mit.edu	37	1	28319944	28319944	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z051-01	TCGA-17-Z051-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:28319944C>T	uc001bpi.1	-	c.1270G>A	c.(1270-1272)GAA>AAA	p.E424K	EYA3_uc010ofs.1_Missense_Mutation_p.E371K|EYA3_uc010oft.1_Missense_Mutation_p.E378K|EYA3_uc001bpj.2_Missense_Mutation_p.E378K|EYA3_uc001bpk.1_Non-coding_Transcript|EYA3_uc010ofu.1_Non-coding_Transcript	NM_001990	NP_001981	Q99504	EYA3_HUMAN	eyes absent 3	424					anatomical structure morphogenesis|double-strand break repair|histone dephosphorylation|multicellular organismal development|positive regulation of DNA repair|regulation of transcription, DNA-dependent|response to ionizing radiation|transcription, DNA-dependent|visual perception	cytoplasm	metal ion binding|protein binding|protein tyrosine phosphatase activity			ovary(2)	2		Colorectal(325;3.46e-05)|all_lung(284;0.000414)|Lung NSC(340;0.000432)|Renal(390;0.00121)|Breast(348;0.00345)|Ovarian(437;0.00503)|all_neural(195;0.0208)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0484)|OV - Ovarian serous cystadenocarcinoma(117;1.25e-24)|Colorectal(126;2.96e-08)|COAD - Colon adenocarcinoma(152;2.8e-06)|STAD - Stomach adenocarcinoma(196;0.00364)|KIRC - Kidney renal clear cell carcinoma(1967;0.00378)|BRCA - Breast invasive adenocarcinoma(304;0.00718)|READ - Rectum adenocarcinoma(331;0.0642)										0.078014	-0.284068	25.384301	11	130	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	28319944	28319944	5524	1	C	T	T	T	416	32	EYA3	2	2
GJA9	81025	broad.mit.edu	37	1	39340384	39340384	+	Missense_Mutation	SNP	G	C	C			TCGA-17-Z051-01	TCGA-17-Z051-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:39340384G>C	uc001cct.1	-	c.1387C>G	c.(1387-1389)CAA>GAA	p.Q463E	RRAGC_uc001ccr.2_5'Flank|MYCBP_uc001ccs.2_5'Flank	NM_030772	NP_110399	P57773	CXA9_HUMAN	gap junction protein, alpha 9, 59kDa	463	Cytoplasmic (Potential).				cell communication	connexon complex|integral to membrane					0	Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0393)	OV - Ovarian serous cystadenocarcinoma(33;8.23e-17)											0.129771	30.776747	48.259689	17	114	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	39340384	39340384	6674	1	G	C	C	C	585	45	GJA9	3	3
GJA9	81025	broad.mit.edu	37	1	39341674	39341674	+	Nonsense_Mutation	SNP	G	A	A			TCGA-17-Z051-01	TCGA-17-Z051-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:39341674G>A	uc001cct.1	-	c.97C>T	c.(97-99)CGA>TGA	p.R33*	RRAGC_uc001ccr.2_5'Flank|MYCBP_uc001ccs.2_5'Flank	NM_030772	NP_110399	P57773	CXA9_HUMAN	gap junction protein, alpha 9, 59kDa	33	Helical; (Potential).				cell communication	connexon complex|integral to membrane					0	Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0393)	OV - Ovarian serous cystadenocarcinoma(33;8.23e-17)											0.172897	151.044376	194.249866	74	354	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	39341674	39341674	6674	1	G	A	A	A	480	37	GJA9	5	1
PPIE	10450	broad.mit.edu	37	1	40207573	40207573	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z051-01	TCGA-17-Z051-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:40207573G>A	uc001cdw.2	+	c.181G>A	c.(181-183)GCA>ACA	p.A61T	PPIE_uc001cds.1_Missense_Mutation_p.A61T|PPIE_uc001cdt.1_5'UTR|PPIE_uc010oiy.1_5'UTR|PPIE_uc001cdu.1_Non-coding_Transcript|PPIE_uc001cdv.2_Missense_Mutation_p.A61T|PPIE_uc001cdx.1_5'Flank	NM_006112	NP_006103	Q9UNP9	PPIE_HUMAN	peptidylprolyl isomerase E isoform 1	61	RRM.|Poly-Ala.				nuclear mRNA splicing, via spliceosome|protein folding|regulation of transcription, DNA-dependent	catalytic step 2 spliceosome	cyclosporin A binding|nucleotide binding|peptidyl-prolyl cis-trans isomerase activity|protein binding|RNA binding				0	all_cancers(7;1.63e-13)|all_lung(5;2.27e-16)|all_epithelial(6;1.35e-15)|Lung NSC(20;1.49e-06)|Ovarian(52;0.00167)|all_hematologic(146;0.0501)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;1.87e-18)|Epithelial(16;2.7e-17)|all cancers(16;5.5e-16)|LUSC - Lung squamous cell carcinoma(16;0.000261)|Lung(16;0.000457)											0.123457	20.544829	42.970299	20	142	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	40207573	40207573	12757	1	G	A	A	A	598	46	PPIE	2	2
PTPRF	5792	broad.mit.edu	37	1	44069399	44069399	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z051-01	TCGA-17-Z051-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:44069399G>T	uc001cjr.2	+	c.2576G>T	c.(2575-2577)CGG>CTG	p.R859L	PTPRF_uc001cjs.2_Missense_Mutation_p.R850L|PTPRF_uc001cju.2_Intron|PTPRF_uc009vwt.2_Missense_Mutation_p.R419L|PTPRF_uc001cjv.2_Missense_Mutation_p.R319L|PTPRF_uc001cjw.2_Missense_Mutation_p.R85L	NM_002840	NP_002831	P10586	PTPRF_HUMAN	protein tyrosine phosphatase, receptor type, F	859	Extracellular (Potential).|Fibronectin type-III 6.				transmembrane receptor protein tyrosine phosphatase signaling pathway	integral to plasma membrane	transmembrane receptor protein tyrosine phosphatase activity			ovary(4)|lung(1)|kidney(1)|central_nervous_system(1)|skin(1)	8	all_hematologic(146;0.0958)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0333)												0.3	49.257474	51.384424	18	42	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	44069399	44069399	13258	1	G	T	T	T	507	39	PTPRF	1	1
EFCAB7	84455	broad.mit.edu	37	1	63999765	63999765	+	Splice_Site_SNP	SNP	G	C	C			TCGA-17-Z051-01	TCGA-17-Z051-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:63999765G>C	uc001dbf.2	+	c.683_splice	c.e6-1	p.G228_splice		NM_032437	NP_115813			EF-hand calcium binding domain 7								calcium ion binding				0														0.341969	196.960149	201.233714	66	127	KEEP	---	---	---	---	capture		Splice_Site_SNP	SNP	63999765	63999765	5127	1	G	C	C	C	455	35	EFCAB7	5	3
INSM1	3642	broad.mit.edu	37	20	20349775	20349775	+	Silent	SNP	G	T	T			TCGA-17-Z051-01	TCGA-17-Z051-01										Phase_I	Unspecified				Illumina GAIIx	g.chr20:20349775G>T	uc002wrx.2	+	c.864G>T	c.(862-864)TCG>TCT	p.S288S		NM_002196	NP_002187	Q01101	INSM1_HUMAN	insulinoma-associated 1	288					endocrine pancreas development|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1				READ - Rectum adenocarcinoma(2;0.0649)										0.277778	9.938274	10.761349	5	13	KEEP	---	---	---	---	capture		Silent	SNP	20349775	20349775	8072	20	G	T	T	T	483	38	INSM1	1	1
SALL4	57167	broad.mit.edu	37	20	50408809	50408809	+	Silent	SNP	C	A	A			TCGA-17-Z051-01	TCGA-17-Z051-01										Phase_I	Unspecified				Illumina GAIIx	g.chr20:50408809C>A	uc002xwh.3	-	c.213G>T	c.(211-213)ACG>ACT	p.T71T	SALL4_uc010gii.2_Silent_p.T71T|SALL4_uc002xwi.3_Intron	NM_020436	NP_065169	Q9UJQ4	SALL4_HUMAN	sal-like 4	71					transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(2)	2														0.202532	35.995803	42.459068	16	63	KEEP	---	---	---	---	capture		Silent	SNP	50408809	50408809	14293	20	C	A	A	A	340	27	SALL4	1	1
MYO18B	84700	broad.mit.edu	37	22	26164635	26164635	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z051-01	TCGA-17-Z051-01										Phase_I	Unspecified				Illumina GAIIx	g.chr22:26164635C>T	uc003abz.1	+	c.752C>T	c.(751-753)ACA>ATA	p.T251I	MYO18B_uc003aca.1_Missense_Mutation_p.T132I|MYO18B_uc010guy.1_Missense_Mutation_p.T132I|MYO18B_uc010guz.1_Missense_Mutation_p.T132I|MYO18B_uc011aka.1_5'UTR|MYO18B_uc011akb.1_5'Flank	NM_032608	NP_115997	Q8IUG5	MY18B_HUMAN	myosin XVIIIB	251						nucleus|sarcomere|unconventional myosin complex	actin binding|ATP binding|motor activity			ovary(5)|central_nervous_system(3)|large_intestine(2)|breast(2)	12										968				0.125	3.60738	6.905771	3	21	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	26164635	26164635	10461	22	C	T	T	T	221	17	MYO18B	2	2
RAC2	5880	broad.mit.edu	37	22	37627429	37627429	+	Nonsense_Mutation	SNP	C	T	T			TCGA-17-Z051-01	TCGA-17-Z051-01										Phase_I	Unspecified				Illumina GAIIx	g.chr22:37627429C>T	uc003arc.2	-	c.290G>A	c.(289-291)TGG>TAG	p.W97*		NM_002872	NP_002863	P15153	RAC2_HUMAN	ras-related C3 botulinum toxin substrate 2	97					axon guidance|platelet activation|regulation of hydrogen peroxide metabolic process|regulation of respiratory burst|regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol|plasma membrane	GTP binding|GTPase activity|protein binding			breast(2)|central_nervous_system(1)	3														0.347826	21.992079	22.462622	8	15	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	37627429	37627429	13434	22	C	T	T	T	273	21	RAC2	5	2
CARD10	29775	broad.mit.edu	37	22	37893099	37893099	+	Missense_Mutation	SNP	C	G	G			TCGA-17-Z051-01	TCGA-17-Z051-01										Phase_I	Unspecified				Illumina GAIIx	g.chr22:37893099C>G	uc003asx.1	-	c.1874G>C	c.(1873-1875)GGG>GCG	p.G625A	CARD10_uc003ast.1_Non-coding_Transcript|CARD10_uc003asv.1_5'Flank|CARD10_uc011ank.1_5'Flank|CARD10_uc003asw.1_Missense_Mutation_p.G339A|CARD10_uc003asy.1_Missense_Mutation_p.G625A	NM_014550	NP_055365	Q9BWT7	CAR10_HUMAN	caspase recruitment domain protein 10	625					activation of NF-kappaB-inducing kinase activity|protein complex assembly|regulation of apoptosis	CBM complex	receptor signaling complex scaffold activity			ovary(1)|kidney(1)	2	Melanoma(58;0.0574)									672				0.417722	100.968184	101.432914	33	46	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	37893099	37893099	2763	22	C	G	G	G	286	22	CARD10	3	3
CDC42EP1	11135	broad.mit.edu	37	22	37964470	37964470	+	Silent	SNP	C	T	T			TCGA-17-Z051-01	TCGA-17-Z051-01										Phase_I	Unspecified				Illumina GAIIx	g.chr22:37964470C>T	uc003asz.3	+	c.819C>T	c.(817-819)CCC>CCT	p.P273P		NM_152243	NP_689449	Q00587	BORG5_HUMAN	CDC42 effector protein 1	273	8.|8 X 7 AA tandem repeats of [PT]-[AT]-A- [ENT]-[PT]-[PTS]-[AG].				positive regulation of pseudopodium assembly|regulation of cell shape	actin cytoskeleton|endomembrane system|Golgi apparatus|plasma membrane	protein binding				0	Melanoma(58;0.0574)													0.375	9.485519	9.571335	3	5	KEEP	---	---	---	---	capture		Silent	SNP	37964470	37964470	3203	22	C	T	T	T	275	22	CDC42EP1	2	2
CELSR1	9620	broad.mit.edu	37	22	46780524	46780524	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z051-01	TCGA-17-Z051-01										Phase_I	Unspecified				Illumina GAIIx	g.chr22:46780524C>A	uc003bhw.1	-	c.6799G>T	c.(6799-6801)GAC>TAC	p.D2267Y	CELSR1_uc011arc.1_Missense_Mutation_p.D588Y	NM_014246	NP_055061	Q9NYQ6	CELR1_HUMAN	cadherin EGF LAG seven-pass G-type receptor 1	2267	Extracellular (Potential).				central nervous system development|homophilic cell adhesion|neural tube closure|neuropeptide signaling pathway	integral to plasma membrane	calcium ion binding|G-protein coupled receptor activity|protein dimerization activity			pancreas(2)|skin(1)	3		Ovarian(80;0.00142)|Breast(42;0.00296)|all_neural(38;0.0416)|Colorectal(5;0.0766)		UCEC - Uterine corpus endometrioid carcinoma (28;0.00643)|BRCA - Breast invasive adenocarcinoma(115;0.171)										0.277778	11.065413	11.866688	5	13	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	46780524	46780524	3354	22	C	A	A	A	403	31	CELSR1	1	1
MOV10L1	54456	broad.mit.edu	37	22	50580512	50580512	+	Silent	SNP	T	C	C			TCGA-17-Z051-01	TCGA-17-Z051-01										Phase_I	Unspecified				Illumina GAIIx	g.chr22:50580512T>C	uc003bjj.2	+	c.2073T>C	c.(2071-2073)AAT>AAC	p.N691N	MOV10L1_uc003bjk.3_Silent_p.N691N|MOV10L1_uc011arp.1_Silent_p.N671N|MOV10L1_uc011arq.1_Silent_p.N452N|MOV10L1_uc010hao.1_Non-coding_Transcript	NM_018995	NP_061868	Q9BXT6	M10L1_HUMAN	MOV10-like 1 isoform 1	691					germ cell development|multicellular organismal development|spermatogenesis	intracellular	ATP binding|ATP-dependent RNA helicase activity|magnesium ion binding|RNA binding			ovary(2)	2		all_cancers(38;3.31e-11)|all_epithelial(38;5.69e-10)|all_lung(38;3.73e-05)|Breast(42;0.000525)|Lung NSC(38;0.000954)|Ovarian(80;0.0367)|Lung SC(80;0.114)		LUAD - Lung adenocarcinoma(64;0.0215)|BRCA - Breast invasive adenocarcinoma(115;0.24)										0.45283	84.798025	84.900212	24	29	KEEP	---	---	---	---	capture		Silent	SNP	50580512	50580512	10111	22	T	C	C	C	634	49	MOV10L1	4	4
RIF1	55183	broad.mit.edu	37	2	152318776	152318776	+	Missense_Mutation	SNP	A	G	G			TCGA-17-Z051-01	TCGA-17-Z051-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:152318776A>G	uc002txm.2	+	c.3248A>G	c.(3247-3249)TAT>TGT	p.Y1083C	RIF1_uc002txl.2_Missense_Mutation_p.Y1083C|RIF1_uc002txn.2_Missense_Mutation_p.Y1083C|RIF1_uc002txo.2_Missense_Mutation_p.Y1083C|RIF1_uc002txp.2_5'Flank	NM_018151	NP_060621	Q5UIP0	RIF1_HUMAN	RAP1 interacting factor 1	1083					cell cycle|response to DNA damage stimulus	chromosome, telomeric region|cytoplasm|nucleus|spindle	binding			ovary(5)|breast(4)|lung(2)|kidney(1)	12				BRCA - Breast invasive adenocarcinoma(221;0.0429)						950				0.587302	140.591634	141.012753	37	26	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	152318776	152318776	13834	2	A	G	G	G	208	16	RIF1	4	4
NEB	4703	broad.mit.edu	37	2	152426796	152426796	+	Missense_Mutation	SNP	A	C	C			TCGA-17-Z051-01	TCGA-17-Z051-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:152426796A>C	uc010fnx.2	-	c.12126T>G	c.(12124-12126)AAT>AAG	p.N4042K	NEB_uc002txr.2_Missense_Mutation_p.N465K	NM_004543	NP_004534	P20929	NEBU_HUMAN	nebulin isoform 3	4042	Nebulin 110.				muscle filament sliding|muscle organ development|regulation of actin filament length|somatic muscle development	actin cytoskeleton|cytosol|Z disc	actin binding|structural constituent of muscle			ovary(8)|large_intestine(5)|breast(3)|central_nervous_system(1)|skin(1)|pancreas(1)	19				BRCA - Breast invasive adenocarcinoma(221;0.219)										0.27027	30.743629	32.498619	10	27	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	152426796	152426796	10701	2	A	C	C	C	102	8	NEB	4	4
GAD1	2571	broad.mit.edu	37	2	171687701	171687701	+	Silent	SNP	A	T	T			TCGA-17-Z051-01	TCGA-17-Z051-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:171687701A>T	uc002ugi.2	+	c.546A>T	c.(544-546)ACA>ACT	p.T182T	GAD1_uc002ugh.2_Silent_p.T182T	NM_000817	NP_000808	Q99259	DCE1_HUMAN	glutamate decarboxylase 1 isoform GAD67	182					glutamate decarboxylation to succinate|neurotransmitter biosynthetic process|neurotransmitter secretion|protein-pyridoxal-5-phosphate linkage	clathrin sculpted gamma-aminobutyric acid transport vesicle membrane|plasma membrane	glutamate decarboxylase activity|protein binding|pyridoxal phosphate binding			ovary(1)	1					L-Glutamic Acid(DB00142)|Pyridoxal Phosphate(DB00114)									0.447059	123.241457	123.448752	38	47	KEEP	---	---	---	---	capture		Silent	SNP	171687701	171687701	6430	2	A	T	T	T	80	7	GAD1	3	3
TTN	7273	broad.mit.edu	37	2	179447076	179447076	+	Missense_Mutation	SNP	T	G	G			TCGA-17-Z051-01	TCGA-17-Z051-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:179447076T>G	uc010zfg.1	-	c.58403A>C	c.(58402-58404)TAT>TCT	p.Y19468S	TTN_uc010zfh.1_Missense_Mutation_p.Y13163S|TTN_uc010zfi.1_Missense_Mutation_p.Y13096S|TTN_uc010zfj.1_Missense_Mutation_p.Y12971S	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	2684										ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1)	153			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)							8722				0.387755	62.469289	62.99058	19	30	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	179447076	179447076	17290	2	T	G	G	G	637	49	TTN	4	4
SLC11A1	6556	broad.mit.edu	37	2	219255992	219255992	+	Silent	SNP	C	G	G			TCGA-17-Z051-01	TCGA-17-Z051-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:219255992C>G	uc002vhv.2	+	c.1026C>G	c.(1024-1026)GCC>GCG	p.A342A	SLC11A1_uc010fvp.1_Silent_p.A342A|SLC11A1_uc010fvq.1_Silent_p.A275A|SLC11A1_uc010zkc.1_Silent_p.A275A|SLC11A1_uc002vhu.1_Silent_p.A137A|SLC11A1_uc002vhw.2_Silent_p.A224A|SLC11A1_uc010fvr.2_Silent_p.A137A	NM_000578	NP_000569	P49279	NRAM1_HUMAN	natural resistance-associated macrophage protein	342	Extracellular (Potential).				activation of protein kinase activity|antigen processing and presentation of peptide antigen|cadmium ion transmembrane transport|cellular cadmium ion homeostasis|cellular iron ion homeostasis|defense response to Gram-negative bacterium|defense response to protozoan|divalent metal ion export|inflammatory response|interleukin-2 production|interleukin-3 production|iron ion transport|L-arginine import|macrophage activation|MHC class II biosynthetic process|mRNA stabilization|multicellular organismal iron ion homeostasis|negative regulation of cytokine production|nitrite transport|phagocytosis|positive regulation of dendritic cell antigen processing and presentation|positive regulation of interferon-gamma production|positive regulation of phagocytosis|positive regulation of T-helper 1 type immune response|positive regulation of transcription from RNA polymerase II promoter|respiratory burst|response to interferon-gamma|response to lipopolysaccharide|T cell cytokine production|T cell proliferation involved in immune response|vacuolar acidification|wound healing	integral to plasma membrane|late endosome membrane|lysosome|phagocytic vesicle membrane|tertiary granule membrane	manganese ion transmembrane transporter activity|metal ion:hydrogen antiporter activity|protein homodimerization activity			ovary(3)|central_nervous_system(1)	4		Renal(207;0.0474)		Epithelial(149;1.16e-06)|all cancers(144;0.000195)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)										0.222222	61.966524	70.319437	26	91	KEEP	---	---	---	---	capture		Silent	SNP	219255992	219255992	14875	2	C	G	G	G	288	23	SLC11A1	3	3
WNT6	7475	broad.mit.edu	37	2	219736487	219736487	+	Silent	SNP	A	T	T			TCGA-17-Z051-01	TCGA-17-Z051-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:219736487A>T	uc002vjc.1	+	c.582A>T	c.(580-582)GGA>GGT	p.G194G		NM_006522	NP_006513	Q9Y6F9	WNT6_HUMAN	wingless-type MMTV integration site family,	194					anterior/posterior pattern formation|axis specification|canonical Wnt receptor signaling pathway|cellular response to retinoic acid|cornea development in camera-type eye|negative regulation of gene-specific transcription from RNA polymerase II promoter|neuron differentiation|odontogenesis of dentine-containing tooth|positive regulation of gene-specific transcription|positive regulation of tooth mineralization|Wnt receptor signaling pathway, calcium modulating pathway	extracellular space|plasma membrane|proteinaceous extracellular matrix	G-protein-coupled receptor binding|signal transducer activity			ovary(2)|skin(1)	3		Renal(207;0.0474)		Epithelial(149;4.53e-07)|all cancers(144;9.3e-05)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)										0.315789	16.846458	17.418146	6	13	KEEP	---	---	---	---	capture		Silent	SNP	219736487	219736487	17967	2	A	T	T	T	119	10	WNT6	3	3
CXCR7	57007	broad.mit.edu	37	2	237490078	237490078	+	Missense_Mutation	SNP	T	C	C			TCGA-17-Z051-01	TCGA-17-Z051-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:237490078T>C	uc010fyq.2	+	c.970T>C	c.(970-972)TAC>CAC	p.Y324H	CXCR7_uc002vwd.2_Missense_Mutation_p.Y324H	NM_020311	NP_064707	P25106	CXCR7_HUMAN	chemokine orphan receptor 1	324	Cytoplasmic (Potential).				interspecies interaction between organisms	integral to membrane|plasma membrane	G-protein coupled receptor activity|protein binding			large_intestine(1)|central_nervous_system(1)|skin(1)	3		Breast(86;0.000182)|Renal(207;0.00339)|all_hematologic(139;0.0048)|Acute lymphoblastic leukemia(138;0.0775)|Ovarian(221;0.089)|all_lung(227;0.147)|all_neural(83;0.223)		Epithelial(121;8.35e-24)|OV - Ovarian serous cystadenocarcinoma(60;7.09e-11)|Kidney(56;1.11e-07)|KIRC - Kidney renal clear cell carcinoma(57;3.03e-06)|BRCA - Breast invasive adenocarcinoma(100;0.000176)|Lung(119;0.00468)|LUSC - Lung squamous cell carcinoma(224;0.008)|COAD - Colon adenocarcinoma(134;0.118)						49				0.241935	38.492527	42.262797	15	47	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	237490078	237490078	4256	2	T	C	C	C	741	57	CXCR7	4	4
EMILIN1	11117	broad.mit.edu	37	2	27303041	27303041	+	Missense_Mutation	SNP	A	G	G			TCGA-17-Z051-01	TCGA-17-Z051-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:27303041A>G	uc002rii.3	+	c.193A>G	c.(193-195)ACC>GCC	p.T65A	EMILIN1_uc010eyq.1_Missense_Mutation_p.T65A	NM_007046	NP_008977	Q9Y6C2	EMIL1_HUMAN	elastin microfibril interfacer 1 precursor	65	EMI.				cell adhesion	collagen				pancreas(1)	1	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)													0.475	127.354014	127.396553	38	42	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	27303041	27303041	5285	2	A	G	G	G	130	10	EMILIN1	4	4
SLC30A6	55676	broad.mit.edu	37	2	32445602	32445602	+	Silent	SNP	A	C	C			TCGA-17-Z051-01	TCGA-17-Z051-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:32445602A>C	uc002rof.1	+	c.1326A>C	c.(1324-1326)CTA>CTC	p.L442L	SLC30A6_uc002roe.1_Silent_p.L402L|SLC30A6_uc010ymw.1_Silent_p.L373L|SLC30A6_uc010ezr.1_Silent_p.L379L|SLC30A6_uc002rog.1_Silent_p.L205L|SLC30A6_uc010ezs.1_Silent_p.L328L|SLC30A6_uc002roh.1_Silent_p.L205L	NM_017964	NP_060434	Q6NXT4	ZNT6_HUMAN	solute carrier family 30 (zinc transporter),	402	Cytoplasmic (Potential).					Golgi membrane|integral to membrane	zinc ion transmembrane transporter activity				0	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.208)													0.362869	290.994431	294.912127	86	151	KEEP	---	---	---	---	capture		Silent	SNP	32445602	32445602	15056	2	A	C	C	C	158	13	SLC30A6	4	4
ZNF638	27332	broad.mit.edu	37	2	71591198	71591198	+	Silent	SNP	A	T	T			TCGA-17-Z051-01	TCGA-17-Z051-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:71591198A>T	uc002shx.2	+	c.1533A>T	c.(1531-1533)CCA>CCT	p.P511P	ZNF638_uc010fec.2_Silent_p.P617P|ZNF638_uc010yqw.1_Silent_p.P90P|ZNF638_uc002shw.2_Silent_p.P511P|ZNF638_uc002shy.2_Silent_p.P511P|ZNF638_uc002shz.2_Silent_p.P511P|ZNF638_uc002sia.2_Silent_p.P511P|ZNF638_uc002sib.1_Silent_p.P511P|ZNF638_uc010fed.2_5'Flank	NM_014497	NP_055312	Q14966	ZN638_HUMAN	zinc finger protein 638	511	Arg-rich.				RNA splicing	cytoplasm|nuclear speck	double-stranded DNA binding|nucleotide binding|RNA binding|zinc ion binding			pancreas(2)|ovary(1)	3														0.410072	162.745261	163.727479	57	82	KEEP	---	---	---	---	capture		Silent	SNP	71591198	71591198	18650	2	A	T	T	T	54	5	ZNF638	3	3
REG1B	5968	broad.mit.edu	37	2	79312722	79312722	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z051-01	TCGA-17-Z051-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:79312722C>A	uc002sny.2	-	c.329G>T	c.(328-330)CGC>CTC	p.R110L	REG1B_uc010ffv.1_3'UTR	NM_006507	NP_006498	P48304	REG1B_HUMAN	regenerating islet-derived 1 beta precursor	110	C-type lectin.				cell proliferation	extracellular region	sugar binding			central_nervous_system(1)	1														0.342105	78.330299	80.002827	26	50	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	79312722	79312722	13680	2	C	A	A	A	351	27	REG1B	1	1
C3orf36	80111	broad.mit.edu	37	3	133647605	133647605	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z051-01	TCGA-17-Z051-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:133647605G>A	uc003epz.1	-	c.43C>T	c.(43-45)CCC>TCC	p.P15S		NM_025041	NP_079317	Q3SXR2	CC036_HUMAN	hypothetical protein LOC80111	15										ovary(1)	1														0.050725	-15.922525	13.531124	7	131	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	133647605	133647605	2319	3	G	A	A	A	572	44	C3orf36	2	2
CLRN1	7401	broad.mit.edu	37	3	150690460	150690460	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z051-01	TCGA-17-Z051-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:150690460C>A	uc003eyk.1	-	c.36G>T	c.(34-36)ATG>ATT	p.M12I	CLRN1OS_uc011bny.1_Intron|CLRN1OS_uc003eyl.2_5'Flank	NM_174878	NP_777367	P58418	CLRN1_HUMAN	clarin 1 isoform a	12	Helical; (Potential).				equilibrioception|photoreceptor cell maintenance|response to stimulus|sensory perception of sound	integral to membrane					0			LUSC - Lung squamous cell carcinoma(72;0.0538)|Lung(72;0.066)											0.247126	105.839157	115.968463	43	131	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	150690460	150690460	3695	3	C	A	A	A	273	21	CLRN1	2	2
DAZL	1618	broad.mit.edu	37	3	16640098	16640098	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z051-01	TCGA-17-Z051-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:16640098G>T	uc003cba.2	-	c.71C>A	c.(70-72)GCA>GAA	p.A24E	DAZL_uc003cbb.2_Missense_Mutation_p.A4E	NM_001351	NP_001342	Q92904	DAZL_HUMAN	deleted in azoospermia-like	4					germ cell development|multicellular organismal development|positive regulation of translational initiation|spermatogenesis	cytoplasm|nucleus	nucleotide binding|protein binding|RNA binding|translation activator activity				0														0.047619	-13.067836	9.766246	5	100	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	16640098	16640098	4417	3	G	T	T	T	598	46	DAZL	2	2
MECOM	2122	broad.mit.edu	37	3	168833655	168833655	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z051-01	TCGA-17-Z051-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:168833655C>A	uc011bpj.1	-	c.2005G>T	c.(2005-2007)GCT>TCT	p.A669S	MECOM_uc010hwk.1_Missense_Mutation_p.A504S|MECOM_uc003ffj.3_Missense_Mutation_p.A546S|MECOM_uc003ffi.3_Missense_Mutation_p.A481S|MECOM_uc011bpi.1_Missense_Mutation_p.A482S|MECOM_uc003ffn.3_Missense_Mutation_p.A481S|MECOM_uc003ffk.2_Missense_Mutation_p.A481S|MECOM_uc003ffl.2_Missense_Mutation_p.A641S|MECOM_uc011bpk.1_Missense_Mutation_p.A471S|MECOM_uc010hwn.2_Missense_Mutation_p.A669S	NM_004991	NP_004982	Q13465	MDS1_HUMAN	MDS1 and EVI1 complex locus isoform c	Error:Variant_position_missing_in_Q13465_after_alignment							sequence-specific DNA binding transcription factor activity			lung(3)|skin(2)|ovary(1)|pancreas(1)|central_nervous_system(1)	8										646				0.210863	147.659737	171.898413	66	247	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	168833655	168833655	9811	3	C	A	A	A	325	25	MECOM	2	2
AP2M1	1173	broad.mit.edu	37	3	183897989	183897989	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z051-01	TCGA-17-Z051-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:183897989G>A	uc011bqx.1	+	c.373G>A	c.(373-375)GAG>AAG	p.E125K	AP2M1_uc003fmw.2_Missense_Mutation_p.E125K|AP2M1_uc003fmx.2_Missense_Mutation_p.E125K|AP2M1_uc003fmy.2_Missense_Mutation_p.E125K|AP2M1_uc011bqy.1_5'Flank|AP2M1_uc011bqz.1_5'Flank	NM_004068	NP_004059	Q96CW1	AP2M1_HUMAN	adaptor-related protein complex 2, mu 1 subunit	125					axon guidance|cellular membrane organization|epidermal growth factor receptor signaling pathway|intracellular protein transport|negative regulation of epidermal growth factor receptor signaling pathway|nerve growth factor receptor signaling pathway|regulation of defense response to virus by virus|synaptic transmission|vesicle-mediated transport|viral reproduction	clathrin adaptor complex|clathrin coat of coated pit|cytosol|endocytic vesicle membrane|peroxisomal membrane	lipid binding|protein binding|transporter activity				0	all_cancers(143;1.12e-10)|Ovarian(172;0.0339)		Epithelial(37;2.92e-34)|OV - Ovarian serous cystadenocarcinoma(80;2.72e-22)											0.151515	8.091601	11.899532	5	28	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	183897989	183897989	752	3	G	A	A	A	481	37	AP2M1	1	1
TRIM71	131405	broad.mit.edu	37	3	32933252	32933252	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z051-01	TCGA-17-Z051-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:32933252C>A	uc003cff.2	+	c.2556C>A	c.(2554-2556)GAC>GAA	p.D852E		NM_001039111	NP_001034200	Q2Q1W2	LIN41_HUMAN	tripartite motif-containing 71	852	NHL 6.				multicellular organismal development	cytoplasm	zinc ion binding			ovary(2)|large_intestine(1)	3														0.71875	165.979721	168.733963	46	18	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	32933252	32933252	17093	3	C	A	A	A	246	19	TRIM71	1	1
CDC25A	993	broad.mit.edu	37	3	48209380	48209380	+	Missense_Mutation	SNP	T	C	C			TCGA-17-Z051-01	TCGA-17-Z051-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:48209380T>C	uc003csh.1	-	c.985A>G	c.(985-987)ATT>GTT	p.I329V	CDC25A_uc003csi.1_Missense_Mutation_p.I289V	NM_001789	NP_001780	P30304	MPIP1_HUMAN	cell division cycle 25A isoform a	329					cell cycle checkpoint|cell division|cell proliferation|cellular response to UV|DNA replication|G1/S transition of mitotic cell cycle|G2/M transition of mitotic cell cycle|mitosis|regulation of cyclin-dependent protein kinase activity|S phase of mitotic cell cycle	cytosol|nucleoplasm	protein binding|protein tyrosine phosphatase activity			lung(2)|kidney(1)|skin(1)	4				BRCA - Breast invasive adenocarcinoma(193;0.000685)|KIRC - Kidney renal clear cell carcinoma(197;0.00596)|Kidney(197;0.00684)						123				0.666667	30.85018	31.218283	10	5	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	48209380	48209380	3190	3	T	C	C	C	663	51	CDC25A	4	4
NFKB1	4790	broad.mit.edu	37	4	103517299	103517299	+	Silent	SNP	C	G	G			TCGA-17-Z051-01	TCGA-17-Z051-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:103517299C>G	uc011cep.1	+	c.1305C>G	c.(1303-1305)ACC>ACG	p.T435T	NFKB1_uc011ceq.1_Silent_p.T434T|NFKB1_uc011cer.1_Silent_p.T254T	NM_003998	NP_003989	P19838	NFKB1_HUMAN	nuclear factor kappa-B, subunit 1 isoform 1	434		Cleavage (when cotranslationally processed).			anti-apoptosis|apoptosis|cellular response to mechanical stimulus|inflammatory response|innate immune response|membrane protein intracellular domain proteolysis|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|negative regulation of calcidiol 1-monooxygenase activity|negative regulation of cellular protein metabolic process|negative regulation of cholesterol transport|negative regulation of gene-specific transcription from RNA polymerase II promoter|negative regulation of vitamin D biosynthetic process|nerve growth factor receptor signaling pathway|positive regulation of canonical Wnt receptor signaling pathway|positive regulation of lipid storage|positive regulation of macrophage derived foam cell differentiation|positive regulation of NF-kappaB transcription factor activity|positive regulation of transcription, DNA-dependent|T cell receptor signaling pathway|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|transcription from RNA polymerase II promoter	cytosol|I-kappaB/NF-kappaB complex|mitochondrion|nucleoplasm	promoter binding|protein binding|protein binding|sequence-specific DNA binding transcription factor activity|transcription activator activity			ovary(2)|breast(2)	4		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;6.59e-08)	Dexamethasone(DB01234)|Pranlukast(DB01411)|Thalidomide(DB01041)					318				0.670886	172.59118	174.632687	53	26	KEEP	---	---	---	---	capture		Silent	SNP	103517299	103517299	10775	4	C	G	G	G	262	21	NFKB1	3	3
COL25A1	84570	broad.mit.edu	37	4	109784494	109784494	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z051-01	TCGA-17-Z051-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:109784494G>A	uc003hze.1	-	c.1133C>T	c.(1132-1134)CCT>CTT	p.P378L	COL25A1_uc003hzg.2_Missense_Mutation_p.P378L|COL25A1_uc003hzd.2_Non-coding_Transcript|COL25A1_uc003hzf.2_Missense_Mutation_p.P159L	NM_198721	NP_942014	Q9BXS0	COPA1_HUMAN	collagen, type XXV, alpha 1 isoform 1	378	Extracellular (Potential).|Collagen-like 5.					collagen|extracellular space	beta-amyloid binding|heparin binding			ovary(2)	2		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;0.000173)										0.724138	73.987258	75.298412	21	8	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	109784494	109784494	3822	4	G	A	A	A	455	35	COL25A1	2	2
C4orf21	55345	broad.mit.edu	37	4	113505306	113505306	+	Missense_Mutation	SNP	C	G	G			TCGA-17-Z051-01	TCGA-17-Z051-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:113505306C>G	uc003iau.2	-	c.4126G>C	c.(4126-4128)GGA>CGA	p.G1376R	C4orf21_uc003iav.2_Non-coding_Transcript	NM_018392	NP_060862	Q6ZU11	YD002_HUMAN	prematurely terminated mRNA decay factor-like	198						integral to membrane	zinc ion binding				0		Ovarian(17;0.156)		OV - Ovarian serous cystadenocarcinoma(123;0.000676)										0.863636	71.340296	74.157345	19	3	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	113505306	113505306	2349	4	C	G	G	G	273	21	C4orf21	3	3
ATP10D	57205	broad.mit.edu	37	4	47527626	47527626	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z051-01	TCGA-17-Z051-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:47527626C>A	uc003gxk.1	+	c.743C>A	c.(742-744)CCA>CAA	p.P248Q	ATP10D_uc003gxj.3_Missense_Mutation_p.P248Q	NM_020453	NP_065186	Q9P241	AT10D_HUMAN	ATPase, class V, type 10D	248	Cytoplasmic (Potential).				ATP biosynthetic process|cation transport	integral to membrane|plasma membrane	ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|magnesium ion binding|phospholipid-translocating ATPase activity			ovary(2)|pancreas(1)	3														0.307692	54.371727	56.516951	20	45	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	47527626	47527626	1137	4	C	A	A	A	273	21	ATP10D	2	2
SHROOM3	57619	broad.mit.edu	37	4	77675663	77675663	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z051-01	TCGA-17-Z051-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:77675663G>T	uc011cbx.1	+	c.4027G>T	c.(4027-4029)GTC>TTC	p.V1343F	SHROOM3_uc003hkg.2_Missense_Mutation_p.V1121F	NM_020859	NP_065910	Q8TF72	SHRM3_HUMAN	shroom family member 3 protein	1343					apical protein localization|cell morphogenesis|cellular pigment accumulation|pattern specification process|regulation of cell shape	adherens junction|apical junction complex|apical plasma membrane|cytoplasm|microtubule	actin binding			ovary(1)	1			Lung(101;0.0903)											0.875	183.052573	191.944564	56	8	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	77675663	77675663	14790	4	G	T	T	T	572	44	SHROOM3	2	2
AQPEP	206338	broad.mit.edu	37	5	115350954	115350954	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z051-01	TCGA-17-Z051-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:115350954C>A	uc003kro.2	+	c.2456C>A	c.(2455-2457)CCT>CAT	p.P819H	AQPEP_uc003krp.2_Non-coding_Transcript|AQPEP_uc003krq.2_Non-coding_Transcript|AQPEP_uc003krr.2_Non-coding_Transcript|AQPEP_uc003krs.2_Non-coding_Transcript	NM_173800	NP_776161	Q6Q4G3	AMPQ_HUMAN	laeverin	819	Lumenal (Potential).				proteolysis	integral to membrane	metallopeptidase activity|zinc ion binding				0														0.764706	86.864423	89.041618	26	8	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	115350954	115350954	845	5	C	A	A	A	312	24	AQPEP	2	2
CSF2	1437	broad.mit.edu	37	5	131409603	131409603	+	Silent	SNP	C	A	A			TCGA-17-Z051-01	TCGA-17-Z051-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:131409603C>A	uc003kwf.2	+	c.87C>A	c.(85-87)CCC>CCA	p.P29P		NM_000758	NP_000749	P04141	CSF2_HUMAN	colony stimulating factor 2 precursor	29					immune response|negative regulation of cytolysis|positive regulation of DNA replication|positive regulation of interleukin-23 production|positive regulation of macrophage derived foam cell differentiation|positive regulation of podosome assembly|positive regulation of tyrosine phosphorylation of Stat5 protein	extracellular space	cytokine activity|granulocyte macrophage colony-stimulating factor receptor binding|growth factor activity				0		all_cancers(142;4.28e-07)|all_lung(232;2.81e-05)|Lung NSC(810;0.000693)|Lung SC(612;0.122)|Breast(839;0.198)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)		Sargramostim(DB00020)					33				0.764706	40.979469	42.067202	13	4	KEEP	---	---	---	---	capture		Silent	SNP	131409603	131409603	4074	5	C	A	A	A	301	24	CSF2	2	2
PCDHGA3	56112	broad.mit.edu	37	5	140725827	140725827	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z051-01	TCGA-17-Z051-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:140725827G>T	uc003ljm.1	+	c.2227G>T	c.(2227-2229)GCG>TCG	p.A743S	PCDHGA1_uc003lji.1_Intron|PCDHGA2_uc003ljk.1_Intron|PCDHGA3_uc010jfx.1_Missense_Mutation_p.A503S|PCDHGA3_uc011dap.1_Missense_Mutation_p.A743S	NM_018916	NP_061739	Q9Y5H0	PCDG3_HUMAN	protocadherin gamma subfamily A, 3 isoform 1	743	Cytoplasmic (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)											0.733333	104.874722	107.081656	33	12	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	140725827	140725827	11975	5	G	T	T	T	494	38	PCDHGA3	1	1
CDH18	1016	broad.mit.edu	37	5	19473547	19473547	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z051-01	TCGA-17-Z051-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:19473547C>A	uc003jgc.2	-	c.2161G>T	c.(2161-2163)GCA>TCA	p.A721S	CDH18_uc003jgd.2_Missense_Mutation_p.A721S|CDH18_uc011cnm.1_3'UTR	NM_004934	NP_004925	Q13634	CAD18_HUMAN	cadherin 18, type 2 preproprotein	721	Cytoplasmic (Potential).				adherens junction organization|cell junction assembly|homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(5)|large_intestine(1)	6	Lung NSC(1;0.00734)|all_lung(1;0.0197)													0.110738	27.900829	72.532502	33	265	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	19473547	19473547	3232	5	C	A	A	A	338	26	CDH18	2	2
IRX2	153572	broad.mit.edu	37	5	2749503	2749503	+	Silent	SNP	C	T	T			TCGA-17-Z051-01	TCGA-17-Z051-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:2749503C>T	uc003jda.2	-	c.648G>A	c.(646-648)GAG>GAA	p.E216E	C5orf38_uc003jdc.2_5'Flank|C5orf38_uc011cmg.1_5'Flank|C5orf38_uc011cmh.1_5'Flank|C5orf38_uc011cmi.1_5'Flank|C5orf38_uc011cmj.1_5'Flank|IRX2_uc003jdb.2_Silent_p.E216E	NM_001134222	NP_001127694	Q9BZI1	IRX2_HUMAN	iroquois homeobox 2	216					regulation of transcription, DNA-dependent	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription regulator activity			skin(1)	1				GBM - Glioblastoma multiforme(108;0.204)										0.066667	-4.048738	10.52126	5	70	KEEP	---	---	---	---	capture		Silent	SNP	2749503	2749503	8148	5	C	T	T	T	311	24	IRX2	2	2
ENPP3	5169	broad.mit.edu	37	6	132014711	132014711	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z051-01	TCGA-17-Z051-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:132014711C>A	uc003qcu.3	+	c.1359C>A	c.(1357-1359)AAC>AAA	p.N453K	ENPP3_uc010kfq.2_Non-coding_Transcript|ENPP3_uc003qcv.2_Missense_Mutation_p.N453K	NM_005021	NP_005012	O14638	ENPP3_HUMAN	ectonucleotide pyrophosphatase/phosphodiesterase	453	Extracellular (Potential).|Phosphodiesterase.				immune response|nucleoside triphosphate catabolic process|phosphate metabolic process	extracellular region|integral to plasma membrane|perinuclear region of cytoplasm	metal ion binding|nucleic acid binding|nucleoside-triphosphate diphosphatase activity|nucleotide diphosphatase activity|phosphodiesterase I activity|polysaccharide binding|scavenger receptor activity			ovary(3)	3	Breast(56;0.0753)			GBM - Glioblastoma multiforme(226;0.0252)|OV - Ovarian serous cystadenocarcinoma(155;0.0511)										0.167513	70.756268	91.388466	33	164	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	132014711	132014711	5324	6	C	A	A	A	246	19	ENPP3	1	1
GPR126	57211	broad.mit.edu	37	6	142729338	142729338	+	Missense_Mutation	SNP	A	G	G			TCGA-17-Z051-01	TCGA-17-Z051-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:142729338A>G	uc010khe.2	+	c.2320A>G	c.(2320-2322)ATT>GTT	p.I774V	GPR126_uc010khc.2_Missense_Mutation_p.I774V|GPR126_uc010khd.2_Missense_Mutation_p.I746V|GPR126_uc010khf.2_Missense_Mutation_p.I746V	NM_198569	NP_940971	Q86SQ4	GP126_HUMAN	G protein-coupled receptor 126 beta 1 precursor	774	Extracellular (Potential).				neuropeptide signaling pathway	integral to membrane|plasma membrane	G-protein coupled receptor activity			ovary(1)	1	Breast(32;0.176)			OV - Ovarian serous cystadenocarcinoma(155;9.33e-06)|GBM - Glioblastoma multiforme(68;0.00121)										0.5	50.852111	50.852111	14	14	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	142729338	142729338	6914	6	A	G	G	G	208	16	GPR126	4	4
COL9A1	1297	broad.mit.edu	37	6	70944245	70944245	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z051-01	TCGA-17-Z051-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:70944245G>T	uc003pfg.3	-	c.2311C>A	c.(2311-2313)CAA>AAA	p.Q771K	COL9A1_uc003pfe.3_Missense_Mutation_p.Q320K|COL9A1_uc003pff.3_Missense_Mutation_p.Q528K	NM_001851	NP_001842	P20849	CO9A1_HUMAN	alpha 1 type IX collagen isoform 1 precursor	771	Nonhelical region (NC2).				axon guidance|cell adhesion|organ morphogenesis	collagen type IX	extracellular matrix structural constituent conferring tensile strength|metal ion binding			ovary(4)	4														0.491071	173.016243	173.024119	55	57	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	70944245	70944245	3845	6	G	T	T	T	624	48	COL9A1	2	2
ZAN	7455	broad.mit.edu	37	7	100389676	100389676	+	Missense_Mutation	SNP	G	C	C			TCGA-17-Z051-01	TCGA-17-Z051-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:100389676G>C	uc003uwj.2	+	c.7618G>C	c.(7618-7620)GCG>CCG	p.A2540P	ZAN_uc003uwk.2_Missense_Mutation_p.A2540P|ZAN_uc003uwl.2_Non-coding_Transcript|ZAN_uc010lhh.2_Non-coding_Transcript|ZAN_uc010lhi.2_Non-coding_Transcript|ZAN_uc011kke.1_Missense_Mutation_p.W532C	NM_003386	NP_003377	Q9Y493	ZAN_HUMAN	zonadhesin isoform 3	2540	Extracellular (Potential).				binding of sperm to zona pellucida|cell-cell adhesion	integral to membrane|plasma membrane				ovary(4)|large_intestine(3)|central_nervous_system(2)|pancreas(2)	11	Lung NSC(181;0.041)|all_lung(186;0.0581)		STAD - Stomach adenocarcinoma(171;0.19)											0.103448	2.41991	6.94735	3	26	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	100389676	100389676	18096	7	G	C	C	C	546	42	ZAN	3	3
ZAN	7455	broad.mit.edu	37	7	100389686	100389686	+	Missense_Mutation	SNP	G	C	C			TCGA-17-Z051-01	TCGA-17-Z051-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:100389686G>C	uc003uwj.2	+	c.7628G>C	c.(7627-7629)AGC>ACC	p.S2543T	ZAN_uc003uwk.2_Missense_Mutation_p.S2543T|ZAN_uc003uwl.2_Non-coding_Transcript|ZAN_uc010lhh.2_Non-coding_Transcript|ZAN_uc010lhi.2_Non-coding_Transcript|ZAN_uc011kke.1_Missense_Mutation_p.A536P	NM_003386	NP_003377	Q9Y493	ZAN_HUMAN	zonadhesin isoform 3	2543	Extracellular (Potential).				binding of sperm to zona pellucida|cell-cell adhesion	integral to membrane|plasma membrane				ovary(4)|large_intestine(3)|central_nervous_system(2)|pancreas(2)	11	Lung NSC(181;0.041)|all_lung(186;0.0581)		STAD - Stomach adenocarcinoma(171;0.19)											0.147059	9.959253	14.02187	5	29	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	100389686	100389686	18096	7	G	C	C	C	442	34	ZAN	3	3
MUC17	140453	broad.mit.edu	37	7	100681801	100681801	+	Silent	SNP	T	A	A			TCGA-17-Z051-01	TCGA-17-Z051-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:100681801T>A	uc003uxp.1	+	c.7104T>A	c.(7102-7104)CCT>CCA	p.P2368P	MUC17_uc010lho.1_Non-coding_Transcript	NM_001040105	NP_001035194	Q685J3	MUC17_HUMAN	mucin 17 precursor	2368	Extracellular (Potential).|59 X approximate tandem repeats.|38.|Ser-rich.					extracellular region|integral to membrane|plasma membrane	extracellular matrix constituent, lubricant activity			ovary(14)|breast(3)|lung(2)	19	Lung NSC(181;0.136)|all_lung(186;0.182)													0.359375	65.504418	66.619895	23	41	KEEP	---	---	---	---	capture		Silent	SNP	100681801	100681801	10368	7	T	A	A	A	704	55	MUC17	3	3
TSGA13	114960	broad.mit.edu	37	7	130356550	130356550	+	Silent	SNP	G	A	A			TCGA-17-Z051-01	TCGA-17-Z051-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:130356550G>A	uc003vqi.2	-	c.609C>T	c.(607-609)TAC>TAT	p.Y203Y	COPG2_uc003vqh.1_5'Flank|TSGA13_uc003vqj.2_Silent_p.Y203Y	NM_052933	NP_443165	Q96PP4	TSG13_HUMAN	testis specific, 13	203										ovary(2)	2	Melanoma(18;0.0435)													0.129693	47.749209	86.89459	38	255	KEEP	---	---	---	---	capture		Silent	SNP	130356550	130356550	17170	7	G	A	A	A	568	44	TSGA13	2	2
CHRM2	1129	broad.mit.edu	37	7	136700194	136700194	+	Silent	SNP	C	A	A			TCGA-17-Z051-01	TCGA-17-Z051-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:136700194C>A	uc003vtf.1	+	c.582C>A	c.(580-582)GCC>GCA	p.A194A	CHRM2_uc003vtg.1_Silent_p.A194A|CHRM2_uc003vtj.1_Silent_p.A194A|CHRM2_uc003vtk.1_Silent_p.A194A|CHRM2_uc003vtl.1_Silent_p.A194A|CHRM2_uc003vtm.1_Silent_p.A194A|CHRM2_uc003vti.1_Silent_p.A194A|CHRM2_uc003vto.1_Silent_p.A194A|CHRM2_uc003vtn.1_Silent_p.A194A	NM_001006630	NP_001006631	P08172	ACM2_HUMAN	cholinergic receptor, muscarinic 2	194	Helical; Name=5; (By similarity).				activation of phospholipase C activity by muscarinic acetylcholine receptor signaling pathway|G-protein signaling, coupled to cAMP nucleotide second messenger|nervous system development|regulation of heart contraction|response to virus	cell junction|integral to plasma membrane|postsynaptic membrane	muscarinic acetylcholine receptor activity|protein binding			ovary(4)|central_nervous_system(1)	5					Anisotropine Methylbromide(DB00517)|Atropine(DB00572)|Benzquinamide(DB00767)|Carbachol(DB00411)|Cryptenamine(DB00785)|Cyclizine(DB01176)|Desipramine(DB01151)|Diphenidol(DB01231)|Doxacurium(DB01334)|Doxacurium chloride(DB01135)|Flavoxate(DB01148)|Gallamine Triethiodide(DB00483)|Homatropine Methylbromide(DB00725)|Hyoscyamine(DB00424)|Ipratropium(DB00332)|Methotrimeprazine(DB01403)|Metixene(DB00340)|Metocurine(DB01336)|Mivacurium(DB01226)|Olanzapine(DB00334)|Oxybutynin(DB01062)|Oxyphencyclimine(DB00383)|Pilocarpine(DB01085)|Procyclidine(DB00387)|Promazine(DB00420)|Promethazine(DB01069)|Propiomazine(DB00777)|Rocuronium(DB00728)|Thiethylperazine(DB00372)|Tolterodine(DB01036)|Tridihexethyl(DB00505)|Triflupromazine(DB00508)									0.490741	152.915002	152.924203	53	55	KEEP	---	---	---	---	capture		Silent	SNP	136700194	136700194	3511	7	C	A	A	A	301	24	CHRM2	2	2
CUL1	8454	broad.mit.edu	37	7	148481085	148481085	+	Missense_Mutation	SNP	A	G	G			TCGA-17-Z051-01	TCGA-17-Z051-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:148481085A>G	uc010lpg.2	+	c.1214A>G	c.(1213-1215)AAC>AGC	p.N405S	CUL1_uc003wey.2_Missense_Mutation_p.N405S|CUL1_uc003wez.2_Missense_Mutation_p.N295S|CUL1_uc003wfa.2_Missense_Mutation_p.N66S	NM_003592	NP_003583	Q13616	CUL1_HUMAN	cullin 1	405					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|cell cycle arrest|G1/S transition of mitotic cell cycle|induction of apoptosis by intracellular signals|interspecies interaction between organisms|negative regulation of cell proliferation|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|protein ubiquitination|S phase of mitotic cell cycle|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process	cytosol|nucleoplasm|SCF ubiquitin ligase complex	ubiquitin protein ligase binding			lung(1)	1	Melanoma(164;0.15)		OV - Ovarian serous cystadenocarcinoma(82;0.00291)											0.350877	62.786496	63.902986	20	37	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	148481085	148481085	4214	7	A	G	G	G	26	2	CUL1	4	4
ABP1	26	broad.mit.edu	37	7	150554719	150554719	+	Silent	SNP	C	G	G			TCGA-17-Z051-01	TCGA-17-Z051-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:150554719C>G	uc003wia.1	+	c.1161C>G	c.(1159-1161)CCC>CCG	p.P387P	ABP1_uc003why.1_Silent_p.P387P|ABP1_uc003whz.1_Silent_p.P387P	NM_001091	NP_001082	P19801	ABP1_HUMAN	amiloride binding protein 1 precursor	387					amine metabolic process|oxidation-reduction process	extracellular space|peroxisome	copper ion binding|diamine oxidase activity|heparin binding|histamine oxidase activity|methylputrescine oxidase activity|primary amine oxidase activity|propane-1,3-diamine oxidase activity|quinone binding			ovary(2)|breast(2)	4	all_neural(206;0.219)		OV - Ovarian serous cystadenocarcinoma(82;0.0121)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)	Amiloride(DB00594)|Spermine(DB00127)	Pancreas(195;1227 3054 24912 28503)								0.444444	109.624534	109.835113	36	45	KEEP	---	---	---	---	capture		Silent	SNP	150554719	150554719	99	7	C	G	G	G	288	23	ABP1	3	3
CRYGN	155051	broad.mit.edu	37	7	151135181	151135181	+	Silent	SNP	G	A	A			TCGA-17-Z051-01	TCGA-17-Z051-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:151135181G>A	uc003wke.2	-	c.171C>T	c.(169-171)TTC>TTT	p.F57F	CRYGN_uc003wkf.2_Silent_p.F57F|CRYGN_uc003wkg.2_Non-coding_Transcript|CRYGN_uc010lqd.1_5'Flank	NM_144727	NP_653328	Q8WXF5	CRGN_HUMAN	gammaN-crystallin	57	Beta/gamma crystallin 'Greek key' 2.										0			OV - Ovarian serous cystadenocarcinoma(82;0.00358)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)										0.227273	33.056511	37.604626	15	51	KEEP	---	---	---	---	capture		Silent	SNP	151135181	151135181	4057	7	G	A	A	A	529	41	CRYGN	2	2
PKD1L1	168507	broad.mit.edu	37	7	47988007	47988007	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z051-01	TCGA-17-Z051-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:47988007C>T	uc003tny.1	-	c.31G>A	c.(31-33)GAT>AAT	p.D11N		NM_138295	NP_612152	Q8TDX9	PK1L1_HUMAN	polycystin-1L1	11	Extracellular (Potential).				cell-cell adhesion	integral to membrane				ovary(7)|breast(1)	8														0.24	59.045882	65.218925	24	76	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	47988007	47988007	12388	7	C	T	T	T	377	29	PKD1L1	2	2
WBSCR17	64409	broad.mit.edu	37	7	70800688	70800688	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z051-01	TCGA-17-Z051-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:70800688G>T	uc003tvy.2	+	c.391G>T	c.(391-393)GAC>TAC	p.D131Y	WBSCR17_uc003tvz.2_5'UTR	NM_022479	NP_071924	Q6IS24	GLTL3_HUMAN	UDP-GalNAc:polypeptide	131	Lumenal (Potential).					Golgi membrane|integral to membrane	polypeptide N-acetylgalactosaminyltransferase activity|sugar binding			ovary(1)|central_nervous_system(1)|pancreas(1)	3		all_cancers(73;0.2)|Lung NSC(55;0.094)|all_lung(88;0.125)												0.445652	111.040515	111.280014	41	51	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	70800688	70800688	17836	7	G	T	T	T	533	41	WBSCR17	2	2
CALCR	799	broad.mit.edu	37	7	93065484	93065484	+	Splice_Site_SNP	SNP	T	C	C			TCGA-17-Z051-01	TCGA-17-Z051-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:93065484T>C	uc003umv.1	-	c.1033_splice	c.e13-1	p.V345_splice	CALCR_uc011kia.1_Splice_Site_SNP_p.V125_splice|CALCR_uc003ums.1_Splice_Site_SNP|CALCR_uc003umt.1_Splice_Site_SNP|CALCR_uc003umu.1_Splice_Site_SNP_p.V311_splice|CALCR_uc003umw.2_Splice_Site_SNP_p.V311_splice	NM_001742	NP_001733			calcitonin receptor isoform 2 precursor						activation of adenylate cyclase activity by G-protein signaling pathway|elevation of cytosolic calcium ion concentration|positive regulation of adenylate cyclase activity|response to glucocorticoid stimulus	integral to plasma membrane	calcitonin binding|calcitonin binding|calcitonin receptor activity|calcitonin receptor activity|protein binding			ovary(3)|lung(1)|pancreas(1)	5	all_cancers(62;3.18e-12)|all_epithelial(64;1.34e-11)|Breast(17;0.000675)|Lung NSC(181;0.207)		STAD - Stomach adenocarcinoma(171;0.000244)		Salmon Calcitonin(DB00017)									0.515152	104.25046	104.263641	34	32	KEEP	---	---	---	---	capture		Splice_Site_SNP	SNP	93065484	93065484	2695	7	T	C	C	C	715	55	CALCR	5	4
TRAPPC9	83696	broad.mit.edu	37	8	141310603	141310603	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z051-01	TCGA-17-Z051-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:141310603G>A	uc003yvh.2	-	c.2027C>T	c.(2026-2028)GCA>GTA	p.A676V	TRAPPC9_uc003yvj.2_Missense_Mutation_p.A578V|TRAPPC9_uc003yvi.1_Missense_Mutation_p.A569V	NM_031466	NP_113654	Q96Q05	TPPC9_HUMAN	trafficking protein particle complex 9 isoform	578					cell differentiation	endoplasmic reticulum|Golgi apparatus					0														0.217742	104.231048	122.67951	54	194	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	141310603	141310603	17009	8	G	A	A	A	598	46	TRAPPC9	2	2
TEX15	56154	broad.mit.edu	37	8	30699884	30699884	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z051-01	TCGA-17-Z051-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:30699884G>A	uc003xil.2	-	c.6650C>T	c.(6649-6651)TCT>TTT	p.S2217F		NM_031271	NP_112561	Q9BXT5	TEX15_HUMAN	testis expressed 15	2217										ovary(3)	3				KIRC - Kidney renal clear cell carcinoma(542;0.0918)|Kidney(114;0.111)										0.080537	2.407052	29.110334	12	137	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	30699884	30699884	16306	8	G	A	A	A	429	33	TEX15	2	2
TEX15	56154	broad.mit.edu	37	8	30700551	30700551	+	Nonsense_Mutation	SNP	G	A	A			TCGA-17-Z051-01	TCGA-17-Z051-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:30700551G>A	uc003xil.2	-	c.5983C>T	c.(5983-5985)CAG>TAG	p.Q1995*		NM_031271	NP_112561	Q9BXT5	TEX15_HUMAN	testis expressed 15	1995										ovary(3)	3				KIRC - Kidney renal clear cell carcinoma(542;0.0918)|Kidney(114;0.111)										0.142857	18.406332	29.602527	13	78	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	30700551	30700551	16306	8	G	A	A	A	585	45	TEX15	5	2
C9orf50	375759	broad.mit.edu	37	9	132382763	132382763	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z051-01	TCGA-17-Z051-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:132382763G>A	uc004byc.3	-	c.91C>T	c.(91-93)CGG>TGG	p.R31W	C9orf50_uc004byb.3_Intron	NM_199350	NP_955382	Q5SZB4	CI050_HUMAN	hypothetical protein LOC375759	31										ovary(1)|central_nervous_system(1)	2		Ovarian(14;0.00556)												1	7.276726	7.053463	2	0	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	132382763	132382763	2602	9	G	A	A	A	493	38	C9orf50	1	1
VPS13A	23230	broad.mit.edu	37	9	79929509	79929509	+	Silent	SNP	A	G	G			TCGA-17-Z051-01	TCGA-17-Z051-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:79929509A>G	uc004akr.2	+	c.4341A>G	c.(4339-4341)ACA>ACG	p.T1447T	VPS13A_uc004akp.3_Silent_p.T1447T|VPS13A_uc004akq.3_Silent_p.T1447T|VPS13A_uc004aks.2_Silent_p.T1408T|VPS13A_uc010mpo.1_Silent_p.T43T	NM_033305	NP_150648	Q96RL7	VP13A_HUMAN	vacuolar protein sorting 13A isoform A	1447					Golgi to endosome transport|protein transport	intracellular	protein binding			pancreas(3)|ovary(2)|large_intestine(1)|central_nervous_system(1)	7														0.343434	97.820492	99.963913	34	65	KEEP	---	---	---	---	capture		Silent	SNP	79929509	79929509	17756	9	A	G	G	G	93	8	VPS13A	4	4
IRS4	8471	broad.mit.edu	37	X	107976487	107976487	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z051-01	TCGA-17-Z051-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:107976487C>A	uc004eoc.2	-	c.3088G>T	c.(3088-3090)GCT>TCT	p.A1030S		NM_003604	NP_003595	O14654	IRS4_HUMAN	insulin receptor substrate 4	1030						plasma membrane	insulin receptor binding|SH3/SH2 adaptor activity|signal transducer activity			ovary(4)|large_intestine(2)|lung(1)|breast(1)|pancreas(1)	9														0.358491	98.412028	100.284537	38	68	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	107976487	107976487	8146	23	C	A	A	A	338	26	IRS4	2	2
IRS4	8471	broad.mit.edu	37	X	107978335	107978335	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z051-01	TCGA-17-Z051-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:107978335G>T	uc004eoc.2	-	c.1240C>A	c.(1240-1242)CTG>ATG	p.L414M		NM_003604	NP_003595	O14654	IRS4_HUMAN	insulin receptor substrate 4	414						plasma membrane	insulin receptor binding|SH3/SH2 adaptor activity|signal transducer activity			ovary(4)|large_intestine(2)|lung(1)|breast(1)|pancreas(1)	9														0.333333	50.430943	51.759905	18	36	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	107978335	107978335	8146	23	G	T	T	T	464	36	IRS4	2	2
PGRMC1	10857	broad.mit.edu	37	X	118370574	118370574	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z051-01	TCGA-17-Z051-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:118370574G>T	uc004erb.2	+	c.248G>T	c.(247-249)GGC>GTC	p.G83V	PGRMC1_uc011mts.1_Missense_Mutation_p.G83V	NM_006667	NP_006658	O00264	PGRC1_HUMAN	progesterone receptor membrane component 1	83	Cytochrome b5 heme-binding.|Cytoplasmic (Potential).					cell surface|endoplasmic reticulum membrane|integral to membrane|microsome|nucleolus	heme binding|protein binding|receptor activity|steroid binding				0														0.407407	29.517541	29.720253	11	16	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	118370574	118370574	12229	23	G	T	T	T	546	42	PGRMC1	2	2
XIAP	331	broad.mit.edu	37	X	123019558	123019558	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z051-01	TCGA-17-Z051-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:123019558G>T	uc010nqu.2	+	c.46G>T	c.(46-48)GAC>TAC	p.D16Y	XIAP_uc004etx.2_Missense_Mutation_p.D16Y|XIAP_uc010nqv.2_Intron	NM_001167	NP_001158	P98170	XIAP_HUMAN	baculoviral IAP repeat-containing protein 4	16					anti-apoptosis|apoptosis|induction of apoptosis by intracellular signals|response to DNA damage stimulus	cytosol	caspase inhibitor activity|ligase activity|protein binding|zinc ion binding			ovary(1)|lung(1)	2										93				0.253521	41.008981	44.930787	18	53	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	123019558	123019558	18009	23	G	T	T	T	429	33	XIAP	2	2
SOX3	6658	broad.mit.edu	37	X	139586817	139586818	+	Missense_Mutation	DNP	CC	AA	AA			TCGA-17-Z051-01	TCGA-17-Z051-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:139586817_139586818CC>AA	uc004fbd.1	-	c.408_409GG>TT	c.(406-411)CAGGAC>CATTAC	p.136_137QD>HY		NM_005634	NP_005625	P41225	SOX3_HUMAN	SRY (sex determining region Y)-box 3	136_137					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding			pancreas(1)	1	Acute lymphoblastic leukemia(192;7.65e-05)													0.384615	67.860953	68.618777	25	40	KEEP	---	---	---	---	capture		Missense_Mutation	DNP	139586817	139586818	15451	23	CC	AA	AA	AA	390	30	SOX3	2	2
SLITRK4	139065	broad.mit.edu	37	X	142716995	142716995	+	Silent	SNP	G	T	T			TCGA-17-Z051-01	TCGA-17-Z051-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:142716995G>T	uc004fbx.2	-	c.1930C>A	c.(1930-1932)CGA>AGA	p.R644R	SLITRK4_uc004fby.2_Silent_p.R644R	NM_173078	NP_775101	Q8IW52	SLIK4_HUMAN	slit and trk like 4 protein precursor	644	Cytoplasmic (Potential).					integral to membrane				upper_aerodigestive_tract(1)|large_intestine(1)	2	Acute lymphoblastic leukemia(192;6.56e-05)													0.434043	302.164079	303.043196	102	133	KEEP	---	---	---	---	capture		Silent	SNP	142716995	142716995	15243	23	G	T	T	T	493	38	SLITRK4	1	1
PASD1	139135	broad.mit.edu	37	X	150840817	150840817	+	Nonsense_Mutation	SNP	G	T	T			TCGA-17-Z051-01	TCGA-17-Z051-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:150840817G>T	uc004fev.3	+	c.1600G>T	c.(1600-1602)GAG>TAG	p.E534*		NM_173493	NP_775764	Q8IV76	PASD1_HUMAN	PAS domain containing 1	534	Lys-rich.					nucleus	signal transducer activity			ovary(3)	3	Acute lymphoblastic leukemia(192;6.56e-05)													0.4	7.38021	7.472157	4	6	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	150840817	150840817	11888	23	G	T	T	T	533	41	PASD1	5	2
EMD	2010	broad.mit.edu	37	X	153609469	153609469	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z051-01	TCGA-17-Z051-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:153609469G>T	uc004fkl.2	+	c.677G>T	c.(676-678)TGG>TTG	p.W226L		NM_000117	NP_000108	P50402	EMD_HUMAN	emerin	226	Helical; (Potential).				cellular response to growth factor stimulus|muscle contraction|muscle organ development|negative regulation of catenin import into nucleus|negative regulation of fibroblast proliferation|positive regulation of protein export from nucleus|regulation of canonical Wnt receptor signaling pathway	endoplasmic reticulum|integral to membrane|microtubule|nuclear inner membrane|nuclear outer membrane	actin binding|beta-tubulin binding				0	all_cancers(53;3.7e-16)|all_epithelial(53;2.97e-10)|all_lung(58;1.84e-07)|Lung NSC(58;5.84e-07)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)													0.3	29.583152	31.013703	12	28	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	153609469	153609469	5279	23	G	T	T	T	611	47	EMD	2	2
SCML2	10389	broad.mit.edu	37	X	18278317	18278317	+	Missense_Mutation	SNP	C	G	G			TCGA-17-Z051-01	TCGA-17-Z051-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:18278317C>G	uc004cyl.2	-	c.1043G>C	c.(1042-1044)GGG>GCG	p.G348A	SCML2_uc004cyk.3_Non-coding_Transcript|SCML2_uc010nfd.1_Missense_Mutation_p.G348A|SCML2_uc011miz.1_Missense_Mutation_p.G282A|SCML2_uc010nfc.2_Missense_Mutation_p.G84A	NM_006089	NP_006080	Q9UQR0	SCML2_HUMAN	sex comb on midleg-like 2	348					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)								0.395349	100.72956	101.55446	34	52	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	18278317	18278317	14392	23	C	G	G	G	286	22	SCML2	3	3
ARSH	347527	broad.mit.edu	37	X	2951409	2951409	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z051-01	TCGA-17-Z051-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:2951409C>T	uc011mhj.1	+	c.1672C>T	c.(1672-1674)CTT>TTT	p.L558F		NM_001011719	NP_001011719	Q5FYA8	ARSH_HUMAN	arylsulfatase family, member H	558						integral to membrane	arylsulfatase activity|metal ion binding			lung(1)	1		all_cancers(21;9e-05)|all_epithelial(21;6.22e-06)|all_lung(23;0.000597)|Lung NSC(23;0.00901)|Lung SC(21;0.186)												0.184211	16.710861	20.258875	7	31	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	2951409	2951409	1011	23	C	T	T	T	312	24	ARSH	2	2
ARSF	416	broad.mit.edu	37	X	3002623	3002623	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z051-01	TCGA-17-Z051-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:3002623G>T	uc004cre.1	+	c.746G>T	c.(745-747)CGG>CTG	p.R249L	ARSF_uc004crf.1_Missense_Mutation_p.R249L	NM_004042	NP_004033	P54793	ARSF_HUMAN	arylsulfatase F precursor	249						extracellular region	arylsulfatase activity|metal ion binding			ovary(2)	2		all_cancers(21;4.28e-07)|all_epithelial(21;2.07e-08)|all_lung(23;2.81e-05)|Lung NSC(23;0.000693)|Lung SC(21;0.122)												0.38806	76.238327	76.972343	26	41	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	3002623	3002623	1009	23	G	T	T	T	507	39	ARSF	1	1
TAB3	257397	broad.mit.edu	37	X	30877604	30877604	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z051-01	TCGA-17-Z051-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:30877604C>A	uc004dcj.2	-	c.102G>T	c.(100-102)CAG>CAT	p.Q34H	TAB3_uc004dck.2_Missense_Mutation_p.Q34H|TAB3_uc010ngl.2_Missense_Mutation_p.Q34H	NM_152787	NP_690000	Q8N5C8	TAB3_HUMAN	mitogen-activated protein kinase kinase kinase 7	34	CUE.				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)								0.295775	55.863862	58.50388	21	50	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	30877604	30877604	16018	23	C	A	A	A	311	24	TAB3	2	2
MXRA5	25878	broad.mit.edu	37	X	3229155	3229155	+	Silent	SNP	C	T	T			TCGA-17-Z051-01	TCGA-17-Z051-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:3229155C>T	uc004crg.3	-	c.7089G>A	c.(7087-7089)GTG>GTA	p.V2363V		NM_015419	NP_056234	Q9NR99	MXRA5_HUMAN	adlican precursor	2363	Ig-like C2-type 8.					extracellular region				ovary(5)|lung(1)|central_nervous_system(1)	7		all_lung(23;0.00031)|Lung NSC(23;0.000946)												0.372093	87.126986	88.343219	32	54	KEEP	---	---	---	---	capture		Silent	SNP	3229155	3229155	10397	23	C	T	T	T	262	21	MXRA5	2	2
TMEM47	83604	broad.mit.edu	37	X	34675059	34675059	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z051-01	TCGA-17-Z051-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:34675059C>A	uc004ddh.2	-	c.88G>T	c.(88-90)GCG>TCG	p.A30S	TMEM47_uc010ngs.2_5'Flank	NM_031442	NP_113630	Q9BQJ4	TMM47_HUMAN	transmembrane protein 47	30	Helical; (Potential).					integral to membrane				lung(1)	1														0.25	6.51863	7.20114	3	9	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	34675059	34675059	16710	23	C	A	A	A	338	26	TMEM47	2	2
RPGR	6103	broad.mit.edu	37	X	38129066	38129066	+	Missense_Mutation	SNP	A	G	G			TCGA-17-Z051-01	TCGA-17-Z051-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:38129066A>G	uc004deb.2	-	c.2261T>C	c.(2260-2262)GTC>GCC	p.V754A	RPGR_uc004dea.2_Non-coding_Transcript|RPGR_uc004dec.2_Non-coding_Transcript	NM_000328	NP_000319	Q92834	RPGR_HUMAN	retinitis pigmentosa GTPase regulator isoform A	759	Glu-rich.				intracellular protein transport|response to stimulus|visual perception	Golgi apparatus|photoreceptor outer segment	guanyl-nucleotide exchange factor activity|protein binding			ovary(1)	1														0.166667	12.638071	16.423474	6	30	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	38129066	38129066	14027	23	A	G	G	G	130	10	RPGR	4	4
HDAC6	10013	broad.mit.edu	37	X	48665048	48665048	+	Silent	SNP	C	T	T			TCGA-17-Z051-01	TCGA-17-Z051-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:48665048C>T	uc011mmi.1	+	c.567C>T	c.(565-567)GGC>GGT	p.G189G	HDAC6_uc004dks.1_Silent_p.G189G|HDAC6_uc010nig.1_Silent_p.G37G|HDAC6_uc004dkt.1_Silent_p.G189G|HDAC6_uc004dku.3_3'UTR|HDAC6_uc011mmj.1_Silent_p.G134G|HDAC6_uc011mmk.1_Silent_p.G170G	NM_006044	NP_006035	Q9UBN7	HDAC6_HUMAN	histone deacetylase 6	189	Histone deacetylase 1.				aggresome assembly|cellular response to hydrogen peroxide|Hsp90 deacetylation|lysosome localization|macroautophagy|misfolded or incompletely synthesized protein catabolic process|negative regulation of hydrogen peroxide metabolic process|negative regulation of oxidoreductase activity|negative regulation of proteolysis|peptidyl-lysine deacetylation|polyubiquitinated misfolded protein transport|positive regulation of apoptosis|positive regulation of cellular chaperone-mediated protein complex assembly|positive regulation of epithelial cell migration|positive regulation of receptor biosynthetic process|positive regulation of signal transduction|regulation of androgen receptor signaling pathway|regulation of microtubule-based movement|regulation of receptor activity|regulation of transcription, DNA-dependent|response to growth factor stimulus|response to toxin|transcription, DNA-dependent|tubulin deacetylation	aggresome|caveola|cell leading edge|cytosol|histone deacetylase complex|microtubule associated complex|perinuclear region of cytoplasm	actin binding|alpha-tubulin binding|beta-catenin binding|dynein complex binding|histone deacetylase activity (H3-K16 specific)|histone deacetylase binding|Hsp90 protein binding|microtubule binding|NAD-dependent histone deacetylase activity (H3-K14 specific)|NAD-dependent histone deacetylase activity (H3-K9 specific)|NAD-dependent histone deacetylase activity (H4-K16 specific)|polyubiquitin binding|specific transcriptional repressor activity|tau protein binding|tubulin deacetylase activity|zinc ion binding			ovary(3)	3					Vorinostat(DB02546)	Pancreas(112;205 1675 2305 8976 15959)				170				0.233083	71.451257	80.131003	31	102	KEEP	---	---	---	---	capture		Silent	SNP	48665048	48665048	7294	23	C	T	T	T	353	28	HDAC6	2	2
TIMM17B	10245	broad.mit.edu	37	X	48754090	48754090	+	Silent	SNP	G	T	T			TCGA-17-Z051-01	TCGA-17-Z051-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:48754090G>T	uc004dla.1	-	c.78C>A	c.(76-78)ATC>ATA	p.I26I	PQBP1_uc004dle.2_5'Flank|PQBP1_uc004dlf.2_5'Flank|PQBP1_uc004dlg.2_5'Flank|PQBP1_uc004dld.2_5'Flank|PQBP1_uc004dlh.2_5'Flank|PQBP1_uc004dli.2_5'Flank|PQBP1_uc004dlj.1_5'Flank|PQBP1_uc004dln.2_5'Flank|PQBP1_uc010nih.2_5'Flank|PQBP1_uc010nii.2_5'Flank|PQBP1_uc004dlk.2_5'Flank|PQBP1_uc004dll.2_5'Flank|PQBP1_uc004dlm.2_5'Flank|PQBP1_uc010nij.2_5'Flank|TIMM17B_uc004dlb.1_Nonsense_Mutation_p.S12*|TIMM17B_uc004dlc.1_Silent_p.I26I	NM_005834	NP_005825	O60830	TI17B_HUMAN	translocase of inner mitochondrial membrane 17	26	Helical; (Potential).				protein targeting to mitochondrion	integral to membrane|microtubule cytoskeleton|mitochondrial inner membrane presequence translocase complex	P-P-bond-hydrolysis-driven protein transmembrane transporter activity			ovary(1)	1														0.325581	38.934487	40.095504	14	29	KEEP	---	---	---	---	capture		Silent	SNP	48754090	48754090	16438	23	G	T	T	T	473	37	TIMM17B	1	1
PIM2	11040	broad.mit.edu	37	X	48771550	48771550	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z051-01	TCGA-17-Z051-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:48771550C>T	uc004dls.2	-	c.794G>A	c.(793-795)CGG>CAG	p.R265Q	SLC35A2_uc004dlo.1_5'Flank|SLC35A2_uc011mml.1_5'Flank|SLC35A2_uc004dlp.1_5'Flank|SLC35A2_uc011mmm.1_5'Flank|SLC35A2_uc011mmn.1_5'Flank|SLC35A2_uc004dlq.2_5'Flank|SLC35A2_uc011mmo.1_5'Flank	NM_006875	NP_006866	Q9P1W9	PIM2_HUMAN	serine/threonine protein kinase pim-2	265	Protein kinase.				anti-apoptosis|cell proliferation|male meiosis|positive regulation of autophagy|positive regulation of I-kappaB kinase/NF-kappaB cascade|protein phosphorylation|response to virus		ATP binding|protein serine/threonine kinase activity			lung(2)|stomach(1)	3										33				0.225806	18.357233	20.463684	7	24	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	48771550	48771550	12352	23	C	T	T	T	299	23	PIM2	1	1
APEX2	27301	broad.mit.edu	37	X	55029451	55029451	+	Missense_Mutation	SNP	C	A	A	rs75862529		TCGA-17-Z051-01	TCGA-17-Z051-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:55029451C>A	uc004dtz.2	+	c.479C>A	c.(478-480)GCG>GAG	p.A160E	APEX2_uc011mom.1_5'UTR	NM_014481	NP_055296	Q9UBZ4	APEX2_HUMAN	apurinic/apyrimidinic endonuclease 2	160					cell cycle|DNA recombination|DNA repair	nucleus	DNA binding|DNA-(apurinic or apyrimidinic site) lyase activity|endonuclease activity|exonuclease activity|zinc ion binding				0														0.323529	31.722631	32.657622	11	23	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	55029451	55029451	780	23	C	A	A	A	351	27	APEX2	1	1
ZC3H12B	340554	broad.mit.edu	37	X	64722832	64722832	+	Missense_Mutation	SNP	A	G	G			TCGA-17-Z051-01	TCGA-17-Z051-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:64722832A>G	uc010nko.2	+	c.2221A>G	c.(2221-2223)ATG>GTG	p.M741V		NM_001010888	NP_001010888	Q5HYM0	ZC12B_HUMAN	zinc finger CCCH-type containing 12B	741							endonuclease activity|nucleic acid binding|zinc ion binding			lung(1)|kidney(1)|pancreas(1)	3														0.415094	58.405728	58.746497	22	31	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	64722832	64722832	18150	23	A	G	G	G	104	8	ZC3H12B	4	4
MED12	9968	broad.mit.edu	37	X	70342079	70342079	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z051-01	TCGA-17-Z051-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:70342079G>T	uc004dyy.2	+	c.1131G>T	c.(1129-1131)TTG>TTT	p.L377F	MED12_uc011mpq.1_Missense_Mutation_p.L377F|MED12_uc004dyz.2_Missense_Mutation_p.L377F|MED12_uc004dza.2_Missense_Mutation_p.L224F	NM_005120	NP_005111	Q93074	MED12_HUMAN	mediator complex subunit 12	377					androgen receptor signaling pathway|negative regulation of Wnt receptor signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription initiation from RNA polymerase II promoter	mediator complex	ligand-dependent nuclear receptor transcription coactivator activity|protein C-terminus binding|protein domain specific binding|receptor activity|RNA polymerase II transcription mediator activity|thyroid hormone receptor binding|transcription activator activity|vitamin D receptor binding			ovary(1)|breast(1)|central_nervous_system(1)|skin(1)	4	Renal(35;0.156)													0.029494	-134.994133	38.152246	21	691	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	70342079	70342079	9817	23	G	T	T	T	607	47	MED12	2	2
NLGN3	54413	broad.mit.edu	37	X	70389605	70389605	+	Missense_Mutation	SNP	A	T	T			TCGA-17-Z051-01	TCGA-17-Z051-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:70389605A>T	uc004dzb.2	+	c.2145A>T	c.(2143-2145)AAA>AAT	p.K715N	NLGN3_uc004dzc.2_Missense_Mutation_p.K598N|NLGN3_uc011mps.1_Missense_Mutation_p.K695N|NLGN3_uc004dze.2_Missense_Mutation_p.K533N	NM_018977	NP_061850	Q9NZ94	NLGN3_HUMAN	neuroligin 3	735	Cytoplasmic (Potential).				neuron cell-cell adhesion|positive regulation of synaptogenesis|receptor-mediated endocytosis|regulation of synaptic transmission|social behavior|synapse assembly	cell surface|endocytic vesicle|integral to plasma membrane|synapse	carboxylesterase activity|protein binding|receptor activity			ovary(1)	1	Renal(35;0.156)					Esophageal Squamous(103;760 1488 16849 22250 40351)								0.285714	13.535711	14.406205	6	15	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	70389605	70389605	10866	23	A	T	T	T	24	2	NLGN3	3	3
KIAA2022	340533	broad.mit.edu	37	X	73962891	73962891	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z051-01	TCGA-17-Z051-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:73962891C>A	uc004eby.2	-	c.1501G>T	c.(1501-1503)GGT>TGT	p.G501C		NM_001008537	NP_001008537	Q5QGS0	K2022_HUMAN	hypothetical protein LOC340533	501					base-excision repair, gap-filling|DNA replication proofreading|DNA replication, removal of RNA primer|nucleotide-excision repair, DNA gap filling|regulation of mitotic cell cycle|S phase of mitotic cell cycle	delta DNA polymerase complex	3'-5'-exodeoxyribonuclease activity|DNA-directed DNA polymerase activity			ovary(7)|large_intestine(4)|skin(2)|central_nervous_system(1)	14										126				0.420635	147.032766	147.729094	53	73	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	73962891	73962891	8580	23	C	A	A	A	286	22	KIAA2022	2	2
MAGEE1	57692	broad.mit.edu	37	X	75649284	75649284	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z051-01	TCGA-17-Z051-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:75649284C>T	uc004ecm.1	+	c.961C>T	c.(961-963)CCG>TCG	p.P321S		NM_020932	NP_065983	Q9HCI5	MAGE1_HUMAN	melanoma antigen family E, 1	321	Pro-rich.					dendrite|nucleus|perinuclear region of cytoplasm|postsynaptic membrane				breast(3)|ovary(1)|pancreas(1)|skin(1)	6														0.294118	12.581189	13.218657	5	12	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	75649284	75649284	9568	23	C	T	T	T	338	26	MAGEE1	2	2
SH3BGRL	6451	broad.mit.edu	37	X	80552722	80552722	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z051-01	TCGA-17-Z051-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:80552722C>A	uc010nmn.2	+	c.452C>A	c.(451-453)GCA>GAA	p.A151E	SH3BGRL_uc004eef.2_Missense_Mutation_p.A114E|SH3BGRL_uc011mqs.1_Non-coding_Transcript|SH3BGRL_uc010nml.2_Non-coding_Transcript|SH3BGRL_uc010nmm.2_Missense_Mutation_p.A151E	NM_003022	NP_003013	O75368	SH3L1_HUMAN	SH3 domain binding glutamic acid-rich protein	114						cytoplasm|nucleus	SH3 domain binding|SH3/SH2 adaptor activity			ovary(1)	1		all_lung(315;5.94e-05)												0.336538	97.6682	100.138519	35	69	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	80552722	80552722	14732	23	C	A	A	A	325	25	SH3BGRL	2	2
ERCC6	2074	broad.mit.edu	37	10	50732305	50732305	+	Frame_Shift_Del	DEL	C	-	-			TCGA-17-Z051-01	TCGA-17-Z051-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:50732305_50732305delC	uc001jhs.3	-	c.1171_1171delG	c.(1171-1173)GCAfs	p.A391fs	PGBD3_uc001jht.2_5'UTR|PGBD3_uc009xoe.2_Frame_Shift_Del_p.A391fs|PGBD3_uc001jhu.2_Frame_Shift_Del_p.A391fs	NM_000124	NP_000115	Q03468	ERCC6_HUMAN	excision repair cross-complementing rodent	391	Asp/Glu-rich (acidic).				base-excision repair|positive regulation of transcription elongation, DNA-dependent|transcription from RNA polymerase II promoter|transcription-coupled nucleotide-excision repair	nucleolus|soluble fraction|transcription elongation factor complex	ATP binding|chromatin binding|DNA binding|DNA-dependent ATPase activity|helicase activity|protein C-terminus binding|protein complex binding|protein N-terminus binding|transcription elongation regulator activity			breast(5)|ovary(2)|large_intestine(2)|lung(1)	10										738				0.44			17	22		---	---	---	---	capture_indel		Frame_Shift_Del	DEL	50732305	50732305	5410	10	C	-	-	-	338	26	ERCC6	5	5
CHRM4	1132	broad.mit.edu	37	11	46407277	46407278	+	Frame_Shift_Ins	INS	-	G	G			TCGA-17-Z051-01	TCGA-17-Z051-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:46407277_46407278insG	uc001nct.1	-	c.830_831insC	c.(829-831)CCGfs	p.P277fs		NM_000741	NP_000732	P08173	ACM4_HUMAN	cholinergic receptor, muscarinic 4	277	Cytoplasmic (By similarity).				cell proliferation	cell junction|integral to plasma membrane|postsynaptic membrane	muscarinic acetylcholine receptor activity				0				GBM - Glioblastoma multiforme(35;0.0254)|Lung(87;0.14)	Atropine(DB00572)|Benzquinamide(DB00767)|Cryptenamine(DB00785)|Homatropine Methylbromide(DB00725)|Methotrimeprazine(DB01403)|Metixene(DB00340)|Olanzapine(DB00334)|Procyclidine(DB00387)|Promazine(DB00420)|Promethazine(DB01069)|Propiomazine(DB00777)|Thiethylperazine(DB00372)|Tropicamide(DB00809)	Esophageal Squamous(171;1020 1936 4566 30205 42542)								0.33			2	4		---	---	---	---	capture_indel		Frame_Shift_Ins	INS	46407277	46407278	3513	11	-	G	G	G	340	27	CHRM4	5	5
MEGF6	1953	broad.mit.edu	37	1	3496416	3496417	+	Frame_Shift_Ins	INS	-	G	G	rs115018369	by1000genomes	TCGA-17-Z051-01	TCGA-17-Z051-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:3496416_3496417insG	uc001akl.2	-	c.453_454insC	c.(451-456)CCCGGCfs	p.P151fs		NM_001409	NP_001400	O75095	MEGF6_HUMAN	EGF-like-domain, multiple 3 precursor	151_152	EGF-like 1.					extracellular region	calcium ion binding			large_intestine(1)	1	all_cancers(77;0.00681)|all_epithelial(69;0.00301)|Ovarian(185;0.0634)|Lung NSC(156;0.0969)|all_lung(157;0.105)	all_epithelial(116;7.41e-22)|all_lung(118;8.3e-09)|Lung NSC(185;3.55e-06)|Breast(487;0.000659)|Renal(390;0.00121)|Hepatocellular(190;0.00308)|Myeloproliferative disorder(586;0.0255)|Lung SC(97;0.0262)|Ovarian(437;0.0308)|Medulloblastoma(700;0.211)		Epithelial(90;3.78e-37)|OV - Ovarian serous cystadenocarcinoma(86;6.86e-22)|GBM - Glioblastoma multiforme(42;1.96e-12)|Colorectal(212;6.15e-05)|COAD - Colon adenocarcinoma(227;0.000241)|Kidney(185;0.000448)|BRCA - Breast invasive adenocarcinoma(365;0.000779)|KIRC - Kidney renal clear cell carcinoma(229;0.00645)|STAD - Stomach adenocarcinoma(132;0.00669)|Lung(427;0.213)		Ovarian(73;978 3658)								0.33			2	4		---	---	---	---	capture_indel		Frame_Shift_Ins	INS	3496416	3496417	9851	1	-	G	G	G	299	23	MEGF6	5	5
CARD10	29775	broad.mit.edu	37	22	37900248	37900249	+	Frame_Shift_Ins	INS	-	G	G			TCGA-17-Z051-01	TCGA-17-Z051-01										Phase_I	Unspecified				Illumina GAIIx	g.chr22:37900248_37900249insG	uc003asx.1	-	c.1578_1579insC	c.(1576-1581)CCCAGTfs	p.P526fs	CARD10_uc003ast.1_Non-coding_Transcript|CARD10_uc003asw.1_Frame_Shift_Ins_p.P240fs|CARD10_uc003asy.1_Frame_Shift_Ins_p.P526fs	NM_014550	NP_055365	Q9BWT7	CAR10_HUMAN	caspase recruitment domain protein 10	526_527					activation of NF-kappaB-inducing kinase activity|protein complex assembly|regulation of apoptosis	CBM complex	receptor signaling complex scaffold activity			ovary(1)|kidney(1)	2	Melanoma(58;0.0574)									672				0.40			4	6		---	---	---	---	capture_indel		Frame_Shift_Ins	INS	37900248	37900249	2763	22	-	G	G	G	715	55	CARD10	5	5
PTPN18	26469	broad.mit.edu	37	2	131129929	131129934	+	In_Frame_Del	DEL	GACGGG	-	-			TCGA-17-Z051-01	TCGA-17-Z051-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:131129929_131129934delGACGGG	uc002trc.2	+	c.1113_1118delGACGGG	c.(1111-1119)CAGACGGGG>CAG	p.TG378del	PTPN18_uc002trd.2_In_Frame_Del_p.TG357del|PTPN18_uc002trb.2_In_Frame_Del_p.TG271del|PTPN18_uc002tre.2_In_Frame_Del_p.TG29del	NM_014369	NP_055184	Q99952	PTN18_HUMAN	protein tyrosine phosphatase, non-receptor type	378_379				Missing (in Ref. 1; CAA56105).		cytoplasm|nucleus	non-membrane spanning protein tyrosine phosphatase activity			ovary(3)|kidney(1)	4	Colorectal(110;0.1)													0.38			3	5		---	---	---	---	capture_indel		In_Frame_Del	DEL	131129929	131129934	13239	2	GACGGG	-	-	-	425	33	PTPN18	5	5
