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
SLC25A28	81894	broad.mit.edu	37	10	101370759	101370759	+	Silent	SNP	C	A	A			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:101370759C>A	uc001kpx.2	-	c.942G>T	c.(940-942)ACG>ACT	p.T314T	SLC25A28_uc001kpy.2_Silent_p.T127T	NM_031212	NP_112489	Q96A46	MFRN2_HUMAN	solute carrier family 25, member 28	314	Solcar 3.				ion transport|iron ion homeostasis	integral to membrane|mitochondrial inner membrane					0		Colorectal(252;0.234)		Epithelial(162;2.57e-10)|all cancers(201;2.01e-08)										0.356589	131.453877	133.773151	46	83	KEEP	---	---	---	---	capture		Silent	SNP	101370759	101370759	14988	10	C	A	A	A	288	23	SLC25A28	1	1
C10orf79	80217	broad.mit.edu	37	10	105928572	105928572	+	Missense_Mutation	SNP	T	A	A			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:105928572T>A	uc001kxw.2	-	c.2621A>T	c.(2620-2622)AAG>ATG	p.K874M	C10orf79_uc009xxq.2_Missense_Mutation_p.K182M|C10orf79_uc001kxx.3_Missense_Mutation_p.K875M	NM_025145	NP_079421	Q8NDM7	WDR96_HUMAN	hypothetical protein LOC80217	874											0		Colorectal(252;0.178)		Epithelial(162;4.83e-10)|all cancers(201;2.26e-08)|BRCA - Breast invasive adenocarcinoma(275;0.0194)										0.489796	667.681584	667.721496	216	225	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	105928572	105928572	1655	10	T	A	A	A	728	56	C10orf79	3	3
PNLIPRP3	119548	broad.mit.edu	37	10	118236276	118236276	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:118236276C>A	uc001lcl.3	+	c.1285C>A	c.(1285-1287)CAG>AAG	p.Q429K		NM_001011709	NP_001011709	Q17RR3	LIPR3_HUMAN	pancreatic lipase-related protein 3 precursor	429	PLAT.				lipid catabolic process	extracellular region	triglyceride lipase activity			ovary(1)	1				all cancers(201;0.0131)										0.449568	473.622282	474.395577	156	191	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	118236276	118236276	12578	10	C	A	A	A	377	29	PNLIPRP3	2	2
PNLIPRP2	5408	broad.mit.edu	37	10	118386475	118386475	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:118386475G>T	uc001lcq.2	+	c.434G>T	c.(433-435)GGG>GTG	p.G145V	PNLIPRP2_uc009xyu.1_Non-coding_Transcript|PNLIPRP2_uc009xyv.1_Non-coding_Transcript	NM_005396	NP_005387	P54317	LIPR2_HUMAN	pancreatic lipase-related protein 2	144					galactolipid catabolic process|lipid digestion|phospholipid catabolic process|triglyceride metabolic process	extracellular space	acylglycerol lipase activity|calcium ion binding|galactolipase activity|phospholipase activity|triglyceride lipase activity			large_intestine(1)	1				all cancers(201;0.015)										0.380952	21.896612	22.156928	8	13	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	118386475	118386475	12577	10	G	T	T	T	559	43	PNLIPRP2	2	2
WDR11	55717	broad.mit.edu	37	10	122643308	122643308	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:122643308G>T	uc010qtf.1	+	c.1756G>T	c.(1756-1758)GTA>TTA	p.V586L	WDR11_uc010qte.1_Missense_Mutation_p.V188L|WDR11_uc001lfd.1_Missense_Mutation_p.V104L|WDR11_uc009xzn.2_5'Flank	NM_018117	NP_060587	Q9BZH6	WDR11_HUMAN	bromodomain and WD repeat domain containing 2	586	WD 5.					integral to membrane					0														0.465753	229.200658	229.336109	68	78	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	122643308	122643308	17846	10	G	T	T	T	520	40	WDR11	1	1
TACC2	10579	broad.mit.edu	37	10	123846990	123846990	+	Nonsense_Mutation	SNP	G	T	T			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:123846990G>T	uc001lfv.2	+	c.4975G>T	c.(4975-4977)GAA>TAA	p.E1659*	TACC2_uc001lfw.2_Intron|TACC2_uc009xzx.2_Nonsense_Mutation_p.E1659*|TACC2_uc010qtv.1_Nonsense_Mutation_p.E1659*	NM_206862	NP_996744	O95359	TACC2_HUMAN	transforming, acidic coiled-coil containing	1659						microtubule organizing center|nucleus	nuclear hormone receptor binding			ovary(4)|breast(3)|central_nervous_system(1)	8		all_neural(114;0.0656)|Lung NSC(174;0.136)|all_lung(145;0.17)|Breast(234;0.197)												0.438356	89.872834	90.117028	32	41	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	123846990	123846990	16023	10	G	T	T	T	585	45	TACC2	5	2
DMBT1	1755	broad.mit.edu	37	10	124390487	124390487	+	Missense_Mutation	SNP	G	C	C			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:124390487G>C	uc001lgk.1	+	c.5649G>C	c.(5647-5649)TTG>TTC	p.L1883F	DMBT1_uc001lgl.1_Missense_Mutation_p.L1873F|DMBT1_uc001lgm.1_Missense_Mutation_p.L1255F|DMBT1_uc009xzz.1_Missense_Mutation_p.L1883F|DMBT1_uc010qtx.1_Missense_Mutation_p.L603F|DMBT1_uc009yab.1_Missense_Mutation_p.L586F|DMBT1_uc009yac.1_Missense_Mutation_p.L177F	NM_007329	NP_015568	Q9UGM3	DMBT1_HUMAN	deleted in malignant brain tumors 1 isoform b	1883	SRCR 14.				epithelial cell differentiation|induction of bacterial agglutination|innate immune response|interspecies interaction between organisms|protein transport|response to virus	extrinsic to membrane|phagocytic vesicle membrane|zymogen granule membrane	calcium-dependent protein binding|Gram-negative bacterial cell surface binding|Gram-positive bacterial cell surface binding|pattern recognition receptor activity|scavenger receptor activity|zymogen binding			central_nervous_system(7)	7		all_neural(114;0.0765)|Lung NSC(174;0.132)|all_lung(145;0.163)|Breast(234;0.238)				Ovarian(182;93 2026 18125 22222 38972)								0.4	109.89575	110.591505	32	48	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	124390487	124390487	4757	10	G	C	C	C	581	45	DMBT1	3	3
CUBN	8029	broad.mit.edu	37	10	17083166	17083166	+	Missense_Mutation	SNP	C	G	G			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:17083166C>G	uc001ioo.2	-	c.3883G>C	c.(3883-3885)GGG>CGG	p.G1295R		NM_001081	NP_001072	O60494	CUBN_HUMAN	cubilin precursor	1295	CUB 8.				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				0.367521	262.006137	265.608956	86	148	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	17083166	17083166	4211	10	C	G	G	G	312	24	CUBN	3	3
MLLT10	8028	broad.mit.edu	37	10	21962822	21962822	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:21962822G>T	uc001iqs.2	+	c.1595G>T	c.(1594-1596)AGT>ATT	p.S532I	MLLT10_uc001iqt.2_Missense_Mutation_p.S532I|MLLT10_uc001iqv.2_Non-coding_Transcript|MLLT10_uc001iqy.2_Missense_Mutation_p.S532I|MLLT10_uc001ira.2_5'UTR|MLLT10_uc001irb.2_Non-coding_Transcript|MLLT10_uc001iqz.2_Missense_Mutation_p.S287I	NM_004641	NP_004632	P55197	AF10_HUMAN	myeloid/lymphoid or mixed-lineage leukemia	532	DNA-binding.				positive regulation of transcription from RNA polymerase II promoter	cytoplasm|nucleus	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			skin(1)	1										395				0.395973	187.288445	188.701245	59	90	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	21962822	21962822	10016	10	G	T	T	T	468	36	MLLT10	2	2
GPR158	57512	broad.mit.edu	37	10	25861792	25861792	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:25861792C>T	uc001isj.2	+	c.1729C>T	c.(1729-1731)CGC>TGC	p.R577C		NM_020752	NP_065803	Q5T848	GP158_HUMAN	G protein-coupled receptor 158 precursor	577	Extracellular (Potential).					integral to membrane|plasma membrane	G-protein coupled receptor activity			ovary(4)|large_intestine(2)|pancreas(1)	7														0.343511	139.140108	141.971634	45	86	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	25861792	25861792	6938	10	C	T	T	T	299	23	GPR158	1	1
GPR158	57512	broad.mit.edu	37	10	25887861	25887861	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:25887861G>T	uc001isj.2	+	c.3306G>T	c.(3304-3306)GAG>GAT	p.E1102D	GPR158_uc001isk.2_Missense_Mutation_p.E477D	NM_020752	NP_065803	Q5T848	GP158_HUMAN	G protein-coupled receptor 158 precursor	1102	Cytoplasmic (Potential).					integral to membrane|plasma membrane	G-protein coupled receptor activity			ovary(4)|large_intestine(2)|pancreas(1)	7														0.377778	173.692158	176.072807	68	112	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	25887861	25887861	6938	10	G	T	T	T	425	33	GPR158	2	2
MAP3K8	1326	broad.mit.edu	37	10	30747105	30747105	+	Silent	SNP	G	A	A			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:30747105G>A	uc001ivi.1	+	c.966G>A	c.(964-966)ACG>ACA	p.T322T	MAP3K8_uc009xlf.1_Silent_p.T322T|MAP3K8_uc001ivj.1_Silent_p.T322T	NM_005204	NP_005195	P41279	M3K8_HUMAN	mitogen-activated protein kinase kinase kinase	322	Protein kinase.				cell cycle|protein phosphorylation|T cell costimulation	cytosol	ATP binding|magnesium ion binding|MAP kinase kinase kinase activity|protein binding			breast(3)|central_nervous_system(1)	4		Prostate(175;0.151)								197				0.49505	161.749784	161.751893	50	51	KEEP	---	---	---	---	capture		Silent	SNP	30747105	30747105	9639	10	G	A	A	A	496	39	MAP3K8	1	1
A1CF	29974	broad.mit.edu	37	10	52603771	52603771	+	Nonsense_Mutation	SNP	C	A	A			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:52603771C>A	uc010qho.1	-	c.235G>T	c.(235-237)GAG>TAG	p.E79*	A1CF_uc010qhn.1_Nonsense_Mutation_p.E79*|A1CF_uc001jji.2_Nonsense_Mutation_p.E71*|A1CF_uc001jjj.2_Nonsense_Mutation_p.E71*|A1CF_uc001jjh.2_Nonsense_Mutation_p.E79*|A1CF_uc009xov.2_Nonsense_Mutation_p.E71*|A1CF_uc001jjk.1_Nonsense_Mutation_p.E71*	NM_138933	NP_620311	Q9NQ94	A1CF_HUMAN	apobec-1 complementation factor isoform 3	71	RRM 1.				cytidine to uridine editing|mRNA modification|mRNA processing|protein stabilization	apolipoprotein B mRNA editing enzyme complex|endoplasmic reticulum|nucleoplasm	nucleotide binding|protein binding|single-stranded RNA binding			central_nervous_system(1)	1														0.432258	201.088182	201.710733	67	88	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	52603771	52603771	2	10	C	A	A	A	377	29	A1CF	5	2
ASB13	79754	broad.mit.edu	37	10	5683788	5683788	+	Silent	SNP	C	T	T			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:5683788C>T	uc001iig.2	-	c.654G>A	c.(652-654)CCG>CCA	p.P218P	ASB13_uc001iii.2_Non-coding_Transcript|ASB13_uc001iih.2_Non-coding_Transcript|ASB13_uc009xic.2_Silent_p.P218P	NM_024701	NP_078977	Q8WXK3	ASB13_HUMAN	ankyrin repeat and SOCS box-containing protein	218					intracellular signal transduction		protein binding			ovary(1)	1				GBM - Glioblastoma multiforme(2;9.59e-09)										0.241379	14.815794	16.582464	7	22	KEEP	---	---	---	---	capture		Silent	SNP	5683788	5683788	1035	10	C	T	T	T	236	19	ASB13	1	1
BICC1	80114	broad.mit.edu	37	10	60461881	60461881	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:60461881G>T	uc001jki.1	+	c.285G>T	c.(283-285)AAG>AAT	p.K95N		NM_001080512	NP_001073981	Q9H694	BICC1_HUMAN	bicaudal C homolog 1	95					multicellular organismal development		RNA binding			ovary(2)|lung(1)	3														0.42029	81.856637	82.240593	29	40	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	60461881	60461881	1452	10	G	T	T	T	425	33	BICC1	2	2
ANK3	288	broad.mit.edu	37	10	61829123	61829123	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:61829123C>A	uc001jky.2	-	c.11516G>T	c.(11515-11517)TGT>TTT	p.C3839F	ANK3_uc001jkw.2_Intron|ANK3_uc009xpa.2_Intron|ANK3_uc001jkx.2_Intron|ANK3_uc010qih.1_Intron|ANK3_uc001jkz.3_Intron|ANK3_uc001jkv.2_Intron|ANK3_uc009xpb.1_Intron	NM_020987	NP_066267	Q12955	ANK3_HUMAN	ankyrin 3 isoform 1	3839					establishment of protein localization|signal transduction	basolateral plasma membrane|cytoplasm|cytoskeleton	protein binding			ovary(6)|pancreas(2)|central_nervous_system(1)|skin(1)	10														0.378815	641.668019	648.853139	211	346	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	61829123	61829123	625	10	C	A	A	A	221	17	ANK3	2	2
CDH23	64072	broad.mit.edu	37	10	73550964	73550964	+	Missense_Mutation	SNP	T	A	A			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:73550964T>A	uc001jrx.3	+	c.6125T>A	c.(6124-6126)CTG>CAG	p.L2042Q		NM_022124	NP_071407	Q9H251	CAD23_HUMAN	cadherin-like 23 isoform 1 precursor	2042	Cadherin 19.|Extracellular (Potential).				calcium ion transport|calcium-dependent cell-cell adhesion|cytosolic calcium ion homeostasis|equilibrioception|homophilic cell adhesion|photoreceptor cell maintenance|response to stimulus|sensory perception of sound	integral to membrane|plasma membrane|stereocilium	calcium ion binding|protein binding			central_nervous_system(5)|large_intestine(4)|ovary(2)	11														0.473684	27.170337	27.181954	9	10	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	73550964	73550964	3237	10	T	A	A	A	715	55	CDH23	3	3
CDH23	64072	broad.mit.edu	37	10	73553269	73553269	+	Missense_Mutation	SNP	A	G	G			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:73553269A>G	uc001jrx.3	+	c.6584A>G	c.(6583-6585)AAT>AGT	p.N2195S	CDH23_uc001jsg.3_5'Flank|CDH23_uc001jsh.3_5'Flank	NM_022124	NP_071407	Q9H251	CAD23_HUMAN	cadherin-like 23 isoform 1 precursor	2195	Cadherin 21.|Extracellular (Potential).			EFLNPIQTVSVLESAEPGTVIANITAIDHDLNPKLEYHIVG IVAKDDTDRLVPNQEDAFAVNIN -> ASWEGQSHVTQAYE EAVGPPQPQVPDSTGDRHPLWGLGGFGQEHPWEGQILGGSS QAEPGLVWS (in Ref. 6; BAB61902).	calcium ion transport|calcium-dependent cell-cell adhesion|cytosolic calcium ion homeostasis|equilibrioception|homophilic cell adhesion|photoreceptor cell maintenance|response to stimulus|sensory perception of sound	integral to membrane|plasma membrane|stereocilium	calcium ion binding|protein binding			central_nervous_system(5)|large_intestine(4)|ovary(2)	11														0.35	87.169441	88.760195	28	52	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	73553269	73553269	3237	10	A	G	G	G	52	4	CDH23	4	4
SH2D4B	387694	broad.mit.edu	37	10	82403749	82403749	+	Missense_Mutation	SNP	G	C	C			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:82403749G>C	uc001kck.1	+	c.986G>C	c.(985-987)GGA>GCA	p.G329A	SH2D4B_uc001kcl.1_Missense_Mutation_p.G281A|SH2D4B_uc001kcm.1_Missense_Mutation_p.E150Q|SH2D4B_uc001kcn.1_Non-coding_Transcript	NM_207372	NP_997255	Q5SQS7	SH24B_HUMAN	SH2 domain containing 4B isoform 1	328	SH2.										0			Colorectal(32;0.229)											0.468927	280.126304	280.272073	83	94	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	82403749	82403749	14727	10	G	C	C	C	533	41	SH2D4B	3	3
LRIT1	26103	broad.mit.edu	37	10	85992365	85992365	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:85992365G>T	uc001kcz.1	-	c.1190C>A	c.(1189-1191)TCT>TAT	p.S397Y		NM_015613	NP_056428	Q9P2V4	LRIT1_HUMAN	retina specific protein PAL	397	Lumenal (Potential).					integral to endoplasmic reticulum membrane					0														0.464286	69.03771	69.099074	26	30	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	85992365	85992365	9320	10	G	T	T	T	429	33	LRIT1	2	2
DLAT	1737	broad.mit.edu	37	11	111922022	111922022	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:111922022G>T	uc001pmo.2	+	c.1463G>T	c.(1462-1464)TGT>TTT	p.C488F	DLAT_uc009yyk.1_Missense_Mutation_p.C383F|DLAT_uc010rwr.1_Missense_Mutation_p.C361F	NM_001931	NP_001922	P10515	ODP2_HUMAN	dihydrolipoamide S-acetyltransferase precursor	488	Catalytic (By similarity).				glycolysis|regulation of acetyl-CoA biosynthetic process from pyruvate	mitochondrial pyruvate dehydrogenase complex	dihydrolipoyllysine-residue acetyltransferase activity|protein binding				0		all_cancers(61;4.53e-11)|all_epithelial(67;2.76e-06)|Melanoma(852;9.42e-06)|all_hematologic(158;0.000885)|Acute lymphoblastic leukemia(157;0.000966)|Breast(348;0.0512)|Medulloblastoma(222;0.0523)|all_neural(223;0.0663)		Epithelial(105;4.87e-07)|BRCA - Breast invasive adenocarcinoma(274;6.83e-07)|all cancers(92;9.63e-06)|OV - Ovarian serous cystadenocarcinoma(223;0.0557)	NADH(DB00157)									0.562044	261.688979	262.147896	77	60	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	111922022	111922022	4729	11	G	T	T	T	624	48	DLAT	2	2
TTC12	54970	broad.mit.edu	37	11	113194102	113194102	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:113194102G>A	uc001pnv.2	+	c.151G>A	c.(151-153)GAC>AAC	p.D51N	TTC12_uc001pnu.2_Missense_Mutation_p.D51N|TTC12_uc001pnw.2_Non-coding_Transcript|TTC12_uc001pnx.2_5'UTR	NM_017868	NP_060338	Q9H892	TTC12_HUMAN	tetratricopeptide repeat domain 12	51							binding			pancreas(2)|central_nervous_system(1)	3		all_cancers(61;2.73e-16)|all_epithelial(67;8.64e-10)|Melanoma(852;1.46e-05)|all_hematologic(158;0.00014)|Acute lymphoblastic leukemia(157;0.000967)|Breast(348;0.0101)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)|Prostate(24;0.183)|Renal(330;0.187)		BRCA - Breast invasive adenocarcinoma(274;5.3e-06)|Epithelial(105;8.37e-05)|all cancers(92;0.000694)										0.468553	478.257697	478.530413	149	169	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	113194102	113194102	17233	11	G	A	A	A	429	33	TTC12	2	2
ZW10	9183	broad.mit.edu	37	11	113607342	113607343	+	Missense_Mutation	DNP	CG	GA	GA			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:113607342_113607343CG>GA	uc001poe.2	-	c.2218_2219CG>TC	c.(2218-2220)CGG>TCG	p.R740S	ZW10_uc009yyv.2_Non-coding_Transcript	NM_004724	NP_004715	O43264	ZW10_HUMAN	centromere/kinetochore protein zw10	740					cell division|ER to Golgi vesicle-mediated transport|establishment of mitotic spindle orientation|meiosis|mitotic cell cycle checkpoint|mitotic metaphase plate congression|mitotic prometaphase|protein complex assembly|protein localization to kinetochore|protein transport|regulation of exit from mitosis	condensed chromosome kinetochore|cytosol|endoplasmic reticulum membrane|kinetochore microtubule|nucleus|spindle pole	centromeric DNA binding|protein binding			central_nervous_system(1)	1		all_cancers(61;3.84e-16)|all_epithelial(67;1e-09)|Melanoma(852;1.46e-05)|all_hematologic(158;0.000237)|Acute lymphoblastic leukemia(157;0.000967)|Breast(348;0.0101)|all_neural(223;0.0281)|Prostate(24;0.0421)|Medulloblastoma(222;0.0425)		BRCA - Breast invasive adenocarcinoma(274;2.94e-06)|Epithelial(105;0.000103)|all cancers(92;0.000786)										0.328302	464.376869	478.177299	174	356	KEEP	---	---	---	---	capture		Missense_Mutation	DNP	113607342	113607343	18852	11	CG	GA	GA	GA	299	23	ZW10	3	3
FEZ1	9638	broad.mit.edu	37	11	125330404	125330404	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:125330404C>A	uc001qbx.2	-	c.657G>T	c.(655-657)TGG>TGT	p.W219C	FEZ1_uc010sbc.1_Missense_Mutation_p.W190C	NM_005103	NP_005094	Q99689	FEZ1_HUMAN	zygin 1 isoform 1	219					axon guidance|cell adhesion|transport	microtubule|plasma membrane				central_nervous_system(3)|ovary(1)	4	all_hematologic(175;0.228)	Breast(109;0.0021)|Lung NSC(97;0.0126)|all_lung(97;0.0132)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;1.49e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0934)		Melanoma(180;509 2033 10762 15939 24711)								0.518248	226.311754	226.350807	71	66	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	125330404	125330404	6060	11	C	A	A	A	234	18	FEZ1	2	2
FLI1	2313	broad.mit.edu	37	11	128680420	128680420	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:128680420G>T	uc010sbu.1	+	c.896G>T	c.(895-897)TGT>TTT	p.C299F	FLI1_uc010sbt.1_Missense_Mutation_p.C106F|FLI1_uc010sbv.1_Missense_Mutation_p.C266F|FLI1_uc009zci.2_Missense_Mutation_p.C233F	NM_002017	NP_002008	Q01543	FLI1_HUMAN	Friend leukemia virus integration 1	299	ETS.				hemostasis|organ morphogenesis|regulation of transcription, DNA-dependent	nucleus	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity		EWSR1/FLI1(2262)	bone(2208)|soft_tissue(46)|autonomic_ganglia(4)|central_nervous_system(4)|ovary(2)|pancreas(2)|lung(1)	2267	all_hematologic(175;0.0641)	Lung NSC(97;0.00588)|all_lung(97;0.00764)|Breast(109;0.0115)|Medulloblastoma(222;0.0523)|all_neural(223;0.0862)|all_hematologic(192;0.182)		OV - Ovarian serous cystadenocarcinoma(99;0.01)|LUSC - Lung squamous cell carcinoma(976;0.0324)|Lung(977;0.0327)						400				0.352941	35.58886	36.237683	12	22	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	128680420	128680420	6162	11	G	T	T	T	624	48	FLI1	2	2
FLI1	2313	broad.mit.edu	37	11	128680554	128680554	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:128680554G>T	uc010sbu.1	+	c.1030G>T	c.(1030-1032)GAT>TAT	p.D344Y	FLI1_uc010sbt.1_Missense_Mutation_p.D151Y|FLI1_uc010sbv.1_Missense_Mutation_p.D311Y|FLI1_uc009zci.2_Missense_Mutation_p.D278Y	NM_002017	NP_002008	Q01543	FLI1_HUMAN	Friend leukemia virus integration 1	344	ETS.				hemostasis|organ morphogenesis|regulation of transcription, DNA-dependent	nucleus	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity		EWSR1/FLI1(2262)	bone(2208)|soft_tissue(46)|autonomic_ganglia(4)|central_nervous_system(4)|ovary(2)|pancreas(2)|lung(1)	2267	all_hematologic(175;0.0641)	Lung NSC(97;0.00588)|all_lung(97;0.00764)|Breast(109;0.0115)|Medulloblastoma(222;0.0523)|all_neural(223;0.0862)|all_hematologic(192;0.182)		OV - Ovarian serous cystadenocarcinoma(99;0.01)|LUSC - Lung squamous cell carcinoma(976;0.0324)|Lung(977;0.0327)					p.D344N(EVSAT-Tumor)	400				0.560606	117.679396	117.890005	37	29	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	128680554	128680554	6162	11	G	T	T	T	585	45	FLI1	2	2
PDE3B	5140	broad.mit.edu	37	11	14665857	14665857	+	Missense_Mutation	SNP	G	C	C			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:14665857G>C	uc001mln.2	+	c.236G>C	c.(235-237)CGC>CCC	p.R79P	PDE3B_uc001mlm.2_Missense_Mutation_p.R79P|PDE3B_uc010rcr.1_Missense_Mutation_p.R79P|PSMA1_uc001mll.2_5'Flank	NM_000922	NP_000913	Q13370	PDE3B_HUMAN	phosphodiesterase 3B	79					cAMP catabolic process|insulin receptor signaling pathway|negative regulation of cAMP-mediated signaling|negative regulation of cell adhesion mediated by integrin|negative regulation of lipid catabolic process|platelet activation	cytosol|endoplasmic reticulum|Golgi apparatus|guanyl-nucleotide exchange factor complex|integral to membrane|microsome	3',5'-cyclic-AMP phosphodiesterase activity|3',5'-cyclic-GMP phosphodiesterase activity|cGMP-inhibited cyclic-nucleotide phosphodiesterase activity|metal ion binding|protein kinase B binding				0														0.8	29.507707	30.346437	8	2	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	14665857	14665857	12059	11	G	C	C	C	494	38	PDE3B	3	3
PLEKHA7	144100	broad.mit.edu	37	11	16838565	16838565	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:16838565C>A	uc010rcu.1	-	c.1648G>T	c.(1648-1650)GAC>TAC	p.D550Y	PLEKHA7_uc001mmo.2_Missense_Mutation_p.D550Y|PLEKHA7_uc010rcv.1_Missense_Mutation_p.D124Y|PLEKHA7_uc001mmn.2_Missense_Mutation_p.D258Y	NM_175058	NP_778228	Q6IQ23	PKHA7_HUMAN	pleckstrin homology domain containing, family A	550	Interaction with CTNND1.				epithelial cell-cell adhesion|zonula adherens maintenance	centrosome|zonula adherens	delta-catenin binding			skin(1)	1														0.863636	180.404718	188.957839	57	9	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	16838565	16838565	12487	11	C	A	A	A	403	31	PLEKHA7	1	1
GYLTL1B	120071	broad.mit.edu	37	11	45946098	45946098	+	Silent	SNP	C	G	G			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:45946098C>G	uc001nbv.1	+	c.534C>G	c.(532-534)CTC>CTG	p.L178L	GYLTL1B_uc001nbw.1_Silent_p.L147L|GYLTL1B_uc001nbx.1_Silent_p.L178L|GYLTL1B_uc001nby.1_5'Flank	NM_152312	NP_689525	Q8N3Y3	LARG2_HUMAN	glycosyltransferase-like 1B	178	Lumenal (Potential).				muscle cell homeostasis	Golgi membrane|integral to membrane	transferase activity, transferring glycosyl groups			ovary(2)	2				GBM - Glioblastoma multiforme(35;0.226)										0.177778	20.571029	24.971133	8	37	KEEP	---	---	---	---	capture		Silent	SNP	45946098	45946098	7187	11	C	G	G	G	405	32	GYLTL1B	3	3
MADD	8567	broad.mit.edu	37	11	47317082	47317082	+	Silent	SNP	A	T	T			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:47317082A>T	uc001ner.1	+	c.3552A>T	c.(3550-3552)CCA>CCT	p.P1184P	MADD_uc001neq.2_Silent_p.P1146P|MADD_uc001nev.1_Silent_p.P1103P|MADD_uc001nes.1_Silent_p.P1123P|MADD_uc001net.1_Silent_p.P1166P|MADD_uc009yln.1_Silent_p.P1103P|MADD_uc001neu.1_Silent_p.P1103P|MADD_uc001nex.2_Silent_p.P1184P|MADD_uc001nez.2_Silent_p.P1103P|MADD_uc001new.2_Silent_p.P1146P|MADD_uc009ylo.2_Silent_p.P102P	NM_003682	NP_003673	Q8WXG6	MADD_HUMAN	MAP-kinase activating death domain-containing	1184	Ser-rich.				activation of MAPK activity|apoptosis|cell surface receptor linked signaling pathway|regulation of apoptosis|regulation of cell cycle	cytoplasm|integral to membrane|plasma membrane	death receptor binding|protein kinase activator activity|Rab guanyl-nucleotide exchange factor activity			ovary(5)|skin(3)|central_nervous_system(2)	10				Lung(87;0.182)						5				0.321429	106.576843	109.740373	36	76	KEEP	---	---	---	---	capture		Silent	SNP	47317082	47317082	9529	11	A	T	T	T	80	7	MADD	3	3
OR5D18	219438	broad.mit.edu	37	11	55587917	55587917	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:55587917C>A	uc010rin.1	+	c.812C>A	c.(811-813)ACA>AAA	p.T271K		NM_001001952	NP_001001952	Q8NGL1	OR5DI_HUMAN	olfactory receptor, family 5, subfamily D,	271	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)	1		all_epithelial(135;0.208)												0.374429	241.488926	244.522948	82	137	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	55587917	55587917	11567	11	C	A	A	A	221	17	OR5D18	2	2
OR5B2	390190	broad.mit.edu	37	11	58190697	58190697	+	Missense_Mutation	SNP	A	G	G			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:58190697A>G	uc010rkg.1	-	c.38T>C	c.(37-39)CTA>CCA	p.L13P		NM_001005566	NP_001005566	Q96R09	OR5B2_HUMAN	olfactory receptor, family 5, subfamily B,	13	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(3)	3	Esophageal squamous(5;0.0027)	Breast(21;0.0778)												0.111392	58.95132	117.881006	44	351	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	58190697	58190697	11560	11	A	G	G	G	195	15	OR5B2	4	4
OR56B4	196335	broad.mit.edu	37	11	6129756	6129756	+	Missense_Mutation	SNP	C	T	T	rs58431577	byFrequency;by1000genomes	TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:6129756C>T	uc010qzx.1	+	c.748C>T	c.(748-750)CAC>TAC	p.H250Y		NM_001005181	NP_001005181	Q8NH76	O56B4_HUMAN	olfactory receptor, family 56, subfamily B,	250	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;1.31e-08)|BRCA - Breast invasive adenocarcinoma(625;0.135)										0.823129	406.843191	421.293086	121	26	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	6129756	6129756	11548	11	C	T	T	T	273	21	OR56B4	2	2
OVOL1	5017	broad.mit.edu	37	11	65561659	65561659	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:65561659C>A	uc001ofp.2	+	c.258C>A	c.(256-258)GAC>GAA	p.D86E	OVOL1_uc001ofq.2_Missense_Mutation_p.D24E	NM_004561	NP_004552	O14753	OVOL1_HUMAN	OVO-like 1 binding protein	86					transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			central_nervous_system(1)	1				READ - Rectum adenocarcinoma(159;0.17)										0.406977	103.707932	104.356628	35	51	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	65561659	65561659	11739	11	C	A	A	A	220	17	OVOL1	2	2
SART1	9092	broad.mit.edu	37	11	65745041	65745041	+	Silent	SNP	G	T	T			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:65745041G>T	uc001ogl.2	+	c.1953G>T	c.(1951-1953)CTG>CTT	p.L651L		NM_005146	NP_005137	O43290	SNUT1_HUMAN	squamous cell carcinoma antigen recognized by T	651					cell cycle arrest|induction of apoptosis by intracellular signals|positive regulation of cytotoxic T cell differentiation|spliceosomal snRNP assembly	Cajal body|catalytic step 2 spliceosome|cytosol				ovary(1)	1														0.258065	38.153357	41.459531	16	46	KEEP	---	---	---	---	capture		Silent	SNP	65745041	65745041	14327	11	G	T	T	T	600	47	SART1	2	2
KLC2	64837	broad.mit.edu	37	11	66031147	66031147	+	Nonsense_Mutation	SNP	A	T	T			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:66031147A>T	uc010rov.1	+	c.769A>T	c.(769-771)AAG>TAG	p.K257*	KLC2_uc010row.1_Nonsense_Mutation_p.K257*|KLC2_uc009yra.2_Intron|KLC2_uc001ohb.2_Nonsense_Mutation_p.K257*|KLC2_uc010rox.1_Nonsense_Mutation_p.K180*|KLC2_uc001ohc.2_Nonsense_Mutation_p.K257*|KLC2_uc001ohd.2_Nonsense_Mutation_p.K180*|KLC2_uc001ohe.1_Nonsense_Mutation_p.K118*	NM_001134775	NP_001128247	Q9H0B6	KLC2_HUMAN	kinesin light chain 2 isoform 1	257	TPR 2.				blood coagulation	cytosol|kinesin complex|microtubule	microtubule motor activity|protein binding				0														0.45098	276.041673	276.470604	92	112	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	66031147	66031147	8646	11	A	T	T	T	65	5	KLC2	5	3
ODZ4	26011	broad.mit.edu	37	11	78381572	78381572	+	Missense_Mutation	SNP	G	C	C			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:78381572G>C	uc001ozl.3	-	c.5818C>G	c.(5818-5820)CAG>GAG	p.Q1940E	ODZ4_uc001ozk.3_Missense_Mutation_p.Q165E|ODZ4_uc009yvb.1_Missense_Mutation_p.Q524E	NM_001098816	NP_001092286	Q6N022	TEN4_HUMAN	odz, odd Oz/ten-m homolog 4	1940	Extracellular (Potential).|YD 6.				signal transduction	integral to membrane				ovary(2)|pancreas(2)	4														0.5	214.345824	214.345824	69	69	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	78381572	78381572	11242	11	G	C	C	C	611	47	ODZ4	3	3
FAM181B	220382	broad.mit.edu	37	11	82443607	82443607	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:82443607G>A	uc001ozp.2	-	c.1165C>T	c.(1165-1167)CAT>TAT	p.H389Y		NM_175885	NP_787081	A6NEQ2	F181B_HUMAN	hypothetical protein LOC220382	389										large_intestine(1)	1														0.314286	31.621253	32.690626	11	24	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	82443607	82443607	5716	11	G	A	A	A	611	47	FAM181B	2	2
NAALAD2	10003	broad.mit.edu	37	11	89885637	89885637	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:89885637G>T	uc001pdf.3	+	c.781G>T	c.(781-783)GGC>TGC	p.G261C	NAALAD2_uc009yvx.2_Missense_Mutation_p.G261C|NAALAD2_uc009yvy.2_Missense_Mutation_p.G261C|NAALAD2_uc001pdd.2_Missense_Mutation_p.G261C|NAALAD2_uc001pde.2_Missense_Mutation_p.G261C	NM_005467	NP_005458	Q9Y3Q0	NALD2_HUMAN	N-acetylated alpha-linked acidic dipeptidase 2	261	Extracellular (Potential).				proteolysis	integral to membrane	carboxypeptidase activity|dipeptidase activity|dipeptidyl-peptidase activity|metal ion binding|metallopeptidase activity|serine-type peptidase activity			pancreas(1)	1		Acute lymphoblastic leukemia(157;2.31e-05)|all_hematologic(158;0.00556)												0.527559	202.201014	202.283223	67	60	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	89885637	89885637	10523	11	G	T	T	T	455	35	NAALAD2	2	2
DENND5A	23258	broad.mit.edu	37	11	9215202	9215202	+	Missense_Mutation	SNP	C	G	G			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:9215202C>G	uc001mhl.2	-	c.976G>C	c.(976-978)GAG>CAG	p.E326Q	DENND5A_uc010rbw.1_Missense_Mutation_p.E326Q|DENND5A_uc010rbx.1_Non-coding_Transcript	NM_015213	NP_056028	Q6IQ26	DEN5A_HUMAN	RAB6 interacting protein 1	326	DENN.									liver(1)	1														0.84127	192.706912	199.69616	53	10	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	9215202	9215202	4615	11	C	G	G	G	390	30	DENND5A	3	3
HEPHL1	341208	broad.mit.edu	37	11	93815724	93815724	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:93815724C>A	uc001pep.2	+	c.1857C>A	c.(1855-1857)AAC>AAA	p.N619K		NM_001098672	NP_001092142	Q6MZM0	HPHL1_HUMAN	hephaestin-like 1 precursor	619	Plastocyanin-like 4.|Extracellular (Potential).				copper ion transport|oxidation-reduction process	integral to membrane	copper ion binding|oxidoreductase activity			ovary(3)	3		Acute lymphoblastic leukemia(157;2.34e-05)|all_hematologic(158;0.00824)												0.277778	38.999585	41.400502	15	39	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	93815724	93815724	7338	11	C	A	A	A	233	18	HEPHL1	2	2
MRE11A	4361	broad.mit.edu	37	11	94180429	94180429	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:94180429C>T	uc001peu.2	-	c.1739G>A	c.(1738-1740)AGA>AAA	p.R580K	MRE11A_uc001pev.2_Missense_Mutation_p.R580K|MRE11A_uc009ywj.2_Missense_Mutation_p.R583K	NM_005591	NP_005582	P49959	MRE11_HUMAN	meiotic recombination 11 homolog A isoform 1	580					DNA duplex unwinding|double-strand break repair via homologous recombination|double-strand break repair via nonhomologous end joining|negative regulation of DNA endoreduplication|positive regulation of kinase activity|positive regulation of protein autophosphorylation|reciprocal meiotic recombination|regulation of mitotic recombination|sister chromatid cohesion|telomere maintenance via telomerase	Mre11 complex|nucleoplasm	3'-5' exonuclease activity|double-stranded DNA binding|manganese ion binding|protein C-terminus binding|single-stranded DNA specific endodeoxyribonuclease activity			breast(3)|lung(1)	4		Acute lymphoblastic leukemia(157;2.37e-05)|all_hematologic(158;0.00824)								377				0.355322	704.660985	716.974054	237	430	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	94180429	94180429	10151	11	C	T	T	T	416	32	MRE11A	2	2
UTP20	27340	broad.mit.edu	37	12	101767525	101767525	+	Missense_Mutation	SNP	A	G	G			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:101767525A>G	uc001tia.1	+	c.7111A>G	c.(7111-7113)ACT>GCT	p.T2371A		NM_014503	NP_055318	O75691	UTP20_HUMAN	down-regulated in metastasis	2371					endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)|endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)|endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA)|negative regulation of cell proliferation	90S preribosome|cytoplasm|nucleolus|nucleoplasm|preribosome, small subunit precursor|small-subunit processome	protein binding			ovary(2)|breast(2)	4														0.300813	104.147769	108.495988	37	86	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	101767525	101767525	17664	12	A	G	G	G	78	6	UTP20	4	4
BTBD11	121551	broad.mit.edu	37	12	107937716	107937716	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:107937716C>A	uc001tmk.1	+	c.1290C>A	c.(1288-1290)GAC>GAA	p.D430E	BTBD11_uc009zut.1_Missense_Mutation_p.D430E|BTBD11_uc001tmj.2_Missense_Mutation_p.D430E	NM_001018072	NP_001018082	A6QL63	BTBDB_HUMAN	BTB (POZ) domain containing 11 isoform a	430						integral to membrane	DNA binding			ovary(1)	1														0.352941	69.986992	71.280392	24	44	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	107937716	107937716	1571	12	C	A	A	A	233	18	BTBD11	2	2
SART3	9733	broad.mit.edu	37	12	108954775	108954775	+	Silent	SNP	C	A	A			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:108954775C>A	uc001tmz.1	-	c.156G>T	c.(154-156)GGG>GGT	p.G52G	SART3_uc009zux.1_5'UTR|SART3_uc010swx.1_Silent_p.G52G|SART3_uc010swz.1_Silent_p.G52G|SART3_uc001tna.1_Non-coding_Transcript|SART3_uc001tnb.2_Silent_p.G52G|ISCU_uc010sxa.1_5'Flank|ISCU_uc010sxb.1_5'Flank|ISCU_uc001tnc.3_5'Flank|ISCU_uc010sxc.1_5'Flank|ISCU_uc009zuy.2_5'Flank|ISCU_uc010sxd.1_5'Flank	NM_014706	NP_055521	Q15020	SART3_HUMAN	squamous cell carcinoma antigen recognized by T	52					RNA processing	cytoplasm|nuclear speck	nucleotide binding|protein binding|RNA binding			pancreas(1)	1														0.27907	25.169919	27.067453	12	31	KEEP	---	---	---	---	capture		Silent	SNP	108954775	108954775	14328	12	C	A	A	A	327	26	SART3	2	2
TAS2R19	259294	broad.mit.edu	37	12	11175115	11175115	+	Missense_Mutation	SNP	A	G	G			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:11175115A>G	uc010shj.1	-	c.56T>C	c.(55-57)CTT>CCT	p.L19P	PRR4_uc009zhp.2_Intron|PRH1_uc001qzb.3_Intron|PRH1_uc001qzc.2_Intron|PRB4_uc001qzf.1_Intron|PRH1_uc001qzj.2_Intron	NM_176888	NP_795369	P59542	T2R19_HUMAN	taste receptor, type 2, member 19	19	Helical; Name=1; (Potential).				sensory perception of taste	integral to membrane	G-protein coupled receptor activity				0														0.822917	305.788891	315.220022	79	17	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	11175115	11175115	16092	12	A	G	G	G	39	3	TAS2R19	4	4
DDX54	79039	broad.mit.edu	37	12	113603731	113603731	+	Silent	SNP	G	A	A			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:113603731G>A	uc001tuq.3	-	c.1521C>T	c.(1519-1521)GGC>GGT	p.G507G	DDX54_uc001tup.2_Silent_p.G507G	NM_001111322	NP_001104792	Q8TDD1	DDX54_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 54	507					estrogen receptor signaling pathway|regulation of transcription, DNA-dependent|RNA processing|transcription, DNA-dependent	nucleolus	ATP binding|ATP-dependent RNA helicase activity|estrogen receptor binding|RNA binding|transcription corepressor activity			central_nervous_system(1)|skin(1)	2														0.256757	44.566767	48.488598	19	55	KEEP	---	---	---	---	capture		Silent	SNP	113603731	113603731	4543	12	G	A	A	A	535	42	DDX54	2	2
PLBD2	196463	broad.mit.edu	37	12	113824843	113824843	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:113824843G>T	uc001tve.2	+	c.1388G>T	c.(1387-1389)CGG>CTG	p.R463L	PLBD2_uc001tvf.2_Missense_Mutation_p.R431L	NM_173542	NP_775813	Q8NHP8	PLBL2_HUMAN	phospholipase B domain containing 2 isoform 1	463					lipid catabolic process	lysosomal lumen	hydrolase activity				0														0.423529	213.625411	214.477403	72	98	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	113824843	113824843	12452	12	G	T	T	T	507	39	PLBD2	1	1
TBX3	6926	broad.mit.edu	37	12	115112301	115112301	+	Missense_Mutation	SNP	G	C	C			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:115112301G>C	uc001tvt.1	-	c.1439C>G	c.(1438-1440)GCG>GGG	p.A480G	TBX3_uc001tvu.1_Missense_Mutation_p.A460G	NM_016569	NP_057653	O15119	TBX3_HUMAN	T-box 3 protein isoform 2	480					anterior/posterior axis specification, embryo|anti-apoptosis|cell aging|embryonic arm morphogenesis|embryonic digit morphogenesis|female genitalia development|follicle-stimulating hormone secretion|luteinizing hormone secretion|male genitalia development|mesoderm morphogenesis|negative regulation of myoblast differentiation|negative regulation of transcription, DNA-dependent|positive regulation of cell cycle|positive regulation of cell proliferation|regulation of transcription from RNA polymerase II promoter|skeletal system development	nucleus	general transcriptional repressor activity|RNA polymerase II transcription factor activity|sequence-specific DNA binding			ovary(2)	2	Medulloblastoma(191;0.163)|all_neural(191;0.178)			BRCA - Breast invasive adenocarcinoma(302;0.0574)										0.4	6.449215	6.492883	2	3	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	115112301	115112301	16185	12	G	C	C	C	494	38	TBX3	3	3
TAOK3	51347	broad.mit.edu	37	12	118599693	118599693	+	Missense_Mutation	SNP	T	A	A			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:118599693T>A	uc001twx.2	-	c.2039A>T	c.(2038-2040)CAG>CTG	p.Q680L	TAOK3_uc001twv.2_Missense_Mutation_p.Q220L|TAOK3_uc001tww.2_Missense_Mutation_p.Q510L|TAOK3_uc001twy.3_Missense_Mutation_p.Q680L	NM_016281	NP_057365	Q9H2K8	TAOK3_HUMAN	TAO kinase 3	680					MAPKKK cascade|negative regulation of JNK cascade|positive regulation of JNK cascade|protein autophosphorylation	mitochondrion|plasma membrane	ATP binding|protein kinase inhibitor activity|protein serine/threonine kinase activity			lung(5)|central_nervous_system(1)	6	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)									500				0.316017	203.379175	210.341771	73	158	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	118599693	118599693	16070	12	T	A	A	A	715	55	TAOK3	3	3
OASL	8638	broad.mit.edu	37	12	121469379	121469379	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:121469379C>A	uc001tzj.1	-	c.523G>T	c.(523-525)GTG>TTG	p.V175L	OASL_uc001tzk.1_Missense_Mutation_p.V175L	NM_003733	NP_003724	Q15646	OASL_HUMAN	2'-5'-oligoadenylate synthetase-like isoform a	175					interferon-gamma-mediated signaling pathway|type I interferon-mediated signaling pathway	cytoplasm|nucleolus	ATP binding|DNA binding|double-stranded RNA binding|thyroid hormone receptor binding|transferase activity				0	all_neural(191;0.0684)|Medulloblastoma(191;0.0922)					Colon(192;517 2041 31392 31913 39966)								0.512953	317.520762	317.548619	99	94	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	121469379	121469379	11207	12	C	A	A	A	221	17	OASL	2	2
TMEM132D	121256	broad.mit.edu	37	12	129559374	129559374	+	Silent	SNP	C	A	A			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:129559374C>A	uc009zyl.1	-	c.2346G>T	c.(2344-2346)CGG>CGT	p.R782R	TMEM132D_uc001uia.2_Silent_p.R320R	NM_133448	NP_597705	Q14C87	T132D_HUMAN	transmembrane protein 132D precursor	782	Extracellular (Potential).					integral to membrane				ovary(10)|pancreas(2)	12	all_neural(191;0.101)|Medulloblastoma(191;0.163)	all_epithelial(31;0.0934)|Breast(359;0.133)		OV - Ovarian serous cystadenocarcinoma(86;0.000288)|Epithelial(86;0.0116)|all cancers(50;0.0246)										0.55303	638.354021	639.312072	219	177	KEEP	---	---	---	---	capture		Silent	SNP	129559374	129559374	16579	12	C	A	A	A	379	30	TMEM132D	2	2
TMEM132D	121256	broad.mit.edu	37	12	129566381	129566381	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:129566381C>A	uc009zyl.1	-	c.1846G>T	c.(1846-1848)GTG>TTG	p.V616L	TMEM132D_uc001uia.2_Missense_Mutation_p.V154L	NM_133448	NP_597705	Q14C87	T132D_HUMAN	transmembrane protein 132D precursor	616	Extracellular (Potential).					integral to membrane				ovary(10)|pancreas(2)	12	all_neural(191;0.101)|Medulloblastoma(191;0.163)	all_epithelial(31;0.0934)|Breast(359;0.133)		OV - Ovarian serous cystadenocarcinoma(86;0.000288)|Epithelial(86;0.0116)|all cancers(50;0.0246)										0.088	1.607817	23.004565	11	114	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	129566381	129566381	16579	12	C	A	A	A	234	18	TMEM132D	2	2
TMEM132D	121256	broad.mit.edu	37	12	130184440	130184440	+	Missense_Mutation	SNP	T	C	C			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:130184440T>C	uc009zyl.1	-	c.883A>G	c.(883-885)ATA>GTA	p.I295V		NM_133448	NP_597705	Q14C87	T132D_HUMAN	transmembrane protein 132D precursor	295	Extracellular (Potential).					integral to membrane				ovary(10)|pancreas(2)	12	all_neural(191;0.101)|Medulloblastoma(191;0.163)	all_epithelial(31;0.0934)|Breast(359;0.133)		OV - Ovarian serous cystadenocarcinoma(86;0.000288)|Epithelial(86;0.0116)|all cancers(50;0.0246)										0.26	40.361382	42.962933	13	37	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	130184440	130184440	16579	12	T	C	C	C	637	49	TMEM132D	4	4
ANKLE2	23141	broad.mit.edu	37	12	133306845	133306845	+	Missense_Mutation	SNP	T	C	C			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:133306845T>C	uc001ukx.2	-	c.1903A>G	c.(1903-1905)ATT>GTT	p.I635V	ANKLE2_uc009zyw.1_5'UTR	NM_015114	NP_055929	Q86XL3	ANKL2_HUMAN	ankyrin repeat and LEM domain containing 2	635						cytoplasm|integral to membrane|nuclear envelope					0	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_epithelial(31;0.0176)|Lung NSC(355;0.204)		OV - Ovarian serous cystadenocarcinoma(86;2.3e-08)|Epithelial(86;1.56e-07)|all cancers(50;4.94e-06)										0.555556	13.872385	13.896205	5	4	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	133306845	133306845	636	12	T	C	C	C	663	51	ANKLE2	4	4
ZNF268	10795	broad.mit.edu	37	12	133764456	133764456	+	Splice_Site_SNP	SNP	A	T	T			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:133764456A>T	uc010tcf.1	+	c.34_splice	c.e3-2	p.V12_splice	ZNF268_uc010tbv.1_Splice_Site_SNP|ZNF268_uc010tbw.1_Splice_Site_SNP|ZNF268_uc010tbx.1_Intron|ZNF268_uc010tby.1_Intron|ZNF268_uc010tbz.1_Splice_Site_SNP|ZNF268_uc010tca.1_Intron|ZNF268_uc010tcb.1_Splice_Site_SNP|ZNF268_uc010tcc.1_Intron|ZNF268_uc010tcd.1_Splice_Site_SNP|ZNF268_uc010tce.1_Intron|ZNF268_uc010tcg.1_Splice_Site_SNP|ZNF268_uc010tch.1_Splice_Site_SNP_p.V12_splice	NM_003415	NP_003406			zinc finger protein 268 isoform a						regulation of transcription, DNA-dependent	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)	1	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_cancers(7;0.000215)|all_epithelial(31;0.096)		OV - Ovarian serous cystadenocarcinoma(86;3.58e-08)|Epithelial(86;6.6e-07)|all cancers(50;2.28e-05)										0.061224	-3.216475	6.632576	3	46	KEEP	---	---	---	---	capture		Splice_Site_SNP	SNP	133764456	133764456	18399	12	A	T	T	T	91	7	ZNF268	5	3
ABCC9	10060	broad.mit.edu	37	12	22065815	22065815	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:22065815G>T	uc001rfh.2	-	c.1002C>A	c.(1000-1002)AAC>AAA	p.N334K	ABCC9_uc001rfi.1_Missense_Mutation_p.N334K|ABCC9_uc001rfj.1_Missense_Mutation_p.N334K	NM_020297	NP_064693	O60706	ABCC9_HUMAN	ATP-binding cassette, sub-family C, member 9	334	Extracellular (Potential).|ABC transmembrane type-1 1.				defense response to virus|potassium ion import	ATP-sensitive potassium channel complex	ATP binding|ATPase activity, coupled to transmembrane movement of substances|potassium channel regulator activity|sulfonylurea receptor activity			ovary(4)	4					Adenosine triphosphate(DB00171)|Glibenclamide(DB01016)									0.863014	218.173687	227.484922	63	10	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	22065815	22065815	60	12	G	T	T	T	620	48	ABCC9	2	2
C12orf40	283461	broad.mit.edu	37	12	40076498	40076498	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:40076498G>A	uc001rmc.2	+	c.772G>A	c.(772-774)GAC>AAC	p.D258N	C12orf40_uc009zjv.1_Non-coding_Transcript	NM_001031748	NP_001026918	Q86WS4	CL040_HUMAN	hypothetical protein LOC283461	258										ovary(6)	6														0.920245	533.068897	562.440888	150	13	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	40076498	40076498	1730	12	G	A	A	A	429	33	C12orf40	2	2
PDZRN4	29951	broad.mit.edu	37	12	41966201	41966201	+	Silent	SNP	C	T	T			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:41966201C>T	uc010skn.1	+	c.1023C>T	c.(1021-1023)GAC>GAT	p.D341D	PDZRN4_uc001rmq.3_Silent_p.D282D|PDZRN4_uc009zjz.2_Silent_p.D280D|PDZRN4_uc001rmr.2_Silent_p.D167D	NM_013377	NP_037509	Q6ZMN7	PZRN4_HUMAN	PDZ domain containing RING finger 4 isoform 2	540							ubiquitin-protein ligase activity|zinc ion binding			lung(3)|ovary(2)|large_intestine(1)|kidney(1)|pancreas(1)	8	all_cancers(12;0.000673)	Lung NSC(34;0.0205)|all_lung(34;0.0264)								467				0.656442	334.968767	338.497798	107	56	KEEP	---	---	---	---	capture		Silent	SNP	41966201	41966201	12131	12	C	T	T	T	220	17	PDZRN4	2	2
TMBIM6	7009	broad.mit.edu	37	12	50135996	50135996	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:50135996G>T	uc001ruy.2	+	c.77G>T	c.(76-78)TGG>TTG	p.W26L	TMBIM6_uc001rux.2_Intron|TMBIM6_uc010sml.1_Intron|TMBIM6_uc001ruz.2_5'UTR	NM_001098576	NP_001092046	P55061	BI1_HUMAN	testis enhanced gene transcript (BAX inhibitor	Error:Variant_position_missing_in_P55061_after_alignment					apoptosis|negative regulation of apoptosis	endoplasmic reticulum|insoluble fraction|integral to plasma membrane|nucleus					0														0.653846	55.381433	55.924225	17	9	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	50135996	50135996	16513	12	G	T	T	T	611	47	TMBIM6	2	2
FAIM2	23017	broad.mit.edu	37	12	50294975	50294975	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:50294975C>A	uc001rvj.1	-	c.149G>T	c.(148-150)GGG>GTG	p.G50V	FAIM2_uc001rvi.1_Missense_Mutation_p.G4V|FAIM2_uc001rvk.1_Non-coding_Transcript	NM_012306	NP_036438	Q9BWQ8	FAIM2_HUMAN	Fas apoptotic inhibitory molecule 2	50					anti-apoptosis|apoptosis	cell junction|integral to membrane|postsynaptic membrane				large_intestine(1)|ovary(1)	2														0.456522	61.300642	61.371358	21	25	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	50294975	50294975	5573	12	C	A	A	A	286	22	FAIM2	2	2
KRT85	3891	broad.mit.edu	37	12	52758935	52758935	+	Missense_Mutation	SNP	T	A	A			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:52758935T>A	uc001sag.2	-	c.440A>T	c.(439-441)CAG>CTG	p.Q147L		NM_002283	NP_002274	P78386	KRT85_HUMAN	keratin 85	147	Rod.|Coil 1A.				epidermis development	keratin filament	protein binding|structural molecule activity			ovary(1)	1	Myeloproliferative disorder(4;0.0484)|all_hematologic(5;0.088)			BRCA - Breast invasive adenocarcinoma(357;0.189)										0.188679	20.94443	25.732681	10	43	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	52758935	52758935	8814	12	T	A	A	A	715	55	KRT85	3	3
CALCOCO1	57658	broad.mit.edu	37	12	54105846	54105846	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:54105846C>A	uc001sef.2	-	c.1958G>T	c.(1957-1959)TGG>TTG	p.W653L	CALCOCO1_uc001see.2_Missense_Mutation_p.W178L|CALCOCO1_uc010som.1_Missense_Mutation_p.W568L|CALCOCO1_uc010son.1_Missense_Mutation_p.W530L|CALCOCO1_uc001seh.2_3'UTR|CALCOCO1_uc009znd.2_Missense_Mutation_p.W652L|CALCOCO1_uc001seg.2_Missense_Mutation_p.W478L	NM_020898	NP_065949	Q9P1Z2	CACO1_HUMAN	coiled-coil transcriptional coactivator isoform	653	C-terminal AD (CTNNB1 binding site) (By similarity).				steroid hormone receptor signaling pathway|transcription, DNA-dependent|Wnt receptor signaling pathway	cytoplasm	armadillo repeat domain binding|beta-catenin binding|ligand-dependent nuclear receptor transcription coactivator activity|protein C-terminus binding|sequence-specific DNA binding|transcription regulatory region DNA binding			ovary(1)	1														0.48913	136.264445	136.273931	45	47	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	54105846	54105846	2693	12	C	A	A	A	273	21	CALCOCO1	2	2
NCKAP1L	3071	broad.mit.edu	37	12	54925989	54925989	+	Silent	SNP	C	A	A			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:54925989C>A	uc001sgc.3	+	c.2817C>A	c.(2815-2817)CCC>CCA	p.P939P	NCKAP1L_uc010sox.1_Silent_p.P481P|NCKAP1L_uc010soy.1_Silent_p.P889P	NM_005337	NP_005328	P55160	NCKPL_HUMAN	NCK-associated protein 1-like	939					actin polymerization-dependent cell motility|B cell homeostasis|B cell receptor signaling pathway|cortical actin cytoskeleton organization|erythrocyte development|maintenance of cell polarity|myeloid cell homeostasis|negative regulation of apoptosis|negative regulation of interleukin-17 production|negative regulation of interleukin-6 production|negative regulation of myosin-light-chain-phosphatase activity|neutrophil chemotaxis|positive regulation of actin filament polymerization|positive regulation of B cell differentiation|positive regulation of B cell proliferation|positive regulation of CD4-positive, alpha-beta T cell differentiation|positive regulation of CD8-positive, alpha-beta T cell differentiation|positive regulation of cell adhesion mediated by integrin|positive regulation of erythrocyte differentiation|positive regulation of gamma-delta T cell differentiation|positive regulation of neutrophil chemotaxis|positive regulation of phagocytosis, engulfment|positive regulation of T cell proliferation|protein complex assembly|response to drug|T cell homeostasis	cytosol|integral to plasma membrane|membrane fraction|SCAR complex	protein complex binding|protein kinase activator activity|Rac GTPase activator activity			ovary(3)|central_nervous_system(1)	4														0.535912	305.66055	305.861641	97	84	KEEP	---	---	---	---	capture		Silent	SNP	54925989	54925989	10621	12	C	A	A	A	262	21	NCKAP1L	2	2
DCD	117159	broad.mit.edu	37	12	55040935	55040935	+	Missense_Mutation	SNP	C	G	G			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:55040935C>G	uc001sgj.2	-	c.67G>C	c.(67-69)GAG>CAG	p.E23Q	DCD_uc009znt.2_Missense_Mutation_p.E23Q|DCD_uc009znu.2_Non-coding_Transcript	NM_053283	NP_444513	P81605	DCD_HUMAN	dermcidin preproprotein	23					defense response to bacterium|defense response to fungus|killing of cells of other organism	extracellular region	protein binding			ovary(1)	1		Myeloproliferative disorder(1001;0.0255)												0.551724	57.003109	57.070585	16	13	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	55040935	55040935	4454	12	C	G	G	G	416	32	DCD	3	3
INHBC	3626	broad.mit.edu	37	12	57828906	57828906	+	Silent	SNP	C	T	T			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:57828906C>T	uc001snv.1	+	c.237C>T	c.(235-237)CTC>CTT	p.L79L		NM_005538	NP_005529	P55103	INHBC_HUMAN	inhibin beta C chain preproprotein	79					growth	extracellular region	growth factor activity|hormone activity|transforming growth factor beta receptor binding				0														0.362069	121.139772	123.072704	42	74	KEEP	---	---	---	---	capture		Silent	SNP	57828906	57828906	8044	12	C	T	T	T	379	30	INHBC	2	2
GLI1	2735	broad.mit.edu	37	12	57858626	57858626	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:57858626G>T	uc001snx.2	+	c.364G>T	c.(364-366)GGT>TGT	p.G122C	GLI1_uc009zpp.2_Non-coding_Transcript|GLI1_uc009zpq.2_5'UTR|GLI1_uc009zpr.1_Non-coding_Transcript	NM_005269	NP_005260	P08151	GLI1_HUMAN	GLI family zinc finger 1 isoform 1	122					epidermal cell differentiation|negative regulation of canonical Wnt receptor signaling pathway|osteoblast differentiation|positive regulation of DNA replication|positive regulation of gene-specific transcription|positive regulation of smoothened signaling pathway|positive regulation of transcription from RNA polymerase II promoter	cytosol|nucleus	promoter binding|transcription activator activity|zinc ion binding			ovary(4)|breast(3)|skin(3)|central_nervous_system(1)|urinary_tract(1)|kidney(1)|pancreas(1)	14			GBM - Glioblastoma multiforme(3;3.99e-32)			Pancreas(157;841 1936 10503 41495 50368)				277				0.324427	241.000753	248.160596	85	177	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	57858626	57858626	6705	12	G	T	T	T	507	39	GLI1	1	1
METTL1	4234	broad.mit.edu	37	12	58162892	58162892	+	Nonsense_Mutation	SNP	C	A	A			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:58162892C>A	uc010ssd.1	-	c.718G>T	c.(718-720)GAG>TAG	p.E240*	CYP27B1_uc001spz.1_5'Flank|CYP27B1_uc001sqa.1_5'Flank|METTL1_uc009zqc.2_3'UTR	NM_005371	NP_005362	Q9UBP6	TRMB_HUMAN	methyltransferase-like protein 1 isoform a	240	S-adenosyl-L-methionine binding.					cytoplasm|nucleus	protein binding|tRNA (guanine-N7-)-methyltransferase activity|tRNA binding				0	all_cancers(7;6.73e-81)|Lung NSC(6;1.07e-25)|all_lung(6;8.25e-24)|all_epithelial(6;4.6e-17)|Glioma(12;6.95e-05)|all_neural(12;0.00016)|Melanoma(17;0.122)		BRCA - Breast invasive adenocarcinoma(9;0.211)											0.348485	180.600043	184.618263	69	129	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	58162892	58162892	9882	12	C	A	A	A	390	30	METTL1	5	2
AVPR1A	552	broad.mit.edu	37	12	63544125	63544125	+	Silent	SNP	C	T	T			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:63544125C>T	uc001sro.1	-	c.492G>A	c.(490-492)GCG>GCA	p.A164A		NM_000706	NP_000697	P37288	V1AR_HUMAN	arginine vasopressin receptor 1A	164	Cytoplasmic (Potential).				activation of phospholipase C activity|elevation of cytosolic calcium ion concentration|generation of precursor metabolites and energy	endosome|integral to plasma membrane	protein kinase C binding|vasopressin receptor activity				0			BRCA - Breast invasive adenocarcinoma(9;0.193)	GBM - Glioblastoma multiforme(28;0.0569)	Conivaptan(DB00872)|Desmopressin(DB00035)|Felypressin(DB00093)|Terlipressin(DB02638)|Vasopressin(DB00067)									0.395522	146.032388	147.315153	53	81	KEEP	---	---	---	---	capture		Silent	SNP	63544125	63544125	1252	12	C	T	T	T	340	27	AVPR1A	1	1
HMGA2	8091	broad.mit.edu	37	12	66232336	66232336	+	Missense_Mutation	SNP	G	C	C			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:66232336G>C	uc001ssu.1	+	c.236G>C	c.(235-237)AGA>ACA	p.R79T	HMGA2_uc001ssw.1_Missense_Mutation_p.R79T|HMGA2_uc001ssx.2_Missense_Mutation_p.R79T|HMGA2_uc010ssv.1_Non-coding_Transcript|HMGA2_uc001sss.1_Non-coding_Transcript|HMGA2_uc001sst.1_Missense_Mutation_p.R79T|HMGA2_uc001ssv.2_Missense_Mutation_p.R79T|HMGA2_uc001ssy.2_Non-coding_Transcript	NM_003483	NP_003474	P52926	HMGA2_HUMAN	high mobility group AT-hook 2 isoform a	79	A.T hook 3.				cell division|chromatin organization|mitosis|multicellular organismal development|regulation of growth|transcription, DNA-dependent	chromatin	AT DNA binding		HMGA2/LPP(161)|HMGA2/WIF1_ENST00000286574(12)|HMGA2/RAD51L1(11)|HMGA2/NFIB_ENST00000397581(8)|HMGA2/FHIT_ENST00000476844(4)|HMGA2/CCNB1IP1(2)|HMGA2/ALDH2_ENST00000261733(2)|HMGA2/EBF1(2)|HMGA2/LHFP(2)|HMGA2/COX6C(2)	soft_tissue(159)|bone(27)|salivary_gland(20)	206	all_cancers(1;5.78e-46)		GBM - Glioblastoma multiforme(1;0.00179)|LUSC - Lung squamous cell carcinoma(43;0.156)	GBM - Glioblastoma multiforme(28;0.0386)						109				0.337838	84.551027	86.27257	25	49	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	66232336	66232336	7515	12	G	C	C	C	429	33	HMGA2	3	3
USP5	8078	broad.mit.edu	37	12	6965284	6965284	+	Silent	SNP	G	T	T			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:6965284G>T	uc001qri.3	+	c.408G>T	c.(406-408)CTG>CTT	p.L136L	USP5_uc001qrh.3_Silent_p.L136L	NM_001098536	NP_001092006	P45974	UBP5_HUMAN	ubiquitin specific peptidase 5 isoform 1	136					positive regulation of proteasomal ubiquitin-dependent protein catabolic process|protein K48-linked deubiquitination|ubiquitin-dependent protein catabolic process	lysosome	cysteine-type endopeptidase activity|omega peptidase activity|protein binding|ubiquitin thiolesterase activity|zinc ion binding				0														0.849057	297.586702	309.992018	90	16	KEEP	---	---	---	---	capture		Silent	SNP	6965284	6965284	17645	12	G	T	T	T	600	47	USP5	2	2
TRHDE	29953	broad.mit.edu	37	12	72936116	72936116	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:72936116G>T	uc001sxa.2	+	c.1633G>T	c.(1633-1635)GTT>TTT	p.V545F		NM_013381	NP_037513	Q9UKU6	TRHDE_HUMAN	thyrotropin-releasing hormone degrading enzyme	545	Extracellular (Potential).				cell-cell signaling|proteolysis|signal transduction	integral to plasma membrane	aminopeptidase activity|metallopeptidase activity|zinc ion binding			ovary(2)	2														0.366667	99.926837	101.342799	33	57	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	72936116	72936116	17023	12	G	T	T	T	468	36	TRHDE	2	2
TRHDE	29953	broad.mit.edu	37	12	72936124	72936124	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:72936124G>T	uc001sxa.2	+	c.1641G>T	c.(1639-1641)CAG>CAT	p.Q547H		NM_013381	NP_037513	Q9UKU6	TRHDE_HUMAN	thyrotropin-releasing hormone degrading enzyme	547	Extracellular (Potential).				cell-cell signaling|proteolysis|signal transduction	integral to plasma membrane	aminopeptidase activity|metallopeptidase activity|zinc ion binding			ovary(2)	2														0.366667	91.243444	92.653251	33	57	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	72936124	72936124	17023	12	G	T	T	T	425	33	TRHDE	2	2
NAV3	89795	broad.mit.edu	37	12	78592410	78592410	+	Missense_Mutation	SNP	C	G	G			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:78592410C>G	uc001syp.2	+	c.6472C>G	c.(6472-6474)CAG>GAG	p.Q2158E	NAV3_uc001syo.2_Missense_Mutation_p.Q2136E|NAV3_uc010sub.1_Missense_Mutation_p.Q1615E|NAV3_uc009zsf.2_Missense_Mutation_p.Q967E	NM_014903	NP_055718	Q8IVL0	NAV3_HUMAN	neuron navigator 3	2158						nuclear outer membrane	ATP binding|nucleoside-triphosphatase activity			large_intestine(6)|ovary(5)|lung(2)|breast(1)|kidney(1)|pancreas(1)	16										1091				0.263514	127.161749	134.642843	39	109	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	78592410	78592410	10581	12	C	G	G	G	377	29	NAV3	3	3
ACSS3	79611	broad.mit.edu	37	12	81568589	81568589	+	Missense_Mutation	SNP	A	T	T			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:81568589A>T	uc001szl.1	+	c.1121A>T	c.(1120-1122)GAT>GTT	p.D374V	ACSS3_uc001szm.1_Missense_Mutation_p.D373V|ACSS3_uc001szn.1_Missense_Mutation_p.D56V	NM_024560	NP_078836	Q9H6R3	ACSS3_HUMAN	acyl-CoA synthetase short-chain family member 3	374						mitochondrion	acetate-CoA ligase activity|ATP binding			ovary(1)|lung(1)|central_nervous_system(1)	3														0.263636	72.038372	77.58756	29	81	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	81568589	81568589	191	12	A	T	T	T	156	12	ACSS3	3	3
CCDC59	29080	broad.mit.edu	37	12	82750917	82750917	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:82750917G>A	uc001szp.3	-	c.286C>T	c.(286-288)CTC>TTC	p.L96F	C12orf26_uc001szq.2_5'Flank	NM_014167	NP_054886	Q9P031	TAP26_HUMAN	coiled-coil domain containing 59	96					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	protein binding				0														0.450704	203.988632	204.288305	64	78	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	82750917	82750917	2952	12	G	A	A	A	429	33	CCDC59	2	2
ZIC5	85416	broad.mit.edu	37	13	100622616	100622616	+	Missense_Mutation	SNP	C	G	G			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr13:100622616C>G	uc001vom.1	-	c.1314G>C	c.(1312-1314)ATG>ATC	p.M438I		NM_033132	NP_149123	Q96T25	ZIC5_HUMAN	zinc finger protein of the cerebellum 5	438					cell differentiation	nucleus	DNA binding|zinc ion binding				0	all_neural(89;0.0837)|Medulloblastoma(90;0.18)|Lung SC(71;0.184)													0.578947	77.255658	77.462357	22	16	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	100622616	100622616	18273	13	C	G	G	G	325	25	ZIC5	3	3
MYO16	23026	broad.mit.edu	37	13	109817397	109817397	+	Silent	SNP	C	A	A			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr13:109817397C>A	uc010agk.1	+	c.5313C>A	c.(5311-5313)TCC>TCA	p.S1771S	MYO16_uc001vqt.1_Silent_p.S1749S	NM_015011	NP_055826	Q9Y6X6	MYO16_HUMAN	myosin heavy chain Myr 8	1749					cerebellum development|negative regulation of cell proliferation|negative regulation of S phase of mitotic cell cycle	myosin complex|nucleoplasm|perinuclear region of cytoplasm|plasma membrane	actin filament binding|ATP binding|motor activity			ovary(5)|large_intestine(1)|kidney(1)|breast(1)|central_nervous_system(1)	9	all_lung(23;0.000332)|all_neural(89;0.00294)|Medulloblastoma(90;0.00596)|Lung NSC(43;0.00751)|Lung SC(71;0.104)		BRCA - Breast invasive adenocarcinoma(86;0.19)|all cancers(43;0.201)											0.290909	43.774785	45.930859	16	39	KEEP	---	---	---	---	capture		Silent	SNP	109817397	109817397	10459	13	C	A	A	A	262	21	MYO16	2	2
RNF17	56163	broad.mit.edu	37	13	25373689	25373689	+	Missense_Mutation	SNP	A	T	T			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr13:25373689A>T	uc001upr.2	+	c.1556A>T	c.(1555-1557)GAT>GTT	p.D519V	RNF17_uc010tdd.1_Missense_Mutation_p.D378V|RNF17_uc010aab.2_Non-coding_Transcript|RNF17_uc010tde.1_Missense_Mutation_p.D519V|RNF17_uc001ups.2_Missense_Mutation_p.D458V	NM_031277	NP_112567	Q9BXT8	RNF17_HUMAN	ring finger protein 17	519					multicellular organismal development	cytoplasm|nucleus	hydrolase activity, acting on ester bonds|nucleic acid binding|zinc ion binding			ovary(1)	1		Lung SC(185;0.0225)|Breast(139;0.077)		all cancers(112;0.0114)|OV - Ovarian serous cystadenocarcinoma(117;0.0311)|Epithelial(112;0.0524)										0.787879	178.422877	183.475194	52	14	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	25373689	25373689	13938	13	A	T	T	T	156	12	RNF17	3	3
C13orf33	84935	broad.mit.edu	37	13	31480658	31480658	+	Silent	SNP	G	T	T			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr13:31480658G>T	uc001uth.3	+	c.6G>T	c.(4-6)GCG>GCT	p.A2A		NM_032849	NP_116238	Q5VYS4	CM033_HUMAN	hypothetical protein LOC84935	2											0		Lung SC(185;0.0281)		all cancers(112;0.00914)|Epithelial(112;0.0474)|OV - Ovarian serous cystadenocarcinoma(117;0.0559)|GBM - Glioblastoma multiforme(144;0.244)										0.888889	25.89708	26.951024	8	1	KEEP	---	---	---	---	capture		Silent	SNP	31480658	31480658	1774	13	G	T	T	T	496	39	C13orf33	1	1
TRPC4	7223	broad.mit.edu	37	13	38320545	38320545	+	Silent	SNP	G	A	A			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr13:38320545G>A	uc010abx.2	-	c.426C>T	c.(424-426)GAC>GAT	p.D142D	TRPC4_uc010abv.2_5'UTR|TRPC4_uc001uwt.2_Silent_p.D142D|TRPC4_uc001uws.2_Silent_p.D142D|TRPC4_uc010tey.1_Silent_p.D142D|TRPC4_uc010abw.2_Intron|TRPC4_uc010aby.2_Silent_p.D142D	NM_003306	NP_003297	Q9UBN4	TRPC4_HUMAN	transient receptor potential cation channel,	142	Cytoplasmic (Potential).|ANK 4.|Multimerization domain (By similarity).				axon guidance|calcium ion import	basolateral plasma membrane|calcium channel complex|cell surface|cortical cytoskeleton	beta-catenin binding|cadherin binding|store-operated calcium channel activity			ovary(3)|breast(1)	4				all cancers(112;1.92e-08)|Epithelial(112;5.04e-06)|OV - Ovarian serous cystadenocarcinoma(117;0.000677)|GBM - Glioblastoma multiforme(144;0.00623)|BRCA - Breast invasive adenocarcinoma(63;0.0126)										0.755869	510.35167	523.105753	161	52	KEEP	---	---	---	---	capture		Silent	SNP	38320545	38320545	17131	13	G	A	A	A	620	48	TRPC4	2	2
RB1	5925	broad.mit.edu	37	13	48916851	48916851	+	Splice_Site_SNP	SNP	G	T	T			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr13:48916851G>T	uc001vcb.2	+	c.380_splice	c.e3+1	p.S127_splice	RB1_uc010acs.1_Intron	NM_000321	NP_000312			retinoblastoma 1						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.?(6)		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)			6	(NCIH1876-Tumor)	568	TCGA GBM(7;6.82e-08)|TSP Lung(12;0.097)|TCGA Ovarian(6;0.080)			0.709677	151.823706	154.26947	44	18	KEEP	---	---	---	---	capture		Splice_Site_SNP	SNP	48916851	48916851	13559	13	G	T	T	T	572	44	RB1	5	2
TDRD3	81550	broad.mit.edu	37	13	61083900	61083900	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr13:61083900G>A	uc010aeg.2	+	c.862G>A	c.(862-864)GAT>AAT	p.D288N	TDRD3_uc010aef.2_Missense_Mutation_p.D20N|TDRD3_uc001via.2_Missense_Mutation_p.D195N|TDRD3_uc001vhz.3_Missense_Mutation_p.D195N|TDRD3_uc001vib.3_Missense_Mutation_p.D194N	NM_001146070	NP_001139542	Q9H7E2	TDRD3_HUMAN	tudor domain containing 3 isoform 1	195	UBA.				chromatin modification	cytoplasm|nucleus	chromatin binding|methylated histone residue binding|nucleic acid binding|transcription coactivator activity				0		Prostate(109;0.173)|Breast(118;0.174)		GBM - Glioblastoma multiforme(99;0.000291)		Colon(36;164 906 35820 50723)								0.400722	321.02486	323.424087	111	166	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	61083900	61083900	16259	13	G	A	A	A	585	45	TDRD3	2	2
TDRD3	81550	broad.mit.edu	37	13	61083927	61083927	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr13:61083927G>A	uc010aeg.2	+	c.889G>A	c.(889-891)GAA>AAA	p.E297K	TDRD3_uc010aef.2_Missense_Mutation_p.E29K|TDRD3_uc001via.2_Missense_Mutation_p.E204K|TDRD3_uc001vhz.3_Missense_Mutation_p.E204K|TDRD3_uc001vib.3_Missense_Mutation_p.E203K	NM_001146070	NP_001139542	Q9H7E2	TDRD3_HUMAN	tudor domain containing 3 isoform 1	204	UBA.				chromatin modification	cytoplasm|nucleus	chromatin binding|methylated histone residue binding|nucleic acid binding|transcription coactivator activity				0		Prostate(109;0.173)|Breast(118;0.174)		GBM - Glioblastoma multiforme(99;0.000291)		Colon(36;164 906 35820 50723)								0.4	280.507555	282.56103	94	141	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	61083927	61083927	16259	13	G	A	A	A	533	41	TDRD3	2	2
KLHL1	57626	broad.mit.edu	37	13	70293521	70293521	+	Silent	SNP	C	A	A			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr13:70293521C>A	uc001vip.2	-	c.1995G>T	c.(1993-1995)CGG>CGT	p.R665R	KLHL1_uc010thm.1_Silent_p.R604R	NM_020866	NP_065917	Q9NR64	KLHL1_HUMAN	kelch-like 1 protein	665	Kelch 5.				actin cytoskeleton organization	cytoplasm|cytoskeleton	actin binding				0		Breast(118;0.000162)		COAD - Colon adenocarcinoma(199;0.000193)|GBM - Glioblastoma multiforme(99;0.000211)										0.567568	515.255859	516.450001	168	128	KEEP	---	---	---	---	capture		Silent	SNP	70293521	70293521	8677	13	C	A	A	A	327	26	KLHL1	2	2
MYCBP2	23077	broad.mit.edu	37	13	77748446	77748446	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr13:77748446C>T	uc001vkf.2	-	c.5537G>A	c.(5536-5538)AGG>AAG	p.R1846K	MYCBP2_uc010aev.2_Missense_Mutation_p.R1250K	NM_015057	NP_055872	O75592	MYCB2_HUMAN	MYC binding protein 2	1846					regulation of mitotic metaphase/anaphase transition|regulation of transcription, DNA-dependent|transcription, DNA-dependent	anaphase-promoting complex	ligase activity|protein binding|zinc ion binding			ovary(4)|breast(4)|lung(2)|pancreas(1)	11		Breast(118;0.212)|Acute lymphoblastic leukemia(28;0.22)		GBM - Glioblastoma multiforme(99;0.109)										0.32	267.391228	275.314472	88	187	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	77748446	77748446	10413	13	C	T	T	T	312	24	MYCBP2	2	2
GPC5	2262	broad.mit.edu	37	13	92345880	92345880	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr13:92345880G>T	uc010tif.1	+	c.765G>T	c.(763-765)ATG>ATT	p.M255I		NM_004466	NP_004457	P78333	GPC5_HUMAN	glypican 5 precursor	255						anchored to membrane|extracellular space|integral to plasma membrane|proteinaceous extracellular matrix	heparan sulfate proteoglycan binding			ovary(2)	2	all_cancers(3;1.43e-07)|all_neural(89;0.0804)|Medulloblastoma(90;0.163)	Lung NSC(4;0.00454)												0.623377	154.706772	155.732726	48	29	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	92345880	92345880	6875	13	G	T	T	T	598	46	GPC5	2	2
TRAF3	7187	broad.mit.edu	37	14	103369758	103369758	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr14:103369758G>A	uc001ymc.1	+	c.1127G>A	c.(1126-1128)CGG>CAG	p.R376Q	TRAF3_uc001yme.1_Missense_Mutation_p.R351Q|TRAF3_uc001ymd.1_Missense_Mutation_p.R376Q|TRAF3_uc010txy.1_Missense_Mutation_p.R293Q|TRAF3_uc001ymf.1_Missense_Mutation_p.R109Q	NM_145725	NP_663777	Q13114	TRAF3_HUMAN	TNF receptor-associated factor 3 isoform 1	376					apoptosis|induction of apoptosis|negative regulation of NF-kappaB transcription factor activity|negative regulation of type I interferon production|regulation of defense response to virus|regulation of interferon-beta production|regulation of proteolysis|toll-like receptor signaling pathway|tumor necrosis factor-mediated signaling pathway	CD40 receptor complex|cytosol|endosome|internal side of plasma membrane|mitochondrion	signal transducer activity|ubiquitin-protein ligase activity|zinc ion binding				0		all_cancers(154;7.87e-06)|all_epithelial(191;0.0024)		Epithelial(152;9.92e-24)|all cancers(159;2.23e-21)|OV - Ovarian serous cystadenocarcinoma(161;7.85e-12)|Colorectal(3;0.0971)										0.254545	35.820607	38.831227	14	41	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	103369758	103369758	16983	14	G	A	A	A	507	39	TRAF3	1	1
AHNAK2	113146	broad.mit.edu	37	14	105416009	105416009	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr14:105416009C>A	uc010axc.1	-	c.5779G>T	c.(5779-5781)GAT>TAT	p.D1927Y	AHNAK2_uc001ypx.2_Missense_Mutation_p.D1827Y	NM_138420	NP_612429	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	1927						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)											0.358696	86.047035	87.664944	33	59	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	105416009	105416009	418	14	C	A	A	A	416	32	AHNAK2	2	2
AHNAK2	113146	broad.mit.edu	37	14	105416572	105416572	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr14:105416572C>A	uc010axc.1	-	c.5216G>T	c.(5215-5217)GGG>GTG	p.G1739V	AHNAK2_uc001ypx.2_Missense_Mutation_p.G1639V	NM_138420	NP_612429	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	1739						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)											0.4	59.834675	60.316583	22	33	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	105416572	105416572	418	14	C	A	A	A	286	22	AHNAK2	2	2
OR4K17	390436	broad.mit.edu	37	14	20586172	20586172	+	Missense_Mutation	SNP	A	T	T			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr14:20586172A>T	uc001vwo.1	+	c.607A>T	c.(607-609)AAT>TAT	p.N203Y		NM_001004715	NP_001004715	Q8NGC6	OR4KH_HUMAN	olfactory receptor, family 4, subfamily K,	175	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0	all_cancers(95;0.00108)		Epithelial(56;7.58e-07)|all cancers(55;3.77e-06)	GBM - Glioblastoma multiforme(265;0.0144)										0.505618	889.955733	889.970618	270	264	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	20586172	20586172	11481	14	A	T	T	T	65	5	OR4K17	3	3
TPPP2	122664	broad.mit.edu	37	14	21498833	21498833	+	Silent	SNP	C	A	A			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr14:21498833C>A	uc001vzh.2	+	c.93C>A	c.(91-93)TCC>TCA	p.S31S	NDRG2_uc010tll.1_Intron	NM_173846	NP_776245	P59282	TPPP2_HUMAN	tubulin polymerization-promoting protein family	31						cytoplasm					0	all_cancers(95;0.000759)		OV - Ovarian serous cystadenocarcinoma(11;6.85e-11)|Epithelial(56;9.49e-09)|all cancers(55;3.84e-08)	GBM - Glioblastoma multiforme(265;0.0191)										0.466667	151.477976	151.57774	49	56	KEEP	---	---	---	---	capture		Silent	SNP	21498833	21498833	16958	14	C	A	A	A	262	21	TPPP2	2	2
EFS	10278	broad.mit.edu	37	14	23828857	23828857	+	Missense_Mutation	SNP	T	A	A			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr14:23828857T>A	uc001wjo.2	-	c.830A>T	c.(829-831)CAG>CTG	p.Q277L	EFS_uc001wjp.2_Missense_Mutation_p.Q184L|EFS_uc010tnm.1_Missense_Mutation_p.Q108L	NM_005864	NP_005855	O43281	EFS_HUMAN	embryonal Fyn-associated substrate isoform 1	277	Pro-rich.				cell adhesion|intracellular signal transduction	cytoplasm	SH3 domain binding			large_intestine(1)	1	all_cancers(95;7.12e-06)			GBM - Glioblastoma multiforme(265;0.00649)										0.466667	98.897499	98.971163	35	40	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	23828857	23828857	5148	14	T	A	A	A	715	55	EFS	3	3
TM9SF1	10548	broad.mit.edu	37	14	24659658	24659658	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr14:24659658C>A	uc010tob.1	-	c.2060G>T	c.(2059-2061)CGG>CTG	p.R687L	IPO4_uc001wmu.2_5'Flank|IPO4_uc001wmv.1_5'Flank|IPO4_uc001wmx.1_5'Flank|IPO4_uc001wmy.1_5'Flank|IPO4_uc010tnz.1_5'Flank|IPO4_uc001wmw.1_5'Flank|IPO4_uc001wmz.1_5'UTR|TM9SF1_uc010toa.1_Missense_Mutation_p.R365L|TM9SF1_uc001wna.1_Non-coding_Transcript|TM9SF1_uc001wnb.1_Missense_Mutation_p.R452L|TM9SF1_uc001wnc.2_Missense_Mutation_p.R452L	NM_006405	NP_006396	O15321	TM9S1_HUMAN	transmembrane 9 superfamily member 1 isoform a	452					autophagy	autophagic vacuole membrane|cytoplasmic vesicle|integral to membrane|lysosomal membrane				ovary(1)	1				GBM - Glioblastoma multiforme(265;0.0183)										0.504505	355.637774	355.641286	112	110	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	24659658	24659658	16507	14	C	A	A	A	299	23	TM9SF1	1	1
NFATC4	4776	broad.mit.edu	37	14	24842998	24842998	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr14:24842998G>T	uc010tol.1	+	c.1846G>T	c.(1846-1848)GTG>TTG	p.V616L	NFATC4_uc010tok.1_Missense_Mutation_p.V616L|NFATC4_uc010alr.2_Missense_Mutation_p.V616L|NFATC4_uc010als.2_Missense_Mutation_p.V566L|NFATC4_uc010tom.1_Missense_Mutation_p.V566L|NFATC4_uc010ton.1_Missense_Mutation_p.V566L|NFATC4_uc010too.1_Missense_Mutation_p.V566L|NFATC4_uc010alt.2_Missense_Mutation_p.V585L|NFATC4_uc010top.1_Missense_Mutation_p.V585L|NFATC4_uc010toq.1_Missense_Mutation_p.V585L|NFATC4_uc010alu.2_Missense_Mutation_p.V245L|NFATC4_uc001wpc.2_Missense_Mutation_p.V553L|NFATC4_uc010tor.1_Missense_Mutation_p.V553L|NFATC4_uc010tos.1_Missense_Mutation_p.V483L|NFATC4_uc010tot.1_Missense_Mutation_p.V541L|NFATC4_uc010tou.1_Missense_Mutation_p.V483L|NFATC4_uc010tov.1_Missense_Mutation_p.V541L|NFATC4_uc010tow.1_Missense_Mutation_p.V483L|NFATC4_uc010alv.2_Missense_Mutation_p.V541L|NFATC4_uc010tox.1_Missense_Mutation_p.V483L|NFATC4_uc001wpd.2_Missense_Mutation_p.V88L|NFATC4_uc010toy.1_Missense_Mutation_p.V88L|NFATC4_uc010toz.1_Missense_Mutation_p.V88L|NFATC4_uc010tpa.1_5'UTR|NFATC4_uc010tpb.1_5'UTR	NM_004554	NP_004545	Q14934	NFAC4_HUMAN	nuclear factor of activated T-cells,	553	RHD.				cell differentiation|inflammatory response|regulation of transcription, DNA-dependent|transcription from RNA polymerase II promoter	cytoplasm|intermediate filament cytoskeleton|nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|transcription coactivator activity			ovary(1)|central_nervous_system(1)	2				GBM - Glioblastoma multiforme(265;0.018)										0.516854	145.088308	145.113034	46	43	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	24842998	24842998	10765	14	G	T	T	T	572	44	NFATC4	2	2
HECTD1	25831	broad.mit.edu	37	14	31642916	31642916	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr14:31642916C>T	uc001wrc.1	-	c.700G>A	c.(700-702)GAG>AAG	p.E234K		NM_015382	NP_056197	Q9ULT8	HECD1_HUMAN	HECT domain containing 1	234					protein ubiquitination involved in ubiquitin-dependent protein catabolic process	intracellular	metal ion binding|protein binding|ubiquitin-protein ligase activity			ovary(2)|large_intestine(1)	3	Hepatocellular(127;0.0877)|Breast(36;0.176)		LUAD - Lung adenocarcinoma(48;0.00292)|Lung(238;0.0164)|BRCA - Breast invasive adenocarcinoma(188;0.111)|STAD - Stomach adenocarcinoma(7;0.173)	GBM - Glioblastoma multiforme(265;0.00617)										0.541667	38.774158	38.810129	13	11	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	31642916	31642916	7322	14	C	T	T	T	377	29	HECTD1	2	2
PRPF39	55015	broad.mit.edu	37	14	45565408	45565408	+	Missense_Mutation	SNP	G	C	C			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr14:45565408G>C	uc001wvz.3	+	c.427G>C	c.(427-429)GAC>CAC	p.D143H	PRPF39_uc001wvy.3_5'UTR|PRPF39_uc010and.2_5'UTR	NM_017922	NP_060392	Q86UA1	PRP39_HUMAN	PRP39 pre-mRNA processing factor 39 homolog	143	HAT 2.				mRNA processing|RNA splicing	nucleus	binding			ovary(1)|breast(1)	2														0.44	39.923711	40.001789	11	14	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	45565408	45565408	13012	14	G	C	C	C	481	37	PRPF39	3	3
C14orf183	196913	broad.mit.edu	37	14	50551964	50551964	+	Missense_Mutation	SNP	C	G	G			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr14:50551964C>G	uc010tqk.1	-	c.500G>C	c.(499-501)TGG>TCG	p.W167S		NM_001014830	NP_001014830	Q8WXQ3	CN183_HUMAN	hypothetical protein LOC196913	167											0														0.176471	6.416756	8.091955	3	14	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	50551964	50551964	1815	14	C	G	G	G	273	21	C14orf183	3	3
PYGL	5836	broad.mit.edu	37	14	51378963	51378963	+	Missense_Mutation	SNP	G	C	C			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr14:51378963G>C	uc001wyu.2	-	c.1679C>G	c.(1678-1680)CCA>CGA	p.P560R	PYGL_uc010tqq.1_Missense_Mutation_p.P526R|PYGL_uc001wyv.2_Missense_Mutation_p.P234R	NM_002863	NP_002854	P06737	PYGL_HUMAN	liver glycogen phosphorylase isoform 1	560					glucose homeostasis|glucose metabolic process|glycogen catabolic process	cytosol|soluble fraction	AMP binding|ATP binding|bile acid binding|drug binding|glucose binding|glycogen phosphorylase activity|protein homodimerization activity|purine base binding|pyridoxal phosphate binding				0	all_epithelial(31;0.00825)|Breast(41;0.148)				Adenosine monophosphate(DB00131)|Pyridoxal Phosphate(DB00114)|Riboflavin(DB00140)									0.546763	513.00995	513.53738	152	126	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	51378963	51378963	13319	14	G	C	C	C	611	47	PYGL	3	3
SIX4	51804	broad.mit.edu	37	14	61190693	61190693	+	Missense_Mutation	SNP	C	G	G			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr14:61190693C>G	uc001xfc.2	-	c.100G>C	c.(100-102)GAA>CAA	p.E34Q	SIX4_uc010app.1_Missense_Mutation_p.E26Q	NM_017420	NP_059116	Q9UIU6	SIX4_HUMAN	sine oculis homeobox homolog 4	34						nucleus	transcription regulator activity			breast(3)|ovary(1)	4				OV - Ovarian serous cystadenocarcinoma(108;0.0275)						127				0.298013	144.229799	149.728865	45	106	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	61190693	61190693	14844	14	C	G	G	G	416	32	SIX4	3	3
C14orf4	64207	broad.mit.edu	37	14	77492209	77492209	+	Missense_Mutation	SNP	C	G	G			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr14:77492209C>G	uc001xsy.2	-	c.1927G>C	c.(1927-1929)GGC>CGC	p.G643R		NM_024496	NP_078772	Q9H1B7	I2BPL_HUMAN	chromosome 14 open reading frame 4	643						nucleus					0			Kidney(204;0.164)	BRCA - Breast invasive adenocarcinoma(234;0.00347)|KIRC - Kidney renal clear cell carcinoma(182;0.0878)										0.454545	29.845556	29.885367	10	12	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	77492209	77492209	1823	14	C	G	G	G	273	21	C14orf4	3	3
SERPINA10	51156	broad.mit.edu	37	14	94756524	94756524	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr14:94756524G>T	uc001yct.2	-	c.407C>A	c.(406-408)ACC>AAC	p.T136N	SERPINA10_uc001ycu.3_Missense_Mutation_p.T136N	NM_016186	NP_057270	Q9UK55	ZPI_HUMAN	serine (or cysteine) proteinase inhibitor, clade	136					regulation of proteolysis	extracellular region	serine-type endopeptidase inhibitor activity			ovary(2)|skin(1)	3		all_cancers(154;0.105)		Epithelial(152;0.135)|COAD - Colon adenocarcinoma(157;0.207)|all cancers(159;0.221)										0.361963	174.70867	177.429785	59	104	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	94756524	94756524	14575	14	G	T	T	T	572	44	SERPINA10	2	2
LRRK1	79705	broad.mit.edu	37	15	101605612	101605612	+	Missense_Mutation	SNP	T	C	C			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr15:101605612T>C	uc002bwr.2	+	c.4970T>C	c.(4969-4971)GTG>GCG	p.V1657A	LRRK1_uc010usb.1_Non-coding_Transcript|LRRK1_uc010usc.1_Non-coding_Transcript|LRRK1_uc002bws.2_Non-coding_Transcript	NM_024652	NP_078928	Q38SD2	LRRK1_HUMAN	leucine-rich repeat kinase 1	1657					protein phosphorylation|small GTPase mediated signal transduction	mitochondrion	ATP binding|GTP binding|metal ion binding|protein binding|protein serine/threonine kinase activity			ovary(4)|lung(4)|central_nervous_system(3)|large_intestine(1)	12	Melanoma(26;0.00505)|Lung NSC(78;0.00793)|all_lung(78;0.0094)		OV - Ovarian serous cystadenocarcinoma(32;0.000932)|LUSC - Lung squamous cell carcinoma(107;0.187)|Lung(145;0.23)							1100				0.325301	139.453251	143.917905	54	112	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	101605612	101605612	9408	15	T	C	C	C	767	59	LRRK1	4	4
MKRN3	7681	broad.mit.edu	37	15	23811302	23811302	+	Missense_Mutation	SNP	A	G	G			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr15:23811302A>G	uc001ywh.3	+	c.373A>G	c.(373-375)AAG>GAG	p.K125E	MKRN3_uc001ywi.2_Intron|MKRN3_uc010ayi.1_Missense_Mutation_p.K125E	NM_005664	NP_005655	Q13064	MKRN3_HUMAN	makorin ring finger protein 3	125						ribonucleoprotein complex	ligase activity|nucleic acid binding|zinc ion binding			large_intestine(2)|ovary(2)	4		all_cancers(20;8.44e-25)|all_epithelial(15;3.69e-22)|Lung NSC(15;2.96e-18)|all_lung(15;2.8e-17)|Breast(32;0.000353)|Colorectal(260;0.14)		all cancers(64;3.02e-06)|Epithelial(43;1.94e-05)|BRCA - Breast invasive adenocarcinoma(123;0.0012)						79				0.445783	114.247938	114.461976	37	46	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	23811302	23811302	9998	15	A	G	G	G	117	9	MKRN3	4	4
MAGEL2	54551	broad.mit.edu	37	15	23889965	23889965	+	Silent	SNP	G	T	T			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr15:23889965G>T	uc001ywj.3	-	c.1116C>A	c.(1114-1116)ACC>ACA	p.T372T		NM_019066	NP_061939			MAGE-like protein 2												0		all_cancers(20;1.78e-24)|all_epithelial(15;7.75e-22)|Lung NSC(15;2.96e-18)|all_lung(15;2.8e-17)|Breast(32;0.000625)|Colorectal(260;0.14)		all cancers(64;1.84e-06)|Epithelial(43;1.2e-05)|BRCA - Breast invasive adenocarcinoma(123;0.00177)										0.62963	55.526539	55.95429	17	10	KEEP	---	---	---	---	capture		Silent	SNP	23889965	23889965	9572	15	G	T	T	T	444	35	MAGEL2	2	2
MAGEL2	54551	broad.mit.edu	37	15	23890368	23890368	+	Missense_Mutation	SNP	T	A	A			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr15:23890368T>A	uc001ywj.3	-	c.713A>T	c.(712-714)AAT>ATT	p.N238I		NM_019066	NP_061939			MAGE-like protein 2												0		all_cancers(20;1.78e-24)|all_epithelial(15;7.75e-22)|Lung NSC(15;2.96e-18)|all_lung(15;2.8e-17)|Breast(32;0.000625)|Colorectal(260;0.14)		all cancers(64;1.84e-06)|Epithelial(43;1.2e-05)|BRCA - Breast invasive adenocarcinoma(123;0.00177)										0.356436	107.798353	109.620456	36	65	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	23890368	23890368	9572	15	T	A	A	A	676	52	MAGEL2	3	3
RYR3	6263	broad.mit.edu	37	15	33842510	33842510	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr15:33842510C>A	uc001zhi.2	+	c.965C>A	c.(964-966)GCA>GAA	p.A322E	RYR3_uc010bar.2_Missense_Mutation_p.A322E	NM_001036	NP_001027	Q15413	RYR3_HUMAN	ryanodine receptor 3	322	Cytoplasmic (By similarity).|MIR 4.				cellular calcium ion homeostasis	integral to membrane	calcium ion binding|receptor activity|ryanodine-sensitive calcium-release channel activity			ovary(5)|central_nervous_system(4)|lung(1)	10		all_lung(180;7.18e-09)		all cancers(64;8.95e-12)|GBM - Glioblastoma multiforme(186;0.00109)|BRCA - Breast invasive adenocarcinoma(123;0.0363)										0.578947	71.857212	72.064443	22	16	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	33842510	33842510	14250	15	C	A	A	A	325	25	RYR3	2	2
RYR3	6263	broad.mit.edu	37	15	34042406	34042406	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr15:34042406C>T	uc001zhi.2	+	c.8318C>T	c.(8317-8319)ACT>ATT	p.T2773I	RYR3_uc010bar.2_Missense_Mutation_p.T2773I	NM_001036	NP_001027	Q15413	RYR3_HUMAN	ryanodine receptor 3	2773	4.|Cytoplasmic (By similarity).|4 X approximate repeats.				cellular calcium ion homeostasis	integral to membrane	calcium ion binding|receptor activity|ryanodine-sensitive calcium-release channel activity			ovary(5)|central_nervous_system(4)|lung(1)	10		all_lung(180;7.18e-09)		all cancers(64;8.95e-12)|GBM - Glioblastoma multiforme(186;0.00109)|BRCA - Breast invasive adenocarcinoma(123;0.0363)										0.217391	12.062695	13.756281	5	18	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	34042406	34042406	14250	15	C	T	T	T	260	20	RYR3	2	2
RASGRP1	10125	broad.mit.edu	37	15	38800034	38800034	+	Missense_Mutation	SNP	T	C	C			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr15:38800034T>C	uc001zke.3	-	c.1135A>G	c.(1135-1137)AAC>GAC	p.N379D	RASGRP1_uc010bbe.2_Non-coding_Transcript|RASGRP1_uc010bbf.2_Missense_Mutation_p.N241D|RASGRP1_uc010bbg.2_Missense_Mutation_p.N241D|RASGRP1_uc001zkd.3_Missense_Mutation_p.N379D	NM_005739	NP_005730	O95267	GRP1_HUMAN	RAS guanyl releasing protein 1 isoform a	379	Ras-GEF.				cell differentiation|platelet activation|Ras protein signal transduction|regulation of small GTPase mediated signal transduction	cytosol|endoplasmic reticulum membrane|Golgi membrane|membrane fraction|plasma membrane	calcium ion binding|guanyl-nucleotide exchange factor activity|lipid binding|protein binding			large_intestine(1)|ovary(1)	2		all_cancers(109;6.38e-17)|all_epithelial(112;5.51e-15)|Lung NSC(122;2.12e-11)|all_lung(180;5.63e-10)|Melanoma(134;0.0574)		GBM - Glioblastoma multiforme(113;1.97e-07)|BRCA - Breast invasive adenocarcinoma(123;0.00248)										0.545455	63.153174	63.212551	18	15	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	38800034	38800034	13535	15	T	C	C	C	806	62	RASGRP1	4	4
RASGRP1	10125	broad.mit.edu	37	15	38800056	38800056	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr15:38800056G>T	uc001zke.3	-	c.1113C>A	c.(1111-1113)GAC>GAA	p.D371E	RASGRP1_uc010bbe.2_Non-coding_Transcript|RASGRP1_uc010bbf.2_Missense_Mutation_p.D233E|RASGRP1_uc010bbg.2_Missense_Mutation_p.D233E|RASGRP1_uc001zkd.3_Missense_Mutation_p.D371E	NM_005739	NP_005730	O95267	GRP1_HUMAN	RAS guanyl releasing protein 1 isoform a	371	Ras-GEF.				cell differentiation|platelet activation|Ras protein signal transduction|regulation of small GTPase mediated signal transduction	cytosol|endoplasmic reticulum membrane|Golgi membrane|membrane fraction|plasma membrane	calcium ion binding|guanyl-nucleotide exchange factor activity|lipid binding|protein binding			large_intestine(1)|ovary(1)	2		all_cancers(109;6.38e-17)|all_epithelial(112;5.51e-15)|Lung NSC(122;2.12e-11)|all_lung(180;5.63e-10)|Melanoma(134;0.0574)		GBM - Glioblastoma multiforme(113;1.97e-07)|BRCA - Breast invasive adenocarcinoma(123;0.00248)										0.513514	60.724702	60.730533	19	18	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	38800056	38800056	13535	15	G	T	T	T	464	36	RASGRP1	2	2
SORD	6652	broad.mit.edu	37	15	45361251	45361251	+	Splice_Site_SNP	SNP	G	T	T			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr15:45361251G>T	uc001zul.3	+	c.786_splice	c.e7+1	p.Y262_splice	SORD_uc010uel.1_Splice_Site_SNP|SORD_uc001zum.3_Splice_Site_SNP_p.Y262_splice|SORD_uc010bdz.2_Splice_Site_SNP_p.Y183_splice	NM_003104	NP_003095			sorbitol dehydrogenase						fructose biosynthetic process|glucose metabolic process|L-xylitol catabolic process|oxidation-reduction process|sorbitol catabolic process|sperm motility	cilium|extracellular space|flagellum|membrane fraction|mitochondrial membrane|soluble fraction	L-iditol 2-dehydrogenase activity|NAD binding|sugar binding|zinc ion binding				0		all_cancers(109;3.43e-12)|all_epithelial(112;2.33e-10)|Lung NSC(122;6.01e-07)|all_lung(180;4.38e-06)|Melanoma(134;0.0122)		all cancers(107;1.6e-18)|GBM - Glioblastoma multiforme(94;4.95e-07)|COAD - Colon adenocarcinoma(120;0.0704)|Colorectal(133;0.0706)	NADH(DB00157)									0.236364	33.447746	36.942122	13	42	KEEP	---	---	---	---	capture		Splice_Site_SNP	SNP	45361251	45361251	15433	15	G	T	T	T	520	40	SORD	5	1
SLC12A1	6557	broad.mit.edu	37	15	48500073	48500073	+	Nonsense_Mutation	SNP	G	T	T			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr15:48500073G>T	uc001zwn.3	+	c.157G>T	c.(157-159)GAA>TAA	p.E53*	SLC12A1_uc010uew.1_Intron|SLC12A1_uc010bem.2_Nonsense_Mutation_p.E53*|SLC12A1_uc010uex.1_Nonsense_Mutation_p.E53*	NM_000338	NP_000329	Q13621	S12A1_HUMAN	sodium potassium chloride cotransporter 2	53	Cytoplasmic (Potential).				potassium ion transport|sodium ion transport	integral to membrane|membrane fraction	sodium:potassium:chloride symporter activity			ovary(1)|central_nervous_system(1)	2		all_lung(180;0.00219)		all cancers(107;1.76e-09)|GBM - Glioblastoma multiforme(94;1.48e-06)	Bumetanide(DB00887)|Chlormerodrin(DB00534)|Chlorthalidone(DB00310)|Ethacrynic acid(DB00903)|Furosemide(DB00695)|Hydroflumethiazide(DB00774)|Methyclothiazide(DB00232)|Metolazone(DB00524)|Potassium Chloride(DB00761)|Torasemide(DB00214)|Trichlormethiazide(DB01021)									0.337662	71.919993	73.717693	26	51	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	48500073	48500073	14877	15	G	T	T	T	585	45	SLC12A1	5	2
FBN1	2200	broad.mit.edu	37	15	48741007	48741007	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr15:48741007G>A	uc001zwx.1	-	c.5629C>T	c.(5629-5631)CAC>TAC	p.H1877Y	FBN1_uc010beo.1_Non-coding_Transcript	NM_000138	NP_000129	P35555	FBN1_HUMAN	fibrillin 1 precursor	1877	EGF-like 31; calcium-binding.				heart development|negative regulation of BMP signaling pathway by extracellular sequestering of BMP|negative regulation of transforming growth factor beta receptor signaling pathway by extracellular sequestering of TGFbeta|skeletal system development	basement membrane|extracellular space|microfibril	calcium ion binding|extracellular matrix structural constituent|protein binding			ovary(2)|large_intestine(1)	3		all_lung(180;0.00279)		all cancers(107;4.24e-07)|GBM - Glioblastoma multiforme(94;1.41e-05)						2933				0.450704	99.301053	99.449536	32	39	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	48741007	48741007	5938	15	G	A	A	A	611	47	FBN1	2	2
COPS2	9318	broad.mit.edu	37	15	49426538	49426538	+	Silent	SNP	T	C	C			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr15:49426538T>C	uc001zxh.2	-	c.735A>G	c.(733-735)AGA>AGG	p.R245R	COPS2_uc001zxf.2_Silent_p.R238R|COPS2_uc010ufa.1_Silent_p.R174R	NM_001143887	NP_001137359	P61201	CSN2_HUMAN	COP9 constitutive photomorphogenic homolog	238					transcription from RNA polymerase II promoter	cytoplasm|signalosome	protein binding|signal transducer activity			lung(1)	1		all_lung(180;0.0428)		all cancers(107;1.34e-07)|GBM - Glioblastoma multiforme(94;3.02e-05)		NSCLC(36;322 1063 10349 30082 48062)|Esophageal Squamous(122;685 1633 15569 21293 52803)								0.408163	63.487344	63.849242	20	29	KEEP	---	---	---	---	capture		Silent	SNP	49426538	49426538	3871	15	T	C	C	C	699	54	COPS2	4	4
TLN2	83660	broad.mit.edu	37	15	62948149	62948150	+	Missense_Mutation	DNP	GG	AT	AT			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr15:62948149_62948150GG>AT	uc002alb.3	+	c.524_525GG>AT	c.(523-525)TGG>TAT	p.W175Y		NM_015059	NP_055874	Q9Y4G6	TLN2_HUMAN	talin 2	175	FERM.				cell adhesion|cell-cell junction assembly|cytoskeletal anchoring at plasma membrane	actin cytoskeleton|cell-cell junction|cytoplasm|focal adhesion|ruffle|synapse	actin binding|insulin receptor binding|structural constituent of cytoskeleton			ovary(4)|breast(2)	6														0.324324	63.971543	65.999959	24	50	KEEP	---	---	---	---	capture		Missense_Mutation	DNP	62948149	62948150	16478	15	GG	AT	AT	AT	611	47	TLN2	2	2
TLN2	83660	broad.mit.edu	37	15	62989969	62989969	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr15:62989969G>T	uc002alb.3	+	c.1375G>T	c.(1375-1377)GGC>TGC	p.G459C		NM_015059	NP_055874	Q9Y4G6	TLN2_HUMAN	talin 2	459					cell adhesion|cell-cell junction assembly|cytoskeletal anchoring at plasma membrane	actin cytoskeleton|cell-cell junction|cytoplasm|focal adhesion|ruffle|synapse	actin binding|insulin receptor binding|structural constituent of cytoskeleton			ovary(4)|breast(2)	6														0.383838	108.442061	109.607162	38	61	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	62989969	62989969	16478	15	G	T	T	T	559	43	TLN2	2	2
SNX1	6642	broad.mit.edu	37	15	64423929	64423929	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr15:64423929G>T	uc010uio.1	+	c.1059G>T	c.(1057-1059)ATG>ATT	p.M353I	SNX1_uc010bgv.2_Missense_Mutation_p.M67I|SNX1_uc002amv.2_Missense_Mutation_p.M353I|SNX1_uc002amw.2_Missense_Mutation_p.M353I|SNX1_uc002amx.2_Missense_Mutation_p.M288I|SNX1_uc002amy.2_Missense_Mutation_p.M282I|SNX1_uc010bgw.2_Missense_Mutation_p.M255I	NM_003099	NP_003090	Q13596	SNX1_HUMAN	sorting nexin 1 isoform a	353	BAR.				cell communication|early endosome to Golgi transport|endocytosis|intracellular protein transport	early endosome membrane|Golgi apparatus	phosphatidylinositol binding|protein binding|protein transporter activity				0														0.388235	95.048946	95.981273	33	52	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	64423929	64423929	15380	15	G	T	T	T	598	46	SNX1	2	2
TLE3	7090	broad.mit.edu	37	15	70342448	70342448	+	Silent	SNP	C	T	T			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr15:70342448C>T	uc002asl.2	-	c.2307G>A	c.(2305-2307)GAG>GAA	p.E769E	TLE3_uc002ask.2_Silent_p.E696E|TLE3_uc010ukd.1_Silent_p.E759E|TLE3_uc010bik.1_Silent_p.E350E|TLE3_uc010bil.1_Silent_p.E766E|TLE3_uc002asn.2_Silent_p.E757E|TLE3_uc002asm.2_Silent_p.E769E|TLE3_uc002asp.2_Silent_p.E761E|TLE3_uc002aso.2_Silent_p.E764E	NM_001105192	NP_001098662	Q04726	TLE3_HUMAN	transducin-like enhancer protein 3 isoform b	769	WD 7.				organ morphogenesis|regulation of transcription, DNA-dependent|transcription, DNA-dependent|Wnt receptor signaling pathway	nucleus	protein binding|protein binding				0														0.374269	203.207526	205.561368	64	107	KEEP	---	---	---	---	capture		Silent	SNP	70342448	70342448	16470	15	C	T	T	T	311	24	TLE3	2	2
NEO1	4756	broad.mit.edu	37	15	73468860	73468860	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr15:73468860G>T	uc002avm.3	+	c.1132G>T	c.(1132-1134)GGG>TGG	p.G378W	NEO1_uc010ukx.1_Missense_Mutation_p.G378W|NEO1_uc010uky.1_Missense_Mutation_p.G378W|NEO1_uc010ukz.1_5'UTR|NEO1_uc002avn.3_Missense_Mutation_p.G23W	NM_002499	NP_002490	Q92859	NEO1_HUMAN	neogenin homolog 1 precursor	378	Extracellular (Potential).|Ig-like C2-type 4.				axon guidance|cell adhesion|positive regulation of muscle cell differentiation	Golgi apparatus|integral to plasma membrane|nucleus				pancreas(1)	1														0.384615	92.433222	93.343138	30	48	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	73468860	73468860	10735	15	G	T	T	T	611	47	NEO1	2	2
PML	5371	broad.mit.edu	37	15	74337262	74337262	+	Missense_Mutation	SNP	G	C	C			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr15:74337262G>C	uc002awv.2	+	c.2562G>C	c.(2560-2562)TTG>TTC	p.L854F	PML_uc002awu.2_Missense_Mutation_p.L806F|PML_uc010ule.1_Missense_Mutation_p.L415F	NM_033238	NP_150241	P29590	PML_HUMAN	promyelocytic leukemia protein isoform 1	854					cell cycle arrest|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|DNA damage response, signal transduction resulting in induction of apoptosis|endoplasmic reticulum calcium ion homeostasis|induction of apoptosis|interferon-gamma-mediated signaling pathway|interspecies interaction between organisms|maintenance of protein location in nucleus|negative regulation of angiogenesis|negative regulation of cell growth|negative regulation of cell proliferation|negative regulation of mitotic cell cycle|negative regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process|negative regulation of telomerase activity|negative regulation of telomere maintenance via telomerase|negative regulation of transcription, DNA-dependent|negative regulation of translation in response to oxidative stress|PML body organization|PML body organization|positive regulation of defense response to virus by host|positive regulation of histone deacetylation|protein complex assembly|protein stabilization|protein targeting|regulation of calcium ion transport into cytosol|regulation of protein phosphorylation|response to hypoxia|response to virus|transcription, DNA-dependent	cytoplasm|cytosol|early endosome membrane|extrinsic to endoplasmic reticulum membrane|insoluble fraction|nuclear matrix|nuclear membrane|nucleolus|nucleus|PML body	cobalt ion binding|DNA binding|protein binding|protein binding|protein heterodimerization activity|protein homodimerization activity|SUMO binding|transcription coactivator activity|transcription repressor activity|ubiquitin protein ligase binding|zinc ion binding|zinc ion binding			central_nervous_system(2)|kidney(2)	4										214				0.412903	206.076272	207.101552	64	91	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	74337262	74337262	12561	15	G	C	C	C	607	47	PML	3	3
NTRK3	4916	broad.mit.edu	37	15	88576116	88576116	+	Silent	SNP	C	T	T			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr15:88576116C>T	uc002bme.1	-	c.1557G>A	c.(1555-1557)CAG>CAA	p.Q519Q	NTRK3_uc002bmh.2_Silent_p.Q511Q|NTRK3_uc002bmf.1_Silent_p.Q519Q|NTRK3_uc010upl.1_Silent_p.Q421Q|NTRK3_uc010bnh.1_Silent_p.Q511Q|NTRK3_uc002bmg.2_Silent_p.Q519Q|NTRK3_uc010bni.2_Non-coding_Transcript	NM_001012338	NP_001012338	Q16288	NTRK3_HUMAN	neurotrophic tyrosine kinase, receptor, type 3	519	Cytoplasmic (Potential).				transmembrane receptor protein tyrosine kinase signaling pathway	integral to plasma membrane	ATP binding|transmembrane receptor protein tyrosine kinase activity		ETV6/NTRK3(234)	soft_tissue(85)|kidney(66)|breast(56)|salivary_gland(26)|lung(13)|ovary(5)|central_nervous_system(3)|haematopoietic_and_lymphoid_tissue(2)|stomach(1)|skin(1)|pancreas(1)	259			BRCA - Breast invasive adenocarcinoma(143;0.211)							506	TSP Lung(13;0.10)			0.431818	115.73206	116.089402	38	50	KEEP	---	---	---	---	capture		Silent	SNP	88576116	88576116	11113	15	C	T	T	T	311	24	NTRK3	2	2
ACAN	176	broad.mit.edu	37	15	89385034	89385034	+	Silent	SNP	G	A	A			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr15:89385034G>A	uc010upo.1	+	c.693G>A	c.(691-693)AGG>AGA	p.R231R	ACAN_uc002bmx.2_Silent_p.R231R|ACAN_uc010upp.1_Silent_p.R231R|ACAN_uc002bna.2_Non-coding_Transcript	NM_013227	NP_037359			aggrecan isoform 2 precursor											ovary(2)|central_nervous_system(1)	3	Lung NSC(78;0.0392)|all_lung(78;0.077)		BRCA - Breast invasive adenocarcinoma(143;0.146)											0.443709	194.651953	195.058904	67	84	KEEP	---	---	---	---	capture		Silent	SNP	89385034	89385034	118	15	G	A	A	A	529	41	ACAN	2	2
POLG	5428	broad.mit.edu	37	15	89870507	89870507	+	Nonsense_Mutation	SNP	C	A	A			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr15:89870507C>A	uc002bns.3	-	c.1324G>T	c.(1324-1326)GAG>TAG	p.E442*	POLG_uc002bnr.3_Nonsense_Mutation_p.E442*	NM_002693	NP_002684	P54098	DPOG1_HUMAN	DNA-directed DNA polymerase gamma	442					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)								0.393443	64.503355	65.103675	24	37	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	89870507	89870507	12628	15	C	A	A	A	390	30	POLG	5	2
CPPED1	55313	broad.mit.edu	37	16	12798851	12798851	+	Silent	SNP	C	A	A			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:12798851C>A	uc002dca.3	-	c.345G>T	c.(343-345)GTG>GTT	p.V115V	CPPED1_uc002dcb.3_Intron|CPPED1_uc002dbz.3_Non-coding_Transcript	NM_018340	NP_060810	Q9BRF8	CPPED_HUMAN	calcineurin-like phosphoesterase domain	115							hydrolase activity|metal ion binding				0														0.807018	149.176992	154.194371	46	11	KEEP	---	---	---	---	capture		Silent	SNP	12798851	12798851	3960	16	C	A	A	A	262	21	CPPED1	2	2
BAIAP3	8938	broad.mit.edu	37	16	1394319	1394319	+	Splice_Site_SNP	SNP	G	A	A			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:1394319G>A	uc002clk.1	+	c.1707_splice	c.e17+1	p.K569_splice	BAIAP3_uc002clj.2_Splice_Site_SNP_p.K551_splice|BAIAP3_uc010uuz.1_Splice_Site_SNP_p.K534_splice|BAIAP3_uc010uva.1_Splice_Site_SNP_p.K506_splice|BAIAP3_uc010uvc.1_Splice_Site_SNP_p.K498_splice	NM_003933	NP_003924			BAI1-associated protein 3						G-protein coupled receptor protein signaling pathway|neurotransmitter secretion		protein C-terminus binding			pancreas(1)	1		Hepatocellular(780;0.0893)												0.730769	57.827359	59.076133	19	7	KEEP	---	---	---	---	capture		Splice_Site_SNP	SNP	1394319	1394319	1325	16	G	A	A	A	572	44	BAIAP3	5	2
PARN	5073	broad.mit.edu	37	16	14693769	14693769	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:14693769C>A	uc010uzd.1	-	c.832G>T	c.(832-834)GCT>TCT	p.A278S	PARN_uc010uzc.1_Missense_Mutation_p.A217S|PARN_uc010uze.1_Missense_Mutation_p.A232S|PARN_uc010uzf.1_Missense_Mutation_p.A103S|PARN_uc010uzg.1_Non-coding_Transcript	NM_002582	NP_002573	O95453	PARN_HUMAN	poly(A)-specific ribonuclease (deadenylation	278					female gamete generation|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay|nuclear-transcribed mRNA poly(A) tail shortening|RNA modification	cytosol|nucleolus	metal ion binding|mRNA 3'-UTR binding|nucleotide binding|poly(A)-specific ribonuclease activity|protein binding			ovary(2)	2														0.797468	216.165119	222.654642	63	16	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	14693769	14693769	11870	16	C	A	A	A	325	25	PARN	2	2
NDE1	54820	broad.mit.edu	37	16	15785139	15785139	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:15785139G>T	uc002ddt.1	+	c.662G>T	c.(661-663)GGA>GTA	p.G221V	NDE1_uc010uzy.1_Missense_Mutation_p.G221V|NDE1_uc002dds.2_Missense_Mutation_p.G221V|NDE1_uc002ddu.1_Missense_Mutation_p.G158V	NM_017668	NP_060138	Q9NXR1	NDE1_HUMAN	nuclear distribution gene E homolog 1	221	Interaction with CENPF (By similarity).				cell differentiation|cell division|centrosome duplication|establishment of chromosome localization|establishment of mitotic spindle orientation|G2/M transition of mitotic cell cycle|mitotic prometaphase|nervous system development	cleavage furrow|condensed chromosome kinetochore|cytosol|microtubule|spindle pole centrosome	microtubule binding			ovary(1)	1										8				0.935484	98.08857	100.983973	29	2	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	15785139	15785139	10642	16	G	T	T	T	533	41	NDE1	2	2
ACSM1	116285	broad.mit.edu	37	16	20648732	20648732	+	Silent	SNP	C	A	A			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:20648732C>A	uc002dhm.1	-	c.1158G>T	c.(1156-1158)CCG>CCT	p.P386P	ACSM1_uc002dhn.1_Non-coding_Transcript|ACSM1_uc010bwg.1_Silent_p.P386P	NM_052956	NP_443188	Q08AH1	ACSM1_HUMAN	acyl-CoA synthetase medium-chain family member	386					benzoate metabolic process|butyrate metabolic process|energy derivation by oxidation of organic compounds|fatty acid oxidation|xenobiotic metabolic process	mitochondrial matrix	acyl-CoA ligase activity|ATP binding|butyrate-CoA ligase activity|GTP binding|metal ion binding			central_nervous_system(1)	1														0.788732	394.851154	405.792965	112	30	KEEP	---	---	---	---	capture		Silent	SNP	20648732	20648732	183	16	C	A	A	A	288	23	ACSM1	1	1
SCNN1G	6340	broad.mit.edu	37	16	23197657	23197657	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:23197657C>T	uc002dlm.1	+	c.65C>T	c.(64-66)GCG>GTG	p.A22V		NM_001039	NP_001030	P51170	SCNNG_HUMAN	sodium channel, nonvoltage-gated 1, gamma	22	Cytoplasmic (By similarity).				excretion|sensory perception of taste	apical plasma membrane|integral to plasma membrane	ligand-gated sodium channel activity|WW domain binding			ovary(2)|large_intestine(1)|pancreas(1)	4				GBM - Glioblastoma multiforme(48;0.0366)	Amiloride(DB00594)|Triamterene(DB00384)									0.344262	55.085578	56.378586	21	40	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	23197657	23197657	14412	16	C	T	T	T	351	27	SCNN1G	1	1
C16orf82	162083	broad.mit.edu	37	16	27078670	27078670	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:27078670G>T	uc010vcm.1	+	c.354G>T	c.(352-354)CAG>CAT	p.Q118H		NM_001145545	NP_001139017	Q7Z2V1	TNT_HUMAN	hypothetical protein LOC162083	181											0														0.636364	18.01566	18.192903	7	4	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	27078670	27078670	1891	16	G	T	T	T	451	35	C16orf82	2	2
NDRG4	65009	broad.mit.edu	37	16	58545443	58545443	+	Missense_Mutation	SNP	T	A	A			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:58545443T>A	uc002enm.2	+	c.1139T>A	c.(1138-1140)CTG>CAG	p.L380Q	NDRG4_uc002enk.2_Missense_Mutation_p.L360Q|NDRG4_uc010vif.1_Missense_Mutation_p.L360Q|NDRG4_uc010cdk.2_Missense_Mutation_p.L346Q|NDRG4_uc002eno.2_Missense_Mutation_p.L341Q|NDRG4_uc010vig.1_Missense_Mutation_p.L358Q|NDRG4_uc010vih.1_Missense_Mutation_p.L273Q|NDRG4_uc010vii.1_Missense_Mutation_p.L346Q|NDRG4_uc002enp.2_Missense_Mutation_p.L328Q|NDRG4_uc002enq.1_Intron	NM_001130487	NP_001123959	Q9ULP0	NDRG4_HUMAN	NDRG family member 4 isoform 2	341					cell differentiation|cell growth|multicellular organismal development|response to stress	cytoplasm					0														0.769231	67.312469	69.040365	20	6	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	58545443	58545443	10653	16	T	A	A	A	715	55	NDRG4	3	3
MTSS1L	92154	broad.mit.edu	37	16	70698083	70698083	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:70698083C>T	uc002ezj.2	-	c.1741G>A	c.(1741-1743)GCT>ACT	p.A581T		NM_138383	NP_612392	Q765P7	MTSSL_HUMAN	metastasis suppressor 1-like	581					filopodium assembly|signal transduction		actin binding|cytoskeletal adaptor activity|SH3 domain binding			central_nervous_system(1)	1														0.5	42.033291	42.033291	15	15	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	70698083	70698083	10356	16	C	T	T	T	351	27	MTSS1L	1	1
HYDIN	54768	broad.mit.edu	37	16	70926379	70926379	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:70926379G>A	uc002ezr.2	-	c.9299C>T	c.(9298-9300)TCA>TTA	p.S3100L		NM_032821	NP_116210	Q4G0P3	HYDIN_HUMAN	hydrocephalus inducing isoform a	3101										ovary(1)	1		Ovarian(137;0.0654)												0.195876	80.606284	97.376694	38	156	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	70926379	70926379	7767	16	G	A	A	A	585	45	HYDIN	2	2
HYDIN	54768	broad.mit.edu	37	16	71007911	71007911	+	Missense_Mutation	SNP	G	C	C			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:71007911G>C	uc002ezr.2	-	c.5047C>G	c.(5047-5049)CCA>GCA	p.P1683A		NM_032821	NP_116210	Q4G0P3	HYDIN_HUMAN	hydrocephalus inducing isoform a	1684										ovary(1)	1		Ovarian(137;0.0654)												0.186441	27.591478	33.02483	11	48	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	71007911	71007911	7767	16	G	C	C	C	546	42	HYDIN	3	3
CHST6	4166	broad.mit.edu	37	16	75513119	75513119	+	Missense_Mutation	SNP	T	A	A			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:75513119T>A	uc002fef.2	-	c.608A>T	c.(607-609)GAC>GTC	p.D203V	CHST6_uc002feg.1_Non-coding_Transcript|CHST6_uc002feh.1_Missense_Mutation_p.D203V	NM_021615	NP_067628	Q9GZX3	CHST6_HUMAN	carbohydrate (N-acetylglucosamine 6-O)	203	PAPS (By similarity).|Lumenal (Potential).				keratan sulfate biosynthetic process|N-acetylglucosamine metabolic process	Golgi membrane|integral to membrane	N-acetylglucosamine 6-O-sulfotransferase activity				0														0.888889	23.377612	24.030979	8	1	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	75513119	75513119	3542	16	T	A	A	A	754	58	CHST6	3	3
BCMO1	53630	broad.mit.edu	37	16	81324046	81324046	+	Missense_Mutation	SNP	C	G	G			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:81324046C>G	uc002fgn.1	+	c.1508C>G	c.(1507-1509)GCC>GGC	p.A503G	BCMO1_uc010vnp.1_Missense_Mutation_p.A434G	NM_017429	NP_059125	Q9HAY6	BCDO1_HUMAN	beta-carotene 15,15'-monooxygenase	503					oxidation-reduction process|retinoid metabolic process|steroid metabolic process	cytosol	beta-carotene 15,15'-monooxygenase activity|metal ion binding				0														0.792079	288.838864	296.812106	80	21	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	81324046	81324046	1405	16	C	G	G	G	338	26	BCMO1	3	3
MYO15A	51168	broad.mit.edu	37	17	18058425	18058425	+	Silent	SNP	C	A	A			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:18058425C>A	uc010vxh.1	+	c.8226C>A	c.(8224-8226)GCC>GCA	p.A2742A	MYO15A_uc010vxi.1_Silent_p.A6A|MYO15A_uc010vxj.1_5'UTR|MYO15A_uc010vxk.1_Intron|MYO15A_uc010vxl.1_5'Flank	NM_016239	NP_057323	Q9UKN7	MYO15_HUMAN	myosin XV	2742	Tail.				sensory perception of sound	cytoplasm|myosin complex|stereocilium	actin binding|ATP binding|calmodulin binding|motor activity			ovary(2)|pancreas(1)|breast(1)|central_nervous_system(1)|skin(1)	6	all_neural(463;0.228)													0.6	20.251942	20.339386	6	4	KEEP	---	---	---	---	capture		Silent	SNP	18058425	18058425	10458	17	C	A	A	A	275	22	MYO15A	2	2
LGALS9C	654346	broad.mit.edu	37	17	18392259	18392259	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:18392259C>A	uc002gtw.2	+	c.449C>A	c.(448-450)CCC>CAC	p.P150H	LGALS9C_uc010vyb.1_Missense_Mutation_p.P62H	NM_001040078	NP_001035167	Q6DKI2	LEG9C_HUMAN	galectin 9 like	150							sugar binding			ovary(1)	1														0.34	46.457851	47.590182	17	33	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	18392259	18392259	9076	17	C	A	A	A	286	22	LGALS9C	2	2
WSB1	26118	broad.mit.edu	37	17	25630530	25630530	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:25630530G>T	uc002gzd.1	+	c.347G>T	c.(346-348)GGG>GTG	p.G116V	WSB1_uc010vzy.1_Missense_Mutation_p.G116V|WSB1_uc010vzz.1_Missense_Mutation_p.G85V|WSB1_uc010crf.1_Intron|WSB1_uc002gze.1_Intron|WSB1_uc002gzf.1_Non-coding_Transcript	NM_015626	NP_056441	Q9Y6I7	WSB1_HUMAN	WD repeat and SOCS box-containing 1 isoform 1	116					intracellular signal transduction	intracellular	protein binding				0	all_cancers(1;2e-13)|all_epithelial(1;4.8e-15)|Lung NSC(42;0.00152)		BRCA - Breast invasive adenocarcinoma(3;0.0152)	UCEC - Uterine corpus endometrioid carcinoma (53;0.154)										0.603834	582.665367	585.60506	189	124	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	25630530	25630530	17978	17	G	T	T	T	559	43	WSB1	2	2
OR3A1	4994	broad.mit.edu	37	17	3195487	3195487	+	Nonsense_Mutation	SNP	G	T	T			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:3195487G>T	uc002fvh.1	-	c.390C>A	c.(388-390)TGC>TGA	p.C130*		NM_002550	NP_002541	P47881	OR3A1_HUMAN	olfactory receptor, family 3, subfamily A,	130	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			kidney(2)|central_nervous_system(1)	3						GBM(20;287 516 18743 28660 36594)								0.882353	479.883696	504.717171	150	20	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	3195487	3195487	11443	17	G	T	T	T	542	42	OR3A1	5	2
UNC45B	146862	broad.mit.edu	37	17	33495200	33495200	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:33495200G>T	uc002hja.2	+	c.1272G>T	c.(1270-1272)GAG>GAT	p.E424D	UNC45B_uc002hjb.2_Missense_Mutation_p.E424D|UNC45B_uc002hjc.2_Missense_Mutation_p.E424D|UNC45B_uc010cto.2_Missense_Mutation_p.E424D	NM_173167	NP_775259	Q8IWX7	UN45B_HUMAN	cardiomyopathy associated 4 isoform 1	424					cell differentiation|muscle organ development		binding			ovary(3)|central_nervous_system(2)|breast(1)	6		Ovarian(249;0.17)												0.358209	65.377344	66.565273	24	43	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	33495200	33495200	17547	17	G	T	T	T	425	33	UNC45B	2	2
FBXO47	494188	broad.mit.edu	37	17	37101330	37101330	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:37101330G>T	uc002hrc.2	-	c.676C>A	c.(676-678)CAT>AAT	p.H226N		NM_001008777	NP_001008777	Q5MNV8	FBX47_HUMAN	F-box protein 47	226											0														0.171779	47.378722	64.00558	28	135	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	37101330	37101330	5993	17	G	T	T	T	585	45	FBXO47	2	2
ERBB2	2064	broad.mit.edu	37	17	37879576	37879576	+	Missense_Mutation	SNP	C	G	G			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:37879576C>G	uc002hso.2	+	c.1951C>G	c.(1951-1953)CTG>GTG	p.L651V	ERBB2_uc002hsm.2_Missense_Mutation_p.L621V|ERBB2_uc010cwa.2_Missense_Mutation_p.L636V|ERBB2_uc002hsp.2_Missense_Mutation_p.L454V|ERBB2_uc010cwb.2_Missense_Mutation_p.L651V|ERBB2_uc010wek.1_Missense_Mutation_p.L375V	NM_004448	NP_004439	P04626	ERBB2_HUMAN	erbB-2 isoform a	651	Extracellular (Potential).				cell proliferation|heart development|phosphatidylinositol 3-kinase cascade|phosphatidylinositol-mediated signaling|positive regulation of cell adhesion|positive regulation of epithelial cell proliferation|positive regulation of MAP kinase activity|protein autophosphorylation|regulation of angiogenesis|regulation of transcription, DNA-dependent|transcription, DNA-dependent|wound healing	integral to membrane|nucleus|perinuclear region of cytoplasm|receptor complex	ATP binding|DNA binding|epidermal growth factor receptor activity|ErbB-3 class receptor binding|identical protein binding|protein C-terminus binding|protein heterodimerization activity|protein phosphatase binding|receptor signaling protein tyrosine kinase activity			lung(71)|central_nervous_system(16)|ovary(13)|stomach(12)|breast(5)|upper_aerodigestive_tract(4)|large_intestine(3)|liver(3)|endometrium(2)|pancreas(1)	130	all_cancers(6;1.06e-93)|all_epithelial(6;2.33e-113)|Breast(7;9.37e-100)|Lung NSC(9;9.76e-10)|all_lung(9;5.34e-09)|Colorectal(19;0.000442)|Esophageal squamous(10;0.052)	Ovarian(249;0.0547)|Colorectal(1115;0.234)	UCEC - Uterine corpus endometrioid carcinoma (11;0.000126)|Epithelial(3;9.42e-64)|all cancers(3;5.61e-57)|BRCA - Breast invasive adenocarcinoma(8;2.5e-45)|STAD - Stomach adenocarcinoma(3;9.03e-13)|Colorectal(5;6.23e-08)|COAD - Colon adenocarcinoma(5;8.58e-06)|Lung(15;0.00193)|LUAD - Lung adenocarcinoma(14;0.0664)|OV - Ovarian serous cystadenocarcinoma(8;0.0917)|LUSC - Lung squamous cell carcinoma(15;0.171)	UCEC - Uterine corpus endometrioid carcinoma (308;0.0767)	Lapatinib(DB01259)|Letrozole(DB01006)|Trastuzumab(DB00072)			1		271	TCGA GBM(5;<1E-8)			0.522222	489.371924	489.487225	141	129	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	37879576	37879576	5399	17	C	G	G	G	415	32	ERBB2	3	3
KRTAP4-3	85290	broad.mit.edu	37	17	39324424	39324424	+	Missense_Mutation	SNP	T	C	C			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:39324424T>C	uc010cxl.2	-	c.1A>G	c.(1-3)ATG>GTG	p.M1V		NM_033187	NP_149443	Q9BYR4	KRA43_HUMAN	keratin associated protein 4-3	1						keratin filament					0		Breast(137;0.000496)	STAD - Stomach adenocarcinoma(17;0.000449)											0.453608	128.785467	128.967503	44	53	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	39324424	39324424	8874	17	T	C	C	C	663	51	KRTAP4-3	4	4
RAB5C	5878	broad.mit.edu	37	17	40278776	40278776	+	Missense_Mutation	SNP	T	G	G			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:40278776T>G	uc010cxx.2	-	c.631A>C	c.(631-633)ATA>CTA	p.I211L	RAB5C_uc002hyz.2_Missense_Mutation_p.I178L|RAB5C_uc002hza.2_Missense_Mutation_p.I178L|RAB5C_uc010cxy.2_Missense_Mutation_p.I90L	NM_201434	NP_958842	P51148	RAB5C_HUMAN	RAB5C, member RAS oncogene family isoform a	178					protein transport|small GTPase mediated signal transduction	early endosome membrane|melanosome|plasma membrane	GTP binding|GTPase activity|protein binding			large_intestine(1)|skin(1)	2		all_cancers(22;1.24e-06)|all_epithelial(22;4.33e-05)|Breast(137;0.000143)		BRCA - Breast invasive adenocarcinoma(366;0.128)										0.366667	479.635109	485.725949	143	247	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	40278776	40278776	13409	17	T	G	G	G	676	52	RAB5C	4	4
HCRT	3060	broad.mit.edu	37	17	40336456	40336456	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:40336456C>T	uc002hzc.1	-	c.112G>A	c.(112-114)GAC>AAC	p.D38N		NM_001524	NP_001515	O43612	OREX_HUMAN	orexin precursor	38					neuropeptide signaling pathway	cell junction|extracellular region|rough endoplasmic reticulum|synaptic vesicle					0		all_cancers(22;1.39e-06)|all_epithelial(22;9.98e-06)|Breast(137;0.000143)|Ovarian(249;0.0221)|Myeloproliferative disorder(1115;0.0255)|Colorectal(1115;0.069)		BRCA - Breast invasive adenocarcinoma(366;0.124)										0.5	25.957476	25.957476	9	9	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	40336456	40336456	7283	17	C	T	T	T	403	31	HCRT	1	1
ZZEF1	23140	broad.mit.edu	37	17	4045901	4045901	+	Missense_Mutation	SNP	G	C	C			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:4045901G>C	uc002fxe.2	-	c.289C>G	c.(289-291)CTG>GTG	p.L97V	ZZEF1_uc002fxk.1_Missense_Mutation_p.L97V|CYB5D2_uc002fxm.3_5'Flank|CYB5D2_uc010cko.2_5'Flank|CYB5D2_uc002fxl.3_5'Flank	NM_015113	NP_055928	O43149	ZZEF1_HUMAN	zinc finger, ZZ type with EF hand domain 1	97					regulation of mitotic metaphase/anaphase transition	anaphase-promoting complex	calcium ion binding|zinc ion binding			ovary(1)|pancreas(1)	2														0.555556	52.727792	52.800261	15	12	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	4045901	4045901	18861	17	G	C	C	C	425	33	ZZEF1	3	3
FZD2	2535	broad.mit.edu	37	17	42635672	42635672	+	Nonsense_Mutation	SNP	A	T	T			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:42635672A>T	uc002igx.1	+	c.616A>T	c.(616-618)AAG>TAG	p.K206*		NM_001466	NP_001457	Q14332	FZD2_HUMAN	frizzled 2 precursor	206	Extracellular (Potential).				axonogenesis|brain development|canonical Wnt receptor signaling pathway|epithelial cell differentiation|G-protein signaling, coupled to cGMP nucleotide second messenger|gonad development|positive regulation of cGMP metabolic process|positive regulation of transcription regulator activity|positive regulation of transcription, DNA-dependent|regulation of gene-specific transcription from RNA polymerase II promoter|vasculature development|Wnt receptor signaling pathway, calcium modulating pathway	apical part of cell|cytoplasm|integral to membrane|neuron projection membrane	G-protein coupled receptor activity|PDZ domain binding|Wnt receptor activity|Wnt-protein binding			ovary(2)	2		Prostate(33;0.0181)		BRCA - Breast invasive adenocarcinoma(366;0.189)										0.525	66.675722	66.697488	21	19	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	42635672	42635672	6381	17	A	T	T	T	65	5	FZD2	5	3
FZD2	2535	broad.mit.edu	37	17	42636025	42636025	+	Silent	SNP	G	A	A			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:42636025G>A	uc002igx.1	+	c.969G>A	c.(967-969)AAG>AAA	p.K323K		NM_001466	NP_001457	Q14332	FZD2_HUMAN	frizzled 2 precursor	323	Extracellular (Potential).				axonogenesis|brain development|canonical Wnt receptor signaling pathway|epithelial cell differentiation|G-protein signaling, coupled to cGMP nucleotide second messenger|gonad development|positive regulation of cGMP metabolic process|positive regulation of transcription regulator activity|positive regulation of transcription, DNA-dependent|regulation of gene-specific transcription from RNA polymerase II promoter|vasculature development|Wnt receptor signaling pathway, calcium modulating pathway	apical part of cell|cytoplasm|integral to membrane|neuron projection membrane	G-protein coupled receptor activity|PDZ domain binding|Wnt receptor activity|Wnt-protein binding			ovary(2)	2		Prostate(33;0.0181)		BRCA - Breast invasive adenocarcinoma(366;0.189)										0.322222	80.540918	83.068168	29	61	KEEP	---	---	---	---	capture		Silent	SNP	42636025	42636025	6381	17	G	A	A	A	425	33	FZD2	2	2
ARHGAP27	201176	broad.mit.edu	37	17	43481636	43481636	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:43481636C>A	uc002iix.2	-	c.455G>T	c.(454-456)AGG>ATG	p.R152M	ARHGAP27_uc010dak.2_Missense_Mutation_p.R125M|ARHGAP27_uc010wjl.1_Intron	NM_199282	NP_954976	Q6ZUM4	RHG27_HUMAN	Rho GTPase activating protein 27 isoform a	493					positive regulation of Cdc42 GTPase activity|receptor-mediated endocytosis|signal transduction	cytoplasm|membrane	Rac GTPase activator activity|SH3 domain binding				0	Renal(3;0.0405)													0.329545	75.037098	77.307677	29	59	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	43481636	43481636	888	17	C	A	A	A	312	24	ARHGAP27	2	2
IGF2BP1	10642	broad.mit.edu	37	17	47115536	47115536	+	Silent	SNP	C	T	T			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:47115536C>T	uc002iom.2	+	c.408C>T	c.(406-408)ATC>ATT	p.I136I	IGF2BP1_uc010dbj.2_Intron	NM_006546	NP_006537	Q9NZI8	IF2B1_HUMAN	insulin-like growth factor 2 mRNA binding	136	RRM 2.				CRD-mediated mRNA stabilization|negative regulation of translation|regulation of cytokine biosynthetic process|regulation of mRNA stability involved in response to stress	CRD-mediated mRNA stability complex|cytosol|dendritic spine|lamellipodium|nucleus|plasma membrane|stress granule	mRNA 3'-UTR binding|mRNA 5'-UTR binding|nucleotide binding|protein binding|translation regulator activity			kidney(1)	1						Esophageal Squamous(198;1041 2123 8248 37119 38268)								0.372483	310.622659	314.888392	111	187	KEEP	---	---	---	---	capture		Silent	SNP	47115536	47115536	7874	17	C	T	T	T	369	29	IGF2BP1	2	2
USP32	84669	broad.mit.edu	37	17	58270219	58270219	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:58270219C>A	uc002iyo.1	-	c.3507G>T	c.(3505-3507)TGG>TGT	p.W1169C	USP32_uc002iyn.1_Missense_Mutation_p.W839C	NM_032582	NP_115971	Q8NFA0	UBP32_HUMAN	ubiquitin specific protease 32	1169					protein deubiquitination|ubiquitin-dependent protein catabolic process	Golgi apparatus|membrane	calcium ion binding|cysteine-type peptidase activity|ubiquitin thiolesterase activity			large_intestine(1)	1	all_neural(34;0.0878)|Medulloblastoma(34;0.0922)		Epithelial(12;2.02e-11)|all cancers(12;5.23e-10)|Colorectal(3;0.198)											0.35545	227.975518	231.855616	75	136	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	58270219	58270219	17627	17	C	A	A	A	234	18	USP32	2	2
PPM1D	8493	broad.mit.edu	37	17	58678173	58678173	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:58678173C>T	uc002iyt.1	+	c.398C>T	c.(397-399)TCC>TTC	p.S133F	PPM1D_uc010ddm.1_Non-coding_Transcript	NM_003620	NP_003611	O15297	PPM1D_HUMAN	protein phosphatase 1D	133	PP2C-like.				negative regulation of cell proliferation|protein dephosphorylation|response to radiation	nucleus|protein serine/threonine phosphatase complex	metal ion binding|protein binding|protein serine/threonine phosphatase activity				0	all_neural(34;0.0878)|Medulloblastoma(34;0.0922)		Epithelial(12;6.75e-12)|all cancers(12;1.96e-10)											0.309735	89.997496	93.636063	35	78	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	58678173	58678173	12772	17	C	T	T	T	390	30	PPM1D	2	2
TBX2	6909	broad.mit.edu	37	17	59479175	59479175	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:59479175G>T	uc010wox.1	+	c.526G>T	c.(526-528)GGC>TGC	p.G176C	TBX2_uc002ize.2_Missense_Mutation_p.G166C|TBX2_uc002izg.2_Missense_Mutation_p.G22C	NM_005994	NP_005985	Q13207	TBX2_HUMAN	T-box 2	176	T-box.			AGKA -> TDKT (in Ref. 4; AAB36216).	cell aging|positive regulation of cell proliferation		sequence-specific DNA binding|transcription repressor activity				0						GBM(3;187 253 11467 14965 23079)								0.363636	20.69231	21.052843	8	14	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	59479175	59479175	16181	17	G	T	T	T	559	43	TBX2	2	2
MAP3K3	4215	broad.mit.edu	37	17	61768535	61768535	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:61768535G>T	uc002jbe.2	+	c.1379G>T	c.(1378-1380)GGC>GTC	p.G460V	MAP3K3_uc002jbf.2_Missense_Mutation_p.G460V|MAP3K3_uc002jbg.2_Missense_Mutation_p.G429V|MAP3K3_uc002jbh.2_Missense_Mutation_p.G456V|MAP3K3_uc010wpo.1_Missense_Mutation_p.G344V|MAP3K3_uc010wpp.1_Missense_Mutation_p.G425V	NM_203351	NP_976226	Q99759	M3K3_HUMAN	mitogen-activated protein kinase kinase kinase 3	429	Protein kinase.				MAPKKK cascade|positive regulation of I-kappaB kinase/NF-kappaB cascade|protein autophosphorylation	cytosol	ATP binding|MAP kinase kinase kinase activity|metal ion binding|protein binding			lung(3)|large_intestine(1)	4										183				0.482759	123.243195	123.265727	42	45	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	61768535	61768535	9634	17	G	T	T	T	546	42	MAP3K3	2	2
ERN1	2081	broad.mit.edu	37	17	62135165	62135165	+	Silent	SNP	G	A	A			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:62135165G>A	uc002jdz.2	-	c.1395C>T	c.(1393-1395)CCC>CCT	p.P465P		NM_001433	NP_001424	O75460	ERN1_HUMAN	endoplasmic reticulum to nucleus signalling 1	465	Cytoplasmic (Potential).				activation of signaling protein activity involved in unfolded protein response|apoptosis|cell cycle arrest|induction of apoptosis|mRNA processing|regulation of transcription, DNA-dependent|transcription, DNA-dependent	integral to endoplasmic reticulum membrane	ATP binding|endoribonuclease activity, producing 5'-phosphomonoesters|magnesium ion binding|protein binding|protein serine/threonine kinase activity			central_nervous_system(4)|lung(2)|stomach(1)|ovary(1)|kidney(1)	9										295				0.125	13.074882	25.157678	11	77	KEEP	---	---	---	---	capture		Silent	SNP	62135165	62135165	5430	17	G	A	A	A	548	43	ERN1	2	2
CCDC46	201134	broad.mit.edu	37	17	63746823	63746823	+	Missense_Mutation	SNP	T	A	A			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:63746823T>A	uc002jfl.2	-	c.2414A>T	c.(2413-2415)CAG>CTG	p.Q805L	CCDC46_uc010deo.2_Intron|CCDC46_uc002jfm.2_Missense_Mutation_p.Q805L|CCDC46_uc010dep.2_Missense_Mutation_p.Q763L|CCDC46_uc002jfk.2_Missense_Mutation_p.Q61L	NM_145036	NP_659473	Q8N8E3	CCD46_HUMAN	coiled-coil domain containing 46 isoform a	805	Potential.										0			BRCA - Breast invasive adenocarcinoma(6;1.53e-06)											0.300532	328.42456	341.791957	113	263	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	63746823	63746823	2940	17	T	A	A	A	715	55	CCDC46	3	3
TP53	7157	broad.mit.edu	37	17	7577531	7577532	+	Missense_Mutation	DNP	GG	AA	AA			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:7577531_7577532GG>AA	uc002gim.2	-	c.749_750CC>TT	c.(748-750)CCC>CTT	p.P250L	TP53_uc002gig.1_Missense_Mutation_p.P250L|TP53_uc002gih.2_Missense_Mutation_p.P250L|TP53_uc010cne.1_5'Flank|TP53_uc010cnf.1_Missense_Mutation_p.P118L|TP53_uc010cng.1_Missense_Mutation_p.P118L|TP53_uc002gii.1_Missense_Mutation_p.P118L|TP53_uc010cnh.1_Missense_Mutation_p.P250L|TP53_uc010cni.1_Missense_Mutation_p.P250L|TP53_uc002gij.2_Missense_Mutation_p.P250L|TP53_uc010cnj.1_Non-coding_Transcript|TP53_uc002gin.2_Missense_Mutation_p.P157L|TP53_uc002gio.2_Missense_Mutation_p.P118L	NM_001126112	NP_001119584	P04637	P53_HUMAN	tumor protein p53 isoform a	250	|Interaction with HIPK1 (By similarity).|Interaction with AXIN1 (By similarity).		P -> L (in sporadic cancers; somatic mutation).|RP -> SA (in a sporadic cancer; somatic mutation).|P -> F (in sporadic cancers; somatic mutation; requires 2 nucleotide substitutions).|RP -> SS (in sporadic cancers; somatic mutation).|P -> T (in sporadic cancers; somatic mutation).|P -> Q (in sporadic cancers; somatic mutation).|P -> A (in sporadic cancers; somatic mutation).|P -> S (in sporadic cancers; somatic mutation).|P -> N (in sporadic cancers; somatic mutation; requires 2 nucleotide substitutions).|P -> H (in sporadic cancers; somatic mutation).		activation of caspase activity by cytochrome c|base-excision repair|blood coagulation|cell cycle arrest|cell differentiation|cell proliferation|cellular protein localization|cellular response to drug|cellular response to glucose starvation|cellular response to hypoxia|cellular response to ionizing radiation|cellular response to UV|determination of adult lifespan|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator|ER overload response|interspecies interaction between organisms|negative regulation of apoptosis|negative regulation of cell growth|negative regulation of cell proliferation|negative regulation of gene-specific transcription from RNA polymerase II promoter|negative regulation of helicase activity|negative regulation of transcription from RNA polymerase II promoter|nucleotide-excision repair|oxidative stress-induced premature senescence|positive regulation of gene-specific transcription from RNA polymerase II promoter|positive regulation of histone deacetylation|positive regulation of neuron apoptosis|positive regulation of peptidyl-tyrosine phosphorylation|positive regulation of reactive oxygen species metabolic process|positive regulation of thymocyte apoptosis|positive regulation of transcription from RNA polymerase II promoter|protein localization|protein tetramerization|Ras protein signal transduction|regulation of mitochondrial membrane permeability|replicative senescence|response to antibiotic|response to gamma radiation|response to X-ray	chromatin|cytoplasm|cytosol|endoplasmic reticulum|insoluble fraction|mitochondrion|nuclear matrix|nucleolus|nucleus|PML body|protein complex|replication fork	ATP binding|chaperone binding|chromatin binding|copper ion binding|damaged DNA binding|DNA strand annealing activity|histone acetyltransferase binding|p53 binding|promoter binding|promoter binding|protease binding|protein heterodimerization activity|protein kinase binding|protein N-terminus binding|protein phosphatase 2A binding|sequence-specific DNA binding transcription factor activity|specific transcriptional repressor activity|transcription activator activity|transcription factor binding|ubiquitin protein ligase binding|zinc ion binding	p.P250L(37)|p.0?(6)|p.P250P(4)|p.P250F(3)|p.P250N(2)|p.M246_P250delMNRRP(2)|p.P250_L252delPIL(2)|p.P250Q(2)|p.N247_P250delNRRP(1)|p.R248_P250delRRP(1)|p.P250H(1)|p.P250_T253delPILT(1)|p.P250_I251insXXXXXX(1)|p.P250_I251insXXXXXXX(1)|p.R249_P250delRP(1)|p.P250_I251insX(1)|p.I251fs*96(1)|p.R249_T256delRPILTIIT(1)|p.I251fs*94(1)|p.R249_I251delRPI(1)|p.I251fs*13(1)		large_intestine(4614)|breast(2344)|upper_aerodigestive_tract(2150)|lung(1958)|ovary(1559)|oesophagus(1462)|haematopoietic_and_lymphoid_tissue(1212)|stomach(1127)|urinary_tract(1113)|central_nervous_system(1072)|liver(805)|skin(693)|pancreas(370)|biliary_tract(247)|soft_tissue(209)|prostate(192)|endometrium(150)|bone(102)|vulva(79)|kidney(79)|cervix(68)|thyroid(54)|salivary_gland(41)|adrenal_gland(37)|peritoneum(33)|eye(24)|thymus(21)|genital_tract(16)|autonomic_ganglia(16)|small_intestine(14)|testis(11)|penis(10)|vagina(6)|meninges(5)|pituitary(4)|pleura(3)|gastrointestinal_tract_(site_indeterminate)(1)|NS(1)|Fallopian tube(1)|placenta(1)	21904		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)		Pancreas(47;798 1329 9957 10801)		111	p.P250L(HT1376-Tumor)	690	TCGA GBM(1;<1E-8)|TSP Lung(2;<1E-8)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)			0.857143	581.229331	607.165539	180	30	KEEP	---	---	---	---	capture		Missense_Mutation	DNP	7577531	7577532	16923	17	GG	AA	AA	AA	600	47	TP53	2	2
USP36	57602	broad.mit.edu	37	17	76802278	76802278	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:76802278G>A	uc002jvz.1	-	c.2176C>T	c.(2176-2178)CAC>TAC	p.H726Y	USP36_uc002jwa.1_Missense_Mutation_p.H726Y|USP36_uc002jwb.1_Missense_Mutation_p.H363Y|USP36_uc002jwc.1_Missense_Mutation_p.H426Y	NM_025090	NP_079366	Q9P275	UBP36_HUMAN	ubiquitin specific peptidase 36	726					ubiquitin-dependent protein catabolic process	nucleolus	cysteine-type peptidase activity|ubiquitin thiolesterase activity			ovary(1)|kidney(1)	2			BRCA - Breast invasive adenocarcinoma(99;0.000842)|OV - Ovarian serous cystadenocarcinoma(97;0.151)											0.380952	104.324553	105.645641	40	65	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	76802278	76802278	17631	17	G	A	A	A	585	45	USP36	2	2
RNF213	57674	broad.mit.edu	37	17	78320202	78320202	+	Silent	SNP	C	T	T			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:78320202C>T	uc002jyh.1	+	c.2286C>T	c.(2284-2286)ATC>ATT	p.I762I		NM_020914	NP_065965	Q9HCF4	ALO17_HUMAN	ring finger protein 213	Error:Variant_position_missing_in_Q9HCF4_after_alignment										ovary(8)|large_intestine(2)|central_nervous_system(1)|pancreas(1)	12	all_neural(118;0.0538)		BRCA - Breast invasive adenocarcinoma(99;0.0252)|OV - Ovarian serous cystadenocarcinoma(97;0.057)											0.280899	64.314058	68.172671	25	64	KEEP	---	---	---	---	capture		Silent	SNP	78320202	78320202	13955	17	C	T	T	T	395	31	RNF213	1	1
MYH10	4628	broad.mit.edu	37	17	8393742	8393742	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:8393742C>A	uc002glm.2	-	c.4800G>T	c.(4798-4800)ATG>ATT	p.M1600I	MYH10_uc002gll.2_Missense_Mutation_p.M1569I|MYH10_uc010cnx.2_Missense_Mutation_p.M1578I	NM_005964	NP_005955	P35580	MYH10_HUMAN	myosin, heavy polypeptide 10, non-muscle	1569	Potential.				actin filament-based movement|axon guidance|cytokinesis after mitosis|regulation of cell shape	cell cortex|cleavage furrow|midbody|myosin complex|stress fiber	actin filament binding|actin-dependent ATPase activity|ADP binding|ATP binding|calmodulin binding|microfilament motor activity			ovary(2)	2										971				0.437299	398.677062	399.753583	136	175	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	8393742	8393742	10425	17	C	A	A	A	325	25	MYH10	2	2
RIT2	6014	broad.mit.edu	37	18	40554090	40554090	+	Silent	SNP	G	C	C			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr18:40554090G>C	uc002lav.2	-	c.183C>G	c.(181-183)GTC>GTG	p.V61V	RIT2_uc010dnf.2_Silent_p.V61V	NM_002930	NP_002921	Q99578	RIT2_HUMAN	Ras-like without CAAX 2	61					nerve growth factor receptor signaling pathway|small GTPase mediated signal transduction|synaptic transmission	intracellular|plasma membrane	calmodulin binding|GTP binding|GTPase activity			ovary(1)	1														0.431034	93.672387	93.911705	25	33	KEEP	---	---	---	---	capture		Silent	SNP	40554090	40554090	13864	18	G	C	C	C	574	45	RIT2	3	3
SETBP1	26040	broad.mit.edu	37	18	42529998	42529998	+	Silent	SNP	C	A	A			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr18:42529998C>A	uc010dni.2	+	c.693C>A	c.(691-693)GTC>GTA	p.V231V		NM_015559	NP_056374	Q9Y6X0	SETBP_HUMAN	SET binding protein 1 isoform a	231						nucleus	DNA binding			large_intestine(1)	1				Colorectal(1;0.0622)|COAD - Colon adenocarcinoma(74;0.201)										0.486957	332.472349	332.506526	112	118	KEEP	---	---	---	---	capture		Silent	SNP	42529998	42529998	14617	18	C	A	A	A	366	29	SETBP1	2	2
RTTN	25914	broad.mit.edu	37	18	67794780	67794780	+	Missense_Mutation	SNP	C	G	G			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr18:67794780C>G	uc002lkp.2	-	c.3341G>C	c.(3340-3342)GGG>GCG	p.G1114A	RTTN_uc002lko.2_Non-coding_Transcript|RTTN_uc010xfb.1_Missense_Mutation_p.G202A	NM_173630	NP_775901	Q86VV8	RTTN_HUMAN	rotatin	1114							binding			ovary(3)|pancreas(2)|breast(1)|central_nervous_system(1)	7		Esophageal squamous(42;0.129)												0.562092	285.457117	285.996475	86	67	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	67794780	67794780	14217	18	C	G	G	G	286	22	RTTN	3	3
NETO1	81832	broad.mit.edu	37	18	70461478	70461478	+	Silent	SNP	C	T	T			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr18:70461478C>T	uc002lkw.2	-	c.513G>A	c.(511-513)GCG>GCA	p.A171A	NETO1_uc002lkx.1_Silent_p.A170A|NETO1_uc002lky.1_Silent_p.A171A	NM_138966	NP_620416	Q8TDF5	NETO1_HUMAN	neuropilin- and tolloid-like protein 1 isoform 3	171	Extracellular (Potential).				memory|regulation of long-term neuronal synaptic plasticity|visual learning	cell junction|excitatory synapse|extracellular region|integral to membrane|postsynaptic density|postsynaptic membrane	receptor activity			ovary(2)	2		Esophageal squamous(42;0.129)		READ - Rectum adenocarcinoma(1;0.0487)										0.336634	92.990554	95.388976	34	67	KEEP	---	---	---	---	capture		Silent	SNP	70461478	70461478	10738	18	C	T	T	T	236	19	NETO1	1	1
LDLR	3949	broad.mit.edu	37	19	11213428	11213428	+	Silent	SNP	G	A	A			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:11213428G>A	uc002mqk.3	+	c.279G>A	c.(277-279)GTG>GTA	p.V93V	LDLR_uc010xlk.1_Silent_p.V93V|LDLR_uc010xll.1_Intron|LDLR_uc010xlm.1_Intron|LDLR_uc010xln.1_Silent_p.V93V|LDLR_uc010xlo.1_Silent_p.V93V	NM_000527	NP_000518	P01130	LDLR_HUMAN	low density lipoprotein receptor precursor	93	Extracellular (Potential).|LDL-receptor class A 2.				cholesterol homeostasis|cholesterol metabolic process|interspecies interaction between organisms|intestinal cholesterol absorption|low-density lipoprotein particle clearance|receptor-mediated endocytosis	clathrin-coated endocytic vesicle membrane|coated pit|early endosome|endosome membrane|external side of plasma membrane|integral to plasma membrane|low-density lipoprotein particle|lysosome	calcium ion binding|low-density lipoprotein receptor activity|protein binding|very-low-density lipoprotein particle receptor activity			ovary(2)	2		Lung NSC(9;0.000245)|Renal(1328;0.0007)|Hepatocellular(1079;0.0524)		GBM - Glioblastoma multiforme(1328;1.36e-05)|STAD - Stomach adenocarcinoma(1328;0.000766)|Lung(535;0.197)	Methyl aminolevulinate(DB00992)|Porfimer(DB00707)	GBM(18;201 575 7820 21545)				1109				0.482927	304.355445	304.409491	99	106	KEEP	---	---	---	---	capture		Silent	SNP	11213428	11213428	9028	19	G	A	A	A	600	47	LDLR	2	2
LOC55908	55908	broad.mit.edu	37	19	11350393	11350393	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:11350393C>A	uc010dxx.2	+	c.239C>A	c.(238-240)CCA>CAA	p.P80Q	DOCK6_uc010xlq.1_5'Flank|DOCK6_uc002mqs.3_Intron|LOC55908_uc010dxw.2_Intron	NM_018687	NP_061157	Q6UXH0	TD26_HUMAN	hepatocellular carcinoma-associated gene TD26	27						extracellular region					0														0.590909	195.682582	196.483981	65	45	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	11350393	11350393	9237	19	C	A	A	A	273	21	LOC55908	2	2
CCDC151	115948	broad.mit.edu	37	19	11541544	11541545	+	Missense_Mutation	DNP	GG	TC	TC			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:11541544_11541545GG>TC	uc002mrs.2	-	c.418_419CC>GA	c.(418-420)CCA>GAA	p.P140E	CCDC151_uc002mrr.2_Missense_Mutation_p.P75E|CCDC151_uc010dxz.2_Intron	NM_145045	NP_659482	A5D8V7	CC151_HUMAN	coiled-coil domain containing 151	140	Potential.									ovary(1)	1														0.481982	329.713531	329.77608	107	115	KEEP	---	---	---	---	capture		Missense_Mutation	DNP	11541544	11541545	2906	19	GG	TC	TC	TC	611	47	CCDC151	2	2
RFX1	5989	broad.mit.edu	37	19	14080874	14080874	+	Silent	SNP	G	A	A			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:14080874G>A	uc002mxv.2	-	c.1428C>T	c.(1426-1428)AAC>AAT	p.N476N	RFX1_uc010dzi.2_Silent_p.N476N	NM_002918	NP_002909	P22670	RFX1_HUMAN	regulatory factor X1	476	RFX-type winged-helix.				immune response|regulation of transcription, DNA-dependent	nucleus	DNA binding|protein binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|transcription regulator activity			lung(1)|pancreas(1)	2			OV - Ovarian serous cystadenocarcinoma(19;6.67e-23)											0.428571	59.35714	59.576354	21	28	KEEP	---	---	---	---	capture		Silent	SNP	14080874	14080874	13734	19	G	A	A	A	516	40	RFX1	1	1
CALR3	125972	broad.mit.edu	37	19	16593367	16593367	+	Missense_Mutation	SNP	T	A	A			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:16593367T>A	uc002ned.2	-	c.812A>T	c.(811-813)CAT>CTT	p.H271L	MED26_uc002nee.2_Non-coding_Transcript	NM_145046	NP_659483	Q96L12	CALR3_HUMAN	calreticulin 3 precursor	271	3 X approximate repeats.|P-domain.|2-2.				protein folding	endoplasmic reticulum lumen	calcium ion binding|sugar binding|unfolded protein binding				0														0.42446	191.020851	191.708136	59	80	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	16593367	16593367	2710	19	T	A	A	A	663	51	CALR3	3	3
NWD1	284434	broad.mit.edu	37	19	16870093	16870093	+	Silent	SNP	G	T	T			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:16870093G>T	uc002net.3	+	c.1422G>T	c.(1420-1422)CTG>CTT	p.L474L	NWD1_uc002neu.3_Silent_p.L609L|NWD1_uc002nev.3_Silent_p.L403L	NM_001007525	NP_001007526	Q149M9	NWD1_HUMAN	NACHT and WD repeat domain containing 1	609	NACHT.						ATP binding			ovary(2)|pancreas(2)	4														0.403846	246.257884	247.938602	84	124	KEEP	---	---	---	---	capture		Silent	SNP	16870093	16870093	11186	19	G	T	T	T	587	46	NWD1	2	2
FAM125A	93343	broad.mit.edu	37	19	17533201	17533201	+	Missense_Mutation	SNP	A	T	T			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:17533201A>T	uc002ngo.1	+	c.347A>T	c.(346-348)GAC>GTC	p.D116V	FAM125A_uc002ngp.1_Missense_Mutation_p.D24V|FAM125A_uc002ngq.1_Missense_Mutation_p.D12V	NM_138401	NP_612410	Q96EY5	F125A_HUMAN	family with sequence similarity 125, member A	116	MABP.				protein transport	late endosome membrane|microtubule organizing center|nucleus	SH3 domain binding				0														0.471429	95.464139	95.514103	33	37	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	17533201	17533201	5624	19	A	T	T	T	130	10	FAM125A	3	3
GLT25D1	79709	broad.mit.edu	37	19	17691563	17691563	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:17691563G>T	uc002nhc.1	+	c.1450G>T	c.(1450-1452)GTG>TTG	p.V484L	GLT25D1_uc010eax.1_Missense_Mutation_p.V212L|GLT25D1_uc010eay.1_Missense_Mutation_p.V13L	NM_024656	NP_078932	Q8NBJ5	GT251_HUMAN	glycosyltransferase 25 domain containing 1	484					lipopolysaccharide biosynthetic process	endoplasmic reticulum lumen	procollagen galactosyltransferase activity				0														0.522989	294.117292	294.216447	91	83	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	17691563	17691563	6734	19	G	T	T	T	520	40	GLT25D1	1	1
JAK3	3718	broad.mit.edu	37	19	17945771	17945771	+	Silent	SNP	G	T	T			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:17945771G>T	uc002nhn.3	-	c.2089C>A	c.(2089-2091)CGG>AGG	p.R697R	JAK3_uc010ebh.2_Intron|JAK3_uc002nho.2_Silent_p.R697R	NM_000215	NP_000206	P52333	JAK3_HUMAN	Janus kinase 3	697	Protein kinase 1.				B cell differentiation|cytokine-mediated signaling pathway|enzyme linked receptor protein signaling pathway|intracellular protein kinase cascade|negative regulation of dendritic cell cytokine production|negative regulation of FasL biosynthetic process|negative regulation of interleukin-10 production|negative regulation of interleukin-12 production|negative regulation of T-helper 1 cell differentiation|negative regulation of thymocyte apoptosis|peptidyl-tyrosine phosphorylation|positive regulation of anti-apoptosis|response to interleukin-15|response to interleukin-2|response to interleukin-4|response to interleukin-9|T cell homeostasis	cytoskeleton|cytosol|endomembrane system|membrane	ATP binding|non-membrane spanning protein tyrosine kinase activity|protein binding			haematopoietic_and_lymphoid_tissue(36)|lung(3)|ovary(3)|stomach(2)|breast(2)	46								2		364				0.462185	342.827134	343.121479	110	128	KEEP	---	---	---	---	capture		Silent	SNP	17945771	17945771	8243	19	G	T	T	T	506	39	JAK3	1	1
ADAT3	113179	broad.mit.edu	37	19	1913034	1913034	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:1913034G>T	uc002luh.2	+	c.940G>T	c.(940-942)GAC>TAC	p.D314Y	SCAMP4_uc002lui.1_Intron|SCAMP4_uc002luj.2_Intron|SCAMP4_uc002luk.2_Intron|SCAMP4_uc010dss.2_Intron	NM_138422	NP_612431	Q96EY9	ADAT3_HUMAN	tRNA-specific adenosine deaminase 3	314					tRNA processing		hydrolase activity|zinc ion binding			breast(1)	1		Ovarian(11;2.11e-07)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)										0.225806	11.729759	13.859778	7	24	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	1913034	1913034	287	19	G	T	T	T	481	37	ADAT3	1	1
NCAN	1463	broad.mit.edu	37	19	19344697	19344697	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:19344697G>T	uc002nlz.2	+	c.3119G>T	c.(3118-3120)GGG>GTG	p.G1040V	NCAN_uc010ecc.1_Missense_Mutation_p.G604V	NM_004386	NP_004377	O14594	NCAN_HUMAN	chondroitin sulfate proteoglycan 3 precursor	1040	EGF-like 1.				axon guidance|cell adhesion	extracellular region	calcium ion binding|hyaluronic acid binding|sugar binding			ovary(4)	4			Epithelial(12;0.00544)											0.362694	202.191174	205.394919	70	123	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	19344697	19344697	10603	19	G	T	T	T	559	43	NCAN	2	2
ZNF208	7757	broad.mit.edu	37	19	22155984	22155984	+	Missense_Mutation	SNP	A	G	G			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:22155984A>G	uc002nqp.2	-	c.1552T>C	c.(1552-1554)TTT>CTT	p.F518L	ZNF208_uc002nqo.1_Intron	NM_007153	NP_009084			zinc finger protein 208											ovary(5)	5		all_lung(12;0.0961)|Lung NSC(12;0.103)												0.45	347.008868	347.486632	99	121	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	22155984	22155984	18357	19	A	G	G	G	39	3	ZNF208	4	4
ZNF536	9745	broad.mit.edu	37	19	30935852	30935852	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:30935852G>T	uc002nsu.1	+	c.1383G>T	c.(1381-1383)AAG>AAT	p.K461N	ZNF536_uc010edd.1_Missense_Mutation_p.K461N	NM_014717	NP_055532	O15090	ZN536_HUMAN	zinc finger protein 536	461					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	zinc ion binding			ovary(7)|large_intestine(2)	9	Esophageal squamous(110;0.0834)													0.598214	207.934521	208.87871	67	45	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	30935852	30935852	18568	19	G	T	T	T	451	35	ZNF536	2	2
TSHZ3	57616	broad.mit.edu	37	19	31768280	31768280	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:31768280G>T	uc002nsy.3	-	c.2419C>A	c.(2419-2421)CTT>ATT	p.L807I		NM_020856	NP_065907	Q63HK5	TSH3_HUMAN	zinc finger protein 537	807					regulation of respiratory gaseous exchange by neurological system process|regulation of transcription, DNA-dependent	growth cone|nucleus	chromatin binding|protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription repressor activity|zinc ion binding			ovary(4)|pancreas(1)|lung(1)|skin(1)	7	Esophageal squamous(110;0.226)													0.476636	146.830522	146.885736	51	56	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	31768280	31768280	17176	19	G	T	T	T	442	34	TSHZ3	2	2
ZNF527	84503	broad.mit.edu	37	19	37879596	37879596	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:37879596G>T	uc010efk.1	+	c.645G>T	c.(643-645)GAG>GAT	p.E215D	ZNF527_uc002ogf.3_Missense_Mutation_p.E183D|ZNF527_uc010xtq.1_Non-coding_Transcript	NM_032453	NP_115829	Q8NB42	ZN527_HUMAN	zinc finger protein 527	215					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(2)	2			COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)											0.324503	134.020591	138.149114	49	102	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	37879596	37879596	18562	19	G	T	T	T	425	33	ZNF527	2	2
RYR1	6261	broad.mit.edu	37	19	39037100	39037100	+	Nonsense_Mutation	SNP	G	T	T			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:39037100G>T	uc002oit.2	+	c.12028G>T	c.(12028-12030)GAG>TAG	p.E4010*	RYR1_uc002oiu.2_Nonsense_Mutation_p.E4005*|RYR1_uc002oiv.1_Nonsense_Mutation_p.E919*	NM_000540	NP_000531	P21817	RYR1_HUMAN	skeletal muscle ryanodine receptor isoform 1	4010					muscle contraction|release of sequestered calcium ion into cytosol|response to caffeine|response to hypoxia	cell cortex|I band|integral to plasma membrane|junctional sarcoplasmic reticulum membrane|smooth endoplasmic reticulum|terminal cisterna	calcium ion binding|calmodulin binding|receptor activity|ryanodine-sensitive calcium-release channel activity			ovary(7)|pancreas(2)|breast(1)	10	all_cancers(60;7.91e-06)		Lung(45;0.00172)|LUSC - Lung squamous cell carcinoma(53;0.00272)		Dantrolene(DB01219)									0.39726	89.863727	90.536491	29	44	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	39037100	39037100	14248	19	G	T	T	T	481	37	RYR1	5	1
PRX	57716	broad.mit.edu	37	19	40902381	40902381	+	Silent	SNP	G	T	T			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:40902381G>T	uc002onr.2	-	c.1878C>A	c.(1876-1878)GTC>GTA	p.V626V	PRX_uc002onq.2_Silent_p.V487V|PRX_uc002ons.2_3'UTR	NM_181882	NP_870998	Q9BXM0	PRAX_HUMAN	periaxin isoform 2	626	31.|55 X 5 AA approximate tandem repeats of [LVMAG]-[PSREQC]-[EDKL]-[LIVMAP]- [AQKHRPE]; that may have a tripeptide spacer of [LV]-P-[KER].				axon ensheathment	cytoplasm|nucleus|plasma membrane	protein binding			ovary(2)	2			Lung(22;6.24e-05)|LUSC - Lung squamous cell carcinoma(20;0.000384)											0.477064	731.293153	731.545706	260	285	KEEP	---	---	---	---	capture		Silent	SNP	40902381	40902381	13093	19	G	T	T	T	522	41	PRX	2	2
SPTBN4	57731	broad.mit.edu	37	19	40996038	40996038	+	Silent	SNP	G	T	T			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:40996038G>T	uc002ony.2	+	c.378G>T	c.(376-378)GCG>GCT	p.A126A	SPTBN4_uc002onx.2_Silent_p.A126A|SPTBN4_uc002onz.2_Silent_p.A126A	NM_020971	NP_066022	Q9H254	SPTN4_HUMAN	spectrin, beta, non-erythrocytic 4 isoform	126	CH 1.|Actin-binding.				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)											0.384	145.162368	146.638798	48	77	KEEP	---	---	---	---	capture		Silent	SNP	40996038	40996038	15635	19	G	T	T	T	483	38	SPTBN4	1	1
ANKRD24	170961	broad.mit.edu	37	19	4210294	4210294	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:4210294G>T	uc010dtt.1	+	c.984G>T	c.(982-984)AGG>AGT	p.R328S	ANKRD24_uc002lzs.2_Missense_Mutation_p.R299S|ANKRD24_uc002lzt.2_Missense_Mutation_p.R300S	NM_133475	NP_597732	Q8TF21	ANR24_HUMAN	ankyrin repeat domain 24	328	Potential.										0				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0233)|STAD - Stomach adenocarcinoma(1328;0.181)										0.424242	40.476365	40.633293	14	19	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	4210294	4210294	658	19	G	T	T	T	542	42	ANKRD24	2	2
ANKRD24	170961	broad.mit.edu	37	19	4218088	4218088	+	Silent	SNP	C	T	T			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:4218088C>T	uc010dtt.1	+	c.2931C>T	c.(2929-2931)AAC>AAT	p.N977N	ANKRD24_uc002lzs.2_Silent_p.N948N|ANKRD24_uc002lzt.2_Silent_p.N949N	NM_133475	NP_597732	Q8TF21	ANR24_HUMAN	ankyrin repeat domain 24	977	Potential.										0				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0233)|STAD - Stomach adenocarcinoma(1328;0.181)										0.333333	14.27107	14.639544	5	10	KEEP	---	---	---	---	capture		Silent	SNP	4218088	4218088	658	19	C	T	T	T	246	19	ANKRD24	1	1
PSG11	5680	broad.mit.edu	37	19	43519365	43519365	+	Silent	SNP	A	T	T			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:43519365A>T	uc002ovn.1	-	c.885T>A	c.(883-885)CCT>CCA	p.P295P	PSG11_uc002ouw.2_Intron|PSG10_uc002ouv.1_Intron|PSG6_uc002ovh.1_Intron|PSG6_uc002ovi.2_Intron|PSG6_uc010xwk.1_Intron|PSG11_uc002ovk.1_Intron|PSG11_uc002ovm.1_Silent_p.P289P|PSG11_uc002ovo.1_Silent_p.P167P|PSG11_uc002ovp.1_Silent_p.P167P	NM_002785	NP_002776	Q9UQ72	PSG11_HUMAN	pregnancy specific beta-1-glycoprotein 11	289	Ig-like C2-type 2.				female pregnancy	extracellular region					0		Prostate(69;0.00682)												0.277143	242.919482	258.570523	97	253	KEEP	---	---	---	---	capture		Silent	SNP	43519365	43519365	13107	19	A	T	T	T	132	11	PSG11	3	3
CD177	57126	broad.mit.edu	37	19	43859867	43859867	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:43859867G>T	uc002owi.2	+	c.434G>T	c.(433-435)GGG>GTG	p.G145V	CD177_uc010eis.2_Non-coding_Transcript|CD177_uc002owj.2_Non-coding_Transcript	NM_020406	NP_065139	Q8N6Q3	CD177_HUMAN	CD177 molecule precursor	145	UPAR/Ly6 1.				blood coagulation|leukocyte migration	anchored to membrane|plasma membrane					0		Prostate(69;0.00682)												0.45	177.207801	177.510549	63	77	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	43859867	43859867	3098	19	G	T	T	T	559	43	CD177	2	2
RSPH6A	81492	broad.mit.edu	37	19	46318261	46318261	+	Silent	SNP	T	A	A			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:46318261T>A	uc002pdm.2	-	c.174A>T	c.(172-174)TCA>TCT	p.S58S		NM_030785	NP_110412	Q9H0K4	RSH6A_HUMAN	radial spokehead-like 1	58						intracellular				ovary(1)|central_nervous_system(1)	2														0.454545	75.370327	75.468806	25	30	KEEP	---	---	---	---	capture		Silent	SNP	46318261	46318261	14187	19	T	A	A	A	756	59	RSPH6A	3	3
SYMPK	8189	broad.mit.edu	37	19	46345509	46345509	+	Silent	SNP	C	A	A			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:46345509C>A	uc002pdn.2	-	c.1086G>T	c.(1084-1086)CTG>CTT	p.L362L	SYMPK_uc002pdo.1_Silent_p.L362L|SYMPK_uc002pdp.1_Silent_p.L362L|SYMPK_uc002pdq.1_Silent_p.L362L	NM_004819	NP_004810	Q92797	SYMPK_HUMAN	symplekin	362					cell adhesion|mRNA processing	cytoplasm|cytoskeleton|nucleoplasm|tight junction	protein binding			ovary(1)	1		all_neural(266;0.0299)|Ovarian(192;0.0308)		OV - Ovarian serous cystadenocarcinoma(262;0.00509)|GBM - Glioblastoma multiforme(486;0.0593)										0.5	346.564074	346.564074	112	112	KEEP	---	---	---	---	capture		Silent	SNP	46345509	46345509	15960	19	C	A	A	A	262	21	SYMPK	2	2
NOVA2	4858	broad.mit.edu	37	19	46443836	46443836	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:46443836G>T	uc002pdv.2	-	c.764C>A	c.(763-765)CCC>CAC	p.P255H		NM_002516	NP_002507	Q9UNW9	NOVA2_HUMAN	neuro-oncological ventral antigen 2	255	Ala-rich.					nucleus	RNA binding				0		all_neural(266;0.113)|Ovarian(192;0.127)		OV - Ovarian serous cystadenocarcinoma(262;0.00245)|GBM - Glioblastoma multiforme(486;0.0782)|Epithelial(262;0.179)										0.4	6.349024	6.392753	2	3	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	46443836	46443836	10959	19	G	T	T	T	559	43	NOVA2	2	2
HIF3A	64344	broad.mit.edu	37	19	46834463	46834463	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:46834463G>T	uc002peh.2	+	c.1763G>T	c.(1762-1764)GGA>GTA	p.G588V	HIF3A_uc002peg.3_Missense_Mutation_p.G588V|HIF3A_uc002pei.3_Missense_Mutation_p.G532V|HIF3A_uc002pej.1_Intron|HIF3A_uc002pek.2_Missense_Mutation_p.G532V|HIF3A_uc010xxy.1_Missense_Mutation_p.G519V|HIF3A_uc002pel.2_Missense_Mutation_p.G586V|HIF3A_uc010xxz.1_Missense_Mutation_p.G537V	NM_152795	NP_690008	Q9Y2N7	HIF3A_HUMAN	hypoxia inducible factor 3, alpha subunit	588					regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	DNA binding|signal transducer activity|transcription regulator activity			central_nervous_system(1)|skin(1)	2		Ovarian(192;0.00965)|all_neural(266;0.0887)		OV - Ovarian serous cystadenocarcinoma(262;0.00204)|all cancers(93;0.0107)|GBM - Glioblastoma multiforme(486;0.0489)|Epithelial(262;0.136)										0.521739	241.835642	241.899819	84	77	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	46834463	46834463	7390	19	G	T	T	T	533	41	HIF3A	2	2
SLC8A2	6543	broad.mit.edu	37	19	47940789	47940789	+	Silent	SNP	C	G	G			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:47940789C>G	uc002pgx.2	-	c.2040G>C	c.(2038-2040)ACG>ACC	p.T680T	SLC8A2_uc010xyq.1_Silent_p.T436T|SLC8A2_uc010xyr.1_Silent_p.T143T|SLC8A2_uc010ele.2_Silent_p.T680T	NM_015063	NP_055878	Q9UPR5	NAC2_HUMAN	solute carrier family 8 member 2 precursor	680	Cytoplasmic (Potential).				cell communication|platelet activation	integral to membrane|plasma membrane	calcium:sodium antiporter activity|calmodulin binding			ovary(1)	1		all_cancers(25;3.05e-07)|all_lung(116;4.19e-06)|Lung NSC(112;7.16e-06)|all_epithelial(76;7.65e-06)|all_neural(266;0.0652)|Ovarian(192;0.086)|Breast(70;0.173)		OV - Ovarian serous cystadenocarcinoma(262;0.000501)|all cancers(93;0.00058)|Epithelial(262;0.0181)|GBM - Glioblastoma multiforme(486;0.0457)										0.435484	283.806433	284.468482	81	105	KEEP	---	---	---	---	capture		Silent	SNP	47940789	47940789	15204	19	C	G	G	G	392	31	SLC8A2	3	3
LIG1	3978	broad.mit.edu	37	19	48643258	48643258	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:48643258C>A	uc002pia.1	-	c.1057G>T	c.(1057-1059)GTC>TTC	p.V353F	LIG1_uc010xze.1_Missense_Mutation_p.V46F|LIG1_uc002phz.1_Non-coding_Transcript|LIG1_uc002pib.1_Non-coding_Transcript|LIG1_uc010xzf.1_Missense_Mutation_p.V285F|LIG1_uc010xzg.1_Missense_Mutation_p.V322F|LIG1_uc010xzh.1_Non-coding_Transcript	NM_000234	NP_000225	P18858	DNLI1_HUMAN	DNA ligase I	353					anatomical structure morphogenesis|base-excision repair|cell division|DNA ligation involved in DNA repair|DNA strand elongation involved in DNA replication|double-strand break repair via homologous recombination|nucleotide-excision repair, DNA gap filling|S phase of mitotic cell cycle|telomere maintenance via recombination|telomere maintenance via semi-conservative replication|transcription-coupled nucleotide-excision repair	nucleoplasm	ATP binding|DNA binding|DNA ligase (ATP) activity|metal ion binding			large_intestine(2)	2		all_epithelial(76;3.1e-06)|all_lung(116;4.39e-06)|Lung NSC(112;8.96e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)|Breast(70;0.203)		OV - Ovarian serous cystadenocarcinoma(262;8.45e-05)|all cancers(93;0.000423)|Epithelial(262;0.0177)|GBM - Glioblastoma multiforme(486;0.0329)	Bleomycin(DB00290)									0.521739	225.298903	225.355579	72	66	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	48643258	48643258	9107	19	C	A	A	A	221	17	LIG1	2	2
SIGLEC9	27180	broad.mit.edu	37	19	51628959	51628959	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:51628959C>T	uc010yct.1	+	c.527C>T	c.(526-528)CCT>CTT	p.P176L	SIGLEC9_uc002pvu.2_Missense_Mutation_p.P176L	NM_014441	NP_055256	Q9Y336	SIGL9_HUMAN	sialic acid binding Ig-like lectin 9 precursor	176	Extracellular (Potential).|Ig-like C2-type 1.				cell adhesion|cell surface receptor linked signaling pathway	integral to plasma membrane	sugar binding				0		all_neural(266;0.0529)		GBM - Glioblastoma multiforme(134;0.000826)|OV - Ovarian serous cystadenocarcinoma(262;0.00295)										0.501845	435.860578	435.861248	136	135	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	51628959	51628959	14810	19	C	T	T	T	312	24	SIGLEC9	2	2
SIGLEC10	89790	broad.mit.edu	37	19	51920674	51920674	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:51920674G>A	uc002pwo.2	-	c.83C>T	c.(82-84)TCA>TTA	p.S28L	SIGLEC10_uc002pwp.2_Missense_Mutation_p.S28L|SIGLEC10_uc002pwq.2_Missense_Mutation_p.S28L|SIGLEC10_uc002pwr.2_Missense_Mutation_p.S28L|SIGLEC10_uc010ycy.1_Missense_Mutation_p.S28L|SIGLEC10_uc010ycz.1_Missense_Mutation_p.S28L|SIGLEC10_uc010eow.2_Intron|SIGLEC10_uc002pws.1_Missense_Mutation_p.S12L	NM_033130	NP_149121	Q96LC7	SIG10_HUMAN	sialic acid binding Ig-like lectin 10 precursor	28	Extracellular (Potential).|Ig-like V-type.			S -> P (in Ref. 4; AAK51124).	cell adhesion	extracellular region|integral to membrane|plasma membrane	sugar binding				0		all_neural(266;0.0199)		GBM - Glioblastoma multiforme(134;0.000668)|OV - Ovarian serous cystadenocarcinoma(262;0.0101)										0.557447	384.313762	384.975066	131	104	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	51920674	51920674	14801	19	G	A	A	A	585	45	SIGLEC10	2	2
CACNG6	59285	broad.mit.edu	37	19	54502970	54502970	+	Silent	SNP	C	A	A			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:54502970C>A	uc002qct.2	+	c.489C>A	c.(487-489)CTC>CTA	p.L163L	CACNG6_uc002qcu.2_Intron|CACNG6_uc002qcv.2_Intron	NM_145814	NP_665813	Q9BXT2	CCG6_HUMAN	voltage-dependent calcium channel gamma-6	163	Helical; (Potential).					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)										0.350877	616.064693	628.384549	220	407	KEEP	---	---	---	---	capture		Silent	SNP	54502970	54502970	2677	19	C	A	A	A	366	29	CACNG6	2	2
FCAR	2204	broad.mit.edu	37	19	55399520	55399520	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:55399520C>A	uc002qhr.1	+	c.508C>A	c.(508-510)CAA>AAA	p.Q170K	FCAR_uc002qhq.2_Missense_Mutation_p.Q170K|FCAR_uc002qhs.1_Intron|FCAR_uc002qht.1_Missense_Mutation_p.Q143K|FCAR_uc010esi.1_Intron|FCAR_uc002qhu.1_Intron|FCAR_uc002qhv.1_Missense_Mutation_p.Q170K|FCAR_uc002qhw.1_Missense_Mutation_p.Q158K|FCAR_uc002qhx.1_Intron|FCAR_uc002qhy.1_Missense_Mutation_p.Q158K|FCAR_uc002qhz.1_Missense_Mutation_p.Q158K|FCAR_uc002qia.1_Missense_Mutation_p.Q61K	NM_002000	NP_001991	P24071	FCAR_HUMAN	Fc alpha receptor isoform a precursor	170	Ig-like C2-type 2.|Extracellular (Potential).				immune response	extracellular region|integral to plasma membrane	IgA binding|receptor activity			ovary(1)	1				GBM - Glioblastoma multiforme(193;0.0443)										0.5	91.671541	91.671541	29	29	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	55399520	55399520	6010	19	C	A	A	A	273	21	FCAR	2	2
NLRP13	126204	broad.mit.edu	37	19	56423995	56423995	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:56423995C>A	uc010ygg.1	-	c.1188G>T	c.(1186-1188)ATG>ATT	p.M396I		NM_176810	NP_789780	Q86W25	NAL13_HUMAN	NACHT, leucine rich repeat and PYD containing	396	NACHT.						ATP binding			ovary(3)|skin(2)|pancreas(1)|lung(1)	7		Colorectal(82;3.48e-05)|Ovarian(87;0.0481)|Renal(1328;0.218)		GBM - Glioblastoma multiforme(193;0.0642)										0.556075	354.056779	354.632452	119	95	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	56423995	56423995	10878	19	C	A	A	A	377	29	NLRP13	2	2
NLRP13	126204	broad.mit.edu	37	19	56424114	56424114	+	Missense_Mutation	SNP	C	G	G			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:56424114C>G	uc010ygg.1	-	c.1069G>C	c.(1069-1071)GCT>CCT	p.A357P		NM_176810	NP_789780	Q86W25	NAL13_HUMAN	NACHT, leucine rich repeat and PYD containing	357	NACHT.						ATP binding			ovary(3)|skin(2)|pancreas(1)|lung(1)	7		Colorectal(82;3.48e-05)|Ovarian(87;0.0481)|Renal(1328;0.218)		GBM - Glioblastoma multiforme(193;0.0642)										0.372197	254.512099	257.731008	83	140	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	56424114	56424114	10878	19	C	G	G	G	338	26	NLRP13	3	3
NLRP5	126206	broad.mit.edu	37	19	56569690	56569690	+	Silent	SNP	C	T	T			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:56569690C>T	uc002qmj.2	+	c.3384C>T	c.(3382-3384)AAC>AAT	p.N1128N	NLRP5_uc002qmi.2_Silent_p.N1109N	NM_153447	NP_703148	P59047	NALP5_HUMAN	NACHT, LRR and PYD containing protein 5	1128	LRR 13.					mitochondrion|nucleolus	ATP binding			ovary(3)|skin(2)|kidney(1)	6		Colorectal(82;3.46e-05)|Ovarian(87;0.0481)|Renal(1328;0.157)		GBM - Glioblastoma multiforme(193;0.0326)										0.477273	125.519956	125.559788	42	46	KEEP	---	---	---	---	capture		Silent	SNP	56569690	56569690	10883	19	C	T	T	T	233	18	NLRP5	2	2
ZSCAN5B	342933	broad.mit.edu	37	19	56701605	56701605	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:56701605C>A	uc010ygh.1	-	c.1079G>T	c.(1078-1080)TGC>TTC	p.C360F		NM_001080456	NP_001073925	A6NJL1	ZSA5B_HUMAN	zinc finger and SCAN domain containing 5B	360	C2H2-type 1.				regulation of transcription, DNA-dependent|viral reproduction	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)	1														0.460377	369.29936	369.663692	122	143	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	56701605	56701605	18843	19	C	A	A	A	325	25	ZSCAN5B	2	2
PEG3	5178	broad.mit.edu	37	19	57328635	57328635	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:57328635C>T	uc002qnu.2	-	c.1175G>A	c.(1174-1176)AGG>AAG	p.R392K	ZIM2_uc010ygq.1_Intron|ZIM2_uc010ygr.1_Intron|ZIM2_uc002qnr.2_Intron|ZIM2_uc002qnq.2_Intron|ZIM2_uc010etp.2_Intron|ZIM2_uc010ygs.1_Intron|PEG3_uc002qnt.2_Missense_Mutation_p.R363K|PEG3_uc002qnv.2_Missense_Mutation_p.R392K|PEG3_uc002qnw.2_Missense_Mutation_p.R268K|PEG3_uc002qnx.2_Missense_Mutation_p.R266K|PEG3_uc010etr.2_Missense_Mutation_p.R392K	NM_001146186	NP_001139658	Q9GZU2	PEG3_HUMAN	paternally expressed 3 isoform 1	392					apoptosis|regulation of transcription, DNA-dependent|viral reproduction	cytoplasm|nucleus	nucleic acid binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(7)|large_intestine(1)|pancreas(1)	9		Colorectal(82;0.000256)|all_neural(62;0.103)|Ovarian(87;0.243)		GBM - Glioblastoma multiforme(193;0.0269)										0.356627	446.93064	454.46702	148	267	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	57328635	57328635	12141	19	C	T	T	T	312	24	PEG3	2	2
FUT3	2525	broad.mit.edu	37	19	5844847	5844847	+	Missense_Mutation	SNP	C	G	G			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:5844847C>G	uc002mdk.2	-	c.4G>C	c.(4-6)GAT>CAT	p.D2H	FUT3_uc002mdm.2_Missense_Mutation_p.D2H|FUT3_uc002mdj.2_Missense_Mutation_p.D2H|FUT3_uc002mdl.2_Missense_Mutation_p.D2H	NM_001097641	NP_001091110	P21217	FUT3_HUMAN	fucosyltransferase 3	2	Cytoplasmic (Potential).				protein glycosylation	Golgi cisterna membrane|integral to membrane|membrane fraction	3-galactosyl-N-acetylglucosaminide 4-alpha-L-fucosyltransferase activity				0						Esophageal Squamous(82;745 1728 24593 44831)								0.420561	150.3633	150.950568	45	62	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	5844847	5844847	6356	19	C	G	G	G	390	30	FUT3	3	3
SLC25A41	284427	broad.mit.edu	37	19	6430113	6430113	+	Missense_Mutation	SNP	C	G	G			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:6430113C>G	uc010dus.2	-	c.423G>C	c.(421-423)CAG>CAC	p.Q141H	SLC25A41_uc010dut.2_Missense_Mutation_p.Q3H	NM_173637	NP_775908	Q8N5S1	S2541_HUMAN	solute carrier family 25, member 41	141	Solcar 1.				transmembrane transport	integral to membrane|mitochondrial inner membrane	binding				0														0.583333	45.35083	45.495874	14	10	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	6430113	6430113	15003	19	C	G	G	G	311	24	SLC25A41	3	3
SLC25A23	79085	broad.mit.edu	37	19	6454458	6454458	+	Missense_Mutation	SNP	T	C	C			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:6454458T>C	uc002mex.1	-	c.671A>G	c.(670-672)AAC>AGC	p.N224S	SLC25A23_uc002mev.2_Non-coding_Transcript|SLC25A23_uc010xjd.1_Missense_Mutation_p.N41S	NM_024103	NP_077008	Q9BV35	SCMC3_HUMAN	solute carrier family 25, member 23	224	Solcar 1.|Mitochondrial matrix (Potential).				transmembrane transport	integral to membrane|mitochondrial inner membrane	calcium ion binding			ovary(1)|pancreas(1)	2														0.468966	234.666844	234.789673	68	77	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	6454458	6454458	14983	19	T	C	C	C	780	60	SLC25A23	4	4
KIAA1543	57662	broad.mit.edu	37	19	7671671	7671671	+	Silent	SNP	G	T	T			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:7671671G>T	uc002mgu.3	+	c.630G>T	c.(628-630)ACG>ACT	p.T210T	KIAA1543_uc002mgv.3_Intron	NM_001080429	NP_001073898	Q9P1Y5	CAMP3_HUMAN	NEZHA isoform 1	207	CH.				epithelial cell-cell adhesion|microtubule anchoring|regulation of microtubule cytoskeleton organization|zonula adherens maintenance	cytoplasm|microtubule|zonula adherens	microtubule minus-end binding			pancreas(1)	1														0.75	40.705467	41.613624	12	4	KEEP	---	---	---	---	capture		Silent	SNP	7671671	7671671	8552	19	G	T	T	T	483	38	KIAA1543	1	1
MYO1F	4542	broad.mit.edu	37	19	8601852	8601852	+	Silent	SNP	G	T	T			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:8601852G>T	uc002mkg.2	-	c.1780C>A	c.(1780-1782)CGA>AGA	p.R594R		NM_012335	NP_036467	O00160	MYO1F_HUMAN	myosin IF	594	Myosin head-like.					unconventional myosin complex	actin binding|ATP binding|calmodulin binding|motor activity			ovary(2)	2														0.411765	40.1443	40.373812	14	20	KEEP	---	---	---	---	capture		Silent	SNP	8601852	8601852	10468	19	G	T	T	T	506	39	MYO1F	1	1
MUC16	94025	broad.mit.edu	37	19	9085589	9085589	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:9085589C>A	uc002mkp.2	-	c.6226G>T	c.(6226-6228)GGC>TGC	p.G2076C		NM_024690	NP_078966	Q8WXI7	MUC16_HUMAN	mucin 16	2076	Ser-rich.|Thr-rich.|Extracellular (Potential).				cell adhesion	extracellular space|extrinsic to membrane|integral to membrane|plasma membrane	protein binding			ovary(15)|large_intestine(1)|pancreas(1)|breast(1)|skin(1)	19														0.409704	865.846178	871.154164	304	438	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	9085589	9085589	10367	19	C	A	A	A	312	24	MUC16	2	2
KIF1B	23095	broad.mit.edu	37	1	10338104	10338104	+	Silent	SNP	C	T	T			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:10338104C>T	uc001aqz.2	+	c.1098C>T	c.(1096-1098)GCC>GCT	p.A366A	KIF1B_uc001aqv.3_Silent_p.A360A|KIF1B_uc001aqw.3_Silent_p.A360A|KIF1B_uc001aqx.3_Silent_p.A366A|KIF1B_uc001aqy.2_Silent_p.A366A|KIF1B_uc001ara.2_Silent_p.A366A|KIF1B_uc001arb.2_Silent_p.A366A	NM_015074	NP_055889	O60333	KIF1B_HUMAN	kinesin family member 1B isoform b	366	Potential.				anterograde axon cargo transport|apoptosis|nerve-nerve synaptic transmission|neuromuscular synaptic transmission	cytoplasmic vesicle membrane|microtubule|microtubule associated complex|mitochondrion	ATP binding|ATPase activity|kinesin binding|microtubule motor activity|protein binding			ovary(2)	2	Ovarian(185;0.203)	all_lung(284;1.31e-05)|Lung NSC(185;2.2e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Hepatocellular(190;0.00913)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0259)|Colorectal(212;9.79e-07)|COAD - Colon adenocarcinoma(227;0.000143)|BRCA - Breast invasive adenocarcinoma(304;0.000413)|Kidney(185;0.00134)|KIRC - Kidney renal clear cell carcinoma(229;0.0037)|STAD - Stomach adenocarcinoma(132;0.0113)|READ - Rectum adenocarcinoma(331;0.0642)										0.267081	112.941784	120.840017	43	118	KEEP	---	---	---	---	capture		Silent	SNP	10338104	10338104	8595	1	C	T	T	T	262	21	KIF1B	2	2
COL11A1	1301	broad.mit.edu	37	1	103496798	103496799	+	Missense_Mutation	DNP	CC	AA	AA			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:103496798_103496799CC>AA	uc001dum.2	-	c.653_654GG>TT	c.(652-654)GGG>GTT	p.G218V	COL11A1_uc001duk.2_5'UTR|COL11A1_uc001dul.2_Missense_Mutation_p.G218V|COL11A1_uc001dun.2_Missense_Mutation_p.G218V|COL11A1_uc009weh.2_Missense_Mutation_p.G218V	NM_080629	NP_542196	P12107	COBA1_HUMAN	alpha 1 type XI collagen isoform B	218	TSP N-terminal.				collagen fibril organization|detection of mechanical stimulus involved in sensory perception of sound|visual perception	collagen type XI	extracellular matrix binding|extracellular matrix structural constituent|protein binding, bridging			ovary(6)|breast(3)|central_nervous_system(1)|pancreas(1)	11		all_epithelial(167;2.52e-07)|all_lung(203;3.11e-05)|Lung NSC(277;6.61e-05)|Breast(1374;0.181)		Lung(183;0.186)|all cancers(265;0.242)|Epithelial(280;0.248)										0.388889	39.741452	40.130819	14	22	KEEP	---	---	---	---	capture		Missense_Mutation	DNP	103496798	103496799	3805	1	CC	AA	AA	AA	275	22	COL11A1	2	2
FNDC7	163479	broad.mit.edu	37	1	109268418	109268418	+	Silent	SNP	C	T	T			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:109268418C>T	uc001dvx.2	+	c.903C>T	c.(901-903)GGC>GGT	p.G301G	FNDC7_uc010ova.1_Silent_p.G68G	NM_001144937	NP_001138409	Q5VTL7	FNDC7_HUMAN	fibronectin type III domain containing 7	302	Fibronectin type-III 4.					extracellular region				ovary(1)	1		all_lung(203;0.00439)|Lung NSC(277;0.00683)|all_epithelial(167;0.00728)		Colorectal(144;0.0314)|Lung(183;0.0924)|COAD - Colon adenocarcinoma(174;0.119)|Epithelial(280;0.173)|all cancers(265;0.244)										0.404372	203.974427	205.41786	74	109	KEEP	---	---	---	---	capture		Silent	SNP	109268418	109268418	6215	1	C	T	T	T	327	26	FNDC7	2	2
LRIG2	9860	broad.mit.edu	37	1	113661947	113661947	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:113661947G>T	uc001edf.1	+	c.2773G>T	c.(2773-2775)GCT>TCT	p.A925S	LRIG2_uc009wgn.1_Missense_Mutation_p.A822S	NM_014813	NP_055628	O94898	LRIG2_HUMAN	leucine-rich repeats and immunoglobulin-like	925	Cytoplasmic (Potential).					cytoplasm|integral to membrane|plasma membrane				ovary(3)	3	Lung SC(450;0.246)	all_cancers(81;1.56e-05)|all_epithelial(167;2.62e-05)|all_lung(203;0.000665)|Lung NSC(69;0.000986)		Lung(183;0.0279)|Colorectal(144;0.0885)|COAD - Colon adenocarcinoma(174;0.134)|all cancers(265;0.139)|Epithelial(280;0.143)|LUSC - Lung squamous cell carcinoma(189;0.15)										0.421053	207.233661	208.170801	72	99	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	113661947	113661947	9318	1	G	T	T	T	598	46	LRIG2	2	2
IGSF3	3321	broad.mit.edu	37	1	117146563	117146563	+	Missense_Mutation	SNP	G	A	A	rs61786578	by1000genomes	TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:117146563G>A	uc001egq.1	-	c.1367C>T	c.(1366-1368)ACG>ATG	p.T456M	IGSF3_uc001egr.1_Missense_Mutation_p.T436M|IGSF3_uc001egs.1_Missense_Mutation_p.T109M	NM_001542	NP_001533	O75054	IGSF3_HUMAN	immunoglobulin superfamily, member 3 isoform 1	436	Ig-like C2-type 4.|Extracellular (Potential).					integral to membrane				ovary(2)	2	Lung SC(450;0.225)	all_cancers(81;1.24e-06)|all_epithelial(167;4.85e-07)|all_lung(203;1.66e-06)|Lung NSC(69;1.11e-05)		Lung(183;0.0142)|Colorectal(144;0.0929)|LUSC - Lung squamous cell carcinoma(189;0.108)|COAD - Colon adenocarcinoma(174;0.139)|all cancers(265;0.159)|Epithelial(280;0.166)										0.409722	169.926651	170.942505	59	85	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	117146563	117146563	7902	1	G	A	A	A	520	40	IGSF3	1	1
VPS13D	55187	broad.mit.edu	37	1	12304475	12304475	+	Silent	SNP	C	T	T			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:12304475C>T	uc001atv.2	+	c.348C>T	c.(346-348)GCC>GCT	p.A116A	VPS13D_uc001atw.2_Silent_p.A116A	NM_015378	NP_056193	Q5THJ4	VP13D_HUMAN	vacuolar protein sorting 13D isoform 1	116					protein localization					ovary(4)|pancreas(1)	5	Ovarian(185;0.249)	Lung NSC(185;4.08e-05)|all_lung(284;4.55e-05)|Renal(390;0.000147)|Colorectal(325;0.00058)|Breast(348;0.00093)|Ovarian(437;0.00965)|Hepatocellular(190;0.0202)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0327)|Colorectal(212;4.63e-06)|BRCA - Breast invasive adenocarcinoma(304;0.000289)|COAD - Colon adenocarcinoma(227;0.000801)|Kidney(185;0.00216)|KIRC - Kidney renal clear cell carcinoma(229;0.00544)|STAD - Stomach adenocarcinoma(313;0.012)|READ - Rectum adenocarcinoma(331;0.0476)|Lung(427;0.209)										0.415301	240.267944	241.414014	76	107	KEEP	---	---	---	---	capture		Silent	SNP	12304475	12304475	17759	1	C	T	T	T	275	22	VPS13D	2	2
SF3B4	10262	broad.mit.edu	37	1	149897745	149897745	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:149897745C>T	uc001etj.1	-	c.896G>A	c.(895-897)GGT>GAT	p.G299D	SF3B4_uc001eti.1_Missense_Mutation_p.G63D|SF3B4_uc001etk.1_Missense_Mutation_p.G299D|SF3B4_uc009wll.1_Missense_Mutation_p.G299D	NM_005850	NP_005841	Q15427	SF3B4_HUMAN	splicing factor 3b, subunit 4	299					nuclear mRNA splicing, via spliceosome	nucleoplasm|U12-type spliceosomal complex	nucleotide binding|protein binding|RNA binding			ovary(1)	1	Breast(34;0.0009)|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)											0.306818	72.410692	75.328684	27	61	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	149897745	149897745	14642	1	C	T	T	T	234	18	SF3B4	2	2
IVL	3713	broad.mit.edu	37	1	152883676	152883676	+	Missense_Mutation	SNP	A	T	T			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:152883676A>T	uc001fau.2	+	c.1403A>T	c.(1402-1404)AAG>ATG	p.K468M		NM_005547	NP_005538	P07476	INVO_HUMAN	involucrin	468	39 X 10 AA approximate tandem repeats of [LP]-[EKG]-[LHVYQEK]-[PLSQE]-[EQDV]- [QHEKRGA]-Q-[EMVQLP]-[GKLE]-[QHVNLD].|32.				isopeptide cross-linking via N6-(L-isoglutamyl)-L-lysine|keratinization|response to UV-B	cornified envelope|cytoplasm	protein binding, bridging|structural molecule activity			ovary(3)	3	Lung NSC(65;3.97e-29)|Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.171)											0.571429	11.499183	11.530072	4	3	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	152883676	152883676	8233	1	A	T	T	T	39	3	IVL	3	3
KCNN3	3782	broad.mit.edu	37	1	154680544	154680544	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:154680544C>A	uc001ffp.2	-	c.2104G>T	c.(2104-2106)GTG>TTG	p.V702L	KCNN3_uc001ffo.2_Missense_Mutation_p.V397L	NM_002249	NP_002240	Q9UGI6	KCNN3_HUMAN	small conductance calcium-activated potassium	707						integral to membrane	calmodulin binding			lung(1)	1	all_lung(78;2.29e-27)|all_hematologic(923;0.088)|Hepatocellular(266;0.108)|all_neural(408;0.245)		BRCA - Breast invasive adenocarcinoma(34;0.00819)											0.45082	155.966518	156.22832	55	67	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	154680544	154680544	8385	1	C	A	A	A	260	20	KCNN3	2	2
ARHGEF2	9181	broad.mit.edu	37	1	155935171	155935171	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:155935171C>A	uc001fmu.2	-	c.638G>T	c.(637-639)CGC>CTC	p.R213L	ARHGEF2_uc001fmr.2_Missense_Mutation_p.R141L|ARHGEF2_uc001fms.2_Missense_Mutation_p.R168L|ARHGEF2_uc001fmt.2_Missense_Mutation_p.R168L|ARHGEF2_uc010pgt.1_Missense_Mutation_p.R141L|ARHGEF2_uc010pgu.1_Missense_Mutation_p.R213L	NM_004723	NP_004714	Q92974	ARHG2_HUMAN	Rho/Rac guanine nucleotide exchange factor 2	168					actin filament organization|apoptosis|cell division|cell morphogenesis|induction of apoptosis by extracellular signals|intracellular protein transport|mitosis|negative regulation of microtubule depolymerization|nerve growth factor receptor signaling pathway|positive regulation of NF-kappaB transcription factor activity|regulation of cell proliferation|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol|Golgi apparatus|microtubule|ruffle membrane|spindle|tight junction	microtubule binding|Rac GTPase binding|Rac guanyl-nucleotide exchange factor activity|zinc ion binding			ovary(1)	1	Hepatocellular(266;0.133)|all_hematologic(923;0.145)|all_neural(408;0.195)					Melanoma(178;35 2768 6610 28839)								0.314685	127.7667	132.113089	45	98	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	155935171	155935171	917	1	C	A	A	A	351	27	ARHGEF2	1	1
CD1C	911	broad.mit.edu	37	1	158260984	158260984	+	Missense_Mutation	SNP	G	C	C			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:158260984G>C	uc001fru.2	+	c.122G>C	c.(121-123)TGG>TCG	p.W41S	CD1C_uc001frv.2_5'Flank	NM_001765	NP_001756	P29017	CD1C_HUMAN	CD1C antigen precursor	41	Extracellular (Potential).				antigen processing and presentation|T cell activation involved in immune response	endosome membrane|integral to plasma membrane	endogenous lipid antigen binding|exogenous lipid antigen binding|glycolipid binding|lipopeptide binding			ovary(2)|pancreas(1)	3	all_hematologic(112;0.0378)													0.457143	370.882893	371.272841	112	133	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	158260984	158260984	3103	1	G	C	C	C	611	47	CD1C	3	3
HSPA6	3310	broad.mit.edu	37	1	161495987	161495987	+	Silent	SNP	C	T	T			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:161495987C>T	uc001gap.2	+	c.1539C>T	c.(1537-1539)AGC>AGT	p.S513S	HSPA6_uc001gaq.2_Silent_p.S513S	NM_002155	NP_002146	P17066	HSP76_HUMAN	heat shock 70kDa protein 6 (HSP70B')	513					response to unfolded protein		ATP binding			skin(1)	1	all_cancers(52;4.89e-16)|all_hematologic(112;0.0207)		BRCA - Breast invasive adenocarcinoma(70;0.00376)											0.37931	58.631404	59.374006	22	36	KEEP	---	---	---	---	capture		Silent	SNP	161495987	161495987	7714	1	C	T	T	T	324	25	HSPA6	2	2
GPA33	10223	broad.mit.edu	37	1	167038196	167038196	+	Silent	SNP	C	T	T			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:167038196C>T	uc001gea.1	-	c.378G>A	c.(376-378)GAG>GAA	p.E126E		NM_005814	NP_005805	Q99795	GPA33_HUMAN	transmembrane glycoprotein A33 precursor	126	Ig-like V-type.|Extracellular (Potential).					integral to plasma membrane	receptor activity				0														0.40404	124.420778	125.205047	40	59	KEEP	---	---	---	---	capture		Silent	SNP	167038196	167038196	6860	1	C	T	T	T	311	24	GPA33	2	2
DUSP27	92235	broad.mit.edu	37	1	167096834	167096834	+	Silent	SNP	C	T	T			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:167096834C>T	uc001geb.1	+	c.2466C>T	c.(2464-2466)CCC>CCT	p.P822P		NM_001080426	NP_001073895	Q5VZP5	DUS27_HUMAN	dual specificity phosphatase 27	822					protein dephosphorylation		protein tyrosine/serine/threonine phosphatase activity			ovary(3)	3														0.317241	135.701664	140.005852	46	99	KEEP	---	---	---	---	capture		Silent	SNP	167096834	167096834	5009	1	C	T	T	T	262	21	DUSP27	2	2
MPZL1	9019	broad.mit.edu	37	1	167741611	167741611	+	Missense_Mutation	SNP	A	G	G			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:167741611A>G	uc001geo.2	+	c.358A>G	c.(358-360)ATC>GTC	p.I120V	MPZL1_uc001gen.3_Missense_Mutation_p.I120V|MPZL1_uc001gep.2_Missense_Mutation_p.I120V|MPZL1_uc001geq.2_Intron|MPZL1_uc009wvh.2_Intron	NM_003953	NP_003944	O95297	MPZL1_HUMAN	myelin protein zero-like 1 isoform a	120	Extracellular (Potential).|Ig-like V-type.				cell-cell signaling|transmembrane receptor protein tyrosine kinase signaling pathway	integral to plasma membrane	protein binding|structural molecule activity			ovary(2)	2	all_hematologic(923;0.215)													0.455696	380.075095	380.479964	108	129	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	167741611	167741611	10141	1	A	G	G	G	52	4	MPZL1	4	4
SELE	6401	broad.mit.edu	37	1	169698390	169698391	+	Nonsense_Mutation	DNP	CC	AT	AT			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:169698390_169698391CC>AT	uc001ggm.3	-	c.1026_1027GG>AT	c.(1024-1029)CAGGGA>CAATGA	p.G343*	C1orf112_uc001ggj.2_Intron	NM_000450	NP_000441	P16581	LYAM2_HUMAN	selectin E precursor	343	Extracellular (Potential).|Sushi 3.				actin filament-based process|activation of phospholipase C activity|calcium-mediated signaling|heterophilic cell-cell adhesion|leukocyte migration involved in inflammatory response|leukocyte tethering or rolling|positive regulation of receptor internalization|regulation of inflammatory response|response to interleukin-1|response to lipopolysaccharide|response to tumor necrosis factor	caveola|coated pit|cortical cytoskeleton|extracellular space|integral to membrane|perinuclear region of cytoplasm	oligosaccharide binding|phospholipase binding|sialic acid binding|transmembrane receptor activity			ovary(3)	3	all_hematologic(923;0.208)													0.605505	208.663397	209.724053	66	43	KEEP	---	---	---	---	capture		Nonsense_Mutation	DNP	169698390	169698391	14499	1	CC	AT	AT	AT	286	22	SELE	5	2
SELE	6401	broad.mit.edu	37	1	169698684	169698684	+	Missense_Mutation	SNP	C	G	G			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:169698684C>G	uc001ggm.3	-	c.846G>C	c.(844-846)CAG>CAC	p.Q282H	C1orf112_uc001ggj.2_Intron	NM_000450	NP_000441	P16581	LYAM2_HUMAN	selectin E precursor	282	Sushi 2.|Extracellular (Potential).				actin filament-based process|activation of phospholipase C activity|calcium-mediated signaling|heterophilic cell-cell adhesion|leukocyte migration involved in inflammatory response|leukocyte tethering or rolling|positive regulation of receptor internalization|regulation of inflammatory response|response to interleukin-1|response to lipopolysaccharide|response to tumor necrosis factor	caveola|coated pit|cortical cytoskeleton|extracellular space|integral to membrane|perinuclear region of cytoplasm	oligosaccharide binding|phospholipase binding|sialic acid binding|transmembrane receptor activity			ovary(3)	3	all_hematologic(923;0.208)													0.264706	133.996378	142.505659	45	125	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	169698684	169698684	14499	1	C	G	G	G	415	32	SELE	3	3
SLC9A11	284525	broad.mit.edu	37	1	173569258	173569258	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:173569258C>T	uc001giz.2	-	c.226G>A	c.(226-228)GAG>AAG	p.E76K	SLC9A11_uc010pmq.1_Intron	NM_178527	NP_848622	Q5TAH2	S9A11_HUMAN	solute carrier family 9, member 11	76					sodium ion transport	integral to membrane	solute:hydrogen antiporter activity			ovary(2)	2														0.416667	76.982859	77.341456	25	35	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	173569258	173569258	15208	1	C	T	T	T	377	29	SLC9A11	2	2
SOAT1	6646	broad.mit.edu	37	1	179320569	179320569	+	Missense_Mutation	SNP	A	G	G			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:179320569A>G	uc001gml.2	+	c.1568A>G	c.(1567-1569)TAT>TGT	p.Y523C	SOAT1_uc010pni.1_Missense_Mutation_p.Y458C|SOAT1_uc001gmm.2_Missense_Mutation_p.Y465C|SOAT1_uc010pnj.1_Missense_Mutation_p.Y259C|SOAT1_uc010pnk.1_Missense_Mutation_p.Y458C	NM_003101	NP_003092	P35610	SOAT1_HUMAN	sterol O-acyltransferase 1	523					cholesterol efflux|cholesterol esterification|cholesterol homeostasis|cholesterol metabolic process|cholesterol storage|macrophage derived foam cell differentiation|positive regulation of amyloid precursor protein biosynthetic process|very-low-density lipoprotein particle assembly	endoplasmic reticulum membrane|integral to membrane|microsome	cholesterol binding|cholesterol O-acyltransferase activity|fatty-acyl-CoA binding			central_nervous_system(1)	1					Ezetimibe(DB00973)|Hesperetin(DB01094)									0.430769	784.702991	786.877136	224	296	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	179320569	179320569	15410	1	A	G	G	G	208	16	SOAT1	4	4
CACNA1E	777	broad.mit.edu	37	1	181689367	181689367	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:181689367G>A	uc001gow.2	+	c.1777G>A	c.(1777-1779)GTG>ATG	p.V593M	CACNA1E_uc009wxs.2_Missense_Mutation_p.V500M	NM_000721	NP_000712	Q15878	CAC1E_HUMAN	calcium channel, voltage-dependent, R type,	593	Cytoplasmic (Potential).|II.				energy reserve metabolic process|membrane depolarization|synaptic transmission	voltage-gated calcium channel complex	voltage-gated calcium channel activity			ovary(3)|central_nervous_system(2)|pancreas(1)	6														0.367347	102.773411	104.289682	36	62	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	181689367	181689367	2658	1	G	A	A	A	572	44	CACNA1E	2	2
KCNT2	343450	broad.mit.edu	37	1	196285039	196285039	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:196285039G>T	uc001gtd.1	-	c.2466C>A	c.(2464-2466)AAC>AAA	p.N822K	KCNT2_uc009wyt.1_Non-coding_Transcript|KCNT2_uc001gte.1_Missense_Mutation_p.N748K|KCNT2_uc001gtf.1_Missense_Mutation_p.N798K|KCNT2_uc001gtg.1_Non-coding_Transcript|KCNT2_uc009wyu.2_Missense_Mutation_p.N798K|KCNT2_uc001gth.1_Missense_Mutation_p.N319K	NM_198503	NP_940905	Q6UVM3	KCNT2_HUMAN	potassium channel, subfamily T, member 2	822	Cytoplasmic (Potential).					voltage-gated potassium channel complex	ATP binding|calcium-activated potassium channel activity|catalytic activity|voltage-gated potassium channel activity			ovary(4)|breast(1)	5														0.26	36.566178	39.1649	13	37	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	196285039	196285039	8397	1	G	T	T	T	516	40	KCNT2	1	1
CRB1	23418	broad.mit.edu	37	1	197404099	197404099	+	Nonsense_Mutation	SNP	G	T	T			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:197404099G>T	uc001gtz.2	+	c.3106G>T	c.(3106-3108)GAA>TAA	p.E1036*	CRB1_uc010poz.1_Nonsense_Mutation_p.E1012*|CRB1_uc010ppa.1_Non-coding_Transcript|CRB1_uc009wza.2_Nonsense_Mutation_p.E924*|CRB1_uc010ppb.1_Intron|CRB1_uc010ppd.1_Nonsense_Mutation_p.E517*|CRB1_uc001gub.1_Nonsense_Mutation_p.E685*	NM_201253	NP_957705	P82279	CRUM1_HUMAN	crumbs homolog 1 precursor	1036	Extracellular (Potential).|Laminin G-like 3.				cell-cell signaling|establishment or maintenance of cell polarity|response to stimulus|visual perception	apical plasma membrane|extracellular region|integral to membrane	calcium ion binding|protein binding			ovary(5)|large_intestine(1)	6														0.407643	195.880952	197.04651	64	93	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	197404099	197404099	3987	1	G	T	T	T	481	37	CRB1	5	1
PTPRC	5788	broad.mit.edu	37	1	198677262	198677262	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:198677262G>T	uc001gur.1	+	c.899G>T	c.(898-900)GGG>GTG	p.G300V	PTPRC_uc001gus.1_Missense_Mutation_p.G252V|PTPRC_uc001gut.1_Missense_Mutation_p.G139V|PTPRC_uc009wzf.1_Missense_Mutation_p.G188V|PTPRC_uc010ppg.1_Missense_Mutation_p.G236V	NM_002838	NP_002829	P08575	PTPRC_HUMAN	protein tyrosine phosphatase, receptor type, C	300	Extracellular (Potential).				axon guidance|B cell proliferation|B cell receptor signaling pathway|defense response to virus|immunoglobulin biosynthetic process|negative regulation of cytokine-mediated signaling pathway|negative regulation of protein kinase activity|negative regulation of T cell mediated cytotoxicity|positive regulation of antigen receptor-mediated signaling pathway|positive regulation of B cell proliferation|positive regulation of protein kinase activity|positive regulation of T cell proliferation|regulation of S phase|release of sequestered calcium ion into cytosol|T cell differentiation|T cell receptor signaling pathway	focal adhesion|integral to plasma membrane|membrane raft	protein kinase binding|transmembrane receptor protein tyrosine phosphatase activity			breast(4)|skin(2)|ovary(2)|lung(1)|kidney(1)|pancreas(1)	11										815				0.342593	97.833529	100.201685	37	71	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	198677262	198677262	13254	1	G	T	T	T	559	43	PTPRC	2	2
FAM58B	339521	broad.mit.edu	37	1	200182807	200182807	+	Missense_Mutation	SNP	T	C	C			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:200182807T>C	uc009wzi.1	+	c.116T>C	c.(115-117)ATG>ACG	p.M39T		NM_001105517	NP_001098987	P0C7Q3	FA58B_HUMAN	family with sequence similarity 58 member B	39											0	Prostate(682;0.19)													0.385827	151.045796	152.496318	49	78	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	200182807	200182807	5813	1	T	C	C	C	663	51	FAM58B	4	4
TNNT2	7139	broad.mit.edu	37	1	201334414	201334414	+	Nonsense_Mutation	SNP	C	A	A			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:201334414C>A	uc001gwf.2	-	c.316G>T	c.(316-318)GAG>TAG	p.E106*	TNNT2_uc001gwg.2_Nonsense_Mutation_p.E96*|TNNT2_uc001gwh.2_Nonsense_Mutation_p.E91*|TNNT2_uc001gwi.2_Intron|TNNT2_uc009wzr.2_Nonsense_Mutation_p.E37*|TNNT2_uc001gwj.1_5'Flank|TNNT2_uc009wzs.1_Nonsense_Mutation_p.E71*|TNNT2_uc001gwk.1_Nonsense_Mutation_p.E37*|TNNT2_uc009wzt.1_Nonsense_Mutation_p.E96*	NM_000364	NP_000355	P45379	TNNT2_HUMAN	troponin T type 2, cardiac isoform 1	106					ATP catabolic process|muscle filament sliding|negative regulation of ATPase activity|positive regulation of ATPase activity|regulation of heart contraction|response to calcium ion|response to calcium ion|ventricular cardiac muscle tissue morphogenesis	cytosol|troponin complex	actin binding|tropomyosin binding|troponin C binding|troponin I binding				0														0.377309	379.467757	384.495102	143	236	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	201334414	201334414	16872	1	C	A	A	A	390	30	TNNT2	5	2
SOX13	9580	broad.mit.edu	37	1	204082127	204082127	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:204082127G>T	uc001ham.2	+	c.84G>T	c.(82-84)GAG>GAT	p.E28D	SOX13_uc001hal.2_Missense_Mutation_p.E28D|SOX13_uc010pqp.1_Missense_Mutation_p.E28D	NM_005686	NP_005677	Q9UN79	SOX13_HUMAN	SRY-box 13	28					anatomical structure morphogenesis|regulation of transcription, DNA-dependent	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			breast(1)|central_nervous_system(1)	2	all_cancers(21;0.0754)|Breast(84;0.116)|all_epithelial(62;0.189)		KIRC - Kidney renal clear cell carcinoma(13;0.0584)|Kidney(21;0.0934)|BRCA - Breast invasive adenocarcinoma(75;0.109)											0.555556	25.943981	25.993792	10	8	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	204082127	204082127	15444	1	G	T	T	T	425	33	SOX13	2	2
NFASC	23114	broad.mit.edu	37	1	204985663	204985663	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:204985663C>A	uc001hbj.2	+	c.3719C>A	c.(3718-3720)GCC>GAC	p.A1240D	NFASC_uc010pra.1_Missense_Mutation_p.A1174D|NFASC_uc001hbi.2_Missense_Mutation_p.A1169D|NFASC_uc010prb.1_Missense_Mutation_p.A1189D|NFASC_uc010prc.1_Missense_Mutation_p.A740D|NFASC_uc001hbl.1_Missense_Mutation_p.A316D|NFASC_uc001hbm.1_Missense_Mutation_p.A263D|NFASC_uc009xbh.1_Missense_Mutation_p.P95T|NFASC_uc001hbo.1_Missense_Mutation_p.P116T	NM_001005388	NP_001005388	O94856	NFASC_HUMAN	neurofascin isoform 1 precursor	1347	Cytoplasmic (Potential).				axon guidance|cell adhesion|myelination|peripheral nervous system development	integral to membrane|node of Ranvier|plasma membrane	protein binding			ovary(3)|breast(1)	4	all_cancers(21;0.0375)|Breast(84;0.0437)|all_epithelial(62;0.171)|Prostate(682;0.19)		KIRC - Kidney renal clear cell carcinoma(13;0.0584)|Kidney(21;0.0934)|BRCA - Breast invasive adenocarcinoma(75;0.158)											0.455446	127.222645	127.398767	46	55	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	204985663	204985663	10759	1	C	A	A	A	338	26	NFASC	2	2
C1orf186	440712	broad.mit.edu	37	1	206239438	206239438	+	Missense_Mutation	SNP	A	G	G			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:206239438A>G	uc001hdt.1	-	c.460T>C	c.(460-462)TGG>CGG	p.W154R		NM_001007544	NP_001007545	Q6ZWK4	CA186_HUMAN	hypothetical protein LOC440712	154						integral to membrane					0			BRCA - Breast invasive adenocarcinoma(75;0.0754)											0.469388	151.042303	151.122144	46	52	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	206239438	206239438	2088	1	A	G	G	G	91	7	C1orf186	4	4
LGTN	1939	broad.mit.edu	37	1	206767041	206767041	+	Silent	SNP	G	T	T			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:206767041G>T	uc001heh.2	-	c.1611C>A	c.(1609-1611)GCC>GCA	p.A537A	LGTN_uc009xbw.2_Silent_p.A413A	NM_006893	NP_008824	P41214	EIF2D_HUMAN	ligatin	537	SUI1.				intracellular protein transport	cytoplasm	protein binding|receptor activity|translation initiation factor activity				0	Breast(84;0.183)		BRCA - Breast invasive adenocarcinoma(75;0.166)											0.488235	245.235051	245.254449	83	87	KEEP	---	---	---	---	capture		Silent	SNP	206767041	206767041	9086	1	G	T	T	T	548	43	LGTN	2	2
IL19	29949	broad.mit.edu	37	1	206972271	206972271	+	Missense_Mutation	SNP	C	G	G			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:206972271C>G	uc001heo.2	+	c.32C>G	c.(31-33)TCT>TGT	p.S11C		NM_153758	NP_715639	Q9UHD0	IL19_HUMAN	interleukin 19 isoform 1 precursor	Error:Variant_position_missing_in_Q9UHD0_after_alignment					apoptosis|immune response|signal transduction	extracellular space	cytokine activity			ovary(1)	1			BRCA - Breast invasive adenocarcinoma(75;0.211)											0.477612	118.297859	118.327036	32	35	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	206972271	206972271	7950	1	C	G	G	G	416	32	IL19	3	3
KCTD3	51133	broad.mit.edu	37	1	215793472	215793472	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:215793472C>T	uc001hks.2	+	c.1960C>T	c.(1960-1962)CCT>TCT	p.P654S	KCTD3_uc001hkt.2_Missense_Mutation_p.P652S|KCTD3_uc010pub.1_Missense_Mutation_p.P552S|KCTD3_uc009xdn.2_Missense_Mutation_p.P378S	NM_016121	NP_057205	Q9Y597	KCTD3_HUMAN	potassium channel tetramerisation domain	654						voltage-gated potassium channel complex	protein binding|voltage-gated potassium channel activity			ovary(2)	2				all cancers(67;0.0164)|OV - Ovarian serous cystadenocarcinoma(81;0.019)|GBM - Glioblastoma multiforme(131;0.0862)|Epithelial(68;0.13)										0.423077	130.582159	131.119074	44	60	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	215793472	215793472	8416	1	C	T	T	T	390	30	KCTD3	2	2
TGFB2	7042	broad.mit.edu	37	1	218607550	218607550	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:218607550C>A	uc001hln.2	+	c.721C>A	c.(721-723)CAT>AAT	p.H241N	TGFB2_uc001hlm.2_Missense_Mutation_p.H213N|TGFB2_uc010pue.1_Non-coding_Transcript|TGFB2_uc001hlo.2_Non-coding_Transcript	NM_001135599	NP_001129071	P61812	TGFB2_HUMAN	transforming growth factor, beta 2 isoform 1	213					activation of protein kinase activity|angiogenesis|cardiac epithelial to mesenchymal transition|cardiac muscle cell proliferation|cardioblast differentiation|catagen|cell cycle arrest|cell death|cell growth|cell-cell junction organization|cell-cell signaling|collagen fibril organization|dopamine biosynthetic process|embryonic digestive tract development|eye development|glial cell migration|hair follicle morphogenesis|hemopoiesis|menstrual cycle phase|negative regulation of alkaline phosphatase activity|negative regulation of cell growth|negative regulation of epithelial cell proliferation|negative regulation of immune response|negative regulation of macrophage cytokine production|neuron development|neutrophil chemotaxis|odontogenesis|pathway-restricted SMAD protein phosphorylation|platelet activation|platelet degranulation|positive regulation of cardioblast differentiation|positive regulation of catagen|positive regulation of cell adhesion mediated by integrin|positive regulation of cell cycle|positive regulation of cell division|positive regulation of cell growth|positive regulation of cell proliferation|positive regulation of epithelial cell migration|positive regulation of epithelial to mesenchymal transition|positive regulation of heart contraction|positive regulation of immune response|positive regulation of integrin biosynthetic process|positive regulation of neuron apoptosis|positive regulation of ossification|positive regulation of phosphatidylinositol 3-kinase cascade|positive regulation of protein secretion|positive regulation of stress-activated MAPK cascade|regulation of transforming growth factor-beta2 production|response to hypoxia|response to progesterone stimulus|salivary gland morphogenesis|SMAD protein import into nucleus|somatic stem cell division|transforming growth factor beta receptor signaling pathway	axon|extracellular matrix|extracellular space|neuronal cell body|platelet alpha granule lumen	beta-amyloid binding|cytokine activity|growth factor activity|protein heterodimerization activity|protein homodimerization activity|receptor signaling protein serine/threonine kinase activity|type II transforming growth factor beta receptor binding				0				all cancers(67;0.0459)|OV - Ovarian serous cystadenocarcinoma(81;0.049)|GBM - Glioblastoma multiforme(131;0.0776)						137				0.366337	96.606139	98.208274	37	64	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	218607550	218607550	16346	1	C	A	A	A	273	21	TGFB2	2	2
RAB3GAP2	25782	broad.mit.edu	37	1	220332740	220332740	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:220332740C>A	uc010puk.1	-	c.3249G>T	c.(3247-3249)AGG>AGT	p.R1083S	RAB3GAP2_uc001hmf.2_Non-coding_Transcript|RAB3GAP2_uc001hmg.2_Missense_Mutation_p.R663S|RAB3GAP2_uc001hmh.2_Missense_Mutation_p.R27S	NM_012414	NP_036546	Q9H2M9	RBGPR_HUMAN	rab3 GTPase-activating protein, non-catalytic	1083					intracellular protein transport	cytoplasm|soluble fraction	GTPase activator activity|protein heterodimerization activity			central_nervous_system(1)	1				GBM - Glioblastoma multiforme(131;0.0443)										0.34375	31.420034	32.107869	11	21	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	220332740	220332740	13395	1	C	A	A	A	233	18	RAB3GAP2	2	2
CELA3B	23436	broad.mit.edu	37	1	22310714	22310714	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:22310714G>T	uc001bfk.2	+	c.532G>T	c.(532-534)GCC>TCC	p.A178S	CELA3B_uc009vqf.2_Intron	NM_007352	NP_031378	P08861	CEL3B_HUMAN	elastase 3B, pancreatic preproprotein	178	Peptidase S1.				cholesterol metabolic process|proteolysis	extracellular region	serine-type endopeptidase activity			ovary(1)	1														0.349206	57.828361	59.093544	22	41	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	22310714	22310714	3347	1	G	T	T	T	546	42	CELA3B	2	2
LEFTY1	10637	broad.mit.edu	37	1	226076566	226076566	+	Silent	SNP	G	A	A			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:226076566G>A	uc001hpo.2	-	c.201C>T	c.(199-201)CGC>CGT	p.R67R	LEFTY1_uc010pvj.1_Intron|LEFTY1_uc009xej.1_Silent_p.R67R	NM_020997	NP_066277	O75610	LFTY1_HUMAN	left-right determination, factor B	67					cell growth|multicellular organismal development|transforming growth factor beta receptor signaling pathway	extracellular space	cytokine activity|growth factor activity|transforming growth factor beta receptor binding				0	Breast(184;0.197)													0.533333	45.496523	45.525229	16	14	KEEP	---	---	---	---	capture		Silent	SNP	226076566	226076566	9039	1	G	A	A	A	587	46	LEFTY1	2	2
HIST3H2BB	128312	broad.mit.edu	37	1	228646196	228646196	+	Silent	SNP	C	T	T			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:228646196C>T	uc001hsz.2	+	c.366C>T	c.(364-366)TAC>TAT	p.Y122Y	HIST3H2A_uc001hsy.2_5'Flank	NM_175055	NP_778225	Q8N257	H2B3B_HUMAN	histone cluster 3, H2bb	122					nucleosome assembly	nucleosome|nucleus	DNA binding				0		Prostate(94;0.183)												0.342105	33.547541	34.392037	13	25	KEEP	---	---	---	---	capture		Silent	SNP	228646196	228646196	7474	1	C	T	T	T	220	17	HIST3H2BB	2	2
LYST	1130	broad.mit.edu	37	1	235827894	235827894	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:235827894C>A	uc001hxj.2	-	c.11066G>T	c.(11065-11067)TGG>TTG	p.W3689L	LYST_uc001hxi.2_Missense_Mutation_p.W913L	NM_000081	NP_000072	Q99698	LYST_HUMAN	lysosomal trafficking regulator	3689	WD 5.				defense response to bacterium|defense response to protozoan|defense response to virus|endosome to lysosome transport via multivesicular body sorting pathway|leukocyte chemotaxis|mast cell secretory granule organization|melanosome organization|natural killer cell mediated cytotoxicity|protein transport	cytoplasm|microtubule cytoskeleton	protein binding			ovary(6)|breast(4)|central_nervous_system(2)	12	Ovarian(103;0.0634)|Breast(184;0.23)	all_cancers(173;0.00246)|Prostate(94;0.0771)|Acute lymphoblastic leukemia(190;0.228)	OV - Ovarian serous cystadenocarcinoma(106;0.000674)											0.426471	88.66238	88.983458	29	39	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	235827894	235827894	9505	1	C	A	A	A	273	21	LYST	2	2
NID1	4811	broad.mit.edu	37	1	236192981	236192981	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:236192981C>A	uc001hxo.2	-	c.1607G>T	c.(1606-1608)CGG>CTG	p.R536L	NID1_uc009xgd.2_Missense_Mutation_p.R536L	NM_002508	NP_002499	P14543	NID1_HUMAN	nidogen 1 precursor	536	Nidogen G2 beta-barrel.				bioluminescence|cell-matrix adhesion|protein-chromophore linkage	basement membrane|membrane	calcium ion binding			large_intestine(1)|pancreas(1)	2	Ovarian(103;0.0544)|Breast(184;0.23)	all_cancers(173;0.00491)|Prostate(94;0.184)|Acute lymphoblastic leukemia(190;0.229)	OV - Ovarian serous cystadenocarcinoma(106;0.00162)		Becaplermin(DB00102)|Urokinase(DB00013)									0.352941	34.289424	34.93796	12	22	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	236192981	236192981	10815	1	C	A	A	A	299	23	NID1	1	1
MTR	4548	broad.mit.edu	37	1	237058851	237058851	+	Splice_Site_SNP	SNP	G	T	T			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:237058851G>T	uc001hyi.3	+	c.3598_splice	c.e31+1	p.G1200_splice	MTR_uc010pxw.1_Splice_Site_SNP_p.G793_splice|MTR_uc010pxx.1_Splice_Site_SNP_p.G1149_splice|MTR_uc010pxy.1_Splice_Site_SNP_p.G1054_splice	NM_000254	NP_000245			5-methyltetrahydrofolate-homocysteine						nervous system development|xenobiotic metabolic process	cytosol	cobalamin binding|homocysteine S-methyltransferase activity|methionine synthase activity|protein binding|zinc ion binding			ovary(1)|central_nervous_system(1)|pancreas(1)	3	Ovarian(103;0.0634)|Breast(184;0.221)	all_cancers(173;2.79e-22)|all_epithelial(177;4.84e-14)|Breast(1374;0.00123)|Prostate(94;0.0181)|Lung SC(1967;0.0262)|Acute lymphoblastic leukemia(190;0.117)	OV - Ovarian serous cystadenocarcinoma(106;0.0106)	KIRC - Kidney renal clear cell carcinoma(1967;0.248)	Hydroxocobalamin(DB00200)|L-Methionine(DB00134)|Tetrahydrofolic acid(DB00116)									0.5	16.874994	16.874994	5	5	KEEP	---	---	---	---	capture		Splice_Site_SNP	SNP	237058851	237058851	10351	1	G	T	T	T	572	44	MTR	5	2
RYR2	6262	broad.mit.edu	37	1	237656285	237656285	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:237656285G>T	uc001hyl.1	+	c.1859G>T	c.(1858-1860)TGC>TTC	p.C620F		NM_001035	NP_001026	Q92736	RYR2_HUMAN	cardiac muscle ryanodine receptor	620	Cytoplasmic (By similarity).|B30.2/SPRY 1.				cardiac muscle contraction|detection of calcium ion|induction of apoptosis by ionic changes|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum|response to caffeine|response to hypoxia|response to redox state	calcium channel complex|plasma membrane|plasma membrane enriched fraction|sarcoplasmic reticulum membrane	calcium ion binding|calmodulin binding|identical protein binding|protein kinase A catalytic subunit binding|protein kinase A regulatory subunit binding|receptor activity|ryanodine-sensitive calcium-release channel activity|suramin binding			ovary(17)|large_intestine(6)|central_nervous_system(6)|pancreas(3)|breast(1)	33	Ovarian(103;0.103)	all_cancers(173;0.000368)|Melanoma(53;0.0179)|all_epithelial(177;0.0225)	OV - Ovarian serous cystadenocarcinoma(106;0.00606)											0.35	20.418706	20.815871	7	13	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	237656285	237656285	14249	1	G	T	T	T	598	46	RYR2	2	2
RYR2	6262	broad.mit.edu	37	1	237711738	237711738	+	Missense_Mutation	SNP	C	G	G			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:237711738C>G	uc001hyl.1	+	c.2914C>G	c.(2914-2916)CTG>GTG	p.L972V		NM_001035	NP_001026	Q92736	RYR2_HUMAN	cardiac muscle ryanodine receptor	972	Cytoplasmic (By similarity).|2.|4 X approximate repeats.				cardiac muscle contraction|detection of calcium ion|induction of apoptosis by ionic changes|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum|response to caffeine|response to hypoxia|response to redox state	calcium channel complex|plasma membrane|plasma membrane enriched fraction|sarcoplasmic reticulum membrane	calcium ion binding|calmodulin binding|identical protein binding|protein kinase A catalytic subunit binding|protein kinase A regulatory subunit binding|receptor activity|ryanodine-sensitive calcium-release channel activity|suramin binding			ovary(17)|large_intestine(6)|central_nervous_system(6)|pancreas(3)|breast(1)	33	Ovarian(103;0.103)	all_cancers(173;0.000368)|Melanoma(53;0.0179)|all_epithelial(177;0.0225)	OV - Ovarian serous cystadenocarcinoma(106;0.00606)											0.421053	52.595199	52.801352	16	22	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	237711738	237711738	14249	1	C	G	G	G	363	28	RYR2	3	3
CHML	1122	broad.mit.edu	37	1	241798259	241798259	+	Missense_Mutation	SNP	T	A	A			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:241798259T>A	uc001hzd.2	-	c.810A>T	c.(808-810)GAA>GAT	p.E270D	OPN3_uc001hza.2_Intron|OPN3_uc001hzb.2_Intron|OPN3_uc001hzc.2_Intron	NM_001821	NP_001812	P26374	RAE2_HUMAN	choroideremia-like Rab escort protein 2	270					intracellular protein transport|visual perception	Rab-protein geranylgeranyltransferase complex	GTPase activator activity|Rab geranylgeranyltransferase activity			ovary(4)	4	Ovarian(103;0.103)|all_lung(81;0.23)	all_cancers(173;0.0231)	OV - Ovarian serous cystadenocarcinoma(106;0.0125)											0.385417	104.949634	106.055325	37	59	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	241798259	241798259	3485	1	T	A	A	A	725	56	CHML	3	3
CHML	1122	broad.mit.edu	37	1	241798846	241798846	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:241798846C>A	uc001hzd.2	-	c.223G>T	c.(223-225)GTA>TTA	p.V75L	OPN3_uc001hza.2_Intron|OPN3_uc001hzb.2_Intron|OPN3_uc001hzc.2_Intron	NM_001821	NP_001812	P26374	RAE2_HUMAN	choroideremia-like Rab escort protein 2	75					intracellular protein transport|visual perception	Rab-protein geranylgeranyltransferase complex	GTPase activator activity|Rab geranylgeranyltransferase activity			ovary(4)	4	Ovarian(103;0.103)|all_lung(81;0.23)	all_cancers(173;0.0231)	OV - Ovarian serous cystadenocarcinoma(106;0.0125)											0.275862	232.528968	246.986053	88	231	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	241798846	241798846	3485	1	C	A	A	A	221	17	CHML	2	2
PLCH2	9651	broad.mit.edu	37	1	2428372	2428372	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:2428372G>T	uc001aji.1	+	c.2039G>T	c.(2038-2040)CGC>CTC	p.R680L	PLCH2_uc010nyz.1_Missense_Mutation_p.R468L|PLCH2_uc009vle.1_Missense_Mutation_p.R468L|PLCH2_uc001ajj.1_Missense_Mutation_p.R468L|PLCH2_uc001ajk.1_Missense_Mutation_p.R468L|PLCH2_uc001ajl.1_5'Flank	NM_014638	NP_055453	O75038	PLCH2_HUMAN	phospholipase C, eta 2	680	PI-PLC Y-box.	Substrate (By similarity).			intracellular signal transduction|lipid catabolic process	cytoplasm|plasma membrane	calcium ion binding|phosphatidylinositol phospholipase C activity|signal transducer activity			central_nervous_system(3)|ovary(1)|skin(1)	5	all_cancers(77;0.000161)|all_epithelial(69;5.98e-05)|all_lung(157;0.016)|Lung NSC(156;0.0376)|Ovarian(185;0.0634)	all_epithelial(116;7.32e-16)|all_lung(118;1.15e-06)|Lung NSC(185;6.26e-05)|Renal(390;0.00571)|Breast(487;0.00832)|Hepatocellular(190;0.0268)|Myeloproliferative disorder(586;0.028)|Ovarian(437;0.127)|Medulloblastoma(700;0.151)|Lung SC(97;0.217)		Epithelial(90;1.44e-37)|OV - Ovarian serous cystadenocarcinoma(86;6.78e-23)|GBM - Glioblastoma multiforme(42;2.8e-08)|Colorectal(212;4.19e-05)|COAD - Colon adenocarcinoma(227;0.000195)|Kidney(185;0.00034)|BRCA - Breast invasive adenocarcinoma(365;0.00443)|KIRC - Kidney renal clear cell carcinoma(229;0.00548)|STAD - Stomach adenocarcinoma(132;0.00644)|Lung(427;0.2)										0.538462	39.526316	39.557901	14	12	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	2428372	2428372	12464	1	G	T	T	T	494	38	PLCH2	1	1
OR2B11	127623	broad.mit.edu	37	1	247615073	247615073	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:247615073G>T	uc010pyx.1	-	c.212C>A	c.(211-213)TCC>TAC	p.S71Y		NM_001004492	NP_001004492	Q5JQS5	OR2BB_HUMAN	olfactory receptor, family 2, subfamily B,	71	Helical; Name=2; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0	all_cancers(71;4.51e-05)|all_epithelial(71;1.3e-05)|Breast(184;0.0149)|Ovarian(71;0.0377)|all_lung(81;0.0662)|Lung NSC(105;0.0724)	all_cancers(173;0.241)	OV - Ovarian serous cystadenocarcinoma(106;0.0188)											0.416452	436.422862	438.804034	162	227	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	247615073	247615073	11394	1	G	T	T	T	533	41	OR2B11	2	2
OR2C3	81472	broad.mit.edu	37	1	247695285	247695285	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:247695285G>T	uc009xgy.2	-	c.529C>A	c.(529-531)CAC>AAC	p.H177N	C1orf150_uc009xgw.2_Intron|C1orf150_uc001ida.3_Intron|C1orf150_uc001idb.3_Intron|C1orf150_uc009xgx.2_Intron|LOC148824_uc001idd.2_5'Flank	NM_198074	NP_932340	Q8N628	OR2C3_HUMAN	olfactory receptor, family 2, subfamily C,	177	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)	1	all_cancers(71;4.51e-05)|all_epithelial(71;1.3e-05)|Breast(184;0.0149)|Ovarian(71;0.0377)|all_lung(81;0.0662)|Lung NSC(105;0.0724)	all_cancers(173;0.0242)	OV - Ovarian serous cystadenocarcinoma(106;0.0241)											0.415094	64.316428	64.654611	22	31	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	247695285	247695285	11399	1	G	T	T	T	611	47	OR2C3	2	2
OR2M5	127059	broad.mit.edu	37	1	248309178	248309178	+	Silent	SNP	T	C	C			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:248309178T>C	uc010pze.1	+	c.729T>C	c.(727-729)TCT>TCC	p.S243S		NM_001004690	NP_001004690	A3KFT3	OR2M5_HUMAN	olfactory receptor, family 2, subfamily M,	243	Helical; Name=6; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(2)|kidney(1)	3	all_cancers(71;0.000149)|all_epithelial(71;1.27e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0388)											0.453155	797.211437	798.209443	237	286	KEEP	---	---	---	---	capture		Silent	SNP	248309178	248309178	11419	1	T	C	C	C	691	54	OR2M5	4	4
OR14C36	127066	broad.mit.edu	37	1	248512562	248512562	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:248512562C>A	uc010pzl.1	+	c.486C>A	c.(484-486)TTC>TTA	p.F162L		NM_001001918	NP_001001918	Q8NHC7	O14CZ_HUMAN	olfactory receptor, family 14, subfamily C,	162	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)|central_nervous_system(1)	2														0.429752	140.578749	141.098376	52	69	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	248512562	248512562	11352	1	C	A	A	A	389	30	OR14C36	2	2
GMEB1	10691	broad.mit.edu	37	1	29040746	29040746	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:29040746C>T	uc001bra.2	+	c.1183C>T	c.(1183-1185)CCT>TCT	p.P395S	GMEB1_uc001bqz.2_Missense_Mutation_p.P385S|GMEB1_uc001brb.2_Missense_Mutation_p.P385S	NM_006582	NP_006573	Q9Y692	GMEB1_HUMAN	glucocorticoid modulatory element binding	395					regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	DNA binding|metal ion binding|transcription coactivator activity				0		Colorectal(325;3.46e-05)|Lung NSC(340;0.000451)|all_lung(284;0.00063)|Breast(348;0.00502)|Renal(390;0.00555)|all_neural(195;0.0227)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0563)|Medulloblastoma(700;0.123)		Colorectal(126;2.96e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|STAD - Stomach adenocarcinoma(196;0.00299)|BRCA - Breast invasive adenocarcinoma(304;0.0221)|KIRC - Kidney renal clear cell carcinoma(1967;0.0296)|READ - Rectum adenocarcinoma(331;0.0649)										0.431373	63.957446	64.162925	22	29	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	29040746	29040746	6756	1	C	T	T	T	390	30	GMEB1	2	2
CSMD2	114784	broad.mit.edu	37	1	34238314	34238314	+	Missense_Mutation	SNP	C	G	G			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:34238314C>G	uc001bxm.1	-	c.1702G>C	c.(1702-1704)GCA>CCA	p.A568P	CSMD2_uc001bxn.1_Missense_Mutation_p.A528P	NM_052896	NP_443128	Q7Z408	CSMD2_HUMAN	CUB and Sushi multiple domains 2	528	Sushi 3.|Extracellular (Potential).					integral to membrane|plasma membrane	protein binding			ovary(5)|pancreas(1)	6		Myeloproliferative disorder(586;0.0294)|all_neural(195;0.249)												0.043478	-13.024828	12.655976	5	110	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	34238314	34238314	4086	1	C	G	G	G	325	25	CSMD2	3	3
DMBX1	127343	broad.mit.edu	37	1	46972733	46972733	+	Silent	SNP	C	T	T			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:46972733C>T	uc001cpx.2	+	c.51C>T	c.(49-51)CTC>CTT	p.L17L	DMBX1_uc001cpw.2_Silent_p.L17L	NM_147192	NP_671725	Q8NFW5	DMBX1_HUMAN	diencephalon/mesencephalon homeobox 1 isoform b	17	Interacts with OXT2 and is required for repressor activity (By similarity).				brain development|developmental growth|negative regulation of transcription, DNA-dependent	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription repressor activity			ovary(1)	1	Acute lymphoblastic leukemia(166;0.155)													0.348684	140.634374	143.702965	53	99	KEEP	---	---	---	---	capture		Silent	SNP	46972733	46972733	4758	1	C	T	T	T	366	29	DMBX1	2	2
ZCCHC11	23318	broad.mit.edu	37	1	52926896	52926896	+	Splice_Site_SNP	SNP	C	A	A			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:52926896C>A	uc001cty.2	-	c.3232_splice	c.e19-1	p.A1078_splice	ZCCHC11_uc001ctx.2_Splice_Site_SNP_p.A1078_splice|ZCCHC11_uc001ctz.2_Splice_Site_SNP_p.A1078_splice|ZCCHC11_uc009vze.1_Splice_Site_SNP_p.A1078_splice|ZCCHC11_uc009vzf.1_Splice_Site_SNP_p.A837_splice|ZCCHC11_uc001cua.1_Splice_Site_SNP	NM_001009881	NP_001009881			zinc finger, CCHC domain containing 11 isoform						miRNA catabolic process|pre-microRNA processing|RNA 3'-end processing|stem cell maintenance	cytoplasm|nucleolus	nucleic acid binding|protein binding|protein binding|RNA uridylyltransferase activity|zinc ion binding			ovary(2)	2														0.404494	103.877031	104.588188	36	53	KEEP	---	---	---	---	capture		Splice_Site_SNP	SNP	52926896	52926896	18168	1	C	A	A	A	312	24	ZCCHC11	5	2
GPX7	2882	broad.mit.edu	37	1	53072521	53072521	+	Missense_Mutation	SNP	A	T	T			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:53072521A>T	uc001cue.2	+	c.304A>T	c.(304-306)AGC>TGC	p.S102C		NM_015696	NP_056511	Q96SL4	GPX7_HUMAN	glutathione peroxidase 7 precursor	102					oxidation-reduction process|response to oxidative stress	extracellular region	glutathione peroxidase activity				0					Glutathione(DB00143)									0.391473	271.049189	273.697173	101	157	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	53072521	53072521	7021	1	A	T	T	T	143	11	GPX7	3	3
JAK1	3716	broad.mit.edu	37	1	65330594	65330594	+	Missense_Mutation	SNP	T	C	C			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:65330594T>C	uc001dbu.1	-	c.1052A>G	c.(1051-1053)AAG>AGG	p.K351R	JAK1_uc009wam.1_Missense_Mutation_p.K339R	NM_002227	NP_002218	P23458	JAK1_HUMAN	janus kinase 1	351	FERM.				interferon-gamma-mediated signaling pathway|regulation of interferon-gamma-mediated signaling pathway|regulation of type I interferon-mediated signaling pathway|response to antibiotic|type I interferon-mediated signaling pathway	cytoskeleton|cytosol|endomembrane system|membrane|nucleus	ATP binding|growth hormone receptor binding|non-membrane spanning protein tyrosine kinase activity			haematopoietic_and_lymphoid_tissue(30)|prostate(7)|soft_tissue(6)|lung(4)|central_nervous_system(2)|liver(2)|large_intestine(1)|stomach(1)|breast(1)|ovary(1)	55				BRCA - Breast invasive adenocarcinoma(111;0.0485)						1025				0.385057	234.390809	236.40415	67	107	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	65330594	65330594	8241	1	T	C	C	C	728	56	JAK1	4	4
USP33	23032	broad.mit.edu	37	1	78181454	78181454	+	Missense_Mutation	SNP	T	A	A			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:78181454T>A	uc001dht.2	-	c.2111A>T	c.(2110-2112)AAT>ATT	p.N704I	USP33_uc001dhs.2_Missense_Mutation_p.N425I|USP33_uc001dhu.2_Missense_Mutation_p.N673I|USP33_uc001dhv.2_Missense_Mutation_p.N509I|USP33_uc001dhw.2_Missense_Mutation_p.N696I	NM_015017	NP_055832	Q8TEY7	UBP33_HUMAN	ubiquitin specific protease 33 isoform 1	704					axon guidance|cell migration|endocytosis|protein K48-linked deubiquitination|protein K63-linked deubiquitination|regulation of G-protein coupled receptor protein signaling pathway|ubiquitin-dependent protein catabolic process	perinuclear region of cytoplasm|VCB complex	cysteine-type endopeptidase activity|G-protein-coupled receptor binding|protein binding|ubiquitin thiolesterase activity|ubiquitin-specific protease activity|zinc ion binding			ovary(1)	1						Melanoma(152;72 1870 11110 26780 42647)								0.453125	92.069198	92.191447	29	35	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	78181454	78181454	17628	1	T	A	A	A	676	52	USP33	3	3
ELTD1	64123	broad.mit.edu	37	1	79403639	79403639	+	Missense_Mutation	SNP	C	G	G			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:79403639C>G	uc001diq.3	-	c.613G>C	c.(613-615)GAT>CAT	p.D205H		NM_022159	NP_071442	Q9HBW9	ELTD1_HUMAN	EGF, latrophilin and seven transmembrane domain	205	Extracellular (Potential).				neuropeptide signaling pathway	integral to membrane|plasma membrane	calcium ion binding|G-protein coupled receptor activity			ovary(1)	1				COAD - Colon adenocarcinoma(225;0.0905)|Colorectal(170;0.103)|all cancers(265;0.105)|Epithelial(280;0.148)										0.428571	249.586523	250.331352	72	96	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	79403639	79403639	5276	1	C	G	G	G	390	30	ELTD1	3	3
LPHN2	23266	broad.mit.edu	37	1	82456358	82456358	+	Silent	SNP	A	T	T			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:82456358A>T	uc001dit.3	+	c.3741A>T	c.(3739-3741)GCA>GCT	p.A1247A	LPHN2_uc001dis.2_Silent_p.A227A|LPHN2_uc001diu.2_Silent_p.A1247A|LPHN2_uc001div.2_3'UTR|LPHN2_uc009wcd.2_3'UTR|LPHN2_uc001diw.2_Silent_p.A874A	NM_012302	NP_036434	O95490	LPHN2_HUMAN	latrophilin 2 precursor	1303	Cytoplasmic (Potential).				neuropeptide signaling pathway	integral to membrane|plasma membrane	G-protein coupled receptor activity|latrotoxin receptor activity|sugar binding			ovary(2)|central_nervous_system(1)	3				all cancers(265;0.00142)|Epithelial(280;0.00829)|OV - Ovarian serous cystadenocarcinoma(397;0.077)|STAD - Stomach adenocarcinoma(256;0.248)										0.378378	82.581174	83.541782	28	46	KEEP	---	---	---	---	capture		Silent	SNP	82456358	82456358	9289	1	A	T	T	T	80	7	LPHN2	3	3
CLCA2	9635	broad.mit.edu	37	1	86891153	86891153	+	Nonsense_Mutation	SNP	T	A	A			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:86891153T>A	uc001dlr.3	+	c.318T>A	c.(316-318)TAT>TAA	p.Y106*		NM_006536	NP_006527	Q9UQC9	CLCA2_HUMAN	chloride channel accessory 2 precursor	106	Extracellular (Potential).				cell adhesion	basal plasma membrane|cell junction|extracellular region|integral to plasma membrane	chloride channel activity			ovary(1)|breast(1)	2		Lung NSC(277;0.238)		all cancers(265;0.0233)|Epithelial(280;0.0452)		Melanoma(157;1000 1898 5363 5664 48018)|Ovarian(88;135 1366 2838 28875 34642)								0.518519	94.602955	94.61915	28	26	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	86891153	86891153	3594	1	T	A	A	A	660	51	CLCA2	5	3
ABCA4	24	broad.mit.edu	37	1	94481334	94481334	+	Missense_Mutation	SNP	T	G	G			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:94481334T>G	uc001dqh.2	-	c.5273A>C	c.(5272-5274)GAA>GCA	p.E1758A	ABCA4_uc009wdp.1_Missense_Mutation_p.E26A	NM_000350	NP_000341	P78363	ABCA4_HUMAN	ATP-binding cassette, sub-family A member 4	1758					phototransduction, visible light|visual perception	integral to plasma membrane|membrane fraction	ATP binding|ATPase activity, coupled to transmembrane movement of substances			ovary(4)|central_nervous_system(2)|breast(1)	7		all_lung(203;0.000757)|Lung NSC(277;0.00335)		all cancers(265;0.00432)|GBM - Glioblastoma multiforme(16;0.00715)|Epithelial(280;0.171)										0.444444	107.718259	107.906489	32	40	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	94481334	94481334	35	1	T	G	G	G	806	62	ABCA4	4	4
DPYD	1806	broad.mit.edu	37	1	98157295	98157295	+	Missense_Mutation	SNP	A	C	C			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:98157295A>C	uc001drv.2	-	c.740T>G	c.(739-741)CTA>CGA	p.L247R	DPYD_uc010oub.1_Non-coding_Transcript	NM_000110	NP_000101	Q12882	DPYD_HUMAN	dihydropyrimidine dehydrogenase isoform 1	247					'de novo' pyrimidine base biosynthetic process|oxidation-reduction process|purine base catabolic process|thymidine catabolic process|thymine catabolic process|UMP biosynthetic process|uracil catabolic process	cytosol	4 iron, 4 sulfur cluster binding|dihydroorotate oxidase activity|dihydropyrimidine dehydrogenase (NADP+) activity|electron carrier activity|flavin adenine dinucleotide binding|metal ion binding|NADP binding|protein homodimerization activity			ovary(3)|breast(2)	5		all_epithelial(167;0.000185)|all_lung(203;0.00318)|Lung NSC(277;0.00994)		Colorectal(170;0.0165)|Epithelial(280;0.0526)|all cancers(265;0.104)|READ - Rectum adenocarcinoma(84;0.171)|Lung(183;0.216)	Capecitabine(DB01101)|Enfuvirtide(DB00109)					533				0.432836	193.828909	194.355721	58	76	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	98157295	98157295	4929	1	A	C	C	C	195	15	DPYD	4	4
ZNF133	7692	broad.mit.edu	37	20	18297071	18297071	+	Nonsense_Mutation	SNP	G	T	T			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr20:18297071G>T	uc010zrv.1	+	c.1585G>T	c.(1585-1587)GAG>TAG	p.E529*	ZNF133_uc010gcq.2_Nonsense_Mutation_p.E526*|ZNF133_uc010zrw.1_Nonsense_Mutation_p.E463*|ZNF133_uc010gcr.2_Nonsense_Mutation_p.E526*|ZNF133_uc010zrx.1_Nonsense_Mutation_p.E431*|ZNF133_uc002wql.3_Nonsense_Mutation_p.E525*|ZNF133_uc010gcs.2_Nonsense_Mutation_p.E525*|ZNF133_uc010zry.1_Nonsense_Mutation_p.E431*|ZNF133_uc002wqm.2_Nonsense_Mutation_p.E526*	NM_003434	NP_003425	P52736	ZN133_HUMAN	zinc finger protein 133	526	C2H2-type 12.				regulation of transcription, DNA-dependent	nucleus	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)|pancreas(1)	2														0.360656	115.088165	117.163495	44	78	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	18297071	18297071	18314	20	G	T	T	T	429	33	ZNF133	5	2
MYLK2	85366	broad.mit.edu	37	20	30408011	30408011	+	Silent	SNP	G	C	C			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr20:30408011G>C	uc002wwq.2	+	c.135G>C	c.(133-135)CCG>CCC	p.P45P		NM_033118	NP_149109	Q9H1R3	MYLK2_HUMAN	skeletal myosin light chain kinase	45					cardiac muscle contraction|cardiac muscle tissue morphogenesis|regulation of muscle filament sliding	sarcomere	ATP binding|calmodulin binding|calmodulin-dependent protein kinase activity|myosin light chain kinase activity			lung(2)|skin(2)|ovary(1)|central_nervous_system(1)	6			Colorectal(19;0.00306)|COAD - Colon adenocarcinoma(19;0.0347)							150				0.607843	94.32528	94.845238	31	20	KEEP	---	---	---	---	capture		Silent	SNP	30408011	30408011	10452	20	G	C	C	C	496	39	MYLK2	3	3
FAM83C	128876	broad.mit.edu	37	20	33874960	33874960	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr20:33874960G>A	uc010zux.1	-	c.1622C>T	c.(1621-1623)CCA>CTA	p.P541L	EIF6_uc002xbv.1_5'Flank|EIF6_uc002xbx.1_5'Flank|EIF6_uc002xbz.1_5'Flank|EIF6_uc002xby.1_5'Flank|FAM83C_uc002xcb.1_Missense_Mutation_p.P196L	NM_178468	NP_848563	Q9BQN1	FA83C_HUMAN	hypothetical protein LOC128876	541										ovary(2)	2			BRCA - Breast invasive adenocarcinoma(18;0.00252)											0.397436	81.177764	81.903795	31	47	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	33874960	33874960	5861	20	G	A	A	A	611	47	FAM83C	2	2
RBM12	10137	broad.mit.edu	37	20	34240756	34240756	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr20:34240756C>A	uc002xdq.2	-	c.2489G>T	c.(2488-2490)GGC>GTC	p.G830V	CPNE1_uc010zvj.1_Intron|CPNE1_uc002xde.2_Intron|CPNE1_uc002xdf.2_Intron|CPNE1_uc002xdg.2_Intron|CPNE1_uc010gfi.2_Intron|CPNE1_uc010gfj.2_Intron|CPNE1_uc002xdh.2_Intron|CPNE1_uc002xdi.2_Intron|CPNE1_uc002xdj.2_Intron|CPNE1_uc002xdk.2_Intron|CPNE1_uc002xdl.2_Intron|CPNE1_uc002xdm.2_Intron|CPNE1_uc010gfk.1_Intron|CPNE1_uc002xdn.1_Intron|CPNE1_uc002xdo.1_Intron|CPNE1_uc002xdp.1_Intron|RBM12_uc002xdr.2_Missense_Mutation_p.G830V|RBM12_uc002xds.2_Missense_Mutation_p.G830V	NM_152838	NP_690051	Q9NTZ6	RBM12_HUMAN	RNA binding motif protein 12	830	Gly-rich.|Pro-rich.					nucleus	nucleotide binding|protein binding|RNA binding			ovary(3)	3	Lung NSC(9;0.00608)|all_lung(11;0.00918)		BRCA - Breast invasive adenocarcinoma(18;0.00953)											0.548387	46.671118	46.73426	17	14	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	34240756	34240756	13574	20	C	A	A	A	338	26	RBM12	2	2
EMILIN3	90187	broad.mit.edu	37	20	39992303	39992303	+	Nonsense_Mutation	SNP	G	T	T			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr20:39992303G>T	uc002xjy.1	-	c.489C>A	c.(487-489)TAC>TAA	p.Y163*		NM_052846	NP_443078	Q9NT22	EMIL3_HUMAN	elastin microfibril interfacer 3	163						proteinaceous extracellular matrix				ovary(1)	1		Myeloproliferative disorder(115;0.00425)												0.357143	99.8924	101.656244	35	63	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	39992303	39992303	5287	20	G	T	T	T	620	48	EMILIN3	5	2
R3HDML	140902	broad.mit.edu	37	20	42973925	42973925	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr20:42973925G>T	uc002xls.1	+	c.536G>T	c.(535-537)CGG>CTG	p.R179L		NM_178491	NP_848586	Q9H3Y0	CRSPL_HUMAN	R3H domain containing-like precursor	179						extracellular region	peptidase inhibitor activity				0		Myeloproliferative disorder(115;0.028)	COAD - Colon adenocarcinoma(18;0.00189)											0.436975	336.981053	337.801805	104	134	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	42973925	42973925	13348	20	G	T	T	T	507	39	R3HDML	1	1
CDH22	64405	broad.mit.edu	37	20	44856177	44856177	+	Nonsense_Mutation	SNP	C	A	A			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr20:44856177C>A	uc002xrm.2	-	c.640G>T	c.(640-642)GAG>TAG	p.E214*	CDH22_uc010ghk.1_Nonsense_Mutation_p.E214*	NM_021248	NP_067071	Q9UJ99	CAD22_HUMAN	cadherin 22 precursor	214	Extracellular (Potential).|Cadherin 2.				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(4)	4		Myeloproliferative disorder(115;0.0122)												0.538462	79.114069	79.183593	28	24	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	44856177	44856177	3236	20	C	A	A	A	403	31	CDH22	5	1
TSHZ2	128553	broad.mit.edu	37	20	51872703	51872703	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr20:51872703C>A	uc002xwo.2	+	c.2706C>A	c.(2704-2706)AAC>AAA	p.N902K		NM_173485	NP_775756	Q9NRE2	TSH2_HUMAN	teashirt zinc finger homeobox 2	902	Homeobox; atypical.				multicellular organismal development|regulation of transcription, DNA-dependent	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(4)	4			STAD - Stomach adenocarcinoma(23;0.1)											0.634146	267.739525	269.686098	78	45	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	51872703	51872703	17175	20	C	A	A	A	246	19	TSHZ2	1	1
LAMA5	3911	broad.mit.edu	37	20	60910172	60910172	+	Missense_Mutation	SNP	T	A	A			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr20:60910172T>A	uc002ycq.2	-	c.2387A>T	c.(2386-2388)CAG>CTG	p.Q796L		NM_005560	NP_005551	O15230	LAMA5_HUMAN	laminin alpha 5 precursor	796	Laminin EGF-like 10.				angiogenesis|cell proliferation|cell recognition|cytoskeleton organization|endothelial cell differentiation|focal adhesion assembly|integrin-mediated signaling pathway|regulation of cell adhesion|regulation of cell migration|regulation of embryonic development|substrate adhesion-dependent cell spreading	extracellular space|laminin-1 complex|laminin-10 complex|laminin-11 complex	integrin binding|receptor activity|structural molecule activity			pancreas(1)	1	Breast(26;1.57e-08)		BRCA - Breast invasive adenocarcinoma(19;4.36e-06)		Alteplase(DB00009)|Anistreplase(DB00029)|Reteplase(DB00015)|Tenecteplase(DB00031)									0.555556	17.67649	17.700762	5	4	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	60910172	60910172	8932	20	T	A	A	A	715	55	LAMA5	3	3
TPD52L2	7165	broad.mit.edu	37	20	62521253	62521253	+	Silent	SNP	A	T	T			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr20:62521253A>T	uc002ygy.2	+	c.645A>T	c.(643-645)TCA>TCT	p.S215S	TPD52L2_uc002ygz.2_Silent_p.S206S|TPD52L2_uc002yha.2_Silent_p.S195S|TPD52L2_uc002yhb.2_Silent_p.S186S|TPD52L2_uc002yhc.2_Silent_p.S192S|TPD52L2_uc002yhd.2_Silent_p.S172S|TPD52L2_uc011abk.1_Silent_p.S143S|TPD52L2_uc011abl.1_Silent_p.S149S|TPD52L2_uc002yhe.2_Silent_p.S91S	NM_199360	NP_955392	O43399	TPD54_HUMAN	tumor protein D52-like 2 isoform a	192					regulation of cell proliferation	perinuclear region of cytoplasm	protein binding|protein homodimerization activity			ovary(1)	1	all_cancers(38;1.3e-12)|all_epithelial(29;2.23e-14)|Lung NSC(23;5.92e-10)|all_lung(23;2.08e-09)													0.193548	10.336799	13.061032	6	25	KEEP	---	---	---	---	capture		Silent	SNP	62521253	62521253	16943	20	A	T	T	T	80	7	TPD52L2	3	3
TPTE	7179	broad.mit.edu	37	21	10934087	10934087	+	Missense_Mutation	SNP	T	A	A			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr21:10934087T>A	uc002yip.1	-	c.890A>T	c.(889-891)AAT>ATT	p.N297I	TPTE_uc002yis.1_Non-coding_Transcript|TPTE_uc002yiq.1_Missense_Mutation_p.N279I|TPTE_uc002yir.1_Missense_Mutation_p.N259I|TPTE_uc010gkv.1_Missense_Mutation_p.N159I	NM_199261	NP_954870	P56180	TPTE_HUMAN	transmembrane phosphatase with tensin homology	297	Phosphatase tensin-type.				signal transduction	integral to membrane	ion channel activity|protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity			ovary(2)|lung(1)|breast(1)|skin(1)	5			Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723)	UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247)										0.333333	139.328491	142.943545	49	98	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	10934087	10934087	16974	21	T	A	A	A	676	52	TPTE	3	3
NCAM2	4685	broad.mit.edu	37	21	22658668	22658668	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr21:22658668C>A	uc002yld.1	+	c.417C>A	c.(415-417)AGC>AGA	p.S139R	NCAM2_uc011acb.1_Intron|NCAM2_uc011acc.1_Missense_Mutation_p.S164R	NM_004540	NP_004531	O15394	NCAM2_HUMAN	neural cell adhesion molecule 2 precursor	139	Ig-like C2-type 2.|Extracellular (Potential).				neuron cell-cell adhesion	integral to membrane|plasma membrane				ovary(4)	4		Lung NSC(9;0.195)		all cancers(11;0.00102)|OV - Ovarian serous cystadenocarcinoma(11;0.00121)|Epithelial(23;0.00147)|Colorectal(24;0.174)										0.437037	173.01778	173.480406	59	76	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	22658668	22658668	10602	21	C	A	A	A	324	25	NCAM2	2	2
KRTAP19-7	337974	broad.mit.edu	37	21	31933578	31933578	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr21:31933578G>T	uc011adb.1	-	c.31C>A	c.(31-33)CTA>ATA	p.L11I		NM_181614	NP_853645	Q3SYF9	KR197_HUMAN	keratin associated protein 19-7	11						intermediate filament					0														0.337838	66.870656	68.582704	25	49	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	31933578	31933578	8849	21	G	T	T	T	451	35	KRTAP19-7	2	2
KRTAP21-1	337977	broad.mit.edu	37	21	32127565	32127565	+	Silent	SNP	G	T	T			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr21:32127565G>T	uc011adi.1	-	c.132C>A	c.(130-132)TCC>TCA	p.S44S		NM_181619	NP_853650	Q3LI58	KR211_HUMAN	keratin associated protein 21-1	44						intermediate filament				breast(1)	1														0.321212	132.339701	137.013143	53	112	KEEP	---	---	---	---	capture		Silent	SNP	32127565	32127565	8857	21	G	T	T	T	548	43	KRTAP21-1	2	2
PRDM15	63977	broad.mit.edu	37	21	43279791	43279791	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr21:43279791C>A	uc002yzq.1	-	c.941G>T	c.(940-942)TGT>TTT	p.C314F	PRDM15_uc002yzo.2_Missense_Mutation_p.C51F|PRDM15_uc002yzp.2_Missense_Mutation_p.C51F|PRDM15_uc002yzr.1_Missense_Mutation_p.C51F	NM_022115	NP_071398	P57071	PRD15_HUMAN	PR domain containing 15 isoform 1	314					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0														0.25	19.783263	21.602235	8	24	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	43279791	43279791	12898	21	C	A	A	A	221	17	PRDM15	2	2
TRAPPC10	7109	broad.mit.edu	37	21	45504114	45504114	+	Nonsense_Mutation	SNP	G	T	T			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr21:45504114G>T	uc002zea.2	+	c.2350G>T	c.(2350-2352)GAG>TAG	p.E784*	TRAPPC10_uc010gpo.2_Nonsense_Mutation_p.E495*|TRAPPC10_uc011afa.1_Nonsense_Mutation_p.E203*	NM_003274	NP_003265	P48553	TPC10_HUMAN	trafficking protein particle complex 10	784					vesicle-mediated transport	Golgi apparatus|integral to membrane	binding|sodium ion transmembrane transporter activity			ovary(1)|skin(1)	2														0.357143	37.314289	38.068588	15	27	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	45504114	45504114	17001	21	G	T	T	T	533	41	TRAPPC10	5	2
KRTAP12-2	353323	broad.mit.edu	37	21	46086733	46086733	+	Missense_Mutation	SNP	C	G	G			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr21:46086733C>G	uc002zfu.2	-	c.71G>C	c.(70-72)TGT>TCT	p.C24S	C21orf29_uc002zfe.1_Intron|C21orf29_uc010gpv.1_Intron	NM_181684	NP_859012	P59991	KR122_HUMAN	keratin associated protein 12-2	24	3.|23 X 5 AA approximate repeats.					keratin filament					0														0.514286	128.308012	128.32075	36	34	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	46086733	46086733	8834	21	C	G	G	G	221	17	KRTAP12-2	3	3
DGCR14	8220	broad.mit.edu	37	22	19132106	19132106	+	Silent	SNP	C	A	A			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr22:19132106C>A	uc002zou.2	-	c.48G>T	c.(46-48)GCG>GCT	p.A16A	DGCR14_uc002zot.2_5'UTR|DGCR14_uc002zov.2_Non-coding_Transcript	NM_022719	NP_073210	Q96DF8	DGC14_HUMAN	DiGeorge syndrome critical region protein 14	16					nervous system development|nuclear mRNA splicing, via spliceosome	catalytic step 2 spliceosome				ovary(1)	1	Colorectal(54;0.0993)									49				1	29.316868	29.312957	8	0	KEEP	---	---	---	---	capture		Silent	SNP	19132106	19132106	4639	22	C	A	A	A	236	19	DGCR14	1	1
LZTR1	8216	broad.mit.edu	37	22	21340155	21340155	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr22:21340155C>T	uc002zto.2	+	c.289C>T	c.(289-291)CGG>TGG	p.R97W	LZTR1_uc002ztn.2_Missense_Mutation_p.R56W|LZTR1_uc011ahy.1_Intron|LZTR1_uc010gsr.1_5'Flank	NM_006767	NP_006758	Q8N653	LZTR1_HUMAN	leucine-zipper-like transcription regulator 1	97	Kelch 1.				anatomical structure morphogenesis		sequence-specific DNA binding transcription factor activity			ovary(2)|lung(2)	4	all_cancers(11;1.83e-25)|all_epithelial(7;9.19e-23)|Lung NSC(8;3.06e-15)|all_lung(8;5.05e-14)|Melanoma(16;0.000465)|Ovarian(15;0.0028)|Colorectal(54;0.0332)|all_neural(72;0.142)	Lung SC(17;0.0262)	LUSC - Lung squamous cell carcinoma(15;0.000204)|Lung(15;0.00494)|Epithelial(17;0.195)							1299				0.913043	68.854229	72.654904	21	2	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	21340155	21340155	9514	22	C	T	T	T	347	27	LZTR1	1	1
SEZ6L	23544	broad.mit.edu	37	22	26688759	26688759	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr22:26688759C>A	uc003acb.2	+	c.482C>A	c.(481-483)ACG>AAG	p.T161K	SEZ6L_uc003acc.2_Missense_Mutation_p.T161K|SEZ6L_uc011akc.1_Missense_Mutation_p.T161K|SEZ6L_uc003acd.2_Missense_Mutation_p.T161K|SEZ6L_uc011akd.1_Missense_Mutation_p.T161K|SEZ6L_uc003ace.2_Missense_Mutation_p.T161K|SEZ6L_uc003acf.1_5'UTR|SEZ6L_uc010gvc.1_5'UTR	NM_021115	NP_066938	Q9BYH1	SE6L1_HUMAN	seizure related 6 homolog (mouse)-like	161	Extracellular (Potential).					endoplasmic reticulum membrane|integral to membrane		p.T161M(1)		ovary(4)|central_nervous_system(1)|pancreas(1)	6														0.863636	533.360351	556.12634	152	24	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	26688759	26688759	14632	22	C	A	A	A	247	19	SEZ6L	1	1
PMM1	5372	broad.mit.edu	37	22	41974850	41974850	+	Silent	SNP	C	T	T			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr22:41974850C>T	uc003bal.2	-	c.510G>A	c.(508-510)CTG>CTA	p.L170L		NM_002676	NP_002667	Q92871	PMM1_HUMAN	phosphomannomutase 1	170					dolichol-linked oligosaccharide biosynthetic process|GDP-mannose biosynthetic process|post-translational protein modification|protein N-linked glycosylation via asparagine	cytosol	metal ion binding|phosphomannomutase activity				0														0.875	22.836204	23.927816	7	1	KEEP	---	---	---	---	capture		Silent	SNP	41974850	41974850	12562	22	C	T	T	T	366	29	PMM1	2	2
ZBED4	9889	broad.mit.edu	37	22	50278348	50278348	+	Silent	SNP	G	T	T			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr22:50278348G>T	uc003bix.2	+	c.1038G>T	c.(1036-1038)ACG>ACT	p.T346T		NM_014838	NP_055653	O75132	ZBED4_HUMAN	zinc finger, BED-type containing 4	346						cytoplasm|nucleus	DNA binding|metal ion binding|protein dimerization activity			ovary(2)	2		all_cancers(38;8.58e-10)|all_epithelial(38;1.15e-08)|all_lung(38;0.000109)|Lung NSC(38;0.0018)|Breast(42;0.00191)|Ovarian(80;0.0164)|Lung SC(80;0.164)		UCEC - Uterine corpus endometrioid carcinoma (28;0.168)|BRCA - Breast invasive adenocarcinoma(115;0.2)|LUAD - Lung adenocarcinoma(64;0.247)										0.903226	95.466242	100.467953	28	3	KEEP	---	---	---	---	capture		Silent	SNP	50278348	50278348	18104	22	G	T	T	T	496	39	ZBED4	1	1
PLXNB2	23654	broad.mit.edu	37	22	50721207	50721207	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr22:50721207C>T	uc003bkv.3	-	c.2920G>A	c.(2920-2922)GGC>AGC	p.G974S	PLXNB2_uc003bkt.1_5'Flank|PLXNB2_uc003bku.1_5'Flank	NM_012401	NP_036533	O15031	PLXB2_HUMAN	plexin B2 precursor	974	Extracellular (Potential).|IPT/TIG 2.				regulation of small GTPase mediated signal transduction	integral to membrane|intracellular	GTPase activator activity|protein binding|receptor activity			ovary(4)|central_nervous_system(1)	5		all_cancers(38;5.78e-13)|all_epithelial(38;1.71e-11)|all_lung(38;3.89e-05)|Breast(42;0.000523)|Lung NSC(38;0.000992)|Ovarian(80;0.0221)|Hepatocellular(38;0.0691)|Lung SC(80;0.113)		BRCA - Breast invasive adenocarcinoma(115;0.205)|LUAD - Lung adenocarcinoma(64;0.247)										1	32.291668	32.289711	9	0	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	50721207	50721207	12550	22	C	T	T	T	299	23	PLXNB2	1	1
LMF2	91289	broad.mit.edu	37	22	50944120	50944120	+	Missense_Mutation	SNP	C	A	A	rs113089468		TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr22:50944120C>A	uc003blp.2	-	c.899G>T	c.(898-900)CGC>CTC	p.R300L	LMF2_uc010hba.2_Missense_Mutation_p.R122L|LMF2_uc003blo.2_Missense_Mutation_p.R275L|NCAPH2_uc003blq.3_5'Flank|NCAPH2_uc003blv.2_5'Flank|NCAPH2_uc003blr.3_5'Flank|NCAPH2_uc010hbb.2_5'Flank|NCAPH2_uc003blu.3_5'Flank|NCAPH2_uc003bls.3_5'Flank|NCAPH2_uc003blt.3_5'Flank|NCAPH2_uc003blw.3_5'Flank|NCAPH2_uc003blx.3_5'Flank|NCAPH2_uc003bly.3_5'Flank	NM_033200	NP_149977	Q9BU23	LMF2_HUMAN	lipase maturation factor 2	300						endoplasmic reticulum membrane|integral to membrane				breast(1)	1		all_cancers(38;1.31e-09)|all_epithelial(38;1.81e-08)|all_lung(38;0.000817)|Breast(42;0.00387)|Lung NSC(38;0.0124)|Ovarian(80;0.104)|Lung SC(80;0.162)|Hepatocellular(38;0.178)		BRCA - Breast invasive adenocarcinoma(115;0.205)|LUAD - Lung adenocarcinoma(64;0.247)										1	25.645099	25.637302	7	0	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	50944120	50944120	9175	22	C	A	A	A	351	27	LMF2	1	1
RNF149	284996	broad.mit.edu	37	2	101924963	101924963	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:101924963C>A	uc002taz.1	-	c.88G>T	c.(88-90)GCC>TCC	p.A30S	RNF149_uc002tax.1_Non-coding_Transcript	NM_173647	NP_775918	Q8NC42	RN149_HUMAN	ring finger protein 149 precursor	30						integral to membrane	ligase activity|zinc ion binding			ovary(1)|breast(1)	2						Colon(25;331 612 6521 7355 31028)								0.55	31.222346	31.265529	11	9	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	101924963	101924963	13927	2	C	A	A	A	338	26	RNF149	2	2
CNTNAP5	129684	broad.mit.edu	37	2	125671764	125671764	+	Missense_Mutation	SNP	A	T	T			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:125671764A>T	uc010flu.2	+	c.3823A>T	c.(3823-3825)ATG>TTG	p.M1275L	CNTNAP5_uc002tno.2_Missense_Mutation_p.M1274L	NM_130773	NP_570129	Q8WYK1	CNTP5_HUMAN	contactin associated protein-like 5 precursor	1274	Cytoplasmic (Potential).				cell adhesion|signal transduction	integral to membrane	receptor binding			ovary(10)	10				BRCA - Breast invasive adenocarcinoma(221;0.248)										0.234899	181.017278	200.161619	70	228	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	125671764	125671764	3788	2	A	T	T	T	156	12	CNTNAP5	3	3
GPR148	344561	broad.mit.edu	37	2	131487498	131487498	+	Silent	SNP	G	T	T			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:131487498G>T	uc002trv.1	+	c.774G>T	c.(772-774)CGG>CGT	p.R258R		NM_207364	NP_997247	Q8TDV2	GP148_HUMAN	G protein-coupled receptor 148	258	Cytoplasmic (Potential).					integral to membrane|plasma membrane	G-protein coupled receptor activity				0	Colorectal(110;0.1)													0.321839	221.441093	228.782035	84	177	KEEP	---	---	---	---	capture		Silent	SNP	131487498	131487498	6928	2	G	T	T	T	548	43	GPR148	2	2
ZEB2	9839	broad.mit.edu	37	2	145156031	145156031	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:145156031G>T	uc002tvu.2	-	c.2723C>A	c.(2722-2724)ACT>AAT	p.T908N	ZEB2_uc002tvv.2_Missense_Mutation_p.T902N|ZEB2_uc010zbm.1_Missense_Mutation_p.T879N|ZEB2_uc010fnp.2_Intron|ZEB2_uc010fnq.1_Missense_Mutation_p.T937N	NM_014795	NP_055610	O60315	ZEB2_HUMAN	zinc finger homeobox 1b	908					negative regulation of transcription, DNA-dependent	cytoplasm|nucleolus	phosphatase regulator activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|SMAD binding|zinc ion binding			ovary(5)|pancreas(2)|large_intestine(1)	8				BRCA - Breast invasive adenocarcinoma(221;0.112)		Melanoma(33;1235 1264 5755 16332)								0.46831	417.02424	417.274231	133	151	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	145156031	145156031	18212	2	G	T	T	T	468	36	ZEB2	2	2
TPO	7173	broad.mit.edu	37	2	1481057	1481057	+	Missense_Mutation	SNP	T	G	G			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:1481057T>G	uc002qww.2	+	c.1019T>G	c.(1018-1020)CTG>CGG	p.L340R	TPO_uc010ewj.2_Intron|TPO_uc002qwu.2_Missense_Mutation_p.L340R|TPO_uc002qwr.2_Missense_Mutation_p.L340R|TPO_uc002qwx.2_Missense_Mutation_p.L340R|TPO_uc010yio.1_Intron|TPO_uc010yip.1_Missense_Mutation_p.L340R	NM_000547	NP_000538	P07202	PERT_HUMAN	thyroid peroxidase isoform a	340	Extracellular (Potential).				cellular nitrogen compound metabolic process|hormone biosynthetic process|hydrogen peroxide catabolic process|oxidation-reduction process	cell surface|cytoplasm|integral to plasma membrane	calcium ion binding|heme binding|iodide peroxidase activity			ovary(6)|pancreas(6)|skin(3)|lung(1)|kidney(1)	17	all_hematologic(175;0.0487)|Acute lymphoblastic leukemia(172;0.0627)	all_cancers(51;0.0338)		all cancers(51;0.0356)|OV - Ovarian serous cystadenocarcinoma(76;0.0748)|Epithelial(75;0.12)	Carbimazole(DB00389)|Methimazole(DB00763)|Propylthiouracil(DB00550)					723				0.583333	24.526571	24.599305	7	5	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	1481057	1481057	16954	2	T	G	G	G	715	55	TPO	4	4
DDX1	1653	broad.mit.edu	37	2	15770224	15770224	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:15770224G>T	uc002rce.2	+	c.2082G>T	c.(2080-2082)AGG>AGT	p.R694S		NM_004939	NP_004930	Q92499	DDX1_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 1	694	Necessary for interaction with HNRNPK.				DNA duplex unwinding|double-strand break repair|multicellular organismal development|regulation of transcription, DNA-dependent|regulation of translational initiation|spliceosome assembly|transcription, DNA-dependent	nucleus|stress granule|tRNA-splicing ligase complex	ATP binding|ATP-dependent helicase activity|chromatin binding|DNA binding|DNA/RNA helicase activity|exonuclease activity|poly(A) RNA binding|protein binding|RNA helicase activity|transcription cofactor activity			central_nervous_system(2)|upper_aerodigestive_tract(1)|ovary(1)	4	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.197)	all_epithelial(98;2.96e-07)|Acute lymphoblastic leukemia(84;4.24e-05)|Ovarian(717;0.0694)	GBM - Glioblastoma multiforme(3;0.00969)	Epithelial(75;4.35e-05)|OV - Ovarian serous cystadenocarcinoma(76;0.133)						1245				0.063584	-11.619557	22.678348	11	162	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	15770224	15770224	4512	2	G	T	T	T	555	43	DDX1	2	2
PXDN	7837	broad.mit.edu	37	2	1653092	1653092	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:1653092C>A	uc002qxa.2	-	c.2460G>T	c.(2458-2460)CAG>CAT	p.Q820H		NM_012293	NP_036425	Q92626	PXDN_HUMAN	peroxidasin precursor	820					extracellular matrix organization|hydrogen peroxide catabolic process|immune response|oxidation-reduction process	endoplasmic reticulum|extracellular space|proteinaceous extracellular matrix	extracellular matrix structural constituent|heme binding|interleukin-1 receptor antagonist activity|peroxidase activity			pancreas(6)|ovary(2)	8	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.0797)	all_cancers(51;0.0845)|Lung NSC(108;0.00641)|all_epithelial(98;0.00716)		all cancers(51;0.0492)|OV - Ovarian serous cystadenocarcinoma(76;0.0973)|Epithelial(75;0.17)|GBM - Glioblastoma multiforme(21;0.228)						2093				0.6	92.046127	92.481877	30	20	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	1653092	1653092	13305	2	C	A	A	A	259	20	PXDN	2	2
SCN3A	6328	broad.mit.edu	37	2	165948941	165948941	+	Missense_Mutation	SNP	T	A	A			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:165948941T>A	uc002ucx.2	-	c.4630A>T	c.(4630-4632)ATG>TTG	p.M1544L	SCN3A_uc010zcy.1_Missense_Mutation_p.M27L|SCN3A_uc002ucy.2_Missense_Mutation_p.M1495L|SCN3A_uc002ucz.2_Missense_Mutation_p.M1495L	NM_006922	NP_008853	Q9NY46	SCN3A_HUMAN	sodium channel, voltage-gated, type III, alpha	1544	Helical; Name=S1 of repeat IV; (Potential).					voltage-gated sodium channel complex	voltage-gated sodium channel activity			ovary(4)|breast(3)|central_nervous_system(1)	8					Lamotrigine(DB00555)									0.538462	174.695746	174.828908	56	48	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	165948941	165948941	14400	2	T	A	A	A	650	50	SCN3A	3	3
XIRP2	129446	broad.mit.edu	37	2	168067310	168067310	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:168067310G>T	uc002udx.2	+	c.628G>T	c.(628-630)GTG>TTG	p.V210L	XIRP2_uc010fpn.2_Missense_Mutation_p.V243L|XIRP2_uc010fpo.2_Missense_Mutation_p.V210L|XIRP2_uc010fpp.2_Missense_Mutation_p.V210L|XIRP2_uc002udy.2_Missense_Mutation_p.V35L|XIRP2_uc010fpq.2_5'UTR|XIRP2_uc010fpr.2_5'UTR	NM_152381	NP_689594	A4UGR9	XIRP2_HUMAN	xin actin-binding repeat containing 2 isoform 1	35					actin cytoskeleton organization	cell junction	actin binding			ovary(6)|pancreas(1)|skin(1)	8														0.333333	212.935475	218.306624	73	146	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	168067310	168067310	18011	2	G	T	T	T	624	48	XIRP2	2	2
XIRP2	129446	broad.mit.edu	37	2	168101776	168101776	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:168101776G>T	uc002udx.2	+	c.3874G>T	c.(3874-3876)GAC>TAC	p.D1292Y	XIRP2_uc010fpn.2_Intron|XIRP2_uc010fpo.2_Intron|XIRP2_uc010fpp.2_Intron|XIRP2_uc002udy.2_Missense_Mutation_p.D1117Y|XIRP2_uc010fpq.2_Missense_Mutation_p.D1070Y|XIRP2_uc010fpr.2_Intron|XIRP2_uc010fps.1_5'Flank	NM_152381	NP_689594	A4UGR9	XIRP2_HUMAN	xin actin-binding repeat containing 2 isoform 1	1117					actin cytoskeleton organization	cell junction	actin binding			ovary(6)|pancreas(1)|skin(1)	8														0.360129	311.197045	316.560419	112	199	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	168101776	168101776	18011	2	G	T	T	T	585	45	XIRP2	2	2
LRP2	4036	broad.mit.edu	37	2	170063751	170063751	+	Missense_Mutation	SNP	T	C	C			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:170063751T>C	uc002ues.2	-	c.6479A>G	c.(6478-6480)TAT>TGT	p.Y2160C		NM_004525	NP_004516	P98164	LRP2_HUMAN	low density lipoprotein-related protein 2	2160	LDL-receptor class B 21.|Extracellular (Potential).				hormone biosynthetic process|protein glycosylation|receptor-mediated endocytosis|vitamin D metabolic process	coated pit|integral to membrane|lysosome	calcium ion binding|receptor activity|SH3 domain binding			ovary(13)|central_nervous_system(4)|large_intestine(3)|kidney(2)|pancreas(1)	23				STAD - Stomach adenocarcinoma(1183;0.000766)|COAD - Colon adenocarcinoma(177;0.0101)	Gentamicin(DB00798)|Insulin Glargine recombinant(DB00047)|Insulin Lyspro recombinant(DB00046)|Insulin recombinant(DB00030)|Insulin, porcine(DB00071)|Urokinase(DB00013)					2055				0.546392	196.214497	196.402128	53	44	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	170063751	170063751	9329	2	T	C	C	C	637	49	LRP2	4	4
LRP2	4036	broad.mit.edu	37	2	170097780	170097780	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:170097780C>A	uc002ues.2	-	c.3763G>T	c.(3763-3765)GAC>TAC	p.D1255Y	LRP2_uc010zdf.1_Missense_Mutation_p.D1118Y	NM_004525	NP_004516	P98164	LRP2_HUMAN	low density lipoprotein-related protein 2	1255	Extracellular (Potential).|LDL-receptor class A 13.				hormone biosynthetic process|protein glycosylation|receptor-mediated endocytosis|vitamin D metabolic process	coated pit|integral to membrane|lysosome	calcium ion binding|receptor activity|SH3 domain binding			ovary(13)|central_nervous_system(4)|large_intestine(3)|kidney(2)|pancreas(1)	23				STAD - Stomach adenocarcinoma(1183;0.000766)|COAD - Colon adenocarcinoma(177;0.0101)	Gentamicin(DB00798)|Insulin Glargine recombinant(DB00047)|Insulin Lyspro recombinant(DB00046)|Insulin recombinant(DB00030)|Insulin, porcine(DB00071)|Urokinase(DB00013)					2055				0.522449	379.531908	379.635606	128	117	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	170097780	170097780	9329	2	C	A	A	A	416	32	LRP2	2	2
RAPGEF4	11069	broad.mit.edu	37	2	173855582	173855582	+	Silent	SNP	T	C	C			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:173855582T>C	uc002uhv.3	+	c.1419T>C	c.(1417-1419)GAT>GAC	p.D473D	RAPGEF4_uc002uhw.3_Silent_p.D329D|RAPGEF4_uc010zec.1_Silent_p.D320D|RAPGEF4_uc010zed.1_Silent_p.D302D|RAPGEF4_uc010zee.1_Silent_p.D320D|RAPGEF4_uc010fqo.2_Silent_p.D302D|RAPGEF4_uc010zef.1_Silent_p.D253D|RAPGEF4_uc010zeg.1_Silent_p.D300D|RAPGEF4_uc010zeh.1_Silent_p.D253D	NM_007023	NP_008954	Q8WZA2	RPGF4_HUMAN	Rap guanine nucleotide exchange factor (GEF) 4	473	cAMP 2.				blood coagulation|energy reserve metabolic process|G-protein coupled receptor protein signaling pathway|regulation of insulin secretion|regulation of protein phosphorylation|regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cAMP-dependent protein kinase complex|membrane fraction|plasma membrane	cAMP binding|cAMP-dependent protein kinase regulator activity|Ras GTPase binding|Ras guanyl-nucleotide exchange factor activity			large_intestine(2)|kidney(1)|central_nervous_system(1)	4			OV - Ovarian serous cystadenocarcinoma(117;0.194)											0.360656	68.934627	69.976645	22	39	KEEP	---	---	---	---	capture		Silent	SNP	173855582	173855582	13506	2	T	C	C	C	660	51	RAPGEF4	4	4
RAPGEF4	11069	broad.mit.edu	37	2	173891808	173891808	+	Splice_Site_SNP	SNP	G	T	T			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:173891808G>T	uc002uhv.3	+	c.2380_splice	c.e25-1	p.L794_splice	RAPGEF4_uc002uhw.3_Splice_Site_SNP_p.L650_splice	NM_007023	NP_008954			Rap guanine nucleotide exchange factor (GEF) 4						blood coagulation|energy reserve metabolic process|G-protein coupled receptor protein signaling pathway|regulation of insulin secretion|regulation of protein phosphorylation|regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cAMP-dependent protein kinase complex|membrane fraction|plasma membrane	cAMP binding|cAMP-dependent protein kinase regulator activity|Ras GTPase binding|Ras guanyl-nucleotide exchange factor activity			large_intestine(2)|kidney(1)|central_nervous_system(1)	4			OV - Ovarian serous cystadenocarcinoma(117;0.194)											0.48	146.090834	146.125815	48	52	KEEP	---	---	---	---	capture		Splice_Site_SNP	SNP	173891808	173891808	13506	2	G	T	T	T	442	34	RAPGEF4	5	2
TTN	7273	broad.mit.edu	37	2	179484542	179484542	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:179484542G>T	uc010zfg.1	-	c.38798C>A	c.(38797-38799)GCA>GAA	p.A12933E	TTN_uc010zfh.1_Missense_Mutation_p.A6628E|TTN_uc010zfi.1_Missense_Mutation_p.A6561E|TTN_uc010zfj.1_Missense_Mutation_p.A6436E	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	3260										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				0.533981	347.851142	348.056965	110	96	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	179484542	179484542	17290	2	G	T	T	T	598	46	TTN	2	2
PDE1A	5136	broad.mit.edu	37	2	183104919	183104919	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:183104919C>A	uc002uoq.1	-	c.316G>T	c.(316-318)GGG>TGG	p.G106W	PDE1A_uc010zfp.1_Missense_Mutation_p.G2W|PDE1A_uc010zfq.1_Missense_Mutation_p.G106W|PDE1A_uc002uor.2_Missense_Mutation_p.G90W|PDE1A_uc002uos.2_Missense_Mutation_p.G106W|PDE1A_uc002uou.2_Missense_Mutation_p.G72W	NM_005019	NP_005010	P54750	PDE1A_HUMAN	phosphodiesterase 1A isoform 1	106					activation of phospholipase C activity|nerve growth factor receptor signaling pathway|platelet activation	cytosol	3',5'-cyclic-AMP phosphodiesterase activity|3',5'-cyclic-GMP phosphodiesterase activity|calmodulin binding|calmodulin-dependent cyclic-nucleotide phosphodiesterase activity|metal ion binding			ovary(1)	1			OV - Ovarian serous cystadenocarcinoma(117;0.061)											0.315186	278.316845	288.874473	110	239	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	183104919	183104919	12054	2	C	A	A	A	286	22	PDE1A	2	2
ZNF804A	91752	broad.mit.edu	37	2	185798332	185798332	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:185798332G>T	uc002uph.2	+	c.258G>T	c.(256-258)AGG>AGT	p.R86S		NM_194250	NP_919226	Q7Z570	Z804A_HUMAN	zinc finger protein 804A	86						intracellular	zinc ion binding			ovary(6)|large_intestine(1)|pancreas(1)	8														0.264151	66.174594	71.492181	28	78	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	185798332	185798332	18768	2	G	T	T	T	542	42	ZNF804A	2	2
ZNF804A	91752	broad.mit.edu	37	2	185802533	185802533	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:185802533G>T	uc002uph.2	+	c.2410G>T	c.(2410-2412)GCT>TCT	p.A804S		NM_194250	NP_919226	Q7Z570	Z804A_HUMAN	zinc finger protein 804A	804						intracellular	zinc ion binding			ovary(6)|large_intestine(1)|pancreas(1)	8														0.282258	94.37276	99.654465	35	89	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	185802533	185802533	18768	2	G	T	T	T	598	46	ZNF804A	2	2
CALCRL	10203	broad.mit.edu	37	2	188247947	188247947	+	Missense_Mutation	SNP	T	A	A			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:188247947T>A	uc002upv.3	-	c.137A>T	c.(136-138)TAT>TTT	p.Y46F	CALCRL_uc010frt.2_Missense_Mutation_p.Y46F	NM_005795	NP_005786	Q16602	CALRL_HUMAN	calcitonin receptor-like precursor	46	Extracellular (Potential).					integral to plasma membrane				ovary(1)	1			OV - Ovarian serous cystadenocarcinoma(117;0.0554)|Epithelial(96;0.227)											0.446701	273.489585	273.974321	88	109	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	188247947	188247947	2696	2	T	A	A	A	637	49	CALCRL	3	3
PARD3B	117583	broad.mit.edu	37	2	206023618	206023618	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:206023618G>T	uc002var.1	+	c.1607G>T	c.(1606-1608)GGC>GTC	p.G536V	PARD3B_uc010fub.1_Missense_Mutation_p.G536V|PARD3B_uc002vao.1_Missense_Mutation_p.G536V|PARD3B_uc002vap.1_Intron|PARD3B_uc002vaq.1_Missense_Mutation_p.G536V	NM_152526	NP_689739	Q8TEW8	PAR3L_HUMAN	par-3 partitioning defective 3 homolog B isoform	536	PDZ 3.				cell cycle|cell division	endomembrane system|tight junction				ovary(1)|breast(1)	2		all_cancers(1;2.88e-06)|all_epithelial(1;3.23e-06)		Epithelial(149;0.0739)										0.302752	88.513769	92.312769	33	76	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	206023618	206023618	11861	2	G	T	T	T	546	42	PARD3B	2	2
FZD5	7855	broad.mit.edu	37	2	208632887	208632887	+	Missense_Mutation	SNP	G	C	C			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:208632887G>C	uc002vcj.2	-	c.577C>G	c.(577-579)CGC>GGC	p.R193G		NM_003468	NP_003459	Q13467	FZD5_HUMAN	frizzled 5 precursor	193	Extracellular (Potential).				angiogenesis|anterior/posterior axis specification, embryo|axonogenesis|brain development|canonical Wnt receptor signaling pathway|cellular response to molecule of bacterial origin|embryonic camera-type eye development|gonad development|labyrinthine layer blood vessel development|positive regulation of gene-specific transcription from RNA polymerase II promoter|positive regulation of interferon-gamma production|post-embryonic camera-type eye development|Spemann organizer formation|T cell differentiation in thymus|Wnt receptor signaling pathway involved in dorsal/ventral axis specification	cell projection|cell surface|Golgi membrane|integral to membrane|plasma membrane	G-protein coupled receptor activity|PDZ domain binding|protein kinase binding|Wnt receptor activity|Wnt-protein binding			ovary(2)	2				LUSC - Lung squamous cell carcinoma(261;0.0703)|Epithelial(149;0.13)|Lung(261;0.134)										0.241379	18.012883	19.887761	7	22	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	208632887	208632887	6384	2	G	C	C	C	481	37	FZD5	3	3
CCDC108	255101	broad.mit.edu	37	2	219886523	219886523	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:219886523C>T	uc002vjl.1	-	c.3109G>A	c.(3109-3111)GCC>ACC	p.A1037T	CCDC108_uc002vjm.3_5'Flank	NM_194302	NP_919278	Q6ZU64	CC108_HUMAN	coiled-coil domain containing 108 isoform 1	1037						integral to membrane	structural molecule activity			ovary(2)|pancreas(1)	3		Renal(207;0.0915)		Epithelial(149;1.12e-06)|all cancers(144;0.000196)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)										0.55814	69.497548	69.623444	24	19	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	219886523	219886523	2863	2	C	T	T	T	338	26	CCDC108	2	2
SPEG	10290	broad.mit.edu	37	2	220342497	220342497	+	Nonsense_Mutation	SNP	G	T	T			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:220342497G>T	uc010fwg.2	+	c.4816G>T	c.(4816-4818)GAG>TAG	p.E1606*		NM_005876	NP_005867	Q15772	SPEG_HUMAN	SPEG complex locus	1606	Protein kinase 1.				muscle organ development|negative regulation of cell proliferation|protein phosphorylation	nucleus	ATP binding|protein serine/threonine kinase activity			ovary(4)|stomach(2)|central_nervous_system(1)	7		Renal(207;0.0183)		Epithelial(149;4.5e-10)|all cancers(144;7.93e-08)|Lung(261;0.00639)|LUSC - Lung squamous cell carcinoma(224;0.00829)|READ - Rectum adenocarcinoma(5;0.163)						482				0.632653	91.114288	91.867552	31	18	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	220342497	220342497	15548	2	G	T	T	T	533	41	SPEG	5	2
SLC4A3	6508	broad.mit.edu	37	2	220504305	220504305	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:220504305G>T	uc002vmo.3	+	c.3206G>T	c.(3205-3207)GGG>GTG	p.G1069V	SLC4A3_uc002vmp.3_Missense_Mutation_p.G1042V|SLC4A3_uc010fwm.2_Missense_Mutation_p.G592V	NM_201574	NP_963868	P48751	B3A3_HUMAN	solute carrier family 4, anion exchanger, member	1042	Helical; (Potential).|Membrane (anion exchange).				bicarbonate transport	integral to plasma membrane|membrane fraction	inorganic anion exchanger activity			ovary(1)|breast(1)	2		Renal(207;0.0183)		Epithelial(149;2.53e-07)|all cancers(144;5.57e-05)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)										0.25	42.220452	46.321618	18	54	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	220504305	220504305	15152	2	G	T	T	T	559	43	SLC4A3	2	2
COL4A4	1286	broad.mit.edu	37	2	227872247	227872247	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:227872247G>T	uc010zlt.1	-	c.4867C>A	c.(4867-4869)CTG>ATG	p.L1623M		NM_000092	NP_000083	P53420	CO4A4_HUMAN	alpha 4 type IV collagen precursor	1623	Collagen IV NC1.				axon guidance|glomerular basement membrane development	basal lamina|collagen type IV	extracellular matrix structural constituent|protein binding			ovary(5)|central_nervous_system(3)|breast(1)|pancreas(1)	10		Renal(207;0.00844)|all_lung(227;0.0187)|Lung NSC(271;0.0879)|all_hematologic(139;0.21)|Esophageal squamous(248;0.242)		Epithelial(121;6.7e-11)|all cancers(144;5.39e-08)|Lung(261;0.0132)|LUSC - Lung squamous cell carcinoma(224;0.0181)										0.300813	98.026353	102.386483	37	86	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	227872247	227872247	3831	2	G	T	T	T	451	35	COL4A4	2	2
COL4A4	1286	broad.mit.edu	37	2	227973939	227973939	+	Splice_Site_SNP	SNP	C	A	A			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:227973939C>A	uc010zlt.1	-	c.657_splice	c.e10+1	p.V219_splice		NM_000092	NP_000083			alpha 4 type IV collagen precursor						axon guidance|glomerular basement membrane development	basal lamina|collagen type IV	extracellular matrix structural constituent|protein binding			ovary(5)|central_nervous_system(3)|breast(1)|pancreas(1)	10		Renal(207;0.00844)|all_lung(227;0.0187)|Lung NSC(271;0.0879)|all_hematologic(139;0.21)|Esophageal squamous(248;0.242)		Epithelial(121;6.7e-11)|all cancers(144;5.39e-08)|Lung(261;0.0132)|LUSC - Lung squamous cell carcinoma(224;0.0181)										0.2891	164.499328	172.906635	61	150	KEEP	---	---	---	---	capture		Splice_Site_SNP	SNP	227973939	227973939	3831	2	C	A	A	A	234	18	COL4A4	5	2
COL4A4	1286	broad.mit.edu	37	2	228009238	228009238	+	Silent	SNP	T	C	C			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:228009238T>C	uc010zlt.1	-	c.108A>G	c.(106-108)GTA>GTG	p.V36V		NM_000092	NP_000083	P53420	CO4A4_HUMAN	alpha 4 type IV collagen precursor	36					axon guidance|glomerular basement membrane development	basal lamina|collagen type IV	extracellular matrix structural constituent|protein binding			ovary(5)|central_nervous_system(3)|breast(1)|pancreas(1)	10		Renal(207;0.00844)|all_lung(227;0.0187)|Lung NSC(271;0.0879)|all_hematologic(139;0.21)|Esophageal squamous(248;0.242)		Epithelial(121;6.7e-11)|all cancers(144;5.39e-08)|Lung(261;0.0132)|LUSC - Lung squamous cell carcinoma(224;0.0181)										0.4875	140.219558	140.230479	39	41	KEEP	---	---	---	---	capture		Silent	SNP	228009238	228009238	3831	2	T	C	C	C	626	49	COL4A4	4	4
PID1	55022	broad.mit.edu	37	2	230020584	230020584	+	Missense_Mutation	SNP	G	C	C			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:230020584G>C	uc002vpr.3	-	c.226C>G	c.(226-228)CTG>GTG	p.L76V	PID1_uc002vps.3_Missense_Mutation_p.L74V|PID1_uc002vpt.3_Missense_Mutation_p.L43V|PID1_uc002vpu.3_Intron	NM_001100818	NP_001094288	Q7Z2X4	PCLI1_HUMAN	phosphotyrosine interaction domain containing 1	76						cytoplasm				breast(3)	3		Renal(207;0.0112)|all_lung(227;0.0191)|Lung NSC(271;0.0851)|all_hematologic(139;0.104)|Acute lymphoblastic leukemia(138;0.171)		Epithelial(121;3.08e-11)|all cancers(144;2.28e-08)|LUSC - Lung squamous cell carcinoma(224;0.0145)|Lung(261;0.0189)										0.251534	112.402985	121.541252	41	122	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	230020584	230020584	12306	2	G	C	C	C	438	34	PID1	3	3
ARMC9	80210	broad.mit.edu	37	2	232072915	232072915	+	Missense_Mutation	SNP	T	A	A			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:232072915T>A	uc002vrq.3	+	c.127T>A	c.(127-129)TGT>AGT	p.C43S	ARMC9_uc002vrp.3_Missense_Mutation_p.C43S	NM_025139	NP_079415	Q7Z3E5	ARMC9_HUMAN	armadillo repeat containing 9	43							binding			ovary(1)	1		Renal(207;0.0112)|all_lung(227;0.0744)|all_hematologic(139;0.0749)|Acute lymphoblastic leukemia(138;0.167)|Medulloblastoma(418;0.184)|Lung NSC(271;0.205)		Epithelial(121;1.43e-10)|LUSC - Lung squamous cell carcinoma(224;0.017)|Lung(119;0.0189)										0.295455	36.5629	38.206705	13	31	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	232072915	232072915	976	2	T	A	A	A	767	59	ARMC9	3	3
UGT1A10	54575	broad.mit.edu	37	2	234545533	234545533	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:234545533C>T	uc002vur.2	+	c.365C>T	c.(364-366)TCG>TTG	p.S122L	UGT1A8_uc010zmv.1_Intron|UGT1A8_uc002vup.2_Intron|UGT1A10_uc002vuq.3_Missense_Mutation_p.S122L	NM_019075	NP_061948	Q9HAW8	UD110_HUMAN	UDP glycosyltransferase 1 family, polypeptide	122					flavone metabolic process	endoplasmic reticulum membrane|integral to membrane|microsome	glucuronosyltransferase activity|protein heterodimerization activity|protein homodimerization activity|protein kinase C binding			ovary(2)	2		Breast(86;0.000766)|all_lung(227;0.00271)|Renal(207;0.00339)|all_hematologic(139;0.0116)|Acute lymphoblastic leukemia(138;0.0334)|Lung NSC(271;0.0461)|Lung SC(224;0.128)		Epithelial(121;1.96e-17)|BRCA - Breast invasive adenocarcinoma(100;0.000468)|Lung(119;0.00381)|LUSC - Lung squamous cell carcinoma(224;0.008)										0.517588	326.616529	326.669506	103	96	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	234545533	234545533	17503	2	C	T	T	T	403	31	UGT1A10	1	1
UGT1A5	54579	broad.mit.edu	37	2	234676544	234676544	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:234676544C>A	uc002vuw.2	+	c.1049C>A	c.(1048-1050)ACG>AAG	p.T350K	UGT1A8_uc010zmv.1_Missense_Mutation_p.T346K|UGT1A8_uc002vup.2_Missense_Mutation_p.T346K|UGT1A10_uc002vuq.3_Missense_Mutation_p.T346K|UGT1A10_uc002vur.2_Missense_Mutation_p.T346K|UGT1A9_uc010zmw.1_Missense_Mutation_p.T346K|UGT1A9_uc002vus.2_Missense_Mutation_p.T346K|UGT1A7_uc010zmx.1_Missense_Mutation_p.T346K|UGT1A7_uc002vut.2_Missense_Mutation_p.T346K|UGT1A6_uc002vuu.2_Missense_Mutation_p.T81K|UGT1A6_uc010zmy.1_Missense_Mutation_p.T348K|UGT1A6_uc002vuv.3_Missense_Mutation_p.T348K|UGT1A5_uc010zmz.1_Missense_Mutation_p.T350K|UGT1A4_uc010zna.1_Missense_Mutation_p.T350K|UGT1A4_uc002vux.2_Missense_Mutation_p.T350K|UGT1A3_uc010znb.1_Missense_Mutation_p.T350K|UGT1A3_uc002vuy.2_Missense_Mutation_p.T350K|UGT1A9_uc002vva.2_Non-coding_Transcript|UGT1A1_uc010znc.1_Missense_Mutation_p.T349K|UGT1A1_uc002vvb.2_Missense_Mutation_p.T349K	NM_019078	NP_061951	P35504	UD15_HUMAN	UDP glycosyltransferase 1 family, polypeptide A5	350					xenobiotic metabolic process	endoplasmic reticulum membrane|integral to membrane|microsome	glucuronosyltransferase activity				0		Breast(86;0.000765)|all_lung(227;0.00267)|Renal(207;0.00339)|all_hematologic(139;0.0116)|Acute lymphoblastic leukemia(138;0.0328)|Lung NSC(271;0.0457)|Lung SC(224;0.128)		Epithelial(121;4.51e-18)|BRCA - Breast invasive adenocarcinoma(100;0.000523)|Lung(119;0.00271)|LUSC - Lung squamous cell carcinoma(224;0.00645)										0.222857	100.736751	113.098823	39	136	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	234676544	234676544	17506	2	C	A	A	A	247	19	UGT1A5	1	1
COL6A3	1293	broad.mit.edu	37	2	238263564	238263564	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:238263564C>T	uc002vwl.2	-	c.6605G>A	c.(6604-6606)CGA>CAA	p.R2202Q	COL6A3_uc002vwo.2_Missense_Mutation_p.R1996Q|COL6A3_uc010znj.1_Missense_Mutation_p.R1595Q|COL6A3_uc002vwp.1_Missense_Mutation_p.R23Q	NM_004369	NP_004360	P12111	CO6A3_HUMAN	alpha 3 type VI collagen isoform 1 precursor	2202	Triple-helical region.|Collagen-like 3.				axon guidance|cell adhesion|muscle organ development	collagen type VI|extracellular space	serine-type endopeptidase inhibitor activity			ovary(8)|central_nervous_system(6)|pancreas(1)	15		Breast(86;0.000301)|Renal(207;0.000966)|all_hematologic(139;0.067)|Ovarian(221;0.0694)|all_lung(227;0.0943)|Melanoma(123;0.203)		Epithelial(121;1.23e-21)|OV - Ovarian serous cystadenocarcinoma(60;1.34e-10)|Kidney(56;5.71e-09)|KIRC - Kidney renal clear cell carcinoma(57;1.51e-07)|BRCA - Breast invasive adenocarcinoma(100;0.00025)|Lung(119;0.0142)|LUSC - Lung squamous cell carcinoma(224;0.034)										0.234043	26.503048	29.543887	11	36	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	238263564	238263564	3839	2	C	T	T	T	403	31	COL6A3	1	1
AQP12A	375318	broad.mit.edu	37	2	241631351	241631351	+	Silent	SNP	C	T	T			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:241631351C>T	uc002vzu.2	+	c.21C>T	c.(19-21)TCC>TCT	p.S7S	AQP12A_uc002vzv.2_Intron	NM_198998	NP_945349	Q8IXF9	AQ12A_HUMAN	aquaporin 12A	7	Helical; Name=1; (Potential).					integral to membrane	transporter activity				0		all_epithelial(40;7.49e-12)|Breast(86;0.000148)|Renal(207;0.00571)|Ovarian(221;0.104)|all_neural(83;0.107)|all_hematologic(139;0.182)|all_lung(227;0.186)|Melanoma(123;0.238)		Epithelial(32;2.2e-31)|all cancers(36;1.08e-28)|OV - Ovarian serous cystadenocarcinoma(60;2.13e-15)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;7.52e-06)|Lung(119;0.00163)|LUSC - Lung squamous cell carcinoma(224;0.008)|Colorectal(34;0.0124)|COAD - Colon adenocarcinoma(134;0.0757)										0.419753	97.620954	98.078314	34	47	KEEP	---	---	---	---	capture		Silent	SNP	241631351	241631351	835	2	C	T	T	T	275	22	AQP12A	2	2
PDCD1	5133	broad.mit.edu	37	2	242794882	242794882	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:242794882G>T	uc002wcq.3	-	c.327C>A	c.(325-327)AGC>AGA	p.S109R	PDCD1_uc010fzs.2_Missense_Mutation_p.S40R|PDCD1_uc010fzt.2_Intron	NM_005018	NP_005009	Q15116	PDCD1_HUMAN	programmed cell death 1 precursor	109	Ig-like V-type.|Extracellular (Potential).				apoptosis|humoral immune response|multicellular organismal development|T cell costimulation	integral to membrane	protein tyrosine phosphatase activity|signal transducer activity			ovary(1)	1		all_cancers(19;1.09e-40)|all_epithelial(40;2.03e-18)|Breast(86;1.53e-05)|all_lung(227;0.00338)|Renal(207;0.00502)|Ovarian(221;0.00716)|Lung NSC(271;0.012)|Esophageal squamous(248;0.129)|Melanoma(123;0.144)|all_hematologic(139;0.158)|all_neural(83;0.243)|Hepatocellular(293;0.244)		Epithelial(32;3.84e-33)|all cancers(36;8.08e-31)|OV - Ovarian serous cystadenocarcinoma(60;7.41e-15)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;1.63e-06)|Lung(119;0.000152)|LUSC - Lung squamous cell carcinoma(224;0.00154)|Colorectal(34;0.0129)|COAD - Colon adenocarcinoma(134;0.0219)						259				0.225806	16.308965	18.449744	7	24	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	242794882	242794882	12036	2	G	T	T	T	490	38	PDCD1	1	1
C2orf71	388939	broad.mit.edu	37	2	29294983	29294984	+	Missense_Mutation	DNP	GG	TT	TT			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:29294983_29294984GG>TT	uc002rmt.1	-	c.2144_2145CC>AA	c.(2143-2145)GCC>GAA	p.A715E		NM_001029883	NP_001025054	A6NGG8	CB071_HUMAN	hypothetical protein LOC388939	715					response to stimulus|visual perception	photoreceptor outer segment					0														0.598485	259.05597	260.180185	79	53	KEEP	---	---	---	---	capture		Missense_Mutation	DNP	29294983	29294984	2279	2	GG	TT	TT	TT	600	47	C2orf71	2	2
SLC30A6	55676	broad.mit.edu	37	2	32418022	32418022	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:32418022C>A	uc002rof.1	+	c.521C>A	c.(520-522)ACG>AAG	p.T174K	SLC30A6_uc002roe.1_Missense_Mutation_p.T134K|SLC30A6_uc010ymw.1_Missense_Mutation_p.T105K|SLC30A6_uc010ezr.1_Missense_Mutation_p.T134K|SLC30A6_uc002rog.1_5'UTR|SLC30A6_uc010ezs.1_Missense_Mutation_p.T60K|SLC30A6_uc002roh.1_5'UTR	NM_017964	NP_060434	Q6NXT4	ZNT6_HUMAN	solute carrier family 30 (zinc transporter),	134	Extracellular (Potential).					Golgi membrane|integral to membrane	zinc ion transmembrane transporter activity				0	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.208)													0.6	10.42605	10.469789	3	2	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	32418022	32418022	15056	2	C	A	A	A	247	19	SLC30A6	1	1
BIRC6	57448	broad.mit.edu	37	2	32724693	32724693	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:32724693G>A	uc010ezu.2	+	c.8548G>A	c.(8548-8550)GTC>ATC	p.V2850I		NM_016252	NP_057336	Q9NR09	BIRC6_HUMAN	baculoviral IAP repeat-containing 6	2850					anti-apoptosis|apoptosis|post-translational protein modification	intracellular	acid-amino acid ligase activity|cysteine-type endopeptidase inhibitor activity|protein binding			ovary(5)|skin(4)|lung(2)|central_nervous_system(1)|breast(1)|pancreas(1)	14	Acute lymphoblastic leukemia(172;0.155)					Pancreas(94;175 1509 16028 18060 45422)				1555				0.32	143.344991	147.664198	48	102	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	32724693	32724693	1463	2	G	A	A	A	468	36	BIRC6	2	2
PRKCE	5581	broad.mit.edu	37	2	46211818	46211818	+	Missense_Mutation	SNP	A	T	T			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:46211818A>T	uc002rut.2	+	c.822A>T	c.(820-822)AAA>AAT	p.K274N		NM_005400	NP_005391	Q02156	KPCE_HUMAN	protein kinase C, epsilon	274	Phorbol-ester/DAG-type 2.				activation of phospholipase C activity|induction of apoptosis|intracellular signal transduction|nerve growth factor receptor signaling pathway|platelet activation|protein phosphorylation	cytosol|endoplasmic reticulum|plasma membrane	ATP binding|enzyme activator activity|metal ion binding|signal transducer activity			lung(3)|ovary(2)|large_intestine(1)|kidney(1)	7		all_hematologic(82;0.155)|Acute lymphoblastic leukemia(82;0.209)	LUSC - Lung squamous cell carcinoma(58;0.171)							460				0.361186	389.32838	395.628263	134	237	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	46211818	46211818	12954	2	A	T	T	T	37	3	PRKCE	3	3
LHCGR	3973	broad.mit.edu	37	2	48921418	48921418	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:48921418C>T	uc002rwu.3	-	c.892G>A	c.(892-894)GAA>AAA	p.E298K	GTF2A1L_uc002rwt.2_Intron|LHCGR_uc002rwv.2_Non-coding_Transcript	NM_000233	NP_000224	P22888	LSHR_HUMAN	luteinizing hormone/choriogonadotropin receptor	298	Extracellular (Potential).				male genitalia development|male gonad development	endosome|integral to plasma membrane	luteinizing hormone receptor activity			ovary(3)|breast(1)	4		all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.176)	Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151)		Cetrorelix(DB00050)|Choriogonadotropin alfa(DB00097)|Goserelin(DB00014)|Lutropin alfa(DB00044)|Menotropins(DB00032)									0.360656	60.627724	61.672573	22	39	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	48921418	48921418	9088	2	C	T	T	T	377	29	LHCGR	2	2
FSHR	2492	broad.mit.edu	37	2	49190382	49190382	+	Missense_Mutation	SNP	C	G	G			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:49190382C>G	uc002rww.2	-	c.1578G>C	c.(1576-1578)TTG>TTC	p.L526F	FSHR_uc002rwx.2_Missense_Mutation_p.L464F|FSHR_uc010fbn.2_Missense_Mutation_p.L500F	NM_000145	NP_000136	P23945	FSHR_HUMAN	follicle stimulating hormone receptor isoform 1	526	Extracellular (Potential).				female gamete generation|male gonad development|spermatogenesis	integral to membrane|plasma membrane	follicle-stimulating hormone receptor activity|protein binding			ovary(4)	4		all_hematologic(82;0.152)|Acute lymphoblastic leukemia(82;0.181)	Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151)		Choriogonadotropin alfa(DB00097)|Follitropin beta(DB00066)|Menotropins(DB00032)|Urofollitropin(DB00094)									0.466667	124.921147	124.993552	35	40	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	49190382	49190382	6324	2	C	G	G	G	220	17	FSHR	3	3
SPTBN1	6711	broad.mit.edu	37	2	54844783	54844783	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:54844783G>T	uc002rxu.2	+	c.605G>T	c.(604-606)TGG>TTG	p.W202L	SPTBN1_uc002rxv.1_Missense_Mutation_p.W202L|SPTBN1_uc002rxx.2_Missense_Mutation_p.W189L	NM_003128	NP_003119	Q01082	SPTB2_HUMAN	spectrin, beta, non-erythrocytic 1 isoform 1	202	CH 2.|Actin-binding.				actin filament capping|axon guidance	cytosol|nucleolus|plasma membrane|sarcomere|spectrin	actin binding|calmodulin binding|protein binding|structural constituent of cytoskeleton			ovary(2)|breast(2)|central_nervous_system(2)	6			Lung(47;0.24)											0.621951	163.833597	164.902282	51	31	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	54844783	54844783	15633	2	G	T	T	T	611	47	SPTBN1	2	2
COMMD1	150684	broad.mit.edu	37	2	62228015	62228015	+	Silent	SNP	G	T	T			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:62228015G>T	uc002sbp.2	+	c.360G>T	c.(358-360)CGG>CGT	p.R120R	COMMD1_uc002sbq.1_Non-coding_Transcript	NM_152516	NP_689729	Q8N668	COMD1_HUMAN	MURR1	120	COMM.				copper ion homeostasis|negative regulation of NF-kappaB transcription factor activity|positive regulation of protein ubiquitination|regulation of proteasomal ubiquitin-dependent protein catabolic process	cell junction|Cul2-RING ubiquitin ligase complex|cytoplasm|nucleolus	copper ion binding|protein homodimerization activity			ovary(1)	1	Lung NSC(7;0.035)|all_lung(7;0.0691)		LUSC - Lung squamous cell carcinoma(7;4.73e-07)|Epithelial(17;0.0216)|all cancers(80;0.0934)											0.453333	104.343527	104.48505	34	41	KEEP	---	---	---	---	capture		Silent	SNP	62228015	62228015	3852	2	G	T	T	T	548	43	COMMD1	2	2
MDH1	4190	broad.mit.edu	37	2	63832432	63832432	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:63832432G>T	uc010ypv.1	+	c.748G>T	c.(748-750)GCT>TCT	p.A250S	MDH1_uc002scj.1_Missense_Mutation_p.A232S|MDH1_uc010ypw.1_Missense_Mutation_p.A137S	NM_005917	NP_005908	P40925	MDHC_HUMAN	cytosolic malate dehydrogenase	232					gluconeogenesis|tricarboxylic acid cycle	centrosome|cytosol	L-malate dehydrogenase activity|malic enzyme activity			kidney(2)	2					NADH(DB00157)									0.326087	43.013021	44.245341	15	31	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	63832432	63832432	9797	2	G	T	T	T	494	38	MDH1	1	1
RSAD2	91543	broad.mit.edu	37	2	7035938	7035938	+	Silent	SNP	G	T	T			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:7035938G>T	uc002qyp.1	+	c.951G>T	c.(949-951)CGG>CGT	p.R317R		NM_080657	NP_542388	Q8WXG1	RSAD2_HUMAN	radical S-adenosyl methionine domain containing	317					defense response to virus	endoplasmic reticulum membrane|Golgi apparatus	catalytic activity|iron-sulfur cluster binding|metal ion binding				0	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)			OV - Ovarian serous cystadenocarcinoma(76;0.191)										0.348485	122.461581	125.157684	46	86	KEEP	---	---	---	---	capture		Silent	SNP	7035938	7035938	14175	2	G	T	T	T	522	41	RSAD2	2	2
SNRPG	6637	broad.mit.edu	37	2	70508813	70508813	+	Missense_Mutation	SNP	T	C	C			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:70508813T>C	uc002sgp.2	-	c.184A>G	c.(184-186)ATA>GTA	p.I62V	SNRPG_uc002sgo.2_Non-coding_Transcript	NM_003096	NP_003087	P62308	RUXG_HUMAN	small nuclear ribonucleoprotein polypeptide G	62					histone mRNA metabolic process|ncRNA metabolic process|spliceosomal snRNP assembly|spliceosome assembly|termination of RNA polymerase II transcription	catalytic step 2 spliceosome|cytosol|nucleoplasm|U12-type spliceosomal complex|U7 snRNP	protein binding|RNA binding				0						NSCLC(57;761 1258 15082 39958 48415)								0.367925	134.683398	136.313904	39	67	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	70508813	70508813	15369	2	T	C	C	C	676	52	SNRPG	4	4
ACTG2	72	broad.mit.edu	37	2	74135818	74135818	+	Missense_Mutation	SNP	T	C	C			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:74135818T>C	uc002sjw.2	+	c.274T>C	c.(274-276)TAC>CAC	p.Y92H	ACTG2_uc010fey.2_Missense_Mutation_p.Y92H|ACTG2_uc010yrn.1_Missense_Mutation_p.Y49H	NM_001615	NP_001606	P63267	ACTH_HUMAN	actin, gamma 2 propeptide	92					muscle contraction	cytoskeleton|cytosol	ATP binding				0														0.492537	112.872094	112.875356	33	34	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	74135818	74135818	198	2	T	C	C	C	689	53	ACTG2	4	4
ATOH8	84913	broad.mit.edu	37	2	85981923	85981923	+	Missense_Mutation	SNP	A	G	G			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:85981923A>G	uc002sqm.3	+	c.611A>G	c.(610-612)CAG>CGG	p.Q204R	ATOH8_uc002sqn.2_Missense_Mutation_p.Q204R	NM_032827	NP_116216	Q96SQ7	ATOH8_HUMAN	atonal homolog 8	204					cell differentiation|nervous system development|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|transcription regulator activity				0														0.281818	76.476401	81.184022	31	79	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	85981923	85981923	1133	2	A	G	G	G	91	7	ATOH8	4	4
TMEM131	23505	broad.mit.edu	37	2	98378537	98378537	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:98378537C>A	uc002syh.3	-	c.4850G>T	c.(4849-4851)CGG>CTG	p.R1617L	TMEM131_uc002syg.2_5'Flank	NM_015348	NP_056163	Q92545	TM131_HUMAN	RW1 protein	1617						integral to membrane				ovary(4)|central_nervous_system(2)	6														0.591837	90.351395	90.708184	29	20	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	98378537	98378537	16575	2	C	A	A	A	299	23	TMEM131	1	1
INPP4A	3631	broad.mit.edu	37	2	99203983	99203983	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:99203983G>T	uc002syy.2	+	c.2846G>T	c.(2845-2847)CGC>CTC	p.R949L	INPP4A_uc010yvk.1_Missense_Mutation_p.R910L|INPP4A_uc002syx.2_Missense_Mutation_p.R944L|INPP4A_uc010fik.2_Missense_Mutation_p.R278L	NM_001134224	NP_001127696	Q96PE3	INP4A_HUMAN	inositol polyphosphate-4-phosphatase, type 1	949					signal transduction		phosphatidylinositol-3,4-bisphosphate 4-phosphatase activity|phosphatidylinositol-4,5-bisphosphate 4-phosphatase activity			kidney(1)	1														0.490909	91.029349	91.033109	27	28	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	99203983	99203983	8053	2	G	T	T	T	494	38	INPP4A	1	1
IRAK2	3656	broad.mit.edu	37	3	10242074	10242074	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:10242074G>T	uc003bve.1	+	c.299G>T	c.(298-300)AGG>ATG	p.R100M		NM_001570	NP_001561	O43187	IRAK2_HUMAN	interleukin-1 receptor-associated kinase 2	100					activation of MAPK activity|I-kappaB kinase/NF-kappaB cascade|inflammatory response|innate immune response|interleukin-1-mediated signaling pathway|JNK cascade|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|negative regulation of NF-kappaB transcription factor activity|positive regulation of NF-kappaB transcription factor activity|regulation of cytokine-mediated signaling pathway|stress-activated MAPK cascade|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway	cell surface|cytosol|endosome membrane|plasma membrane	ATP binding|NF-kappaB-inducing kinase activity|protein heterodimerization activity|protein homodimerization activity			lung(5)|breast(3)	8										288				0.418675	393.952166	395.841631	139	193	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	10242074	10242074	8126	3	G	T	T	T	455	35	IRAK2	2	2
DZIP3	9666	broad.mit.edu	37	3	108403123	108403123	+	Missense_Mutation	SNP	G	C	C			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:108403123G>C	uc003dxd.2	+	c.2944G>C	c.(2944-2946)GTT>CTT	p.V982L	DZIP3_uc003dxf.1_Missense_Mutation_p.V982L|DZIP3_uc011bhm.1_Missense_Mutation_p.V433L	NM_014648	NP_055463	Q86Y13	DZIP3_HUMAN	DAZ interacting protein 3, zinc finger	982					protein polyubiquitination	cytoplasm	polyubiquitin binding|RNA binding|ubiquitin-protein ligase activity|zinc ion binding			ovary(1)|central_nervous_system(1)	2														0.39759	781.698893	787.028399	231	350	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	108403123	108403123	5051	3	G	C	C	C	624	48	DZIP3	3	3
CCDC80	151887	broad.mit.edu	37	3	112324420	112324420	+	Silent	SNP	C	A	A			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:112324420C>A	uc003dzf.2	-	c.2697G>T	c.(2695-2697)CGG>CGT	p.R899R	CCDC80_uc011bhv.1_Silent_p.R872R|CCDC80_uc003dzg.2_Silent_p.R899R	NM_199512	NP_955806	Q76M96	CCD80_HUMAN	steroid-sensitive protein 1 precursor	899										ovary(2)	2														0.443548	153.391957	153.738327	55	69	KEEP	---	---	---	---	capture		Silent	SNP	112324420	112324420	2978	3	C	A	A	A	379	30	CCDC80	2	2
SEMA5B	54437	broad.mit.edu	37	3	122667529	122667529	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:122667529G>T	uc003efz.1	-	c.152C>A	c.(151-153)GCT>GAT	p.A51D	SEMA5B_uc011bju.1_5'UTR|SEMA5B_uc003ega.1_Non-coding_Transcript|SEMA5B_uc003egb.1_Missense_Mutation_p.A51D|SEMA5B_uc010hro.1_5'UTR|SEMA5B_uc010hrp.1_Non-coding_Transcript	NM_001031702	NP_001026872	Q9P283	SEM5B_HUMAN	semaphorin 5B isoform 1	51	Extracellular (Potential).				cell differentiation|nervous system development	integral to membrane	receptor activity			ovary(2)|breast(2)|pancreas(2)|central_nervous_system(1)	7				GBM - Glioblastoma multiforme(114;0.0367)						383				0.24	43.937969	48.548702	18	57	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	122667529	122667529	14524	3	G	T	T	T	442	34	SEMA5B	2	2
KALRN	8997	broad.mit.edu	37	3	124211729	124211729	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:124211729G>T	uc003ehg.2	+	c.4826G>T	c.(4825-4827)AGG>ATG	p.R1609M	KALRN_uc010hrv.1_Missense_Mutation_p.R1600M|KALRN_uc003ehf.1_Missense_Mutation_p.R1609M|KALRN_uc011bjy.1_Missense_Mutation_p.R1600M	NM_001024660	NP_001019831	O60229	KALRN_HUMAN	kalirin, RhoGEF kinase isoform 1	1609					apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|nervous system development|protein phosphorylation|regulation of Rho protein signal transduction|small GTPase mediated signal transduction|vesicle-mediated transport	actin cytoskeleton|cytosol	ATP binding|GTPase activator activity|metal ion binding|protein binding|protein serine/threonine kinase activity|Rho guanyl-nucleotide exchange factor activity			large_intestine(2)|ovary(2)|central_nervous_system(1)	5										1865				0.376812	70.615938	71.539378	26	43	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	124211729	124211729	8279	3	G	T	T	T	455	35	KALRN	2	2
TMCC1	23023	broad.mit.edu	37	3	129389291	129389291	+	Nonsense_Mutation	SNP	C	A	A			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:129389291C>A	uc003emz.3	-	c.1393G>T	c.(1393-1395)GAG>TAG	p.E465*	TMCC1_uc003emy.3_Nonsense_Mutation_p.E141*|TMCC1_uc011blc.1_Nonsense_Mutation_p.E286*|TMCC1_uc010htg.2_Nonsense_Mutation_p.E351*	NM_001017395	NP_001017395	O94876	TMCC1_HUMAN	transmembrane and coiled-coil domain family 1	465	Potential.					integral to membrane					0														0.481481	231.323946	231.377387	78	84	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	129389291	129389291	16522	3	C	A	A	A	377	29	TMCC1	5	2
COL6A6	131873	broad.mit.edu	37	3	130289995	130289995	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:130289995C>A	uc010htl.2	+	c.2735C>A	c.(2734-2736)CCC>CAC	p.P912H		NM_001102608	NP_001096078	A6NMZ7	CO6A6_HUMAN	collagen type VI alpha 6 precursor	912	VWFA 5.|Nonhelical region.				axon guidance|cell adhesion	collagen				ovary(6)|central_nervous_system(1)|pancreas(1)	8														0.433333	116.416406	116.763899	39	51	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	130289995	130289995	3841	3	C	A	A	A	286	22	COL6A6	2	2
MRPL3	11222	broad.mit.edu	37	3	131208916	131208916	+	Silent	SNP	T	A	A			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:131208916T>A	uc011blp.1	-	c.558A>T	c.(556-558)ACA>ACT	p.T186T	MRPL3_uc011blo.1_Silent_p.T54T|MRPL3_uc003eoh.2_Silent_p.T159T	NM_007208	NP_009139	P09001	RM03_HUMAN	mitochondrial ribosomal protein L3	159					translation	mitochondrial large ribosomal subunit	RNA binding|structural constituent of ribosome				0														0.495726	196.350062	196.351886	58	59	KEEP	---	---	---	---	capture		Silent	SNP	131208916	131208916	10186	3	T	A	A	A	652	51	MRPL3	3	3
TF	7018	broad.mit.edu	37	3	133486935	133486935	+	Missense_Mutation	SNP	T	A	A			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:133486935T>A	uc003epu.1	+	c.1549T>A	c.(1549-1551)TGT>AGT	p.C517S	TF_uc011blt.1_Missense_Mutation_p.C390S|TF_uc003epw.1_Intron|TF_uc003epv.1_Missense_Mutation_p.C517S	NM_001063	NP_001054	P02787	TRFE_HUMAN	transferrin precursor	517	Transferrin-like 2.				cellular iron ion homeostasis|platelet activation|platelet degranulation|transferrin transport|transmembrane transport	apical plasma membrane|basal plasma membrane|coated pit|early endosome|endocytic vesicle|endosome membrane|extracellular region|late endosome|perinuclear region of cytoplasm|recycling endosome|stored secretory granule	ferric iron binding			ovary(1)	1					Aluminium(DB01370)|Bismuth(DB01402)|Iron Dextran(DB00893)									0.387879	200.373799	202.187217	64	101	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	133486935	133486935	16313	3	T	A	A	A	767	59	TF	3	3
SLCO2A1	6578	broad.mit.edu	37	3	133674019	133674019	+	Missense_Mutation	SNP	T	A	A			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:133674019T>A	uc003eqa.3	-	c.416A>T	c.(415-417)CAG>CTG	p.Q139L	SLCO2A1_uc003eqb.3_Intron|SLCO2A1_uc011blv.1_Intron|SLCO2A1_uc010htw.1_5'UTR	NM_005630	NP_005621	Q92959	SO2A1_HUMAN	solute carrier organic anion transporter family,	139	Extracellular (Potential).				sodium-independent organic anion transport	integral to plasma membrane|membrane fraction	prostaglandin transmembrane transporter activity|protein binding			central_nervous_system(1)	1														0.416667	30.553375	30.69664	10	14	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	133674019	133674019	15223	3	T	A	A	A	715	55	SLCO2A1	3	3
NCK1	4690	broad.mit.edu	37	3	136664548	136664548	+	Missense_Mutation	SNP	A	G	G			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:136664548A>G	uc003erh.2	+	c.350A>G	c.(349-351)TAC>TGC	p.Y117C	NCK1_uc011bme.1_Missense_Mutation_p.Y53C	NM_006153	NP_006144	P16333	NCK1_HUMAN	NCK adaptor protein 1	117	SH3 2.				axon guidance|positive regulation of actin filament polymerization|positive regulation of T cell proliferation|regulation of translation|signal complex assembly|T cell activation|T cell receptor signaling pathway	cytosol|endoplasmic reticulum|nucleus	cytoskeletal adaptor activity|receptor binding|receptor signaling complex scaffold activity			pancreas(1)	1														0.416185	503.458553	505.574979	144	202	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	136664548	136664548	10618	3	A	G	G	G	182	14	NCK1	4	4
RBP2	5948	broad.mit.edu	37	3	139173624	139173624	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:139173624C>T	uc003eth.2	-	c.301G>A	c.(301-303)GAG>AAG	p.E101K		NM_004164	NP_004155	P50120	RET2_HUMAN	retinol binding protein 2, cellular	101					epidermis development|retinoid metabolic process|steroid metabolic process|vitamin A metabolic process	cytosol	retinal binding|retinol binding|transporter activity				0					Vitamin A(DB00162)									0.431227	344.230968	345.34348	116	153	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	139173624	139173624	13625	3	C	T	T	T	390	30	RBP2	2	2
ZIC1	7545	broad.mit.edu	37	3	147128400	147128400	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:147128400C>A	uc003ewe.2	+	c.501C>A	c.(499-501)TTC>TTA	p.F167L		NM_003412	NP_003403	Q15915	ZIC1_HUMAN	zinc finger protein of the cerebellum 1	167					behavior|brain development|cell differentiation|inner ear morphogenesis|pattern specification process|positive regulation of protein import into nucleus|regulation of smoothened signaling pathway|regulation of transcription, DNA-dependent	cytoplasm|nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|transcription activator activity|zinc ion binding			ovary(1)|central_nervous_system(1)	2														0.52381	27.917968	27.927945	11	10	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	147128400	147128400	18269	3	C	A	A	A	415	32	ZIC1	2	2
CP	1356	broad.mit.edu	37	3	148917570	148917570	+	Missense_Mutation	SNP	G	A	A	rs35331711		TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:148917570G>A	uc003ewy.3	-	c.1430C>T	c.(1429-1431)CCG>CTG	p.P477L	CP_uc011bnr.1_Non-coding_Transcript|CP_uc003ewx.3_Missense_Mutation_p.P258L|CP_uc003ewz.2_Missense_Mutation_p.P477L|CP_uc010hvf.1_Missense_Mutation_p.P203L	NM_000096	NP_000087	P00450	CERU_HUMAN	ceruloplasmin precursor	477	Plastocyanin-like 3.|F5/8 type A 2.				cellular iron ion homeostasis|copper ion transport|oxidation-reduction process|transmembrane transport	extracellular space	chaperone binding|ferroxidase activity			ovary(1)	1		Prostate(884;0.00217)|Hepatocellular(537;0.00826)|Myeloproliferative disorder(1037;0.0122)|all_neural(597;0.0189)|Melanoma(1037;0.152)	LUSC - Lung squamous cell carcinoma(72;0.0473)|Lung(72;0.0607)		Drotrecogin alfa(DB00055)									0.393443	228.954854	230.775276	72	111	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	148917570	148917570	3925	3	G	A	A	A	507	39	CP	1	1
FGD5	152273	broad.mit.edu	37	3	14939087	14939087	+	Missense_Mutation	SNP	G	C	C			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:14939087G>C	uc003bzc.2	+	c.2820G>C	c.(2818-2820)GAG>GAC	p.E940D	FGD5_uc011avk.1_Missense_Mutation_p.E940D|FGD5_uc003bzd.2_Missense_Mutation_p.E18D	NM_152536	NP_689749	Q6ZNL6	FGD5_HUMAN	FYVE, RhoGEF and PH domain containing 5	940	DH.				actin cytoskeleton organization|filopodium assembly|regulation of Cdc42 GTPase activity|regulation of cell shape	cytoskeleton|Golgi apparatus|lamellipodium|ruffle	metal ion binding|Rho guanyl-nucleotide exchange factor activity|small GTPase binding			ovary(3)|kidney(1)|pancreas(1)	5														0.466667	24.024034	24.038525	7	8	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	14939087	14939087	6073	3	G	C	C	C	451	35	FGD5	3	3
SI	6476	broad.mit.edu	37	3	164780197	164780197	+	Nonsense_Mutation	SNP	C	A	A			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:164780197C>A	uc003fei.2	-	c.982G>T	c.(982-984)GGA>TGA	p.G328*		NM_001041	NP_001032	P14410	SUIS_HUMAN	sucrase-isomaltase	328	Lumenal.|Isomaltase.				carbohydrate metabolic process|polysaccharide digestion	apical plasma membrane|brush border|Golgi apparatus|integral to membrane	carbohydrate binding|oligo-1,6-glucosidase activity|sucrose alpha-glucosidase activity			ovary(7)|pancreas(1)	8		Prostate(884;0.00314)|Melanoma(1037;0.0153)|all_neural(597;0.0199)			Acarbose(DB00284)									0.333333	69.946564	71.793329	25	50	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	164780197	164780197	14792	3	C	A	A	A	312	24	SI	5	2
HTR3C	170572	broad.mit.edu	37	3	183777831	183777831	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:183777831G>T	uc003fmk.2	+	c.1141G>T	c.(1141-1143)GGC>TGC	p.G381C		NM_130770	NP_570126	Q8WXA8	5HT3C_HUMAN	5-hydroxytryptamine receptor 3 subunit C	381	Cytoplasmic (Potential).					integral to membrane|plasma membrane|postsynaptic membrane	extracellular ligand-gated ion channel activity|receptor activity			large_intestine(1)|ovary(1)|central_nervous_system(1)	3	all_cancers(143;2.33e-10)|Ovarian(172;0.0303)		Epithelial(37;1.74e-35)|OV - Ovarian serous cystadenocarcinoma(80;3.11e-22)											0.266667	9.392761	10.130936	4	11	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	183777831	183777831	7746	3	G	T	T	T	611	47	HTR3C	2	2
FETUB	26998	broad.mit.edu	37	3	186358877	186358877	+	Missense_Mutation	SNP	T	C	C			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:186358877T>C	uc010hyq.2	+	c.284T>C	c.(283-285)GTG>GCG	p.V95A	FETUB_uc011brz.1_Intron|FETUB_uc003fqn.2_Missense_Mutation_p.V95A|FETUB_uc003fqo.2_5'UTR|FETUB_uc010hyr.2_Intron|FETUB_uc010hys.2_5'UTR|FETUB_uc003fqp.3_Intron	NM_014375	NP_055190	Q9UGM5	FETUB_HUMAN	fetuin B precursor	95	Cystatin fetuin-B-type 1.					extracellular space	cysteine-type endopeptidase inhibitor activity			ovary(1)|lung(1)	2	all_cancers(143;6.64e-12)|Ovarian(172;0.0339)		OV - Ovarian serous cystadenocarcinoma(80;5.73e-20)	GBM - Glioblastoma multiforme(93;0.0479)										0.272727	34.996884	37.56073	15	40	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	186358877	186358877	6058	3	T	C	C	C	767	59	FETUB	4	4
OSBPL10	114884	broad.mit.edu	37	3	31789593	31789593	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:31789593C>T	uc003cev.2	-	c.749G>A	c.(748-750)GGG>GAG	p.G250E	OSBPL10_uc003ceu.1_Missense_Mutation_p.G7E|OSBPL10_uc011axf.1_Missense_Mutation_p.G186E	NM_017784	NP_060254	Q9BXB5	OSB10_HUMAN	oxysterol-binding protein-like protein 10	250					lipid transport		lipid binding				0				STAD - Stomach adenocarcinoma(1;0.00406)										0.413223	145.132996	145.926717	50	71	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	31789593	31789593	11686	3	C	T	T	T	286	22	OSBPL10	2	2
SCN5A	6331	broad.mit.edu	37	3	38622698	38622698	+	Silent	SNP	G	T	T			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:38622698G>T	uc003cio.2	-	c.2952C>A	c.(2950-2952)CTC>CTA	p.L984L	SCN5A_uc003cin.2_Silent_p.L984L|SCN5A_uc003cil.3_Silent_p.L984L|SCN5A_uc010hhi.2_Silent_p.L984L|SCN5A_uc010hhk.2_Silent_p.L984L|SCN5A_uc011ayr.1_Silent_p.L984L|SCN5A_uc010hhj.1_Silent_p.L595L	NM_198056	NP_932173	Q14524	SCN5A_HUMAN	voltage-gated sodium channel type V alpha	984					blood circulation|muscle contraction|regulation of heart contraction	sarcolemma|voltage-gated sodium channel complex	protein binding|voltage-gated sodium channel activity			ovary(4)|pancreas(2)|central_nervous_system(1)	7	Medulloblastoma(35;0.163)			KIRC - Kidney renal clear cell carcinoma(284;0.0822)|Kidney(284;0.1)	Benzonatate(DB00868)|Bepridil(DB01244)|Carbamazepine(DB00564)|Cocaine(DB00907)|Dibucaine(DB00527)|Disopyramide(DB00280)|Encainide(DB01228)|Ethotoin(DB00754)|Flecainide(DB01195)|Fosphenytoin(DB01320)|Hexylcaine(DB00473)|Indecainide(DB00192)|Lamotrigine(DB00555)|Lidocaine(DB00281)|Mephenytoin(DB00532)|Mexiletine(DB00379)|Mibefradil(DB01388)|Moricizine(DB00680)|Oxcarbazepine(DB00776)|Phenytoin(DB00252)|Prilocaine(DB00750)|Procainamide(DB01035)|Propafenone(DB01182)|Quinidine(DB00908)|Riluzole(DB00740)|Tocainide(DB01056)|Verapamil(DB00661)									0.5	21.999856	21.999856	8	8	KEEP	---	---	---	---	capture		Silent	SNP	38622698	38622698	14404	3	G	T	T	T	522	41	SCN5A	2	2
TTC21A	199223	broad.mit.edu	37	3	39162658	39162658	+	Silent	SNP	G	A	A			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:39162658G>A	uc003cje.2	+	c.1095G>A	c.(1093-1095)AAG>AAA	p.K365K	TTC21A_uc003cjc.2_Silent_p.K365K|TTC21A_uc003cjd.2_Non-coding_Transcript|TTC21A_uc011ayx.1_Silent_p.K316K	NM_001105513	NP_001098983	Q8NDW8	TT21A_HUMAN	tetratricopeptide repeat domain 21A isoform 1	365	TPR 6.						binding			ovary(1)	1				KIRC - Kidney renal clear cell carcinoma(284;0.0588)|Kidney(284;0.0738)										0.424658	102.614517	102.97579	31	42	KEEP	---	---	---	---	capture		Silent	SNP	39162658	39162658	17241	3	G	A	A	A	451	35	TTC21A	2	2
CHL1	10752	broad.mit.edu	37	3	419556	419556	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:419556G>A	uc003bot.2	+	c.1807G>A	c.(1807-1809)GGT>AGT	p.G603S	CHL1_uc003bou.2_Missense_Mutation_p.G587S|CHL1_uc003bow.1_Missense_Mutation_p.G587S|CHL1_uc011asi.1_Missense_Mutation_p.G603S	NM_006614	NP_006605	O00533	CHL1_HUMAN	cell adhesion molecule with homology to L1CAM	587	Ig-like C2-type 6.|Extracellular (Potential).				axon guidance|cell adhesion|signal transduction	integral to membrane|plasma membrane|proteinaceous extracellular matrix				central_nervous_system(4)|large_intestine(2)|ovary(1)	7		all_cancers(2;1.14e-06)|all_epithelial(2;0.00367)|all_lung(1;0.061)|Lung NSC(2;0.201)		Epithelial(13;5.36e-06)|all cancers(10;1.4e-05)|OV - Ovarian serous cystadenocarcinoma(96;0.00323)|COAD - Colon adenocarcinoma(1;0.00925)|Colorectal(20;0.0198)						659				0.422414	320.210784	321.429889	98	134	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	419556	419556	3483	3	G	A	A	A	455	35	CHL1	2	2
SETD2	29072	broad.mit.edu	37	3	47098321	47098321	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:47098321G>A	uc003cqv.2	-	c.7154C>T	c.(7153-7155)CCA>CTA	p.P2385L	SETD2_uc003cqs.2_Missense_Mutation_p.P2318L	NM_014159	NP_054878	Q9BYW2	SETD2_HUMAN	SET domain containing 2	2318	Gln-rich.|Low charge region.				oxidation-reduction process|regulation of transcription, DNA-dependent|transcription, DNA-dependent	chromosome|nucleus	DNA binding|histone-lysine N-methyltransferase activity|oxidoreductase activity|transition metal ion binding			kidney(24)|ovary(5)|skin(1)|central_nervous_system(1)|breast(1)	32		Acute lymphoblastic leukemia(5;0.0169)		BRCA - Breast invasive adenocarcinoma(193;0.000302)|KIRC - Kidney renal clear cell carcinoma(197;0.00732)|Kidney(197;0.00844)										0.413534	163.058678	163.93634	55	78	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	47098321	47098321	14620	3	G	A	A	A	611	47	SETD2	2	2
CACNA1D	776	broad.mit.edu	37	3	53804040	53804040	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:53804040C>T	uc003dgu.3	+	c.3971C>T	c.(3970-3972)CCT>CTT	p.P1324L	CACNA1D_uc003dgv.3_Missense_Mutation_p.P1304L|CACNA1D_uc003dgy.3_Intron|CACNA1D_uc003dgw.3_Missense_Mutation_p.P971L|CACNA1D_uc003dgx.1_Missense_Mutation_p.P480L	NM_000720	NP_000711	Q01668	CAC1D_HUMAN	calcium channel, voltage-dependent, L type,	1304	Extracellular (Potential).|IV.				axon guidance|energy reserve metabolic process|regulation of insulin secretion	voltage-gated calcium channel complex	voltage-gated calcium channel activity			ovary(6)|liver(1)	7				BRCA - Breast invasive adenocarcinoma(193;0.00029)|KIRC - Kidney renal clear cell carcinoma(284;0.0145)|Kidney(284;0.0175)|OV - Ovarian serous cystadenocarcinoma(275;0.0613)	Verapamil(DB00661)									0.369048	284.701359	288.50122	93	159	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	53804040	53804040	2657	3	C	T	T	T	312	24	CACNA1D	2	2
CACNA2D3	55799	broad.mit.edu	37	3	54603855	54603855	+	Missense_Mutation	SNP	T	C	C			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:54603855T>C	uc003dhf.2	+	c.710T>C	c.(709-711)ATT>ACT	p.I237T	CACNA2D3_uc011beu.1_Non-coding_Transcript|CACNA2D3_uc003dhg.1_Missense_Mutation_p.I143T|CACNA2D3_uc003dhh.1_Non-coding_Transcript|CACNA2D3_uc010hmv.1_5'UTR	NM_018398	NP_060868	Q8IZS8	CA2D3_HUMAN	calcium channel, voltage-dependent, alpha	237	Extracellular (Potential).					integral to membrane	calcium channel activity|metal ion binding|voltage-gated ion channel activity			large_intestine(3)|ovary(1)|breast(1)|central_nervous_system(1)|skin(1)	7				KIRC - Kidney renal clear cell carcinoma(284;0.00287)|Kidney(284;0.00327)										0.307692	12.197229	12.62462	4	9	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	54603855	54603855	2666	3	T	C	C	C	676	52	CACNA2D3	4	4
C3orf63	23272	broad.mit.edu	37	3	56683054	56683054	+	Missense_Mutation	SNP	T	A	A			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:56683054T>A	uc003did.3	-	c.1400A>T	c.(1399-1401)TAC>TTC	p.Y467F	C3orf63_uc003dic.3_Missense_Mutation_p.Y71F|C3orf63_uc003die.3_Missense_Mutation_p.Y467F	NM_015224	NP_056039	Q9UK61	CC063_HUMAN	retinoblastoma-associated protein 140 isoform b	467										ovary(3)|kidney(1)|central_nervous_system(1)	5				KIRC - Kidney renal clear cell carcinoma(284;0.0126)|Kidney(284;0.0147)										0.391892	86.26051	87.01679	29	45	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	56683054	56683054	2332	3	T	A	A	A	741	57	C3orf63	3	3
IL17RD	54756	broad.mit.edu	37	3	57148729	57148729	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:57148729C>A	uc003dil.2	-	c.301G>T	c.(301-303)GGG>TGG	p.G101W	IL17RD_uc003dik.2_Missense_Mutation_p.G77W|IL17RD_uc010hna.2_De_novo_Start_OutOfFrame|IL17RD_uc011bex.1_De_novo_Start_OutOfFrame	NM_017563	NP_060033	Q8NFM7	I17RD_HUMAN	interleukin 17 receptor D precursor	101	Extracellular (Potential).					Golgi membrane|integral to membrane|plasma membrane	receptor activity				0				KIRC - Kidney renal clear cell carcinoma(284;0.0173)|Kidney(284;0.0204)						213				0.545455	95.051042	95.149545	30	25	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	57148729	57148729	7943	3	C	A	A	A	312	24	IL17RD	2	2
PDZRN3	23024	broad.mit.edu	37	3	73433528	73433528	+	Missense_Mutation	SNP	T	C	C			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:73433528T>C	uc003dpl.1	-	c.2189A>G	c.(2188-2190)AAC>AGC	p.N730S	PDZRN3_uc011bgh.1_Missense_Mutation_p.N387S|PDZRN3_uc010hoe.1_Missense_Mutation_p.N428S|PDZRN3_uc011bgf.1_Missense_Mutation_p.N447S|PDZRN3_uc011bgg.1_Missense_Mutation_p.N450S	NM_015009	NP_055824	Q9UPQ7	PZRN3_HUMAN	PDZ domain containing ring finger 3	730							ubiquitin-protein ligase activity|zinc ion binding			ovary(2)|pancreas(2)|large_intestine(1)	5		Prostate(10;0.114)|Lung NSC(201;0.187)|Lung SC(41;0.236)		BRCA - Breast invasive adenocarcinoma(55;0.00041)|Epithelial(33;0.0023)|LUSC - Lung squamous cell carcinoma(21;0.0048)|Lung(16;0.0105)|KIRC - Kidney renal clear cell carcinoma(39;0.111)|Kidney(39;0.134)										0.5	30.075353	30.075353	9	9	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	73433528	73433528	12130	3	T	C	C	C	780	60	PDZRN3	4	4
EPHA3	2042	broad.mit.edu	37	3	89499354	89499354	+	Silent	SNP	C	A	A			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:89499354C>A	uc003dqy.2	+	c.2524C>A	c.(2524-2526)CGA>AGA	p.R842R	EPHA3_uc010hon.1_Non-coding_Transcript	NM_005233	NP_005224	P29320	EPHA3_HUMAN	ephrin receptor EphA3 isoform a precursor	842	Cytoplasmic (Potential).|Protein kinase.				protein phosphorylation|transmembrane receptor protein tyrosine kinase signaling pathway	extracellular region|integral to plasma membrane	ATP binding			lung(15)|ovary(7)|large_intestine(4)|central_nervous_system(2)|pancreas(1)	29	all_cancers(8;0.0406)|Melanoma(1;0.00142)|all_epithelial(1;0.0612)	Lung NSC(201;0.0782)		LUSC - Lung squamous cell carcinoma(29;0.00344)|Lung(72;0.00942)						416	TSP Lung(6;0.00050)			0.379747	88.630575	89.632881	30	49	KEEP	---	---	---	---	capture		Silent	SNP	89499354	89499354	5361	3	C	A	A	A	399	31	EPHA3	1	1
OR5H6	79295	broad.mit.edu	37	3	97983469	97983469	+	Missense_Mutation	SNP	T	C	C			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:97983469T>C	uc003dsi.1	+	c.341T>C	c.(340-342)ATG>ACG	p.M114T		NM_001005479	NP_001005479	Q8NGV6	OR5H6_HUMAN	olfactory receptor, family 5, subfamily H,	114	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			large_intestine(1)|skin(1)	2														0.41954	225.075049	226.072134	73	101	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	97983469	97983469	11573	3	T	C	C	C	663	51	OR5H6	4	4
CRELD1	78987	broad.mit.edu	37	3	9979755	9979755	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:9979755G>A	uc003buf.2	+	c.425G>A	c.(424-426)TGC>TAC	p.C142Y	CIDEC_uc003bto.2_Intron|CRELD1_uc003bug.2_Missense_Mutation_p.C142Y|CRELD1_uc003buh.2_Missense_Mutation_p.C142Y|CRELD1_uc003bui.2_Missense_Mutation_p.C142Y|CRELD1_uc003buj.2_Non-coding_Transcript	NM_001031717	NP_001026887	Q96HD1	CREL1_HUMAN	cysteine-rich with EGF-like domains 1 isoform 1	142	Extracellular (Potential).				cardiac septum development|endocardial cushion development	integral to membrane	calcium ion binding			ovary(1)	1														0.361111	32.944297	33.563627	13	23	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	9979755	9979755	4005	3	G	A	A	A	598	46	CRELD1	2	2
BANK1	55024	broad.mit.edu	37	4	102992455	102992455	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:102992455C>A	uc003hvy.3	+	c.2236C>A	c.(2236-2238)CCA>ACA	p.P746T	BANK1_uc003hvx.3_Missense_Mutation_p.P731T|BANK1_uc010ill.2_Missense_Mutation_p.P613T|BANK1_uc003hvz.3_Missense_Mutation_p.P716T	NM_017935	NP_060405	Q8NDB2	BANK1_HUMAN	B-cell scaffold protein with ankyrin repeats 1	746					B cell activation					ovary(2)	2		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;2.7e-07)										0.341014	195.565424	200.421559	74	143	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	102992455	102992455	1330	4	C	A	A	A	390	30	BANK1	2	2
ANK2	287	broad.mit.edu	37	4	114290764	114290764	+	Missense_Mutation	SNP	G	C	C			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:114290764G>C	uc003ibe.3	+	c.11413G>C	c.(11413-11415)GCA>CCA	p.A3805P	ANK2_uc003ibd.3_Missense_Mutation_p.A1711P|ANK2_uc003ibf.3_Missense_Mutation_p.A1720P|ANK2_uc011cgc.1_Missense_Mutation_p.A896P|ANK2_uc003ibg.3_Missense_Mutation_p.A704P|ANK2_uc003ibh.3_Missense_Mutation_p.A394P|ANK2_uc011cgd.1_Missense_Mutation_p.A1107P	NM_001148	NP_001139	Q01484	ANK2_HUMAN	ankyrin 2 isoform 1	3772					axon guidance|signal transduction	apical plasma membrane|basolateral plasma membrane|cytoskeleton|cytosol|sarcomere	protein binding|protein binding			central_nervous_system(7)|ovary(3)|large_intestine(2)|breast(1)	13		Ovarian(17;0.0448)|Hepatocellular(203;0.218)		OV - Ovarian serous cystadenocarcinoma(123;4.92e-05)										0.490909	183.638413	183.646451	54	56	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	114290764	114290764	624	4	G	C	C	C	598	46	ANK2	3	3
NDST4	64579	broad.mit.edu	37	4	115997337	115997337	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:115997337C>T	uc003ibu.2	-	c.856G>A	c.(856-858)GAT>AAT	p.D286N	NDST4_uc010imw.2_Intron	NM_022569	NP_072091	Q9H3R1	NDST4_HUMAN	heparan sulfate N-deacetylase/N-sulfotransferase	286	Lumenal (Potential).|Heparan sulfate N-deacetylase 4.					Golgi membrane|integral to membrane	[heparan sulfate]-glucosamine N-sulfotransferase activity|hydrolase activity			ovary(1)	1		Ovarian(17;0.156)		OV - Ovarian serous cystadenocarcinoma(123;0.000562)										0.356037	342.037401	347.933625	115	208	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	115997337	115997337	10657	4	C	T	T	T	416	32	NDST4	2	2
QRFPR	84109	broad.mit.edu	37	4	122250803	122250803	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:122250803C>A	uc010inj.1	-	c.962G>T	c.(961-963)GGA>GTA	p.G321V	QRFPR_uc010ink.1_Non-coding_Transcript|QRFPR_uc003ids.2_3'UTR	NM_198179	NP_937822	Q96P65	QRFPR_HUMAN	G protein-coupled receptor 103	321	Helical; Name=7; (Potential).					integral to membrane|plasma membrane	neuropeptide Y receptor activity				0														0.297872	36.533107	38.248933	14	33	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	122250803	122250803	13336	4	C	A	A	A	390	30	QRFPR	2	2
TRPC3	7222	broad.mit.edu	37	4	122825509	122825509	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:122825509C>A	uc003ieg.2	-	c.2221G>T	c.(2221-2223)GCT>TCT	p.A741S	TRPC3_uc010inr.2_Missense_Mutation_p.A613S|TRPC3_uc003ief.2_Missense_Mutation_p.A668S|TRPC3_uc011cgl.1_Missense_Mutation_p.A405S	NM_001130698	NP_001124170	Q13507	TRPC3_HUMAN	transient receptor potential cation channel,	656	Helical; (Potential).				axon guidance|phototransduction|platelet activation	integral to plasma membrane	protein binding|store-operated calcium channel activity			ovary(2)	2														0.217391	12.361797	14.05595	5	18	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	122825509	122825509	17130	4	C	A	A	A	325	25	TRPC3	2	2
PRSS48	345062	broad.mit.edu	37	4	152212601	152212601	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:152212601G>A	uc011cif.1	+	c.983G>A	c.(982-984)AGA>AAA	p.R328K	PRSS48_uc011cig.1_Missense_Mutation_p.R185K	NM_183375	NP_899231	Q7RTY5	PRS48_HUMAN	epidermis-specific serine protease-like protein	328					proteolysis	extracellular region	serine-type endopeptidase activity			large_intestine(1)	1														0.510638	72.196516	72.201033	24	23	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	152212601	152212601	13081	4	G	A	A	A	429	33	PRSS48	2	2
KIAA0922	23240	broad.mit.edu	37	4	154510157	154510157	+	Silent	SNP	C	T	T			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:154510157C>T	uc010ipp.2	+	c.1668C>T	c.(1666-1668)TGC>TGT	p.C556C	KIAA0922_uc003inm.3_Silent_p.C555C|KIAA0922_uc010ipq.2_Silent_p.C408C|KIAA0922_uc010ips.1_3'UTR	NM_001131007	NP_001124479	A2VDJ0	T131L_HUMAN	hypothetical protein LOC23240 isoform 1	555	Extracellular (Potential).					integral to membrane				ovary(1)	1	all_hematologic(180;0.093)	Renal(120;0.118)												0.341176	76.142417	78.040407	29	56	KEEP	---	---	---	---	capture		Silent	SNP	154510157	154510157	8508	4	C	T	T	T	324	25	KIAA0922	2	2
TLR2	7097	broad.mit.edu	37	4	154626008	154626008	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:154626008G>T	uc003inq.2	+	c.1949G>T	c.(1948-1950)CGG>CTG	p.R650L	TLR2_uc003inr.2_Missense_Mutation_p.R650L|TLR2_uc003ins.2_Missense_Mutation_p.R650L	NM_003264	NP_003255	O60603	TLR2_HUMAN	toll-like receptor 2 precursor	650	TIR.|Cytoplasmic (Potential).				cellular response to diacyl bacterial lipopeptide|cellular response to lipoteichoic acid|cellular response to triacyl bacterial lipopeptide|detection of diacyl bacterial lipopeptide|detection of triacyl bacterial lipopeptide|I-kappaB phosphorylation|induction of apoptosis|inflammatory response|innate immune response|MyD88-dependent toll-like receptor signaling pathway|positive regulation of chemokine production|positive regulation of gene-specific transcription from RNA polymerase II promoter|positive regulation of inflammatory response|positive regulation of interferon-beta production|positive regulation of interleukin-12 production|positive regulation of interleukin-18 production|positive regulation of interleukin-6 production|positive regulation of interleukin-8 production|positive regulation of NF-kappaB import into nucleus|positive regulation of NF-kappaB transcription factor activity|positive regulation of nitric-oxide synthase biosynthetic process|positive regulation of toll-like receptor signaling pathway|positive regulation of tumor necrosis factor production|positive regulation of Wnt receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway	cytoplasm|integral to plasma membrane|Toll-like receptor 1-Toll-like receptor 2 protein complex	Gram-positive bacterial cell surface binding|lipopolysaccharide receptor activity|peptidoglycan binding|protein heterodimerization activity|transmembrane receptor activity|triacyl lipopeptide binding				0	all_hematologic(180;0.093)	Renal(120;0.117)												0.370787	101.758731	103.061654	33	56	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	154626008	154626008	16481	4	G	T	T	T	507	39	TLR2	1	1
CC2D2A	57545	broad.mit.edu	37	4	15591208	15591208	+	Missense_Mutation	SNP	A	C	C			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:15591208A>C	uc010idv.2	+	c.4220A>C	c.(4219-4221)TAT>TCT	p.Y1407S	CC2D2A_uc003gnx.2_Missense_Mutation_p.Y1299S|CC2D2A_uc003gnz.1_Non-coding_Transcript|CC2D2A_uc003goa.1_Non-coding_Transcript	NM_001080522	NP_001073991	Q9P2K1	C2D2A_HUMAN	coiled-coil and C2 domain containing 2A isoform	1407					cell projection organization	cilium|microtubule basal body				pancreas(2)|ovary(1)	3														0.531915	470.73036	470.943269	125	110	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	15591208	15591208	2848	4	A	C	C	C	208	16	CC2D2A	4	4
FSTL5	56884	broad.mit.edu	37	4	162508658	162508659	+	Nonsense_Mutation	DNP	AG	TT	TT			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:162508658_162508659AG>TT	uc003iqh.2	-	c.963_964CT>AA	c.(961-966)TGCTAT>TGAAAT	p.321_322CY>*N	FSTL5_uc003iqi.2_Nonsense_Mutation_p.320_321CY>*N|FSTL5_uc010iqv.2_Nonsense_Mutation_p.320_321CY>*N	NM_020116	NP_064501	Q8N475	FSTL5_HUMAN	follistatin-like 5 isoform a	321_322	Ig-like 1.					extracellular region	calcium ion binding			ovary(2)|pancreas(2)|large_intestine(1)|central_nervous_system(1)	6	all_hematologic(180;0.24)			COAD - Colon adenocarcinoma(41;0.179)										0.318182	83.968386	86.554436	28	60	KEEP	---	---	---	---	capture		Nonsense_Mutation	DNP	162508658	162508659	6331	4	AG	TT	TT	TT	195	15	FSTL5	5	3
TLL1	7092	broad.mit.edu	37	4	166986903	166986903	+	Silent	SNP	C	T	T			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:166986903C>T	uc011cjn.1	+	c.2145C>T	c.(2143-2145)TTC>TTT	p.F715F	TLL1_uc003irh.1_Silent_p.F692F|TLL1_uc011cjo.1_Silent_p.F516F	NM_012464	NP_036596	O43897	TLL1_HUMAN	tolloid-like 1 precursor	692	CUB 3.				cell differentiation|proteolysis|skeletal system development	extracellular region	calcium ion binding|metalloendopeptidase activity|zinc ion binding			ovary(2)|breast(1)|central_nervous_system(1)	4	all_hematologic(180;0.221)	Melanoma(52;0.0315)|Prostate(90;0.0405)		GBM - Glioblastoma multiforme(119;0.103)										0.401235	202.134451	203.518692	65	97	KEEP	---	---	---	---	capture		Silent	SNP	166986903	166986903	16475	4	C	T	T	T	415	32	TLL1	2	2
GPM6A	2823	broad.mit.edu	37	4	176556066	176556066	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:176556066G>T	uc003iuf.2	-	c.827C>A	c.(826-828)GCA>GAA	p.A276E	GPM6A_uc011ckj.1_Missense_Mutation_p.A269E|GPM6A_uc003iug.2_Missense_Mutation_p.A276E|GPM6A_uc003iuh.2_Missense_Mutation_p.A265E	NM_201591	NP_963885	P51674	GPM6A_HUMAN	glycoprotein M6A isoform 2	276	Cytoplasmic (Potential).					cell surface|integral to membrane					0		Breast(14;7.35e-05)|Melanoma(52;0.00909)|Prostate(90;0.00996)|Renal(120;0.0183)|all_hematologic(60;0.107)|all_neural(102;0.164)		all cancers(43;9.21e-19)|Epithelial(43;3.01e-17)|OV - Ovarian serous cystadenocarcinoma(60;2.02e-09)|STAD - Stomach adenocarcinoma(60;0.00083)|GBM - Glioblastoma multiforme(59;0.00168)|LUSC - Lung squamous cell carcinoma(193;0.0388)										0.35567	202.720424	206.281095	69	125	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	176556066	176556066	6889	4	G	T	T	T	598	46	GPM6A	2	2
STOX2	56977	broad.mit.edu	37	4	184938371	184938371	+	Silent	SNP	G	T	T			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:184938371G>T	uc003ivz.1	+	c.2715G>T	c.(2713-2715)CCG>CCT	p.P905P	STOX2_uc003iwa.1_3'UTR	NM_020225	NP_064610	Q9P2F5	STOX2_HUMAN	storkhead box 2	905					embryo development|maternal placenta development						0		all_lung(41;1.89e-12)|Lung NSC(41;3.48e-12)|Colorectal(36;0.00435)|Renal(120;0.0246)|Hepatocellular(41;0.0268)|all_hematologic(60;0.027)|Prostate(90;0.0283)		all cancers(43;2.85e-26)|Epithelial(43;2.27e-22)|OV - Ovarian serous cystadenocarcinoma(60;3.4e-10)|Colorectal(24;8.23e-06)|GBM - Glioblastoma multiforme(59;1.64e-05)|STAD - Stomach adenocarcinoma(60;3.6e-05)|COAD - Colon adenocarcinoma(29;4.37e-05)|LUSC - Lung squamous cell carcinoma(40;0.008)|READ - Rectum adenocarcinoma(43;0.227)										0.44	33.62023	33.698832	11	14	KEEP	---	---	---	---	capture		Silent	SNP	184938371	184938371	15840	4	G	T	T	T	470	37	STOX2	1	1
LRP2BP	55805	broad.mit.edu	37	4	186294187	186294187	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:186294187G>A	uc003ixj.1	-	c.626C>T	c.(625-627)TCC>TTC	p.S209F	LRP2BP_uc003ixk.1_Missense_Mutation_p.S183F|LRP2BP_uc011ckr.1_Missense_Mutation_p.S209F	NM_018409	NP_060879	Q9P2M1	LR2BP_HUMAN	LRP2 binding protein	209	Sel1-like 4.					cytoplasm	protein binding				0		all_lung(41;1.3e-11)|Lung NSC(41;2.25e-11)|Melanoma(20;0.00109)|Colorectal(36;0.0215)|Renal(120;0.0246)|Hepatocellular(41;0.0268)|Prostate(90;0.0283)|all_hematologic(60;0.0749)		all cancers(43;2.14e-25)|Epithelial(43;1.55e-22)|OV - Ovarian serous cystadenocarcinoma(60;1.34e-11)|BRCA - Breast invasive adenocarcinoma(30;8.01e-05)|GBM - Glioblastoma multiforme(59;0.000132)|STAD - Stomach adenocarcinoma(60;0.000766)|Colorectal(24;0.00116)|LUSC - Lung squamous cell carcinoma(40;0.00904)|COAD - Colon adenocarcinoma(29;0.0101)|READ - Rectum adenocarcinoma(43;0.161)										0.351852	165.54233	168.67102	57	105	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	186294187	186294187	9330	4	G	A	A	A	533	41	LRP2BP	2	2
ZNF141	7700	broad.mit.edu	37	4	337570	337570	+	Splice_Site_SNP	SNP	G	A	A			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:337570G>A	uc003gaa.2	+	c.4_splice	c.e3-1	p.E2_splice	ZNF141_uc003fzz.2_Splice_Site_SNP_p.E2_splice|ZNF141_uc003gab.2_Splice_Site_SNP_p.E2_splice	NM_003441	NP_003432			zinc finger protein 141						anatomical structure morphogenesis|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|specific RNA polymerase II transcription factor activity|zinc ion binding				0														0.343284	72.0037	73.457826	23	44	KEEP	---	---	---	---	capture		Splice_Site_SNP	SNP	337570	337570	18321	4	G	A	A	A	455	35	ZNF141	5	2
TLR6	10333	broad.mit.edu	37	4	38829072	38829072	+	Nonsense_Mutation	SNP	C	A	A			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:38829072C>A	uc003gtm.2	-	c.2023G>T	c.(2023-2025)GAG>TAG	p.E675*	TLR6_uc010ifg.1_Nonsense_Mutation_p.E675*	NM_006068	NP_006059	Q9Y2C9	TLR6_HUMAN	toll-like receptor 6 precursor	675	TIR.|Cytoplasmic (Potential).				activation of NF-kappaB-inducing kinase activity|cellular response to diacyl bacterial lipopeptide|defense response to bacterium|detection of diacyl bacterial lipopeptide|inflammatory response|innate immune response|MyD88-dependent toll-like receptor signaling pathway|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of interleukin-6 biosynthetic process|positive regulation of JUN kinase activity|T-helper 1 type immune response|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway	integral to plasma membrane|phagocytic vesicle membrane	lipopeptide binding|transmembrane receptor activity			ovary(2)	2														0.481982	328.932479	328.993766	107	115	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	38829072	38829072	16485	4	C	A	A	A	377	29	TLR6	5	2
FAM114A1	92689	broad.mit.edu	37	4	38937413	38937413	+	Splice_Site_SNP	SNP	T	A	A			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:38937413T>A	uc003gtn.2	+	c.1536_splice	c.e13+2	p.G512_splice	FAM114A1_uc011byh.1_Splice_Site_SNP_p.G305_splice|FAM114A1_uc010ifi.2_Splice_Site_SNP_p.G170_splice	NM_138389	NP_612398			hypothetical protein LOC92689							cytoplasm				ovary(1)	1														0.367816	92.078188	93.413981	32	55	KEEP	---	---	---	---	capture		Splice_Site_SNP	SNP	38937413	38937413	5600	4	T	A	A	A	741	57	FAM114A1	5	3
EVC	2121	broad.mit.edu	37	4	5750010	5750010	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:5750010G>T	uc003gil.1	+	c.1075G>T	c.(1075-1077)GAT>TAT	p.D359Y	EVC_uc003gim.1_Non-coding_Transcript|CRMP1_uc003gin.1_Missense_Mutation_p.R465S	NM_153717	NP_714928	P57679	EVC_HUMAN	Ellis van Creveld syndrome protein	359					muscle organ development	integral to membrane				ovary(1)	1		Myeloproliferative disorder(84;0.117)												0.323529	119.856514	123.614354	44	92	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	5750010	5750010	5478	4	G	T	T	T	481	37	EVC	1	1
CPZ	8532	broad.mit.edu	37	4	8621242	8621242	+	Silent	SNP	C	T	T			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:8621242C>T	uc003glm.2	+	c.1857C>T	c.(1855-1857)CTC>CTT	p.L619L	CPZ_uc003gll.2_Non-coding_Transcript|CPZ_uc003gln.2_Silent_p.L482L|CPZ_uc003glo.2_Silent_p.L608L|CPZ_uc003glp.2_Non-coding_Transcript	NM_001014447	NP_001014447	Q66K79	CBPZ_HUMAN	carboxypeptidase Z isoform 1	619					proteolysis|Wnt receptor signaling pathway	proteinaceous extracellular matrix	metallocarboxypeptidase activity|zinc ion binding			ovary(2)|pancreas(1)	3														0.362319	69.381352	70.521574	25	44	KEEP	---	---	---	---	capture		Silent	SNP	8621242	8621242	3978	4	C	T	T	T	379	30	CPZ	2	2
UNC5C	8633	broad.mit.edu	37	4	96222767	96222767	+	Silent	SNP	C	T	T			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:96222767C>T	uc003htp.1	-	c.480G>A	c.(478-480)GTG>GTA	p.V160V	UNC5C_uc010ilc.1_Silent_p.V160V|UNC5C_uc003htq.2_Silent_p.V160V	NM_003728	NP_003719	O95185	UNC5C_HUMAN	unc5C precursor	160	Extracellular (Potential).				apoptosis|axon guidance|brain development	integral to membrane	netrin receptor activity			ovary(3)|pancreas(1)	4		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;8.72e-10)										0.271605	104.848615	112.4576	44	118	KEEP	---	---	---	---	capture		Silent	SNP	96222767	96222767	17551	4	C	T	T	T	314	25	UNC5C	2	2
AQPEP	206338	broad.mit.edu	37	5	115298845	115298845	+	Silent	SNP	C	T	T			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:115298845C>T	uc003kro.2	+	c.531C>T	c.(529-531)GAC>GAT	p.D177D	AQPEP_uc003krp.2_Non-coding_Transcript	NM_173800	NP_776161	Q6Q4G3	AMPQ_HUMAN	laeverin	177	Lumenal (Potential).				proteolysis	integral to membrane	metallopeptidase activity|zinc ion binding				0														0.085106	0.069328	8.27221	4	43	KEEP	---	---	---	---	capture		Silent	SNP	115298845	115298845	845	5	C	T	T	T	246	19	AQPEP	1	1
HSD17B4	3295	broad.mit.edu	37	5	118877683	118877683	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:118877683G>T	uc003ksj.2	+	c.2205G>T	c.(2203-2205)AAG>AAT	p.K735N	HSD17B4_uc011cwg.1_Missense_Mutation_p.K711N|HSD17B4_uc011cwh.1_Missense_Mutation_p.K717N|HSD17B4_uc011cwi.1_Missense_Mutation_p.K760N|HSD17B4_uc003ksk.3_Missense_Mutation_p.K588N|HSD17B4_uc011cwj.1_Missense_Mutation_p.K588N|HSD17B4_uc010jcn.1_Missense_Mutation_p.K473N|HSD17B4_uc010jco.1_3'UTR	NM_000414	NP_000405	P51659	DHB4_HUMAN	hydroxysteroid (17-beta) dehydrogenase 4	735	Microbody targeting signal (Potential).|SCP2.				bile acid biosynthetic process|fatty acid beta-oxidation using acyl-CoA oxidase	peroxisomal matrix	3-hydroxyacyl-CoA dehydrogenase activity|3alpha,7alpha,12alpha-trihydroxy-5beta-cholest-24-enoyl-CoA hydratase activity|estradiol 17-beta-dehydrogenase activity|isomerase activity|long-chain-enoyl-CoA hydratase activity|protein binding|sterol binding|sterol transporter activity			ovary(1)|pancreas(1)	2		all_cancers(142;0.0206)|Prostate(80;0.0322)		OV - Ovarian serous cystadenocarcinoma(64;0.000247)|Epithelial(69;0.000849)|all cancers(49;0.0122)	NADH(DB00157)	Colon(35;490 801 34689 41394 43344)								0.451613	127.957519	128.143921	42	51	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	118877683	118877683	7681	5	G	T	T	T	438	34	HSD17B4	2	2
SNX2	6643	broad.mit.edu	37	5	122163148	122163148	+	Missense_Mutation	SNP	A	T	T			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:122163148A>T	uc003kte.2	+	c.1431A>T	c.(1429-1431)AGA>AGT	p.R477S	SNX2_uc011cwn.1_Missense_Mutation_p.R360S	NM_003100	NP_003091	O60749	SNX2_HUMAN	sorting nexin 2	477					cell communication|endocytosis|intracellular protein transport	early endosome membrane	phosphatidylinositol binding|protein binding|protein transporter activity			kidney(1)	1		all_cancers(142;1.14e-44)|all_lung(232;1.03e-13)|Lung NSC(810;2.5e-13)|Breast(839;0.000812)|Myeloproliferative disorder(839;0.0122)|Prostate(80;0.0235)|all_hematologic(541;0.0592)|all_neural(839;0.243)	KIRC - Kidney renal clear cell carcinoma(527;0.0897)|Kidney(363;0.137)	all cancers(49;2.13e-24)|Epithelial(69;6.15e-22)|OV - Ovarian serous cystadenocarcinoma(64;5.6e-11)|BRCA - Breast invasive adenocarcinoma(61;0.00013)|GBM - Glioblastoma multiforme(465;0.000357)|COAD - Colon adenocarcinoma(49;0.000887)|Lung(113;0.0109)										0.422535	178.245495	178.994312	60	82	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	122163148	122163148	15391	5	A	T	T	T	154	12	SNX2	3	3
MEGF10	84466	broad.mit.edu	37	5	126776464	126776464	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:126776464C>A	uc003kuh.3	+	c.2267C>A	c.(2266-2268)GCA>GAA	p.A756E	MEGF10_uc003kui.3_Missense_Mutation_p.A756E	NM_032446	NP_115822	Q96KG7	MEG10_HUMAN	multiple EGF-like-domains 10 precursor	756	Extracellular (Potential).|Necessary for interaction with AP2M1, self-assembly and formation of the irregular, mosaic-like adhesion pattern.|EGF-like 14.				cell adhesion|phagocytosis	basolateral plasma membrane|cell projection|integral to membrane|phagocytic cup				ovary(4)	4		Prostate(80;0.165)	KIRC - Kidney renal clear cell carcinoma(527;0.0268)|Kidney(363;0.0488)	OV - Ovarian serous cystadenocarcinoma(64;0.0657)|Epithelial(69;0.123)										0.458874	317.476079	317.819411	106	125	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	126776464	126776464	9849	5	C	A	A	A	325	25	MEGF10	2	2
SLC27A6	28965	broad.mit.edu	37	5	128368829	128368829	+	Missense_Mutation	SNP	C	G	G			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:128368829C>G	uc003kuy.2	+	c.1714C>G	c.(1714-1716)CTA>GTA	p.L572V	SLC27A6_uc003kuz.2_Missense_Mutation_p.L572V	NM_014031	NP_054750	Q9Y2P4	S27A6_HUMAN	solute carrier family 27 (fatty acid	572					long-chain fatty acid transport|transmembrane transport|very long-chain fatty acid metabolic process	integral to membrane|sarcolemma	fatty acid transporter activity|long-chain fatty acid-CoA ligase activity|nucleotide binding				0		all_cancers(142;0.0483)|Prostate(80;0.055)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)	Epithelial(69;0.171)|OV - Ovarian serous cystadenocarcinoma(64;0.186)										0.4	56.892621	57.242326	16	24	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	128368829	128368829	15027	5	C	G	G	G	259	20	SLC27A6	3	3
CHSY3	337876	broad.mit.edu	37	5	129521158	129521158	+	Missense_Mutation	SNP	T	C	C			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:129521158T>C	uc003kvd.2	+	c.2323T>C	c.(2323-2325)TGG>CGG	p.W775R		NM_175856	NP_787052	Q70JA7	CHSS3_HUMAN	chondroitin sulfate synthase 3	775	Lumenal (Potential).					Golgi cisterna membrane|integral to membrane	glucuronosyl-N-acetylgalactosaminyl-proteoglycan 4-beta-N-acetylgalactosaminyltransferase activity|metal ion binding|N-acetylgalactosaminyl-proteoglycan 3-beta-glucuronosyltransferase activity			ovary(2)|pancreas(1)	3		all_cancers(142;0.0227)|Breast(839;0.198)|Prostate(80;0.215)|Lung NSC(810;0.239)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)	OV - Ovarian serous cystadenocarcinoma(64;0.136)										0.408163	306.459209	308.262408	100	145	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	129521158	129521158	3547	5	T	C	C	C	819	63	CHSY3	4	4
RAPGEF6	51735	broad.mit.edu	37	5	130897670	130897670	+	Splice_Site_SNP	SNP	C	A	A			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:130897670C>A	uc003kvp.1	-	c.501_splice	c.e6+1	p.V167_splice	RAPGEF6_uc003kvn.1_Splice_Site_SNP_p.V117_splice|RAPGEF6_uc003kvo.1_Splice_Site_SNP_p.V117_splice|RAPGEF6_uc010jdi.1_Splice_Site_SNP_p.V117_splice|RAPGEF6_uc010jdj.1_Splice_Site_SNP_p.V117_splice|RAPGEF6_uc003kvr.2_Splice_Site_SNP_p.V117_splice|RAPGEF6_uc011cxe.1_Splice_Site_SNP|RAPGEF6_uc010jdk.2_Splice_Site_SNP_p.V117_splice	NM_016340	NP_057424			PDZ domain-containing guanine nucleotide						Ras protein signal transduction|regulation of GTPase activity|regulation of small GTPase mediated signal transduction	cytoplasm|plasma membrane	GTP-dependent protein binding|guanyl-nucleotide exchange factor activity|Ras GTPase binding			ovary(1)|lung(1)|central_nervous_system(1)	3			KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)	Lung(113;0.0721)		Melanoma(168;435 1955 13113 13877 23213)								0.33125	158.526692	162.56103	53	107	KEEP	---	---	---	---	capture		Splice_Site_SNP	SNP	130897670	130897670	13508	5	C	A	A	A	234	18	RAPGEF6	5	2
KIF3A	11127	broad.mit.edu	37	5	132062049	132062049	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:132062049G>T	uc011cxf.1	-	c.422C>A	c.(421-423)ACA>AAA	p.T141K	KIF3A_uc003kxn.2_Missense_Mutation_p.T100K|KIF3A_uc003kxo.2_Missense_Mutation_p.T141K|KIF3A_uc003kxp.2_Missense_Mutation_p.T141K	NM_007054	NP_008985	Q9Y496	KIF3A_HUMAN	kinesin family member 3A	141	Kinesin-motor.				blood coagulation|organelle organization|plus-end-directed vesicle transport along microtubule	centrosome|cytosol|kinesin II complex|spindle microtubule	ATP binding|plus-end-directed microtubule motor activity|protein binding			pancreas(1)	1		all_cancers(142;0.0751)|Breast(839;0.198)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)											0.327044	149.647271	153.864915	52	107	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	132062049	132062049	8611	5	G	T	T	T	624	48	KIF3A	2	2
HNRNPA0	10949	broad.mit.edu	37	5	137089259	137089259	+	Missense_Mutation	SNP	T	A	A			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:137089259T>A	uc003lbt.2	-	c.497A>T	c.(496-498)CAT>CTT	p.H166L	MYOT_uc011cye.1_Intron|HNRNPA0_uc010jeo.2_Intron	NM_006805	NP_006796	Q13151	ROA0_HUMAN	heterogeneous nuclear ribonucleoprotein A0	166	RRM 2.				nuclear mRNA splicing, via spliceosome	heterogeneous nuclear ribonucleoprotein complex|nucleoplasm	nucleotide binding|RNA binding				0			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)											0.564103	75.956093	76.095977	22	17	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	137089259	137089259	7548	5	T	A	A	A	663	51	HNRNPA0	3	3
CTNNA1	1495	broad.mit.edu	37	5	138260225	138260225	+	Nonsense_Mutation	SNP	A	T	T			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:138260225A>T	uc003ldh.2	+	c.1573A>T	c.(1573-1575)AAA>TAA	p.K525*	CTNNA1_uc011cyx.1_Nonsense_Mutation_p.K422*|CTNNA1_uc011cyy.1_Nonsense_Mutation_p.K402*|CTNNA1_uc003ldi.2_Nonsense_Mutation_p.K223*|CTNNA1_uc003ldj.2_Nonsense_Mutation_p.K525*|CTNNA1_uc003ldl.2_Nonsense_Mutation_p.K155*	NM_001903	NP_001894	P35221	CTNA1_HUMAN	catenin, alpha 1	525					adherens junction organization|apical junction assembly|cell adhesion|cellular response to indole-3-methanol|muscle cell differentiation|positive regulation of muscle cell differentiation	actin cytoskeleton|catenin complex|cytosol	beta-catenin binding|cadherin binding|gamma-catenin binding|structural molecule activity|vinculin binding			breast(6)|ovary(2)|large_intestine(2)|kidney(1)	11			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00325)											0.356688	167.634682	170.483809	56	101	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	138260225	138260225	4171	5	A	T	T	T	65	5	CTNNA1	5	3
NRG2	9542	broad.mit.edu	37	5	139232109	139232109	+	Silent	SNP	G	T	T			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:139232109G>T	uc003lev.1	-	c.1476C>A	c.(1474-1476)GTC>GTA	p.V492V	NRG2_uc003lew.1_Silent_p.V486V|NRG2_uc003lex.1_Silent_p.V484V|NRG2_uc003ley.1_Silent_p.V478V	NM_013982	NP_053585	O14511	NRG2_HUMAN	neuregulin 2 isoform 3	484	Cytoplasmic (Potential).				embryo development	extracellular region|integral to membrane|plasma membrane	growth factor activity			pancreas(2)|ovary(1)	3			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)											0.386861	147.724448	149.267044	53	84	KEEP	---	---	---	---	capture		Silent	SNP	139232109	139232109	11053	5	G	T	T	T	574	45	NRG2	2	2
WDR55	54853	broad.mit.edu	37	5	140048960	140048960	+	Silent	SNP	C	G	G			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:140048960C>G	uc003lgr.3	+	c.873C>G	c.(871-873)GGC>GGG	p.G291G	WDR55_uc011czl.1_Silent_p.G130G	NM_017706	NP_060176	Q9H6Y2	WDR55_HUMAN	WD repeat domain 55	291					rRNA processing	cytoplasm|nucleolus				ovary(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)											0.173077	14.671122	19.826831	9	43	KEEP	---	---	---	---	capture		Silent	SNP	140048960	140048960	17880	5	C	G	G	G	327	26	WDR55	3	3
PCDHA1	56147	broad.mit.edu	37	5	140167592	140167592	+	Missense_Mutation	SNP	A	C	C			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:140167592A>C	uc003lhb.2	+	c.1717A>C	c.(1717-1719)ACT>CCT	p.T573P	PCDHA1_uc003lha.2_Intron|PCDHA1_uc003lgz.2_Missense_Mutation_p.T573P	NM_018900	NP_061723	Q9Y5I3	PCDA1_HUMAN	protocadherin alpha 1 isoform 1 precursor	573	Extracellular (Potential).				homophilic cell adhesion|nervous system development	extracellular region|integral to plasma membrane	calcium ion binding|protein binding				0			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)											0.397849	107.501752	108.364453	37	56	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	140167592	140167592	11939	5	A	C	C	C	78	6	PCDHA1	4	4
PCDHB1	29930	broad.mit.edu	37	5	140432991	140432991	+	Missense_Mutation	SNP	C	G	G			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:140432991C>G	uc003lik.1	+	c.1936C>G	c.(1936-1938)CAG>GAG	p.Q646E		NM_013340	NP_037472	Q9Y5F3	PCDB1_HUMAN	protocadherin beta 1 precursor	646	Cadherin 6.|Extracellular (Potential).				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding				0			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)											0.386503	217.082978	218.924322	63	100	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	140432991	140432991	11954	5	C	G	G	G	377	29	PCDHB1	3	3
PCDHB10	56126	broad.mit.edu	37	5	140572514	140572514	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:140572514C>A	uc003lix.2	+	c.389C>A	c.(388-390)GCG>GAG	p.A130E		NM_018930	NP_061753	Q9UN67	PCDBA_HUMAN	protocadherin beta 10 precursor	130	Extracellular (Potential).|Cadherin 1.				calcium-dependent cell-cell adhesion|homophilic cell adhesion|synapse assembly|synaptic transmission	integral to membrane|plasma membrane	calcium ion binding			ovary(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)											0.326203	165.582717	170.608942	61	126	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	140572514	140572514	11955	5	C	A	A	A	351	27	PCDHB10	1	1
PCDHB12	56124	broad.mit.edu	37	5	140590240	140590240	+	Silent	SNP	C	A	A			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:140590240C>A	uc003liz.2	+	c.1761C>A	c.(1759-1761)ACC>ACA	p.T587T	PCDHB12_uc011dak.1_Silent_p.T250T	NM_018932	NP_061755	Q9Y5F1	PCDBC_HUMAN	protocadherin beta 12 precursor	587	Extracellular (Potential).|Cadherin 6.				homophilic cell adhesion|nervous system development	integral to plasma membrane	calcium ion binding			ovary(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)											0.096154	8.816439	34.323551	15	141	KEEP	---	---	---	---	capture		Silent	SNP	140590240	140590240	11957	5	C	A	A	A	262	21	PCDHB12	2	2
PCDHGB7	56099	broad.mit.edu	37	5	140798221	140798221	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:140798221G>T	uc003lkn.1	+	c.795G>T	c.(793-795)AAG>AAT	p.K265N	PCDHGA1_uc003lji.1_Intron|PCDHGA2_uc003ljk.1_Intron|PCDHGA3_uc003ljm.1_Intron|PCDHGA3_uc010jfx.1_Intron|PCDHGB1_uc003ljo.1_Intron|PCDHGA4_uc003ljq.1_Intron|PCDHGB2_uc003ljs.1_Intron|PCDHGA5_uc003lju.1_Intron|PCDHGB3_uc003ljw.1_Intron|PCDHGA6_uc003ljy.1_Intron|PCDHGA7_uc003lka.1_Intron|PCDHGB4_uc003lkc.1_Intron|PCDHGA8_uc003lkd.1_Intron|PCDHGB5_uc003lkf.1_Intron|PCDHGA9_uc003lkh.1_Intron|PCDHGB6_uc003lkj.1_Intron|PCDHGA10_uc003lkl.1_Intron|PCDHGB7_uc003lkm.2_Missense_Mutation_p.K265N|PCDHGA11_uc003lko.1_5'Flank|PCDHGA11_uc003lkp.1_5'Flank|PCDHGA11_uc003lkq.1_5'Flank	NM_018927	NP_061750	Q9Y5F8	PCDGJ_HUMAN	protocadherin gamma subfamily B, 7 isoform 1	265	Extracellular (Potential).|Cadherin 3.				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(2)	2			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)											0.367647	71.098931	72.129055	25	43	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	140798221	140798221	11988	5	G	T	T	T	451	35	PCDHGB7	2	2
ARAP3	64411	broad.mit.edu	37	5	141036183	141036183	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:141036183C>A	uc003llm.2	-	c.3677G>T	c.(3676-3678)CGG>CTG	p.R1226L	ARAP3_uc003lll.2_Missense_Mutation_p.R177L|ARAP3_uc011dbe.1_Missense_Mutation_p.R888L|ARAP3_uc003lln.2_Missense_Mutation_p.R1057L	NM_022481	NP_071926	Q8WWN8	ARAP3_HUMAN	ArfGAP with RhoGAP domain, ankyrin repeat and PH	1226	PH 3.				cytoskeleton organization|negative regulation of cell migration|negative regulation of Rho protein signal transduction|regulation of ARF GTPase activity|regulation of cell shape|small GTPase mediated signal transduction|vesicle-mediated transport	cytoskeleton|cytosol|lamellipodium|plasma membrane|ruffle	ARF GTPase activator activity|phosphatidylinositol-3,4,5-trisphosphate binding|phosphatidylinositol-3,4-bisphosphate binding|Rho GTPase activator activity|zinc ion binding			breast(5)|ovary(1)|large_intestine(1)	7														0.461538	54.235925	54.286952	18	21	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	141036183	141036183	851	5	C	A	A	A	299	23	ARAP3	1	1
PDE6A	5145	broad.mit.edu	37	5	149286877	149286877	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:149286877G>T	uc003lrg.3	-	c.1063C>A	c.(1063-1065)CTG>ATG	p.L355M		NM_000440	NP_000431	P16499	PDE6A_HUMAN	phosphodiesterase 6A	355	GAF 2.				cytosolic calcium ion homeostasis|GMP metabolic process|platelet activation|signal transduction|visual perception	cytosol|plasma membrane	3',5'-cyclic-GMP phosphodiesterase activity|metal ion binding			ovary(1)|pancreas(1)	2			KIRC - Kidney renal clear cell carcinoma(527;0.000962)|Kidney(363;0.00147)											0.440299	541.118552	542.36681	177	225	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	149286877	149286877	12066	5	G	T	T	T	451	35	PDE6A	2	2
SGCD	6444	broad.mit.edu	37	5	156186253	156186253	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:156186253G>T	uc003lwc.3	+	c.725G>T	c.(724-726)AGG>ATG	p.R242M	SGCD_uc003lwd.3_Missense_Mutation_p.R241M	NM_000337	NP_000328	Q92629	SGCD_HUMAN	delta-sarcoglycan isoform 1	241	Extracellular (Potential).				cytoskeleton organization|muscle organ development	cytoplasm|cytoskeleton|integral to membrane|sarcoglycan complex|sarcolemma					0	Renal(175;0.00488)	Medulloblastoma(196;0.0378)|all_neural(177;0.106)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)											0.392857	192.305815	193.996676	66	102	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	156186253	156186253	14692	5	G	T	T	T	455	35	SGCD	2	2
CYFIP2	26999	broad.mit.edu	37	5	156787323	156787323	+	Silent	SNP	C	T	T			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:156787323C>T	uc003lwq.2	+	c.2851C>T	c.(2851-2853)CTG>TTG	p.L951L	CYFIP2_uc011ddn.1_Silent_p.L925L|CYFIP2_uc011ddo.1_Silent_p.L755L|CYFIP2_uc003lwr.2_Silent_p.L951L|CYFIP2_uc003lws.2_Silent_p.L951L|CYFIP2_uc003lwt.2_Silent_p.L854L|CYFIP2_uc011ddp.1_Silent_p.L685L	NM_001037333	NP_001032410	Q96F07	CYFP2_HUMAN	cytoplasmic FMR1 interacting protein 2	976					apoptosis|cell-cell adhesion	cell junction|perinuclear region of cytoplasm|synapse|synaptosome	protein binding				0	Renal(175;0.00212)	Medulloblastoma(196;0.0306)|all_neural(177;0.0897)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)											0.392638	190.762288	192.407298	64	99	KEEP	---	---	---	---	capture		Silent	SNP	156787323	156787323	4303	5	C	T	T	T	259	20	CYFIP2	2	2
ODZ2	57451	broad.mit.edu	37	5	167689762	167689762	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:167689762G>T	uc010jjd.2	+	c.8245G>T	c.(8245-8247)GAC>TAC	p.D2749Y	ODZ2_uc003lzr.3_Missense_Mutation_p.D2519Y|ODZ2_uc003lzt.3_Missense_Mutation_p.D2122Y|ODZ2_uc010jje.2_Missense_Mutation_p.D2013Y	NM_001122679	NP_001116151			odz, odd Oz/ten-m homolog 2											ovary(6)|central_nervous_system(4)	10	Renal(175;0.00124)|Lung NSC(126;0.136)|all_lung(126;0.242)	Medulloblastoma(196;0.0241)|all_neural(177;0.026)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	all cancers(165;0.0444)|OV - Ovarian serous cystadenocarcinoma(192;0.0694)|Epithelial(171;0.124)										0.611111	30.014873	30.20698	11	7	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	167689762	167689762	11240	5	G	T	T	T	429	33	ODZ2	2	2
LCP2	3937	broad.mit.edu	37	5	169677861	169677861	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:169677861G>A	uc003man.1	-	c.1352C>T	c.(1351-1353)TCT>TTT	p.S451F	C5orf58_uc003mal.2_Intron|LCP2_uc011des.1_Missense_Mutation_p.S246F|LCP2_uc011det.1_Missense_Mutation_p.S280F	NM_005565	NP_005556	Q13094	LCP2_HUMAN	lymphocyte cytosolic protein 2	451	SH2.				immune response|platelet activation|T cell receptor signaling pathway|transmembrane receptor protein tyrosine kinase signaling pathway	cytosol	protein binding			ovary(1)	1	Renal(175;0.000159)|Lung NSC(126;0.0221)|all_lung(126;0.0337)	Medulloblastoma(196;0.0109)|all_neural(177;0.0146)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	OV - Ovarian serous cystadenocarcinoma(192;0.247)										0.408602	116.029065	116.70876	38	55	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	169677861	169677861	9016	5	G	A	A	A	429	33	LCP2	2	2
STK10	6793	broad.mit.edu	37	5	171509412	171509412	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:171509412C>A	uc003mbo.1	-	c.1907G>T	c.(1906-1908)CGG>CTG	p.R636L		NM_005990	NP_005981	O94804	STK10_HUMAN	serine/threonine kinase 10	636	Potential.				protein phosphorylation		ATP binding|protein serine/threonine kinase activity			ovary(3)|testis(1)|lung(1)|pancreas(1)	6	Renal(175;0.000159)|Lung NSC(126;0.0056)|all_lung(126;0.0094)	Medulloblastoma(196;0.00868)|all_neural(177;0.026)	Kidney(164;7.24e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000516)						p.R636Q(REH-Tumor)	570				0.38806	154.723068	156.207194	52	82	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	171509412	171509412	15806	5	C	A	A	A	299	23	STK10	1	1
CDHR2	54825	broad.mit.edu	37	5	175995737	175995737	+	Silent	SNP	G	C	C			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:175995737G>C	uc003mem.1	+	c.183G>C	c.(181-183)GGG>GGC	p.G61G	CDHR2_uc003men.1_Silent_p.G61G	NM_017675	NP_060145	Q9BYE9	CDHR2_HUMAN	protocadherin LKC precursor	61	Extracellular (Potential).|Cadherin 1.				homophilic cell adhesion|negative regulation of cell growth	apical plasma membrane|cell junction|integral to membrane	calcium ion binding|protein binding			ovary(2)	2														0.402597	106.409228	107.048196	31	46	KEEP	---	---	---	---	capture		Silent	SNP	175995737	175995737	3248	5	G	C	C	C	522	41	CDHR2	3	3
ZNF354C	30832	broad.mit.edu	37	5	178505712	178505712	+	Silent	SNP	A	G	G			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:178505712A>G	uc003mju.2	+	c.279A>G	c.(277-279)GCA>GCG	p.A93A		NM_014594	NP_055409	Q86Y25	Z354C_HUMAN	zinc finger protein 354C	93					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1	all_cancers(89;0.00065)|all_epithelial(37;0.000153)|Renal(175;0.000159)|Lung NSC(126;0.00175)|all_lung(126;0.00309)	all_cancers(40;0.19)|all_neural(177;0.00802)|Medulloblastoma(196;0.0145)|all_hematologic(541;0.248)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	all cancers(165;0.247)										0.509615	158.24354	158.251456	53	51	KEEP	---	---	---	---	capture		Silent	SNP	178505712	178505712	18458	5	A	G	G	G	93	8	ZNF354C	4	4
PRDM9	56979	broad.mit.edu	37	5	23527761	23527761	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:23527761C>A	uc003jgo.2	+	c.2564C>A	c.(2563-2565)ACA>AAA	p.T855K		NM_020227	NP_064612	Q9NQV7	PRDM9_HUMAN	PR domain containing 9	855					meiosis|regulation of transcription, DNA-dependent|transcription, DNA-dependent	chromosome|nucleoplasm	histone-lysine N-methyltransferase activity|nucleic acid binding|zinc ion binding			ovary(3)|large_intestine(2)|pancreas(1)	6														0.334586	242.474995	248.925261	89	177	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	23527761	23527761	12906	5	C	A	A	A	221	17	PRDM9	2	2
WDR70	55100	broad.mit.edu	37	5	37381788	37381788	+	Splice_Site_SNP	SNP	G	T	T			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:37381788G>T	uc003jkv.2	+	c.175_splice	c.e3+1	p.E59_splice	WDR70_uc010iva.1_Splice_Site_SNP_p.E59_splice	NM_018034	NP_060504			WD repeat domain 70											ovary(1)|central_nervous_system(1)	2	all_lung(31;0.000285)		COAD - Colon adenocarcinoma(61;0.14)|Colorectal(62;0.202)											0.488372	213.125354	213.140379	63	66	KEEP	---	---	---	---	capture		Splice_Site_SNP	SNP	37381788	37381788	17894	5	G	T	T	T	572	44	WDR70	5	2
NDUFS4	4724	broad.mit.edu	37	5	52942075	52942075	+	Missense_Mutation	SNP	T	G	G			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:52942075T>G	uc003jpe.2	+	c.190T>G	c.(190-192)TTA>GTA	p.L64V		NM_002495	NP_002486	O43181	NDUS4_HUMAN	NADH dehydrogenase (ubiquinone) Fe-S protein 4	64					brain development|cAMP-mediated signaling|mitochondrial electron transport, NADH to ubiquinone|mitochondrial respiratory chain complex I assembly|positive regulation of fibroblast proliferation|reactive oxygen species metabolic process|regulation of protein phosphorylation|response to cAMP|transport	mitochondrial respiratory chain complex I	NADH dehydrogenase (ubiquinone) activity				0		Lung NSC(810;8.27e-05)|Breast(144;0.0848)			NADH(DB00157)									0.466667	77.477498	77.520371	21	24	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	52942075	52942075	10693	5	T	G	G	G	829	64	NDUFS4	4	4
CDC20B	166979	broad.mit.edu	37	5	54420672	54420672	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:54420672C>A	uc003jpo.1	-	c.1174G>T	c.(1174-1176)GGC>TGC	p.G392C	CDC20B_uc003jpn.1_Missense_Mutation_p.G392C|CDC20B_uc010ivu.1_Missense_Mutation_p.G392C|CDC20B_uc010ivv.1_3'UTR	NM_152623	NP_689836	Q86Y33	CD20B_HUMAN	CDC20 cell division cycle 20 homolog B isoform	392	WD 4.										0		Lung NSC(810;0.000744)|Breast(144;0.159)|Prostate(74;0.194)	LUSC - Lung squamous cell carcinoma(15;0.225)											0.493827	116.397039	116.399635	40	41	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	54420672	54420672	3188	5	C	A	A	A	286	22	CDC20B	2	2
CCNO	10309	broad.mit.edu	37	5	54527339	54527339	+	Missense_Mutation	SNP	C	G	G			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:54527339C>G	uc003jpw.2	-	c.917G>C	c.(916-918)GGA>GCA	p.G306A	CCNO_uc003jpv.2_Non-coding_Transcript	NM_021147	NP_066970	P22674	CCNO_HUMAN	cyclin domain containing	306					cell cycle|cell division|depyrimidination	nucleoplasm	uracil DNA N-glycosylase activity				0		Lung NSC(810;4.08e-05)|Breast(144;0.0735)|Prostate(74;0.183)	LUSC - Lung squamous cell carcinoma(15;0.142)|Lung(15;0.161)											0.25	13.765276	14.901589	5	15	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	54527339	54527339	3060	5	C	G	G	G	390	30	CCNO	3	3
IQGAP2	10788	broad.mit.edu	37	5	75979002	75979002	+	Silent	SNP	G	T	T			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:75979002G>T	uc003kek.2	+	c.3723G>T	c.(3721-3723)CTG>CTT	p.L1241L	IQGAP2_uc011csv.1_Silent_p.L737L|IQGAP2_uc003kel.2_Silent_p.L737L|IQGAP2_uc010izw.1_5'UTR	NM_006633	NP_006624	Q13576	IQGA2_HUMAN	IQ motif containing GTPase activating protein 2	1241					small GTPase mediated signal transduction	actin cytoskeleton	actin binding|calmodulin binding|GTPase inhibitor activity|Ras GTPase activator activity			ovary(6)|central_nervous_system(1)	7		all_lung(232;0.000514)|Lung NSC(167;0.00135)|Prostate(461;0.00838)|Ovarian(174;0.0149)		all cancers(79;1.38e-36)										0.332192	279.069453	286.357385	97	195	KEEP	---	---	---	---	capture		Silent	SNP	75979002	75979002	8118	5	G	T	T	T	600	47	IQGAP2	2	2
VCAN	1462	broad.mit.edu	37	5	82834200	82834200	+	Missense_Mutation	SNP	T	C	C			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:82834200T>C	uc003kii.3	+	c.5378T>C	c.(5377-5379)TTT>TCT	p.F1793S	VCAN_uc003kij.3_Missense_Mutation_p.F806S|VCAN_uc010jau.2_Intron|VCAN_uc003kik.3_Intron|VCAN_uc003kil.3_Missense_Mutation_p.F457S	NM_004385	NP_004376	P13611	CSPG2_HUMAN	versican isoform 1 precursor	1793	GAG-beta.				cell adhesion|cell recognition|glial cell migration	extracellular space|proteinaceous extracellular matrix	calcium ion binding|hyaluronic acid binding|sugar binding			ovary(7)|skin(3)|lung(2)|central_nervous_system(1)	13		Lung NSC(167;0.0216)|all_lung(232;0.0251)|Ovarian(174;0.142)		OV - Ovarian serous cystadenocarcinoma(54;2.47e-41)|Epithelial(54;2.51e-34)|all cancers(79;5.19e-29)										0.402062	270.117162	271.742785	78	116	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	82834200	82834200	17703	5	T	C	C	C	832	64	VCAN	4	4
VCAN	1462	broad.mit.edu	37	5	82875805	82875805	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:82875805G>A	uc003kii.3	+	c.9887G>A	c.(9886-9888)TGC>TAC	p.C3296Y	VCAN_uc003kij.3_Missense_Mutation_p.C2309Y|VCAN_uc010jau.2_Missense_Mutation_p.C1542Y|VCAN_uc003kik.3_Missense_Mutation_p.C555Y|VCAN_uc003kil.3_Missense_Mutation_p.C1960Y	NM_004385	NP_004376	P13611	CSPG2_HUMAN	versican isoform 1 precursor	3296	Sushi.				cell adhesion|cell recognition|glial cell migration	extracellular space|proteinaceous extracellular matrix	calcium ion binding|hyaluronic acid binding|sugar binding			ovary(7)|skin(3)|lung(2)|central_nervous_system(1)	13		Lung NSC(167;0.0216)|all_lung(232;0.0251)|Ovarian(174;0.142)		OV - Ovarian serous cystadenocarcinoma(54;2.47e-41)|Epithelial(54;2.51e-34)|all cancers(79;5.19e-29)										0.466667	322.690665	322.919944	112	128	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	82875805	82875805	17703	5	G	A	A	A	598	46	VCAN	2	2
GPR98	84059	broad.mit.edu	37	5	90021007	90021007	+	Silent	SNP	T	G	G			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:90021007T>G	uc003kju.2	+	c.10011T>G	c.(10009-10011)CTT>CTG	p.L3337L	GPR98_uc003kjt.2_Silent_p.L1043L|GPR98_uc003kjv.2_Silent_p.L937L	NM_032119	NP_115495	Q8WXG9	GPR98_HUMAN	G protein-coupled receptor 98 precursor	3337	Extracellular (Potential).|EAR 2.				cell communication|cell-cell adhesion|maintenance of organ identity|neuropeptide signaling pathway|photoreceptor cell maintenance	cell surface|cytoplasm|integral to membrane|plasma membrane	calcium ion binding|G-protein coupled receptor activity			ovary(11)|central_nervous_system(3)|pancreas(2)	16		all_cancers(142;1.05e-09)|all_epithelial(76;1.81e-12)|all_lung(232;5.41e-06)|Lung NSC(167;1.72e-05)|Ovarian(174;0.00948)|Colorectal(57;0.133)|Breast(839;0.192)		OV - Ovarian serous cystadenocarcinoma(54;7.01e-30)|Epithelial(54;6.79e-25)|all cancers(79;1.88e-20)										0.222222	16.238056	18.152594	6	21	KEEP	---	---	---	---	capture		Silent	SNP	90021007	90021007	6997	5	T	G	G	G	782	61	GPR98	4	4
GPR98	84059	broad.mit.edu	37	5	90085636	90085636	+	Nonsense_Mutation	SNP	A	T	T			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:90085636A>T	uc003kju.2	+	c.14011A>T	c.(14011-14013)AGA>TGA	p.R4671*	GPR98_uc003kjt.2_Nonsense_Mutation_p.R2377*|GPR98_uc003kjw.2_Nonsense_Mutation_p.R332*	NM_032119	NP_115495	Q8WXG9	GPR98_HUMAN	G protein-coupled receptor 98 precursor	4671	Extracellular (Potential).				cell communication|cell-cell adhesion|maintenance of organ identity|neuropeptide signaling pathway|photoreceptor cell maintenance	cell surface|cytoplasm|integral to membrane|plasma membrane	calcium ion binding|G-protein coupled receptor activity			ovary(11)|central_nervous_system(3)|pancreas(2)	16		all_cancers(142;1.05e-09)|all_epithelial(76;1.81e-12)|all_lung(232;5.41e-06)|Lung NSC(167;1.72e-05)|Ovarian(174;0.00948)|Colorectal(57;0.133)|Breast(839;0.192)		OV - Ovarian serous cystadenocarcinoma(54;7.01e-30)|Epithelial(54;6.79e-25)|all cancers(79;1.88e-20)										1	12.248822	12.131008	3	0	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	90085636	90085636	6997	5	A	T	T	T	88	7	GPR98	5	3
SEMA5A	9037	broad.mit.edu	37	5	9108286	9108286	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:9108286C>A	uc003jek.2	-	c.2039G>T	c.(2038-2040)TGT>TTT	p.C680F		NM_003966	NP_003957	Q13591	SEM5A_HUMAN	semaphorin 5A precursor	680	TSP type-1 3.|Extracellular (Potential).				cell adhesion|cell-cell signaling	integral to membrane|plasma membrane				ovary(1)|central_nervous_system(1)	2														0.28125	26.090721	27.449145	9	23	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	9108286	9108286	14523	5	C	A	A	A	221	17	SEMA5A	2	2
NR2F1	7025	broad.mit.edu	37	5	92921132	92921132	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:92921132C>A	uc003kkj.2	+	c.403C>A	c.(403-405)CGC>AGC	p.R135S		NM_005654	NP_005645	P10589	COT1_HUMAN	nuclear receptor subfamily 2, group F, member 1	135	NR C4-type.|Nuclear receptor.				negative regulation of transcription from RNA polymerase II promoter|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor	nucleoplasm	ligand-regulated transcription factor activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|steroid hormone receptor activity|transcription coactivator activity|zinc ion binding			urinary_tract(1)|ovary(1)|lung(1)	3		all_cancers(142;1.62e-05)|all_epithelial(76;1.51e-07)|all_lung(232;0.0126)|Lung NSC(167;0.0155)|Ovarian(174;0.0218)|Prostate(281;0.173)|Colorectal(57;0.19)		UCEC - Uterine corpus endometrioid carcinoma (5;0.0416)|all cancers(79;9.57e-18)						48				0.414634	53.072976	53.332365	17	24	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	92921132	92921132	11032	5	C	A	A	A	299	23	NR2F1	1	1
LNPEP	4012	broad.mit.edu	37	5	96315554	96315554	+	Silent	SNP	C	T	T			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:96315554C>T	uc003kmv.1	+	c.732C>T	c.(730-732)GCC>GCT	p.A244A	LNPEP_uc003kmw.1_Silent_p.A230A	NM_005575	NP_005566	Q9UIQ6	LCAP_HUMAN	leucyl/cystinyl aminopeptidase isoform 1	244	Extracellular (Potential).				cell-cell signaling|female pregnancy|proteolysis	extracellular region|integral to plasma membrane	aminopeptidase activity|metallopeptidase activity|zinc ion binding			ovary(3)|breast(1)	4		all_cancers(142;7e-07)|all_epithelial(76;9.52e-10)|all_lung(232;0.00101)|Lung NSC(167;0.00137)|Ovarian(225;0.024)|Colorectal(57;0.0269)|Breast(839;0.244)		COAD - Colon adenocarcinoma(37;0.072)										0.448864	232.222643	232.632897	79	97	KEEP	---	---	---	---	capture		Silent	SNP	96315554	96315554	9193	5	C	T	T	T	262	21	LNPEP	2	2
MICAL1	64780	broad.mit.edu	37	6	109769445	109769445	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:109769445G>T	uc011eaq.1	-	c.1873C>A	c.(1873-1875)CAC>AAC	p.H625N	MICAL1_uc003ptj.2_Missense_Mutation_p.H606N|MICAL1_uc003ptk.2_Missense_Mutation_p.H606N|MICAL1_uc010kdr.2_Missense_Mutation_p.H520N	NM_022765	NP_073602	Q8TDZ2	MICA1_HUMAN	microtubule associated monoxygenase, calponin	606	CH.				cytoskeleton organization|oxidation-reduction process|signal transduction	cytoplasm|intermediate filament	SH3 domain binding|zinc ion binding			breast(2)|ovary(1)	3		all_cancers(87;0.000189)|Acute lymphoblastic leukemia(125;3.07e-08)|all_hematologic(75;3.33e-06)|all_epithelial(87;0.00686)|Lung SC(18;0.0743)|Colorectal(196;0.101)|all_lung(197;0.149)		Epithelial(106;0.0142)|all cancers(137;0.0197)|OV - Ovarian serous cystadenocarcinoma(136;0.0233)|BRCA - Breast invasive adenocarcinoma(108;0.0574)										0.605505	207.86115	208.923292	66	43	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	109769445	109769445	9959	6	G	T	T	T	611	47	MICAL1	2	2
KPNA5	3841	broad.mit.edu	37	6	117043355	117043355	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:117043355G>T	uc003pxh.2	+	c.823G>T	c.(823-825)GTG>TTG	p.V275L		NM_002269	NP_002260	O15131	IMA5_HUMAN	karyopherin alpha 5	272	ARM 5.				NLS-bearing substrate import into nucleus	cytoplasm|nuclear pore	protein binding|protein transporter activity			breast(3)	3		all_cancers(87;0.0314)|all_epithelial(87;0.0216)|Colorectal(196;0.234)		GBM - Glioblastoma multiforme(226;0.0298)|all cancers(137;0.0461)|OV - Ovarian serous cystadenocarcinoma(136;0.0513)|Epithelial(106;0.212)						205				0.4	211.798822	213.21545	66	99	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	117043355	117043355	8747	6	G	T	T	T	520	40	KPNA5	1	1
RFX6	222546	broad.mit.edu	37	6	117246757	117246757	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:117246757C>A	uc003pxm.2	+	c.1820C>A	c.(1819-1821)CCT>CAT	p.P607H		NM_173560	NP_775831	Q8HWS3	RFX6_HUMAN	regulatory factor X, 6	607					glucose homeostasis|pancreatic A cell differentiation|pancreatic D cell differentiation|pancreatic E cell differentiation|positive regulation of transcription, DNA-dependent|regulation of insulin secretion|transcription, DNA-dependent|type B pancreatic cell differentiation	nucleus	promoter binding|protein binding|transcription activator activity			ovary(1)|pancreas(1)	2														0.383929	119.486144	120.812994	43	69	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	117246757	117246757	13739	6	C	A	A	A	312	24	RFX6	2	2
LAMA2	3908	broad.mit.edu	37	6	129774214	129774214	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:129774214G>T	uc003qbn.2	+	c.6511G>T	c.(6511-6513)GTT>TTT	p.V2171F	LAMA2_uc003qbo.2_Missense_Mutation_p.V2171F	NM_000426	NP_000417	P24043	LAMA2_HUMAN	laminin alpha 2 subunit isoform a precursor	2171	Laminin G-like 1.				cell adhesion|muscle organ development|regulation of cell adhesion|regulation of cell migration|regulation of embryonic development	laminin-1 complex	receptor binding|structural molecule activity			ovary(8)|breast(1)	9				OV - Ovarian serous cystadenocarcinoma(136;0.178)|all cancers(137;0.245)										0.4	114.808676	115.645159	38	57	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	129774214	129774214	8929	6	G	T	T	T	624	48	LAMA2	2	2
MAP3K5	4217	broad.mit.edu	37	6	136926374	136926374	+	Silent	SNP	C	A	A			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:136926374C>A	uc003qhc.2	-	c.2652G>T	c.(2650-2652)CTG>CTT	p.L884L	MAP3K5_uc011edj.1_Silent_p.L131L|MAP3K5_uc011edk.1_Silent_p.L729L	NM_005923	NP_005914	Q99683	M3K5_HUMAN	mitogen-activated protein kinase kinase kinase	884	Protein kinase.				activation of JUN kinase activity|activation of MAPKK activity|apoptosis|induction of apoptosis by extracellular signals|interspecies interaction between organisms		ATP binding|caspase activator activity|magnesium ion binding|MAP kinase kinase kinase activity|protein homodimerization activity|protein phosphatase binding			ovary(2)	2	Colorectal(23;0.24)			GBM - Glioblastoma multiforme(68;0.00137)|OV - Ovarian serous cystadenocarcinoma(155;0.00569)						1151				0.372385	253.142121	256.549238	89	150	KEEP	---	---	---	---	capture		Silent	SNP	136926374	136926374	9636	6	C	A	A	A	262	21	MAP3K5	2	2
KIAA1244	57221	broad.mit.edu	37	6	138576798	138576798	+	Silent	SNP	G	T	T			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:138576798G>T	uc003qhu.2	+	c.996G>T	c.(994-996)CTG>CTT	p.L332L		NM_020340	NP_065073	Q5TH69	BIG3_HUMAN	brefeldin A-inhibited guanine	332					regulation of ARF protein signal transduction	cytoplasm|integral to membrane	ARF guanyl-nucleotide exchange factor activity			ovary(1)|skin(1)	2	Breast(32;0.135)			OV - Ovarian serous cystadenocarcinoma(155;0.00102)|GBM - Glioblastoma multiforme(68;0.00259)										0.4	26.588788	26.82194	10	15	KEEP	---	---	---	---	capture		Silent	SNP	138576798	138576798	8526	6	G	T	T	T	600	47	KIAA1244	2	2
HIVEP2	3097	broad.mit.edu	37	6	143092972	143092972	+	Silent	SNP	G	A	A			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:143092972G>A	uc003qjd.2	-	c.2904C>T	c.(2902-2904)AGC>AGT	p.S968S		NM_006734	NP_006725	P31629	ZEP2_HUMAN	human immunodeficiency virus type I enhancer	968	Ser-rich.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(3)|central_nervous_system(1)	4				OV - Ovarian serous cystadenocarcinoma(155;1.61e-05)|GBM - Glioblastoma multiforme(68;0.0102)		Esophageal Squamous(107;843 1510 13293 16805 42198)								0.522523	176.28121	176.333016	58	53	KEEP	---	---	---	---	capture		Silent	SNP	143092972	143092972	7478	6	G	A	A	A	542	42	HIVEP2	2	2
UNC93A	54346	broad.mit.edu	37	6	167728843	167728843	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:167728843G>T	uc003qvq.2	+	c.1277G>T	c.(1276-1278)GGG>GTG	p.G426V	UNC93A_uc003qvr.2_Missense_Mutation_p.G384V	NM_018974	NP_061847	Q86WB7	UN93A_HUMAN	unc-93 homolog A isoform 1	426						integral to membrane|plasma membrane					0		Breast(66;7.62e-05)|Ovarian(120;0.105)		OV - Ovarian serous cystadenocarcinoma(33;2.22e-20)|BRCA - Breast invasive adenocarcinoma(81;6.17e-07)|GBM - Glioblastoma multiforme(31;0.00492)										0.341067	403.735621	413.336777	147	284	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	167728843	167728843	17555	6	G	T	T	T	559	43	UNC93A	2	2
MLLT4	4301	broad.mit.edu	37	6	168370608	168370608	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:168370608C>T	uc003qwd.2	+	c.5498C>T	c.(5497-5499)ACA>ATA	p.T1833I		NM_001040001	NP_001035090	E9PHS7	E9PHS7_HUMAN	myeloid/lymphoid or mixed-lineage leukemia	Error:Variant_position_missing_in_E9PHS7_after_alignment					signal transduction					ovary(2)|kidney(1)|central_nervous_system(1)	4		Breast(66;1.07e-05)|Ovarian(120;0.024)		Epithelial(4;2.38e-32)|OV - Ovarian serous cystadenocarcinoma(33;9.99e-23)|BRCA - Breast invasive adenocarcinoma(4;1.2e-11)|GBM - Glioblastoma multiforme(31;0.00117)						1250				0.5	15.941752	15.941752	6	6	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	168370608	168370608	10019	6	C	T	T	T	221	17	MLLT4	2	2
FAM120B	84498	broad.mit.edu	37	6	170626835	170626835	+	Missense_Mutation	SNP	C	G	G			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:170626835C>G	uc003qxp.2	+	c.357C>G	c.(355-357)ATC>ATG	p.I119M	FAM120B_uc003qxo.1_Missense_Mutation_p.I119M|FAM120B_uc011ehd.1_Intron	NM_032448	NP_115824	Q96EK7	F120B_HUMAN	family with sequence similarity 120B	119					cell differentiation|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	protein binding			ovary(1)	1		Breast(66;0.000338)|Esophageal squamous(34;0.241)		OV - Ovarian serous cystadenocarcinoma(33;3.94e-22)|BRCA - Breast invasive adenocarcinoma(81;6.47e-06)|GBM - Glioblastoma multiforme(31;0.0899)										0.5	203.027652	203.027652	55	55	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	170626835	170626835	5614	6	C	G	G	G	369	29	FAM120B	3	3
HIST1H2BI	8346	broad.mit.edu	37	6	26273485	26273485	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:26273485G>T	uc003nhk.2	+	c.282G>T	c.(280-282)GAG>GAT	p.E94D	HIST1H3G_uc003nhi.2_5'Flank	NM_003525	NP_003516	P62807	H2B1C_HUMAN	histone cluster 1, H2bi	94					defense response to bacterium|nucleosome assembly	nucleosome|nucleus	DNA binding|protein binding				0														0.451852	161.224397	161.499657	61	74	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	26273485	26273485	7433	6	G	T	T	T	425	33	HIST1H2BI	2	2
HIST1H2AJ	8331	broad.mit.edu	37	6	27782408	27782408	+	Missense_Mutation	SNP	T	A	A			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:27782408T>A	uc003njn.1	-	c.111A>T	c.(109-111)AAA>AAT	p.K37N	HIST1H2BM_uc003njo.2_5'Flank	NM_021066	NP_066544	Q99878	H2A1J_HUMAN	histone cluster 1, H2aj	37					nucleosome assembly	nucleosome|nucleus	DNA binding				0														0.352941	17.744897	18.069115	6	11	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	27782408	27782408	7421	6	T	A	A	A	725	56	HIST1H2AJ	3	3
ITPR3	3710	broad.mit.edu	37	6	33652605	33652605	+	Missense_Mutation	SNP	A	C	C			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:33652605A>C	uc011drk.1	+	c.5192A>C	c.(5191-5193)GAG>GCG	p.E1731A	ITPR3_uc003oey.2_5'Flank	NM_002224	NP_002215	Q14573	ITPR3_HUMAN	inositol 1,4,5-triphosphate receptor, type 3	1731	Cytoplasmic (Potential).				activation of phospholipase C activity|calcium ion transport into cytosol|energy reserve metabolic process|G-protein coupled receptor protein signaling pathway|nerve growth factor receptor signaling pathway|platelet activation|protein heterooligomerization|protein homooligomerization|regulation of insulin secretion|response to calcium ion	apical part of cell|brush border|endoplasmic reticulum membrane|integral to plasma membrane|myelin sheath|neuronal cell body|nuclear outer membrane|platelet dense tubular network membrane	inositol 1,3,4,5 tetrakisphosphate binding|inositol 1,4,5 trisphosphate binding|inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity|inositol hexakisphosphate binding|intracellular ligand-gated calcium channel activity|protein binding			central_nervous_system(5)|ovary(3)|lung(1)|kidney(1)	10														0.387097	94.132449	95.216121	36	57	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	33652605	33652605	8226	6	A	C	C	C	143	11	ITPR3	4	4
SLC26A8	116369	broad.mit.edu	37	6	35923158	35923158	+	Missense_Mutation	SNP	A	G	G			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:35923158A>G	uc003olm.2	-	c.2003T>C	c.(2002-2004)GTG>GCG	p.V668A	SLC26A8_uc010jwa.2_Non-coding_Transcript|SLC26A8_uc003olk.2_Missense_Mutation_p.V250A|SLC26A8_uc003oln.2_Missense_Mutation_p.V668A|SLC26A8_uc003oll.2_Missense_Mutation_p.V563A	NM_052961	NP_443193	Q96RN1	S26A8_HUMAN	solute carrier family 26, member 8 isoform a	668	Interaction with RACGAP1.|STAS.|Cytoplasmic (Potential).				cell differentiation|meiosis|multicellular organismal development|spermatogenesis	integral to membrane|plasma membrane	anion:anion antiporter activity|chloride channel activity|oxalate transmembrane transporter activity|protein binding|sulfate transmembrane transporter activity			ovary(2)	2														0.379653	450.60925	455.75187	153	250	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	35923158	35923158	15020	6	A	G	G	G	78	6	SLC26A8	4	4
MOCS1	4337	broad.mit.edu	37	6	39883915	39883915	+	Silent	SNP	C	A	A			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:39883915C>A	uc003opb.2	-	c.480G>T	c.(478-480)CTG>CTT	p.L160L	MOCS1_uc003opa.2_Silent_p.L160L|MOCS1_uc003opc.2_Silent_p.L160L|MOCS1_uc003opd.2_Silent_p.L160L|MOCS1_uc003ope.2_Silent_p.L73L	NM_005942	NP_005933	Q9NZB8	MOCS1_HUMAN	molybdenum cofactor synthesis-step 1 protein	160	Molybdenum cofactor biosynthesis protein A.				Mo-molybdopterin cofactor biosynthetic process|Mo-molybdopterin cofactor biosynthetic process|water-soluble vitamin metabolic process	cytosol|molybdopterin synthase complex|nucleus	4 iron, 4 sulfur cluster binding|4 iron, 4 sulfur cluster binding|catalytic activity|GTP binding|metal ion binding			ovary(1)|liver(1)|central_nervous_system(1)	3	Ovarian(28;0.0355)|Colorectal(47;0.196)					NSCLC(84;861 1413 23785 24908 42279)|Melanoma(182;611 2047 9114 11847 26639)								0.428571	19.248013	19.310288	6	8	KEEP	---	---	---	---	capture		Silent	SNP	39883915	39883915	10081	6	C	A	A	A	262	21	MOCS1	2	2
TREML4	285852	broad.mit.edu	37	6	41197840	41197840	+	Silent	SNP	C	A	A			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:41197840C>A	uc003oqc.2	+	c.486C>A	c.(484-486)TCC>TCA	p.S162S	TREML4_uc003oqd.2_Non-coding_Transcript	NM_198153	NP_937796	Q6UXN2	TRML4_HUMAN	triggering receptor expressed on myeloid	162						extracellular region				breast(1)	1	Ovarian(28;0.0327)|Colorectal(47;0.196)													0.341935	152.520648	155.945948	53	102	KEEP	---	---	---	---	capture		Silent	SNP	41197840	41197840	17018	6	C	A	A	A	262	21	TREML4	2	2
HSP90AB1	3326	broad.mit.edu	37	6	44221316	44221316	+	Missense_Mutation	SNP	G	C	C	rs76772157	byFrequency;by1000genomes	TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:44221316G>C	uc003oxa.1	+	c.2156G>C	c.(2155-2157)CGC>CCC	p.R719P	HSP90AB1_uc011dvr.1_Missense_Mutation_p.R709P|HSP90AB1_uc003oxb.1_Missense_Mutation_p.R719P|HSP90AB1_uc011dvs.1_Missense_Mutation_p.R539P|HSP90AB1_uc003oxc.1_Missense_Mutation_p.R357P	NM_007355	NP_031381	P08238	HS90B_HUMAN	heat shock 90kDa protein 1, beta	719					axon guidance|negative regulation of proteasomal ubiquitin-dependent protein catabolic process|positive regulation of nitric oxide biosynthetic process|protein folding|regulation of interferon-gamma-mediated signaling pathway|regulation of type I interferon-mediated signaling pathway|response to unfolded protein	cytosol|melanosome	ATP binding|nitric-oxide synthase regulator activity|TPR domain binding|unfolded protein binding				0	all_cancers(18;1.7e-05)|all_lung(25;0.00747)|Hepatocellular(11;0.00908)|Ovarian(13;0.0273)		Colorectal(64;0.00337)|COAD - Colon adenocarcinoma(64;0.00536)							186		OREG0017471	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	0.049751	-21.346792	21.841553	10	191	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	44221316	44221316	7701	6	G	C	C	C	494	38	HSP90AB1	3	3
TDRD6	221400	broad.mit.edu	37	6	46663671	46663671	+	Nonsense_Mutation	SNP	G	T	T			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:46663671G>T	uc003oyj.2	+	c.6160G>T	c.(6160-6162)GAA>TAA	p.E2054*	TDRD6_uc010jze.2_Nonsense_Mutation_p.E2048*	NM_001010870	NP_001010870	O60522	TDRD6_HUMAN	tudor domain containing 6	2054	Tudor 8.				cell differentiation|multicellular organismal development|spermatogenesis	chromatoid body	nucleic acid binding			breast(3)|ovary(2)	5			Lung(136;0.192)											0.150617	92.148524	139.631013	61	344	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	46663671	46663671	16261	6	G	T	T	T	429	33	TDRD6	5	2
PKHD1	5314	broad.mit.edu	37	6	51613225	51613225	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:51613225G>T	uc003pah.1	-	c.9189C>A	c.(9187-9189)AAC>AAA	p.N3063K	PKHD1_uc010jzn.1_Missense_Mutation_p.N1046K|PKHD1_uc003pai.2_Missense_Mutation_p.N3063K	NM_138694	NP_619639	P08F94	PKHD1_HUMAN	fibrocystin isoform 1	3063	Extracellular (Potential).				cell-cell adhesion|cilium assembly|homeostatic process|kidney development|negative regulation of cellular component movement	anchored to external side of plasma membrane|apical plasma membrane|integral to membrane|microtubule basal body	protein binding|receptor activity			ovary(12)|large_intestine(5)|central_nervous_system(3)	20	Lung NSC(77;0.0605)									1537				0.428016	342.019226	343.176794	110	147	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	51613225	51613225	12396	6	G	T	T	T	568	44	PKHD1	2	2
KIAA1586	57691	broad.mit.edu	37	6	56915638	56915638	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:56915638G>T	uc003pdj.2	+	c.172G>T	c.(172-174)GCC>TCC	p.A58S	KIAA1586_uc011dxm.1_Intron	NM_020931	NP_065982	Q9HCI6	K1586_HUMAN	hypothetical protein LOC57691	58							nucleic acid binding				0	Lung NSC(77;0.0969)		LUSC - Lung squamous cell carcinoma(124;0.0785)|Lung(124;0.13)											0.387097	146.981605	148.362755	48	76	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	56915638	56915638	8554	6	G	T	T	T	494	38	KIAA1586	1	1
EYS	346007	broad.mit.edu	37	6	66204803	66204803	+	Silent	SNP	C	A	A			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:66204803C>A	uc011dxu.1	-	c.501G>T	c.(499-501)GTG>GTT	p.V167V	EYS_uc003peq.2_Silent_p.V167V|EYS_uc003per.1_Silent_p.V167V|EYS_uc010kaj.1_Non-coding_Transcript	NM_001142800	NP_001136272	Q5T1H1	EYS_HUMAN	eyes shut homolog isoform 1	167					response to stimulus|visual perception	extracellular region	calcium ion binding			ovary(1)	1														0.464567	176.09437	176.234773	59	68	KEEP	---	---	---	---	capture		Silent	SNP	66204803	66204803	5526	6	C	A	A	A	366	29	EYS	2	2
COL19A1	1310	broad.mit.edu	37	6	70850845	70850845	+	Splice_Site_SNP	SNP	G	T	T			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:70850845G>T	uc003pfc.1	+	c.1447_splice	c.e20-1	p.G483_splice	COL19A1_uc010kam.1_Splice_Site_SNP_p.G379_splice	NM_001858	NP_001849			alpha 1 type XIX collagen precursor						cell differentiation|cell-cell adhesion|extracellular matrix organization|skeletal system development	collagen	extracellular matrix structural constituent|protein binding, bridging			ovary(2)|breast(2)	4														0.382979	326.245436	329.627142	108	174	KEEP	---	---	---	---	capture		Splice_Site_SNP	SNP	70850845	70850845	3814	6	G	T	T	T	455	35	COL19A1	5	2
TMEM30A	55754	broad.mit.edu	37	6	75968498	75968498	+	Missense_Mutation	SNP	T	C	C			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:75968498T>C	uc003phw.2	-	c.890A>G	c.(889-891)TAC>TGC	p.Y297C	TMEM30A_uc003phx.2_Missense_Mutation_p.Y261C	NM_018247	NP_060717	Q9NV96	CC50A_HUMAN	transmembrane protein 30A isoform 1	297						integral to membrane					0														0.483871	107.254923	107.268536	30	32	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	75968498	75968498	16692	6	T	C	C	C	741	57	TMEM30A	4	4
FHL5	9457	broad.mit.edu	37	6	97053948	97053948	+	Splice_Site_SNP	SNP	G	T	T			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:97053948G>T	uc003pos.1	+	c.504_splice	c.e5+1	p.K168_splice	FHL5_uc003pot.1_Splice_Site_SNP_p.K168_splice	NM_020482	NP_065228			activator of cAMP-responsive element modulator							nucleus	zinc ion binding			ovary(2)	2		all_cancers(76;1.57e-07)|Acute lymphoblastic leukemia(125;4.93e-10)|all_hematologic(75;3.55e-07)|all_epithelial(107;0.00266)|Colorectal(196;0.0341)|Lung NSC(302;0.204)		BRCA - Breast invasive adenocarcinoma(108;0.0948)										0.385417	118.056144	119.159837	37	59	KEEP	---	---	---	---	capture		Splice_Site_SNP	SNP	97053948	97053948	6119	6	G	T	T	T	572	44	FHL5	5	2
MUC17	140453	broad.mit.edu	37	7	100676862	100676862	+	Nonsense_Mutation	SNP	C	A	A	rs71530303		TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:100676862C>A	uc003uxp.1	+	c.2165C>A	c.(2164-2166)TCA>TAA	p.S722*	MUC17_uc010lho.1_Non-coding_Transcript	NM_001040105	NP_001035194	Q685J3	MUC17_HUMAN	mucin 17 precursor	722	Extracellular (Potential).|Ser-rich.|10.|59 X approximate tandem repeats.					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)													0.067227	-32.846404	59.60871	32	444	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	100676862	100676862	10368	7	C	A	A	A	377	29	MUC17	5	2
MUC17	140453	broad.mit.edu	37	7	100696652	100696652	+	Nonsense_Mutation	SNP	G	A	A			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:100696652G>A	uc003uxp.1	+	c.13298G>A	c.(13297-13299)TGG>TAG	p.W4433*	MUC17_uc010lho.1_Non-coding_Transcript	NM_001040105	NP_001035194	Q685J3	MUC17_HUMAN	mucin 17 precursor	4433	Cytoplasmic (Potential).					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)													0.5	211.546367	211.546367	66	66	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	100696652	100696652	10368	7	G	A	A	A	611	47	MUC17	5	2
RELN	5649	broad.mit.edu	37	7	103276694	103276694	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:103276694C>A	uc003vca.2	-	c.2291G>T	c.(2290-2292)AGC>ATC	p.S764I	RELN_uc010liz.2_Missense_Mutation_p.S764I	NM_005045	NP_005036	P78509	RELN_HUMAN	reelin isoform a	764					axon guidance|cell adhesion|cerebral cortex tangential migration|glial cell differentiation|neuron migration|peptidyl-tyrosine phosphorylation|positive regulation of protein kinase activity|positive regulation of small GTPase mediated signal transduction|response to pain|spinal cord patterning	cytoplasm|dendrite|extracellular space|proteinaceous extracellular matrix	metal ion binding|protein serine/threonine/tyrosine kinase activity|serine-type peptidase activity			ovary(8)|large_intestine(2)|central_nervous_system(2)|pancreas(1)|skin(1)	14				COAD - Colon adenocarcinoma(1;8.98e-05)|Colorectal(1;0.00184)		NSCLC(146;835 1944 15585 22231 52158)								0.325	36.561318	37.648281	13	27	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	103276694	103276694	13689	7	C	A	A	A	364	28	RELN	2	2
RELN	5649	broad.mit.edu	37	7	103294653	103294653	+	Splice_Site_SNP	SNP	C	G	G			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:103294653C>G	uc003vca.2	-	c.1442_splice	c.e13-1	p.G481_splice	RELN_uc010liz.2_Splice_Site_SNP_p.G481_splice	NM_005045	NP_005036			reelin isoform a						axon guidance|cell adhesion|cerebral cortex tangential migration|glial cell differentiation|neuron migration|peptidyl-tyrosine phosphorylation|positive regulation of protein kinase activity|positive regulation of small GTPase mediated signal transduction|response to pain|spinal cord patterning	cytoplasm|dendrite|extracellular space|proteinaceous extracellular matrix	metal ion binding|protein serine/threonine/tyrosine kinase activity|serine-type peptidase activity			ovary(8)|large_intestine(2)|central_nervous_system(2)|pancreas(1)|skin(1)	14				COAD - Colon adenocarcinoma(1;8.98e-05)|Colorectal(1;0.00184)		NSCLC(146;835 1944 15585 22231 52158)								0.430493	304.044439	304.98739	96	127	KEEP	---	---	---	---	capture		Splice_Site_SNP	SNP	103294653	103294653	13689	7	C	G	G	G	312	24	RELN	5	3
CDHR3	222256	broad.mit.edu	37	7	105656440	105656441	+	Missense_Mutation	DNP	CT	TA	TA			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:105656440_105656441CT>TA	uc003vdl.3	+	c.1395_1396CT>TA	c.(1393-1398)TCCTAT>TCTAAT	p.Y466N	CDHR3_uc003vdk.2_Missense_Mutation_p.Y114N|CDHR3_uc003vdm.3_Missense_Mutation_p.Y453N|CDHR3_uc011klt.1_Missense_Mutation_p.Y378N|CDHR3_uc003vdn.2_Missense_Mutation_p.Y183N	NM_152750	NP_689963	Q6ZTQ4	CDHR3_HUMAN	hypothetical protein LOC222256 precursor	466	Cadherin 4.|Extracellular (Potential).|Cadherin 5.				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(1)	1														0.464286	80.64267	80.705097	26	30	KEEP	---	---	---	---	capture		Missense_Mutation	DNP	105656440	105656441	3249	7	CT	TA	TA	TA	301	24	CDHR3	2	2
IFRD1	3475	broad.mit.edu	37	7	112096994	112096994	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:112096994G>A	uc003vgh.2	+	c.310G>A	c.(310-312)GAA>AAA	p.E104K	IFRD1_uc011kmn.1_Missense_Mutation_p.E54K|IFRD1_uc003vgi.2_Missense_Mutation_p.E104K|IFRD1_uc003vgj.2_Missense_Mutation_p.E104K|IFRD1_uc011kmo.1_Non-coding_Transcript|IFRD1_uc011kmp.1_Missense_Mutation_p.E54K	NM_001007245	NP_001007246	O00458	IFRD1_HUMAN	interferon-related developmental regulator 1	104					multicellular organismal development|myoblast cell fate determination		binding			kidney(1)|central_nervous_system(1)	2														0.371981	215.612173	218.595802	77	130	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	112096994	112096994	7854	7	G	A	A	A	585	45	IFRD1	2	2
ST7	7982	broad.mit.edu	37	7	116830916	116830916	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:116830916G>T	uc003vin.2	+	c.1180G>T	c.(1180-1182)GGG>TGG	p.G394W	ST7_uc011knl.1_Missense_Mutation_p.G371W|ST7_uc003vio.2_Missense_Mutation_p.G371W|ST7_uc003viq.2_Missense_Mutation_p.G348W|ST7_uc011knm.1_Missense_Mutation_p.G351W|ST7_uc003vir.2_Missense_Mutation_p.G319W|ST7_uc011knn.1_Missense_Mutation_p.G342W|ST7_uc003vix.1_Missense_Mutation_p.G207W|ST7OT3_uc003viy.1_Non-coding_Transcript	NM_021908	NP_068708	Q9NRC1	ST7_HUMAN	suppression of tumorigenicity 7 isoform b	394						integral to membrane	binding			central_nervous_system(1)	1	all_cancers(3;3.88e-07)|all_epithelial(6;3.42e-07)|Lung NSC(10;0.00072)|all_lung(10;0.000847)		STAD - Stomach adenocarcinoma(10;0.000512)	LUSC - Lung squamous cell carcinoma(290;0.133)										0.288732	97.468976	103.123648	41	101	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	116830916	116830916	15747	7	G	T	T	T	559	43	ST7	2	2
TSPAN12	23554	broad.mit.edu	37	7	120446688	120446688	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:120446688C>A	uc003vjk.2	-	c.527G>T	c.(526-528)TGG>TTG	p.W176L	TSPAN12_uc010lkj.2_Missense_Mutation_p.W49L	NM_012338	NP_036470	O95859	TSN12_HUMAN	transmembrane 4 superfamily member 12	176	Extracellular (Potential).				angiogenesis|cell surface receptor linked signaling pathway|regulation of angiogenesis|retina layer formation	integral to plasma membrane|membrane fraction					0	all_neural(327;0.117)													0.456897	162.664518	162.851496	53	63	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	120446688	120446688	17187	7	C	A	A	A	273	21	TSPAN12	2	2
GRM8	2918	broad.mit.edu	37	7	126173024	126173024	+	Silent	SNP	T	A	A			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:126173024T>A	uc003vlr.2	-	c.2412A>T	c.(2410-2412)ACA>ACT	p.T804T	GRM8_uc003vls.2_Non-coding_Transcript|GRM8_uc011kof.1_Non-coding_Transcript|GRM8_uc003vlt.2_Silent_p.T804T|GRM8_uc010lkz.1_Non-coding_Transcript	NM_000845	NP_000836	O00222	GRM8_HUMAN	glutamate receptor, metabotropic 8 isoform a	804	Extracellular (Potential).				negative regulation of cAMP biosynthetic process|sensory perception of smell|visual perception	integral to plasma membrane				ovary(5)|pancreas(1)	6		Prostate(267;0.186)			L-Glutamic Acid(DB00142)									0.469799	229.3432	229.460906	70	79	KEEP	---	---	---	---	capture		Silent	SNP	126173024	126173024	7082	7	T	A	A	A	704	55	GRM8	3	3
AHCYL2	23382	broad.mit.edu	37	7	129064950	129064950	+	Missense_Mutation	SNP	A	T	T			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:129064950A>T	uc011kov.1	+	c.1676A>T	c.(1675-1677)AAG>ATG	p.K559M	AHCYL2_uc003vot.2_Missense_Mutation_p.K558M|AHCYL2_uc003vov.2_Missense_Mutation_p.K456M|AHCYL2_uc011kow.1_Missense_Mutation_p.K457M|AHCYL2_uc011kox.1_Missense_Mutation_p.K456M	NM_015328	NP_056143	Q96HN2	SAHH3_HUMAN	S-adenosylhomocysteine hydrolase-like 2 isoform	559					one-carbon metabolic process		adenosylhomocysteinase activity			ovary(2)	2						Pancreas(160;1736 1964 29875 40941 45605)								0.470588	449.921472	450.155666	144	162	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	129064950	129064950	414	7	A	T	T	T	39	3	AHCYL2	3	3
TAS2R41	259287	broad.mit.edu	37	7	143175182	143175182	+	Missense_Mutation	SNP	A	G	G			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:143175182A>G	uc003wdc.1	+	c.217A>G	c.(217-219)AAG>GAG	p.K73E		NM_176883	NP_795364	P59536	T2R41_HUMAN	taste receptor, type 2, member 41	73	Extracellular (Potential).				sensory perception of taste	integral to membrane	G-protein coupled receptor activity			pancreas(1)	1	Melanoma(164;0.15)													0.245033	209.011578	226.887645	74	228	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	143175182	143175182	16101	7	A	G	G	G	117	9	TAS2R41	4	4
ZNF425	155054	broad.mit.edu	37	7	148801676	148801676	+	Silent	SNP	C	T	T			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:148801676C>T	uc003wfj.2	-	c.1287G>A	c.(1285-1287)CTG>CTA	p.L429L		NM_001001661	NP_001001661	Q6IV72	ZN425_HUMAN	zinc finger protein 425	429	C2H2-type 8.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			breast(2)|ovary(1)	3	Melanoma(164;0.15)		OV - Ovarian serous cystadenocarcinoma(82;0.00463)											0.511765	263.820209	263.840674	87	83	KEEP	---	---	---	---	capture		Silent	SNP	148801676	148801676	18492	7	C	T	T	T	366	29	ZNF425	2	2
GIMAP8	155038	broad.mit.edu	37	7	150174341	150174341	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:150174341G>A	uc003whj.2	+	c.1471G>A	c.(1471-1473)GTT>ATT	p.V491I		NM_175571	NP_783161	Q8ND71	GIMA8_HUMAN	GTPase, IMAP family member 8	491	Poly-Val.					endoplasmic reticulum|Golgi apparatus|mitochondrion	GTP binding			ovary(1)|breast(1)|central_nervous_system(1)	3			OV - Ovarian serous cystadenocarcinoma(82;0.0218)	UCEC - Uterine corpus endometrioid carcinoma (81;0.17)										0.412088	210.56587	211.800009	75	107	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	150174341	150174341	6653	7	G	A	A	A	572	44	GIMAP8	2	2
HOXA5	3202	broad.mit.edu	37	7	27183196	27183196	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:27183196C>A	uc003syn.1	-	c.31G>T	c.(31-33)GGT>TGT	p.G11C		NM_019102	NP_061975	P20719	HXA5_HUMAN	homeobox A5	11					negative regulation of angiogenesis|negative regulation of erythrocyte differentiation|positive regulation of apoptosis|positive regulation of myeloid cell differentiation|positive regulation of receptor biosynthetic process|positive regulation of transcription from RNA polymerase II promoter	nucleus	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription regulator activity				0						Colon(119;75 2200 7557 42868)								0.483146	288.016873	288.05619	86	92	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	27183196	27183196	7587	7	C	A	A	A	299	23	HOXA5	1	1
CHN2	1124	broad.mit.edu	37	7	29519962	29519962	+	Missense_Mutation	SNP	A	G	G			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:29519962A>G	uc011jzs.1	+	c.869A>G	c.(868-870)CAC>CGC	p.H290R	CHN2_uc003szz.2_Missense_Mutation_p.H215R|CHN2_uc010kva.2_Intron|CHN2_uc010kvb.2_Intron|CHN2_uc010kvc.2_Missense_Mutation_p.H180R|CHN2_uc011jzt.1_Missense_Mutation_p.H228R|CHN2_uc010kvd.2_Missense_Mutation_p.H71R|CHN2_uc011jzu.1_Missense_Mutation_p.H200R|CHN2_uc010kvg.2_Missense_Mutation_p.H79R|CHN2_uc010kvh.2_Missense_Mutation_p.H79R|CHN2_uc010kvi.2_Missense_Mutation_p.H79R|CHN2_uc010kve.2_Missense_Mutation_p.H79R|CHN2_uc003taa.2_Missense_Mutation_p.H79R|CHN2_uc010kvf.2_Missense_Mutation_p.H79R|CHN2_uc010kvj.2_Intron|CHN2_uc010kvk.2_Intron|CHN2_uc010kvl.2_Intron|CHN2_uc010kvm.2_Intron	NM_004067	NP_004058	P52757	CHIO_HUMAN	beta chimerin isoform 2	215	Phorbol-ester/DAG-type.				regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol|membrane	GTPase activator activity|metal ion binding|SH3/SH2 adaptor activity			ovary(2)	2						Ovarian(1;44 48 13232 18918 31480)								0.378906	280.899934	284.196216	97	159	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	29519962	29519962	3497	7	A	G	G	G	78	6	CHN2	4	4
GLI3	2737	broad.mit.edu	37	7	42004046	42004046	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:42004046C>A	uc011kbh.1	-	c.4625G>T	c.(4624-4626)CGG>CTG	p.R1542L	GLI3_uc011kbg.1_Missense_Mutation_p.R1483L	NM_000168	NP_000159	P10071	GLI3_HUMAN	GLI-Kruppel family member GLI3	1542					negative regulation of alpha-beta T cell differentiation|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of smoothened signaling pathway|negative regulation of transcription from RNA polymerase II promoter|negative thymic T cell selection|positive regulation of alpha-beta T cell differentiation|positive regulation of gene-specific transcription from RNA polymerase II promoter|thymocyte apoptosis	cilium|cytosol|nucleolus	beta-catenin binding|histone acetyltransferase binding|histone deacetylase binding|sequence-specific DNA binding transcription factor activity|transcription activator activity|transcription repressor activity|zinc ion binding			large_intestine(2)|ovary(2)|central_nervous_system(1)|lung(1)|kidney(1)|pancreas(1)	8										806				0.411765	103.079924	103.663938	35	50	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	42004046	42004046	6707	7	C	A	A	A	299	23	GLI3	1	1
TNS3	64759	broad.mit.edu	37	7	47440037	47440037	+	Missense_Mutation	SNP	T	A	A			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:47440037T>A	uc003tnv.2	-	c.872A>T	c.(871-873)TAT>TTT	p.Y291F	TNS3_uc003tnw.2_Missense_Mutation_p.Y291F	NM_022748	NP_073585	Q68CZ2	TENS3_HUMAN	tensin 3	291	C2 tensin-type.					focal adhesion	protein binding			ovary(4)	4														0.440994	222.608814	223.0946	71	90	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	47440037	47440037	16885	7	T	A	A	A	637	49	TNS3	3	3
SUN3	256979	broad.mit.edu	37	7	48046777	48046777	+	Silent	SNP	G	A	A			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:48046777G>A	uc003tof.2	-	c.477C>T	c.(475-477)GAC>GAT	p.D159D	SUN3_uc010kyq.2_Silent_p.D59D|SUN3_uc003tog.2_Silent_p.D159D|SUN3_uc011kcf.1_Silent_p.D147D	NM_152782	NP_689995	Q8TAQ9	SUN3_HUMAN	Sad1 and UNC84 domain containing 1	159						integral to membrane				central_nervous_system(1)	1														0.394737	126.246445	127.352729	45	69	KEEP	---	---	---	---	capture		Silent	SNP	48046777	48046777	15913	7	G	A	A	A	568	44	SUN3	2	2
POM121L12	285877	broad.mit.edu	37	7	53103588	53103588	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:53103588C>A	uc003tpz.2	+	c.224C>A	c.(223-225)ACC>AAC	p.T75N		NM_182595	NP_872401	Q8N7R1	P1L12_HUMAN	POM121 membrane glycoprotein-like 12	75											0														0.352941	44.476369	45.429942	18	33	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	53103588	53103588	12669	7	C	A	A	A	234	18	POM121L12	2	2
EIF2AK1	27102	broad.mit.edu	37	7	6068579	6068579	+	Missense_Mutation	SNP	T	C	C			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:6068579T>C	uc003spp.2	-	c.1417A>G	c.(1417-1419)AAC>GAC	p.N473D	EIF2AK1_uc003spq.2_Missense_Mutation_p.N472D|EIF2AK1_uc011jwm.1_Missense_Mutation_p.N349D	NM_014413	NP_055228	Q9BQI3	E2AK1_HUMAN	eukaryotic translation initiation factor 2-alpha	473	Protein kinase.				negative regulation of hemoglobin biosynthetic process|negative regulation of translational initiation by iron|protein autophosphorylation|response to external stimulus|response to stress	cytoplasm	ATP binding|eukaryotic translation initiation factor 2alpha kinase activity|heme binding|protein homodimerization activity			upper_aerodigestive_tract(1)|stomach(1)|lung(1)|central_nervous_system(1)	4		Ovarian(82;0.0423)		UCEC - Uterine corpus endometrioid carcinoma (126;0.106)|OV - Ovarian serous cystadenocarcinoma(56;5.22e-14)						253				0.125954	59.080229	94.903053	33	229	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	6068579	6068579	5185	7	T	C	C	C	806	62	EIF2AK1	4	4
VPS37D	155382	broad.mit.edu	37	7	73085416	73085416	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:73085416G>T	uc003tyr.2	+	c.466G>T	c.(466-468)GCC>TCC	p.A156S		NM_001077621	NP_001071089	Q86XT2	VP37D_HUMAN	vacuolar protein sorting 37D	156	VPS37 C-terminal.				cellular membrane organization|endosome transport|protein transport	late endosome membrane					0		Lung NSC(55;0.0908)|all_lung(88;0.198)												0.323077	58.30689	60.085352	21	44	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	73085416	73085416	17775	7	G	T	T	T	494	38	VPS37D	1	1
CLIP2	7461	broad.mit.edu	37	7	73768238	73768239	+	Missense_Mutation	DNP	GG	AT	AT			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:73768238_73768239GG>AT	uc003uam.2	+	c.707_708GG>AT	c.(706-708)CGG>CAT	p.R236H	CLIP2_uc003uan.2_Missense_Mutation_p.R236H	NM_003388	NP_003379	Q9UDT6	CLIP2_HUMAN	CAP-GLY domain containing linker protein 2	236						microtubule associated complex					0														0.35022	421.665691	430.614239	159	295	KEEP	---	---	---	---	capture		Missense_Mutation	DNP	73768238	73768239	3671	7	GG	AT	AT	AT	507	39	CLIP2	1	1
FGL2	10875	broad.mit.edu	37	7	76828895	76828895	+	Silent	SNP	G	A	A			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:76828895G>A	uc003ugb.2	-	c.216C>T	c.(214-216)TTC>TTT	p.F72F	CCDC146_uc003ufz.1_Intron|CCDC146_uc003uga.2_Intron	NM_006682	NP_006673	Q14314	FGL2_HUMAN	fibrinogen-like 2 precursor	72					signal transduction	fibrinogen complex	receptor binding			skin(1)	1														0.450746	440.343274	441.056129	151	184	KEEP	---	---	---	---	capture		Silent	SNP	76828895	76828895	6110	7	G	A	A	A	581	45	FGL2	2	2
PION	54103	broad.mit.edu	37	7	76984659	76984659	+	Silent	SNP	G	C	C			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:76984659G>C	uc003ugf.2	-	c.1209C>G	c.(1207-1209)CTC>CTG	p.L403L	PION_uc003ugg.1_Silent_p.L188L	NM_017439	NP_059135	A4D1B5	GSAP_HUMAN	pigeon homolog	403					beta-amyloid formation|regulation of proteolysis	trans-Golgi network	beta-amyloid binding			central_nervous_system(1)	1														0.367347	286.10356	289.885739	90	155	KEEP	---	---	---	---	capture		Silent	SNP	76984659	76984659	12358	7	G	C	C	C	418	33	PION	3	3
CACNA2D1	781	broad.mit.edu	37	7	81603792	81603792	+	Missense_Mutation	SNP	T	C	C			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:81603792T>C	uc003uhr.1	-	c.2032A>G	c.(2032-2034)AAA>GAA	p.K678E		NM_000722	NP_000713	P54289	CA2D1_HUMAN	calcium channel, voltage-dependent, alpha	690	Extracellular (Potential).					voltage-gated calcium channel complex	metal ion binding			ovary(5)|pancreas(1)	6					Felodipine(DB01023)|Gabapentin(DB00996)|Ibutilide(DB00308)|Isradipine(DB00270)|Magnesium Sulfate(DB00653)|Nifedipine(DB01115)									0.525	77.175192	77.196841	21	19	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	81603792	81603792	2664	7	T	C	C	C	832	64	CACNA2D1	4	4
DYNC1I1	1780	broad.mit.edu	37	7	95662047	95662047	+	Silent	SNP	T	C	C			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:95662047T>C	uc003uoc.3	+	c.1236T>C	c.(1234-1236)GAT>GAC	p.D412D	DYNC1I1_uc003uod.3_Silent_p.D395D|DYNC1I1_uc003uob.2_Silent_p.D375D|DYNC1I1_uc003uoe.3_Silent_p.D392D|DYNC1I1_uc010lfl.2_Silent_p.D401D	NM_004411	NP_004402	O14576	DC1I1_HUMAN	dynein, cytoplasmic 1, intermediate chain 1	412	WD 3.				vesicle transport along microtubule	condensed chromosome kinetochore|cytoplasmic dynein complex|microtubule|perinuclear region of cytoplasm|spindle pole	microtubule binding|microtubule motor activity			ovary(3)|kidney(1)	4	all_cancers(62;9.39e-10)|all_epithelial(64;2.28e-09)|Lung NSC(181;0.165)|all_lung(186;0.191)		STAD - Stomach adenocarcinoma(171;0.0957)											0.464286	364.843585	365.123805	117	135	KEEP	---	---	---	---	capture		Silent	SNP	95662047	95662047	5028	7	T	C	C	C	660	51	DYNC1I1	4	4
TRRAP	8295	broad.mit.edu	37	7	98557026	98557026	+	Silent	SNP	G	T	T			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:98557026G>T	uc003upp.2	+	c.6381G>T	c.(6379-6381)GTG>GTT	p.V2127V	TRRAP_uc011kis.1_Silent_p.V2109V|TRRAP_uc003upr.2_Silent_p.V1826V	NM_003496	NP_003487	Q9Y4A5	TRRAP_HUMAN	transformation/transcription domain-associated	2127	Interaction with TP53.				histone deubiquitination|histone H2A acetylation|histone H4 acetylation|regulation of transcription, DNA-dependent|transcription, DNA-dependent	NuA4 histone acetyltransferase complex|PCAF complex|STAGA complex|transcription factor TFTC complex	phosphotransferase activity, alcohol group as acceptor|protein binding|transcription cofactor activity			ovary(9)|large_intestine(8)|central_nervous_system(6)|stomach(2)|lung(1)|liver(1)	27	all_cancers(62;6.96e-09)|all_epithelial(64;4.86e-09)|Lung NSC(181;0.01)|all_lung(186;0.016)|Esophageal squamous(72;0.0274)		STAD - Stomach adenocarcinoma(171;0.215)							1847				0.10687	11.248947	31.350441	14	117	KEEP	---	---	---	---	capture		Silent	SNP	98557026	98557026	17152	7	G	T	T	T	574	45	TRRAP	2	2
PABPC1	26986	broad.mit.edu	37	8	101717279	101717279	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:101717279G>A	uc003yjs.1	-	c.1693C>T	c.(1693-1695)CGG>TGG	p.R565W	PABPC1_uc011lhc.1_Missense_Mutation_p.R533W|PABPC1_uc011lhd.1_Missense_Mutation_p.R520W|PABPC1_uc003yjt.1_Missense_Mutation_p.R562W|PABPC1_uc003yju.2_Non-coding_Transcript	NM_002568	NP_002559	P11940	PABP1_HUMAN	poly(A) binding protein, cytoplasmic 1	565	PABC.				mRNA polyadenylation|mRNA stabilization|nuclear mRNA splicing, via spliceosome|nuclear-transcribed mRNA poly(A) tail shortening|translation	catalytic step 2 spliceosome|cytosol	nucleotide binding|poly(A) RNA binding|protein C-terminus binding|translation activator activity				0	all_cancers(14;6.8e-05)|all_epithelial(15;3.16e-07)|Lung NSC(17;0.000453)|all_lung(17;0.00125)		Epithelial(11;6.37e-11)|all cancers(13;1.11e-08)|OV - Ovarian serous cystadenocarcinoma(57;3.91e-05)|STAD - Stomach adenocarcinoma(118;0.206)											0.173333	50.456091	65.571793	26	124	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	101717279	101717279	11776	8	G	A	A	A	519	40	PABPC1	1	1
CSMD3	114788	broad.mit.edu	37	8	113421257	113421257	+	Silent	SNP	C	A	A			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:113421257C>A	uc003ynu.2	-	c.5400G>T	c.(5398-5400)GTG>GTT	p.V1800V	CSMD3_uc003yns.2_Intron|CSMD3_uc003ynt.2_Silent_p.V1760V|CSMD3_uc011lhx.1_Silent_p.V1696V	NM_198123	NP_937756	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3 isoform 1	1800	Extracellular (Potential).|CUB 10.					integral to membrane|plasma membrane				ovary(20)|lung(11)|kidney(8)|large_intestine(6)|skin(3)|central_nervous_system(2)|urinary_tract(1)|breast(1)	52										2888	TCGA Ovarian(7;0.080)			0.492683	315.967692	315.977249	101	104	KEEP	---	---	---	---	capture		Silent	SNP	113421257	113421257	4087	8	C	A	A	A	210	17	CSMD3	2	2
BLK	640	broad.mit.edu	37	8	11400849	11400849	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:11400849C>A	uc003wty.2	+	c.116C>A	c.(115-117)CCG>CAG	p.P39Q	BLK_uc003wtz.2_Intron	NM_001715	NP_001706	P51451	BLK_HUMAN	B lymphoid tyrosine kinase	39					intracellular protein kinase cascade|positive regulation of insulin secretion|protein phosphorylation		ATP binding|non-membrane spanning protein tyrosine kinase activity			large_intestine(1)|ovary(1)	2			STAD - Stomach adenocarcinoma(15;0.00391)	COAD - Colon adenocarcinoma(149;0.207)						676				0.583333	44.647588	44.793257	14	10	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	11400849	11400849	1469	8	C	A	A	A	299	23	BLK	1	1
NOV	4856	broad.mit.edu	37	8	120429208	120429208	+	Silent	SNP	G	T	T			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:120429208G>T	uc003yoq.2	+	c.309G>T	c.(307-309)ACG>ACT	p.T103T		NM_002514	NP_002505	P48745	NOV_HUMAN	nephroblastoma overexpressed precursor	103	IGFBP N-terminal.				regulation of cell growth		growth factor activity|insulin-like growth factor binding			ovary(2)|skin(2)|kidney(1)	5	all_cancers(13;3.84e-26)|Lung NSC(37;1.19e-08)|Ovarian(258;0.0249)|Hepatocellular(40;0.161)		STAD - Stomach adenocarcinoma(47;0.000507)		Insulin Glargine recombinant(DB00047)|Insulin Lyspro recombinant(DB00046)|Insulin recombinant(DB00030)|Insulin, porcine(DB00071)					71		OREG0018940	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	0.290323	22.460403	23.683055	9	22	KEEP	---	---	---	---	capture		Silent	SNP	120429208	120429208	10957	8	G	T	T	T	496	39	NOV	1	1
ENPP2	5168	broad.mit.edu	37	8	120592356	120592356	+	Missense_Mutation	SNP	C	G	G			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:120592356C>G	uc003yos.1	-	c.1936G>C	c.(1936-1938)GAG>CAG	p.E646Q	ENPP2_uc011lic.1_Missense_Mutation_p.A107P|ENPP2_uc003yor.1_Missense_Mutation_p.E229Q|ENPP2_uc003yot.1_Missense_Mutation_p.E594Q|ENPP2_uc010mdd.1_Missense_Mutation_p.A594P	NM_006209	NP_006200	Q13822	ENPP2_HUMAN	autotaxin isoform 1 preproprotein	594					cellular component movement|chemotaxis|G-protein coupled receptor protein signaling pathway|immune response|phosphate metabolic process|phosphatidylcholine catabolic process|regulation of cell migration	extracellular space|integral to plasma membrane	alkylglycerophosphoethanolamine phosphodiesterase activity|calcium ion binding|lysophospholipase activity|nucleic acid binding|nucleotide diphosphatase activity|phosphodiesterase I activity|polysaccharide binding|scavenger receptor activity|transcription factor binding|zinc ion binding			ovary(2)|central_nervous_system(2)|large_intestine(1)|kidney(1)	6	Lung NSC(37;5.03e-06)|Ovarian(258;0.0249)|Hepatocellular(40;0.161)		STAD - Stomach adenocarcinoma(47;0.00185)			Melanoma(20;305 879 2501 4818 31020)								0.411602	900.852651	905.750962	298	426	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	120592356	120592356	5323	8	C	G	G	G	312	24	ENPP2	3	3
FAM49B	51571	broad.mit.edu	37	8	130874493	130874493	+	Missense_Mutation	SNP	C	G	G			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:130874493C>G	uc003yss.2	-	c.283G>C	c.(283-285)GAA>CAA	p.E95Q	FAM49B_uc003yst.2_Missense_Mutation_p.E95Q|FAM49B_uc003ysu.2_Missense_Mutation_p.E95Q|FAM49B_uc003ysv.2_Intron|FAM49B_uc003ysw.2_Missense_Mutation_p.E95Q|FAM49B_uc003ysx.2_Missense_Mutation_p.E95Q|FAM49B_uc003ysy.1_Missense_Mutation_p.E95Q	NM_016623	NP_057707	Q9NUQ9	FA49B_HUMAN	hypothetical protein LOC51571	95											0	Ovarian(5;0.000567)|Esophageal squamous(12;0.00693)|Acute lymphoblastic leukemia(118;0.155)		LUAD - Lung adenocarcinoma(14;0.0989)											0.40625	417.867031	420.092031	117	171	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	130874493	130874493	5798	8	C	G	G	G	403	31	FAM49B	3	3
TG	7038	broad.mit.edu	37	8	133900711	133900711	+	Missense_Mutation	SNP	A	G	G			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:133900711A>G	uc003ytw.2	+	c.2659A>G	c.(2659-2661)AGC>GGC	p.S887G		NM_003235	NP_003226	P01266	THYG_HUMAN	thyroglobulin precursor	887	Thyroglobulin type-1 7.				hormone biosynthetic process|regulation of synaptic transmission|signal transduction		carboxylesterase activity|hormone activity			ovary(8)|breast(4)|pancreas(1)	13	Ovarian(258;0.00438)|Acute lymphoblastic leukemia(118;0.155)	Myeloproliferative disorder(644;0.00878)|Acute lymphoblastic leukemia(644;0.0559)|Breast(495;0.0735)	BRCA - Breast invasive adenocarcinoma(115;0.000701)	KIRC - Kidney renal clear cell carcinoma(542;0.0546)						1778				0.493671	117.501699	117.504729	39	40	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	133900711	133900711	16341	8	A	G	G	G	91	7	TG	4	4
COL22A1	169044	broad.mit.edu	37	8	139614397	139614397	+	Silent	SNP	G	A	A			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:139614397G>A	uc003yvd.2	-	c.4146C>T	c.(4144-4146)GTC>GTT	p.V1382V	COL22A1_uc011ljo.1_Silent_p.V662V	NM_152888	NP_690848	Q8NFW1	COMA1_HUMAN	collagen, type XXII, alpha 1	1382	Pro-rich.|Gly-rich.				cell adhesion	collagen|cytoplasm	structural molecule activity			ovary(10)|pancreas(1)	11	all_epithelial(106;1.55e-12)|Lung NSC(106;1.67e-05)|all_lung(105;3.39e-05)|Ovarian(258;0.00672)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0517)											0.321101	91.100092	94.192131	35	74	KEEP	---	---	---	---	capture		Silent	SNP	139614397	139614397	3819	8	G	A	A	A	522	41	COL22A1	2	2
SLC45A4	57210	broad.mit.edu	37	8	142228515	142228515	+	Silent	SNP	C	A	A			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:142228515C>A	uc003ywd.1	-	c.1071G>T	c.(1069-1071)ACG>ACT	p.T357T	SLC45A4_uc003ywc.1_Silent_p.T357T|SLC45A4_uc010meq.1_Silent_p.T355T	NM_001080431	NP_001073900	Q5BKX6	S45A4_HUMAN	solute carrier family 45, member 4	408					transmembrane transport	integral to membrane				ovary(2)	2	all_cancers(97;1.52e-15)|all_epithelial(106;2.92e-14)|Lung NSC(106;1.23e-05)|all_lung(105;1.75e-05)|Ovarian(258;0.01)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0493)											0.3	16.342909	17.057304	6	14	KEEP	---	---	---	---	capture		Silent	SNP	142228515	142228515	15140	8	C	A	A	A	236	19	SLC45A4	1	1
PLEC	5339	broad.mit.edu	37	8	144995163	144995163	+	Silent	SNP	C	A	A			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:144995163C>A	uc003zaf.1	-	c.9237G>T	c.(9235-9237)CTG>CTT	p.L3079L	PLEC_uc003zab.1_Silent_p.L2942L|PLEC_uc003zac.1_Silent_p.L2946L|PLEC_uc003zad.2_Silent_p.L2942L|PLEC_uc003zae.1_Silent_p.L2910L|PLEC_uc003zag.1_Silent_p.L2920L|PLEC_uc003zah.2_Silent_p.L2928L|PLEC_uc003zaj.2_Silent_p.L2969L	NM_201380	NP_958782	Q15149	PLEC_HUMAN	plectin isoform 1	3079	Globular 2.				cellular component disassembly involved in apoptosis|hemidesmosome assembly	cytosol|focal adhesion|intermediate filament cytoskeleton|sarcolemma	actin binding|structural constituent of muscle|structural constituent of muscle			large_intestine(2)|ovary(2)|pancreas(2)|central_nervous_system(1)	7														0.4	33.791196	34.054329	12	18	KEEP	---	---	---	---	capture		Silent	SNP	144995163	144995163	12478	8	C	A	A	A	314	25	PLEC	2	2
OPLAH	26873	broad.mit.edu	37	8	145114525	145114525	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:145114525C>A	uc003zar.3	-	c.340G>T	c.(340-342)GCC>TCC	p.A114S	OPLAH_uc003zat.1_5'Flank	NM_017570	NP_060040	O14841	OPLA_HUMAN	5-oxoprolinase (ATP-hydrolysing)	114							5-oxoprolinase (ATP-hydrolyzing) activity|ATP binding				0	all_cancers(97;1.06e-10)|all_epithelial(106;1.5e-09)|Lung NSC(106;5.89e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;6.79e-41)|Epithelial(56;1.02e-39)|all cancers(56;2.24e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.105)		L-Glutamic Acid(DB00142)									0.307692	11.095928	11.524061	4	9	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	145114525	145114525	11282	8	C	A	A	A	364	28	OPLAH	2	2
ZNF7	7553	broad.mit.edu	37	8	146068327	146068327	+	Missense_Mutation	SNP	A	G	G			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:146068327A>G	uc010mge.2	+	c.1868A>G	c.(1867-1869)TAT>TGT	p.Y623C	ZNF7_uc003zeg.3_Missense_Mutation_p.Y612C|ZNF7_uc011lln.1_Missense_Mutation_p.Y516C|ZNF7_uc003zeh.2_Intron|ZNF7_uc003zek.3_Missense_Mutation_p.Y516C|COMMD5_uc003zel.1_Intron	NM_003416	NP_003407	P17097	ZNF7_HUMAN	zinc finger protein 7	612					multicellular organismal development|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(3)	3	all_cancers(97;1.03e-11)|all_epithelial(106;6.69e-11)|Lung NSC(106;4.08e-05)|all_lung(105;0.000125)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)	Breast(495;0.0812)|Ovarian(118;0.0822)|Acute lymphoblastic leukemia(644;0.143)	Epithelial(56;8.75e-39)|OV - Ovarian serous cystadenocarcinoma(54;1.13e-38)|all cancers(56;8.48e-34)|BRCA - Breast invasive adenocarcinoma(115;0.0355)|Colorectal(110;0.055)	GBM - Glioblastoma multiforme(99;2.11e-07)										0.434783	174.441812	174.86619	50	65	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	146068327	146068327	18697	8	A	G	G	G	208	16	ZNF7	4	4
MSR1	4481	broad.mit.edu	37	8	16001085	16001085	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:16001085C>T	uc010lsu.2	-	c.1069G>A	c.(1069-1071)GGG>AGG	p.G357R	MSR1_uc003wwz.2_Missense_Mutation_p.G339R|MSR1_uc003wxa.2_Missense_Mutation_p.G339R|MSR1_uc003wxb.2_Missense_Mutation_p.G339R|MSR1_uc011kxz.1_Missense_Mutation_p.G113R	NM_138715	NP_619729	P21757	MSRE_HUMAN	macrophage scavenger receptor 1 isoform type 1	339	Collagen-like.|Extracellular (Potential).				cholesterol transport|plasma lipoprotein particle clearance|positive regulation of cholesterol storage|positive regulation of macrophage derived foam cell differentiation|receptor-mediated endocytosis	collagen|integral to plasma membrane|low-density lipoprotein particle	low-density lipoprotein particle binding|protein binding|scavenger receptor activity			ovary(1)	1				Colorectal(111;0.00475)|COAD - Colon adenocarcinoma(73;0.0164)										0.288136	47.351113	49.725639	17	42	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	16001085	16001085	10279	8	C	T	T	T	286	22	MSR1	2	2
PSD3	23362	broad.mit.edu	37	8	18432723	18432723	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:18432723C>A	uc003wza.2	-	c.2554G>T	c.(2554-2556)GCA>TCA	p.A852S	PSD3_uc003wyx.3_Missense_Mutation_p.A181S|PSD3_uc003wyy.2_Missense_Mutation_p.A318S|PSD3_uc003wyz.2_Missense_Mutation_p.A153S	NM_015310	NP_056125	Q9NYI0	PSD3_HUMAN	ADP-ribosylation factor guanine nucleotide	853	PH.				regulation of ARF protein signal transduction	cell junction|cytoplasm|postsynaptic density|postsynaptic membrane	ARF guanyl-nucleotide exchange factor activity			ovary(3)	3				Colorectal(111;0.0281)|READ - Rectum adenocarcinoma(644;0.183)										0.458333	455.017694	455.524083	154	182	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	18432723	18432723	13101	8	C	A	A	A	338	26	PSD3	2	2
MYOM2	9172	broad.mit.edu	37	8	2000375	2000375	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:2000375G>T	uc003wpx.3	+	c.207G>T	c.(205-207)AGG>AGT	p.R69S	MYOM2_uc011kwi.1_Intron	NM_003970	NP_003961	P54296	MYOM2_HUMAN	myomesin 2	69					muscle contraction	myosin filament	structural constituent of muscle			ovary(4)|central_nervous_system(1)	5		Ovarian(12;0.0572)|Colorectal(14;0.0844)|Hepatocellular(245;0.217)		BRCA - Breast invasive adenocarcinoma(11;1.85e-05)|Colorectal(4;0.0101)|READ - Rectum adenocarcinoma(4;0.148)|COAD - Colon adenocarcinoma(4;0.179)										0.467153	196.270986	196.39972	64	73	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	2000375	2000375	10487	8	G	T	T	T	555	43	MYOM2	2	2
SCARA5	286133	broad.mit.edu	37	8	27823991	27823991	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:27823991C>A	uc003xgj.2	-	c.181G>T	c.(181-183)GCT>TCT	p.A61S	SCARA5_uc010luz.2_Missense_Mutation_p.A61S|SCARA5_uc003xgk.2_Intron|SCARA5_uc003xgl.2_Missense_Mutation_p.A61S	NM_173833	NP_776194	Q6ZMJ2	SCAR5_HUMAN	scavenger receptor class A, member 5	61	Helical; Signal-anchor for type II membrane protein; (Potential).				cellular iron ion homeostasis|endocytosis|iron ion transmembrane transport|protein homotrimerization	integral to plasma membrane	ferritin receptor activity|scavenger receptor activity			central_nervous_system(1)|skin(1)	2		Ovarian(32;0.0218)		UCEC - Uterine corpus endometrioid carcinoma (27;0.023)|KIRC - Kidney renal clear cell carcinoma(542;0.152)|Kidney(114;0.181)|Colorectal(74;0.228)						203				0.409396	359.841083	361.963356	122	176	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	27823991	27823991	14361	8	C	A	A	A	325	25	SCARA5	2	2
CSMD1	64478	broad.mit.edu	37	8	3205673	3205673	+	Silent	SNP	T	A	A			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:3205673T>A	uc011kwk.1	-	c.3318A>T	c.(3316-3318)GGA>GGT	p.G1106G	CSMD1_uc011kwj.1_Silent_p.G498G|CSMD1_uc003wqe.2_Silent_p.G262G	NM_033225	NP_150094	Q96PZ7	CSMD1_HUMAN	CUB and Sushi multiple domains 1 precursor	1106	Extracellular (Potential).|CUB 7.					integral to membrane				breast(20)|large_intestine(5)	25		all_cancers(1;5.7e-41)|all_epithelial(1;2.54e-36)|Lung NSC(1;7.54e-11)|all_lung(1;3.2e-10)|Hepatocellular(1;3.78e-05)|Breast(1;0.000196)|Myeloproliferative disorder(4;0.000374)|Esophageal squamous(1;0.0157)|Ovarian(12;0.091)|Renal(68;0.144)|Colorectal(14;0.234)		all cancers(1;5.03e-41)|Epithelial(1;4.78e-31)|Lung(1;1.14e-14)|LUSC - Lung squamous cell carcinoma(1;2.34e-14)|GBM - Glioblastoma multiforme(1;4.49e-10)|Colorectal(4;1.18e-07)|OV - Ovarian serous cystadenocarcinoma(1;3.2e-07)|BRCA - Breast invasive adenocarcinoma(1;6.17e-07)|COAD - Colon adenocarcinoma(4;0.000539)|READ - Rectum adenocarcinoma(4;0.00896)|Kidney(5;0.00957)|KIRC - Kidney renal clear cell carcinoma(5;0.0689)										0.44186	55.220281	55.34662	19	24	KEEP	---	---	---	---	capture		Silent	SNP	3205673	3205673	4085	8	T	A	A	A	691	54	CSMD1	3	3
CSMD1	64478	broad.mit.edu	37	8	3432588	3432588	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:3432588G>T	uc011kwk.1	-	c.1226C>A	c.(1225-1227)GCG>GAG	p.A409E		NM_033225	NP_150094	Q96PZ7	CSMD1_HUMAN	CUB and Sushi multiple domains 1 precursor	409	Extracellular (Potential).|Sushi 2.					integral to membrane				breast(20)|large_intestine(5)	25		all_cancers(1;5.7e-41)|all_epithelial(1;2.54e-36)|Lung NSC(1;7.54e-11)|all_lung(1;3.2e-10)|Hepatocellular(1;3.78e-05)|Breast(1;0.000196)|Myeloproliferative disorder(4;0.000374)|Esophageal squamous(1;0.0157)|Ovarian(12;0.091)|Renal(68;0.144)|Colorectal(14;0.234)		all cancers(1;5.03e-41)|Epithelial(1;4.78e-31)|Lung(1;1.14e-14)|LUSC - Lung squamous cell carcinoma(1;2.34e-14)|GBM - Glioblastoma multiforme(1;4.49e-10)|Colorectal(4;1.18e-07)|OV - Ovarian serous cystadenocarcinoma(1;3.2e-07)|BRCA - Breast invasive adenocarcinoma(1;6.17e-07)|COAD - Colon adenocarcinoma(4;0.000539)|READ - Rectum adenocarcinoma(4;0.00896)|Kidney(5;0.00957)|KIRC - Kidney renal clear cell carcinoma(5;0.0689)										0.382716	91.392727	92.373444	31	50	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	3432588	3432588	4085	8	G	T	T	T	494	38	CSMD1	1	1
CYP7B1	9420	broad.mit.edu	37	8	65528624	65528624	+	Missense_Mutation	SNP	C	G	G			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:65528624C>G	uc003xvj.2	-	c.474G>C	c.(472-474)ATG>ATC	p.M158I		NM_004820	NP_004811	O75881	CP7B1_HUMAN	cytochrome P450, family 7, subfamily B,	158					bile acid biosynthetic process|cell death|cholesterol metabolic process|oxidation-reduction process|xenobiotic metabolic process	endoplasmic reticulum membrane|microsome	25-hydroxycholesterol 7alpha-hydroxylase activity|electron carrier activity|heme binding|oxysterol 7-alpha-hydroxylase activity			ovary(3)	3		all_cancers(86;0.217)|Lung NSC(129;0.0521)|all_lung(136;0.0906)|all_epithelial(80;0.215)												0.529412	220.120177	220.209306	63	56	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	65528624	65528624	4362	8	C	G	G	G	325	25	CYP7B1	3	3
SULF1	23213	broad.mit.edu	37	8	70533314	70533314	+	Missense_Mutation	SNP	C	G	G			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:70533314C>G	uc010lza.1	+	c.1422C>G	c.(1420-1422)CAC>CAG	p.H474Q	SULF1_uc003xyd.2_Missense_Mutation_p.H474Q|SULF1_uc003xye.2_Missense_Mutation_p.H474Q|SULF1_uc003xyf.2_Missense_Mutation_p.H474Q|SULF1_uc003xyg.2_Missense_Mutation_p.H474Q|SULF1_uc003xyh.1_Non-coding_Transcript	NM_015170	NP_055985	Q8IWU6	SULF1_HUMAN	sulfatase 1 precursor	474					apoptosis|bone development|heparan sulfate proteoglycan metabolic process|kidney development|negative regulation of fibroblast growth factor receptor signaling pathway	cell surface|endoplasmic reticulum|extracellular space|Golgi stack	arylsulfatase activity|calcium ion binding			ovary(2)|central_nervous_system(2)|pancreas(1)	5	Breast(64;0.0654)		Epithelial(68;0.0124)|OV - Ovarian serous cystadenocarcinoma(28;0.0265)|all cancers(69;0.0534)							473				0.438095	158.738267	159.088242	46	59	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	70533314	70533314	15890	8	C	G	G	G	220	17	SULF1	3	3
TRPA1	8989	broad.mit.edu	37	8	72945894	72945894	+	Silent	SNP	G	T	T			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:72945894G>T	uc003xza.2	-	c.2853C>A	c.(2851-2853)GTC>GTA	p.V951V		NM_007332	NP_015628	O75762	TRPA1_HUMAN	ankyrin-like protein 1	951	Helical; Name=6; (Potential).					integral to plasma membrane				ovary(4)|lung(1)|kidney(1)	6			Epithelial(68;0.223)		Menthol(DB00825)									0.349206	117.059695	119.588767	44	82	KEEP	---	---	---	---	capture		Silent	SNP	72945894	72945894	17128	8	G	T	T	T	522	41	TRPA1	2	2
CDH17	1015	broad.mit.edu	37	8	95186447	95186447	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:95186447G>A	uc003ygh.2	-	c.466C>T	c.(466-468)CCG>TCG	p.P156S	CDH17_uc011lgo.1_Intron|CDH17_uc011lgp.1_Missense_Mutation_p.P156S	NM_004063	NP_004054	Q12864	CAD17_HUMAN	cadherin 17 precursor	156	Extracellular (Potential).|Cadherin 2.					integral to membrane	calcium ion binding			ovary(5)	5	Breast(36;4.65e-06)		BRCA - Breast invasive adenocarcinoma(8;0.00691)											0.33871	231.904055	237.61812	84	164	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	95186447	95186447	3231	8	G	A	A	A	533	41	CDH17	2	2
TDRD7	23424	broad.mit.edu	37	9	100243134	100243134	+	Missense_Mutation	SNP	C	G	G			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:100243134C>G	uc004axj.2	+	c.2326C>G	c.(2326-2328)CTT>GTT	p.L776V	TDRD7_uc011lux.1_Missense_Mutation_p.L702V|TDRD7_uc010msp.1_Missense_Mutation_p.L28V|TDRD7_uc011luy.1_Missense_Mutation_p.L96V	NM_014290	NP_055105	Q8NHU6	TDRD7_HUMAN	tudor domain containing 7	776					lens fiber cell differentiation|lens morphogenesis in camera-type eye|posttranscriptional regulation of gene expression|spermatogenesis	chromatoid body	mRNA binding			ovary(2)|pancreas(1)	3		Acute lymphoblastic leukemia(62;0.158)												0.38326	615.74589	621.170465	174	280	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	100243134	100243134	16262	9	C	G	G	G	416	32	TDRD7	3	3
TMOD1	7111	broad.mit.edu	37	9	100315641	100315641	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:100315641C>A	uc004axk.1	+	c.356C>A	c.(355-357)GCC>GAC	p.A119D	TMOD1_uc004axl.1_Missense_Mutation_p.A119D	NM_003275	NP_003266	P28289	TMOD1_HUMAN	tropomodulin 1	119	Tropomyosin-binding (Potential).				muscle filament sliding	cytosol	actin binding				0		Acute lymphoblastic leukemia(62;0.154)		STAD - Stomach adenocarcinoma(157;0.105)										0.375	73.498919	74.489338	27	45	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	100315641	100315641	16773	9	C	A	A	A	338	26	TMOD1	2	2
SEC61B	10952	broad.mit.edu	37	9	101990179	101990179	+	Splice_Site_SNP	SNP	A	G	G			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:101990179A>G	uc004azh.2	+	c.102_splice	c.e3-2	p.R34_splice		NM_006808	NP_006799			Sec61 beta subunit						ER-associated protein catabolic process|protein import into nucleus, translocation|retrograde protein transport, ER to cytosol|transmembrane transport	endoplasmic reticulum Sec complex|integral to membrane	epidermal growth factor binding				0		Acute lymphoblastic leukemia(62;0.0559)												0.407407	60.335306	60.740871	22	32	KEEP	---	---	---	---	capture		Splice_Site_SNP	SNP	101990179	101990179	14488	9	A	G	G	G	91	7	SEC61B	5	4
ACTL7B	10880	broad.mit.edu	37	9	111617113	111617113	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:111617113G>T	uc004bdi.2	-	c.1098C>A	c.(1096-1098)GAC>GAA	p.D366E		NM_006686	NP_006677	Q9Y614	ACL7B_HUMAN	actin-like 7B	366						actin cytoskeleton|cytoplasm	structural constituent of cytoskeleton			pancreas(1)	1														0.304348	19.323914	20.105225	7	16	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	111617113	111617113	202	9	G	T	T	T	620	48	ACTL7B	2	2
PKN3	29941	broad.mit.edu	37	9	131475465	131475465	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:131475465G>T	uc004bvw.2	+	c.970G>T	c.(970-972)GGC>TGC	p.G324C	PKN3_uc010myh.2_Missense_Mutation_p.G324C|PKN3_uc011mbk.1_De_novo_Start_InFrame	NM_013355	NP_037487	Q6P5Z2	PKN3_HUMAN	protein kinase PKNbeta	324					protein phosphorylation|signal transduction	Golgi apparatus|nucleus|perinuclear region of cytoplasm	ATP binding|protein binding|protein kinase C activity			lung(2)	2										307				0.421053	23.096122	23.199602	8	11	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	131475465	131475465	12406	9	G	T	T	T	455	35	PKN3	2	2
FIBCD1	84929	broad.mit.edu	37	9	133780763	133780763	+	Silent	SNP	G	T	T			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:133780763G>T	uc004bzz.2	-	c.984C>A	c.(982-984)GCC>GCA	p.A328A	FIBCD1_uc011mcc.1_Silent_p.A328A	NM_032843	NP_116232	Q8N539	FBCD1_HUMAN	fibrinogen C domain containing 1	328	Fibrinogen C-terminal.|Extracellular (Potential).				signal transduction	extracellular space|integral to membrane	chitin binding|metal ion binding|receptor binding				0	all_hematologic(7;0.0028)			OV - Ovarian serous cystadenocarcinoma(145;3.52e-05)|Epithelial(140;0.00019)										0.4	22.394779	22.570034	8	12	KEEP	---	---	---	---	capture		Silent	SNP	133780763	133780763	6122	9	G	T	T	T	444	35	FIBCD1	2	2
BAT2L1	84726	broad.mit.edu	37	9	134340162	134340162	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:134340162G>T	uc004can.3	+	c.1417G>T	c.(1417-1419)GGC>TGC	p.G473C	BAT2L1_uc010mzj.1_Missense_Mutation_p.G56C	NM_013318	NP_037450	Q5JSZ5	PRC2B_HUMAN	HLA-B associated transcript 2-like	473							protein binding				0														0.4	27.843421	28.062467	10	15	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	134340162	134340162	1341	9	G	T	T	T	559	43	BAT2L1	2	2
SETX	23064	broad.mit.edu	37	9	135172287	135172287	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:135172287C>A	uc004cbk.2	-	c.5936G>T	c.(5935-5937)CGT>CTT	p.R1979L	SETX_uc004cbj.2_Missense_Mutation_p.R1598L|SETX_uc010mzt.2_Missense_Mutation_p.R1598L	NM_015046	NP_055861	Q7Z333	SETX_HUMAN	senataxin	1979					cell death|double-strand break repair|RNA processing	cytoplasm|nucleolus|nucleoplasm	ATP binding|DNA binding|DNA helicase activity			ovary(2)	2		Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;6.82e-06)|Epithelial(140;0.000171)										0.297297	64.320797	67.03942	22	52	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	135172287	135172287	14630	9	C	A	A	A	247	19	SETX	1	1
SARDH	1757	broad.mit.edu	37	9	136573445	136573446	+	Missense_Mutation	DNP	CA	AG	AG			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:136573445_136573446CA>AG	uc004cep.3	-	c.1433_1434TG>CT	c.(1432-1434)CTG>CCT	p.L478P	SARDH_uc004ceo.2_Missense_Mutation_p.L478P|SARDH_uc011mdn.1_Missense_Mutation_p.L478P|SARDH_uc011mdo.1_Missense_Mutation_p.L310P	NM_001134707	NP_001128179	Q9UL12	SARDH_HUMAN	sarcosine dehydrogenase precursor	478					glycine catabolic process|oxidation-reduction process	mitochondrial matrix	aminomethyltransferase activity|sarcosine dehydrogenase activity				0				OV - Ovarian serous cystadenocarcinoma(145;3.21e-07)|Epithelial(140;2.37e-06)|all cancers(34;2.75e-05)										0.227273	25.025888	28.030295	10	34	KEEP	---	---	---	---	capture		Missense_Mutation	DNP	136573445	136573446	14322	9	CA	AG	AG	AG	262	21	SARDH	2	2
CACNA1B	774	broad.mit.edu	37	9	141010115	141010115	+	Missense_Mutation	SNP	A	T	T			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:141010115A>T	uc004cog.2	+	c.5761A>T	c.(5761-5763)AGC>TGC	p.S1921C	CACNA1B_uc004coi.2_Missense_Mutation_p.S1133C	NM_000718	NP_000709	Q00975	CAC1B_HUMAN	calcium channel, voltage-dependent, N type,	1921	Cytoplasmic (Potential).				membrane depolarization|synaptic transmission	voltage-gated calcium channel complex	ATP binding|protein C-terminus binding|voltage-gated calcium channel activity			breast(3)|large_intestine(2)|ovary(1)	6	all_cancers(76;0.166)			OV - Ovarian serous cystadenocarcinoma(145;1.16e-05)|Epithelial(140;0.000476)	Amlodipine(DB00381)|Gabapentin(DB00996)									0.486486	111.69412	111.705971	36	38	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	141010115	141010115	2655	9	A	T	T	T	91	7	CACNA1B	3	3
TEK	7010	broad.mit.edu	37	9	27197413	27197413	+	Silent	SNP	T	C	C			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:27197413T>C	uc003zqi.3	+	c.1725T>C	c.(1723-1725)TAT>TAC	p.Y575Y	TEK_uc011lno.1_Silent_p.Y532Y|TEK_uc011lnp.1_Silent_p.Y428Y|TEK_uc003zqj.1_Silent_p.Y509Y	NM_000459	NP_000450	Q02763	TIE2_HUMAN	TEK tyrosine kinase, endothelial precursor	575	Extracellular (Potential).|Fibronectin type-III 2.				angiogenesis|blood coagulation|cell-cell signaling|leukocyte migration|positive regulation of ERK1 and ERK2 cascade|positive regulation of protein kinase B signaling cascade|protein oligomerization|protein phosphorylation|transmembrane receptor protein tyrosine kinase signaling pathway	apical plasma membrane|basolateral plasma membrane|cell surface|integral to plasma membrane|membrane raft|microvillus	ATP binding|protein binding|transmembrane receptor protein tyrosine kinase activity			ovary(3)|central_nervous_system(3)|breast(3)|lung(2)|kidney(1)	12		all_neural(11;7.57e-10)|Myeloproliferative disorder(762;0.0255)		Lung(218;4.08e-05)|LUSC - Lung squamous cell carcinoma(38;0.00027)						493				0.50813	400.866668	400.880679	125	121	KEEP	---	---	---	---	capture		Silent	SNP	27197413	27197413	16278	9	T	C	C	C	660	51	TEK	4	4
NOL6	65083	broad.mit.edu	37	9	33462736	33462736	+	Missense_Mutation	SNP	G	C	C			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:33462736G>C	uc003zsz.2	-	c.3367C>G	c.(3367-3369)CTG>GTG	p.L1123V	SUGT1P1_uc010mjq.1_Intron|NOL6_uc003zsy.2_Missense_Mutation_p.L177V|NOL6_uc003zta.2_Missense_Mutation_p.L676V|NOL6_uc010mjv.2_Missense_Mutation_p.L1120V|NOL6_uc011lob.1_Missense_Mutation_p.L1071V|NOL6_uc003ztb.1_Intron	NM_022917	NP_075068	Q9H6R4	NOL6_HUMAN	nucleolar protein family 6 alpha isoform	1123					rRNA processing	condensed nuclear chromosome|nucleolus	RNA binding			ovary(2)	2			LUSC - Lung squamous cell carcinoma(29;0.00788)	GBM - Glioblastoma multiforme(74;0.152)										0.496	191.338999	191.340816	62	63	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	33462736	33462736	10928	9	G	C	C	C	451	35	NOL6	3	3
CNTNAP3	79937	broad.mit.edu	37	9	39118245	39118245	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:39118245G>T	uc004abi.2	-	c.2092C>A	c.(2092-2094)CTG>ATG	p.L698M	CNTNAP3_uc004abj.2_Missense_Mutation_p.L697M|CNTNAP3_uc011lqr.1_Non-coding_Transcript|CNTNAP3_uc004abk.1_Missense_Mutation_p.L698M|CNTNAP3_uc011lqs.1_Missense_Mutation_p.L604M	NM_033655	NP_387504	Q9BZ76	CNTP3_HUMAN	cell recognition molecule CASPR3 precursor	698	Fibrinogen C-terminal.|Extracellular (Potential).				cell adhesion|cell recognition|signal transduction	extracellular region|integral to membrane|plasma membrane	receptor binding			ovary(1)	1				GBM - Glioblastoma multiforme(29;0.02)|Lung(182;0.0681)										0.440678	164.182425	164.544289	52	66	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	39118245	39118245	3786	9	G	T	T	T	464	36	CNTNAP3	2	2
FAM75A2	642265	broad.mit.edu	37	9	39887061	39887061	+	Silent	SNP	G	T	T			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:39887061G>T	uc004abp.2	+	c.303G>T	c.(301-303)CTG>CTT	p.L101L		NM_001040065	NP_001035154	Q5RGS2	F75A2_HUMAN	hypothetical protein LOC642265	101						integral to membrane					0				GBM - Glioblastoma multiforme(29;0.02)|Lung(182;0.0681)										0.40625	307.75776	309.721254	104	152	KEEP	---	---	---	---	capture		Silent	SNP	39887061	39887061	5844	9	G	T	T	T	587	46	FAM75A2	2	2
GLDC	2731	broad.mit.edu	37	9	6604786	6604786	+	Splice_Site_SNP	SNP	T	C	C			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:6604786T>C	uc003zkc.2	-	c.862_splice	c.e7-1	p.S288_splice		NM_000170	NP_000161			glycine dehydrogenase (decarboxylating)						glycine catabolic process|oxidation-reduction process	mitochondrion	electron carrier activity|glycine dehydrogenase (decarboxylating) activity|lyase activity|pyridoxal phosphate binding			ovary(2)	2		Acute lymphoblastic leukemia(23;0.161)		GBM - Glioblastoma multiforme(50;0.0421)|Lung(218;0.134)	Glycine(DB00145)|Pyridoxal Phosphate(DB00114)									0.42328	271.870204	272.836525	80	109	KEEP	---	---	---	---	capture		Splice_Site_SNP	SNP	6604786	6604786	6701	9	T	C	C	C	689	53	GLDC	5	4
ANKRD20A4	728747	broad.mit.edu	37	9	69420315	69420315	+	Missense_Mutation	SNP	A	G	G			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:69420315A>G	uc004afn.2	+	c.1205A>G	c.(1204-1206)AAT>AGT	p.N402S		NM_001098805	NP_001092275	Q4UJ75	A20A4_HUMAN	ankyrin repeat domain 20 family, member A4	402											0														0.112676	13.351114	23.862644	8	63	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	69420315	69420315	655	9	A	G	G	G	52	4	ANKRD20A4	4	4
PTPRD	5789	broad.mit.edu	37	9	8521415	8521415	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:8521415C>A	uc003zkk.2	-	c.823G>T	c.(823-825)GAT>TAT	p.D275Y	PTPRD_uc003zkp.2_Missense_Mutation_p.D275Y|PTPRD_uc003zkq.2_Missense_Mutation_p.D275Y|PTPRD_uc003zkr.2_Missense_Mutation_p.D269Y|PTPRD_uc003zks.2_Missense_Mutation_p.D265Y|PTPRD_uc003zkl.2_Missense_Mutation_p.D275Y|PTPRD_uc003zkm.2_Missense_Mutation_p.D262Y|PTPRD_uc003zkn.2_Missense_Mutation_p.D275Y|PTPRD_uc003zko.2_Missense_Mutation_p.D272Y	NM_002839	NP_002830	P23468	PTPRD_HUMAN	protein tyrosine phosphatase, receptor type, D	275	Extracellular (Potential).|Ig-like C2-type 3.				transmembrane receptor protein tyrosine phosphatase signaling pathway	integral to plasma membrane	protein binding|transmembrane receptor protein tyrosine phosphatase activity			lung(10)|large_intestine(3)|ovary(2)|urinary_tract(1)	16		all_cancers(3;3.38e-95)|all_epithelial(3;2.84e-91)|all_lung(3;7.3e-56)|Lung NSC(3;1.82e-52)|Renal(3;3.42e-19)|all_hematologic(3;0.000134)|all_neural(3;0.00409)|Acute lymphoblastic leukemia(23;0.0069)|Melanoma(3;0.0121)|Myeloproliferative disorder(4;0.0122)|Medulloblastoma(3;0.0144)|Lung SC(3;0.0301)|Ovarian(56;0.0694)|Hepatocellular(3;0.0824)		all cancers(1;3.38e-12)|Epithelial(1;2.12e-09)|STAD - Stomach adenocarcinoma(1;1.29e-07)|KIRC - Kidney renal clear cell carcinoma(3;5.49e-07)|Kidney(3;6.36e-07)|GBM - Glioblastoma multiforme(50;9.05e-05)|Lung(1;0.000189)|BRCA - Breast invasive adenocarcinoma(1;0.00178)|LUSC - Lung squamous cell carcinoma(1;0.0115)|LUAD - Lung adenocarcinoma(58;0.119)						1253	TSP Lung(15;0.13)			0.349315	134.155989	137.091926	51	95	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	8521415	8521415	13256	9	C	A	A	A	416	32	PTPRD	2	2
ODZ1	10178	broad.mit.edu	37	X	123785936	123785936	+	Silent	SNP	G	T	T			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:123785936G>T	uc010nqy.2	-	c.1407C>A	c.(1405-1407)GTC>GTA	p.V469V	ODZ1_uc011muj.1_Silent_p.V468V|ODZ1_uc004euj.2_Silent_p.V469V	NM_001163278	NP_001156750	Q9UKZ4	TEN1_HUMAN	odz, odd Oz/ten-m homolog 1 isoform 1	469	Extracellular (Potential).				immune response|negative regulation of cell proliferation|nervous system development|signal transduction	extracellular region	heparin binding			ovary(11)|breast(4)|large_intestine(2)|pancreas(2)|upper_aerodigestive_tract(1)|lung(1)|skin(1)	22										623				0.92	290.968258	308.958894	92	8	KEEP	---	---	---	---	capture		Silent	SNP	123785936	123785936	11239	23	G	T	T	T	574	45	ODZ1	2	2
UBE2NL	389898	broad.mit.edu	37	X	142967530	142967530	+	Missense_Mutation	SNP	C	G	G			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:142967530C>G	uc004fca.2	+	c.328C>G	c.(328-330)CAG>GAG	p.Q110E		NM_001012989	NP_001013007	Q5JXB2	UE2NL_HUMAN	ubiquitin-conjugating enzyme E2N-like	110					post-translational protein modification		acid-amino acid ligase activity				0	Acute lymphoblastic leukemia(192;6.56e-05)													0.935323	611.369623	644.165669	188	13	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	142967530	142967530	17424	23	C	G	G	G	273	21	UBE2NL	3	3
CTAG2	30848	broad.mit.edu	37	X	153880837	153880837	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:153880837G>T	uc004fmi.1	-	c.338C>A	c.(337-339)GCC>GAC	p.A113D	CTAG2_uc004fmh.1_Missense_Mutation_p.A113D	NM_020994	NP_066274	O75638	CTAG2_HUMAN	cancer/testis antigen 2 isoform LAGE-1b	113						centrosome				pancreas(1)	1	all_cancers(53;5.05e-16)|all_epithelial(53;1.87e-10)|all_lung(58;1.84e-07)|Lung NSC(58;5.84e-07)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)													0.942308	157.278249	164.132139	49	3	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	153880837	153880837	4150	23	G	T	T	T	546	42	CTAG2	2	2
MAGEB18	286514	broad.mit.edu	37	X	26158064	26158064	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:26158064G>T	uc004dbq.1	+	c.962G>T	c.(961-963)AGG>ATG	p.R321M		NM_173699	NP_775970	Q96M61	MAGBI_HUMAN	melanoma antigen family B, 18	321							protein binding			central_nervous_system(1)	1														0.842105	49.906354	52.024042	16	3	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	26158064	26158064	9556	23	G	T	T	T	455	35	MAGEB18	2	2
MAGEB10	139422	broad.mit.edu	37	X	27839660	27839660	+	Silent	SNP	C	T	T			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:27839660C>T	uc004dbw.2	+	c.237C>T	c.(235-237)CAC>CAT	p.H79H		NM_182506	NP_872312	Q96LZ2	MAGBA_HUMAN	melanoma antigen family B, 10	79										lung(1)|breast(1)|central_nervous_system(1)	3														1	47.367844	47.367783	14	0	KEEP	---	---	---	---	capture		Silent	SNP	27839660	27839660	9554	23	C	T	T	T	220	17	MAGEB10	2	2
EFHC2	80258	broad.mit.edu	37	X	44109566	44109566	+	Silent	SNP	T	C	C			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:44109566T>C	uc004dgb.3	-	c.732A>G	c.(730-732)GGA>GGG	p.G244G		NM_025184	NP_079460	Q5JST6	EFHC2_HUMAN	EF-hand domain (C-terminal) containing 2	244	DM10 2.						calcium ion binding			breast(3)|ovary(2)|central_nervous_system(1)	6														0.92	88.132661	91.946606	23	2	KEEP	---	---	---	---	capture		Silent	SNP	44109566	44109566	5135	23	T	C	C	C	691	54	EFHC2	4	4
SHROOM4	57477	broad.mit.edu	37	X	50351111	50351111	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:50351111C>A	uc004dpe.2	-	c.3031G>T	c.(3031-3033)GAC>TAC	p.D1011Y	SHROOM4_uc004dpd.3_Non-coding_Transcript	NM_020717	NP_065768	Q9ULL8	SHRM4_HUMAN	shroom family member 4	1011					actin filament organization|brain development|cell morphogenesis|cognition	apical plasma membrane|basal plasma membrane|internal side of plasma membrane|nucleus	actin filament binding				0	Ovarian(276;0.236)													0.920635	188.331525	199.570931	58	5	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	50351111	50351111	14791	23	C	A	A	A	390	30	SHROOM4	2	2
PDE3B	5140	broad.mit.edu	37	11	14865565	14865565	+	Frame_Shift_Del	DEL	C	-	-			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:14865565_14865565delC	uc001mln.2	+	c.2513_2513delC	c.(2512-2514)GCCfs	p.A838fs	PDE3B_uc010rcr.1_Frame_Shift_Del_p.A787fs	NM_000922	NP_000913	Q13370	PDE3B_HUMAN	phosphodiesterase 3B	838	Catalytic (By similarity).				cAMP catabolic process|insulin receptor signaling pathway|negative regulation of cAMP-mediated signaling|negative regulation of cell adhesion mediated by integrin|negative regulation of lipid catabolic process|platelet activation	cytosol|endoplasmic reticulum|Golgi apparatus|guanyl-nucleotide exchange factor complex|integral to membrane|microsome	3',5'-cyclic-AMP phosphodiesterase activity|3',5'-cyclic-GMP phosphodiesterase activity|cGMP-inhibited cyclic-nucleotide phosphodiesterase activity|metal ion binding|protein kinase B binding				0														0.73			134	50		---	---	---	---	capture_indel		Frame_Shift_Del	DEL	14865565	14865565	12059	11	C	-	-	-	338	26	PDE3B	5	5
OR56B1	387748	broad.mit.edu	37	11	5757908	5757908	+	Frame_Shift_Del	DEL	C	-	-			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:5757908_5757908delC	uc001mbt.1	+	c.162_162delC	c.(160-162)ATCfs	p.I54fs	TRIM5_uc001mbq.1_Intron|TRIM22_uc009yet.1_Intron|OR56B1_uc001mbs.1_Frame_Shift_Del_p.I54fs|OR56B1_uc009yev.1_Frame_Shift_Del_p.I54fs	NM_001005180	NP_001005180	Q8NGI3	O56B1_HUMAN	olfactory receptor, family 56, subfamily B,	54	Helical; Name=1; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			central_nervous_system(1)	1		Medulloblastoma(188;0.0075)|all_neural(188;0.0572)|Breast(177;0.086)		Epithelial(150;1.74e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)|LUSC - Lung squamous cell carcinoma(625;0.184)										0.77			91	27		---	---	---	---	capture_indel		Frame_Shift_Del	DEL	5757908	5757908	11547	11	C	-	-	-	382	30	OR56B1	5	5
OR10A6	390093	broad.mit.edu	37	11	7949605	7949605	+	Frame_Shift_Del	DEL	C	-	-			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:7949605_7949605delC	uc010rbh.1	-	c.605_605delG	c.(604-606)GGCfs	p.G202fs		NM_001004461	NP_001004461	Q8NH74	O10A6_HUMAN	olfactory receptor, family 10, subfamily A,	202	Helical; Name=5; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)	1				Epithelial(150;1.38e-07)|BRCA - Breast invasive adenocarcinoma(625;0.189)										0.83			105	21		---	---	---	---	capture_indel		Frame_Shift_Del	DEL	7949605	7949605	11300	11	C	-	-	-	338	26	OR10A6	5	5
ANO2	57101	broad.mit.edu	37	12	5687633	5687633	+	Frame_Shift_Del	DEL	G	-	-			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:5687633_5687633delG	uc001qnm.2	-	c.2285_2285delC	c.(2284-2286)CCTfs	p.P762fs		NM_020373	NP_065106	Q9NQ90	ANO2_HUMAN	anoctamin 2	767	Helical; (Potential).					chloride channel complex|plasma membrane	intracellular calcium activated chloride channel activity			ovary(4)|large_intestine(2)|central_nervous_system(1)	7														0.83			39	8		---	---	---	---	capture_indel		Frame_Shift_Del	DEL	5687633	5687633	705	12	G	-	-	-	455	35	ANO2	5	5
CES7	221223	broad.mit.edu	37	16	55907815	55907815	+	Frame_Shift_Del	DEL	G	-	-			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:55907815_55907815delG	uc002eip.2	-	c.208_208delC	c.(208-210)CTGfs	p.L70fs	CES7_uc002eio.2_Frame_Shift_Del_p.L70fs|CES7_uc002eiq.2_5'UTR|CES7_uc002eir.2_5'UTR	NM_001143685	NP_001137157	Q6NT32	EST5A_HUMAN	carboxylesterase 7 isoform 1	70					regulation of synaptic transmission	extracellular region	methyl indole-3-acetate esterase activity|methyl jasmonate esterase activity|methyl salicylate esterase activity				0				all cancers(182;0.229)|Epithelial(162;0.231)										0.60			24	16		---	---	---	---	capture_indel		Frame_Shift_Del	DEL	55907815	55907815	3405	16	G	-	-	-	451	35	CES7	5	5
TSHZ1	10194	broad.mit.edu	37	18	72999246	72999247	+	Frame_Shift_Ins	INS	-	C	C			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr18:72999246_72999247insC	uc002lly.2	+	c.1749_1750insC	c.(1747-1752)ACGCCCfs	p.T583fs		NM_005786	NP_005777	Q6ZSZ6	TSH1_HUMAN	teashirt family zinc finger 1	628_629					regulation of transcription, DNA-dependent	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding				0		Esophageal squamous(42;0.129)|Prostate(75;0.142)|Melanoma(33;0.211)		Colorectal(1;0.000501)|READ - Rectum adenocarcinoma(2;0.00226)|BRCA - Breast invasive adenocarcinoma(31;0.246)										0.33			31	64		---	---	---	---	capture_indel		Frame_Shift_Ins	INS	72999246	72999247	17174	18	-	C	C	C	483	38	TSHZ1	5	5
LMTK3	114783	broad.mit.edu	37	19	48994680	48994680	+	Frame_Shift_Del	DEL	G	-	-			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:48994680_48994680delG	uc002pjk.2	-	c.4296_4296delC	c.(4294-4296)CCCfs	p.P1432fs		NM_001080434	NP_001073903			lemur tyrosine kinase 3											lung(5)|central_nervous_system(1)	6		all_lung(116;0.000147)|Lung NSC(112;0.000251)|all_epithelial(76;0.000326)|all_neural(266;0.0506)|Ovarian(192;0.113)		OV - Ovarian serous cystadenocarcinoma(262;0.000114)|all cancers(93;0.000141)|Epithelial(262;0.00854)|GBM - Glioblastoma multiforme(486;0.0231)						193				0.44			4	5		---	---	---	---	capture_indel		Frame_Shift_Del	DEL	48994680	48994680	9189	19	G	-	-	-	600	47	LMTK3	5	5
MRPL9	65005	broad.mit.edu	37	1	151732565	151732565	+	Frame_Shift_Del	DEL	T	-	-			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:151732565_151732565delT	uc001eyv.2	-	c.765_765delA	c.(763-765)CAAfs	p.Q255fs	MRPL9_uc009wmz.2_Non-coding_Transcript|OAZ3_uc010pdl.1_5'Flank	NM_031420	NP_113608	Q9BYD2	RM09_HUMAN	mitochondrial ribosomal protein L9 precursor	255					translation	mitochondrial ribosome	structural constituent of ribosome			ovary(1)	1	Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.14)		LUSC - Lung squamous cell carcinoma(543;0.181)											0.38			58	95		---	---	---	---	capture_indel		Frame_Shift_Del	DEL	151732565	151732565	10213	1	T	-	-	-	725	56	MRPL9	5	5
CYP27A1	1593	broad.mit.edu	37	2	219677646	219677646	+	Splice_Site_Del	DEL	G	-	-			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:219677646_219677646delG	uc002viz.3	+	c.845_splice	c.e5-1	p.G282_splice		NM_000784	NP_000775			cytochrome P450, family 27, subfamily A,						bile acid biosynthetic process|oxidation-reduction process|xenobiotic metabolic process	mitochondrial matrix	cholestanetriol 26-monooxygenase activity|electron carrier activity|heme binding			ovary(1)	1		Renal(207;0.0474)		Epithelial(149;9.48e-07)|all cancers(144;0.000171)|LUSC - Lung squamous cell carcinoma(224;0.00813)|Lung(261;0.00981)	Cholecalciferol(DB00169)									0.45			29	35		---	---	---	---	capture_indel		Splice_Site_Del	DEL	219677646	219677646	4323	2	G	-	-	-	455	35	CYP27A1	5	5
GPR98	84059	broad.mit.edu	37	5	90106258	90106258	+	Frame_Shift_Del	DEL	G	-	-			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:90106258_90106258delG	uc003kju.2	+	c.15181_15181delG	c.(15181-15183)GGGfs	p.G5061fs	GPR98_uc003kjt.2_Frame_Shift_Del_p.G2767fs|GPR98_uc003kjw.2_Frame_Shift_Del_p.G722fs	NM_032119	NP_115495	Q8WXG9	GPR98_HUMAN	G protein-coupled receptor 98 precursor	5061	Calx-beta 33.|Extracellular (Potential).				cell communication|cell-cell adhesion|maintenance of organ identity|neuropeptide signaling pathway|photoreceptor cell maintenance	cell surface|cytoplasm|integral to membrane|plasma membrane	calcium ion binding|G-protein coupled receptor activity			ovary(11)|central_nervous_system(3)|pancreas(2)	16		all_cancers(142;1.05e-09)|all_epithelial(76;1.81e-12)|all_lung(232;5.41e-06)|Lung NSC(167;1.72e-05)|Ovarian(174;0.00948)|Colorectal(57;0.133)|Breast(839;0.192)		OV - Ovarian serous cystadenocarcinoma(54;7.01e-30)|Epithelial(54;6.79e-25)|all cancers(79;1.88e-20)										0.40			22	33		---	---	---	---	capture_indel		Frame_Shift_Del	DEL	90106258	90106258	6997	5	G	-	-	-	611	47	GPR98	5	5
TAP2	6891	broad.mit.edu	37	6	32805380	32805380	+	Frame_Shift_Del	DEL	C	-	-			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:32805380_32805380delC	uc011dqf.1	-	c.542_542delG	c.(541-543)GGAfs	p.G181fs	TAP2_uc003ocb.1_Frame_Shift_Del_p.G181fs|TAP2_uc003occ.2_Frame_Shift_Del_p.G181fs|TAP2_uc003ocd.2_Frame_Shift_Del_p.G181fs	NM_018833	NP_061313	Q03519	TAP2_HUMAN	transporter 2, ATP-binding cassette, sub-family	181	Lumenal (Potential).|ABC transmembrane type-1.				antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent|antigen processing and presentation of endogenous peptide antigen via MHC class Ib via ER pathway, TAP-dependent|antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent|cytosol to ER transport|intracellular transport of viral proteins in host cell|peptide antigen transport|positive regulation of antigen processing and presentation of peptide antigen via MHC class I|positive regulation of T cell mediated cytotoxicity	nucleus|plasma membrane|TAP complex	ATP binding|MHC class I protein binding|oligopeptide-transporting ATPase activity|peptide antigen binding|peptide antigen-transporting ATPase activity|TAP1 binding|TAP2 binding|tapasin binding				0														0.33			46	94		---	---	---	---	capture_indel		Frame_Shift_Del	DEL	32805380	32805380	16072	6	C	-	-	-	390	30	TAP2	5	5
SAMD9L	219285	broad.mit.edu	37	7	92762932	92762932	+	Frame_Shift_Del	DEL	C	-	-			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:92762932_92762932delC	uc003umh.1	-	c.2353_2353delG	c.(2353-2355)GTCfs	p.V785fs	SAMD9L_uc003umj.1_Frame_Shift_Del_p.V785fs|SAMD9L_uc003umi.1_Frame_Shift_Del_p.V785fs|SAMD9L_uc010lfb.1_Frame_Shift_Del_p.V785fs|SAMD9L_uc003umk.1_Frame_Shift_Del_p.V785fs|SAMD9L_uc010lfc.1_Frame_Shift_Del_p.V785fs|SAMD9L_uc010lfd.1_Frame_Shift_Del_p.V785fs|SAMD9L_uc011khx.1_Intron	NM_152703	NP_689916	Q8IVG5	SAM9L_HUMAN	sterile alpha motif domain containing 9-like	785										ovary(4)	4	all_cancers(62;4.15e-11)|all_epithelial(64;2.29e-10)|Breast(17;0.000675)|Lung NSC(181;0.0755)|all_lung(186;0.0989)		STAD - Stomach adenocarcinoma(171;0.000302)											0.32			268	557		---	---	---	---	capture_indel		Frame_Shift_Del	DEL	92762932	92762932	14307	7	C	-	-	-	234	18	SAMD9L	5	5
MATN2	4147	broad.mit.edu	37	8	98943445	98943446	+	Frame_Shift_Ins	INS	-	T	T	rs2290470	byFrequency;by1000genomes	TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:98943445_98943446insT	uc003yic.2	+	c.407_408insT	c.(406-408)ACTfs	p.T136fs	MATN2_uc003yib.1_Frame_Shift_Ins_p.T136fs|MATN2_uc010mbh.1_Frame_Shift_Ins_p.T136fs|MATN2_uc003yid.2_Frame_Shift_Ins_p.T136fs|MATN2_uc003yie.1_Frame_Shift_Ins_p.T136fs|MATN2_uc010mbi.1_Frame_Shift_Ins_p.T10fs	NM_002380	NP_002371	O00339	MATN2_HUMAN	matrilin 2 isoform a precursor	136	VWFA 1.					proteinaceous extracellular matrix	calcium ion binding			ovary(2)	2	Breast(36;1.43e-06)		OV - Ovarian serous cystadenocarcinoma(57;0.244)											0.44			32	41		---	---	---	---	capture_indel		Frame_Shift_Ins	INS	98943445	98943446	9718	8	-	T	T	T	260	20	MATN2	5	5
CCIN	881	broad.mit.edu	37	9	36171041	36171042	+	Frame_Shift_Del	DEL	TG	-	-			TCGA-17-Z049-01	TCGA-17-Z049-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:36171041_36171042delTG	uc003zzb.3	+	c.1542_1543delTG	c.(1540-1545)GATGTGfs	p.D514fs		NM_005893	NP_005884	Q13939	CALI_HUMAN	calicin	514_515	Kelch 5.				cell differentiation|multicellular organismal development|spermatogenesis	cytoskeletal calyx	structural constituent of cytoskeleton			ovary(1)	1			STAD - Stomach adenocarcinoma(86;0.228)											0.45			95	114		---	---	---	---	capture_indel		Frame_Shift_Del	DEL	36171041	36171042	3003	9	TG	-	-	-	660	51	CCIN	5	5
