Hugo_Symbol	Entrez_Gene_Id	Center	NCBI_Build	Chromosome	Start_position	End_position	Strand	Variant_Classification	Variant_Type	Reference_Allele	Tumor_Seq_Allele1	Tumor_Seq_Allele2	dbSNP_RS	dbSNP_Val_Status	Tumor_Sample_Barcode	Matched_Norm_Sample_Barcode	Match_Norm_Seq_Allele1	Match_Norm_Seq_Allele2	Tumor_Validation_Allele1	Tumor_Validation_Allele2	Match_Norm_Validation_Allele1	Match_Norm_Validation_Allele2	Verification_Status	Validation_Status	Mutation_Status	Sequencing_Phase	Sequence_Source	Validation_Method	Score	BAM_file	Sequencer	Genome_Change	Annotation_Transcript	Transcript_Strand	cDNA_Change	Codon_Change	Protein_Change	Other_Transcripts	Refseq_mRNA_Id	Refseq_prot_Id	SwissProt_acc_Id	SwissProt_entry_Id	Description	UniProt_AApos	UniProt_Region	UniProt_Site	UniProt_Natural_Variations	UniProt_Experimental_Info	GO_Biological_Process	GO_Cellular_Component	GO_Molecular_Function	COSMIC_overlapping_mutations	COSMIC_fusion_genes	COSMIC_tissue_types_affected	COSMIC_total_alterations_in_gene	Tumorscape_Amplification_Peaks	Tumorscape_Deletion_Peaks	i_TCGAscape_Amplification_Peaks	i_TCGAscape_Deletion_Peaks	DrugBank	i_ACHILLES_Top_Genes	i_CCLE_ONCOMAP_overlapping_mutations	i_CCLE_ONCOMAP_total_mutations_in_gene	i_CCLE_SEQ_overlapping_mutations	i_CCLE_SEQ_total_mutations_in_gene	MUTSIG_Significant_Genes	OREGANNO_ID	OREGANNO_Values	i_tumor_f	i_init_t_lod	i_t_lod_fstar	i_t_alt_count	i_t_ref_count	i_normal_best_gt	i_failure_reasons	i_judgement	validation_status	validation_method	validation_tumor_sample	validation_alt_allele	dataset	TCGAscape_Amplification_Peaks	TCGAscape_Deletion_Peaks	type	classification	start	end	gene	chr	ref_allele	tum_allele1	tum_allele2	context_orig	context65	gene_name	newbase	categ	categ_ignoring_null_categ
FAM13C	220965	broad.mit.edu	36	10	60699831	60699831	+	Missense_Mutation	SNP	C	T	T			TCGA-28-5204-01	TCGA-28-5204-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr10:60699831C>T	uc001jkn.1	-	c.637G>A	c.(637-639)GCA>ACA	p.A213T	FAM13C_uc001jko.1_Missense_Mutation_p.A213T|FAM13C_uc001jkp.2_Missense_Mutation_p.A130T	NM_198215	NP_937858	Q8NE31	FA13C_HUMAN	hypothetical protein LOC220965 isoform 1	213										ovary(1)	1														0.333333	92.170813	95.056682	39	78	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	60699831	60699831	5651	10	C	T	T	25	25	FAM13C	T	2	2
RTKN2	219790	broad.mit.edu	36	10	63627691	63627691	+	Missense_Mutation	SNP	C	G	G			TCGA-28-5204-01	TCGA-28-5204-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr10:63627691C>G	uc001jlw.1	-	c.1812G>C	c.(1810-1812)TGG>TGC	p.W604C	RTKN2_uc009xpf.1_Intron|RTKN2_uc001jlv.1_Missense_Mutation_p.W258C	NM_145307	NP_660350	Q8IZC4	RTKN2_HUMAN	rhotekin 2	604					signal transduction	intracellular					0	Prostate(12;0.0297)|all_hematologic(501;0.215)													0.36	151.040362	153.197538	45	80	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	63627691	63627691	14203	10	C	G	G	26	26	RTKN2	G	3	3
CARD16	114769	broad.mit.edu	36	11	104417351	104417351	+	Missense_Mutation	SNP	G	A	A			TCGA-28-5204-01	TCGA-28-5204-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr11:104417351G>A	uc001pip.1	-	c.580C>T	c.(580-582)CAT>TAT	p.H194Y	CASP1_uc001pil.1_Intron|CASP1_uc001pin.1_Intron|CARD16_uc001pio.1_3'UTR	NM_001017534	NP_001017534	Q5EG05	CAR16_HUMAN	caspase-1 dominant-negative inhibitor pseudo-ICE	194					regulation of apoptosis	intracellular	cysteine-type endopeptidase inhibitor activity				0														0.393443	123.354355	124.57251	48	74	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	104417351	104417351	2766	11	G	A	A	45	45	CARD16	A	2	2
PKP3	11187	broad.mit.edu	36	11	393237	393237	+	Missense_Mutation	SNP	C	A	A			TCGA-28-5204-01	TCGA-28-5204-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr11:393237C>A	uc001lpc.1	+	c.1897C>A	c.(1897-1899)CAG>AAG	p.Q633K		NM_007183	NP_009114	Q9Y446	PKP3_HUMAN	plakophilin 3	633	ARM 6.				cell adhesion	desmosome|nucleus	binding			skin(1)	1		all_cancers(49;3.02e-09)|all_epithelial(84;2.09e-06)|Breast(177;0.000162)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.0538)|all_lung(207;0.0713)												0.272727	6.418773	6.932032	3	8	CC		KEEP	---	---	---	---	capture		all cancers(45;1.56e-27)|Epithelial(43;9.31e-27)|OV - Ovarian serous cystadenocarcinoma(40;1.11e-20)|BRCA - Breast invasive adenocarcinoma(625;3.56e-05)|Lung(200;0.0182)|LUSC - Lung squamous cell carcinoma(625;0.0703)	Missense_Mutation	SNP	393237	393237	12411	11	C	A	A	25	25	PKP3	A	3	3
OR51A2	401667	broad.mit.edu	36	11	4932729	4932729	+	Missense_Mutation	SNP	C	T	T	rs61744535	unknown	TCGA-28-5204-01	TCGA-28-5204-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr11:4932729C>T	uc001lzu.1	-	c.791G>A	c.(790-792)CGC>CAC	p.R264H		NM_001004748	NP_001004748	Q8NGJ7	O51A2_HUMAN	olfactory receptor, family 51, subfamily A,	264	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0		Medulloblastoma(188;0.0075)|all_neural(188;0.0577)|Breast(177;0.086)												0.374502	235.962012	239.441441	94	157	CC		KEEP	---	---	---	---	capture		Epithelial(150;3.22e-11)|BRCA - Breast invasive adenocarcinoma(625;0.0284)|LUSC - Lung squamous cell carcinoma(625;0.19)	Missense_Mutation	SNP	4932729	4932729	11496	11	C	T	T	27	27	OR51A2	T	1	1
OR4C12	283093	broad.mit.edu	36	11	49960296	49960296	+	Silent	SNP	A	G	G			TCGA-28-5204-01	TCGA-28-5204-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr11:49960296A>G	uc001nhc.1	-	c.318T>C	c.(316-318)GGT>GGC	p.G106G		NM_001005270	NP_001005270	Q96R67	OR4CC_HUMAN	olfactory receptor, family 4, subfamily C,	106	Helical; Name=3; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(2)	2														0.373297	422.915924	428.07666	137	230	AA		KEEP	---	---	---	---	capture			Silent	SNP	49960296	49960296	11452	11	A	G	G	6	6	OR4C12	G	4	4
SLC38A1	81539	broad.mit.edu	36	12	44881157	44881157	+	Missense_Mutation	SNP	T	C	C			TCGA-28-5204-01	TCGA-28-5204-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr12:44881157T>C	uc009zkj.1	-	c.994A>G	c.(994-996)ACA>GCA	p.T332A	SLC38A1_uc001rpa.1_Missense_Mutation_p.T332A|SLC38A1_uc001rpb.1_Missense_Mutation_p.T332A|SLC38A1_uc001rpc.1_Missense_Mutation_p.T332A|SLC38A1_uc001rpd.1_Missense_Mutation_p.T332A|SLC38A1_uc001rpe.1_Missense_Mutation_p.T332A|SLC38A1_uc009zkk.1_Missense_Mutation_p.T305A	NM_030674	NP_109599	Q9H2H9	S38A1_HUMAN	amino acid transporter system A1	332	Helical; (Potential).				cellular nitrogen compound metabolic process|neurotransmitter uptake	integral to membrane|plasma membrane	sodium:amino acid symporter activity			ovary(2)|central_nervous_system(1)	3	Lung SC(27;0.137)|Renal(347;0.236)													0.387097	119.185113	120.22164	36	57	TT		KEEP	---	---	---	---	capture	all cancers(1;0.00805)|OV - Ovarian serous cystadenocarcinoma(5;0.0106)|Epithelial(2;0.0344)		Missense_Mutation	SNP	44881157	44881157	15098	12	T	C	C	58	58	SLC38A1	C	4	4
TRPC4	7223	broad.mit.edu	36	13	37164163	37164163	+	Missense_Mutation	SNP	C	T	T			TCGA-28-5204-01	TCGA-28-5204-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr13:37164163C>T	uc010abx.1	-	c.1207G>A	c.(1207-1209)GAG>AAG	p.E403K	TRPC4_uc010abv.1_Intron|TRPC4_uc010abw.1_Missense_Mutation_p.E230K|TRPC4_uc001uws.1_Missense_Mutation_p.E403K|TRPC4_uc001uwt.1_Missense_Mutation_p.E403K|TRPC4_uc010aby.1_Missense_Mutation_p.E403K	NM_016179	NP_057263	Q9UBN4	TRPC4_HUMAN	transient receptor potential cation channel,	403	Cytoplasmic (Potential).				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														0.402985	149.116586	150.220966	54	80	CC		KEEP	---	---	---	---	capture		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)	Missense_Mutation	SNP	37164163	37164163	17131	13	C	T	T	31	31	TRPC4	T	1	1
DACH1	1602	broad.mit.edu	36	13	70951353	70951353	+	Nonsense_Mutation	SNP	C	A	A			TCGA-28-5204-01	TCGA-28-5204-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr13:70951353C>A	uc010aek.1	-	c.1819G>T	c.(1819-1821)GAA>TAA	p.E607*	DACH1_uc010ael.1_Nonsense_Mutation_p.E459*|DACH1_uc010aem.1_Nonsense_Mutation_p.E405*	NM_080759	NP_542937	Q9UI36	DACH1_HUMAN	dachshund homolog 1 isoform a	659	DACHbox-C.|Potential.|Interaction with SIN3A (By similarity).				multicellular organismal development|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleolus	DNA binding|nucleotide binding|protein binding			breast(1)	1		Acute lymphoblastic leukemia(28;0.0503)|Breast(118;0.198)								202				0.38009	216.924283	219.719275	84	137	CC		KEEP	---	---	---	---	capture		GBM - Glioblastoma multiforme(99;0.00032)	Nonsense_Mutation	SNP	70951353	70951353	4386	13	C	A	A	32	32	DACH1	A	5	3
TLN2	83660	broad.mit.edu	36	15	60898861	60898861	+	Missense_Mutation	SNP	G	A	A			TCGA-28-5204-01	TCGA-28-5204-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr15:60898861G>A	uc002alb.2	+	c.6865G>A	c.(6865-6867)GAA>AAA	p.E2289K	TLN2_uc002alc.2_Missense_Mutation_p.E682K	NM_015059	NP_055874	Q9Y4G6	TLN2_HUMAN	talin 2	2289					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														0.204301	8.410005	16.670003	19	74	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	60898861	60898861	16478	15	G	A	A	41	41	TLN2	A	2	2
ACAN	176	broad.mit.edu	36	15	87201791	87201791	+	Silent	SNP	A	T	T			TCGA-28-5204-01	TCGA-28-5204-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr15:87201791A>T	uc002bmy.1	+	c.4629A>T	c.(4627-4629)CCA>CCT	p.P1543P	ACAN_uc002bmz.1_Silent_p.P1543P|ACAN_uc002bna.1_5'UTR	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)													0.42522	406.702601	408.365062	145	196	AA		KEEP	---	---	---	---	capture	BRCA - Breast invasive adenocarcinoma(143;0.146)		Silent	SNP	87201791	87201791	118	15	A	T	T	5	5	ACAN	T	4	4
DPEP1	1800	broad.mit.edu	36	16	88230809	88230809	+	Missense_Mutation	SNP	G	A	A			TCGA-28-5204-01	TCGA-28-5204-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr16:88230809G>A	uc010cin.1	+	c.556G>A	c.(556-558)GAG>AAG	p.E186K	DPEP1_uc002fnr.2_Missense_Mutation_p.E186K|DPEP1_uc002fns.2_Missense_Mutation_p.E186K	NM_001128141	NP_001121613	P16444	DPEP1_HUMAN	dipeptidase 1	186					proteolysis	anchored to membrane|apical plasma membrane|microvillus membrane	dipeptidase activity|dipeptidyl-peptidase activity|metal ion binding|metalloexopeptidase activity|protein binding			large_intestine(1)	1		all_lung(18;0.0054)|all_hematologic(23;0.094)			Cilastatin(DB01597)									0.755814	193.501893	198.62934	65	21	GG		KEEP	---	---	---	---	capture		BRCA - Breast invasive adenocarcinoma(80;0.0258)	Missense_Mutation	SNP	88230809	88230809	4897	16	G	A	A	37	37	DPEP1	A	1	1
DBF4B	80174	broad.mit.edu	36	17	40183774	40183774	+	Missense_Mutation	SNP	G	A	A			TCGA-28-5204-01	TCGA-28-5204-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr17:40183774G>A	uc002ihf.1	+	c.1475G>A	c.(1474-1476)GGC>GAC	p.G492D		NM_145663	NP_663696	Q8NFT6	DBF4B_HUMAN	DBF4 homolog B isoform 1	492					cell cycle	nucleus	nucleic acid binding|zinc ion binding				0		Prostate(33;0.0322)												0.432692	251.495347	252.298156	90	118	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	40183774	40183774	4420	17	G	A	A	42	42	DBF4B	A	2	2
ABCA5	23461	broad.mit.edu	36	17	64775786	64775786	+	Missense_Mutation	SNP	T	A	A			TCGA-28-5204-01	TCGA-28-5204-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr17:64775786T>A	uc002jif.1	-	c.3037A>T	c.(3037-3039)ACT>TCT	p.T1013S	ABCA5_uc002jib.1_5'UTR|ABCA5_uc002jic.1_Missense_Mutation_p.T236S|ABCA5_uc002jid.1_5'UTR|ABCA5_uc002jie.1_Non-coding_Transcript|ABCA5_uc002jig.1_Missense_Mutation_p.T1013S	NM_018672	NP_758424	Q8WWZ7	ABCA5_HUMAN	ATP-binding cassette, sub-family A , member 5	1013					cholesterol efflux|high-density lipoprotein particle remodeling|negative regulation of macrophage derived foam cell differentiation|reverse cholesterol transport	Golgi membrane|integral to membrane|late endosome membrane|lysosomal membrane	ATP binding|ATPase activity			ovary(2)|central_nervous_system(1)	3	Breast(10;3.72e-11)													0.476744	117.070877	117.111001	41	45	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	64775786	64775786	36	17	T	A	A	57	57	ABCA5	A	4	4
TNRC6C	57690	broad.mit.edu	36	17	73594768	73594768	+	Silent	SNP	C	T	T			TCGA-28-5204-01	TCGA-28-5204-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr17:73594768C>T	uc002jud.1	+	c.3801C>T	c.(3799-3801)CTC>CTT	p.L1267L	TNRC6C_uc002juf.1_Silent_p.L543L	NM_018996	NP_061869	Q9HCJ0	TNR6C_HUMAN	trinucleotide repeat containing 6C isoform 2	1267					gene silencing by RNA|regulation of translation		nucleotide binding|RNA binding			ovary(1)|central_nervous_system(1)	2														0.486486	202.163716	202.188069	72	76	CC		KEEP	---	---	---	---	capture	BRCA - Breast invasive adenocarcinoma(99;0.00269)|Lung(188;0.0973)		Silent	SNP	73594768	73594768	16883	17	C	T	T	31	31	TNRC6C	T	1	1
LDLR	3949	broad.mit.edu	36	19	11083312	11083312	+	Missense_Mutation	SNP	G	A	A			TCGA-28-5204-01	TCGA-28-5204-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr19:11083312G>A	uc002mqk.2	+	c.1183G>A	c.(1183-1185)GTG>ATG	p.V395M		NM_000527	NP_000518	P01130	LDLR_HUMAN	low density lipoprotein receptor precursor	395	Extracellular (Potential).				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)			Methyl aminolevulinate(DB00992)|Porfimer(DB00707)	GBM(18;201 575 7820 21545)				1109				0.384615	85.779367	86.848904	35	56	GG		KEEP	---	---	---	---	capture		GBM - Glioblastoma multiforme(1328;1.36e-05)|STAD - Stomach adenocarcinoma(1328;0.000766)|Lung(535;0.197)	Missense_Mutation	SNP	11083312	11083312	9028	19	G	A	A	48	48	LDLR	A	2	2
ZNF554	115196	broad.mit.edu	36	19	2785236	2785236	+	Missense_Mutation	SNP	C	T	T			TCGA-28-5204-01	TCGA-28-5204-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr19:2785236C>T	uc002lwm.2	+	c.1003C>T	c.(1003-1005)CGG>TGG	p.R335W	ZNF554_uc002lwl.2_Missense_Mutation_p.R284W	NM_001102651	NP_001096121	Q86TJ5	ZN554_HUMAN	zinc finger protein 554	335	C2H2-type 2.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1		Hepatocellular(1079;0.137)												0.453202	259.184794	259.569131	92	111	CC		KEEP	---	---	---	---	capture		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)	Missense_Mutation	SNP	2785236	2785236	18580	19	C	T	T	23	23	ZNF554	T	1	1
ZNF235	9310	broad.mit.edu	36	19	49495637	49495637	+	Missense_Mutation	SNP	T	C	C			TCGA-28-5204-01	TCGA-28-5204-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr19:49495637T>C	uc002oza.2	-	c.104A>G	c.(103-105)GAT>GGT	p.D35G	ZNF235_uc002oyx.1_Non-coding_Transcript|ZNF235_uc010eji.1_Missense_Mutation_p.D35G|ZNF235_uc002ozb.2_Missense_Mutation_p.D35G	NM_004234	NP_004225	Q14590	ZN235_HUMAN	zinc finger protein 93 homolog	35	KRAB.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(2)|large_intestine(1)	3		Prostate(69;0.0352)|all_neural(266;0.116)												0.412979	461.863142	464.096634	140	199	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	49495637	49495637	18379	19	T	C	C	50	50	ZNF235	C	4	4
PTPRS	5802	broad.mit.edu	36	19	5174138	5174138	+	Missense_Mutation	SNP	G	A	A			TCGA-28-5204-01	TCGA-28-5204-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr19:5174138G>A	uc002mbv.1	-	c.2665C>T	c.(2665-2667)CGC>TGC	p.R889C	PTPRS_uc002mbu.1_Intron|PTPRS_uc002mbw.1_Missense_Mutation_p.R867C|PTPRS_uc002mbx.1_Intron|PTPRS_uc002mby.1_Intron	NM_002850	NP_002841	Q13332	PTPRS_HUMAN	protein tyrosine phosphatase, receptor type,	889	Extracellular (Potential).|Fibronectin type-III 6.				cell adhesion	integral to plasma membrane	protein binding|transmembrane receptor protein tyrosine phosphatase activity			large_intestine(2)|ovary(1)|central_nervous_system(1)	4														0.75	17.651446	18.105143	6	2	GG		KEEP	---	---	---	---	capture		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0321)|Lung(535;0.182)	Missense_Mutation	SNP	5174138	5174138	13269	19	G	A	A	39	39	PTPRS	A	1	1
FPR2	2358	broad.mit.edu	36	19	56963884	56963884	+	Missense_Mutation	SNP	G	A	A			TCGA-28-5204-01	TCGA-28-5204-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr19:56963884G>A	uc002pxr.1	+	c.161G>A	c.(160-162)CGG>CAG	p.R54Q	FPR2_uc002pxs.2_Missense_Mutation_p.R54Q|FPR2_uc010epf.1_Missense_Mutation_p.R54Q|FPR2_uc010epg.1_Missense_Mutation_p.R54Q	NM_001005738	NP_001453	P25090	FPR2_HUMAN	formyl peptide receptor-like 1	54	Cytoplasmic (Potential).				cell adhesion|cellular component movement|chemotaxis|inflammatory response	integral to membrane|plasma membrane	N-formyl peptide receptor activity			ovary(1)	1														0.386792	229.697277	232.079149	82	130	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	56963884	56963884	6285	19	G	A	A	39	39	FPR2	A	1	1
UBE2M	9040	broad.mit.edu	36	19	63759494	63759494	+	Splice_Site_SNP	SNP	C	T	T			TCGA-28-5204-01	TCGA-28-5204-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr19:63759494C>T	uc002qtl.2	-	c.411_splice	c.e5+1	p.L137_splice	CHMP2A_uc002qti.1_5'Flank|CHMP2A_uc002qtj.1_5'Flank|CHMP2A_uc002qtk.1_5'Flank	NM_003969	NP_003960			ubiquitin-conjugating enzyme E2M						post-translational protein modification|protein neddylation		ATP binding|NEDD8 ligase activity|protein binding|ribosomal S6-glutamic acid ligase activity|ubiquitin-protein ligase activity			ovary(1)|pancreas(1)	2		all_cancers(17;4.4e-22)|all_epithelial(17;2.15e-16)|Lung NSC(17;1.24e-06)|all_lung(17;5.41e-06)|Colorectal(82;3.46e-05)|Renal(17;0.00179)|all_neural(62;0.00607)|Ovarian(87;0.0443)|Breast(46;0.0928)|Medulloblastoma(540;0.184)												0.417526	224.022804	225.178235	81	113	CC		KEEP	---	---	---	---	capture		UCEC - Uterine corpus endometrioid carcinoma (67;0.0434)|all cancers(4;1.39e-13)|Epithelial(4;1.01e-10)|OV - Ovarian serous cystadenocarcinoma(4;2.34e-09)|GBM - Glioblastoma multiforme(193;0.0102)|Lung(386;0.179)	Splice_Site_SNP	SNP	63759494	63759494	17422	19	C	T	T	18	18	UBE2M	T	5	2
YOD1	55432	broad.mit.edu	36	1	205290713	205290713	+	Missense_Mutation	SNP	C	T	T			TCGA-28-5204-01	TCGA-28-5204-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr1:205290713C>T	uc001hfe.1	-	c.286G>A	c.(286-288)GAG>AAG	p.E96K	YOD1_uc001hff.1_Missense_Mutation_p.E52K|PFKFB2_uc001hfg.1_5'Flank|PFKFB2_uc001hfh.1_5'Flank	NM_018566	NP_061036	Q5VVQ6	OTU1_HUMAN	YOD1 OTU deubiquinating enzyme 1 homolog	96	UBX-like.				cellular amino acid metabolic process|endoplasmic reticulum unfolded protein response|ER-associated protein catabolic process|protein K48-linked deubiquitination|protein K63-linked deubiquitination	intracellular	protein binding|ubiquitin-specific protease activity|zinc ion binding				0	Prostate(682;0.19)											OREG0014189	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	0.414365	188.406235	189.556063	75	106	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	205290713	205290713	18071	1	C	T	T	31	31	YOD1	T	1	1
SLC35F3	148641	broad.mit.edu	36	1	232522532	232522532	+	Missense_Mutation	SNP	G	A	A			TCGA-28-5204-01	TCGA-28-5204-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:232522532G>A	uc001hvy.1	+	c.1213G>A	c.(1213-1215)GTC>ATC	p.V405I	SLC35F3_uc001hwa.1_Missense_Mutation_p.V336I	NM_173508	NP_775779	Q8IY50	S35F3_HUMAN	solute carrier family 35, member F3	336	Helical; (Potential).				transport	integral to membrane				ovary(2)	2	Ovarian(103;0.0454)	all_cancers(173;0.145)|Prostate(94;0.0885)												0.450216	284.755863	285.256209	104	127	GG		KEEP	---	---	---	---	capture	OV - Ovarian serous cystadenocarcinoma(106;0.00531)		Missense_Mutation	SNP	232522532	232522532	15087	1	G	A	A	40	40	SLC35F3	A	1	1
OR2W5	441932	broad.mit.edu	36	1	245721416	245721416	+	Missense_Mutation	SNP	C	T	T			TCGA-28-5204-01	TCGA-28-5204-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr1:245721416C>T	uc001icz.1	+	c.364C>T	c.(364-366)CGC>TGC	p.R122C		NM_001004698	NP_001004698	A6NFC9	OR2W5_HUMAN	olfactory receptor, family 2, subfamily W,	122					sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)|breast(1)	2	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;0.222)												0.347826	145.450886	148.740937	56	105	CC		KEEP	---	---	---	---	capture	OV - Ovarian serous cystadenocarcinoma(106;0.0188)		Missense_Mutation	SNP	245721416	245721416	11440	1	C	T	T	23	23	OR2W5	T	1	1
MATN4	8785	broad.mit.edu	36	20	43360464	43360464	+	Missense_Mutation	SNP	C	T	T			TCGA-28-5204-01	TCGA-28-5204-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr20:43360464C>T	uc002xnn.1	-	c.1186G>A	c.(1186-1188)GAG>AAG	p.E396K	MATN4_uc002xno.1_Missense_Mutation_p.E355K|MATN4_uc002xnp.1_Missense_Mutation_p.E314K|MATN4_uc002xnq.1_Missense_Mutation_p.E355K|MATN4_uc002xnr.1_Missense_Mutation_p.E396K	NM_003833	NP_003824	O95460	MATN4_HUMAN	matrilin 4 isoform 1 precursor	437	VWFA 2.					extracellular region	protein binding				0		Myeloproliferative disorder(115;0.0122)												0.47619	105.225551	105.263623	40	44	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	43360464	43360464	9720	20	C	T	T	31	31	MATN4	T	1	1
USP25	29761	broad.mit.edu	36	21	16121276	16121276	+	Missense_Mutation	SNP	C	T	T			TCGA-28-5204-01	TCGA-28-5204-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr21:16121276C>T	uc002yjz.1	+	c.1576C>T	c.(1576-1578)CGG>TGG	p.R526W	USP25_uc002yjy.1_Missense_Mutation_p.R526W|USP25_uc010gla.1_Intron	NM_013396	NP_037528	Q9UHP3	UBP25_HUMAN	ubiquitin specific protease 25	526					protein modification process|ubiquitin-dependent protein catabolic process	cytoplasm|nucleus	ubiquitin thiolesterase activity|ubiquitin-specific protease activity			ovary(3)|liver(2)	5														0.466667	251.594263	251.76682	84	96	CC		KEEP	---	---	---	---	capture		Epithelial(23;7.55e-05)|all cancers(11;0.000429)|COAD - Colon adenocarcinoma(22;0.00543)|OV - Ovarian serous cystadenocarcinoma(11;0.00743)|Colorectal(24;0.0116)|Lung(58;0.0853)|LUSC - Lung squamous cell carcinoma(23;0.0889)	Missense_Mutation	SNP	16121276	16121276	17619	21	C	T	T	23	23	USP25	T	1	1
IL1A	3552	broad.mit.edu	36	2	113249118	113249118	+	Silent	SNP	C	T	T	rs3783588	unknown	TCGA-28-5204-01	TCGA-28-5204-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr2:113249118C>T	uc002tig.1	-	c.813G>A	c.(811-813)GCG>GCA	p.A271A		NM_000575	NP_000566	P01583	IL1A_HUMAN	interleukin 1, alpha proprotein	271					anti-apoptosis|apoptosis|cell proliferation|cellular response to heat|cytokine-mediated signaling pathway|fever generation|immune response|negative regulation of cell proliferation|positive regulation of angiogenesis|positive regulation of cell division|positive regulation of cytokine secretion|positive regulation of interleukin-2 biosynthetic process|positive regulation of mitosis|positive regulation vascular endothelial growth factor production|response to copper ion	cytosol|extracellular space	copper ion binding|cytokine activity|interleukin-1 receptor binding				0										100				0.382022	87.714546	88.805427	34	55	CC		KEEP	---	---	---	---	capture			Silent	SNP	113249118	113249118	7951	2	C	T	T	19	19	IL1A	T	1	1
TTN	7273	broad.mit.edu	36	2	179156719	179156719	+	Silent	SNP	G	A	A			TCGA-28-5204-01	TCGA-28-5204-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr2:179156719G>A	uc002umr.1	-	c.57732C>T	c.(57730-57732)CAC>CAT	p.H19244H	TTN_uc002ums.1_Silent_p.H12939H|TTN_uc010frc.1_Silent_p.H12872H|TTN_uc010frd.1_Silent_p.H12747H	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	20171										ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1)	153										8722				0.45	76.513743	76.64487	27	33	GG		KEEP	---	---	---	---	capture	OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)		Silent	SNP	179156719	179156719	17290	2	G	A	A	44	44	TTN	A	2	2
COL3A1	1281	broad.mit.edu	36	2	189572305	189572305	+	Missense_Mutation	SNP	C	G	G			TCGA-28-5204-01	TCGA-28-5204-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr2:189572305C>G	uc002uqj.1	+	c.2072C>G	c.(2071-2073)GCC>GGC	p.A691G		NM_000090	NP_000081	P02461	CO3A1_HUMAN	collagen type III alpha 1 preproprotein	691	Triple-helical region.				axon guidance|cell-matrix adhesion|collagen biosynthetic process|collagen fibril organization|fibril organization|heart development|integrin-mediated signaling pathway|negative regulation of immune response|peptide cross-linking|platelet activation|response to cytokine stimulus|response to radiation|skin development|transforming growth factor beta receptor signaling pathway	collagen type III|extracellular space	extracellular matrix structural constituent|integrin binding|platelet-derived growth factor binding			central_nervous_system(7)|ovary(4)|large_intestine(2)	13					Collagenase(DB00048)|Palifermin(DB00039)					1079				0.263158	6.615575	7.561437	5	14	CC		KEEP	---	---	---	---	capture	OV - Ovarian serous cystadenocarcinoma(117;0.0106)|Epithelial(96;0.141)		Missense_Mutation	SNP	189572305	189572305	3826	2	C	G	G	26	26	COL3A1	G	3	3
TMPRSS7	344805	broad.mit.edu	36	3	113252237	113252237	+	Missense_Mutation	SNP	A	G	G			TCGA-28-5204-01	TCGA-28-5204-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr3:113252237A>G	uc010hqb.1	+	c.742A>G	c.(742-744)ATC>GTC	p.I248V	TMPRSS7_uc003dyp.1_Missense_Mutation_p.I103V	NM_001042575	NP_001036040	Q7RTY8	TMPS7_HUMAN	transmembrane protease, serine 7	374	Extracellular (Potential).|CUB 2.				proteolysis	integral to membrane|plasma membrane	serine-type endopeptidase activity			ovary(1)|kidney(1)	2														0.41	744.176093	748.409412	246	354	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	113252237	113252237	16793	3	A	G	G	8	8	TMPRSS7	G	4	4
RPL22L1	200916	broad.mit.edu	36	3	172066957	172066957	+	Missense_Mutation	SNP	T	C	C			TCGA-28-5204-01	TCGA-28-5204-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr3:172066957T>C	uc003fhc.2	-	c.275A>G	c.(274-276)GAT>GGT	p.D92G	RPL22L1_uc003fhb.2_Non-coding_Transcript	NM_001099645	NP_001093115	Q6P5R6	RL22L_HUMAN	ribosomal protein L22-like 1	92					translation	ribosome	structural constituent of ribosome				0	all_cancers(22;1.96e-19)|all_lung(20;1.59e-15)|Lung NSC(18;7.08e-15)|Ovarian(172;0.00197)|Breast(254;0.137)													0.388889	45.137991	45.528423	14	22	TT		KEEP	---	---	---	---	capture	LUSC - Lung squamous cell carcinoma(14;1.1e-14)|Lung(28;2.99e-14)		Missense_Mutation	SNP	172066957	172066957	14048	3	T	C	C	50	50	RPL22L1	C	4	4
HRG	3273	broad.mit.edu	36	3	187873312	187873312	+	Missense_Mutation	SNP	C	T	T			TCGA-28-5204-01	TCGA-28-5204-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr3:187873312C>T	uc003fqq.1	+	c.601C>T	c.(601-603)CGG>TGG	p.R201W		NM_000412	NP_000403	P04196	HRG_HUMAN	histidine-rich glycoprotein precursor	201	Cystatin 2.				fibrinolysis|platelet activation|platelet degranulation	extracellular region|plasma membrane|platelet alpha granule lumen	cysteine-type endopeptidase inhibitor activity|heparin binding			ovary(1)|central_nervous_system(1)	2	all_cancers(143;6.64e-12)|Ovarian(172;0.0339)													0.423077	114.170105	114.709345	44	60	CC		KEEP	---	---	---	---	capture	OV - Ovarian serous cystadenocarcinoma(80;5.73e-20)	GBM - Glioblastoma multiforme(93;0.0683)	Missense_Mutation	SNP	187873312	187873312	7646	3	C	T	T	27	27	HRG	T	1	1
PLCXD3	345557	broad.mit.edu	36	5	41418205	41418205	+	Nonsense_Mutation	SNP	G	A	A			TCGA-28-5204-01	TCGA-28-5204-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr5:41418205G>A	uc003jmm.1	-	c.292C>T	c.(292-294)CGA>TGA	p.R98*		NM_001005473	NP_001005473	Q63HM9	PLCX3_HUMAN	phosphatidylinositol-specific phospholipase C, X	98	PI-PLC X-box.				intracellular signal transduction|lipid catabolic process		phospholipase C activity|signal transducer activity			urinary_tract(1)|ovary(1)|lung(1)|central_nervous_system(1)	4														0.467836	220.97272	221.127488	80	91	GG		KEEP	---	---	---	---	capture			Nonsense_Mutation	SNP	41418205	41418205	12469	5	G	A	A	37	37	PLCXD3	A	5	1
OOEP	441161	broad.mit.edu	36	6	74136128	74136128	+	Missense_Mutation	SNP	G	A	A			TCGA-28-5204-01	TCGA-28-5204-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr6:74136128G>A	uc003pgu.2	-	c.109C>T	c.(109-111)CGG>TGG	p.R37W	OOEP_uc003pgv.2_Intron	NM_001080507	NP_001073976	A6NGQ2	OOEP_HUMAN	oocyte expressed protein homolog	37						cytoplasm					0														0.798561	357.286791	368.795899	111	28	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	74136128	74136128	11276	6	G	A	A	39	39	OOEP	A	1	1
CALN1	83698	broad.mit.edu	36	7	71209115	71209115	+	Silent	SNP	G	A	A			TCGA-28-5204-01	TCGA-28-5204-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr7:71209115G>A	uc003twb.2	-	c.345C>T	c.(343-345)AGC>AGT	p.S115S	CALN1_uc003twa.2_Silent_p.S73S|CALN1_uc003twc.2_Silent_p.S73S	NM_031468	NP_113656	Q9BXU9	CABP8_HUMAN	calneuron 1 isoform 1	73	EF-hand 2.|Cytoplasmic (Potential).					Golgi apparatus|integral to membrane|perinuclear region of cytoplasm|plasma membrane	calcium ion binding				0		all_cancers(73;0.069)|Lung NSC(55;0.0658)|all_lung(88;0.0912)|all_epithelial(88;0.161)												0.212598	47.449677	57.159665	27	100	GG		KEEP	---	---	---	---	capture			Silent	SNP	71209115	71209115	2708	7	G	A	A	38	38	CALN1	A	1	1
GNAT3	346562	broad.mit.edu	36	7	79941551	79941551	+	Missense_Mutation	SNP	G	A	A			TCGA-28-5204-01	TCGA-28-5204-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr7:79941551G>A	uc010leb.1	-	c.542C>T	c.(541-543)ACG>ATG	p.T181M	CD36_uc003uhc.1_Intron	NM_001102386	NP_001095856	A8MTJ3	GNAT3_HUMAN	guanine nucleotide binding protein, alpha	181					detection of chemical stimulus involved in sensory perception of bitter taste|G-protein signaling, coupled to cAMP nucleotide second messenger|rhodopsin mediated phototransduction|sensory perception of sweet taste|sensory perception of umami taste	cytoplasm|heterotrimeric G-protein complex|photoreceptor inner segment|photoreceptor outer segment	G-protein beta/gamma-subunit complex binding|G-protein-coupled receptor binding|GTP binding|GTPase activity|signal transducer activity			ovary(1)	1														0.245614	30.718279	34.080608	14	43	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	79941551	79941551	6782	7	G	A	A	40	40	GNAT3	A	1	1
TRRAP	8295	broad.mit.edu	36	7	98447657	98447657	+	Missense_Mutation	SNP	C	T	T			TCGA-28-5204-01	TCGA-28-5204-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr7:98447657C>T	uc003upp.1	+	c.11323C>T	c.(11323-11325)CGG>TGG	p.R3775W	TRRAP_uc003upq.1_Missense_Mutation_p.R3746W|TRRAP_uc003upr.1_Missense_Mutation_p.R3481W|TRRAP_uc003ups.2_5'Flank	NM_003496	NP_003487	Q9Y4A5	TRRAP_HUMAN	transformation/transcription domain-associated	3775	PI3K/PI4K.				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)									1847				0.191358	64.844232	79.255004	31	131	CC		KEEP	---	---	---	---	capture	STAD - Stomach adenocarcinoma(171;0.215)		Missense_Mutation	SNP	98447657	98447657	17152	7	C	T	T	23	23	TRRAP	T	1	1
GJC3	349149	broad.mit.edu	36	7	99359114	99359114	+	Missense_Mutation	SNP	C	G	G			TCGA-28-5204-01	TCGA-28-5204-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr7:99359114C>G	uc003usg.1	-	c.830G>C	c.(829-831)AGA>ACA	p.R277T		NM_181538	NP_853516	Q8NFK1	CXG3_HUMAN	gap junction protein, gamma 3, 30.2kDa	277	Cytoplasmic (Potential).					connexon complex|integral to membrane				ovary(1)	1	Esophageal squamous(72;0.0166)|Lung NSC(181;0.0211)|all_lung(186;0.0323)													0.262673	172.372413	183.429209	57	160	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	99359114	99359114	6684	7	C	G	G	32	32	GJC3	G	3	3
ADAM2	2515	broad.mit.edu	36	8	39797683	39797683	+	Missense_Mutation	SNP	C	T	T			TCGA-28-5204-01	TCGA-28-5204-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr8:39797683C>T	uc003xnj.1	-	c.508G>A	c.(508-510)GTA>ATA	p.V170I	ADAM2_uc003xnk.1_Missense_Mutation_p.V170I|ADAM2_uc003xnl.1_Missense_Mutation_p.V170I	NM_001464	NP_001455	Q99965	ADAM2_HUMAN	ADAM metallopeptidase domain 2 proprotein	170				V -> A (in Ref. 2; AAD04206).	cell adhesion|fusion of sperm to egg plasma membrane|proteolysis	integral to plasma membrane	integrin binding|metalloendopeptidase activity|zinc ion binding			ovary(1)|lung(1)	2		all_cancers(7;2.38e-28)|all_epithelial(6;8.85e-21)|all_lung(54;1.24e-07)|Lung NSC(58;1.94e-07)|Hepatocellular(245;0.00745)|Breast(189;0.00908)|Renal(179;0.0183)|Colorectal(162;0.246)												0.733333	264.533673	270.428345	88	32	CC		KEEP	---	---	---	---	capture	LUSC - Lung squamous cell carcinoma(45;0.000149)	READ - Rectum adenocarcinoma(644;0.0689)|Kidney(114;0.162)	Missense_Mutation	SNP	39797683	39797683	242	8	C	T	T	19	19	ADAM2	T	1	1
CYLC2	1539	broad.mit.edu	36	9	104807411	104807411	+	Missense_Mutation	SNP	A	C	C			TCGA-28-5204-01	TCGA-28-5204-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr9:104807411A>C	uc004bbs.1	+	c.677A>C	c.(676-678)AAG>ACG	p.K226T		NM_001340	NP_001331	Q14093	CYLC2_HUMAN	cylicin 2	226	3 X approximate tandem repeats.|31 X 3 AA repeats of K-K-X.|3.				cell differentiation|multicellular organismal development|spermatogenesis	cytoskeletal calyx	structural constituent of cytoskeleton			skin(1)	1		all_hematologic(171;0.125)												0.763636	141.671999	145.164689	42	13	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	104807411	104807411	4307	9	A	C	C	3	3	CYLC2	C	4	4
RORB	6096	broad.mit.edu	36	9	76439368	76439368	+	Missense_Mutation	SNP	G	T	T			TCGA-28-5204-01	TCGA-28-5204-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr9:76439368G>T	uc004aji.1	+	c.128G>T	c.(127-129)GGA>GTA	p.G43V	RORB_uc004ajh.1_Missense_Mutation_p.G32V	NM_006914	NP_008845	Q92753	RORB_HUMAN	RAR-related orphan receptor B	43	Nuclear receptor.				eye photoreceptor cell development|positive regulation of gene-specific transcription|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor|visual perception	nucleoplasm	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|steroid hormone receptor activity|zinc ion binding			ovary(2)|lung(1)	3														0.380952	55.865471	56.65456	24	39	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	76439368	76439368	14008	9	G	T	T	41	41	RORB	T	3	3
IRS4	8471	broad.mit.edu	36	X	107864558	107864558	+	Nonsense_Mutation	SNP	G	T	T			TCGA-28-5204-01	TCGA-28-5204-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chrX:107864558G>T	uc004eoc.1	-	c.1673C>A	c.(1672-1674)TCA>TAA	p.S558*		NM_003604	NP_003595	O14654	IRS4_HUMAN	insulin receptor substrate 4	558						plasma membrane	insulin receptor binding|SH3/SH2 adaptor activity|signal transducer activity			ovary(4)|large_intestine(2)|lung(1)|breast(1)|pancreas(1)	9														0.894737	602.748599	638.010563	204	24	GG		KEEP	---	---	---	---	capture			Nonsense_Mutation	SNP	107864558	107864558	8146	23	G	T	T	45	45	IRS4	T	5	3
KIAA2022	340533	broad.mit.edu	36	X	73878162	73878162	+	Missense_Mutation	SNP	C	T	T			TCGA-28-5204-01	TCGA-28-5204-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chrX:73878162C>T	uc004eby.1	-	c.2955G>A	c.(2953-2955)ATG>ATA	p.M985I		NM_001008537	NP_001008537	Q5QGS0	K2022_HUMAN	hypothetical protein LOC340533	985					base-excision repair, gap-filling|DNA replication proofreading|DNA replication, removal of RNA primer|nucleotide-excision repair, DNA gap filling|regulation of mitotic cell cycle|S phase of mitotic cell cycle	delta DNA polymerase complex	3'-5'-exodeoxyribonuclease activity|DNA-directed DNA polymerase activity			ovary(7)|large_intestine(4)|skin(2)|central_nervous_system(1)	14										126				0.84058	192.185275	199.804267	58	11	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	73878162	73878162	8580	23	C	T	T	21	21	KIAA2022	T	2	2
TAF3	83860	broad.mit.edu	36	10	8047623	8047631	+	In_Frame_Del	DEL	AGAAGGAGA	-	-			TCGA-28-5204-01	TCGA-28-5204-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:8047623_8047631delAGAAGGAGA	uc009xis.1	+	c.2144_2152delAGAAGGAGA	c.(2143-2154)GAGAAGGAGAAG>GAG	p.KEK719del	TAF3_uc009xir.1_In_Frame_Del_p.KEK718del	NM_031923	NP_114129	Q5VWG9	TAF3_HUMAN	RNA polymerase II transcription factor TAFII140	719_721	Lys-rich.				maintenance of protein location in nucleus|regulation of transcription, DNA-dependent|transcription, DNA-dependent	transcription factor TFIID complex	protein binding|zinc ion binding			ovary(1)	1														0.61			25	16				---	---	---	---	capture_indel			In_Frame_Del	DEL	8047623	8047631	16046	10	AGAAGGAGA	-	-	11	11	TAF3	-	5	5
NEFH	4744	broad.mit.edu	36	22	28216478	28216478	+	Frame_Shift_Del	DEL	C	-	-			TCGA-28-5204-01	TCGA-28-5204-01										Phase_I	Unspecified				Illumina GAIIx	g.chr22:28216478_28216478delC	uc003afo.1	+	c.2849_2849delC	c.(2848-2850)GCAfs	p.A950fs	NEFH_uc003afp.2_Frame_Shift_Del_p.Q16fs	NM_021076	NP_066554	P12036	NFH_HUMAN	neurofilament, heavy polypeptide 200kDa	956	Tail.				cell death|nervous system development	neurofilament					0														0.37			47	79				---	---	---	---	capture_indel			Frame_Shift_Del	DEL	28216478	28216478	10713	22	C	-	-	25	25	NEFH	-	5	5
