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
TACC2	10579	broad.mit.edu	37	10	123843769	123843769	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z013-01	TCGA-17-Z013-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:123843769C>T	uc001lfv.2	+	c.1754C>T	c.(1753-1755)CCA>CTA	p.P585L	TACC2_uc001lfw.2_Intron|TACC2_uc009xzx.2_Missense_Mutation_p.P585L|TACC2_uc010qtv.1_Missense_Mutation_p.P585L	NM_206862	NP_996744	O95359	TACC2_HUMAN	transforming, acidic coiled-coil containing	585						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)												0.481481	41.773791	41.781841	13	14	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	123843769	123843769	16023	10	C	T	T	T	273	21	TACC2	2	2
C10orf11	83938	broad.mit.edu	37	10	77542781	77542781	+	Splice_Site_SNP	SNP	G	T	T			TCGA-17-Z013-01	TCGA-17-Z013-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:77542781G>T	uc001jxi.2	+	c.47_splice	c.e1+1	p.R16_splice		NM_032024	NP_114413			chromosome 10 open reading frame 11												0	Prostate(51;0.0095)|all_epithelial(25;0.0221)													0.076923	-0.476022	11.434017	5	60	KEEP	---	---	---	---	capture		Splice_Site_SNP	SNP	77542781	77542781	1617	10	G	T	T	T	572	44	C10orf11	5	2
DYNC2H1	79659	broad.mit.edu	37	11	103124071	103124071	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z013-01	TCGA-17-Z013-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:103124071G>T	uc001phn.1	+	c.10121G>T	c.(10120-10122)CGC>CTC	p.R3374L	DYNC2H1_uc001pho.2_Missense_Mutation_p.R3367L|DYNC2H1_uc009yxe.1_Intron	NM_001080463	NP_001073932	Q8NCM8	DYHC2_HUMAN	dynein, cytoplasmic 2, heavy chain 1	3367	AAA 5 (By similarity).				cell projection organization|Golgi organization|microtubule-based movement|multicellular organismal development	cilium axoneme|dynein complex|Golgi apparatus|microtubule|plasma membrane	ATP binding|ATPase activity|microtubule motor activity				0		Acute lymphoblastic leukemia(157;0.000966)|all_hematologic(158;0.00348)		BRCA - Breast invasive adenocarcinoma(274;0.000177)|Epithelial(105;0.0785)										0.491803	99.181316	99.183851	30	31	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	103124071	103124071	5032	11	G	T	T	T	494	38	DYNC2H1	1	1
DNHD1	144132	broad.mit.edu	37	11	6588872	6588872	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z013-01	TCGA-17-Z013-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:6588872C>A	uc001mdw.3	+	c.12133C>A	c.(12133-12135)CGC>AGC	p.R4045S	DNHD1_uc001mea.3_Missense_Mutation_p.R314S|DNHD1_uc001meb.2_Missense_Mutation_p.R313S|DNHD1_uc001mec.2_Missense_Mutation_p.R313S|DNHD1_uc010rao.1_Missense_Mutation_p.R303S|DNHD1_uc009yfg.2_5'Flank	NM_144666	NP_653267	Q96M86	DNHD1_HUMAN	dynein heavy chain domain 1 isoform 1	4045					microtubule-based movement	dynein complex	microtubule motor activity			ovary(2)	2		Medulloblastoma(188;0.00776)|all_neural(188;0.0652)|Breast(177;0.171)		Epithelial(150;3.93e-08)|BRCA - Breast invasive adenocarcinoma(625;0.13)										0.447368	53.071156	53.162712	17	21	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	6588872	6588872	4851	11	C	A	A	A	351	27	DNHD1	1	1
C11orf30	56946	broad.mit.edu	37	11	76248892	76248892	+	Missense_Mutation	SNP	A	G	G			TCGA-17-Z013-01	TCGA-17-Z013-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:76248892A>G	uc010rsb.1	+	c.2458A>G	c.(2458-2460)ATG>GTG	p.M820V	C11orf30_uc001oxl.2_Missense_Mutation_p.M805V|C11orf30_uc001oxm.2_Missense_Mutation_p.M721V|C11orf30_uc010rsc.1_Missense_Mutation_p.M820V|C11orf30_uc001oxn.2_Missense_Mutation_p.M806V|C11orf30_uc010rsd.1_Intron|C11orf30_uc001oxo.1_Missense_Mutation_p.M173V|C11orf30_uc010rse.1_Intron	NM_020193	NP_064578	Q7Z589	EMSY_HUMAN	EMSY protein	805					chromatin modification|DNA repair|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus				ovary(5)|skin(1)	6														0.483871	101.548566	101.562525	30	32	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	76248892	76248892	1674	11	A	G	G	G	52	4	C11orf30	4	4
EID3	493861	broad.mit.edu	37	12	104698108	104698108	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z013-01	TCGA-17-Z013-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:104698108G>A	uc001tkw.2	+	c.396G>A	c.(394-396)ATG>ATA	p.M132I	TXNRD1_uc010swk.1_Intron|TXNRD1_uc010swl.1_Intron|TXNRD1_uc010swm.1_Intron|TXNRD1_uc010swn.1_Intron|TXNRD1_uc010swo.1_Intron|TXNRD1_uc010swp.1_Intron|TXNRD1_uc010swq.1_Intron|TXNRD1_uc001tku.2_Intron|TXNRD1_uc001tko.1_Intron|TXNRD1_uc001tkp.1_Intron|TXNRD1_uc001tkv.1_Intron	NM_001008394	NP_001008395	Q8N140	EID3_HUMAN	EP300 interacting inhibitor of differentiation	132					regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus					0														0.056962	-14.261489	18.310978	9	149	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	104698108	104698108	5178	12	G	A	A	A	611	47	EID3	2	2
RFC5	5985	broad.mit.edu	37	12	118462732	118462732	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z013-01	TCGA-17-Z013-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:118462732G>T	uc001twq.2	+	c.498G>T	c.(496-498)CAG>CAT	p.Q166H	RFC5_uc010syx.1_Missense_Mutation_p.Q145H|RFC5_uc010syy.1_Missense_Mutation_p.Q145H|RFC5_uc010syz.1_Missense_Mutation_p.Q81H|RFC5_uc009zwr.2_Missense_Mutation_p.Q166H	NM_007370	NP_031396	P40937	RFC5_HUMAN	replication factor C 5 isoform 1	166					cell cycle checkpoint|DNA strand elongation involved in DNA replication|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	DNA replication factor C complex|nucleoplasm	ATP binding|DNA clamp loader activity|enzyme binding				0	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)													0.101449	6.075409	17.007051	7	62	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	118462732	118462732	13719	12	G	T	T	T	464	36	RFC5	2	2
ADAMTS20	80070	broad.mit.edu	37	12	43858449	43858449	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z013-01	TCGA-17-Z013-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:43858449C>A	uc010skx.1	-	c.1454G>T	c.(1453-1455)GGA>GTA	p.G485V		NM_025003	NP_079279	P59510	ATS20_HUMAN	a disintegrin-like and metalloprotease with	485	Disintegrin.					proteinaceous extracellular matrix	zinc ion binding			central_nervous_system(5)|ovary(4)|lung(3)|large_intestine(2)|skin(2)|urinary_tract(1)|kidney(1)|pancreas(1)	19	all_cancers(12;2.6e-05)|Lung SC(27;0.184)	Lung NSC(34;0.0569)|all_lung(34;0.129)		GBM - Glioblastoma multiforme(48;0.0473)						2149				0.393939	75.709126	76.333782	26	40	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	43858449	43858449	267	12	C	A	A	A	390	30	ADAMTS20	2	2
PIP4K2C	79837	broad.mit.edu	37	12	57992982	57992982	+	Silent	SNP	G	A	A			TCGA-17-Z013-01	TCGA-17-Z013-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:57992982G>A	uc001sou.2	+	c.648G>A	c.(646-648)AAG>AAA	p.K216K	PIP4K2C_uc001sot.2_Silent_p.K216K|PIP4K2C_uc010srs.1_Silent_p.K198K|PIP4K2C_uc010srt.1_Silent_p.K168K	NM_001146258	NP_001139730	Q8TBX8	PI42C_HUMAN	phosphatidylinositol-5-phosphate 4-kinase, type	216	PIPK.					cytoplasm|membrane	1-phosphatidylinositol-5-phosphate 4-kinase activity|ATP binding|identical protein binding			central_nervous_system(2)|lung(1)	3	Melanoma(17;0.122)									258				0.395833	54.343503	54.789326	19	29	KEEP	---	---	---	---	capture		Silent	SNP	57992982	57992982	12362	12	G	A	A	A	464	36	PIP4K2C	2	2
PTPRB	5787	broad.mit.edu	37	12	70983978	70983978	+	Missense_Mutation	SNP	T	C	C			TCGA-17-Z013-01	TCGA-17-Z013-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:70983978T>C	uc001swc.3	-	c.1816A>G	c.(1816-1818)AAT>GAT	p.N606D	PTPRB_uc001swb.3_Missense_Mutation_p.N388D|PTPRB_uc010sto.1_Missense_Mutation_p.N388D|PTPRB_uc010stp.1_Intron|PTPRB_uc001swa.3_Missense_Mutation_p.N606D|PTPRB_uc001swd.3_Missense_Mutation_p.N605D|PTPRB_uc009zrr.1_Missense_Mutation_p.N485D	NM_001109754	NP_001103224	P23467	PTPRB_HUMAN	protein tyrosine phosphatase, receptor type, B	388	Fibronectin type-III 5.|Extracellular (Potential).				angiogenesis	integral to plasma membrane	protein binding|transmembrane receptor protein tyrosine phosphatase activity			lung(2)|skin(1)	3	Renal(347;0.236)		GBM - Glioblastoma multiforme(2;2.17e-05)|Lung(24;0.000636)|OV - Ovarian serous cystadenocarcinoma(12;0.00306)|STAD - Stomach adenocarcinoma(21;0.149)									OREG0021990	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	0.449102	260.724944	261.09862	75	92	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	70983978	70983978	13253	12	T	C	C	C	793	61	PTPRB	4	4
MCF2L	23263	broad.mit.edu	37	13	113728838	113728838	+	Silent	SNP	C	T	T			TCGA-17-Z013-01	TCGA-17-Z013-01										Phase_I	Unspecified				Illumina GAIIx	g.chr13:113728838C>T	uc001vsu.2	+	c.1248C>T	c.(1246-1248)CAC>CAT	p.H416H	MCF2L_uc001vsq.2_Silent_p.H416H|MCF2L_uc010tjr.1_Silent_p.H359H|MCF2L_uc001vsr.2_Silent_p.H363H|MCF2L_uc001vss.3_Silent_p.H357H|MCF2L_uc010tjs.1_Silent_p.H357H|MCF2L_uc001vst.1_Silent_p.H321H	NM_001112732	NP_001106203	O15068	MCF2L_HUMAN	MCF.2 cell line derived transforming	389	Spectrin.				apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol|plasma membrane	Rho guanyl-nucleotide exchange factor activity			ovary(1)|kidney(1)	2	all_lung(23;0.000374)|Lung NSC(43;0.0107)|Lung SC(71;0.0753)|all_neural(89;0.0804)|Hepatocellular(20;0.0877)|Medulloblastoma(90;0.163)	all_cancers(25;0.118)|all_lung(25;0.0368)|all_epithelial(44;0.0396)|Lung NSC(25;0.129)|Breast(118;0.188)												0.62963	51.577923	51.97564	17	10	KEEP	---	---	---	---	capture		Silent	SNP	113728838	113728838	9768	13	C	T	T	T	233	18	MCF2L	2	2
PABPC3	5042	broad.mit.edu	37	13	25670848	25670848	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z013-01	TCGA-17-Z013-01										Phase_I	Unspecified				Illumina GAIIx	g.chr13:25670848G>T	uc001upy.2	+	c.512G>T	c.(511-513)GGA>GTA	p.G171V		NM_030979	NP_112241	Q9H361	PABP3_HUMAN	poly(A) binding protein, cytoplasmic 3	171	RRM 2.				mRNA metabolic process	cytoplasm	nucleotide binding|poly(A) RNA binding			ovary(3)|skin(1)	4		Lung SC(185;0.0225)|Breast(139;0.0602)		all cancers(112;0.0071)|Epithelial(112;0.0398)|OV - Ovarian serous cystadenocarcinoma(117;0.151)|GBM - Glioblastoma multiforme(144;0.222)|Lung(94;0.241)										0.164179	20.481361	27.658069	11	56	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	25670848	25670848	11780	13	G	T	T	T	533	41	PABPC3	2	2
AP4S1	11154	broad.mit.edu	37	14	31549850	31549850	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z013-01	TCGA-17-Z013-01										Phase_I	Unspecified				Illumina GAIIx	g.chr14:31549850G>T	uc001wqw.3	+	c.366G>T	c.(364-366)CAG>CAT	p.Q122H	AP4S1_uc001wqx.3_Missense_Mutation_p.Q122H|AP4S1_uc010amh.2_Intron|AP4S1_uc001wqy.3_Intron|AP4S1_uc001wqz.3_Intron	NM_007077	NP_009008	Q9Y587	AP4S1_HUMAN	adaptor-related protein complex 4, sigma 1	20						coated pit|Golgi apparatus	protein transporter activity				0	Hepatocellular(127;0.0877)|Breast(36;0.176)		LUAD - Lung adenocarcinoma(48;0.00292)|Lung(238;0.0164)|BRCA - Breast invasive adenocarcinoma(188;0.221)	GBM - Glioblastoma multiforme(265;0.00553)		Pancreas(128;620 2365 4508 44145)								0.103448	3.002651	7.543594	3	26	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	31549850	31549850	764	14	G	T	T	T	451	35	AP4S1	2	2
ZDHHC22	283576	broad.mit.edu	37	14	77600032	77600032	+	Missense_Mutation	SNP	A	T	T			TCGA-17-Z013-01	TCGA-17-Z013-01										Phase_I	Unspecified				Illumina GAIIx	g.chr14:77600032A>T	uc010asp.2	-	c.786T>A	c.(784-786)GAT>GAA	p.D262E		NM_174976	NP_777636	Q8N966	ZDH22_HUMAN	zinc finger, DHHC domain containing 22	262						integral to membrane	acyltransferase activity|zinc ion binding				0			Kidney(204;0.164)	BRCA - Breast invasive adenocarcinoma(234;0.0277)										0.542857	57.81055	57.865421	19	16	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	77600032	77600032	18201	14	A	T	T	T	206	16	ZDHHC22	3	3
NTRK3	4916	broad.mit.edu	37	15	88420187	88420187	+	Silent	SNP	G	T	T			TCGA-17-Z013-01	TCGA-17-Z013-01										Phase_I	Unspecified				Illumina GAIIx	g.chr15:88420187G>T	uc002bme.1	-	c.2499C>A	c.(2497-2499)ATC>ATA	p.I833I	NTRK3_uc002bmh.2_Silent_p.I811I|NTRK3_uc002bmf.1_Silent_p.I819I	NM_001012338	NP_001012338	Q16288	NTRK3_HUMAN	neurotrophic tyrosine kinase, receptor, type 3	833	Cytoplasmic (Potential).|Protein kinase.				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)			0.430556	92.412631	92.715674	31	41	KEEP	---	---	---	---	capture		Silent	SNP	88420187	88420187	11113	15	G	T	T	T	421	33	NTRK3	2	2
MAPK7	5598	broad.mit.edu	37	17	19284751	19284751	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z013-01	TCGA-17-Z013-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:19284751G>A	uc002gvn.2	+	c.1229G>A	c.(1228-1230)AGT>AAT	p.S410N	MAPK7_uc002gvo.2_Missense_Mutation_p.S271N|MAPK7_uc002gvq.2_Missense_Mutation_p.S410N|MAPK7_uc002gvp.2_Missense_Mutation_p.S410N	NM_139033	NP_620602	Q13164	MK07_HUMAN	mitogen-activated protein kinase 7 isoform 1	410	May not be required for kinase activity; required to stimulate MEF2C activity (By similarity).|Pro-rich.				cell cycle|cell differentiation|innate immune response|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|nerve growth factor receptor 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	cytosol|nucleoplasm	ATP binding|MAP kinase activity|protein binding			central_nervous_system(3)|lung(1)|skin(1)	5	all_cancers(12;2.87e-05)|all_epithelial(12;0.00114)|Hepatocellular(7;0.00345)|Breast(13;0.206)									176				0.16	3.698118	6.459772	4	21	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	19284751	19284751	9665	17	G	A	A	A	468	36	MAPK7	2	2
ABCA8	10351	broad.mit.edu	37	17	66917630	66917630	+	Missense_Mutation	SNP	A	G	G			TCGA-17-Z013-01	TCGA-17-Z013-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:66917630A>G	uc002jhq.2	-	c.1505T>C	c.(1504-1506)CTG>CCG	p.L502P	ABCA8_uc002jhp.2_Missense_Mutation_p.L502P|ABCA8_uc010wqq.1_Missense_Mutation_p.L502P|ABCA8_uc010wqr.1_Missense_Mutation_p.L441P|ABCA8_uc002jhr.2_Missense_Mutation_p.L502P	NM_007168	NP_009099	O94911	ABCA8_HUMAN	ATP-binding cassette, sub-family A member 8	502	ABC transporter 1.					integral to membrane|plasma membrane	ATP binding|ATPase activity, coupled to transmembrane movement of substances			ovary(2)	2	Breast(10;4.56e-13)													0.492537	111.474573	111.477803	33	34	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	66917630	66917630	39	17	A	G	G	G	91	7	ABCA8	4	4
SRP68	6730	broad.mit.edu	37	17	74035838	74035838	+	Silent	SNP	G	A	A			TCGA-17-Z013-01	TCGA-17-Z013-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:74035838G>A	uc002jqk.1	-	c.1833C>T	c.(1831-1833)ACC>ACT	p.T611T	SRP68_uc010wsu.1_Silent_p.T510T|SRP68_uc002jql.1_Silent_p.T573T|SRP68_uc002jqj.1_Silent_p.T272T	NM_014230	NP_055045	Q9UHB9	SRP68_HUMAN	signal recognition particle 68kDa	611					response to drug	cytosol|endoplasmic reticulum|nucleolus|ribosome|signal recognition particle, endoplasmic reticulum targeting	RNA binding|signal recognition particle binding			ovary(1)	1														0.470588	23.283268	23.29703	8	9	KEEP	---	---	---	---	capture		Silent	SNP	74035838	74035838	15670	17	G	A	A	A	600	47	SRP68	2	2
C18orf19	125228	broad.mit.edu	37	18	13681703	13681703	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z013-01	TCGA-17-Z013-01										Phase_I	Unspecified				Illumina GAIIx	g.chr18:13681703C>A	uc010dlh.2	-	c.374G>T	c.(373-375)CGA>CTA	p.R125L	C18orf19_uc010dlg.2_Missense_Mutation_p.R125L|C18orf19_uc010dli.2_Missense_Mutation_p.R125L|C18orf19_uc002ksj.3_Missense_Mutation_p.R125L|C18orf19_uc010dlj.2_Intron	NM_001098801	NP_001092271	Q96ND0	CR019_HUMAN	hypothetical protein LOC125228	125	DUF1279.					integral to membrane				breast(2)	2														0.089109	0.597819	17.82988	9	92	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	13681703	13681703	1957	18	C	A	A	A	403	31	C18orf19	1	1
HPN	3249	broad.mit.edu	37	19	35540199	35540199	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z013-01	TCGA-17-Z013-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:35540199C>T	uc002nxq.1	+	c.22C>T	c.(22-24)CGG>TGG	p.R8W	HPN_uc002nxr.1_Missense_Mutation_p.R8W|HPN_uc002nxs.1_Intron|HPN_uc010xsh.1_5'UTR|HPN_uc002nxt.1_5'Flank	NM_002151	NP_002142	P05981	HEPS_HUMAN	hepsin	8	Cytoplasmic (Potential).				cell growth|proteolysis	cytoplasm|integral to plasma membrane	scavenger receptor activity|serine-type endopeptidase activity			ovary(1)|central_nervous_system(1)	2	all_lung(56;5.38e-08)|Lung NSC(56;8.61e-08)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0849)		Coagulation factor VIIa(DB00036)									0.488636	132.741329	132.750271	43	45	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	35540199	35540199	7628	19	C	T	T	T	295	23	HPN	1	1
EIF4G3	8672	broad.mit.edu	37	1	21183973	21183973	+	Nonsense_Mutation	SNP	C	A	A			TCGA-17-Z013-01	TCGA-17-Z013-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:21183973C>A	uc001bef.2	-	c.3202G>T	c.(3202-3204)GAA>TAA	p.E1068*	EIF4G3_uc010odi.1_Nonsense_Mutation_p.E636*|EIF4G3_uc010odj.1_Nonsense_Mutation_p.E1031*|EIF4G3_uc009vpz.2_Nonsense_Mutation_p.E752*|EIF4G3_uc001bec.2_Nonsense_Mutation_p.E1032*|EIF4G3_uc001bed.2_Nonsense_Mutation_p.E1032*|EIF4G3_uc001bee.2_Nonsense_Mutation_p.E1038*	NM_003760	NP_003751	O43432	IF4G3_HUMAN	eukaryotic translation initiation factor 4	1032					interspecies interaction between organisms|regulation of translational initiation|RNA metabolic process	eukaryotic translation initiation factor 4F complex	protein binding|RNA cap binding|translation initiation factor activity				0		all_lung(284;2.61e-06)|Lung NSC(340;2.81e-06)|Colorectal(325;3.46e-05)|Renal(390;9.67e-05)|Breast(348;0.00149)|Ovarian(437;0.00338)|Myeloproliferative disorder(586;0.0256)		UCEC - Uterine corpus endometrioid carcinoma (279;0.023)|COAD - Colon adenocarcinoma(152;5.42e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000327)|GBM - Glioblastoma multiforme(114;0.000696)|Kidney(64;0.0018)|STAD - Stomach adenocarcinoma(196;0.00644)|KIRC - Kidney renal clear cell carcinoma(64;0.0185)|READ - Rectum adenocarcinoma(331;0.124)|Lung(427;0.191)										0.122396	66.946379	120.483079	47	337	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	21183973	21183973	5229	1	C	A	A	A	403	31	EIF4G3	5	1
SLC32A1	140679	broad.mit.edu	37	20	37353388	37353388	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z013-01	TCGA-17-Z013-01										Phase_I	Unspecified				Illumina GAIIx	g.chr20:37353388C>A	uc002xjc.2	+	c.21C>A	c.(19-21)AGC>AGA	p.S7R		NM_080552	NP_542119	Q9H598	VIAAT_HUMAN	solute carrier family 32, member 1	7	Cytoplasmic (Potential).				neurotransmitter secretion	clathrin sculpted gamma-aminobutyric acid transport vesicle membrane|integral to membrane|plasma membrane|synaptic vesicle membrane	vesicular hydrogen:amino acid antiporter activity				0		Myeloproliferative disorder(115;0.00878)			Glycine(DB00145)									0.12	3.707573	7.248922	3	22	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	37353388	37353388	15062	20	C	A	A	A	324	25	SLC32A1	2	2
PCK1	5105	broad.mit.edu	37	20	56139562	56139562	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z013-01	TCGA-17-Z013-01										Phase_I	Unspecified				Illumina GAIIx	g.chr20:56139562C>T	uc002xyn.3	+	c.1211C>T	c.(1210-1212)TCG>TTG	p.S404L	PCK1_uc010zzm.1_Missense_Mutation_p.S87L	NM_002591	NP_002582	P35558	PCKGC_HUMAN	cytosolic phosphoenolpyruvate carboxykinase 1	404	Substrate binding.				gluconeogenesis|glucose homeostasis|glycerol biosynthetic process from pyruvate|response to insulin stimulus	cytosol|nucleus	carboxylic acid binding|GTP binding|magnesium ion binding|manganese ion binding|phosphoenolpyruvate carboxykinase (GTP) activity				0	Lung NSC(12;0.000764)|all_lung(29;0.00264)|Melanoma(10;0.242)		BRCA - Breast invasive adenocarcinoma(13;9.88e-12)|Epithelial(14;3.41e-08)|all cancers(14;2.13e-07)											0.506494	121.427432	121.430331	39	38	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	56139562	56139562	12001	20	C	T	T	T	403	31	PCK1	1	1
SLC5A1	6523	broad.mit.edu	37	22	32500780	32500780	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z013-01	TCGA-17-Z013-01										Phase_I	Unspecified				Illumina GAIIx	g.chr22:32500780G>A	uc003amc.2	+	c.1673G>A	c.(1672-1674)CGT>CAT	p.R558H	SLC5A1_uc011alz.1_Missense_Mutation_p.R431H	NM_000343	NP_000334	P13866	SC5A1_HUMAN	solute carrier family 5 (sodium/glucose	558	Cytoplasmic (Potential).				carbohydrate metabolic process	integral to plasma membrane	glucose:sodium symporter activity|protein binding				0														0.894737	58.371731	61.22631	17	2	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	32500780	32500780	15158	22	G	A	A	A	520	40	SLC5A1	1	1
SLC4A10	57282	broad.mit.edu	37	2	162751304	162751304	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z013-01	TCGA-17-Z013-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:162751304G>T	uc002ubx.3	+	c.1310G>T	c.(1309-1311)CGA>CTA	p.R437L	SLC4A10_uc010fpa.1_Missense_Mutation_p.R449L|SLC4A10_uc010zcr.1_Non-coding_Transcript|SLC4A10_uc002uby.3_Missense_Mutation_p.R407L|SLC4A10_uc010zcs.1_Missense_Mutation_p.R418L	NM_022058	NP_071341	Q6U841	S4A10_HUMAN	solute carrier family 4, sodium bicarbonate	437	Cytoplasmic (Potential).				bicarbonate transport|chloride transport|sodium ion transport	integral to membrane|plasma membrane	inorganic anion exchanger activity|symporter activity			ovary(2)|lung(2)|pancreas(1)	5														0.149038	56.992443	81.567457	31	177	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	162751304	162751304	15148	2	G	T	T	T	481	37	SLC4A10	1	1
GCKR	2646	broad.mit.edu	37	2	27746251	27746251	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z013-01	TCGA-17-Z013-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:27746251C>T	uc002rky.2	+	c.1823C>T	c.(1822-1824)CCA>CTA	p.P608L	GCKR_uc010ezd.2_Missense_Mutation_p.P606L|GCKR_uc010ylu.1_Missense_Mutation_p.P418L	NM_001486	NP_001477	Q14397	GCKR_HUMAN	glucokinase regulatory protein	608					carbohydrate metabolic process|glucose transport|negative regulation of glucokinase activity|positive regulation of gene expression|protein import into nucleus, translocation|regulation of glucose transport|response to fructose stimulus|transmembrane transport|triglyceride homeostasis|urate metabolic process	cytosol|nucleoplasm	fructose-6-phosphate binding|protein binding			ovary(2)	2	Acute lymphoblastic leukemia(172;0.155)													0.410714	67.01176	67.402379	23	33	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	27746251	27746251	6560	2	C	T	T	T	273	21	GCKR	2	2
SUCLG1	8802	broad.mit.edu	37	2	84670519	84670519	+	Silent	SNP	G	A	A			TCGA-17-Z013-01	TCGA-17-Z013-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:84670519G>A	uc002son.2	-	c.207C>T	c.(205-207)ACC>ACT	p.T69T	SUCLG1_uc010ysk.1_Silent_p.T56T	NM_003849	NP_003840	P53597	SUCA_HUMAN	succinate-CoA ligase, GDP-forming alpha subunit	69					tricarboxylic acid cycle		ATP citrate synthase activity|GTP binding|succinate-CoA ligase (GDP-forming) activity				0					Succinic acid(DB00139)	Ovarian(48;203 1101 37206 40305 50790)								0.092593	4.233464	13.252421	5	49	KEEP	---	---	---	---	capture		Silent	SNP	84670519	84670519	15884	2	G	A	A	A	444	35	SUCLG1	2	2
TMEM131	23505	broad.mit.edu	37	2	98451367	98451367	+	Missense_Mutation	SNP	T	C	C			TCGA-17-Z013-01	TCGA-17-Z013-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:98451367T>C	uc002syh.3	-	c.826A>G	c.(826-828)AAG>GAG	p.K276E	TMEM131_uc010yvg.1_Non-coding_Transcript	NM_015348	NP_056163	Q92545	TM131_HUMAN	RW1 protein	276						integral to membrane				ovary(4)|central_nervous_system(2)	6														0.471074	173.955286	174.043941	57	64	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	98451367	98451367	16575	2	T	C	C	C	819	63	TMEM131	4	4
SLC25A36	55186	broad.mit.edu	37	3	140692807	140692807	+	Silent	SNP	C	T	T			TCGA-17-Z013-01	TCGA-17-Z013-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:140692807C>T	uc003etr.2	+	c.702C>T	c.(700-702)GCC>GCT	p.A234A	SLC25A36_uc003ets.2_Silent_p.A234A|SLC25A36_uc003etq.2_Silent_p.A77A|SLC25A36_uc011bmz.1_Silent_p.A208A	NM_001104647	NP_001098117	Q96CQ1	S2536_HUMAN	solute carrier family 25, member 36 isoform a	234	Solcar 3.|Helical; Name=5; (Potential).				response to estradiol stimulus|transmembrane transport	integral to membrane|mitochondrial inner membrane	binding				0														0.423729	78.465957	78.765291	25	34	KEEP	---	---	---	---	capture		Silent	SNP	140692807	140692807	14997	3	C	T	T	T	262	21	SLC25A36	2	2
WDR49	151790	broad.mit.edu	37	3	167240228	167240228	+	Missense_Mutation	SNP	T	A	A			TCGA-17-Z013-01	TCGA-17-Z013-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:167240228T>A	uc003fev.1	-	c.1593A>T	c.(1591-1593)AGA>AGT	p.R531S	WDR49_uc003feu.1_Missense_Mutation_p.R356S|WDR49_uc011bpd.1_Intron|WDR49_uc003few.1_Intron	NM_178824	NP_849146	Q8IV35	WDR49_HUMAN	WD repeat domain 49	531										large_intestine(1)|ovary(1)	2														0.577778	165.023931	165.50364	52	38	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	167240228	167240228	17875	3	T	A	A	A	699	54	WDR49	3	3
TTC14	151613	broad.mit.edu	37	3	180327571	180327571	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z013-01	TCGA-17-Z013-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:180327571G>T	uc003fkk.2	+	c.1554G>T	c.(1552-1554)AGG>AGT	p.R518S	TTC14_uc003fkl.2_3'UTR|TTC14_uc003fkm.2_Missense_Mutation_p.R518S	NM_133462	NP_597719	Q96N46	TTC14_HUMAN	tetratricopeptide repeat domain 14 isoform a	518	Ser-rich.						RNA binding			ovary(1)	1	all_cancers(143;9.31e-15)|Ovarian(172;0.0212)		OV - Ovarian serous cystadenocarcinoma(80;5.62e-23)|GBM - Glioblastoma multiforme(14;0.000558)											0.483333	172.604718	172.629812	58	62	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	180327571	180327571	17235	3	G	T	T	T	542	42	TTC14	2	2
KIAA1109	84162	broad.mit.edu	37	4	123192676	123192676	+	Nonsense_Mutation	SNP	C	G	G			TCGA-17-Z013-01	TCGA-17-Z013-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:123192676C>G	uc003ieh.2	+	c.7997C>G	c.(7996-7998)TCA>TGA	p.S2666*	KIAA1109_uc003iel.1_Nonsense_Mutation_p.S601*|KIAA1109_uc003iek.2_Nonsense_Mutation_p.S1285*	NM_015312	NP_056127	Q2LD37	K1109_HUMAN	fragile site-associated protein	2666					regulation of cell growth|regulation of epithelial cell differentiation	integral to membrane|nucleus				ovary(7)|central_nervous_system(1)|pancreas(1)	9														0.3	46.507173	48.293038	15	35	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	123192676	123192676	8516	4	C	G	G	G	377	29	KIAA1109	5	3
CRIPAK	285464	broad.mit.edu	37	4	1389279	1389279	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z013-01	TCGA-17-Z013-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:1389279G>A	uc003gdf.2	+	c.980G>A	c.(979-981)TGT>TAT	p.C327Y		NM_175918	NP_787114	Q8N1N5	CRPAK_HUMAN	cysteine-rich PAK1 inhibitor	327	9.				ER-nucleus signaling pathway|negative regulation of protein kinase activity|regulation of cytoskeleton organization|response to estrogen stimulus	endoplasmic reticulum|nucleus|plasma membrane	protein binding				0			OV - Ovarian serous cystadenocarcinoma(23;0.0106)											0.15	4.011099	6.361984	3	17	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	1389279	1389279	4016	4	G	A	A	A	624	48	CRIPAK	2	2
CLCN3	1182	broad.mit.edu	37	4	170618824	170618824	+	Nonsense_Mutation	SNP	G	A	A			TCGA-17-Z013-01	TCGA-17-Z013-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:170618824G>A	uc003ish.2	+	c.1502G>A	c.(1501-1503)TGG>TAG	p.W501*	CLCN3_uc003isi.2_Nonsense_Mutation_p.W501*|CLCN3_uc011cjz.1_Nonsense_Mutation_p.W484*|CLCN3_uc011cka.1_Nonsense_Mutation_p.W474*|CLCN3_uc003isj.1_Nonsense_Mutation_p.W474*	NM_173872	NP_776297	P51790	CLCN3_HUMAN	chloride channel 3 isoform e	501	Helical; (By similarity).				endosomal lumen acidification	cell surface|early endosome membrane|Golgi membrane|integral to membrane|late endosome membrane|transport vesicle membrane	antiporter activity|ATP binding|PDZ domain binding|protein heterodimerization activity|protein homodimerization activity|voltage-gated chloride channel activity			breast(2)|ovary(1)	3		Prostate(90;0.00601)|Renal(120;0.0183)		GBM - Glioblastoma multiforme(119;0.0233)|LUSC - Lung squamous cell carcinoma(193;0.131)										0.630252	247.082717	248.878055	75	44	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	170618824	170618824	3600	4	G	A	A	A	611	47	CLCN3	5	2
POLN	353497	broad.mit.edu	37	4	2073949	2073949	+	Silent	SNP	C	A	A			TCGA-17-Z013-01	TCGA-17-Z013-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:2073949C>A	uc003ger.2	-	c.2595G>T	c.(2593-2595)CCG>CCT	p.P865P	POLN_uc010icg.1_Silent_p.P304P	NM_181808	NP_861524	Q7Z5Q5	DPOLN_HUMAN	DNA-directed DNA polymerase nu	865					DNA repair|DNA replication	nucleus	DNA binding|DNA-directed DNA polymerase activity			kidney(2)|ovary(1)|skin(1)	4			OV - Ovarian serous cystadenocarcinoma(23;0.0955)											0.5	6.550803	6.550785	2	2	KEEP	---	---	---	---	capture		Silent	SNP	2073949	2073949	12635	4	C	A	A	A	340	27	POLN	1	1
HTT	3064	broad.mit.edu	37	4	3213834	3213834	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z013-01	TCGA-17-Z013-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:3213834C>T	uc011bvq.1	+	c.6599C>T	c.(6598-6600)CCG>CTG	p.P2200L		NM_002111	NP_002102	P42858	HD_HUMAN	huntingtin	2198					establishment of mitotic spindle orientation|Golgi organization|retrograde vesicle-mediated transport, Golgi to ER|vesicle transport along microtubule	autophagic vacuole|axon|cytoplasmic vesicle membrane|cytosol|dendrite|endoplasmic reticulum|Golgi apparatus|late endosome|membrane fraction|nucleus|protein complex	beta-tubulin binding|dynactin binding|dynein intermediate chain binding|p53 binding|transcription factor binding			ovary(1)|lung(1)	2		all_epithelial(65;0.18)		UCEC - Uterine corpus endometrioid carcinoma (64;0.187)										0.333333	18.046387	18.488005	6	12	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	3213834	3213834	7757	4	C	T	T	T	299	23	HTT	1	1
APC	324	broad.mit.edu	37	5	112174160	112174160	+	Nonsense_Mutation	SNP	A	T	T			TCGA-17-Z013-01	TCGA-17-Z013-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:112174160A>T	uc010jby.2	+	c.2869A>T	c.(2869-2871)AAG>TAG	p.K957*	APC_uc011cvt.1_Nonsense_Mutation_p.K939*|APC_uc003kpz.3_Nonsense_Mutation_p.K957*|APC_uc003kpy.3_Nonsense_Mutation_p.K957*|APC_uc010jbz.2_Nonsense_Mutation_p.K674*|APC_uc010jca.2_Nonsense_Mutation_p.K257*	NM_001127511	NP_001120983	P25054	APC_HUMAN	adenomatous polyposis coli	957	Ser-rich.				canonical Wnt receptor signaling pathway|cell adhesion|cell cycle arrest|cell migration|cellular component disassembly involved in apoptosis|cytokinesis after mitosis|mitotic cell cycle spindle assembly checkpoint|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of cyclin-dependent protein kinase activity|negative regulation of microtubule depolymerization|positive regulation of apoptosis|positive regulation of cell migration|positive regulation of protein catabolic process|positive regulation of pseudopodium assembly|protein complex assembly|regulation of attachment of spindle microtubules to kinetochore|response to DNA damage stimulus|tight junction assembly	adherens junction|APC-Axin-1-beta-catenin complex|Axin-APC-beta-catenin-GSK3B complex|beta-catenin destruction complex|centrosome|cytosol|kinetochore|lamellipodium|lateral plasma membrane|nucleus|ruffle membrane|tight junction	beta-catenin binding|gamma-catenin binding|microtubule plus-end binding|protein kinase binding|protein kinase regulator activity	p.?(1)		large_intestine(2012)|stomach(123)|soft_tissue(55)|small_intestine(34)|pancreas(25)|breast(23)|urinary_tract(20)|lung(18)|thyroid(18)|liver(13)|central_nervous_system(10)|ovary(9)|upper_aerodigestive_tract(6)|adrenal_gland(6)|NS(5)|bone(5)|skin(4)|prostate(4)|endometrium(3)|kidney(1)|oesophagus(1)|biliary_tract(1)	2396		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)		12		629	TSP Lung(16;0.13)			0.72973	91.740123	93.501306	27	10	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	112174160	112174160	773	5	A	T	T	T	65	5	APC	5	3
KCNMB1	3779	broad.mit.edu	37	5	169805873	169805873	+	Silent	SNP	G	A	A			TCGA-17-Z013-01	TCGA-17-Z013-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:169805873G>A	uc003maq.1	-	c.411C>T	c.(409-411)TCC>TCT	p.S137S	KCNIP1_uc003map.2_Intron	NM_004137	NP_004128	Q16558	KCMB1_HUMAN	potassium large conductance calcium-activated	137	Extracellular (Potential).				platelet activation|synaptic transmission		calcium-activated potassium channel activity|potassium channel regulator activity			ovary(2)	2	Renal(175;0.000159)|Lung NSC(126;0.0165)|all_lung(126;0.026)	Medulloblastoma(196;0.0109)|all_neural(177;0.0146)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	all cancers(165;0.175)										0.433333	80.446219	80.677385	26	34	KEEP	---	---	---	---	capture		Silent	SNP	169805873	169805873	8379	5	G	A	A	A	496	39	KCNMB1	1	1
ITGA2	3673	broad.mit.edu	37	5	52351368	52351368	+	Silent	SNP	A	G	G			TCGA-17-Z013-01	TCGA-17-Z013-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:52351368A>G	uc003joy.2	+	c.780A>G	c.(778-780)AGA>AGG	p.R260R	ITGA2_uc011cqa.1_Non-coding_Transcript|ITGA2_uc011cqb.1_Non-coding_Transcript|ITGA2_uc011cqc.1_Silent_p.R184R|ITGA2_uc011cqd.1_Non-coding_Transcript|ITGA2_uc011cqe.1_Non-coding_Transcript	NM_002203	NP_002194	P17301	ITA2_HUMAN	integrin alpha 2 precursor	260	Extracellular (Potential).|VWFA.				axon guidance|blood coagulation|cell-matrix adhesion|integrin-mediated signaling pathway|interspecies interaction between organisms|organ morphogenesis	integrin complex	collagen binding|identical protein binding|receptor activity			lung(1)	1		Lung NSC(810;3.11e-05)|Breast(144;0.014)|Prostate(461;0.0181)												0.78125	90.593341	92.927861	25	7	KEEP	---	---	---	---	capture		Silent	SNP	52351368	52351368	8179	5	A	G	G	G	115	9	ITGA2	4	4
DCBLD1	285761	broad.mit.edu	37	6	117859994	117859994	+	Missense_Mutation	SNP	A	G	G			TCGA-17-Z013-01	TCGA-17-Z013-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:117859994A>G	uc003pxs.2	+	c.972A>G	c.(970-972)ATA>ATG	p.I324M	GOPC_uc003pxq.1_Intron|DCBLD1_uc003pxr.1_Missense_Mutation_p.I324M|DCBLD1_uc003pxt.1_5'Flank	NM_173674	NP_775945	Q8N8Z6	DCBD1_HUMAN	discoidin, CUB and LCCL domain containing 1	324	F5/8 type C.|Extracellular (Potential).				cell adhesion	integral to membrane				ovary(1)	1		all_cancers(87;0.171)		GBM - Glioblastoma multiforme(226;0.0447)|OV - Ovarian serous cystadenocarcinoma(136;0.0921)|all cancers(137;0.125)						15				0.210526	9.889262	11.36236	4	15	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	117859994	117859994	4451	6	A	G	G	G	163	13	DCBLD1	4	4
KIF13A	63971	broad.mit.edu	37	6	17855807	17855807	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z013-01	TCGA-17-Z013-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:17855807G>T	uc003ncg.3	-	c.355C>A	c.(355-357)CTG>ATG	p.L119M	KIF13A_uc003ncf.2_Missense_Mutation_p.L119M|KIF13A_uc003nch.3_Missense_Mutation_p.L119M|KIF13A_uc003nci.3_Missense_Mutation_p.L119M	NM_022113	NP_071396	Q9H1H9	KI13A_HUMAN	kinesin family member 13A isoform a	119	Kinesin-motor.				cargo loading into vesicle|cell cycle|cytokinesis|endosome to lysosome transport|Golgi to plasma membrane protein transport|melanosome organization|plus-end-directed vesicle transport along microtubule	centrosome|endosome membrane|microtubule|midbody|trans-Golgi network membrane	ATP binding|microtubule motor activity|protein binding			large_intestine(2)|ovary(2)	4	Breast(50;0.0107)|Ovarian(93;0.016)	all_hematologic(90;0.125)	all cancers(50;0.0865)|Epithelial(50;0.0974)											0.0625	-3.0156	6.560381	3	45	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	17855807	17855807	8585	6	G	T	T	T	438	34	KIF13A	2	2
GPLD1	2822	broad.mit.edu	37	6	24436895	24436895	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z013-01	TCGA-17-Z013-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:24436895C>A	uc003ned.1	-	c.2267G>T	c.(2266-2268)GGC>GTC	p.G756V		NM_001503	NP_001494	P80108	PHLD_HUMAN	glycosylphosphatidylinositol specific	756	FG-GAP 6.					extracellular region	glycosylphosphatidylinositol phospholipase D activity			ovary(2)|kidney(1)	3														0.615385	119.889009	120.64283	40	25	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	24436895	24436895	6888	6	C	A	A	A	338	26	GPLD1	2	2
MET	4233	broad.mit.edu	37	7	116397814	116397814	+	Silent	SNP	A	T	T			TCGA-17-Z013-01	TCGA-17-Z013-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:116397814A>T	uc010lkh.2	+	c.2088A>T	c.(2086-2088)ACA>ACT	p.T696T	MET_uc003vij.2_Silent_p.T696T|MET_uc011kne.1_Silent_p.T668T|MET_uc011knf.1_Silent_p.T696T|MET_uc011kng.1_Silent_p.T696T|MET_uc011knh.1_Silent_p.T696T|MET_uc011kni.1_Silent_p.T696T|MET_uc011knj.1_Silent_p.T266T	NM_001127500	NP_001120972	P08581	MET_HUMAN	met proto-oncogene isoform a precursor	696	Extracellular (Potential).|IPT/TIG 2.				axon guidance|cell proliferation|protein phosphorylation	basal plasma membrane|integral to plasma membrane	ATP binding|hepatocyte growth factor receptor activity|protein binding			upper_aerodigestive_tract(63)|lung(41)|kidney(18)|ovary(5)|thyroid(4)|central_nervous_system(4)|stomach(3)|liver(3)|NS(3)|large_intestine(2)|testis(1)|breast(1)	148	all_cancers(3;1.25e-07)|all_epithelial(6;4.07e-08)|Lung NSC(10;0.00108)|all_lung(10;0.00125)	Ovarian(593;0.133)	GBM - Glioblastoma multiforme(2;2.31e-07)|all cancers(2;0.000419)|STAD - Stomach adenocarcinoma(10;0.000512)							299				0.361905	119.623596	121.384817	38	67	KEEP	---	---	---	---	capture		Silent	SNP	116397814	116397814	9874	7	A	T	T	T	93	8	MET	3	3
MEST	4232	broad.mit.edu	37	7	130137853	130137853	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z013-01	TCGA-17-Z013-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:130137853C>T	uc003vqg.2	+	c.338C>T	c.(337-339)CCG>CTG	p.P113L	MEST_uc003vqc.2_Missense_Mutation_p.P104L|MEST_uc003vqd.2_Missense_Mutation_p.P104L|MEST_uc003vqf.2_Missense_Mutation_p.P104L|MEST_uc011kph.1_Missense_Mutation_p.P99L|MEST_uc010lmg.2_Missense_Mutation_p.P113L	NM_002402	NP_002393	Q5EB52	MEST_HUMAN	mesoderm specific transcript isoform a	113					mesoderm development	endoplasmic reticulum membrane|integral to membrane	hydrolase activity|protein binding			ovary(2)	2	Melanoma(18;0.0435)					Colon(126;2182 2305 6517 35181)								0.366279	186.312219	189.002534	63	109	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	130137853	130137853	9873	7	C	T	T	T	299	23	MEST	1	1
POM121L12	285877	broad.mit.edu	37	7	53104228	53104228	+	Silent	SNP	C	T	T			TCGA-17-Z013-01	TCGA-17-Z013-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:53104228C>T	uc003tpz.2	+	c.864C>T	c.(862-864)ACC>ACT	p.T288T		NM_182595	NP_872401	Q8N7R1	P1L12_HUMAN	POM121 membrane glycoprotein-like 12	288											0														0.393939	76.996433	77.624704	26	40	KEEP	---	---	---	---	capture		Silent	SNP	53104228	53104228	12669	7	C	T	T	T	275	22	POM121L12	2	2
ZNF107	51427	broad.mit.edu	37	7	64168663	64168663	+	Nonsense_Mutation	SNP	G	T	T			TCGA-17-Z013-01	TCGA-17-Z013-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:64168663G>T	uc003ttd.2	+	c.1981G>T	c.(1981-1983)GAG>TAG	p.E661*	ZNF107_uc003tte.2_Nonsense_Mutation_p.E661*	NM_016220	NP_057304	Q9UII5	ZN107_HUMAN	zinc finger protein 107	661					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1		Lung NSC(55;0.00948)|all_lung(88;0.0249)												0.071429	-3.285003	9.971305	5	65	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	64168663	64168663	18306	7	G	T	T	T	429	33	ZNF107	5	2
CSMD1	64478	broad.mit.edu	37	8	3245077	3245077	+	Silent	SNP	G	A	A			TCGA-17-Z013-01	TCGA-17-Z013-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:3245077G>A	uc011kwk.1	-	c.2724C>T	c.(2722-2724)GAC>GAT	p.D908D	CSMD1_uc011kwj.1_Silent_p.D300D|CSMD1_uc003wqe.2_Silent_p.D64D	NM_033225	NP_150094	Q96PZ7	CSMD1_HUMAN	CUB and Sushi multiple domains 1 precursor	908	Extracellular (Potential).|Sushi 5.					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)										0.363636	10.696246	10.876483	4	7	KEEP	---	---	---	---	capture		Silent	SNP	3245077	3245077	4085	8	G	A	A	A	516	40	CSMD1	1	1
ST18	9705	broad.mit.edu	37	8	53071600	53071600	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z013-01	TCGA-17-Z013-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:53071600G>T	uc003xqz.2	-	c.1664C>A	c.(1663-1665)CCT>CAT	p.P555H	ST18_uc011ldq.1_Missense_Mutation_p.P202H|ST18_uc011ldr.1_Missense_Mutation_p.P520H|ST18_uc011lds.1_Missense_Mutation_p.P460H|ST18_uc003xra.2_Missense_Mutation_p.P555H|ST18_uc003xrb.2_Missense_Mutation_p.P555H	NM_014682	NP_055497	O60284	ST18_HUMAN	suppression of tumorigenicity 18	555						nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(4)	4		Lung NSC(129;0.131)|all_epithelial(80;0.217)|all_lung(136;0.229)												0.464286	78.054116	78.114902	26	30	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	53071600	53071600	15730	8	G	T	T	T	455	35	ST18	2	2
EYA1	2138	broad.mit.edu	37	8	72234494	72234494	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z013-01	TCGA-17-Z013-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:72234494C>T	uc003xys.3	-	c.212G>A	c.(211-213)AGC>AAC	p.S71N	EYA1_uc003xyr.3_Missense_Mutation_p.S71N|EYA1_uc003xyt.3_Missense_Mutation_p.S38N|EYA1_uc010lzf.2_5'UTR|EYA1_uc003xyu.2_Missense_Mutation_p.S71N|EYA1_uc011lfe.1_Missense_Mutation_p.S71N|EYA1_uc003xyv.2_5'UTR	NM_172058	NP_742055	Q99502	EYA1_HUMAN	eyes absent 1 isoform b	71					double-strand break repair|histone dephosphorylation|positive regulation of DNA repair|regulation of transcription, DNA-dependent|response to ionizing radiation|sensory perception of sound|transcription, DNA-dependent	cytoplasm|nucleus	metal ion binding|protein tyrosine phosphatase activity			ovary(2)|central_nervous_system(2)|upper_aerodigestive_tract(1)	5	Breast(64;0.046)		Epithelial(68;0.0837)|all cancers(69;0.247)											0.466667	162.067482	162.168973	49	56	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	72234494	72234494	5522	8	C	T	T	T	364	28	EYA1	2	2
GSN	2934	broad.mit.edu	37	9	124088878	124088878	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z013-01	TCGA-17-Z013-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:124088878G>A	uc004blf.1	+	c.1658G>A	c.(1657-1659)CGC>CAC	p.R553H	GSN_uc004bld.1_Missense_Mutation_p.R502H|GSN_uc010mvq.1_Missense_Mutation_p.R513H|GSN_uc010mvr.1_Missense_Mutation_p.R513H|GSN_uc010mvu.1_Missense_Mutation_p.R502H|GSN_uc010mvt.1_Missense_Mutation_p.R502H|GSN_uc010mvs.1_Missense_Mutation_p.R502H|GSN_uc004ble.1_Missense_Mutation_p.R502H|GSN_uc010mvv.1_Missense_Mutation_p.R502H|GSN_uc011lyh.1_Missense_Mutation_p.R519H|GSN_uc011lyi.1_Missense_Mutation_p.R502H|GSN_uc011lyj.1_Missense_Mutation_p.R526H|GSN_uc004blg.1_Missense_Mutation_p.R284H	NM_000177	NP_000168	P06396	GELS_HUMAN	gelsolin isoform a precursor	553	Actin-binding, Ca-sensitive (Potential).				actin filament polymerization|actin filament severing|barbed-end actin filament capping|cellular component disassembly involved in apoptosis|cilium morphogenesis	actin cytoskeleton|cytosol	actin binding|calcium ion binding|protein binding			breast(2)|ovary(1)	3														0.461538	15.133757	15.151719	6	7	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	124088878	124088878	7105	9	G	A	A	A	494	38	GSN	1	1
CERCAM	51148	broad.mit.edu	37	9	131193524	131193524	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z013-01	TCGA-17-Z013-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:131193524G>A	uc004buz.3	+	c.1145G>A	c.(1144-1146)CGC>CAC	p.R382H	CERCAM_uc004buy.1_Missense_Mutation_p.R304H|CERCAM_uc010mxz.2_Missense_Mutation_p.R304H|CERCAM_uc010mya.1_Missense_Mutation_p.R223H	NM_016174	NP_057258	Q5T4B2	GT253_HUMAN	cerebral endothelial cell adhesion molecule 1	382					cellular component movement|leukocyte cell-cell adhesion|lipopolysaccharide biosynthetic process	endoplasmic reticulum lumen|plasma membrane				pancreas(1)	1														0.103448	2.033383	6.548499	3	26	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	131193524	131193524	3399	9	G	A	A	A	494	38	CERCAM	1	1
NUP214	8021	broad.mit.edu	37	9	134077060	134077060	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z013-01	TCGA-17-Z013-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:134077060G>A	uc004cag.2	+	c.5548G>A	c.(5548-5550)GTG>ATG	p.V1850M	NUP214_uc004cah.2_Missense_Mutation_p.V1840M|NUP214_uc004cai.2_Missense_Mutation_p.V1280M|NUP214_uc010mzg.2_Non-coding_Transcript|NUP214_uc011mcg.1_Missense_Mutation_p.V676M	NM_005085	NP_005076	P35658	NU214_HUMAN	nucleoporin 214kDa	1850	Pro/Ser/Thr-rich.|11 X 3 AA approximate repeats.|11 X 5 AA approximate repeats.|18 X 4 AA approximate repeats.				carbohydrate metabolic process|glucose transport|mRNA metabolic process|protein export from nucleus|regulation of glucose transport|transmembrane transport|viral reproduction	cytosol|nuclear pore|nucleoplasm	protein binding			breast(3)|ovary(2)|lung(1)|central_nervous_system(1)	7	all_hematologic(7;0.0028)	Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;3.42e-05)|Epithelial(140;0.000256)		Pancreas(4;24 48 25510 30394 32571)				1058				0.318182	20.116807	20.763462	7	15	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	134077060	134077060	11167	9	G	A	A	A	624	48	NUP214	2	2
DCAF12	25853	broad.mit.edu	37	9	34125044	34125044	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z013-01	TCGA-17-Z013-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:34125044C>A	uc003ztt.2	-	c.310G>T	c.(310-312)GTG>TTG	p.V104L		NM_015397	NP_056212	Q5T6F0	DCA12_HUMAN	DDB1 and CUL4 associated factor 12	104					protein ubiquitination	centrosome|CUL4 RING ubiquitin ligase complex					0														0.081967	0.130969	10.978762	5	56	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	34125044	34125044	4434	9	C	A	A	A	234	18	DCAF12	2	2
ZDHHC9	51114	broad.mit.edu	37	X	128946792	128946792	+	Missense_Mutation	SNP	G	C	C			TCGA-17-Z013-01	TCGA-17-Z013-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:128946792G>C	uc004euv.2	-	c.679C>G	c.(679-681)CTA>GTA	p.L227V	ZDHHC9_uc004euw.2_Missense_Mutation_p.L227V	NM_001008222	NP_001008223	Q9Y397	ZDHC9_HUMAN	zinc finger, DHHC domain containing 9	227	Lumenal (Potential).					endoplasmic reticulum membrane|Golgi membrane|integral to membrane	acyltransferase activity|zinc ion binding			ovary(1)	1														0.255474	102.060688	109.490017	35	102	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	128946792	128946792	18210	23	G	C	C	C	425	33	ZDHHC9	3	3
GPR112	139378	broad.mit.edu	37	X	135429458	135429458	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z013-01	TCGA-17-Z013-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:135429458C>A	uc004ezu.1	+	c.3593C>A	c.(3592-3594)GCC>GAC	p.A1198D	GPR112_uc010nsb.1_Missense_Mutation_p.A993D|GPR112_uc010nsc.1_Missense_Mutation_p.A965D	NM_153834	NP_722576	Q8IZF6	GP112_HUMAN	G-protein coupled receptor 112	1198	Extracellular (Potential).				neuropeptide signaling pathway	integral to membrane|plasma membrane	G-protein coupled receptor activity			ovary(5)|large_intestine(2)|lung(1)|breast(1)|skin(1)|pancreas(1)	11	Acute lymphoblastic leukemia(192;0.000127)									487				0.277027	204.771377	217.989112	82	214	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	135429458	135429458	6903	23	C	A	A	A	338	26	GPR112	2	2
PASD1	139135	broad.mit.edu	37	X	150789453	150789453	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z013-01	TCGA-17-Z013-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:150789453G>A	uc004fev.3	+	c.259G>A	c.(259-261)GAT>AAT	p.D87N		NM_173493	NP_775764	Q8IV76	PASD1_HUMAN	PAS domain containing 1	87	PAS.					nucleus	signal transducer activity			ovary(3)	3	Acute lymphoblastic leukemia(192;6.56e-05)													0.485876	277.439164	277.47006	86	91	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	150789453	150789453	11888	23	G	A	A	A	429	33	PASD1	2	2
MAGEA12	4111	broad.mit.edu	37	X	151900189	151900189	+	Silent	SNP	G	A	A			TCGA-17-Z013-01	TCGA-17-Z013-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:151900189G>A	uc010ntp.2	-	c.612C>T	c.(610-612)ATC>ATT	p.I204I	MAGEA12_uc004fgb.2_Intron|MAGEA12_uc004fgc.2_Silent_p.I204I	NM_005367	NP_005358	P43365	MAGAC_HUMAN	melanoma antigen family A, 12	204	MAGE.										0	Acute lymphoblastic leukemia(192;6.56e-05)													0.060403	-12.594195	17.455515	9	140	KEEP	---	---	---	---	capture		Silent	SNP	151900189	151900189	9543	23	G	A	A	A	473	37	MAGEA12	1	1
MAGEA1	4100	broad.mit.edu	37	X	152482654	152482654	+	Silent	SNP	G	T	T			TCGA-17-Z013-01	TCGA-17-Z013-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:152482654G>T	uc004fhf.2	-	c.357C>A	c.(355-357)GCC>GCA	p.A119A		NM_004988	NP_004979	P43355	MAGA1_HUMAN	melanoma antigen family A, 1	119	MAGE.					cytoplasm|plasma membrane				central_nervous_system(7)|ovary(1)|lung(1)|breast(1)	10	all_hematologic(71;4.25e-06)|Acute lymphoblastic leukemia(192;6.56e-05)													0.274194	45.459412	48.300234	17	45	KEEP	---	---	---	---	capture		Silent	SNP	152482654	152482654	9540	23	G	T	T	T	600	47	MAGEA1	2	2
F8	2157	broad.mit.edu	37	X	154159070	154159070	+	Nonsense_Mutation	SNP	C	A	A			TCGA-17-Z013-01	TCGA-17-Z013-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:154159070C>A	uc004fmt.2	-	c.2995G>T	c.(2995-2997)GGA>TGA	p.G999*		NM_000132	NP_000123	P00451	FA8_HUMAN	coagulation factor VIII isoform a precursor	999	B.				acute-phase response|blood coagulation, intrinsic pathway|cell adhesion|oxidation-reduction process|platelet activation|platelet degranulation	extracellular space|plasma membrane|platelet alpha granule lumen	copper ion binding|oxidoreductase activity|protein binding			ovary(5)|large_intestine(2)|pancreas(2)|upper_aerodigestive_tract(1)|skin(1)	11	all_cancers(53;7.19e-17)|all_epithelial(53;9.83e-11)|all_lung(58;6.63e-07)|Lung NSC(58;2.08e-06)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)|Renal(33;0.214)				Antihemophilic Factor(DB00025)|Coagulation Factor IX(DB00100)|Drotrecogin alfa(DB00055)					359				0.268293	59.319138	63.289552	22	60	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	154159070	154159070	5544	23	C	A	A	A	273	21	F8	5	2
DCAF8L1	139425	broad.mit.edu	37	X	27998441	27998441	+	Silent	SNP	C	A	A			TCGA-17-Z013-01	TCGA-17-Z013-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:27998441C>A	uc004dbx.1	-	c.1011G>T	c.(1009-1011)CTG>CTT	p.L337L		NM_001017930	NP_001017930	A6NGE4	DC8L1_HUMAN	DDB1 and CUL4 associated factor 8-like 1	337	WD 4.									ovary(3)	3														0.205882	33.110807	38.565863	14	54	KEEP	---	---	---	---	capture		Silent	SNP	27998441	27998441	4448	23	C	A	A	A	210	17	DCAF8L1	2	2
KDM5C	8242	broad.mit.edu	37	X	53239738	53239738	+	Missense_Mutation	SNP	T	C	C			TCGA-17-Z013-01	TCGA-17-Z013-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:53239738T>C	uc004drz.2	-	c.1604A>G	c.(1603-1605)TAT>TGT	p.Y535C	KDM5C_uc011moc.1_Non-coding_Transcript|KDM5C_uc011mod.1_Missense_Mutation_p.Y468C|KDM5C_uc004dsa.2_Missense_Mutation_p.Y534C	NM_004187	NP_004178	P41229	KDM5C_HUMAN	jumonji, AT rich interactive domain 1C isoform	535	JmjC.				chromatin modification|oxidation-reduction process|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|protein binding|zinc ion binding	p.W534*(1)		kidney(9)|ovary(5)|salivary_gland(1)|autonomic_ganglia(1)|haematopoietic_and_lymphoid_tissue(1)|oesophagus(1)	18														0.149254	17.848769	25.883398	10	57	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	53239738	53239738	8441	23	T	C	C	C	637	49	KDM5C	4	4
PJA1	64219	broad.mit.edu	37	X	68381557	68381557	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z013-01	TCGA-17-Z013-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:68381557C>A	uc004dxh.2	-	c.1525G>T	c.(1525-1527)GTG>TTG	p.V509L	PJA1_uc011mpi.1_Missense_Mutation_p.V227L|PJA1_uc004dxg.2_Missense_Mutation_p.V321L|PJA1_uc004dxi.2_Missense_Mutation_p.V454L	NM_145119	NP_660095	Q8NG27	PJA1_HUMAN	praja 1 isoform a	509							zinc ion binding				0														0.208333	23.925548	27.706209	10	38	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	68381557	68381557	12385	23	C	A	A	A	260	20	PJA1	2	2
IL2RG	3561	broad.mit.edu	37	X	70331304	70331304	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z013-01	TCGA-17-Z013-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:70331304G>A	uc004dyw.1	-	c.86C>T	c.(85-87)ACG>ATG	p.T29M	IL2RG_uc004dyv.1_5'Flank|IL2RG_uc004dyx.1_De_novo_Start_OutOfFrame	NM_000206	NP_000197	P31785	IL2RG_HUMAN	interleukin 2 receptor, gamma precursor	29	Extracellular (Potential).				immune response|interleukin-4-mediated signaling pathway|interspecies interaction between organisms	external side of plasma membrane|integral to plasma membrane	cytokine receptor activity|interleukin-2 binding			pancreas(1)	1	Renal(35;0.156)				Aldesleukin(DB00041)|Denileukin diftitox(DB00004)									0.085366	1.469039	15.758315	7	75	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	70331304	70331304	7989	23	G	A	A	A	520	40	IL2RG	1	1
CHM	1121	broad.mit.edu	37	X	85233809	85233809	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z013-01	TCGA-17-Z013-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:85233809G>T	uc004eet.2	-	c.276C>A	c.(274-276)GAC>GAA	p.D92E	CHM_uc011mqz.1_Intron|CHM_uc004eeu.3_Non-coding_Transcript|CHM_uc004eev.3_Missense_Mutation_p.D92E	NM_000390	NP_000381	P24386	RAE1_HUMAN	choroideremia isoform a	92					intracellular protein transport|protein geranylgeranylation|response to stimulus|visual perception	Rab-protein geranylgeranyltransferase complex	GTPase activator activity|Rab geranylgeranyltransferase activity			ovary(1)	1		all_lung(315;5.41e-06)												0.212766	25.323808	28.906995	10	37	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	85233809	85233809	3484	23	G	T	T	T	620	48	CHM	2	2
EPS8	2059	broad.mit.edu	37	12	15834162	15834163	+	Frame_Shift_Ins	INS	-	A	A			TCGA-17-Z013-01	TCGA-17-Z013-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:15834162_15834163insA	uc009zif.2	-	c.133_134insT	c.(133-135)TATfs	p.Y45fs	EPS8_uc001rdb.2_Frame_Shift_Ins_p.Y45fs|EPS8_uc009zig.2_De_novo_Start_OutOfFrame	NM_004447	NP_004438	Q12929	EPS8_HUMAN	epidermal growth factor receptor pathway	45					cell proliferation|epidermal growth factor receptor signaling pathway		SH3/SH2 adaptor activity			ovary(2)	2		all_epithelial(100;1.87e-05)|Breast(259;0.000286)|Hepatocellular(102;0.244)		BRCA - Breast invasive adenocarcinoma(232;4.29e-05)|GBM - Glioblastoma multiforme(207;0.0264)										0.39			45	71		---	---	---	---	capture_indel		Frame_Shift_Ins	INS	15834162	15834163	5387	12	-	A	A	A	637	49	EPS8	5	5
SERPINB4	6318	broad.mit.edu	37	18	61324514	61324515	+	Frame_Shift_Ins	INS	-	A	A			TCGA-17-Z013-01	TCGA-17-Z013-01										Phase_I	Unspecified				Illumina GAIIx	g.chr18:61324514_61324515insA	uc002ljg.2	-	c.601_602insT	c.(601-603)TGGfs	p.W201fs	SERPINB3_uc002lji.2_Frame_Shift_Ins_p.W201fs|SERPINB3_uc010dqa.2_Frame_Shift_Ins_p.W201fs	SERPINB4		P48594	SPB4_HUMAN	SubName: Full=Squamous cell carcinoma antigen 2;	201					immune response|regulation of proteolysis	cytoplasm|extracellular region	protein binding|serine-type endopeptidase inhibitor activity			ovary(1)|lung(1)	2										163				0.44			18	23		---	---	---	---	capture_indel		Frame_Shift_Ins	INS	61324514	61324515	14591	18	-	A	A	A	273	21	SERPINB4	5	5
SOX13	9580	broad.mit.edu	37	1	204091465	204091466	+	Frame_Shift_Ins	INS	-	C	C			TCGA-17-Z013-01	TCGA-17-Z013-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:204091465_204091466insC	uc001ham.2	+	c.962_963insC	c.(961-963)CGCfs	p.R321fs	SOX13_uc010pqp.1_Frame_Shift_Ins_p.R320fs|SOX13_uc010pqq.1_Frame_Shift_Ins_p.R188fs	NM_005686	NP_005677	Q9UN79	SOX13_HUMAN	SRY-box 13	321	Pro-rich.				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)											0.33			2	4		---	---	---	---	capture_indel		Frame_Shift_Ins	INS	204091465	204091466	15444	1	-	C	C	C	494	38	SOX13	5	5
AFF3	3899	broad.mit.edu	37	2	100210335	100210340	+	In_Frame_Del	DEL	GGCTGA	-	-			TCGA-17-Z013-01	TCGA-17-Z013-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:100210335_100210340delGGCTGA	uc002taf.2	-	c.1858_1863delTCAGCC	c.(1858-1863)TCAGCCdel	p.SA620del	AFF3_uc002tag.2_In_Frame_Del_p.SA595del|AFF3_uc010fiq.1_In_Frame_Del_p.SA595del|AFF3_uc010yvr.1_In_Frame_Del_p.SA748del|AFF3_uc002tah.1_In_Frame_Del_p.SA620del	NM_001025108	NP_001020279	P51826	AFF3_HUMAN	AF4/FMR2 family, member 3 isoform 2	595_596					multicellular organismal development|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding			ovary(2)|pancreas(1)|lung(1)|kidney(1)|skin(1)	6										693				0.33			2	4		---	---	---	---	capture_indel		In_Frame_Del	DEL	100210335	100210340	359	2	GGCTGA	-	-	-	496	39	AFF3	5	5
LRP1B	53353	broad.mit.edu	37	2	141665648	141665648	+	Splice_Site_Del	DEL	T	-	-			TCGA-17-Z013-01	TCGA-17-Z013-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:141665648_141665648delT	uc002tvj.1	-	c.3320_splice	c.e22-1	p.G1107_splice	LRP1B_uc010fnl.1_Splice_Site_Del_p.G289_splice	NM_018557	NP_061027			low density lipoprotein-related protein 1B						protein transport|receptor-mediated endocytosis	integral to membrane	calcium ion binding			lung(17)|ovary(10)|pancreas(3)|central_nervous_system(2)|liver(1)|kidney(1)	34		all_cancers(3;1.1e-60)|all_epithelial(3;1.94e-59)|all_lung(3;1.09e-24)|Lung NSC(3;5.65e-24)|Esophageal squamous(3;5.41e-13)|Renal(3;0.000147)|Breast(3;0.000527)|Hepatocellular(3;0.011)|all_neural(3;0.014)|Colorectal(150;0.101)		UCEC - Uterine corpus endometrioid carcinoma (2;0.00139)|Epithelial(1;1.25e-24)|all cancers(1;8.86e-24)|OV - Ovarian serous cystadenocarcinoma(1;2.45e-12)|LUSC - Lung squamous cell carcinoma(1;2.97e-10)|Lung(1;6.05e-09)|BRCA - Breast invasive adenocarcinoma(221;0.0103)		Colon(99;50 2074 2507 20106)				2546	TSP Lung(27;0.18)			0.48			21	23		---	---	---	---	capture_indel		Splice_Site_Del	DEL	141665648	141665648	9328	2	T	-	-	-	728	56	LRP1B	5	5
KLHL15	80311	broad.mit.edu	37	X	24006703	24006703	+	Frame_Shift_Del	DEL	C	-	-			TCGA-17-Z013-01	TCGA-17-Z013-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:24006703_24006703delC	uc004dba.3	-	c.1150_1150delG	c.(1150-1152)GTAfs	p.V384fs		NM_030624	NP_085127	Q96M94	KLH15_HUMAN	kelch-like 15	384	Kelch 2.									ovary(1)|breast(1)	2														0.56			63	50		---	---	---	---	capture_indel		Frame_Shift_Del	DEL	24006703	24006703	8683	23	C	-	-	-	247	19	KLHL15	5	5
