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
C10orf137	26098	broad.mit.edu	37	10	127429728	127429728	+	Nonsense_Mutation	SNP	C	T	T			TCGA-05-4434-01	TCGA-05-4434-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:127429728C>T	uc001liq.1	+	c.2329C>T	c.(2329-2331)CAG>TAG	p.Q777*	C10orf137_uc001lin.2_Nonsense_Mutation_p.Q743*|C10orf137_uc001lio.1_Nonsense_Mutation_p.Q743*|C10orf137_uc001lip.1_Nonsense_Mutation_p.Q481*|C10orf137_uc001lir.2_Nonsense_Mutation_p.Q271*|C10orf137_uc001lis.1_Nonsense_Mutation_p.Q103*	NM_015608	NP_056423	Q3B7T1	EDRF1_HUMAN	erythroid differentiation-related factor 1	777					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	binding			ovary(5)|large_intestine(3)	8		all_lung(145;0.0096)|Lung NSC(174;0.0145)|Colorectal(57;0.0846)|all_neural(114;0.0936)												0.125984	15.701593	33.063876	16	111	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	127429728	127429728	1631	10	C	T	T	T	273	21	C10orf137	5	2
SLC22A6	9356	broad.mit.edu	37	11	62752036	62752036	+	Missense_Mutation	SNP	C	T	T			TCGA-05-4434-01	TCGA-05-4434-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:62752036C>T	uc001nwk.2	-	c.127G>A	c.(127-129)GCC>ACC	p.A43T	SLC22A6_uc001nwl.2_Missense_Mutation_p.A43T|SLC22A6_uc001nwj.2_Missense_Mutation_p.A43T|SLC22A6_uc001nwm.2_Missense_Mutation_p.A43T	NM_004790	NP_004781	Q4U2R8	S22A6_HUMAN	solute carrier family 22 member 6 isoform a	43	Extracellular (Potential).				alpha-ketoglutarate transport	basolateral plasma membrane|integral to plasma membrane|membrane fraction	inorganic anion exchanger activity|protein binding				0														0.088235	0.496835	6.327448	3	31	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	62752036	62752036	14955	11	C	T	T	T	325	25	SLC22A6	2	2
ERBB3	2065	broad.mit.edu	37	12	56489568	56489568	+	Missense_Mutation	SNP	G	A	A			TCGA-05-4434-01	TCGA-05-4434-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:56489568G>A	uc001sjh.2	+	c.2033G>A	c.(2032-2034)AGG>AAG	p.R678K	ERBB3_uc009zoj.2_Intron|ERBB3_uc010sqb.1_Missense_Mutation_p.R35K|ERBB3_uc010sqc.1_Missense_Mutation_p.R619K|ERBB3_uc009zok.2_Missense_Mutation_p.R120K|ERBB3_uc001sjk.2_5'Flank	NM_001982	NP_001973	P21860	ERBB3_HUMAN	erbB-3 isoform 1 precursor	678	Cytoplasmic (Potential).				cranial nerve development|heart development|negative regulation of cell adhesion|negative regulation of neuron apoptosis|negative regulation of secretion|negative regulation of signal transduction|neuron apoptosis|phosphatidylinositol 3-kinase cascade|positive regulation of phosphatidylinositol 3-kinase cascade|protein phosphorylation|regulation of cell proliferation|Schwann cell differentiation|transmembrane receptor protein tyrosine kinase signaling pathway|wound healing	basolateral plasma membrane|extracellular space|integral to plasma membrane|receptor complex	ATP binding|growth factor binding|protein heterodimerization activity|protein homodimerization activity|protein tyrosine kinase activator activity|receptor signaling protein tyrosine kinase activity|transmembrane receptor protein tyrosine kinase activity			lung(3)|central_nervous_system(2)|stomach(1)|ovary(1)|skin(1)	8			OV - Ovarian serous cystadenocarcinoma(18;0.112)							322				0.109589	20.988757	43.021098	16	130	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	56489568	56489568	5401	12	G	A	A	A	455	35	ERBB3	2	2
STAC3	246329	broad.mit.edu	37	12	57641974	57641974	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4434-01	TCGA-05-4434-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:57641974C>A	uc001snp.2	-	c.440G>T	c.(439-441)GGT>GTT	p.G147V	STAC3_uc009zpl.2_5'UTR|STAC3_uc001snq.2_Missense_Mutation_p.G108V|STAC3_uc010srm.1_5'UTR	NM_145064	NP_659501	Q96MF2	STAC3_HUMAN	SH3 and cysteine rich domain 3	147					intracellular signal transduction		identical protein binding|metal ion binding			ovary(2)	2														0.312057	116.930169	121.375626	44	97	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	57641974	57641974	15759	12	C	A	A	A	234	18	STAC3	2	2
CD4	920	broad.mit.edu	37	12	6925422	6925422	+	Missense_Mutation	SNP	C	T	T			TCGA-05-4434-01	TCGA-05-4434-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:6925422C>T	uc001qqv.1	+	c.808C>T	c.(808-810)CCT>TCT	p.P270S	CD4_uc009zez.1_3'UTR|CD4_uc009zfa.1_Non-coding_Transcript|CD4_uc009zfb.1_Non-coding_Transcript|CD4_uc010sfj.1_5'UTR|CD4_uc009zfc.1_Missense_Mutation_p.P91S|CD4_uc010sfk.1_5'UTR|CD4_uc010sfl.1_5'UTR|CD4_uc010sfm.1_5'UTR	NM_000616	NP_000607	P01730	CD4_HUMAN	CD4 antigen precursor	270	Extracellular (Potential).|Ig-like C2-type 2.				cell adhesion|entry into host cell|immune response|induction by virus of host cell-cell fusion|initiation of viral infection|maintenance of protein location in cell|positive regulation of interleukin-2 biosynthetic process|positive regulation of protein kinase activity|protein palmitoleylation|regulation of defense response to virus by virus|T cell costimulation|T cell receptor signaling pathway|T cell selection|transmembrane receptor protein tyrosine kinase signaling pathway	early endosome|endoplasmic reticulum membrane|integral to membrane|T cell receptor complex	coreceptor activity|extracellular matrix structural constituent|glycoprotein binding|MHC class II protein binding|protein homodimerization activity|protein kinase binding|transmembrane receptor activity|zinc ion binding				0		Myeloproliferative disorder(1001;0.0122)												0.363636	141.672986	143.828775	48	84	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	6925422	6925422	3142	12	C	T	T	T	286	22	CD4	2	2
PCDH9	5101	broad.mit.edu	37	13	67801491	67801491	+	Missense_Mutation	SNP	C	T	T			TCGA-05-4434-01	TCGA-05-4434-01										Phase_I	Unspecified				Illumina GAIIx	g.chr13:67801491C>T	uc001vik.2	-	c.1082G>A	c.(1081-1083)AGG>AAG	p.R361K	PCDH9_uc001vil.2_Missense_Mutation_p.R361K|PCDH9_uc010thl.1_Missense_Mutation_p.R361K|PCDH9_uc001vin.3_Missense_Mutation_p.R361K	NM_203487	NP_982354	Q9HC56	PCDH9_HUMAN	protocadherin 9 isoform 1 precursor	361	Extracellular (Potential).				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(4)|pancreas(1)	5		Hepatocellular(98;0.0906)|Breast(118;0.107)		GBM - Glioblastoma multiforme(99;0.00819)										0.032847	-47.998316	17.537024	9	265	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	67801491	67801491	11938	13	C	T	T	T	312	24	PCDH9	2	2
RPS6KA5	9252	broad.mit.edu	37	14	91389482	91389482	+	Missense_Mutation	SNP	C	G	G			TCGA-05-4434-01	TCGA-05-4434-01										Phase_I	Unspecified				Illumina GAIIx	g.chr14:91389482C>G	uc001xys.2	-	c.677G>C	c.(676-678)AGA>ACA	p.R226T	RPS6KA5_uc010twi.1_Missense_Mutation_p.R147T|RPS6KA5_uc001xyt.2_Missense_Mutation_p.R226T|RPS6KA5_uc010att.1_Non-coding_Transcript	NM_004755	NP_004746	O75582	KS6A5_HUMAN	ribosomal protein S6 kinase, polypeptide 5	226	Protein kinase 1.				axon guidance|epidermal growth factor receptor signaling pathway|histone phosphorylation|innate immune response|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|nerve growth factor receptor signaling pathway|regulation of transcription, DNA-dependent|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	cytoplasm|nucleoplasm	ATP binding|magnesium ion binding|protein binding|protein serine/threonine kinase activity			ovary(1)	1		all_cancers(154;0.0148)|Melanoma(154;0.099)|all_epithelial(191;0.146)		Epithelial(152;0.182)|BRCA - Breast invasive adenocarcinoma(234;0.201)						302				0.045045	-11.126384	13.433667	5	106	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	91389482	91389482	14134	14	C	G	G	G	416	32	RPS6KA5	3	3
ALDH1A3	220	broad.mit.edu	37	15	101433167	101433167	+	Missense_Mutation	SNP	T	A	A			TCGA-05-4434-01	TCGA-05-4434-01										Phase_I	Unspecified				Illumina GAIIx	g.chr15:101433167T>A	uc002bwn.3	+	c.493T>A	c.(493-495)TTC>ATC	p.F165I	ALDH1A3_uc010bpb.2_Intron	NM_000693	NP_000684	P47895	AL1A3_HUMAN	aldehyde dehydrogenase 1A3	165					oxidation-reduction process|retinal metabolic process	cytoplasm	protein homodimerization activity			central_nervous_system(2)|lung(1)|pancreas(1)	4	Lung NSC(78;0.00144)|all_lung(78;0.0018)|Melanoma(26;0.00852)		OV - Ovarian serous cystadenocarcinoma(32;0.000932)|LUSC - Lung squamous cell carcinoma(107;0.0766)|Lung(145;0.103)		NADH(DB00157)|Vitamin A(DB00162)									0.252174	71.515806	77.934099	29	86	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	101433167	101433167	495	15	T	A	A	A	728	56	ALDH1A3	3	3
ZNF770	54989	broad.mit.edu	37	15	35274487	35274487	+	Silent	SNP	T	C	C			TCGA-05-4434-01	TCGA-05-4434-01										Phase_I	Unspecified				Illumina GAIIx	g.chr15:35274487T>C	uc001ziw.2	-	c.1149A>G	c.(1147-1149)AGA>AGG	p.R383R		NM_014106	NP_054825	Q6IQ21	ZN770_HUMAN	zinc finger protein 770	383					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1		Lung NSC(122;4.59e-10)|all_lung(180;8.78e-09)		all cancers(64;1.97e-18)|GBM - Glioblastoma multiforme(113;2.11e-07)|BRCA - Breast invasive adenocarcinoma(123;0.0643)										0.071429	0.190995	16.078727	6	78	KEEP	---	---	---	---	capture		Silent	SNP	35274487	35274487	18741	15	T	C	C	C	803	62	ZNF770	4	4
ABCC11	85320	broad.mit.edu	37	16	48244898	48244898	+	Silent	SNP	C	T	T			TCGA-05-4434-01	TCGA-05-4434-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:48244898C>T	uc002eff.1	-	c.1569G>A	c.(1567-1569)CTG>CTA	p.L523L	ABCC11_uc002efg.1_Silent_p.L523L|ABCC11_uc002efh.1_Silent_p.L523L|ABCC11_uc010vgk.1_Non-coding_Transcript	NM_033151	NP_149163	Q96J66	ABCCB_HUMAN	ATP-binding cassette, sub-family C, member 11	523	ABC transporter 1.|Cytoplasmic (Potential).					integral to membrane	ATP binding|ATPase activity, coupled to transmembrane movement of substances			ovary(3)|central_nervous_system(1)	4		all_cancers(37;0.127)|all_lung(18;0.132)|Breast(268;0.166)												0.373134	75.457173	76.404643	25	42	KEEP	---	---	---	---	capture		Silent	SNP	48244898	48244898	52	16	C	T	T	T	262	21	ABCC11	2	2
NFAT5	10725	broad.mit.edu	37	16	69724870	69724870	+	Missense_Mutation	SNP	A	G	G			TCGA-05-4434-01	TCGA-05-4434-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:69724870A>G	uc002exl.1	+	c.1802A>G	c.(1801-1803)GAT>GGT	p.D601G	NFAT5_uc002exi.2_Missense_Mutation_p.D507G|NFAT5_uc002exj.1_Missense_Mutation_p.D507G|NFAT5_uc002exk.1_Missense_Mutation_p.D507G|NFAT5_uc002exn.1_Missense_Mutation_p.D600G|NFAT5_uc002exm.1_Missense_Mutation_p.D583G|NFAT5_uc002exo.1_5'Flank	NM_138713	NP_619727	O94916	NFAT5_HUMAN	nuclear factor of activated T-cells 5 isoform b	583					excretion|regulation of transcription, DNA-dependent|signal transduction|transcription from RNA polymerase II promoter	nucleus	DNA binding|RNA polymerase II transcription factor activity|sequence-specific DNA binding transcription factor activity				0														0.186441	87.973878	104.27312	33	144	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	69724870	69724870	10760	16	A	G	G	G	156	12	NFAT5	4	4
PDPR	55066	broad.mit.edu	37	16	70165265	70165265	+	Missense_Mutation	SNP	G	A	A			TCGA-05-4434-01	TCGA-05-4434-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:70165265G>A	uc002eyf.1	+	c.790G>A	c.(790-792)GAA>AAA	p.E264K	CLEC18C_uc002exy.2_Intron|PDPR_uc010vlr.1_Missense_Mutation_p.E164K|PDPR_uc002eyg.1_5'Flank	NM_017990	NP_060460	Q8NCN5	PDPR_HUMAN	pyruvate dehydrogenase phosphatase regulatory	264					glycine catabolic process|pyruvate metabolic process|regulation of acetyl-CoA biosynthetic process from pyruvate	mitochondrial matrix	aminomethyltransferase activity|oxidoreductase activity			breast(1)	1				BRCA - Breast invasive adenocarcinoma(221;0.124)										0.176471	6.215552	7.891708	3	14	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	70165265	70165265	12110	16	G	A	A	A	481	37	PDPR	1	1
PMFBP1	83449	broad.mit.edu	37	16	72174328	72174328	+	Missense_Mutation	SNP	C	T	T			TCGA-05-4434-01	TCGA-05-4434-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:72174328C>T	uc002fcc.3	-	c.790G>A	c.(790-792)GCC>ACC	p.A264T	PMFBP1_uc002fcd.2_Missense_Mutation_p.A264T|PMFBP1_uc002fce.2_Non-coding_Transcript|PMFBP1_uc002fcf.2_Missense_Mutation_p.A119T	NM_031293	NP_112583	Q8TBY8	PMFBP_HUMAN	polyamine modulated factor 1 binding protein 1	264										ovary(1)	1		Ovarian(137;0.179)												0.105751	51.037771	134.227139	57	482	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	72174328	72174328	12560	16	C	T	T	T	338	26	PMFBP1	2	2
MYH1	4619	broad.mit.edu	37	17	10412921	10412921	+	Nonsense_Mutation	SNP	G	A	A			TCGA-05-4434-01	TCGA-05-4434-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:10412921G>A	uc002gmo.2	-	c.1468C>T	c.(1468-1470)CAG>TAG	p.Q490*		NM_005963	NP_005954	P12882	MYH1_HUMAN	myosin, heavy chain 1, skeletal muscle, adult	490	Myosin head-like.					muscle myosin complex|myofibril|myosin filament	actin binding|ATP binding|calmodulin binding|motor activity			ovary(10)|breast(3)|kidney(1)|skin(1)	15										585				0.114428	21.384607	50.844885	23	178	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	10412921	10412921	10424	17	G	A	A	A	624	48	MYH1	5	2
LASP1	3927	broad.mit.edu	37	17	37034383	37034383	+	Silent	SNP	A	G	G			TCGA-05-4434-01	TCGA-05-4434-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:37034383A>G	uc002hra.2	+	c.114A>G	c.(112-114)ACA>ACG	p.T38T	LASP1_uc010wdy.1_Silent_p.T38T|LASP1_uc010cvq.2_5'UTR|LASP1_uc010wdz.1_Missense_Mutation_p.T11A	NM_006148	NP_006139	Q14847	LASP1_HUMAN	LIM and SH3 protein 1	38	LIM zinc-binding.					cortical actin cytoskeleton	ion transmembrane transporter activity|SH3/SH2 adaptor activity|zinc ion binding				0										114				0.186916	44.850051	54.664267	20	87	KEEP	---	---	---	---	capture		Silent	SNP	37034383	37034383	8960	17	A	G	G	G	67	6	LASP1	4	4
RPAIN	84268	broad.mit.edu	37	17	5324728	5324728	+	Missense_Mutation	SNP	T	A	A			TCGA-05-4434-01	TCGA-05-4434-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:5324728T>A	uc010vsz.1	+	c.194T>A	c.(193-195)ATG>AAG	p.M65K	NUP88_uc002gbo.1_5'Flank|NUP88_uc010vsx.1_5'Flank|NUP88_uc010cle.1_5'Flank|NUP88_uc010vsy.1_5'Flank|RPAIN_uc002gbp.1_Missense_Mutation_p.D118E|RPAIN_uc010vta.1_Missense_Mutation_p.M65K|RPAIN_uc002gbq.2_Missense_Mutation_p.M65K|RPAIN_uc010vtb.1_Missense_Mutation_p.M65K|RPAIN_uc002gbs.2_Missense_Mutation_p.D118E|RPAIN_uc002gbt.2_Missense_Mutation_p.M65K|RPAIN_uc002gbu.2_Missense_Mutation_p.D118E|RPAIN_uc002gbv.2_Non-coding_Transcript|RPAIN_uc002gbr.2_Non-coding_Transcript|RPAIN_uc002gbw.2_Missense_Mutation_p.M65K	NM_001160243	NP_001153715	Q86UA6	RIP_HUMAN	RPA interacting protein isoform a	65					DNA recombination|DNA repair|DNA-dependent DNA replication|protein import into nucleus|response to UV	cytoplasm|cytoplasm|nucleolus|PML body|PML body	metal ion binding|protein complex binding				0														0.093458	8.171628	25.94793	10	97	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	5324728	5324728	14019	17	T	A	A	A	663	51	RPAIN	3	3
TEX2	55852	broad.mit.edu	37	17	62230409	62230409	+	Silent	SNP	C	T	T			TCGA-05-4434-01	TCGA-05-4434-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:62230409C>T	uc002jed.2	-	c.3057G>A	c.(3055-3057)AAG>AAA	p.K1019K	TEX2_uc002jec.2_Silent_p.K1012K|TEX2_uc002jee.2_Silent_p.K1012K	NM_018469	NP_060939	Q8IWB9	TEX2_HUMAN	testis expressed sequence 2	1012					signal transduction|sphingolipid metabolic process	integral to membrane				ovary(1)	1			BRCA - Breast invasive adenocarcinoma(8;1.33e-10)	READ - Rectum adenocarcinoma(1115;0.0689)										0.116279	11.683242	24.152251	10	76	KEEP	---	---	---	---	capture		Silent	SNP	62230409	62230409	16308	17	C	T	T	T	415	32	TEX2	2	2
STX8	9482	broad.mit.edu	37	17	9460847	9460847	+	Splice_Site_SNP	SNP	T	A	A			TCGA-05-4434-01	TCGA-05-4434-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:9460847T>A	uc002glx.2	-	c.118_splice	c.e3-1	p.L40_splice		NM_004853	NP_004844			syntaxin 8						transport	endoplasmic reticulum|integral to plasma membrane					0														0.22619	49.892746	55.666709	19	65	KEEP	---	---	---	---	capture		Splice_Site_SNP	SNP	9460847	9460847	15871	17	T	A	A	A	715	55	STX8	5	3
LAMA1	284217	broad.mit.edu	37	18	6980611	6980611	+	Missense_Mutation	SNP	C	G	G			TCGA-05-4434-01	TCGA-05-4434-01										Phase_I	Unspecified				Illumina GAIIx	g.chr18:6980611C>G	uc002knm.2	-	c.5916G>C	c.(5914-5916)TTG>TTC	p.L1972F	LAMA1_uc010wzj.1_Missense_Mutation_p.L1448F	NM_005559	NP_005550	P25391	LAMA1_HUMAN	laminin, alpha 1 precursor	1972	Domain II and I.|Potential.				axon guidance|cell adhesion|cell surface receptor linked signaling pathway|regulation of cell adhesion|regulation of cell migration|regulation of embryonic development	extracellular space|laminin-1 complex|laminin-3 complex	extracellular matrix structural constituent|receptor binding			ovary(8)|large_intestine(4)|breast(2)|pancreas(2)|central_nervous_system(1)	17		Colorectal(10;0.172)			Alteplase(DB00009)|Anistreplase(DB00029)|Reteplase(DB00015)|Tenecteplase(DB00031)					1597				0.067797	-0.548669	10.857731	4	55	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	6980611	6980611	8928	18	C	G	G	G	376	29	LAMA1	3	3
ABCA7	10347	broad.mit.edu	37	19	1063563	1063563	+	Silent	SNP	G	A	A			TCGA-05-4434-01	TCGA-05-4434-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:1063563G>A	uc002lqw.3	+	c.5733G>A	c.(5731-5733)GCG>GCA	p.A1911A	ABCA7_uc002lqy.2_Silent_p.A364A|ABCA7_uc010dsc.2_Non-coding_Transcript|HMHA1_uc010xgd.1_5'Flank	NM_019112	NP_061985	Q8IZY2	ABCA7_HUMAN	ATP-binding cassette, sub-family A, member 7	1911	ABC transporter 2.				phagocytosis|transmembrane transport	ATP-binding cassette (ABC) transporter complex|endosome membrane|Golgi membrane|integral to membrane|plasma membrane	ATP binding|ATPase activity|transporter activity			pancreas(7)|ovary(1)|central_nervous_system(1)	9		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;1.04e-05)|all_lung(49;1.53e-05)|Breast(49;9.42e-05)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)										0.088889	0.867409	8.550245	4	41	KEEP	---	---	---	---	capture		Silent	SNP	1063563	1063563	38	19	G	A	A	A	483	38	ABCA7	1	1
UNC13A	23025	broad.mit.edu	37	19	17780382	17780382	+	Missense_Mutation	SNP	G	A	A			TCGA-05-4434-01	TCGA-05-4434-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:17780382G>A	uc002nhd.2	-	c.638C>T	c.(637-639)ACG>ATG	p.T213M		NM_001080421	NP_001073890	Q9UPW8	UN13A_HUMAN	unc-13 homolog A	125					exocytosis|intracellular signal transduction	cell junction|cytoplasm|presynaptic membrane	metal ion binding			ovary(3)	3														0.2	17.675796	21.025134	8	32	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	17780382	17780382	17542	19	G	A	A	A	520	40	UNC13A	1	1
NLRP5	126206	broad.mit.edu	37	19	56572808	56572808	+	Missense_Mutation	SNP	G	A	A			TCGA-05-4434-01	TCGA-05-4434-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:56572808G>A	uc002qmj.2	+	c.3517G>A	c.(3517-3519)GAA>AAA	p.E1173K	NLRP5_uc002qmi.2_Missense_Mutation_p.E1154K	NM_153447	NP_703148	P59047	NALP5_HUMAN	NACHT, LRR and PYD containing protein 5	1173						mitochondrion|nucleolus	ATP binding			ovary(3)|skin(2)|kidney(1)	6		Colorectal(82;3.46e-05)|Ovarian(87;0.0481)|Renal(1328;0.157)		GBM - Glioblastoma multiforme(193;0.0326)										0.236111	38.117213	42.726915	17	55	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	56572808	56572808	10883	19	G	A	A	A	533	41	NLRP5	2	2
NLRP5	126206	broad.mit.edu	37	19	56572884	56572884	+	Nonsense_Mutation	SNP	G	A	A			TCGA-05-4434-01	TCGA-05-4434-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:56572884G>A	uc002qmj.2	+	c.3593G>A	c.(3592-3594)TGG>TAG	p.W1198*	NLRP5_uc002qmi.2_Nonsense_Mutation_p.W1179*	NM_153447	NP_703148	P59047	NALP5_HUMAN	NACHT, LRR and PYD containing protein 5	1198						mitochondrion|nucleolus	ATP binding			ovary(3)|skin(2)|kidney(1)	6		Colorectal(82;3.46e-05)|Ovarian(87;0.0481)|Renal(1328;0.157)		GBM - Glioblastoma multiforme(193;0.0326)										0.217391	46.345663	53.124493	20	72	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	56572884	56572884	10883	19	G	A	A	A	611	47	NLRP5	5	2
NVL	4931	broad.mit.edu	37	1	224477242	224477242	+	Missense_Mutation	SNP	G	A	A			TCGA-05-4434-01	TCGA-05-4434-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:224477242G>A	uc001hok.2	-	c.1519C>T	c.(1519-1521)CCA>TCA	p.P507S	NVL_uc001hol.2_Missense_Mutation_p.P401S|NVL_uc010pvd.1_Missense_Mutation_p.P416S|NVL_uc010pve.1_Missense_Mutation_p.P318S|NVL_uc010pvf.1_Non-coding_Transcript	NM_002533	NP_002524	O15381	NVL_HUMAN	nuclear VCP-like isoform 1	507						aggresome|cytoplasm|nucleolus	ATP binding|nucleoside-triphosphatase activity				0				GBM - Glioblastoma multiforme(131;0.00501)										0.053333	-7.560499	8.231585	4	71	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	224477242	224477242	11185	1	G	A	A	A	546	42	NVL	2	2
IL28RA	163702	broad.mit.edu	37	1	24484026	24484026	+	Missense_Mutation	SNP	G	A	A			TCGA-05-4434-01	TCGA-05-4434-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:24484026G>A	uc001bis.2	-	c.1157C>T	c.(1156-1158)TCA>TTA	p.S386L	IL28RA_uc001bir.2_Missense_Mutation_p.S357L|IL28RA_uc001bit.2_3'UTR|IL28RA_uc001biu.2_Missense_Mutation_p.S302L	NM_170743	NP_734464	Q8IU57	I28RA_HUMAN	interleukin 28 receptor, alpha isoform 1	386	Cytoplasmic (Potential).				cytokine-mediated signaling pathway|negative regulation of cell proliferation|regulation of defense response to virus by host	interleukin-28 receptor complex	protein binding|receptor activity				0		Colorectal(325;3.46e-05)|Renal(390;0.0007)|Lung NSC(340;0.00117)|all_lung(284;0.00151)|Ovarian(437;0.00348)|Breast(348;0.0126)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|OV - Ovarian serous cystadenocarcinoma(117;3.21e-24)|Colorectal(126;6.61e-08)|COAD - Colon adenocarcinoma(152;3.56e-06)|GBM - Glioblastoma multiforme(114;0.000132)|BRCA - Breast invasive adenocarcinoma(304;0.00104)|KIRC - Kidney renal clear cell carcinoma(1967;0.00374)|STAD - Stomach adenocarcinoma(196;0.00918)|READ - Rectum adenocarcinoma(331;0.0656)|Lung(427;0.0853)|LUSC - Lung squamous cell carcinoma(448;0.185)										0.071429	-1.611387	6.340596	3	39	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	24484026	24484026	7985	1	G	A	A	A	585	45	IL28RA	2	2
CCDC116	164592	broad.mit.edu	37	22	21988400	21988400	+	Silent	SNP	C	T	T			TCGA-05-4434-01	TCGA-05-4434-01										Phase_I	Unspecified				Illumina GAIIx	g.chr22:21988400C>T	uc002zve.2	+	c.162C>T	c.(160-162)AGC>AGT	p.S54S	CCDC116_uc011aih.1_Silent_p.S54S	NM_152612	NP_689825	Q8IYX3	CC116_HUMAN	coiled-coil domain containing 116	54										ovary(1)	1	Colorectal(54;0.105)													0.1375	16.658663	26.765343	11	69	KEEP	---	---	---	---	capture		Silent	SNP	21988400	21988400	2873	22	C	T	T	T	363	28	CCDC116	2	2
NF2	4771	broad.mit.edu	37	22	30035169	30035169	+	Nonsense_Mutation	SNP	C	T	T			TCGA-05-4434-01	TCGA-05-4434-01										Phase_I	Unspecified				Illumina GAIIx	g.chr22:30035169C>T	uc003age.3	+	c.331C>T	c.(331-333)CAG>TAG	p.Q111*	NF2_uc003afy.3_Nonsense_Mutation_p.Q111*|NF2_uc003afz.3_Intron|NF2_uc003agf.3_Nonsense_Mutation_p.Q111*|NF2_uc003agb.3_Nonsense_Mutation_p.Q34*|NF2_uc003agc.3_Nonsense_Mutation_p.Q73*|NF2_uc003agd.3_Intron|NF2_uc003agg.3_Nonsense_Mutation_p.Q111*|NF2_uc003aga.3_Nonsense_Mutation_p.Q69*|NF2_uc003agh.3_Intron|NF2_uc003agi.3_Intron|NF2_uc003agj.3_Nonsense_Mutation_p.Q111*|NF2_uc003agk.3_Nonsense_Mutation_p.Q73*	NM_000268	NP_000259	P35240	MERL_HUMAN	neurofibromin 2 isoform 1	111	FERM.				actin cytoskeleton organization|negative regulation of cell migration|negative regulation of cell proliferation|negative regulation of cell-cell adhesion|negative regulation of cell-matrix adhesion|negative regulation of DNA replication|negative regulation of tyrosine phosphorylation of Stat3 protein|negative regulation of tyrosine phosphorylation of Stat5 protein|positive regulation of stress fiber assembly|regulation of hippo signaling cascade|Schwann cell proliferation	cytoskeleton|early endosome|extrinsic to membrane|filopodium membrane|nucleolus|perinuclear region of cytoplasm|ruffle membrane	cytoskeletal protein binding|protein binding	p.Q111*(2)|p.V86_Q111>E(1)|p.V110_L141del(1)		meninges(371)|soft_tissue(271)|central_nervous_system(20)|kidney(10)|pleura(9)|skin(7)|large_intestine(5)|breast(5)|urinary_tract(3)|thyroid(2)|endometrium(2)|ovary(2)|lung(2)|stomach(2)|bone(2)|pituitary(1)	714										350				0.057851	-15.032405	10.075051	7	114	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	30035169	30035169	10757	22	C	T	T	T	377	29	NF2	5	2
ASCC2	84164	broad.mit.edu	37	22	30197042	30197042	+	Silent	SNP	A	G	G			TCGA-05-4434-01	TCGA-05-4434-01										Phase_I	Unspecified				Illumina GAIIx	g.chr22:30197042A>G	uc003agr.2	-	c.1626T>C	c.(1624-1626)AAT>AAC	p.N542N	ASCC2_uc003ags.2_Non-coding_Transcript|ASCC2_uc003agt.2_Silent_p.N542N|ASCC2_uc011akr.1_Silent_p.N466N	NM_032204	NP_115580	Q9H1I8	ASCC2_HUMAN	activating signal cointegrator 1 complex subunit	542					regulation of transcription, DNA-dependent|transcription, DNA-dependent						0			OV - Ovarian serous cystadenocarcinoma(5;0.000103)|Epithelial(10;0.0169)|all cancers(5;0.0259)											0.152047	45.939758	65.764706	26	145	KEEP	---	---	---	---	capture		Silent	SNP	30197042	30197042	1050	22	A	G	G	G	102	8	ASCC2	4	4
SLC5A1	6523	broad.mit.edu	37	22	32445957	32445957	+	Missense_Mutation	SNP	G	C	C			TCGA-05-4434-01	TCGA-05-4434-01										Phase_I	Unspecified				Illumina GAIIx	g.chr22:32445957G>C	uc003amc.2	+	c.163G>C	c.(163-165)GTT>CTT	p.V55L		NM_000343	NP_000334	P13866	SC5A1_HUMAN	solute carrier family 5 (sodium/glucose	55	Cytoplasmic (Potential).				carbohydrate metabolic process	integral to plasma membrane	glucose:sodium symporter activity|protein binding				0														0.21519	203.926151	227.581472	68	248	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	32445957	32445957	15158	22	G	C	C	C	624	48	SLC5A1	3	3
MYH9	4627	broad.mit.edu	37	22	36708237	36708237	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4434-01	TCGA-05-4434-01										Phase_I	Unspecified				Illumina GAIIx	g.chr22:36708237C>A	uc003apg.2	-	c.1585G>T	c.(1585-1587)GAC>TAC	p.D529Y	MYH9_uc003aph.1_Missense_Mutation_p.D393Y	NM_002473	NP_002464	P35579	MYH9_HUMAN	myosin, heavy polypeptide 9, non-muscle	529	Myosin head-like.				actin cytoskeleton reorganization|actin filament-based movement|angiogenesis|axon guidance|blood vessel endothelial cell migration|cytokinesis|integrin-mediated signaling pathway|leukocyte migration|membrane protein ectodomain proteolysis|monocyte differentiation|platelet formation|protein transport|regulation of cell shape	actomyosin contractile ring|cleavage furrow|cytosol|myosin complex|nucleus|ruffle|stress fiber|uropod	actin filament binding|actin-dependent ATPase activity|ADP binding|ATP binding|calmodulin binding|microfilament motor activity|protein anchor|protein homodimerization activity			breast(3)|ovary(2)|upper_aerodigestive_tract(1)|lung(1)|skin(1)|kidney(1)|pancreas(1)	10										1624				0.098765	4.434924	17.483025	8	73	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	36708237	36708237	10437	22	C	A	A	A	390	30	MYH9	2	2
CHN1	1123	broad.mit.edu	37	2	175742790	175742790	+	Silent	SNP	G	A	A			TCGA-05-4434-01	TCGA-05-4434-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:175742790G>A	uc002uji.2	-	c.327C>T	c.(325-327)CGC>CGT	p.R109R	CHN1_uc010zeq.1_Silent_p.R109R|CHN1_uc002ujj.2_Intron	NM_001822	NP_001813	P15882	CHIN_HUMAN	chimerin (chimaerin) 1 isoform a	109	SH2.				regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol	GTPase activator activity|metal ion binding|SH3/SH2 adaptor activity			ovary(2)|skin(1)	3			OV - Ovarian serous cystadenocarcinoma(117;0.226)							265				0.094118	4.230892	18.305583	8	77	KEEP	---	---	---	---	capture		Silent	SNP	175742790	175742790	3496	2	G	A	A	A	431	34	CHN1	2	2
CAD	790	broad.mit.edu	37	2	27462316	27462316	+	Missense_Mutation	SNP	G	A	A			TCGA-05-4434-01	TCGA-05-4434-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:27462316G>A	uc002rji.2	+	c.5371G>A	c.(5371-5373)GAG>AAG	p.E1791K	CAD_uc010eyw.2_Missense_Mutation_p.E1728K	NM_004341	NP_004332	P27708	PYR1_HUMAN	carbamoylphosphate synthetase 2/aspartate	1791	Linker.				'de novo' pyrimidine base biosynthetic process|glutamine metabolic process|peptidyl-threonine phosphorylation|protein autophosphorylation|pyrimidine nucleoside biosynthetic process|pyrimidine nucleotide biosynthetic process	cytosol|nuclear matrix	aspartate binding|aspartate carbamoyltransferase activity|ATP binding|carbamoyl-phosphate synthase (glutamine-hydrolyzing) activity|dihydroorotase activity|enzyme binding|metal ion binding|protein kinase activity			ovary(4)|large_intestine(2)|kidney(2)|lung(1)|pancreas(1)	10	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)				L-Aspartic Acid(DB00128)|L-Glutamine(DB00130)					653				0.081081	0.195678	6.811645	3	34	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	27462316	27462316	2681	2	G	A	A	A	533	41	CAD	2	2
LRRTM4	80059	broad.mit.edu	37	2	77745685	77745685	+	Missense_Mutation	SNP	G	A	A			TCGA-05-4434-01	TCGA-05-4434-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:77745685G>A	uc002snr.2	-	c.1310C>T	c.(1309-1311)GCC>GTC	p.A437V	LRRTM4_uc002snq.2_Missense_Mutation_p.A437V|LRRTM4_uc002sns.2_Missense_Mutation_p.A437V|LRRTM4_uc002snt.2_Missense_Mutation_p.A438V	NM_001134745	NP_001128217	Q86VH4	LRRT4_HUMAN	leucine rich repeat transmembrane neuronal 4	437	Helical; (Potential).					integral to membrane				pancreas(3)|ovary(1)	4				Colorectal(11;0.059)										0.21978	44.945759	51.532158	20	71	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	77745685	77745685	9418	2	G	A	A	A	546	42	LRRTM4	2	2
C3orf17	25871	broad.mit.edu	37	3	112727277	112727277	+	Missense_Mutation	SNP	C	T	T			TCGA-05-4434-01	TCGA-05-4434-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:112727277C>T	uc003dzr.2	-	c.976G>A	c.(976-978)GAG>AAG	p.E326K	GTPBP8_uc011bhy.1_Intron|C3orf17_uc003dzq.2_5'UTR|C3orf17_uc011bhz.1_5'UTR|C3orf17_uc010hqh.2_5'UTR|C3orf17_uc003dzt.2_Missense_Mutation_p.E229K|C3orf17_uc003dzs.2_Missense_Mutation_p.E190K|C3orf17_uc010hqg.2_Missense_Mutation_p.E151K|C3orf17_uc011bia.1_Missense_Mutation_p.E123K|C3orf17_uc003dzu.2_Missense_Mutation_p.E255K|C3orf17_uc011bib.1_Missense_Mutation_p.E215K|C3orf17_uc011bic.1_Missense_Mutation_p.E159K|C3orf17_uc011bid.1_Non-coding_Transcript	NM_015412	NP_056227	Q6NW34	CC017_HUMAN	hypothetical protein LOC25871	326						integral to membrane					0														0.170543	44.262686	57.511923	22	107	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	112727277	112727277	2303	3	C	T	T	T	390	30	C3orf17	2	2
PARP9	83666	broad.mit.edu	37	3	122274901	122274901	+	Missense_Mutation	SNP	T	A	A			TCGA-05-4434-01	TCGA-05-4434-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:122274901T>A	uc010hri.2	-	c.222A>T	c.(220-222)TTA>TTT	p.L74F	PARP9_uc003eff.3_Missense_Mutation_p.L39F|PARP9_uc011bjs.1_Missense_Mutation_p.L39F|PARP9_uc003efg.2_Intron|PARP9_uc003efi.2_Missense_Mutation_p.L39F|PARP9_uc003efh.2_Missense_Mutation_p.L74F|PARP9_uc003efj.2_Missense_Mutation_p.L39F	NM_001146102	NP_001139574	Q8IXQ6	PARP9_HUMAN	poly (ADP-ribose) polymerase family, member 9	74					cell migration	cytosol|nucleus	NAD+ ADP-ribosyltransferase activity|protein binding			ovary(1)|pancreas(1)	2				GBM - Glioblastoma multiforme(114;0.0519)						175				0.079545	-0.642538	15.234892	7	81	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	122274901	122274901	11883	3	T	A	A	A	790	61	PARP9	3	3
PARP14	54625	broad.mit.edu	37	3	122418783	122418783	+	Missense_Mutation	SNP	A	G	G			TCGA-05-4434-01	TCGA-05-4434-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:122418783A>G	uc003efq.3	+	c.1382A>G	c.(1381-1383)AAA>AGA	p.K461R	PARP14_uc010hrk.2_Non-coding_Transcript|PARP14_uc003efr.2_Missense_Mutation_p.K178R|PARP14_uc003efs.1_Missense_Mutation_p.K178R	NM_017554	NP_060024	Q460N5	PAR14_HUMAN	poly (ADP-ribose) polymerase family, member 14	461					regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus|plasma membrane	NAD+ ADP-ribosyltransferase activity			ovary(2)|pancreas(1)	3				GBM - Glioblastoma multiforme(114;0.0531)										0.178082	33.832773	40.952315	13	60	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	122418783	122418783	11875	3	A	G	G	G	13	1	PARP14	4	4
OXTR	5021	broad.mit.edu	37	3	8809556	8809556	+	Silent	SNP	G	A	A			TCGA-05-4434-01	TCGA-05-4434-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:8809556G>A	uc003brc.2	-	c.318C>T	c.(316-318)TAC>TAT	p.Y106Y		NM_000916	NP_000907	P30559	OXYR_HUMAN	oxytocin receptor	106	Extracellular (Potential).				female pregnancy|lactation|muscle contraction	integral to plasma membrane	oxytocin receptor activity|vasopressin receptor activity				0				OV - Ovarian serous cystadenocarcinoma(96;0.15)	Carbetocin(DB01282)									0.166667	5.413065	7.31007	3	15	KEEP	---	---	---	---	capture		Silent	SNP	8809556	8809556	11751	3	G	A	A	A	516	40	OXTR	1	1
SULT1B1	27284	broad.mit.edu	37	4	70620398	70620398	+	Missense_Mutation	SNP	T	A	A			TCGA-05-4434-01	TCGA-05-4434-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:70620398T>A	uc003hen.2	-	c.267A>T	c.(265-267)TTA>TTT	p.L89F		NM_014465	NP_055280	O43704	ST1B1_HUMAN	sulfotransferase family, cytosolic, 1B, member	89					3'-phosphoadenosine 5'-phosphosulfate metabolic process|cellular biogenic amine metabolic process|flavonoid metabolic process|steroid metabolic process|sulfation|thyroid hormone metabolic process|xenobiotic metabolic process	cytosol					0														0.055556	-8.900141	9.809022	5	85	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	70620398	70620398	15896	4	T	A	A	A	790	61	SULT1B1	3	3
PCDHGA6	56109	broad.mit.edu	37	5	140755505	140755505	+	Missense_Mutation	SNP	G	A	A			TCGA-05-4434-01	TCGA-05-4434-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:140755505G>A	uc003ljy.1	+	c.1855G>A	c.(1855-1857)GTG>ATG	p.V619M	PCDHGA1_uc003lji.1_Intron|PCDHGA2_uc003ljk.1_Intron|PCDHGA3_uc003ljm.1_Intron|PCDHGA3_uc010jfx.1_Intron|PCDHGB1_uc003ljo.1_Intron|PCDHGA4_uc003ljq.1_Intron|PCDHGB2_uc003ljs.1_Intron|PCDHGA5_uc003lju.1_Intron|PCDHGB3_uc003ljw.1_Intron|PCDHGA6_uc011dau.1_Missense_Mutation_p.V619M	NM_018919	NP_061742	Q9Y5G7	PCDG6_HUMAN	protocadherin gamma subfamily A, 6 isoform 1	619	Extracellular (Potential).|Cadherin 6.				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			breast(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)											0.126316	16.13495	29.081335	12	83	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	140755505	140755505	11978	5	G	A	A	A	468	36	PCDHGA6	2	2
BEND3	57673	broad.mit.edu	37	6	107390628	107390628	+	Silent	SNP	C	T	T			TCGA-05-4434-01	TCGA-05-4434-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:107390628C>T	uc003prs.2	-	c.1767G>A	c.(1765-1767)GAG>GAA	p.E589E		NM_001080450	NP_001073919	Q5T5X7	BEND3_HUMAN	BEN domain containing 3	589	BEN 3.									ovary(3)	3														0.134328	11.488679	20.275315	9	58	KEEP	---	---	---	---	capture		Silent	SNP	107390628	107390628	1422	6	C	T	T	T	415	32	BEND3	2	2
FOXF2	2295	broad.mit.edu	37	6	1390684	1390684	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4434-01	TCGA-05-4434-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:1390684C>A	uc003mtm.2	+	c.502C>A	c.(502-504)CCC>ACC	p.P168T	FOXF2_uc003mtn.2_Missense_Mutation_p.P168T	NM_001452	NP_001443	Q12947	FOXF2_HUMAN	forkhead box F2	168	Fork-head.				epithelial to mesenchymal transition|genitalia development|negative regulation of gene-specific transcription from RNA polymerase II promoter|palate development|pattern specification process|positive regulation of gene-specific transcription from RNA polymerase II promoter|regulation of sequence-specific DNA binding transcription factor activity	transcription factor complex	DNA bending activity|double-stranded DNA binding|promoter binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|specific RNA polymerase II transcription factor activity|specific transcriptional repressor activity|transcription activator activity|transcription factor binding				0	Ovarian(93;0.0733)	all_lung(73;0.0713)|all_hematologic(90;0.0895)		OV - Ovarian serous cystadenocarcinoma(45;0.095)										0.053191	-11.196745	8.577043	5	89	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	1390684	1390684	6251	6	C	A	A	A	338	26	FOXF2	2	2
SYNE1	23345	broad.mit.edu	37	6	152751686	152751686	+	Silent	SNP	T	C	C			TCGA-05-4434-01	TCGA-05-4434-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:152751686T>C	uc010kiw.2	-	c.4620A>G	c.(4618-4620)GCA>GCG	p.A1540A	SYNE1_uc003qot.3_Silent_p.A1547A|SYNE1_uc003qou.3_Silent_p.A1540A|SYNE1_uc010kjb.1_Silent_p.A1523A|SYNE1_uc003qow.2_Silent_p.A835A	NM_182961	NP_892006	Q8NF91	SYNE1_HUMAN	spectrin repeat containing, nuclear envelope 1	1540	Cytoplasmic (Potential).				cell death|cytoskeletal anchoring at nuclear membrane|Golgi organization|muscle cell differentiation|nuclear matrix anchoring at nuclear membrane	cytoskeleton|Golgi apparatus|integral to membrane|nuclear outer membrane|postsynaptic membrane|sarcomere|SUN-KASH complex	actin binding|lamin binding			central_nervous_system(15)|ovary(8)|large_intestine(5)|pancreas(2)	30		Ovarian(120;0.0955)	BRCA - Breast invasive adenocarcinoma(37;0.243)	OV - Ovarian serous cystadenocarcinoma(155;2.24e-10)										0.035533	-61.988161	30.336561	14	380	KEEP	---	---	---	---	capture		Silent	SNP	152751686	152751686	15966	6	T	C	C	C	756	59	SYNE1	4	4
SLC22A2	6582	broad.mit.edu	37	6	160679700	160679700	+	Silent	SNP	C	T	T			TCGA-05-4434-01	TCGA-05-4434-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:160679700C>T	uc003qte.1	-	c.90G>A	c.(88-90)TCG>TCA	p.S30S	SLC22A2_uc003qtf.2_Silent_p.S30S|SLC22A2_uc003qth.1_Silent_p.S30S	NM_003058	NP_003049	O15244	S22A2_HUMAN	solute carrier family 22 member 2	30	Helical; (Potential).				body fluid secretion|neurotransmitter biosynthetic process|neurotransmitter secretion	integral to plasma membrane|membrane fraction	neurotransmitter transporter activity|organic cation transmembrane transporter activity			breast(1)	1		Breast(66;0.000776)|Ovarian(120;0.0303)		OV - Ovarian serous cystadenocarcinoma(65;2.28e-17)|BRCA - Breast invasive adenocarcinoma(81;6.29e-06)										0.063492	-3.546755	8.94211	4	59	KEEP	---	---	---	---	capture		Silent	SNP	160679700	160679700	14947	6	C	T	T	T	288	23	SLC22A2	1	1
SLC22A3	6581	broad.mit.edu	37	6	160831831	160831831	+	Missense_Mutation	SNP	C	T	T			TCGA-05-4434-01	TCGA-05-4434-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:160831831C>T	uc003qti.2	+	c.928C>T	c.(928-930)CGC>TGC	p.R310C	SLC22A3_uc011efx.1_Non-coding_Transcript	NM_021977	NP_068812	O75751	S22A3_HUMAN	solute carrier family 22 member 3	310						integral to plasma membrane|membrane fraction	protein binding|quaternary ammonium group transmembrane transporter activity			ovary(1)|central_nervous_system(1)	2		Breast(66;0.00028)|Ovarian(120;0.0308)|Prostate(117;0.218)		OV - Ovarian serous cystadenocarcinoma(65;9.47e-17)|BRCA - Breast invasive adenocarcinoma(81;9.75e-06)						170				0.091837	4.812182	21.244129	9	89	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	160831831	160831831	14952	6	C	T	T	T	247	19	SLC22A3	1	1
IMPG1	3617	broad.mit.edu	37	6	76728564	76728564	+	Silent	SNP	T	A	A			TCGA-05-4434-01	TCGA-05-4434-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:76728564T>A	uc003pik.1	-	c.678A>T	c.(676-678)ACA>ACT	p.T226T		NM_001563	NP_001554	Q17R60	IMPG1_HUMAN	interphotoreceptor matrix proteoglycan 1	226					visual perception	proteinaceous extracellular matrix	extracellular matrix structural constituent|receptor activity			ovary(2)	2		Acute lymphoblastic leukemia(125;0.0418)|all_hematologic(105;0.222)				Pancreas(37;839 1141 2599 26037)								0.4375	133.437951	133.764481	42	54	KEEP	---	---	---	---	capture		Silent	SNP	76728564	76728564	8029	6	T	A	A	A	704	55	IMPG1	3	3
ACTR3B	57180	broad.mit.edu	37	7	152497649	152497649	+	Missense_Mutation	SNP	A	C	C			TCGA-05-4434-01	TCGA-05-4434-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:152497649A>C	uc003wle.1	+	c.134A>C	c.(133-135)GAC>GCC	p.D45A	ACTR3B_uc003wlf.1_Missense_Mutation_p.D45A|ACTR3B_uc003wlg.1_5'UTR|ACTR3B_uc011kvp.1_Intron	NM_020445	NP_065178	Q9P1U1	ARP3B_HUMAN	actin-related protein 3-beta isoform 1	45					regulation of actin filament polymerization	cell projection|cytoplasm|cytoskeleton	actin binding|ATP binding				0		all_hematologic(28;0.0592)|Prostate(32;0.191)	OV - Ovarian serous cystadenocarcinoma(82;0.0287)	UCEC - Uterine corpus endometrioid carcinoma (81;0.0434)										0.11039	22.168349	45.291364	17	137	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	152497649	152497649	214	7	A	C	C	C	130	10	ACTR3B	4	4
SEMA3D	223117	broad.mit.edu	37	7	84644482	84644482	+	Silent	SNP	G	A	A			TCGA-05-4434-01	TCGA-05-4434-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:84644482G>A	uc003uic.2	-	c.1596C>T	c.(1594-1596)CAC>CAT	p.H532H	SEMA3D_uc010led.2_Silent_p.H532H|SEMA3D_uc003uib.2_Silent_p.H171H	NM_152754	NP_689967	O95025	SEM3D_HUMAN	semaphorin 3D precursor	532					cell differentiation|nervous system development	extracellular region|membrane	receptor activity			ovary(3)|large_intestine(2)	5						Ovarian(63;442 1191 17318 29975 31528)								0.144737	16.26912	25.506365	11	65	KEEP	---	---	---	---	capture		Silent	SNP	84644482	84644482	14513	7	G	A	A	A	620	48	SEMA3D	2	2
FBXO43	286151	broad.mit.edu	37	8	101146122	101146122	+	Missense_Mutation	SNP	C	G	G			TCGA-05-4434-01	TCGA-05-4434-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:101146122C>G	uc003yjd.2	-	c.2035G>C	c.(2035-2037)GAA>CAA	p.E679Q	FBXO43_uc003yje.2_Missense_Mutation_p.E645Q	NM_001029860	NP_001025031	Q4G163	FBX43_HUMAN	F-box protein 43 isoform b	679	IBR-type.				meiosis		zinc ion binding			kidney(1)|skin(1)	2	all_cancers(14;0.000139)|all_epithelial(15;2.84e-07)|Lung NSC(17;0.000274)|all_lung(17;0.000798)		Epithelial(11;1.17e-09)|all cancers(13;1.34e-07)|OV - Ovarian serous cystadenocarcinoma(57;3.82e-05)|STAD - Stomach adenocarcinoma(118;0.0957)							303				0.442857	335.13748	335.736526	93	117	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	101146122	101146122	5989	8	C	G	G	G	377	29	FBXO43	3	3
FBXO43	286151	broad.mit.edu	37	8	101154000	101154000	+	Missense_Mutation	SNP	G	C	C			TCGA-05-4434-01	TCGA-05-4434-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:101154000G>C	uc003yjd.2	-	c.482C>G	c.(481-483)TCT>TGT	p.S161C	FBXO43_uc003yje.2_Missense_Mutation_p.S127C|FBXO43_uc010mbp.1_Missense_Mutation_p.S161C	NM_001029860	NP_001025031	Q4G163	FBX43_HUMAN	F-box protein 43 isoform b	161					meiosis		zinc ion binding			kidney(1)|skin(1)	2	all_cancers(14;0.000139)|all_epithelial(15;2.84e-07)|Lung NSC(17;0.000274)|all_lung(17;0.000798)		Epithelial(11;1.17e-09)|all cancers(13;1.34e-07)|OV - Ovarian serous cystadenocarcinoma(57;3.82e-05)|STAD - Stomach adenocarcinoma(118;0.0957)							303				0.056856	-15.980718	45.679782	17	282	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	101154000	101154000	5989	8	G	C	C	C	429	33	FBXO43	3	3
SNX30	401548	broad.mit.edu	37	9	115580031	115580031	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4434-01	TCGA-05-4434-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:115580031G>T	uc004bgj.3	+	c.395G>T	c.(394-396)AGA>ATA	p.R132I		NM_001012994	NP_001013012	Q5VWJ9	SNX30_HUMAN	sorting nexin family member 30	132	PX.				cell communication|protein transport	cytoplasm	phosphatidylinositol binding				0														0.252336	65.567683	71.532768	27	80	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	115580031	115580031	15400	9	G	T	T	T	429	33	SNX30	2	2
SLC2A8	29988	broad.mit.edu	37	9	130162258	130162258	+	Missense_Mutation	SNP	G	A	A			TCGA-05-4434-01	TCGA-05-4434-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:130162258G>A	uc004bqu.2	+	c.499G>A	c.(499-501)GTC>ATC	p.V167I	SLC2A8_uc010mxj.2_Missense_Mutation_p.V167I	NM_014580	NP_055395	Q9NY64	GTR8_HUMAN	solute carrier family 2 (facilitated glucose	167	Helical; Name=5; (Potential).					cytoplasmic vesicle membrane|integral to plasma membrane	D-glucose transmembrane transporter activity			ovary(1)	1														0.15	19.450818	28.84508	12	68	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	130162258	130162258	15048	9	G	A	A	A	520	40	SLC2A8	1	1
CD72	971	broad.mit.edu	37	9	35616193	35616193	+	Silent	SNP	G	C	C			TCGA-05-4434-01	TCGA-05-4434-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:35616193G>C	uc003zxb.2	-	c.435C>G	c.(433-435)CTC>CTG	p.L145L	CD72_uc003zxc.1_5'UTR|CD72_uc010mkt.1_5'UTR|CD72_uc010mku.2_Silent_p.L145L|CD72_uc010mkv.2_3'UTR|CD72_uc010mkw.1_Non-coding_Transcript	NM_001782	NP_001773	P21854	CD72_HUMAN	CD72 molecule	145	Extracellular (Potential).				axon guidance|cell adhesion	integral to plasma membrane	receptor binding|sugar binding|transmembrane receptor activity				0			Lung(28;0.00276)|LUSC - Lung squamous cell carcinoma(32;0.00418)|STAD - Stomach adenocarcinoma(86;0.194)											0.091743	8.364237	26.662913	10	99	KEEP	---	---	---	---	capture		Silent	SNP	35616193	35616193	3162	9	G	C	C	C	574	45	CD72	3	3
FGF16	8823	broad.mit.edu	37	X	76711920	76711920	+	Silent	SNP	T	C	C			TCGA-05-4434-01	TCGA-05-4434-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:76711920T>C	uc011mqp.1	+	c.258T>C	c.(256-258)ACT>ACC	p.T86T		NM_003868	NP_003859	O43320	FGF16_HUMAN	fibroblast growth factor 16	177					cell-cell signaling|fibroblast growth factor receptor signaling pathway|insulin receptor signaling pathway|metabolic process|organ morphogenesis|response to temperature stimulus	extracellular space	growth factor activity				0														0.146789	36.636384	49.692972	16	93	KEEP	---	---	---	---	capture		Silent	SNP	76711920	76711920	6081	23	T	C	C	C	678	53	FGF16	4	4
MAFA	389692	broad.mit.edu	37	8	144511954	144511956	+	In_Frame_Del	DEL	TGG	-	-			TCGA-05-4434-01	TCGA-05-4434-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:144511954_144511956delTGG	uc003yyc.1	-	c.621_623delCCA	c.(619-624)CACCAT>CAT	p.207_208HH>H		NM_201589	NP_963883	Q8NHW3	MAFA_HUMAN	v-maf musculoaponeurotic fibrosarcoma oncogene	207_208	His-rich.				insulin secretion|nitric oxide mediated signal transduction|response to glucose stimulus	nucleus	protein heterodimerization activity|protein homodimerization activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity				0	all_cancers(97;7.39e-11)|all_epithelial(106;5.44e-09)|Lung NSC(106;0.000167)|all_lung(105;0.000459)|Ovarian(258;0.0212)|Acute lymphoblastic leukemia(118;0.155)		Colorectal(110;0.107)|BRCA - Breast invasive adenocarcinoma(115;0.237)											0.33			2	4		---	---	---	---	capture_indel		In_Frame_Del	DEL	144511954	144511956	9534	8	TGG	-	-	-	663	51	MAFA	5	5
KDM5C	8242	broad.mit.edu	37	X	53225159	53225159	+	Frame_Shift_Del	DEL	T	-	-			TCGA-05-4434-01	TCGA-05-4434-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:53225159_53225159delT	uc004drz.2	-	c.3059_3059delA	c.(3058-3060)CAGfs	p.Q1020fs	KDM5C_uc011moc.1_Non-coding_Transcript|KDM5C_uc011mod.1_Frame_Shift_Del_p.Q953fs|KDM5C_uc004dsa.2_Frame_Shift_Del_p.Q1019fs	NM_004187	NP_004178	P41229	KDM5C_HUMAN	jumonji, AT rich interactive domain 1C isoform	1020					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			kidney(9)|ovary(5)|salivary_gland(1)|autonomic_ganglia(1)|haematopoietic_and_lymphoid_tissue(1)|oesophagus(1)	18														0.34			14	27		---	---	---	---	capture_indel		Frame_Shift_Del	DEL	53225159	53225159	8441	23	T	-	-	-	715	55	KDM5C	5	5
