Hugo_Symbol	Entrez_Gene_Id	Center	NCBI_Build	Chromosome	Start_position	End_position	Strand	Variant_Classification	Variant_Type	Reference_Allele	Tumor_Seq_Allele1	Tumor_Seq_Allele2	dbSNP_RS	dbSNP_Val_Status	Tumor_Sample_Barcode	Matched_Norm_Sample_Barcode	Match_Norm_Seq_Allele1	Match_Norm_Seq_Allele2	Tumor_Validation_Allele1	Tumor_Validation_Allele2	Match_Norm_Validation_Allele1	Match_Norm_Validation_Allele2	Verification_Status	Validation_Status	Mutation_Status	Sequencing_Phase	Sequence_Source	Validation_Method	Score	BAM_file	Sequencer	Genome_Change	Annotation_Transcript	Transcript_Strand	cDNA_Change	Codon_Change	Protein_Change	Other_Transcripts	Refseq_mRNA_Id	Refseq_prot_Id	SwissProt_acc_Id	SwissProt_entry_Id	Description	UniProt_AApos	UniProt_Region	UniProt_Site	UniProt_Natural_Variations	UniProt_Experimental_Info	GO_Biological_Process	GO_Cellular_Component	GO_Molecular_Function	COSMIC_overlapping_mutations	COSMIC_fusion_genes	COSMIC_tissue_types_affected	COSMIC_total_alterations_in_gene	Tumorscape_Amplification_Peaks	Tumorscape_Deletion_Peaks	i_TCGAscape_Amplification_Peaks	i_TCGAscape_Deletion_Peaks	DrugBank	i_ACHILLES_Top_Genes	i_CCLE_ONCOMAP_overlapping_mutations	i_CCLE_ONCOMAP_total_mutations_in_gene	i_CCLE_SEQ_overlapping_mutations	i_CCLE_SEQ_total_mutations_in_gene	MUTSIG_Significant_Genes	OREGANNO_ID	OREGANNO_Values	i_tumor_f	i_init_t_lod	i_t_lod_fstar	i_t_alt_count	i_t_ref_count	i_normal_best_gt	i_failure_reasons	i_judgement	validation_status	validation_method	validation_tumor_sample	validation_alt_allele	dataset	TCGAscape_Amplification_Peaks	TCGAscape_Deletion_Peaks	type	classification	start	end	gene	chr	ref_allele	tum_allele1	tum_allele2	context_orig	context65	gene_name	newbase	categ	categ_ignoring_null_categ
USP6NL	9712	broad.mit.edu	36	10	11545274	11545274	+	Silent	SNP	G	A	A			TCGA-06-0155-01	TCGA-06-0155-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr10:11545274G>A	uc001iks.1	-	c.1710C>T	c.(1708-1710)AAC>AAT	p.N570N	USP6NL_uc001ikt.2_Silent_p.N553N	NM_001080491	NP_001073960	Q92738	US6NL_HUMAN	USP6 N-terminal like isoform 2	553						intracellular	Rab GTPase activator activity				0														0.738095	195.758106	200.06031	62	22	GG		KEEP	---	---	---	---	capture			Silent	SNP	11545274	11545274	17651	10	G	A	A	40	40	USP6NL	A	1	1
MMP21	118856	broad.mit.edu	36	10	127446147	127446147	+	Missense_Mutation	SNP	C	G	G			TCGA-06-0155-01	TCGA-06-0155-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr10:127446147C>G	uc001liu.1	-	c.1354G>C	c.(1354-1356)GAC>CAC	p.D452H		NM_147191	NP_671724	Q8N119	MMP21_HUMAN	matrix metalloproteinase 21 preproprotein	452	Hemopexin-like 3.				proteolysis	extracellular matrix	calcium ion binding|metalloendopeptidase activity|zinc ion binding			ovary(2)	2		all_lung(145;0.0096)|Lung NSC(174;0.0145)|Colorectal(57;0.0846)|all_neural(114;0.0936)												0.6	291.000674	292.181074	81	54	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	127446147	127446147	10050	10	C	G	G	32	32	MMP21	G	3	3
PRKCQ	5588	broad.mit.edu	36	10	6593046	6593046	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0155-01	TCGA-06-0155-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr10:6593046C>T	uc001iji.1	-	c.334G>A	c.(334-336)GTG>ATG	p.V112M	PRKCQ_uc009xim.1_Missense_Mutation_p.V79M|PRKCQ_uc001ijj.1_Missense_Mutation_p.V79M|PRKCQ_uc009xin.1_Missense_Mutation_p.V43M	NM_006257	NP_006248	Q04759	KPCT_HUMAN	protein kinase C, theta	79	C2.				axon guidance|cellular component disassembly involved in apoptosis|intracellular signal transduction|membrane protein ectodomain proteolysis|platelet activation|protein phosphorylation|regulation of cell growth|T cell receptor signaling pathway	cytosol	ATP binding|metal ion binding|protein binding|protein kinase C activity			ovary(3)|lung(2)|large_intestine(1)	6						Ovarian(50;572 1126 10530 25349 30594)				435				0.582278	283.519208	284.452858	92	66	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	6593046	6593046	12958	10	C	T	T	19	19	PRKCQ	T	1	1
PPP3CB	5532	broad.mit.edu	36	10	74874537	74874537	+	Missense_Mutation	SNP	T	A	A			TCGA-06-0155-01	TCGA-06-0155-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr10:74874537T>A	uc001juf.1	-	c.1321A>T	c.(1321-1323)ATG>TTG	p.M441L	PPP3CB_uc001jue.1_Missense_Mutation_p.M440L|PPP3CB_uc001jug.1_Missense_Mutation_p.M441L|PPP3CB_uc001juh.1_Missense_Mutation_p.M355L|PPP3CB_uc001jui.1_Missense_Mutation_p.M458L	NM_021132	NP_066955	P16298	PP2BB_HUMAN	protein phosphatase 3 (formerly 2B), catalytic	440										skin(1)	1	Prostate(51;0.0119)									146				0.339286	53.807519	55.086443	19	37	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	74874537	74874537	12834	10	T	A	A	50	50	PPP3CB	A	4	4
PTEN	5728	broad.mit.edu	36	10	89682902	89682902	+	Missense_Mutation	SNP	T	C	C			TCGA-06-0155-01	TCGA-06-0155-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr10:89682902T>C	uc001kfb.1	+	c.406T>C	c.(406-408)TGT>CGT	p.C136R		NM_000314	NP_000305	P60484	PTEN_HUMAN	phosphatase and tensin homolog	136	Phosphatase tensin-type.		C -> Y (in CD; loss of phosphatase activity towards Ins(1,3,4,5)P3).		apoptosis|canonical Wnt receptor signaling pathway|cell proliferation|central nervous system development|induction of apoptosis|inositol phosphate dephosphorylation|negative regulation of cell migration|negative regulation of focal adhesion assembly|negative regulation of protein kinase B signaling cascade|negative regulation of protein phosphorylation|nerve growth factor receptor signaling pathway|phosphatidylinositol dephosphorylation|phosphatidylinositol-mediated signaling|positive regulation of sequence-specific DNA binding transcription factor activity|protein stabilization|regulation of cyclin-dependent protein kinase activity|regulation of neuron projection development|T cell receptor signaling pathway	cytosol|internal side of plasma membrane|PML body	enzyme binding|inositol-1,3,4,5-tetrakisphosphate 3-phosphatase activity|lipid binding|magnesium ion binding|PDZ domain binding|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity|phosphatidylinositol-3,4-bisphosphate 3-phosphatase activity|phosphatidylinositol-3-phosphatase activity|protein serine/threonine phosphatase activity|protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity	p.I135fs*44(3)|p.C136fs*1(2)|p.C136R(2)|p.Y27_N212>Y(2)|p.I135_A137>T(1)|p.T131fs*42(1)|p.I135fs*6(1)|p.A121_F145del(1)|p.F56fs*2(1)		endometrium(831)|central_nervous_system(654)|skin(119)|haematopoietic_and_lymphoid_tissue(101)|prostate(97)|large_intestine(90)|breast(67)|lung(63)|ovary(58)|thyroid(29)|stomach(29)|upper_aerodigestive_tract(25)|cervix(21)|liver(20)|vulva(17)|kidney(15)|NS(14)|soft_tissue(12)|urinary_tract(12)|eye(8)|pancreas(6)|salivary_gland(5)|bone(5)|biliary_tract(4)|autonomic_ganglia(2)|meninges(2)|testis(1)|oesophagus(1)	2308		all_cancers(4;3.61e-31)|all_epithelial(4;3.96e-23)|Prostate(4;8.12e-23)|Breast(4;0.000111)|Melanoma(5;0.00146)|all_hematologic(4;0.00227)|Colorectal(252;0.00494)|all_neural(4;0.00513)|Acute lymphoblastic leukemia(4;0.0116)|Glioma(4;0.0274)|all_lung(38;0.132)						31		264	TCGA GBM(2;<1E-8)|TSP Lung(26;0.18)			0.666667	333.739202	337.574767	104	52	TT		KEEP	---	---	---	---	capture	KIRC - Kidney renal clear cell carcinoma(1;0.214)	UCEC - Uterine corpus endometrioid carcinoma (6;0.000228)|all cancers(1;4.16e-84)|GBM - Glioblastoma multiforme(1;7.77e-49)|Epithelial(1;7.67e-41)|OV - Ovarian serous cystadenocarcinoma(1;6.22e-15)|BRCA - Breast invasive adenocarcinoma(1;1.1e-06)|Lung(2;3.18e-06)|Colorectal(12;4.88e-06)|LUSC - Lung squamous cell carcinoma(2;4.97e-06)|COAD - Colon adenocarcinoma(12;1.13e-05)|Kidney(1;0.000288)|KIRC - Kidney renal clear cell carcinoma(1;0.00037)|STAD - Stomach adenocarcinoma(243;0.218)	Missense_Mutation	SNP	89682902	89682902	13192	10	T	C	C	51	51	PTEN	C	4	4
HTR3A	3359	broad.mit.edu	36	11	113359096	113359096	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0155-01	TCGA-06-0155-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr11:113359096G>A	uc001pon.1	+	c.419G>A	c.(418-420)CGG>CAG	p.R140Q	HTR3A_uc001pom.1_Missense_Mutation_p.R140Q|HTR3A_uc009yyx.1_Non-coding_Transcript	NM_213621	NP_998786	P46098	5HT3A_HUMAN	5-hydroxytryptamine (serotonin) receptor 3A	140	Extracellular (Potential).				digestion|synaptic transmission	cell junction|integral to plasma membrane|postsynaptic membrane	serotonin binding|serotonin receptor activity|serotonin-activated cation-selective channel activity				0		all_cancers(61;2.31e-17)|all_epithelial(67;2.1e-10)|all_hematologic(158;4.64e-05)|Melanoma(852;0.000312)|Acute lymphoblastic leukemia(157;0.000967)|Breast(348;0.0101)|all_neural(223;0.0281)|Prostate(24;0.0294)|Medulloblastoma(222;0.0425)			Alosetron(DB00969)|Chloroprocaine(DB01161)|Cisapride(DB00604)|Dolasetron(DB00757)|Granisetron(DB00889)|Mirtazapine(DB00370)|Ondansetron(DB00904)|Palonosetron(DB00377)|Procaine(DB00721)|Tubocurarine(DB01199)									0.394737	311.429786	314.005335	105	161	GG		KEEP	---	---	---	---	capture		BRCA - Breast invasive adenocarcinoma(274;2.71e-06)|Epithelial(105;2.58e-05)|all cancers(92;0.000238)|OV - Ovarian serous cystadenocarcinoma(223;0.191)	Missense_Mutation	SNP	113359096	113359096	7744	11	G	A	A	39	39	HTR3A	A	1	1
CD44	960	broad.mit.edu	36	11	35189422	35189422	+	Missense_Mutation	SNP	A	G	G			TCGA-06-0155-01	TCGA-06-0155-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr11:35189422A>G	uc001mvu.1	+	c.1660A>G	c.(1660-1662)ACT>GCT	p.T554A	CD44_uc001mvv.1_Missense_Mutation_p.T511A|CD44_uc001mvw.1_Missense_Mutation_p.T305A|CD44_uc001mvx.1_Intron|CD44_uc001mvy.1_Intron|CD44_uc001mwc.2_Missense_Mutation_p.T241A|CD44_uc009ykh.1_Intron|CD44_uc001mwb.1_Non-coding_Transcript|CD44_uc001mvz.1_Missense_Mutation_p.T118A|CD44_uc001mwa.1_Missense_Mutation_p.T82A	NM_000610	NP_000601	P16070	CD44_HUMAN	CD44 antigen isoform 1 precursor	554	Extracellular (Potential).|Stem.				cell-cell adhesion|cell-matrix adhesion|interferon-gamma-mediated signaling pathway|negative regulation of apoptosis|negative regulation of DNA damage response, signal transduction by p53 class mediator|positive regulation of ERK1 and ERK2 cascade|positive regulation of peptidyl-serine phosphorylation|positive regulation of peptidyl-tyrosine phosphorylation	cell surface|Golgi apparatus|integral to plasma membrane	collagen binding|hyaluronic acid binding|receptor activity			pancreas(1)	1	all_cancers(35;0.212)|all_lung(20;0.0874)|all_epithelial(35;0.112)	all_hematologic(20;0.107)			Hyaluronidase(DB00070)					401				0.377224	355.291384	359.00543	106	175	AA		KEEP	---	---	---	---	capture	STAD - Stomach adenocarcinoma(6;0.00731)		Missense_Mutation	SNP	35189422	35189422	3145	11	A	G	G	2	2	CD44	G	4	4
OR52E6	390078	broad.mit.edu	36	11	5819178	5819178	+	Missense_Mutation	SNP	T	G	G			TCGA-06-0155-01	TCGA-06-0155-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr11:5819178T>G	uc001mby.1	-	c.526A>C	c.(526-528)ATC>CTC	p.I176L	TRIM5_uc001mbq.1_Intron	NM_001005167	NP_001005167	Q96RD3	O52E6_HUMAN	olfactory receptor, family 52, subfamily E,	176	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			central_nervous_system(1)	1		Medulloblastoma(188;0.0075)|all_neural(188;0.0577)|Breast(177;0.086)												0.414847	320.512797	321.954802	95	134	TT		KEEP	---	---	---	---	capture		Epithelial(150;2.55e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)	Missense_Mutation	SNP	5819178	5819178	11527	11	T	G	G	51	51	OR52E6	G	4	4
SLC22A9	114571	broad.mit.edu	36	11	62906322	62906322	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0155-01	TCGA-06-0155-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr11:62906322C>T	uc001nww.1	+	c.1070C>T	c.(1069-1071)ACG>ATG	p.T357M	SLC22A9_uc001nwx.1_Non-coding_Transcript	NM_080866	NP_543142	Q8IVM8	S22A9_HUMAN	solute carrier family 22 (organic anion/cation	357	Helical; (Potential).				transmembrane transport	integral to membrane				breast(2)|large_intestine(1)	3														0.382239	286.970857	290.117658	99	160	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	62906322	62906322	14958	11	C	T	T	19	19	SLC22A9	T	1	1
RIMBP2	23504	broad.mit.edu	36	12	129493064	129493064	+	Silent	SNP	G	A	A			TCGA-06-0155-01	TCGA-06-0155-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr12:129493064G>A	uc001uil.2	-	c.735C>T	c.(733-735)AAC>AAT	p.N245N	RIMBP2_uc001uim.2_Silent_p.N153N|RIMBP2_uc001uin.1_De_novo_Start_OutOfFrame	NM_015347	NP_056162	O15034	RIMB2_HUMAN	RIM-binding protein 2	245						cell junction|synapse				ovary(3)|large_intestine(2)|central_nervous_system(2)|pancreas(1)	8	all_neural(191;0.101)|Medulloblastoma(191;0.163)	all_epithelial(31;0.213)												0.331492	155.89368	160.421	60	121	GG		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(86;4.29e-06)|all cancers(50;4.56e-05)|Epithelial(86;5.41e-05)	Silent	SNP	129493064	129493064	13838	12	G	A	A	40	40	RIMBP2	A	1	1
CACNA1C	775	broad.mit.edu	36	12	2437015	2437015	+	Silent	SNP	A	G	G			TCGA-06-0155-01	TCGA-06-0155-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr12:2437015A>G	uc009zdu.1	+	c.639A>G	c.(637-639)GAA>GAG	p.E213E	CACNA1C_uc009zdv.1_Silent_p.E213E|CACNA1C_uc001qkb.2_Silent_p.E213E|CACNA1C_uc001qkc.2_Silent_p.E213E|CACNA1C_uc001qke.2_Silent_p.E213E|CACNA1C_uc001qkf.2_Silent_p.E213E|CACNA1C_uc001qjz.2_Silent_p.E213E|CACNA1C_uc001qkd.2_Silent_p.E213E|CACNA1C_uc001qkg.2_Silent_p.E213E|CACNA1C_uc009zdw.1_Silent_p.E213E|CACNA1C_uc001qkh.2_Silent_p.E213E|CACNA1C_uc001qkl.2_Silent_p.E213E|CACNA1C_uc001qkn.2_Silent_p.E213E|CACNA1C_uc001qko.2_Silent_p.E213E|CACNA1C_uc001qkp.2_Silent_p.E213E|CACNA1C_uc001qkr.2_Silent_p.E213E|CACNA1C_uc001qku.2_Silent_p.E213E|CACNA1C_uc001qkq.2_Silent_p.E213E|CACNA1C_uc001qks.2_Silent_p.E213E|CACNA1C_uc001qkt.2_Silent_p.E213E|CACNA1C_uc001qka.1_5'UTR|CACNA1C_uc001qki.1_5'UTR|CACNA1C_uc001qkj.1_5'UTR|CACNA1C_uc001qkk.1_5'UTR|CACNA1C_uc001qkm.1_5'UTR	NM_199460	NP_955630	Q13936	CAC1C_HUMAN	calcium channel, voltage-dependent, L type,	213	Extracellular (Potential).|I.				axon guidance|calcium ion transport into cytosol|energy reserve metabolic process|regulation of insulin secretion	cytoplasm|postsynaptic density|voltage-gated calcium channel complex	calmodulin binding|voltage-gated calcium channel activity			ovary(10)|central_nervous_system(1)	11					Ibutilide(DB00308)|Isradipine(DB00270)|Magnesium Sulfate(DB00653)|Mibefradil(DB01388)|Nicardipine(DB00622)|Verapamil(DB00661)									0.330472	248.808313	254.736608	77	156	AA		KEEP	---	---	---	---	capture	OV - Ovarian serous cystadenocarcinoma(31;0.00256)	LUAD - Lung adenocarcinoma(1;0.134)	Silent	SNP	2437015	2437015	2656	12	A	G	G	2	2	CACNA1C	G	4	4
PPFIBP1	8496	broad.mit.edu	36	12	27700825	27700825	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0155-01	TCGA-06-0155-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr12:27700825G>A	uc001ric.1	+	c.799G>A	c.(799-801)GCA>ACA	p.A267T	PPFIBP1_uc001rib.1_Missense_Mutation_p.A236T|PPFIBP1_uc001ria.2_Missense_Mutation_p.A236T|PPFIBP1_uc001rid.1_Missense_Mutation_p.A114T|PPFIBP1_uc001rie.1_5'Flank	NM_003622	NP_003613	Q86W92	LIPB1_HUMAN	PTPRF interacting protein binding protein 1	267	Potential.				cell adhesion	plasma membrane	protein binding		PPFIBP1/ALK(3)	soft_tissue(3)|kidney(1)|skin(1)	5	Lung SC(9;0.0873)													0.210526	45.644064	53.010995	20	75	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	27700825	27700825	12743	12	G	A	A	42	42	PPFIBP1	A	2	2
TPH2	121278	broad.mit.edu	36	12	70652596	70652596	+	Silent	SNP	T	A	A			TCGA-06-0155-01	TCGA-06-0155-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr12:70652596T>A	uc009zrw.1	+	c.639T>A	c.(637-639)ACT>ACA	p.T213T	TPH2_uc001swy.2_Silent_p.T123T	NM_173353	NP_775489	Q8IWU9	TPH2_HUMAN	tryptophan hydroxylase 2	213					aromatic amino acid family metabolic process|hormone biosynthetic process|oxidation-reduction process|serotonin biosynthetic process	cytosol	amino acid binding|iron ion binding|tryptophan 5-monooxygenase activity			ovary(2)|central_nervous_system(1)	3					L-Tryptophan(DB00150)									0.376963	639.257363	646.870735	216	357	TT		KEEP	---	---	---	---	capture			Silent	SNP	70652596	70652596	16946	12	T	A	A	55	55	TPH2	A	4	4
MYF5	4617	broad.mit.edu	36	12	79635359	79635359	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0155-01	TCGA-06-0155-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr12:79635359G>A	uc001szg.2	+	c.386G>A	c.(385-387)CGC>CAC	p.R129H		NM_005593	NP_005584	P13349	MYF5_HUMAN	myogenic factor 5	129	Helix-loop-helix motif.				muscle cell fate commitment|positive regulation of muscle cell differentiation|skeletal muscle tissue development	nucleoplasm	DNA binding|protein heterodimerization activity|sequence-specific enhancer binding RNA polymerase II transcription factor activity|transcription regulator activity			ovary(1)	1														0.364078	200.750168	204.104671	75	131	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	79635359	79635359	10422	12	G	A	A	38	38	MYF5	A	1	1
GOLGA2B	55592	broad.mit.edu	36	12	99075543	99075543	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0155-01	TCGA-06-0155-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr12:99075543G>A	uc001tgs.1	-	c.184C>T	c.(184-186)CGG>TGG	p.R62W	GOLGA2B_uc001tgu.1_Missense_Mutation_p.R62W|GOLGA2B_uc001tgt.1_Non-coding_Transcript	NM_017600	NP_060070			golgi autoantigen, golgin subfamily a, 2-like 1												0														0.389474	103.867739	104.878947	37	58	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	99075543	99075543	6822	12	G	A	A	37	37	GOLGA2B	A	1	1
COG6	57511	broad.mit.edu	36	13	39191942	39191942	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0155-01	TCGA-06-0155-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr13:39191942G>A	uc001uxh.1	+	c.1562G>A	c.(1561-1563)CGT>CAT	p.R521H	COG6_uc001uxi.1_Missense_Mutation_p.R469H|COG6_uc010acb.1_Missense_Mutation_p.R521H	NM_020751	NP_065802	Q9Y2V7	COG6_HUMAN	component of oligomeric golgi complex 6 isoform	521					protein transport	Golgi membrane|Golgi transport complex				kidney(1)	1		Lung NSC(96;0.000124)|Breast(139;0.0199)|Prostate(109;0.0233)|Lung SC(185;0.0367)												0.315789	141.273747	146.443736	54	117	GG		KEEP	---	---	---	---	capture		all cancers(112;6.03e-09)|Epithelial(112;7e-07)|OV - Ovarian serous cystadenocarcinoma(117;0.00015)|BRCA - Breast invasive adenocarcinoma(63;0.00438)|GBM - Glioblastoma multiforme(144;0.0168)	Missense_Mutation	SNP	39191942	39191942	3800	13	G	A	A	40	40	COG6	A	1	1
SALL2	6297	broad.mit.edu	36	14	21061250	21061250	+	Missense_Mutation	SNP	C	G	G			TCGA-06-0155-01	TCGA-06-0155-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr14:21061250C>G	uc001wbe.1	-	c.2452G>C	c.(2452-2454)GCA>CCA	p.A818P	SALL2_uc001wbf.2_Intron|SALL2_uc001wbg.1_Intron	NM_005407	NP_005398	Q9Y467	SALL2_HUMAN	sal-like 2	818	Poly-Ala.						DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(2)|large_intestine(1)	3	all_cancers(95;0.000662)													0.1875	6.719853	9.67912	6	26	CC		KEEP	---	---	---	---	capture		GBM - Glioblastoma multiforme(265;0.0151)	Missense_Mutation	SNP	21061250	21061250	14291	14	C	G	G	28	28	SALL2	G	3	3
FANCM	57697	broad.mit.edu	36	14	44726760	44726760	+	Missense_Mutation	SNP	A	G	G			TCGA-06-0155-01	TCGA-06-0155-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr14:44726760A>G	uc001wwd.2	+	c.4699A>G	c.(4699-4701)AAA>GAA	p.K1567E	FANCM_uc010anf.1_Missense_Mutation_p.K1541E|FANCM_uc001wwe.2_Missense_Mutation_p.K1103E|FANCM_uc010ang.1_Missense_Mutation_p.K781E	NM_020937	NP_065988	Q8IYD8	FANCM_HUMAN	Fanconi anemia, complementation group M	1567					DNA repair	Fanconi anaemia nuclear complex	ATP binding|ATP-dependent helicase activity|chromatin binding|DNA binding|nuclease activity|protein binding			ovary(2)|breast(1)	3										793				0.208333	36.204563	41.985731	15	57	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	44726760	44726760	5907	14	A	G	G	9	9	FANCM	G	4	4
TBPL2	387332	broad.mit.edu	36	14	54976926	54976926	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0155-01	TCGA-06-0155-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr14:54976926G>A	uc001xby.1	-	c.91C>T	c.(91-93)CGG>TGG	p.R31W		NM_199047	NP_950248	Q6SJ96	TBPL2_HUMAN	TATA box binding protein like 2	31					multicellular organismal development|transcription initiation from RNA polymerase II promoter	cytoplasm|nucleus	DNA binding|RNA polymerase II transcription factor activity				0														0.418803	137.758806	138.428788	49	68	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	54976926	54976926	16172	14	G	A	A	40	40	TBPL2	A	1	1
EHD4	30844	broad.mit.edu	36	15	39980354	39980354	+	Silent	SNP	G	A	A			TCGA-06-0155-01	TCGA-06-0155-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr15:39980354G>A	uc001zot.1	-	c.1407C>T	c.(1405-1407)AAC>AAT	p.N469N		NM_139265	NP_644670	Q9H223	EHD4_HUMAN	EH-domain containing 4	469	EH.				endocytic recycling|protein homooligomerization	early endosome membrane|endoplasmic reticulum|nucleus|recycling endosome membrane	ATP binding|calcium ion binding|GTP binding|GTPase activity|nucleic acid binding|protein binding			ovary(2)	2		all_cancers(109;2.54e-12)|all_epithelial(112;6.59e-11)|Lung NSC(122;2.17e-07)|all_lung(180;8.79e-07)|Melanoma(134;0.091)												0.308511	75.940724	79.012334	29	65	GG		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(18;1.6e-19)|GBM - Glioblastoma multiforme(94;3.77e-06)|COAD - Colon adenocarcinoma(120;0.0474)|Colorectal(105;0.0538)	Silent	SNP	39980354	39980354	5169	15	G	A	A	40	40	EHD4	A	1	1
SCNN1G	6340	broad.mit.edu	36	16	23134032	23134032	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0155-01	TCGA-06-0155-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr16:23134032G>A	uc002dlm.1	+	c.1691G>A	c.(1690-1692)CGC>CAC	p.R564H		NM_001039	NP_001030	P51170	SCNNG_HUMAN	sodium channel, nonvoltage-gated 1, gamma	564	Cytoplasmic (By similarity).				excretion|sensory perception of taste	apical plasma membrane|integral to plasma membrane	ligand-gated sodium channel activity|WW domain binding			ovary(2)|large_intestine(1)|pancreas(1)	4					Amiloride(DB00594)|Triamterene(DB00384)									0.382353	180.776525	182.823573	65	105	GG		KEEP	---	---	---	---	capture		GBM - Glioblastoma multiforme(48;0.0366)	Missense_Mutation	SNP	23134032	23134032	14412	16	G	A	A	38	38	SCNN1G	A	1	1
RAB11FIP3	9727	broad.mit.edu	36	16	493083	493083	+	Silent	SNP	G	A	A			TCGA-06-0155-01	TCGA-06-0155-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr16:493083G>A	uc002chf.1	+	c.1380G>A	c.(1378-1380)GAG>GAA	p.E460E		NM_014700	NP_055515	O75154	RFIP3_HUMAN	rab11-family interacting protein 3 isoform 1	460					cell cycle|cytokinesis|endocytic recycling|protein transport	centrosome|cleavage furrow|midbody|recycling endosome membrane	ADP-ribosylation factor binding|calcium ion binding|protein homodimerization activity|Rab GTPase binding				0		Hepatocellular(16;0.0218)				Melanoma(160;2366 2595 4474 8099)								0.295238	89.784275	93.722351	31	74	GG		KEEP	---	---	---	---	capture			Silent	SNP	493083	493083	13354	16	G	A	A	35	35	RAB11FIP3	A	2	2
RHBDF1	64285	broad.mit.edu	36	16	53740	53740	+	Missense_Mutation	SNP	G	C	C			TCGA-06-0155-01	TCGA-06-0155-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr16:53740G>C	uc002cfl.2	-	c.307C>G	c.(307-309)CGC>GGC	p.R103G	RHBDF1_uc010bqo.1_Non-coding_Transcript	NM_022450	NP_071895	Q96CC6	RHDF1_HUMAN	rhomboid family 1	103	Cytoplasmic (Potential).				cell migration|cell proliferation|negative regulation of protein secretion|regulation of epidermal growth factor receptor signaling pathway|regulation of proteasomal protein catabolic process	endoplasmic reticulum membrane|Golgi membrane|integral to membrane	serine-type endopeptidase activity			ovary(1)|pancreas(1)	2		all_cancers(16;2.56e-05)|all_epithelial(16;0.000116)|Hepatocellular(780;0.0068)|Lung NSC(18;0.0795)|all_lung(18;0.159)												0.266667	7.659106	10.17807	12	33	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	53740	53740	13794	16	G	C	C	38	38	RHBDF1	C	3	3
MAPT	4137	broad.mit.edu	36	17	41429665	41429665	+	Missense_Mutation	SNP	G	C	C			TCGA-06-0155-01	TCGA-06-0155-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr17:41429665G>C	uc010dau.1	+	c.1625G>C	c.(1624-1626)GGC>GCC	p.G542A	MAPT_uc002ijr.2_Missense_Mutation_p.G524A|MAPT_uc002ijs.2_Missense_Mutation_p.G207A|MAPT_uc002ijx.2_Missense_Mutation_p.G178A|MAPT_uc002ijt.2_Missense_Mutation_p.G149A|MAPT_uc002iju.2_Missense_Mutation_p.G149A|MAPT_uc002ijv.2_Missense_Mutation_p.G156A|STH_uc002ijy.2_5'Flank	NM_001123066	NP_001116538	P10636	TAU_HUMAN	microtubule-associated protein tau isoform 6	524					cellular component disassembly involved in apoptosis|microtubule cytoskeleton organization|negative regulation of microtubule depolymerization|positive regulation of axon extension|positive regulation of microtubule polymerization|regulation of autophagy	axon|cytosol|growth cone|microtubule|microtubule associated complex|nuclear periphery|plasma membrane|tubulin complex	apolipoprotein E binding|enzyme binding|identical protein binding|lipoprotein particle binding|microtubule binding|protein binding|SH3 domain binding|structural constituent of cytoskeleton			pancreas(1)	1		Melanoma(429;0.216)												0.25	7.099021	8.307564	5	15	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	41429665	41429665	9680	17	G	C	C	42	42	MAPT	C	3	3
ASGR2	433	broad.mit.edu	36	17	6945633	6945633	+	Silent	SNP	G	A	A			TCGA-06-0155-01	TCGA-06-0155-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr17:6945633G>A	uc002gep.2	-	c.921C>T	c.(919-921)ACC>ACT	p.T307T	ASGR2_uc002gem.1_Silent_p.T246T|ASGR2_uc002gen.1_Silent_p.T288T|ASGR2_uc002geo.1_Silent_p.T302T|ASGR2_uc002ger.2_Silent_p.T307T|ASGR2_uc002geq.2_Silent_p.T283T	NM_001181	NP_550434	P07307	ASGR2_HUMAN	asialoglycoprotein receptor 2 isoform a	307	Extracellular (Potential).				cell surface receptor linked signaling pathway|endocytosis	focal adhesion|integral to membrane|nucleolus	asialoglycoprotein receptor activity|protein binding|sugar binding			ovary(1)	1					Antihemophilic Factor(DB00025)									0.314286	123.097436	127.368873	44	96	GG		KEEP	---	---	---	---	capture			Silent	SNP	6945633	6945633	1059	17	G	A	A	39	39	ASGR2	A	1	1
ASPSCR1	79058	broad.mit.edu	36	17	77547185	77547185	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0155-01	TCGA-06-0155-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr17:77547185C>T	uc002kcy.1	+	c.461C>T	c.(460-462)ACG>ATG	p.T154M	ASPSCR1_uc002kcw.1_Missense_Mutation_p.T154M|ASPSCR1_uc002kcx.1_Missense_Mutation_p.T154M|ASPSCR1_uc002kcz.1_Missense_Mutation_p.T154M|ASPSCR1_uc002kda.1_Missense_Mutation_p.T77M|ASPSCR1_uc002kdb.1_Missense_Mutation_p.T77M	NM_024083	NP_076988	Q9BZE9	ASPC1_HUMAN	alveolar soft part sarcoma chromosome region,	154							protein binding		ASPSCR1/TFE3(161)	soft_tissue(118)|kidney(43)	161	all_neural(118;0.0878)|Ovarian(332;0.12)|all_lung(278;0.246)									254				0.375	16.346566	16.565795	6	10	CC		KEEP	---	---	---	---	capture	BRCA - Breast invasive adenocarcinoma(99;0.0114)|OV - Ovarian serous cystadenocarcinoma(97;0.0191)		Missense_Mutation	SNP	77547185	77547185	1078	17	C	T	T	19	19	ASPSCR1	T	1	1
MIB1	57534	broad.mit.edu	36	18	17599778	17599778	+	Missense_Mutation	SNP	A	G	G			TCGA-06-0155-01	TCGA-06-0155-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr18:17599778A>G	uc002ktq.1	+	c.277A>G	c.(277-279)ATC>GTC	p.I93V	MIB1_uc002ktp.1_5'UTR	NM_020774	NP_065825	Q86YT6	MIB1_HUMAN	mindbomb homolog 1	93	ZZ-type.				Notch signaling pathway	nuclear membrane|plasma membrane	ubiquitin-protein ligase activity|zinc ion binding			ovary(4)	4														0.409091	271.367366	272.788428	81	117	AA		KEEP	---	---	---	---	capture	STAD - Stomach adenocarcinoma(5;0.212)		Missense_Mutation	SNP	17599778	17599778	9956	18	A	G	G	4	4	MIB1	G	4	4
LMAN1	3998	broad.mit.edu	36	18	55173781	55173781	+	Nonsense_Mutation	SNP	C	A	A			TCGA-06-0155-01	TCGA-06-0155-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr18:55173781C>A	uc002lhz.1	-	c.304G>T	c.(304-306)GAG>TAG	p.E102*		NM_005570	NP_005561	P49257	LMAN1_HUMAN	lectin, mannose-binding, 1 precursor	102	Lumenal (Potential).|L-type lectin-like.				blood coagulation|ER to Golgi vesicle-mediated transport|post-translational protein modification|protein folding|protein N-linked glycosylation via asparagine|protein transport	endoplasmic reticulum membrane|ER to Golgi transport vesicle membrane|ER-Golgi intermediate compartment membrane|Golgi membrane|integral to membrane	mannose binding|unfolded protein binding				0		Colorectal(73;0.0946)			Antihemophilic Factor(DB00025)									0.370588	175.973644	178.47807	63	107	CC		KEEP	---	---	---	---	capture			Nonsense_Mutation	SNP	55173781	55173781	9165	18	C	A	A	29	29	LMAN1	A	5	3
AKAP8	10270	broad.mit.edu	36	19	15345143	15345143	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0155-01	TCGA-06-0155-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr19:15345143C>T	uc002nav.1	-	c.380G>A	c.(379-381)CGC>CAC	p.R127H	AKAP8_uc010dzy.1_5'UTR|AKAP8_uc010dzz.1_Non-coding_Transcript	NM_005858	NP_005849	O43823	AKAP8_HUMAN	A-kinase anchor protein 8	127					signal transduction	nuclear matrix				ovary(1)|breast(1)	2						GBM(190;1671 2163 3274 27186 30476)								0.225	21.057537	23.834299	9	31	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	15345143	15345143	460	19	C	T	T	27	27	AKAP8	T	1	1
OR10H4	126541	broad.mit.edu	36	19	15921302	15921302	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0155-01	TCGA-06-0155-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr19:15921302C>T	uc002nbv.1	+	c.485C>T	c.(484-486)ACG>ATG	p.T162M		NM_001004465	NP_001004465	Q8NGA5	O10H4_HUMAN	olfactory receptor, family 10, subfamily H,	162	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)|breast(1)	2														0.262673	274.486283	296.580939	114	320	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	15921302	15921302	11314	19	C	T	T	19	19	OR10H4	T	1	1
DMWD	1762	broad.mit.edu	36	19	50981927	50981927	+	Missense_Mutation	SNP	G	C	C			TCGA-06-0155-01	TCGA-06-0155-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr19:50981927G>C	uc002pdj.1	-	c.667C>G	c.(667-669)CCT>GCT	p.P223A	DMWD_uc002pdk.1_Missense_Mutation_p.P223A|DMWD_uc010eko.1_5'UTR	NM_004943	NP_004934	Q09019	DMWD_HUMAN	dystrophia myotonica-containing WD repeat motif	223	WD 1.				meiosis						0		Ovarian(192;0.0308)|all_neural(266;0.112)												0.1875	7.249003	10.184992	6	26	GG		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(262;0.00604)|GBM - Glioblastoma multiforme(486;0.0807)|Epithelial(262;0.236)	Missense_Mutation	SNP	50981927	50981927	4775	19	G	C	C	42	42	DMWD	C	3	3
SIGLEC11	114132	broad.mit.edu	36	19	55145174	55145174	+	Silent	SNP	G	T	T			TCGA-06-0155-01	TCGA-06-0155-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr19:55145174G>T	uc002pre.1	-	c.1926C>A	c.(1924-1926)CTC>CTA	p.L642L	SIGLEC11_uc010enr.1_Silent_p.L582L	NM_052884	NP_443116	Q96RL6	SIG11_HUMAN	sialic acid binding Ig-like lectin 11 isoform 1	654	Cytoplasmic (Potential).				cell adhesion	integral to membrane	sugar binding			ovary(3)|central_nervous_system(2)|pancreas(1)	6		all_lung(116;0.00318)|all_neural(266;0.107)|Ovarian(192;0.17)												0.28866	67.052235	70.941999	28	69	GG		KEEP	---	---	---	---	capture		GBM - Glioblastoma multiforme(134;0.00107)|OV - Ovarian serous cystadenocarcinoma(262;0.00517)	Silent	SNP	55145174	55145174	14802	19	G	T	T	33	33	SIGLEC11	T	3	3
TUBB4	10382	broad.mit.edu	36	19	6453176	6453176	+	Silent	SNP	G	T	T			TCGA-06-0155-01	TCGA-06-0155-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr19:6453176G>T	uc002mfg.1	-	c.48C>A	c.(46-48)ATC>ATA	p.I16I	TUBB4_uc002mff.1_5'UTR	NM_006087	NP_006078	P04350	TBB4_HUMAN	tubulin, beta 4	16					'de novo' posttranslational protein folding|G2/M transition of mitotic cell cycle|microtubule-based movement|protein polymerization	cytosol|microtubule	GTP binding|GTPase activity|protein binding|structural molecule activity			ovary(2)	2		Hepatocellular(1079;0.00213)|Renal(1328;0.0183)												0.3	8.121542	8.478672	3	7	GG		KEEP	---	---	---	---	capture		Lung(535;3.23e-05)|STAD - Stomach adenocarcinoma(1328;8.24e-05)|GBM - Glioblastoma multiforme(1328;0.00839)|READ - Rectum adenocarcinoma(264;0.155)	Silent	SNP	6453176	6453176	17313	19	G	T	T	37	37	TUBB4	T	3	3
CD209	30835	broad.mit.edu	36	19	7713928	7713928	+	Silent	SNP	C	T	T			TCGA-06-0155-01	TCGA-06-0155-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr19:7713928C>T	uc002mht.1	-	c.1212G>A	c.(1210-1212)GCG>GCA	p.A404A	CD209_uc010dvp.1_3'UTR|CD209_uc002mhs.1_Silent_p.A334A|CD209_uc002mhq.1_Silent_p.A404A|CD209_uc002mhr.1_Silent_p.A380A|CD209_uc002mhu.1_Silent_p.A312A|CD209_uc010dvq.1_Silent_p.A398A|CD209_uc002mhv.1_Silent_p.A380A|CD209_uc002mhw.1_Silent_p.A268A|CD209_uc002mhx.1_Silent_p.A360A|CD209_uc010dvr.1_Silent_p.A168A	NM_021155	NP_066978	Q9NNX6	CD209_HUMAN	CD209 molecule isoform 1	404	Extracellular (Probable).				cell-cell recognition|endocytosis|heterophilic cell-cell adhesion|innate immune response|intracellular signal transduction|intracellular virion transport|leukocyte cell-cell adhesion|peptide antigen transport|viral genome replication|virion attachment to host cell surface receptor	cytoplasm|extracellular region|integral to membrane|plasma membrane	mannose binding|metal ion binding|peptide antigen binding|receptor activity|virion binding				0														0.266881	203.787795	219.053817	83	228	CC		KEEP	---	---	---	---	capture			Silent	SNP	7713928	7713928	3111	19	C	T	T	19	19	CD209	T	1	1
AP4B1	10717	broad.mit.edu	36	1	114240051	114240051	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0155-01	TCGA-06-0155-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:114240051G>A	uc001eeb.2	-	c.1643C>T	c.(1642-1644)CCG>CTG	p.P548L	AP4B1_uc001eec.2_Missense_Mutation_p.P380L|AP4B1_uc001eed.2_Missense_Mutation_p.P548L|AP4B1_uc001eea.1_3'UTR|AP4B1_uc001eee.1_Missense_Mutation_p.P75L	NM_006594	NP_006585	Q9Y6B7	AP4B1_HUMAN	adaptor-related protein complex 4, beta 1	548					intracellular protein transport|vesicle-mediated transport	clathrin adaptor complex|soluble fraction|trans-Golgi network	protein binding|protein transporter activity			ovary(3)	3	Lung SC(450;0.184)	all_cancers(81;4.5e-08)|all_epithelial(167;1.1e-07)|all_lung(203;1.53e-05)|Lung NSC(69;2.76e-05)												0.383929	128.534625	129.844075	43	69	GG		KEEP	---	---	---	---	capture		Lung(183;0.0234)|Colorectal(144;0.0686)|all cancers(265;0.0792)|Epithelial(280;0.0866)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)	Missense_Mutation	SNP	114240051	114240051	761	1	G	A	A	39	39	AP4B1	A	1	1
CLCNKB	1188	broad.mit.edu	36	1	16251338	16251338	+	Silent	SNP	C	T	T			TCGA-06-0155-01	TCGA-06-0155-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr1:16251338C>T	uc001axw.2	+	c.1467C>T	c.(1465-1467)TTC>TTT	p.F489F	CLCNKB_uc001axx.2_Silent_p.F489F|CLCNKB_uc001axy.2_Silent_p.F320F	NM_000085	NP_000076	P51801	CLCKB_HUMAN	chloride channel Kb	489	Helical; (Potential).				excretion	chloride channel complex|integral to plasma membrane	voltage-gated chloride channel activity				0		Colorectal(325;3.46e-05)|Breast(348;0.000278)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.000567)|Ovarian(437;0.0221)|Myeloproliferative disorder(586;0.0255)												0.209524	48.802634	56.995329	22	83	CC		KEEP	---	---	---	---	capture		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|Colorectal(212;8.04e-08)|COAD - Colon adenocarcinoma(227;5.46e-06)|BRCA - Breast invasive adenocarcinoma(304;9.02e-05)|Kidney(64;0.00016)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(313;0.00655)|READ - Rectum adenocarcinoma(331;0.0649)	Silent	SNP	16251338	16251338	3606	1	C	T	T	31	31	CLCNKB	T	1	1
ANGPTL1	9068	broad.mit.edu	36	1	177100994	177100994	+	Missense_Mutation	SNP	A	G	G			TCGA-06-0155-01	TCGA-06-0155-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr1:177100994A>G	uc001gma.1	-	c.541T>C	c.(541-543)TCC>CCC	p.S181P	RALGPS2_uc001glz.1_Intron|RALGPS2_uc001gly.1_Intron|ANGPTL1_uc001gmb.1_Missense_Mutation_p.S181P	NM_004673	NP_004664	O95841	ANGL1_HUMAN	angiopoietin-like 1 precursor	181						extracellular space	receptor binding				0														0.333333	144.83996	148.156067	45	90	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	177100994	177100994	616	1	A	G	G	9	9	ANGPTL1	G	4	4
OBSCN	84033	broad.mit.edu	36	1	226497768	226497768	+	Missense_Mutation	SNP	G	T	T			TCGA-06-0155-01	TCGA-06-0155-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:226497768G>T	uc009xez.1	+	c.3191G>T	c.(3190-3192)CGC>CTC	p.R1064L	OBSCN_uc001hsn.1_Missense_Mutation_p.R1064L	NM_001098623	NP_001092093	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and	1064	Ig-like 10.				apoptosis|cell differentiation|induction of apoptosis by extracellular signals|multicellular organismal development|nerve growth factor receptor signaling pathway|protein phosphorylation|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol|M band|Z disc	ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity|protein tyrosine kinase activity|Rho guanyl-nucleotide exchange factor activity|structural constituent of muscle|titin binding			large_intestine(7)|breast(5)|ovary(4)|skin(2)|stomach(1)|central_nervous_system(1)|pancreas(1)	21		Prostate(94;0.0405)								4006				0.365385	56.728812	57.550156	19	33	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	226497768	226497768	11217	1	G	T	T	38	38	OBSCN	T	3	3
CHRM3	1131	broad.mit.edu	36	1	238138858	238138858	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0155-01	TCGA-06-0155-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr1:238138858C>T	uc001hyp.1	+	c.1484C>T	c.(1483-1485)GCG>GTG	p.A495V	CHRM3_uc009xgk.1_Missense_Mutation_p.A495V	NM_000740	NP_000731	P20309	ACM3_HUMAN	cholinergic receptor, muscarinic 3	495	Helical; Name=6; (By similarity).				cell proliferation|energy reserve metabolic process|nervous system development|protein modification process|regulation of insulin secretion	basolateral plasma membrane|cell junction|integral to plasma membrane|postsynaptic membrane	muscarinic acetylcholine receptor activity|phosphatidylinositol phospholipase C activity			ovary(4)	4	Ovarian(103;0.127)	all_cancers(173;0.00567)|all_neural(198;0.203)			Anisotropine Methylbromide(DB00517)|Atropine(DB00572)|Benzquinamide(DB00767)|Cevimeline(DB00185)|Cryptenamine(DB00785)|Cyclizine(DB01176)|Darifenacin(DB00496)|Diphemanil Methylsulfate(DB00729)|Diphenidol(DB01231)|Homatropine Methylbromide(DB00725)|Methotrimeprazine(DB01403)|Metixene(DB00340)|Olanzapine(DB00334)|Oxybutynin(DB01062)|Oxyphencyclimine(DB00383)|Promazine(DB00420)|Promethazine(DB01069)|Propiomazine(DB00777)|Solifenacin(DB01591)|Thiethylperazine(DB00372)|Tiotropium(DB01409)|Tolterodine(DB01036)|Tridihexethyl(DB00505)									0.397059	228.928829	230.820998	81	123	CC		KEEP	---	---	---	---	capture	OV - Ovarian serous cystadenocarcinoma(106;0.00989)		Missense_Mutation	SNP	238138858	238138858	3512	1	C	T	T	27	27	CHRM3	T	1	1
RBL1	5933	broad.mit.edu	36	20	35097130	35097130	+	Missense_Mutation	SNP	T	A	A			TCGA-06-0155-01	TCGA-06-0155-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr20:35097130T>A	uc002xgi.1	-	c.2099A>T	c.(2098-2100)CAA>CTA	p.Q700L	RBL1_uc002xgj.1_Missense_Mutation_p.Q700L	NM_002895	NP_002886	P28749	RBL1_HUMAN	retinoblastoma-like protein 1 isoform a	700	Pocket; binds T and E1A.|Spacer.				cell cycle|chromatin modification|interspecies interaction between organisms|regulation of cell cycle|regulation of lipid kinase activity|transcription, DNA-dependent		transcription factor binding			lung(5)|ovary(2)	7		Myeloproliferative disorder(115;0.00878)								419				0.342222	215.395432	220.349439	77	148	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	35097130	35097130	13570	20	T	A	A	63	63	RBL1	A	4	4
DSCAM	1826	broad.mit.edu	36	21	40436384	40436384	+	Missense_Mutation	SNP	A	T	T			TCGA-06-0155-01	TCGA-06-0155-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr21:40436384A>T	uc002yyq.1	-	c.3377T>A	c.(3376-3378)GTC>GAC	p.V1126D	DSCAM_uc002yyr.1_Non-coding_Transcript	NM_001389	NP_001380	O60469	DSCAM_HUMAN	Down syndrome cell adhesion molecule isoform	1126	Extracellular (Potential).|Fibronectin type-III 3.				cell adhesion|dendrite self-avoidance|negative regulation of cell adhesion|positive regulation of axon extension involved in axon guidance|positive regulation of phosphorylation	axon|extracellular region|growth cone|integral to plasma membrane|membrane fraction	protein binding			ovary(6)	6		all_cancers(19;0.186)|Prostate(19;1.15e-05)|all_epithelial(19;0.0103)				Melanoma(134;970 1778 1785 21664 32388)								0.284974	139.844456	147.855367	55	138	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	40436384	40436384	4952	21	A	T	T	10	10	DSCAM	T	4	4
PRDM15	63977	broad.mit.edu	36	21	42103672	42103672	+	Silent	SNP	G	A	A			TCGA-06-0155-01	TCGA-06-0155-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr21:42103672G>A	uc002yzq.1	-	c.3657C>T	c.(3655-3657)CAC>CAT	p.H1219H	PRDM15_uc002yzo.1_Silent_p.H890H|PRDM15_uc002yzp.1_Silent_p.H910H|PRDM15_uc002yzr.1_Silent_p.H910H	NM_022115	NP_071398	P57071	PRD15_HUMAN	PR domain containing 15 isoform 1	1219	C2H2-type 15.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0														0.25	19.391618	21.205126	8	24	GG		KEEP	---	---	---	---	capture			Silent	SNP	42103672	42103672	12898	21	G	A	A	40	40	PRDM15	A	1	1
IL2RB	3560	broad.mit.edu	36	22	35854820	35854820	+	Silent	SNP	C	T	T			TCGA-06-0155-01	TCGA-06-0155-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr22:35854820C>T	uc003aqv.1	-	c.918G>A	c.(916-918)TCG>TCA	p.S306S		NM_000878	NP_000869	P14784	IL2RB_HUMAN	interleukin 2 receptor beta precursor	306	Cytoplasmic (Potential).				interspecies interaction between organisms|positive regulation of survival gene product expression|protein complex assembly	external side of plasma membrane|integral to plasma membrane	interleukin-2 receptor activity				0					Aldesleukin(DB00041)|Basiliximab(DB00074)|Daclizumab(DB00111)|Denileukin diftitox(DB00004)									0.447761	87.74314	87.901943	30	37	CC		KEEP	---	---	---	---	capture			Silent	SNP	35854820	35854820	7988	22	C	T	T	27	27	IL2RB	T	1	1
SCN9A	6335	broad.mit.edu	36	2	166793599	166793599	+	Missense_Mutation	SNP	T	A	A			TCGA-06-0155-01	TCGA-06-0155-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr2:166793599T>A	uc002udq.2	-	c.4021A>T	c.(4021-4023)AAC>TAC	p.N1341Y		NM_002977	NP_002968	Q15858	SCN9A_HUMAN	sodium channel, voltage-gated, type IX, alpha	1352	III.					voltage-gated sodium channel complex	voltage-gated sodium channel activity			ovary(6)|central_nervous_system(5)	11					Lamotrigine(DB00555)|Lidocaine(DB00281)									0.358974	469.767878	477.963992	168	300	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	166793599	166793599	14407	2	T	A	A	61	61	SCN9A	A	4	4
TTN	7273	broad.mit.edu	36	2	179145304	179145304	+	Missense_Mutation	SNP	T	C	C			TCGA-06-0155-01	TCGA-06-0155-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr2:179145304T>C	uc002umr.1	-	c.66097A>G	c.(66097-66099)ATT>GTT	p.I22033V	TTN_uc002ums.1_Missense_Mutation_p.I15728V|TTN_uc010frc.1_Missense_Mutation_p.I15661V|TTN_uc010frd.1_Missense_Mutation_p.I15536V	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	22960										ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1)	153										8722				0.391753	111.630132	112.624794	38	59	TT		KEEP	---	---	---	---	capture	OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)		Missense_Mutation	SNP	179145304	179145304	17290	2	T	C	C	51	51	TTN	C	4	4
CAPN13	92291	broad.mit.edu	36	2	30819873	30819873	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0155-01	TCGA-06-0155-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr2:30819873C>T	uc002rnn.1	-	c.1325G>A	c.(1324-1326)CGC>CAC	p.R442H	CAPN13_uc002rnm.1_Non-coding_Transcript|CAPN13_uc002rno.1_5'UTR	NM_144575	NP_653176	Q6MZZ7	CAN13_HUMAN	calpain 13	442					proteolysis	intracellular	calcium ion binding|calcium-dependent cysteine-type endopeptidase activity			large_intestine(1)|ovary(1)	2	all_hematologic(175;0.0487)|Acute lymphoblastic leukemia(172;0.155)													0.399361	363.985484	366.701299	125	188	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	30819873	30819873	2743	2	C	T	T	27	27	CAPN13	T	1	1
DYSF	8291	broad.mit.edu	36	2	71724619	71724619	+	Missense_Mutation	SNP	A	C	C			TCGA-06-0155-01	TCGA-06-0155-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr2:71724619A>C	uc010fen.1	+	c.4544A>C	c.(4543-4545)GAT>GCT	p.D1515A	DYSF_uc002sie.1_Missense_Mutation_p.D1476A|DYSF_uc002sig.2_Missense_Mutation_p.D1462A|DYSF_uc010fee.1_Missense_Mutation_p.D1497A|DYSF_uc010fef.1_Missense_Mutation_p.D1514A|DYSF_uc010feg.1_Missense_Mutation_p.D1507A|DYSF_uc010feh.1_Missense_Mutation_p.D1483A|DYSF_uc010fei.1_Missense_Mutation_p.D1493A|DYSF_uc010fej.1_Missense_Mutation_p.D1484A|DYSF_uc002sif.1_Missense_Mutation_p.D1477A|DYSF_uc010fek.1_Missense_Mutation_p.D1494A|DYSF_uc010fel.1_Missense_Mutation_p.D1463A|DYSF_uc010fem.1_Missense_Mutation_p.D1498A|DYSF_uc010feo.1_Missense_Mutation_p.D1508A	NM_003494	NP_003485	O75923	DYSF_HUMAN	dysferlin isoform 8	1476	Cytoplasmic (Potential).					cytoplasmic vesicle membrane|integral to membrane|sarcolemma	calcium-dependent phospholipid binding			ovary(3)|breast(2)|pancreas(1)	6														0.352941	38.792704	39.439849	12	22	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	71724619	71724619	5045	2	A	C	C	12	12	DYSF	C	4	4
ZIC1	7545	broad.mit.edu	36	3	148613058	148613058	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0155-01	TCGA-06-0155-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr3:148613058G>A	uc003ewe.1	+	c.1046G>A	c.(1045-1047)CGC>CAC	p.R349H		NM_003412	NP_003403	Q15915	ZIC1_HUMAN	zinc finger protein of the cerebellum 1	349	C2H2-type 4.				behavior|brain development|cell differentiation|inner ear morphogenesis|pattern specification process|positive regulation of protein import into nucleus|regulation of smoothened signaling pathway|regulation of transcription, DNA-dependent	cytoplasm|nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|transcription activator activity|zinc ion binding			ovary(1)|central_nervous_system(1)	2														0.238938	61.723114	68.719541	27	86	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	148613058	148613058	18269	3	G	A	A	38	38	ZIC1	A	1	1
CDHR4	389118	broad.mit.edu	36	3	49811335	49811335	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0155-01	TCGA-06-0155-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr3:49811335C>T	uc003cxp.1	-	c.499G>A	c.(499-501)GCC>ACC	p.A167T	CDHR4_uc010hkz.1_Silent_p.V141V	NM_001007540	NP_001007541	A6H8M9	CDHR4_HUMAN	cadherin-like 29	Error:Variant_position_missing_in_A6H8M9_after_alignment					homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding				0														0.5	56.096121	56.096121	20	20	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	49811335	49811335	3250	3	C	T	T	25	25	CDHR4	T	2	2
QRFPR	84109	broad.mit.edu	36	4	122473601	122473601	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0155-01	TCGA-06-0155-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr4:122473601G>A	uc010inj.1	-	c.622C>T	c.(622-624)CCT>TCT	p.P208S	QRFPR_uc010ink.1_Non-coding_Transcript|QRFPR_uc003ids.2_Missense_Mutation_p.P208S	NM_198179	NP_937822	Q96P65	QRFPR_HUMAN	G protein-coupled receptor 103	208	Extracellular (Potential).					integral to membrane|plasma membrane	neuropeptide Y receptor activity				0														0.379518	192.297466	194.406788	63	103	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	122473601	122473601	13336	4	G	A	A	43	43	QRFPR	A	2	2
SULT1B1	27284	broad.mit.edu	36	4	70630928	70630928	+	Missense_Mutation	SNP	T	G	G			TCGA-06-0155-01	TCGA-06-0155-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr4:70630928T>G	uc003hen.1	-	c.658A>C	c.(658-660)ATC>CTC	p.I220L		NM_014465	NP_055280	O43704	ST1B1_HUMAN	sulfotransferase family, cytosolic, 1B, member	220	PAPS (By similarity).				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														0.350515	109.82565	111.735749	34	63	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	70630928	70630928	15896	4	T	G	G	50	50	SULT1B1	G	4	4
BMP3	651	broad.mit.edu	36	4	82186426	82186426	+	Missense_Mutation	SNP	A	G	G			TCGA-06-0155-01	TCGA-06-0155-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr4:82186426A>G	uc003hmg.2	+	c.827A>G	c.(826-828)CAC>CGC	p.H276R		NM_001201	NP_001192	P12645	BMP3_HUMAN	bone morphogenetic protein 3 preproprotein	276					cartilage development|cell differentiation|cell-cell signaling|growth|ossification	extracellular space	BMP receptor binding|cytokine activity|growth factor activity			ovary(4)|central_nervous_system(1)	5														0.297872	114.797488	119.94611	42	99	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	82186426	82186426	1486	4	A	G	G	6	6	BMP3	G	4	4
SGCD	6444	broad.mit.edu	36	5	155868223	155868223	+	Missense_Mutation	SNP	G	T	T			TCGA-06-0155-01	TCGA-06-0155-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr5:155868223G>T	uc003lwc.2	+	c.227G>T	c.(226-228)GGT>GTT	p.G76V	SGCD_uc003lwa.1_Missense_Mutation_p.G76V|SGCD_uc003lwb.1_Missense_Mutation_p.G76V|SGCD_uc003lwd.2_Missense_Mutation_p.G75V	NM_000337	NP_000328	Q92629	SGCD_HUMAN	delta-sarcoglycan isoform 1	75	Extracellular (Potential).				cytoskeleton organization|muscle organ development	cytoplasm|cytoskeleton|integral to membrane|sarcoglycan complex|sarcolemma					0	Renal(175;0.00488)	Medulloblastoma(196;0.0378)|all_neural(177;0.106)												0.396552	66.410428	66.954262	23	35	GG		KEEP	---	---	---	---	capture	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)		Missense_Mutation	SNP	155868223	155868223	14692	5	G	T	T	44	44	SGCD	T	3	3
FLT4	2324	broad.mit.edu	36	5	179981275	179981275	+	Silent	SNP	C	T	T			TCGA-06-0155-01	TCGA-06-0155-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr5:179981275C>T	uc003mlz.2	-	c.1893G>A	c.(1891-1893)GCG>GCA	p.A631A	FLT4_uc003mma.2_Silent_p.A631A|FLT4_uc003mmb.1_Silent_p.A164A	NM_182925	NP_891555	P35916	VGFR3_HUMAN	fms-related tyrosine kinase 4 isoform 1	631	Ig-like C2-type 6.|Extracellular (Potential).				positive regulation of cell proliferation|protein phosphorylation	integral to plasma membrane	ATP binding|protein binding|vascular endothelial growth factor receptor activity			lung(3)|ovary(1)|central_nervous_system(1)|kidney(1)|skin(1)	7	all_cancers(89;2.21e-05)|all_epithelial(37;5.29e-06)|Renal(175;0.000159)|Lung NSC(126;0.00199)|all_lung(126;0.00351)|Breast(19;0.114)	all_cancers(40;0.00245)|Medulloblastoma(196;0.0133)|all_neural(177;0.0199)|all_hematologic(541;0.163)|Ovarian(839;0.238)			Sorafenib(DB00398)|Sunitinib(DB01268)	Colon(97;1075 1466 27033 27547 35871)				2638				0.361702	44.249832	45.003917	17	30	CC		KEEP	---	---	---	---	capture	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	all cancers(165;0.134)	Silent	SNP	179981275	179981275	6186	5	C	T	T	27	27	FLT4	T	1	1
CARD6	84674	broad.mit.edu	36	5	40889536	40889536	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0155-01	TCGA-06-0155-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr5:40889536G>A	uc003jmg.1	+	c.2345G>A	c.(2344-2346)AGT>AAT	p.S782N		NM_032587	NP_115976	Q9BX69	CARD6_HUMAN	caspase recruitment domain family, member 6	782					apoptosis|regulation of apoptosis	intracellular				ovary(2)|skin(2)|lung(1)	5														0.373362	483.70642	490.192988	171	287	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	40889536	40889536	2769	5	G	A	A	36	36	CARD6	A	2	2
ADAMTS6	11174	broad.mit.edu	36	5	64802610	64802610	+	Silent	SNP	C	T	T			TCGA-06-0155-01	TCGA-06-0155-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr5:64802610C>T	uc003jtp.1	-	c.213G>A	c.(211-213)CGG>CGA	p.R71R	ADAMTS6_uc003jto.1_Non-coding_Transcript|ADAMTS6_uc003jtq.1_Non-coding_Transcript|ADAMTS6_uc003jtr.1_5'UTR	NM_197941	NP_922932	Q9UKP5	ATS6_HUMAN	ADAM metallopeptidase with thrombospondin type 1	71					proteolysis	proteinaceous extracellular matrix	metalloendopeptidase activity|zinc ion binding				0		Lung NSC(167;2.44e-06)|Prostate(74;0.014)|Ovarian(174;0.0549)|Breast(144;0.111)|Colorectal(97;0.235)												0.323232	179.982055	185.448495	64	134	CC		KEEP	---	---	---	---	capture		Lung(70;0.00942)	Silent	SNP	64802610	64802610	271	5	C	T	T	30	30	ADAMTS6	T	2	2
MAP1B	4131	broad.mit.edu	36	5	71529825	71529825	+	Silent	SNP	A	G	G			TCGA-06-0155-01	TCGA-06-0155-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr5:71529825A>G	uc003kbw.2	+	c.4887A>G	c.(4885-4887)GCA>GCG	p.A1629A	MAP1B_uc010iyw.1_Silent_p.A1646A|MAP1B_uc010iyx.1_Silent_p.A1503A|MAP1B_uc010iyy.1_Silent_p.A1503A	NM_005909	NP_005900	P46821	MAP1B_HUMAN	microtubule-associated protein 1B	1629						microtubule|microtubule associated complex	structural molecule activity			large_intestine(2)|ovary(1)|central_nervous_system(1)|pancreas(1)	5		Lung NSC(167;0.00202)|Ovarian(174;0.0175)|Prostate(461;0.142)|Breast(144;0.198)				Melanoma(17;367 822 11631 31730 47712)								0.260274	151.075482	162.47156	57	162	AA		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(47;7.99e-54)	Silent	SNP	71529825	71529825	9611	5	A	G	G	5	5	MAP1B	G	4	4
HSF2	3298	broad.mit.edu	36	6	122785739	122785739	+	Silent	SNP	C	A	A			TCGA-06-0155-01	TCGA-06-0155-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr6:122785739C>A	uc003pyu.1	+	c.1008C>A	c.(1006-1008)ACC>ACA	p.T336T	HSF2_uc003pyv.1_Silent_p.T336T	NM_004506	NP_004497	Q03933	HSF2_HUMAN	heat shock transcription factor 2 isoform a	336					regulation of transcription, DNA-dependent|response to stress|transcription from RNA polymerase II promoter	cytoplasm|nucleus	sequence-specific DNA binding transcription factor activity|transcription coactivator activity				0														0.379085	162.805734	164.770908	58	95	CC		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(136;0.00371)|all cancers(137;0.0299)|GBM - Glioblastoma multiforme(226;0.0586)	Silent	SNP	122785739	122785739	7691	6	C	A	A	24	24	HSF2	A	3	3
QKI	9444	broad.mit.edu	36	6	163819851	163819851	+	Missense_Mutation	SNP	A	C	C			TCGA-06-0155-01	TCGA-06-0155-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr6:163819851A>C	uc003qui.1	+	c.335A>C	c.(334-336)CAA>CCA	p.Q112P	QKI_uc003que.1_Missense_Mutation_p.Q112P|QKI_uc003quf.1_Missense_Mutation_p.Q112P|QKI_uc003qug.1_Missense_Mutation_p.Q112P|QKI_uc003quh.1_Missense_Mutation_p.Q112P|QKI_uc003quj.1_Missense_Mutation_p.Q112P	NM_006775	NP_006766	Q96PU8	QKI_HUMAN	quaking homolog, KH domain RNA binding isoform	112	KH.				mRNA processing|mRNA transport|regulation of translation|RNA splicing	cytoplasm|nucleus|plasma membrane	RNA binding|SH3 domain binding			large_intestine(1)|ovary(1)	2		Breast(66;5e-05)|Prostate(117;0.0235)|all_neural(5;0.0416)|Ovarian(120;0.0448)|Glioma(2;0.203)												0.412214	186.535362	187.4148	54	77	AA		KEEP	---	---	---	---	capture		all cancers(1;4.4e-46)|OV - Ovarian serous cystadenocarcinoma(33;6.91e-23)|GBM - Glioblastoma multiforme(1;2.94e-19)|BRCA - Breast invasive adenocarcinoma(81;1.49e-06)|Kidney(3;0.000199)|KIRC - Kidney renal clear cell carcinoma(3;0.000234)	Missense_Mutation	SNP	163819851	163819851	13331	6	A	C	C	5	5	QKI	C	4	4
ITPR3	3710	broad.mit.edu	36	6	33761860	33761860	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0155-01	TCGA-06-0155-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr6:33761860C>T	uc010jvc.1	+	c.5720C>T	c.(5719-5721)ACG>ATG	p.T1907M	ITPR3_uc003oey.1_De_novo_Start_InFrame	NM_002224	NP_002215	Q14573	ITPR3_HUMAN	inositol 1,4,5-triphosphate receptor, type 3	1907	Cytoplasmic (Potential).				activation of phospholipase C activity|calcium ion transport into cytosol|energy reserve metabolic process|G-protein coupled receptor protein signaling pathway|nerve growth factor receptor signaling pathway|platelet activation|protein heterooligomerization|protein homooligomerization|regulation of insulin secretion|response to calcium ion	apical part of cell|brush border|endoplasmic reticulum membrane|integral to plasma membrane|myelin sheath|neuronal cell body|nuclear outer membrane|platelet dense tubular network membrane	inositol 1,3,4,5 tetrakisphosphate binding|inositol 1,4,5 trisphosphate binding|inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity|inositol hexakisphosphate binding|intracellular ligand-gated calcium channel activity|protein binding			central_nervous_system(5)|ovary(3)|lung(1)|kidney(1)	10														0.324675	64.035933	66.143178	25	52	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	33761860	33761860	8226	6	C	T	T	19	19	ITPR3	T	1	1
GLP1R	2740	broad.mit.edu	36	6	39132190	39132190	+	Nonsense_Mutation	SNP	C	T	T			TCGA-06-0155-01	TCGA-06-0155-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr6:39132190C>T	uc003ooj.2	+	c.118C>T	c.(118-120)CGA>TGA	p.R40*	GLP1R_uc003ooh.2_Non-coding_Transcript|GLP1R_uc003ooi.2_Non-coding_Transcript	NM_002062	NP_002053	P43220	GLP1R_HUMAN	glucagon-like peptide 1 receptor	40	Extracellular (Potential).				activation of adenylate cyclase activity|cAMP-mediated signaling|elevation of cytosolic calcium ion concentration|energy reserve metabolic process|regulation of insulin secretion	integral to membrane|plasma membrane	glucagon receptor activity|peptide receptor activity, G-protein coupled			lung(1)|pancreas(1)	2					Exenatide(DB01276)|Glucagon recombinant(DB00040)									0.296875	49.099591	51.461249	19	45	CC		KEEP	---	---	---	---	capture			Nonsense_Mutation	SNP	39132190	39132190	6720	6	C	T	T	27	27	GLP1R	T	5	1
DST	667	broad.mit.edu	36	6	56613314	56613314	+	Silent	SNP	A	G	G			TCGA-06-0155-01	TCGA-06-0155-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr6:56613314A>G	uc003pcz.2	-	c.1443T>C	c.(1441-1443)TCT>TCC	p.S481S	DST_uc003pcy.2_Silent_p.S155S|DST_uc003pdb.2_Silent_p.S155S|DST_uc003pdc.2_Silent_p.S155S|DST_uc003pdd.2_Silent_p.S155S	NM_183380	NP_899236	Q03001	DYST_HUMAN	dystonin isoform 1	481					cell adhesion|cell cycle arrest|integrin-mediated signaling pathway|intermediate filament cytoskeleton organization	basement membrane|cytoplasmic membrane-bounded vesicle|hemidesmosome|microtubule plus end|nucleus	actin binding|calcium ion binding|integrin binding|microtubule plus-end binding|protein C-terminus binding			ovary(7)|central_nervous_system(6)	13	Lung NSC(77;0.103)									2498				0.331707	217.334201	222.476601	68	137	AA		KEEP	---	---	---	---	capture	LUSC - Lung squamous cell carcinoma(124;0.0485)|Lung(124;0.0956)		Silent	SNP	56613314	56613314	4967	6	A	G	G	3	3	DST	G	4	4
SRPK2	6733	broad.mit.edu	36	7	104569877	104569877	+	Nonsense_Mutation	SNP	G	A	A			TCGA-06-0155-01	TCGA-06-0155-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr7:104569877G>A	uc003vcv.1	-	c.1357C>T	c.(1357-1359)CGA>TGA	p.R453*	SRPK2_uc003vct.1_Nonsense_Mutation_p.R442*|SRPK2_uc003vcu.1_Nonsense_Mutation_p.R442*|SRPK2_uc003vcw.1_Nonsense_Mutation_p.R442*	NM_182692	NP_872634	P78362	SRPK2_HUMAN	SFRS protein kinase 2 isoform a	442	Protein kinase.				angiogenesis|cell differentiation|innate immune response|intracellular protein kinase cascade|negative regulation of viral genome replication|nuclear speck organization|positive regulation of cell cycle|positive regulation of cell proliferation|positive regulation of gene expression|positive regulation of neuron apoptosis|positive regulation of viral genome replication|protein phosphorylation|spliceosome assembly	cytoplasm|nucleolus	14-3-3 protein binding|ATP binding|magnesium ion binding|protein serine/threonine kinase activity			central_nervous_system(3)|ovary(2)	5										326				0.28642	298.816821	315.34338	116	289	GG		KEEP	---	---	---	---	capture			Nonsense_Mutation	SNP	104569877	104569877	15674	7	G	A	A	40	40	SRPK2	A	5	1
GPR37	2861	broad.mit.edu	36	7	124192163	124192163	+	Missense_Mutation	SNP	C	G	G			TCGA-06-0155-01	TCGA-06-0155-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr7:124192163C>G	uc003vli.1	-	c.104G>C	c.(103-105)AGA>ACA	p.R35T		NM_005302	NP_005293	O15354	GPR37_HUMAN	G protein-coupled receptor 37	35	Extracellular (Potential).					endoplasmic reticulum membrane|integral to plasma membrane	G-protein coupled receptor activity			ovary(1)|central_nervous_system(1)	2														0.265306	35.752017	38.1916	13	36	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	124192163	124192163	6966	7	C	G	G	32	32	GPR37	G	3	3
TPST1	8460	broad.mit.edu	36	7	65388977	65388977	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0155-01	TCGA-06-0155-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr7:65388977G>A	uc003tuw.1	+	c.890G>A	c.(889-891)GGA>GAA	p.G297E	TPST1_uc010kzy.1_Non-coding_Transcript|TPST1_uc010kzz.1_Missense_Mutation_p.G297E|TPST1_uc010laa.1_Missense_Mutation_p.G297E	NM_003596	NP_003587	O60507	TPST1_HUMAN	tyrosylprotein sulfotransferase 1	297	Lumenal (Potential).				inflammatory response|peptidyl-tyrosine sulfation	Golgi membrane|integral to membrane|membrane fraction	protein-tyrosine sulfotransferase activity				0														0.25625	105.197018	113.819343	41	119	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	65388977	65388977	16971	7	G	A	A	41	41	TPST1	A	2	2
ATAD2	29028	broad.mit.edu	36	8	124427650	124427650	+	Missense_Mutation	SNP	T	C	C			TCGA-06-0155-01	TCGA-06-0155-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr8:124427650T>C	uc003yqh.2	-	c.2389A>G	c.(2389-2391)ATA>GTA	p.I797V	ATAD2_uc003yqi.2_Non-coding_Transcript|ATAD2_uc003yqj.2_Missense_Mutation_p.I797V	NM_014109	NP_054828	Q6PL18	ATAD2_HUMAN	ATPase family, AAA domain containing 2	797					regulation of transcription, DNA-dependent|transcription, DNA-dependent	mitochondrion|nucleus	ATP binding|ATPase activity			ovary(2)	2	Lung NSC(37;1.25e-09)|Ovarian(258;0.00838)													0.394118	222.593691	224.260445	67	103	TT		KEEP	---	---	---	---	capture	STAD - Stomach adenocarcinoma(47;0.00288)		Missense_Mutation	SNP	124427650	124427650	1090	8	T	C	C	50	50	ATAD2	C	4	4
SPATC1	375686	broad.mit.edu	36	8	145167485	145167485	+	Silent	SNP	G	A	A			TCGA-06-0155-01	TCGA-06-0155-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr8:145167485G>A	uc003zaq.1	+	c.522G>A	c.(520-522)TCG>TCA	p.S174S		NM_198572	NP_940974	Q76KD6	SPERI_HUMAN	spermatogenesis and centriole associated 1	265										ovary(1)|central_nervous_system(1)	2	all_cancers(97;8.2e-11)|all_epithelial(106;1.1e-09)|Lung NSC(106;5.89e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)													0.389535	194.289637	196.126812	67	105	GG		KEEP	---	---	---	---	capture	OV - Ovarian serous cystadenocarcinoma(54;6.79e-41)|Epithelial(56;1.02e-39)|all cancers(56;3.67e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.105)		Silent	SNP	145167485	145167485	15527	8	G	A	A	37	37	SPATC1	A	1	1
DOCK5	80005	broad.mit.edu	36	8	25278070	25278070	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0155-01	TCGA-06-0155-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr8:25278070G>A	uc003xeg.1	+	c.3056G>A	c.(3055-3057)CGT>CAT	p.R1019H	DOCK5_uc010luf.1_Non-coding_Transcript|DOCK5_uc003xei.1_Missense_Mutation_p.R589H|DOCK5_uc003xej.1_Non-coding_Transcript|DOCK5_uc003xeh.1_Missense_Mutation_p.R733H	NM_024940	NP_079216	Q9H7D0	DOCK5_HUMAN	dedicator of cytokinesis 5	1019						cytoplasm	GTP binding|GTPase binding|guanyl-nucleotide exchange factor activity			ovary(3)	3		all_cancers(63;0.0361)|Ovarian(32;0.000711)|all_epithelial(46;0.0153)|Hepatocellular(4;0.115)|Prostate(55;0.13)|Breast(100;0.143)				Pancreas(145;34 1887 3271 10937 30165)								0.357143	27.638557	28.14331	10	18	GG		KEEP	---	---	---	---	capture		UCEC - Uterine corpus endometrioid carcinoma (27;0.0267)|Epithelial(17;1.07e-11)|Colorectal(74;0.0276)|COAD - Colon adenocarcinoma(73;0.0828)	Missense_Mutation	SNP	25278070	25278070	4874	8	G	A	A	40	40	DOCK5	A	1	1
STK3	6788	broad.mit.edu	36	8	99787879	99787879	+	Missense_Mutation	SNP	G	C	C			TCGA-06-0155-01	TCGA-06-0155-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr8:99787879G>C	uc003yio.1	-	c.760C>G	c.(760-762)CCA>GCA	p.P254A	STK3_uc003yip.1_Missense_Mutation_p.P226A|STK3_uc010mbm.1_Intron	NM_006281	NP_006272	Q13188	STK3_HUMAN	serine/threonine kinase 3 (STE20 homolog,	226	Protein kinase.				apoptosis|hippo signaling cascade|intracellular protein kinase cascade|negative regulation of canonical Wnt receptor signaling pathway|positive regulation of apoptosis|protein phosphorylation	cytoplasm|nucleus	ATP binding|magnesium ion binding|protein dimerization activity|protein serine/threonine kinase activator activity|protein serine/threonine kinase activity			lung(2)|ovary(1)	3	Breast(36;2.4e-06)	Breast(495;0.106)								180				0.403509	152.429026	153.356673	46	68	GG		KEEP	---	---	---	---	capture	OV - Ovarian serous cystadenocarcinoma(57;0.0382)	KIRC - Kidney renal clear cell carcinoma(542;9.44e-06)	Missense_Mutation	SNP	99787879	99787879	15815	8	G	C	C	41	41	STK3	C	3	3
DCAF12L2	340578	broad.mit.edu	36	X	125126852	125126852	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0155-01	TCGA-06-0155-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chrX:125126852C>T	uc004euk.1	-	c.737G>A	c.(736-738)CGT>CAT	p.R246H		NM_001013628	NP_001013650	Q5VW00	DC122_HUMAN	WD repeat domain 40C	246										lung(2)|large_intestine(1)|ovary(1)|pancreas(1)	5														0.666667	86.106088	87.139591	28	14	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	125126852	125126852	4436	23	C	T	T	19	19	DCAF12L2	T	1	1
SLITRK4	139065	broad.mit.edu	36	X	142545980	142545980	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0155-01	TCGA-06-0155-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chrX:142545980C>T	uc004fbx.1	-	c.611G>A	c.(610-612)CGT>CAT	p.R204H	SLITRK4_uc004fby.1_Missense_Mutation_p.R204H|SLITRK4_uc010nsn.1_Missense_Mutation_p.R204H	NM_173078	NP_775101	Q8IW52	SLIK4_HUMAN	slit and trk like 4 protein	204	Extracellular (Potential).					integral to membrane				upper_aerodigestive_tract(1)|large_intestine(1)	2	Acute lymphoblastic leukemia(192;6.56e-05)													0.57764	287.681444	288.526457	93	68	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	142545980	142545980	15243	23	C	T	T	19	19	SLITRK4	T	1	1
SPANXN2	494119	broad.mit.edu	36	X	142623103	142623103	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0155-01	TCGA-06-0155-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chrX:142623103C>T	uc004fbz.1	-	c.241G>A	c.(241-243)GTC>ATC	p.V81I		NM_001009615	NP_001009615	Q5MJ10	SPXN2_HUMAN	SPANX-N2 protein	81										ovary(1)	1	Acute lymphoblastic leukemia(192;6.56e-05)													0.791892	960.93272	990.126638	293	77	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	142623103	142623103	15499	23	C	T	T	19	19	SPANXN2	T	1	1
ZMYM3	9203	broad.mit.edu	36	X	70389578	70389578	+	Missense_Mutation	SNP	G	C	C			TCGA-06-0155-01	TCGA-06-0155-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chrX:70389578G>C	uc004dzh.1	-	c.253C>G	c.(253-255)CTG>GTG	p.L85V	ZMYM3_uc004dzi.1_Missense_Mutation_p.L85V|ZMYM3_uc004dzj.1_Missense_Mutation_p.L85V|ZMYM3_uc004dzk.2_Missense_Mutation_p.L85V|ZMYM3_uc004dzl.2_Missense_Mutation_p.L85V|ZMYM3_uc004dzm.2_Missense_Mutation_p.L85V	NM_201599	NP_963893	Q14202	ZMYM3_HUMAN	zinc finger protein 261	85					multicellular organismal development	nucleus	DNA binding|zinc ion binding			ovary(1)	1	Renal(35;0.156)													0.2	6.986794	8.663551	4	16	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	70389578	70389578	18292	23	G	C	C	34	34	ZMYM3	C	3	3
PCDHGC3	5098	broad.mit.edu	36	5	140837951	140837954	+	Frame_Shift_Del	DEL	TTCT	-	-			TCGA-06-0155-01	TCGA-06-0155-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:140837951_140837954delTTCT	uc003lkv.1	+	c.2084_2087delTTCT	c.(2083-2088)CTTCTTfs	p.L695fs	PCDHGA1_uc003lji.1_Intron|PCDHGA2_uc003ljk.1_Intron|PCDHGA3_uc010jfx.1_Intron|PCDHGA3_uc003ljm.1_Intron|PCDHGB1_uc003ljo.1_Intron|PCDHGA4_uc003ljq.1_Intron|PCDHGB2_uc003ljs.1_Intron|PCDHGA5_uc003lju.1_Intron|PCDHGB3_uc003ljw.1_Intron|PCDHGA6_uc003ljy.1_Intron|PCDHGA7_uc003lka.1_Intron|PCDHGB4_uc003lkc.1_Intron|PCDHGA8_uc003lkd.1_Intron|PCDHGB5_uc003lkf.1_Intron|PCDHGA9_uc003lkh.1_Intron|PCDHGB6_uc003lkj.1_Intron|PCDHGA10_uc003lkl.1_Intron|PCDHGB7_uc003lkn.1_Intron|PCDHGA11_uc003lkp.1_Intron|PCDHGA11_uc003lkq.1_Intron|PCDHGA12_uc003lkt.1_Intron|PCDHGC3_uc003lku.1_Frame_Shift_Del_p.L695fs|PCDHGC3_uc003lkw.1_Intron	NM_002588	NP_002579	Q9UN70	PCDGK_HUMAN	protocadherin gamma subfamily C, 3 isoform 1	695_696	Helical; (Potential).				calcium-dependent cell-cell adhesion|homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)									OREG0016865	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	0.34			268	511				---	---	---	---	capture_indel			Frame_Shift_Del	DEL	140837951	140837954	11989	5	TTCT	-	-	56	56	PCDHGC3	-	5	5
