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
SEMA4G	57715	broad.mit.edu	36	10	102722729	102722729	+	Missense_Mutation	SNP	C	T	T			TCGA-06-1087-01	TCGA-06-1087-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr10:102722729C>T	uc001krw.1	+	c.70C>T	c.(70-72)CGG>TGG	p.R24W	SEMA4G_uc001krv.2_Non-coding_Transcript|SEMA4G_uc001krx.2_Missense_Mutation_p.R24W	NM_017893	NP_060363	Q9NTN9	SEM4G_HUMAN	semaphorin 4G	24	Extracellular (Potential).				cell differentiation|nervous system development	integral to membrane	receptor activity			breast(1)	1		Colorectal(252;0.234)		Epithelial(162;3.71e-09)|all cancers(201;2.1e-07)										0.96	88.868534	90.129848	24	1	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	102722729	102722729	14522	10	C	T	T	27	27	SEMA4G	T	1	1
DNAJB12	54788	broad.mit.edu	36	10	73766397	73766397	+	Silent	SNP	G	A	A			TCGA-06-1087-01	TCGA-06-1087-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr10:73766397G>A	uc001jsz.1	-	c.897C>T	c.(895-897)GAC>GAT	p.D299D	DNAJB12_uc001jsy.1_Non-coding_Transcript|DNAJB12_uc001jta.1_Silent_p.D299D	NM_017626	NP_060096	Q9NXW2	DJB12_HUMAN	DnaJ (Hsp40) homolog, subfamily B, member 12	299					protein folding	endoplasmic reticulum|integral to membrane	heat shock protein binding|unfolded protein binding				0														0.290323	14.949864	16.180509	9	22	GG		KEEP	---	---	---	---	capture			Silent	SNP	73766397	73766397	4800	10	G	A	A	48	48	DNAJB12	A	2	2
CCDC87	55231	broad.mit.edu	36	11	66115552	66115552	+	Missense_Mutation	SNP	G	T	T			TCGA-06-1087-01	TCGA-06-1087-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr11:66115552G>T	uc001oiq.2	-	c.1511C>A	c.(1510-1512)TCT>TAT	p.S504Y	CCS_uc001oir.1_5'Flank	NM_018219	NP_060689	Q9NVE4	CCD87_HUMAN	coiled-coil domain containing 87	504										ovary(1)	1														0.105	14.727311	45.768447	21	179	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	66115552	66115552	2987	11	G	T	T	33	33	CCDC87	T	3	3
C2CD3	26005	broad.mit.edu	36	11	73438158	73438158	+	Missense_Mutation	SNP	A	C	C			TCGA-06-1087-01	TCGA-06-1087-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr11:73438158A>C	uc001ouu.2	-	c.5233T>G	c.(5233-5235)TAC>GAC	p.Y1745D	C2CD3_uc001out.2_Non-coding_Transcript	NM_015531	NP_056346	Q4AC94	C2CD3_HUMAN	C2 calcium-dependent domain containing 3	1745										ovary(3)|pancreas(2)	5	Breast(11;4.16e-06)													0.214286	10.710478	12.857383	6	22	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	73438158	73438158	2237	11	A	C	C	14	14	C2CD3	C	4	4
HIP1R	9026	broad.mit.edu	36	12	121901376	121901377	+	Missense_Mutation	DNP	AC	GG	GG			TCGA-06-1087-01	TCGA-06-1087-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:121901376_121901377AC>GG	uc001udj.1	+	c.480_481AC>GG	c.(478-483)GTACTG>GTGGTG	p.L161V	HIP1R_uc001udg.1_Missense_Mutation_p.L149V|HIP1R_uc001udi.1_Missense_Mutation_p.L161V	NM_003959	NP_003950	O75146	HIP1R_HUMAN	huntingtin interacting protein-1-related	161					receptor-mediated endocytosis	clathrin coated vesicle membrane|coated pit|perinuclear region of cytoplasm	actin binding|phosphatidylinositol binding			ovary(1)	1	all_neural(191;0.0837)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;4.6e-05)|Epithelial(86;0.000119)|BRCA - Breast invasive adenocarcinoma(302;0.2)										0.269231	14.812733	16.063251	7	19	AA		KEEP	---	---	---	---	capture			Missense_Mutation	DNP	121901376	121901377	7400	12	AC	GG	GG	14	14	HIP1R	GG	4	4
RDH5	5959	broad.mit.edu	36	12	54404047	54404047	+	Missense_Mutation	SNP	C	T	T			TCGA-06-1087-01	TCGA-06-1087-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr12:54404047C>T	uc001shk.1	+	c.680C>T	c.(679-681)GCA>GTA	p.A227V	RDH5_uc001shj.2_3'UTR|RDH5_uc001shl.1_Missense_Mutation_p.A227V	NM_002905	NP_002896	Q92781	RDH1_HUMAN	retinol dehydrogenase 5 (11-cis and 9-cis)	227					oxidation-reduction process|response to stimulus|visual perception	membrane	binding|retinol dehydrogenase activity			ovary(1)	1					NADH(DB00157)|Vitamin A(DB00162)									0.473684	70.299502	70.334989	27	30	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	54404047	54404047	13664	12	C	T	T	25	25	RDH5	T	2	2
CD4	920	broad.mit.edu	36	12	6798325	6798325	+	Missense_Mutation	SNP	A	C	C			TCGA-06-1087-01	TCGA-06-1087-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr12:6798325A>C	uc001qqv.1	+	c.1330A>C	c.(1330-1332)ACC>CCC	p.T444P	CD4_uc009zfc.1_Missense_Mutation_p.T265P|GPR162_uc001qqw.1_5'Flank|GPR162_uc001qqx.1_5'Flank|GPR162_uc009zfd.1_5'Flank	NM_000616	NP_000607	P01730	CD4_HUMAN	CD4 antigen precursor	444	Cytoplasmic (Potential).|HIV-1 Vpu-susceptibility domain.				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)												0.210526	6.42363	12.778896	16	60	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	6798325	6798325	3142	12	A	C	C	10	10	CD4	C	4	4
KL	9365	broad.mit.edu	36	13	32533828	32533828	+	Missense_Mutation	SNP	T	A	A			TCGA-06-1087-01	TCGA-06-1087-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr13:32533828T>A	uc001uus.1	+	c.2612T>A	c.(2611-2613)ATA>AAA	p.I871K	KL_uc001uur.1_3'UTR	NM_004795	NP_004786	Q9UEF7	KLOT_HUMAN	klotho	871	Glycosyl hydrolase-1 2.|Extracellular (Potential).				aging|carbohydrate metabolic process|insulin receptor signaling pathway|positive regulation of bone mineralization	extracellular space|extracellular space|integral to membrane|integral to plasma membrane|membrane fraction|soluble fraction	beta-glucosidase activity|beta-glucuronidase activity|cation binding|fibroblast growth factor binding|hormone activity|signal transducer activity|vitamin D binding			large_intestine(1)|ovary(1)	2	all_epithelial(80;0.133)	Ovarian(182;1.78e-06)|Breast(139;4.08e-05)|Hepatocellular(188;0.00886)|Lung SC(185;0.0262)		GBM - Glioblastoma multiforme(144;7.13e-230)|all cancers(112;1.33e-165)|OV - Ovarian serous cystadenocarcinoma(117;1.09e-113)|Epithelial(112;3.79e-112)|Lung(94;8.52e-27)|LUSC - Lung squamous cell carcinoma(192;1.4e-13)|Kidney(163;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(186;5.63e-08)|BRCA - Breast invasive adenocarcinoma(63;1.41e-05)										0.2	16.523289	21.988775	13	52	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	32533828	32533828	8643	13	T	A	A	49	49	KL	A	4	4
KIAA0564	23078	broad.mit.edu	36	13	41171293	41171293	+	Missense_Mutation	SNP	T	G	G			TCGA-06-1087-01	TCGA-06-1087-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr13:41171293T>G	uc001uyj.1	-	c.3478A>C	c.(3478-3480)ACA>CCA	p.T1160P		NM_015058	NP_055873	A3KMH1	K0564_HUMAN	hypothetical protein LOC23078 isoform a	1160						extracellular region	ATP binding|ATPase activity			ovary(3)|upper_aerodigestive_tract(1)|kidney(1)	5		Lung NSC(96;4.61e-06)|Prostate(109;0.0167)|Lung SC(185;0.0262)|Breast(139;0.0854)|Hepatocellular(98;0.114)		OV - Ovarian serous cystadenocarcinoma(117;0.000368)|GBM - Glioblastoma multiforme(144;0.0033)|BRCA - Breast invasive adenocarcinoma(63;0.0969)										0.285714	6.443417	7.383632	6	15	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	41171293	41171293	8492	13	T	G	G	60	60	KIAA0564	G	4	4
RB1	5925	broad.mit.edu	36	13	47937229	47937229	+	Nonsense_Mutation	SNP	T	A	A			TCGA-06-1087-01	TCGA-06-1087-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr13:47937229T>A	uc001vcb.1	+	c.2306T>A	c.(2305-2307)TTG>TAG	p.L769*		NM_000321	NP_000312	P06400	RB_HUMAN	retinoblastoma 1	769	Interaction with LIMD1.|Pocket; binds T and E1A.|Domain B.				androgen receptor signaling pathway|cell cycle arrest|chromatin remodeling|G1 phase of mitotic cell cycle|interspecies interaction between organisms|maintenance of mitotic sister chromatid cohesion|mitotic cell cycle G1/S transition checkpoint|myoblast differentiation|negative regulation of cell growth|negative regulation of protein kinase activity|negative regulation of S phase of mitotic cell cycle|negative regulation of sequence-specific DNA binding transcription factor activity|positive regulation of mitotic metaphase/anaphase transition|protein localization to chromosome, centromeric region|Ras protein signal transduction|regulation of centromere complex assembly|regulation of cohesin localization to chromatin|regulation of lipid kinase activity|regulation of transcription involved in G1/S phase of mitotic cell cycle|S phase of mitotic cell cycle|sister chromatid biorientation	chromatin|PML body|Rb-E2F complex|SWI/SNF complex	androgen receptor binding|DNA binding|kinase binding|phosphoprotein binding|sequence-specific DNA binding transcription factor activity|transcription coactivator activity|transcription factor binding|transcription repressor activity|ubiquitin protein ligase binding	p.?(1)		lung(93)|eye(89)|central_nervous_system(47)|bone(22)|breast(20)|urinary_tract(17)|haematopoietic_and_lymphoid_tissue(14)|ovary(10)|soft_tissue(8)|prostate(8)|skin(7)|endometrium(5)|cervix(3)|liver(3)|salivary_gland(2)|stomach(2)|oesophagus(1)|adrenal_gland(1)|kidney(1)|gastrointestinal_tract_(site_indeterminate)(1)|pituitary(1)	355		all_cancers(8;6.9e-71)|all_epithelial(8;4.61e-22)|Acute lymphoblastic leukemia(8;1.1e-21)|all_hematologic(8;2.3e-21)|all_lung(13;1.51e-09)|Lung NSC(96;7.03e-07)|Breast(56;1.53e-05)|Prostate(109;0.000493)|Myeloproliferative disorder(33;0.0179)|Hepatocellular(98;0.0207)|all_neural(104;0.0227)|Glioma(44;0.0286)|Lung SC(185;0.0301)		GBM - Glioblastoma multiforme(2;9.98e-18)|LUSC - Lung squamous cell carcinoma(3;0.013)	Insulin Glargine recombinant(DB00047)|Insulin Lyspro recombinant(DB00046)|Insulin recombinant(DB00030)|Insulin, porcine(DB00071)			6		568	TCGA GBM(7;6.82e-08)|TSP Lung(12;0.097)|TCGA Ovarian(6;0.080)			0.824561	162.852764	168.511919	47	10	TT		KEEP	---	---	---	---	capture			Nonsense_Mutation	SNP	47937229	47937229	13559	13	T	A	A	63	63	RB1	A	5	4
KCNH5	27133	broad.mit.edu	36	14	62542924	62542924	+	Missense_Mutation	SNP	T	A	A			TCGA-06-1087-01	TCGA-06-1087-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr14:62542924T>A	uc001xfx.1	-	c.217A>T	c.(217-219)ACT>TCT	p.T73S	KCNH5_uc001xfy.1_Missense_Mutation_p.T73S|KCNH5_uc001xfz.1_Missense_Mutation_p.T15S|KCNH5_uc001xga.2_Missense_Mutation_p.T15S	NM_139318	NP_647479	Q8NCM2	KCNH5_HUMAN	potassium voltage-gated channel, subfamily H,	73	Cytoplasmic (Potential).|PAS.				regulation of transcription, DNA-dependent	integral to membrane	calmodulin binding|two-component sensor activity|voltage-gated potassium channel activity			ovary(4)|central_nervous_system(1)	5				OV - Ovarian serous cystadenocarcinoma(108;0.00958)|BRCA - Breast invasive adenocarcinoma(234;0.168)										0.290323	24.462774	25.683889	9	22	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	62542924	62542924	8340	14	T	A	A	58	58	KCNH5	A	4	4
MOAP1	64112	broad.mit.edu	36	14	92719751	92719751	+	Missense_Mutation	SNP	A	C	C			TCGA-06-1087-01	TCGA-06-1087-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr14:92719751A>C	uc001ybj.1	-	c.590T>G	c.(589-591)GTG>GGG	p.V197G	MOAP1_uc010aun.1_Missense_Mutation_p.V197G|C14orf109_uc001ybk.2_5'Flank|C14orf109_uc010auo.1_5'Flank|C14orf109_uc010aup.1_5'Flank	NM_022151	NP_071434	Q96BY2	MOAP1_HUMAN	modulator of apoptosis 1	197					activation of caspase activity|apoptotic nuclear change	cytoplasm	protein homodimerization activity			ovary(1)	1		all_cancers(154;0.00528)|Acute lymphoblastic leukemia(33;0.0497)|all_epithelial(191;0.125)|all_neural(303;0.13)		Epithelial(152;0.178)|all cancers(159;0.2)|COAD - Colon adenocarcinoma(157;0.204)										0.185185	6.374214	14.414108	15	66	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	92719751	92719751	10071	14	A	C	C	6	6	MOAP1	C	4	4
ADAMTS17	170691	broad.mit.edu	36	15	98454129	98454129	+	Missense_Mutation	SNP	T	G	G			TCGA-06-1087-01	TCGA-06-1087-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr15:98454129T>G	uc002bvv.1	-	c.2092A>C	c.(2092-2094)ACC>CCC	p.T698P	ADAMTS17_uc002bvx.1_Missense_Mutation_p.T455P	NM_139057	NP_620688	Q8TE56	ATS17_HUMAN	ADAM metallopeptidase with thrombospondin type 1	698	Cys-rich.				proteolysis	intracellular|proteinaceous extracellular matrix	metalloendopeptidase activity|zinc ion binding			ovary(2)|central_nervous_system(1)	3	Lung NSC(78;0.00299)|all_lung(78;0.00457)|Melanoma(26;0.00571)		OV - Ovarian serous cystadenocarcinoma(32;0.0013)|LUSC - Lung squamous cell carcinoma(107;0.132)|Lung(145;0.161)	COAD - Colon adenocarcinoma(1;0.111)|all cancers(203;0.219)										0.182692	14.308003	24.595422	19	85	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	98454129	98454129	263	15	T	G	G	58	58	ADAMTS17	G	4	4
SMG1	23049	broad.mit.edu	36	16	18766645	18766645	+	Silent	SNP	T	G	G			TCGA-06-1087-01	TCGA-06-1087-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr16:18766645T>G	uc002dfm.1	-	c.5835A>C	c.(5833-5835)GTA>GTC	p.V1945V	SMG1_uc010bwa.1_Silent_p.V676V|SMG1_uc010bwb.1_Silent_p.V1805V|SMG1_uc002dfo.2_Silent_p.V243V	NM_015092	NP_055907	Q96Q15	SMG1_HUMAN	PI-3-kinase-related kinase SMG-1	1945					DNA repair|mRNA export from nucleus|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay|peptidyl-serine phosphorylation|phosphatidylinositol phosphorylation|protein autophosphorylation	cytoplasm|nucleus	ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity			breast(5)|lung(4)|kidney(2)|stomach(1)|ovary(1)	13										1101				0.444444	12.900566	12.924416	4	5	TT		KEEP	---	---	---	---	capture			Silent	SNP	18766645	18766645	15293	16	T	G	G	49	49	SMG1	G	4	4
CLUAP1	23059	broad.mit.edu	36	16	3520642	3520642	+	Silent	SNP	C	A	A			TCGA-06-1087-01	TCGA-06-1087-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr16:3520642C>A	uc002cvl.1	+	c.1002C>A	c.(1000-1002)CCC>CCA	p.P334P	CLUAP1_uc002cvk.1_Silent_p.P334P|CLUAP1_uc002cvj.1_Silent_p.P334P|CLUAP1_uc002cvm.1_Silent_p.P168P	NM_015041	NP_055856	Q96AJ1	CLUA1_HUMAN	clusterin associated protein 1 isoform 1	334						nucleus	protein binding			ovary(1)|breast(1)|pancreas(1)	3														0.307692	7.589045	8.021434	4	9	CC		KEEP	---	---	---	---	capture			Silent	SNP	3520642	3520642	3707	16	C	A	A	21	21	CLUAP1	A	3	3
ELMO3	79767	broad.mit.edu	36	16	65792955	65792955	+	Missense_Mutation	SNP	A	G	G			TCGA-06-1087-01	TCGA-06-1087-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr16:65792955A>G	uc002esa.1	+	c.986A>G	c.(985-987)GAC>GGC	p.D329G	ELMO3_uc002esb.1_Missense_Mutation_p.D312G|ELMO3_uc002esc.1_Missense_Mutation_p.D163G	NM_024712	NP_078988	Q96BJ8	ELMO3_HUMAN	engulfment and cell motility 3	276					apoptosis|phagocytosis	cytoplasm|cytoskeleton	SH3 domain binding				0		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.00067)|Epithelial(162;0.00442)|all cancers(182;0.0417)										0.179487	9.299764	13.075604	7	32	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	65792955	65792955	5259	16	A	G	G	10	10	ELMO3	G	4	4
MAP2K3	5606	broad.mit.edu	36	17	21158069	21158069	+	Silent	SNP	C	T	T			TCGA-06-1087-01	TCGA-06-1087-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr17:21158069C>T	uc002gys.1	+	c.978C>T	c.(976-978)ACC>ACT	p.T326T	MAP2K3_uc002gyt.1_Silent_p.T297T|MAP2K3_uc002gyu.1_Silent_p.T297T	NM_145109	NP_002747	P46734	MP2K3_HUMAN	mitogen-activated protein kinase kinase 3	326					activation of MAPK activity|innate immune response|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|positive 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	cytosol|nucleoplasm	ATP binding|MAP kinase kinase activity|protein binding|protein serine/threonine kinase activity|protein tyrosine kinase activity				0				COAD - Colon adenocarcinoma(3;0.0131)|Colorectal(15;0.0553)						346				0.243631	407.66413	445.282657	153	475	CC		KEEP	---	---	---	---	capture			Silent	SNP	21158069	21158069	9621	17	C	T	T	24	24	MAP2K3	T	2	2
KRT36	8689	broad.mit.edu	36	17	36899308	36899308	+	Missense_Mutation	SNP	C	T	T			TCGA-06-1087-01	TCGA-06-1087-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr17:36899308C>T	uc002hwt.1	-	c.335G>A	c.(334-336)CGT>CAT	p.R112H		NM_003771	NP_003762	O76013	KRT36_HUMAN	keratin 36	112	Rod.|Coil 1A.					intermediate filament	protein binding|structural constituent of epidermis				0		Breast(137;0.000286)												0.430769	167.582579	168.12454	56	74	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	36899308	36899308	8788	17	C	T	T	19	19	KRT36	T	1	1
TP53	7157	broad.mit.edu	36	17	7518915	7518915	+	Missense_Mutation	SNP	T	C	C			TCGA-06-1087-01	TCGA-06-1087-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr17:7518915T>C	uc002gim.2	-	c.659A>G	c.(658-660)TAT>TGT	p.Y220C	TP53_uc002gig.1_Missense_Mutation_p.Y220C|TP53_uc002gih.1_Missense_Mutation_p.Y220C|TP53_uc010cne.1_5'Flank|TP53_uc010cnf.1_Missense_Mutation_p.Y88C|TP53_uc010cng.1_Missense_Mutation_p.Y88C|TP53_uc002gii.1_Missense_Mutation_p.Y88C|TP53_uc010cnh.1_Missense_Mutation_p.Y220C|TP53_uc010cni.1_Missense_Mutation_p.Y220C|TP53_uc002gij.2_Missense_Mutation_p.Y220C|TP53_uc010cnj.1_Intron|TP53_uc002gin.2_Missense_Mutation_p.Y127C|TP53_uc002gio.2_Missense_Mutation_p.Y88C	NM_001126112	NP_001119584	P04637	P53_HUMAN	tumor protein p53 isoform a	220	Required for interaction with FBXO42.||Interaction with HIPK1 (By similarity).|Interaction with AXIN1 (By similarity).		Y -> N (in sporadic cancers; somatic mutation).|Y -> H (in sporadic cancers; somatic mutation).|Y -> S (in a brain tumor with no family history; germline mutation and in sporadic cancers; somatic mutation).|Y -> F (in a sporadic cancer; somatic mutation).|Y -> D (in sporadic cancers; somatic mutation).|Y -> C (in LFS; germline mutation and in sporadic cancers; somatic mutation).		activation of caspase activity by cytochrome c|base-excision repair|blood coagulation|cell cycle arrest|cell differentiation|cell proliferation|cellular protein localization|cellular response to drug|cellular response to glucose starvation|cellular response to hypoxia|cellular response to ionizing radiation|cellular response to UV|determination of adult lifespan|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator|ER overload response|interspecies interaction between organisms|negative regulation of apoptosis|negative regulation of cell growth|negative regulation of cell proliferation|negative regulation of gene-specific transcription from RNA polymerase II promoter|negative regulation of helicase activity|negative regulation of transcription from RNA polymerase II promoter|nucleotide-excision repair|oxidative stress-induced premature senescence|positive regulation of gene-specific transcription from RNA polymerase II promoter|positive regulation of histone deacetylation|positive regulation of neuron apoptosis|positive regulation of peptidyl-tyrosine phosphorylation|positive regulation of reactive oxygen species metabolic process|positive regulation of thymocyte apoptosis|positive regulation of transcription from RNA polymerase II promoter|protein localization|protein tetramerization|Ras protein signal transduction|regulation of mitochondrial membrane permeability|replicative senescence|response to antibiotic|response to gamma radiation|response to X-ray	chromatin|cytoplasm|cytosol|endoplasmic reticulum|insoluble fraction|mitochondrion|nuclear matrix|nucleolus|nucleus|PML body|protein complex|replication fork	ATP binding|chaperone binding|chromatin binding|copper ion binding|damaged DNA binding|DNA strand annealing activity|histone acetyltransferase binding|p53 binding|promoter binding|promoter binding|protease binding|protein heterodimerization activity|protein kinase binding|protein N-terminus binding|protein phosphatase 2A binding|sequence-specific DNA binding transcription factor activity|specific transcriptional repressor activity|transcription activator activity|transcription factor binding|ubiquitin protein ligase binding|zinc ion binding	p.Y220C(194)|p.Y220S(9)|p.0?(6)|p.D208fs*1(1)|p.Y220_P223delYEPP(1)|p.Y220H(1)|p.?(1)|p.V218_E224delVPYEPPE(1)|p.V218_E221delVPYE(1)|p.V218_Y220delVPY(1)|p.Y220fs*25(1)|p.V216_Y220delVVVPY(1)|p.Y220fs*2(1)|p.V218fs*26(1)		large_intestine(4614)|breast(2344)|upper_aerodigestive_tract(2150)|lung(1958)|ovary(1559)|oesophagus(1462)|haematopoietic_and_lymphoid_tissue(1212)|stomach(1127)|urinary_tract(1113)|central_nervous_system(1072)|liver(805)|skin(693)|pancreas(370)|biliary_tract(247)|soft_tissue(209)|prostate(192)|endometrium(150)|bone(102)|vulva(79)|kidney(79)|cervix(68)|thyroid(54)|salivary_gland(41)|adrenal_gland(37)|peritoneum(33)|eye(24)|thymus(21)|genital_tract(16)|autonomic_ganglia(16)|small_intestine(14)|testis(11)|penis(10)|vagina(6)|meninges(5)|pituitary(4)|pleura(3)|gastrointestinal_tract_(site_indeterminate)(1)|NS(1)|Fallopian tube(1)|placenta(1)	21904		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)		Pancreas(47;798 1329 9957 10801)		111	p.Y220C(HCC2935-Tumor)|p.Y220C(BXPC3-Tumor)|p.Y220C(HCC366-Tumor)|p.Y220C(TE8-Tumor)|p.Y220C(NUGC3-Tumor)|p.Y220C(HUH7-Tumor)|p.Y220C(COV362-Tumor)|p.Y220C(HCC1419-Tumor)|p.Y220C(MFE319-Tumor)|p.Y220C(T3M4-Tumor)|p.Y220C(NCIH2342-Tumor)|p.Y220C(MFE296-Tumor)	690	TCGA GBM(1;<1E-8)|TSP Lung(2;<1E-8)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)			0.430769	373.176259	374.259246	112	148	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	7518915	7518915	16923	17	T	C	C	49	49	TP53	C	4	4
DSG4	147409	broad.mit.edu	36	18	27247524	27247524	+	Nonsense_Mutation	SNP	C	T	T			TCGA-06-1087-01	TCGA-06-1087-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr18:27247524C>T	uc002kwr.1	+	c.3148C>T	c.(3148-3150)CGA>TGA	p.R1050*	DSG4_uc002kwq.1_Nonsense_Mutation_p.R1031*	NM_177986	NP_817123	Q86SJ6	DSG4_HUMAN	desmoglein 4 isoform 2	1031	Cytoplasmic (Potential).				homophilic cell adhesion	desmosome|integral to membrane	calcium ion binding			central_nervous_system(5)|ovary(3)	8			OV - Ovarian serous cystadenocarcinoma(10;0.00504)											0.598901	363.806957	365.365118	109	73	CC		KEEP	---	---	---	---	capture			Nonsense_Mutation	SNP	27247524	27247524	4963	18	C	T	T	19	19	DSG4	T	5	1
RFX2	5990	broad.mit.edu	36	19	5967270	5967270	+	Missense_Mutation	SNP	A	C	C			TCGA-06-1087-01	TCGA-06-1087-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr19:5967270A>C	uc002meb.1	-	c.610T>G	c.(610-612)TTG>GTG	p.L204V	RFX2_uc002mec.1_Missense_Mutation_p.L179V	NM_000635	NP_000626	P48378	RFX2_HUMAN	regulatory factor X2 isoform a	204	RFX-type winged-helix.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|transcription regulator activity			breast(4)|ovary(1)	5						Colon(38;171 817 19800 47433 48051)								0.206897	21.93079	26.611033	12	46	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	5967270	5967270	13735	19	A	C	C	2	2	RFX2	C	4	4
COL5A3	50509	broad.mit.edu	36	19	9932362	9932362	+	Missense_Mutation	SNP	C	G	G			TCGA-06-1087-01	TCGA-06-1087-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr19:9932362C>G	uc002mmq.1	-	c.5056G>C	c.(5056-5058)GCA>CCA	p.A1686P		NM_015719	NP_056534	P25940	CO5A3_HUMAN	collagen, type V, alpha 3 preproprotein	1686	Fibrillar collagen NC1.				collagen fibril organization|skin development	collagen type V	collagen binding|extracellular matrix structural constituent			ovary(7)|lung(1)|central_nervous_system(1)	9			Epithelial(33;7.11e-05)											0.131579	8.414126	18.446026	10	66	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	9932362	9932362	3836	19	C	G	G	28	28	COL5A3	G	3	3
POGZ	23126	broad.mit.edu	36	1	149680058	149680058	+	Missense_Mutation	SNP	T	A	A			TCGA-06-1087-01	TCGA-06-1087-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr1:149680058T>A	uc001eyd.1	-	c.253A>T	c.(253-255)ACT>TCT	p.T85S	POGZ_uc001eye.1_Intron|POGZ_uc001eyf.1_Intron|POGZ_uc009wmv.1_Missense_Mutation_p.T85S|POGZ_uc001eyg.1_Missense_Mutation_p.T85S	NM_015100	NP_055915	Q7Z3K3	POGZ_HUMAN	pogo transposable element with ZNF domain	85					cell division|kinetochore assembly|mitotic sister chromatid cohesion	cytoplasm|nuclear chromatin	DNA binding|protein binding|zinc ion binding			ovary(3)	3	Lung SC(34;0.00471)|Ovarian(49;0.00672)|Hepatocellular(266;0.0997)|all_hematologic(923;0.127)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.112)|LUSC - Lung squamous cell carcinoma(543;0.181)											0.404762	307.895422	309.894353	102	150	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	149680058	149680058	12614	1	T	A	A	58	58	POGZ	A	4	4
PADI3	51702	broad.mit.edu	36	1	17464802	17464802	+	Silent	SNP	G	A	A			TCGA-06-1087-01	TCGA-06-1087-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:17464802G>A	uc001bai.1	+	c.408G>A	c.(406-408)AAG>AAA	p.K136K		NM_016233	NP_057317	Q9ULW8	PADI3_HUMAN	peptidylarginine deiminase type III	136					peptidyl-citrulline biosynthetic process from peptidyl-arginine	cytoplasm	calcium ion binding|protein-arginine deiminase activity			ovary(1)|breast(1)	2		Colorectal(325;3.46e-05)|Breast(348;0.000162)|all_lung(284;0.000337)|Lung NSC(340;0.000419)|Renal(390;0.000518)|Ovarian(437;0.00409)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00488)|BRCA - Breast invasive adenocarcinoma(304;1.17e-05)|COAD - Colon adenocarcinoma(227;1.18e-05)|Kidney(64;0.000186)|KIRC - Kidney renal clear cell carcinoma(64;0.00272)|STAD - Stomach adenocarcinoma(196;0.00656)|READ - Rectum adenocarcinoma(331;0.0655)|Lung(427;0.189)	L-Citrulline(DB00155)									0.666667	79.961413	80.773004	22	11	GG		KEEP	---	---	---	---	capture			Silent	SNP	17464802	17464802	11795	1	G	A	A	35	35	PADI3	A	2	2
CACNA1E	777	broad.mit.edu	36	1	179813598	179813598	+	Missense_Mutation	SNP	C	T	T			TCGA-06-1087-01	TCGA-06-1087-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr1:179813598C>T	uc001gow.1	+	c.586C>T	c.(586-588)CGG>TGG	p.R196W	CACNA1E_uc009wxr.1_Missense_Mutation_p.R103W|CACNA1E_uc009wxs.1_Missense_Mutation_p.R103W	NM_000721	NP_000712	Q15878	CAC1E_HUMAN	calcium channel, voltage-dependent, R type,	196	Helical; Name=S4 of repeat I.|I.				energy reserve metabolic process|membrane depolarization|synaptic transmission	voltage-gated calcium channel complex	voltage-gated calcium channel activity			ovary(3)|central_nervous_system(2)|pancreas(1)	6														0.528302	554.2129	554.434496	168	150	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	179813598	179813598	2658	1	C	T	T	27	27	CACNA1E	T	1	1
PLXNA2	5362	broad.mit.edu	36	1	206450347	206450347	+	Silent	SNP	C	T	T			TCGA-06-1087-01	TCGA-06-1087-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr1:206450347C>T	uc001hgz.1	-	c.1272G>A	c.(1270-1272)CTG>CTA	p.L424L	PLXNA2_uc001hha.2_Silent_p.L478L	NM_025179	NP_079455	O75051	PLXA2_HUMAN	plexin A2	424	Extracellular (Potential).|Sema.				axon guidance	integral to membrane|intracellular|plasma membrane				ovary(2)	2				OV - Ovarian serous cystadenocarcinoma(81;0.199)										0.369863	75.101246	76.189351	27	46	CC		KEEP	---	---	---	---	capture			Silent	SNP	206450347	206450347	12546	1	C	T	T	17	17	PLXNA2	T	2	2
SCMH1	22955	broad.mit.edu	36	1	41351703	41351703	+	Missense_Mutation	SNP	C	G	G			TCGA-06-1087-01	TCGA-06-1087-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr1:41351703C>G	uc001cgo.1	-	c.554G>C	c.(553-555)TGC>TCC	p.C185S	SCMH1_uc001cgp.1_Missense_Mutation_p.C124S|SCMH1_uc001cgr.1_Missense_Mutation_p.C124S|SCMH1_uc001cgs.1_Missense_Mutation_p.C195S|SCMH1_uc001cgt.1_Missense_Mutation_p.C124S|SCMH1_uc001cgq.1_Missense_Mutation_p.C138S	NM_001031694	NP_001026864	Q96GD3	SCMH1_HUMAN	sex comb on midleg 1 isoform 1	185	MBT 2.				anatomical structure morphogenesis|gene silencing|multicellular organismal development|negative regulation of transcription, DNA-dependent	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|transcription repressor activity				0	Ovarian(52;0.00769)|all_hematologic(146;0.0977)|Acute lymphoblastic leukemia(166;0.155)|Breast(333;0.162)	Myeloproliferative disorder(586;0.0393)												0.208333	8.447674	10.358905	5	19	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	41351703	41351703	14390	1	C	G	G	25	25	SCMH1	G	3	3
HFM1	164045	broad.mit.edu	36	1	91500739	91500739	+	Splice_Site_SNP	SNP	T	A	A			TCGA-06-1087-01	TCGA-06-1087-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr1:91500739T>A	uc001doa.2	-	c.e37_splice_site			HFM1_uc009wdb.1_Splice_Site_SNP|HFM1_uc001dob.2_Splice_Site_SNP	NM_001017975	NP_001017975			HFM1 protein								ATP binding|ATP-dependent helicase activity|nucleic acid binding				0		all_lung(203;0.00961)|Lung NSC(277;0.0351)		all cancers(265;0.000481)|Epithelial(280;0.00863)|OV - Ovarian serous cystadenocarcinoma(397;0.126)|KIRC - Kidney renal clear cell carcinoma(1967;0.171)										0.2	7.730674	10.249766	6	24	TT		KEEP	---	---	---	---	capture			Splice_Site_SNP	SNP	91500739	91500739	7366	1	T	A	A	53	53	HFM1	A	5	4
BCAR3	8412	broad.mit.edu	36	1	93820459	93820459	+	Missense_Mutation	SNP	C	G	G			TCGA-06-1087-01	TCGA-06-1087-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr1:93820459C>G	uc001dpz.1	-	c.1673G>C	c.(1672-1674)AGC>ACC	p.S558T	BCAR3_uc001dpy.1_Missense_Mutation_p.S467T|BCAR3_uc001dqa.1_Missense_Mutation_p.S558T|BCAR3_uc001dqb.1_Missense_Mutation_p.S558T|BCAR3_uc001dpx.2_Missense_Mutation_p.S234T|BCAR3_uc009wdm.1_Missense_Mutation_p.S234T	NM_003567	NP_003558	O75815	BCAR3_HUMAN	breast cancer antiestrogen resistance 3	558	Ras-GEF.				response to drug|small GTPase mediated signal transduction	intracellular	guanyl-nucleotide exchange factor activity|protein binding			ovary(1)|lung(1)|central_nervous_system(1)	3		all_lung(203;0.00145)|Lung NSC(277;0.00662)		all cancers(265;0.0126)|GBM - Glioblastoma multiforme(16;0.0467)|Epithelial(280;0.166)										0.177966	94.801098	117.85251	42	194	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	93820459	93820459	1370	1	C	G	G	28	28	BCAR3	G	3	3
ZNF133	7692	broad.mit.edu	36	20	18244607	18244607	+	Missense_Mutation	SNP	C	G	G			TCGA-06-1087-01	TCGA-06-1087-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr20:18244607C>G	uc010gcq.1	+	c.1112C>G	c.(1111-1113)TCC>TGC	p.S371C	ZNF133_uc010gcr.1_Missense_Mutation_p.S371C|ZNF133_uc002wql.2_Missense_Mutation_p.S370C|ZNF133_uc010gcs.1_Missense_Mutation_p.S370C|ZNF133_uc002wqm.1_Missense_Mutation_p.S371C	NM_003434	NP_003425	P52736	ZN133_HUMAN	zinc finger protein 133	371	C2H2-type 6.				regulation of transcription, DNA-dependent	nucleus	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)|pancreas(1)	2														0.116667	20.30349	72.618368	42	318	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	18244607	18244607	18314	20	C	G	G	30	30	ZNF133	G	3	3
MAP3K2	10746	broad.mit.edu	36	2	127796102	127796102	+	Silent	SNP	T	G	G			TCGA-06-1087-01	TCGA-06-1087-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr2:127796102T>G	uc002toj.1	-	c.1035A>C	c.(1033-1035)CCA>CCC	p.P345P		NM_006609	NP_006600	Q9Y2U5	M3K2_HUMAN	mitogen-activated protein kinase kinase kinase	345					activation of JUN kinase activity|cellular response to mechanical stimulus	nucleus	ATP binding|MAP kinase kinase kinase activity|metal ion binding|protein kinase binding			lung(3)|ovary(2)|large_intestine(1)|central_nervous_system(1)	7	Colorectal(110;0.1)			BRCA - Breast invasive adenocarcinoma(221;0.0706)						211				0.297297	6.529681	8.155495	11	26	TT		KEEP	---	---	---	---	capture			Silent	SNP	127796102	127796102	9633	2	T	G	G	59	59	MAP3K2	G	4	4
ACVR2A	92	broad.mit.edu	36	2	148394348	148394348	+	Missense_Mutation	SNP	G	A	A			TCGA-06-1087-01	TCGA-06-1087-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr2:148394348G>A	uc002twg.1	+	c.1042G>A	c.(1042-1044)GAG>AAG	p.E348K	ACVR2A_uc002twh.1_Missense_Mutation_p.E348K	NM_001616	NP_001607	P27037	AVR2A_HUMAN	activin A receptor, type IIA precursor	348	Cytoplasmic (Potential).|Protein kinase.			E -> V (in Ref. 4; BAA06548).	activin receptor signaling pathway|BMP signaling pathway|positive regulation of activin receptor signaling pathway|positive regulation of bone mineralization|positive regulation of erythrocyte differentiation|positive regulation of osteoblast differentiation|positive regulation of protein phosphorylation|protein phosphorylation	cytoplasm|inhibin-betaglycan-ActRII complex|integral to plasma membrane	ATP binding|coreceptor activity|inhibin beta-A binding|metal ion binding|receptor signaling protein serine/threonine kinase activity|transforming growth factor beta receptor activity			stomach(8)|large_intestine(2)|kidney(1)	11				BRCA - Breast invasive adenocarcinoma(221;0.0969)						196				0.663158	211.251591	213.488527	63	32	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	148394348	148394348	224	2	G	A	A	45	45	ACVR2A	A	2	2
APOB	338	broad.mit.edu	36	2	21082991	21082991	+	Silent	SNP	C	T	T			TCGA-06-1087-01	TCGA-06-1087-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr2:21082991C>T	uc002red.1	-	c.10254G>A	c.(10252-10254)ACG>ACA	p.T3418T		NM_000384	NP_000375	P04114	APOB_HUMAN	apolipoprotein B precursor	3418	Heparin-binding.				cholesterol homeostasis|cholesterol metabolic process|leukocyte migration|low-density lipoprotein particle clearance|low-density lipoprotein particle remodeling|platelet activation|positive regulation of cholesterol storage|positive regulation of macrophage derived foam cell differentiation|receptor-mediated endocytosis|response to virus|very-low-density lipoprotein particle assembly	chylomicron remnant|clathrin-coated endocytic vesicle membrane|endoplasmic reticulum lumen|endoplasmic reticulum membrane|endosome lumen|endosome membrane|intermediate-density lipoprotein particle|low-density lipoprotein particle|mature chylomicron|microsome|plasma membrane|very-low-density lipoprotein particle	cholesterol transporter activity|enzyme binding|heparin binding|low-density lipoprotein particle receptor binding|phospholipid binding|protein heterodimerization activity			ovary(11)|central_nervous_system(3)|large_intestine(2)|pancreas(1)|skin(1)	18	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)				Atorvastatin(DB01076)									0.316384	132.893137	138.226179	56	121	CC		KEEP	---	---	---	---	capture			Silent	SNP	21082991	21082991	796	2	C	T	T	31	31	APOB	T	1	1
COL6A3	1293	broad.mit.edu	36	2	237918137	237918137	+	Missense_Mutation	SNP	C	T	T			TCGA-06-1087-01	TCGA-06-1087-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr2:237918137C>T	uc002vwl.2	-	c.7263G>A	c.(7261-7263)ATG>ATA	p.M2421I	COL6A3_uc002vwj.2_5'Flank|COL6A3_uc002vwk.2_Missense_Mutation_p.M2254I|COL6A3_uc002vwm.2_Missense_Mutation_p.M2220I|COL6A3_uc002vwn.2_Missense_Mutation_p.M2221I|COL6A3_uc002vwo.2_Missense_Mutation_p.M2215I|COL6A3_uc002vwp.1_Missense_Mutation_p.M242I	NM_004369	NP_004360	P12111	CO6A3_HUMAN	alpha 3 type VI collagen isoform 1 precursor	2421	VWFA 11.|Nonhelical region.				axon guidance|cell adhesion|muscle organ development	collagen type VI|extracellular space	serine-type endopeptidase inhibitor activity			ovary(8)|central_nervous_system(6)|pancreas(1)	15		Breast(86;0.000301)|Renal(207;0.000966)|all_hematologic(139;0.067)|Ovarian(221;0.0694)|all_lung(227;0.0943)|Melanoma(123;0.203)		Epithelial(121;1.23e-21)|OV - Ovarian serous cystadenocarcinoma(60;1.34e-10)|Kidney(56;5.71e-09)|KIRC - Kidney renal clear cell carcinoma(57;1.51e-07)|BRCA - Breast invasive adenocarcinoma(100;0.00025)|Lung(119;0.0142)|LUSC - Lung squamous cell carcinoma(224;0.034)										0.159091	36.286505	50.910175	21	111	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	237918137	237918137	3839	2	C	T	T	25	25	COL6A3	T	2	2
COL6A3	1293	broad.mit.edu	36	2	237939165	237939165	+	Missense_Mutation	SNP	C	T	T			TCGA-06-1087-01	TCGA-06-1087-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr2:237939165C>T	uc002vwl.2	-	c.5753G>A	c.(5752-5754)CGC>CAC	p.R1918H	COL6A3_uc002vwk.2_Missense_Mutation_p.R1751H|COL6A3_uc002vwm.2_Missense_Mutation_p.R1717H|COL6A3_uc002vwn.2_Missense_Mutation_p.R1718H|COL6A3_uc002vwo.2_Missense_Mutation_p.R1712H	NM_004369	NP_004360	P12111	CO6A3_HUMAN	alpha 3 type VI collagen isoform 1 precursor	1918	VWFA 10.|Nonhelical region.				axon guidance|cell adhesion|muscle organ development	collagen type VI|extracellular space	serine-type endopeptidase inhibitor activity			ovary(8)|central_nervous_system(6)|pancreas(1)	15		Breast(86;0.000301)|Renal(207;0.000966)|all_hematologic(139;0.067)|Ovarian(221;0.0694)|all_lung(227;0.0943)|Melanoma(123;0.203)		Epithelial(121;1.23e-21)|OV - Ovarian serous cystadenocarcinoma(60;1.34e-10)|Kidney(56;5.71e-09)|KIRC - Kidney renal clear cell carcinoma(57;1.51e-07)|BRCA - Breast invasive adenocarcinoma(100;0.00025)|Lung(119;0.0142)|LUSC - Lung squamous cell carcinoma(224;0.034)										0.25	7.318334	8.001166	3	9	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	237939165	237939165	3839	2	C	T	T	27	27	COL6A3	T	1	1
KIF3C	3797	broad.mit.edu	36	2	26028186	26028186	+	Missense_Mutation	SNP	A	G	G			TCGA-06-1087-01	TCGA-06-1087-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr2:26028186A>G	uc002rgu.2	-	c.1982T>C	c.(1981-1983)TTC>TCC	p.F661S	KIF3C_uc010eyj.1_Non-coding_Transcript	NM_002254	NP_002245	O14782	KIF3C_HUMAN	kinesin family member 3C	661	Globular (Potential).				blood coagulation|microtubule-based movement	cytosol|kinesin complex|microtubule	ATP binding|microtubule motor activity			ovary(3)	3	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)													0.258065	9.421849	11.128388	8	23	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	26028186	26028186	8613	2	A	G	G	9	9	KIF3C	G	4	4
GPN1	11321	broad.mit.edu	36	2	27706310	27706310	+	Silent	SNP	T	C	C			TCGA-06-1087-01	TCGA-06-1087-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr2:27706310T>C	uc002rlf.1	+	c.192T>C	c.(190-192)TTT>TTC	p.F64F	CCDC121_uc002rld.1_5'Flank|CCDC121_uc002rle.1_5'Flank|CCDC121_uc010eze.1_5'Flank|GPN1_uc010ezf.1_Silent_p.F52F|GPN1_uc002rlg.1_Silent_p.F64F|GPN1_uc010ezg.1_5'UTR	NM_007266	NP_009197	Q9HCN4	GPN1_HUMAN	GPN-loop GTPase 1 isoform a	64						cytoplasm	GTP binding|nucleoside-triphosphatase activity|protein binding				0														0.209677	7.952598	13.190742	13	49	TT		KEEP	---	---	---	---	capture			Silent	SNP	27706310	27706310	6891	2	T	C	C	62	62	GPN1	C	4	4
PNPT1	87178	broad.mit.edu	36	2	55774341	55774341	+	Missense_Mutation	SNP	C	T	T			TCGA-06-1087-01	TCGA-06-1087-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr2:55774341C>T	uc002rzf.2	-	c.122G>A	c.(121-123)AGC>AAC	p.S41N	PNPT1_uc002rzg.2_Non-coding_Transcript	NM_033109	NP_149100	Q8TCS8	PNPT1_HUMAN	polyribonucleotide nucleotidyltransferase 1	41					mRNA catabolic process|RNA processing	plasma membrane	3'-5'-exoribonuclease activity|polyribonucleotide nucleotidyltransferase activity|RNA binding				0			LUSC - Lung squamous cell carcinoma(58;0.127)|Lung(47;0.132)											0.560345	214.987116	215.355224	65	51	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	55774341	55774341	12600	2	C	T	T	28	28	PNPT1	T	2	2
GFM1	85476	broad.mit.edu	36	3	159865856	159865856	+	Missense_Mutation	SNP	T	G	G			TCGA-06-1087-01	TCGA-06-1087-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr3:159865856T>G	uc003fce.1	+	c.1417T>G	c.(1417-1419)TTT>GTT	p.F473V	GFM1_uc003fcd.2_Missense_Mutation_p.F473V|GFM1_uc003fcf.1_Non-coding_Transcript|GFM1_uc003fcg.1_Missense_Mutation_p.F404V	NM_024996	NP_079272	Q96RP9	EFGM_HUMAN	G elongation factor, mitochondrial 1	473					mitochondrial translational elongation	mitochondrion	GTP binding|GTPase activity|translation elongation factor activity			ovary(3)|central_nervous_system(1)	4			Lung(72;0.00309)|LUSC - Lung squamous cell carcinoma(72;0.0043)											0.275862	10.923411	12.288693	8	21	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	159865856	159865856	6609	3	T	G	G	60	60	GFM1	G	4	4
KNG1	3827	broad.mit.edu	36	3	187918111	187918111	+	Missense_Mutation	SNP	A	T	T			TCGA-06-1087-01	TCGA-06-1087-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr3:187918111A>T	uc010hyt.1	+	c.86A>T	c.(85-87)AAT>ATT	p.N29I	KNG1_uc003fqr.1_Missense_Mutation_p.N29I	NM_001102416	NP_001095886	P01042	KNG1_HUMAN	kininogen 1 isoform 1	29	Cystatin 1.				blood coagulation, intrinsic pathway|diuresis|elevation of cytosolic calcium ion concentration|inflammatory response|natriuresis|negative regulation of blood coagulation|negative regulation of cell adhesion|platelet activation|platelet degranulation|positive regulation of apoptosis|smooth muscle contraction|vasodilation	extracellular space|plasma membrane|platelet alpha granule lumen	cysteine-type endopeptidase inhibitor activity|heparin binding|receptor binding|zinc ion binding				0	all_cancers(143;8.96e-12)|Ovarian(172;0.0339)		OV - Ovarian serous cystadenocarcinoma(80;4.12e-20)	GBM - Glioblastoma multiforme(93;0.0798)	Ouabain(DB01092)									0.285714	7.08915	7.669836	4	10	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	187918111	187918111	8741	3	A	T	T	4	4	KNG1	T	4	4
MAGI1	9223	broad.mit.edu	36	3	65390809	65390809	+	Silent	SNP	T	C	C			TCGA-06-1087-01	TCGA-06-1087-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr3:65390809T>C	uc003dmn.1	-	c.1593A>G	c.(1591-1593)ACA>ACG	p.T531T	MAGI1_uc003dmm.1_Silent_p.T531T|MAGI1_uc003dmo.1_Silent_p.T531T|MAGI1_uc003dmp.1_Silent_p.T531T	NM_001033057	NP_001028229	Q96QZ7	MAGI1_HUMAN	membrane associated guanylate kinase, WW and PDZ	531	PDZ 2.				cell adhesion|cell surface receptor linked signaling pathway|protein complex assembly	tight junction	ATP binding|protein C-terminus binding			kidney(1)|pancreas(1)	2		Lung NSC(201;0.0016)		BRCA - Breast invasive adenocarcinoma(55;0.00138)|KIRC - Kidney renal clear cell carcinoma(15;0.0988)|Kidney(15;0.133)										0.258065	253.122586	272.859635	96	276	TT		KEEP	---	---	---	---	capture			Silent	SNP	65390809	65390809	9573	3	T	C	C	59	59	MAGI1	C	4	4
STX19	415117	broad.mit.edu	36	3	95216568	95216568	+	Missense_Mutation	SNP	A	T	T			TCGA-06-1087-01	TCGA-06-1087-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr3:95216568A>T	uc003drh.1	-	c.236T>A	c.(235-237)GTG>GAG	p.V79E	ARL13B_uc003drc.1_Intron|ARL13B_uc003drd.1_Intron|ARL13B_uc003dre.1_Intron|ARL13B_uc003drf.1_Intron|ARL13B_uc003drg.1_Intron|ARL13B_uc010hop.1_Intron|STX19_uc010hoq.1_Missense_Mutation_p.V79E	NM_001001850	NP_001001850	Q8N4C7	STX19_HUMAN	syntaxin 19	79					intracellular protein transport|vesicle-mediated transport	membrane	SNAP receptor activity				0														0.118182	15.997092	31.756025	13	97	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	95216568	95216568	15862	3	A	T	T	6	6	STX19	T	4	4
STK32B	55351	broad.mit.edu	36	4	5192559	5192559	+	Missense_Mutation	SNP	C	T	T			TCGA-06-1087-01	TCGA-06-1087-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr4:5192559C>T	uc003gih.1	+	c.79C>T	c.(79-81)CGG>TGG	p.R27W	STK32B_uc010ida.1_5'UTR	NM_018401	NP_060871	Q9NY57	ST32B_HUMAN	serine/threonine kinase 32B	27	Protein kinase.				protein phosphorylation		ATP binding|metal ion binding|protein serine/threonine kinase activity			breast(2)|large_intestine(1)|central_nervous_system(1)|skin(1)	5										175				0.863636	932.708696	972.118353	266	42	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	5192559	5192559	15818	4	C	T	T	27	27	STK32B	T	1	1
UGT2A1	10941	broad.mit.edu	36	4	70547522	70547522	+	Missense_Mutation	SNP	A	G	G			TCGA-06-1087-01	TCGA-06-1087-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr4:70547522A>G	uc003hem.2	-	c.430T>C	c.(430-432)TTT>CTT	p.F144L	UGT2A1_uc010iht.1_Missense_Mutation_p.F144L|UGT2A1_uc010ihu.1_Missense_Mutation_p.F144L	NM_006798	NP_006789	Q9Y4X1	UD2A1_HUMAN	UDP glycosyltransferase 2 family, polypeptide	144	Extracellular (Potential).				detection of chemical stimulus|sensory perception of smell	integral to membrane	glucuronosyltransferase activity|glucuronosyltransferase activity			ovary(1)	1														0.793893	375.67595	386.17858	104	27	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	70547522	70547522	17511	4	A	G	G	2	2	UGT2A1	G	4	4
ODAM	54959	broad.mit.edu	36	4	71098397	71098397	+	Silent	SNP	C	T	T			TCGA-06-1087-01	TCGA-06-1087-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr4:71098397C>T	uc003hfc.1	+	c.309C>T	c.(307-309)GCC>GCT	p.A103A		NM_017855	NP_060325	A1E959	ODAM_HUMAN	odontogenic ameloblast-associated protein	103	Gln-rich.				biomineral tissue development|odontogenesis of dentine-containing tooth	fibril				ovary(3)|large_intestine(1)	4														0.807692	70.585578	72.883255	21	5	CC		KEEP	---	---	---	---	capture			Silent	SNP	71098397	71098397	11229	4	C	T	T	22	22	ODAM	T	2	2
HARS2	23438	broad.mit.edu	36	5	140056946	140056946	+	Missense_Mutation	SNP	T	G	G			TCGA-06-1087-01	TCGA-06-1087-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr5:140056946T>G	uc003lgx.1	+	c.968T>G	c.(967-969)CTC>CGC	p.L323R		NM_012208	NP_036340	P49590	SYHM_HUMAN	histidyl-tRNA synthetase 2 precursor	323					histidyl-tRNA aminoacylation	mitochondrial matrix	ATP binding|histidine-tRNA ligase activity				0			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)											0.265306	69.905402	74.784327	26	72	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	140056946	140056946	7242	5	T	G	G	54	54	HARS2	G	4	4
HSPB3	8988	broad.mit.edu	36	5	53787604	53787604	+	Silent	SNP	C	T	T			TCGA-06-1087-01	TCGA-06-1087-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr5:53787604C>T	uc003jph.1	+	c.228C>T	c.(226-228)GAC>GAT	p.D76D		NM_006308	NP_006299	Q12988	HSPB3_HUMAN	heat shock 27kDa protein 3	76					cell death|response to heat|response to unfolded protein	cytoplasm|nucleus					0		Lung NSC(810;0.00104)												0.441558	104.83921	105.068214	34	43	CC		KEEP	---	---	---	---	capture			Silent	SNP	53787604	53787604	7720	5	C	T	T	19	19	HSPB3	T	1	1
BHMT	635	broad.mit.edu	36	5	78452005	78452005	+	Missense_Mutation	SNP	G	C	C			TCGA-06-1087-01	TCGA-06-1087-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr5:78452005G>C	uc003kfu.2	+	c.362G>C	c.(361-363)GGA>GCA	p.G121A		NM_001713	NP_001704	Q93088	BHMT1_HUMAN	betaine-homocysteine methyltransferase	121	Hcy-binding.				protein methylation|regulation of homocysteine metabolic process	cytoplasm	betaine-homocysteine S-methyltransferase activity|homocysteine S-methyltransferase activity|zinc ion binding			ovary(1)	1		all_lung(232;0.00051)|Lung NSC(167;0.00131)|Ovarian(174;0.0261)|Prostate(461;0.191)		OV - Ovarian serous cystadenocarcinoma(54;1.88e-45)|Epithelial(54;8.07e-41)|all cancers(79;3.51e-36)	L-Methionine(DB00134)									0.079327	9.650122	84.79969	33	383	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	78452005	78452005	1450	5	G	C	C	41	41	BHMT	C	3	3
NCOA7	135112	broad.mit.edu	36	6	126278307	126278307	+	Silent	SNP	C	G	G			TCGA-06-1087-01	TCGA-06-1087-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr6:126278307C>G	uc010kes.1	+	c.2232C>G	c.(2230-2232)ACC>ACG	p.T744T	NCOA7_uc003qae.2_Silent_p.T744T|NCOA7_uc003qah.2_Silent_p.T733T|NCOA7_uc003qai.2_Silent_p.T744T	NM_181782	NP_861447	Q8NI08	NCOA7_HUMAN	nuclear receptor coactivator 7 isoform 1	744					cell wall macromolecule catabolic process|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	protein binding			lung(2)|ovary(1)	3				UCEC - Uterine corpus endometrioid carcinoma (4;0.0803)|GBM - Glioblastoma multiforme(226;0.0193)|all cancers(137;0.237)										0.098522	18.251909	50.985451	20	183	CC		KEEP	---	---	---	---	capture			Silent	SNP	126278307	126278307	10633	6	C	G	G	21	21	NCOA7	G	3	3
SHPRH	257218	broad.mit.edu	36	6	146297983	146297984	+	Missense_Mutation	DNP	GT	AC	AC			TCGA-06-1087-01	TCGA-06-1087-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:146297983_146297984GT>AC	uc003qld.1	-	c.2742_2743AC>GT	c.(2740-2745)ATACCA>ATGTCA	p.914_915IP>MS	SHPRH_uc010kht.1_Missense_Mutation_p.747_748IP>MS|SHPRH_uc003qle.1_Missense_Mutation_p.914_915IP>MS|SHPRH_uc003qlf.1_Missense_Mutation_p.914_915IP>MS|SHPRH_uc003qlg.1_Missense_Mutation_p.470_471IP>MS|SHPRH_uc003qlh.2_5'Flank|SHPRH_uc003qlj.1_Missense_Mutation_p.803_804IP>MS	NM_001042683	NP_001036148	Q149N8	SHPRH_HUMAN	SNF2 histone linker PHD RING helicase isoform a	914_915					DNA repair|nucleosome assembly	nucleosome|nucleus	ATP binding|DNA binding|helicase activity|ligase activity|zinc ion binding			ovary(1)|kidney(1)	2		Ovarian(120;0.0365)		OV - Ovarian serous cystadenocarcinoma(155;1.47e-07)|GBM - Glioblastoma multiforme(68;0.0124)										0.236842	13.344168	15.762645	9	29	GG		KEEP	---	---	---	---	capture			Missense_Mutation	DNP	146297983	146297984	14786	6	GT	AC	AC	44	44	SHPRH	AC	2	2
FOXC1	2296	broad.mit.edu	36	6	1557233	1557233	+	Missense_Mutation	SNP	G	T	T			TCGA-06-1087-01	TCGA-06-1087-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr6:1557233G>T	uc003mtp.1	+	c.1554G>T	c.(1552-1554)TTG>TTT	p.L518F		NM_001453	NP_001444	Q12948	FOXC1_HUMAN	forkhead box C1	518					anti-apoptosis|artery morphogenesis|blood vessel remodeling|brain development|camera-type eye development|cardiac muscle cell proliferation|collagen fibril organization|embryonic heart tube development|germ cell migration|glycosaminoglycan metabolic process|lacrimal gland development|lymphangiogenesis|metanephros development|negative regulation of gene-specific transcription from RNA polymerase II promoter|negative regulation of mitotic cell cycle|neural crest cell fate commitment|Notch signaling pathway|odontogenesis of dentine-containing tooth|ossification|ovarian follicle development|paraxial mesodermal cell fate commitment|positive regulation of gene-specific transcription from RNA polymerase II promoter|regulation of blood vessel size|regulation of organ growth|regulation of sequence-specific DNA binding transcription factor activity|somitogenesis|ureteric bud development|vascular endothelial growth factor receptor signaling pathway|vasculogenesis|ventricular cardiac muscle tissue morphogenesis	nuclear heterochromatin|transcription factor complex	chromatin DNA binding|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			ovary(1)	1	Ovarian(93;0.0733)	all_cancers(2;4.45e-07)|all_epithelial(2;4.33e-05)|all_lung(73;0.0713)|all_hematologic(90;0.0895)		Epithelial(2;0.0904)|OV - Ovarian serous cystadenocarcinoma(45;0.095)|all cancers(2;0.168)		Pancreas(133;719 1821 3197 26645 35015)								0.214286	7.772512	9.966884	6	22	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	1557233	1557233	6236	6	G	T	T	45	45	FOXC1	T	3	3
KCNK5	8645	broad.mit.edu	36	6	39266893	39266893	+	Silent	SNP	G	A	A			TCGA-06-1087-01	TCGA-06-1087-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr6:39266893G>A	uc003oon.1	-	c.1251C>T	c.(1249-1251)GAC>GAT	p.D417D		NM_003740	NP_003731	O95279	KCNK5_HUMAN	potassium channel, subfamily K, member 5	417					excretion	integral to plasma membrane	potassium channel activity|voltage-gated ion channel activity			central_nervous_system(1)	1														0.647059	72.95941	73.609058	22	12	GG		KEEP	---	---	---	---	capture			Silent	SNP	39266893	39266893	8374	6	G	A	A	40	40	KCNK5	A	1	1
PTK7	5754	broad.mit.edu	36	6	43221074	43221074	+	Missense_Mutation	SNP	G	T	T			TCGA-06-1087-01	TCGA-06-1087-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr6:43221074G>T	uc003oub.1	+	c.2566G>T	c.(2566-2568)GCC>TCC	p.A856S	PTK7_uc003ouc.1_Missense_Mutation_p.A800S|PTK7_uc003oud.1_Missense_Mutation_p.A816S|PTK7_uc003oue.1_Missense_Mutation_p.A726S|PTK7_uc003ouf.1_Intron|PTK7_uc003oug.1_Non-coding_Transcript|PTK7_uc010jyj.1_Missense_Mutation_p.A182S	NM_002821	NP_002812	Q13308	PTK7_HUMAN	PTK7 protein tyrosine kinase 7 isoform a	856	Cytoplasmic (Potential).|Protein kinase; inactive.|Interaction with CTNNB1.				actin cytoskeleton reorganization|canonical Wnt receptor signaling pathway|cell adhesion|cell migration|protein phosphorylation	cell-cell junction|integral to plasma membrane	ATP binding|transmembrane receptor protein tyrosine kinase activity			large_intestine(1)	1			Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.00784)|OV - Ovarian serous cystadenocarcinoma(102;0.0423)							398				0.125828	52.747344	94.027815	38	264	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	43221074	43221074	13220	6	G	T	T	38	38	PTK7	T	3	3
TJAP1	93643	broad.mit.edu	36	6	43581357	43581357	+	Missense_Mutation	SNP	A	C	C			TCGA-06-1087-01	TCGA-06-1087-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr6:43581357A>C	uc003ovd.1	+	c.1460A>C	c.(1459-1461)AAC>ACC	p.N487T	TJAP1_uc003ovc.1_Missense_Mutation_p.N477T|TJAP1_uc010jyp.1_Missense_Mutation_p.N446T|TJAP1_uc003ove.1_Missense_Mutation_p.N477T|TJAP1_uc003ovf.1_Missense_Mutation_p.N477T|TJAP1_uc003ovg.1_Missense_Mutation_p.N353T|TJAP1_uc003ovh.1_Missense_Mutation_p.N304T|TJAP1_uc003ovi.1_Missense_Mutation_p.N353T	NM_080604	NP_542171	Q5JTD0	TJAP1_HUMAN	tight junction protein 4 (peripheral)	487						Golgi apparatus|tight junction	protein binding				0	all_lung(25;0.00536)		Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.0122)|OV - Ovarian serous cystadenocarcinoma(102;0.0804)											0.172414	8.6555	21.120075	20	96	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	43581357	43581357	16457	6	A	C	C	2	2	TJAP1	C	4	4
DOCK4	9732	broad.mit.edu	36	7	111299796	111299796	+	Missense_Mutation	SNP	G	T	T			TCGA-06-1087-01	TCGA-06-1087-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr7:111299796G>T	uc003vfy.1	-	c.1805C>A	c.(1804-1806)TCT>TAT	p.S602Y	DOCK4_uc003vfw.1_Missense_Mutation_p.S43Y|DOCK4_uc003vfx.1_Missense_Mutation_p.S602Y|DOCK4_uc003vga.1_Missense_Mutation_p.S207Y	NM_014705	NP_055520	Q8N1I0	DOCK4_HUMAN	dedicator of cytokinesis 4	602	DHR-1.				cell chemotaxis	cytosol|endomembrane system|membrane|stereocilium	GTP binding|guanyl-nucleotide exchange factor activity|PDZ domain binding|Rac GTPase activator activity|Rac GTPase binding|receptor tyrosine kinase binding|SH3 domain binding			ovary(2)|central_nervous_system(1)	3		Acute lymphoblastic leukemia(1;0.0441)												0.446078	288.895809	289.412728	91	113	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	111299796	111299796	4873	7	G	T	T	33	33	DOCK4	T	3	3
FSCN3	29999	broad.mit.edu	36	7	127025881	127025881	+	Missense_Mutation	SNP	C	T	T			TCGA-06-1087-01	TCGA-06-1087-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr7:127025881C>T	uc003vmd.1	+	c.1117C>T	c.(1117-1119)CCA>TCA	p.P373S	FSCN3_uc010llc.1_Missense_Mutation_p.P373S	NM_020369	NP_065102	Q9NQT6	FSCN3_HUMAN	fascin 3	373						actin cytoskeleton|cytoplasm	actin filament binding|protein binding, bridging			ovary(1)	1														0.72549	122.992788	125.327604	37	14	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	127025881	127025881	6319	7	C	T	T	30	30	FSCN3	T	2	2
COBL	23242	broad.mit.edu	36	7	51060459	51060459	+	Silent	SNP	T	G	G			TCGA-06-1087-01	TCGA-06-1087-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr7:51060459T>G	uc003tpr.2	-	c.3609A>C	c.(3607-3609)CCA>CCC	p.P1203P	COBL_uc003tpp.2_Silent_p.P989P|COBL_uc003tpq.2_Intron|COBL_uc003tpo.2_Silent_p.P745P	NM_015198	NP_056013	O75128	COBL_HUMAN	cordon-bleu homolog	1203										ovary(2)|skin(1)	3	Glioma(55;0.08)					NSCLC(189;2119 2138 12223 30818 34679)								0.28	6.647707	7.870016	7	18	TT		KEEP	---	---	---	---	capture			Silent	SNP	51060459	51060459	3791	7	T	G	G	59	59	COBL	G	4	4
DYNC1I1	1780	broad.mit.edu	36	7	95502991	95502991	+	Missense_Mutation	SNP	G	A	A			TCGA-06-1087-01	TCGA-06-1087-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr7:95502991G>A	uc003uoc.2	+	c.1406G>A	c.(1405-1407)CGT>CAT	p.R469H	DYNC1I1_uc003uob.1_Missense_Mutation_p.R432H|DYNC1I1_uc003uod.2_Missense_Mutation_p.R452H|DYNC1I1_uc003uoe.2_Missense_Mutation_p.R449H|DYNC1I1_uc010lfl.1_Missense_Mutation_p.R458H	NM_004411	NP_004402	O14576	DC1I1_HUMAN	dynein, cytoplasmic 1, intermediate chain 1	469	WD 4.				vesicle transport along microtubule	condensed chromosome kinetochore|cytoplasmic dynein complex|microtubule|perinuclear region of cytoplasm|spindle pole	microtubule binding|microtubule motor activity			ovary(3)|kidney(1)	4	all_cancers(62;9.39e-10)|all_epithelial(64;2.28e-09)|Lung NSC(181;0.165)|all_lung(186;0.191)		STAD - Stomach adenocarcinoma(171;0.0957)											0.534826	1381.332222	1382.17667	430	374	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	95502991	95502991	5028	7	G	A	A	40	40	DYNC1I1	A	1	1
DCAF13	25879	broad.mit.edu	36	8	104501794	104501794	+	Missense_Mutation	SNP	G	A	A			TCGA-06-1087-01	TCGA-06-1087-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr8:104501794G>A	uc003yln.1	+	c.653G>A	c.(652-654)CGT>CAT	p.R218H	DCAF13_uc003ylm.1_Intron|DCAF13_uc003ylo.1_De_novo_Start_OutOfFrame	NM_015420	NP_056235	Q9NV06	DCA13_HUMAN	WD repeats and SOF1 domain containing	66	WD 1.				protein ubiquitination|rRNA processing	CUL4 RING ubiquitin ligase complex|nucleolus|ribonucleoprotein complex				breast(1)	1														0.764706	44.182895	45.272846	13	4	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	104501794	104501794	4437	8	G	A	A	40	40	DCAF13	A	1	1
FER1L6	654463	broad.mit.edu	36	8	125131063	125131063	+	Missense_Mutation	SNP	C	G	G			TCGA-06-1087-01	TCGA-06-1087-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr8:125131063C>G	uc003yqw.1	+	c.2759C>G	c.(2758-2760)GCT>GGT	p.A920G		NM_001039112	NP_001034201	Q2WGJ9	FR1L6_HUMAN	fer-1-like 6	920	Cytoplasmic (Potential).					integral to membrane				ovary(5)|central_nervous_system(1)|skin(1)	7	Lung NSC(37;4.1e-12)|Ovarian(258;0.00438)|all_neural(195;0.0741)		STAD - Stomach adenocarcinoma(47;0.00186)											0.185185	7.238908	9.78569	5	22	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	125131063	125131063	6052	8	C	G	G	28	28	FER1L6	G	3	3
CPNE3	8895	broad.mit.edu	36	8	87632446	87632446	+	Splice_Site_SNP	SNP	T	G	G			TCGA-06-1087-01	TCGA-06-1087-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr8:87632446T>G	uc003ydv.1	+	c.e14_splice_site			CPNE3_uc003ydw.1_Splice_Site_SNP	NM_003909	NP_003900			copine III						lipid metabolic process|vesicle-mediated transport	cytosol	calcium-dependent phospholipid binding|protein serine/threonine kinase activity|transporter activity			ovary(1)	1														0.444444	14.786044	14.849035	8	10	TT		KEEP	---	---	---	---	capture			Splice_Site_SNP	SNP	87632446	87632446	3951	8	T	G	G	57	57	CPNE3	G	5	4
OR1L8	138881	broad.mit.edu	36	9	124369829	124369829	+	Missense_Mutation	SNP	G	A	A			TCGA-06-1087-01	TCGA-06-1087-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr9:124369829G>A	uc004bmp.1	-	c.749C>T	c.(748-750)ACG>ATG	p.T250M		NM_001004454	NP_001004454	Q8NGR8	OR1L8_HUMAN	olfactory receptor, family 1, subfamily L,	250	Helical; Name=6; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(2)|central_nervous_system(1)	3														0.368421	77.675541	78.833542	28	48	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	124369829	124369829	11373	9	G	A	A	40	40	OR1L8	A	1	1
SMC5	23137	broad.mit.edu	36	9	72119534	72119534	+	Silent	SNP	T	C	C			TCGA-06-1087-01	TCGA-06-1087-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr9:72119534T>C	uc004ahr.2	+	c.1635T>C	c.(1633-1635)TAT>TAC	p.Y545Y		NM_015110	NP_055925	Q8IY18	SMC5_HUMAN	SMC5 protein	545	Flexible hinge.				DNA recombination|DNA repair	chromosome|nucleus	ATP binding			ovary(2)|central_nervous_system(1)	3														0.3125	14.868758	15.369729	5	11	TT		KEEP	---	---	---	---	capture			Silent	SNP	72119534	72119534	15284	9	T	C	C	51	51	SMC5	C	4	4
KLHL13	90293	broad.mit.edu	36	X	116927469	116927469	+	Missense_Mutation	SNP	G	T	T			TCGA-06-1087-01	TCGA-06-1087-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chrX:116927469G>T	uc004eql.1	-	c.1189C>A	c.(1189-1191)CAG>AAG	p.Q397K	KLHL13_uc004eqk.1_Missense_Mutation_p.Q346K|KLHL13_uc004eqm.1_Missense_Mutation_p.Q346K	NM_033495	NP_277030	Q9P2N7	KLH13_HUMAN	kelch-like 13	397	Kelch 2.				cytokinesis|mitosis|protein ubiquitination	Cul3-RING ubiquitin ligase complex				kidney(1)	1														0.954545	149.86814	153.696187	42	2	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	116927469	116927469	8681	23	G	T	T	48	48	KLHL13	T	3	3
SAGE1	55511	broad.mit.edu	36	X	134815100	134815100	+	Missense_Mutation	SNP	C	T	T			TCGA-06-1087-01	TCGA-06-1087-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chrX:134815100C>T	uc004ezh.1	+	c.337C>T	c.(337-339)CGT>TGT	p.R113C	SAGE1_uc010nry.1_Missense_Mutation_p.R82C	NM_018666	NP_061136	Q9NXZ1	SAGE1_HUMAN	sarcoma antigen 1	113										ovary(1)	1	Acute lymphoblastic leukemia(192;0.000127)													0.981818	202.964951	205.072695	54	1	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	134815100	134815100	14289	23	C	T	T	23	23	SAGE1	T	1	1
PAGE5	90737	broad.mit.edu	36	X	55263765	55263765	+	Missense_Mutation	SNP	C	T	T			TCGA-06-1087-01	TCGA-06-1087-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chrX:55263765C>T	uc004duj.1	+	c.8C>T	c.(7-9)GCG>GTG	p.A3V	PAGE5_uc004duk.1_Intron	NM_130467	NP_001013453	Q96GU1	GGEE1_HUMAN	P antigen family, member 5 isoform 1	3											0														0.75	10.227706	10.454016	3	1	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	55263765	55263765	11809	23	C	T	T	27	27	PAGE5	T	1	1
LRP1	4035	broad.mit.edu	36	12	55834566	55834574	+	In_Frame_Del	DEL	GTGGAACGC	-	-			TCGA-06-1087-01	TCGA-06-1087-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:55834566_55834574delGTGGAACGC	uc001snd.1	+	c.1042_1050delGTGGAACGC	c.(1042-1050)GTGGAACGCdel	p.VER348del	LRP1_uc001snc.1_In_Frame_Del_p.VER348del	NM_002332	NP_002323	Q07954	LRP1_HUMAN	low density lipoprotein-related protein 1	348_350	LDL-receptor class B 2.|Extracellular (Potential).				apoptotic cell clearance|multicellular organismal development|negative regulation of Wnt receptor signaling pathway|positive regulation of cholesterol efflux|regulation of phospholipase A2 activity	coated pit|integral to plasma membrane|nucleus	apolipoprotein E binding|calcium ion binding|lipoprotein particle receptor binding|lipoprotein transporter activity|protein complex binding|receptor activity			ovary(7)|large_intestine(2)|pancreas(2)|skin(1)|central_nervous_system(1)	13				BRCA - Breast invasive adenocarcinoma(357;0.0103)	Alteplase(DB00009)|Anistreplase(DB00029)|Antihemophilic Factor(DB00025)|Becaplermin(DB00102)|Coagulation Factor IX(DB00100)|Tenecteplase(DB00031)					1456				0.32			265	557				---	---	---	---	capture_indel			In_Frame_Del	DEL	55834566	55834574	9324	12	GTGGAACGC	-	-	44	44	LRP1	-	5	5
RASGRP4	115727	broad.mit.edu	36	19	43593637	43593638	+	Frame_Shift_Ins	INS	-	G	G			TCGA-06-1087-01	TCGA-06-1087-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:43593637_43593638insG	uc002oir.2	-	c.1809_1810insC	c.(1807-1812)CCCGGAfs	p.P603fs	RASGRP4_uc010efz.1_Non-coding_Transcript|RASGRP4_uc010ega.1_Non-coding_Transcript|RASGRP4_uc010egb.1_Frame_Shift_Ins_p.P454fs	NM_170604	NP_733749	Q8TDF6	GRP4_HUMAN	RAS guanyl releasing protein 4	603_604					activation of phospholipase C activity|cell growth|cell proliferation|myeloid cell differentiation|positive regulation of Ras protein signal transduction|regulation of G-protein coupled receptor protein signaling pathway|response to extracellular stimulus|small GTPase mediated signal transduction|transmembrane receptor protein tyrosine kinase signaling pathway	cytoplasm|membrane fraction|plasma membrane|soluble fraction	diacylglycerol binding|GTP-dependent protein binding|metal ion binding|Ras guanyl-nucleotide exchange factor activity			pancreas(1)|skin(1)	2	all_cancers(60;4.21e-06)		Lung(45;0.00172)|LUSC - Lung squamous cell carcinoma(53;0.00272)											0.33			2	4				---	---	---	---	capture_indel			Frame_Shift_Ins	INS	43593637	43593638	13538	19	-	G	G	23	23	RASGRP4	G	5	5
SCAP	22937	broad.mit.edu	36	3	47431604	47431605	+	Frame_Shift_Ins	INS	-	T	T			TCGA-06-1087-01	TCGA-06-1087-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:47431604_47431605insT	uc003crh.1	-	c.3126_3127insA	c.(3124-3129)CCCCTGfs	p.P1042fs	SCAP_uc003crg.2_Frame_Shift_Ins_p.P649fs	NM_012235	NP_036367	Q12770	SCAP_HUMAN	SREBF chaperone protein	1042_1043	Interaction with SREBF2 (By similarity).|Cytoplasmic (By similarity).				cholesterol metabolic process|negative regulation of cholesterol biosynthetic process|positive regulation of low-density lipoprotein particle receptor biosynthetic process|positive regulation of transcription via sterol regulatory element binding involved in ER-nuclear sterol response pathway	endoplasmic reticulum membrane|ER to Golgi transport vesicle membrane|Golgi membrane|integral to membrane	unfolded protein binding			ovary(1)	1				BRCA - Breast invasive adenocarcinoma(193;0.000278)|KIRC - Kidney renal clear cell carcinoma(197;0.00592)|Kidney(197;0.00679)		Pancreas(149;978 1908 29304 37806 46700)								0.33			2	4				---	---	---	---	capture_indel			Frame_Shift_Ins	INS	47431604	47431605	14358	3	-	T	T	35	35	SCAP	T	5	5
PDGFC	56034	broad.mit.edu	36	4	158111472	158111472	+	Frame_Shift_Del	DEL	C	-	-			TCGA-06-1087-01	TCGA-06-1087-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:158111472_158111472delC	uc003iph.1	-	c.34_34delG	c.(34-36)GCCfs	p.A12fs	PDGFC_uc003ipi.1_5'UTR	NM_016205	NP_057289	Q9NRA1	PDGFC_HUMAN	platelet-derived growth factor C precursor	12					central nervous system development|platelet-derived growth factor receptor signaling pathway|positive regulation of cell division|positive regulation of DNA replication|positive regulation of fibroblast proliferation|vascular endothelial growth factor receptor signaling pathway	endoplasmic reticulum lumen|extracellular space|Golgi membrane|nucleus	cell surface binding|growth factor activity|platelet-derived growth factor receptor binding|protein homodimerization activity			ovary(1)|lung(1)	2	all_hematologic(180;0.24)	Renal(120;0.0458)		KIRC - Kidney renal clear cell carcinoma(143;0.08)|Kidney(143;0.0977)|COAD - Colon adenocarcinoma(41;0.212)								OREG0016375	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	0.34			14	27				---	---	---	---	capture_indel			Frame_Shift_Del	DEL	158111472	158111472	12080	4	C	-	-	25	25	PDGFC	-	5	5
DSP	1832	broad.mit.edu	36	6	7487147	7487148	+	Start_Codon_Ins	INS	-	A	A			TCGA-06-1087-01	TCGA-06-1087-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:7487147_7487148insA	uc003mxp.1	+				DSP_uc003mxq.1_Start_Codon_Ins	NM_004415	NP_004406			desmoplakin isoform I						cellular component disassembly involved in apoptosis|keratinocyte differentiation|peptide cross-linking	cornified envelope|cytoplasm|desmosome	protein binding, bridging|structural constituent of cytoskeleton			central_nervous_system(6)|ovary(2)	8	Ovarian(93;0.0584)	all_hematologic(90;0.236)		OV - Ovarian serous cystadenocarcinoma(45;0.000508)										0.50			3	3				---	---	---	---	capture_indel			Start_Codon_Ins	INS	7487147	7487148	4965	6	-	A	A	17	17	DSP	A	5	5
