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
PTCHD3	374308	broad.mit.edu	36	10	27742779	27742779	+	Missense_Mutation	SNP	G	A	A			TCGA-28-5220-01	TCGA-28-5220-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr10:27742779G>A	uc001itu.1	-	c.407C>T	c.(406-408)GCG>GTG	p.A136V		NM_001034842	NP_001030014	Q3KNS1	PTHD3_HUMAN	patched domain containing 3	136					spermatid development	integral to membrane	hedgehog receptor activity			ovary(2)|pancreas(1)|skin(1)	4														0.857143	90.024506	94.544475	30	5	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	27742779	27742779	13188	10	G	A	A	38	38	PTCHD3	A	1	1
OR6X1	390260	broad.mit.edu	36	11	123129846	123129846	+	Silent	SNP	G	A	A			TCGA-28-5220-01	TCGA-28-5220-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr11:123129846G>A	uc001pzg.1	-	c.591C>T	c.(589-591)GGC>GGT	p.G197G		NM_001005188	NP_001005188	Q8NH79	OR6X1_HUMAN	olfactory receptor, family 6, subfamily X,	197	Helical; Name=5; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(2)	2		Breast(109;0.0109)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.224)												0.096	11.014684	51.94518	24	226	GG		KEEP	---	---	---	---	capture		BRCA - Breast invasive adenocarcinoma(274;4.88e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0279)	Silent	SNP	123129846	123129846	11623	11	G	A	A	38	38	OR6X1	A	1	1
WT1	7490	broad.mit.edu	36	11	32406140	32406140	+	Missense_Mutation	SNP	G	C	C			TCGA-28-5220-01	TCGA-28-5220-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr11:32406140G>C	uc001mtn.1	-	c.810C>G	c.(808-810)TGC>TGG	p.C270W	WT1_uc001mtl.1_Missense_Mutation_p.C58W|WT1_uc001mtm.1_Missense_Mutation_p.C58W|WT1_uc001mto.1_Missense_Mutation_p.C270W|WT1_uc001mtp.1_Missense_Mutation_p.C270W|WT1_uc001mtq.1_Missense_Mutation_p.C270W|WT1_uc009yjs.1_Non-coding_Transcript	NM_024426	NP_077744	P19544	WT1_HUMAN	Wilms tumor 1 isoform D	202					adrenal gland development|branching involved in ureteric bud morphogenesis|glomerular basement membrane development|glomerular visceral epithelial cell differentiation|induction of apoptosis|male gonad development|metanephric S-shaped body morphogenesis|negative regulation of apoptosis|negative regulation of cell growth|negative regulation of cell proliferation|negative regulation of gene-specific transcription|negative regulation of transcription from RNA polymerase II promoter|negative regulation of translation|positive regulation of gene-specific transcription|sex determination|visceral serous pericardium development	cytoplasm|nuclear speck|nucleoplasm	C2H2 zinc finger domain binding|promoter binding|RNA binding|sequence-specific DNA binding transcription factor activity|specific transcriptional repressor activity|transcription activator activity|transcription repressor activity|zinc ion binding		EWSR1/WT1(231)	haematopoietic_and_lymphoid_tissue(302)|soft_tissue(231)|kidney(132)|pleura(2)|peritoneum(1)|lung(1)	669	Breast(20;0.247)									684				0.346154	8.39866	9.067267	9	17	GG		KEEP	---	---	---	---	capture	OV - Ovarian serous cystadenocarcinoma(30;0.128)		Missense_Mutation	SNP	32406140	32406140	17982	11	G	C	C	42	42	WT1	C	3	3
RBM19	9904	broad.mit.edu	36	12	112766960	112766960	+	Missense_Mutation	SNP	A	G	G			TCGA-28-5220-01	TCGA-28-5220-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr12:112766960A>G	uc009zwi.1	-	c.2681T>C	c.(2680-2682)CTG>CCG	p.L894P	RBM19_uc001tvm.1_Missense_Mutation_p.L894P|RBM19_uc001tvn.2_Missense_Mutation_p.L894P	NM_016196	NP_057280	Q9Y4C8	RBM19_HUMAN	RNA binding motif protein 19	894	RRM 6.				multicellular organismal development|positive regulation of embryonic development	chromosome|cytoplasm|nucleolus|nucleoplasm	nucleotide binding|RNA binding			skin(2)|ovary(1)|liver(1)|central_nervous_system(1)	5	Medulloblastoma(191;0.163)|all_neural(191;0.178)													0.408602	117.636835	118.314154	38	55	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	112766960	112766960	13582	12	A	G	G	7	7	RBM19	G	4	4
RABGGTA	5875	broad.mit.edu	36	14	23809125	23809125	+	Missense_Mutation	SNP	G	A	A			TCGA-28-5220-01	TCGA-28-5220-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr14:23809125G>A	uc001wof.1	-	c.301C>T	c.(301-303)CGG>TGG	p.R101W	RABGGTA_uc001woe.1_Non-coding_Transcript|RABGGTA_uc001wog.1_Missense_Mutation_p.R101W|RABGGTA_uc001woh.1_Non-coding_Transcript|RABGGTA_uc001woi.1_Non-coding_Transcript	NM_004581	NP_004572	Q92696	PGTA_HUMAN	Rab geranylgeranyltransferase, alpha subunit	101	PFTA 2.				visual perception		Rab geranylgeranyltransferase activity|zinc ion binding				0														0.588235	30.953921	31.070238	10	7	GG		KEEP	---	---	---	---	capture		GBM - Glioblastoma multiforme(265;0.0184)	Missense_Mutation	SNP	23809125	23809125	13426	14	G	A	A	38	38	RABGGTA	A	1	1
CORO7	79585	broad.mit.edu	36	16	4354383	4354383	+	Silent	SNP	C	T	T			TCGA-28-5220-01	TCGA-28-5220-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr16:4354383C>T	uc002cwf.1	-	c.1170G>A	c.(1168-1170)CGG>CGA	p.R390R	CORO7_uc002cwe.1_Non-coding_Transcript|CORO7_uc002cwg.2_Silent_p.R170R|CORO7_uc002cwh.2_Silent_p.R390R|CORO7_uc002cwi.1_Silent_p.R170R|CORO7_uc010btp.1_Silent_p.R170R	NM_024535	NP_078811	P57737	CORO7_HUMAN	coronin 7	390						cytoplasmic membrane-bounded vesicle|cytosol|Golgi membrane|integral to membrane of membrane fraction|soluble fraction					0														0.551724	48.195941	48.262828	16	13	CC		KEEP	---	---	---	---	capture			Silent	SNP	4354383	4354383	3897	16	C	T	T	26	26	CORO7	T	2	2
AMAC1	146861	broad.mit.edu	36	17	30545035	30545035	+	Missense_Mutation	SNP	T	A	A			TCGA-28-5220-01	TCGA-28-5220-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr17:30545035T>A	uc002hjd.1	-	c.405A>T	c.(403-405)AAA>AAT	p.K135N		NM_152462	NP_689675	Q8N808	AMAC1_HUMAN	acyl-malonyl condensing enzyme 1	135	DUF6 1.					integral to membrane					0														0.444444	486.631036	487.673219	172	215	TT		KEEP	---	---	---	---	capture		BRCA - Breast invasive adenocarcinoma(366;0.0917)	Missense_Mutation	SNP	30545035	30545035	562	17	T	A	A	56	56	AMAC1	A	4	4
KRT20	54474	broad.mit.edu	36	17	36294872	36294872	+	Missense_Mutation	SNP	G	A	A			TCGA-28-5220-01	TCGA-28-5220-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr17:36294872G>A	uc002hvl.1	-	c.92C>T	c.(91-93)ACG>ATG	p.T31M		NM_019010	NP_061883	P35900	K1C20_HUMAN	keratin 20	31	Head.				apoptosis|intermediate filament organization	Golgi apparatus|intermediate filament	protein binding|structural constituent of cytoskeleton			large_intestine(1)|kidney(1)	2		Breast(137;0.000301)|Ovarian(249;0.15)												0.381295	139.724637	141.447894	53	86	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	36294872	36294872	8773	17	G	A	A	40	40	KRT20	A	1	1
TBKBP1	9755	broad.mit.edu	36	17	43131023	43131023	+	Missense_Mutation	SNP	C	G	G			TCGA-28-5220-01	TCGA-28-5220-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr17:43131023C>G	uc002ilu.1	+	c.517C>G	c.(517-519)CAA>GAA	p.Q173E		NM_014726	NP_055541	A7MCY6	TBKB1_HUMAN	TBK1 binding protein 1	173					innate immune response						0												OREG0024498	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	0.695652	54.671367	55.447554	16	7	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	43131023	43131023	16164	17	C	G	G	25	25	TBKBP1	G	3	3
EXOC7	23265	broad.mit.edu	36	17	71596159	71596159	+	Missense_Mutation	SNP	T	G	G			TCGA-28-5220-01	TCGA-28-5220-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr17:71596159T>G	uc002jqs.1	-	c.1433A>C	c.(1432-1434)GAC>GCC	p.D478A	EXOC7_uc010dgv.1_Missense_Mutation_p.D374A|EXOC7_uc002jqq.1_Missense_Mutation_p.D427A|EXOC7_uc002jqr.1_Missense_Mutation_p.D396A	NM_015219	NP_001013861	Q9UPT5	EXOC7_HUMAN	exocyst complex component 7 isoform 2	478					exocytosis|protein transport	centriolar satellite|cytosol|exocyst|plasma membrane	protein binding				0														0.5	102.381261	102.381261	31	31	TT		KEEP	---	---	---	---	capture	LUSC - Lung squamous cell carcinoma(166;0.187)		Missense_Mutation	SNP	71596159	71596159	5503	17	T	G	G	58	58	EXOC7	G	4	4
ZNF407	55628	broad.mit.edu	36	18	70904648	70904648	+	Missense_Mutation	SNP	G	A	A			TCGA-28-5220-01	TCGA-28-5220-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr18:70904648G>A	uc002llw.2	+	c.5983G>A	c.(5983-5985)GCG>ACG	p.A1995T		NM_017757	NP_060227	Q9C0G0	ZN407_HUMAN	zinc finger protein 407	1995					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(2)	2		Esophageal squamous(42;0.131)|Prostate(75;0.173)												0.326923	39.77617	41.148652	17	35	GG		KEEP	---	---	---	---	capture		BRCA - Breast invasive adenocarcinoma(31;0.184)	Missense_Mutation	SNP	70904648	70904648	18480	18	G	A	A	46	46	ZNF407	A	2	2
COMP	1311	broad.mit.edu	36	19	18756132	18756132	+	Silent	SNP	G	A	A	rs10421797	by-frequency,by-hapmap	TCGA-28-5220-01	TCGA-28-5220-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr19:18756132G>A	uc002nke.1	-	c.1956C>T	c.(1954-1956)AAC>AAT	p.N652N	COMP_uc002nkd.1_Silent_p.N619N	NM_000095	NP_000086	P49747	COMP_HUMAN	cartilage oligomeric matrix protein precursor	652	Mediates cell survival and induction of the IAP family of survival proteins.|TSP C-terminal.				anti-apoptosis|apoptosis|cell adhesion|limb development	extracellular space|proteinaceous extracellular matrix	calcium ion binding|collagen binding|extracellular matrix structural constituent|heparan sulfate proteoglycan binding|heparin binding				0														0.447917	238.705597	239.160812	86	106	GG		KEEP	---	---	---	---	capture			Silent	SNP	18756132	18756132	3862	19	G	A	A	40	40	COMP	A	1	1
PRX	57716	broad.mit.edu	36	19	45592174	45592174	+	Missense_Mutation	SNP	G	C	C			TCGA-28-5220-01	TCGA-28-5220-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr19:45592174G>C	uc002onr.1	-	c.3925C>G	c.(3925-3927)CCC>GCC	p.P1309A	PRX_uc002onq.1_Missense_Mutation_p.P1170A|PRX_uc002ons.1_3'UTR	NM_181882	NP_870998	Q9BXM0	PRAX_HUMAN	periaxin isoform 2	1309					axon ensheathment	cytoplasm|nucleus|plasma membrane	protein binding			ovary(2)	2														0.285714	7.695984	8.272303	4	10	GG		KEEP	---	---	---	---	capture	Lung(22;6.24e-05)|LUSC - Lung squamous cell carcinoma(20;0.000384)		Missense_Mutation	SNP	45592174	45592174	13093	19	G	C	C	42	42	PRX	C	3	3
CCDC155	147872	broad.mit.edu	36	19	54602309	54602309	+	Missense_Mutation	SNP	C	T	T			TCGA-28-5220-01	TCGA-28-5220-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr19:54602309C>T	uc002pnm.1	+	c.877C>T	c.(877-879)CGG>TGG	p.R293W	CCDC155_uc010emx.1_Missense_Mutation_p.R266W	NM_144688	NP_653289	Q8N6L0	CC155_HUMAN	coiled-coil domain containing 155	293	Potential.					integral to membrane	calcium ion binding			ovary(1)	1														0.377358	50.579613	51.280897	20	33	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	54602309	54602309	2910	19	C	T	T	27	27	CCDC155	T	1	1
TBC1D17	79735	broad.mit.edu	36	19	55079583	55079583	+	Silent	SNP	C	T	T			TCGA-28-5220-01	TCGA-28-5220-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr19:55079583C>T	uc002pqo.1	+	c.1299C>T	c.(1297-1299)AAC>AAT	p.N433N	TBC1D17_uc002pqp.1_Silent_p.N84N|TBC1D17_uc002pqq.1_Silent_p.N84N|TBC1D17_uc002pqr.1_Silent_p.N84N|TBC1D17_uc002pqs.1_Non-coding_Transcript	NM_024682	NP_078958	Q9HA65	TBC17_HUMAN	TBC1 domain family, member 17	433	Rab-GAP TBC.					intracellular	Rab GTPase activator activity				0		all_lung(116;0.000338)|Lung NSC(112;0.000446)|all_neural(266;0.107)|Ovarian(192;0.231)												0.434599	298.089265	298.972469	103	134	CC		KEEP	---	---	---	---	capture		GBM - Glioblastoma multiforme(134;0.0116)|OV - Ovarian serous cystadenocarcinoma(262;0.017)	Silent	SNP	55079583	55079583	16128	19	C	T	T	19	19	TBC1D17	T	1	1
SLC2A1	6513	broad.mit.edu	36	1	43169405	43169405	+	Silent	SNP	G	A	A			TCGA-28-5220-01	TCGA-28-5220-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:43169405G>A	uc001cik.2	-	c.174C>T	c.(172-174)CCC>CCT	p.P58P		NM_006516	NP_006507	P11166	GTR1_HUMAN	solute carrier family 2 (facilitated glucose	58	Extracellular (Potential).				carbohydrate metabolic process|energy reserve metabolic process|regulation of insulin secretion|water-soluble vitamin metabolic process	integral to membrane|melanosome|membrane fraction|midbody	D-glucose transmembrane transporter activity|dehydroascorbic acid transporter activity			central_nervous_system(2)|pancreas(2)|ovary(1)	5	Ovarian(52;0.00579)|all_hematologic(146;0.0977)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0122)			Etomidate(DB00292)							OREG0013425	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	0.478571	205.709533	205.765912	67	73	GG		KEEP	---	---	---	---	capture			Silent	SNP	43169405	43169405	15035	1	G	A	A	47	47	SLC2A1	A	2	2
TGM2	7052	broad.mit.edu	36	20	36223276	36223276	+	Silent	SNP	G	A	A			TCGA-28-5220-01	TCGA-28-5220-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr20:36223276G>A	uc002xhr.1	-	c.150C>T	c.(148-150)TAC>TAT	p.Y50Y	TGM2_uc002xhs.1_Silent_p.Y50Y|TGM2_uc002xht.1_Silent_p.Y50Y|TGM2_uc002xhu.2_Silent_p.Y50Y	NM_004613	NP_004604	P21980	TGM2_HUMAN	transglutaminase 2 isoform a	50					apoptotic cell clearance|peptide cross-linking|positive regulation of cell adhesion		acyltransferase activity|metal ion binding|protein binding|protein-glutamine gamma-glutamyltransferase activity			large_intestine(1)|lung(1)|ovary(1)	3		Myeloproliferative disorder(115;0.00878)			L-Glutamine(DB00130)									0.445378	144.221312	144.534325	53	66	GG		KEEP	---	---	---	---	capture			Silent	SNP	36223276	36223276	16358	20	G	A	A	40	40	TGM2	A	1	1
TRPM2	7226	broad.mit.edu	36	21	44611087	44611087	+	Missense_Mutation	SNP	C	G	G			TCGA-28-5220-01	TCGA-28-5220-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr21:44611087C>G	uc010gpt.1	+	c.446C>G	c.(445-447)ACG>AGG	p.T149R	TRPM2_uc002zet.1_Missense_Mutation_p.T149R|TRPM2_uc002zeu.1_Missense_Mutation_p.T149R|TRPM2_uc002zew.1_Missense_Mutation_p.T149R|TRPM2_uc002zex.1_5'Flank	NM_003307	NP_003298	O94759	TRPM2_HUMAN	transient receptor potential cation channel,	149	Cytoplasmic (Potential).					integral to plasma membrane	ADP-ribose diphosphatase activity|calcium channel activity|sodium channel activity			ovary(1)|central_nervous_system(1)|pancreas(1)	3														0.349206	216.913074	220.696304	66	123	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	44611087	44611087	17137	21	C	G	G	19	19	TRPM2	G	3	3
RIBC2	26150	broad.mit.edu	36	22	44192469	44192469	+	Missense_Mutation	SNP	C	T	T			TCGA-28-5220-01	TCGA-28-5220-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr22:44192469C>T	uc003bgf.1	+	c.316C>T	c.(316-318)CGT>TGT	p.R106C		NM_015653	NP_056468	Q9H4K1	RIBC2_HUMAN	RIB43A domain with coiled-coils 2	106											0		Ovarian(80;0.00965)|all_neural(38;0.0416)												0.425926	67.117185	67.375282	23	31	CC		KEEP	---	---	---	---	capture		UCEC - Uterine corpus endometrioid carcinoma (28;0.0178)	Missense_Mutation	SNP	44192469	44192469	13828	22	C	T	T	23	23	RIBC2	T	1	1
TGFBRAP1	9392	broad.mit.edu	36	2	105263596	105263596	+	Missense_Mutation	SNP	C	T	T			TCGA-28-5220-01	TCGA-28-5220-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr2:105263596C>T	uc002tcq.1	-	c.1138G>A	c.(1138-1140)GTC>ATC	p.V380I	TGFBRAP1_uc010fjc.1_Missense_Mutation_p.V150I|TGFBRAP1_uc002tcr.2_Missense_Mutation_p.V380I	NM_004257	NP_004248	Q8WUH2	TGFA1_HUMAN	transforming growth factor, beta receptor	380					regulation of transcription, DNA-dependent|transforming growth factor beta receptor signaling pathway	cytoplasm|membrane	SMAD binding|small GTPase regulator activity|transforming growth factor beta receptor binding			central_nervous_system(1)|skin(1)	2						Esophageal Squamous(183;794 2019 9730 21801 48859)								0.483333	79.864917	79.879668	29	31	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	105263596	105263596	16352	2	C	T	T	17	17	TGFBRAP1	T	2	2
CNTNAP5	129684	broad.mit.edu	36	2	125083868	125083868	+	Missense_Mutation	SNP	G	A	A			TCGA-28-5220-01	TCGA-28-5220-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr2:125083868G>A	uc002tno.1	+	c.1774G>A	c.(1774-1776)GAG>AAG	p.E592K	CNTNAP5_uc010flu.1_Missense_Mutation_p.E593K	NM_130773	NP_570129	Q8WYK1	CNTP5_HUMAN	contactin associated protein-like 5	592	Extracellular (Potential).|Fibrinogen C-terminal.				cell adhesion|signal transduction	integral to membrane	receptor binding			ovary(10)	10														0.423469	242.6942	243.694463	83	113	GG		KEEP	---	---	---	---	capture		BRCA - Breast invasive adenocarcinoma(221;0.248)	Missense_Mutation	SNP	125083868	125083868	3788	2	G	A	A	37	37	CNTNAP5	A	1	1
PDE11A	50940	broad.mit.edu	36	2	178644705	178644705	+	Missense_Mutation	SNP	C	G	G			TCGA-28-5220-01	TCGA-28-5220-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr2:178644705C>G	uc002ulq.1	-	c.706G>C	c.(706-708)GAC>CAC	p.D236H	PDE11A_uc002ulr.1_Intron|PDE11A_uc002ult.1_Intron	NM_016953	NP_001070664	Q9HCR9	PDE11_HUMAN	phosphodiesterase 11A isoform 4	236	GAF 1.				platelet activation|signal transduction	cytosol	3',5'-cyclic-AMP phosphodiesterase activity|3',5'-cyclic-GMP phosphodiesterase activity|metal ion binding			ovary(3)|large_intestine(1)	4														0.389163	265.074021	267.260487	79	124	CC		KEEP	---	---	---	---	capture	OV - Ovarian serous cystadenocarcinoma(117;0.00121)|Epithelial(96;0.00455)|all cancers(119;0.02)		Missense_Mutation	SNP	178644705	178644705	12052	2	C	G	G	29	29	PDE11A	G	3	3
SPHKAP	80309	broad.mit.edu	36	2	228591128	228591128	+	Missense_Mutation	SNP	C	T	T			TCGA-28-5220-01	TCGA-28-5220-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr2:228591128C>T	uc002vpq.1	-	c.2686G>A	c.(2686-2688)GAA>AAA	p.E896K	SPHKAP_uc002vpp.1_Missense_Mutation_p.E896K	NM_030623	NP_085126	Q2M3C7	SPKAP_HUMAN	sphingosine kinase type 1-interacting protein	896						cytoplasm	protein binding			ovary(4)|lung(1)	5		Renal(207;0.025)|all_hematologic(139;0.15)|all_lung(227;0.204)|Acute lymphoblastic leukemia(138;0.205)|Esophageal squamous(248;0.23)												0.430857	1133.044755	1136.691149	377	498	CC		KEEP	---	---	---	---	capture		Epithelial(121;8.17e-11)|all cancers(144;7.92e-08)|Lung(261;0.0168)|LUSC - Lung squamous cell carcinoma(224;0.0232)	Missense_Mutation	SNP	228591128	228591128	15560	2	C	T	T	31	31	SPHKAP	T	1	1
PDGFRB	5159	broad.mit.edu	36	5	149484080	149484080	+	Missense_Mutation	SNP	G	A	A			TCGA-28-5220-01	TCGA-28-5220-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr5:149484080G>A	uc003lro.1	-	c.1949C>T	c.(1948-1950)TCG>TTG	p.S650L	PDGFRB_uc010jhd.1_Missense_Mutation_p.S489L	NM_002609	NP_002600	P09619	PGFRB_HUMAN	platelet-derived growth factor receptor beta	650	Cytoplasmic (Potential).|Protein kinase.				cardiac myofibril assembly|cell chemotaxis|hemopoiesis|metanephric glomerular capillary formation|metanephric glomerular mesangial cell proliferation involved in metanephros development|peptidyl-tyrosine phosphorylation|positive regulation of calcium ion import|positive regulation of chemotaxis|positive regulation of ERK1 and ERK2 cascade|positive regulation of MAP kinase activity|positive regulation of mitosis|positive regulation of phosphatidylinositol 3-kinase cascade|positive regulation of reactive oxygen species metabolic process|positive regulation of smooth muscle cell migration|positive regulation of smooth muscle cell proliferation|protein autophosphorylation|retina vasculature development in camera-type eye	apical plasma membrane|cytoplasm|integral to plasma membrane|nucleus	ATP binding|platelet activating factor receptor activity|platelet-derived growth factor beta-receptor activity|platelet-derived growth factor binding|platelet-derived growth factor receptor binding|vascular endothelial growth factor receptor activity			central_nervous_system(4)|lung(3)|large_intestine(1)|stomach(1)|breast(1)|ovary(1)	11		all_hematologic(541;0.224)			Becaplermin(DB00102)|Dasatinib(DB01254)|Imatinib(DB00619)|Sorafenib(DB00398)|Sunitinib(DB01268)					880				0.396226	117.561632	118.578854	42	64	GG		KEEP	---	---	---	---	capture	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)		Missense_Mutation	SNP	149484080	149484080	12083	5	G	A	A	37	37	PDGFRB	A	1	1
HEATR7B2	133558	broad.mit.edu	36	5	41106705	41106705	+	Missense_Mutation	SNP	G	T	T			TCGA-28-5220-01	TCGA-28-5220-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr5:41106705G>T	uc003jmj.2	-	c.7C>A	c.(7-9)CTT>ATT	p.L3I		NM_173489	NP_775760	Q7Z745	HTRB2_HUMAN	HEAT repeat family member 7B2	3							binding			ovary(6)|central_nervous_system(2)	8														0.254237	37.693242	40.930728	15	44	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	41106705	41106705	7318	5	G	T	T	36	36	HEATR7B2	T	3	3
ENC1	8507	broad.mit.edu	36	5	73967408	73967408	+	Missense_Mutation	SNP	T	C	C			TCGA-28-5220-01	TCGA-28-5220-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr5:73967408T>C	uc003kdc.2	-	c.659A>G	c.(658-660)TAT>TGT	p.Y220C	ENC1_uc010izg.1_Missense_Mutation_p.Y220C	NM_003633	NP_003624	O14682	ENC1_HUMAN	ectodermal-neural cortex (with BTB-like domain)	220					nervous system development	cytoplasm|cytoskeleton|nuclear matrix	actin binding			ovary(1)|pancreas(1)|skin(1)	3		all_lung(232;0.0154)|Lung NSC(167;0.0331)|Ovarian(174;0.0798)												0.429185	338.811524	339.81927	100	133	TT		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(47;1.45e-59)	Missense_Mutation	SNP	73967408	73967408	5306	5	T	C	C	49	49	ENC1	C	4	4
RELN	5649	broad.mit.edu	36	7	102978906	102978906	+	Missense_Mutation	SNP	G	A	A			TCGA-28-5220-01	TCGA-28-5220-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr7:102978906G>A	uc003vca.1	-	c.6146C>T	c.(6145-6147)GCG>GTG	p.A2049V	RELN_uc010liz.1_Missense_Mutation_p.A2049V	NM_005045	NP_005036	P78509	RELN_HUMAN	reelin isoform a	2049	BNR 9.				axon guidance|cell adhesion|cerebral cortex tangential migration|glial cell differentiation|neuron migration|peptidyl-tyrosine phosphorylation|positive regulation of protein kinase activity|positive regulation of small GTPase mediated signal transduction|response to pain|spinal cord patterning	cytoplasm|dendrite|extracellular space|proteinaceous extracellular matrix	metal ion binding|protein serine/threonine/tyrosine kinase activity|serine-type peptidase activity			ovary(8)|large_intestine(2)|central_nervous_system(2)|pancreas(1)|skin(1)	14						NSCLC(146;835 1944 15585 22231 52158)								0.370968	58.104234	59.012526	23	39	GG		KEEP	---	---	---	---	capture		COAD - Colon adenocarcinoma(1;8.98e-05)|Colorectal(1;0.00184)	Missense_Mutation	SNP	102978906	102978906	13689	7	G	A	A	38	38	RELN	A	1	1
RNF32	140545	broad.mit.edu	36	7	156143982	156143982	+	Missense_Mutation	SNP	C	G	G			TCGA-28-5220-01	TCGA-28-5220-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr7:156143982C>G	uc003wmo.1	+	c.641C>G	c.(640-642)CCT>CGT	p.P214R	RNF32_uc010lql.1_Non-coding_Transcript|RNF32_uc010lqm.1_Missense_Mutation_p.P214R|RNF32_uc003wmq.2_Missense_Mutation_p.P214R|RNF32_uc003wmr.1_Missense_Mutation_p.P214R|RNF32_uc003wms.2_Missense_Mutation_p.P214R|RNF32_uc003wmu.1_Non-coding_Transcript|RNF32_uc003wmt.2_Missense_Mutation_p.P214R	NM_030936	NP_112198	Q9H0A6	RNF32_HUMAN	ring finger protein 32	214	IQ.					aggresome|endosome	protein binding|zinc ion binding				0	Ovarian(565;0.218)	all_hematologic(28;0.0592)												0.283898	195.633775	205.525605	67	169	CC		KEEP	---	---	---	---	capture	OV - Ovarian serous cystadenocarcinoma(82;0.00291)	UCEC - Uterine corpus endometrioid carcinoma (81;0.169)	Missense_Mutation	SNP	156143982	156143982	13967	7	C	G	G	24	24	RNF32	G	3	3
AQP1	358	broad.mit.edu	36	7	30928359	30928359	+	Missense_Mutation	SNP	C	T	T			TCGA-28-5220-01	TCGA-28-5220-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr7:30928359C>T	uc003tbv.1	+	c.538C>T	c.(538-540)CAC>TAC	p.H180Y	AQP1_uc010kwf.1_Missense_Mutation_p.H97Y|AQP1_uc010kwg.1_Missense_Mutation_p.H61Y|AQP1_uc010kwh.1_Missense_Mutation_p.H129Y	NM_198098	NP_932766	P29972	AQP1_HUMAN	aquaporin 1	180	Helical; Name=Helix 5.	Substrate discrimination.			ammonium transport|cell volume homeostasis|cellular hyperosmotic response|cellular response to cAMP|cellular response to copper ion|cellular response to dexamethasone stimulus|cellular response to hydrogen peroxide|cellular response to hypoxia|cellular response to mechanical stimulus|cellular response to mercury ion|cellular response to nitric oxide|cellular response to retinoic acid|cellular response to salt stress|cellular response to UV|cerebrospinal fluid secretion|cGMP biosynthetic process|establishment or maintenance of actin cytoskeleton polarity|lateral ventricle development|maintenance of symbiont-containing vacuole via substance secreted by host|negative regulation of apoptosis|odontogenesis|pancreatic juice secretion|positive regulation of angiogenesis|positive regulation of fibroblast proliferation|positive regulation of saliva secretion|renal water transport|response to drug|transepithelial water transport	apical plasma membrane|basal plasma membrane|brush border membrane|cytoplasm|integral to plasma membrane|nuclear membrane|sarcolemma|symbiont-containing vacuole	ammonia transmembrane transporter activity|carbon dioxide transmembrane transporter activity|glycerol transmembrane transporter activity|intracellular cGMP activated cation channel activity|nitric oxide transmembrane transporter activity|potassium channel activity|potassium ion transmembrane transporter activity|protein binding|water channel activity				0		Melanoma(862;0.16)			Acetazolamide(DB00819)									0.373333	73.776152	74.83455	28	47	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	30928359	30928359	832	7	C	T	T	17	17	AQP1	T	2	2
SDK1	221935	broad.mit.edu	36	7	3977655	3977655	+	Missense_Mutation	SNP	C	A	A			TCGA-28-5220-01	TCGA-28-5220-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr7:3977655C>A	uc003smx.1	+	c.1746C>A	c.(1744-1746)GAC>GAA	p.D582E		NM_152744	NP_689957	Q7Z5N4	SDK1_HUMAN	sidekick 1 isoform 1	582	Ig-like C2-type 6.				cell adhesion	integral to membrane				large_intestine(3)|ovary(2)	5		all_cancers(1;0.127)|Ovarian(82;0.0177)|Myeloproliferative disorder(862;0.194)												0.278846	77.130581	81.705877	29	75	CC		KEEP	---	---	---	---	capture		UCEC - Uterine corpus endometrioid carcinoma (126;0.121)|OV - Ovarian serous cystadenocarcinoma(56;9.65e-15)	Missense_Mutation	SNP	3977655	3977655	14454	7	C	A	A	18	18	SDK1	A	3	3
PKD1L1	168507	broad.mit.edu	36	7	47806906	47806906	+	Missense_Mutation	SNP	G	A	A			TCGA-28-5220-01	TCGA-28-5220-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr7:47806906G>A	uc003tny.1	-	c.8059C>T	c.(8059-8061)CCC>TCC	p.P2687S	C7orf69_uc003tnz.2_Intron|C7orf69_uc003toa.1_Intron	NM_138295	NP_612152	Q8TDX9	PK1L1_HUMAN	polycystin-1L1	2687	Extracellular (Potential).				cell-cell adhesion	integral to membrane				ovary(7)|breast(1)	8														0.291339	312.46825	327.330134	111	270	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	47806906	47806906	12388	7	G	A	A	43	43	PKD1L1	A	2	2
COL14A1	7373	broad.mit.edu	36	8	121288451	121288451	+	Silent	SNP	C	T	T			TCGA-28-5220-01	TCGA-28-5220-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr8:121288451C>T	uc003yox.1	+	c.1128C>T	c.(1126-1128)GCC>GCT	p.A376A	COL14A1_uc010mde.1_Silent_p.A54A|COL14A1_uc003yoy.2_Silent_p.A54A	NM_021110	NP_066933	Q05707	COEA1_HUMAN	collagen, type XIV, alpha 1	376	Fibronectin type-III 2.				cell-cell adhesion|collagen fibril organization	collagen type XIV|extracellular space	collagen binding|extracellular matrix structural constituent|protein binding, bridging			ovary(4)|kidney(4)|skin(2)|pancreas(1)|central_nervous_system(1)	12	Lung NSC(37;6.52e-07)|Ovarian(258;0.00769)|Hepatocellular(40;0.161)									1131				0.436364	147.886388	148.274173	48	62	CC		KEEP	---	---	---	---	capture	OV - Ovarian serous cystadenocarcinoma(1;6.47e-38)|STAD - Stomach adenocarcinoma(47;0.00503)		Silent	SNP	121288451	121288451	3809	8	C	T	T	22	22	COL14A1	T	2	2
LYN	4067	broad.mit.edu	36	8	57025610	57025610	+	Missense_Mutation	SNP	A	G	G			TCGA-28-5220-01	TCGA-28-5220-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr8:57025610A>G	uc003xsk.2	+	c.323A>G	c.(322-324)AAA>AGA	p.K108R	LYN_uc003xsl.2_Missense_Mutation_p.K87R	NM_002350	NP_002341	P07948	LYN_HUMAN	Yamaguchi sarcoma viral (v-yes-1) oncogene	108	SH3.				erythrocyte differentiation|interspecies interaction between organisms|leukocyte migration|platelet activation|positive regulation of cellular component movement|positive regulation of stress-activated protein kinase signaling cascade|positive regulation of tyrosine phosphorylation of STAT protein|response to DNA damage stimulus|T cell costimulation	cytosol|Golgi apparatus|membrane raft|nucleus|perinuclear region of cytoplasm	ATP binding|ion channel binding|non-membrane spanning protein tyrosine kinase activity|receptor signaling protein tyrosine kinase activity			ovary(1)|breast(1)|central_nervous_system(1)	3		all_lung(136;0.0555)|Lung NSC(129;0.0726)|all_epithelial(80;0.0772)								240				0.466667	774.656308	775.104392	217	248	AA		KEEP	---	---	---	---	capture	Epithelial(17;0.000834)|all cancers(17;0.00598)		Missense_Mutation	SNP	57025610	57025610	9484	8	A	G	G	1	1	LYN	G	4	4
FOXB2	442425	broad.mit.edu	36	9	78825032	78825032	+	Silent	SNP	C	T	T			TCGA-28-5220-01	TCGA-28-5220-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr9:78825032C>T	uc004ako.1	+	c.642C>T	c.(640-642)CCC>CCT	p.P214P		NM_001013735	NP_001013757	Q5VYV0	FOXB2_HUMAN	forkhead box B2	214					brain development|embryo development|negative regulation of gene-specific transcription from RNA polymerase II promoter|pattern specification process|regulation of sequence-specific DNA binding transcription factor activity|tissue development	transcription factor complex	DNA bending activity|double-stranded DNA binding|promoter binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|specific RNA polymerase II transcription factor activity|specific transcriptional repressor activity|transcription activator activity|transcription factor binding				0														0.8	23.290103	24.121465	8	2	CC		KEEP	---	---	---	---	capture			Silent	SNP	78825032	78825032	6235	9	C	T	T	23	23	FOXB2	T	1	1
SMC1A	8243	broad.mit.edu	36	X	53449047	53449047	+	Missense_Mutation	SNP	G	T	T			TCGA-28-5220-01	TCGA-28-5220-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chrX:53449047G>T	uc004dsg.1	-	c.1913C>A	c.(1912-1914)ACA>AAA	p.T638K	SMC1A_uc004dsh.1_Missense_Mutation_p.T616K	NM_006306	NP_006297	Q14683	SMC1A_HUMAN	structural maintenance of chromosomes 1A	638	Flexible hinge.				cell cycle checkpoint|cell division|DNA repair|meiosis|mitotic metaphase/anaphase transition|mitotic prometaphase|mitotic sister chromatid cohesion|mitotic spindle organization|negative regulation of DNA endoreduplication|nuclear mRNA splicing, via spliceosome|response to radiation|signal transduction in response to DNA damage	cohesin core heterodimer|condensed chromosome kinetochore|condensed nuclear chromosome|cytoplasm|meiotic cohesin complex|nucleoplasm	ATP binding|chromatin binding|microtubule motor activity|protein heterodimerization activity			ovary(5)	5														0.886792	162.157863	169.981762	47	6	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	53449047	53449047	15279	23	G	T	T	48	48	SMC1A	T	3	3
ZNF101	94039	broad.mit.edu	36	19	19651246	19651247	+	Frame_Shift_Ins	INS	-	C	C			TCGA-28-5220-01	TCGA-28-5220-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:19651246_19651247insC	uc002nni.1	+	c.448_449insC	c.(448-450)TCCfs	p.S150fs	ZNF101_uc010ecg.1_Frame_Shift_Ins_p.S30fs|ZNF101_uc002nnj.1_Frame_Shift_Ins_p.S30fs	NM_033204	NP_149981	Q8IZC7	ZN101_HUMAN	zinc finger protein 101	150					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(2)	2														0.30			92	214				---	---	---	---	capture_indel			Frame_Shift_Ins	INS	19651246	19651247	18305	19	-	C	C	54	54	ZNF101	C	5	5
GALNT5	11227	broad.mit.edu	36	2	157822926	157822927	+	Frame_Shift_Ins	INS	-	C	C			TCGA-28-5220-01	TCGA-28-5220-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:157822926_157822927insC	uc002tzg.1	+	c.86_87insC	c.(85-87)GACfs	p.D29fs		NM_014568	NP_055383	Q7Z7M9	GALT5_HUMAN	UDP-N-acetyl-alpha-D-galactosamine:polypeptide	29	Helical; Signal-anchor for type II membrane protein; (Potential).				glycosaminoglycan biosynthetic process	Golgi membrane|integral to membrane	polypeptide N-acetylgalactosaminyltransferase activity|sugar binding			breast(3)	3														0.35			113	213				---	---	---	---	capture_indel			Frame_Shift_Ins	INS	157822926	157822927	6480	2	-	C	C	10	10	GALNT5	C	5	5
C9orf150	286343	broad.mit.edu	36	9	12765861	12765862	+	In_Frame_Ins	INS	-	GGCGGC	GGCGGC			TCGA-28-5220-01	TCGA-28-5220-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:12765861_12765862insGGCGGC	uc003zkw.1	+	c.147_148insGGCGGC	c.(145-150)insGGCGGC	p.55_56insGG		NM_203403	NP_981948	Q8IV03	CI150_HUMAN	hypothetical protein LOC286343	58_59	Gly-rich.										0				GBM - Glioblastoma multiforme(1;1.64e-13)										0.33			3	6				---	---	---	---	capture_indel			In_Frame_Ins	INS	12765861	12765862	2576	9	-	GGCGGC	GGCGGC	59	59	C9orf150	GGCGGC	5	5
