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
LOXL4	84171	broad.mit.edu	36	10	100010684	100010684	+	Missense_Mutation	SNP	T	G	G			TCGA-06-0686-01	TCGA-06-0686-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr10:100010684T>G	uc001kpa.1	-	c.647A>C	c.(646-648)GAC>GCC	p.D216A		NM_032211	NP_115587	Q96JB6	LOXL4_HUMAN	lysyl oxidase-like 4 precursor	216	SRCR 2.				oxidation-reduction process	extracellular space|membrane	copper ion binding|protein binding|scavenger receptor activity			ovary(3)|breast(1)	4		Colorectal(252;0.234)												0.666667	9.796734	9.943479	4	2	TT		KEEP	---	---	---	---	capture		Epithelial(162;2.14e-11)|all cancers(201;2.49e-09)	Missense_Mutation	SNP	100010684	100010684	9275	10	T	G	G	58	58	LOXL4	G	4	4
IL15RA	3601	broad.mit.edu	36	10	6035116	6035116	+	Missense_Mutation	SNP	C	A	A			TCGA-06-0686-01	TCGA-06-0686-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr10:6035116C>A	uc001iiv.1	-	c.752G>T	c.(751-753)TGG>TTG	p.W251L	IL15RA_uc001iiu.1_Intron|IL15RA_uc001iiw.1_Missense_Mutation_p.W215L|IL15RA_uc001iix.1_Missense_Mutation_p.W182L|IL15RA_uc001iiy.1_Missense_Mutation_p.W99L	NM_002189	NP_751950	Q13261	I15RA_HUMAN	interleukin 15 receptor, alpha isoform 1	251	Cytoplasmic (Potential).				cell proliferation	cytoplasmic vesicle membrane|endoplasmic reticulum membrane|extracellular space|Golgi membrane|integral to membrane|nuclear membrane	cytokine receptor activity				0														0.80597	172.380418	178.228848	54	13	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	6035116	6035116	7933	10	C	A	A	21	21	IL15RA	A	3	3
MUC2	4583	broad.mit.edu	36	11	1068153	1068153	+	Missense_Mutation	SNP	G	T	T			TCGA-06-0686-01	TCGA-06-0686-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr11:1068153G>T	uc001lsx.1	+	c.520G>T	c.(520-522)GGC>TGC	p.G174C		NM_002457	NP_002448	Q02817	MUC2_HUMAN	mucin 2 precursor	174	VWFD 1.					inner mucus layer|outer mucus layer	protein binding			lung(1)|breast(1)	2		all_cancers(49;1.08e-07)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.191)			Pranlukast(DB01411)									0.166667	7.585767	10.113664	4	20	GG		KEEP	---	---	---	---	capture		BRCA - Breast invasive adenocarcinoma(625;0.000207)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)	Missense_Mutation	SNP	1068153	1068153	10369	11	G	T	T	39	39	MUC2	T	3	3
GYLTL1B	120071	broad.mit.edu	36	11	45902683	45902683	+	Silent	SNP	A	C	C			TCGA-06-0686-01	TCGA-06-0686-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr11:45902683A>C	uc001nbv.1	+	c.543A>C	c.(541-543)CTA>CTC	p.L181L	GYLTL1B_uc001nbw.1_Silent_p.L150L|GYLTL1B_uc001nbx.1_Silent_p.L181L|GYLTL1B_uc001nby.1_5'Flank	NM_152312	NP_689525	Q8N3Y3	LARG2_HUMAN	glycosyltransferase-like 1B	181	Lumenal (Potential).				muscle cell homeostasis	Golgi membrane|integral to membrane	transferase activity, transferring glycosyl groups			ovary(2)	2														0.328767	75.981861	77.876052	24	49	AA		KEEP	---	---	---	---	capture		GBM - Glioblastoma multiforme(35;0.226)	Silent	SNP	45902683	45902683	7187	11	A	C	C	13	13	GYLTL1B	C	4	4
OR4S2	219431	broad.mit.edu	36	11	55175864	55175864	+	Missense_Mutation	SNP	T	A	A			TCGA-06-0686-01	TCGA-06-0686-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr11:55175864T>A	uc001nhs.1	+	c.909T>A	c.(907-909)AAT>AAA	p.N303K		NM_001004059	NP_001004059	Q8NH73	OR4S2_HUMAN	olfactory receptor, family 4, subfamily S,	303	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)|skin(1)	2		all_epithelial(135;0.0748)												0.261628	124.101392	132.941713	45	127	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	55175864	55175864	11493	11	T	A	A	51	51	OR4S2	A	4	4
ME3	10873	broad.mit.edu	36	11	85839062	85839062	+	Missense_Mutation	SNP	T	C	C			TCGA-06-0686-01	TCGA-06-0686-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr11:85839062T>C	uc001pbz.1	-	c.946A>G	c.(946-948)ATC>GTC	p.I316V	ME3_uc001pca.1_Missense_Mutation_p.I316V|ME3_uc009yvk.1_Missense_Mutation_p.I316V	NM_001014811	NP_006671	Q16798	MAON_HUMAN	malic enzyme 3, NADP(+)-dependent,	316					aerobic respiration|malate metabolic process|oxygen metabolic process|pyruvate metabolic process	mitochondrial matrix	malate dehydrogenase (oxaloacetate-decarboxylating) (NADP+) activity|metal ion binding|NAD binding			ovary(1)	1		Acute lymphoblastic leukemia(157;4.34e-06)|all_hematologic(158;0.00252)			NADH(DB00157)									0.222222	6.392523	7.670503	4	14	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	85839062	85839062	9808	11	T	C	C	50	50	ME3	C	4	4
TMEM120B	144404	broad.mit.edu	36	12	120698002	120698002	+	Missense_Mutation	SNP	G	C	C			TCGA-06-0686-01	TCGA-06-0686-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr12:120698002G>C	uc001uaz.1	+	c.1011G>C	c.(1009-1011)AAG>AAC	p.K337N	TMEM120B_uc009zxh.1_3'UTR|TMEM120B_uc001uba.1_5'Flank	NM_001080825	NP_001074294	A0PK00	T120B_HUMAN	transmembrane protein 120B	337						integral to membrane					0	all_neural(191;0.0684)|Medulloblastoma(191;0.0922)											OREG0022207	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	0.257143	6.413563	8.528267	9	26	GG		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(86;5.75e-05)|Epithelial(86;0.000128)|BRCA - Breast invasive adenocarcinoma(302;0.238)	Missense_Mutation	SNP	120698002	120698002	16565	12	G	C	C	34	34	TMEM120B	C	3	3
EP400	57634	broad.mit.edu	36	12	131074419	131074419	+	Missense_Mutation	SNP	G	C	C			TCGA-06-0686-01	TCGA-06-0686-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr12:131074419G>C	uc001ujn.1	+	c.4835G>C	c.(4834-4836)GGC>GCC	p.G1612A	EP400_uc001ujl.1_Missense_Mutation_p.G1611A|EP400_uc001ujm.1_Missense_Mutation_p.G1531A	NM_015409	NP_056224	Q96L91	EP400_HUMAN	E1A binding protein p400	1648					histone H2A acetylation|histone H4 acetylation	NuA4 histone acetyltransferase complex|nuclear speck	ATP binding|DNA binding|helicase activity			central_nervous_system(4)|ovary(3)|breast(3)	10	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_epithelial(31;0.198)												0.225806	9.104584	11.265989	7	24	GG		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(86;3.01e-08)|Epithelial(86;3.43e-07)|all cancers(50;2.01e-06)	Missense_Mutation	SNP	131074419	131074419	5342	12	G	C	C	42	42	EP400	C	3	3
INHBE	83729	broad.mit.edu	36	12	56135710	56135710	+	Missense_Mutation	SNP	C	G	G			TCGA-06-0686-01	TCGA-06-0686-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr12:56135710C>G	uc001snw.1	+	c.124C>G	c.(124-126)CTG>GTG	p.L42V		NM_031479	NP_113667	P58166	INHBE_HUMAN	activin beta E	42					growth	extracellular region	growth factor activity|hormone activity			breast(2)|central_nervous_system(1)	3						GBM(191;1808 2166 15720 36624 50371)								0.901515	1285.997843	1349.836743	357	39	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	56135710	56135710	8045	12	C	G	G	32	32	INHBE	G	3	3
KCNRG	283518	broad.mit.edu	36	13	49487663	49487663	+	Silent	SNP	G	C	C			TCGA-06-0686-01	TCGA-06-0686-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr13:49487663G>C	uc001vdu.1	+	c.33G>C	c.(31-33)GTG>GTC	p.V11V	DLEU2_uc001vdn.1_Intron|DLEU2_uc001vdo.1_Intron|TRIM13_uc001vdp.1_3'UTR|TRIM13_uc001vdq.1_3'UTR|TRIM13_uc001vdr.1_3'UTR|TRIM13_uc001vds.1_3'UTR|KCNRG_uc001vdt.1_Silent_p.V11V	NM_173605	NP_775876	Q8N5I3	KCNRG_HUMAN	potassium channel regulator isoform 1	11	BTB.					voltage-gated potassium channel complex	identical protein binding|voltage-gated potassium channel activity				0		Acute lymphoblastic leukemia(7;3.41e-06)|Lung NSC(96;3.08e-05)|Breast(56;9.7e-05)|Prostate(109;0.00174)|Hepatocellular(98;0.0207)|Myeloproliferative disorder(33;0.163)|Lung SC(185;0.187)|all_neural(104;0.19)												0.437956	184.165035	184.62701	60	77	GG		KEEP	---	---	---	---	capture		GBM - Glioblastoma multiforme(99;1.48e-10)|COAD - Colon adenocarcinoma(199;0.204)	Silent	SNP	49487663	49487663	8392	13	G	C	C	47	47	KCNRG	C	3	3
CTSG	1511	broad.mit.edu	36	14	24113407	24113407	+	Nonsense_Mutation	SNP	G	A	A			TCGA-06-0686-01	TCGA-06-0686-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr14:24113407G>A	uc001wpq.1	-	c.478C>T	c.(478-480)CGA>TGA	p.R160*		NM_001911	NP_001902	P08311	CATG_HUMAN	cathepsin G preproprotein	160	Peptidase S1.				immune response|proteolysis	cell surface|extracellular space|plasma membrane|stored secretory granule	heparin binding|serine-type endopeptidase activity			ovary(2)	2														0.444444	187.799387	188.182141	64	80	GG		KEEP	---	---	---	---	capture		GBM - Glioblastoma multiforme(265;0.0269)	Nonsense_Mutation	SNP	24113407	24113407	4194	14	G	A	A	39	39	CTSG	A	5	1
DACT1	51339	broad.mit.edu	36	14	58183129	58183129	+	Missense_Mutation	SNP	T	G	G			TCGA-06-0686-01	TCGA-06-0686-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr14:58183129T>G	uc001xdw.1	+	c.2035T>G	c.(2035-2037)TGG>GGG	p.W679G	DACT1_uc001xdx.1_Missense_Mutation_p.W642G	NM_016651	NP_057735	Q9NYF0	DACT1_HUMAN	dapper 1 isoform 1	679					multicellular organismal development|Wnt receptor signaling pathway	cytoplasm|nucleus				large_intestine(2)|lung(2)|ovary(1)	5														0.4	13.410535	13.663557	10	15	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	58183129	58183129	4388	14	T	G	G	59	59	DACT1	G	4	4
ZNF609	23060	broad.mit.edu	36	15	62753583	62753583	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0686-01	TCGA-06-0686-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr15:62753583G>A	uc002ann.1	+	c.1477G>A	c.(1477-1479)GTC>ATC	p.V493I		NM_015042	NP_055857	O15014	ZN609_HUMAN	zinc finger protein 609	493						nucleus	zinc ion binding			ovary(1)	1														0.449275	179.018904	179.329516	62	76	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	62753583	62753583	18630	15	G	A	A	40	40	ZNF609	A	1	1
ISLR	3671	broad.mit.edu	36	15	72255497	72255497	+	Silent	SNP	G	C	C			TCGA-06-0686-01	TCGA-06-0686-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr15:72255497G>C	uc002axg.1	+	c.1245G>C	c.(1243-1245)CTG>CTC	p.L415L	ISLR_uc002axh.1_Silent_p.L415L|ISLR_uc010bjh.1_Silent_p.L415L	NM_005545	NP_958934	O14498	ISLR_HUMAN	immunoglobulin superfamily containing	415					cell adhesion	extracellular region				large_intestine(1)|ovary(1)	2														0.344444	82.093187	84.018622	31	59	GG		KEEP	---	---	---	---	capture			Silent	SNP	72255497	72255497	8162	15	G	C	C	47	47	ISLR	C	3	3
C15orf26	161502	broad.mit.edu	36	15	79215979	79215979	+	Missense_Mutation	SNP	A	G	G			TCGA-06-0686-01	TCGA-06-0686-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr15:79215979A>G	uc002bgb.1	+	c.227A>G	c.(226-228)GAT>GGT	p.D76G	C15orf26_uc010blp.1_Missense_Mutation_p.D51G	NM_173528	NP_775799	Q6P656	CO026_HUMAN	hypothetical protein LOC161502	76											0														0.293478	72.770388	76.295845	27	65	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	79215979	79215979	1837	15	A	G	G	12	12	C15orf26	G	4	4
MYH11	4629	broad.mit.edu	36	16	15749000	15749000	+	Missense_Mutation	SNP	T	C	C			TCGA-06-0686-01	TCGA-06-0686-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr16:15749000T>C	uc002ddx.1	-	c.2360A>G	c.(2359-2361)GAG>GGG	p.E787G	MYH11_uc002ddv.1_Missense_Mutation_p.E787G|MYH11_uc002ddw.1_Missense_Mutation_p.E780G|MYH11_uc002ddy.1_Missense_Mutation_p.E780G|MYH11_uc010bvg.1_Missense_Mutation_p.E612G	NM_001040114	NP_001035203	P35749	MYH11_HUMAN	smooth muscle myosin heavy chain 11 isoform	780	Myosin head-like.				axon guidance|cardiac muscle fiber development|elastic fiber assembly|skeletal muscle myosin thick filament assembly|smooth muscle contraction	cytosol|melanosome|muscle myosin complex|myosin filament	actin binding|ATP binding|calmodulin binding|motor activity|structural constituent of muscle			ovary(4)|skin(2)|lung(1)	7										1257				0.093023	7.735258	22.060485	8	78	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	15749000	15749000	10426	16	T	C	C	54	54	MYH11	C	4	4
RBBP6	5930	broad.mit.edu	36	16	24490428	24490428	+	Missense_Mutation	SNP	A	C	C			TCGA-06-0686-01	TCGA-06-0686-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr16:24490428A>C	uc002dmh.1	+	c.4540A>C	c.(4540-4542)AAA>CAA	p.K1514Q	RBBP6_uc002dmi.1_Missense_Mutation_p.K1480Q|RBBP6_uc010bxr.1_Missense_Mutation_p.K674Q|RBBP6_uc002dmk.1_Missense_Mutation_p.K1347Q	NM_006910	NP_008841	Q7Z6E9	RBBP6_HUMAN	retinoblastoma-binding protein 6 isoform 1	1514	Interaction with p53 (By similarity).				protein ubiquitination involved in ubiquitin-dependent protein catabolic process	chromosome|nucleolus|ubiquitin ligase complex	nucleic acid binding|protein binding|ubiquitin-protein ligase activity|zinc ion binding			ovary(3)|pancreas(1)	4														0.558824	69.130653	69.233358	19	15	AA		KEEP	---	---	---	---	capture		GBM - Glioblastoma multiforme(48;0.0518)	Missense_Mutation	SNP	24490428	24490428	13564	16	A	C	C	13	13	RBBP6	C	4	4
PAQR4	124222	broad.mit.edu	36	16	2961598	2961598	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0686-01	TCGA-06-0686-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr16:2961598C>T	uc002csj.2	+	c.470C>T	c.(469-471)TCG>TTG	p.S157L	PAQR4_uc002csk.2_Missense_Mutation_p.S118L|PAQR4_uc002csl.2_Missense_Mutation_p.S83L	NM_152341	NP_689554	Q8N4S7	PAQR4_HUMAN	progestin and adipoQ receptor family member IV	157	Helical; (Potential).					integral to membrane	receptor activity				0														0.42515	200.906209	201.715139	71	96	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	2961598	2961598	11854	16	C	T	T	31	31	PAQR4	T	1	1
CNGB1	1258	broad.mit.edu	36	16	56552291	56552291	+	Missense_Mutation	SNP	T	C	C			TCGA-06-0686-01	TCGA-06-0686-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr16:56552291T>C	uc002emt.1	-	c.488A>G	c.(487-489)GAG>GGG	p.E163G	CNGB1_uc010cdh.1_Missense_Mutation_p.E163G|CNGB1_uc002emu.1_Missense_Mutation_p.E163G	NM_001297	NP_001288	Q14028	CNGB1_HUMAN	cyclic nucleotide gated channel beta 1 isoform	163					sensory perception of smell	intracellular cyclic nucleotide activated cation channel complex	cAMP binding|intracellular cAMP activated cation channel activity			breast(3)|pancreas(1)	4						Colon(156;1293 1853 16336 28962 38659)								0.25	7.088049	8.001315	4	12	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	56552291	56552291	3738	16	T	C	C	54	54	CNGB1	C	4	4
ZNF23	7571	broad.mit.edu	36	16	70040734	70040734	+	Missense_Mutation	SNP	C	A	A			TCGA-06-0686-01	TCGA-06-0686-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr16:70040734C>A	uc002fai.2	-	c.812G>T	c.(811-813)AGC>ATC	p.S271I	ZNF23_uc002fae.1_Missense_Mutation_p.S174I|ZNF23_uc002faf.1_Missense_Mutation_p.S232I|ZNF23_uc002fah.1_Missense_Mutation_p.S232I|ZNF23_uc002fad.2_Missense_Mutation_p.S174I|ZNF23_uc002fag.2_Missense_Mutation_p.S174I	NM_145911	NP_666016	P17027	ZNF23_HUMAN	zinc finger protein 23	232	C2H2-type 3.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0		Ovarian(137;0.00768)												0.316901	114.208064	118.450653	45	97	CC		KEEP	---	---	---	---	capture		BRCA - Breast invasive adenocarcinoma(221;0.0686)	Missense_Mutation	SNP	70040734	70040734	18374	16	C	A	A	28	28	ZNF23	A	3	3
SMARCD2	6603	broad.mit.edu	36	17	59266530	59266530	+	Nonsense_Mutation	SNP	G	A	A			TCGA-06-0686-01	TCGA-06-0686-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr17:59266530G>A	uc010deb.1	-	c.697C>T	c.(697-699)CGA>TGA	p.R233*	SMARCD2_uc010dea.1_Nonsense_Mutation_p.R158*|SMARCD2_uc010dec.1_Nonsense_Mutation_p.R212*	NM_001098426	NP_001091896	Q92925	SMRD2_HUMAN	SWI/SNF-related matrix-associated	233					chromatin modification|regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	SWI/SNF complex	protein binding|transcription coactivator activity				0														0.397436	90.710943	91.427985	31	47	GG		KEEP	---	---	---	---	capture			Nonsense_Mutation	SNP	59266530	59266530	15276	17	G	A	A	39	39	SMARCD2	A	5	1
ABCA8	10351	broad.mit.edu	36	17	64440155	64440155	+	Silent	SNP	A	T	T			TCGA-06-0686-01	TCGA-06-0686-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr17:64440155A>T	uc002jhq.1	-	c.666T>A	c.(664-666)ACT>ACA	p.T222T	ABCA8_uc002jhp.1_Silent_p.T222T|ABCA8_uc002jhs.1_Silent_p.T222T|ABCA8_uc002jht.1_Silent_p.T222T	NM_007168	NP_009099	O94911	ABCA8_HUMAN	ATP-binding cassette, sub-family A member 8	222	Helical; (Potential).					integral to membrane|plasma membrane	ATP binding|ATPase activity, coupled to transmembrane movement of substances			ovary(2)	2	Breast(10;4.56e-13)													0.412371	124.682694	125.333043	40	57	AA		KEEP	---	---	---	---	capture			Silent	SNP	64440155	64440155	39	17	A	T	T	7	7	ABCA8	T	4	4
FBF1	85302	broad.mit.edu	36	17	71422802	71422802	+	Missense_Mutation	SNP	A	C	C			TCGA-06-0686-01	TCGA-06-0686-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr17:71422802A>C	uc002jqc.2	-	c.2474T>G	c.(2473-2475)GTG>GGG	p.V825G	FBF1_uc002jqa.1_Non-coding_Transcript|FBF1_uc002jqb.2_Non-coding_Transcript|FBF1_uc010dgr.1_Missense_Mutation_p.V136G	NM_001080542	NP_001074011	A6NLR5	A6NLR5_HUMAN	Fas (TNFRSF6) binding factor 1	825											0														0.545455	6.508684	6.506069	6	5	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	71422802	71422802	5931	17	A	C	C	6	6	FBF1	C	4	4
WRAP53	55135	broad.mit.edu	36	17	7545820	7545820	+	Missense_Mutation	SNP	C	G	G			TCGA-06-0686-01	TCGA-06-0686-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr17:7545820C>G	uc002gip.1	+	c.943C>G	c.(943-945)CGA>GGA	p.R315G	WRAP53_uc002giq.1_Non-coding_Transcript|WRAP53_uc002gir.1_Missense_Mutation_p.R315G|WRAP53_uc010cnl.1_Missense_Mutation_p.R282G	NM_018081	NP_060551	Q9BUR4	WAP53_HUMAN	WD repeat domain 79	315					positive regulation of telomerase activity|telomere formation via telomerase	Cajal body|cytoplasm|telomerase holoenzyme complex	protein binding|RNA binding				0														0.228571	8.614262	11.093531	8	27	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	7545820	7545820	17974	17	C	G	G	23	23	WRAP53	G	3	3
FASN	2194	broad.mit.edu	36	17	77636495	77636495	+	Missense_Mutation	SNP	T	G	G			TCGA-06-0686-01	TCGA-06-0686-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr17:77636495T>G	uc002kdu.1	-	c.4195A>C	c.(4195-4197)ACG>CCG	p.T1399P	FASN_uc002kdw.1_Missense_Mutation_p.T615P	NM_004104	NP_004095	P49327	FAS_HUMAN	fatty acid synthase	1399					energy reserve metabolic process|fatty acid biosynthetic process|long-chain fatty-acyl-CoA biosynthetic process|pantothenate metabolic process|positive regulation of cellular metabolic process|triglyceride biosynthetic process	cytosol|Golgi apparatus|melanosome|plasma membrane	3-hydroxypalmitoyl-[acyl-carrier-protein] dehydratase activity|3-oxoacyl-[acyl-carrier-protein] reductase activity|3-oxoacyl-[acyl-carrier-protein] synthase activity|[acyl-carrier-protein] S-acetyltransferase activity|[acyl-carrier-protein] S-malonyltransferase activity|acyl carrier activity|cofactor binding|enoyl-[acyl-carrier-protein] reductase (NADPH, B-specific) activity|myristoyl-[acyl-carrier-protein] hydrolase activity|oleoyl-[acyl-carrier-protein] hydrolase activity|palmitoyl-[acyl-carrier-protein] hydrolase activity|phosphopantetheine binding|protein binding|zinc ion binding			central_nervous_system(1)	1	all_neural(118;0.0878)|Ovarian(332;0.227)|all_lung(278;0.246)				Cerulenin(DB01034)|Orlistat(DB01083)|Pyrazinamide(DB00339)	Colon(59;314 1043 11189 28578 32273)				1201				0.230769	11.930506	13.672784	6	20	TT		KEEP	---	---	---	---	capture	OV - Ovarian serous cystadenocarcinoma(97;0.0211)|BRCA - Breast invasive adenocarcinoma(99;0.0237)		Missense_Mutation	SNP	77636495	77636495	5919	17	T	G	G	59	59	FASN	G	4	4
CD7	924	broad.mit.edu	36	17	77868075	77868075	+	Missense_Mutation	SNP	C	A	A			TCGA-06-0686-01	TCGA-06-0686-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr17:77868075C>A	uc002kel.1	-	c.154G>T	c.(154-156)GGG>TGG	p.G52W	CD7_uc010din.1_Missense_Mutation_p.G52W|CD7_uc002kem.1_Missense_Mutation_p.R33L	NM_006137	NP_006128	P09564	CD7_HUMAN	CD7 antigen precursor	52	Ig-like.|Extracellular (Probable).				immune response|T cell activation|transmembrane receptor protein tyrosine kinase signaling pathway	integral to membrane|membrane fraction|plasma membrane	receptor activity				0	Breast(20;0.000675)|all_neural(118;0.0804)|Lung NSC(278;0.128)|all_lung(278;0.145)|Ovarian(332;0.249)					Pancreas(45;804 1068 19702 28207 28798)								0.43617	124.167805	124.500056	41	53	CC		KEEP	---	---	---	---	capture	OV - Ovarian serous cystadenocarcinoma(97;0.00463)|BRCA - Breast invasive adenocarcinoma(99;0.0667)		Missense_Mutation	SNP	77868075	77868075	3160	17	C	A	A	23	23	CD7	A	3	3
CYP4F3	4051	broad.mit.edu	36	19	15619065	15619065	+	Silent	SNP	G	A	A			TCGA-06-0686-01	TCGA-06-0686-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr19:15619065G>A	uc002nbj.1	+	c.456G>A	c.(454-456)ACG>ACA	p.T152T	CYP4F3_uc002nbk.1_Silent_p.T152T	NM_000896	NP_000887	Q08477	CP4F3_HUMAN	cytochrome P450, family 4, subfamily F,	152					leukotriene metabolic process|oxidation-reduction process|xenobiotic metabolic process	endoplasmic reticulum membrane|integral to membrane|microsome	electron carrier activity|heme binding|leukotriene-B4 20-monooxygenase activity|oxygen binding			ovary(3)	3														0.487179	163.566527	163.58314	57	60	GG		KEEP	---	---	---	---	capture			Silent	SNP	15619065	15619065	4355	19	G	A	A	38	38	CYP4F3	A	1	1
ZNF493	284443	broad.mit.edu	36	19	21398820	21398820	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0686-01	TCGA-06-0686-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr19:21398820C>T	uc002npw.1	+	c.1519C>T	c.(1519-1521)CAT>TAT	p.H507Y	ZNF493_uc002npx.1_Missense_Mutation_p.H379Y|ZNF493_uc002npy.1_Missense_Mutation_p.H379Y|ZNF493_uc010ect.1_Missense_Mutation_p.H379Y	NM_001076678	NP_787106	Q6ZR52	ZN493_HUMAN	zinc finger protein 493 isoform 3	379	C2H2-type 13.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1														0.222222	17.07658	19.636612	8	28	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	21398820	21398820	18538	19	C	T	T	17	17	ZNF493	T	2	2
SIPA1L3	23094	broad.mit.edu	36	19	43347359	43347359	+	Missense_Mutation	SNP	G	C	C			TCGA-06-0686-01	TCGA-06-0686-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr19:43347359G>C	uc002ohk.1	+	c.4181G>C	c.(4180-4182)GGC>GCC	p.G1394A		NM_015073	NP_055888	O60292	SI1L3_HUMAN	signal-induced proliferation-associated 1 like	1394					regulation of small GTPase mediated signal transduction	intracellular	GTPase activator activity			ovary(1)|central_nervous_system(1)	2														0.6	9.758893	9.832911	6	4	GG		KEEP	---	---	---	---	capture	Lung(45;0.000246)|LUSC - Lung squamous cell carcinoma(53;0.000292)		Missense_Mutation	SNP	43347359	43347359	14826	19	G	C	C	42	42	SIPA1L3	C	3	3
MUC16	94025	broad.mit.edu	36	19	8876333	8876333	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0686-01	TCGA-06-0686-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr19:8876333C>T	uc002mkp.1	-	c.38255G>A	c.(38254-38256)AGA>AAA	p.R12752K		NM_024690	NP_078966	Q8WXI7	MUC16_HUMAN	mucin 16	12754	SEA 5.|Extracellular (Potential).			Missing (in Ref. 3; AAK74120).	cell adhesion	extracellular space|extrinsic to membrane|integral to membrane|plasma membrane	protein binding			ovary(15)|large_intestine(1)|pancreas(1)|breast(1)|skin(1)	19														0.361446	83.125671	84.528561	30	53	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	8876333	8876333	10367	19	C	T	T	32	32	MUC16	T	2	2
FAM132A	388581	broad.mit.edu	36	1	1168345	1168345	+	Missense_Mutation	SNP	A	G	G			TCGA-06-0686-01	TCGA-06-0686-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr1:1168345A>G	uc001adl.1	-	c.691T>C	c.(691-693)TGT>CGT	p.C231R		NM_001014980	NP_001014980	Q5T7M4	F132A_HUMAN	family with sequence similarity 132, member A	231						extracellular region					0	all_cancers(77;0.00164)|all_epithelial(69;0.000959)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;9.48e-15)|all_lung(118;9.67e-07)|Lung NSC(185;5.59e-05)|Renal(390;0.00571)|Breast(487;0.0183)|Hepatocellular(190;0.0268)|Myeloproliferative disorder(586;0.028)|Ovarian(437;0.127)|Lung SC(97;0.217)								448				0.272727	6.922178	7.433316	3	8	AA		KEEP	---	---	---	---	capture		Epithelial(90;2.83e-35)|OV - Ovarian serous cystadenocarcinoma(86;2.22e-21)|Colorectal(212;0.000155)|COAD - Colon adenocarcinoma(227;0.000193)|Kidney(185;0.00227)|BRCA - Breast invasive adenocarcinoma(365;0.0025)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0339)|Lung(427;0.199)	Missense_Mutation	SNP	1168345	1168345	5639	1	A	G	G	6	6	FAM132A	G	4	4
GON4L	54856	broad.mit.edu	36	1	153988942	153988942	+	Missense_Mutation	SNP	A	G	G			TCGA-06-0686-01	TCGA-06-0686-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr1:153988942A>G	uc001flz.2	-	c.5906T>C	c.(5905-5907)CTC>CCC	p.L1969P	GON4L_uc001fly.1_Missense_Mutation_p.L1968P|GON4L_uc009wrh.1_Missense_Mutation_p.L1968P|GON4L_uc001fma.1_Missense_Mutation_p.L1969P|GON4L_uc001flx.1_5'Flank|GON4L_uc009wrg.1_Non-coding_Transcript	NM_001037533	NP_001032622	Q3T8J9	GON4L_HUMAN	gon-4-like isoform a	1969					regulation of transcription, DNA-dependent	cytoplasm|nucleus	DNA binding			ovary(3)	3	Hepatocellular(266;0.0997)|all_hematologic(923;0.145)|all_neural(408;0.195)													0.333333	7.832545	8.44626	7	14	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	153988942	153988942	6845	1	A	G	G	11	11	GON4L	G	4	4
KIAA1751	85452	broad.mit.edu	36	1	1886225	1886225	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0686-01	TCGA-06-0686-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:1886225G>A	uc009vkz.1	-	c.1537C>T	c.(1537-1539)CGC>TGC	p.R513C	KIAA1751_uc001aim.1_Missense_Mutation_p.R513C	NM_001080484	NP_001073953	Q9C0B2	K1751_HUMAN	hypothetical protein LOC85452	513										pancreas(1)	1	all_cancers(77;0.000708)|all_epithelial(69;0.000943)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;6.04e-15)|all_lung(118;9.67e-07)|Lung NSC(185;5.59e-05)|Renal(390;0.00571)|Breast(487;0.0183)|Hepatocellular(190;0.0268)|Myeloproliferative disorder(586;0.028)|Ovarian(437;0.127)|Medulloblastoma(700;0.151)|Lung SC(97;0.217)												0.45614	76.844244	76.939531	26	31	GG		KEEP	---	---	---	---	capture		Epithelial(90;8.79e-39)|OV - Ovarian serous cystadenocarcinoma(86;9.61e-25)|GBM - Glioblastoma multiforme(42;1.2e-07)|Colorectal(212;4.84e-05)|COAD - Colon adenocarcinoma(227;0.000214)|Kidney(185;0.00254)|BRCA - Breast invasive adenocarcinoma(365;0.00461)|STAD - Stomach adenocarcinoma(132;0.00645)|KIRC - Kidney renal clear cell carcinoma(229;0.037)|Lung(427;0.205)	Missense_Mutation	SNP	1886225	1886225	8567	1	G	A	A	40	40	KIAA1751	A	1	1
HHIPL2	79802	broad.mit.edu	36	1	220784100	220784100	+	Missense_Mutation	SNP	G	C	C			TCGA-06-0686-01	TCGA-06-0686-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:220784100G>C	uc001hnh.1	-	c.376C>G	c.(376-378)CTC>GTC	p.L126V		NM_024746	NP_079022	Q6UWX4	HIPL2_HUMAN	HHIP-like 2	126					carbohydrate metabolic process	extracellular region	oxidoreductase activity, acting on the CH-OH group of donors, quinone or similar compound as acceptor|quinone binding			ovary(1)	1														0.413333	304.839432	306.313586	93	132	GG		KEEP	---	---	---	---	capture		GBM - Glioblastoma multiforme(131;0.0185)	Missense_Mutation	SNP	220784100	220784100	7378	1	G	C	C	33	33	HHIPL2	C	3	3
SNAP47	116841	broad.mit.edu	36	1	226002348	226002348	+	Missense_Mutation	SNP	T	A	A			TCGA-06-0686-01	TCGA-06-0686-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr1:226002348T>A	uc001hrf.1	+	c.423T>A	c.(421-423)CAT>CAA	p.H141Q	SNAP47_uc001hqz.1_Missense_Mutation_p.H96Q|SNAP47_uc001hra.1_Intron|SNAP47_uc001hrd.2_Missense_Mutation_p.H141Q|SNAP47_uc001hre.2_Intron|SNAP47_uc001hrg.1_Missense_Mutation_p.H96Q	NM_053052	NP_444280	Q5SQN1	SNP47_HUMAN	synaptosomal-associated protein, 47kDa	141						endomembrane system|membrane|perinuclear region of cytoplasm				ovary(1)	1														0.125	8.753461	17.550602	8	56	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	226002348	226002348	15332	1	T	A	A	52	52	SNAP47	A	4	4
OR6F1	343169	broad.mit.edu	36	1	245942255	245942255	+	Silent	SNP	C	T	T			TCGA-06-0686-01	TCGA-06-0686-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr1:245942255C>T	uc001idj.1	-	c.426G>A	c.(424-426)GCG>GCA	p.A142A		NM_001005286	NP_001005286	Q8NGZ6	OR6F1_HUMAN	olfactory receptor, family 6, subfamily F,	142	Helical; Name=4; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0	all_cancers(71;3.24e-05)|all_epithelial(71;1.3e-05)|Breast(184;0.0149)|Ovarian(71;0.0377)|all_lung(81;0.0662)|Lung NSC(105;0.0724)													0.493243	213.962109	213.967915	73	75	CC		KEEP	---	---	---	---	capture	OV - Ovarian serous cystadenocarcinoma(106;0.0168)		Silent	SNP	245942255	245942255	11611	1	C	T	T	27	27	OR6F1	T	1	1
GFI1	2672	broad.mit.edu	36	1	92719114	92719114	+	Nonsense_Mutation	SNP	G	A	A			TCGA-06-0686-01	TCGA-06-0686-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:92719114G>A	uc001dou.2	-	c.418C>T	c.(418-420)CGA>TGA	p.R140*	GFI1_uc001dov.2_Nonsense_Mutation_p.R140*|GFI1_uc001dow.2_Nonsense_Mutation_p.R140*	NM_001127215	NP_001120687	Q99684	GFI1_HUMAN	growth factor independent 1	140					negative regulation of calcidiol 1-monooxygenase activity|negative regulation of gene-specific transcription from RNA polymerase II promoter|negative regulation of vitamin D biosynthetic process|regulation of transcription involved in G1/S phase of mitotic cell cycle|transcription, DNA-dependent|viral reproduction	nucleus	promoter binding|protein binding|zinc ion binding			large_intestine(1)	1		all_lung(203;0.00292)|Lung NSC(277;0.0115)|all_neural(321;0.185)|Glioma(108;0.203)												0.636364	66.684183	67.225456	21	12	GG		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(397;9.04e-07)|Epithelial(280;1.17e-05)|all cancers(265;5.61e-05)|GBM - Glioblastoma multiforme(16;0.0191)	Nonsense_Mutation	SNP	92719114	92719114	6607	1	G	A	A	39	39	GFI1	A	5	1
CBS	875	broad.mit.edu	36	21	43351342	43351342	+	Missense_Mutation	SNP	G	C	C			TCGA-06-0686-01	TCGA-06-0686-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr21:43351342G>C	uc002zct.1	-	c.1449C>G	c.(1447-1449)ATC>ATG	p.I483M	CBS_uc002zcs.1_Missense_Mutation_p.I378M|CBS_uc002zcu.1_Missense_Mutation_p.I483M|CBS_uc002zcv.1_Missense_Mutation_p.I483M|CBS_uc002zcw.2_Missense_Mutation_p.I483M|CBS_uc002zcx.1_Missense_Mutation_p.I102M	NM_000071	NP_000062	P35520	CBS_HUMAN	cystathionine-beta-synthase	483					cysteine biosynthetic process from serine|cysteine biosynthetic process via cystathionine|homocysteine catabolic process|hydrogen sulfide biosynthetic process|L-cysteine catabolic process|L-serine catabolic process	cytosol|nucleolus	cystathionine beta-synthase activity|heme binding|protein homodimerization activity|pyridoxal phosphate binding|ubiquitin protein ligase binding				0					L-Cysteine(DB00151)|L-Serine(DB00133)|Pyridoxal Phosphate(DB00114)|Pyridoxine(DB00165)|S-Adenosylmethionine(DB00118)									0.415385	88.214549	88.620694	27	38	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	43351342	43351342	2830	21	G	C	C	33	33	CBS	C	3	3
SLC7A4	6545	broad.mit.edu	36	22	19715682	19715682	+	Nonsense_Mutation	SNP	G	T	T			TCGA-06-0686-01	TCGA-06-0686-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr22:19715682G>T	uc002zud.1	-	c.420C>A	c.(418-420)TAC>TAA	p.Y140*	SLC7A4_uc002zue.1_Nonsense_Mutation_p.Y140*	NM_004173	NP_004164	O43246	CTR4_HUMAN	solute carrier family 7 (cationic amino acid	140					cellular amino acid metabolic process	integral to membrane	basic amino acid transmembrane transporter activity			ovary(1)|lung(1)	2	all_cancers(11;2.85e-22)|Lung NSC(8;4.21e-14)|all_lung(8;6.08e-13)|Melanoma(16;0.000465)|Ovarian(15;0.0028)|Colorectal(54;0.0968)	Lung SC(17;0.0262)			L-Arginine(DB00125)|L-Lysine(DB00123)|L-Ornithine(DB00129)									0.2	7.594925	9.264907	4	16	GG		KEEP	---	---	---	---	capture	LUSC - Lung squamous cell carcinoma(15;0.000204)|Lung(15;0.00494)|Epithelial(17;0.195)		Nonsense_Mutation	SNP	19715682	19715682	15196	22	G	T	T	44	44	SLC7A4	T	5	3
CNTNAP5	129684	broad.mit.edu	36	2	125377053	125377053	+	Silent	SNP	G	A	A			TCGA-06-0686-01	TCGA-06-0686-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr2:125377053G>A	uc002tno.1	+	c.3558G>A	c.(3556-3558)GCG>GCA	p.A1186A		NM_130773	NP_570129	Q8WYK1	CNTP5_HUMAN	contactin associated protein-like 5	1186	Extracellular (Potential).|Laminin G-like 4.				cell adhesion|signal transduction	integral to membrane	receptor binding			ovary(10)	10														0.380952	21.494976	21.755939	8	13	GG		KEEP	---	---	---	---	capture		BRCA - Breast invasive adenocarcinoma(221;0.248)	Silent	SNP	125377053	125377053	3788	2	G	A	A	38	38	CNTNAP5	A	1	1
TTN	7273	broad.mit.edu	36	2	179147197	179147197	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0686-01	TCGA-06-0686-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr2:179147197G>A	uc002umr.1	-	c.64204C>T	c.(64204-64206)CGG>TGG	p.R21402W	TTN_uc002ums.1_Missense_Mutation_p.R15097W|TTN_uc010frc.1_Missense_Mutation_p.R15030W|TTN_uc010frd.1_Missense_Mutation_p.R14905W	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	22329								p.R21402C(1)		ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1)	153										8722				0.349398	81.550502	83.211355	29	54	GG		KEEP	---	---	---	---	capture	OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)		Missense_Mutation	SNP	179147197	179147197	17290	2	G	A	A	40	40	TTN	A	1	1
TTN	7273	broad.mit.edu	36	2	179277604	179277604	+	Missense_Mutation	SNP	A	C	C			TCGA-06-0686-01	TCGA-06-0686-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr2:179277604A>C	uc002umr.1	-	c.26108T>G	c.(26107-26109)TTT>TGT	p.F8703C	TTN_uc002ums.1_Intron|TTN_uc010frc.1_Intron|TTN_uc010frd.1_Intron|TTN_uc002umz.1_Missense_Mutation_p.F5364C|TTN_uc010fre.1_5'Flank	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	9630										ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1)	153										8722				0.526316	69.809639	69.833354	20	18	AA		KEEP	---	---	---	---	capture	OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)		Missense_Mutation	SNP	179277604	179277604	17290	2	A	C	C	1	1	TTN	C	4	4
ALPPL2	251	broad.mit.edu	36	2	232980623	232980623	+	Missense_Mutation	SNP	T	C	C			TCGA-06-0686-01	TCGA-06-0686-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr2:232980623T>C	uc002vss.2	+	c.376T>C	c.(376-378)TTC>CTC	p.F126L		NM_031313	NP_112603	P10696	PPBN_HUMAN	placental-like alkaline phosphatase	126					phosphorylation	anchored to membrane|plasma membrane	alkaline phosphatase activity|metal ion binding				0		all_hematologic(139;0.00793)|Renal(207;0.0112)|Acute lymphoblastic leukemia(138;0.0182)|all_lung(227;0.0449)|Lung NSC(271;0.132)			Amifostine(DB01143)|Levamisole(DB00848)									0.359375	75.80878	76.922566	23	41	TT		KEEP	---	---	---	---	capture		Epithelial(121;4.45e-22)|Kidney(3;4.42e-11)|KIRC - Kidney renal clear cell carcinoma(3;1.9e-09)|BRCA - Breast invasive adenocarcinoma(100;0.000767)|Lung(119;0.00566)|LUSC - Lung squamous cell carcinoma(224;0.00746)|STAD - Stomach adenocarcinoma(3;0.0181)|GBM - Glioblastoma multiforme(43;0.196)	Missense_Mutation	SNP	232980623	232980623	552	2	T	C	C	56	56	ALPPL2	C	4	4
ALLC	55821	broad.mit.edu	36	2	3705396	3705396	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0686-01	TCGA-06-0686-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr2:3705396G>A	uc010ewt.1	+	c.235G>A	c.(235-237)GTT>ATT	p.V79I		NM_018436	NP_060906	Q8N6M5	ALLC_HUMAN	allantoicase isoform a	98							allantoicase activity			central_nervous_system(1)	1	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.088)	all_cancers(51;0.24)												0.433333	147.182345	147.646671	52	68	GG		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(76;0.088)|all cancers(51;0.151)|Epithelial(75;0.206)	Missense_Mutation	SNP	3705396	3705396	537	2	G	A	A	40	40	ALLC	A	1	1
TGFA	7039	broad.mit.edu	36	2	70533954	70533954	+	Nonsense_Mutation	SNP	G	A	A			TCGA-06-0686-01	TCGA-06-0686-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr2:70533954G>A	uc010fdq.1	-	c.397C>T	c.(397-399)CGA>TGA	p.R133*	TGFA_uc010fdr.1_Nonsense_Mutation_p.R132*|TGFA_uc002sgs.2_Nonsense_Mutation_p.R127*|TGFA_uc002sgt.2_Nonsense_Mutation_p.R126*|TGFA_uc002sgu.2_Nonsense_Mutation_p.R126*|TGFA_uc002sgv.2_Nonsense_Mutation_p.R127*|TGFA_uc002sgw.2_Nonsense_Mutation_p.R126*	NM_003236	NP_003227	P01135	TGFA_HUMAN	transforming growth factor, alpha isoform 1	127	Cytoplasmic (Potential).				activation of MAPK activity|cell proliferation|positive regulation of cell division|positive regulation of epidermal growth factor receptor activity|positive regulation of epithelial cell proliferation|positive regulation of mitosis	cell surface|extracellular space|integral to membrane|plasma membrane	epidermal growth factor receptor binding|growth factor activity|MAP kinase kinase activity|signal transducer activity				0														0.438849	186.258708	186.71096	61	78	GG		KEEP	---	---	---	---	capture			Nonsense_Mutation	SNP	70533954	70533954	16343	2	G	A	A	39	39	TGFA	A	5	1
GHSR	2693	broad.mit.edu	36	3	173648691	173648691	+	Silent	SNP	C	T	T			TCGA-06-0686-01	TCGA-06-0686-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr3:173648691C>T	uc003fib.1	-	c.207G>A	c.(205-207)TCG>TCA	p.S69S	GHSR_uc003fic.1_Silent_p.S69S	NM_198407	NP_940799	Q92847	GHSR_HUMAN	growth hormone secretagogue receptor isoform 1a	69	Cytoplasmic (Potential).				actin polymerization or depolymerization|adult feeding behavior|decidualization|growth hormone secretion|hormone-mediated signaling pathway|negative regulation of inflammatory response|negative regulation of interleukin-1 beta production|negative regulation of interleukin-6 biosynthetic process|negative regulation of tumor necrosis factor biosynthetic process|positive regulation of appetite|positive regulation of multicellular organism growth	cell surface|integral to membrane|membrane raft|neuron projection|plasma membrane	growth hormone secretagogue receptor activity|growth hormone-releasing hormone receptor activity			ovary(1)|central_nervous_system(1)	2	Ovarian(172;0.00143)|Breast(254;0.197)					Esophageal Squamous(93;641 1401 20883 29581 34638)								0.451613	117.547525	117.734787	42	51	CC		KEEP	---	---	---	---	capture	Lung(28;3.93e-15)|LUSC - Lung squamous cell carcinoma(14;1.48e-14)|STAD - Stomach adenocarcinoma(35;0.235)		Silent	SNP	173648691	173648691	6643	3	C	T	T	27	27	GHSR	T	1	1
NPY5R	4889	broad.mit.edu	36	4	164492100	164492100	+	Missense_Mutation	SNP	A	G	G			TCGA-06-0686-01	TCGA-06-0686-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr4:164492100A>G	uc003iqn.1	+	c.1225A>G	c.(1225-1227)ATT>GTT	p.I409V	NPY5R_uc003iqo.2_Missense_Mutation_p.I409V	NM_006174	NP_006165	Q15761	NPY5R_HUMAN	neuropeptide Y receptor Y5	409	Helical; Name=7; (Potential).				cardiac left ventricle morphogenesis|outflow tract morphogenesis	integral to plasma membrane					0	all_hematologic(180;0.166)	Prostate(90;0.109)				Melanoma(139;1287 1774 9781 19750 25599)								0.460784	151.316664	151.45299	47	55	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	164492100	164492100	11015	4	A	G	G	8	8	NPY5R	G	4	4
PALLD	23022	broad.mit.edu	36	4	170052333	170052333	+	Missense_Mutation	SNP	G	C	C			TCGA-06-0686-01	TCGA-06-0686-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr4:170052333G>C	uc003iru.1	+	c.2129G>C	c.(2128-2130)CGT>CCT	p.R710P	PALLD_uc003irv.1_Missense_Mutation_p.R328P|PALLD_uc003irw.1_Missense_Mutation_p.R212P	NM_016081	NP_057165	Q8WX93	PALLD_HUMAN	palladin	934					cytoskeleton organization	actin filament|focal adhesion|lamellipodium|nucleus|ruffle|sarcomere	actin binding|muscle alpha-actinin binding			ovary(1)	1		Prostate(90;0.00996)|Renal(120;0.0203)|Melanoma(52;0.144)				Esophageal Squamous(109;1482 1532 18347 40239 51172)								0.235294	7.736478	8.796216	4	13	GG		KEEP	---	---	---	---	capture		GBM - Glioblastoma multiforme(119;0.204)	Missense_Mutation	SNP	170052333	170052333	11823	4	G	C	C	40	40	PALLD	C	3	3
TRIML1	339976	broad.mit.edu	36	4	189302249	189302249	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0686-01	TCGA-06-0686-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr4:189302249C>T	uc003izm.1	+	c.824C>T	c.(823-825)ACG>ATG	p.T275M	TRIML1_uc003izn.1_De_novo_Start_InFrame	NM_178556	NP_848651	Q8N9V2	TRIML_HUMAN	tripartite motif family-like 1	275	B30.2/SPRY.				multicellular organismal development		ligase activity|zinc ion binding	p.T275T(1)		ovary(1)|breast(1)|pancreas(1)	3		all_cancers(14;1.33e-43)|all_epithelial(14;7.86e-31)|all_lung(41;4.3e-13)|Lung NSC(41;9.69e-13)|Melanoma(20;7.86e-05)|Breast(6;0.000148)|Hepatocellular(41;0.0218)|Renal(120;0.0376)|Prostate(90;0.0513)|all_hematologic(60;0.062)				Melanoma(31;213 1036 16579 23968 32372)								0.392157	55.08509	55.605325	20	31	CC		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(60;1.52e-11)|BRCA - Breast invasive adenocarcinoma(30;4.19e-06)|GBM - Glioblastoma multiforme(59;0.000232)|STAD - Stomach adenocarcinoma(60;0.000279)|LUSC - Lung squamous cell carcinoma(40;0.00902)|READ - Rectum adenocarcinoma(43;0.156)	Missense_Mutation	SNP	189302249	189302249	17100	4	C	T	T	19	19	TRIML1	T	1	1
FRYL	285527	broad.mit.edu	36	4	48232603	48232603	+	Splice_Site_SNP	SNP	T	C	C			TCGA-06-0686-01	TCGA-06-0686-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr4:48232603T>C	uc003gyh.1	-	c.6394_splice	c.e48-1	p.V2132_splice	FRYL_uc003gyg.1_Splice_Site_SNP_p.V828_splice|FRYL_uc003gyi.1_Splice_Site_SNP_p.V1020_splice|FRYL_uc003gyj.1_Splice_Site_SNP_p.V427_splice	NM_015030	NP_055845			furry-like						regulation of transcription, DNA-dependent|transcription, DNA-dependent		protein binding			skin(1)	1														0.263158	15.267327	16.230467	5	14	TT		KEEP	---	---	---	---	capture			Splice_Site_SNP	SNP	48232603	48232603	6314	4	T	C	C	53	53	FRYL	C	5	4
GAK	2580	broad.mit.edu	36	4	852325	852325	+	Splice_Site_SNP	SNP	A	C	C			TCGA-06-0686-01	TCGA-06-0686-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr4:852325A>C	uc003gbm.2	-	c.2395_splice	c.e20+1	p.E799_splice	GAK_uc010ibi.1_5'Flank|GAK_uc010ibj.1_Splice_Site_SNP|GAK_uc003gbl.2_Splice_Site_SNP_p.E663_splice|GAK_uc003gbn.2_Splice_Site_SNP_p.E720_splice|GAK_uc010ibk.1_Splice_Site_SNP_p.E693_splice	NM_005255	NP_005246			cyclin G associated kinase						cell cycle|protein phosphorylation	focal adhesion|Golgi apparatus|perinuclear region of cytoplasm	ATP binding|heat shock protein binding|protein serine/threonine kinase activity			lung(2)|central_nervous_system(1)	3										679				0.222222	8.089393	9.368834	4	14	AA		KEEP	---	---	---	---	capture		Colorectal(103;0.219)	Splice_Site_SNP	SNP	852325	852325	6459	4	A	C	C	14	14	GAK	C	5	4
CTNND2	1501	broad.mit.edu	36	5	11135954	11135954	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0686-01	TCGA-06-0686-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr5:11135954G>A	uc003jfa.1	-	c.2642C>T	c.(2641-2643)TCA>TTA	p.S881L	CTNND2_uc010itt.1_Missense_Mutation_p.S790L|CTNND2_uc010itu.1_Non-coding_Transcript	NM_001332	NP_001323	Q9UQB3	CTND2_HUMAN	catenin (cadherin-associated protein), delta 2	881					multicellular organismal development|neuron cell-cell adhesion|regulation of transcription, DNA-dependent|signal transduction|transcription, DNA-dependent	adherens junction|cytoplasm|nucleus	protein binding			large_intestine(2)|ovary(2)|pancreas(1)|lung(1)|skin(1)	7														0.442623	80.715791	80.890948	27	34	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	11135954	11135954	4179	5	G	A	A	45	45	CTNND2	A	2	2
PPIC	5480	broad.mit.edu	36	5	122387533	122387533	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0686-01	TCGA-06-0686-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr5:122387533G>A	uc003kth.1	-	c.575C>T	c.(574-576)TCG>TTG	p.S192L		NM_000943	NP_000934	P45877	PPIC_HUMAN	peptidylprolyl isomerase C	192	PPIase cyclophilin-type.				protein folding|signal transduction	cytoplasm	cyclosporin A binding|peptidyl-prolyl cis-trans isomerase activity|unfolded protein binding			ovary(1)	1		all_cancers(142;0.0168)|Prostate(80;0.0322)|Lung NSC(810;0.102)|all_lung(232;0.163)			L-Proline(DB00172)	Ovarian(99;690 1502 20765 45543 49568)								0.365854	256.577374	260.473026	90	156	GG		KEEP	---	---	---	---	capture	KIRC - Kidney renal clear cell carcinoma(527;0.0897)|Kidney(363;0.137)	OV - Ovarian serous cystadenocarcinoma(64;0.000331)|Epithelial(69;0.000553)|all cancers(49;0.00505)	Missense_Mutation	SNP	122387533	122387533	12755	5	G	A	A	37	37	PPIC	A	1	1
SLC12A2	6558	broad.mit.edu	36	5	127547971	127547971	+	Missense_Mutation	SNP	A	G	G			TCGA-06-0686-01	TCGA-06-0686-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr5:127547971A>G	uc003kus.1	+	c.3314A>G	c.(3313-3315)GAG>GGG	p.E1105G	SLC12A2_uc010jdf.1_Non-coding_Transcript	NM_001046	NP_001037	P55011	S12A2_HUMAN	solute carrier family 12	1105	Cytoplasmic (Potential).				potassium ion transport|sodium ion transport|transepithelial ammonium transport|transepithelial chloride transport	integral to plasma membrane|membrane fraction	ammonia transmembrane transporter activity|sodium:potassium:chloride symporter activity			ovary(2)	2		all_cancers(142;0.0972)|Prostate(80;0.151)			Bumetanide(DB00887)|Potassium Chloride(DB00761)									0.346939	55.160773	56.173929	17	32	AA		KEEP	---	---	---	---	capture	KIRC - Kidney renal clear cell carcinoma(527;0.0268)|Kidney(363;0.0488)	Epithelial(69;0.0433)|OV - Ovarian serous cystadenocarcinoma(64;0.0978)	Missense_Mutation	SNP	127547971	127547971	14878	5	A	G	G	11	11	SLC12A2	G	4	4
PDGFRB	5159	broad.mit.edu	36	5	149484080	149484080	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0686-01	TCGA-06-0686-01	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				0.362319	71.154772	72.306337	25	44	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
GABRG2	2566	broad.mit.edu	36	5	161453542	161453542	+	Missense_Mutation	SNP	A	G	G			TCGA-06-0686-01	TCGA-06-0686-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr5:161453542A>G	uc010jjc.1	+	c.238A>G	c.(238-240)AAA>GAA	p.K80E	GABRG2_uc003lyy.2_Missense_Mutation_p.K80E|GABRG2_uc003lyz.2_Missense_Mutation_p.K80E	NM_198903	NP_944493	P18507	GBRG2_HUMAN	gamma-aminobutyric acid A receptor, gamma 2	80	Extracellular (Probable).				gamma-aminobutyric acid signaling pathway	cell junction|chloride channel complex|integral to plasma membrane|postsynaptic membrane	benzodiazepine receptor activity|chloride channel activity|extracellular ligand-gated ion channel activity|GABA-A receptor activity|protein binding			ovary(4)	4	Renal(175;0.000319)	Medulloblastoma(196;0.0208)|all_neural(177;0.0672)												0.369748	148.276273	150.047815	44	75	AA		KEEP	---	---	---	---	capture	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	all cancers(165;0.0734)|OV - Ovarian serous cystadenocarcinoma(192;0.135)|Epithelial(171;0.136)	Missense_Mutation	SNP	161453542	161453542	6423	5	A	G	G	13	13	GABRG2	G	4	4
AP3B1	8546	broad.mit.edu	36	5	77347089	77347089	+	Missense_Mutation	SNP	A	G	G			TCGA-06-0686-01	TCGA-06-0686-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr5:77347089A>G	uc003kfj.1	-	c.3032T>C	c.(3031-3033)ATT>ACT	p.I1011T		NM_003664	NP_003655	O00203	AP3B1_HUMAN	adaptor-related protein complex 3, beta 1	1011					endocytosis|melanosome organization	clathrin coated vesicle membrane|Golgi apparatus|membrane coat	protein phosphatase binding|protein transporter activity			central_nervous_system(1)	1		all_lung(232;0.000397)|Lung NSC(167;0.00106)|Ovarian(174;0.0105)|Prostate(461;0.215)												0.466667	95.09805	95.155814	28	32	AA		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(54;8.23e-47)|Epithelial(54;2.74e-41)|all cancers(79;4.8e-36)	Missense_Mutation	SNP	77347089	77347089	754	5	A	G	G	4	4	AP3B1	G	4	4
GPR150	285601	broad.mit.edu	36	5	94982461	94982461	+	Silent	SNP	C	T	T			TCGA-06-0686-01	TCGA-06-0686-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr5:94982461C>T	uc003kle.1	+	c.726C>T	c.(724-726)GTC>GTT	p.V242V		NM_199243	NP_954713	Q8NGU9	GP150_HUMAN	G protein-coupled receptor 150	242	Helical; Name=5; (Potential).					integral to membrane|plasma membrane	G-protein coupled receptor activity				0		all_cancers(142;0.000462)|all_epithelial(76;2.44e-06)|all_lung(232;0.0318)|Lung NSC(167;0.041)|Ovarian(225;0.051)												0.555556	15.87614	15.900403	5	4	CC		KEEP	---	---	---	---	capture		all cancers(79;1.82e-16)	Silent	SNP	94982461	94982461	6931	5	C	T	T	31	31	GPR150	T	1	1
ZNF184	7738	broad.mit.edu	36	6	27528939	27528939	+	Silent	SNP	T	G	G			TCGA-06-0686-01	TCGA-06-0686-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr6:27528939T>G	uc003nji.1	-	c.378A>C	c.(376-378)ATA>ATC	p.I126I	ZNF184_uc003njj.1_Silent_p.I126I|ZNF184_uc010jqv.1_Silent_p.I126I	NM_007149	NP_009080	Q99676	ZN184_HUMAN	zinc finger protein 184	126					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1														0.284024	136.536003	143.610242	48	121	TT		KEEP	---	---	---	---	capture			Silent	SNP	27528939	27528939	18342	6	T	G	G	53	53	ZNF184	G	4	4
OR10C1	442194	broad.mit.edu	36	6	29516292	29516292	+	Missense_Mutation	SNP	C	T	T	rs2074466	by-cluster,by-frequency,by-hapmap	TCGA-06-0686-01	TCGA-06-0686-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr6:29516292C>T	uc003nmh.1	+	c.521C>T	c.(520-522)CCG>CTG	p.P174L	OR11A1_uc010jrh.1_Intron	NM_013941	NP_039229	Q6IFQ5	Q6IFQ5_HUMAN	olfactory receptor, family 10, subfamily C,	174						integral to membrane	olfactory receptor activity				0														0.444915	315.402548	316.014224	105	131	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	29516292	29516292	11304	6	C	T	T	23	23	OR10C1	T	1	1
OR2H1	26716	broad.mit.edu	36	6	29538384	29538384	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0686-01	TCGA-06-0686-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr6:29538384G>A	uc003nmi.1	+	c.859G>A	c.(859-861)GTA>ATA	p.V287I	OR2H1_uc003nmj.1_Missense_Mutation_p.V287I|OR2H1_uc010jri.1_Missense_Mutation_p.V209I|OR2H1_uc010jrj.1_Missense_Mutation_p.V209I|OR2H1_uc010jrk.1_Missense_Mutation_p.V287I	NM_030883	NP_112145	Q9GZK4	OR2H1_HUMAN	olfactory receptor, family 2, subfamily H,	287	Helical; Name=7; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0														0.254098	73.884685	80.569319	31	91	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	29538384	29538384	11407	6	G	A	A	40	40	OR2H1	A	1	1
PDE1C	5137	broad.mit.edu	36	7	31829369	31829369	+	Silent	SNP	C	T	T			TCGA-06-0686-01	TCGA-06-0686-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr7:31829369C>T	uc003tco.1	-	c.1605G>A	c.(1603-1605)TCG>TCA	p.S535S	PDE1C_uc003tcm.1_Silent_p.S475S|PDE1C_uc003tcn.1_Silent_p.S475S|PDE1C_uc003tcr.1_Silent_p.S475S|PDE1C_uc003tcs.1_Silent_p.S475S	NM_005020	NP_005011	Q14123	PDE1C_HUMAN	phosphodiesterase 1C, calmodulin-dependent	475	Catalytic (By similarity).				activation of phospholipase C activity|nerve growth factor receptor signaling pathway	cytosol	calmodulin binding|calmodulin-dependent cyclic-nucleotide phosphodiesterase activity|metal ion binding			central_nervous_system(1)	1														0.280576	103.290489	109.291501	39	100	CC		KEEP	---	---	---	---	capture	GBM - Glioblastoma multiforme(11;0.216)		Silent	SNP	31829369	31829369	12056	7	C	T	T	19	19	PDE1C	T	1	1
SUN3	256979	broad.mit.edu	36	7	48002267	48002267	+	Silent	SNP	T	A	A			TCGA-06-0686-01	TCGA-06-0686-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr7:48002267T>A	uc003tof.1	-	c.579A>T	c.(577-579)GGA>GGT	p.G193G	SUN3_uc010kyq.1_Silent_p.G93G|SUN3_uc003tog.1_Silent_p.G193G	NM_152782	NP_689995	Q8TAQ9	SUN3_HUMAN	Sad1 and UNC84 domain containing 1	193	SUN.					integral to membrane				central_nervous_system(1)	1														0.173077	31.783302	42.284792	18	86	TT		KEEP	---	---	---	---	capture			Silent	SNP	48002267	48002267	15913	7	T	A	A	54	54	SUN3	A	4	4
ADAM22	53616	broad.mit.edu	36	7	87542906	87542906	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0686-01	TCGA-06-0686-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr7:87542906G>A	uc003ujp.1	+	c.509G>A	c.(508-510)AGA>AAA	p.R170K	ADAM22_uc003uji.1_Missense_Mutation_p.R117K|ADAM22_uc003ujj.1_Missense_Mutation_p.R118K|ADAM22_uc003ujk.1_Missense_Mutation_p.R118K|ADAM22_uc003ujl.1_Missense_Mutation_p.R118K|ADAM22_uc003ujn.1_Missense_Mutation_p.R118K|ADAM22_uc003ujm.1_Missense_Mutation_p.R118K|ADAM22_uc003ujo.1_Missense_Mutation_p.R118K	NM_004194	NP_004185	Q9P0K1	ADA22_HUMAN	ADAM metallopeptidase domain 22 isoform 4	118					cell adhesion|central nervous system development|negative regulation of cell adhesion|proteolysis	integral to membrane	integrin binding|metalloendopeptidase activity|protein binding|receptor activity|zinc ion binding			ovary(4)|skin(2)|lung(1)|kidney(1)	8	Esophageal squamous(14;0.00202)									704				0.22619	48.480004	54.26307	19	65	GG		KEEP	---	---	---	---	capture	STAD - Stomach adenocarcinoma(171;0.215)		Missense_Mutation	SNP	87542906	87542906	245	7	G	A	A	33	33	ADAM22	A	2	2
AZGP1	563	broad.mit.edu	36	7	99402585	99402585	+	Missense_Mutation	SNP	C	G	G			TCGA-06-0686-01	TCGA-06-0686-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr7:99402585C>G	uc003ush.1	-	c.874G>C	c.(874-876)GTG>CTG	p.V292L		NM_001185	NP_001176	P25311	ZA2G_HUMAN	alpha-2-glycoprotein 1, zinc	292	Ig-like C1-type.				antigen processing and presentation|cell adhesion|immune response|lipid catabolic process|negative regulation of cell proliferation	extracellular region|MHC class I protein complex	fatty acid binding|protein transmembrane transporter activity|ribonuclease activity			ovary(1)|central_nervous_system(1)	2	Esophageal squamous(72;0.0166)|Lung NSC(181;0.0211)|all_lung(186;0.0323)													0.181548	151.435059	183.403799	61	275	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	99402585	99402585	1260	7	C	G	G	19	19	AZGP1	G	3	3
ENPP2	5168	broad.mit.edu	36	8	120639011	120639011	+	Silent	SNP	C	T	T			TCGA-06-0686-01	TCGA-06-0686-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr8:120639011C>T	uc003yos.1	-	c.2679G>A	c.(2677-2679)AAG>AAA	p.K893K	ENPP2_uc003yot.1_Silent_p.K841K|ENPP2_uc010mdd.1_Silent_p.K866K|ENPP2_uc003yor.1_Silent_p.K476K	NM_006209	NP_006200	Q13822	ENPP2_HUMAN	autotaxin isoform 1 preproprotein	841	Required for secretion (By similarity).				cellular component movement|chemotaxis|G-protein coupled receptor protein signaling pathway|immune response|phosphate metabolic process|phosphatidylcholine catabolic process|regulation of cell migration	extracellular space|integral to plasma membrane	alkylglycerophosphoethanolamine phosphodiesterase activity|calcium ion binding|lysophospholipase activity|nucleic acid binding|nucleotide diphosphatase activity|phosphodiesterase I activity|polysaccharide binding|scavenger receptor activity|transcription factor binding|zinc ion binding			ovary(2)|central_nervous_system(2)|large_intestine(1)|kidney(1)	6	Lung NSC(37;5.03e-06)|Ovarian(258;0.0249)|Hepatocellular(40;0.161)					Melanoma(20;305 879 2501 4818 31020)								0.401575	150.457558	151.514258	51	76	CC		KEEP	---	---	---	---	capture	STAD - Stomach adenocarcinoma(47;0.00185)		Silent	SNP	120639011	120639011	5323	8	C	T	T	32	32	ENPP2	T	2	2
CHD7	55636	broad.mit.edu	36	8	61931863	61931863	+	Silent	SNP	G	A	A			TCGA-06-0686-01	TCGA-06-0686-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr8:61931863G>A	uc003xue.1	+	c.7470G>A	c.(7468-7470)TCG>TCA	p.S2490S		NM_017780	NP_060250	Q9P2D1	CHD7_HUMAN	chromodomain helicase DNA binding protein 7	2490					central nervous system development|chromatin assembly or disassembly|chromatin modification|cognition|cranial nerve development|face development|heart morphogenesis|in utero embryonic development|inner ear morphogenesis|nose development|palate development|regulation of growth hormone secretion|regulation of transcription, DNA-dependent|retina development in camera-type eye|skeletal system development|T cell differentiation|transcription, DNA-dependent	chromatin|nucleus	ATP binding|chromatin binding|DNA binding|helicase activity			ovary(4)|large_intestine(1)|lung(1)|breast(1)|pancreas(1)	8		all_cancers(86;0.2)|all_lung(136;0.0402)|Lung NSC(129;0.0459)|all_epithelial(80;0.0477)												0.392344	231.899455	234.021464	82	127	GG		KEEP	---	---	---	---	capture	BRCA - Breast invasive adenocarcinoma(89;0.143)		Silent	SNP	61931863	61931863	3464	8	G	A	A	38	38	CHD7	A	1	1
C8orf34	116328	broad.mit.edu	36	8	69783867	69783867	+	Silent	SNP	C	T	T			TCGA-06-0686-01	TCGA-06-0686-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr8:69783867C>T	uc010lyz.1	+	c.1068C>T	c.(1066-1068)TTC>TTT	p.F356F	C8orf34_uc003xyb.1_Silent_p.F331F	NM_052958	NP_443190	Q49A92	CH034_HUMAN	hypothetical protein LOC116328	356					signal transduction		cAMP-dependent protein kinase regulator activity			large_intestine(1)	1														0.59375	61.430956	61.676994	19	13	CC		KEEP	---	---	---	---	capture	Epithelial(68;0.0117)|OV - Ovarian serous cystadenocarcinoma(28;0.0227)|all cancers(69;0.0502)		Silent	SNP	69783867	69783867	2532	8	C	T	T	31	31	C8orf34	T	1	1
KCNB2	9312	broad.mit.edu	36	8	74012142	74012142	+	Silent	SNP	G	A	A			TCGA-06-0686-01	TCGA-06-0686-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr8:74012142G>A	uc003xzb.1	+	c.1998G>A	c.(1996-1998)ACG>ACA	p.T666T		NM_004770	NP_004761	Q92953	KCNB2_HUMAN	potassium voltage-gated channel, Shab-related	666	Cytoplasmic (Potential).				regulation of smooth muscle contraction	voltage-gated potassium channel complex	delayed rectifier potassium channel activity|protein binding			large_intestine(1)|ovary(1)|central_nervous_system(1)|pancreas(1)	4	Breast(64;0.137)													0.481203	190.391708	190.432542	64	69	GG		KEEP	---	---	---	---	capture	Epithelial(68;0.105)		Silent	SNP	74012142	74012142	8318	8	G	A	A	38	38	KCNB2	A	1	1
CCNE2	9134	broad.mit.edu	36	8	95969382	95969382	+	Missense_Mutation	SNP	A	C	C			TCGA-06-0686-01	TCGA-06-0686-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr8:95969382A>C	uc003yhc.1	-	c.549T>G	c.(547-549)AAT>AAG	p.N183K	CCNE2_uc003yhd.1_Missense_Mutation_p.N183K	NM_057749	NP_477097	O96020	CCNE2_HUMAN	cyclin E2	183					cell cycle checkpoint|cell division|G1/S transition of mitotic cell cycle|regulation of cyclin-dependent protein kinase activity	cytosol|nucleoplasm	protein binding				0	Breast(36;8.75e-07)													0.422222	133.043032	133.516297	38	52	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	95969382	95969382	3048	8	A	C	C	16	16	CCNE2	C	4	4
SARDH	1757	broad.mit.edu	36	9	135587530	135587530	+	Missense_Mutation	SNP	G	C	C			TCGA-06-0686-01	TCGA-06-0686-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr9:135587530G>C	uc004cep.2	-	c.346C>G	c.(346-348)CTG>GTG	p.L116V	SARDH_uc004ceo.1_Missense_Mutation_p.L116V	NM_007101	NP_009032	Q9UL12	SARDH_HUMAN	sarcosine dehydrogenase precursor	116					glycine catabolic process|oxidation-reduction process	mitochondrial matrix	aminomethyltransferase activity|sarcosine dehydrogenase activity				0														0.24	9.329828	10.881501	6	19	GG		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(145;3.21e-07)|Epithelial(140;2.37e-06)|all cancers(34;2.75e-05)	Missense_Mutation	SNP	135587530	135587530	14322	9	G	C	C	34	34	SARDH	C	3	3
BMP15	9210	broad.mit.edu	36	X	50676171	50676171	+	Missense_Mutation	SNP	C	A	A			TCGA-06-0686-01	TCGA-06-0686-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chrX:50676171C>A	uc004dpg.1	+	c.1003C>A	c.(1003-1005)CCC>ACC	p.P335T		NM_005448	NP_005439	O95972	BMP15_HUMAN	bone morphogenetic protein 15 precursor	335					female gamete generation|granulosa cell development|ovarian follicle development	extracellular space	cytokine activity|growth factor activity			ovary(2)	2	Ovarian(276;0.236)													0.818182	169.975988	176.24673	54	12	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	50676171	50676171	1483	23	C	A	A	22	22	BMP15	A	3	3
TPRX1	284355	broad.mit.edu	36	19	52997355	52997378	+	In_Frame_Del	DEL	GGGCCTGGGATCGGGCCTGGGTTC	-	-			TCGA-06-0686-01	TCGA-06-0686-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:52997355_52997378delGGGCCTGGGATCGGGCCTGGGTTC	uc002php.1	-	c.702_725delGAACCCAGGCCCGATCCCAGGCCC	c.(700-726)CCGAACCCAGGCCCGATCCCAGGCCCA>CCA	p.234_242PNPGPIPGP>P		NM_198479	NP_940881	Q8N7U7	TPRX1_HUMAN	tetra-peptide repeat homeobox	234_242	Gly-rich.				regulation of transcription, DNA-dependent	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity				0		all_cancers(25;3.02e-09)|all_epithelial(76;7e-07)|all_lung(116;2.48e-06)|Lung NSC(112;5.15e-06)|Ovarian(192;0.0139)|all_neural(266;0.0146)|Breast(70;0.133)		OV - Ovarian serous cystadenocarcinoma(262;0.000241)|all cancers(93;0.00036)|Epithelial(262;0.0127)|GBM - Glioblastoma multiforme(486;0.048)		Esophageal Squamous(123;175 2281 3051 32395)								0.45			5	6				---	---	---	---	capture_indel			In_Frame_Del	DEL	52997355	52997378	16966	19	GGGCCTGGGATCGGGCCTGGGTTC	-	-	47	47	TPRX1	-	5	5
OR2T35	403244	broad.mit.edu	36	1	246868225	246868226	+	Frame_Shift_Ins	INS	-	CA	CA			TCGA-06-0686-01	TCGA-06-0686-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:246868225_246868226insCA	uc001ies.1	-	c.957_958insTG	c.(955-960)GTGATCfs	p.V319fs		NM_001001827	NP_001001827	Q8NGX2	O2T35_HUMAN	olfactory receptor, family 2, subfamily T,	319_320	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0	all_cancers(71;2.04e-05)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)	all_cancers(173;0.237)	OV - Ovarian serous cystadenocarcinoma(106;0.0265)											0.38			3	5				---	---	---	---	capture_indel			Frame_Shift_Ins	INS	246868225	246868226	11432	1	-	CA	CA	50	50	OR2T35	CA	5	5
