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
MMP13	4322	broad.mit.edu	36	11	102328088	102328088	+	Missense_Mutation	SNP	G	A	A			TCGA-12-3652-01	TCGA-12-3652-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr11:102328088G>A	uc001phl.1	-	c.662C>T	c.(661-663)GCG>GTG	p.A221V		NM_002427	NP_002418	P45452	MMP13_HUMAN	matrix metalloproteinase 13 preproprotein	221					collagen catabolic process|proteolysis	extracellular space	metalloendopeptidase activity|zinc ion binding			ovary(2)	2		all_hematologic(158;0.00092)|Acute lymphoblastic leukemia(157;0.000967)												0.409326	215.684648	217.070413	79	114	GG		KEEP	---	---	---	---	capture		BRCA - Breast invasive adenocarcinoma(274;0.0144)	Missense_Mutation	SNP	102328088	102328088	10042	11	G	A	A	38	38	MMP13	A	1	1
LRRC55	219527	broad.mit.edu	36	11	56706430	56706430	+	Silent	SNP	C	T	T			TCGA-12-3652-01	TCGA-12-3652-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr11:56706430C>T	uc001njl.1	+	c.487C>T	c.(487-489)CTG>TTG	p.L163L		NM_001005210	NP_001005210	Q6ZSA7	LRC55_HUMAN	leucine rich repeat containing 55	133	LRR 3.					integral to membrane					0														0.317073	39.461719	40.680816	13	28	CC		KEEP	---	---	---	---	capture			Silent	SNP	56706430	56706430	9386	11	C	T	T	24	24	LRRC55	T	2	2
OR5AN1	390195	broad.mit.edu	36	11	58889016	58889016	+	Missense_Mutation	SNP	G	T	T			TCGA-12-3652-01	TCGA-12-3652-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr11:58889016G>T	uc001nnv.1	+	c.509G>T	c.(508-510)TGT>TTT	p.C170F		NM_001004729	NP_001004729	Q8NGI8	O5AN1_HUMAN	olfactory receptor, family 5, subfamily AN,	170	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)	1														0.424242	352.338591	353.664091	112	152	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	58889016	58889016	11553	11	G	T	T	48	48	OR5AN1	T	3	3
RNFT2	84900	broad.mit.edu	36	12	115701419	115701419	+	Silent	SNP	C	T	T			TCGA-12-3652-01	TCGA-12-3652-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr12:115701419C>T	uc009zwn.1	+	c.765C>T	c.(763-765)GAC>GAT	p.D255D	RNFT2_uc001twb.2_Silent_p.D255D|RNFT2_uc001twa.2_Silent_p.D165D|RNFT2_uc001twc.2_Silent_p.D3D	NM_001109903	NP_001103373	Q96EX2	RNFT2_HUMAN	transmembrane protein 118 isoform 1	255	Extracellular (Potential).					integral to membrane	zinc ion binding				0	all_neural(191;0.117)|Medulloblastoma(191;0.163)													0.443038	328.913171	329.587224	105	132	CC		KEEP	---	---	---	---	capture		BRCA - Breast invasive adenocarcinoma(302;0.034)	Silent	SNP	115701419	115701419	13981	12	C	T	T	20	20	RNFT2	T	2	2
VSIG10	54621	broad.mit.edu	36	12	117001590	117001590	+	Missense_Mutation	SNP	C	A	A			TCGA-12-3652-01	TCGA-12-3652-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr12:117001590C>A	uc001tws.1	-	c.869G>T	c.(868-870)TGT>TTT	p.C290F		NM_019086	NP_061959	Q8N0Z9	VSI10_HUMAN	hypothetical protein FLJ20674	290	Ig-like C2-type 3.|Extracellular (Potential).					integral to membrane					0														0.521127	116.496418	116.52573	37	34	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	117001590	117001590	17790	12	C	A	A	17	17	VSIG10	A	3	3
CCDC60	160777	broad.mit.edu	36	12	118427336	118427336	+	Missense_Mutation	SNP	G	A	A			TCGA-12-3652-01	TCGA-12-3652-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr12:118427336G>A	uc001txe.1	+	c.728G>A	c.(727-729)CGG>CAG	p.R243Q		NM_178499	NP_848594	Q8IWA6	CCD60_HUMAN	coiled-coil domain containing 60	243										ovary(2)	2	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)													0.458167	353.69679	354.078441	115	136	GG		KEEP	---	---	---	---	capture		BRCA - Breast invasive adenocarcinoma(302;0.207)	Missense_Mutation	SNP	118427336	118427336	2954	12	G	A	A	39	39	CCDC60	A	1	1
NR4A1	3164	broad.mit.edu	36	12	50734823	50734823	+	Silent	SNP	G	T	T			TCGA-12-3652-01	TCGA-12-3652-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr12:50734823G>T	uc001rzq.1	+	c.606G>T	c.(604-606)CCG>CCT	p.P202P	NR4A1_uc001rzr.2_Silent_p.P148P|NR4A1_uc009zmb.1_Silent_p.P148P|NR4A1_uc001rzs.1_Silent_p.P148P|NR4A1_uc001rzt.1_Silent_p.P148P|NR4A1_uc009zmc.1_5'Flank	NM_173157	NP_775180	P22736	NR4A1_HUMAN	nuclear receptor subfamily 4, group A, member 1	148					nerve growth factor receptor signaling pathway|phosphatidylinositol-mediated signaling|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor		steroid hormone receptor activity|zinc ion binding				0														0.526316	93.838287	93.872786	30	27	GG		KEEP	---	---	---	---	capture		BRCA - Breast invasive adenocarcinoma(357;0.0967)	Silent	SNP	50734823	50734823	11037	12	G	T	T	38	38	NR4A1	T	3	3
ESYT1	23344	broad.mit.edu	36	12	54822446	54822446	+	Missense_Mutation	SNP	G	T	T			TCGA-12-3652-01	TCGA-12-3652-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr12:54822446G>T	uc001sjr.1	+	c.2733G>T	c.(2731-2733)CAG>CAT	p.Q911H	ESYT1_uc001sjq.1_Missense_Mutation_p.Q901H	NM_015292	NP_056107	Q9BSJ8	ESYT1_HUMAN	family with sequence similarity 62 (C2 domain	901						integral to membrane				ovary(4)	4														0.451613	126.319685	126.511523	42	51	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	54822446	54822446	5457	12	G	T	T	35	35	ESYT1	T	3	3
RNF17	56163	broad.mit.edu	36	13	24323654	24323654	+	Missense_Mutation	SNP	C	T	T			TCGA-12-3652-01	TCGA-12-3652-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr13:24323654C>T	uc001upr.1	+	c.3265C>T	c.(3265-3267)CGT>TGT	p.R1089C	RNF17_uc010aab.1_Non-coding_Transcript|RNF17_uc001ups.1_Missense_Mutation_p.R1028C|RNF17_uc010aac.1_Missense_Mutation_p.R287C|RNF17_uc010aad.1_Missense_Mutation_p.R141C	NM_031277	NP_112567	Q9BXT8	RNF17_HUMAN	ring finger protein 17	1089					multicellular organismal development	cytoplasm|nucleus	hydrolase activity, acting on ester bonds|nucleic acid binding|zinc ion binding			ovary(1)	1		Lung SC(185;0.0225)|Breast(139;0.077)												0.756757	92.316576	94.539503	28	9	CC		KEEP	---	---	---	---	capture		all cancers(112;0.0114)|OV - Ovarian serous cystadenocarcinoma(117;0.0311)|Epithelial(112;0.0524)	Missense_Mutation	SNP	24323654	24323654	13938	13	C	T	T	27	27	RNF17	T	1	1
INTS6	26512	broad.mit.edu	36	13	50924179	50924179	+	Missense_Mutation	SNP	T	G	G			TCGA-12-3652-01	TCGA-12-3652-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr13:50924179T>G	uc001vfk.1	-	c.125A>C	c.(124-126)GAC>GCC	p.D42A	INTS6_uc001vfj.1_Missense_Mutation_p.D29A|INTS6_uc001vfl.1_5'UTR|INTS6_uc001vfm.1_Missense_Mutation_p.D42A	NM_012141	NP_001035026	Q9UL03	INT6_HUMAN	integrator complex subunit 6 isoform a	42	VWFA.				snRNA processing	actin cytoskeleton|integrator complex	protein binding|transmembrane receptor activity			ovary(1)|lung(1)	2		Breast(56;0.000286)|Lung NSC(96;0.00145)|Prostate(109;0.00403)|Hepatocellular(98;0.065)|Myeloproliferative disorder(33;0.163)|all_neural(104;0.19)												0.25	6.718538	7.401185	3	9	TT		KEEP	---	---	---	---	capture		GBM - Glioblastoma multiforme(99;7.7e-08)	Missense_Mutation	SNP	50924179	50924179	8083	13	T	G	G	58	58	INTS6	G	4	4
PCDH9	5101	broad.mit.edu	36	13	66103381	66103381	+	Missense_Mutation	SNP	T	C	C			TCGA-12-3652-01	TCGA-12-3652-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr13:66103381T>C	uc001vik.1	-	c.3302A>G	c.(3301-3303)AAG>AGG	p.K1101R	PCDH9_uc010aei.1_Non-coding_Transcript|PCDH9_uc001vil.1_Missense_Mutation_p.K1067R	NM_203487	NP_982354	Q9HC56	PCDH9_HUMAN	protocadherin 9 isoform 1 precursor	1101	Cytoplasmic (Potential).				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(4)|pancreas(1)	5		Hepatocellular(98;0.0906)|Breast(118;0.107)												0.421769	220.830962	221.615058	62	85	TT		KEEP	---	---	---	---	capture		GBM - Glioblastoma multiforme(99;0.00819)	Missense_Mutation	SNP	66103381	66103381	11938	13	T	C	C	56	56	PCDH9	C	4	4
KLF12	11278	broad.mit.edu	36	13	73285377	73285377	+	Missense_Mutation	SNP	C	T	T			TCGA-12-3652-01	TCGA-12-3652-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr13:73285377C>T	uc001vjf.1	-	c.719G>A	c.(718-720)AGT>AAT	p.S240N	KLF12_uc010aeq.1_Missense_Mutation_p.S240N|KLF12_uc001vjg.2_Missense_Mutation_p.S240N	NM_007249	NP_009180	Q9Y4X4	KLF12_HUMAN	Kruppel-like factor 12	240					negative regulation of transcription from RNA polymerase II promoter	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|transcription corepressor activity|zinc ion binding			ovary(1)	1		Prostate(6;0.00217)|Breast(118;0.0838)												0.267123	99.552402	106.709235	39	107	CC		KEEP	---	---	---	---	capture		GBM - Glioblastoma multiforme(99;0.00677)	Missense_Mutation	SNP	73285377	73285377	8652	13	C	T	T	20	20	KLF12	T	2	2
SLC8A3	6547	broad.mit.edu	36	14	69704320	69704320	+	Silent	SNP	G	A	A	rs35952723	unknown	TCGA-12-3652-01	TCGA-12-3652-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr14:69704320G>A	uc001xly.1	-	c.573C>T	c.(571-573)GAC>GAT	p.D191D	SLC8A3_uc001xlw.1_Silent_p.D191D|SLC8A3_uc001xlx.1_Silent_p.D191D|SLC8A3_uc001xlz.1_Silent_p.D191D|SLC8A3_uc010ara.1_Non-coding_Transcript	NM_183002	NP_892114	P57103	NAC3_HUMAN	solute carrier family 8 (sodium/calcium	191	Cytoplasmic (Potential).				cell communication|platelet activation	integral to membrane|plasma membrane	calcium:sodium antiporter activity|calmodulin binding			ovary(2)|breast(2)	4														0.47541	87.469507	87.501645	29	32	GG		KEEP	---	---	---	---	capture		BRCA - Breast invasive adenocarcinoma(234;0.0079)|all cancers(60;0.0102)|OV - Ovarian serous cystadenocarcinoma(108;0.0555)	Silent	SNP	69704320	69704320	15205	14	G	A	A	40	40	SLC8A3	A	1	1
RYR3	6263	broad.mit.edu	36	15	31837052	31837052	+	Missense_Mutation	SNP	G	A	A			TCGA-12-3652-01	TCGA-12-3652-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr15:31837052G>A	uc001zhi.1	+	c.8668G>A	c.(8668-8670)GGA>AGA	p.G2890R	RYR3_uc010bar.1_Missense_Mutation_p.G2890R	NM_001036	NP_001027	Q15413	RYR3_HUMAN	ryanodine receptor 3	2890	Cytoplasmic (By similarity).				cellular calcium ion homeostasis	integral to membrane	calcium ion binding|receptor activity|ryanodine-sensitive calcium-release channel activity			ovary(5)|central_nervous_system(4)|lung(1)	10		all_lung(180;7.18e-09)												0.45	29.173377	29.216827	9	11	GG		KEEP	---	---	---	---	capture		all cancers(64;8.95e-12)|GBM - Glioblastoma multiforme(186;0.00109)|BRCA - Breast invasive adenocarcinoma(123;0.0363)	Missense_Mutation	SNP	31837052	31837052	14250	15	G	A	A	39	39	RYR3	A	1	1
SPTBN5	51332	broad.mit.edu	36	15	39949345	39949345	+	Missense_Mutation	SNP	G	A	A			TCGA-12-3652-01	TCGA-12-3652-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr15:39949345G>A	uc001zos.1	-	c.5734C>T	c.(5734-5736)CGC>TGC	p.R1912C		NM_016642	NP_057726	Q9NRC6	SPTN5_HUMAN	spectrin, beta, non-erythrocytic 5	1947	Spectrin 16.				actin cytoskeleton organization|actin filament capping|axon guidance	cytosol|membrane|spectrin				ovary(1)|central_nervous_system(1)	2		all_cancers(109;1.84e-17)|all_epithelial(112;1.12e-15)|Lung NSC(122;7.6e-10)|all_lung(180;4.15e-09)|Melanoma(134;0.0179)|Ovarian(310;0.143)|Colorectal(260;0.173)												0.55	36.627778	36.671468	11	9	GG		KEEP	---	---	---	---	capture		all cancers(2;4.33e-34)|Epithelial(2;1.72e-25)|OV - Ovarian serous cystadenocarcinoma(18;8.32e-20)|GBM - Glioblastoma multiforme(94;4.69e-07)|Colorectal(2;0.00104)|COAD - Colon adenocarcinoma(120;0.0405)|READ - Rectum adenocarcinoma(92;0.0908)	Missense_Mutation	SNP	39949345	39949345	15636	15	G	A	A	39	39	SPTBN5	A	1	1
GALK2	2585	broad.mit.edu	36	15	47407469	47407469	+	Missense_Mutation	SNP	A	G	G			TCGA-12-3652-01	TCGA-12-3652-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr15:47407469A>G	uc001zxj.1	+	c.1198A>G	c.(1198-1200)ACT>GCT	p.T400A	GALK2_uc001zxi.1_Missense_Mutation_p.T389A|GALK2_uc001zxk.1_Non-coding_Transcript	NM_002044	NP_002035	Q01415	GALK2_HUMAN	galactokinase 2 isoform 1	400					galactose metabolic process	cytoplasm	ATP binding|galactokinase activity|N-acetylgalactosamine kinase activity			breast(1)	1		all_lung(180;0.000325)												0.387324	191.003751	192.579736	55	87	AA		KEEP	---	---	---	---	capture		all cancers(107;3.71e-08)|GBM - Glioblastoma multiforme(94;7e-05)	Missense_Mutation	SNP	47407469	47407469	6468	15	A	G	G	14	14	GALK2	G	4	4
SLC24A1	9187	broad.mit.edu	36	15	63704268	63704268	+	Missense_Mutation	SNP	C	A	A			TCGA-12-3652-01	TCGA-12-3652-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr15:63704268C>A	uc002apf.1	+	c.797C>A	c.(796-798)GCA>GAA	p.A266E	SLC24A1_uc010bhm.1_5'UTR|SLC24A1_uc002apg.1_5'UTR	NM_004727	NP_004718	O60721	NCKX1_HUMAN	solute carrier family 24	266	Extracellular (Potential).				response to light intensity|visual perception	integral to plasma membrane|membrane fraction|outer membrane	calcium, potassium:sodium antiporter activity|protein binding|symporter activity				0														0.437037	179.766809	180.239263	59	76	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	63704268	63704268	14962	15	C	A	A	25	25	SLC24A1	A	3	3
MYO15A	51168	broad.mit.edu	36	17	17993279	17993279	+	Silent	SNP	G	A	A			TCGA-12-3652-01	TCGA-12-3652-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr17:17993279G>A	uc010cpt.1	+	c.6981G>A	c.(6979-6981)TCG>TCA	p.S2327S	MYO15A_uc010cpu.1_Silent_p.S2327S	NM_016239	NP_057323	Q9UKN7	MYO15_HUMAN	myosin XV	2327	Tail.				sensory perception of sound	cytoplasm|myosin complex|stereocilium	actin binding|ATP binding|calmodulin binding|motor activity			ovary(2)|pancreas(1)|breast(1)|central_nervous_system(1)|skin(1)	6	all_neural(463;0.228)													0.512821	66.901325	66.906905	20	19	GG		KEEP	---	---	---	---	capture			Silent	SNP	17993279	17993279	10458	17	G	A	A	39	39	MYO15A	A	1	1
MYO1D	4642	broad.mit.edu	36	17	28131903	28131903	+	Silent	SNP	C	T	T			TCGA-12-3652-01	TCGA-12-3652-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr17:28131903C>T	uc002hho.1	-	c.108G>A	c.(106-108)GGG>GGA	p.G36G	MYO1D_uc002hhp.1_Silent_p.G36G	NM_015194	NP_056009	O94832	MYO1D_HUMAN	myosin ID	36	Myosin head-like.					myosin complex	actin binding|ATP binding|calmodulin binding			large_intestine(1)|ovary(1)|central_nervous_system(1)	3														0.472222	104.100931	104.143524	34	38	CC		KEEP	---	---	---	---	capture	BRCA - Breast invasive adenocarcinoma(9;0.0362)		Silent	SNP	28131903	28131903	10466	17	C	T	T	26	26	MYO1D	T	2	2
SLC4A1	6521	broad.mit.edu	36	17	39690947	39690947	+	Silent	SNP	G	A	A			TCGA-12-3652-01	TCGA-12-3652-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr17:39690947G>A	uc002igf.2	-	c.1215C>T	c.(1213-1215)GTC>GTT	p.V405V	SLC4A1_uc002igg.2_Silent_p.V405V	NM_000342	NP_000333	P02730	B3AT_HUMAN	solute carrier family 4, anion exchanger, member	405	Helical; (Potential).|Membrane (anion exchange).		Missing (in EL4).		bicarbonate transport|cellular ion homeostasis	basolateral plasma membrane|cortical cytoskeleton|integral to plasma membrane|Z disc	ankyrin binding|chloride transmembrane transporter activity|inorganic anion exchanger activity|protein anchor|protein homodimerization activity			ovary(1)|central_nervous_system(1)|skin(1)	3		Breast(137;0.014)|Prostate(33;0.0181)												0.380165	125.847665	127.360334	46	75	GG		KEEP	---	---	---	---	capture		BRCA - Breast invasive adenocarcinoma(366;0.115)	Silent	SNP	39690947	39690947	15147	17	G	A	A	41	41	SLC4A1	A	2	2
DNAH2	146754	broad.mit.edu	36	17	7612076	7612076	+	Missense_Mutation	SNP	G	A	A			TCGA-12-3652-01	TCGA-12-3652-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr17:7612076G>A	uc002giu.1	+	c.3809G>A	c.(3808-3810)CGC>CAC	p.R1270H		NM_020877	NP_065928	Q9P225	DYH2_HUMAN	dynein heavy chain domain 3	1270	Stem (By similarity).				ciliary or flagellar motility|microtubule-based movement	axonemal dynein complex|cilium axoneme|cytoplasm|microtubule	ATP binding|ATPase activity|microtubule motor activity			ovary(6)|central_nervous_system(1)	7		all_cancers(10;4.66e-07)|Prostate(122;0.081)												0.452632	124.009545	124.195379	43	52	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	7612076	7612076	4785	17	G	A	A	38	38	DNAH2	A	1	1
RBBP8	5932	broad.mit.edu	36	18	18818926	18818926	+	Silent	SNP	T	C	C			TCGA-12-3652-01	TCGA-12-3652-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr18:18818926T>C	uc002kua.1	+	c.684T>C	c.(682-684)TAT>TAC	p.Y228Y	RBBP8_uc002ktw.1_Silent_p.Y228Y|RBBP8_uc002ktx.1_Silent_p.Y228Y|RBBP8_uc002kty.1_Silent_p.Y228Y|RBBP8_uc002ktz.1_Silent_p.Y228Y	NM_203291	NP_976036	Q99708	COM1_HUMAN	retinoblastoma binding protein 8 isoform a	228					cell cycle checkpoint|DNA double-strand break processing involved in repair via single-strand annealing|meiosis|regulation of transcription from RNA polymerase II promoter	nucleus	damaged DNA binding|protein binding|single-stranded DNA specific endodeoxyribonuclease activity			ovary(1)|skin(1)	2	all_cancers(21;4.34e-05)|all_epithelial(16;8.3e-07)|Lung NSC(20;0.0107)|Colorectal(14;0.0202)|all_lung(20;0.0291)|Ovarian(20;0.19)								p.Y228Y(OCUM1-Tumor)	470				0.358491	108.720565	110.589656	38	68	TT		KEEP	---	---	---	---	capture	OV - Ovarian serous cystadenocarcinoma(1;0.00196)		Silent	SNP	18818926	18818926	13566	18	T	C	C	51	51	RBBP8	C	4	4
FKBP8	23770	broad.mit.edu	36	19	18510190	18510190	+	Missense_Mutation	SNP	G	A	A			TCGA-12-3652-01	TCGA-12-3652-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr19:18510190G>A	uc002njj.1	-	c.608C>T	c.(607-609)ACG>ATG	p.T203M	FKBP8_uc002nji.1_Missense_Mutation_p.T40M|FKBP8_uc002njk.1_Missense_Mutation_p.T202M|FKBP8_uc002njl.1_Missense_Mutation_p.T203M|FKBP8_uc002njm.1_Missense_Mutation_p.T202M|FKBP8_uc010ebr.1_Missense_Mutation_p.T41M|FKBP8_uc002njn.1_Non-coding_Transcript	NM_012181	NP_036313	Q14318	FKBP8_HUMAN	FK506-binding protein 8	202	PPIase FKBP-type.				apoptosis|interspecies interaction between organisms|intracellular signal transduction|protein folding	integral to endoplasmic reticulum membrane|mitochondrial membrane	FK506 binding|peptidyl-prolyl cis-trans isomerase activity			ovary(1)	1														0.297297	57.021519	59.740062	22	52	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	18510190	18510190	6152	19	G	A	A	40	40	FKBP8	A	1	1
NPHS1	4868	broad.mit.edu	36	19	41031001	41031001	+	Missense_Mutation	SNP	C	T	T			TCGA-12-3652-01	TCGA-12-3652-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr19:41031001C>T	uc002oby.2	-	c.1309G>A	c.(1309-1311)GTA>ATA	p.V437I		NM_004646	NP_004637	O60500	NPHN_HUMAN	nephrin precursor	437	Extracellular (Potential).				cell adhesion|excretion|muscle organ development	integral to plasma membrane				ovary(4)	4	all_lung(56;7.14e-07)|Lung NSC(56;1.12e-06)|Esophageal squamous(110;0.162)													0.260274	142.179673	153.571734	57	162	CC		KEEP	---	---	---	---	capture	LUSC - Lung squamous cell carcinoma(66;0.0515)		Missense_Mutation	SNP	41031001	41031001	10986	19	C	T	T	19	19	NPHS1	T	1	1
TTYH1	57348	broad.mit.edu	36	19	59622187	59622187	+	Missense_Mutation	SNP	T	C	C			TCGA-12-3652-01	TCGA-12-3652-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr19:59622187T>C	uc002qfr.1	+	c.200T>C	c.(199-201)ATC>ACC	p.I67T	TTYH1_uc002qfq.1_Missense_Mutation_p.I67T|TTYH1_uc002qfs.1_Non-coding_Transcript|TTYH1_uc002qft.1_Missense_Mutation_p.I67T|TTYH1_uc002qfu.1_5'UTR	NM_001005367	NP_001005367	Q9H313	TTYH1_HUMAN	tweety 1 isoform 2	67	Cytoplasmic (Potential).				cell adhesion	chloride channel complex|plasma membrane	chloride channel activity|iron ion transmembrane transporter activity				0	Ovarian(34;0.19)													0.285714	125.53847	132.465738	48	120	TT		KEEP	---	---	---	---	capture		GBM - Glioblastoma multiforme(193;0.0767)	Missense_Mutation	SNP	59622187	59622187	17294	19	T	C	C	50	50	TTYH1	C	4	4
C3	718	broad.mit.edu	36	19	6628900	6628900	+	Missense_Mutation	SNP	G	T	T			TCGA-12-3652-01	TCGA-12-3652-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr19:6628900G>T	uc002mfm.1	-	c.4985C>A	c.(4984-4986)CCC>CAC	p.P1662H	C3_uc002mfl.1_Missense_Mutation_p.P398H	NM_000064	NP_000055	P01024	CO3_HUMAN	complement component 3 precursor	1662					complement activation, alternative pathway|complement activation, classical pathway|G-protein coupled receptor protein signaling pathway|inflammatory response|positive regulation vascular endothelial growth factor production	extracellular space	endopeptidase inhibitor activity|receptor binding			ovary(1)|pancreas(1)	2														0.330189	91.295683	94.001657	35	71	GG		KEEP	---	---	---	---	capture		GBM - Glioblastoma multiforme(1328;1.36e-05)|Lung(535;0.00661)	Missense_Mutation	SNP	6628900	6628900	2296	19	G	T	T	43	43	C3	T	3	3
C1orf187	374946	broad.mit.edu	36	1	11688912	11688912	+	Missense_Mutation	SNP	C	G	G			TCGA-12-3652-01	TCGA-12-3652-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr1:11688912C>G	uc001asr.1	+	c.10C>G	c.(10-12)CCT>GCT	p.P4A		NM_198545	NP_940947	Q8NBI3	DRAXI_HUMAN	chromosome 1 open reading frame 187	4					axon guidance|commissural neuron differentiation in spinal cord|dorsal spinal cord development|forebrain development|negative regulation of canonical Wnt receptor signaling pathway|Wnt receptor signaling pathway	extracellular region					0	Ovarian(185;0.249)	Lung NSC(185;4.15e-05)|all_lung(284;4.76e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Hepatocellular(190;0.00826)|Ovarian(437;0.00965)|Myeloproliferative disorder(586;0.0255)												0.272727	6.637603	7.139151	3	8	CC		KEEP	---	---	---	---	capture		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;6.48e-06)|COAD - Colon adenocarcinoma(227;0.000283)|BRCA - Breast invasive adenocarcinoma(304;0.000316)|Kidney(185;0.000841)|KIRC - Kidney renal clear cell carcinoma(229;0.00269)|STAD - Stomach adenocarcinoma(313;0.00754)|READ - Rectum adenocarcinoma(331;0.0651)	Missense_Mutation	SNP	11688912	11688912	2089	1	C	G	G	26	26	C1orf187	G	3	3
SPRR2B	6701	broad.mit.edu	36	1	151309757	151309757	+	Silent	SNP	T	A	A			TCGA-12-3652-01	TCGA-12-3652-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr1:151309757T>A	uc001fbg.1	-	c.183A>T	c.(181-183)CCA>CCT	p.P61P	SPRR2A_uc001fbe.1_Intron|SPRR2A_uc001fbf.1_Intron	NM_001017418	NP_001017418	P35325	SPR2B_HUMAN	small proline-rich protein 2B	61					keratinization	cornified envelope|cytoplasm					0	Lung NSC(65;1.49e-28)|Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)													0.466667	164.300586	164.452914	63	72	TT		KEEP	---	---	---	---	capture	LUSC - Lung squamous cell carcinoma(543;0.171)		Silent	SNP	151309757	151309757	15612	1	T	A	A	59	59	SPRR2B	A	4	4
ADCY10	55811	broad.mit.edu	36	1	166081569	166081569	+	Missense_Mutation	SNP	G	A	A			TCGA-12-3652-01	TCGA-12-3652-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:166081569G>A	uc001ger.1	-	c.2863C>T	c.(2863-2865)CGC>TGC	p.R955C	ADCY10_uc009wvk.1_Missense_Mutation_p.R863C|ADCY10_uc009wvl.1_Missense_Mutation_p.R954C	NM_018417	NP_060887	Q96PN6	ADCYA_HUMAN	soluble adenylyl cyclase	955					intracellular signal transduction|spermatogenesis	cytoskeleton|cytosol|perinuclear region of cytoplasm|plasma membrane|soluble fraction	adenylate cyclase activity|ATP binding|magnesium ion binding			central_nervous_system(2)|ovary(1)	3														0.423729	157.965305	158.555231	50	68	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	166081569	166081569	294	1	G	A	A	39	39	ADCY10	A	1	1
KIAA1614	57710	broad.mit.edu	36	1	179171056	179171056	+	Missense_Mutation	SNP	G	A	A			TCGA-12-3652-01	TCGA-12-3652-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:179171056G>A	uc001gok.2	+	c.1388G>A	c.(1387-1389)CGT>CAT	p.R463H	KIAA1614_uc001gol.1_Missense_Mutation_p.R84H|KIAA1614_uc001gom.1_Intron	NM_020950	NP_066001	Q5VZ46	K1614_HUMAN	hypothetical protein LOC57710	463										ovary(3)	3														0.6	26.276113	26.407562	9	6	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	179171056	179171056	8557	1	G	A	A	40	40	KIAA1614	A	1	1
GLUL	2752	broad.mit.edu	36	1	180623030	180623030	+	Missense_Mutation	SNP	C	T	T			TCGA-12-3652-01	TCGA-12-3652-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr1:180623030C>T	uc001gpa.1	-	c.187G>A	c.(187-189)GAT>AAT	p.D63N	GLUL_uc001gpb.1_Missense_Mutation_p.D63N|GLUL_uc001gpc.1_Missense_Mutation_p.D63N|GLUL_uc001gpd.1_Missense_Mutation_p.D63N	NM_001033056	NP_002056	P15104	GLNA_HUMAN	glutamine synthetase	63					cell proliferation|glutamine biosynthetic process|neurotransmitter uptake	cytosol|Golgi apparatus|mitochondrion	ATP binding|glutamate decarboxylase activity|glutamate-ammonia ligase activity|identical protein binding				0					Asparaginase(DB00023)|L-Glutamic Acid(DB00142)|L-Glutamine(DB00130)|L-Methionine(DB00134)									0.456	176.499177	176.704024	57	68	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	180623030	180623030	6746	1	C	T	T	31	31	GLUL	T	1	1
HLX	3142	broad.mit.edu	36	1	219124239	219124239	+	Missense_Mutation	SNP	A	G	G			TCGA-12-3652-01	TCGA-12-3652-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr1:219124239A>G	uc001hmv.2	+	c.1037A>G	c.(1036-1038)GAG>GGG	p.E346G		NM_021958	NP_068777	Q14774	HLX_HUMAN	H2.0-like homeobox	346					cell differentiation|regulation of transcription, DNA-dependent	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription regulator activity			ovary(2)	2														0.482759	46.849607	46.857043	14	15	AA		KEEP	---	---	---	---	capture		GBM - Glioblastoma multiforme(131;0.00914)	Missense_Mutation	SNP	219124239	219124239	7507	1	A	G	G	11	11	HLX	G	4	4
HHIPL2	79802	broad.mit.edu	36	1	220772075	220772075	+	Nonsense_Mutation	SNP	G	A	A			TCGA-12-3652-01	TCGA-12-3652-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:220772075G>A	uc001hnh.1	-	c.1579C>T	c.(1579-1581)CGA>TGA	p.R527*		NM_024746	NP_079022	Q6UWX4	HIPL2_HUMAN	HHIP-like 2	527					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														0.477273	62.869406	62.889309	21	23	GG		KEEP	---	---	---	---	capture		GBM - Glioblastoma multiforme(131;0.0185)	Nonsense_Mutation	SNP	220772075	220772075	7378	1	G	A	A	37	37	HHIPL2	A	5	1
OBSCN	84033	broad.mit.edu	36	1	226529063	226529063	+	Missense_Mutation	SNP	G	C	C			TCGA-12-3652-01	TCGA-12-3652-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:226529063G>C	uc009xez.1	+	c.5851G>C	c.(5851-5853)GCC>CCC	p.A1951P	OBSCN_uc001hsn.1_Missense_Mutation_p.A1951P|OBSCN_uc001hsp.1_5'Flank	NM_001098623	NP_001092093	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and	1951	Ig-like 19.				apoptosis|cell differentiation|induction of apoptosis by extracellular signals|multicellular organismal development|nerve growth factor receptor signaling pathway|protein phosphorylation|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol|M band|Z disc	ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity|protein tyrosine kinase activity|Rho guanyl-nucleotide exchange factor activity|structural constituent of muscle|titin binding			large_intestine(7)|breast(5)|ovary(4)|skin(2)|stomach(1)|central_nervous_system(1)|pancreas(1)	21		Prostate(94;0.0405)							p.A1951P(NCIH1355-Tumor)	4006				0.5	8.160979	8.160979	4	4	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	226529063	226529063	11217	1	G	C	C	38	38	OBSCN	C	3	3
RYR2	6262	broad.mit.edu	36	1	236014175	236014175	+	Silent	SNP	C	T	T			TCGA-12-3652-01	TCGA-12-3652-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr1:236014175C>T	uc001hyl.1	+	c.12540C>T	c.(12538-12540)GGC>GGT	p.G4180G		NM_001035	NP_001026	Q92736	RYR2_HUMAN	cardiac muscle ryanodine receptor	4180					cardiac muscle contraction|detection of calcium ion|induction of apoptosis by ionic changes|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum|response to caffeine|response to hypoxia|response to redox state	calcium channel complex|plasma membrane|plasma membrane enriched fraction|sarcoplasmic reticulum membrane	calcium ion binding|calmodulin binding|identical protein binding|protein kinase A catalytic subunit binding|protein kinase A regulatory subunit binding|receptor activity|ryanodine-sensitive calcium-release channel activity|suramin binding			ovary(17)|large_intestine(6)|central_nervous_system(6)|pancreas(3)|breast(1)	33	Ovarian(103;0.103)	all_cancers(173;0.000368)|Melanoma(53;0.0179)|all_epithelial(177;0.0225)												0.382979	153.244039	154.92667	54	87	CC		KEEP	---	---	---	---	capture	OV - Ovarian serous cystadenocarcinoma(106;0.00606)		Silent	SNP	236014175	236014175	14249	1	C	T	T	27	27	RYR2	T	1	1
ARHGEF16	27237	broad.mit.edu	36	1	3384317	3384317	+	Missense_Mutation	SNP	G	A	A			TCGA-12-3652-01	TCGA-12-3652-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:3384317G>A	uc001akg.2	+	c.1492G>A	c.(1492-1494)GCC>ACC	p.A498T	ARHGEF16_uc001aki.1_Missense_Mutation_p.A210T|ARHGEF16_uc001akj.1_Missense_Mutation_p.A210T	NM_014448	NP_055263	Q5VV41	ARHGG_HUMAN	Rho guanine exchange factor 16	498					activation of Cdc42 GTPase activity|activation of Rac GTPase activity|apoptosis|cell chemotaxis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|positive regulation of establishment of protein localization in plasma membrane|small GTPase mediated signal transduction	cytosol	PDZ domain binding|receptor tyrosine kinase binding|Rho GTPase binding|Rho guanyl-nucleotide exchange factor activity			ovary(1)	1	all_cancers(77;0.00276)|all_epithelial(69;0.00102)|Ovarian(185;0.0634)|Lung NSC(156;0.0969)|all_lung(157;0.101)	all_epithelial(116;7.14e-21)|all_lung(118;2.24e-08)|Lung NSC(185;3.55e-06)|Breast(487;0.000765)|Renal(390;0.00121)|Hepatocellular(190;0.0046)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0308)|Lung SC(97;0.0847)|Medulloblastoma(700;0.211)												0.487179	107.022566	107.03421	38	40	GG		KEEP	---	---	---	---	capture		Epithelial(90;8.62e-38)|OV - Ovarian serous cystadenocarcinoma(86;3.62e-22)|GBM - Glioblastoma multiforme(42;2.49e-12)|Colorectal(212;4.25e-05)|COAD - Colon adenocarcinoma(227;0.000196)|Kidney(185;0.000342)|BRCA - Breast invasive adenocarcinoma(365;0.000681)|KIRC - Kidney renal clear cell carcinoma(229;0.00549)|STAD - Stomach adenocarcinoma(132;0.00644)|Lung(427;0.201)	Missense_Mutation	SNP	3384317	3384317	913	1	G	A	A	46	46	ARHGEF16	A	2	2
SEMG2	6407	broad.mit.edu	36	20	43284680	43284680	+	Silent	SNP	A	G	G			TCGA-12-3652-01	TCGA-12-3652-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr20:43284680A>G	uc010ggz.1	+	c.993A>G	c.(991-993)ACA>ACG	p.T331T	SEMG2_uc002xnk.1_Silent_p.T331T|SEMG2_uc002xnl.1_Silent_p.T331T	NM_003008	NP_002999	Q02383	SEMG2_HUMAN	semenogelin II precursor	331	Repeat-rich region.|4 X 60 AA tandem repeats, type I.				sexual reproduction	extracellular space|stored secretory granule	structural molecule activity				0		Myeloproliferative disorder(115;0.0122)												0.275168	114.800918	121.591714	41	108	AA		KEEP	---	---	---	---	capture			Silent	SNP	43284680	43284680	14531	20	A	G	G	5	5	SEMG2	G	4	4
WFDC8	90199	broad.mit.edu	36	20	43614198	43614198	+	Missense_Mutation	SNP	G	A	A			TCGA-12-3652-01	TCGA-12-3652-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr20:43614198G>A	uc002xow.1	-	c.607C>T	c.(607-609)CGC>TGC	p.R203C	WFDC8_uc002xox.1_Missense_Mutation_p.R203C	NM_181510	NP_852611	Q8IUA0	WFDC8_HUMAN	WAP four-disulfide core domain 8 precursor	203	WAP 3.					extracellular region	serine-type endopeptidase inhibitor activity				0		Myeloproliferative disorder(115;0.0122)												0.319149	245.543716	253.743863	90	192	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	43614198	43614198	17930	20	G	A	A	40	40	WFDC8	A	1	1
PROKR2	128674	broad.mit.edu	36	20	5231335	5231335	+	Missense_Mutation	SNP	G	A	A			TCGA-12-3652-01	TCGA-12-3652-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr20:5231335G>A	uc002wlx.2	-	c.506C>T	c.(505-507)ACG>ATG	p.T169M	PROKR2_uc010gbj.1_Missense_Mutation_p.T169M|PROKR2_uc010gbk.1_Missense_Mutation_p.T169M	NM_144773	NP_658986	Q8NFJ6	PKR2_HUMAN	prokineticin receptor 2	169	Cytoplasmic (Potential).					integral to membrane|plasma membrane	neuropeptide Y receptor activity			ovary(3)|central_nervous_system(1)|pancreas(1)	5														0.3	214.461985	224.116276	81	189	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	5231335	5231335	12996	20	G	A	A	40	40	PROKR2	A	1	1
UMODL1	89766	broad.mit.edu	36	21	42369257	42369257	+	Missense_Mutation	SNP	G	C	C			TCGA-12-3652-01	TCGA-12-3652-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr21:42369257G>C	uc002zag.1	+	c.151G>C	c.(151-153)GTG>CTG	p.V51L	UMODL1_uc002zad.1_5'UTR|UMODL1_uc002zae.1_5'UTR|UMODL1_uc002zaf.1_Missense_Mutation_p.V51L	NM_173568	NP_775839	Q5DID0	UROL1_HUMAN	uromodulin-like 1 isoform 2 precursor	51	Extracellular (Potential).|EMI.					cytoplasm|extracellular region|integral to membrane|plasma membrane	calcium ion binding|peptidase inhibitor activity			ovary(2)	2						Pancreas(122;680 807 13940 14411 22888 25505 31742 36028 36332 38435)								0.41048	319.531131	321.127301	94	135	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	42369257	42369257	17538	21	G	C	C	40	40	UMODL1	C	3	3
CECR2	27443	broad.mit.edu	36	22	16362144	16362144	+	Silent	SNP	C	G	G			TCGA-12-3652-01	TCGA-12-3652-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr22:16362144C>G	uc010gqw.1	+	c.555C>G	c.(553-555)TCC>TCG	p.S185S	CECR2_uc010gqv.1_Silent_p.S64S|CECR2_uc002zml.2_Silent_p.S64S|CECR2_uc002zmm.1_Silent_p.S64S	NM_031413	NP_113601	Q9BXF3	CECR2_HUMAN	cat eye syndrome chromosome region, candidate 2	227					chromatin modification|cytokinesis|cytoskeleton organization|DNA fragmentation involved in apoptotic nuclear change|vesicle-mediated transport		protein binding			ovary(1)|skin(1)	2		all_epithelial(15;0.139)												0.25	7.019236	7.701091	3	9	CC		KEEP	---	---	---	---	capture		Lung(27;0.146)	Silent	SNP	16362144	16362144	3339	22	C	G	G	23	23	CECR2	G	3	3
INPP1	3628	broad.mit.edu	36	2	190944373	190944373	+	Nonstop_Mutation	SNP	G	C	C			TCGA-12-3652-01	TCGA-12-3652-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr2:190944373G>C	uc002ury.2	+	c.1200G>C	c.(1198-1200)TAG>TAC	p.*400Y	INPP1_uc010fsb.1_Nonstop_Mutation_p.*400Y|INPP1_uc002urx.2_Nonstop_Mutation_p.*400Y	NM_001128928	NP_001122400	P49441	INPP_HUMAN	inositol polyphosphate-1-phosphatase	400					signal transduction		inositol-1,4-bisphosphate 1-phosphatase activity|metal ion binding			ovary(1)|lung(1)	2					Lithium(DB01356)	Melanoma(130;184 1743 2185 19805 38428)								0.47541	104.872674	104.904727	29	32	GG		KEEP	---	---	---	---	capture	OV - Ovarian serous cystadenocarcinoma(117;0.000286)|Epithelial(96;0.0186)|all cancers(119;0.057)		Nonstop_Mutation	SNP	190944373	190944373	8052	2	G	C	C	33	33	INPP1	C	5	3
ALMS1	7840	broad.mit.edu	36	2	73531156	73531156	+	Missense_Mutation	SNP	A	G	G			TCGA-12-3652-01	TCGA-12-3652-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr2:73531156A>G	uc002sje.1	+	c.3997A>G	c.(3997-3999)ACT>GCT	p.T1333A	ALMS1_uc002sjf.1_Missense_Mutation_p.T1289A|ALMS1_uc002sjg.2_Missense_Mutation_p.T719A|ALMS1_uc002sjh.1_Missense_Mutation_p.T719A	NM_015120	NP_055935	Q8TCU4	ALMS1_HUMAN	ALMS1	1331	17.|34 X 47 AA approximate tandem repeat.				G2/M transition of mitotic cell cycle|visual perception	centrosome|cilium|cytosol|microtubule basal body|spindle pole				ovary(2)|breast(2)|lung(1)|pancreas(1)	6														0.393382	369.991012	372.689946	107	165	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	73531156	73531156	538	2	A	G	G	14	14	ALMS1	G	4	4
RPL32	6161	broad.mit.edu	36	3	12855946	12855946	+	Silent	SNP	A	G	G			TCGA-12-3652-01	TCGA-12-3652-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr3:12855946A>G	uc003bxl.1	-	c.180T>C	c.(178-180)TAT>TAC	p.Y60Y	RPL32_uc003bxm.1_Silent_p.Y60Y|RPL32_uc003bxn.1_Silent_p.Y60Y	NM_001007074	NP_001007075	P62910	RL32_HUMAN	ribosomal protein L32	60					endocrine pancreas development|translational elongation|translational termination|viral transcription	cytosol|ribosome	protein binding|structural constituent of ribosome			ovary(1)	1														0.392777	510.138275	514.601346	174	269	AA		KEEP	---	---	---	---	capture			Silent	SNP	12855946	12855946	14061	3	A	G	G	8	8	RPL32	G	4	4
IQSEC1	9922	broad.mit.edu	36	3	12952752	12952752	+	Missense_Mutation	SNP	G	A	A			TCGA-12-3652-01	TCGA-12-3652-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr3:12952752G>A	uc003bxt.1	-	c.806C>T	c.(805-807)CCG>CTG	p.P269L	IQSEC1_uc003bxu.2_Missense_Mutation_p.P147L	NM_014869	NP_055684	Q6DN90	IQEC1_HUMAN	IQ motif and Sec7 domain 1 isoform b	269					regulation of ARF protein signal transduction	cytoplasm|nucleus	ARF guanyl-nucleotide exchange factor activity			ovary(1)	1														0.516393	196.064242	196.095301	63	59	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	12952752	12952752	8120	3	G	A	A	39	39	IQSEC1	A	1	1
ZNF385D	79750	broad.mit.edu	36	3	21581172	21581172	+	Silent	SNP	C	T	T			TCGA-12-3652-01	TCGA-12-3652-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr3:21581172C>T	uc003cce.1	-	c.174G>A	c.(172-174)CCG>CCA	p.P58P	ZNF385D_uc010hfb.1_Non-coding_Transcript	NM_024697	NP_078973	Q9H6B1	Z385D_HUMAN	zinc finger protein 385D	58						nucleus	nucleic acid binding|zinc ion binding			large_intestine(2)|ovary(1)	3														0.333333	122.691709	125.860351	43	86	CC		KEEP	---	---	---	---	capture			Silent	SNP	21581172	21581172	18470	3	C	T	T	31	31	ZNF385D	T	1	1
CAV3	859	broad.mit.edu	36	3	8762341	8762341	+	Missense_Mutation	SNP	G	A	A			TCGA-12-3652-01	TCGA-12-3652-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr3:8762341G>A	uc003bra.1	+	c.244G>A	c.(244-246)GTC>ATC	p.V82I	C3orf32_uc003bqz.1_5'Flank|CAV3_uc003brb.1_Missense_Mutation_p.V82I	NM_001234	NP_203123	P56539	CAV3_HUMAN	caveolin 3	82	Cytoplasmic (Potential).|Required for interaction with DAG1.				cell growth|elevation of cytosolic calcium ion concentration|muscle organ development|negative regulation of cardiac muscle hypertrophy|negative regulation of cell size|negative regulation of MAP kinase activity|negative regulation of sarcomere organization|positive regulation of microtubule polymerization|regulation of skeletal muscle contraction|regulation of ventricular cardiomyocyte membrane repolarization|T-tubule organization	caveola|dystrophin-associated glycoprotein complex|Golgi membrane|neuromuscular junction|T-tubule	protein C-terminus binding|protein complex binding|protein complex scaffold|sodium channel regulator activity				0														0.487805	59.402639	59.407702	20	21	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	8762341	8762341	2814	3	G	A	A	40	40	CAV3	A	1	1
CFI	3426	broad.mit.edu	36	4	110883195	110883195	+	Missense_Mutation	SNP	C	T	T			TCGA-12-3652-01	TCGA-12-3652-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr4:110883195C>T	uc003hzr.2	-	c.1435G>A	c.(1435-1437)GAA>AAA	p.E479K	CFI_uc003hzq.1_Missense_Mutation_p.E276K|CFI_uc003hzs.2_Missense_Mutation_p.E472K	NM_000204	NP_000195	P05156	CFAI_HUMAN	complement factor I preproprotein	479	Peptidase S1.				complement activation, classical pathway|innate immune response|proteolysis	extracellular space|membrane	scavenger receptor activity|serine-type endopeptidase activity				0		Hepatocellular(203;0.217)							p.E472K(HT115-Tumor)	317				0.436364	145.785638	146.173593	48	62	CC		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(123;0.000331)	Missense_Mutation	SNP	110883195	110883195	3422	4	C	T	T	31	31	CFI	T	1	1
FAT1	2195	broad.mit.edu	36	4	187778096	187778096	+	Missense_Mutation	SNP	T	A	A			TCGA-12-3652-01	TCGA-12-3652-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr4:187778096T>A	uc003izf.1	-	c.6638A>T	c.(6637-6639)AAA>ATA	p.K2213I		NM_005245	NP_005236	Q14517	FAT1_HUMAN	FAT tumor suppressor 1 precursor	2213	Extracellular (Potential).|Cadherin 20.				actin filament organization|anatomical structure morphogenesis|cell migration|cell-cell signaling|establishment or maintenance of cell polarity|homophilic cell adhesion	cell-cell junction|integral to plasma membrane|nucleus|perinuclear region of cytoplasm	calcium ion binding|protein binding			ovary(10)|central_nervous_system(1)|pancreas(1)	12						Colon(197;1040 2055 4143 4984 49344)								0.437984	327.330561	328.196386	113	145	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	187778096	187778096	5925	4	T	A	A	64	64	FAT1	A	4	4
PCDH7	5099	broad.mit.edu	36	4	30335209	30335209	+	Missense_Mutation	SNP	G	T	T			TCGA-12-3652-01	TCGA-12-3652-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr4:30335209G>T	uc010iez.1	+	c.2926G>T	c.(2926-2928)GAT>TAT	p.D976Y	PCDH7_uc003gsj.1_Missense_Mutation_p.D1023Y|PCDH7_uc003gsk.1_Missense_Mutation_p.D1023Y	NM_032457	NP_115833	O60245	PCDH7_HUMAN	protocadherin 7 isoform c precursor	1023	Cytoplasmic (Potential).				homophilic cell adhesion	integral to plasma membrane	calcium ion binding			upper_aerodigestive_tract(1)|ovary(1)|liver(1)|skin(1)	4														0.494118	119.408031	119.411095	42	43	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	30335209	30335209	11936	4	G	T	T	33	33	PCDH7	T	3	3
KLB	152831	broad.mit.edu	36	4	39112233	39112233	+	Silent	SNP	G	A	A			TCGA-12-3652-01	TCGA-12-3652-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr4:39112233G>A	uc003gua.1	+	c.834G>A	c.(832-834)TCG>TCA	p.S278S		NM_175737	NP_783864	Q86Z14	KLOTB_HUMAN	klotho beta	278	Extracellular (Potential).|Glycosyl hydrolase-1 1.				carbohydrate metabolic process	integral to membrane|plasma membrane	cation binding|fibroblast growth factor binding|hydrolase activity, hydrolyzing O-glycosyl compounds			skin(1)	1														0.452174	160.187272	160.416283	52	63	GG		KEEP	---	---	---	---	capture			Silent	SNP	39112233	39112233	8644	4	G	A	A	37	37	KLB	A	1	1
MAN2B2	23324	broad.mit.edu	36	4	6629265	6629265	+	Silent	SNP	C	T	T			TCGA-12-3652-01	TCGA-12-3652-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr4:6629265C>T	uc003gjf.1	+	c.198C>T	c.(196-198)CGC>CGT	p.R66R	MAN2B2_uc003gje.1_Silent_p.R66R	NM_015274	NP_056089	Q9Y2E5	MA2B2_HUMAN	mannosidase, alpha, class 2B, member 2	66					mannose metabolic process	extracellular region	alpha-mannosidase activity|carbohydrate binding|zinc ion binding			ovary(2)	2														0.395833	149.73051	151.067504	57	87	CC		KEEP	---	---	---	---	capture			Silent	SNP	6629265	6629265	9600	4	C	T	T	27	27	MAN2B2	T	1	1
NPFFR2	10886	broad.mit.edu	36	4	73231836	73231836	+	Missense_Mutation	SNP	G	T	T			TCGA-12-3652-01	TCGA-12-3652-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr4:73231836G>T	uc003hgg.1	+	c.1012G>T	c.(1012-1014)GTC>TTC	p.V338F	NPFFR2_uc010iig.1_Missense_Mutation_p.V120F|NPFFR2_uc003hgh.1_Missense_Mutation_p.V236F|NPFFR2_uc003hgi.1_Missense_Mutation_p.V239F|NPFFR2_uc003hgj.1_Non-coding_Transcript	NM_004885	NP_444264	Q9Y5X5	NPFF2_HUMAN	neuropeptide FF receptor 2 isoform 1	338	Helical; Name=5; (Potential).				detection of abiotic stimulus	actin cytoskeleton|integral to plasma membrane	neuropeptide receptor activity			ovary(2)|central_nervous_system(1)	3														0.397959	120.504561	121.397442	39	59	GG		KEEP	---	---	---	---	capture	Lung(101;0.0935)|LUSC - Lung squamous cell carcinoma(112;0.138)		Missense_Mutation	SNP	73231836	73231836	10982	4	G	T	T	48	48	NPFFR2	T	3	3
TMSL3	7117	broad.mit.edu	36	4	91979160	91979160	+	Missense_Mutation	SNP	G	C	C			TCGA-12-3652-01	TCGA-12-3652-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr4:91979160G>C	uc003hsy.1	-	c.52C>G	c.(52-54)CTG>GTG	p.L18V	FAM190A_uc003hsv.2_Intron|FAM190A_uc010ikv.1_Intron|FAM190A_uc003hsx.2_Intron	NM_183049	NP_898870	A8MW06	TMSL3_HUMAN	thymosin-like 3	18					actin cytoskeleton organization|sequestering of actin monomers	cytoplasm|cytoskeleton	actin binding				0		all_cancers(2;6.48e-24)|all_epithelial(2;3.86e-25)|Colorectal(2;8.52e-12)|all_lung(2;3.73e-07)|Lung NSC(2;7.99e-07)|Renal(2;0.0243)|Hepatocellular(203;0.0411)												0.373913	278.490616	281.702068	86	144	GG		KEEP	---	---	---	---	capture		Epithelial(2;5.28e-11)|OV - Ovarian serous cystadenocarcinoma(123;8.9e-10)|all cancers(2;3.21e-09)|STAD - Stomach adenocarcinoma(1;0.0201)	Missense_Mutation	SNP	91979160	91979160	16800	4	G	C	C	36	36	TMSL3	C	3	3
PCDHA12	56137	broad.mit.edu	36	5	140236852	140236852	+	Silent	SNP	G	A	A			TCGA-12-3652-01	TCGA-12-3652-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr5:140236852G>A	uc003lic.1	+	c.1611G>A	c.(1609-1611)GCG>GCA	p.A537A	PCDHA1_uc003lha.1_Intron|PCDHA1_uc003lhb.1_Intron|PCDHA2_uc003lhd.1_Intron|PCDHA3_uc003lhf.1_Intron|PCDHA4_uc003lhh.1_Intron|PCDHA4_uc003lhi.1_Intron|PCDHA5_uc003lhk.1_Intron|PCDHA5_uc003lhl.1_Intron|PCDHA6_uc003lho.1_Intron|PCDHA6_uc003lhn.1_Intron|PCDHA7_uc003lhq.1_Intron|PCDHA8_uc003lhs.1_Intron|PCDHA9_uc003lhu.1_Intron|PCDHA10_uc003lhx.1_Intron|PCDHA10_uc003lhw.1_Intron|PCDHA11_uc003lia.1_Intron|PCDHA12_uc003lib.1_Silent_p.A537A	NM_018903	NP_061726	Q9UN75	PCDAC_HUMAN	protocadherin alpha 12 isoform 1 precursor	537	Cadherin 5.|Extracellular (Potential).				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding|protein binding				0						Pancreas(113;759 1672 13322 24104 50104)								0.377483	153.186899	155.155628	57	94	GG		KEEP	---	---	---	---	capture	KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)		Silent	SNP	140236852	140236852	11942	5	G	A	A	38	38	PCDHA12	A	1	1
CDH9	1007	broad.mit.edu	36	5	26938526	26938526	+	Nonsense_Mutation	SNP	G	A	A			TCGA-12-3652-01	TCGA-12-3652-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr5:26938526G>A	uc003jgs.1	-	c.1069C>T	c.(1069-1071)CGA>TGA	p.R357*		NM_016279	NP_057363	Q9ULB4	CADH9_HUMAN	cadherin 9, type 2 preproprotein	357	Cadherin 3.|Extracellular (Potential).				adherens junction organization|cell junction assembly|homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(5)	5						Melanoma(8;187 585 15745 40864 52829)								0.746479	168.216842	172.159052	53	18	GG		KEEP	---	---	---	---	capture			Nonsense_Mutation	SNP	26938526	26938526	3246	5	G	A	A	40	40	CDH9	A	5	1
MTX3	345778	broad.mit.edu	36	5	79320143	79320143	+	Missense_Mutation	SNP	C	G	G			TCGA-12-3652-01	TCGA-12-3652-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr5:79320143C>G	uc010jag.1	-	c.402G>C	c.(400-402)TTG>TTC	p.L134F	MTX3_uc010jah.1_Missense_Mutation_p.L134F|MTX3_uc003kge.2_Missense_Mutation_p.L73F|MTX3_uc003kgf.1_5'Flank	NM_001010891	NP_001010891	Q5HYI7	MTX3_HUMAN	metaxin 3	134					protein targeting to mitochondrion	mitochondrial outer membrane					0		Lung NSC(167;0.00428)|all_lung(232;0.00455)|Ovarian(174;0.0261)												0.444444	56.296325	56.393067	16	20	CC		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(54;1.63e-45)|Epithelial(54;2.9e-40)|all cancers(79;4.68e-35)	Missense_Mutation	SNP	79320143	79320143	10362	5	C	G	G	29	29	MTX3	G	3	3
GPR98	84059	broad.mit.edu	36	5	89979222	89979222	+	Silent	SNP	A	G	G			TCGA-12-3652-01	TCGA-12-3652-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr5:89979222A>G	uc003kju.1	+	c.3174A>G	c.(3172-3174)GGA>GGG	p.G1058G	GPR98_uc003kjt.1_5'UTR	NM_032119	NP_115495	Q8WXG9	GPR98_HUMAN	G protein-coupled receptor 98 precursor	1058	Calx-beta 8.|Extracellular (Potential).				cell communication|cell-cell adhesion|maintenance of organ identity|neuropeptide signaling pathway|photoreceptor cell maintenance	cell surface|cytoplasm|integral to membrane|plasma membrane	calcium ion binding|G-protein coupled receptor activity			ovary(11)|central_nervous_system(3)|pancreas(2)	16		all_cancers(142;1.05e-09)|all_epithelial(76;1.81e-12)|all_lung(232;5.41e-06)|Lung NSC(167;1.72e-05)|Ovarian(174;0.00948)|Colorectal(57;0.133)|Breast(839;0.192)												0.390533	225.308868	227.083694	66	103	AA		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(54;7.01e-30)|Epithelial(54;6.79e-25)|all cancers(79;1.88e-20)	Silent	SNP	89979222	89979222	6997	5	A	G	G	11	11	GPR98	G	4	4
SIM1	6492	broad.mit.edu	36	6	100945617	100945617	+	Nonsense_Mutation	SNP	G	A	A			TCGA-12-3652-01	TCGA-12-3652-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr6:100945617G>A	uc003pqj.2	-	c.1642C>T	c.(1642-1644)CGA>TGA	p.R548*	SIM1_uc010kct.1_Nonsense_Mutation_p.R548*|SIM1_uc010kcu.1_Nonsense_Mutation_p.R548*	NM_005068	NP_005059	P81133	SIM1_HUMAN	single-minded homolog 1	548	Single-minded C-terminal.				cell differentiation|nervous system development|regulation of transcription, DNA-dependent	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|signal transducer activity			ovary(4)	4		all_cancers(76;9.88e-06)|Acute lymphoblastic leukemia(125;4.99e-11)|all_hematologic(75;5.82e-08)|all_epithelial(107;0.0248)|Colorectal(196;0.13)												0.432624	188.950098	189.508696	61	80	GG		KEEP	---	---	---	---	capture		BRCA - Breast invasive adenocarcinoma(108;0.0774)	Nonsense_Mutation	SNP	100945617	100945617	14818	6	G	A	A	39	39	SIM1	A	5	1
SHPRH	257218	broad.mit.edu	36	6	146257046	146257046	+	Missense_Mutation	SNP	A	G	G			TCGA-12-3652-01	TCGA-12-3652-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr6:146257046A>G	uc003qld.1	-	c.4640T>C	c.(4639-4641)ATT>ACT	p.I1547T	SHPRH_uc010kht.1_Missense_Mutation_p.I1376T|SHPRH_uc003qle.1_Missense_Mutation_p.I1547T|SHPRH_uc003qlf.1_Missense_Mutation_p.I1543T	NM_001042683	NP_001036148	Q149N8	SHPRH_HUMAN	SNF2 histone linker PHD RING helicase isoform a	1543	Helicase C-terminal.				DNA repair|nucleosome assembly	nucleosome|nucleus	ATP binding|DNA binding|helicase activity|ligase activity|zinc ion binding			ovary(1)|kidney(1)	2		Ovarian(120;0.0365)												0.452055	112.869794	113.015577	33	40	AA		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(155;1.47e-07)|GBM - Glioblastoma multiforme(68;0.0124)	Missense_Mutation	SNP	146257046	146257046	14786	6	A	G	G	4	4	SHPRH	G	4	4
WNT2	7472	broad.mit.edu	36	7	116747916	116747916	+	Missense_Mutation	SNP	C	T	T			TCGA-12-3652-01	TCGA-12-3652-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr7:116747916C>T	uc003viz.1	-	c.251G>A	c.(250-252)CGC>CAC	p.R84H	WNT2_uc003vja.1_Silent_p.P9P	NM_003391	NP_003382	P09544	WNT2_HUMAN	wingless-type MMTV integration site family	84					atrial cardiac muscle tissue morphogenesis|canonical Wnt receptor signaling pathway|cardiac epithelial to mesenchymal transition|cellular response to retinoic acid|cellular response to transforming growth factor beta stimulus|dorsal/ventral axis specification|iris morphogenesis|labyrinthine layer blood vessel development|lens development in camera-type eye|lung induction|mammary gland epithelium development|negative regulation of gene-specific transcription from RNA polymerase II promoter|neuron differentiation|positive regulation of canonical Wnt receptor signaling pathway|positive regulation of cardiac muscle cell proliferation|positive regulation of epithelial cell proliferation involved in lung morphogenesis|positive regulation of fibroblast proliferation|positive regulation of mesenchymal cell proliferation|positive regulation of sequence-specific DNA binding transcription factor activity|positive regulation of transcription from RNA polymerase II promoter|Wnt receptor signaling pathway, calcium modulating pathway	cytoplasm|extracellular space|proteinaceous extracellular matrix	cytokine activity|frizzled binding|frizzled-2 binding|signal transducer activity			central_nervous_system(2)|ovary(1)|breast(1)	4	all_epithelial(6;2.24e-06)|Lung NSC(10;0.000936)|all_lung(10;0.00109)													0.516129	48.999293	49.00624	16	15	CC		KEEP	---	---	---	---	capture	STAD - Stomach adenocarcinoma(10;0.000512)	LUSC - Lung squamous cell carcinoma(290;0.133)	Missense_Mutation	SNP	116747916	116747916	17960	7	C	T	T	27	27	WNT2	T	1	1
MGAM	8972	broad.mit.edu	36	7	141380530	141380530	+	Splice_Site_SNP	SNP	G	T	T			TCGA-12-3652-01	TCGA-12-3652-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr7:141380530G>T	uc003vwy.1	+	c.1670_splice	c.e15-1	p.R557_splice		NM_004668	NP_004659			maltase-glucoamylase						polysaccharide digestion|starch catabolic process	apical plasma membrane|integral to membrane	carbohydrate binding|glucan 1,4-alpha-glucosidase activity|maltose alpha-glucosidase activity			ovary(2)	2	Melanoma(164;0.0272)				Acarbose(DB00284)|Miglitol(DB00491)|Voglibose(DB04878)									0.388889	20.420341	20.615235	7	11	GG		KEEP	---	---	---	---	capture			Splice_Site_SNP	SNP	141380530	141380530	9931	7	G	T	T	35	35	MGAM	T	5	3
NOD1	10392	broad.mit.edu	36	7	30458890	30458890	+	Missense_Mutation	SNP	C	T	T			TCGA-12-3652-01	TCGA-12-3652-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr7:30458890C>T	uc003tav.1	-	c.668G>A	c.(667-669)CGG>CAG	p.R223Q	NOD1_uc010kvs.1_Intron	NM_006092	NP_006083	Q9Y239	NOD1_HUMAN	nucleotide-binding oligomerization domain	223	NACHT.				activation of caspase activity|activation of MAPK activity|detection of bacterium|induction of apoptosis|inflammatory response|innate immune response|interleukin-8 biosynthetic process|JNK cascade|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|positive regulation of dendritic cell antigen processing and presentation|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of NF-kappaB transcription factor activity|protein oligomerization|stress-activated MAPK cascade|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway	basolateral plasma membrane|cytosol	ATP binding|CARD domain binding|caspase activator activity|peptidoglycan binding|protein homodimerization activity			ovary(1)	1														0.349057	105.856369	107.981367	37	69	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	30458890	30458890	10919	7	C	T	T	23	23	NOD1	T	1	1
EGFR	1956	broad.mit.edu	36	7	55189205	55189205	+	Missense_Mutation	SNP	G	C	C			TCGA-12-3652-01	TCGA-12-3652-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr7:55189205G>C	uc003tqk.1	+	c.755G>C	c.(754-756)CGC>CCC	p.R252P	EGFR_uc003tqh.1_Missense_Mutation_p.R252P|EGFR_uc003tqi.1_Missense_Mutation_p.R252P|EGFR_uc003tqj.1_Missense_Mutation_p.R252P|EGFR_uc010kzg.1_Missense_Mutation_p.R207P	NM_005228	NP_005219	P00533	EGFR_HUMAN	epidermal growth factor receptor isoform a	252	Approximate.|Extracellular (Potential).				activation of phospholipase A2 activity by calcium-mediated signaling|activation of phospholipase C activity|axon guidance|cell proliferation|cell-cell adhesion|negative regulation of apoptosis|negative regulation of epidermal growth factor receptor signaling pathway|ossification|positive regulation of catenin import into nucleus|positive regulation of cell migration|positive regulation of cyclin-dependent protein kinase activity involved in G1/S|positive regulation of epithelial cell proliferation|positive regulation of MAP kinase activity|positive regulation of nitric oxide biosynthetic process|positive regulation of phosphorylation|positive regulation of protein kinase B signaling cascade|protein autophosphorylation|protein insertion into membrane|regulation of nitric-oxide synthase activity|regulation of peptidyl-tyrosine phosphorylation|response to stress|response to UV-A	basolateral plasma membrane|endoplasmic reticulum membrane|endosome|extracellular space|Golgi membrane|integral to membrane|nuclear membrane|Shc-EGFR complex	actin filament binding|ATP binding|double-stranded DNA binding|epidermal growth factor receptor activity|identical protein binding|MAP/ERK kinase kinase activity|protein heterodimerization activity|protein phosphatase binding|receptor signaling protein tyrosine kinase activity	p.V30_R297>G(10)		lung(8200)|central_nervous_system(103)|upper_aerodigestive_tract(37)|prostate(32)|ovary(31)|thyroid(23)|breast(11)|peritoneum(9)|oesophagus(9)|salivary_gland(9)|large_intestine(8)|stomach(6)|urinary_tract(6)|skin(5)|adrenal_gland(5)|kidney(4)|soft_tissue(4)|bone(3)|NS(2)|haematopoietic_and_lymphoid_tissue(2)|thymus(2)|liver(2)|eye(1)|pancreas(1)	8515	all_cancers(1;1.57e-46)|all_epithelial(1;5.62e-37)|Lung NSC(1;9.29e-25)|all_lung(1;4.39e-23)|Esophageal squamous(2;7.55e-08)|Breast(14;0.0318)				Cetuximab(DB00002)|Erlotinib(DB00530)|Gefitinib(DB00317)|Lapatinib(DB01259)|Lidocaine(DB00281)|Panitumumab(DB01269)|Trastuzumab(DB00072)			8		608	TCGA GBM(3;<1E-8)|TSP Lung(4;<1E-8)			0.100752	73.248911	179.045562	67	598	GG		KEEP	---	---	---	---	capture	GBM - Glioblastoma multiforme(1;0)|all cancers(1;2.19e-314)|Lung(13;4.65e-05)|LUSC - Lung squamous cell carcinoma(13;0.000168)|STAD - Stomach adenocarcinoma(5;0.00164)|Epithelial(13;0.0607)		Missense_Mutation	SNP	55189205	55189205	5156	7	G	C	C	38	38	EGFR	C	3	3
FAM135B	51059	broad.mit.edu	36	8	139233745	139233745	+	Nonsense_Mutation	SNP	G	A	A			TCGA-12-3652-01	TCGA-12-3652-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr8:139233745G>A	uc003yuy.1	-	c.2155C>T	c.(2155-2157)CGA>TGA	p.R719*	FAM135B_uc003yux.1_Nonsense_Mutation_p.R620*|FAM135B_uc003yuz.1_Non-coding_Transcript|FAM135B_uc003yva.2_Nonsense_Mutation_p.R281*|FAM135B_uc003yvb.2_Nonsense_Mutation_p.R281*	NM_015912	NP_056996	Q49AJ0	F135B_HUMAN	hypothetical protein LOC51059	719										ovary(7)	7	all_epithelial(106;8.29e-14)|Lung NSC(106;6.88e-06)|all_lung(105;1.44e-05)|Ovarian(258;0.00672)|Acute lymphoblastic leukemia(118;0.155)													0.112676	8.648831	19.164644	8	63	GG		KEEP	---	---	---	---	capture	BRCA - Breast invasive adenocarcinoma(115;0.0805)		Nonsense_Mutation	SNP	139233745	139233745	5646	8	G	A	A	37	37	FAM135B	A	5	1
NRBP2	340371	broad.mit.edu	36	8	144990027	144990027	+	Missense_Mutation	SNP	C	T	T			TCGA-12-3652-01	TCGA-12-3652-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr8:144990027C>T	uc003yzw.1	-	c.764G>A	c.(763-765)AGC>AAC	p.S255N	NRBP2_uc003yzv.2_Missense_Mutation_p.S220N|NRBP2_uc010mfl.1_Silent_p.Q285Q|NRBP2_uc010mfm.1_Intron|NRBP2_uc003yzx.1_Non-coding_Transcript|NRBP2_uc003yzy.1_Missense_Mutation_p.S220N|NRBP2_uc003yzz.1_Silent_p.Q143Q	NM_178564	NP_848659	Q9NSY0	NRBP2_HUMAN	nuclear receptor binding protein 2	463					negative regulation of neuron apoptosis|neuron differentiation|protein phosphorylation	cytoplasm	ATP binding|protein kinase activity			central_nervous_system(2)	2	all_cancers(97;2.31e-11)|all_epithelial(106;1.58e-09)|Lung NSC(106;0.00013)|all_lung(105;0.000374)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)									69				0.3	8.622161	8.978919	3	7	CC		KEEP	---	---	---	---	capture	OV - Ovarian serous cystadenocarcinoma(54;2.46e-41)|Epithelial(56;1.23e-39)|all cancers(56;6.82e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.18)		Missense_Mutation	SNP	144990027	144990027	11048	8	C	T	T	28	28	NRBP2	T	2	2
EHMT1	79813	broad.mit.edu	36	9	139849213	139849213	+	Missense_Mutation	SNP	C	T	T			TCGA-12-3652-01	TCGA-12-3652-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr9:139849213C>T	uc004coc.1	+	c.3791C>T	c.(3790-3792)GCC>GTC	p.A1264V	EHMT1_uc004coe.1_Missense_Mutation_p.A200V	NM_024757	NP_079033	Q9H9B1	EHMT1_HUMAN	euchromatic histone-lysine N-methyltransferase	1295	Poly-Ala.				DNA methylation|embryo development|peptidyl-lysine dimethylation|peptidyl-lysine monomethylation	chromosome|nucleus	histone methyltransferase activity (H3-K27 specific)|histone methyltransferase activity (H3-K9 specific)|p53 binding|zinc ion binding			breast(2)|pancreas(1)	3	all_cancers(76;0.164)													0.444444	10.460051	10.472522	4	5	CC		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(145;0.000183)|Epithelial(140;0.000728)	Missense_Mutation	SNP	139849213	139849213	5172	9	C	T	T	26	26	EHMT1	T	2	2
BNC2	54796	broad.mit.edu	36	9	16409622	16409622	+	Missense_Mutation	SNP	G	A	A			TCGA-12-3652-01	TCGA-12-3652-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr9:16409622G>A	uc003zml.1	-	c.2665C>T	c.(2665-2667)CGT>TGT	p.R889C	BNC2_uc003zmm.2_3'UTR|BNC2_uc010mii.1_3'UTR|BNC2_uc003zmi.1_Missense_Mutation_p.R676C|BNC2_uc003zmj.1_3'UTR|BNC2_uc003zmk.1_Non-coding_Transcript	NM_017637	NP_060107	Q6ZN30	BNC2_HUMAN	basonuclin 2	889					regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus|plasma membrane	zinc ion binding			ovary(2)|central_nervous_system(1)	3														0.178947	32.307965	41.536222	17	78	GG		KEEP	---	---	---	---	capture		GBM - Glioblastoma multiforme(50;9.01e-08)	Missense_Mutation	SNP	16409622	16409622	1500	9	G	A	A	37	37	BNC2	A	1	1
LINGO2	158038	broad.mit.edu	36	9	27940347	27940347	+	Missense_Mutation	SNP	C	T	T			TCGA-12-3652-01	TCGA-12-3652-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr9:27940347C>T	uc003zqu.1	-	c.323G>A	c.(322-324)CGT>CAT	p.R108H	LINGO2_uc010mjf.1_Missense_Mutation_p.R108H|LINGO2_uc003zqv.1_Missense_Mutation_p.R108H|LINGO2_uc010mjg.1_Missense_Mutation_p.R108H	NM_152570	NP_689783	Q7L985	LIGO2_HUMAN	leucine rich repeat and Ig domain containing 2	108	LRR 3.|Extracellular (Potential).					integral to membrane				ovary(1)|central_nervous_system(1)	2	Melanoma(11;0.242)	all_neural(11;2.78e-09)												0.783951	408.715217	420.809703	127	35	CC		KEEP	---	---	---	---	capture		UCEC - Uterine corpus endometrioid carcinoma (5;0.0818)|GBM - Glioblastoma multiforme(2;1.31e-34)|all cancers(2;2.37e-25)|Lung(2;7.48e-08)|LUSC - Lung squamous cell carcinoma(38;5.09e-07)|KIRC - Kidney renal clear cell carcinoma(2;0.0465)|Kidney(2;0.0604)	Missense_Mutation	SNP	27940347	27940347	9142	9	C	T	T	19	19	LINGO2	T	1	1
WNK2	65268	broad.mit.edu	36	9	95091237	95091237	+	Silent	SNP	A	G	G			TCGA-12-3652-01	TCGA-12-3652-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr9:95091237A>G	uc004ati.1	+	c.4491A>G	c.(4489-4491)CCA>CCG	p.P1497P	WNK2_uc004atj.1_Silent_p.P1460P|WNK2_uc004atk.2_Silent_p.P1097P|WNK2_uc004atl.1_Silent_p.P55P	NM_006648	NP_006639	Q9Y3S1	WNK2_HUMAN	WNK lysine deficient protein kinase 2	1497					intracellular protein kinase cascade|protein phosphorylation		ATP binding|protein binding|protein serine/threonine kinase activity			ovary(2)|lung(2)|stomach(1)|large_intestine(1)|central_nervous_system(1)	7										1420				0.705882	40.405907	41.050544	12	5	AA		KEEP	---	---	---	---	capture			Silent	SNP	95091237	95091237	17952	9	A	G	G	7	7	WNK2	G	4	4
ENOX2	10495	broad.mit.edu	36	X	129627386	129627386	+	Missense_Mutation	SNP	A	C	C			TCGA-12-3652-01	TCGA-12-3652-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chrX:129627386A>C	uc004evw.1	-	c.1013T>G	c.(1012-1014)GTG>GGG	p.V338G	ENOX2_uc004evv.1_Missense_Mutation_p.V165G|ENOX2_uc004evx.1_Missense_Mutation_p.V309G|ENOX2_uc004evy.1_Missense_Mutation_p.V309G	NM_182314	NP_006366	Q16206	ENOX2_HUMAN	ecto-NOX disulfide-thiol exchanger 2 isoform b	338					cell growth|electron transport chain|regulation of growth|transport|ultradian rhythm	cytosol|external side of plasma membrane|extracellular space	nucleic acid binding|nucleotide binding|protein disulfide oxidoreductase activity			ovary(1)	1						Ovarian(101;828 1506 2951 9500 35258)								0.428571	7.988671	8.0793	6	8	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	129627386	129627386	5320	23	A	C	C	6	6	ENOX2	C	4	4
MAGEB4	4115	broad.mit.edu	36	X	30170423	30170423	+	Missense_Mutation	SNP	G	A	A			TCGA-12-3652-01	TCGA-12-3652-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chrX:30170423G>A	uc004dcb.1	+	c.250G>A	c.(250-252)GAC>AAC	p.D84N	MAGEB1_uc004dcc.1_5'Flank|MAGEB1_uc004dcd.1_5'Flank	NM_002367	NP_002358	O15481	MAGB4_HUMAN	melanoma antigen family B, 4	84										ovary(1)	1														0.1875	6.315458	7.778662	3	13	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	30170423	30170423	9559	23	G	A	A	37	37	MAGEB4	A	1	1
KDM5D	8284	broad.mit.edu	36	Y	20356640	20356640	+	Missense_Mutation	SNP	T	A	A			TCGA-12-3652-01	TCGA-12-3652-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chrY:20356640T>A	uc004fug.1	-	c.919A>T	c.(919-921)AGC>TGC	p.S307C	KDM5D_uc010nwy.1_Missense_Mutation_p.S250C|KDM5D_uc004fuh.1_Missense_Mutation_p.S262C	NM_004653	NP_004644	Q9BY66	KDM5D_HUMAN	jumonji, AT rich interactive domain 1D	307					chromatin modification|oxidation-reduction process|spermatogenesis	nucleus	DNA binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|protein binding|zinc ion binding			skin(1)	1					Vitamin C(DB00126)									0.893333	233.679302	245.196157	67	8	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	20356640	20356640	8442	24	T	A	A	55	55	KDM5D	A	4	4
SFRP1	6422	broad.mit.edu	36	8	41285795	41285797	+	In_Frame_Del	DEL	GCT	-	-			TCGA-12-3652-01	TCGA-12-3652-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:41285795_41285797delGCT	uc003xnt.1	-	c.39_41delAGC	c.(37-42)GCAGCC>GCC	p.13_14AA>A		NM_003012	NP_003003	Q8N474	SFRP1_HUMAN	secreted frizzled-related protein 1	13_14				Missing (in Ref. 1 and 3).	brain development|canonical Wnt receptor signaling pathway|cellular response to BMP stimulus|cellular response to estradiol stimulus|cellular response to fibroblast growth factor stimulus|cellular response to heparin|cellular response to hypoxia|cellular response to interleukin-1|cellular response to prostaglandin E stimulus|cellular response to starvation|cellular response to transforming growth factor beta stimulus|cellular response to tumor necrosis factor|cellular response to vitamin D|DNA fragmentation involved in apoptotic nuclear change|dorsal/ventral axis specification|hemopoietic progenitor cell differentiation|hemopoietic stem cell differentiation|menstrual cycle phase|negative regulation of androgen receptor signaling pathway|negative regulation of B cell differentiation|negative regulation of bone remodeling|negative regulation of canonical Wnt receptor signaling pathway involved in controlling type B pancreatic cell proliferation|negative regulation of cell growth|negative regulation of cell migration|negative regulation of cysteine-type endopeptidase activity|negative regulation of epithelial cell proliferation|negative regulation of epithelial to mesenchymal transition|negative regulation of fibroblast apoptosis|negative regulation of fibroblast proliferation|negative regulation of gene-specific transcription|negative regulation of insulin secretion|negative regulation of ossification|negative regulation of osteoblast proliferation|negative regulation of peptidyl-tyrosine phosphorylation|negative regulation of Wnt receptor signaling pathway involved in dorsal/ventral axis specification|osteoblast differentiation|positive regulation of canonical Wnt receptor signaling pathway|positive regulation of cell growth|positive regulation of epithelial cell proliferation|positive regulation of fat cell differentiation|positive regulation of fibroblast apoptosis|positive regulation of focal adhesion assembly|positive regulation of gene-specific transcription|positive regulation of non-canonical Wnt receptor signaling pathway|positive regulation of Rac GTPase activity|positive regulation of smoothened signaling pathway|positive regulation of stress fiber assembly|regulation of angiogenesis|regulation of cell cycle process|regulation of gene-specific transcription from RNA polymerase II promoter|response to drug|response to organic cyclic compound|vasculature development	cell surface|cytosol|extracellular space|plasma membrane|proteinaceous extracellular matrix	cysteine-type endopeptidase activity|drug binding|frizzled binding|heparin binding|identical protein binding|PDZ domain binding|specific transcriptional repressor activity|transcription activator activity|Wnt receptor activity|Wnt-protein binding			central_nervous_system(1)	1	Breast(1;9.19e-13)|Ovarian(28;0.00769)|Colorectal(14;0.0305)|Lung SC(25;0.211)	all_lung(54;0.0034)|Lung NSC(58;0.0134)|Hepatocellular(245;0.023)|Esophageal squamous(32;0.0559)	BRCA - Breast invasive adenocarcinoma(1;1.11e-10)|LUSC - Lung squamous cell carcinoma(45;0.00894)|COAD - Colon adenocarcinoma(11;0.0174)											0.40			4	6				---	---	---	---	capture_indel			In_Frame_Del	DEL	41285795	41285797	14650	8	GCT	-	-	42	42	SFRP1	-	5	5
