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
HKDC1	80201	broad.mit.edu	36	10	70695358	70695358	+	Missense_Mutation	SNP	C	G	G			TCGA-06-2563-01	TCGA-06-2563-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr10:70695358C>G	uc001jpf.2	+	c.2384C>G	c.(2383-2385)GCC>GGC	p.A795G	HKDC1_uc009xqb.1_Non-coding_Transcript	NM_025130	NP_079406	Q2TB90	HKDC1_HUMAN	hexokinase domain containing 1	795					glycolysis	mitochondrion|nucleus	ATP binding|hexokinase activity			ovary(4)	4														0.258065	7.780203	9.54216	8	23	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	70695358	70695358	7484	10	C	G	G	26	26	HKDC1	G	3	3
IDE	3416	broad.mit.edu	36	10	94257938	94257938	+	Missense_Mutation	SNP	C	G	G			TCGA-06-2563-01	TCGA-06-2563-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr10:94257938C>G	uc001kia.2	-	c.1065G>C	c.(1063-1065)TGG>TGC	p.W355C		NM_004969	NP_004960	P14735	IDE_HUMAN	insulysin	355					beta-amyloid metabolic process|bradykinin catabolic process|interspecies interaction between organisms|sex differentiation	cell surface|extracellular space|soluble fraction	ATP binding|metalloendopeptidase activity|protein homodimerization activity|signal transducer activity|zinc ion binding			ovary(2)|central_nervous_system(1)	3					Bacitracin(DB00626)|Insulin Glargine recombinant(DB00047)|Insulin Lyspro recombinant(DB00046)|Insulin recombinant(DB00030)|Insulin, porcine(DB00071)									0.413284	342.565865	344.363878	112	159	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	94257938	94257938	7793	10	C	G	G	22	22	IDE	G	3	3
MUC2	4583	broad.mit.edu	36	11	1074268	1074268	+	Missense_Mutation	SNP	T	G	G			TCGA-06-2563-01	TCGA-06-2563-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr11:1074268T>G	uc001lsx.1	+	c.2400T>G	c.(2398-2400)TGT>TGG	p.C800W		NM_002457	NP_002448	Q02817	MUC2_HUMAN	mucin 2 precursor	800						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)									0.5625	12.254338	12.269832	9	7	TT		KEEP	---	---	---	---	capture		BRCA - Breast invasive adenocarcinoma(625;0.000207)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)	Missense_Mutation	SNP	1074268	1074268	10369	11	T	G	G	59	59	MUC2	G	4	4
SIRT3	23410	broad.mit.edu	36	11	223173	223173	+	Missense_Mutation	SNP	A	C	C			TCGA-06-2563-01	TCGA-06-2563-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr11:223173A>C	uc001lok.2	-	c.516T>G	c.(514-516)GAT>GAG	p.D172E	SIRT3_uc001loj.2_Missense_Mutation_p.D30E|SIRT3_uc009ybt.1_Non-coding_Transcript	NM_012239	NP_001017524	Q9NTG7	SIRT3_HUMAN	sirtuin 3 isoform a	172	Deacetylase sirtuin-type.				chromatin silencing|protein ADP-ribosylation|protein deacetylation	mitochondrial matrix	hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides|NAD+ ADP-ribosyltransferase activity|NAD+ binding|protein binding|zinc ion binding			urinary_tract(1)	1		all_cancers(49;1.58e-09)|all_epithelial(84;2.71e-06)|Breast(177;0.000162)|Ovarian(85;0.000626)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.0538)|all_lung(207;0.0713)												0.396552	71.804194	72.349474	23	35	AA		KEEP	---	---	---	---	capture		all cancers(45;3.66e-27)|Epithelial(43;2.02e-26)|OV - Ovarian serous cystadenocarcinoma(40;2.9e-21)|BRCA - Breast invasive adenocarcinoma(625;3.88e-05)|Lung(200;0.111)|LUSC - Lung squamous cell carcinoma(625;0.129)	Missense_Mutation	SNP	223173	223173	14834	11	A	C	C	12	12	SIRT3	C	4	4
OR51M1	390059	broad.mit.edu	36	11	5367752	5367752	+	Missense_Mutation	SNP	C	G	G			TCGA-06-2563-01	TCGA-06-2563-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr11:5367752C>G	uc001mat.1	+	c.548C>G	c.(547-549)TCT>TGT	p.S183C	HBG2_uc001mak.1_Intron|HBE1_uc001mam.1_Intron|OR51B5_uc001maq.1_Intron	NM_001004756	NP_001004756	B2RNI9	B2RNI9_HUMAN	olfactory receptor, family 51, subfamily M,	183						integral to membrane	olfactory receptor activity				0		Medulloblastoma(188;0.0075)|all_neural(188;0.0572)|Breast(177;0.0675)												0.418519	374.317412	375.88378	113	157	CC		KEEP	---	---	---	---	capture		Epithelial(150;1.98e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)	Missense_Mutation	SNP	5367752	5367752	11513	11	C	G	G	32	32	OR51M1	G	3	3
VWCE	220001	broad.mit.edu	36	11	60804955	60804955	+	Silent	SNP	C	T	T			TCGA-06-2563-01	TCGA-06-2563-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr11:60804955C>T	uc001nra.1	-	c.1116G>A	c.(1114-1116)AGG>AGA	p.R372R	VWCE_uc001nrb.1_Non-coding_Transcript	NM_152718	NP_689931	Q96DN2	VWCE_HUMAN	von Willebrand factor C and EGF domains	372						extracellular region	calcium ion binding			ovary(1)	1														0.421053	25.697157	25.800438	8	11	CC		KEEP	---	---	---	---	capture			Silent	SNP	60804955	60804955	17816	11	C	T	T	22	22	VWCE	T	2	2
CLEC1A	51267	broad.mit.edu	36	12	10115281	10115281	+	Missense_Mutation	SNP	C	T	T			TCGA-06-2563-01	TCGA-06-2563-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr12:10115281C>T	uc001qxb.1	-	c.761G>A	c.(760-762)CGT>CAT	p.R254H	CLEC1A_uc009zhf.1_Missense_Mutation_p.R166H|CLEC1A_uc001qxc.1_Missense_Mutation_p.R166H|CLEC1A_uc001qxd.1_Missense_Mutation_p.R211H	NM_016511	NP_057595	Q8NC01	CLC1A_HUMAN	C-type lectin-like receptor-1	254	C-type lectin.|Extracellular (Potential).				cell surface receptor linked signaling pathway|defense response	integral to plasma membrane|intracellular	sugar binding|transmembrane receptor activity			ovary(1)|central_nervous_system(1)	2														0.357143	308.067291	313.601922	110	198	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	10115281	10115281	3642	12	C	T	T	19	19	CLEC1A	T	1	1
WSCD2	9671	broad.mit.edu	36	12	107124309	107124309	+	Missense_Mutation	SNP	C	T	T			TCGA-06-2563-01	TCGA-06-2563-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr12:107124309C>T	uc001tms.1	+	c.496C>T	c.(496-498)CGG>TGG	p.R166W	WSCD2_uc001tmt.1_Missense_Mutation_p.R166W	NM_014653	NP_055468	Q2TBF2	WSCD2_HUMAN	WSC domain containing 2	166	WSC 1.					integral to membrane				ovary(1)|large_intestine(1)|breast(1)	3														0.337079	85.524429	87.613043	30	59	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	107124309	107124309	17981	12	C	T	T	19	19	WSCD2	T	1	1
RNF34	80196	broad.mit.edu	36	12	120345608	120345608	+	Missense_Mutation	SNP	A	C	C			TCGA-06-2563-01	TCGA-06-2563-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr12:120345608A>C	uc001uam.1	+	c.965A>C	c.(964-966)GAC>GCC	p.D322A	RNF34_uc001uak.1_Missense_Mutation_p.D323A|RNF34_uc001ual.1_Missense_Mutation_p.D322A	NM_025126	NP_079402	Q969K3	RNF34_HUMAN	ring finger protein 34 isoform 2	322					apoptosis	endomembrane system|membrane|nuclear speck	ligase activity|zinc ion binding				0	all_neural(191;0.0684)|Medulloblastoma(191;0.0922)													0.210526	6.894312	8.365044	4	15	AA		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(86;0.000432)|Epithelial(86;0.00233)	Missense_Mutation	SNP	120345608	120345608	13968	12	A	C	C	10	10	RNF34	C	4	4
TMEM132D	121256	broad.mit.edu	36	12	128750422	128750422	+	Missense_Mutation	SNP	C	T	T			TCGA-06-2563-01	TCGA-06-2563-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr12:128750422C>T	uc009zyl.1	-	c.854G>A	c.(853-855)CGT>CAT	p.R285H		NM_133448	NP_597705	Q14C87	T132D_HUMAN	transmembrane protein 132D	285	Extracellular (Potential).					integral to membrane				ovary(10)|pancreas(2)	12	all_neural(191;0.101)|Medulloblastoma(191;0.163)	all_epithelial(31;0.0934)|Breast(359;0.133)												0.426667	90.584114	90.936302	32	43	CC		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(86;0.000288)|Epithelial(86;0.0116)|all cancers(50;0.0246)	Missense_Mutation	SNP	128750422	128750422	16579	12	C	T	T	19	19	TMEM132D	T	1	1
KRT18	3875	broad.mit.edu	36	12	51629488	51629488	+	Silent	SNP	C	T	T			TCGA-06-2563-01	TCGA-06-2563-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr12:51629488C>T	uc001sbe.1	+	c.264C>T	c.(262-264)AAC>AAT	p.N88N	KRT8_uc009zml.1_Intron|KRT8_uc009zmm.1_Intron|KRT18_uc009zmn.1_Silent_p.N88N|KRT18_uc001sbf.1_De_novo_Start_OutOfFrame|KRT18_uc001sbg.1_Silent_p.N88N|KRT18_uc009zmo.1_Silent_p.N88N	NM_199187	NP_954657	P05783	K1C18_HUMAN	keratin 18	88	Coil 1A.|Rod.|Interaction with TRADD.|Necessary for interaction with PNN.				anatomical structure morphogenesis|cell cycle|Golgi to plasma membrane CFTR protein transport|interspecies interaction between organisms|negative regulation of apoptosis	centriolar satellite|keratin filament|perinuclear region of cytoplasm	protein binding|structural molecule activity				0														0.358491	52.809701	53.744518	19	34	CC		KEEP	---	---	---	---	capture			Silent	SNP	51629488	51629488	8770	12	C	T	T	19	19	KRT18	T	1	1
SCNN1A	6337	broad.mit.edu	36	12	6334186	6334186	+	Nonsense_Mutation	SNP	G	T	T			TCGA-06-2563-01	TCGA-06-2563-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr12:6334186G>T	uc001qnw.1	-	c.1410C>A	c.(1408-1410)TAC>TAA	p.Y470*	SCNN1A_uc001qnv.1_Nonsense_Mutation_p.Y111*|SCNN1A_uc001qnx.1_Nonsense_Mutation_p.Y411*	NM_001038	NP_001029	P37088	SCNNA_HUMAN	sodium channel, nonvoltage-gated 1 alpha	411	Extracellular (By similarity).				excretion|response to stimulus|sensory perception of taste	apical plasma membrane	WW domain binding				0					Amiloride(DB00594)|Triamterene(DB00384)									0.408602	112.129228	112.808774	38	55	GG		KEEP	---	---	---	---	capture			Nonsense_Mutation	SNP	6334186	6334186	14409	12	G	T	T	48	48	SCNN1A	T	5	3
PTPRR	5801	broad.mit.edu	36	12	69381252	69381252	+	Silent	SNP	G	T	T			TCGA-06-2563-01	TCGA-06-2563-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr12:69381252G>T	uc001swi.1	-	c.1126C>A	c.(1126-1128)CGA>AGA	p.R376R	PTPRR_uc001swh.1_Silent_p.R131R|PTPRR_uc009zrs.1_Silent_p.R170R	NM_002849	NP_002840	Q15256	PTPRR_HUMAN	protein tyrosine phosphatase, receptor type, R	376	Cytoplasmic (Potential).				in utero embryonic development	cell surface|Golgi apparatus|integral to membrane|nucleus|perinuclear region of cytoplasm|plasma membrane	protein kinase binding|transmembrane receptor protein tyrosine phosphatase activity			ovary(1)|skin(1)	2														0.362205	141.718266	143.839195	46	81	GG		KEEP	---	---	---	---	capture	GBM - Glioblastoma multiforme(2;5.67e-07)|Lung(24;0.00283)|OV - Ovarian serous cystadenocarcinoma(12;0.00578)|LUSC - Lung squamous cell carcinoma(43;0.132)	COAD - Colon adenocarcinoma(1;0.136)	Silent	SNP	69381252	69381252	13268	12	G	T	T	39	39	PTPRR	T	3	3
PPFIA2	8499	broad.mit.edu	36	12	80195325	80195325	+	Splice_Site_SNP	SNP	C	T	T			TCGA-06-2563-01	TCGA-06-2563-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr12:80195325C>T	uc001szo.1	-	c.3213_splice	c.e28-1	p.R1071_splice	PPFIA2_uc009zsh.1_Splice_Site_SNP|PPFIA2_uc009zsi.1_Splice_Site_SNP	NM_003625	NP_003616			PTPRF interacting protein alpha 2						cell-matrix adhesion	cell surface|cytoplasm	protein binding			ovary(3)|lung(2)|pancreas(1)	6														0.444444	7.831388	7.864312	4	5	CC		KEEP	---	---	---	---	capture			Splice_Site_SNP	SNP	80195325	80195325	12740	12	C	T	T	32	32	PPFIA2	T	5	2
FAM70B	348013	broad.mit.edu	36	13	113611620	113611620	+	Silent	SNP	G	C	C			TCGA-06-2563-01	TCGA-06-2563-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr13:113611620G>C	uc001vuh.1	-	c.354C>G	c.(352-354)CCC>CCG	p.P118P		NM_182614	NP_872420	Q8WV15	FA70B_HUMAN	family with sequence similarity 70, member B	118						integral to membrane					0	Lung NSC(43;0.00976)|all_neural(89;0.0337)|Hepatocellular(20;0.0877)|Medulloblastoma(90;0.163)|Lung SC(71;0.218)	all_lung(25;0.123)|all_epithelial(44;0.133)												0.555556	91.720051	91.862369	30	24	GG		KEEP	---	---	---	---	capture	all cancers(43;0.181)		Silent	SNP	113611620	113611620	5829	13	G	C	C	43	43	FAM70B	C	3	3
OR11H6	122748	broad.mit.edu	36	14	19762258	19762258	+	Missense_Mutation	SNP	C	A	A			TCGA-06-2563-01	TCGA-06-2563-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr14:19762258C>A	uc001vwr.1	+	c.550C>A	c.(550-552)CTT>ATT	p.L184I		NM_001004480	NP_001004480	Q8NGC7	O11H6_HUMAN	olfactory receptor, family 11, subfamily H,	184	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(2)	2	all_cancers(95;0.00108)													0.558442	136.631556	136.8605	43	34	CC		KEEP	---	---	---	---	capture	Epithelial(56;1.75e-06)|all cancers(55;1.22e-05)	GBM - Glioblastoma multiforme(265;0.0143)	Missense_Mutation	SNP	19762258	19762258	11335	14	C	A	A	20	20	OR11H6	A	3	3
CHRNA7	1139	broad.mit.edu	36	15	30247570	30247570	+	Silent	SNP	G	A	A			TCGA-06-2563-01	TCGA-06-2563-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr15:30247570G>A	uc001zft.1	+	c.1128G>A	c.(1126-1128)CCG>CCA	p.P376P	CHRNA7_uc010baf.1_Silent_p.P195P|CHRNA7_uc010bak.1_Silent_p.P291P	NM_000746	NP_683709	P36544	ACHA7_HUMAN	cholinergic receptor, nicotinic, alpha 7	376	Cytoplasmic (Potential).				activation of MAPK activity|calcium ion transport|cellular calcium ion homeostasis|memory|negative regulation of tumor necrosis factor production|positive regulation of angiogenesis|positive regulation of cell proliferation|response to hypoxia|response to nicotine	cell junction|nicotinic acetylcholine-gated receptor-channel complex|postsynaptic membrane	acetylcholine receptor activity|beta-amyloid binding|chloride channel regulator activity|nicotinic acetylcholine-activated cation-selective channel activity|protein homodimerization activity|toxin binding			ovary(1)	1		all_lung(180;6.35e-11)			Nicotine(DB00184)|Varenicline(DB01273)	Esophageal Squamous(193;529 2900 40232 43193)								0.166667	12.873832	17.929603	8	40	GG		KEEP	---	---	---	---	capture		all cancers(64;3.34e-21)|Epithelial(43;2.64e-15)|GBM - Glioblastoma multiforme(186;5.17e-06)|BRCA - Breast invasive adenocarcinoma(123;0.00112)|Lung(196;0.227)	Silent	SNP	30247570	30247570	3522	15	G	A	A	38	38	CHRNA7	A	1	1
MAPKBP1	23005	broad.mit.edu	36	15	39894061	39894061	+	Silent	SNP	G	A	A			TCGA-06-2563-01	TCGA-06-2563-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr15:39894061G>A	uc001zok.2	+	c.1020G>A	c.(1018-1020)GCG>GCA	p.A340A	MAPKBP1_uc001zoj.2_Silent_p.A334A|MAPKBP1_uc010bci.1_Silent_p.A334A|MAPKBP1_uc010bcj.1_Intron|MAPKBP1_uc010bck.1_5'UTR|MAPKBP1_uc010bcl.1_Intron	NM_001128608	NP_001122080	O60336	MABP1_HUMAN	mitogen-activated protein kinase binding protein	340										central_nervous_system(4)|breast(2)|pancreas(1)	7		all_cancers(109;7.71e-14)|all_epithelial(112;5.15e-12)|Lung NSC(122;3.74e-08)|all_lung(180;1.81e-07)|Melanoma(134;0.0262)								360				0.407767	382.015159	384.304748	126	183	GG		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(18;3.95e-17)|GBM - Glioblastoma multiforme(94;5.71e-07)|Lung(196;0.0436)|BRCA - Breast invasive adenocarcinoma(123;0.203)|LUSC - Lung squamous cell carcinoma(244;0.225)	Silent	SNP	39894061	39894061	9675	15	G	A	A	37	37	MAPKBP1	A	1	1
MAPKBP1	23005	broad.mit.edu	36	15	39898366	39898366	+	Missense_Mutation	SNP	G	A	A			TCGA-06-2563-01	TCGA-06-2563-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr15:39898366G>A	uc001zok.2	+	c.2228G>A	c.(2227-2229)CGT>CAT	p.R743H	MAPKBP1_uc001zoj.2_Missense_Mutation_p.R737H|MAPKBP1_uc010bci.1_Missense_Mutation_p.R737H|MAPKBP1_uc010bcj.1_Missense_Mutation_p.R244H|MAPKBP1_uc010bck.1_5'UTR|MAPKBP1_uc010bcl.1_Missense_Mutation_p.R244H	NM_001128608	NP_001122080	O60336	MABP1_HUMAN	mitogen-activated protein kinase binding protein	743										central_nervous_system(4)|breast(2)|pancreas(1)	7		all_cancers(109;7.71e-14)|all_epithelial(112;5.15e-12)|Lung NSC(122;3.74e-08)|all_lung(180;1.81e-07)|Melanoma(134;0.0262)								360				0.377358	55.18801	55.886981	20	33	GG		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(18;3.95e-17)|GBM - Glioblastoma multiforme(94;5.71e-07)|Lung(196;0.0436)|BRCA - Breast invasive adenocarcinoma(123;0.203)|LUSC - Lung squamous cell carcinoma(244;0.225)	Missense_Mutation	SNP	39898366	39898366	9675	15	G	A	A	40	40	MAPKBP1	A	1	1
ATP8B4	79895	broad.mit.edu	36	15	48126951	48126951	+	Missense_Mutation	SNP	A	T	T			TCGA-06-2563-01	TCGA-06-2563-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr15:48126951A>T	uc001zxu.1	-	c.90T>A	c.(88-90)GAT>GAA	p.D30E	ATP8B4_uc010ber.1_5'UTR	NM_024837	NP_079113	Q8TF62	AT8B4_HUMAN	ATPase class I type 8B member 4	30	Cytoplasmic (Potential).				ATP biosynthetic process	integral to membrane	ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|magnesium ion binding|phospholipid-translocating ATPase activity	p.D30D(1)		ovary(2)|breast(2)|large_intestine(1)	5		all_lung(180;0.00183)												0.368421	105.097235	106.543921	35	60	AA		KEEP	---	---	---	---	capture		all cancers(107;2.41e-07)|GBM - Glioblastoma multiforme(94;8.28e-05)	Missense_Mutation	SNP	48126951	48126951	1216	15	A	T	T	16	16	ATP8B4	T	4	4
PTX4	390667	broad.mit.edu	36	16	1476135	1476135	+	Missense_Mutation	SNP	C	T	T			TCGA-06-2563-01	TCGA-06-2563-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr16:1476135C>T	uc002clx.1	-	c.1228G>A	c.(1228-1230)GAC>AAC	p.D410N		NM_001013658	NP_001013680	Q96A99	PTX4_HUMAN	hypothetical protein LOC390667	415	Pentaxin.					extracellular region	metal ion binding				0														0.377358	58.988511	59.687528	20	33	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	1476135	1476135	13281	16	C	T	T	31	31	PTX4	T	1	1
DNAH3	55567	broad.mit.edu	36	16	20940874	20940874	+	Missense_Mutation	SNP	C	T	T			TCGA-06-2563-01	TCGA-06-2563-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr16:20940874C>T	uc002did.1	-	c.5696G>A	c.(5695-5697)CGC>CAC	p.R1899H		NM_017539	NP_060009	Q8TD57	DYH3_HUMAN	dynein, axonemal, heavy chain 3	1899	AAA 2 (By similarity).				ciliary or flagellar motility|microtubule-based movement	axonemal dynein complex|cilium axoneme|cytoplasm|microtubule	ATP binding|ATPase activity|microtubule motor activity			ovary(10)|large_intestine(2)|central_nervous_system(2)	14														0.5	95.704157	95.704157	33	33	CC		KEEP	---	---	---	---	capture		GBM - Glioblastoma multiforme(48;0.207)	Missense_Mutation	SNP	20940874	20940874	4786	16	C	T	T	27	27	DNAH3	T	1	1
SRRM2	23524	broad.mit.edu	36	16	2757215	2757215	+	Missense_Mutation	SNP	G	C	C			TCGA-06-2563-01	TCGA-06-2563-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr16:2757215G>C	uc002crk.1	+	c.6685G>C	c.(6685-6687)GCC>CCC	p.A2229P	SRRM2_uc002crj.1_Missense_Mutation_p.A2133P|SRRM2_uc002crl.1_Missense_Mutation_p.A2229P|SRRM2_uc010bsu.1_Missense_Mutation_p.A2133P	NM_016333	NP_057417	Q9UQ35	SRRM2_HUMAN	splicing coactivator subunit SRm300	2229	Ala-rich.|Ser-rich.				nuclear mRNA splicing, via spliceosome	Cajal body|catalytic step 2 spliceosome|nuclear speck	C2H2 zinc finger domain binding|protein N-terminus binding|RNA binding			ovary(1)|central_nervous_system(1)|pancreas(1)	3														0.420455	123.860102	124.346163	37	51	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	2757215	2757215	15683	16	G	C	C	46	46	SRRM2	C	3	3
C17orf39	79018	broad.mit.edu	36	17	17883786	17883786	+	Missense_Mutation	SNP	G	A	A			TCGA-06-2563-01	TCGA-06-2563-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr17:17883786G>A	uc002gsg.1	+	c.283G>A	c.(283-285)GGT>AGT	p.G95S	ATPAF2_uc002gsd.1_5'Flank|ATPAF2_uc002gse.1_5'Flank|ATPAF2_uc002gsf.1_5'Flank	NM_024052	NP_076957	Q8IVV7	CQ039_HUMAN	hypothetical protein LOC79018	95	Pro-rich.										0	all_neural(463;0.228)													0.5	15.275008	15.275008	5	5	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	17883786	17883786	1911	17	G	A	A	39	39	C17orf39	A	1	1
ACACA	31	broad.mit.edu	36	17	32688858	32688858	+	Missense_Mutation	SNP	C	T	T			TCGA-06-2563-01	TCGA-06-2563-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr17:32688858C>T	uc002hno.1	-	c.1706G>A	c.(1705-1707)CGC>CAC	p.R569H	ACACA_uc002hnk.1_Missense_Mutation_p.R454H|ACACA_uc002hnl.1_Missense_Mutation_p.R474H|ACACA_uc002hnm.1_Missense_Mutation_p.R532H|ACACA_uc002hnn.1_Missense_Mutation_p.R532H|ACACA_uc010cuz.1_Missense_Mutation_p.R532H	NM_198834	NP_942135	Q13085	ACACA_HUMAN	acetyl-Coenzyme A carboxylase alpha isoform 1	532	Biotin carboxylation.				acetyl-CoA metabolic process|energy reserve metabolic process|fatty acid biosynthetic process|long-chain fatty-acyl-CoA biosynthetic process|positive regulation of cellular metabolic process|protein homotetramerization|triglyceride biosynthetic process	cytosol	acetyl-CoA carboxylase activity|ATP binding|biotin carboxylase activity|metal ion binding|protein binding			large_intestine(1)|ovary(1)	2		Breast(25;0.00157)|Ovarian(249;0.15)			Biotin(DB00121)	Colon(23;82 258 739 2117 10493 24037 27661 34815 35438 36249)				742				0.5	190.239491	190.239491	62	62	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	32688858	32688858	107	17	C	T	T	27	27	ACACA	T	1	1
KRT33A	3883	broad.mit.edu	36	17	36756668	36756668	+	Missense_Mutation	SNP	C	T	T			TCGA-06-2563-01	TCGA-06-2563-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr17:36756668C>T	uc002hwk.1	-	c.830G>A	c.(829-831)CGC>CAC	p.R277H		NM_004138	NP_004129	O76009	KT33A_HUMAN	keratin 33A	277	Coil 2.|Rod.					intermediate filament	protein binding|structural molecule activity				0		Breast(137;0.000496)												0.403756	254.321382	256.041656	86	127	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	36756668	36756668	8784	17	C	T	T	27	27	KRT33A	T	1	1
KRT19	3880	broad.mit.edu	36	17	36934769	36934769	+	Missense_Mutation	SNP	G	A	A			TCGA-06-2563-01	TCGA-06-2563-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr17:36934769G>A	uc002hxd.2	-	c.512C>T	c.(511-513)ACG>ATG	p.T171M		NM_002276	NP_002267	P08727	K1C19_HUMAN	keratin 19	171	Coil 1B.|Rod.				interspecies interaction between organisms|response to estrogen stimulus|sarcomere organization	costamere|intermediate filament	protein binding|structural constituent of cytoskeleton|structural constituent of muscle				0		Breast(137;0.00038)												0.364162	176.270446	179.081565	63	110	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	36934769	36934769	8771	17	G	A	A	40	40	KRT19	A	1	1
EPN3	55040	broad.mit.edu	36	17	45969387	45969387	+	Silent	SNP	G	A	A			TCGA-06-2563-01	TCGA-06-2563-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr17:45969387G>A	uc002ira.2	+	c.471G>A	c.(469-471)GAG>GAA	p.E157E	EPN3_uc002irb.2_Silent_p.E101E	NM_017957	NP_060427	Q9H201	EPN3_HUMAN	epsin 3	157						clathrin-coated vesicle|nucleus|perinuclear region of cytoplasm	lipid binding			ovary(1)	1	Breast(11;1.23e-18)													0.294118	14.567986	15.213021	5	12	GG		KEEP	---	---	---	---	capture	BRCA - Breast invasive adenocarcinoma(22;2.88e-09)		Silent	SNP	45969387	45969387	5380	17	G	A	A	35	35	EPN3	A	2	2
POLR2A	5430	broad.mit.edu	36	17	7345003	7345003	+	Silent	SNP	G	A	A			TCGA-06-2563-01	TCGA-06-2563-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr17:7345003G>A	uc002ghf.2	+	c.1902G>A	c.(1900-1902)GAG>GAA	p.E634E		NM_000937	NP_000928	P24928	RPB1_HUMAN	DNA directed RNA polymerase II polypeptide A	634					mRNA capping|nuclear mRNA splicing, via spliceosome|positive regulation of viral transcription|regulation of transcription, DNA-dependent|transcription elongation from RNA polymerase II promoter|transcription initiation from RNA polymerase II promoter|transcription-coupled nucleotide-excision repair|viral reproduction	DNA-directed RNA polymerase II, core complex	DNA binding|DNA-directed RNA polymerase activity|metal ion binding|RNA-directed RNA polymerase activity|ubiquitin protein ligase binding			pancreas(1)	1		Prostate(122;0.173)												0.358974	82.887632	84.249541	28	50	GG		KEEP	---	---	---	---	capture			Silent	SNP	7345003	7345003	12642	17	G	A	A	34	34	POLR2A	A	2	2
TP53	7157	broad.mit.edu	36	17	7519266	7519266	+	Missense_Mutation	SNP	A	G	G			TCGA-06-2563-01	TCGA-06-2563-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr17:7519266A>G	uc002gim.2	-	c.389T>C	c.(388-390)CTC>CCC	p.L130P	TP53_uc002gig.1_Missense_Mutation_p.L130P|TP53_uc002gih.1_Missense_Mutation_p.L130P|TP53_uc010cne.1_5'Flank|TP53_uc010cnf.1_5'UTR|TP53_uc010cng.1_5'UTR|TP53_uc002gii.1_5'UTR|TP53_uc010cnh.1_Missense_Mutation_p.L130P|TP53_uc010cni.1_Missense_Mutation_p.L130P|TP53_uc002gij.2_Missense_Mutation_p.L130P|TP53_uc010cnj.1_Non-coding_Transcript|TP53_uc002gin.2_Missense_Mutation_p.L37P|TP53_uc002gio.2_5'UTR	NM_001126112	NP_001119584	P04637	P53_HUMAN	tumor protein p53 isoform a	130	Required for interaction with FBXO42.||Interaction with HIPK1 (By similarity).|Interaction with AXIN1 (By similarity).		L -> H (in sporadic cancers; somatic mutation).|L -> F (in sporadic cancers; somatic mutation).|L -> I (in a sporadic cancer; somatic mutation).|L -> R (in sporadic cancers; somatic mutation).|L -> V (in sporadic cancers; somatic mutation).|L -> P (in sporadic cancers; somatic mutation).		activation of caspase activity by cytochrome c|base-excision repair|blood coagulation|cell cycle arrest|cell differentiation|cell proliferation|cellular protein localization|cellular response to drug|cellular response to glucose starvation|cellular response to hypoxia|cellular response to ionizing radiation|cellular response to UV|determination of adult lifespan|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator|ER overload response|interspecies interaction between organisms|negative regulation of apoptosis|negative regulation of cell growth|negative regulation of cell proliferation|negative regulation of gene-specific transcription from RNA polymerase II promoter|negative regulation of helicase activity|negative regulation of transcription from RNA polymerase II promoter|nucleotide-excision repair|oxidative stress-induced premature senescence|positive regulation of gene-specific transcription from RNA polymerase II promoter|positive regulation of histone deacetylation|positive regulation of neuron apoptosis|positive regulation of peptidyl-tyrosine phosphorylation|positive regulation of reactive oxygen species metabolic process|positive regulation of thymocyte apoptosis|positive regulation of transcription from RNA polymerase II promoter|protein localization|protein tetramerization|Ras protein signal transduction|regulation of mitochondrial membrane permeability|replicative senescence|response to antibiotic|response to gamma radiation|response to X-ray	chromatin|cytoplasm|cytosol|endoplasmic reticulum|insoluble fraction|mitochondrion|nuclear matrix|nucleolus|nucleus|PML body|protein complex|replication fork	ATP binding|chaperone binding|chromatin binding|copper ion binding|damaged DNA binding|DNA strand annealing activity|histone acetyltransferase binding|p53 binding|promoter binding|promoter binding|protease binding|protein heterodimerization activity|protein kinase binding|protein N-terminus binding|protein phosphatase 2A binding|sequence-specific DNA binding transcription factor activity|specific transcriptional repressor activity|transcription activator activity|transcription factor binding|ubiquitin protein ligase binding|zinc ion binding	p.L130R(7)|p.0?(6)|p.Y126_K132delYSPALNK(6)|p.Y126_N131delYSPALN(3)|p.L130H(2)|p.L130fs*41(2)|p.N131fs*27(2)|p.V73fs*9(1)|p.S127fs*36(1)|p.A129_K132delALNK(1)|p.Y126fs*11(1)|p.Y126fs*18(1)|p.L130P(1)|p.S127_Q136del10(1)|p.L130fs*39(1)|p.L130_M133delLNKM(1)|p.A129_N131delALN(1)|p.L130fs*16(1)|p.L130del(1)		large_intestine(4614)|breast(2344)|upper_aerodigestive_tract(2150)|lung(1958)|ovary(1559)|oesophagus(1462)|haematopoietic_and_lymphoid_tissue(1212)|stomach(1127)|urinary_tract(1113)|central_nervous_system(1072)|liver(805)|skin(693)|pancreas(370)|biliary_tract(247)|soft_tissue(209)|prostate(192)|endometrium(150)|bone(102)|vulva(79)|kidney(79)|cervix(68)|thyroid(54)|salivary_gland(41)|adrenal_gland(37)|peritoneum(33)|eye(24)|thymus(21)|genital_tract(16)|autonomic_ganglia(16)|small_intestine(14)|testis(11)|penis(10)|vagina(6)|meninges(5)|pituitary(4)|pleura(3)|gastrointestinal_tract_(site_indeterminate)(1)|NS(1)|Fallopian tube(1)|placenta(1)	21904		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)				Pancreas(47;798 1329 9957 10801)		111		690	TCGA GBM(1;<1E-8)|TSP Lung(2;<1E-8)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)			0.380952	53.990959	54.512768	16	26	AA		KEEP	---	---	---	---	capture		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Missense_Mutation	SNP	7519266	7519266	16923	17	A	G	G	11	11	TP53	G	4	4
HOOK2	29911	broad.mit.edu	36	19	12737980	12737980	+	Missense_Mutation	SNP	T	C	C			TCGA-06-2563-01	TCGA-06-2563-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr19:12737980T>C	uc002muy.2	-	c.1448A>G	c.(1447-1449)GAG>GGG	p.E483G	HOOK2_uc002muz.2_Missense_Mutation_p.E483G	NM_013312	NP_037444	Q96ED9	HOOK2_HUMAN	hook homolog 2 isoform 1	483	Sufficient for interaction with microtubules.|Potential.				early endosome to late endosome transport|endocytosis|endosome organization|endosome to lysosome transport|lysosome organization|microtubule cytoskeleton organization|protein transport	centrosome|FHF complex|microtubule	identical protein binding|microtubule binding			ovary(1)|breast(1)	2												OREG0025273	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	0.615385	15.346698	15.487719	8	5	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	12737980	12737980	7575	19	T	C	C	54	54	HOOK2	C	4	4
TJP3	27134	broad.mit.edu	36	19	3697621	3697621	+	Missense_Mutation	SNP	T	C	C			TCGA-06-2563-01	TCGA-06-2563-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr19:3697621T>C	uc002lym.1	+	c.2248T>C	c.(2248-2250)TCC>CCC	p.S750P	TJP3_uc002lyk.1_Missense_Mutation_p.S717P|TJP3_uc002lyl.1_Missense_Mutation_p.S726P|TJP3_uc002lyn.1_Missense_Mutation_p.S717P	NM_014428	NP_055243	O95049	ZO3_HUMAN	tight junction protein 3	731	Guanylate kinase-like.					tight junction	protein binding			ovary(1)|central_nervous_system(1)	2														0.3125	7.558554	8.129081	5	11	TT		KEEP	---	---	---	---	capture		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0118)|STAD - Stomach adenocarcinoma(1328;0.18)	Missense_Mutation	SNP	3697621	3697621	16460	19	T	C	C	54	54	TJP3	C	4	4
APBA3	9546	broad.mit.edu	36	19	3710564	3710564	+	Missense_Mutation	SNP	T	C	C			TCGA-06-2563-01	TCGA-06-2563-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr19:3710564T>C	uc002lyp.1	-	c.611A>G	c.(610-612)CAG>CGG	p.Q204R		NM_004886	NP_004877	O96018	APBA3_HUMAN	amyloid beta (A4) precursor protein-binding,	204					intracellular signal transduction|protein transport	membrane	protein binding				0		Hepatocellular(1079;0.137)												0.173913	9.887387	12.194109	4	19	TT		KEEP	---	---	---	---	capture		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.00467)|STAD - Stomach adenocarcinoma(1328;0.18)	Missense_Mutation	SNP	3710564	3710564	768	19	T	C	C	55	55	APBA3	C	4	4
PSG7	5676	broad.mit.edu	36	19	48125532	48125532	+	Missense_Mutation	SNP	A	T	T			TCGA-06-2563-01	TCGA-06-2563-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr19:48125532A>T	uc002ovl.2	-	c.611T>A	c.(610-612)CTA>CAA	p.L204Q	PSG10_uc002ouv.1_Intron|PSG6_uc002ovi.2_Intron|PSG3_uc002ouf.1_Intron|PSG7_uc002ous.1_5'Flank|PSG7_uc002out.1_Missense_Mutation_p.L23Q|PSG11_uc002ouw.1_Intron|PSG6_uc002ovh.1_Intron|PSG11_uc002ovk.1_Intron	NM_002783	NP_002774	Q13046	PSG7_HUMAN	pregnancy specific beta-1-glycoprotein 7	204	Ig-like C2-type 1.				female pregnancy	extracellular region					0		Prostate(69;0.00682)												0.278562	581.802446	616.125179	217	562	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	48125532	48125532	13113	19	A	T	T	15	15	PSG7	T	4	4
MYBPC2	4606	broad.mit.edu	36	19	55637293	55637293	+	Silent	SNP	C	A	A			TCGA-06-2563-01	TCGA-06-2563-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr19:55637293C>A	uc002psf.2	+	c.813C>A	c.(811-813)GGC>GGA	p.G271G		NM_004533	NP_004524	Q14324	MYPC2_HUMAN	myosin binding protein C, fast type	271	Ig-like C2-type 2.				cell adhesion|muscle filament sliding	cytosol|myosin filament	actin binding|structural constituent of muscle			breast(1)	1		all_neural(266;0.057)												0.222222	9.894572	11.169223	4	14	CC		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(262;0.0079)|GBM - Glioblastoma multiforme(134;0.0144)	Silent	SNP	55637293	55637293	10407	19	C	A	A	25	25	MYBPC2	A	3	3
CLPP	8192	broad.mit.edu	36	19	6317351	6317351	+	Missense_Mutation	SNP	C	T	T			TCGA-06-2563-01	TCGA-06-2563-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr19:6317351C>T	uc002mem.1	+	c.638C>T	c.(637-639)ACC>ATC	p.T213I	CLPP_uc002men.1_Missense_Mutation_p.T15I	NM_006012	NP_006003	Q16740	CLPP_HUMAN	endopeptidase Clp precursor	213					proteolysis	mitochondrial matrix	ATP binding|protein binding|serine-type endopeptidase activity			ovary(1)	1														0.227273	24.527798	27.53088	10	34	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	6317351	6317351	3690	19	C	T	T	18	18	CLPP	T	2	2
VAV1	7409	broad.mit.edu	36	19	6723889	6723889	+	Missense_Mutation	SNP	C	A	A			TCGA-06-2563-01	TCGA-06-2563-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr19:6723889C>A	uc002mfu.1	+	c.71C>A	c.(70-72)ACC>AAC	p.T24N	VAV1_uc010dva.1_Missense_Mutation_p.T24N	NM_005428	NP_005419	P15498	VAV_HUMAN	vav 1 guanine nucleotide exchange factor	24	CH.				apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|platelet activation|regulation of Rho protein signal transduction|small GTPase mediated signal transduction|T cell costimulation	cytosol|plasma membrane	metal ion binding|protein binding|sequence-specific DNA binding transcription factor activity			ovary(3)|lung(2)|central_nervous_system(2)|kidney(2)|skin(1)	10										494				0.232558	50.256888	55.888423	20	66	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	6723889	6723889	17696	19	C	A	A	18	18	VAV1	A	3	3
ANKRD35	148741	broad.mit.edu	36	1	144270198	144270198	+	Missense_Mutation	SNP	C	T	T			TCGA-06-2563-01	TCGA-06-2563-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr1:144270198C>T	uc001eob.1	+	c.460C>T	c.(460-462)CGT>TGT	p.R154C		NM_144698	NP_653299	Q8N283	ANR35_HUMAN	ankyrin repeat domain 35	154	ANK 4.									ovary(4)	4	all_hematologic(18;0.0187)|Acute lymphoblastic leukemia(18;0.0786)					Melanoma(9;127 754 22988 51047)								0.391304	206.170814	208.070108	72	112	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	144270198	144270198	672	1	C	T	T	19	19	ANKRD35	T	1	1
SPRR1A	6698	broad.mit.edu	36	1	151224398	151224398	+	Missense_Mutation	SNP	A	T	T			TCGA-06-2563-01	TCGA-06-2563-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr1:151224398A>T	uc009wnu.1	+	c.68A>T	c.(67-69)CAA>CTA	p.Q23L	SPRR1A_uc001faw.1_Missense_Mutation_p.Q23L|SPRR1A_uc009wnv.1_Missense_Mutation_p.Q23L	NM_005987	NP_005978	P35321	SPR1A_HUMAN	small proline-rich protein 1A	23	2.|2 X 12 AA approximate repeats.				keratinization|peptide cross-linking	cornified envelope|cytoplasm	protein binding, bridging|structural molecule activity				0	Lung NSC(65;1.46e-29)|Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)													0.368984	189.060517	191.866953	69	118	AA		KEEP	---	---	---	---	capture	LUSC - Lung squamous cell carcinoma(543;0.171)		Missense_Mutation	SNP	151224398	151224398	15609	1	A	T	T	5	5	SPRR1A	T	4	4
C1orf116	79098	broad.mit.edu	36	1	205262198	205262198	+	Missense_Mutation	SNP	C	T	T			TCGA-06-2563-01	TCGA-06-2563-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr1:205262198C>T	uc001hfd.2	-	c.1534G>A	c.(1534-1536)GGC>AGC	p.G512S	C1orf116_uc009xcb.1_Missense_Mutation_p.G266S	NM_023938	NP_001077393	Q9BW04	SARG_HUMAN	specifically androgen-regulated protein isoform	512						cytoplasm|plasma membrane	receptor activity			ovary(1)|central_nervous_system(1)	2	Prostate(682;0.19)													0.5	63.424809	63.424809	19	19	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	205262198	205262198	2056	1	C	T	T	22	22	C1orf116	T	2	2
HIST3H3	8290	broad.mit.edu	36	1	226679301	226679301	+	Missense_Mutation	SNP	G	A	A			TCGA-06-2563-01	TCGA-06-2563-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:226679301G>A	uc001hsx.1	-	c.349C>T	c.(349-351)CGG>TGG	p.R117W		NM_003493	NP_003484	Q16695	H31T_HUMAN	histone cluster 3, H3	117					nucleosome assembly|telomere maintenance	nucleoplasm|nucleosome	DNA binding|protein binding				0		Prostate(94;0.0724)												0.395833	111.532893	112.44334	38	58	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	226679301	226679301	7475	1	G	A	A	40	40	HIST3H3	A	1	1
HIST3H2A	92815	broad.mit.edu	36	1	226711750	226711750	+	Silent	SNP	C	T	T			TCGA-06-2563-01	TCGA-06-2563-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr1:226711750C>T	uc001hsy.1	-	c.392G>A	c.(391-393)TGA>TAA	p.*131*	HIST3H2BB_uc001hsz.1_5'Flank	NM_033445	NP_254280	Q7L7L0	H2A3_HUMAN	histone cluster 3, H2a	131					nucleosome assembly	nucleosome|nucleus	DNA binding			ovary(1)	1		Prostate(94;0.183)												0.5	39.795257	39.795257	15	15	CC		KEEP	---	---	---	---	capture			Silent	SNP	226711750	226711750	7473	1	C	T	T	29	29	HIST3H2A	T	2	2
PLCH2	9651	broad.mit.edu	36	1	2401264	2401264	+	Missense_Mutation	SNP	G	A	A			TCGA-06-2563-01	TCGA-06-2563-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:2401264G>A	uc001aji.1	+	c.503G>A	c.(502-504)CGC>CAC	p.R168H	PLCH2_uc009vle.1_5'Flank|PLCH2_uc001ajj.1_5'Flank|PLCH2_uc001ajk.1_5'Flank	NM_014638	NP_055453	O75038	PLCH2_HUMAN	phospholipase C, eta 2	168					intracellular signal transduction|lipid catabolic process	cytoplasm|plasma membrane	calcium ion binding|phosphatidylinositol phospholipase C activity|signal transducer activity			central_nervous_system(3)|ovary(1)|skin(1)	5	all_cancers(77;0.000161)|all_epithelial(69;5.98e-05)|all_lung(157;0.016)|Lung NSC(156;0.0376)|Ovarian(185;0.0634)	all_epithelial(116;7.32e-16)|all_lung(118;1.15e-06)|Lung NSC(185;6.26e-05)|Renal(390;0.00571)|Breast(487;0.00832)|Hepatocellular(190;0.0268)|Myeloproliferative disorder(586;0.028)|Ovarian(437;0.127)|Medulloblastoma(700;0.151)|Lung SC(97;0.217)												0.489796	67.788143	67.792758	24	25	GG		KEEP	---	---	---	---	capture		Epithelial(90;1.44e-37)|OV - Ovarian serous cystadenocarcinoma(86;6.78e-23)|GBM - Glioblastoma multiforme(42;2.8e-08)|Colorectal(212;4.19e-05)|COAD - Colon adenocarcinoma(227;0.000195)|Kidney(185;0.00034)|BRCA - Breast invasive adenocarcinoma(365;0.00443)|KIRC - Kidney renal clear cell carcinoma(229;0.00548)|STAD - Stomach adenocarcinoma(132;0.00644)|Lung(427;0.2)	Missense_Mutation	SNP	2401264	2401264	12464	1	G	A	A	38	38	PLCH2	A	1	1
OR2C3	81472	broad.mit.edu	36	1	245761818	245761818	+	Missense_Mutation	SNP	A	G	G			TCGA-06-2563-01	TCGA-06-2563-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr1:245761818A>G	uc009xgy.1	-	c.619T>C	c.(619-621)TTT>CTT	p.F207L	C1orf150_uc009xgw.1_Intron|C1orf150_uc001ida.2_Intron|C1orf150_uc001idb.2_Intron|C1orf150_uc009xgx.1_Intron|OR2C3_uc001idd.1_5'Flank|OR2C3_uc009xgz.1_Missense_Mutation_p.F206L	NM_198074	NP_932340	Q8N628	OR2C3_HUMAN	olfactory receptor, family 2, subfamily C,	207	Helical; Name=5; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)	1	all_cancers(71;4.51e-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)	all_cancers(173;0.0242)												0.396825	82.06194	82.648705	25	38	AA		KEEP	---	---	---	---	capture	OV - Ovarian serous cystadenocarcinoma(106;0.0241)		Missense_Mutation	SNP	245761818	245761818	11399	1	A	G	G	3	3	OR2C3	G	4	4
NCDN	23154	broad.mit.edu	36	1	35800822	35800822	+	Splice_Site_SNP	SNP	G	A	A			TCGA-06-2563-01	TCGA-06-2563-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:35800822G>A	uc001bza.1	+	c.1385_splice	c.e5+1	p.R462_splice	NCDN_uc001bzb.1_Splice_Site_SNP_p.R462_splice|NCDN_uc001bzc.1_Splice_Site_SNP_p.R445_splice	NM_001014839	NP_001014841			neurochondrin isoform 1						neuron projection development	cytosol|dendrite|neuronal cell body				large_intestine(2)|pancreas(1)	3		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0887)												0.421053	47.700876	47.905558	16	22	GG		KEEP	---	---	---	---	capture			Splice_Site_SNP	SNP	35800822	35800822	10613	1	G	A	A	44	44	NCDN	A	5	2
C1orf173	127254	broad.mit.edu	36	1	74881317	74881317	+	Missense_Mutation	SNP	C	A	A			TCGA-06-2563-01	TCGA-06-2563-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr1:74881317C>A	uc001dgg.1	-	c.297G>T	c.(295-297)GAG>GAT	p.E99D		NM_001002912	NP_001002912	Q5RHP9	CA173_HUMAN	hypothetical protein LOC127254	99										ovary(3)|central_nervous_system(1)	4														0.395683	165.384138	166.711202	55	84	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	74881317	74881317	2081	1	C	A	A	28	28	C1orf173	A	3	3
TGM3	7053	broad.mit.edu	36	20	2246103	2246103	+	Missense_Mutation	SNP	C	A	A			TCGA-06-2563-01	TCGA-06-2563-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr20:2246103C>A	uc002wfx.2	+	c.955C>A	c.(955-957)CCC>ACC	p.P319T		NM_003245	NP_003236	Q08188	TGM3_HUMAN	transglutaminase 3 precursor	319					cell envelope organization|hair follicle morphogenesis|keratinization|peptide cross-linking|protein tetramerization	cytoplasm|extrinsic to internal side of plasma membrane	acyltransferase activity|calcium ion binding|GDP binding|GTP binding|GTPase activity|magnesium ion binding|protein-glutamine gamma-glutamyltransferase activity			large_intestine(4)|ovary(3)|breast(1)	8					L-Glutamine(DB00130)									0.275325	260.656383	278.117692	106	279	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	2246103	2246103	16359	20	C	A	A	22	22	TGM3	A	3	3
TRPM2	7226	broad.mit.edu	36	21	44613616	44613616	+	Missense_Mutation	SNP	G	A	A			TCGA-06-2563-01	TCGA-06-2563-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr21:44613616G>A	uc010gpt.1	+	c.733G>A	c.(733-735)GGC>AGC	p.G245S	TRPM2_uc002zet.1_Missense_Mutation_p.G245S|TRPM2_uc002zeu.1_Missense_Mutation_p.G245S|TRPM2_uc002zew.1_Missense_Mutation_p.G245S|TRPM2_uc002zex.1_Missense_Mutation_p.G31S	NM_003307	NP_003298	O94759	TRPM2_HUMAN	transient receptor potential cation channel,	245	Cytoplasmic (Potential).					integral to plasma membrane	ADP-ribose diphosphatase activity|calcium channel activity|sodium channel activity			ovary(1)|central_nervous_system(1)|pancreas(1)	3														0.414634	46.985172	47.239708	17	24	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	44613616	44613616	17137	21	G	A	A	43	43	TRPM2	A	2	2
GLI2	2736	broad.mit.edu	36	2	121463541	121463541	+	Missense_Mutation	SNP	G	A	A			TCGA-06-2563-01	TCGA-06-2563-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr2:121463541G>A	uc010flp.1	+	c.3581G>A	c.(3580-3582)AGC>AAC	p.S1194N	GLI2_uc002tmq.1_Intron|GLI2_uc002tmr.1_Intron|GLI2_uc002tmt.2_Missense_Mutation_p.S866N|GLI2_uc002tmu.2_Missense_Mutation_p.S849N	NM_005270	NP_005261	P10070	GLI2_HUMAN	GLI-Kruppel family member GLI2	1194					axon guidance|branching morphogenesis of a tube|cell proliferation|cerebellar cortex morphogenesis|developmental growth|embryonic digestive tract development|epidermal cell differentiation|floor plate formation|heart development|hindgut morphogenesis|kidney development|lung development|negative regulation of transcription from RNA polymerase II promoter|odontogenesis of dentine-containing tooth|osteoblast development|osteoblast differentiation|pituitary gland development|positive regulation of DNA replication|positive regulation of T cell differentiation in thymus|positive regulation of transcription from RNA polymerase II promoter|proximal/distal pattern formation|skeletal system development|smoothened signaling pathway involved in ventral spinal cord interneuron specification|spinal cord ventral commissure morphogenesis	nucleus|nucleus	protein binding|sequence-specific DNA binding transcription factor activity|transcription activator activity|zinc ion binding			ovary(7)|central_nervous_system(1)	8	Renal(3;0.0496)	Prostate(154;0.0623)								376				0.166667	7.784151	10.31316	4	20	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	121463541	121463541	6706	2	G	A	A	34	34	GLI2	A	2	2
LY75	4065	broad.mit.edu	36	2	160463690	160463690	+	Missense_Mutation	SNP	C	T	T			TCGA-06-2563-01	TCGA-06-2563-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr2:160463690C>T	uc002ubb.2	-	c.221G>A	c.(220-222)CGG>CAG	p.R74Q	LY75_uc010fos.1_Missense_Mutation_p.R74Q|LY75_uc002ubc.2_Missense_Mutation_p.R74Q|LY75_uc010fot.1_Missense_Mutation_p.R74Q	NM_002349	NP_002340	O60449	LY75_HUMAN	lymphocyte antigen 75	74	Extracellular (Potential).|Ricin B-type lectin.				endocytosis|immune response|inflammatory response	integral to plasma membrane	receptor activity|sugar binding				0														0.379747	184.06456	186.067811	60	98	CC		KEEP	---	---	---	---	capture		COAD - Colon adenocarcinoma(177;0.132)	Missense_Mutation	SNP	160463690	160463690	9476	2	C	T	T	23	23	LY75	T	1	1
LRP2	4036	broad.mit.edu	36	2	169798338	169798338	+	Missense_Mutation	SNP	G	A	A			TCGA-06-2563-01	TCGA-06-2563-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr2:169798338G>A	uc002ues.1	-	c.4927C>T	c.(4927-4929)CGG>TGG	p.R1643W		NM_004525	NP_004516	P98164	LRP2_HUMAN	low density lipoprotein-related protein 2	1643	LDL-receptor class B 13.|Extracellular (Potential).				hormone biosynthetic process|protein glycosylation|receptor-mediated endocytosis|vitamin D metabolic process	coated pit|integral to membrane|lysosome	calcium ion binding|receptor activity|SH3 domain binding			ovary(13)|central_nervous_system(4)|large_intestine(3)|kidney(2)|pancreas(1)	23					Gentamicin(DB00798)|Insulin Glargine recombinant(DB00047)|Insulin Lyspro recombinant(DB00046)|Insulin recombinant(DB00030)|Insulin, porcine(DB00071)|Urokinase(DB00013)					2055				0.329114	72.425234	74.4693	26	53	GG		KEEP	---	---	---	---	capture		STAD - Stomach adenocarcinoma(1183;0.000766)|COAD - Colon adenocarcinoma(177;0.0101)	Missense_Mutation	SNP	169798338	169798338	9329	2	G	A	A	40	40	LRP2	A	1	1
PLXND1	23129	broad.mit.edu	36	3	130764656	130764656	+	Missense_Mutation	SNP	G	C	C			TCGA-06-2563-01	TCGA-06-2563-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr3:130764656G>C	uc003emx.2	-	c.4639C>G	c.(4639-4641)CTG>GTG	p.L1547V	PLXND1_uc010htf.1_Non-coding_Transcript	NM_015103	NP_055918	Q9Y4D7	PLXD1_HUMAN	plexin D1	1547	Cytoplasmic (Potential).				axon guidance	integral to membrane|intracellular|plasma membrane				large_intestine(1)	1						Ovarian(97;366 1484 3738 22084 39045)								0.25	6.818367	7.500861	3	9	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	130764656	130764656	12553	3	G	C	C	34	34	PLXND1	C	3	3
GRIP2	80852	broad.mit.edu	36	3	14533599	14533599	+	Missense_Mutation	SNP	C	T	T			TCGA-06-2563-01	TCGA-06-2563-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr3:14533599C>T	uc003byt.1	-	c.1577G>A	c.(1576-1578)CGA>CAA	p.R526Q	GRIP2_uc003bys.1_Missense_Mutation_p.R57Q	NM_001080423	NP_001073892	Q9C0E4	GRIP2_HUMAN	glutamate receptor interacting protein 2	428					synaptic transmission	cytosol|plasma membrane	protein binding			pancreas(1)	1														0.315789	16.542887	17.116505	6	13	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	14533599	14533599	7067	3	C	T	T	31	31	GRIP2	T	1	1
TLR9	54106	broad.mit.edu	36	3	52230407	52230407	+	Missense_Mutation	SNP	G	T	T			TCGA-06-2563-01	TCGA-06-2563-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr3:52230407G>T	uc003ddb.1	-	c.3070C>A	c.(3070-3072)CGC>AGC	p.R1024S	TLR9_uc003dda.1_Missense_Mutation_p.R989S	NM_017442	NP_059138	Q9NR96	TLR9_HUMAN	toll-like receptor 9 isoform A precursor	989	TIR.|Cytoplasmic (Potential).				defense response to bacterium|fibroblast growth factor receptor signaling pathway|I-kappaB phosphorylation|inflammatory response|innate immune response|insulin receptor signaling pathway|maintenance of gastrointestinal epithelium|negative regulation of interleukin-6 production|negative regulation of interleukin-8 production|negative regulation of NF-kappaB transcription factor activity|negative regulation of toll-like receptor signaling pathway|positive regulation of chemokine production|positive regulation of gene-specific transcription from RNA polymerase II promoter|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of inflammatory response|positive regulation of interferon-alpha biosynthetic process|positive regulation of interferon-beta biosynthetic process|positive regulation of interferon-beta production|positive regulation of interferon-gamma biosynthetic process|positive regulation of interleukin-10 production|positive regulation of interleukin-12 production|positive regulation of interleukin-18 production|positive regulation of interleukin-6 production|positive regulation of interleukin-8 production|positive regulation of JNK cascade|positive regulation of JUN kinase activity|positive regulation of NF-kappaB import into nucleus|positive regulation of NF-kappaB transcription factor activity|positive regulation of nitric-oxide synthase biosynthetic process|positive regulation of toll-like receptor signaling pathway|positive regulation of tumor necrosis factor production|response to molecule of bacterial origin	apical plasma membrane|basolateral plasma membrane|early phagosome|endoplasmic reticulum membrane|endosome membrane|extracellular region|integral to membrane|lysosome	interleukin-1 receptor binding|siRNA binding|transmembrane receptor activity			large_intestine(2)|skin(1)	3					Chloroquine(DB00608)					82				0.476923	90.80046	90.831396	31	34	GG		KEEP	---	---	---	---	capture		BRCA - Breast invasive adenocarcinoma(193;2.41e-05)|Kidney(197;0.000537)|KIRC - Kidney renal clear cell carcinoma(197;0.000716)	Missense_Mutation	SNP	52230407	52230407	16488	3	G	T	T	39	39	TLR9	T	3	3
LMCD1	29995	broad.mit.edu	36	3	8582284	8582284	+	Missense_Mutation	SNP	G	C	C			TCGA-06-2563-01	TCGA-06-2563-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr3:8582284G>C	uc003bqq.1	+	c.890G>C	c.(889-891)GGC>GCC	p.G297A		NM_014583	NP_055398	Q9NZU5	LMCD1_HUMAN	LIM and cysteine-rich domains 1	297	LIM zinc-binding 1.				positive regulation of calcineurin-NFAT signaling pathway|regulation of cardiac muscle hypertrophy|transcription, DNA-dependent	cytoplasm|extracellular space|nucleus	transcription corepressor activity|zinc ion binding			ovary(1)	1														0.285714	8.694213	9.27154	4	10	GG		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(96;0.124)	Missense_Mutation	SNP	8582284	8582284	9173	3	G	C	C	42	42	LMCD1	C	3	3
TNIP3	79931	broad.mit.edu	36	4	122295192	122295192	+	Missense_Mutation	SNP	C	G	G			TCGA-06-2563-01	TCGA-06-2563-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr4:122295192C>G	uc010ing.1	-	c.456G>C	c.(454-456)AAG>AAC	p.K152N	TNIP3_uc010inh.1_Missense_Mutation_p.K152N|TNIP3_uc010ini.1_Missense_Mutation_p.K152N	NM_024873	NP_079149	Q96KP6	TNIP3_HUMAN	TNFAIP3 interacting protein 3	152	Potential.									ovary(1)	1														0.448087	270.925059	271.354308	82	101	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	122295192	122295192	16857	4	C	G	G	24	24	TNIP3	G	3	3
SLCO6A1	133482	broad.mit.edu	36	5	101843904	101843904	+	Missense_Mutation	SNP	G	T	T			TCGA-06-2563-01	TCGA-06-2563-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr5:101843904G>T	uc003knn.2	-	c.492C>A	c.(490-492)TTC>TTA	p.F164L	SLCO6A1_uc003kno.2_Missense_Mutation_p.F164L|SLCO6A1_uc003knp.1_Missense_Mutation_p.F164L|SLCO6A1_uc003knq.1_Missense_Mutation_p.F164L	NM_173488	NP_775759	Q86UG4	SO6A1_HUMAN	solute carrier organic anion transporter family,	164	Helical; Name=2; (Potential).					integral to membrane|plasma membrane	transporter activity			ovary(3)|central_nervous_system(1)	4		all_cancers(142;8e-09)|all_epithelial(76;2.83e-12)|Prostate(80;0.00125)|Colorectal(57;0.00342)|Ovarian(225;0.024)|Lung NSC(167;0.0259)|all_lung(232;0.0323)												0.405405	219.181402	220.630526	75	110	GG		KEEP	---	---	---	---	capture		Epithelial(69;1.47e-15)|COAD - Colon adenocarcinoma(37;0.0113)	Missense_Mutation	SNP	101843904	101843904	15229	5	G	T	T	33	33	SLCO6A1	T	3	3
CHSY3	337876	broad.mit.edu	36	5	129547863	129547863	+	Missense_Mutation	SNP	G	A	A			TCGA-06-2563-01	TCGA-06-2563-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr5:129547863G>A	uc003kvd.1	+	c.1129G>A	c.(1129-1131)GGT>AGT	p.G377S		NM_175856	NP_787052	Q70JA7	CHSS3_HUMAN	chondroitin sulfate synthase 3	377	Lumenal (Potential).					Golgi cisterna membrane|integral to membrane	glucuronosyl-N-acetylgalactosaminyl-proteoglycan 4-beta-N-acetylgalactosaminyltransferase activity|metal ion binding|N-acetylgalactosaminyl-proteoglycan 3-beta-glucuronosyltransferase activity			ovary(2)|pancreas(1)	3		all_cancers(142;0.0227)|Breast(839;0.198)|Prostate(80;0.215)|Lung NSC(810;0.239)												0.463918	136.563812	136.673893	45	52	GG		KEEP	---	---	---	---	capture	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)	OV - Ovarian serous cystadenocarcinoma(64;0.136)	Missense_Mutation	SNP	129547863	129547863	3547	5	G	A	A	43	43	CHSY3	A	2	2
FBXO38	81545	broad.mit.edu	36	5	147764486	147764486	+	Missense_Mutation	SNP	T	G	G			TCGA-06-2563-01	TCGA-06-2563-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr5:147764486T>G	uc003lpf.1	+	c.638T>G	c.(637-639)CTT>CGT	p.L213R	FBXO38_uc003lpg.1_Missense_Mutation_p.L213R|FBXO38_uc003lph.2_Missense_Mutation_p.L213R	NM_205836	NP_995308	Q6PIJ6	FBX38_HUMAN	F-box protein 38 isoform b	213						cytoplasm|nucleus				ovary(4)|skin(1)	5														0.477876	167.911456	167.961138	54	59	TT		KEEP	---	---	---	---	capture	KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)		Missense_Mutation	SNP	147764486	147764486	5983	5	T	G	G	56	56	FBXO38	G	4	4
SLIT3	6586	broad.mit.edu	36	5	168145494	168145494	+	Silent	SNP	G	A	A			TCGA-06-2563-01	TCGA-06-2563-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr5:168145494G>A	uc010jjg.1	-	c.1147C>T	c.(1147-1149)CTG>TTG	p.L383L	SLIT3_uc003mab.1_Silent_p.L383L|SLIT3_uc003mac.1_Silent_p.L180L|SLIT3_uc010jji.1_Silent_p.L383L	NM_003062	NP_003053	O75094	SLIT3_HUMAN	slit homolog 3	383	LRR 10.				apoptosis involved in luteolysis|axon extension involved in axon guidance|cellular response to hormone stimulus|negative chemotaxis|negative regulation of cell growth|negative regulation of chemokine-mediated signaling pathway|response to cortisol stimulus|Roundabout signaling pathway	extracellular space|mitochondrion	calcium ion binding|Roundabout binding			ovary(3)	3	Renal(175;0.000159)|Lung NSC(126;0.0174)|all_lung(126;0.0392)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)				Ovarian(29;311 847 10864 17279 24903)								0.328571	66.199419	68.024196	23	47	GG		KEEP	---	---	---	---	capture	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)		Silent	SNP	168145494	168145494	15239	5	G	A	A	34	34	SLIT3	A	2	2
NSD1	64324	broad.mit.edu	36	5	176570911	176570911	+	Missense_Mutation	SNP	G	A	A			TCGA-06-2563-01	TCGA-06-2563-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr5:176570911G>A	uc003mfr.2	+	c.2905G>A	c.(2905-2907)GGA>AGA	p.G969R	NSD1_uc003mft.2_Missense_Mutation_p.G700R|NSD1_uc003mfs.1_Missense_Mutation_p.G866R	NM_022455	NP_071900	Q96L73	NSD1_HUMAN	nuclear receptor binding SET domain protein 1	969					negative regulation of transcription from RNA polymerase II promoter|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	chromosome|nucleus	androgen receptor binding|chromatin binding|estrogen receptor binding|histone methyltransferase activity (H3-K36 specific)|histone methyltransferase activity (H4-K20 specific)|ligand-dependent nuclear receptor binding|retinoid X receptor binding|thyroid hormone receptor binding|transcription corepressor activity|zinc ion binding			ovary(2)|kidney(1)	3	all_cancers(89;1.57e-05)|Renal(175;0.000269)|Lung NSC(126;0.00111)|all_lung(126;0.002)	all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)								492				0.44086	124.863502	125.146453	41	52	GG		KEEP	---	---	---	---	capture	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)|Epithelial(233;0.198)	Kidney(146;0.235)	Missense_Mutation	SNP	176570911	176570911	11074	5	G	A	A	43	43	NSD1	A	2	2
BRD9	65980	broad.mit.edu	36	5	918623	918623	+	Missense_Mutation	SNP	G	C	C			TCGA-06-2563-01	TCGA-06-2563-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr5:918623G>C	uc003jbo.1	-	c.1311C>G	c.(1309-1311)GAC>GAG	p.D437E	BRD9_uc003jbl.1_Missense_Mutation_p.D417E|BRD9_uc003jbm.1_Non-coding_Transcript|BRD9_uc003jbn.1_Non-coding_Transcript	NM_023924	NP_076413	Q9H8M2	BRD9_HUMAN	bromodomain containing 9 isoform 1	533							nucleic acid binding				0														0.329032	160.389252	164.397179	51	104	GG		KEEP	---	---	---	---	capture	Epithelial(17;0.00202)|OV - Ovarian serous cystadenocarcinoma(19;0.00353)|all cancers(22;0.00815)|Lung(60;0.185)		Missense_Mutation	SNP	918623	918623	1538	5	G	C	C	44	44	BRD9	C	3	3
TIAM2	26230	broad.mit.edu	36	6	155613741	155613741	+	Silent	SNP	A	C	C			TCGA-06-2563-01	TCGA-06-2563-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr6:155613741A>C	uc003qqb.1	+	c.3954A>C	c.(3952-3954)GTA>GTC	p.V1318V	TIAM2_uc003qqd.1_Silent_p.V1318V|TIAM2_uc003qqe.1_Silent_p.V1318V|TIAM2_uc010kjj.1_Silent_p.V880V|TIAM2_uc003qqf.1_Silent_p.V694V|TIAM2_uc003qqg.1_Silent_p.V630V|TIAM2_uc003qqh.1_Silent_p.V243V	NM_012454	NP_036586	Q8IVF5	TIAM2_HUMAN	T-cell lymphoma invasion and metastasis 2	1318					apoptosis|cellular lipid metabolic process|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol|filopodium|growth cone|lamellipodium	receptor signaling protein activity|Rho guanyl-nucleotide exchange factor activity			ovary(3)|breast(1)	4		Ovarian(120;0.196)												0.401099	247.05024	248.603469	73	109	AA		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(155;8.1e-13)|BRCA - Breast invasive adenocarcinoma(81;0.0053)	Silent	SNP	155613741	155613741	16419	6	A	C	C	13	13	TIAM2	C	4	4
PNPLA1	285848	broad.mit.edu	36	6	36367246	36367246	+	Missense_Mutation	SNP	G	A	A			TCGA-06-2563-01	TCGA-06-2563-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr6:36367246G>A	uc010jwe.1	+	c.92G>A	c.(91-93)CGC>CAC	p.R31H	PNPLA1_uc003olw.1_Missense_Mutation_p.R31H|PNPLA1_uc010jwf.1_Missense_Mutation_p.R126H	NM_173676	NP_775947	Q8N8W4	PLPL1_HUMAN	patatin-like phospholipase domain containing 1	126	Patatin.				lipid catabolic process		hydrolase activity			large_intestine(1)|breast(1)|pancreas(1)	3														0.430769	79.088095	79.359959	28	37	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	36367246	36367246	12591	6	G	A	A	38	38	PNPLA1	A	1	1
PRICKLE4	29964	broad.mit.edu	36	6	41861961	41861961	+	Missense_Mutation	SNP	A	G	G			TCGA-06-2563-01	TCGA-06-2563-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr6:41861961A>G	uc003ore.1	+	c.700A>G	c.(700-702)AGC>GGC	p.S234G	PRICKLE4_uc003ord.1_Non-coding_Transcript|TOMM6_uc003org.1_5'Flank	NM_013397	NP_037529	Q2TBC4	PRIC4_HUMAN	over-expressed breast tumor protein	194	LIM zinc-binding 2.					nucleus	zinc ion binding				0	Ovarian(28;0.0355)|Colorectal(47;0.121)													0.425926	73.317551	73.575601	23	31	AA		KEEP	---	---	---	---	capture	Epithelial(12;8.38e-05)|STAD - Stomach adenocarcinoma(11;0.000204)|Colorectal(64;0.00062)|COAD - Colon adenocarcinoma(64;0.00152)		Missense_Mutation	SNP	41861961	41861961	12932	6	A	G	G	3	3	PRICKLE4	G	4	4
SLC26A3	1811	broad.mit.edu	36	7	107215187	107215187	+	Missense_Mutation	SNP	G	C	C			TCGA-06-2563-01	TCGA-06-2563-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr7:107215187G>C	uc003ver.2	-	c.739C>G	c.(739-741)CTA>GTA	p.L247V	SLC26A3_uc003ves.2_Missense_Mutation_p.L212V	NM_000111	NP_000102	P40879	S26A3_HUMAN	solute carrier family 26, member 3	247					excretion	integral to membrane|membrane fraction	inorganic anion exchanger activity|secondary active sulfate transmembrane transporter activity|sequence-specific DNA binding transcription factor activity|transcription cofactor activity			ovary(3)	3														0.244186	124.463087	134.719219	42	130	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	107215187	107215187	15015	7	G	C	C	36	36	SLC26A3	C	3	3
KEL	3792	broad.mit.edu	36	7	142359818	142359818	+	Missense_Mutation	SNP	C	A	A			TCGA-06-2563-01	TCGA-06-2563-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr7:142359818C>A	uc003wcb.1	-	c.1103G>T	c.(1102-1104)GGG>GTG	p.G368V		NM_000420	NP_000411	P23276	KELL_HUMAN	Kell blood group, metallo-endopeptidase	368	Extracellular (Potential).				proteolysis|vasoconstriction	integral to membrane|plasma membrane	metal ion binding|metalloendopeptidase activity|protein binding			ovary(3)|central_nervous_system(1)	4	Melanoma(164;0.059)													0.362069	116.089313	118.001232	42	74	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	142359818	142359818	8448	7	C	A	A	22	22	KEL	A	3	3
KCNH2	3757	broad.mit.edu	36	7	150280478	150280478	+	Missense_Mutation	SNP	C	T	T			TCGA-06-2563-01	TCGA-06-2563-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr7:150280478C>T	uc003wic.1	-	c.1525G>A	c.(1525-1527)GAC>AAC	p.D509N	KCNH2_uc003wib.1_Missense_Mutation_p.D169N|KCNH2_uc003wid.1_Missense_Mutation_p.D169N|KCNH2_uc003wie.1_Missense_Mutation_p.D509N	NM_000238	NP_000229	Q12809	KCNH2_HUMAN	voltage-gated potassium channel, subfamily H,	509	Helical; Name=Segment S3; (Potential).				blood circulation|muscle contraction|regulation of heart contraction|regulation of transcription, DNA-dependent	voltage-gated potassium channel complex	delayed rectifier potassium channel activity|two-component sensor activity			ovary(1)|skin(1)	2	all_neural(206;0.219)				Amiodarone(DB01118)|Amsacrine(DB00276)|Astemizole(DB00637)|Carvedilol(DB01136)|Cisapride(DB00604)|Dofetilide(DB00204)|Halofantrine(DB01218)|Ibutilide(DB00308)|Pimozide(DB01100)|Propafenone(DB01182)|Quinidine(DB00908)|Sertindole(DB06144)|Sotalol(DB00489)|Terfenadine(DB00342)|Verapamil(DB00661)	GBM(137;110 1844 13671 20123 45161)				314				0.365079	64.405927	65.415443	23	40	CC		KEEP	---	---	---	---	capture	OV - Ovarian serous cystadenocarcinoma(82;0.0121)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)	Missense_Mutation	SNP	150280478	150280478	8337	7	C	T	T	31	31	KCNH2	T	1	1
HECW1	23072	broad.mit.edu	36	7	43451592	43451592	+	Missense_Mutation	SNP	G	A	A			TCGA-06-2563-01	TCGA-06-2563-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr7:43451592G>A	uc003tid.1	+	c.2296G>A	c.(2296-2298)GCT>ACT	p.A766T		NM_015052	NP_055867	Q76N89	HECW1_HUMAN	NEDD4-like ubiquitin-protein ligase 1	766					protein ubiquitination involved in ubiquitin-dependent protein catabolic process	cytoplasm|nucleus	ubiquitin-protein ligase activity			ovary(7)|breast(2)|skin(2)|pancreas(1)|lung(1)	13										944				0.418919	82.030397	82.449077	31	43	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	43451592	43451592	7325	7	G	A	A	38	38	HECW1	A	1	1
ZPBP	11055	broad.mit.edu	36	7	50091979	50091979	+	Nonsense_Mutation	SNP	G	A	A			TCGA-06-2563-01	TCGA-06-2563-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr7:50091979G>A	uc003tou.1	-	c.271C>T	c.(271-273)CGA>TGA	p.R91*	ZPBP_uc010kyw.1_Nonsense_Mutation_p.R91*	NM_007009	NP_008940	Q9BS86	ZPBP1_HUMAN	zona pellucida binding protein	91					binding of sperm to zona pellucida	extracellular region					0	Glioma(55;0.08)|all_neural(89;0.245)													0.350877	171.550009	174.90389	60	111	GG		KEEP	---	---	---	---	capture			Nonsense_Mutation	SNP	50091979	50091979	18823	7	G	A	A	38	38	ZPBP	A	5	1
EGFR	1956	broad.mit.edu	36	7	55189204	55189204	+	Missense_Mutation	SNP	C	T	T			TCGA-06-2563-01	TCGA-06-2563-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr7:55189204C>T	uc003tqk.1	+	c.754C>T	c.(754-756)CGC>TGC	p.R252C	EGFR_uc003tqh.1_Missense_Mutation_p.R252C|EGFR_uc003tqi.1_Missense_Mutation_p.R252C|EGFR_uc003tqj.1_Missense_Mutation_p.R252C|EGFR_uc010kzg.1_Missense_Mutation_p.R207C	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)|p.R252C(1)		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)			0.943455	3205.458914	3316.365931	901	54	CC		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	55189204	55189204	5156	7	C	T	T	23	23	EGFR	T	1	1
CCDC146	57639	broad.mit.edu	36	7	76760257	76760257	+	Missense_Mutation	SNP	T	C	C			TCGA-06-2563-01	TCGA-06-2563-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr7:76760257T>C	uc003uga.1	+	c.2468T>C	c.(2467-2469)CTT>CCT	p.L823P	CCDC146_uc010ldp.1_Missense_Mutation_p.L537P|CCDC146_uc003ugc.1_Missense_Mutation_p.L160P	NM_020879	NP_065930	Q8IYE0	CC146_HUMAN	coiled-coil domain containing 146	823	Potential.									ovary(1)|central_nervous_system(1)	2		all_cancers(73;0.128)|all_lung(88;0.0986)|all_epithelial(88;0.163)|Myeloproliferative disorder(862;0.205)												0.325301	168.141974	172.665881	54	112	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	76760257	76760257	2900	7	T	C	C	56	56	CCDC146	C	4	4
PCLO	27445	broad.mit.edu	36	7	82225834	82225834	+	Missense_Mutation	SNP	G	A	A			TCGA-06-2563-01	TCGA-06-2563-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr7:82225834G>A	uc003uhx.2	-	c.15422C>T	c.(15421-15423)ACG>ATG	p.T5141M		NM_033026	NP_149015	Q9Y6V0	PCLO_HUMAN	piccolo isoform 1	5064					cytoskeleton organization|synaptic vesicle exocytosis	cell junction|cytoskeleton|synaptic vesicle	calcium ion binding|calcium-dependent phospholipid binding|profilin binding|transporter activity|zinc ion binding			ovary(7)	7														0.264368	421.292846	451.86659	161	448	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	82225834	82225834	12003	7	G	A	A	40	40	PCLO	A	1	1
PCLO	27445	broad.mit.edu	36	7	82418586	82418586	+	Missense_Mutation	SNP	G	T	T			TCGA-06-2563-01	TCGA-06-2563-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr7:82418586G>T	uc003uhx.2	-	c.9254C>A	c.(9253-9255)TCT>TAT	p.S3085Y	PCLO_uc003uhv.2_Missense_Mutation_p.S3085Y|PCLO_uc010lec.1_Missense_Mutation_p.S50Y	NM_033026	NP_149015	Q9Y6V0	PCLO_HUMAN	piccolo isoform 1	3016					cytoskeleton organization|synaptic vesicle exocytosis	cell junction|cytoskeleton|synaptic vesicle	calcium ion binding|calcium-dependent phospholipid binding|profilin binding|transporter activity|zinc ion binding			ovary(7)	7														0.175	12.399447	16.386468	7	33	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	82418586	82418586	12003	7	G	T	T	33	33	PCLO	T	3	3
RIMS2	9699	broad.mit.edu	36	8	104991568	104991568	+	Missense_Mutation	SNP	C	T	T			TCGA-06-2563-01	TCGA-06-2563-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr8:104991568C>T	uc003yls.2	+	c.989C>T	c.(988-990)ACG>ATG	p.T330M	RIMS2_uc003ylp.2_Missense_Mutation_p.T552M|RIMS2_uc003ylw.2_Missense_Mutation_p.T360M|RIMS2_uc003ylq.2_Missense_Mutation_p.T360M|RIMS2_uc003ylr.2_Intron|RIMS2_uc003ylt.2_5'Flank	NM_014677	NP_055492	Q9UQ26	RIMS2_HUMAN	regulating synaptic membrane exocytosis 2	630					intracellular protein transport	cell junction|presynaptic membrane	Rab GTPase binding|zinc ion binding			ovary(6)|lung(2)|breast(2)|large_intestine(1)|central_nervous_system(1)|skin(1)|pancreas(1)	14										728				0.384615	209.809871	211.933181	70	112	CC		KEEP	---	---	---	---	capture	OV - Ovarian serous cystadenocarcinoma(57;7.7e-07)|STAD - Stomach adenocarcinoma(118;0.229)		Missense_Mutation	SNP	104991568	104991568	13845	8	C	T	T	19	19	RIMS2	T	1	1
CSMD3	114788	broad.mit.edu	36	8	114057462	114057462	+	Silent	SNP	A	T	T			TCGA-06-2563-01	TCGA-06-2563-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr8:114057462A>T	uc003ynu.1	-	c.1122T>A	c.(1120-1122)CCT>CCA	p.P374P	CSMD3_uc003ynt.1_Silent_p.P334P|CSMD3_uc003ynv.1_Intron	NM_198123	NP_937756	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3 isoform 1	374	Extracellular (Potential).					integral to membrane|plasma membrane				ovary(20)|lung(11)|kidney(8)|large_intestine(6)|skin(3)|central_nervous_system(2)|urinary_tract(1)|breast(1)	52										2888	TCGA Ovarian(7;0.080)			0.461538	221.285848	221.486321	72	84	AA		KEEP	---	---	---	---	capture			Silent	SNP	114057462	114057462	4087	8	A	T	T	7	7	CSMD3	T	4	4
CYP7B1	9420	broad.mit.edu	36	8	65679863	65679863	+	Missense_Mutation	SNP	C	T	T			TCGA-06-2563-01	TCGA-06-2563-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr8:65679863C>T	uc003xvj.2	-	c.1163G>A	c.(1162-1164)CGA>CAA	p.R388Q		NM_004820	NP_004811	O75881	CP7B1_HUMAN	cytochrome P450, family 7, subfamily B,	388					bile acid biosynthetic process|cell death|cholesterol metabolic process|oxidation-reduction process|xenobiotic metabolic process	endoplasmic reticulum membrane|microsome	25-hydroxycholesterol 7alpha-hydroxylase activity|electron carrier activity|heme binding|oxysterol 7-alpha-hydroxylase activity			ovary(3)	3		all_cancers(86;0.217)|Lung NSC(129;0.0521)|all_lung(136;0.0906)|all_epithelial(80;0.215)												0.47619	154.840102	154.891994	50	55	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	65679863	65679863	4362	8	C	T	T	31	31	CYP7B1	T	1	1
OR13C2	392376	broad.mit.edu	36	9	106407037	106407037	+	Silent	SNP	G	A	A			TCGA-06-2563-01	TCGA-06-2563-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr9:106407037G>A	uc004bce.1	-	c.693C>T	c.(691-693)TCC>TCT	p.S231S		NM_001004481	NP_001004481	Q8NGS9	O13C2_HUMAN	olfactory receptor, family 13, subfamily C,	231	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0														0.406417	236.491889	237.914322	76	111	GG		KEEP	---	---	---	---	capture			Silent	SNP	106407037	106407037	11340	9	G	A	A	39	39	OR13C2	A	1	1
GUCY2F	2986	broad.mit.edu	36	X	108560198	108560198	+	Silent	SNP	G	A	A			TCGA-06-2563-01	TCGA-06-2563-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chrX:108560198G>A	uc004eod.2	-	c.1785C>T	c.(1783-1785)TTC>TTT	p.F595F	GUCY2F_uc010npo.1_Silent_p.F595F	NM_001522	NP_001513	P51841	GUC2F_HUMAN	guanylate cyclase 2F	595	Protein kinase.|Cytoplasmic (Potential).				intracellular signal transduction|protein phosphorylation|receptor guanylyl cyclase signaling pathway|visual perception	integral to plasma membrane|nuclear outer membrane	ATP binding|GTP binding|guanylate cyclase activity|protein kinase activity|receptor activity			lung(4)|breast(3)|central_nervous_system(1)	8										308				0.382294	570.138011	576.17429	190	307	GG		KEEP	---	---	---	---	capture			Silent	SNP	108560198	108560198	7178	23	G	A	A	37	37	GUCY2F	A	1	1
GRIA3	2892	broad.mit.edu	36	X	122360188	122360188	+	Silent	SNP	C	T	T			TCGA-06-2563-01	TCGA-06-2563-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chrX:122360188C>T	uc004etq.2	+	c.933C>T	c.(931-933)CAC>CAT	p.H311H	GRIA3_uc004etr.2_Silent_p.H311H|GRIA3_uc004ets.2_Non-coding_Transcript	NM_007325	NP_015564	P42263	GRIA3_HUMAN	glutamate receptor, ionotrophic, AMPA 3 isoform	311	Extracellular (Potential).				glutamate signaling pathway|synaptic transmission	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane	alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity			ovary(3)|pancreas(1)	4					L-Glutamic Acid(DB00142)					217				0.342857	66.889801	68.411621	24	46	CC		KEEP	---	---	---	---	capture			Silent	SNP	122360188	122360188	7047	23	C	T	T	19	19	GRIA3	T	1	1
SMARCA1	6594	broad.mit.edu	36	X	128484906	128484906	+	Silent	SNP	G	A	A			TCGA-06-2563-01	TCGA-06-2563-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chrX:128484906G>A	uc004eun.2	-	c.123C>T	c.(121-123)GCC>GCT	p.A41A	SMARCA1_uc004eup.2_Silent_p.A41A	NM_003069	NP_003060	P28370	SMCA1_HUMAN	SWI/SNF-related matrix-associated	41					ATP-dependent chromatin remodeling|brain development|neuron differentiation|positive regulation of gene-specific transcription|transcription, DNA-dependent	NURF complex	ATP binding|DNA binding|helicase activity|nucleosome binding|protein binding|transcription regulator activity			ovary(3)|skin(1)	4														0.348624	99.656614	101.842528	38	71	GG		KEEP	---	---	---	---	capture			Silent	SNP	128484906	128484906	15266	23	G	A	A	39	39	SMARCA1	A	1	1
MAGEC1	9947	broad.mit.edu	36	X	140823310	140823310	+	Silent	SNP	C	T	T			TCGA-06-2563-01	TCGA-06-2563-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chrX:140823310C>T	uc004fbt.1	+	c.2454C>T	c.(2452-2454)CCC>CCT	p.P818P	MAGEC1_uc010nsl.1_Intron	NM_005462	NP_005453	O60732	MAGC1_HUMAN	melanoma antigen family C, 1	818							protein binding			ovary(1)|kidney(1)|central_nervous_system(1)	3	Acute lymphoblastic leukemia(192;6.56e-05)													0.383966	560.8083	566.41354	182	292	CC		KEEP	---	---	---	---	capture			Silent	SNP	140823310	140823310	9561	23	C	T	T	24	24	MAGEC1	T	2	2
AFF2	2334	broad.mit.edu	36	X	147842881	147842881	+	Missense_Mutation	SNP	C	T	T			TCGA-06-2563-01	TCGA-06-2563-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chrX:147842881C>T	uc004fcp.1	+	c.1469C>T	c.(1468-1470)TCG>TTG	p.S490L	AFF2_uc004fcq.1_Missense_Mutation_p.S480L|AFF2_uc004fcr.1_Missense_Mutation_p.S451L|AFF2_uc004fcs.1_Missense_Mutation_p.S457L	NM_002025	NP_002016	P51816	AFF2_HUMAN	fragile X mental retardation 2	490					brain development|mRNA processing|regulation of RNA splicing|RNA splicing	nuclear speck	G-quadruplex RNA binding|protein binding			ovary(3)|pancreas(2)	5	Acute lymphoblastic leukemia(192;6.56e-05)													0.387097	241.543151	243.968586	84	133	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	147842881	147842881	358	23	C	T	T	31	31	AFF2	T	1	1
CXorf23	256643	broad.mit.edu	36	X	19878873	19878873	+	Missense_Mutation	SNP	C	T	T			TCGA-06-2563-01	TCGA-06-2563-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chrX:19878873C>T	uc004czp.1	-	c.1664G>A	c.(1663-1665)CGA>CAA	p.R555Q	CXorf23_uc010nfn.1_Non-coding_Transcript|CXorf23_uc004czo.1_Missense_Mutation_p.R505Q	NM_198279	NP_938020	A2AJT9	CX023_HUMAN	hypothetical protein LOC256643	555						mitochondrion				lung(1)|skin(1)	2														0.379487	223.206657	225.689968	74	121	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	19878873	19878873	4263	23	C	T	T	31	31	CXorf23	T	1	1
OPHN1	4983	broad.mit.edu	36	X	67338252	67338252	+	Missense_Mutation	SNP	T	C	C			TCGA-06-2563-01	TCGA-06-2563-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chrX:67338252T>C	uc004dww.2	-	c.959A>G	c.(958-960)TAC>TGC	p.Y320C		NM_002547	NP_002538	O60890	OPHN1_HUMAN	oligophrenin 1	320	PH.				axon guidance|endocytosis|filopodium assembly|small GTPase mediated signal transduction|substrate-dependent cell migration, cell extension	axon|cell junction|cytosol|dendritic spine|synapse	cytoskeletal adaptor activity|Rho GTPase activator activity|SH3 domain binding			ovary(2)	2														0.438298	357.130204	357.918709	103	132	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	67338252	67338252	11281	23	T	C	C	57	57	OPHN1	C	4	4
LPAR4	2846	broad.mit.edu	36	X	77897945	77897945	+	Missense_Mutation	SNP	C	A	A			TCGA-06-2563-01	TCGA-06-2563-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chrX:77897945C>A	uc010nme.1	+	c.923C>A	c.(922-924)CCT>CAT	p.P308H	LPAR4_uc004edd.1_Missense_Mutation_p.P308H	NM_005296	NP_005287	Q99677	LPAR4_HUMAN	lysophosphatidic acid receptor 4	308	Helical; Name=7; (Potential).					integral to plasma membrane	lipid binding|purinergic nucleotide receptor activity, G-protein coupled			ovary(3)	3														0.366379	249.164227	252.785731	85	147	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	77897945	77897945	9280	23	C	A	A	24	24	LPAR4	A	3	3
POF1B	79983	broad.mit.edu	36	X	84520982	84520982	+	Missense_Mutation	SNP	T	C	C			TCGA-06-2563-01	TCGA-06-2563-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chrX:84520982T>C	uc004ees.2	-	c.134A>G	c.(133-135)AAA>AGA	p.K45R	POF1B_uc004eer.2_Missense_Mutation_p.K45R	NM_024921	NP_079197	Q8WVV4	POF1B_HUMAN	premature ovarian failure, 1B	45							actin binding				0														0.351852	61.209356	62.254426	19	35	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	84520982	84520982	12610	23	T	C	C	64	64	POF1B	C	4	4
RPL10L	140801	broad.mit.edu	36	14	46190591	46190591	+	Frame_Shift_Del	DEL	G	-	-			TCGA-06-2563-01	TCGA-06-2563-01										Phase_I	Unspecified				Illumina GAIIx	g.chr14:46190591_46190591delG	uc001wwg.1	-	c.99_99delC	c.(97-99)ATCfs	p.I33fs		NM_080746	NP_542784	Q96L21	RL10L_HUMAN	ribosomal protein L10-like protein	33					spermatogenesis|translation	cytosolic large ribosomal subunit|nucleus	structural constituent of ribosome			ovary(1)	1														0.41			65	92				---	---	---	---	capture_indel			Frame_Shift_Del	DEL	46190591	46190591	14035	14	G	-	-	33	33	RPL10L	-	5	5
ZNF280C	55609	broad.mit.edu	36	X	129198278	129198279	+	Frame_Shift_Del	DEL	TG	-	-			TCGA-06-2563-01	TCGA-06-2563-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:129198278_129198279delTG	uc004evm.1	-	c.509_510delCA	c.(508-510)TCAfs	p.S170fs	ZNF280C_uc010nrf.1_Frame_Shift_Del_p.S170fs	NM_017666	NP_060136	Q8ND82	Z280C_HUMAN	zinc finger protein 280C	170	Ser-rich.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			skin(2)|ovary(1)	3														0.48			46	49				---	---	---	---	capture_indel			Frame_Shift_Del	DEL	129198278	129198279	18408	23	TG	-	-	51	51	ZNF280C	-	5	5
