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
PTEN	5728	broad.mit.edu	36	10	89682884	89682884	+	Nonsense_Mutation	SNP	C	T	T			TCGA-28-1745-01	TCGA-28-1745-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr10:89682884C>T	uc001kfb.1	+	c.388C>T	c.(388-390)CGA>TGA	p.R130*		NM_000314	NP_000305	P60484	PTEN_HUMAN	phosphatase and tensin homolog	130	Phosphatase tensin-type.		R -> L (in CD and endometrial hyperplasia; loss of phosphatase activity towards Ins(1,3,4,5)P4; retains ability to bind phospholipid membranes).|R -> Q (in CD; loss of phosphatase activity towards Ins(1,3,4,5)P4; retains ability to bind phospholipid membranes).|R -> G (loss of phosphatase activity towards Ins(1,3,4,5)P4 and PtdIns(3,4,5)P3).	R->M: Does not affect the ability to inhibit AKT/PKB activation.	apoptosis|canonical Wnt receptor signaling pathway|cell proliferation|central nervous system development|induction of apoptosis|inositol phosphate dephosphorylation|negative regulation of cell migration|negative regulation of focal adhesion assembly|negative regulation of protein kinase B signaling cascade|negative regulation of protein phosphorylation|nerve growth factor receptor signaling pathway|phosphatidylinositol dephosphorylation|phosphatidylinositol-mediated signaling|positive regulation of sequence-specific DNA binding transcription factor activity|protein stabilization|regulation of cyclin-dependent protein kinase activity|regulation of neuron projection development|T cell receptor signaling pathway	cytosol|internal side of plasma membrane|PML body	enzyme binding|inositol-1,3,4,5-tetrakisphosphate 3-phosphatase activity|lipid binding|magnesium ion binding|PDZ domain binding|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity|phosphatidylinositol-3,4-bisphosphate 3-phosphatase activity|phosphatidylinositol-3-phosphatase activity|protein serine/threonine phosphatase activity|protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity	p.R130G(64)|p.R130*(60)|p.K128_R130del(3)|p.R130Q(2)|p.Y27_N212>Y(2)|p.K128fs*47(1)|p.R130R(1)|p.A121_F145del(1)|p.F56fs*2(1)|p.G129fs*50(1)|p.G129fs*51(1)		endometrium(831)|central_nervous_system(654)|skin(119)|haematopoietic_and_lymphoid_tissue(101)|prostate(97)|large_intestine(90)|breast(67)|lung(63)|ovary(58)|thyroid(29)|stomach(29)|upper_aerodigestive_tract(25)|cervix(21)|liver(20)|vulva(17)|kidney(15)|NS(14)|soft_tissue(12)|urinary_tract(12)|eye(8)|pancreas(6)|salivary_gland(5)|bone(5)|biliary_tract(4)|autonomic_ganglia(2)|meninges(2)|testis(1)|oesophagus(1)	2308		all_cancers(4;3.61e-31)|all_epithelial(4;3.96e-23)|Prostate(4;8.12e-23)|Breast(4;0.000111)|Melanoma(5;0.00146)|all_hematologic(4;0.00227)|Colorectal(252;0.00494)|all_neural(4;0.00513)|Acute lymphoblastic leukemia(4;0.0116)|Glioma(4;0.0274)|all_lung(38;0.132)	KIRC - Kidney renal clear cell carcinoma(1;0.214)	UCEC - Uterine corpus endometrioid carcinoma (6;0.000228)|all cancers(1;4.16e-84)|GBM - Glioblastoma multiforme(1;7.77e-49)|Epithelial(1;7.67e-41)|OV - Ovarian serous cystadenocarcinoma(1;6.22e-15)|BRCA - Breast invasive adenocarcinoma(1;1.1e-06)|Lung(2;3.18e-06)|Colorectal(12;4.88e-06)|LUSC - Lung squamous cell carcinoma(2;4.97e-06)|COAD - Colon adenocarcinoma(12;1.13e-05)|Kidney(1;0.000288)|KIRC - Kidney renal clear cell carcinoma(1;0.00037)|STAD - Stomach adenocarcinoma(243;0.218)			R130G(OV56_OVARY)|R130G(KMBC2_URINARY_TRACT)	31	p.R130G(OV56-Tumor)|p.KGR128del(A2780-Tumor)|p.R130G(KMBC2-Tumor)|p.G129fs(U937-Tumor)	264	TCGA GBM(2;<1E-8)|TSP Lung(26;0.18)			0.219388	115.726378	129.937534	43	153	CC		KEEP	---	---	---	---	capture			Nonsense_Mutation	SNP	89682884	89682884	13192	10	C	T	T	19	19	PTEN	T	5	1
MYOF	26509	broad.mit.edu	36	10	95062781	95062781	+	Missense_Mutation	SNP	C	T	T			TCGA-28-1745-01	TCGA-28-1745-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr10:95062781C>T	uc001kin.1	-	c.5875G>A	c.(5875-5877)GCC>ACC	p.A1959T	MYOF_uc001kio.1_Missense_Mutation_p.A1946T|MYOF_uc009xue.1_Non-coding_Transcript	NM_013451	NP_038479	Q9NZM1	MYOF_HUMAN	myoferlin isoform a	1959	Cytoplasmic (Potential).				blood circulation|muscle contraction|plasma membrane repair	caveola|cytoplasmic vesicle membrane|integral to membrane|nuclear membrane	phospholipid binding|protein binding			ovary(3)|breast(1)	4														0.272727	11.642047	12.667766	6	16	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	95062781	95062781	10484	10	C	T	T	27	27	MYOF	T	1	1
C12orf24	29902	broad.mit.edu	36	12	109412251	109412251	+	Missense_Mutation	SNP	G	C	C			TCGA-28-1745-01	TCGA-28-1745-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr12:109412251G>C	uc001tqu.2	+	c.748G>C	c.(748-750)GAA>CAA	p.E250Q	C12orf24_uc001tqv.2_Non-coding_Transcript|C12orf24_uc009zvp.1_Non-coding_Transcript	NM_013300	NP_037432	Q8WUB2	CL024_HUMAN	hypothetical protein LOC29902	250											0														0.104651	9.919953	23.280686	9	77	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	109412251	109412251	1722	12	G	C	C	41	41	C12orf24	C	3	3
ABCB9	23457	broad.mit.edu	36	12	121999138	121999138	+	Missense_Mutation	SNP	C	T	T			TCGA-28-1745-01	TCGA-28-1745-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr12:121999138C>T	uc001udm.2	-	c.1039G>A	c.(1039-1041)GGC>AGC	p.G347S	ABCB9_uc001udo.2_Missense_Mutation_p.G347S|ABCB9_uc009zxr.1_Intron|ABCB9_uc001udp.1_Missense_Mutation_p.G347S|ABCB9_uc001udq.2_Missense_Mutation_p.G129S|ABCB9_uc001udr.2_Missense_Mutation_p.G347S	NM_019625	NP_982269	Q9NP78	ABCB9_HUMAN	ATP-binding cassette, sub-family B (MDR/TAP),	347	ABC transmembrane type-1.				positive regulation of T cell mediated cytotoxicity|protein transport	lysosomal membrane|plasma membrane|TAP complex	ATP binding|MHC class I protein binding|oligopeptide-transporting ATPase activity|peptide antigen binding|protein homodimerization activity|TAP1 binding|TAP2 binding|tapasin binding				0	all_neural(191;0.0837)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;6.84e-05)|Epithelial(86;0.000152)|BRCA - Breast invasive adenocarcinoma(302;0.111)		Ovarian(49;786 1333 9175 38236)								0.26087	16.342857	17.531159	6	17	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	121999138	121999138	49	12	C	T	T	23	23	ABCB9	T	1	1
OR6C3	254786	broad.mit.edu	36	12	54011900	54011900	+	Missense_Mutation	SNP	C	A	A			TCGA-28-1745-01	TCGA-28-1745-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr12:54011900C>A	uc001sgv.1	+	c.149C>A	c.(148-150)TCC>TAC	p.S50Y		NM_054104	NP_473445	Q9NZP0	OR6C3_HUMAN	olfactory receptor, family 6, subfamily C,	50	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0														0.112319	31.121388	72.11956	31	245	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	54011900	54011900	11602	12	C	A	A	30	30	OR6C3	A	3	3
CLDN10	9071	broad.mit.edu	36	13	95003014	95003014	+	Silent	SNP	T	A	A			TCGA-28-1745-01	TCGA-28-1745-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr13:95003014T>A	uc001vmh.1	+	c.6T>A	c.(4-6)GCT>GCA	p.A2A	CLDN10_uc001vmg.1_Intron	NM_006984	NP_008915	P78369	CLD10_HUMAN	claudin 10 isoform b	2	Helical; (Potential).				calcium-independent cell-cell adhesion	integral to membrane|tight junction	identical protein binding|structural molecule activity			ovary(1)	1	all_neural(89;0.0878)|Breast(111;0.148)|Medulloblastoma(90;0.163)		BRCA - Breast invasive adenocarcinoma(86;0.18)											0.444444	8.29005	8.315307	4	5	TT		KEEP	---	---	---	---	capture			Silent	SNP	95003014	95003014	3608	13	T	A	A	53	53	CLDN10	A	4	4
BDKRB2	624	broad.mit.edu	36	14	95776811	95776811	+	Silent	SNP	C	G	G			TCGA-28-1745-01	TCGA-28-1745-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr14:95776811C>G	uc010avm.1	+	c.393C>G	c.(391-393)CGC>CGG	p.R131R	BDKRB2_uc010avl.1_3'UTR|BDKRB2_uc001yfg.2_Silent_p.R131R	NM_000623	NP_000614	P30411	BKRB2_HUMAN	bradykinin receptor B2	131	Extracellular (Potential).				arachidonic acid secretion|elevation of cytosolic calcium ion concentration|inflammatory response|regulation of vascular permeability|regulation of vasoconstriction|smooth muscle contraction|transmembrane receptor protein tyrosine kinase signaling pathway	endosome|integral to plasma membrane	bradykinin receptor activity|phosphatidylinositol phospholipase C activity|protease binding|protein heterodimerization activity|type 1 angiotensin receptor binding			ovary(3)|kidney(1)	4		all_cancers(154;0.0678)|Melanoma(154;0.155)|all_epithelial(191;0.179)		COAD - Colon adenocarcinoma(157;0.226)										0.227273	7.660919	9.16755	5	17	CC		KEEP	---	---	---	---	capture			Silent	SNP	95776811	95776811	1415	14	C	G	G	27	27	BDKRB2	G	3	3
PGBD4	161779	broad.mit.edu	36	15	32183273	32183273	+	Silent	SNP	A	C	C			TCGA-28-1745-01	TCGA-28-1745-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr15:32183273A>C	uc001zho.1	+	c.1249A>C	c.(1249-1251)AGG>CGG	p.R417R	C15orf24_uc001zhm.1_5'Flank|C15orf24_uc001zhn.1_5'Flank	NM_152595	NP_689808	Q96DM1	PGBD4_HUMAN	piggyBac transposable element derived 4	417											0		all_lung(180;1.76e-08)		all cancers(64;1.22e-17)|GBM - Glioblastoma multiforme(113;1.78e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0242)										0.153846	8.397493	15.871367	10	55	AA		KEEP	---	---	---	---	capture			Silent	SNP	32183273	32183273	12206	15	A	C	C	3	3	PGBD4	C	4	4
PRR14	78994	broad.mit.edu	36	16	30573706	30573706	+	Missense_Mutation	SNP	C	T	T			TCGA-28-1745-01	TCGA-28-1745-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr16:30573706C>T	uc002dyy.1	+	c.914C>T	c.(913-915)CCC>CTC	p.P305L	PRR14_uc002dyz.1_Missense_Mutation_p.P150L|PRR14_uc002dza.1_Missense_Mutation_p.P305L|PRR14_uc002dzb.1_Missense_Mutation_p.P119L	NM_024031	NP_076936	Q9BWN1	PRR14_HUMAN	proline rich 14	305	Pro-rich.										0			Colorectal(24;0.103)											0.482759	39.225921	39.234085	14	15	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	30573706	30573706	13029	16	C	T	T	22	22	PRR14	T	2	2
SRL	6345	broad.mit.edu	36	16	4182385	4182385	+	Missense_Mutation	SNP	G	A	A			TCGA-28-1745-01	TCGA-28-1745-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr16:4182385G>A	uc002cvz.2	-	c.1192C>T	c.(1192-1194)CGC>TGC	p.R398C	SRL_uc002cvy.2_Non-coding_Transcript	NM_001098814	NP_001092284	Q86TD4	SRCA_HUMAN	sarcalumenin	857						sarcoplasmic reticulum lumen	GTP binding|GTPase activity			ovary(3)	3														0.194805	36.784448	43.471199	15	62	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	4182385	4182385	15664	16	G	A	A	39	39	SRL	A	1	1
NOD2	64127	broad.mit.edu	36	16	49291271	49291271	+	Missense_Mutation	SNP	G	A	A			TCGA-28-1745-01	TCGA-28-1745-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr16:49291271G>A	uc002egm.1	+	c.445G>A	c.(445-447)GTG>ATG	p.V149M	NOD2_uc010cbj.1_Missense_Mutation_p.V122M|NOD2_uc010cbk.1_Missense_Mutation_p.V122M|NOD2_uc002egl.1_De_novo_Start_OutOfFrame	NM_022162	NP_071445	Q9HC29	NOD2_HUMAN	nucleotide-binding oligomerization domain	149	CARD 2.				activation of MAPK activity involved in innate immune response|cytokine production involved in immune response|detection of bacterium|detection of muramyl dipeptide|JNK cascade|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|negative regulation of macrophage apoptosis|nucleotide-binding oligomerization domain containing 2 signaling pathway|positive regulation of B cell activation|positive regulation of dendritic cell antigen processing and presentation|positive regulation of epithelial cell proliferation|positive regulation of ERK1 and ERK2 cascade|positive regulation of gamma-delta T cell activation|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of interleukin-1 beta secretion|positive regulation of interleukin-10 production|positive regulation of interleukin-17 production|positive regulation of interleukin-6 production|positive regulation of JNK cascade|positive regulation of NF-kappaB transcription factor activity|positive regulation of nitric-oxide synthase biosynthetic process|positive regulation of Notch signaling pathway|positive regulation of phosphatidylinositol 3-kinase activity|positive regulation of prostaglandin-E synthase activity|positive regulation of prostaglandin-endoperoxide synthase activity|positive regulation of stress-activated MAPK cascade|positive regulation of tumor necrosis factor production|positive regulation of type 2 immune response|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	cell surface|cytosol|plasma membrane|vesicle	ATP binding|CARD domain binding|muramyl dipeptide binding|protein kinase binding			ovary(3)	3		all_cancers(37;0.0156)												0.1875	8.527903	11.461351	6	26	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	49291271	49291271	10920	16	G	A	A	48	48	NOD2	A	2	2
FTO	79068	broad.mit.edu	36	16	52417297	52417297	+	Silent	SNP	A	G	G			TCGA-28-1745-01	TCGA-28-1745-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr16:52417297A>G	uc002ehr.1	+	c.144A>G	c.(142-144)AAA>AAG	p.K48K		NM_001080432	NP_001073901	Q9C0B1	FTO_HUMAN	fat mass and obesity associated	48	Fe2OG dioxygenase domain.				DNA dealkylation involved in DNA repair|oxidative single-stranded DNA demethylation|oxidative single-stranded RNA demethylation|RNA repair	nucleus	DNA-N1-methyladenine dioxygenase activity|ferrous iron binding|oxidative DNA demethylase activity|oxidative RNA demethylase activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen				0														0.185185	9.561305	12.069444	5	22	AA		KEEP	---	---	---	---	capture			Silent	SNP	52417297	52417297	6337	16	A	G	G	2	2	FTO	G	4	4
CNGB1	1258	broad.mit.edu	36	16	56554388	56554388	+	Silent	SNP	G	A	A			TCGA-28-1745-01	TCGA-28-1745-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr16:56554388G>A	uc002emt.1	-	c.372C>T	c.(370-372)GAC>GAT	p.D124D	CNGB1_uc010cdh.1_Silent_p.D124D|CNGB1_uc002emu.1_Silent_p.D124D	NM_001297	NP_001288	Q14028	CNGB1_HUMAN	cyclic nucleotide gated channel beta 1 isoform	124					sensory perception of smell	intracellular cyclic nucleotide activated cation channel complex	cAMP binding|intracellular cAMP activated cation channel activity			breast(3)|pancreas(1)	4						Colon(156;1293 1853 16336 28962 38659)								0.164179	9.806468	16.983648	11	56	GG		KEEP	---	---	---	---	capture			Silent	SNP	56554388	56554388	3738	16	G	A	A	44	44	CNGB1	A	2	2
MAPK7	5598	broad.mit.edu	36	17	19224887	19224887	+	Missense_Mutation	SNP	C	T	T			TCGA-28-1745-01	TCGA-28-1745-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr17:19224887C>T	uc002gvn.1	+	c.772C>T	c.(772-774)CGG>TGG	p.R258W	B9D1_uc010cqm.1_5'Flank|B9D1_uc002gvl.2_5'Flank|MAPK7_uc002gvo.1_Missense_Mutation_p.R119W|MAPK7_uc002gvp.1_Missense_Mutation_p.R258W|MAPK7_uc002gvq.1_Missense_Mutation_p.R258W	NM_139033	NP_620601	Q13164	MK07_HUMAN	mitogen-activated protein kinase 7 isoform 1	258	Necessary for oligomerization (By similarity).|Protein kinase.				cell cycle|cell differentiation|innate immune response|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|nerve growth factor receptor signaling pathway|stress-activated MAPK cascade|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway	cytosol|nucleoplasm	ATP binding|MAP kinase activity|protein binding			central_nervous_system(3)|lung(1)|skin(1)	5	all_cancers(12;2.87e-05)|all_epithelial(12;0.00114)|Hepatocellular(7;0.00345)|Breast(13;0.206)									176				0.181818	8.594514	10.681018	4	18	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	19224887	19224887	9665	17	C	T	T	23	23	MAPK7	T	1	1
ANKRD13B	124930	broad.mit.edu	36	17	24963273	24963273	+	Missense_Mutation	SNP	C	A	A			TCGA-28-1745-01	TCGA-28-1745-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr17:24963273C>A	uc002hei.1	+	c.1114C>A	c.(1114-1116)CTG>ATG	p.L372M	ANKRD13B_uc002heh.1_Missense_Mutation_p.L240M|ANKRD13B_uc002hej.2_Non-coding_Transcript|ANKRD13B_uc002hek.1_5'Flank	NM_152345	NP_689558	Q86YJ7	AN13B_HUMAN	ankyrin repeat domain 13B	372											0														0.148148	6.79708	9.994143	4	23	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	24963273	24963273	645	17	C	A	A	28	28	ANKRD13B	A	3	3
SLFN11	91607	broad.mit.edu	36	17	30714243	30714243	+	Nonsense_Mutation	SNP	C	A	A			TCGA-28-1745-01	TCGA-28-1745-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr17:30714243C>A	uc010ctp.1	-	c.697G>T	c.(697-699)GAA>TAA	p.E233*	SLFN11_uc010ctq.1_Nonsense_Mutation_p.E233*|SLFN11_uc002hjh.2_Nonsense_Mutation_p.E233*|SLFN11_uc002hjg.2_Nonsense_Mutation_p.E233*|SLFN11_uc010ctr.1_Nonsense_Mutation_p.E233*	NM_001104588	NP_689483	Q7Z7L1	SLN11_HUMAN	schlafen family member 11	233						nucleus	ATP binding			large_intestine(1)|ovary(1)	2		Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0182)										0.177419	92.46688	116.762543	44	204	CC		KEEP	---	---	---	---	capture			Nonsense_Mutation	SNP	30714243	30714243	15230	17	C	A	A	32	32	SLFN11	A	5	3
ITGAE	3682	broad.mit.edu	36	17	3607755	3607755	+	Silent	SNP	G	A	A			TCGA-28-1745-01	TCGA-28-1745-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr17:3607755G>A	uc002fwo.2	-	c.1014C>T	c.(1012-1014)GCC>GCT	p.A338A		NM_002208	NP_002199	P38570	ITAE_HUMAN	integrin, alpha E precursor	338	VWFA.|Extracellular (Potential).				cell adhesion|integrin-mediated signaling pathway	integrin complex	receptor activity			large_intestine(2)|breast(1)|pancreas(1)	4				UCEC - Uterine corpus endometrioid carcinoma (3;0.0813)		NSCLC(182;635 2928 8995 38788)				37				0.210526	9.98947	11.462257	4	15	GG		KEEP	---	---	---	---	capture			Silent	SNP	3607755	3607755	8189	17	G	A	A	47	47	ITGAE	A	2	2
CBX4	8535	broad.mit.edu	36	17	75423379	75423379	+	Silent	SNP	A	C	C			TCGA-28-1745-01	TCGA-28-1745-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr17:75423379A>C	uc002jxe.1	-	c.657T>G	c.(655-657)GGT>GGG	p.G219G		NM_003655	NP_003646	O00257	CBX4_HUMAN	chromobox homolog 4	219					anti-apoptosis|chromatin assembly or disassembly|chromatin modification|transcription, DNA-dependent	chromatin|Golgi apparatus|nucleus	enzyme binding|transcription corepressor activity				0			OV - Ovarian serous cystadenocarcinoma(97;0.0102)|BRCA - Breast invasive adenocarcinoma(99;0.0224)									OREG0024799	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	0.333333	7.524361	7.744587	3	6	AA		KEEP	---	---	---	---	capture			Silent	SNP	75423379	75423379	2839	17	A	C	C	6	6	CBX4	C	4	4
DNAH2	146754	broad.mit.edu	36	17	7623387	7623387	+	Silent	SNP	C	T	T			TCGA-28-1745-01	TCGA-28-1745-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr17:7623387C>T	uc002giu.1	+	c.5643C>T	c.(5641-5643)GCC>GCT	p.A1881A		NM_020877	NP_065928	Q9P225	DYH2_HUMAN	dynein heavy chain domain 3	1881	AAA 1 (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)												0.115942	9.057735	19.076996	8	61	CC		KEEP	---	---	---	---	capture			Silent	SNP	7623387	7623387	4785	17	C	T	T	23	23	DNAH2	T	1	1
PSG4	5672	broad.mit.edu	36	19	48394257	48394257	+	Silent	SNP	G	A	A			TCGA-28-1745-01	TCGA-28-1745-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr19:48394257G>A	uc002ovy.1	-	c.441C>T	c.(439-441)CCC>CCT	p.P147P	PSG4_uc002ovz.1_Silent_p.P147P|PSG4_uc002owa.1_Non-coding_Transcript|PSG4_uc002owb.1_Intron	NM_002780	NP_002771	Q00888	PSG4_HUMAN	pregnancy specific beta-1-glycoprotein 4 isoform	147	Ig-like C2-type 1.				defense response|female pregnancy	extracellular region				ovary(1)	1		Prostate(69;0.00682)												0.13617	56.64778	86.765726	32	203	GG		KEEP	---	---	---	---	capture			Silent	SNP	48394257	48394257	13110	19	G	A	A	47	47	PSG4	A	2	2
WDR47	22911	broad.mit.edu	36	1	109348739	109348739	+	Missense_Mutation	SNP	C	T	T			TCGA-28-1745-01	TCGA-28-1745-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr1:109348739C>T	uc001dwi.1	-	c.1255G>A	c.(1255-1257)GAG>AAG	p.E419K	WDR47_uc001dwj.1_Missense_Mutation_p.E418K|WDR47_uc001dwk.1_Missense_Mutation_p.E390K|WDR47_uc001dwl.1_Missense_Mutation_p.E426K	NM_014969	NP_055784	O94967	WDR47_HUMAN	WD repeat domain 47 isoform 2	418										ovary(1)	1		all_lung(203;0.00519)|all_epithelial(167;0.00611)|Lung NSC(277;0.00822)		Colorectal(144;0.0165)|Lung(183;0.0484)|COAD - Colon adenocarcinoma(174;0.128)|Epithelial(280;0.168)|all cancers(265;0.201)|LUSC - Lung squamous cell carcinoma(189;0.244)										0.140351	12.559236	19.68046	8	49	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	109348739	109348739	17873	1	C	T	T	29	29	WDR47	T	2	2
PRG4	10216	broad.mit.edu	36	1	184543890	184543890	+	Missense_Mutation	SNP	A	C	C			TCGA-28-1745-01	TCGA-28-1745-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr1:184543890A>C	uc001gru.2	+	c.2416A>C	c.(2416-2418)ACC>CCC	p.T806P	PRG4_uc001grt.2_Missense_Mutation_p.T765P|PRG4_uc009wyl.1_Missense_Mutation_p.T713P|PRG4_uc009wym.1_Missense_Mutation_p.T672P	NM_005807	NP_005798	Q92954	PRG4_HUMAN	proteoglycan 4 isoform A	806	59 X 8 AA repeats of K-X-P-X-P-T-T-X.|53; approximate.				cell proliferation|immune response	extracellular region	polysaccharide binding|protein binding|scavenger receptor activity				0														0.5	6.312447	6.312447	3	3	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	184543890	184543890	12924	1	A	C	C	6	6	PRG4	C	4	4
KCNT2	343450	broad.mit.edu	36	1	194703541	194703541	+	Splice_Site_SNP	SNP	T	A	A			TCGA-28-1745-01	TCGA-28-1745-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr1:194703541T>A	uc001gtd.1	-	c.e7_splice_site			KCNT2_uc009wyt.1_Splice_Site_SNP|KCNT2_uc001gte.1_Splice_Site_SNP|KCNT2_uc001gtf.1_Splice_Site_SNP|KCNT2_uc001gtg.1_Splice_Site_SNP|KCNT2_uc009wyu.1_Splice_Site_SNP|KCNT2_uc009wyv.1_Splice_Site_SNP	NM_198503	NP_940905			potassium channel, subfamily T, member 2							voltage-gated potassium channel complex	ATP binding|calcium-activated potassium channel activity|catalytic activity|voltage-gated potassium channel activity			ovary(4)|breast(1)	5														0.235294	19.681858	21.862156	8	26	TT		KEEP	---	---	---	---	capture			Splice_Site_SNP	SNP	194703541	194703541	8397	1	T	A	A	55	55	KCNT2	A	5	4
IKBKE	9641	broad.mit.edu	36	1	204719017	204719017	+	Silent	SNP	A	G	G			TCGA-28-1745-01	TCGA-28-1745-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr1:204719017A>G	uc001hdz.1	+	c.1101A>G	c.(1099-1101)GCA>GCG	p.A367A	IKBKE_uc009xbv.1_Silent_p.A367A|IKBKE_uc001hea.1_Silent_p.A282A	NM_014002	NP_054721	Q14164	IKKE_HUMAN	IKK-related kinase epsilon	367					DNA damage response, signal transduction resulting in induction of apoptosis|innate immune response|MyD88-independent toll-like receptor signaling pathway|negative regulation of type I interferon production|positive regulation of I-kappaB kinase/NF-kappaB cascade|protein phosphorylation|Toll signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway	cytosol|endosome membrane|plasma membrane|PML body	ATP binding|IkappaB kinase activity|NF-kappaB-inducing kinase activity|protein binding			ovary(3)|lung(1)|central_nervous_system(1)|skin(1)	6	Breast(84;0.137)									537				0.307692	7.290996	7.722223	4	9	AA		KEEP	---	---	---	---	capture			Silent	SNP	204719017	204719017	7913	1	A	G	G	6	6	IKBKE	G	4	4
OR2T12	127064	broad.mit.edu	36	1	246524571	246524571	+	Missense_Mutation	SNP	G	C	C			TCGA-28-1745-01	TCGA-28-1745-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:246524571G>C	uc001iee.1	-	c.933C>G	c.(931-933)CAC>CAG	p.H311Q		NM_001004692	NP_001004692	Q8NG77	O2T12_HUMAN	olfactory receptor, family 2, subfamily T,	311	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)	1	all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0201)											0.14786	73.110168	103.602111	38	219	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	246524571	246524571	11425	1	G	C	C	44	44	OR2T12	C	3	3
LPHN2	23266	broad.mit.edu	36	1	82188617	82188617	+	Missense_Mutation	SNP	C	T	T			TCGA-28-1745-01	TCGA-28-1745-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr1:82188617C>T	uc001dit.2	+	c.1355C>T	c.(1354-1356)ACA>ATA	p.T452I	LPHN2_uc001dis.1_Intron|LPHN2_uc001diu.1_Missense_Mutation_p.T452I|LPHN2_uc001div.1_Missense_Mutation_p.T452I|LPHN2_uc009wcd.1_Missense_Mutation_p.T452I|LPHN2_uc001diw.1_Missense_Mutation_p.T23I	NM_012302	NP_036434	O95490	LPHN2_HUMAN	latrophilin 2 precursor	452	Extracellular (Potential).				neuropeptide signaling pathway	integral to membrane|plasma membrane	G-protein coupled receptor activity|latrotoxin receptor activity|sugar binding			ovary(2)|central_nervous_system(1)	3				all cancers(265;0.00142)|Epithelial(280;0.00829)|OV - Ovarian serous cystadenocarcinoma(397;0.077)|STAD - Stomach adenocarcinoma(256;0.248)										0.1875	26.865752	32.715348	12	52	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	82188617	82188617	9289	1	C	T	T	17	17	LPHN2	T	2	2
PCSK2	5126	broad.mit.edu	36	20	17394023	17394023	+	Missense_Mutation	SNP	C	T	T			TCGA-28-1745-01	TCGA-28-1745-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr20:17394023C>T	uc002wpm.1	+	c.1255C>T	c.(1255-1257)CGG>TGG	p.R419W	PCSK2_uc002wpl.1_Missense_Mutation_p.R400W|PCSK2_uc002wpn.1_Missense_Mutation_p.R73W	NM_002594	NP_002585	P16519	NEC2_HUMAN	proprotein convertase subtilisin/kexin type 2	419					enkephalin processing|insulin processing|islet amyloid polypeptide processing	extracellular space|membrane|soluble fraction|transport vesicle	serine-type endopeptidase activity	p.R419W(1)		ovary(3)|central_nervous_system(2)|large_intestine(1)|pancreas(1)	7					Insulin Glargine recombinant(DB00047)|Insulin Lyspro recombinant(DB00046)|Insulin recombinant(DB00030)|Insulin, porcine(DB00071)									0.244898	29.991796	32.885913	12	37	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	17394023	17394023	12022	20	C	T	T	19	19	PCSK2	T	1	1
IL17RA	23765	broad.mit.edu	36	22	15966757	15966757	+	Missense_Mutation	SNP	T	G	G			TCGA-28-1745-01	TCGA-28-1745-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr22:15966757T>G	uc002zly.1	+	c.958T>G	c.(958-960)TGG>GGG	p.W320G	IL17RA_uc010gqt.1_Intron	NM_014339	NP_055154	Q96F46	I17RA_HUMAN	interleukin 17A receptor precursor	320	Extracellular (Potential).				fibroblast activation|positive regulation of interleukin-23 production	integral to plasma membrane	interleukin-17 receptor activity				0		all_epithelial(15;0.0181)|Lung NSC(13;0.109)|all_lung(157;0.132)		Colorectal(9;0.241)										0.263158	8.866124	9.831477	5	14	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	15966757	15966757	7940	22	T	G	G	59	59	IL17RA	G	4	4
XPNPEP3	63929	broad.mit.edu	36	22	39650381	39650381	+	Missense_Mutation	SNP	A	C	C			TCGA-28-1745-01	TCGA-28-1745-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr22:39650381A>C	uc003azh.1	+	c.1306A>C	c.(1306-1308)ATG>CTG	p.M436L	XPNPEP3_uc003azi.1_Missense_Mutation_p.M357L	NM_022098	NP_071381	Q9NQH7	XPP3_HUMAN	X-prolyl aminopeptidase (aminopeptidase P) 3,	436					cellular process	mitochondrion	aminopeptidase activity|manganese ion binding|metallopeptidase activity				0						Ovarian(145;306 1841 7037 21878 30110)								0.203593	79.861495	93.479453	34	133	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	39650381	39650381	18027	22	A	C	C	8	8	XPNPEP3	C	4	4
BUB1	699	broad.mit.edu	36	2	111141715	111141715	+	Missense_Mutation	SNP	G	A	A			TCGA-28-1745-01	TCGA-28-1745-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr2:111141715G>A	uc002tgc.1	-	c.659C>T	c.(658-660)TCT>TTT	p.S220F	BUB1_uc010fkb.1_Missense_Mutation_p.S220F|BUB1_uc002tgd.1_Missense_Mutation_p.S220F	NM_004336	NP_004327	O43683	BUB1_HUMAN	budding uninhibited by benzimidazoles 1	220					apoptosis|cell division|chromosome segregation|interspecies interaction between organisms|mitotic cell cycle spindle assembly checkpoint|mitotic prometaphase|protein phosphorylation|regulation of sister chromatid cohesion	condensed chromosome kinetochore|cytosol	ATP binding|protein binding|protein serine/threonine kinase activity			ovary(1)|lung(1)|kidney(1)	3		Ovarian(717;0.0822)		BRCA - Breast invasive adenocarcinoma(221;0.0556)						375				0.181818	27.059411	33.337389	12	54	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	111141715	111141715	1604	2	G	A	A	33	33	BUB1	A	2	2
ARHGAP31	57514	broad.mit.edu	36	3	120615595	120615595	+	Missense_Mutation	SNP	C	G	G			TCGA-28-1745-01	TCGA-28-1745-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr3:120615595C>G	uc003ecj.2	+	c.2129C>G	c.(2128-2130)CCA>CGA	p.P710R		NM_020754	NP_065805	Q2M1Z3	RHG31_HUMAN	Cdc42 GTPase-activating protein	710	Pro-rich.				regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol|focal adhesion|lamellipodium	GTPase activator activity			ovary(2)	2						Pancreas(7;176 297 5394 51128 51241)								0.189474	22.571826	31.179413	18	77	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	120615595	120615595	892	3	C	G	G	21	21	ARHGAP31	G	3	3
CASR	846	broad.mit.edu	36	3	123486115	123486115	+	Missense_Mutation	SNP	G	C	C			TCGA-28-1745-01	TCGA-28-1745-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr3:123486115G>C	uc003eew.2	+	c.2654G>C	c.(2653-2655)AGC>ACC	p.S885T	CASR_uc003eev.2_Missense_Mutation_p.S875T	NM_000388	NP_000379	P41180	CASR_HUMAN	calcium-sensing receptor	875	Cytoplasmic (Potential).				anatomical structure morphogenesis|calcium ion import|cellular calcium ion homeostasis|chemosensory behavior|detection of calcium ion|ossification	integral to plasma membrane	G-protein coupled receptor activity|phosphatidylinositol phospholipase C activity			ovary(4)	4				GBM - Glioblastoma multiforme(114;0.226)	Cinacalcet(DB01012)									0.35514	114.320796	116.298808	38	69	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	123486115	123486115	2801	3	G	C	C	34	34	CASR	C	3	3
TMEM144	55314	broad.mit.edu	36	4	159373579	159373579	+	Missense_Mutation	SNP	G	A	A			TCGA-28-1745-01	TCGA-28-1745-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr4:159373579G>A	uc003ipx.1	+	c.490G>A	c.(490-492)GAG>AAG	p.E164K	TMEM144_uc010iqi.1_Non-coding_Transcript	NM_018342	NP_060812	Q7Z5S9	TM144_HUMAN	transmembrane protein 144	164						integral to membrane					0	all_hematologic(180;0.24)	Renal(120;0.0854)		COAD - Colon adenocarcinoma(41;0.0539)										0.162162	24.949813	32.983129	12	62	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	159373579	159373579	16590	4	G	A	A	33	33	TMEM144	A	2	2
EPHA5	2044	broad.mit.edu	36	4	65952718	65952718	+	Missense_Mutation	SNP	C	T	T			TCGA-28-1745-01	TCGA-28-1745-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr4:65952718C>T	uc003hcy.1	-	c.1759G>A	c.(1759-1761)GCA>ACA	p.A587T	EPHA5_uc003hcx.1_Missense_Mutation_p.A519T|EPHA5_uc003hcz.1_Missense_Mutation_p.A587T|EPHA5_uc003hda.1_Missense_Mutation_p.A588T	NM_004439	NP_004430	P54756	EPHA5_HUMAN	ephrin receptor EphA5 isoform a precursor	587	Helical; (Potential).				cAMP-mediated signaling|ephrin receptor signaling pathway|neuron development|protein phosphorylation	dendrite|external side of plasma membrane|integral to plasma membrane|neuronal cell body|perinuclear region of cytoplasm|rough endoplasmic reticulum	ATP binding|transmembrane-ephrin receptor activity			lung(12)|ovary(2)|central_nervous_system(1)	15										537	TSP Lung(17;0.13)			0.124031	17.084346	34.900285	16	113	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	65952718	65952718	5363	4	C	T	T	26	26	EPHA5	T	2	2
ATP10B	23120	broad.mit.edu	36	5	159972399	159972399	+	Missense_Mutation	SNP	G	A	A			TCGA-28-1745-01	TCGA-28-1745-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr5:159972399G>A	uc003lym.1	-	c.2765C>T	c.(2764-2766)GCG>GTG	p.A922V	ATP10B_uc010jit.1_Missense_Mutation_p.A239V|ATP10B_uc003lyn.2_Missense_Mutation_p.A480V	NM_025153	NP_079429	O94823	AT10B_HUMAN	ATPase, class V, type 10B	922	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			ovary(3)|central_nervous_system(1)|pancreas(1)	5	Renal(175;0.00196)	Medulloblastoma(196;0.0377)|all_neural(177;0.121)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)											0.160714	13.738463	19.880604	9	47	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	159972399	159972399	1136	5	G	A	A	38	38	ATP10B	A	1	1
SLIT3	6586	broad.mit.edu	36	5	168026139	168026139	+	Silent	SNP	G	A	A			TCGA-28-1745-01	TCGA-28-1745-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr5:168026139G>A	uc010jjg.1	-	c.4491C>T	c.(4489-4491)ACC>ACT	p.T1497T	SLIT3_uc003mab.1_Silent_p.T1490T	NM_003062	NP_003053	O75094	SLIT3_HUMAN	slit homolog 3	1490	CTCK.				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)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			Ovarian(29;311 847 10864 17279 24903)								0.222222	11.371066	13.93996	8	28	GG		KEEP	---	---	---	---	capture			Silent	SNP	168026139	168026139	15239	5	G	A	A	43	43	SLIT3	A	2	2
GCNT2	2651	broad.mit.edu	36	6	10729624	10729624	+	Missense_Mutation	SNP	A	C	C			TCGA-28-1745-01	TCGA-28-1745-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr6:10729624A>C	uc010joo.1	+	c.980A>C	c.(979-981)AAG>ACG	p.K327T	GCNT2_uc010jol.1_Missense_Mutation_p.K41T|GCNT2_uc010jom.1_Non-coding_Transcript|GCNT2_uc010jop.1_Non-coding_Transcript|GCNT2_uc003mza.1_Non-coding_Transcript|GCNT2_uc003mzc.2_Missense_Mutation_p.K326T|GCNT2_uc003mzd.1_Missense_Mutation_p.K325T|GCNT2_uc003mze.1_Missense_Mutation_p.K327T	NM_145649	NP_663624	Q8N0V5	GNT2A_HUMAN	glucosaminyl (N-acetyl) transferase 2,	327	Lumenal (Potential).					Golgi membrane|integral to membrane	N-acetyllactosaminide beta-1,6-N-acetylglucosaminyltransferase activity			ovary(2)	2	Ovarian(93;0.107)|Breast(50;0.148)	all_hematologic(90;0.107)		KIRC - Kidney renal clear cell carcinoma(1;0.099)|Kidney(1;0.119)						312				0.164835	15.661709	25.39238	15	76	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	10729624	10729624	6567	6	A	C	C	3	3	GCNT2	C	4	4
ADAT2	134637	broad.mit.edu	36	6	143795406	143795406	+	Nonsense_Mutation	SNP	G	A	A			TCGA-28-1745-01	TCGA-28-1745-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr6:143795406G>A	uc003qjj.1	-	c.388C>T	c.(388-390)CGA>TGA	p.R130*		NM_182503	NP_872309	Q7Z6V5	ADAT2_HUMAN	deaminase domain containing 1	130					tRNA processing		hydrolase activity|zinc ion binding				0				OV - Ovarian serous cystadenocarcinoma(155;5.61e-06)|GBM - Glioblastoma multiforme(68;0.0115)										0.253012	53.43682	58.035244	21	62	GG		KEEP	---	---	---	---	capture			Nonsense_Mutation	SNP	143795406	143795406	286	6	G	A	A	40	40	ADAT2	A	5	1
EGFR	1956	broad.mit.edu	36	7	55236460	55236460	+	Missense_Mutation	SNP	T	A	A			TCGA-28-1745-01	TCGA-28-1745-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr7:55236460T>A	uc003tqk.1	+	c.3032T>A	c.(3031-3033)GTG>GAG	p.V1011E	EGFR_uc010kzg.1_Missense_Mutation_p.V966E	NM_005228	NP_005219	P00533	EGFR_HUMAN	epidermal growth factor receptor isoform a	1011	Cytoplasmic (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			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)		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)		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)			0.189189	89.326428	109.392437	42	180	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	55236460	55236460	5156	7	T	A	A	59	59	EGFR	A	4	4
ZFAT	57623	broad.mit.edu	36	8	135718954	135718954	+	Missense_Mutation	SNP	T	C	C			TCGA-28-1745-01	TCGA-28-1745-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr8:135718954T>C	uc003yup.1	-	c.380A>G	c.(379-381)AAC>AGC	p.N127S	ZFAT_uc003yun.1_Missense_Mutation_p.N115S|ZFAT_uc003yuo.1_Missense_Mutation_p.N115S|ZFAT_uc010meh.1_Missense_Mutation_p.N115S|ZFAT_uc010mei.1_Non-coding_Transcript|ZFAT_uc003yuq.1_Missense_Mutation_p.N115S|ZFAT_uc010mej.1_Missense_Mutation_p.N127S|ZFAT_uc003yur.1_Missense_Mutation_p.N115S	NM_020863	NP_065914	Q9P243	ZFAT_HUMAN	zinc finger protein 406 isoform ZFAT-1	127	C2H2-type 2; degenerate.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytosol|nucleus	DNA binding|zinc ion binding			central_nervous_system(1)	1	all_epithelial(106;8.26e-19)|Lung NSC(106;3.47e-07)|all_lung(105;1.39e-06)|Ovarian(258;0.0102)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0432)											0.153226	36.94562	51.211166	19	105	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	135718954	135718954	18220	8	T	C	C	60	60	ZFAT	C	4	4
TNC	3371	broad.mit.edu	36	9	116889192	116889192	+	Silent	SNP	G	A	A			TCGA-28-1745-01	TCGA-28-1745-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr9:116889192G>A	uc004bjj.2	-	c.639C>T	c.(637-639)GGC>GGT	p.G213G	TNC_uc010mvf.1_Silent_p.G213G	NM_002160	NP_002151	P24821	TENA_HUMAN	tenascin C precursor	213	EGF-like 2.				cell adhesion|response to wounding|signal transduction	extracellular space	receptor binding|syndecan binding			central_nervous_system(4)|ovary(1)	5														0.419753	96.773994	97.217927	34	47	GG		KEEP	---	---	---	---	capture			Silent	SNP	116889192	116889192	16811	9	G	A	A	38	38	TNC	A	1	1
TLE1	7088	broad.mit.edu	36	9	83418227	83418227	+	Missense_Mutation	SNP	T	A	A			TCGA-28-1745-01	TCGA-28-1745-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr9:83418227T>A	uc004alz.1	-	c.978A>T	c.(976-978)AAA>AAT	p.K326N	TLE1_uc004aly.1_Missense_Mutation_p.K316N|TLE1_uc004ama.1_Missense_Mutation_p.K316N	NM_005077	NP_005068	Q04724	TLE1_HUMAN	transducin-like enhancer protein 1	316	Pro/Ser-rich.				negative regulation of Wnt receptor signaling pathway|organ morphogenesis|transcription, DNA-dependent|Wnt receptor signaling pathway		transcription factor binding			ovary(1)	1						NSCLC(155;1437 1995 30668 39354 45875)|Melanoma(16;266 781 14000 47728 51870)				350				0.54	266.322023	266.525812	81	69	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	83418227	83418227	16468	9	T	A	A	52	52	TLE1	A	4	4
TDRD7	23424	broad.mit.edu	36	9	99262838	99262838	+	Silent	SNP	A	G	G			TCGA-28-1745-01	TCGA-28-1745-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr9:99262838A>G	uc004axj.1	+	c.1413A>G	c.(1411-1413)GAA>GAG	p.E471E		NM_014290	NP_055105	Q8NHU6	TDRD7_HUMAN	tudor domain containing 7	471					lens fiber cell differentiation|lens morphogenesis in camera-type eye|posttranscriptional regulation of gene expression|spermatogenesis	chromatoid body	mRNA binding			ovary(2)|pancreas(1)	3		Acute lymphoblastic leukemia(62;0.158)												0.100917	11.450605	28.769466	11	98	AA		KEEP	---	---	---	---	capture			Silent	SNP	99262838	99262838	16262	9	A	G	G	2	2	TDRD7	G	4	4
FAM47A	158724	broad.mit.edu	36	X	34058779	34058779	+	Missense_Mutation	SNP	C	T	T			TCGA-28-1745-01	TCGA-28-1745-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chrX:34058779C>T	uc004ddg.1	-	c.1538G>A	c.(1537-1539)CGG>CAG	p.R513Q		NM_203408	NP_981953	Q5JRC9	FA47A_HUMAN	hypothetical protein LOC158724	513										ovary(4)|central_nervous_system(1)	5														0.25	10.769028	11.903414	5	15	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	34058779	34058779	5790	23	C	T	T	23	23	FAM47A	T	1	1
FAM47A	158724	broad.mit.edu	36	X	34058818	34058818	+	Missense_Mutation	SNP	C	T	T			TCGA-28-1745-01	TCGA-28-1745-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chrX:34058818C>T	uc004ddg.1	-	c.1499G>A	c.(1498-1500)CGG>CAG	p.R500Q		NM_203408	NP_981953	Q5JRC9	FA47A_HUMAN	hypothetical protein LOC158724	500			Missing.							ovary(4)|central_nervous_system(1)	5														0.4	42.243332	42.549254	14	21	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	34058818	34058818	5790	23	C	T	T	23	23	FAM47A	T	1	1
IGF2	3481	broad.mit.edu	36	11	2110817	2110818	+	Frame_Shift_Ins	INS	-	G	G			TCGA-28-1745-01	TCGA-28-1745-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:2110817_2110818insG	uc009ydf.1	-	c.686_687insC	c.(685-687)CCAfs	p.P229fs	IGF2_uc001lvf.1_Non-coding_Transcript|IGF2_uc009yde.1_Frame_Shift_Ins_p.P173fs|IGF2_uc001lvg.1_Frame_Shift_Ins_p.P173fs|IGF2_uc001lvh.1_Frame_Shift_Ins_p.P173fs|INS-IGF2_uc001lvi.1_Non-coding_Transcript	NM_001127598	NP_001121070	P01344	IGF2_HUMAN	insulin-like growth factor 2 isoform 2	173					glucose metabolic process|insulin receptor signaling pathway|ossification|positive regulation of cell division|positive regulation of cell proliferation|positive regulation of insulin receptor signaling pathway|positive regulation of MAPKKK cascade|positive regulation of mitosis|positive regulation of protein kinase B signaling cascade|regulation of gene expression by genetic imprinting|regulation of gene-specific transcription|skeletal system development	extracellular space	growth factor activity|hormone activity|insulin receptor binding|insulin-like growth factor receptor binding			central_nervous_system(1)	1		all_epithelial(84;5.04e-06)|Breast(177;0.000777)|Ovarian(85;0.0014)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.191)|all_lung(207;0.24)	Colorectal(5;0.0179)|COAD - Colon adenocarcinoma(6;0.029)	BRCA - Breast invasive adenocarcinoma(625;1.09e-05)|LUSC - Lung squamous cell carcinoma(625;0.082)|Lung(200;0.153)										0.44			4	5				---	---	---	---	capture_indel			Frame_Shift_Ins	INS	2110817	2110818	7873	11	-	G	G	55	55	IGF2	G	5	5
HGS	9146	broad.mit.edu	36	17	77273839	77273840	+	Frame_Shift_Ins	INS	-	G	G			TCGA-28-1745-01	TCGA-28-1745-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:77273839_77273840insG	uc002kbg.1	+	c.1441_1442insG	c.(1441-1443)CGGfs	p.R481fs		NM_004712	NP_004703	O14964	HGS_HUMAN	hepatocyte growth factor-regulated tyrosine	481	Interaction with STAM1 (By similarity).|Interaction with SNAP25 and TRAK2 (By similarity).|Interaction with SNX1 (By similarity).|Interaction with NF2.				cellular membrane organization|endosome transport|epidermal growth factor receptor signaling pathway|intracellular protein transport|negative regulation of cell proliferation|negative regulation of epidermal growth factor receptor signaling pathway|negative regulation of JAK-STAT cascade|regulation of protein catabolic process	cytosol|early endosome membrane|multivesicular body membrane	protein domain specific binding|zinc ion binding			ovary(1)	1	all_neural(118;0.0878)|all_lung(278;0.23)		BRCA - Breast invasive adenocarcinoma(99;0.0101)|OV - Ovarian serous cystadenocarcinoma(97;0.0955)											0.50			3	3				---	---	---	---	capture_indel			Frame_Shift_Ins	INS	77273839	77273840	7371	17	-	G	G	23	23	HGS	G	5	5
PTP4A3	11156	broad.mit.edu	36	8	142504373	142504373	+	Frame_Shift_Del	DEL	A	-	-			TCGA-28-1745-01	TCGA-28-1745-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:142504373_142504373delA	uc003ywg.1	+	c.149_149delA	c.(148-150)GAAfs	p.E50fs	PTP4A3_uc003ywh.1_Frame_Shift_Del_p.E50fs|PTP4A3_uc010met.1_Intron	NM_032611	NP_116000	O75365	TP4A3_HUMAN	protein tyrosine phosphatase type IVA, member 3	50						early endosome|plasma membrane	identical protein binding|prenylated protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity				0	all_cancers(97;2.55e-15)|all_epithelial(106;1.39e-13)|Lung NSC(106;2.07e-05)|all_lung(105;2.89e-05)|Ovarian(258;0.0303)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0474)											0.33			2	4				---	---	---	---	capture_indel			Frame_Shift_Del	DEL	142504373	142504373	13227	8	A	-	-	9	9	PTP4A3	-	5	5
