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
C10orf96	374355	broad.mit.edu	36	10	118074578	118074578	+	Missense_Mutation	SNP	G	A	A			TCGA-28-2510-01	TCGA-28-2510-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr10:118074578G>A	uc001lck.1	+	c.65G>A	c.(64-66)CGT>CAT	p.R22H		NM_198515	NP_940917	P0C7W6	CJ096_HUMAN	hypothetical protein LOC374355	22	Potential.									ovary(2)	2		Lung NSC(174;0.204)|all_lung(145;0.248)												0.269231	17.016484	18.264224	7	19	GG		KEEP	---	---	---	---	capture		all cancers(201;0.014)	Missense_Mutation	SNP	118074578	118074578	1664	10	G	A	A	40	40	C10orf96	A	1	1
PTEN	5728	broad.mit.edu	36	10	89701880	89701880	+	Missense_Mutation	SNP	G	A	A			TCGA-28-2510-01	TCGA-28-2510-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr10:89701880G>A	uc001kfb.1	+	c.518G>A	c.(517-519)CGC>CAC	p.R173H		NM_000314	NP_000305	P60484	PTEN_HUMAN	phosphatase and tensin homolog	173	Phosphatase tensin-type.		R -> C (in endometrial hyperplasia; loss of phosphatase activity towards Ins(1,3,4,5)P4 and PtdIns(3,4,5)P3; retains ability to bind phospholipid membranes).|R -> P (loss of phosphatase activity towards Ins(1,3,4,5)P4).|R -> H (loss of phosphatase activity towards Ins(1,3,4,5)P4).		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.R173H(22)|p.R173C(5)|p.V166fs*17(3)|p.G165fs*9(3)|p.Y27_N212>Y(2)|p.G165_K342del(1)|p.G165_*404del(1)|p.R173P(1)|p.R172fs*5(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)					R173H(RL952_ENDOMETRIUM)	31	p.R173H(RL952-Tumor)	264	TCGA GBM(2;<1E-8)|TSP Lung(26;0.18)			0.158537	21.723843	30.837158	13	69	GG		KEEP	---	---	---	---	capture	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)	Missense_Mutation	SNP	89701880	89701880	13192	10	G	A	A	38	38	PTEN	A	1	1
AHNAK	79026	broad.mit.edu	36	11	62052586	62052586	+	Missense_Mutation	SNP	A	G	G			TCGA-28-2510-01	TCGA-28-2510-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr11:62052586A>G	uc001ntl.1	-	c.5879T>C	c.(5878-5880)GTG>GCG	p.V1960A	AHNAK_uc001ntk.1_Intron	NM_001620	NP_001611	Q09666	AHNK_HUMAN	AHNAK nucleoprotein isoform 1	1960					nervous system development	nucleus	protein binding			ovary(10)|pancreas(4)	14		Melanoma(852;0.155)												0.171233	46.784353	61.755466	25	121	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	62052586	62052586	417	11	A	G	G	6	6	AHNAK	G	4	4
TTC9C	283237	broad.mit.edu	36	11	62259570	62259570	+	Missense_Mutation	SNP	G	C	C			TCGA-28-2510-01	TCGA-28-2510-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr11:62259570G>C	uc001nux.1	+	c.778G>C	c.(778-780)GCC>CCC	p.A260P	TTC9C_uc001nuy.1_Missense_Mutation_p.A127P	NM_173810	NP_776171	Q8N5M4	TTC9C_HUMAN	tetratricopeptide repeat domain 9C	127	TPR 3.						binding			ovary(1)|pancreas(1)	2														0.294118	10.934592	11.541849	5	12	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	62259570	62259570	17272	11	G	C	C	42	42	TTC9C	C	3	3
STAB2	55576	broad.mit.edu	36	12	102508929	102508929	+	Missense_Mutation	SNP	G	A	A			TCGA-28-2510-01	TCGA-28-2510-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr12:102508929G>A	uc001tjw.1	+	c.206G>A	c.(205-207)CGA>CAA	p.R69Q		NM_017564	NP_060034	Q8WWQ8	STAB2_HUMAN	stabilin 2 precursor	69	Extracellular (Potential).				angiogenesis|cell adhesion|defense response to bacterium|receptor-mediated endocytosis	cytoplasm|external side of plasma membrane|integral to plasma membrane	Gram-negative bacterial cell surface binding|hyaluronic acid binding|low-density lipoprotein receptor activity|protein disulfide oxidoreductase activity|scavenger receptor activity			ovary(9)|skin(1)	10														0.138889	16.308678	25.375966	10	62	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	102508929	102508929	15756	12	G	A	A	37	37	STAB2	A	1	1
CUX2	23316	broad.mit.edu	36	12	110232592	110232592	+	Silent	SNP	C	T	T			TCGA-28-2510-01	TCGA-28-2510-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr12:110232592C>T	uc001tsa.1	+	c.1623C>T	c.(1621-1623)GGC>GGT	p.G541G		NM_015267	NP_056082	O14529	CUX2_HUMAN	cut-like 2	541						nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			ovary(3)|breast(1)	4														0.230769	6.452276	7.292538	3	10	CC		KEEP	---	---	---	---	capture			Silent	SNP	110232592	110232592	4225	12	C	T	T	27	27	CUX2	T	1	1
KCNA6	3742	broad.mit.edu	36	12	4790534	4790534	+	Missense_Mutation	SNP	T	C	C			TCGA-28-2510-01	TCGA-28-2510-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr12:4790534T>C	uc001qnf.1	+	c.1066T>C	c.(1066-1068)TCC>CCC	p.S356P		NM_002235	NP_002226	P17658	KCNA6_HUMAN	potassium voltage-gated channel, shaker-related	356	Helical; Voltage-sensor; Name=Segment S4; (Potential).					voltage-gated potassium channel complex	voltage-gated potassium channel activity			ovary(1)|skin(1)	2														0.25	8.791366	9.701235	4	12	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	4790534	4790534	8312	12	T	C	C	54	54	KCNA6	C	4	4
ENO2	2026	broad.mit.edu	36	12	6901186	6901186	+	Silent	SNP	G	C	C	rs17849663	unknown	TCGA-28-2510-01	TCGA-28-2510-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr12:6901186G>C	uc001qru.1	+	c.1047G>C	c.(1045-1047)TCG>TCC	p.S349S	ENO2_uc009zfi.1_Silent_p.S349S|ENO2_uc001qrv.1_Silent_p.S349S|ATN1_uc001qrw.1_5'Flank	NM_001975	NP_001966	P09104	ENOG_HUMAN	enolase 2	349					gluconeogenesis|glycolysis	phosphopyruvate hydratase complex|plasma membrane	magnesium ion binding|phosphopyruvate hydratase activity				0														0.230769	7.164041	7.996059	3	10	GG		KEEP	---	---	---	---	capture			Silent	SNP	6901186	6901186	5315	12	G	C	C	39	39	ENO2	C	3	3
RBM25	58517	broad.mit.edu	36	14	72648056	72648056	+	Silent	SNP	T	C	C			TCGA-28-2510-01	TCGA-28-2510-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr14:72648056T>C	uc001xno.1	+	c.2085T>C	c.(2083-2085)TTT>TTC	p.F695F	RBM25_uc001xnp.1_Silent_p.F490F	NM_021239	NP_067062	P49756	RBM25_HUMAN	RNA binding motif protein 25	695					apoptosis|mRNA processing|regulation of alternative nuclear mRNA splicing, via spliceosome|RNA splicing	cytoplasm|nuclear speck	mRNA binding|nucleotide binding|protein binding			central_nervous_system(2)|ovary(1)|breast(1)	4														0.285714	57.127241	59.720982	18	45	TT		KEEP	---	---	---	---	capture		BRCA - Breast invasive adenocarcinoma(234;0.00362)|OV - Ovarian serous cystadenocarcinoma(108;0.0688)	Silent	SNP	72648056	72648056	13587	14	T	C	C	61	61	RBM25	C	4	4
ADAM10	102	broad.mit.edu	36	15	56691388	56691388	+	Missense_Mutation	SNP	A	C	C			TCGA-28-2510-01	TCGA-28-2510-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr15:56691388A>C	uc002afd.1	-	c.1606T>G	c.(1606-1608)TGT>GGT	p.C536G	ADAM10_uc010bgc.1_Non-coding_Transcript|ADAM10_uc002afe.1_Intron|ADAM10_uc002aff.1_Missense_Mutation_p.C73G	NM_001110	NP_001101	O14672	ADA10_HUMAN	ADAM metallopeptidase domain 10	536	Extracellular (Potential).|Disintegrin.				cell-cell signaling|constitutive protein ectodomain proteolysis|epidermal growth factor receptor signaling pathway|in utero embryonic development|integrin-mediated signaling pathway|monocyte activation|negative regulation of cell adhesion|Notch receptor processing|Notch signaling pathway|PMA-inducible membrane protein ectodomain proteolysis|positive regulation of cell growth|positive regulation of cell proliferation|positive regulation of T cell chemotaxis|protein phosphorylation|response to tumor necrosis factor	cell surface|endomembrane system|Golgi-associated vesicle|integral to membrane|nucleus|plasma membrane	integrin binding|metalloendopeptidase activity|protein homodimerization activity|protein kinase binding|SH3 domain binding|zinc ion binding			skin(1)	1										515				0.139535	12.537448	17.919613	6	37	AA		KEEP	---	---	---	---	capture		GBM - Glioblastoma multiforme(80;0.202)	Missense_Mutation	SNP	56691388	56691388	235	15	A	C	C	8	8	ADAM10	C	4	4
RLTPR	146206	broad.mit.edu	36	16	66239658	66239658	+	Missense_Mutation	SNP	C	T	T			TCGA-28-2510-01	TCGA-28-2510-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr16:66239658C>T	uc002etn.1	+	c.1274C>T	c.(1273-1275)TCC>TTC	p.S425F	RLTPR_uc010cel.1_Missense_Mutation_p.S425F	NM_001013838	NP_001013860	Q6F5E8	LR16C_HUMAN	RGD motif, leucine rich repeats, tropomodulin	425										breast(1)	1		Acute lymphoblastic leukemia(13;3.23e-05)|all_hematologic(13;0.00251)|Ovarian(137;0.192)												0.3	7.320344	7.678199	3	7	CC		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(108;0.0146)|Epithelial(162;0.0481)|all cancers(182;0.232)	Missense_Mutation	SNP	66239658	66239658	13871	16	C	T	T	30	30	RLTPR	T	2	2
CTAGE1	64693	broad.mit.edu	36	18	18251764	18251764	+	Silent	SNP	G	A	A			TCGA-28-2510-01	TCGA-28-2510-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr18:18251764G>A	uc002ktv.1	-	c.9C>T	c.(7-9)CCC>CCT	p.P3P		NM_172241	NP_758441	Q96RT6	CTGE2_HUMAN	cutaneous T-cell lymphoma-associated antigen 1	3						integral to membrane				ovary(1)	1	all_cancers(21;0.000361)|all_epithelial(16;9.61e-06)|Colorectal(14;0.0533)|Lung NSC(20;0.0605)|Ovarian(2;0.116)|all_lung(20;0.135)													0.307692	10.59487	11.023616	4	9	GG		KEEP	---	---	---	---	capture			Silent	SNP	18251764	18251764	4151	18	G	A	A	39	39	CTAGE1	A	1	1
OR7A5	26659	broad.mit.edu	36	19	14799368	14799368	+	Missense_Mutation	SNP	G	A	A			TCGA-28-2510-01	TCGA-28-2510-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr19:14799368G>A	uc002mzw.1	-	c.686C>T	c.(685-687)TCA>TTA	p.S229L	OR7A5_uc010dzt.1_Missense_Mutation_p.S229L	NM_017506	NP_059976	Q15622	OR7A5_HUMAN	olfactory receptor, family 7, subfamily A,	229	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			central_nervous_system(1)	1														0.148936	11.699046	17.252734	7	40	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	14799368	14799368	11627	19	G	A	A	45	45	OR7A5	A	2	2
USE1	55850	broad.mit.edu	36	19	17191035	17191035	+	Missense_Mutation	SNP	T	G	G			TCGA-28-2510-01	TCGA-28-2510-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr19:17191035T>G	uc002nfo.2	+	c.436T>G	c.(436-438)TCC>GCC	p.S146A	USE1_uc010eal.1_Intron	NM_018467	NP_060937	Q9NZ43	USE1_HUMAN	uncharacterized hematopoietic stem/progenitor	146	Cytoplasmic (Potential).				lysosomal transport|protein catabolic process|protein transport|secretion by cell|vesicle-mediated transport	endoplasmic reticulum membrane|integral to membrane	protein binding				0														0.357143	9.988464	10.275167	5	9	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	17191035	17191035	17593	19	T	G	G	58	58	USE1	G	4	4
HIPK4	147746	broad.mit.edu	36	19	45581883	45581883	+	Missense_Mutation	SNP	T	C	C			TCGA-28-2510-01	TCGA-28-2510-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr19:45581883T>C	uc002onp.1	-	c.469A>G	c.(469-471)ATT>GTT	p.I157V		NM_144685	NP_653286	Q8NE63	HIPK4_HUMAN	homeodomain interacting protein kinase 4	157	Protein kinase.				protein phosphorylation	cytoplasm	ATP binding|protein serine/threonine kinase activity			ovary(1)	1										108				0.160714	19.240539	25.374615	9	47	TT		KEEP	---	---	---	---	capture	Lung(22;4.95e-05)|LUSC - Lung squamous cell carcinoma(20;0.000292)		Missense_Mutation	SNP	45581883	45581883	7404	19	T	C	C	50	50	HIPK4	C	4	4
NLRP4	147945	broad.mit.edu	36	19	61064612	61064612	+	Silent	SNP	C	A	A			TCGA-28-2510-01	TCGA-28-2510-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr19:61064612C>A	uc002qmd.2	+	c.1905C>A	c.(1903-1905)ACC>ACA	p.T635T	NLRP4_uc002qme.1_Silent_p.T635T|NLRP4_uc002qmf.1_Silent_p.T560T|NLRP4_uc010etf.1_Silent_p.T466T	NM_134444	NP_604393	Q96MN2	NALP4_HUMAN	NLR family, pyrin domain containing 4	635							ATP binding			ovary(5)|lung(3)|kidney(1)|pancreas(1)	10		Colorectal(82;0.0002)|Ovarian(87;0.221)												0.151515	8.252588	12.091617	5	28	CC		KEEP	---	---	---	---	capture		GBM - Glioblastoma multiforme(193;0.0606)	Silent	SNP	61064612	61064612	10882	19	C	A	A	21	21	NLRP4	A	3	3
FLG	2312	broad.mit.edu	36	1	150546689	150546689	+	Missense_Mutation	SNP	T	C	C			TCGA-28-2510-01	TCGA-28-2510-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr1:150546689T>C	uc001ezu.1	-	c.7297A>G	c.(7297-7299)ACC>GCC	p.T2433A		NM_002016	NP_002007	P20930	FILA_HUMAN	filaggrin	2433	Ser-rich.				keratinocyte differentiation	cytoplasmic membrane-bounded vesicle|intermediate filament	calcium ion binding|structural molecule activity			ovary(9)	9	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)													0.123853	40.464564	70.585961	27	191	TT		KEEP	---	---	---	---	capture	LUSC - Lung squamous cell carcinoma(543;0.206)		Missense_Mutation	SNP	150546689	150546689	6160	1	T	C	C	58	58	FLG	C	4	4
PABPC4	8761	broad.mit.edu	36	1	39814069	39814069	+	Missense_Mutation	SNP	T	G	G			TCGA-28-2510-01	TCGA-28-2510-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr1:39814069T>G	uc001cdl.1	-	c.142A>C	c.(142-144)ACC>CCC	p.T48P	PABPC4_uc001cdm.1_Missense_Mutation_p.T48P|PABPC4_uc001cdn.1_Missense_Mutation_p.T48P	NM_003819	NP_003810	Q13310	PABP4_HUMAN	poly A binding protein, cytoplasmic 4 isoform 2	48	RRM 1.				blood coagulation|RNA catabolic process|RNA processing|translation	cytoplasm|ribonucleoprotein complex	nucleotide binding|poly(A) RNA binding|poly(U) RNA binding|protein binding				0	Lung NSC(20;1.55e-06)|Ovarian(52;0.00769)|all_hematologic(146;0.0501)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)												0.25	8.189251	9.101407	4	12	TT		KEEP	---	---	---	---	capture	OV - Ovarian serous cystadenocarcinoma(33;2.89e-18)|Epithelial(16;6.17e-17)|all cancers(16;1.18e-15)|LUSC - Lung squamous cell carcinoma(16;0.000261)|Lung(16;0.000457)		Missense_Mutation	SNP	39814069	39814069	11781	1	T	G	G	59	59	PABPC4	G	4	4
SEMA4C	54910	broad.mit.edu	36	2	96890742	96890742	+	Missense_Mutation	SNP	G	C	C			TCGA-28-2510-01	TCGA-28-2510-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr2:96890742G>C	uc002sxg.2	-	c.2009C>G	c.(2008-2010)GCC>GGC	p.A670G	SEMA4C_uc002sxf.2_Missense_Mutation_p.A117G|SEMA4C_uc002sxh.2_Missense_Mutation_p.A617G|SEMA4C_uc002sxe.2_Missense_Mutation_p.A158G	NM_017789	NP_060259	Q9C0C4	SEM4C_HUMAN	semaphorin 4C	617	Extracellular (Potential).|Ig-like C2-type.				muscle cell differentiation|nervous system development|positive regulation of stress-activated MAPK cascade	cell junction|integral to membrane|postsynaptic density|postsynaptic membrane|synaptic vesicle membrane	receptor activity			skin(1)	1														0.5	7.454185	7.454185	5	5	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	96890742	96890742	14519	2	G	C	C	42	42	SEMA4C	C	3	3
MUC4	4585	broad.mit.edu	36	3	197000447	197000447	+	Missense_Mutation	SNP	G	A	A			TCGA-28-2510-01	TCGA-28-2510-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr3:197000447G>A	uc010hzt.1	-	c.2399C>T	c.(2398-2400)GCG>GTG	p.A800V	MUC4_uc003fvo.1_Intron|MUC4_uc003fvp.1_Intron|MUC4_uc010hzu.1_Missense_Mutation_p.A682V	NM_018406	NP_060876	Q99102	MUC4_HUMAN	mucin 4 isoform a	805	Ser-rich.				cell-matrix adhesion	integral to plasma membrane|proteinaceous extracellular matrix	ErbB-2 class receptor binding|extracellular matrix constituent, lubricant activity				0	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)												0.130952	12.592791	23.69902	11	73	GG		KEEP	---	---	---	---	capture	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)	Missense_Mutation	SNP	197000447	197000447	10372	3	G	A	A	38	38	MUC4	A	1	1
CLCN3	1182	broad.mit.edu	36	4	170846941	170846941	+	Missense_Mutation	SNP	C	G	G			TCGA-28-2510-01	TCGA-28-2510-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr4:170846941C>G	uc003ish.1	+	c.591C>G	c.(589-591)ATC>ATG	p.I197M	CLCN3_uc003isi.1_Missense_Mutation_p.I197M|CLCN3_uc003isj.1_Missense_Mutation_p.I170M	NM_173872	NP_776297	P51790	CLCN3_HUMAN	chloride channel 3 isoform e	197					endosomal lumen acidification	cell surface|early endosome membrane|Golgi membrane|integral to membrane|late endosome membrane|transport vesicle membrane	antiporter activity|ATP binding|PDZ domain binding|protein heterodimerization activity|protein homodimerization activity|voltage-gated chloride channel activity			breast(2)|ovary(1)	3		Prostate(90;0.00601)|Renal(120;0.0183)												0.134615	12.786058	19.520013	7	45	CC		KEEP	---	---	---	---	capture		GBM - Glioblastoma multiforme(119;0.0233)|LUSC - Lung squamous cell carcinoma(193;0.131)	Missense_Mutation	SNP	170846941	170846941	3600	4	C	G	G	29	29	CLCN3	G	3	3
LIN54	132660	broad.mit.edu	36	4	84124822	84124822	+	Missense_Mutation	SNP	G	C	C			TCGA-28-2510-01	TCGA-28-2510-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr4:84124822G>C	uc003hnx.2	-	c.200C>G	c.(199-201)ACA>AGA	p.T67R	LIN54_uc003hnz.2_Intron|LIN54_uc003hny.2_Intron|LIN54_uc010ijt.1_Missense_Mutation_p.T67R|LIN54_uc010iju.1_5'UTR|LIN54_uc010ijv.1_Intron	NM_194282	NP_919258	Q6MZP7	LIN54_HUMAN	lin-54 homolog isoform a	67					cell cycle|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding				0		Hepatocellular(203;0.114)												0.161765	25.879264	33.279446	11	57	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	84124822	84124822	9136	4	G	C	C	48	48	LIN54	C	3	3
SAMD9	54809	broad.mit.edu	36	7	92569799	92569799	+	Missense_Mutation	SNP	G	A	A			TCGA-28-2510-01	TCGA-28-2510-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr7:92569799G>A	uc003umf.1	-	c.3548C>T	c.(3547-3549)CCG>CTG	p.P1183L	SAMD9_uc003umg.1_Missense_Mutation_p.P1183L|SAMD9_uc010lfa.1_Missense_Mutation_p.P1183L	NM_017654	NP_060124	Q5K651	SAMD9_HUMAN	sterile alpha motif domain containing 9	1183						cytoplasm				ovary(3)|breast(1)|central_nervous_system(1)	5	all_cancers(62;5.71e-11)|all_epithelial(64;3.25e-10)|Breast(17;0.000675)|Lung NSC(181;0.0969)|all_lung(186;0.125)													0.116883	21.572358	43.778701	18	136	GG		KEEP	---	---	---	---	capture	STAD - Stomach adenocarcinoma(171;0.000302)		Missense_Mutation	SNP	92569799	92569799	14306	7	G	A	A	39	39	SAMD9	A	1	1
PKHD1L1	93035	broad.mit.edu	36	8	110532394	110532394	+	Missense_Mutation	SNP	C	A	A			TCGA-28-2510-01	TCGA-28-2510-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr8:110532394C>A	uc003yne.1	+	c.6190C>A	c.(6190-6192)CAA>AAA	p.Q2064K		NM_177531	NP_803875	Q86WI1	PKHL1_HUMAN	fibrocystin L	2064	Extracellular (Potential).|IPT/TIG 13.				immune response	cytosol|extracellular space|integral to membrane	receptor activity			ovary(9)|central_nervous_system(2)|large_intestine(1)|breast(1)|pancreas(1)	14												OREG0018931	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	0.25	7.289538	8.201878	4	12	CC		KEEP	---	---	---	---	capture	OV - Ovarian serous cystadenocarcinoma(57;9.88e-13)		Missense_Mutation	SNP	110532394	110532394	12397	8	C	A	A	25	25	PKHD1L1	A	3	3
NUP188	23511	broad.mit.edu	36	9	130804004	130804004	+	Silent	SNP	A	G	G			TCGA-28-2510-01	TCGA-28-2510-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr9:130804004A>G	uc004bws.1	+	c.4065A>G	c.(4063-4065)GGA>GGG	p.G1355G	NUP188_uc004bwu.2_Silent_p.G698G	NM_015354	NP_056169	Q5SRE5	NU188_HUMAN	nucleoporin 188kDa	1355					carbohydrate metabolic process|glucose transport|mRNA transport|protein transport|regulation of glucose transport|transmembrane transport|viral reproduction	nuclear pore	protein binding			ovary(2)|central_nervous_system(2)|kidney(1)|breast(1)	6														0.214286	9.054011	11.292368	6	22	AA		KEEP	---	---	---	---	capture			Silent	SNP	130804004	130804004	11163	9	A	G	G	11	11	NUP188	G	4	4
SNAPC4	6621	broad.mit.edu	36	9	138402740	138402740	+	Missense_Mutation	SNP	C	G	G			TCGA-28-2510-01	TCGA-28-2510-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr9:138402740C>G	uc004chh.1	-	c.1100G>C	c.(1099-1101)GGC>GCC	p.G367A		NM_003086	NP_003077	Q5SXM2	SNPC4_HUMAN	small nuclear RNA activating complex,	367	Myb-like 2.				regulation of transcription, DNA-dependent|snRNA transcription from RNA polymerase II promoter|snRNA transcription from RNA polymerase III promoter	snRNA-activating protein complex	DNA binding|sequence-specific DNA binding transcription factor activity				0		Myeloproliferative disorder(178;0.0511)												0.222222	7.588294	8.868781	4	14	CC		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(145;5.31e-06)|Epithelial(140;7.13e-06)	Missense_Mutation	SNP	138402740	138402740	15337	9	C	G	G	26	26	SNAPC4	G	3	3
BEND2	139105	broad.mit.edu	36	X	18105632	18105632	+	Silent	SNP	C	T	T			TCGA-28-2510-01	TCGA-28-2510-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chrX:18105632C>T	uc004cyj.2	-	c.1608G>A	c.(1606-1608)CCG>CCA	p.P536P	BEND2_uc010nfb.1_Silent_p.P445P	NM_153346	NP_699177	Q8NDZ0	BEND2_HUMAN	BEN domain containing 2	536	BEN 1.							p.P536P(1)		ovary(3)|kidney(1)|central_nervous_system(1)	5														0.23053	179.8197	201.157525	74	247	CC		KEEP	---	---	---	---	capture			Silent	SNP	18105632	18105632	1421	23	C	T	T	31	31	BEND2	T	1	1
YY2	404281	broad.mit.edu	36	X	21785272	21785272	+	Missense_Mutation	SNP	C	T	T			TCGA-28-2510-01	TCGA-28-2510-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chrX:21785272C>T	uc010nfq.1	+	c.1403C>T	c.(1402-1404)CCT>CTT	p.P468L	MBTPS2_uc004dab.1_Intron|MBTPS2_uc004dac.1_Intron|MBTPS2_uc010nfr.1_Intron|YY2_uc004dad.1_Missense_Mutation_p.P250L	NM_206923	NP_996806	O15391	TYY2_HUMAN	YY2 transcription factor	250	Mediates transcriptional repression.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus|plasma membrane	DNA binding|zinc ion binding			breast(1)|skin(1)	2														0.3	192.056681	199.928335	66	154	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	21785272	21785272	18092	23	C	T	T	24	24	YY2	T	2	2
