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
TMPRSS13	84000	broad.mit.edu	36	11	117294610	117294610	+	Missense_Mutation	SNP	C	T	T			TCGA-76-4928-01	TCGA-76-4928-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr11:117294610C>T	uc001prs.1	-	c.175G>A	c.(175-177)GCA>ACA	p.A59T	TMPRSS13_uc009yzr.1_5'UTR|TMPRSS13_uc001prt.1_5'UTR|TMPRSS13_uc001pru.1_Missense_Mutation_p.A59T	NM_001077263	NP_001070731	Q1RMF8	Q1RMF8_HUMAN	transmembrane protease, serine 13	59					proteolysis	membrane	scavenger receptor activity|serine-type endopeptidase activity			pancreas(1)	1	all_hematologic(175;0.0487)	Medulloblastoma(222;0.0425)|all_hematologic(192;0.196)|all_neural(223;0.234)												0.23	47.659336	54.36219	23	77	CC		KEEP	---	---	---	---	capture		BRCA - Breast invasive adenocarcinoma(274;1.78e-05)|Epithelial(105;0.00106)	Missense_Mutation	SNP	117294610	117294610	16786	11	C	T	T	26	26	TMPRSS13	T	2	2
TREH	11181	broad.mit.edu	36	11	118035385	118035385	+	Missense_Mutation	SNP	T	C	C			TCGA-76-4928-01	TCGA-76-4928-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr11:118035385T>C	uc001pty.1	-	c.1336A>G	c.(1336-1338)ACT>GCT	p.T446A	TREH_uc009zaj.1_Missense_Mutation_p.T415A|TREH_uc001ptz.1_Missense_Mutation_p.T323A	NM_007180	NP_009111	O43280	TREA_HUMAN	trehalase	446					polysaccharide digestion|trehalose catabolic process	anchored to plasma membrane	alpha,alpha-trehalase activity			pancreas(1)	1	all_hematologic(175;0.0839)	Medulloblastoma(222;0.0425)|all_hematologic(192;0.0564)|all_neural(223;0.112)										OREG0021385	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	0.222222	7.988311	9.27001	4	14	TT		KEEP	---	---	---	---	capture		BRCA - Breast invasive adenocarcinoma(274;3.16e-05)	Missense_Mutation	SNP	118035385	118035385	17013	11	T	C	C	58	58	TREH	C	4	4
LUZP2	338645	broad.mit.edu	36	11	25056729	25056729	+	Silent	SNP	A	G	G			TCGA-76-4928-01	TCGA-76-4928-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr11:25056729A>G	uc001mqs.1	+	c.990A>G	c.(988-990)AAA>AAG	p.K330K	LUZP2_uc009yif.1_Silent_p.K244K|LUZP2_uc009yig.1_Silent_p.K288K	NM_001009909	NP_001009909	Q86TE4	LUZP2_HUMAN	leucine zipper protein 2	330						extracellular region				ovary(1)	1														0.113636	24.136069	43.564054	15	117	AA		KEEP	---	---	---	---	capture			Silent	SNP	25056729	25056729	9463	11	A	G	G	2	2	LUZP2	G	4	4
SPRYD5	84767	broad.mit.edu	36	11	55412131	55412131	+	Missense_Mutation	SNP	G	T	T			TCGA-76-4928-01	TCGA-76-4928-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr11:55412131G>T	uc001nia.1	+	c.78G>T	c.(76-78)AAG>AAT	p.K26N		NM_032681	NP_116070	Q9BSJ1	SPRY5_HUMAN	SPRY domain containing 5	185						intracellular	zinc ion binding				0		all_epithelial(135;0.226)												0.142857	16.906157	28.1025	13	78	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	55412131	55412131	15625	11	G	T	T	33	33	SPRYD5	T	3	3
MRPS35	60488	broad.mit.edu	36	12	27799642	27799642	+	Missense_Mutation	SNP	G	A	A			TCGA-76-4928-01	TCGA-76-4928-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr12:27799642G>A	uc001rih.1	+	c.964G>A	c.(964-966)GTG>ATG	p.V322M	MRPS35_uc001rii.1_3'UTR	NM_021821	NP_068593	P82673	RT35_HUMAN	mitochondrial ribosomal protein S35	322					DNA damage response, detection of DNA damage|peptide biosynthetic process	mitochondrial small ribosomal subunit					0	Lung SC(9;0.0873)													0.126866	38.343684	74.768698	34	234	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	27799642	27799642	10237	12	G	A	A	48	48	MRPS35	A	2	2
CCND2	894	broad.mit.edu	36	12	4268290	4268290	+	Missense_Mutation	SNP	C	G	G			TCGA-76-4928-01	TCGA-76-4928-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr12:4268290C>G	uc001qmo.1	+	c.593C>G	c.(592-594)CCA>CGA	p.P198R		NM_001759	NP_001750	P30279	CCND2_HUMAN	cyclin D2	198					cell division|positive regulation of cyclin-dependent protein kinase activity|positive regulation of protein phosphorylation	cyclin-dependent protein kinase holoenzyme complex|cytoplasm|membrane|nucleus	protein kinase binding			kidney(1)	1										84				0.114754	53.779224	107.314641	42	324	CC		KEEP	---	---	---	---	capture	all cancers(3;4.15e-10)|GBM - Glioblastoma multiforme(3;6.34e-05)|Colorectal(7;0.00245)|OV - Ovarian serous cystadenocarcinoma(31;0.00301)|COAD - Colon adenocarcinoma(12;0.0264)|STAD - Stomach adenocarcinoma(119;0.206)		Missense_Mutation	SNP	4268290	4268290	3044	12	C	G	G	21	21	CCND2	G	3	3
GLI1	2735	broad.mit.edu	36	12	56150385	56150385	+	Missense_Mutation	SNP	G	A	A			TCGA-76-4928-01	TCGA-76-4928-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr12:56150385G>A	uc001snx.1	+	c.1595G>A	c.(1594-1596)CGC>CAC	p.R532H		NM_005269	NP_005260	P08151	GLI1_HUMAN	glioma-associated oncogene homolog 1	532					epidermal cell differentiation|negative regulation of canonical Wnt receptor signaling pathway|osteoblast differentiation|positive regulation of DNA replication|positive regulation of gene-specific transcription|positive regulation of smoothened signaling pathway|positive regulation of transcription from RNA polymerase II promoter	cytosol|nucleus	promoter binding|transcription activator activity|zinc ion binding			ovary(4)|breast(3)|skin(3)|central_nervous_system(1)|urinary_tract(1)|kidney(1)|pancreas(1)	14						Pancreas(157;841 1936 10503 41495 50368)				277				0.207018	111.090207	133.764125	59	226	GG		KEEP	---	---	---	---	capture	GBM - Glioblastoma multiforme(3;3.99e-32)		Missense_Mutation	SNP	56150385	56150385	6705	12	G	A	A	38	38	GLI1	A	1	1
ACSM4	341392	broad.mit.edu	36	12	7361956	7361956	+	Missense_Mutation	SNP	G	A	A			TCGA-76-4928-01	TCGA-76-4928-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr12:7361956G>A	uc001qsx.1	+	c.832G>A	c.(832-834)GCC>ACC	p.A278T		NM_001080454	NP_001073923	P0C7M7	ACSM4_HUMAN	acyl-CoA synthetase medium-chain family member	278					fatty acid metabolic process	mitochondrial matrix	ATP binding|butyrate-CoA ligase activity|metal ion binding				0														0.118644	11.378999	28.231331	14	104	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	7361956	7361956	187	12	G	A	A	38	38	ACSM4	A	1	1
SLC6A15	55117	broad.mit.edu	36	12	83794477	83794477	+	Missense_Mutation	SNP	A	T	T			TCGA-76-4928-01	TCGA-76-4928-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr12:83794477A>T	uc001szv.1	-	c.797T>A	c.(796-798)ATT>AAT	p.I266N		NM_182767	NP_877499	Q9H2J7	S6A15_HUMAN	solute carrier family 6, member 15 isoform 1	266	Helical; Name=5; (Potential).				cellular nitrogen compound metabolic process|leucine transport|proline transport	integral to plasma membrane	amino acid transmembrane transporter activity|neurotransmitter:sodium symporter activity			pancreas(2)|ovary(1)	3														0.23741	85.708083	94.46334	33	106	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	83794477	83794477	15175	12	A	T	T	4	4	SLC6A15	T	4	4
ATP12A	479	broad.mit.edu	36	13	24161441	24161441	+	Silent	SNP	G	A	A			TCGA-76-4928-01	TCGA-76-4928-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr13:24161441G>A	uc010aaa.1	+	c.474G>A	c.(472-474)ACG>ACA	p.T158T	ATP12A_uc001upp.1_Silent_p.T158T	NM_001676	NP_001667	P54707	AT12A_HUMAN	hydrogen/potassium-exchanging ATPase 12A	158	Helical; (Potential).				ATP biosynthetic process	hydrogen:potassium-exchanging ATPase complex	ATP binding|hydrogen:potassium-exchanging ATPase activity|metal ion binding			ovary(2)|central_nervous_system(2)|large_intestine(1)|breast(1)	6		Lung SC(185;0.0225)|Breast(139;0.077)			Esomeprazole(DB00736)|Pantoprazole(DB00213)	Pancreas(156;1582 1935 18898 22665 26498)								0.124294	25.715941	50.161227	22	155	GG		KEEP	---	---	---	---	capture		all cancers(112;0.0307)|Epithelial(112;0.086)|OV - Ovarian serous cystadenocarcinoma(117;0.228)	Silent	SNP	24161441	24161441	1141	13	G	A	A	39	39	ATP12A	A	1	1
TTC5	91875	broad.mit.edu	36	14	19837405	19837405	+	Missense_Mutation	SNP	G	A	A			TCGA-76-4928-01	TCGA-76-4928-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr14:19837405G>A	uc001vwt.1	-	c.439C>T	c.(439-441)CGT>TGT	p.R147C	TTC5_uc001vwu.1_Missense_Mutation_p.R4C	NM_138376	NP_612385	Q8N0Z6	TTC5_HUMAN	tetratricopeptide repeat domain 5	147					DNA repair	cytoplasm|nucleus	binding			ovary(1)	1	all_cancers(95;0.00092)													0.178862	40.671287	52.614338	22	101	GG		KEEP	---	---	---	---	capture	Epithelial(56;1.1e-06)|all cancers(55;8.07e-06)	GBM - Glioblastoma multiforme(265;0.0106)	Missense_Mutation	SNP	19837405	19837405	17266	14	G	A	A	37	37	TTC5	A	1	1
ISM2	145501	broad.mit.edu	36	14	77018731	77018731	+	Silent	SNP	G	A	A			TCGA-76-4928-01	TCGA-76-4928-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr14:77018731G>A	uc001xtz.1	-	c.660C>T	c.(658-660)GCC>GCT	p.A220A	ISM2_uc001xty.1_Silent_p.A132A|ISM2_uc001xua.1_Intron	NM_199296	NP_954874	Q6H9L7	ISM2_HUMAN	isthmin 2 homolog isoform 1	220						extracellular region					0														0.106481	18.975823	52.182598	23	193	GG		KEEP	---	---	---	---	capture			Silent	SNP	77018731	77018731	8165	14	G	A	A	39	39	ISM2	A	1	1
HYDIN	54768	broad.mit.edu	36	16	69475390	69475390	+	Missense_Mutation	SNP	C	T	T			TCGA-76-4928-01	TCGA-76-4928-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr16:69475390C>T	uc002ezr.1	-	c.9910G>A	c.(9910-9912)GGC>AGC	p.G3304S		NM_032821	NP_116210	Q4G0P3	HYDIN_HUMAN	hydrocephalus inducing isoform a	3305										ovary(1)	1		Ovarian(137;0.0654)												0.143836	30.755756	48.528775	21	125	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	69475390	69475390	7767	16	C	T	T	23	23	HYDIN	T	1	1
GRIN2A	2903	broad.mit.edu	36	16	9764672	9764672	+	Silent	SNP	C	T	T			TCGA-76-4928-01	TCGA-76-4928-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr16:9764672C>T	uc002czp.1	-	c.4230G>A	c.(4228-4230)TCG>TCA	p.S1410S	GRIN2A_uc002czq.1_Silent_p.S1410S|GRIN2A_uc002czr.2_3'UTR|GRIN2A_uc002czo.2_5'Flank	NM_000833	NP_000824	Q12879	NMDE1_HUMAN	N-methyl-D-aspartate receptor subunit 2A isoform	1410	Cytoplasmic (Potential).				response to ethanol	cell junction|N-methyl-D-aspartate selective glutamate receptor complex|outer membrane-bounded periplasmic space|postsynaptic membrane	N-methyl-D-aspartate selective glutamate receptor activity|zinc ion binding			ovary(4)|lung(1)|breast(1)|kidney(1)|skin(1)	8					Felbamate(DB00949)|Glycine(DB00145)|L-Glutamic Acid(DB00142)|Loperamide(DB00836)|Memantine(DB01043)					324				0.114943	7.18175	19.913927	10	77	CC		KEEP	---	---	---	---	capture			Silent	SNP	9764672	9764672	7058	16	C	T	T	19	19	GRIN2A	T	1	1
MYH8	4626	broad.mit.edu	36	17	10256768	10256768	+	Missense_Mutation	SNP	C	T	T			TCGA-76-4928-01	TCGA-76-4928-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr17:10256768C>T	uc002gmm.2	-	c.1150G>A	c.(1150-1152)GCT>ACT	p.A384T		NM_002472	NP_002463	P13535	MYH8_HUMAN	myosin, heavy chain 8, skeletal muscle,	384	Myosin head-like.				muscle filament sliding	cytosol|muscle myosin complex|myofibril|myosin filament	actin binding|ATP binding|calmodulin binding|motor activity|structural constituent of muscle			ovary(3)|breast(2)	5														0.227106	133.32475	151.978165	62	211	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	10256768	10256768	10436	17	C	T	T	27	27	MYH8	T	1	1
ORMDL3	94103	broad.mit.edu	36	17	35333924	35333924	+	Missense_Mutation	SNP	C	T	T			TCGA-76-4928-01	TCGA-76-4928-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr17:35333924C>T	uc002htj.1	-	c.59G>A	c.(58-60)CGT>CAT	p.R20H	ORMDL3_uc002hti.1_Non-coding_Transcript|ORMDL3_uc002htk.1_Missense_Mutation_p.R20H	NM_139280	NP_644809	Q8N138	ORML3_HUMAN	ORM1-like 3	20	Cytoplasmic (Potential).				ceramide metabolic process	integral to membrane|SPOTS complex	protein binding				0	Colorectal(19;0.000442)									24				0.230159	62.706338	71.12036	29	97	CC		KEEP	---	---	---	---	capture	Lung(15;0.0234)		Missense_Mutation	SNP	35333924	35333924	11682	17	C	T	T	19	19	ORMDL3	T	1	1
CNTNAP1	8506	broad.mit.edu	36	17	38090561	38090561	+	Silent	SNP	G	A	A			TCGA-76-4928-01	TCGA-76-4928-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr17:38090561G>A	uc002iay.1	+	c.390G>A	c.(388-390)TCG>TCA	p.S130S		NM_003632	NP_003623	P78357	CNTP1_HUMAN	contactin associated protein 1 precursor	130	Extracellular (Potential).|F5/8 type C.				axon guidance|cell adhesion	paranode region of axon	receptor activity|receptor binding|SH3 domain binding|SH3/SH2 adaptor activity			ovary(2)	2		Breast(137;0.000143)												0.212766	42.58798	49.727489	20	74	GG		KEEP	---	---	---	---	capture		BRCA - Breast invasive adenocarcinoma(366;0.143)	Silent	SNP	38090561	38090561	3784	17	G	A	A	39	39	CNTNAP1	A	1	1
WIPI1	55062	broad.mit.edu	36	17	63960673	63960673	+	Missense_Mutation	SNP	C	T	T			TCGA-76-4928-01	TCGA-76-4928-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr17:63960673C>T	uc010dey.1	-	c.136G>A	c.(136-138)GAG>AAG	p.E46K	WIPI1_uc002jhd.2_Non-coding_Transcript|WIPI1_uc002jhe.2_Intron	NM_017983	NP_060453	Q5MNZ9	WIPI1_HUMAN	WD repeat domain, phosphoinositide interacting	46					macroautophagy|vesicle targeting, trans-Golgi to endosome	autophagic vacuole membrane|clathrin-coated vesicle|cytosol|endosome membrane|PAS complex|pre-autophagosomal structure membrane|trans-Golgi network	androgen receptor binding|estrogen receptor binding|phosphatidylinositol-3,5-bisphosphate binding|phosphatidylinositol-3-phosphate binding				0														0.21519	37.932627	43.84915	17	62	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	63960673	63960673	17944	17	C	T	T	30	30	WIPI1	T	2	2
SLC16A5	9121	broad.mit.edu	36	17	70608015	70608015	+	Missense_Mutation	SNP	G	A	A			TCGA-76-4928-01	TCGA-76-4928-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr17:70608015G>A	uc002jmr.1	+	c.662G>A	c.(661-663)CGG>CAG	p.R221Q	SLC16A5_uc002jms.1_Missense_Mutation_p.R221Q|SLC16A5_uc002jmt.1_Missense_Mutation_p.R221Q|SLC16A5_uc002jmu.1_Missense_Mutation_p.R221Q	NM_004695	NP_004686	O15375	MOT6_HUMAN	solute carrier family 16, member 5	221	Cytoplasmic (Potential).				organic anion transport	integral to plasma membrane|membrane fraction	secondary active monocarboxylate transmembrane transporter activity|symporter activity			central_nervous_system(1)	1	all_lung(278;0.226)				Pyruvic acid(DB00119)									0.189781	48.181677	60.506166	26	111	GG		KEEP	---	---	---	---	capture	LUSC - Lung squamous cell carcinoma(166;0.162)|Lung(188;0.235)		Missense_Mutation	SNP	70608015	70608015	14907	17	G	A	A	39	39	SLC16A5	A	1	1
EIF4A1	1973	broad.mit.edu	36	17	7421648	7421648	+	Missense_Mutation	SNP	C	A	A			TCGA-76-4928-01	TCGA-76-4928-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr17:7421648C>A	uc002gho.1	+	c.806C>A	c.(805-807)ACC>AAC	p.T269N	EIF4A1_uc002ghr.1_Missense_Mutation_p.T269N|EIF4A1_uc002ghq.1_Missense_Mutation_p.T269N|EIF4A1_uc002ghp.1_Missense_Mutation_p.T269N|SNORA67_uc010cml.1_5'Flank|CD68_uc002ghv.1_5'Flank|CD68_uc002ghu.1_5'Flank	NM_001416	NP_001407	P60842	IF4A1_HUMAN	eukaryotic translation initiation factor 4A	269	Helicase C-terminal.				nuclear-transcribed mRNA poly(A) tail shortening	cytosol|eukaryotic translation initiation factor 4F complex	ATP binding|ATP-dependent helicase activity|mRNA binding|protein binding|RNA cap binding|translation initiation factor activity			ovary(1)	1						Melanoma(120;278 1668 15796 27423 46368)				115				0.18617	71.769758	89.081132	35	153	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	7421648	7421648	5215	17	C	A	A	18	18	EIF4A1	A	3	3
ST8SIA5	29906	broad.mit.edu	36	18	42514033	42514033	+	Silent	SNP	G	A	A			TCGA-76-4928-01	TCGA-76-4928-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr18:42514033G>A	uc002lcj.1	-	c.1101C>T	c.(1099-1101)CGC>CGT	p.R367R	ST8SIA5_uc002lci.1_Silent_p.R214R	NM_013305	NP_037437	O15466	SIA8E_HUMAN	ST8 alpha-N-acetyl-neuraminide	367	Lumenal (Potential).				glycosphingolipid biosynthetic process|protein glycosylation	integral to Golgi membrane				ovary(1)|pancreas(1)	2														0.253165	42.490901	46.844021	20	59	GG		KEEP	---	---	---	---	capture			Silent	SNP	42514033	42514033	15753	18	G	A	A	38	38	ST8SIA5	A	1	1
KLK15	55554	broad.mit.edu	36	19	56022117	56022117	+	Missense_Mutation	SNP	G	A	A			TCGA-76-4928-01	TCGA-76-4928-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr19:56022117G>A	uc002ptl.1	-	c.310C>T	c.(310-312)CGC>TGC	p.R104C	KLK15_uc002ptn.1_Missense_Mutation_p.R104C|KLK15_uc002ptm.1_Missense_Mutation_p.R104C|KLK15_uc002pto.1_Missense_Mutation_p.R103C|KLK15_uc010eod.1_Non-coding_Transcript	NM_017509	NP_059979	Q9H2R5	KLK15_HUMAN	kallikrein-related peptidase 15 isoform 4	104	Peptidase S1.				proteolysis	extracellular region	serine-type endopeptidase activity			lung(1)|breast(1)	2		all_neural(266;0.057)				Pancreas(140;10 2513 7143 9246)								0.226415	79.925868	90.849449	36	123	GG		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(262;0.00758)|GBM - Glioblastoma multiforme(134;0.0143)	Missense_Mutation	SNP	56022117	56022117	8717	19	G	A	A	39	39	KLK15	A	1	1
NLRP5	126206	broad.mit.edu	36	19	61231469	61231469	+	Silent	SNP	C	T	T			TCGA-76-4928-01	TCGA-76-4928-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr19:61231469C>T	uc002qmj.1	+	c.2058C>T	c.(2056-2058)GAC>GAT	p.D686D	NLRP5_uc002qmi.1_Silent_p.D667D	NM_153447	NP_703148	P59047	NALP5_HUMAN	NACHT, LRR and PYD containing protein 5	686						mitochondrion|nucleolus	ATP binding			ovary(3)|skin(2)|kidney(1)	6		Colorectal(82;3.46e-05)|Ovarian(87;0.0481)|Renal(1328;0.157)												0.186047	85.277021	109.09721	48	210	CC		KEEP	---	---	---	---	capture		GBM - Glioblastoma multiforme(193;0.0326)	Silent	SNP	61231469	61231469	10883	19	C	T	T	19	19	NLRP5	T	1	1
PEX14	5195	broad.mit.edu	36	1	10477930	10477930	+	Missense_Mutation	SNP	C	G	G			TCGA-76-4928-01	TCGA-76-4928-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr1:10477930C>G	uc001arn.1	+	c.49C>G	c.(49-51)CCA>GCA	p.P17A	PEX14_uc001arl.2_Non-coding_Transcript|PEX14_uc001arm.1_Non-coding_Transcript|PEX14_uc009vmu.1_Missense_Mutation_p.P17A|PEX14_uc009vmv.1_5'UTR	NM_004565	NP_004556	O75381	PEX14_HUMAN	peroxisomal biogenesis factor 14	17					negative regulation of gene-specific transcription|negative regulation of sequence-specific DNA binding transcription factor activity|protein homooligomerization|protein import into peroxisome matrix|transmembrane transport	integral to membrane|nucleus|peroxisomal membrane|protein complex	protein N-terminus binding|transcription corepressor activity			breast(1)	1	Ovarian(185;0.203)	all_lung(284;6.02e-06)|Lung NSC(185;9.62e-06)|Renal(390;0.000147)|Breast(348;0.000932)|Colorectal(325;0.00215)|Hepatocellular(190;0.00913)|Ovarian(437;0.023)|Myeloproliferative disorder(586;0.0255)										OREG0013090	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	0.135135	18.797114	28.345808	10	64	CC		KEEP	---	---	---	---	capture		UCEC - Uterine corpus endometrioid carcinoma (279;0.0292)|Colorectal(212;9.13e-08)|COAD - Colon adenocarcinoma(227;2.07e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000482)|Kidney(185;0.00174)|KIRC - Kidney renal clear cell carcinoma(229;0.00457)|STAD - Stomach adenocarcinoma(132;0.0249)|READ - Rectum adenocarcinoma(331;0.0419)	Missense_Mutation	SNP	10477930	10477930	12164	1	C	G	G	30	30	PEX14	G	3	3
DENND2C	163259	broad.mit.edu	36	1	114969504	114969504	+	Missense_Mutation	SNP	G	C	C			TCGA-76-4928-01	TCGA-76-4928-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:114969504G>C	uc001efd.1	-	c.625C>G	c.(625-627)CCT>GCT	p.P209A	DENND2C_uc001eez.2_Non-coding_Transcript|DENND2C_uc001efc.1_Missense_Mutation_p.P209A	NM_198459	NP_940861	Q68D51	DEN2C_HUMAN	DENN/MADD domain containing 2C	209											0	all_epithelial(7;9.54e-05)|all_lung(7;0.000179)|Lung NSC(6;0.00195)|Lung SC(450;0.211)	all_cancers(81;4.64e-07)|all_epithelial(167;4.2e-07)|all_lung(203;9.97e-06)|Lung NSC(69;1.74e-05)												0.076087	7.144325	57.969054	21	255	GG		KEEP	---	---	---	---	capture		Lung(183;0.0234)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|all cancers(265;0.112)|Epithelial(280;0.124)|LUSC - Lung squamous cell carcinoma(189;0.133)	Missense_Mutation	SNP	114969504	114969504	4609	1	G	C	C	41	41	DENND2C	C	3	3
HIST2H3D	653604	broad.mit.edu	36	1	148051850	148051850	+	Missense_Mutation	SNP	G	C	C			TCGA-76-4928-01	TCGA-76-4928-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:148051850G>C	uc009wli.1	-	c.11C>G	c.(10-12)ACT>AGT	p.T4S	HIST2H2BF_uc001esr.1_5'Flank	NM_001123375	NP_066403	Q71DI3	H32_HUMAN	histone cluster 2, H3d	4					blood coagulation|nucleosome assembly	nucleoplasm|nucleosome	DNA binding|protein binding				0														0.1875	38.077569	45.392025	15	65	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	148051850	148051850	7470	1	G	C	C	36	36	HIST2H3D	C	3	3
FLG	2312	broad.mit.edu	36	1	150552538	150552538	+	Missense_Mutation	SNP	C	A	A			TCGA-76-4928-01	TCGA-76-4928-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr1:150552538C>A	uc001ezu.1	-	c.1448G>T	c.(1447-1449)GGA>GTA	p.G483V		NM_002016	NP_002007	P20930	FILA_HUMAN	filaggrin	483	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)													0.125813	54.604535	117.682113	58	403	CC		KEEP	---	---	---	---	capture	LUSC - Lung squamous cell carcinoma(543;0.206)		Missense_Mutation	SNP	150552538	150552538	6160	1	C	A	A	30	30	FLG	A	3	3
ILDR2	387597	broad.mit.edu	36	1	165157093	165157093	+	Silent	SNP	G	C	C			TCGA-76-4928-01	TCGA-76-4928-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:165157093G>C	uc001gdx.1	-	c.1359C>G	c.(1357-1359)GGC>GGG	p.G453G		NM_199351	NP_955383	Q71H61	ILDR2_HUMAN	immunoglobulin-like domain containing receptor	453	Cytoplasmic (Potential).					integral to membrane				ovary(1)	1														0.384615	6.941339	7.1347	5	8	GG		KEEP	---	---	---	---	capture			Silent	SNP	165157093	165157093	8011	1	G	C	C	38	38	ILDR2	C	3	3
FUCA1	2517	broad.mit.edu	36	1	24053486	24053486	+	Missense_Mutation	SNP	C	T	T			TCGA-76-4928-01	TCGA-76-4928-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr1:24053486C>T	uc001bie.1	-	c.920G>A	c.(919-921)CGT>CAT	p.R307H	FUCA1_uc009vqt.1_Non-coding_Transcript	NM_000147	NP_000138	P04066	FUCO_HUMAN	fucosidase, alpha-L-1, tissue	307					fucose metabolic process|glycosaminoglycan catabolic process	lysosome	alpha-L-fucosidase activity|cation binding			breast(1)	1		Colorectal(325;3.46e-05)|Renal(390;0.000219)|Lung NSC(340;0.000233)|all_lung(284;0.000321)|Ovarian(437;0.00348)|Breast(348;0.00957)|Myeloproliferative disorder(586;0.0255)												0.210332	115.719587	136.768206	57	214	CC		KEEP	---	---	---	---	capture		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|OV - Ovarian serous cystadenocarcinoma(117;1.11e-24)|Colorectal(126;5.69e-08)|COAD - Colon adenocarcinoma(152;3.15e-06)|GBM - Glioblastoma multiforme(114;9.04e-06)|BRCA - Breast invasive adenocarcinoma(304;0.000986)|KIRC - Kidney renal clear cell carcinoma(1967;0.00342)|STAD - Stomach adenocarcinoma(196;0.0128)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.144)	Missense_Mutation	SNP	24053486	24053486	6345	1	C	T	T	19	19	FUCA1	T	1	1
PTPRF	5792	broad.mit.edu	36	1	43856988	43856988	+	Missense_Mutation	SNP	G	A	A			TCGA-76-4928-01	TCGA-76-4928-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:43856988G>A	uc001cjr.1	+	c.4472G>A	c.(4471-4473)CGC>CAC	p.R1491H	PTPRF_uc001cjs.1_Missense_Mutation_p.R1482H|PTPRF_uc001cju.1_Missense_Mutation_p.R880H|PTPRF_uc009vwt.1_Missense_Mutation_p.R1051H|PTPRF_uc001cjv.1_Missense_Mutation_p.R962H|PTPRF_uc001cjw.1_Missense_Mutation_p.R717H	NM_002840	NP_002831	P10586	PTPRF_HUMAN	protein tyrosine phosphatase, receptor type, F	1491	Tyrosine-protein phosphatase 1.|Cytoplasmic (Potential).				transmembrane receptor protein tyrosine phosphatase signaling pathway	integral to plasma membrane	transmembrane receptor protein tyrosine phosphatase activity			ovary(4)|lung(1)|kidney(1)|central_nervous_system(1)|skin(1)	8	all_hematologic(146;0.0958)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0333)												0.219512	91.267728	106.12774	45	160	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	43856988	43856988	13258	1	G	A	A	38	38	PTPRF	A	1	1
CHD5	26038	broad.mit.edu	36	1	6106638	6106638	+	Silent	SNP	G	C	C			TCGA-76-4928-01	TCGA-76-4928-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:6106638G>C	uc001amb.1	-	c.4656C>G	c.(4654-4656)CCC>CCG	p.P1552P	CHD5_uc001alz.1_Silent_p.P409P|CHD5_uc001ama.1_Non-coding_Transcript|CHD5_uc001amc.1_Non-coding_Transcript|CHD5_uc009vlx.1_Non-coding_Transcript	NM_015557	NP_056372	Q8TDI0	CHD5_HUMAN	chromodomain helicase DNA binding protein 5	1552					chromatin assembly or disassembly|chromatin modification|regulation of transcription, DNA-dependent|transcription, DNA-dependent	chromatin|nucleus	ATP binding|ATP-dependent helicase activity|chromatin binding|DNA binding|zinc ion binding			breast(3)|central_nervous_system(3)|ovary(1)|lung(1)|pancreas(1)	9	Ovarian(185;0.0634)	all_cancers(23;5.36e-32)|all_epithelial(116;2.32e-17)|all_neural(13;3.68e-06)|all_lung(118;3.94e-06)|all_hematologic(16;2.39e-05)|Lung NSC(185;5.33e-05)|Acute lymphoblastic leukemia(12;0.000372)|Glioma(11;0.00127)|Renal(390;0.00188)|Colorectal(325;0.00342)|Breast(487;0.00373)|Hepatocellular(190;0.0218)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.15)								2304				0.222222	9.09084	10.368801	4	14	GG		KEEP	---	---	---	---	capture		Epithelial(90;3.08e-37)|GBM - Glioblastoma multiforme(13;1.36e-31)|OV - Ovarian serous cystadenocarcinoma(86;7.7e-19)|Colorectal(212;9.97e-08)|COAD - Colon adenocarcinoma(227;1.07e-05)|Kidney(185;6.16e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.00109)|BRCA - Breast invasive adenocarcinoma(365;0.0012)|STAD - Stomach adenocarcinoma(132;0.00346)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.193)	Silent	SNP	6106638	6106638	3462	1	G	C	C	39	39	CHD5	C	3	3
TGM3	7053	broad.mit.edu	36	20	2260692	2260692	+	Missense_Mutation	SNP	C	T	T			TCGA-76-4928-01	TCGA-76-4928-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr20:2260692C>T	uc002wfx.2	+	c.1378C>T	c.(1378-1380)CTT>TTT	p.L460F		NM_003245	NP_003236	Q08188	TGM3_HUMAN	transglutaminase 3 precursor	460					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)									0.238636	105.854637	116.840237	42	134	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	2260692	2260692	16359	20	C	T	T	20	20	TGM3	T	2	2
RPRD1B	58490	broad.mit.edu	36	20	36121273	36121273	+	Nonsense_Mutation	SNP	C	T	T			TCGA-76-4928-01	TCGA-76-4928-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr20:36121273C>T	uc002xho.2	+	c.592C>T	c.(592-594)CGA>TGA	p.R198*		NM_021215	NP_067038	Q9NQG5	RPR1B_HUMAN	Regulation of nuclear pre-mRNA domain containing	198										pancreas(1)	1														0.095541	6.811094	32.581337	15	142	CC		KEEP	---	---	---	---	capture			Nonsense_Mutation	SNP	36121273	36121273	14095	20	C	T	T	23	23	RPRD1B	T	5	1
LBP	3929	broad.mit.edu	36	20	36428849	36428849	+	Missense_Mutation	SNP	G	A	A			TCGA-76-4928-01	TCGA-76-4928-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr20:36428849G>A	uc002xic.1	+	c.944G>A	c.(943-945)CGA>CAA	p.R315Q		NM_004139	NP_004130	P18428	LBP_HUMAN	lipopolysaccharide-binding protein precursor	315					acute-phase response|cellular defense response|cellular response to lipoteichoic acid|defense response to Gram-negative bacterium|defense response to Gram-positive bacterium|detection of molecule of bacterial origin|innate immune response|lipid transport|lipopolysaccharide transport|lipopolysaccharide-mediated signaling pathway|macrophage activation involved in immune response|negative regulation of tumor necrosis factor production|opsonization|positive regulation of interleukin-6 production|positive regulation of interleukin-8 production|positive regulation of macrophage activation|positive regulation of respiratory burst involved in inflammatory response|positive regulation of toll-like receptor 4 signaling pathway|positive regulation of tumor necrosis factor production|Toll signaling pathway	extracellular space	Gram-negative bacterial cell surface binding|Gram-positive bacterial cell surface binding|lipid binding|lipopolysaccharide binding|lipoteichoic acid binding|receptor binding			ovary(1)|central_nervous_system(1)	2		Myeloproliferative disorder(115;0.00878)												0.193833	85.566019	105.429104	44	183	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	36428849	36428849	8974	20	G	A	A	37	37	LBP	A	1	1
CHD6	84181	broad.mit.edu	36	20	39499338	39499338	+	Missense_Mutation	SNP	T	G	G			TCGA-76-4928-01	TCGA-76-4928-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr20:39499338T>G	uc002xka.1	-	c.4058A>C	c.(4057-4059)CAG>CCG	p.Q1353P	CHD6_uc002xkb.1_Missense_Mutation_p.Q119P	NM_032221	NP_115597	Q8TD26	CHD6_HUMAN	chromodomain helicase DNA binding protein 6	1353					chromatin assembly or disassembly|chromatin remodeling|nervous system development|regulation of transcription, DNA-dependent|transcription, DNA-dependent	chromatin|nucleus	ATP binding|ATP-dependent helicase activity|chromatin binding|DNA binding			ovary(6)|lung(2)|central_nervous_system(1)|skin(1)	10		Myeloproliferative disorder(115;0.00425)												0.211009	110.136453	126.971647	46	172	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	39499338	39499338	3463	20	T	G	G	55	55	CHD6	G	4	4
KRTAP20-2	337976	broad.mit.edu	36	21	30929487	30929487	+	Missense_Mutation	SNP	C	T	T			TCGA-76-4928-01	TCGA-76-4928-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr21:30929487C>T	uc002yor.1	+	c.34C>T	c.(34-36)CGT>TGT	p.R12C		NM_181616	NP_853647	Q3LI61	KR202_HUMAN	keratin associated protein 20-2	12						intermediate filament				central_nervous_system(1)	1														0.132075	21.454214	42.390303	21	138	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	30929487	30929487	8855	21	C	T	T	27	27	KRTAP20-2	T	1	1
MAPK1	5594	broad.mit.edu	36	22	20472632	20472632	+	Missense_Mutation	SNP	T	C	C			TCGA-76-4928-01	TCGA-76-4928-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr22:20472632T>C	uc002zvn.1	-	c.770A>G	c.(769-771)AAT>AGT	p.N257S	MAPK1_uc002zvo.1_Missense_Mutation_p.N257S|MAPK1_uc010gtk.1_Intron	NM_002745	NP_620407	P28482	MK01_HUMAN	mitogen-activated protein kinase 1	257	Protein kinase.				activation of MAPK activity|activation of MAPKK activity|axon guidance|cell cycle|epidermal growth factor receptor signaling pathway|ERK1 and ERK2 cascade|induction of apoptosis|innate immune response|insulin receptor signaling pathway|interspecies interaction between organisms|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|nerve growth factor receptor signaling pathway|platelet activation|Ras protein signal transduction|regulation of sequence-specific DNA binding transcription factor activity|stress-activated MAPK cascade|synaptic transmission|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|transcription, DNA-dependent	cytosol|nucleoplasm	ATP binding|DNA binding|MAP kinase activity|phosphatase binding|RNA polymerase II carboxy-terminal domain kinase activity			ovary(1)	1	Colorectal(54;0.105)	all_lung(157;3.89e-05)			Arsenic trioxide(DB01169)					164				0.268908	94.150996	99.883899	32	87	TT		KEEP	---	---	---	---	capture		READ - Rectum adenocarcinoma(21;0.0689)	Missense_Mutation	SNP	20472632	20472632	9654	22	T	C	C	52	52	MAPK1	C	4	4
TMPRSS6	164656	broad.mit.edu	36	22	35800661	35800661	+	Missense_Mutation	SNP	C	T	T			TCGA-76-4928-01	TCGA-76-4928-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr22:35800661C>T	uc003aqt.1	-	c.1376G>A	c.(1375-1377)GGA>GAA	p.G459E	TMPRSS6_uc003aqs.1_Missense_Mutation_p.G468E	NM_153609	NP_705837	Q8IU80	TMPS6_HUMAN	transmembrane protease, serine 6	468	LDL-receptor class A 1.|Extracellular (Potential).				angiogenesis|extracellular matrix organization|fibrinolysis|intracellular signal transduction|proteolysis	integral to membrane|plasma membrane	serine-type endopeptidase activity			breast(4)|ovary(1)	5														0.224138	29.958863	34.00578	13	45	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	35800661	35800661	16792	22	C	T	T	30	30	TMPRSS6	T	2	2
UPK3A	7380	broad.mit.edu	36	22	44061929	44061929	+	Missense_Mutation	SNP	A	C	C			TCGA-76-4928-01	TCGA-76-4928-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr22:44061929A>C	uc003bfy.1	+	c.421A>C	c.(421-423)ACC>CCC	p.T141P	UPK3A_uc010gzy.1_Intron	NM_006953	NP_008884	O75631	UPK3A_HUMAN	uroplakin 3A precursor	141	Lumenal (Potential).				epithelial cell differentiation	endoplasmic reticulum membrane|integral to membrane					0		Ovarian(80;0.00965)|all_neural(38;0.0416)												0.315789	9.078296	9.691004	6	13	AA		KEEP	---	---	---	---	capture		UCEC - Uterine corpus endometrioid carcinoma (28;0.0178)	Missense_Mutation	SNP	44061929	44061929	17570	22	A	C	C	10	10	UPK3A	C	4	4
SLC9A4	389015	broad.mit.edu	36	2	102507984	102507984	+	Missense_Mutation	SNP	C	T	T			TCGA-76-4928-01	TCGA-76-4928-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr2:102507984C>T	uc002tbz.2	+	c.1888C>T	c.(1888-1890)CGC>TGC	p.R630C		NM_001011552	NP_001011552	Q6AI14	SL9A4_HUMAN	solute carrier family 9 (sodium/hydrogen	630	Cytoplasmic (Potential).				regulation of pH	apical plasma membrane|basolateral plasma membrane|integral to membrane	sodium:hydrogen antiporter activity			central_nervous_system(1)	1														0.210667	166.33245	195.368674	79	296	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	102507984	102507984	15213	2	C	T	T	23	23	SLC9A4	T	1	1
LY75	4065	broad.mit.edu	36	2	160419289	160419289	+	Missense_Mutation	SNP	C	T	T			TCGA-76-4928-01	TCGA-76-4928-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr2:160419289C>T	uc002ubb.2	-	c.2423G>A	c.(2422-2424)CGT>CAT	p.R808H	LY75_uc010fos.1_Missense_Mutation_p.R808H|LY75_uc002ubc.2_Missense_Mutation_p.R808H	NM_002349	NP_002340	O60449	LY75_HUMAN	lymphocyte antigen 75	808	Extracellular (Potential).				endocytosis|immune response|inflammatory response	integral to plasma membrane	receptor activity|sugar binding				0														0.117117	12.209238	28.204568	13	98	CC		KEEP	---	---	---	---	capture		COAD - Colon adenocarcinoma(177;0.132)	Missense_Mutation	SNP	160419289	160419289	9476	2	C	T	T	19	19	LY75	T	1	1
APOB	338	broad.mit.edu	36	2	21083838	21083838	+	Missense_Mutation	SNP	C	T	T			TCGA-76-4928-01	TCGA-76-4928-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr2:21083838C>T	uc002red.1	-	c.9407G>A	c.(9406-9408)CGT>CAT	p.R3136H		NM_000384	NP_000375	P04114	APOB_HUMAN	apolipoprotein B precursor	3136					cholesterol homeostasis|cholesterol metabolic process|leukocyte migration|low-density lipoprotein particle clearance|low-density lipoprotein particle remodeling|platelet activation|positive regulation of cholesterol storage|positive regulation of macrophage derived foam cell differentiation|receptor-mediated endocytosis|response to virus|very-low-density lipoprotein particle assembly	chylomicron remnant|clathrin-coated endocytic vesicle membrane|endoplasmic reticulum lumen|endoplasmic reticulum membrane|endosome lumen|endosome membrane|intermediate-density lipoprotein particle|low-density lipoprotein particle|mature chylomicron|microsome|plasma membrane|very-low-density lipoprotein particle	cholesterol transporter activity|enzyme binding|heparin binding|low-density lipoprotein particle receptor binding|phospholipid binding|protein heterodimerization activity			ovary(11)|central_nervous_system(3)|large_intestine(2)|pancreas(1)|skin(1)	18	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)				Atorvastatin(DB01076)									0.196	91.441595	112.988979	49	201	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	21083838	21083838	796	2	C	T	T	19	19	APOB	T	1	1
NEU4	129807	broad.mit.edu	36	2	242406849	242406849	+	Nonsense_Mutation	SNP	C	A	A			TCGA-76-4928-01	TCGA-76-4928-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr2:242406849C>A	uc002wcn.1	+	c.1293C>A	c.(1291-1293)TAC>TAA	p.Y431*	NEU4_uc002wcl.1_Non-coding_Transcript|NEU4_uc010fzr.1_Nonsense_Mutation_p.Y419*|NEU4_uc002wcm.1_Nonsense_Mutation_p.Y419*|NEU4_uc002wco.1_Nonsense_Mutation_p.Y419*|NEU4_uc002wcp.1_Nonsense_Mutation_p.Y431*	NM_080741	NP_542779	Q8WWR8	NEUR4_HUMAN	sialidase 4	419		Nucleophile (By similarity).				lysosomal lumen|organelle inner membrane	exo-alpha-sialidase activity|protein binding				0		all_cancers(19;1.09e-40)|all_epithelial(40;2.03e-18)|Breast(86;1.53e-05)|all_lung(227;0.00338)|Renal(207;0.00502)|Ovarian(221;0.00716)|Lung NSC(271;0.012)|Esophageal squamous(248;0.129)|Melanoma(123;0.144)|all_hematologic(139;0.158)|all_neural(83;0.243)|Hepatocellular(293;0.244)												0.227273	6.957254	8.47654	5	17	CC		KEEP	---	---	---	---	capture		Epithelial(32;3.84e-33)|all cancers(36;8.08e-31)|OV - Ovarian serous cystadenocarcinoma(60;7.41e-15)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;1.63e-06)|Lung(119;0.000152)|LUSC - Lung squamous cell carcinoma(224;0.00154)|Colorectal(34;0.0129)|COAD - Colon adenocarcinoma(134;0.0825)	Nonsense_Mutation	SNP	242406849	242406849	10743	2	C	A	A	20	20	NEU4	A	5	3
CEP97	79598	broad.mit.edu	36	3	102934058	102934058	+	Missense_Mutation	SNP	T	G	G			TCGA-76-4928-01	TCGA-76-4928-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr3:102934058T>G	uc003dvk.1	+	c.598T>G	c.(598-600)TTG>GTG	p.L200V	CEP97_uc010hpm.1_Missense_Mutation_p.L166V|CEP97_uc003dvl.1_5'UTR|CEP97_uc003dvm.1_Missense_Mutation_p.L38V	NM_024548	NP_078824	Q8IW35	CEP97_HUMAN	centrosomal protein 97kDa	200	LRR 8.					centrosome|nucleus	protein binding			ovary(2)	2														0.209302	75.760461	85.844306	27	102	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	102934058	102934058	3396	3	T	G	G	60	60	CEP97	G	4	4
TMPRSS7	344805	broad.mit.edu	36	3	113282501	113282501	+	Missense_Mutation	SNP	G	T	T			TCGA-76-4928-01	TCGA-76-4928-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr3:113282501G>T	uc010hqb.1	+	c.2034G>T	c.(2032-2034)TGG>TGT	p.W678C	TMPRSS7_uc003dyp.1_Missense_Mutation_p.W533C	NM_001042575	NP_001036040	Q7RTY8	TMPS7_HUMAN	transmembrane protease, serine 7	804	Extracellular (Potential).|Peptidase S1.				proteolysis	integral to membrane|plasma membrane	serine-type endopeptidase activity			ovary(1)|kidney(1)	2														0.202091	110.267099	133.955233	58	229	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	113282501	113282501	16793	3	G	T	T	41	41	TMPRSS7	T	3	3
MECOM	2122	broad.mit.edu	36	3	170331951	170331951	+	Silent	SNP	G	A	A			TCGA-76-4928-01	TCGA-76-4928-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr3:170331951G>A	uc003ffl.2	-	c.489C>T	c.(487-489)AGC>AGT	p.S163S	MECOM_uc010hwn.1_Silent_p.S191S|MECOM_uc010hwk.1_Silent_p.S26S|MECOM_uc010hwl.1_Silent_p.S67S|MECOM_uc003ffi.2_Silent_p.S3S|MECOM_uc003ffj.2_Silent_p.S67S|MECOM_uc003ffn.2_5'UTR|MECOM_uc010hwm.1_Silent_p.S3S|MECOM_uc003ffk.2_5'UTR|MECOM_uc003ffm.1_Silent_p.S67S	NM_005241	NP_005232	Q13465	MDS1_HUMAN	ecotropic viral integration site 1 isoform b	98							sequence-specific DNA binding transcription factor activity			lung(3)|skin(2)|ovary(1)|pancreas(1)|central_nervous_system(1)	8										646				0.182796	26.964317	35.722869	17	76	GG		KEEP	---	---	---	---	capture			Silent	SNP	170331951	170331951	9811	3	G	A	A	38	38	MECOM	A	1	1
PIK3CA	5290	broad.mit.edu	36	3	180399548	180399548	+	Missense_Mutation	SNP	G	A	A			TCGA-76-4928-01	TCGA-76-4928-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr3:180399548G>A	uc003fjk.1	+	c.241G>A	c.(241-243)GAA>AAA	p.E81K		NM_006218	NP_006209	P42336	PK3CA_HUMAN	phosphoinositide-3-kinase, catalytic, alpha	81					epidermal growth factor receptor signaling pathway|fibroblast growth factor receptor signaling pathway|insulin receptor signaling pathway|leukocyte migration|nerve growth factor receptor signaling pathway|phosphatidylinositol-mediated signaling|platelet activation|T cell costimulation|T cell receptor signaling pathway		1-phosphatidylinositol-3-kinase activity|ATP binding|phosphatidylinositol-4,5-bisphosphate 3-kinase activity	p.E81K(2)		breast(1506)|large_intestine(749)|endometrium(244)|urinary_tract(195)|ovary(136)|skin(112)|stomach(89)|thyroid(77)|central_nervous_system(69)|lung(61)|upper_aerodigestive_tract(48)|haematopoietic_and_lymphoid_tissue(27)|cervix(25)|biliary_tract(22)|liver(20)|oesophagus(17)|pancreas(11)|penis(8)|pituitary(8)|autonomic_ganglia(4)|kidney(2)|prostate(2)|meninges(1)|eye(1)|NS(1)|soft_tissue(1)|bone(1)	3437	all_cancers(143;1.19e-17)|Ovarian(172;0.00769)|Breast(254;0.155)					Colon(199;1504 1750 3362 26421 31210 32040)		57		621	TCGA GBM(8;5.49e-07)			0.143617	43.894802	66.898503	27	161	GG		KEEP	---	---	---	---	capture	OV - Ovarian serous cystadenocarcinoma(80;9.59e-28)|GBM - Glioblastoma multiforme(14;0.003)|BRCA - Breast invasive adenocarcinoma(182;0.0282)		Missense_Mutation	SNP	180399548	180399548	12337	3	G	A	A	33	33	PIK3CA	A	2	2
LAMP3	27074	broad.mit.edu	36	3	184352884	184352884	+	Silent	SNP	G	A	A			TCGA-76-4928-01	TCGA-76-4928-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr3:184352884G>A	uc003flh.2	-	c.861C>T	c.(859-861)GGC>GGT	p.G287G		NM_014398	NP_055213	Q9UQV4	LAMP3_HUMAN	lysosomal-associated membrane protein 3	287	Lumenal (Potential).				cell proliferation	integral to membrane|lysosomal membrane				ovary(2)|central_nervous_system(1)	3	all_cancers(143;9.14e-14)|Ovarian(172;0.0355)													0.157895	71.52306	105.452612	48	256	GG		KEEP	---	---	---	---	capture	all cancers(12;2.91e-44)|Epithelial(37;5.52e-38)|LUSC - Lung squamous cell carcinoma(7;7.12e-25)|Lung(8;6.39e-23)|OV - Ovarian serous cystadenocarcinoma(80;4.16e-21)		Silent	SNP	184352884	184352884	8942	3	G	A	A	38	38	LAMP3	A	1	1
LSG1	55341	broad.mit.edu	36	3	195854852	195854852	+	Silent	SNP	C	T	T			TCGA-76-4928-01	TCGA-76-4928-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr3:195854852C>T	uc003fui.1	-	c.1068G>A	c.(1066-1068)CAG>CAA	p.Q356Q		NM_018385	NP_060855	Q9H089	LSG1_HUMAN	large subunit GTPase 1	356					nuclear export|protein transport	Cajal body|endoplasmic reticulum	GTP binding|hydrolase activity				0	all_cancers(143;1.68e-08)|Ovarian(172;0.0634)													0.130699	59.680316	103.338626	43	286	CC		KEEP	---	---	---	---	capture	OV - Ovarian serous cystadenocarcinoma(49;4.34e-18)|LUSC - Lung squamous cell carcinoma(58;3.55e-06)|Lung(62;4.19e-06)	GBM - Glioblastoma multiforme(46;7.55e-06)	Silent	SNP	195854852	195854852	9425	3	C	T	T	32	32	LSG1	T	2	2
TRANK1	9881	broad.mit.edu	36	3	36873735	36873735	+	Missense_Mutation	SNP	C	T	T			TCGA-76-4928-01	TCGA-76-4928-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr3:36873735C>T	uc003cgj.2	-	c.700G>A	c.(700-702)GAC>AAC	p.D234N		NM_014831	NP_055646	O15050	TRNK1_HUMAN	lupus brain antigen 1	784					DNA repair		ATP binding|ATP-dependent DNA helicase activity|DNA binding			ovary(1)|central_nervous_system(1)	2														0.248175	320.905351	352.542659	136	412	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	36873735	36873735	16998	3	C	T	T	30	30	TRANK1	T	2	2
ADH1A	124	broad.mit.edu	36	4	100427752	100427752	+	Missense_Mutation	SNP	G	A	A			TCGA-76-4928-01	TCGA-76-4928-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr4:100427752G>A	uc003hur.1	-	c.112C>T	c.(112-114)CGT>TGT	p.R38C	ADH1A_uc010ilf.1_5'Flank|ADH1A_uc010ilg.1_Missense_Mutation_p.R38C	NM_000667	NP_000658	P07327	ADH1A_HUMAN	class I alcohol dehydrogenase, alpha subunit	38					ethanol oxidation|xenobiotic metabolic process	cytosol	alcohol dehydrogenase activity, zinc-dependent|protein binding|transcription regulator activity|zinc ion binding			large_intestine(1)|ovary(1)	2					Fomepizole(DB01213)|NADH(DB00157)									0.201613	48.812575	59.069362	25	99	GG		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(123;9.56e-08)	Missense_Mutation	SNP	100427752	100427752	308	4	G	A	A	37	37	ADH1A	A	1	1
TLL1	7092	broad.mit.edu	36	4	167183904	167183904	+	Silent	SNP	T	C	C			TCGA-76-4928-01	TCGA-76-4928-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr4:167183904T>C	uc003irh.1	+	c.1407T>C	c.(1405-1407)AAT>AAC	p.N469N		NM_012464	NP_036596	O43897	TLL1_HUMAN	tolloid-like 1	469	CUB 2.				cell differentiation|proteolysis|skeletal system development	extracellular region	calcium ion binding|metalloendopeptidase activity|zinc ion binding			ovary(2)|breast(1)|central_nervous_system(1)	4	all_hematologic(180;0.221)	Melanoma(52;0.0315)|Prostate(90;0.0405)												0.11041	42.106611	89.695105	35	282	TT		KEEP	---	---	---	---	capture		GBM - Glioblastoma multiforme(119;0.103)	Silent	SNP	167183904	167183904	16475	4	T	C	C	51	51	TLL1	C	4	4
PCDH7	5099	broad.mit.edu	36	4	30334906	30334906	+	Missense_Mutation	SNP	T	C	C			TCGA-76-4928-01	TCGA-76-4928-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr4:30334906T>C	uc010iez.1	+	c.2623T>C	c.(2623-2625)TTT>CTT	p.F875L	PCDH7_uc003gsj.1_Missense_Mutation_p.F922L|PCDH7_uc003gsk.1_Missense_Mutation_p.F922L	NM_032457	NP_115833	O60245	PCDH7_HUMAN	protocadherin 7 isoform c precursor	922	Cytoplasmic (Potential).				homophilic cell adhesion	integral to plasma membrane	calcium ion binding			upper_aerodigestive_tract(1)|ovary(1)|liver(1)|skin(1)	4														0.313725	104.068277	107.214963	32	70	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	30334906	30334906	11936	4	T	C	C	56	56	PCDH7	C	4	4
SMR3B	10879	broad.mit.edu	36	4	71290107	71290107	+	Missense_Mutation	SNP	G	A	A			TCGA-76-4928-01	TCGA-76-4928-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr4:71290107G>A	uc003hfh.1	+	c.193G>A	c.(193-195)GCA>ACA	p.A65T		NM_006685	NP_006676	P02814	SMR3B_HUMAN	submaxillary gland androgen regulated protein 3	65	Poly-Pro.|Pro-rich.					extracellular space				skin(1)	1		all_hematologic(202;0.196)												0.282407	138.068984	147.268838	61	155	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	71290107	71290107	15312	4	G	A	A	38	38	SMR3B	A	1	1
AFM	173	broad.mit.edu	36	4	74583818	74583818	+	Silent	SNP	T	A	A			TCGA-76-4928-01	TCGA-76-4928-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr4:74583818T>A	uc003hhb.1	+	c.1413T>A	c.(1411-1413)GTT>GTA	p.V471V		NM_001133	NP_001124	P43652	AFAM_HUMAN	afamin precursor	471	Albumin 3.				transport					ovary(2)	2	Breast(15;0.00102)													0.278689	43.114351	45.830045	17	44	TT		KEEP	---	---	---	---	capture	Epithelial(6;5.69e-05)|OV - Ovarian serous cystadenocarcinoma(6;0.000324)|all cancers(17;0.000555)|Lung(101;0.103)|LUSC - Lung squamous cell carcinoma(112;0.154)		Silent	SNP	74583818	74583818	362	4	T	A	A	63	63	AFM	A	4	4
SHROOM3	57619	broad.mit.edu	36	4	77881074	77881074	+	Silent	SNP	C	A	A			TCGA-76-4928-01	TCGA-76-4928-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr4:77881074C>A	uc003hke.1	+	c.2721C>A	c.(2719-2721)CCC>CCA	p.P907P	SHROOM3_uc003hkf.1_Silent_p.P783P|SHROOM3_uc003hkg.1_Silent_p.P686P	NM_020859	NP_065910	Q8TF72	SHRM3_HUMAN	shroom family member 3 protein	908					apical protein localization|cell morphogenesis|cellular pigment accumulation|pattern specification process|regulation of cell shape	adherens junction|apical junction complex|apical plasma membrane|cytoplasm|microtubule	actin binding			ovary(1)	1														0.214286	7.019524	8.073256	3	11	CC		KEEP	---	---	---	---	capture	Lung(101;0.0903)		Silent	SNP	77881074	77881074	14790	4	C	A	A	23	23	SHROOM3	A	3	3
KLHL8	57563	broad.mit.edu	36	4	88310262	88310262	+	Silent	SNP	G	A	A			TCGA-76-4928-01	TCGA-76-4928-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr4:88310262G>A	uc003hql.1	-	c.1530C>T	c.(1528-1530)TAC>TAT	p.Y510Y	KLHL8_uc003hqm.1_Silent_p.Y434Y|KLHL8_uc003hqn.1_Silent_p.Y327Y|KLHL8_uc010ikj.1_Silent_p.Y159Y	NM_020803	NP_065854	Q9P2G9	KLHL8_HUMAN	kelch-like 8	510	Kelch 5.										0		Hepatocellular(203;0.114)|all_hematologic(202;0.21)|Acute lymphoblastic leukemia(40;0.242)												0.125541	32.309824	63.952424	29	202	GG		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(123;0.000603)	Silent	SNP	88310262	88310262	8709	4	G	A	A	40	40	KLHL8	A	1	1
PCDHA2	56146	broad.mit.edu	36	5	140155032	140155032	+	Missense_Mutation	SNP	C	T	T			TCGA-76-4928-01	TCGA-76-4928-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr5:140155032C>T	uc003lhd.1	+	c.299C>T	c.(298-300)GCG>GTG	p.A100V	PCDHA1_uc003lha.1_Intron|PCDHA1_uc003lhb.1_Intron|PCDHA2_uc003lhc.1_Missense_Mutation_p.A100V	NM_018905	NP_061728	Q9Y5H9	PCDA2_HUMAN	protocadherin alpha 2 isoform 1 precursor	100	Extracellular (Potential).|Cadherin 1.				homophilic cell adhesion|nervous system development	integral to plasma membrane	calcium ion binding|protein binding			ovary(4)	4														0.112583	18.491177	63.274723	34	268	CC		KEEP	---	---	---	---	capture	KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)		Missense_Mutation	SNP	140155032	140155032	11944	5	C	T	T	27	27	PCDHA2	T	1	1
PCDHB6	56130	broad.mit.edu	36	5	140511708	140511708	+	Silent	SNP	G	A	A			TCGA-76-4928-01	TCGA-76-4928-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr5:140511708G>A	uc003lir.1	+	c.1686G>A	c.(1684-1686)CCG>CCA	p.P562P		NM_018939	NP_061762	Q9Y5E3	PCDB6_HUMAN	protocadherin beta 6 precursor	562	Extracellular (Potential).				calcium-dependent cell-cell adhesion|homophilic cell adhesion|synapse assembly|synaptic transmission	integral to plasma membrane	calcium ion binding				0														0.201613	47.204097	57.469255	25	99	GG		KEEP	---	---	---	---	capture	KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)		Silent	SNP	140511708	140511708	11966	5	G	A	A	38	38	PCDHB6	A	1	1
ANKRD55	79722	broad.mit.edu	36	5	55443308	55443308	+	Missense_Mutation	SNP	G	A	A			TCGA-76-4928-01	TCGA-76-4928-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr5:55443308G>A	uc003jqu.1	-	c.1024C>T	c.(1024-1026)CGG>TGG	p.R342W	ANKRD55_uc003jqt.1_Missense_Mutation_p.R54W	NM_024669	NP_001035024	Q3KP44	ANR55_HUMAN	ankyrin repeat domain 55 isoform 1	341											0		Lung NSC(810;8.69e-05)|Prostate(74;0.00634)|Breast(144;0.0334)|Ovarian(174;0.223)												0.093301	9.305892	78.856942	39	379	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	55443308	55443308	689	5	G	A	A	40	40	ANKRD55	A	1	1
SKIV2L	6499	broad.mit.edu	36	6	32044233	32044233	+	Missense_Mutation	SNP	G	A	A			TCGA-76-4928-01	TCGA-76-4928-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr6:32044233G>A	uc003nyn.1	+	c.3008G>A	c.(3007-3009)CGG>CAG	p.R1003Q	STK19_uc003nyt.1_5'Flank	NM_006929	NP_008860	Q15477	SKIV2_HUMAN	superkiller viralicidic activity 2-like homolog	1003						nucleus	ATP binding|ATP-dependent RNA helicase activity|protein binding|RNA binding			ovary(1)|large_intestine(1)|breast(1)|central_nervous_system(1)	4														0.232558	47.869344	53.492597	20	66	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	32044233	32044233	14854	6	G	A	A	39	39	SKIV2L	A	1	1
DNAH8	1769	broad.mit.edu	36	6	39011410	39011410	+	Missense_Mutation	SNP	A	G	G			TCGA-76-4928-01	TCGA-76-4928-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr6:39011410A>G	uc003ooe.1	+	c.10871A>G	c.(10870-10872)GAA>GGA	p.E3624G	DNAH8_uc003oog.1_Missense_Mutation_p.E73G	NM_001371	NP_001362	Q96JB1	DYH8_HUMAN	dynein, axonemal, heavy polypeptide 8	3624	Potential.|AAA 5 (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)|skin(5)|lung(2)|large_intestine(1)|central_nervous_system(1)|kidney(1)|pancreas(1)	17										2979				0.125668	82.574735	133.728395	47	327	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	39011410	39011410	4790	6	A	G	G	9	9	DNAH8	G	4	4
PKHD1	5314	broad.mit.edu	36	6	51605393	51605393	+	Missense_Mutation	SNP	A	T	T			TCGA-76-4928-01	TCGA-76-4928-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr6:51605393A>T	uc003pah.1	-	c.11594T>A	c.(11593-11595)CTG>CAG	p.L3865Q		NM_138694	NP_619639	P08F94	PKHD1_HUMAN	fibrocystin isoform 1	3865	Helical; (Potential).				cell-cell adhesion|cilium assembly|homeostatic process|kidney development|negative regulation of cellular component movement	anchored to external side of plasma membrane|apical plasma membrane|integral to membrane|microtubule basal body	protein binding|receptor activity			ovary(12)|large_intestine(5)|central_nervous_system(3)	20	Lung NSC(77;0.0605)									1537				0.246914	97.126463	106.568563	40	122	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	51605393	51605393	12396	6	A	T	T	7	7	PKHD1	T	4	4
C7orf53	286006	broad.mit.edu	36	7	111917199	111917199	+	Nonsense_Mutation	SNP	C	T	T			TCGA-76-4928-01	TCGA-76-4928-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr7:111917199C>T	uc003vgm.1	+	c.355C>T	c.(355-357)CGA>TGA	p.R119*	C7orf53_uc003vgl.1_Non-coding_Transcript	NM_182597	NP_872403	Q8N8F7	CG053_HUMAN	hypothetical protein LOC286006	119	Potential.					integral to membrane				ovary(1)	1														0.171429	68.721053	93.716992	42	203	CC		KEEP	---	---	---	---	capture			Nonsense_Mutation	SNP	111917199	111917199	2509	7	C	T	T	27	27	C7orf53	T	5	1
PLXNA4	91584	broad.mit.edu	36	7	131468462	131468462	+	Silent	SNP	G	A	A			TCGA-76-4928-01	TCGA-76-4928-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr7:131468462G>A	uc003vra.2	-	c.5475C>T	c.(5473-5475)AGC>AGT	p.S1825S	PLXNA4_uc003vqz.2_Silent_p.S110S	NM_020911	NP_065962	Q9HCM2	PLXA4_HUMAN	plexin A4 isoform 1	1825	Cytoplasmic (Potential).					integral to membrane|intracellular|plasma membrane				ovary(1)	1														0.193133	85.942142	106.427401	45	188	GG		KEEP	---	---	---	---	capture			Silent	SNP	131468462	131468462	12548	7	G	A	A	38	38	PLXNA4	A	1	1
BRAF	673	broad.mit.edu	36	7	140099605	140099605	+	Missense_Mutation	SNP	A	T	T			TCGA-76-4928-01	TCGA-76-4928-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr7:140099605A>T	uc003vwc.2	-	c.1799T>A	c.(1798-1800)GTG>GAG	p.V600E		NM_004333	NP_004324	P15056	BRAF_HUMAN	B-Raf	600	Protein kinase.		V -> D (in a melanoma cell line; requires 2 nucleotide substitutions).|V -> E (in sarcoma, colorectal adenocarcinoma, metastatic melanoma, ovarian serous carcinoma, pilocytic astrocytoma; somatic mutation; most common mutation; constitutive and elevated kinase activity; efficiently induces cell transformation; suppression of mutation in melanoma causes growth arrest and promotes apoptosis).		activation of MAPKK activity|anti-apoptosis|nerve growth factor receptor signaling pathway|organ morphogenesis|positive regulation of peptidyl-serine phosphorylation|small GTPase mediated signal transduction|synaptic transmission	cytosol|nucleus|plasma membrane	ATP binding|metal ion binding	p.V600E(15573)|p.V600?(188)|p.V600K(165)|p.V600R(36)|p.V600A(23)|p.V600D(21)|p.V600G(11)|p.V600_K601>E(8)|p.T599_R603>I(2)|p.V600_W604del(1)|p.V600L(1)|p.V600_S605>DV(1)|p.V600_S605>D(1)|p.T599_V600insV(1)|p.T599_V600insT(1)|p.T599_V600insDFGLAT(1)	KIAA1549/BRAF(211)|AKAP9_ENST00000356239/BRAF(10)|AGTRAP/BRAF(2)|FCHSD1/BRAF(2)|SLC45A3/BRAF(2)	thyroid(7681)|large_intestine(4665)|skin(3221)|NS(366)|central_nervous_system(264)|ovary(219)|lung(77)|eye(53)|prostate(44)|endometrium(30)|biliary_tract(27)|soft_tissue(27)|haematopoietic_and_lymphoid_tissue(22)|breast(16)|upper_aerodigestive_tract(13)|stomach(13)|pancreas(10)|small_intestine(10)|testis(7)|bone(6)|cervix(5)|genital_tract(4)|oesophagus(3)|urinary_tract(3)|adrenal_gland(3)|gastrointestinal_tract_(site_indeterminate)(2)|liver(2)|meninges(1)|kidney(1)|autonomic_ganglia(1)|pituitary(1)|salivary_gland(1)	16798	Melanoma(164;0.00956)				Sorafenib(DB00398)	Colon(40;35 892 2973 5743 27438)	V600E(UACC257_SKIN)|V600D(K029AX_SKIN)|V600E(HS695T_SKIN)|V600E(COLO679_SKIN)|V600E(BT474_BREAST)|V600E(IGR39_SKIN)|V600E(A101D_SKIN)|V600E(COLO783_SKIN)|V600E(IGR37_SKIN)|V600E(A375_SKIN)|V600E(WM793_SKIN)|V600E(COLO818_SKIN)|V600E(HS294T_SKIN)|V600E(SKMEL28_SKIN)|V600E(DU4475_BREAST)|V600E(SIGM5_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|V600E(IGR1_SKIN)|V600E(SKHEP1_LIVER)|V600E(WM983B_SKIN)|V600E(GCT_SOFT_TISSUE)|V600E(RVH421_SKIN)|V600D(WM2664_SKIN)|V600E(CL34_LARGE_INTESTINE)|V600E(SKMEL24_SKIN)|V600D(WM115_SKIN)|V600E(MALME3M_SKIN)|V600E(A673_BONE)|V600E(C32_SKIN)|V600E(DBTRG05MG_CENTRAL_NERVOUS_SYSTEM)|V600E(COLO800_SKIN)|V600E(COLO741_SKIN)|V600E(HS939T_SKIN)|V600E(COLO205_LARGE_INTESTINE)|V600E(K029AX_SKIN)|V600E(AM38_CENTRAL_NERVOUS_SYSTEM)|V600E(SH4_SKIN)|V600E(WM88_SKIN)|V600E(KG1C_CENTRAL_NERVOUS_SYSTEM)|V600E(COLO849_SKIN)|V600E(MELHO_SKIN)|V600E(BHT101_THYROID)|V600E(G361_SKIN)|V600E(UACC62_SKIN)|V600E(BCPAP_THYROID)|V600E(8505C_THYROID)|V600E(SW1417_LARGE_INTESTINE)|V600E(COLO829_SKIN)|V600E(RKO_LARGE_INTESTINE)|V600E(A2058_SKIN)|V600E(RPMI7951_SKIN)|V600E(OUMS23_LARGE_INTESTINE)|V600E(SKMEL5_SKIN)|V600E(ES2_OVARY)|V600E(LOXIMVI_SKIN)	61	p.V600E(G361-Tumor)|p.V600E(HT144-Tumor)|p.V600E(MDAMB361-Tumor)|p.V600E(COLO783-Tumor)|p.V600E(COLO201-Tumor)|p.V600E(8505C-Tumor)|p.V600E(COLO205-Tumor)|p.V600E(A673-Tumor)|p.V600E(WM88-Tumor)|p.V600E(LOXIMVI-Tumor)|p.V600D(WM2664-Tumor)|p.V600K(MDST8-Tumor)|p.V600E(HT29-Tumor)|p.V600E(CL34-Tumor)|p.V600E(COLO818-Tumor)|p.V600E(COLO741-Tumor)|p.V600E(LS411N-Tumor)|p.V600E(SKMEL28-Tumor)|p.V600E(NMCG1-Tumor)|p.V600E(MELHO-Tumor)|p.V600E(WM983B-Tumor)|p.V600E(OUMS23-Tumor)|p.V600E(NCIH854-Tumor)|p.V600E(IGR39-Tumor)|p.V600E(SKHEP1-Tumor)|p.V600E(COLO679-Tumor)|p.V600E(SKMEL5-Tumor)|p.V600E(UACC257-Tumor)|p.V600E(HS695T-Tumor)|p.V600E(A375-Tumor)|p.V600E(MALME3M-Tumor)|p.V600E(AM38-Tumor)|p.V600E(SIGM5-Tumor)|p.V600E(DBTRG05MG-Tumor)|p.V600E(8305C-Tumor)|p.V600E(SKMEL24-Tumor)|p.V600E(WM793-Tumor)|p.V600E(BCPAP-Tumor)|p.V600D(WM115-Tumor)|p.V600E(SNUC5-Tumor)|p.V600E(GCT-Tumor)|p.V600E(ES2-Tumor)|p.V600E(SW1417-Tumor)|p.V600E(MDAMB435S-Tumor)|p.V600E(HS294T-Tumor)|p.V600E(DU4475-Tumor)|p.V600E(C32-Tumor)|p.V600E(A101D-Tumor)|p.V600E(COLO829-Tumor)|p.V600E(SKMEL3-Tumor)|p.V600E(SKMEL1-Tumor)|p.V600E(WM1799-Tumor)|p.V600E(RKO-Tumor)|p.V600E(IGR37-Tumor)|p.V600E(K029AX-Tumor)|p.V600E(JHOM2B-Tumor)|p.V600E(SH4-Tumor)	451				0.100559	15.625099	44.130705	18	161	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	140099605	140099605	1527	7	A	T	T	6	6	BRAF	T	4	4
EIF2AK1	27102	broad.mit.edu	36	7	6047156	6047156	+	Missense_Mutation	SNP	T	C	C			TCGA-76-4928-01	TCGA-76-4928-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr7:6047156T>C	uc003spp.1	-	c.1012A>G	c.(1012-1014)ATT>GTT	p.I338V	EIF2AK1_uc003spq.1_Missense_Mutation_p.I337V|EIF2AK1_uc003spr.1_Missense_Mutation_p.I130V	NM_014413	NP_055228	Q9BQI3	E2AK1_HUMAN	eukaryotic translation initiation factor 2-alpha	338	Protein kinase.				negative regulation of hemoglobin biosynthetic process|negative regulation of translational initiation by iron|protein autophosphorylation|response to external stimulus|response to stress	cytoplasm	ATP binding|eukaryotic translation initiation factor 2alpha kinase activity|heme binding|protein homodimerization activity			upper_aerodigestive_tract(1)|stomach(1)|lung(1)|central_nervous_system(1)	4		Ovarian(82;0.0423)								253				0.146789	29.736127	42.795979	16	93	TT		KEEP	---	---	---	---	capture		UCEC - Uterine corpus endometrioid carcinoma (126;0.106)|OV - Ovarian serous cystadenocarcinoma(56;5.22e-14)	Missense_Mutation	SNP	6047156	6047156	5185	7	T	C	C	52	52	EIF2AK1	C	4	4
GATS	352954	broad.mit.edu	36	7	99659579	99659579	+	Silent	SNP	G	A	A			TCGA-76-4928-01	TCGA-76-4928-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr7:99659579G>A	uc003uua.2	-	c.273C>T	c.(271-273)AAC>AAT	p.N91N	GATS_uc003uty.2_Non-coding_Transcript|GATS_uc010lgt.1_Non-coding_Transcript|GATS_uc003utz.2_Non-coding_Transcript|GATS_uc003uuc.1_Silent_p.N91N|GATS_uc003uud.1_5'Flank|GATS_uc010lgu.1_Non-coding_Transcript	NM_178831	NP_849153	Q8NAP1	GATS_HUMAN	stromal antigen 3 opposite strand	91											0	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)									9				0.139535	19.079934	35.287081	18	111	GG		KEEP	---	---	---	---	capture			Silent	SNP	99659579	99659579	6528	7	G	A	A	40	40	GATS	A	1	1
NPBWR1	2831	broad.mit.edu	36	8	54015849	54015849	+	Missense_Mutation	SNP	A	G	G			TCGA-76-4928-01	TCGA-76-4928-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr8:54015849A>G	uc003xrg.1	+	c.829A>G	c.(829-831)ACC>GCC	p.T277A		NM_005285	NP_005276	P48145	NPBW1_HUMAN	G protein-coupled receptor 7	277	Extracellular (Potential).				synaptic transmission	integral to membrane|plasma membrane	opioid receptor activity|protein binding			ovary(2)|breast(1)	3		Lung NSC(129;0.0222)|all_epithelial(80;0.0301)|all_lung(136;0.0431)												0.184615	24.175282	30.229991	12	53	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	54015849	54015849	10972	8	A	G	G	6	6	NPBWR1	G	4	4
KCNS2	3788	broad.mit.edu	36	8	99510240	99510240	+	Missense_Mutation	SNP	C	A	A			TCGA-76-4928-01	TCGA-76-4928-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr8:99510240C>A	uc003yin.1	+	c.857C>A	c.(856-858)ACT>AAT	p.T286N	KCNS2_uc010mbl.1_Missense_Mutation_p.T286N	NM_020697	NP_065748	Q9ULS6	KCNS2_HUMAN	potassium voltage-gated channel,	286	Extracellular (Potential).					voltage-gated potassium channel complex	voltage-gated potassium channel activity			ovary(1)	1	Breast(36;2.4e-06)					Pancreas(138;844 2489 9202 24627)								0.247748	129.006206	141.869039	55	167	CC		KEEP	---	---	---	---	capture	OV - Ovarian serous cystadenocarcinoma(57;0.0448)		Missense_Mutation	SNP	99510240	99510240	8394	8	C	A	A	20	20	KCNS2	A	3	3
LHX2	9355	broad.mit.edu	36	9	125834734	125834734	+	Missense_Mutation	SNP	C	T	T			TCGA-76-4928-01	TCGA-76-4928-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr9:125834734C>T	uc010mwi.1	+	c.1172C>T	c.(1171-1173)ACT>ATT	p.T391I	LHX2_uc004boe.1_Missense_Mutation_p.T383I	NM_004789	NP_004780	P50458	LHX2_HUMAN	LIM homeobox protein 2	383						nucleus	sequence-specific DNA binding transcription factor activity|transcription regulator activity|zinc ion binding				0														0.136	22.183958	38.233886	17	108	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	125834734	125834734	9097	9	C	T	T	20	20	LHX2	T	2	2
KCNV2	169522	broad.mit.edu	36	9	2708127	2708127	+	Missense_Mutation	SNP	A	C	C			TCGA-76-4928-01	TCGA-76-4928-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr9:2708127A>C	uc003zho.1	+	c.388A>C	c.(388-390)ACC>CCC	p.T130P		NM_133497	NP_598004	Q8TDN2	KCNV2_HUMAN	potassium channel, subfamily V, member 2	130	Cytoplasmic (Potential).				response to stimulus|visual perception	voltage-gated potassium channel complex	voltage-gated potassium channel activity			central_nervous_system(1)	1														0.428571	6.419363	6.451232	3	4	AA		KEEP	---	---	---	---	capture		GBM - Glioblastoma multiforme(50;0.0257)	Missense_Mutation	SNP	2708127	2708127	8400	9	A	C	C	6	6	KCNV2	C	4	4
FBP1	2203	broad.mit.edu	36	9	96407613	96407613	+	Missense_Mutation	SNP	C	A	A			TCGA-76-4928-01	TCGA-76-4928-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr9:96407613C>A	uc004auw.2	-	c.772G>T	c.(772-774)GTC>TTC	p.V258F	FBP1_uc010mrl.1_Missense_Mutation_p.V258F	NM_000507	NP_001121100	P09467	F16P1_HUMAN	fructose-1,6-bisphosphatase 1	258					gluconeogenesis	cytosol	fructose 1,6-bisphosphate 1-phosphatase activity|fructose-2,6-bisphosphate 2-phosphatase activity|identical protein binding|metal ion binding				0		Acute lymphoblastic leukemia(62;0.136)			Adenosine monophosphate(DB00131)	Ovarian(142;590 2466 25593 44496)								0.211111	41.372023	48.32285	19	71	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	96407613	96407613	5941	9	C	A	A	18	18	FBP1	A	3	3
FATE1	89885	broad.mit.edu	36	X	150636524	150636524	+	Missense_Mutation	SNP	A	T	T			TCGA-76-4928-01	TCGA-76-4928-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chrX:150636524A>T	uc004fex.1	+	c.231A>T	c.(229-231)AAA>AAT	p.K77N		NM_033085	NP_149076	Q969F0	FATE1_HUMAN	fetal and adult testis expressed transcript	77						endoplasmic reticulum|integral to membrane				ovary(1)	1	Acute lymphoblastic leukemia(192;6.56e-05)													0.225296	116.938103	134.485326	57	196	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	150636524	150636524	5929	23	A	T	T	1	1	FATE1	T	4	4
GJB1	2705	broad.mit.edu	36	X	70360779	70360779	+	Missense_Mutation	SNP	T	G	G			TCGA-76-4928-01	TCGA-76-4928-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chrX:70360779T>G	uc004dzf.2	+	c.497T>G	c.(496-498)GTC>GGC	p.V166G	GJB1_uc004dzg.2_Missense_Mutation_p.V166G|GJB1_uc010nlc.1_Missense_Mutation_p.V166G	NM_001097642	NP_001091111	P08034	CXB1_HUMAN	gap junction protein, beta 1, 32kDa	166	Extracellular (Probable).				cell-cell signaling|cellular membrane organization|gap junction assembly|nervous system development	connexon complex|endoplasmic reticulum membrane|integral to membrane	gap junction channel activity			breast(1)	1	Renal(35;0.156)													0.4375	12.287253	12.362633	7	9	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	70360779	70360779	6675	23	T	G	G	58	58	GJB1	G	4	4
BRWD3	254065	broad.mit.edu	36	X	79886369	79886369	+	Missense_Mutation	SNP	C	T	T			TCGA-76-4928-01	TCGA-76-4928-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chrX:79886369C>T	uc004edt.2	-	c.631G>A	c.(631-633)GAT>AAT	p.D211N	BRWD3_uc004edo.2_5'UTR|BRWD3_uc004edp.2_Missense_Mutation_p.D40N|BRWD3_uc004edq.2_5'UTR|BRWD3_uc010nmj.1_5'UTR|BRWD3_uc004edr.2_5'UTR|BRWD3_uc004eds.2_5'UTR|BRWD3_uc004edu.2_5'UTR|BRWD3_uc004edv.2_5'UTR|BRWD3_uc004edw.2_5'UTR|BRWD3_uc004edx.2_5'UTR|BRWD3_uc004edy.2_5'UTR|BRWD3_uc004edz.2_5'UTR|BRWD3_uc004eea.2_5'UTR|BRWD3_uc004eeb.2_Intron	NM_153252	NP_694984	Q6RI45	BRWD3_HUMAN	bromodomain and WD repeat domain containing 3	211	WD 2.									ovary(4)	4														0.240909	118.35822	131.841088	53	167	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	79886369	79886369	1557	23	C	T	T	29	29	BRWD3	T	2	2
