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
PTCHD3	374308	broad.mit.edu	36	10	27728097	27728097	+	Missense_Mutation	SNP	A	T	T			TCGA-15-0742-01	TCGA-15-0742-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr10:27728097A>T	uc001itu.1	-	c.1436T>A	c.(1435-1437)ATG>AAG	p.M479K		NM_001034842	NP_001030014	Q3KNS1	PTHD3_HUMAN	patched domain containing 3	479	SSD.				spermatid development	integral to membrane	hedgehog receptor activity			ovary(2)|pancreas(1)|skin(1)	4														0.802326	244.224388	251.546392	69	17	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	27728097	27728097	13188	10	A	T	T	8	8	PTCHD3	T	4	4
CARD16	114769	broad.mit.edu	36	11	104420594	104420594	+	Missense_Mutation	SNP	G	T	T			TCGA-15-0742-01	TCGA-15-0742-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr11:104420594G>T	uc001pip.1	-	c.9C>A	c.(7-9)GAC>GAA	p.D3E	CASP1_uc001pil.1_Intron|CASP1_uc001pin.1_Intron|CARD16_uc001pio.1_Missense_Mutation_p.D3E	NM_001017534	NP_001017534	Q5EG05	CAR16_HUMAN	caspase-1 dominant-negative inhibitor pseudo-ICE	3	CARD.				regulation of apoptosis	intracellular	cysteine-type endopeptidase inhibitor activity				0														0.444231	742.047858	743.458503	231	289	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	104420594	104420594	2766	11	G	T	T	48	48	CARD16	T	3	3
ANO1	55107	broad.mit.edu	36	11	69602403	69602403	+	Missense_Mutation	SNP	C	T	T			TCGA-15-0742-01	TCGA-15-0742-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr11:69602403C>T	uc001opj.1	+	c.43C>T	c.(43-45)CGC>TGC	p.R15C	ANO1_uc001opi.1_Missense_Mutation_p.R15C	NM_018043	NP_060513	Q5XXA6	ANO1_HUMAN	transmembrane protein 16A	15	Cytoplasmic (Potential).				multicellular organismal development	chloride channel complex|cytoplasm|plasma membrane	intracellular calcium activated chloride channel activity			ovary(1)|pancreas(1)	2														0.321429	24.567147	25.359133	9	19	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	69602403	69602403	703	11	C	T	T	23	23	ANO1	T	1	1
SYT9	143425	broad.mit.edu	36	11	7280855	7280855	+	Missense_Mutation	SNP	T	C	C			TCGA-15-0742-01	TCGA-15-0742-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr11:7280855T>C	uc001mfe.1	+	c.155T>C	c.(154-156)GTG>GCG	p.V52A	SYT9_uc001mfd.2_Non-coding_Transcript|SYT9_uc009yfi.1_Non-coding_Transcript	NM_175733	NP_783860	Q86SS6	SYT9_HUMAN	synaptotagmin IX	52	Vesicular (Potential).					cell junction|integral to membrane|synaptic vesicle membrane	metal ion binding|transporter activity			ovary(2)|large_intestine(1)	3														0.435644	279.478339	280.221342	88	114	TT		KEEP	---	---	---	---	capture		Epithelial(150;1.34e-07)|LUSC - Lung squamous cell carcinoma(625;0.0949)	Missense_Mutation	SNP	7280855	7280855	16002	11	T	C	C	59	59	SYT9	C	4	4
NOX4	50507	broad.mit.edu	36	11	88794733	88794733	+	Missense_Mutation	SNP	G	A	A			TCGA-15-0742-01	TCGA-15-0742-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr11:88794733G>A	uc001pct.1	-	c.614C>T	c.(613-615)ACG>ATG	p.T205M	NOX4_uc001pcx.1_Intron|NOX4_uc001pcu.1_Missense_Mutation_p.T131M|NOX4_uc001pcv.1_Missense_Mutation_p.T205M|NOX4_uc009yvo.1_Non-coding_Transcript|NOX4_uc009yvp.1_Missense_Mutation_p.T205M|NOX4_uc001pcw.1_Intron|NOX4_uc009yvq.1_Missense_Mutation_p.T181M|NOX4_uc009yvr.1_Missense_Mutation_p.T180M|NOX4_uc009yvs.1_Non-coding_Transcript	NM_016931	NP_058627	Q9NPH5	NOX4_HUMAN	NADPH oxidase 4 isoform a	205	Helical; (Potential).|Ferric oxidoreductase.				cell aging|cell morphogenesis|inflammatory response|negative regulation of cell proliferation|oxidation-reduction process|superoxide anion generation	endoplasmic reticulum membrane|focal adhesion|integral to membrane|nucleus	electron carrier activity|flavin adenine dinucleotide binding|heme binding|NAD(P)H oxidase activity|nucleotide binding|oxygen sensor activity			ovary(1)|central_nervous_system(1)	2		Acute lymphoblastic leukemia(157;2.26e-05)|all_hematologic(158;0.011)												0.432099	108.014644	108.339865	35	46	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	88794733	88794733	10962	11	G	A	A	40	40	NOX4	A	1	1
OLR1	4973	broad.mit.edu	36	12	10210605	10210605	+	Missense_Mutation	SNP	T	A	A			TCGA-15-0742-01	TCGA-15-0742-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr12:10210605T>A	uc001qxo.1	-	c.397A>T	c.(397-399)ACA>TCA	p.T133S		NM_002543	NP_002534	P78380	OLR1_HUMAN	oxidized low density lipoprotein (lectin-like)	133	Extracellular (Potential).|Neck.				blood circulation|blood coagulation|inflammatory response|leukocyte migration|proteolysis	extracellular region|integral to plasma membrane|membrane fraction	sugar binding			ovary(1)	1														0.395652	267.57467	269.766682	91	139	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	10210605	10210605	11268	12	T	A	A	60	60	OLR1	A	4	4
RIMBP2	23504	broad.mit.edu	36	12	129493094	129493094	+	Silent	SNP	G	A	A			TCGA-15-0742-01	TCGA-15-0742-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr12:129493094G>A	uc001uil.2	-	c.705C>T	c.(703-705)AAC>AAT	p.N235N	RIMBP2_uc001uim.2_Silent_p.N143N|RIMBP2_uc001uin.1_De_novo_Start_OutOfFrame	NM_015347	NP_056162	O15034	RIMB2_HUMAN	RIM-binding protein 2	235						cell junction|synapse				ovary(3)|large_intestine(2)|central_nervous_system(2)|pancreas(1)	8	all_neural(191;0.101)|Medulloblastoma(191;0.163)	all_epithelial(31;0.213)												0.491124	251.708304	251.720023	83	86	GG		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(86;4.29e-06)|all cancers(50;4.56e-05)|Epithelial(86;5.41e-05)	Silent	SNP	129493094	129493094	13838	12	G	A	A	40	40	RIMBP2	A	1	1
EP400	57634	broad.mit.edu	36	12	131056769	131056769	+	Missense_Mutation	SNP	T	G	G			TCGA-15-0742-01	TCGA-15-0742-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr12:131056769T>G	uc001ujn.1	+	c.3095T>G	c.(3094-3096)CTG>CGG	p.L1032R	EP400_uc001ujl.1_Missense_Mutation_p.L1031R|EP400_uc001ujm.1_Missense_Mutation_p.L1032R	NM_015409	NP_056224	Q96L91	EP400_HUMAN	E1A binding protein p400	1068	Interactions with RUVBL1 and RUVBL2.				histone H2A acetylation|histone H4 acetylation	NuA4 histone acetyltransferase complex|nuclear speck	ATP binding|DNA binding|helicase activity			central_nervous_system(4)|ovary(3)|breast(3)	10	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_epithelial(31;0.198)												0.385135	179.637868	181.350304	57	91	TT		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(86;3.01e-08)|Epithelial(86;3.43e-07)|all cancers(50;2.01e-06)	Missense_Mutation	SNP	131056769	131056769	5342	12	T	G	G	55	55	EP400	G	4	4
CSRNP2	81566	broad.mit.edu	36	12	49744214	49744214	+	Missense_Mutation	SNP	G	A	A			TCGA-15-0742-01	TCGA-15-0742-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr12:49744214G>A	uc001rxu.1	-	c.1214C>T	c.(1213-1215)ACG>ATG	p.T405M		NM_030809	NP_110436	Q9H175	CSRN2_HUMAN	TGF-beta induced apoptosis protein 12	405					apoptosis|positive regulation of transcription from RNA polymerase II promoter	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity				0														0.422727	277.746918	278.890579	93	127	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	49744214	49744214	4105	12	G	A	A	40	40	CSRNP2	A	1	1
IL22	50616	broad.mit.edu	36	12	66932819	66932819	+	Missense_Mutation	SNP	C	T	T			TCGA-15-0742-01	TCGA-15-0742-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr12:66932819C>T	uc001sty.1	-	c.244G>A	c.(244-246)GGA>AGA	p.G82R		NM_020525	NP_065386	Q9GZX6	IL22_HUMAN	interleukin 22	82					acute-phase response|cell-cell signaling	extracellular space	cytokine activity|interleukin-22 receptor binding				0		Myeloproliferative disorder(1001;0.0255)												0.390728	179.292628	180.871104	59	92	CC		KEEP	---	---	---	---	capture	Lung(24;0.000131)|LUAD - Lung adenocarcinoma(15;0.00107)|STAD - Stomach adenocarcinoma(21;0.018)	GBM - Glioblastoma multiforme(7;5.06e-05)|BRCA - Breast invasive adenocarcinoma(357;0.00104)	Missense_Mutation	SNP	66932819	66932819	7973	12	C	T	T	23	23	IL22	T	1	1
KCNC2	3747	broad.mit.edu	36	12	73730842	73730842	+	Missense_Mutation	SNP	C	T	T			TCGA-15-0742-01	TCGA-15-0742-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr12:73730842C>T	uc001sxg.1	-	c.1210G>A	c.(1210-1212)GAG>AAG	p.E404K	KCNC2_uc009zry.1_Missense_Mutation_p.E404K|KCNC2_uc001sxe.1_Missense_Mutation_p.E404K|KCNC2_uc001sxf.1_Missense_Mutation_p.E404K	NM_139137	NP_631875	Q96PR1	KCNC2_HUMAN	Shaw-related voltage-gated potassium channel	404					energy reserve metabolic process|regulation of insulin secretion	voltage-gated potassium channel complex	voltage-gated potassium channel activity			breast(2)|pancreas(2)|skin(1)|lung(1)	6														0.4	181.474246	182.784619	60	90	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	73730842	73730842	8320	12	C	T	T	31	31	KCNC2	T	1	1
LTBP2	4053	broad.mit.edu	36	14	74039224	74039224	+	Silent	SNP	G	A	A			TCGA-15-0742-01	TCGA-15-0742-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr14:74039224G>A	uc001xqa.1	-	c.5055C>T	c.(5053-5055)ACC>ACT	p.T1685T		NM_000428	NP_000419	Q14767	LTBP2_HUMAN	latent transforming growth factor beta binding	1685					protein secretion|protein targeting|transforming growth factor beta receptor signaling pathway	extracellular space|proteinaceous extracellular matrix	calcium ion binding|growth factor binding			liver(1)	1														0.461538	244.041842	244.258217	78	91	GG		KEEP	---	---	---	---	capture		BRCA - Breast invasive adenocarcinoma(234;0.00219)|READ - Rectum adenocarcinoma(1;0.0649)	Silent	SNP	74039224	74039224	9450	14	G	A	A	39	39	LTBP2	A	1	1
PROX2	283571	broad.mit.edu	36	14	74399302	74399302	+	Missense_Mutation	SNP	G	C	C			TCGA-15-0742-01	TCGA-15-0742-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr14:74399302G>C	uc001xqr.1	-	c.989C>G	c.(988-990)GCA>GGA	p.A330G	PROX2_uc001xqq.1_Intron	NM_001080408	NP_001073877	Q3B8N5	PROX2_HUMAN	prospero homeobox 2	330					multicellular organismal development|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|transcription regulator activity				0														0.471591	286.893742	287.018571	83	93	GG		KEEP	---	---	---	---	capture	KIRC - Kidney renal clear cell carcinoma(43;0.238)	BRCA - Breast invasive adenocarcinoma(234;0.00652)	Missense_Mutation	SNP	74399302	74399302	13004	14	G	C	C	46	46	PROX2	C	3	3
CPPED1	55313	broad.mit.edu	36	16	12782568	12782568	+	Silent	SNP	G	A	A			TCGA-15-0742-01	TCGA-15-0742-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr16:12782568G>A	uc002dca.2	-	c.264C>T	c.(262-264)TGC>TGT	p.C88C	CPPED1_uc002dcb.2_Silent_p.C88C	NM_018340	NP_060810	Q9BRF8	CPPED_HUMAN	hypothetical protein LOC55313 isoform a	88							hydrolase activity|metal ion binding				0														0.545455	56.149993	56.209131	18	15	GG		KEEP	---	---	---	---	capture			Silent	SNP	12782568	12782568	3960	16	G	A	A	38	38	CPPED1	A	1	1
SPNS1	83985	broad.mit.edu	36	16	28894164	28894164	+	Missense_Mutation	SNP	T	G	G			TCGA-15-0742-01	TCGA-15-0742-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr16:28894164T>G	uc002drw.1	+	c.326T>G	c.(325-327)GTG>GGG	p.V109G	SPNS1_uc002drx.1_5'UTR|SPNS1_uc002dry.1_Missense_Mutation_p.V64G|SPNS1_uc002dsa.1_Missense_Mutation_p.V64G|SPNS1_uc002drz.1_Missense_Mutation_p.V64G|SPNS1_uc010byp.1_Missense_Mutation_p.V64G|SPNS1_uc010byq.1_5'UTR	NM_032038	NP_114427	Q9H2V7	SPNS1_HUMAN	spinster homolog 1 isoform 1	64	Helical; (Potential).				lipid transport|transmembrane transport	integral to membrane|mitochondrial inner membrane	protein binding				0														0.4	10.939128	11.099547	6	9	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	28894164	28894164	15587	16	T	G	G	59	59	SPNS1	G	4	4
CIRH1A	84916	broad.mit.edu	36	16	67758552	67758552	+	Missense_Mutation	SNP	G	A	A	rs34057086	unknown	TCGA-15-0742-01	TCGA-15-0742-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr16:67758552G>A	uc002ews.2	+	c.1907G>A	c.(1906-1908)CGC>CAC	p.R636H	CIRH1A_uc002ewr.2_3'UTR|CIRH1A_uc002ewt.2_Missense_Mutation_p.R553H|CIRH1A_uc010cfi.1_Missense_Mutation_p.R438H	NM_032830	NP_116219	Q969X6	CIR1A_HUMAN	cirhin	636						nucleolus	protein binding				0						Melanoma(69;1156 1278 4951 8715 52012)								0.403727	188.936855	190.243187	65	96	GG		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(108;0.125)	Missense_Mutation	SNP	67758552	67758552	3568	16	G	A	A	38	38	CIRH1A	A	1	1
MSLNL	401827	broad.mit.edu	36	16	764302	764302	+	Missense_Mutation	SNP	C	T	T			TCGA-15-0742-01	TCGA-15-0742-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr16:764302C>T	uc002cjz.1	-	c.1855G>A	c.(1855-1857)GTG>ATG	p.V619M		NM_001025190	NP_001020361	Q96KJ4	MSLNL_HUMAN	mesothelin-like	268	Extracellular (Potential).				cell adhesion	integral to membrane				breast(3)|ovary(1)	4														0.6	9.725947	9.769694	3	2	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	764302	764302	10275	16	C	T	T	19	19	MSLNL	T	1	1
MYH2	4620	broad.mit.edu	36	17	10370780	10370780	+	Missense_Mutation	SNP	G	A	A			TCGA-15-0742-01	TCGA-15-0742-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr17:10370780G>A	uc010coi.1	-	c.4048C>T	c.(4048-4050)CGG>TGG	p.R1350W	MYH2_uc002gmp.2_Missense_Mutation_p.R1350W|MYH2_uc010coj.1_Intron	NM_001100112	NP_060004	Q9UKX2	MYH2_HUMAN	myosin, heavy chain 2, skeletal muscle, adult	1350	Potential.				muscle filament sliding	muscle myosin complex|myosin filament|sarcomere	actin binding|ATP binding|calmodulin binding|microfilament motor activity|structural constituent of muscle			ovary(5)|pancreas(4)|lung(1)|kidney(1)	11														0.402542	270.365998	272.328621	95	141	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	10370780	10370780	10430	17	G	A	A	38	38	MYH2	A	1	1
DCC	1630	broad.mit.edu	36	18	48988174	48988174	+	Missense_Mutation	SNP	C	G	G			TCGA-15-0742-01	TCGA-15-0742-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr18:48988174C>G	uc002lfe.1	+	c.1850C>G	c.(1849-1851)ACA>AGA	p.T617R	DCC_uc010dpf.1_Missense_Mutation_p.T272R	NM_005215	NP_005206	P43146	DCC_HUMAN	deleted in colorectal carcinoma	617	Extracellular (Potential).				apoptosis|induction of apoptosis	cytosol|integral to membrane				ovary(6)|large_intestine(1)|central_nervous_system(1)|skin(1)	9		all_cancers(7;0.11)|all_epithelial(6;0.00126)												0.488281	432.577609	432.607504	125	131	CC		KEEP	---	---	---	---	capture		Colorectal(16;0.0251)|COAD - Colon adenocarcinoma(17;0.0942)	Missense_Mutation	SNP	48988174	48988174	4453	18	C	G	G	17	17	DCC	G	3	3
PTPRM	5797	broad.mit.edu	36	18	7878281	7878281	+	Missense_Mutation	SNP	T	A	A			TCGA-15-0742-01	TCGA-15-0742-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr18:7878281T>A	uc010dkv.1	+	c.374T>A	c.(373-375)CTG>CAG	p.L125Q	PTPRM_uc002knn.2_Missense_Mutation_p.L125Q	NM_001105244	NP_001098714	P28827	PTPRM_HUMAN	protein tyrosine phosphatase, receptor type, M	125	MAM.|Extracellular (Potential).				homophilic cell adhesion|negative regulation of angiogenesis|negative regulation of endothelial cell migration|negative regulation of endothelial cell proliferation|response to drug|retina layer formation|retinal ganglion cell axon guidance	cell-cell adherens junction|integral to plasma membrane|lamellipodium|perinuclear region of cytoplasm	cadherin binding|transmembrane receptor protein tyrosine phosphatase activity			lung(3)|ovary(1)|central_nervous_system(1)	5		Colorectal(10;0.234)												0.42381	273.938044	275.00185	89	121	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	7878281	7878281	13263	18	T	A	A	55	55	PTPRM	A	4	4
GAPDHS	26330	broad.mit.edu	36	19	40721352	40721352	+	Nonsense_Mutation	SNP	C	T	T			TCGA-15-0742-01	TCGA-15-0742-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr19:40721352C>T	uc002oaf.1	+	c.376C>T	c.(376-378)CGA>TGA	p.R126*		NM_014364	NP_055179	O14556	G3PT_HUMAN	glyceraldehyde-3-phosphate dehydrogenase,	126					gluconeogenesis|glycolysis|oxidation-reduction process|positive regulation of glycolysis|sperm motility	cytosol	glyceraldehyde-3-phosphate dehydrogenase (phosphorylating) activity|NAD binding|protein binding				0	all_lung(56;1.05e-07)|Lung NSC(56;1.63e-07)|Esophageal squamous(110;0.162)				NADH(DB00157)									0.422222	61.227648	61.462568	19	26	CC		KEEP	---	---	---	---	capture	LUSC - Lung squamous cell carcinoma(66;0.0724)		Nonsense_Mutation	SNP	40721352	40721352	6501	19	C	T	T	23	23	GAPDHS	T	5	1
NLRP5	126206	broad.mit.edu	36	19	61231620	61231620	+	Missense_Mutation	SNP	C	T	T			TCGA-15-0742-01	TCGA-15-0742-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr19:61231620C>T	uc002qmj.1	+	c.2209C>T	c.(2209-2211)CGG>TGG	p.R737W	NLRP5_uc002qmi.1_Missense_Mutation_p.R718W	NM_153447	NP_703148	P59047	NALP5_HUMAN	NACHT, LRR and PYD containing protein 5	737	LRR 2.					mitochondrion|nucleolus	ATP binding			ovary(3)|skin(2)|kidney(1)	6		Colorectal(82;3.46e-05)|Ovarian(87;0.0481)|Renal(1328;0.157)												0.433846	428.245891	429.48141	141	184	CC		KEEP	---	---	---	---	capture		GBM - Glioblastoma multiforme(193;0.0326)	Missense_Mutation	SNP	61231620	61231620	10883	19	C	T	T	31	31	NLRP5	T	1	1
MUC16	94025	broad.mit.edu	36	19	8928947	8928947	+	Missense_Mutation	SNP	G	C	C			TCGA-15-0742-01	TCGA-15-0742-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr19:8928947G>C	uc002mkp.1	-	c.19499C>G	c.(19498-19500)ACA>AGA	p.T6500R		NM_024690	NP_078966	Q8WXI7	MUC16_HUMAN	mucin 16	6502	Thr-rich.|Extracellular (Potential).				cell adhesion	extracellular space|extrinsic to membrane|integral to membrane|plasma membrane	protein binding			ovary(15)|large_intestine(1)|pancreas(1)|breast(1)|skin(1)	19														0.447761	101.139676	101.299254	30	37	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	8928947	8928947	10367	19	G	C	C	48	48	MUC16	C	3	3
KIF1B	23095	broad.mit.edu	36	1	10348085	10348085	+	Missense_Mutation	SNP	G	A	A			TCGA-15-0742-01	TCGA-15-0742-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:10348085G>A	uc001aqz.2	+	c.4544G>A	c.(4543-4545)CGT>CAT	p.R1515H	KIF1B_uc001aqw.2_Missense_Mutation_p.R1469H|KIF1B_uc001aqx.2_Missense_Mutation_p.R1515H|KIF1B_uc001aqy.2_Missense_Mutation_p.R1489H|KIF1B_uc001ara.2_Missense_Mutation_p.R1475H|KIF1B_uc001arb.2_Missense_Mutation_p.R1501H	NM_015074	NP_055889	O60333	KIF1B_HUMAN	kinesin family member 1B isoform b	1515					anterograde axon cargo transport|apoptosis|nerve-nerve synaptic transmission|neuromuscular synaptic transmission	cytoplasmic vesicle membrane|microtubule|microtubule associated complex|mitochondrion	ATP binding|ATPase activity|kinesin binding|microtubule motor activity|protein binding			ovary(2)	2	Ovarian(185;0.203)	all_lung(284;1.31e-05)|Lung NSC(185;2.2e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Hepatocellular(190;0.00913)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)												0.438596	151.034673	151.408982	50	64	GG		KEEP	---	---	---	---	capture		UCEC - Uterine corpus endometrioid carcinoma (279;0.0259)|Colorectal(212;9.79e-07)|COAD - Colon adenocarcinoma(227;0.000143)|BRCA - Breast invasive adenocarcinoma(304;0.000413)|Kidney(185;0.00134)|KIRC - Kidney renal clear cell carcinoma(229;0.0037)|STAD - Stomach adenocarcinoma(132;0.0113)|READ - Rectum adenocarcinoma(331;0.0642)	Missense_Mutation	SNP	10348085	10348085	8595	1	G	A	A	40	40	KIF1B	A	1	1
KIAA1751	85452	broad.mit.edu	36	1	1878002	1878002	+	Missense_Mutation	SNP	C	T	T			TCGA-15-0742-01	TCGA-15-0742-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr1:1878002C>T	uc009vkz.1	-	c.1933G>A	c.(1933-1935)GTT>ATT	p.V645I	KIAA1751_uc001aim.1_Missense_Mutation_p.V645I	NM_001080484	NP_001073953	Q9C0B2	K1751_HUMAN	hypothetical protein LOC85452	645										pancreas(1)	1	all_cancers(77;0.000708)|all_epithelial(69;0.000943)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;6.04e-15)|all_lung(118;9.67e-07)|Lung NSC(185;5.59e-05)|Renal(390;0.00571)|Breast(487;0.0183)|Hepatocellular(190;0.0268)|Myeloproliferative disorder(586;0.028)|Ovarian(437;0.127)|Medulloblastoma(700;0.151)|Lung SC(97;0.217)												0.424242	80.588025	80.918474	28	38	CC		KEEP	---	---	---	---	capture		Epithelial(90;8.79e-39)|OV - Ovarian serous cystadenocarcinoma(86;9.61e-25)|GBM - Glioblastoma multiforme(42;1.2e-07)|Colorectal(212;4.84e-05)|COAD - Colon adenocarcinoma(227;0.000214)|Kidney(185;0.00254)|BRCA - Breast invasive adenocarcinoma(365;0.00461)|STAD - Stomach adenocarcinoma(132;0.00645)|KIRC - Kidney renal clear cell carcinoma(229;0.037)|Lung(427;0.205)	Missense_Mutation	SNP	1878002	1878002	8567	1	C	T	T	19	19	KIAA1751	T	1	1
CNKSR1	10256	broad.mit.edu	36	1	26379664	26379664	+	Silent	SNP	C	T	T			TCGA-15-0742-01	TCGA-15-0742-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr1:26379664C>T	uc001bln.2	+	c.186C>T	c.(184-186)GGC>GGT	p.G62G	CNKSR1_uc001blm.2_Silent_p.G62G|CNKSR1_uc009vsd.1_5'UTR|CNKSR1_uc009vse.1_5'UTR|CNKSR1_uc001blo.1_5'UTR	NM_006314	NP_006305	Q969H4	CNKR1_HUMAN	connector enhancer of kinase suppressor of Ras	62	SAM.				Rho protein signal transduction|transmembrane receptor protein tyrosine kinase signaling pathway	cell cortex|cell-cell junction	protein binding, bridging			kidney(1)	1		Colorectal(325;3.46e-05)|all_lung(284;0.000116)|Lung NSC(340;0.000154)|Renal(390;0.0007)|Ovarian(437;0.00473)|Breast(348;0.0133)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0298)				NSCLC(180;1396 2109 28270 30756 34275)								0.450704	196.49271	196.791433	64	78	CC		KEEP	---	---	---	---	capture		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|OV - Ovarian serous cystadenocarcinoma(117;2.72e-26)|Colorectal(126;1.24e-08)|COAD - Colon adenocarcinoma(152;9.31e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.00072)|BRCA - Breast invasive adenocarcinoma(304;0.000959)|STAD - Stomach adenocarcinoma(196;0.00151)|GBM - Glioblastoma multiforme(114;0.00823)|READ - Rectum adenocarcinoma(331;0.0649)	Silent	SNP	26379664	26379664	3744	1	C	T	T	27	27	CNKSR1	T	1	1
KNCN	148930	broad.mit.edu	36	1	46787488	46787488	+	Missense_Mutation	SNP	C	T	T			TCGA-15-0742-01	TCGA-15-0742-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr1:46787488C>T	uc009vyh.1	-	c.190G>A	c.(190-192)GGG>AGG	p.G64R	KNCN_uc001cpy.2_5'UTR	NM_001097611	NP_001091080	A6PVL3	KNCN_HUMAN	kinocilin	87						integral to membrane					0	Acute lymphoblastic leukemia(166;0.155)													0.488889	71.152067	71.156742	22	23	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	46787488	46787488	8739	1	C	T	T	23	23	KNCN	T	1	1
TACSTD2	4070	broad.mit.edu	36	1	58815086	58815086	+	Missense_Mutation	SNP	C	T	T			TCGA-15-0742-01	TCGA-15-0742-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr1:58815086C>T	uc001cyz.2	-	c.331G>A	c.(331-333)GAG>AAG	p.E111K		NM_002353	NP_002344	P09758	TACD2_HUMAN	tumor-associated calcium signal transducer 2	111	Extracellular (Potential).|Thyroglobulin type-1.				cell proliferation|cell surface receptor linked signaling pathway|visual perception	cytosol|integral to plasma membrane	receptor activity				0	all_cancers(7;6.54e-05)													0.310345	24.064867	24.993735	9	20	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	58815086	58815086	16029	1	C	T	T	31	31	TACSTD2	T	1	1
CCDC18	343099	broad.mit.edu	36	1	93470637	93470637	+	Missense_Mutation	SNP	G	A	A			TCGA-15-0742-01	TCGA-15-0742-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:93470637G>A	uc001dpq.1	+	c.2713G>A	c.(2713-2715)GTT>ATT	p.V905I	CCDC18_uc009wdl.1_Missense_Mutation_p.V422I	NM_206886	NP_996769			sarcoma antigen NY-SAR-41											ovary(2)|breast(2)|pancreas(1)	5		all_lung(203;0.00196)|Lung NSC(277;0.00903)|Melanoma(281;0.099)|all_neural(321;0.185)|Glioma(108;0.203)												0.411111	218.018438	219.259864	74	106	GG		KEEP	---	---	---	---	capture		all cancers(265;0.00166)|GBM - Glioblastoma multiforme(16;0.00551)|Epithelial(280;0.0967)	Missense_Mutation	SNP	93470637	93470637	2916	1	G	A	A	40	40	CCDC18	A	1	1
TMC2	117532	broad.mit.edu	36	20	2487347	2487347	+	Missense_Mutation	SNP	C	T	T			TCGA-15-0742-01	TCGA-15-0742-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr20:2487347C>T	uc002wgf.1	+	c.328C>T	c.(328-330)CGG>TGG	p.R110W	TMC2_uc002wgg.1_Missense_Mutation_p.R94W|TMC2_uc010gap.1_5'UTR	NM_080751	NP_542789	Q8TDI7	TMC2_HUMAN	transmembrane cochlear-expressed protein 2	110	Arg/Asp/Glu/Lys-rich (highly charged).|Cytoplasmic (Potential).					integral to membrane				ovary(3)	3														0.311111	33.32883	34.761517	14	31	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	2487347	2487347	16515	20	C	T	T	27	27	TMC2	T	1	1
C20orf111	51526	broad.mit.edu	36	20	42259591	42259591	+	Missense_Mutation	SNP	C	T	T			TCGA-15-0742-01	TCGA-15-0742-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr20:42259591C>T	uc002xlk.1	-	c.394G>A	c.(394-396)GGA>AGA	p.G132R		NM_016470	NP_057554	Q9NX31	CT111_HUMAN	oxidative stress responsive 1	132											0		Myeloproliferative disorder(115;0.028)												0.233974	193.018845	213.220145	73	239	CC		KEEP	---	---	---	---	capture	COAD - Colon adenocarcinoma(18;0.00189)		Missense_Mutation	SNP	42259591	42259591	2156	20	C	T	T	24	24	C20orf111	T	2	2
PCK1	5105	broad.mit.edu	36	20	55572149	55572149	+	Silent	SNP	C	T	T			TCGA-15-0742-01	TCGA-15-0742-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr20:55572149C>T	uc002xyn.2	+	c.921C>T	c.(919-921)TGC>TGT	p.C307C		NM_002591	NP_002582	P35558	PCKGC_HUMAN	cytosolic phosphoenolpyruvate carboxykinase 1	307					gluconeogenesis|glucose homeostasis|glycerol biosynthetic process from pyruvate|response to insulin stimulus	cytosol|nucleus	carboxylic acid binding|GTP binding|magnesium ion binding|manganese ion binding|phosphoenolpyruvate carboxykinase (GTP) activity				0	Lung NSC(12;0.000764)|all_lung(29;0.00264)|Melanoma(10;0.242)													0.278873	250.587194	266.193442	99	256	CC		KEEP	---	---	---	---	capture	BRCA - Breast invasive adenocarcinoma(13;9.88e-12)|Epithelial(14;3.41e-08)|all cancers(14;2.13e-07)		Silent	SNP	55572149	55572149	12001	20	C	T	T	27	27	PCK1	T	1	1
DSCAM	1826	broad.mit.edu	36	21	40387535	40387535	+	Missense_Mutation	SNP	A	C	C			TCGA-15-0742-01	TCGA-15-0742-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr21:40387535A>C	uc002yyq.1	-	c.3833T>G	c.(3832-3834)GTC>GGC	p.V1278G	DSCAM_uc002yyr.1_Non-coding_Transcript	NM_001389	NP_001380	O60469	DSCAM_HUMAN	Down syndrome cell adhesion molecule isoform	1278	Fibronectin type-III 4.|Extracellular (Potential).				cell adhesion|dendrite self-avoidance|negative regulation of cell adhesion|positive regulation of axon extension involved in axon guidance|positive regulation of phosphorylation	axon|extracellular region|growth cone|integral to plasma membrane|membrane fraction	protein binding			ovary(6)	6		all_cancers(19;0.186)|Prostate(19;1.15e-05)|all_epithelial(19;0.0103)				Melanoma(134;970 1778 1785 21664 32388)								0.222222	15.287034	17.840361	8	28	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	40387535	40387535	4952	21	A	C	C	10	10	DSCAM	C	4	4
C2CD2	25966	broad.mit.edu	36	21	42200205	42200205	+	Missense_Mutation	SNP	C	T	T			TCGA-15-0742-01	TCGA-15-0742-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr21:42200205C>T	uc002yzw.1	-	c.1283G>A	c.(1282-1284)CGC>CAC	p.R428H	C2CD2_uc002yzu.1_Missense_Mutation_p.R260H|C2CD2_uc002yzv.1_Missense_Mutation_p.R273H|C2CD2_uc002yzx.1_Missense_Mutation_p.R273H|C2CD2_uc002yzt.1_Missense_Mutation_p.R44H	NM_015500	NP_950251	Q9Y426	CU025_HUMAN	C2 calcium-dependent domain containing 2 isoform	428						cytosol|extracellular region|nucleus				ovary(1)	1														0.350746	126.679493	129.314992	47	87	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	42200205	42200205	2235	21	C	T	T	27	27	C2CD2	T	1	1
ABCG1	9619	broad.mit.edu	36	21	42584830	42584830	+	Silent	SNP	C	T	T			TCGA-15-0742-01	TCGA-15-0742-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr21:42584830C>T	uc002zaq.1	+	c.1684C>T	c.(1684-1686)CTG>TTG	p.L562L	ABCG1_uc002zan.1_Silent_p.L552L|ABCG1_uc002zam.1_Silent_p.L528L|ABCG1_uc002zao.1_Silent_p.L547L|ABCG1_uc002zap.1_Silent_p.L550L|ABCG1_uc002zar.1_Silent_p.L561L|ABCG1_uc010gpb.1_Silent_p.L172L	NM_004915	NP_004906	P45844	ABCG1_HUMAN	ATP-binding cassette sub-family G member 1	562	ABC transmembrane type-2.|Cytoplasmic (Potential).				amyloid precursor protein catabolic process|cholesterol efflux|cholesterol homeostasis|cholesterol metabolic process|detection of hormone stimulus|high-density lipoprotein particle remodeling|intracellular cholesterol transport|lipoprotein metabolic process|low-density lipoprotein particle remodeling|negative regulation of cholesterol storage|negative regulation of macrophage derived foam cell differentiation|phospholipid efflux|phospholipid homeostasis|positive regulation of cholesterol biosynthetic process|regulation of cholesterol esterification|regulation of transcription, DNA-dependent|response to lipid|reverse cholesterol transport	endoplasmic reticulum membrane|external side of plasma membrane|Golgi membrane|integral to plasma membrane|recycling endosome	ADP binding|ATP binding|cholesterol binding|cholesterol transporter activity|glycoprotein transporter activity|phospholipid binding|phospholipid transporter activity|protein heterodimerization activity|protein homodimerization activity|sterol-transporting ATPase activity|toxin transporter activity			ovary(2)	2					Adenosine triphosphate(DB00171)									0.342105	38.662269	39.499915	13	25	CC		KEEP	---	---	---	---	capture			Silent	SNP	42584830	42584830	69	21	C	T	T	24	24	ABCG1	T	2	2
ITGB2	3689	broad.mit.edu	36	21	45144770	45144770	+	Missense_Mutation	SNP	C	A	A			TCGA-15-0742-01	TCGA-15-0742-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr21:45144770C>A	uc002zgd.1	-	c.790G>T	c.(790-792)GAT>TAT	p.D264Y	ITGB2_uc002zge.1_Missense_Mutation_p.D264Y|ITGB2_uc002zgf.2_Missense_Mutation_p.D264Y|ITGB2_uc010gpw.1_Missense_Mutation_p.D207Y|ITGB2_uc002zgg.1_Missense_Mutation_p.D264Y	NM_001127491	NP_001120963	P05107	ITB2_HUMAN	integrin, beta 2 precursor	264	Extracellular (Potential).|VWFA.				apoptosis|blood coagulation|cell-cell signaling|cell-matrix adhesion|inflammatory response|integrin-mediated signaling pathway|leukocyte cell-cell adhesion|multicellular organismal development|neutrophil chemotaxis|regulation of cell shape|regulation of immune response|regulation of peptidyl-tyrosine phosphorylation	integrin complex	glycoprotein binding|protein kinase binding|receptor activity			ovary(3)|central_nervous_system(3)|breast(2)	8					Simvastatin(DB00641)									0.341176	72.938765	74.838466	29	56	CC		KEEP	---	---	---	---	capture		Colorectal(79;0.0669)	Missense_Mutation	SNP	45144770	45144770	8198	21	C	A	A	29	29	ITGB2	A	3	3
LONRF2	164832	broad.mit.edu	36	2	100282737	100282737	+	Nonsense_Mutation	SNP	C	A	A			TCGA-15-0742-01	TCGA-15-0742-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr2:100282737C>A	uc002tal.2	-	c.1141G>T	c.(1141-1143)GAA>TAA	p.E381*		NM_198461	NP_940863	Q1L5Z9	LONF2_HUMAN	LON peptidase N-terminal domain and ring finger	381					proteolysis		ATP-dependent peptidase activity|zinc ion binding			large_intestine(1)	1														0.526316	210.610414	210.68815	70	63	CC		KEEP	---	---	---	---	capture			Nonsense_Mutation	SNP	100282737	100282737	9267	2	C	A	A	29	29	LONRF2	A	5	3
LRP1B	53353	broad.mit.edu	36	2	140789006	140789006	+	Missense_Mutation	SNP	T	C	C			TCGA-15-0742-01	TCGA-15-0742-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr2:140789006T>C	uc002tvj.1	-	c.12773A>G	c.(12772-12774)CAG>CGG	p.Q4258R		NM_018557	NP_061027	Q9NZR2	LRP1B_HUMAN	low density lipoprotein-related protein 1B	4258	Extracellular (Potential).|EGF-like 11.				protein transport|receptor-mediated endocytosis	integral to membrane	calcium ion binding			lung(17)|ovary(10)|pancreas(3)|central_nervous_system(2)|liver(1)|kidney(1)	34		all_cancers(3;1.1e-60)|all_epithelial(3;1.94e-59)|all_lung(3;1.09e-24)|Lung NSC(3;5.65e-24)|Esophageal squamous(3;5.41e-13)|Renal(3;0.000147)|Breast(3;0.000527)|Hepatocellular(3;0.011)|all_neural(3;0.014)|Colorectal(150;0.101)				Colon(99;50 2074 2507 20106)				2546	TSP Lung(27;0.18)			0.434426	173.656563	174.114022	53	69	TT		KEEP	---	---	---	---	capture		UCEC - Uterine corpus endometrioid carcinoma (2;0.00139)|Epithelial(1;1.25e-24)|all cancers(1;8.86e-24)|OV - Ovarian serous cystadenocarcinoma(1;2.45e-12)|LUSC - Lung squamous cell carcinoma(1;2.97e-10)|Lung(1;6.05e-09)|BRCA - Breast invasive adenocarcinoma(221;0.0103)	Missense_Mutation	SNP	140789006	140789006	9328	2	T	C	C	55	55	LRP1B	C	4	4
LRP1B	53353	broad.mit.edu	36	2	140789103	140789103	+	Missense_Mutation	SNP	T	C	C			TCGA-15-0742-01	TCGA-15-0742-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr2:140789103T>C	uc002tvj.1	-	c.12676A>G	c.(12676-12678)AGA>GGA	p.R4226G		NM_018557	NP_061027	Q9NZR2	LRP1B_HUMAN	low density lipoprotein-related protein 1B	4226	Extracellular (Potential).|EGF-like 10.				protein transport|receptor-mediated endocytosis	integral to membrane	calcium ion binding			lung(17)|ovary(10)|pancreas(3)|central_nervous_system(2)|liver(1)|kidney(1)	34		all_cancers(3;1.1e-60)|all_epithelial(3;1.94e-59)|all_lung(3;1.09e-24)|Lung NSC(3;5.65e-24)|Esophageal squamous(3;5.41e-13)|Renal(3;0.000147)|Breast(3;0.000527)|Hepatocellular(3;0.011)|all_neural(3;0.014)|Colorectal(150;0.101)				Colon(99;50 2074 2507 20106)				2546	TSP Lung(27;0.18)			0.484848	172.494453	172.51429	48	51	TT		KEEP	---	---	---	---	capture		UCEC - Uterine corpus endometrioid carcinoma (2;0.00139)|Epithelial(1;1.25e-24)|all cancers(1;8.86e-24)|OV - Ovarian serous cystadenocarcinoma(1;2.45e-12)|LUSC - Lung squamous cell carcinoma(1;2.97e-10)|Lung(1;6.05e-09)|BRCA - Breast invasive adenocarcinoma(221;0.0103)	Missense_Mutation	SNP	140789103	140789103	9328	2	T	C	C	56	56	LRP1B	C	4	4
LRP1B	53353	broad.mit.edu	36	2	140808600	140808600	+	Splice_Site_SNP	SNP	T	C	C			TCGA-15-0742-01	TCGA-15-0742-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr2:140808600T>C	uc002tvj.1	-	c.12117_splice	c.e79-1	p.G4039_splice		NM_018557	NP_061027			low density lipoprotein-related protein 1B						protein transport|receptor-mediated endocytosis	integral to membrane	calcium ion binding			lung(17)|ovary(10)|pancreas(3)|central_nervous_system(2)|liver(1)|kidney(1)	34		all_cancers(3;1.1e-60)|all_epithelial(3;1.94e-59)|all_lung(3;1.09e-24)|Lung NSC(3;5.65e-24)|Esophageal squamous(3;5.41e-13)|Renal(3;0.000147)|Breast(3;0.000527)|Hepatocellular(3;0.011)|all_neural(3;0.014)|Colorectal(150;0.101)				Colon(99;50 2074 2507 20106)				2546	TSP Lung(27;0.18)			0.426573	180.657742	181.328293	61	82	TT		KEEP	---	---	---	---	capture		UCEC - Uterine corpus endometrioid carcinoma (2;0.00139)|Epithelial(1;1.25e-24)|all cancers(1;8.86e-24)|OV - Ovarian serous cystadenocarcinoma(1;2.45e-12)|LUSC - Lung squamous cell carcinoma(1;2.97e-10)|Lung(1;6.05e-09)|BRCA - Breast invasive adenocarcinoma(221;0.0103)	Splice_Site_SNP	SNP	140808600	140808600	9328	2	T	C	C	55	55	LRP1B	C	5	4
LOXL3	84695	broad.mit.edu	36	2	74633142	74633142	+	Missense_Mutation	SNP	C	T	T			TCGA-15-0742-01	TCGA-15-0742-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr2:74633142C>T	uc002smp.1	-	c.128G>A	c.(127-129)CGG>CAG	p.R43Q	LOXL3_uc002smo.1_5'Flank|LOXL3_uc010ffm.1_Missense_Mutation_p.R43Q|LOXL3_uc002smq.1_Missense_Mutation_p.R43Q|LOXL3_uc010ffn.1_Missense_Mutation_p.R43Q|DOK1_uc002smr.1_Intron|DOK1_uc002sms.1_5'Flank|DOK1_uc010ffo.1_5'Flank|DOK1_uc002smt.1_5'Flank|DOK1_uc002smu.1_5'Flank|DOK1_uc002smv.1_5'Flank|DOK1_uc002smw.1_5'Flank	NM_032603	NP_115992	P58215	LOXL3_HUMAN	lysyl oxidase-like 3 precursor	43					oxidation-reduction process	extracellular space|membrane	copper ion binding|protein-lysine 6-oxidase activity|scavenger receptor activity				0														0.485714	158.953932	158.970712	51	54	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	74633142	74633142	9274	2	C	T	T	23	23	LOXL3	T	1	1
COL6A5	256076	broad.mit.edu	36	3	131670653	131670653	+	Missense_Mutation	SNP	A	T	T			TCGA-15-0742-01	TCGA-15-0742-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr3:131670653A>T	uc010htj.1	+	c.7115A>T	c.(7114-7116)CAT>CTT	p.H2372L	COL6A5_uc010hti.1_Non-coding_Transcript|COL6A5_uc010htk.1_Missense_Mutation_p.H411L	NM_153264	NP_694996	A8TX70	CO6A5_HUMAN	collagen, type XXIX, alpha 1	2372	VWFA 10.|Nonhelical region.				axon guidance|cell adhesion	collagen					0														0.466667	187.912287	188.025772	56	64	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	131670653	131670653	3840	3	A	T	T	8	8	COL6A5	T	4	4
PLSCR1	5359	broad.mit.edu	36	3	147722344	147722344	+	Missense_Mutation	SNP	C	T	T			TCGA-15-0742-01	TCGA-15-0742-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr3:147722344C>T	uc003evx.2	-	c.542G>A	c.(541-543)TGT>TAT	p.C181Y	PLSCR1_uc003evy.2_Missense_Mutation_p.C174Y|PLSCR1_uc003evz.2_Intron	NM_021105	NP_066928	O15162	PLS1_HUMAN	phospholipid scramblase 1	181	Cytoplasmic.|Cys-rich.				phospholipid scrambling|platelet activation|response to virus	integral to membrane|plasma membrane	calcium ion binding|phospholipid scramblase activity|SH3 domain binding			ovary(2)	2														0.493333	221.738301	221.744232	74	76	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	147722344	147722344	12535	3	C	T	T	17	17	PLSCR1	T	2	2
SI	6476	broad.mit.edu	36	3	166182770	166182770	+	Silent	SNP	G	A	A			TCGA-15-0742-01	TCGA-15-0742-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr3:166182770G>A	uc003fei.1	-	c.5370C>T	c.(5368-5370)AAC>AAT	p.N1790N		NM_001041	NP_001032	P14410	SUIS_HUMAN	sucrase-isomaltase (alpha-glucosidase)	1790	Sucrase.|Lumenal.				carbohydrate metabolic process|polysaccharide digestion	apical plasma membrane|brush border|Golgi apparatus|integral to membrane	carbohydrate binding|oligo-1,6-glucosidase activity|sucrose alpha-glucosidase activity			ovary(7)|pancreas(1)	8		Prostate(884;0.00314)|Melanoma(1037;0.0153)|all_neural(597;0.0199)			Acarbose(DB00284)									0.397727	102.205305	103.010915	35	53	GG		KEEP	---	---	---	---	capture			Silent	SNP	166182770	166182770	14792	3	G	A	A	40	40	SI	A	1	1
TMEM207	131920	broad.mit.edu	36	3	191630185	191630185	+	Missense_Mutation	SNP	C	G	G			TCGA-15-0742-01	TCGA-15-0742-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr3:191630185C>G	uc003fsj.1	-	c.334G>C	c.(334-336)GGA>CGA	p.G112R		NM_207316	NP_997199	Q6UWW9	TM207_HUMAN	transmembrane protein 207	112						integral to membrane					0	all_cancers(143;3.61e-10)|Ovarian(172;0.0991)													0.496855	261.806302	261.807777	79	80	CC		KEEP	---	---	---	---	capture	Lung(62;2.23e-05)|LUSC - Lung squamous cell carcinoma(58;3.15e-05)	GBM - Glioblastoma multiforme(93;0.0176)	Missense_Mutation	SNP	191630185	191630185	16667	3	C	G	G	21	21	TMEM207	G	3	3
NEK10	152110	broad.mit.edu	36	3	27208559	27208559	+	Missense_Mutation	SNP	C	T	T			TCGA-15-0742-01	TCGA-15-0742-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr3:27208559C>T	uc010hfk.1	-	c.406G>A	c.(406-408)GTC>ATC	p.V136I	NEK10_uc003cds.1_Missense_Mutation_p.V221I|NEK10_uc010hfj.1_Missense_Mutation_p.V136I|NEK10_uc003cdr.1_Missense_Mutation_p.V136I	NM_001031741	NP_001026911	Q6ZWH5	NEK10_HUMAN	cDNA FLJ32685 fis, clone TESTI2000154, weakly similar to PUTATIVE SERINE/THREONINE-PROTEIN KINASE D1044.3 IN CHROMOSOME III (EC 2.7.1.-) (NIMA (Never in mitosis gene a)-related kinase 10, isoform CRA_a).	824					protein phosphorylation		ATP binding|metal ion binding|protein serine/threonine kinase activity|protein tyrosine kinase activity			ovary(5)|lung(2)|central_nervous_system(2)|pancreas(1)|skin(1)	11									p.V136I(SKMEL30-Tumor)	332				0.528986	221.775687	221.876157	73	65	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	27208559	27208559	10721	3	C	T	T	19	19	NEK10	T	1	1
SCN11A	11280	broad.mit.edu	36	3	38926643	38926643	+	Missense_Mutation	SNP	G	A	A			TCGA-15-0742-01	TCGA-15-0742-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr3:38926643G>A	uc010hhm.1	-	c.1019C>T	c.(1018-1020)ACG>ATG	p.T340M		NM_014139	NP_054858	Q9UI33	SCNBA_HUMAN	sodium channel, voltage-gated, type XI, alpha	340	I.				response to drug	voltage-gated sodium channel complex	voltage-gated sodium channel activity			ovary(1)|pancreas(1)|skin(1)	3					Cocaine(DB00907)									0.422764	159.182578	159.822039	52	71	GG		KEEP	---	---	---	---	capture		Kidney(284;0.00202)|KIRC - Kidney renal clear cell carcinoma(284;0.00226)	Missense_Mutation	SNP	38926643	38926643	14395	3	G	A	A	40	40	SCN11A	A	1	1
CHL1	10752	broad.mit.edu	36	3	414999	414999	+	Missense_Mutation	SNP	C	T	T			TCGA-15-0742-01	TCGA-15-0742-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr3:414999C>T	uc003bot.1	+	c.3184C>T	c.(3184-3186)CGC>TGC	p.R1062C	CHL1_uc003bou.1_Missense_Mutation_p.R1046C|CHL1_uc003bow.1_Missense_Mutation_p.R1046C	NM_006614	NP_006605	O00533	CHL1_HUMAN	cell adhesion molecule with homology to L1CAM	1046	Extracellular (Potential).				axon guidance|cell adhesion|signal transduction	integral to membrane|plasma membrane|proteinaceous extracellular matrix				central_nervous_system(4)|large_intestine(2)|ovary(1)	7		all_cancers(2;1.14e-06)|all_epithelial(2;0.00367)|all_lung(1;0.061)|Lung NSC(2;0.201)							p.R1062C(JHUEM7-Tumor)	659				0.363636	93.177284	94.616451	32	56	CC		KEEP	---	---	---	---	capture		Epithelial(13;5.36e-06)|all cancers(10;1.4e-05)|OV - Ovarian serous cystadenocarcinoma(96;0.00323)|COAD - Colon adenocarcinoma(1;0.00925)|Colorectal(20;0.0198)	Missense_Mutation	SNP	414999	414999	3483	3	C	T	T	31	31	CHL1	T	1	1
CCDC158	339965	broad.mit.edu	36	4	77524591	77524591	+	Nonsense_Mutation	SNP	G	A	A			TCGA-15-0742-01	TCGA-15-0742-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr4:77524591G>A	uc003hkb.2	-	c.400C>T	c.(400-402)CGA>TGA	p.R134*	CCDC158_uc010ijg.1_Non-coding_Transcript|CCDC158_uc003hkd.2_Nonsense_Mutation_p.R134*	NM_001042784	NP_001036249	Q5M9N0	CD158_HUMAN	hypothetical protein LOC339965	134	Potential.									ovary(2)|pancreas(1)	3														0.392157	116.973382	118.013451	40	62	GG		KEEP	---	---	---	---	capture			Nonsense_Mutation	SNP	77524591	77524591	2912	4	G	A	A	40	40	CCDC158	A	5	1
SNX24	28966	broad.mit.edu	36	5	122309728	122309728	+	Missense_Mutation	SNP	G	A	A			TCGA-15-0742-01	TCGA-15-0742-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr5:122309728G>A	uc003ktg.1	+	c.224G>A	c.(223-225)CGA>CAA	p.R75Q	SNX24_uc003ktf.1_Missense_Mutation_p.R75Q|SNX24_uc010jcy.1_Missense_Mutation_p.R75Q	NM_014035	NP_054754	Q9Y343	SNX24_HUMAN	SBBI31 protein	75	PX.				cell communication|protein transport	cytoplasmic vesicle membrane	phosphatidylinositol binding				0		Prostate(80;0.0387)												0.440476	112.061164	112.320876	37	47	GG		KEEP	---	---	---	---	capture	KIRC - Kidney renal clear cell carcinoma(527;0.0897)|Kidney(363;0.137)	OV - Ovarian serous cystadenocarcinoma(64;0.000654)|Epithelial(69;0.0016)|all cancers(49;0.0139)	Missense_Mutation	SNP	122309728	122309728	15395	5	G	A	A	37	37	SNX24	A	1	1
PCDHGB6	56100	broad.mit.edu	36	5	140768000	140768000	+	Missense_Mutation	SNP	T	G	G			TCGA-15-0742-01	TCGA-15-0742-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr5:140768000T>G	uc003lkj.1	+	c.47T>G	c.(46-48)GTG>GGG	p.V16G	PCDHGA1_uc003lji.1_Intron|PCDHGA2_uc003ljk.1_Intron|PCDHGA3_uc010jfx.1_Intron|PCDHGA3_uc003ljm.1_Intron|PCDHGB1_uc003ljo.1_Intron|PCDHGA4_uc003ljq.1_Intron|PCDHGB2_uc003ljs.1_Intron|PCDHGA5_uc003lju.1_Intron|PCDHGB3_uc003ljw.1_Intron|PCDHGA6_uc003ljy.1_Intron|PCDHGA7_uc003lka.1_Intron|PCDHGB4_uc003lkc.1_Intron|PCDHGA8_uc003lkd.1_Intron|PCDHGB5_uc003lkf.1_Intron|PCDHGA9_uc003lkh.1_Intron|PCDHGB6_uc003lki.1_Missense_Mutation_p.V16G	NM_018926	NP_061749	Q9Y5F9	PCDGI_HUMAN	protocadherin gamma subfamily B, 6 isoform 1	16					homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding				0												OREG0016861	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	0.375	8.511397	8.742424	6	10	TT		KEEP	---	---	---	---	capture	KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)		Missense_Mutation	SNP	140768000	140768000	11987	5	T	G	G	59	59	PCDHGB6	G	4	4
G3BP1	10146	broad.mit.edu	36	5	151150743	151150743	+	Missense_Mutation	SNP	A	G	G			TCGA-15-0742-01	TCGA-15-0742-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr5:151150743A>G	uc003lun.1	+	c.278A>G	c.(277-279)CAG>CGG	p.Q93R	G3BP1_uc010jhy.1_Missense_Mutation_p.Q93R|G3BP1_uc003lum.1_Missense_Mutation_p.Q93R|G3BP1_uc010jhz.1_5'UTR	NM_005754	NP_938405	Q13283	G3BP1_HUMAN	Ras-GTPase-activating protein SH3-domain-binding	93	NTF2.				Ras protein signal transduction|transport	cytosol|nucleus|plasma membrane	ATP binding|ATP-dependent DNA helicase activity|ATP-dependent RNA helicase activity|DNA binding|endonuclease activity|protein binding|RNA binding			ovary(1)	1		all_hematologic(541;0.0338)|Medulloblastoma(196;0.091)												0.403756	250.369652	252.10382	86	127	AA		KEEP	---	---	---	---	capture	Kidney(363;0.000171)|KIRC - Kidney renal clear cell carcinoma(527;0.000785)		Missense_Mutation	SNP	151150743	151150743	6392	5	A	G	G	7	7	G3BP1	G	4	4
COL23A1	91522	broad.mit.edu	36	5	177601725	177601725	+	Missense_Mutation	SNP	C	A	A			TCGA-15-0742-01	TCGA-15-0742-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr5:177601725C>A	uc003mje.1	-	c.1505G>T	c.(1504-1506)GGG>GTG	p.G502V	COL23A1_uc010jkt.1_Missense_Mutation_p.G384V	NM_173465	NP_775736	Q86Y22	CONA1_HUMAN	collagen, type XXIII, alpha 1	502	Extracellular (Potential).|Collagen-like 5.|Gly-rich.					collagen|integral to membrane|plasma membrane	protein binding			central_nervous_system(1)	1	all_cancers(89;0.00188)|Renal(175;0.000159)|Lung NSC(126;0.00814)|all_lung(126;0.0129)	all_neural(177;0.00802)|Medulloblastoma(196;0.0145)|all_hematologic(541;0.248)												0.571429	11.299771	11.330772	4	3	CC		KEEP	---	---	---	---	capture	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	OV - Ovarian serous cystadenocarcinoma(192;0.153)|all cancers(165;0.172)	Missense_Mutation	SNP	177601725	177601725	3820	5	C	A	A	22	22	COL23A1	A	3	3
HEATR7B2	133558	broad.mit.edu	36	5	41086859	41086859	+	Missense_Mutation	SNP	G	T	T			TCGA-15-0742-01	TCGA-15-0742-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr5:41086859G>T	uc003jmj.2	-	c.1321C>A	c.(1321-1323)CCA>ACA	p.P441T	HEATR7B2_uc003jmi.2_5'UTR	NM_173489	NP_775760	Q7Z745	HTRB2_HUMAN	HEAT repeat family member 7B2	441	HEAT 5.						binding			ovary(6)|central_nervous_system(2)	8														0.511628	67.054505	67.059776	22	21	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	41086859	41086859	7318	5	G	T	T	43	43	HEATR7B2	T	3	3
AHRR	57491	broad.mit.edu	36	5	480793	480793	+	Silent	SNP	C	G	G			TCGA-15-0742-01	TCGA-15-0742-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr5:480793C>G	uc003jav.1	+	c.762C>G	c.(760-762)CCC>CCG	p.P254P	AHRR_uc003jaw.1_Intron|AHRR_uc010isy.1_Intron|AHRR_uc010isz.1_Intron|AHRR_uc003jax.1_Intron|AHRR_uc003jay.1_Intron	NM_020731	NP_065782	A9YTQ3	AHRR_HUMAN	arylhydrocarbon receptor repressor	240					regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	DNA binding|signal transducer activity|transcription regulator activity			breast(2)	2														0.185714	8.812311	15.658575	13	57	CC		KEEP	---	---	---	---	capture	Epithelial(17;0.0011)|OV - Ovarian serous cystadenocarcinoma(19;0.00353)|all cancers(22;0.00354)|Lung(60;0.0863)		Silent	SNP	480793	480793	420	5	C	G	G	23	23	AHRR	G	3	3
BCLAF1	9774	broad.mit.edu	36	6	136634824	136634824	+	Splice_Site_SNP	SNP	A	C	C			TCGA-15-0742-01	TCGA-15-0742-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr6:136634824A>C	uc003qgx.1	-	c.2043_splice	c.e8+1	p.K681_splice	BCLAF1_uc003qgw.1_Splice_Site_SNP_p.K508_splice|BCLAF1_uc003qgy.1_Splice_Site_SNP_p.K679_splice	NM_014739	NP_055554			BCL2-associated transcription factor 1 isoform						induction of apoptosis|negative regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleolus	DNA binding|protein binding|transcription repressor activity			ovary(1)	1	Colorectal(23;0.24)					Colon(142;1534 1789 5427 7063 28491)								0.208333	8.250654	10.158271	5	19	AA		KEEP	---	---	---	---	capture		GBM - Glioblastoma multiforme(68;0.00226)|OV - Ovarian serous cystadenocarcinoma(155;0.00331)	Splice_Site_SNP	SNP	136634824	136634824	1404	6	A	C	C	14	14	BCLAF1	C	5	4
NOX3	50508	broad.mit.edu	36	6	155817876	155817876	+	Missense_Mutation	SNP	G	A	A			TCGA-15-0742-01	TCGA-15-0742-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr6:155817876G>A	uc003qqm.1	-	c.128C>T	c.(127-129)ACA>ATA	p.T43I		NM_015718	NP_056533	Q9HBY0	NOX3_HUMAN	NADPH oxidase 3	43	Extracellular (Potential).				oxidation-reduction process		electron carrier activity|flavin adenine dinucleotide binding|iron ion binding			ovary(1)	1		Breast(66;0.0183)												0.828571	93.492911	97.062537	29	6	GG		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(155;2.18e-12)|BRCA - Breast invasive adenocarcinoma(81;0.00815)	Missense_Mutation	SNP	155817876	155817876	10961	6	G	A	A	48	48	NOX3	A	2	2
MDC1	9656	broad.mit.edu	36	6	30779503	30779503	+	Missense_Mutation	SNP	C	G	G			TCGA-15-0742-01	TCGA-15-0742-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr6:30779503C>G	uc003nrg.2	-	c.5436G>C	c.(5434-5436)AAG>AAC	p.K1812N	MDC1_uc003nrf.2_Missense_Mutation_p.K443N	NM_014641	NP_055456	Q14676	MDC1_HUMAN	mediator of DNA damage checkpoint 1	1812	Required for nuclear localization (NLS2).				cell cycle|double-strand break repair via homologous recombination|intra-S DNA damage checkpoint	focal adhesion|nucleoplasm	FHA domain binding|protein C-terminus binding			breast(2)|ovary(1)|kidney(1)	4														0.446429	510.813114	511.652469	150	186	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	30779503	30779503	9792	6	C	G	G	32	32	MDC1	G	3	3
KIAA1586	57691	broad.mit.edu	36	6	57026024	57026024	+	Missense_Mutation	SNP	A	C	C			TCGA-15-0742-01	TCGA-15-0742-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr6:57026024A>C	uc003pdj.1	+	c.768A>C	c.(766-768)TTA>TTC	p.L256F		NM_020931	NP_065982	Q9HCI6	K1586_HUMAN	hypothetical protein LOC57691	256							nucleic acid binding				0	Lung NSC(77;0.0969)													0.404255	60.117297	60.49341	19	28	AA		KEEP	---	---	---	---	capture	LUSC - Lung squamous cell carcinoma(124;0.0785)|Lung(124;0.13)		Missense_Mutation	SNP	57026024	57026024	8554	6	A	C	C	15	15	KIAA1586	C	4	4
KCNQ5	56479	broad.mit.edu	36	6	73961170	73961170	+	Missense_Mutation	SNP	C	T	T			TCGA-15-0742-01	TCGA-15-0742-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr6:73961170C>T	uc003pgk.1	+	c.2111C>T	c.(2110-2112)GCG>GTG	p.A704V	KCNQ5_uc010kat.1_Missense_Mutation_p.A695V	NM_019842	NP_062816	Q9NR82	KCNQ5_HUMAN	potassium voltage-gated channel, KQT-like	704					protein complex assembly|synaptic transmission	voltage-gated potassium channel complex	inward rectifier potassium channel activity			ovary(4)|large_intestine(2)	6		all_epithelial(107;0.116)|Lung NSC(302;0.219)				GBM(142;1375 1859 14391 23261 44706)								0.758621	222.392328	227.703148	66	21	CC		KEEP	---	---	---	---	capture		COAD - Colon adenocarcinoma(1;0.0107)|Colorectal(1;0.0583)	Missense_Mutation	SNP	73961170	73961170	8391	6	C	T	T	27	27	KCNQ5	T	1	1
IMPG1	3617	broad.mit.edu	36	6	76808456	76808456	+	Nonsense_Mutation	SNP	G	A	A			TCGA-15-0742-01	TCGA-15-0742-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr6:76808456G>A	uc003pik.1	-	c.175C>T	c.(175-177)CGA>TGA	p.R59*		NM_001563	NP_001554	Q17R60	IMPG1_HUMAN	interphotoreceptor matrix proteoglycan 1	59					visual perception	proteinaceous extracellular matrix	extracellular matrix structural constituent|receptor activity			ovary(2)	2		Acute lymphoblastic leukemia(125;0.0418)|all_hematologic(105;0.222)				Pancreas(37;839 1141 2599 26037)								0.853448	333.49874	347.426828	99	17	GG		KEEP	---	---	---	---	capture			Nonsense_Mutation	SNP	76808456	76808456	8029	6	G	A	A	40	40	IMPG1	A	5	1
SLC26A3	1811	broad.mit.edu	36	7	107221432	107221432	+	Missense_Mutation	SNP	C	T	T			TCGA-15-0742-01	TCGA-15-0742-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr7:107221432C>T	uc003ver.2	-	c.262G>A	c.(262-264)GTA>ATA	p.V88I	SLC26A3_uc003ves.2_Missense_Mutation_p.V53I	NM_000111	NP_000102	P40879	S26A3_HUMAN	solute carrier family 26, member 3	88	Helical; (Potential).				excretion	integral to membrane|membrane fraction	inorganic anion exchanger activity|secondary active sulfate transmembrane transporter activity|sequence-specific DNA binding transcription factor activity|transcription cofactor activity			ovary(3)	3														0.291139	57.689133	60.779143	23	56	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	107221432	107221432	15015	7	C	T	T	19	19	SLC26A3	T	1	1
SPAM1	6677	broad.mit.edu	36	7	123382369	123382369	+	Missense_Mutation	SNP	G	A	A			TCGA-15-0742-01	TCGA-15-0742-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr7:123382369G>A	uc003vle.1	+	c.1037G>A	c.(1036-1038)CGA>CAA	p.R346Q	SPAM1_uc003vld.1_Missense_Mutation_p.R346Q|SPAM1_uc003vlf.2_Missense_Mutation_p.R346Q|SPAM1_uc010lku.1_Missense_Mutation_p.R346Q	NM_003117	NP_003108	P38567	HYALP_HUMAN	sperm adhesion molecule 1 isoform 1	346					binding of sperm to zona pellucida|carbohydrate metabolic process|cell adhesion|fusion of sperm to egg plasma membrane	anchored to membrane|plasma membrane	hyalurononglucosaminidase activity			ovary(3)|kidney(1)	4					Hyaluronidase(DB00070)									0.316832	263.979081	273.025563	96	207	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	123382369	123382369	15489	7	G	A	A	37	37	SPAM1	A	1	1
SVOPL	136306	broad.mit.edu	36	7	137961331	137961331	+	Missense_Mutation	SNP	C	T	T			TCGA-15-0742-01	TCGA-15-0742-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr7:137961331C>T	uc003vue.1	-	c.730G>A	c.(730-732)GGC>AGC	p.G244S	SVOPL_uc003vud.1_Non-coding_Transcript	NM_174959	NP_777619	Q8N434	SVOPL_HUMAN	SVOP-like isoform 2	396	Helical; (Potential).				transmembrane transport	integral to membrane	transporter activity				0														0.166667	25.530124	33.744027	13	65	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	137961331	137961331	15944	7	C	T	T	23	23	SVOPL	T	1	1
EGFR	1956	broad.mit.edu	36	7	55206388	55206388	+	Missense_Mutation	SNP	G	A	A			TCGA-15-0742-01	TCGA-15-0742-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr7:55206388G>A	uc003tqk.1	+	c.1907G>A	c.(1906-1908)TGT>TAT	p.C636Y	EGFR_uc010kzg.1_Missense_Mutation_p.C591Y	NM_005228	NP_005219	P00533	EGFR_HUMAN	epidermal growth factor receptor isoform a	636	Extracellular (Potential).				activation of phospholipase A2 activity by calcium-mediated signaling|activation of phospholipase C activity|axon guidance|cell proliferation|cell-cell adhesion|negative regulation of apoptosis|negative regulation of epidermal growth factor receptor signaling pathway|ossification|positive regulation of catenin import into nucleus|positive regulation of cell migration|positive regulation of cyclin-dependent protein kinase activity involved in G1/S|positive regulation of epithelial cell proliferation|positive regulation of MAP kinase activity|positive regulation of nitric oxide biosynthetic process|positive regulation of phosphorylation|positive regulation of protein kinase B signaling cascade|protein autophosphorylation|protein insertion into membrane|regulation of nitric-oxide synthase activity|regulation of peptidyl-tyrosine phosphorylation|response to stress|response to UV-A	basolateral plasma membrane|endoplasmic reticulum membrane|endosome|extracellular space|Golgi membrane|integral to membrane|nuclear membrane|Shc-EGFR complex	actin filament binding|ATP binding|double-stranded DNA binding|epidermal growth factor receptor activity|identical protein binding|MAP/ERK kinase kinase activity|protein heterodimerization activity|protein phosphatase binding|receptor signaling protein tyrosine kinase activity	p.C636Y(1)		lung(8200)|central_nervous_system(103)|upper_aerodigestive_tract(37)|prostate(32)|ovary(31)|thyroid(23)|breast(11)|peritoneum(9)|oesophagus(9)|salivary_gland(9)|large_intestine(8)|stomach(6)|urinary_tract(6)|skin(5)|adrenal_gland(5)|kidney(4)|soft_tissue(4)|bone(3)|NS(2)|haematopoietic_and_lymphoid_tissue(2)|thymus(2)|liver(2)|eye(1)|pancreas(1)	8515	all_cancers(1;1.57e-46)|all_epithelial(1;5.62e-37)|Lung NSC(1;9.29e-25)|all_lung(1;4.39e-23)|Esophageal squamous(2;7.55e-08)|Breast(14;0.0318)				Cetuximab(DB00002)|Erlotinib(DB00530)|Gefitinib(DB00317)|Lapatinib(DB01259)|Lidocaine(DB00281)|Panitumumab(DB01269)|Trastuzumab(DB00072)			8		608	TCGA GBM(3;<1E-8)|TSP Lung(4;<1E-8)			0.955929	3090.733765	3195.55901	911	42	GG		KEEP	---	---	---	---	capture	GBM - Glioblastoma multiforme(1;0)|all cancers(1;2.19e-314)|Lung(13;4.65e-05)|LUSC - Lung squamous cell carcinoma(13;0.000168)|STAD - Stomach adenocarcinoma(5;0.00164)|Epithelial(13;0.0607)		Missense_Mutation	SNP	55206388	55206388	5156	7	G	A	A	48	48	EGFR	A	2	2
CCL24	6369	broad.mit.edu	36	7	75280899	75280899	+	Missense_Mutation	SNP	G	A	A			TCGA-15-0742-01	TCGA-15-0742-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr7:75280899G>A	uc003udu.2	-	c.71C>T	c.(70-72)ACG>ATG	p.T24M		NM_002991	NP_002982	O00175	CCL24_HUMAN	small inducible cytokine A24 precursor	24					cell-cell signaling|chemotaxis|immune response|inflammatory response|positive regulation of actin filament polymerization|positive regulation of cell migration|positive regulation of endothelial cell proliferation|positive regulation of Rac GTPase activity|signal transduction	extracellular space	chemokine activity				0														0.333333	235.819697	242.017207	84	168	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	75280899	75280899	3021	7	G	A	A	40	40	CCL24	A	1	1
HGF	3082	broad.mit.edu	36	7	81169915	81169915	+	Missense_Mutation	SNP	C	T	T			TCGA-15-0742-01	TCGA-15-0742-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr7:81169915C>T	uc003uhl.1	-	c.2105G>A	c.(2104-2106)CGT>CAT	p.R702H	HGF_uc003uhm.1_Missense_Mutation_p.R697H	NM_000601	NP_000592	P14210	HGF_HUMAN	hepatocyte growth factor isoform 1	702	Peptidase S1.				epithelial to mesenchymal transition|mitosis|platelet activation|platelet degranulation|proteolysis|regulation of branching involved in salivary gland morphogenesis by mesenchymal-epithelial signaling	platelet alpha granule lumen	growth factor activity|serine-type endopeptidase activity			ovary(2)|central_nervous_system(2)	4										800				0.302817	115.169888	120.099071	43	99	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	81169915	81169915	7369	7	C	T	T	19	19	HGF	T	1	1
ZNF804B	219578	broad.mit.edu	36	7	88801531	88801531	+	Silent	SNP	C	A	A			TCGA-15-0742-01	TCGA-15-0742-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr7:88801531C>A	uc003uju.1	+	c.1299C>A	c.(1297-1299)ACC>ACA	p.T433T		NM_181646	NP_857597	A4D1E1	Z804B_HUMAN	zinc finger protein 804B	433						intracellular	zinc ion binding			ovary(5)|pancreas(2)	7	all_hematologic(106;0.125)|Lung NSC(181;0.15)|all_lung(186;0.151)													0.29697	129.823139	135.898082	49	116	CC		KEEP	---	---	---	---	capture	STAD - Stomach adenocarcinoma(171;0.0513)		Silent	SNP	88801531	88801531	18769	7	C	A	A	22	22	ZNF804B	A	3	3
ZNF706	51123	broad.mit.edu	36	8	102283137	102283137	+	Silent	SNP	A	G	G			TCGA-15-0742-01	TCGA-15-0742-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr8:102283137A>G	uc003yka.1	-	c.9T>C	c.(7-9)CGT>CGC	p.R3R	ZNF706_uc003ykb.1_Silent_p.R3R	NM_001042510	NP_057180	Q9Y5V0	ZN706_HUMAN	HSPC038 protein	3						intracellular	zinc ion binding			ovary(2)	2	all_cancers(14;3.3e-07)|all_epithelial(15;3.47e-09)|Lung NSC(17;3.44e-05)|all_lung(17;0.000117)													0.204082	20.621192	24.607318	10	39	AA		KEEP	---	---	---	---	capture	Epithelial(11;8.57e-11)|all cancers(13;1.43e-08)|OV - Ovarian serous cystadenocarcinoma(57;1.43e-05)		Silent	SNP	102283137	102283137	18706	8	A	G	G	6	6	ZNF706	G	4	4
RIMS2	9699	broad.mit.edu	36	8	105070726	105070726	+	Missense_Mutation	SNP	G	A	A			TCGA-15-0742-01	TCGA-15-0742-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr8:105070726G>A	uc003yls.2	+	c.2279G>A	c.(2278-2280)GGG>GAG	p.G760E	RIMS2_uc003ylp.2_Missense_Mutation_p.G982E|RIMS2_uc003ylw.2_Missense_Mutation_p.G774E|RIMS2_uc003ylq.2_Missense_Mutation_p.G774E|RIMS2_uc003ylr.2_Missense_Mutation_p.G821E	NM_014677	NP_055492	Q9UQ26	RIMS2_HUMAN	regulating synaptic membrane exocytosis 2	1044					intracellular protein transport	cell junction|presynaptic membrane	Rab GTPase binding|zinc ion binding			ovary(6)|lung(2)|breast(2)|large_intestine(1)|central_nervous_system(1)|skin(1)|pancreas(1)	14										728				0.319249	198.723415	204.907997	68	145	GG		KEEP	---	---	---	---	capture	OV - Ovarian serous cystadenocarcinoma(57;7.7e-07)|STAD - Stomach adenocarcinoma(118;0.229)		Missense_Mutation	SNP	105070726	105070726	13845	8	G	A	A	43	43	RIMS2	A	2	2
CSMD3	114788	broad.mit.edu	36	8	114360000	114360000	+	Missense_Mutation	SNP	C	T	T			TCGA-15-0742-01	TCGA-15-0742-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr8:114360000C>T	uc003ynu.1	-	c.511G>A	c.(511-513)GAA>AAA	p.E171K	CSMD3_uc003ynt.1_Missense_Mutation_p.E131K|CSMD3_uc003ynv.1_Missense_Mutation_p.E134K|CSMD3_uc010mcx.1_Missense_Mutation_p.E171K	NM_198123	NP_937756	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3 isoform 1	171	Extracellular (Potential).|CUB 1.					integral to membrane|plasma membrane				ovary(20)|lung(11)|kidney(8)|large_intestine(6)|skin(3)|central_nervous_system(2)|urinary_tract(1)|breast(1)	52									p.E131K(MEWO-Tumor)	2888	TCGA Ovarian(7;0.080)			0.537037	91.576805	91.641008	29	25	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	114360000	114360000	4087	8	C	T	T	31	31	CSMD3	T	1	1
BAT2L1	84726	broad.mit.edu	36	9	133356667	133356667	+	Missense_Mutation	SNP	A	C	C			TCGA-15-0742-01	TCGA-15-0742-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr9:133356667A>C	uc004can.2	+	c.6260A>C	c.(6259-6261)CAG>CCG	p.Q2087P	BAT2L1_uc004cao.2_Missense_Mutation_p.Q1444P|BAT2L1_uc004cap.2_Missense_Mutation_p.Q233P	NM_013318	NP_037450	Q5JSZ5	PRC2B_HUMAN	HLA-B associated transcript 2-like	2087							protein binding				0														0.294118	8.202362	8.894251	5	12	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	133356667	133356667	1341	9	A	C	C	7	7	BAT2L1	C	4	4
SURF4	6836	broad.mit.edu	36	9	135220340	135220340	+	Silent	SNP	G	A	A			TCGA-15-0742-01	TCGA-15-0742-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr9:135220340G>A	uc004cdj.1	-	c.660C>T	c.(658-660)AAC>AAT	p.N220N	SURF4_uc010nal.1_3'UTR	NM_033161	NP_149351	O15260	SURF4_HUMAN	surfeit 4	220	Helical; (Potential).					endoplasmic reticulum membrane|ER-Golgi intermediate compartment membrane|Golgi membrane|integral to membrane	protein binding				0														0.793103	150.779716	155.397914	46	12	GG		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(145;5.32e-07)|Epithelial(140;4.56e-06)|all cancers(34;4.25e-05)	Silent	SNP	135220340	135220340	15925	9	G	A	A	40	40	SURF4	A	1	1
IFNA21	3452	broad.mit.edu	36	9	21156247	21156247	+	Missense_Mutation	SNP	C	G	G			TCGA-15-0742-01	TCGA-15-0742-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr9:21156247C>G	uc003zom.2	-	c.365G>C	c.(364-366)TGC>TCC	p.C122S		NM_002175	NP_002166	P01568	IFN21_HUMAN	interferon, alpha 21	122					blood coagulation|regulation of type I interferon-mediated signaling pathway|response to virus|type I interferon-mediated signaling pathway	extracellular space	cytokine activity|cytokine receptor binding			central_nervous_system(1)	1														0.928205	690.42515	727.180464	181	14	CC		KEEP	---	---	---	---	capture		GBM - Glioblastoma multiforme(5;1.93e-187)|Lung(24;2.12e-22)|LUSC - Lung squamous cell carcinoma(38;1.4e-13)	Missense_Mutation	SNP	21156247	21156247	7839	9	C	G	G	25	25	IFNA21	G	3	3
S1PR3	1903	broad.mit.edu	36	9	90806443	90806443	+	Missense_Mutation	SNP	G	A	A			TCGA-15-0742-01	TCGA-15-0742-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr9:90806443G>A	uc004aqe.1	+	c.508G>A	c.(508-510)GCC>ACC	p.A170T	S1PR3_uc010mqm.1_Missense_Mutation_p.A170T	NM_005226	NP_005217	Q99500	S1PR3_HUMAN	sphingosine-1-phosphate receptor 3	170	Helical; Name=4; (By similarity).				anatomical structure morphogenesis|elevation of cytosolic calcium ion concentration|inflammatory response|positive regulation of cell proliferation	integral to plasma membrane	lipid binding|lysosphingolipid and lysophosphatidic acid receptor activity			ovary(2)|central_nervous_system(1)	3												OREG0019291	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	0.516949	183.532468	183.565955	61	57	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	90806443	90806443	14275	9	G	A	A	38	38	S1PR3	A	1	1
GRIA3	2892	broad.mit.edu	36	X	122287713	122287713	+	Missense_Mutation	SNP	G	A	A			TCGA-15-0742-01	TCGA-15-0742-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chrX:122287713G>A	uc004etq.2	+	c.664G>A	c.(664-666)GAA>AAA	p.E222K	GRIA3_uc004etr.2_Missense_Mutation_p.E222K|GRIA3_uc004ets.2_Non-coding_Transcript	NM_007325	NP_015564	P42263	GRIA3_HUMAN	glutamate receptor, ionotrophic, AMPA 3 isoform	222	Extracellular (Potential).				glutamate signaling pathway|synaptic transmission	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane	alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity			ovary(3)|pancreas(1)	4					L-Glutamic Acid(DB00142)					217				0.938776	315.695606	329.769585	92	6	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	122287713	122287713	7047	23	G	A	A	37	37	GRIA3	A	1	1
MAGEB1	4112	broad.mit.edu	36	X	30179535	30179535	+	Missense_Mutation	SNP	G	A	A			TCGA-15-0742-01	TCGA-15-0742-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chrX:30179535G>A	uc004dcc.1	+	c.1004G>A	c.(1003-1005)CGT>CAT	p.R335H	MAGEB1_uc004dcd.1_Missense_Mutation_p.R335H|MAGEB1_uc004dce.1_Missense_Mutation_p.R335H|MAGEB1_uc010ngh.1_Missense_Mutation_p.R335H	NM_002363	NP_803134	P43366	MAGB1_HUMAN	melanoma antigen family B, 1	335											0														0.888889	212.047449	222.810309	64	8	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	30179535	30179535	9553	23	G	A	A	40	40	MAGEB1	A	1	1
PIK3CA	5290	broad.mit.edu	36	3	180399545	180399547	+	In_Frame_Del	DEL	GAA	-	-			TCGA-15-0742-01	TCGA-15-0742-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:180399545_180399547delGAA	uc003fjk.1	+	c.238_240delGAA	c.(238-240)GAAdel	p.E81del		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			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)		OV - Ovarian serous cystadenocarcinoma(80;9.59e-28)|GBM - Glioblastoma multiforme(14;0.003)|BRCA - Breast invasive adenocarcinoma(182;0.0282)			Colon(199;1504 1750 3362 26421 31210 32040)		57		621	TCGA GBM(8;5.49e-07)			0.41			62	91				---	---	---	---	capture_indel			In_Frame_Del	DEL	180399545	180399547	12337	3	GAA	-	-	41	41	PIK3CA	-	5	5
CPEB2	132864	broad.mit.edu	36	4	14614836	14614837	+	In_Frame_Ins	INS	-	GCG	GCG			TCGA-15-0742-01	TCGA-15-0742-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:14614836_14614837insGCG	uc003gnk.1	+	c.130_131insGCG	c.(130-132)AGC>AGCGGC	p.50_51insG	CPEB2_uc003gni.1_In_Frame_Ins_p.50_51insG|CPEB2_uc003gnj.1_In_Frame_Ins_p.50_51insG|CPEB2_uc003gnl.1_In_Frame_Ins_p.50_51insG|CPEB2_uc003gnm.1_In_Frame_Ins_p.50_51insG|CPEB2_uc003gnn.1_In_Frame_Ins_p.50_51insG	NM_182485	NP_872291	Q7Z5Q1	CPEB2_HUMAN	cytoplasmic polyadenylation element binding	50_51	Pro-rich.				regulation of translation	cytoplasm	nucleotide binding|RNA binding				0														0.31			4	9				---	---	---	---	capture_indel			In_Frame_Ins	INS	14614836	14614837	3939	4	-	GCG	GCG	11	11	CPEB2	GCG	5	5
