Hugo_Symbol	Entrez_Gene_Id	Center	NCBI_Build	Chromosome	Start_position	End_position	Strand	Variant_Classification	Variant_Type	Reference_Allele	Tumor_Seq_Allele1	Tumor_Seq_Allele2	dbSNP_RS	dbSNP_Val_Status	Tumor_Sample_Barcode	Matched_Norm_Sample_Barcode	Match_Norm_Seq_Allele1	Match_Norm_Seq_Allele2	Tumor_Validation_Allele1	Tumor_Validation_Allele2	Match_Norm_Validation_Allele1	Match_Norm_Validation_Allele2	Verification_Status	Validation_Status	Mutation_Status	Sequencing_Phase	Sequence_Source	Validation_Method	Score	BAM_file	Sequencer	Genome_Change	Annotation_Transcript	Transcript_Strand	cDNA_Change	Codon_Change	Protein_Change	Other_Transcripts	Refseq_mRNA_Id	Refseq_prot_Id	SwissProt_acc_Id	SwissProt_entry_Id	Description	UniProt_AApos	UniProt_Region	UniProt_Site	UniProt_Natural_Variations	UniProt_Experimental_Info	GO_Biological_Process	GO_Cellular_Component	GO_Molecular_Function	COSMIC_overlapping_mutations	COSMIC_fusion_genes	COSMIC_tissue_types_affected	COSMIC_total_alterations_in_gene	Tumorscape_Amplification_Peaks	Tumorscape_Deletion_Peaks	i_TCGAscape_Amplification_Peaks	i_TCGAscape_Deletion_Peaks	DrugBank	i_ACHILLES_Top_Genes	i_CCLE_ONCOMAP_overlapping_mutations	i_CCLE_ONCOMAP_total_mutations_in_gene	i_CCLE_SEQ_overlapping_mutations	i_CCLE_SEQ_total_mutations_in_gene	MUTSIG_Significant_Genes	OREGANNO_ID	OREGANNO_Values	i_tumor_f	i_init_t_lod	i_t_lod_fstar	i_t_alt_count	i_t_ref_count	i_normal_best_gt	i_failure_reasons	i_judgement	validation_status	validation_method	validation_tumor_sample	validation_alt_allele	dataset	TCGAscape_Amplification_Peaks	TCGAscape_Deletion_Peaks	type	classification	start	end	gene	chr	ref_allele	tum_allele1	tum_allele2	context_orig	context65	gene_name	newbase	categ	categ_ignoring_null_categ
PTEN	5728	broad.mit.edu	36	10	89682821	89682821	+	Missense_Mutation	SNP	G	A	A			TCGA-14-1034-01	TCGA-14-1034-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr10:89682821G>A	uc001kfb.1	+	c.325G>A	c.(325-327)GAC>AAC	p.D109N		NM_000314	NP_000305	P60484	PTEN_HUMAN	phosphatase and tensin homolog	109	Phosphatase tensin-type.				apoptosis|canonical Wnt receptor signaling pathway|cell proliferation|central nervous system development|induction of apoptosis|inositol phosphate dephosphorylation|negative regulation of cell migration|negative regulation of focal adhesion assembly|negative regulation of protein kinase B signaling cascade|negative regulation of protein phosphorylation|nerve growth factor receptor signaling pathway|phosphatidylinositol dephosphorylation|phosphatidylinositol-mediated signaling|positive regulation of sequence-specific DNA binding transcription factor activity|protein stabilization|regulation of cyclin-dependent protein kinase activity|regulation of neuron projection development|T cell receptor signaling pathway	cytosol|internal side of plasma membrane|PML body	enzyme binding|inositol-1,3,4,5-tetrakisphosphate 3-phosphatase activity|lipid binding|magnesium ion binding|PDZ domain binding|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity|phosphatidylinositol-3,4-bisphosphate 3-phosphatase activity|phosphatidylinositol-3-phosphatase activity|protein serine/threonine phosphatase activity|protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity	p.Y27_N212>Y(2)|p.L108_D109del(2)|p.F56fs*2(1)|p.D109fs*6(1)		endometrium(831)|central_nervous_system(654)|skin(119)|haematopoietic_and_lymphoid_tissue(101)|prostate(97)|large_intestine(90)|breast(67)|lung(63)|ovary(58)|thyroid(29)|stomach(29)|upper_aerodigestive_tract(25)|cervix(21)|liver(20)|vulva(17)|kidney(15)|NS(14)|soft_tissue(12)|urinary_tract(12)|eye(8)|pancreas(6)|salivary_gland(5)|bone(5)|biliary_tract(4)|autonomic_ganglia(2)|meninges(2)|testis(1)|oesophagus(1)	2308		all_cancers(4;3.61e-31)|all_epithelial(4;3.96e-23)|Prostate(4;8.12e-23)|Breast(4;0.000111)|Melanoma(5;0.00146)|all_hematologic(4;0.00227)|Colorectal(252;0.00494)|all_neural(4;0.00513)|Acute lymphoblastic leukemia(4;0.0116)|Glioma(4;0.0274)|all_lung(38;0.132)						31		264	TCGA GBM(2;<1E-8)|TSP Lung(26;0.18)			0.42735	141.923954	142.463984	50	67	GG		KEEP	---	---	---	---	capture	KIRC - Kidney renal clear cell carcinoma(1;0.214)	UCEC - Uterine corpus endometrioid carcinoma (6;0.000228)|all cancers(1;4.16e-84)|GBM - Glioblastoma multiforme(1;7.77e-49)|Epithelial(1;7.67e-41)|OV - Ovarian serous cystadenocarcinoma(1;6.22e-15)|BRCA - Breast invasive adenocarcinoma(1;1.1e-06)|Lung(2;3.18e-06)|Colorectal(12;4.88e-06)|LUSC - Lung squamous cell carcinoma(2;4.97e-06)|COAD - Colon adenocarcinoma(12;1.13e-05)|Kidney(1;0.000288)|KIRC - Kidney renal clear cell carcinoma(1;0.00037)|STAD - Stomach adenocarcinoma(243;0.218)	Missense_Mutation	SNP	89682821	89682821	13192	10	G	A	A	45	45	PTEN	A	2	2
MUC2	4583	broad.mit.edu	36	11	1083411	1083411	+	Missense_Mutation	SNP	A	C	C	rs55824838	unknown	TCGA-14-1034-01	TCGA-14-1034-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr11:1083411A>C	uc001lsx.1	+	c.12316A>C	c.(12316-12318)ACG>CCG	p.T4106P		NM_002457	NP_002448	Q02817	MUC2_HUMAN	mucin 2 precursor	4106						inner mucus layer|outer mucus layer	protein binding			lung(1)|breast(1)	2		all_cancers(49;1.08e-07)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.191)			Pranlukast(DB01411)									0.2	7.017276	8.272221	3	12	AA		KEEP	---	---	---	---	capture		BRCA - Breast invasive adenocarcinoma(625;0.000207)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)	Missense_Mutation	SNP	1083411	1083411	10369	11	A	C	C	6	6	MUC2	C	4	4
PPP2R1B	5519	broad.mit.edu	36	11	111118502	111118502	+	Missense_Mutation	SNP	T	C	C			TCGA-14-1034-01	TCGA-14-1034-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr11:111118502T>C	uc001plw.1	-	c.1652A>G	c.(1651-1653)AAT>AGT	p.N551S	PPP2R1B_uc001plx.1_Missense_Mutation_p.N551S	NM_181699	NP_859050	P30154	2AAB_HUMAN	beta isoform of regulatory subunit A, protein	551	HEAT 14.						protein binding				0		all_cancers(61;2.34e-15)|all_epithelial(67;1.72e-09)|Melanoma(852;1.91e-06)|all_hematologic(158;0.000405)|Acute lymphoblastic leukemia(157;0.000967)|Breast(348;0.0112)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)												0.283951	67.792056	71.186161	23	58	TT		KEEP	---	---	---	---	capture		BRCA - Breast invasive adenocarcinoma(274;1.13e-06)|Epithelial(105;2.36e-06)|all cancers(92;3.78e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.0761)	Missense_Mutation	SNP	111118502	111118502	12819	11	T	C	C	52	52	PPP2R1B	C	4	4
SCGB1C1	147199	broad.mit.edu	36	11	183135	183135	+	Silent	SNP	C	T	T			TCGA-14-1034-01	TCGA-14-1034-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr11:183135C>T	uc001loa.1	+	c.36C>T	c.(34-36)CTC>CTT	p.L12L		NM_145651	NP_663626	Q8TD33	SG1C1_HUMAN	secretoglobin, family 1C, member 1	12						extracellular region	binding				0		all_cancers(49;1.58e-09)|all_epithelial(84;2.71e-06)|Breast(177;0.000162)|Ovarian(85;0.000626)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.0538)|all_lung(207;0.0713)												0.2	8.603776	10.266679	4	16	CC		KEEP	---	---	---	---	capture		all cancers(45;3.95e-27)|Epithelial(43;2.66e-26)|OV - Ovarian serous cystadenocarcinoma(40;5.55e-21)|BRCA - Breast invasive adenocarcinoma(625;3.56e-05)|Lung(200;0.105)|LUSC - Lung squamous cell carcinoma(625;0.122)	Silent	SNP	183135	183135	14376	11	C	T	T	29	29	SCGB1C1	T	2	2
DCDC1	341019	broad.mit.edu	36	11	31042743	31042743	+	Missense_Mutation	SNP	G	T	T			TCGA-14-1034-01	TCGA-14-1034-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr11:31042743G>T	uc001msu.1	-	c.1297C>A	c.(1297-1299)CAA>AAA	p.Q433K				P59894	DCDC1_HUMAN	cDNA FLJ44078 fis, clone TESTI4039038.	10					intracellular signal transduction						0	Lung SC(675;0.225)													0.335443	148.201011	151.999185	53	105	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	31042743	31042743	4455	11	G	T	T	46	46	DCDC1	T	3	3
CKAP5	9793	broad.mit.edu	36	11	46749103	46749103	+	Silent	SNP	C	T	T			TCGA-14-1034-01	TCGA-14-1034-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr11:46749103C>T	uc001ndi.1	-	c.2997G>A	c.(2995-2997)CTG>CTA	p.L999L	CKAP5_uc009ylg.1_Silent_p.L885L|CKAP5_uc001ndj.1_Silent_p.L999L|CKAP5_uc001ndh.1_5'Flank	NM_001008938	NP_001008938	Q14008	CKAP5_HUMAN	colonic and hepatic tumor over-expressed protein	999					cell division|centrosome organization|establishment or maintenance of microtubule cytoskeleton polarity|G2/M transition of mitotic cell cycle|mitotic prometaphase|RNA transport|spindle organization	centrosome|cytosol	protein binding|protein binding			ovary(1)	1						Ovarian(4;85 273 2202 4844 13323)								0.346535	84.446257	86.567869	35	66	CC		KEEP	---	---	---	---	capture			Silent	SNP	46749103	46749103	3581	11	C	T	T	21	21	CKAP5	T	2	2
FXC1	26515	broad.mit.edu	36	11	6460024	6460024	+	Silent	SNP	C	T	T			TCGA-14-1034-01	TCGA-14-1034-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr11:6460024C>T	uc001mdn.2	+	c.309C>T	c.(307-309)AGC>AGT	p.S103S	ARFIP2_uc001mdk.1_5'Flank|ARFIP2_uc001mdl.1_5'Flank|ARFIP2_uc001mdm.1_5'Flank|ARFIP2_uc009yfe.1_5'Flank|FXC1_uc001mdo.2_Non-coding_Transcript	NM_012192	NP_036324	Q9Y5J6	TIM9B_HUMAN	fractured callus expressed transcript 1	103					cell-matrix adhesion|protein import into mitochondrial inner membrane|transmembrane transport	mitochondrial inner membrane|mitochondrial intermembrane space protein transporter complex	metal ion binding				0		Medulloblastoma(188;0.00263)|all_neural(188;0.026)|Breast(177;0.029)												0.315789	10.889032	11.494535	6	13	CC		KEEP	---	---	---	---	capture		Epithelial(150;3.26e-08)|BRCA - Breast invasive adenocarcinoma(625;0.189)	Silent	SNP	6460024	6460024	6364	11	C	T	T	28	28	FXC1	T	2	2
NOX4	50507	broad.mit.edu	36	11	88712965	88712965	+	Missense_Mutation	SNP	G	A	A			TCGA-14-1034-01	TCGA-14-1034-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr11:88712965G>A	uc001pct.1	-	c.1360C>T	c.(1360-1362)CTT>TTT	p.L454F	NOX4_uc001pcx.1_Missense_Mutation_p.L107F|NOX4_uc001pcu.1_Missense_Mutation_p.L380F|NOX4_uc001pcv.1_Missense_Mutation_p.L414F|NOX4_uc009yvo.1_Non-coding_Transcript|NOX4_uc009yvp.1_Missense_Mutation_p.L218F|NOX4_uc001pcw.1_Missense_Mutation_p.L147F|NOX4_uc009yvq.1_Missense_Mutation_p.L430F	NM_016931	NP_058627	Q9NPH5	NOX4_HUMAN	NADPH oxidase 4 isoform a	454	Cytoplasmic (Potential).|Mediates interaction with TLR4.				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)												0.314136	161.043755	166.908333	60	131	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	88712965	88712965	10962	11	G	A	A	34	34	NOX4	A	2	2
GALNT8	26290	broad.mit.edu	36	12	4724876	4724876	+	Missense_Mutation	SNP	G	A	A			TCGA-14-1034-01	TCGA-14-1034-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr12:4724876G>A	uc001qne.1	+	c.881G>A	c.(880-882)CGG>CAG	p.R294Q		NM_017417	NP_059113	Q9NY28	GALT8_HUMAN	polypeptide N-acetylgalactosaminyltransferase 8	294	Lumenal (Potential).|Catalytic subdomain A.					Golgi membrane|integral to membrane	polypeptide N-acetylgalactosaminyltransferase activity|sugar binding			ovary(1)|pancreas(1)	2						Colon(108;631 1558 7270 20097 39846)								0.37963	125.261478	126.629546	41	67	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	4724876	4724876	6483	12	G	A	A	39	39	GALNT8	A	1	1
SRGAP1	57522	broad.mit.edu	36	12	62795883	62795883	+	Missense_Mutation	SNP	G	A	A			TCGA-14-1034-01	TCGA-14-1034-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr12:62795883G>A	uc001sru.1	+	c.2167G>A	c.(2167-2169)GGT>AGT	p.G723S	SRGAP1_uc001srv.1_Missense_Mutation_p.G660S	NM_020762	NP_065813	Q7Z6B7	SRGP1_HUMAN	SLIT-ROBO Rho GTPase activating protein 1	723					axon guidance	cytosol				ovary(2)|central_nervous_system(2)	4														0.285714	24.316701	25.773128	10	25	GG		KEEP	---	---	---	---	capture	GBM - Glioblastoma multiforme(3;0.000139)|BRCA - Breast invasive adenocarcinoma(9;0.225)	GBM - Glioblastoma multiforme(28;0.0608)	Missense_Mutation	SNP	62795883	62795883	15659	12	G	A	A	39	39	SRGAP1	A	1	1
CD163	9332	broad.mit.edu	36	12	7530824	7530824	+	Silent	SNP	C	T	T			TCGA-14-1034-01	TCGA-14-1034-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr12:7530824C>T	uc001qsz.2	-	c.2076G>A	c.(2074-2076)TCG>TCA	p.S692S	CD163_uc001qta.2_Silent_p.S692S|CD163_uc009zfw.1_Silent_p.S725S	NM_004244	NP_004235	Q86VB7	C163A_HUMAN	CD163 antigen isoform a	692	Extracellular (Potential).				acute-phase response	extracellular region|integral to plasma membrane	protein binding|scavenger receptor activity			ovary(6)|pancreas(1)|skin(1)	8														0.303704	112.137154	116.77187	41	94	CC		KEEP	---	---	---	---	capture			Silent	SNP	7530824	7530824	3094	12	C	T	T	19	19	CD163	T	1	1
SLITRK6	84189	broad.mit.edu	36	13	85268547	85268547	+	Missense_Mutation	SNP	G	C	C			TCGA-14-1034-01	TCGA-14-1034-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr13:85268547G>C	uc001vll.1	-	c.98C>G	c.(97-99)TCT>TGT	p.S33C	SLITRK6_uc010afe.1_5'Flank|SLITRK6_uc010aff.1_Missense_Mutation_p.S33C	NM_032229	NP_115605	Q9H5Y7	SLIK6_HUMAN	slit and trk like 6	33	LRRNT 1.|Extracellular (Potential).					integral to membrane				large_intestine(1)|ovary(1)|central_nervous_system(1)	3	all_neural(89;0.117)|Medulloblastoma(90;0.163)													0.529915	217.858902	217.949999	62	55	GG		KEEP	---	---	---	---	capture		GBM - Glioblastoma multiforme(99;0.0456)	Missense_Mutation	SNP	85268547	85268547	15245	13	G	C	C	33	33	SLITRK6	C	3	3
AHNAK2	113146	broad.mit.edu	36	14	104480712	104480712	+	Missense_Mutation	SNP	C	T	T			TCGA-14-1034-01	TCGA-14-1034-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr14:104480712C>T	uc010axc.1	-	c.12121G>A	c.(12121-12123)GTG>ATG	p.V4041M	AHNAK2_uc001ypx.2_Missense_Mutation_p.V3941M	NM_138420	NP_612429	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	4041						nucleus				ovary(1)	1		all_cancers(154;0.115)|Melanoma(154;0.155)|all_epithelial(191;0.183)												0.301802	164.666848	172.33099	67	155	CC		KEEP	---	---	---	---	capture	all cancers(16;0.000479)|OV - Ovarian serous cystadenocarcinoma(23;0.00659)|Epithelial(46;0.0151)|GBM - Glioblastoma multiforme(11;0.116)		Missense_Mutation	SNP	104480712	104480712	418	14	C	T	T	19	19	AHNAK2	T	1	1
SYT16	83851	broad.mit.edu	36	14	61620750	61620750	+	Silent	SNP	G	A	A			TCGA-14-1034-01	TCGA-14-1034-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr14:61620750G>A	uc001xfu.1	+	c.1518G>A	c.(1516-1518)GCG>GCA	p.A506A		NM_031914	NP_114120	Q17RD7	SYT16_HUMAN	synaptotagmin XIV-like	506										central_nervous_system(1)	1														0.326087	116.513114	120.223733	45	93	GG		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(108;0.0438)|BRCA - Breast invasive adenocarcinoma(234;0.118)	Silent	SNP	61620750	61620750	15993	14	G	A	A	38	38	SYT16	A	1	1
LOXL1	4016	broad.mit.edu	36	15	72006731	72006731	+	Missense_Mutation	SNP	T	C	C			TCGA-14-1034-01	TCGA-14-1034-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr15:72006731T>C	uc002awc.1	+	c.554T>C	c.(553-555)GTC>GCC	p.V185A		NM_005576	NP_005567	Q08397	LOXL1_HUMAN	lysyl oxidase-like 1 preproprotein	185					oxidation-reduction process|protein deamination	extracellular space	copper ion binding				0														0.466667	10.477567	10.503224	7	8	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	72006731	72006731	9272	15	T	C	C	58	58	LOXL1	C	4	4
HYDIN	54768	broad.mit.edu	36	16	69498824	69498824	+	Missense_Mutation	SNP	G	A	A			TCGA-14-1034-01	TCGA-14-1034-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr16:69498824G>A	uc002ezr.1	-	c.8465C>T	c.(8464-8466)ACG>ATG	p.T2822M	HYDIN_uc002ezs.1_Missense_Mutation_p.T354M	NM_032821	NP_116210	Q4G0P3	HYDIN_HUMAN	hydrocephalus inducing isoform a	2823										ovary(1)	1		Ovarian(137;0.0654)												0.14121	75.554301	118.642682	49	298	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	69498824	69498824	7767	16	G	A	A	40	40	HYDIN	A	1	1
HYDIN	54768	broad.mit.edu	36	16	69546929	69546929	+	Missense_Mutation	SNP	C	T	T			TCGA-14-1034-01	TCGA-14-1034-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr16:69546929C>T	uc002ezr.1	-	c.6163G>A	c.(6163-6165)GTG>ATG	p.V2055M	HYDIN_uc002ezt.1_Non-coding_Transcript|HYDIN_uc002ezu.1_Missense_Mutation_p.V358M	NM_032821	NP_116210	Q4G0P3	HYDIN_HUMAN	hydrocephalus inducing isoform a	2056										ovary(1)	1		Ovarian(137;0.0654)												0.148876	85.381068	127.464809	53	303	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	69546929	69546929	7767	16	C	T	T	19	19	HYDIN	T	1	1
PLCG2	5336	broad.mit.edu	36	16	80510715	80510715	+	Missense_Mutation	SNP	G	A	A			TCGA-14-1034-01	TCGA-14-1034-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr16:80510715G>A	uc002fgt.1	+	c.2180G>A	c.(2179-2181)CGA>CAA	p.R727Q	PLCG2_uc010chg.1_Missense_Mutation_p.R727Q	NM_002661	NP_002652	P16885	PLCG2_HUMAN	phospholipase C, gamma 2	727	SH2 2.				intracellular signal transduction|phospholipid catabolic process|platelet activation	plasma membrane	phosphatidylinositol phospholipase C activity|protein binding|signal transducer activity			large_intestine(4)|lung(2)|ovary(1)|skin(1)	8									p.R727Q(SNU81-Tumor)	1880				0.254386	73.022092	79.262341	29	85	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	80510715	80510715	12462	16	G	A	A	37	37	PLCG2	A	1	1
NECAB2	54550	broad.mit.edu	36	16	82592968	82592968	+	Missense_Mutation	SNP	G	A	A			TCGA-14-1034-01	TCGA-14-1034-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr16:82592968G>A	uc002fhd.1	+	c.1078G>A	c.(1078-1080)GTC>ATC	p.V360I	NECAB2_uc002fhe.1_Missense_Mutation_p.V277I	NM_019065	NP_061938	Q7Z6G3	NECA2_HUMAN	neuronal calcium-binding protein 2	360	ABM.				antibiotic biosynthetic process	cytoplasm	calcium ion binding|oxidoreductase activity|protein binding			ovary(2)	2														0.363636	66.11676	67.181888	24	42	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	82592968	82592968	10704	16	G	A	A	40	40	NECAB2	A	1	1
KIAA1609	57707	broad.mit.edu	36	16	83086872	83086872	+	Missense_Mutation	SNP	C	T	T			TCGA-14-1034-01	TCGA-14-1034-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr16:83086872C>T	uc002fib.1	-	c.302G>A	c.(301-303)GGA>GAA	p.G101E	KIAA1609_uc002fic.1_Non-coding_Transcript	NM_020947	NP_065998	Q6P9B6	K1609_HUMAN	hypothetical protein LOC57707	101							protein binding			ovary(2)	2														0.272727	100.368221	107.022419	39	104	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	83086872	83086872	8556	16	C	T	T	30	30	KIAA1609	T	2	2
HNF1B	6928	broad.mit.edu	36	17	33139126	33139126	+	Missense_Mutation	SNP	G	A	A			TCGA-14-1034-01	TCGA-14-1034-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr17:33139126G>A	uc002hok.2	-	c.1250C>T	c.(1249-1251)ACG>ATG	p.T417M		NM_000458	NP_000449	P35680	HNF1B_HUMAN	transcription factor 2	417					endocrine pancreas development|genitalia development|kidney development|positive regulation of transcription, DNA-dependent	nucleus	DNA binding|protein homodimerization activity|sequence-specific DNA binding transcription factor activity|transcription activator activity			ovary(3)	3		Breast(25;0.00765)|Ovarian(249;0.15)				Colon(71;102 1179 9001 27917 43397)				411				0.306818	72.295503	75.221848	27	61	GG		KEEP	---	---	---	---	capture	STAD - Stomach adenocarcinoma(1;0.0142)		Missense_Mutation	SNP	33139126	33139126	7544	17	G	A	A	40	40	HNF1B	A	1	1
GSG2	83903	broad.mit.edu	36	17	3575098	3575098	+	Missense_Mutation	SNP	C	T	T			TCGA-14-1034-01	TCGA-14-1034-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr17:3575098C>T	uc002fwp.1	+	c.1120C>T	c.(1120-1122)CCT>TCT	p.P374S	ITGAE_uc002fwn.2_5'Flank|ITGAE_uc002fwo.2_Intron	NM_031965	NP_114171	Q8TF76	HASP_HUMAN	haspin	374					cell cycle|chromatin modification|intracellular protein kinase cascade|protein phosphorylation	nucleus	ATP binding|protein serine/threonine kinase activity				0										41				0.323529	119.706755	123.492212	44	92	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	3575098	3575098	7102	17	C	T	T	30	30	GSG2	T	2	2
EPX	8288	broad.mit.edu	36	17	53635590	53635590	+	Missense_Mutation	SNP	G	A	A			TCGA-14-1034-01	TCGA-14-1034-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr17:53635590G>A	uc002ivq.2	+	c.1858G>A	c.(1858-1860)GCT>ACT	p.A620T		NM_000502	NP_000493	P11678	PERE_HUMAN	eosinophil peroxidase	620					hydrogen peroxide catabolic process|oxidation-reduction process		heme binding|peroxidase activity|protein binding			ovary(2)	2														0.316456	131.124625	135.842008	50	108	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	53635590	53635590	5393	17	G	A	A	38	38	EPX	A	1	1
TP53	7157	broad.mit.edu	36	17	7520099	7520099	+	Missense_Mutation	SNP	C	G	G			TCGA-14-1034-01	TCGA-14-1034-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr17:7520099C>G	uc002gim.2	-	c.313G>C	c.(313-315)GGC>CGC	p.G105R	TP53_uc002gig.1_Missense_Mutation_p.G105R|TP53_uc002gih.1_Missense_Mutation_p.G105R|TP53_uc010cne.1_5'Flank|TP53_uc010cnf.1_5'Flank|TP53_uc010cng.1_5'Flank|TP53_uc002gii.1_5'Flank|TP53_uc010cnh.1_Missense_Mutation_p.G105R|TP53_uc010cni.1_Missense_Mutation_p.G105R|TP53_uc002gij.2_Missense_Mutation_p.G105R|TP53_uc010cnj.1_5'Flank|TP53_uc002gin.2_Intron|TP53_uc002gio.2_Intron|TP53_uc010cnk.1_Missense_Mutation_p.G120R	NM_001126112	NP_001119584	P04637	P53_HUMAN	tumor protein p53 isoform a	105	Interaction with HIPK1 (By similarity).||Interaction with WWOX.		G -> D (in sporadic cancers; somatic mutation).|G -> S (in a sporadic cancer; somatic mutation).|G -> V (in sporadic cancers; somatic mutation).|G -> C (in LFS; germline mutation and in sporadic cancers; somatic mutation).|G -> R (in sporadic cancers; somatic mutation).		activation of caspase activity by cytochrome c|base-excision repair|blood coagulation|cell cycle arrest|cell differentiation|cell proliferation|cellular protein localization|cellular response to drug|cellular response to glucose starvation|cellular response to hypoxia|cellular response to ionizing radiation|cellular response to UV|determination of adult lifespan|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator|ER overload response|interspecies interaction between organisms|negative regulation of apoptosis|negative regulation of cell growth|negative regulation of cell proliferation|negative regulation of gene-specific transcription from RNA polymerase II promoter|negative regulation of helicase activity|negative regulation of transcription from RNA polymerase II promoter|nucleotide-excision repair|oxidative stress-induced premature senescence|positive regulation of gene-specific transcription from RNA polymerase II promoter|positive regulation of histone deacetylation|positive regulation of neuron apoptosis|positive regulation of peptidyl-tyrosine phosphorylation|positive regulation of reactive oxygen species metabolic process|positive regulation of thymocyte apoptosis|positive regulation of transcription from RNA polymerase II promoter|protein localization|protein tetramerization|Ras protein signal transduction|regulation of mitochondrial membrane permeability|replicative senescence|response to antibiotic|response to gamma radiation|response to X-ray	chromatin|cytoplasm|cytosol|endoplasmic reticulum|insoluble fraction|mitochondrion|nuclear matrix|nucleolus|nucleus|PML body|protein complex|replication fork	ATP binding|chaperone binding|chromatin binding|copper ion binding|damaged DNA binding|DNA strand annealing activity|histone acetyltransferase binding|p53 binding|promoter binding|promoter binding|protease binding|protein heterodimerization activity|protein kinase binding|protein N-terminus binding|protein phosphatase 2A binding|sequence-specific DNA binding transcription factor activity|specific transcriptional repressor activity|transcription activator activity|transcription factor binding|ubiquitin protein ligase binding|zinc ion binding	p.0?(6)|p.G105C(5)|p.G59fs*23(3)|p.G105R(2)|p.G105fs*18(1)|p.V73fs*9(1)|p.G105_T125del21(1)|p.G105S(1)|p.W91fs*13(1)|p.Y103_G112>C(1)|p.P13fs*18(1)|p.S33fs*23(1)|p.Y103_L111>L(1)|p.Y103fs*15(1)		large_intestine(4614)|breast(2344)|upper_aerodigestive_tract(2150)|lung(1958)|ovary(1559)|oesophagus(1462)|haematopoietic_and_lymphoid_tissue(1212)|stomach(1127)|urinary_tract(1113)|central_nervous_system(1072)|liver(805)|skin(693)|pancreas(370)|biliary_tract(247)|soft_tissue(209)|prostate(192)|endometrium(150)|bone(102)|vulva(79)|kidney(79)|cervix(68)|thyroid(54)|salivary_gland(41)|adrenal_gland(37)|peritoneum(33)|eye(24)|thymus(21)|genital_tract(16)|autonomic_ganglia(16)|small_intestine(14)|testis(11)|penis(10)|vagina(6)|meninges(5)|pituitary(4)|pleura(3)|gastrointestinal_tract_(site_indeterminate)(1)|NS(1)|Fallopian tube(1)|placenta(1)	21904		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)				Pancreas(47;798 1329 9957 10801)		111		690	TCGA GBM(1;<1E-8)|TSP Lung(2;<1E-8)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)			0.442308	71.320062	71.470307	23	29	CC		KEEP	---	---	---	---	capture		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Missense_Mutation	SNP	7520099	7520099	16923	17	C	G	G	22	22	TP53	G	3	3
SETBP1	26040	broad.mit.edu	36	18	40897232	40897232	+	Silent	SNP	C	T	T			TCGA-14-1034-01	TCGA-14-1034-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr18:40897232C>T	uc010dni.1	+	c.4200C>T	c.(4198-4200)CGC>CGT	p.R1400R	SETBP1_uc002laz.1_Silent_p.R1400R|SETBP1_uc002lba.2_5'Flank	NM_015559	NP_056374	Q9Y6X0	SETBP_HUMAN	SET binding protein 1 isoform a	1454	A.T hook 3.					nucleus	DNA binding			large_intestine(1)	1														0.473684	27.976887	27.988021	9	10	CC		KEEP	---	---	---	---	capture		Colorectal(1;0.0622)|COAD - Colon adenocarcinoma(74;0.201)	Silent	SNP	40897232	40897232	14617	18	C	T	T	27	27	SETBP1	T	1	1
ST8SIA3	51046	broad.mit.edu	36	18	53175412	53175412	+	Silent	SNP	C	T	T			TCGA-14-1034-01	TCGA-14-1034-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr18:53175412C>T	uc002lgn.1	+	c.573C>T	c.(571-573)TTC>TTT	p.F191F		NM_015879	NP_056963	O43173	SIA8C_HUMAN	ST8 alpha-N-acetyl-neuraminide	191	Lumenal (Potential).				glycosphingolipid biosynthetic process|N-glycan processing|post-translational protein modification|protein N-linked glycosylation via asparagine	integral to Golgi membrane	alpha-N-acetylneuraminate alpha-2,8-sialyltransferase activity			breast(1)	1														0.285714	138.139583	145.630411	52	130	CC		KEEP	---	---	---	---	capture		READ - Rectum adenocarcinoma(59;0.19)|Colorectal(16;0.205)	Silent	SNP	53175412	53175412	15751	18	C	T	T	31	31	ST8SIA3	T	1	1
HMHA1	23526	broad.mit.edu	36	19	1031274	1031274	+	Missense_Mutation	SNP	G	A	A			TCGA-14-1034-01	TCGA-14-1034-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr19:1031274G>A	uc002lqz.1	+	c.1724G>A	c.(1723-1725)CGG>CAG	p.R575Q	HMHA1_uc002lra.1_Missense_Mutation_p.R415Q|HMHA1_uc002lrb.1_Missense_Mutation_p.R458Q|HMHA1_uc002lrc.1_Missense_Mutation_p.R210Q|HMHA1_uc002lrd.1_5'Flank|HMHA1_uc010dsd.1_5'Flank	NM_012292	NP_036424	Q92619	HMHA1_HUMAN	minor histocompatibility antigen HA-1	575					regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol	GTPase activator activity|metal ion binding			lung(1)	1		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;1.04e-05)|all_lung(49;1.53e-05)|Breast(49;9.42e-05)|Hepatocellular(1079;0.137)												0.242152	138.69821	152.178422	54	169	GG		KEEP	---	---	---	---	capture		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)	Missense_Mutation	SNP	1031274	1031274	7532	19	G	A	A	39	39	HMHA1	A	1	1
EMR3	84658	broad.mit.edu	36	19	14619015	14619015	+	Missense_Mutation	SNP	G	A	A			TCGA-14-1034-01	TCGA-14-1034-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr19:14619015G>A	uc002mzi.2	-	c.860C>T	c.(859-861)ACG>ATG	p.T287M	EMR3_uc010dzp.1_Missense_Mutation_p.T235M	NM_032571	NP_115960	Q9BY15	EMR3_HUMAN	egf-like module-containing mucin-like receptor	287	Extracellular (Potential).				neuropeptide signaling pathway	extracellular space|integral to membrane|plasma membrane	calcium ion binding|G-protein coupled receptor activity			ovary(5)	5														0.257143	245.33665	265.930722	99	286	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	14619015	14619015	5299	19	G	A	A	40	40	EMR3	A	1	1
ZNF676	163223	broad.mit.edu	36	19	22155998	22155998	+	Missense_Mutation	SNP	C	T	T			TCGA-14-1034-01	TCGA-14-1034-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr19:22155998C>T	uc002nqs.1	-	c.361G>A	c.(361-363)GTC>ATC	p.V121I		NM_001001411	NP_001001411	Q8N7Q3	ZN676_HUMAN	zinc finger protein 676	121					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0		Lung NSC(12;0.0207)|all_lung(12;0.0214)|all_epithelial(12;0.114)												0.233898	162.228174	181.343284	69	226	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	22155998	22155998	18678	19	C	T	T	19	19	ZNF676	T	1	1
TLE2	7089	broad.mit.edu	36	19	2956947	2956947	+	Missense_Mutation	SNP	C	T	T			TCGA-14-1034-01	TCGA-14-1034-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr19:2956947C>T	uc010dth.1	-	c.1523G>A	c.(1522-1524)CGT>CAT	p.R508H	TLE2_uc002lww.1_Missense_Mutation_p.R507H|TLE2_uc010dti.1_Missense_Mutation_p.R521H	NM_003260	NP_003251	Q04725	TLE2_HUMAN	transducin-like enhancer protein 2 isoform 1	507	WD 2.				negative regulation of canonical Wnt receptor signaling pathway|negative regulation of transcription, DNA-dependent|organ morphogenesis|transcription, DNA-dependent|Wnt receptor signaling pathway	nucleus	protein binding|transcription corepressor activity				0														0.195402	34.325734	41.852942	17	70	CC		KEEP	---	---	---	---	capture		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)	Missense_Mutation	SNP	2956947	2956947	16469	19	C	T	T	19	19	TLE2	T	1	1
KIRREL2	84063	broad.mit.edu	36	19	41043345	41043345	+	Silent	SNP	C	T	T			TCGA-14-1034-01	TCGA-14-1034-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr19:41043345C>T	uc002ocb.2	+	c.864C>T	c.(862-864)CCC>CCT	p.P288P	KIRREL2_uc002obz.2_Silent_p.P288P|KIRREL2_uc002oca.2_Silent_p.P238P|KIRREL2_uc002occ.2_Silent_p.P235P|KIRREL2_uc002ocd.2_Silent_p.P285P	NM_199180	NP_954649	Q6UWL6	KIRR2_HUMAN	kin of IRRE-like 2 isoform c	288	Ig-like C2-type 3.|Extracellular (Potential).				cell adhesion	integral to membrane|plasma membrane				ovary(1)|central_nervous_system(1)	2	all_lung(56;7.14e-07)|Lung NSC(56;1.12e-06)|Esophageal squamous(110;0.162)													0.230769	63.847541	71.567457	27	90	CC		KEEP	---	---	---	---	capture	LUSC - Lung squamous cell carcinoma(66;0.0515)		Silent	SNP	41043345	41043345	8637	19	C	T	T	23	23	KIRREL2	T	1	1
ZNF780B	163131	broad.mit.edu	36	19	45233565	45233565	+	Missense_Mutation	SNP	C	G	G			TCGA-14-1034-01	TCGA-14-1034-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr19:45233565C>G	uc002omu.1	-	c.1032G>C	c.(1030-1032)AAG>AAC	p.K344N	ZNF780B_uc002omv.1_Missense_Mutation_p.K199N	NM_001005851	NP_001005851	Q9Y6R6	Z780B_HUMAN	zinc finger protein 780B	347	C2H2-type 7.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)|pancreas(1)	2	all_cancers(60;9.55e-06)|all_lung(34;1.17e-07)|Lung NSC(34;1.41e-07)|Ovarian(47;0.0925)													0.347518	149.628581	152.524146	49	92	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	45233565	45233565	18751	19	C	G	G	28	28	ZNF780B	G	3	3
KCNA7	3743	broad.mit.edu	36	19	54267261	54267261	+	Missense_Mutation	SNP	G	C	C			TCGA-14-1034-01	TCGA-14-1034-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr19:54267261G>C	uc002pmg.1	-	c.394C>G	c.(394-396)CTT>GTT	p.L132V		NM_031886	NP_114092	Q96RP8	KCNA7_HUMAN	potassium voltage-gated channel, shaker-related	132						voltage-gated potassium channel complex	voltage-gated potassium channel activity			central_nervous_system(1)	1		all_lung(116;1.7e-06)|Lung NSC(112;3.55e-06)|all_epithelial(76;3.83e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)				Colon(74;686 1235 3793 23366 48562)								0.421053	7.373734	7.538789	8	11	GG		KEEP	---	---	---	---	capture		all cancers(93;0.000397)|OV - Ovarian serous cystadenocarcinoma(262;0.000519)|GBM - Glioblastoma multiforme(486;0.00541)|Epithelial(262;0.0441)	Missense_Mutation	SNP	54267261	54267261	8313	19	G	C	C	34	34	KCNA7	C	3	3
NLRP7	199713	broad.mit.edu	36	19	60141401	60141401	+	Missense_Mutation	SNP	G	A	A			TCGA-14-1034-01	TCGA-14-1034-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr19:60141401G>A	uc010esl.1	-	c.2036C>T	c.(2035-2037)CCG>CTG	p.P679L	NLRP7_uc002qig.2_Intron|NLRP7_uc002qii.2_Missense_Mutation_p.P651L|NLRP7_uc002qih.2_Missense_Mutation_p.P651L|NLRP7_uc010esk.1_Missense_Mutation_p.P651L	NM_001127255	NP_001120727	Q8WX94	NALP7_HUMAN	NACHT, leucine rich repeat and PYD containing 7	651			P -> S (in HYDM).				ATP binding			large_intestine(1)|breast(1)|central_nervous_system(1)	3														0.247253	122.386904	132.965698	45	137	GG		KEEP	---	---	---	---	capture		GBM - Glioblastoma multiforme(193;0.0325)	Missense_Mutation	SNP	60141401	60141401	10885	19	G	A	A	39	39	NLRP7	A	1	1
MUC16	94025	broad.mit.edu	36	19	8936321	8936321	+	Missense_Mutation	SNP	G	A	A			TCGA-14-1034-01	TCGA-14-1034-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr19:8936321G>A	uc002mkp.1	-	c.12125C>T	c.(12124-12126)GCG>GTG	p.A4042V		NM_024690	NP_078966	Q8WXI7	MUC16_HUMAN	mucin 16	4044	Thr-rich.|Extracellular (Potential).|Ser-rich.				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														0.250996	151.200529	165.345898	63	188	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	8936321	8936321	10367	19	G	A	A	38	38	MUC16	A	1	1
CNN2	1265	broad.mit.edu	36	19	983680	983680	+	Silent	SNP	C	T	T			TCGA-14-1034-01	TCGA-14-1034-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr19:983680C>T	uc002lqu.1	+	c.375C>T	c.(373-375)CTC>CTT	p.L125L	CNN2_uc002lqt.1_Silent_p.L125L|CNN2_uc010drz.1_Intron|CNN2_uc002lqv.1_Silent_p.L125L	NM_004368	NP_004359	Q99439	CNN2_HUMAN	calponin 2 isoform a	125	CH.				actomyosin structure organization|cellular response to mechanical stimulus|regulation of actin filament-based process	cell-cell junction|stress fiber	actin binding|calmodulin binding				0		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;1.04e-05)|all_lung(49;1.53e-05)|Breast(49;9.42e-05)|Hepatocellular(1079;0.137)												0.302326	34.560956	36.059729	13	30	CC		KEEP	---	---	---	---	capture		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)	Silent	SNP	983680	983680	3748	19	C	T	T	31	31	CNN2	T	1	1
TDRD10	126668	broad.mit.edu	36	1	152783133	152783133	+	Missense_Mutation	SNP	G	A	A			TCGA-14-1034-01	TCGA-14-1034-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:152783133G>A	uc009wow.1	+	c.574G>A	c.(574-576)GTC>ATC	p.V192I	TDRD10_uc001ffd.1_Missense_Mutation_p.V192I|TDRD10_uc001ffe.1_Missense_Mutation_p.V113I	NM_001098475	NP_001091945	Q5VZ19	TDR10_HUMAN	tudor domain containing 10 isoform a	192							nucleotide binding|RNA binding			ovary(1)	1	all_lung(78;1.72e-29)|Lung NSC(65;2.96e-27)|Hepatocellular(266;0.0877)|all_hematologic(923;0.088)													0.312849	141.139664	146.718362	56	123	GG		KEEP	---	---	---	---	capture	LUSC - Lung squamous cell carcinoma(543;0.185)		Missense_Mutation	SNP	152783133	152783133	16257	1	G	A	A	40	40	TDRD10	A	1	1
CACNA1S	779	broad.mit.edu	36	1	199275833	199275833	+	Missense_Mutation	SNP	C	T	T			TCGA-14-1034-01	TCGA-14-1034-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr1:199275833C>T	uc001gvv.1	-	c.5371G>A	c.(5371-5373)GCT>ACT	p.A1791T		NM_000069	NP_000060	Q13698	CAC1S_HUMAN	calcium channel, voltage-dependent, L type,	1791	Cytoplasmic (Potential).				axon guidance	I band|T-tubule|voltage-gated calcium channel complex	high voltage-gated calcium channel activity			ovary(3)|central_nervous_system(1)	4					Magnesium Sulfate(DB00653)|Verapamil(DB00661)									0.390625	66.547984	67.222157	25	39	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	199275833	199275833	2663	1	C	T	T	26	26	CACNA1S	T	2	2
LAD1	3898	broad.mit.edu	36	1	199622227	199622227	+	Silent	SNP	C	G	G			TCGA-14-1034-01	TCGA-14-1034-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr1:199622227C>G	uc001gwm.1	-	c.885G>C	c.(883-885)CCG>CCC	p.P295P	LAD1_uc009wzu.1_Silent_p.P317P	NM_005558	NP_005549	O00515	LAD1_HUMAN	ladinin 1	295						basement membrane	structural molecule activity				0														0.290323	11.263476	12.56516	9	22	CC		KEEP	---	---	---	---	capture			Silent	SNP	199622227	199622227	8922	1	C	G	G	27	27	LAD1	G	3	3
EDARADD	128178	broad.mit.edu	36	1	234657351	234657351	+	Missense_Mutation	SNP	G	A	A			TCGA-14-1034-01	TCGA-14-1034-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:234657351G>A	uc001hxu.1	+	c.197G>A	c.(196-198)CGA>CAA	p.R66Q	EDARADD_uc001hxv.1_Missense_Mutation_p.R56Q	NM_145861	NP_665860	Q8WWZ3	EDAD_HUMAN	EDAR-associated death domain isoform A	66					cell differentiation|signal transduction	cytoplasm					0	Ovarian(103;0.0634)|Breast(184;0.247)	all_cancers(173;0.0232)|Prostate(94;0.174)												0.411765	85.192664	85.653568	28	40	GG		KEEP	---	---	---	---	capture	OV - Ovarian serous cystadenocarcinoma(106;0.00117)		Missense_Mutation	SNP	234657351	234657351	5093	1	G	A	A	37	37	EDARADD	A	1	1
SH3BP5L	80851	broad.mit.edu	36	1	247073921	247073921	+	Missense_Mutation	SNP	A	C	C			TCGA-14-1034-01	TCGA-14-1034-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr1:247073921A>C	uc001iew.1	-	c.601T>G	c.(601-603)TGC>GGC	p.C201G	SH3BP5L_uc001iev.1_Missense_Mutation_p.C82G	NM_030645	NP_085148	Q7L8J4	3BP5L_HUMAN	SH3-binding domain protein 5-like	201	Potential.										0	all_cancers(71;3.33e-06)|all_epithelial(71;2.41e-06)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.0458)|Lung NSC(105;0.0494)|Melanoma(84;0.199)	all_cancers(173;0.19)												0.3	7.594236	8.411009	6	14	AA		KEEP	---	---	---	---	capture	OV - Ovarian serous cystadenocarcinoma(106;0.00805)		Missense_Mutation	SNP	247073921	247073921	14739	1	A	C	C	6	6	SH3BP5L	C	4	4
ASXL1	171023	broad.mit.edu	36	20	30486006	30486006	+	Silent	SNP	C	T	T			TCGA-14-1034-01	TCGA-14-1034-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr20:30486006C>T	uc002wxs.1	+	c.1830C>T	c.(1828-1830)GGC>GGT	p.G610G	ASXL1_uc010gea.1_Silent_p.G610G|ASXL1_uc010geb.1_Silent_p.G501G	NM_015338	NP_056153	Q8IXJ9	ASXL1_HUMAN	additional sex combs like 1	610					chromatin modification|regulation of transcription, DNA-dependent|transcription, DNA-dependent	PR-DUB complex	metal ion binding|protein binding	p.G610G(1)		haematopoietic_and_lymphoid_tissue(131)|large_intestine(6)|central_nervous_system(2)|ovary(1)	140														0.345238	79.084895	80.844945	29	55	CC		KEEP	---	---	---	---	capture			Silent	SNP	30486006	30486006	1085	20	C	T	T	27	27	ASXL1	T	1	1
KRTAP10-10	353333	broad.mit.edu	36	21	44881924	44881924	+	Silent	SNP	G	A	A			TCGA-14-1034-01	TCGA-14-1034-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr21:44881924G>A	uc002zfq.1	+	c.162G>A	c.(160-162)CAG>CAA	p.Q54Q	C21orf29_uc002zfe.1_Intron|C21orf29_uc010gpv.1_Intron	NM_181688	NP_859016	P60014	KR10A_HUMAN	keratin associated protein 10-10	54	3.|15 X 5 AA repeats of C-C-X(3).					keratin filament					0														0.544643	197.170863	197.363902	61	51	GG		KEEP	---	---	---	---	capture			Silent	SNP	44881924	44881924	8821	21	G	A	A	33	33	KRTAP10-10	A	2	2
COL18A1	80781	broad.mit.edu	36	21	45735602	45735602	+	Silent	SNP	C	T	T			TCGA-14-1034-01	TCGA-14-1034-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr21:45735602C>T	uc002zhi.1	+	c.2643C>T	c.(2641-2643)GGC>GGT	p.G881G	COL18A1_uc002zhg.1_Silent_p.G701G	NM_030582	NP_085059	P39060	COIA1_HUMAN	alpha 1 type XVIII collagen isoform 1 precursor	1116	Triple-helical region 4 (COL4).				cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception	collagen|extracellular space	extracellular matrix structural constituent|metal ion binding|protein binding			central_nervous_system(1)	1										1836				0.4375	55.642059	55.808282	21	27	CC		KEEP	---	---	---	---	capture		Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929)	Silent	SNP	45735602	45735602	3813	21	C	T	T	26	26	COL18A1	T	2	2
COL6A2	1292	broad.mit.edu	36	21	46362977	46362977	+	Missense_Mutation	SNP	C	T	T			TCGA-14-1034-01	TCGA-14-1034-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr21:46362977C>T	uc002zia.1	+	c.1138C>T	c.(1138-1140)CGC>TGC	p.R380C	COL6A2_uc002zhy.1_Missense_Mutation_p.R380C|COL6A2_uc002zhz.1_Missense_Mutation_p.R380C|COL6A2_uc002zib.1_Intron	NM_001849	NP_001840	P12110	CO6A2_HUMAN	alpha 2 type VI collagen isoform 2C2 precursor	380	Triple-helical region.				axon guidance|cell-cell adhesion|extracellular matrix organization|protein heterotrimerization	collagen|extracellular space|protein complex	extracellular matrix structural constituent|protein binding, bridging			central_nervous_system(7)|ovary(1)	8	Breast(49;0.245)													0.275	24.94176	26.74541	11	29	CC		KEEP	---	---	---	---	capture		Colorectal(79;0.0303)|READ - Rectum adenocarcinoma(84;0.0649)	Missense_Mutation	SNP	46362977	46362977	3838	21	C	T	T	19	19	COL6A2	T	1	1
PSD4	23550	broad.mit.edu	36	2	113666589	113666589	+	Missense_Mutation	SNP	G	A	A			TCGA-14-1034-01	TCGA-14-1034-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr2:113666589G>A	uc002tjc.1	+	c.1790G>A	c.(1789-1791)CGC>CAC	p.R597H	PSD4_uc002tjd.1_Missense_Mutation_p.R218H|PSD4_uc002tje.1_Missense_Mutation_p.R568H|PSD4_uc002tjf.1_Missense_Mutation_p.R218H	NM_012455	NP_036587	Q8NDX1	PSD4_HUMAN	pleckstrin and Sec7 domain containing 4	597	SEC7.				regulation of ARF protein signal transduction	cytoplasm|plasma membrane	ARF guanyl-nucleotide exchange factor activity			ovary(2)	2														0.232877	71.283157	80.82075	34	112	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	113666589	113666589	13102	2	G	A	A	38	38	PSD4	A	1	1
TTN	7273	broad.mit.edu	36	2	179182277	179182277	+	Silent	SNP	G	A	A			TCGA-14-1034-01	TCGA-14-1034-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr2:179182277G>A	uc002umr.1	-	c.44301C>T	c.(44299-44301)CGC>CGT	p.R14767R	TTN_uc002ums.1_Silent_p.R8462R|TTN_uc010frc.1_Silent_p.R8395R|TTN_uc010frd.1_Silent_p.R8270R	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	15694										ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1)	153										8722				0.328571	61.90415	63.726537	23	47	GG		KEEP	---	---	---	---	capture	OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)		Silent	SNP	179182277	179182277	17290	2	G	A	A	38	38	TTN	A	1	1
B3GNT2	10678	broad.mit.edu	36	2	62303712	62303712	+	Missense_Mutation	SNP	A	G	G			TCGA-14-1034-01	TCGA-14-1034-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr2:62303712A>G	uc002sbs.1	+	c.853A>G	c.(853-855)AAG>GAG	p.K285E	B3GNT2_uc010fco.1_Missense_Mutation_p.K285E	NM_006577	NP_006568	Q9NY97	B3GN2_HUMAN	UDP-GlcNAc:betaGal	285	Lumenal (Potential).					Golgi membrane|integral to membrane	UDP-galactose:beta-N-acetylglucosamine beta-1,3-galactosyltransferase activity			ovary(1)	1	Lung NSC(7;0.031)|all_lung(7;0.0634)													0.296089	164.014295	170.665308	53	126	AA		KEEP	---	---	---	---	capture	LUSC - Lung squamous cell carcinoma(7;3.55e-06)|Epithelial(17;0.0963)		Missense_Mutation	SNP	62303712	62303712	1278	2	A	G	G	13	13	B3GNT2	G	4	4
SIDT1	54847	broad.mit.edu	36	3	114734763	114734763	+	Missense_Mutation	SNP	A	C	C			TCGA-14-1034-01	TCGA-14-1034-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr3:114734763A>C	uc003eak.1	+	c.205A>C	c.(205-207)ACC>CCC	p.T69P	SIDT1_uc003eaj.1_Missense_Mutation_p.T69P	NM_017699	NP_060169	Q9NXL6	SIDT1_HUMAN	SID1 transmembrane family, member 1	69	Extracellular (Potential).					integral to membrane				ovary(3)|pancreas(1)|skin(1)	5														0.461538	7.005542	7.043394	6	7	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	114734763	114734763	14797	3	A	C	C	6	6	SIDT1	C	4	4
LRRC31	79782	broad.mit.edu	36	3	171062205	171062205	+	Missense_Mutation	SNP	T	C	C			TCGA-14-1034-01	TCGA-14-1034-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr3:171062205T>C	uc003fgc.1	-	c.266A>G	c.(265-267)AAG>AGG	p.K89R	LRRC31_uc010hwp.1_Missense_Mutation_p.K89R	NM_024727	NP_079003	Q6UY01	LRC31_HUMAN	leucine rich repeat containing 31	89										ovary(2)	2	all_cancers(22;2.76e-22)|all_epithelial(15;4.73e-27)|all_lung(20;9.24e-17)|Lung NSC(18;3.85e-16)|Ovarian(172;0.000223)|Breast(254;0.197)													0.348131	484.251007	492.961262	149	279	TT		KEEP	---	---	---	---	capture	Lung(28;2.71e-13)|STAD - Stomach adenocarcinoma(35;0.00943)		Missense_Mutation	SNP	171062205	171062205	9361	3	T	C	C	56	56	LRRC31	C	4	4
ZNF445	353274	broad.mit.edu	36	3	44463337	44463337	+	Missense_Mutation	SNP	G	C	C			TCGA-14-1034-01	TCGA-14-1034-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr3:44463337G>C	uc003cnf.2	-	c.2830C>G	c.(2830-2832)CTA>GTA	p.L944V		NM_181489	NP_852466	P59923	ZN445_HUMAN	zinc finger protein 445	944					regulation of transcription, DNA-dependent|viral reproduction	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)	1														0.26087	139.415698	148.939144	48	136	GG		KEEP	---	---	---	---	capture		KIRC - Kidney renal clear cell carcinoma(197;0.0514)|Kidney(197;0.0646)	Missense_Mutation	SNP	44463337	44463337	18511	3	G	C	C	34	34	ZNF445	C	3	3
DNAH1	25981	broad.mit.edu	36	3	52392519	52392519	+	Silent	SNP	C	T	T			TCGA-14-1034-01	TCGA-14-1034-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr3:52392519C>T	uc003dds.1	+	c.8019C>T	c.(8017-8019)GAC>GAT	p.D2673D	DNAH1_uc003ddu.1_Non-coding_Transcript|DNAH1_uc003ddv.1_5'Flank	NM_015512	NP_056327	Q9P2D7	DYH1_HUMAN	dynein, axonemal, heavy chain 1	2673	AAA 4 (By similarity).				ciliary or flagellar motility|microtubule-based movement|response to mechanical stimulus	axonemal dynein complex|cilium axoneme|cytoplasm|microtubule	ATP binding|ATPase activity|microtubule motor activity			large_intestine(3)	3														0.395349	47.662484	48.075476	17	26	CC		KEEP	---	---	---	---	capture		BRCA - Breast invasive adenocarcinoma(193;2.02e-05)|OV - Ovarian serous cystadenocarcinoma(275;0.000207)|Kidney(197;0.0022)|KIRC - Kidney renal clear cell carcinoma(197;0.00245)	Silent	SNP	52392519	52392519	4779	3	C	T	T	19	19	DNAH1	T	1	1
OR5K4	403278	broad.mit.edu	36	3	99555395	99555395	+	Missense_Mutation	SNP	G	T	T			TCGA-14-1034-01	TCGA-14-1034-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr3:99555395G>T	uc003dsk.1	+	c.8G>T	c.(7-9)AGG>ATG	p.R3M		NM_001005517	NP_001005517	A6NMS3	OR5K4_HUMAN	olfactory receptor, family 5, subfamily K,	3	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			central_nervous_system(1)	1														0.328859	127.059745	130.910845	49	100	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	99555395	99555395	11579	3	G	T	T	35	35	OR5K4	T	3	3
TLL1	7092	broad.mit.edu	36	4	167182697	167182697	+	Missense_Mutation	SNP	C	T	T			TCGA-14-1034-01	TCGA-14-1034-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr4:167182697C>T	uc003irh.1	+	c.1330C>T	c.(1330-1332)CGT>TGT	p.R444C		NM_012464	NP_036596	O43897	TLL1_HUMAN	tolloid-like 1	444	CUB 1.				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)												0.35023	217.639026	221.931409	76	141	CC		KEEP	---	---	---	---	capture		GBM - Glioblastoma multiforme(119;0.103)	Missense_Mutation	SNP	167182697	167182697	16475	4	C	T	T	31	31	TLL1	T	1	1
CMBL	134147	broad.mit.edu	36	5	10343849	10343849	+	Missense_Mutation	SNP	G	A	A			TCGA-14-1034-01	TCGA-14-1034-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr5:10343849G>A	uc003jes.1	-	c.26C>T	c.(25-27)CCG>CTG	p.P9L		NM_138809	NP_620164	Q96DG6	CMBL_HUMAN	carboxymethylenebutenolidase	9						cytosol	hydrolase activity|protein binding				0														0.349315	143.777667	146.704034	51	95	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	10343849	10343849	3714	5	G	A	A	39	39	CMBL	A	1	1
TRPC7	57113	broad.mit.edu	36	5	135720735	135720735	+	Silent	SNP	G	A	A			TCGA-14-1034-01	TCGA-14-1034-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr5:135720735G>A	uc003lbn.1	-	c.237C>T	c.(235-237)AAC>AAT	p.N79N	TRPC7_uc010jef.1_Silent_p.N71N|TRPC7_uc010jeg.1_Non-coding_Transcript|TRPC7_uc010jeh.1_Silent_p.N71N|TRPC7_uc010jei.1_Silent_p.N71N|TRPC7_uc010jej.1_De_novo_Start_OutOfFrame	NM_020389	NP_065122	Q9HCX4	TRPC7_HUMAN	transient receptor potential cation channel,	80	Cytoplasmic (Potential).|ANK 2.				axon guidance|platelet activation	integral to membrane|plasma membrane	calcium channel activity|protein binding				0														0.292517	109.638016	115.263528	43	104	GG		KEEP	---	---	---	---	capture	KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)		Silent	SNP	135720735	135720735	17135	5	G	A	A	40	40	TRPC7	A	1	1
PPARGC1B	133522	broad.mit.edu	36	5	149192768	149192768	+	Silent	SNP	C	T	T			TCGA-14-1034-01	TCGA-14-1034-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr5:149192768C>T	uc003lrc.1	+	c.939C>T	c.(937-939)CCC>CCT	p.P313P	PPARGC1B_uc003lrb.1_Silent_p.P313P|PPARGC1B_uc003lrd.1_Silent_p.P274P|PPARGC1B_uc003lre.1_Silent_p.P292P|PPARGC1B_uc003lrf.1_Silent_p.P292P	NM_133263	NP_573570	Q86YN6	PRGC2_HUMAN	peroxisome proliferator-activated receptor	313					estrogen receptor signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	mediator complex	AF-2 domain binding|estrogen receptor binding|ligand-dependent nuclear receptor transcription coactivator activity|nucleotide binding|receptor activator activity|RNA binding|RNA polymerase II transcription mediator activity				0														0.321739	94.235275	97.481157	37	78	CC		KEEP	---	---	---	---	capture	KIRC - Kidney renal clear cell carcinoma(527;0.000962)|Kidney(363;0.00147)		Silent	SNP	149192768	149192768	12731	5	C	T	T	21	21	PPARGC1B	T	2	2
FAT2	2196	broad.mit.edu	36	5	150881659	150881659	+	Missense_Mutation	SNP	G	A	A			TCGA-14-1034-01	TCGA-14-1034-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr5:150881659G>A	uc003lue.2	-	c.10688C>T	c.(10687-10689)ACG>ATG	p.T3563M	FAT2_uc003lud.2_Missense_Mutation_p.T256M	NM_001447	NP_001438	Q9NYQ8	FAT2_HUMAN	FAT tumor suppressor 2 precursor	3563	Cadherin 32.|Extracellular (Potential).				epithelial cell migration|homophilic cell adhesion	cell-cell adherens junction|integral to membrane|nucleus	calcium ion binding			ovary(4)	4		Medulloblastoma(196;0.0912)|all_hematologic(541;0.104)												0.376812	73.03244	73.951525	26	43	GG		KEEP	---	---	---	---	capture	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)		Missense_Mutation	SNP	150881659	150881659	5926	5	G	A	A	40	40	FAT2	A	1	1
PRELID1	27166	broad.mit.edu	36	5	176666174	176666174	+	Silent	SNP	G	T	T			TCGA-14-1034-01	TCGA-14-1034-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr5:176666174G>T	uc003mfx.1	+	c.657G>T	c.(655-657)GTG>GTT	p.V219V	RAB24_uc003mfu.1_5'Flank|RAB24_uc003mfv.1_5'Flank|RAB24_uc003mfw.1_5'Flank|PRELID1_uc003mfy.1_Silent_p.V217V|MXD3_uc010jkk.1_3'UTR	NM_013237	NP_037369	Q9Y255	PRLD1_HUMAN	PRELI domain containing 1	219					immune response|multicellular organismal development	mitochondrion|nucleus					0	all_cancers(89;2.49e-05)|Renal(175;0.000269)|Lung NSC(126;0.00111)|all_lung(126;0.002)	all_neural(177;0.00802)|Medulloblastoma(196;0.0145)|all_hematologic(541;0.248)												0.363636	8.897248	9.076957	4	7	GG		KEEP	---	---	---	---	capture	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)		Silent	SNP	176666174	176666174	12914	5	G	T	T	48	48	PRELID1	T	3	3
HCN1	348980	broad.mit.edu	36	5	45298658	45298658	+	Missense_Mutation	SNP	A	G	G			TCGA-14-1034-01	TCGA-14-1034-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr5:45298658A>G	uc003jok.1	-	c.1795T>C	c.(1795-1797)TCA>CCA	p.S599P		NM_021072	NP_066550	O60741	HCN1_HUMAN	hyperpolarization activated cyclic	599	Cytoplasmic (Potential).					integral to membrane	cAMP binding|sodium channel activity|voltage-gated potassium channel activity			ovary(1)	1														0.301887	99.963323	103.675617	32	74	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	45298658	45298658	7278	5	A	G	G	9	9	HCN1	G	4	4
SLC9A3	6550	broad.mit.edu	36	5	545029	545029	+	Silent	SNP	G	A	A			TCGA-14-1034-01	TCGA-14-1034-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr5:545029G>A	uc003jbe.1	-	c.369C>T	c.(367-369)ATC>ATT	p.I123I		NM_004174	NP_004165	P48764	SL9A3_HUMAN	solute carrier family 9 (sodium/hydrogen	123	Helical; Name=D/M4; (Potential).					cell surface|integral to membrane	sodium:hydrogen antiporter activity				0														0.333333	13.17306	13.540543	5	10	GG		KEEP	---	---	---	---	capture	Epithelial(17;0.000529)|OV - Ovarian serous cystadenocarcinoma(19;0.00153)|all cancers(22;0.00186)|Lung(60;0.0863)		Silent	SNP	545029	545029	15210	5	G	A	A	37	37	SLC9A3	A	1	1
USP45	85015	broad.mit.edu	36	6	100037390	100037390	+	Missense_Mutation	SNP	G	A	A			TCGA-14-1034-01	TCGA-14-1034-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr6:100037390G>A	uc003ppx.1	-	c.805C>T	c.(805-807)CCA>TCA	p.P269S	USP45_uc003ppw.1_Intron|USP45_uc003ppy.1_Non-coding_Transcript|USP45_uc010kcq.1_Missense_Mutation_p.P269S|USP45_uc003ppz.1_Missense_Mutation_p.P269S|USP45_uc003pqa.1_Missense_Mutation_p.P269S	NM_001080481	NP_001073950	Q70EL2	UBP45_HUMAN	ubiquitin specific peptidase 45	269					ubiquitin-dependent protein catabolic process		cysteine-type peptidase activity|ubiquitin thiolesterase activity|zinc ion binding			ovary(1)	1		all_cancers(76;0.000208)|Acute lymphoblastic leukemia(125;8.41e-11)|all_hematologic(75;2.56e-07)|all_epithelial(107;0.122)|Colorectal(196;0.133)												0.319018	140.23588	144.984114	52	111	GG		KEEP	---	---	---	---	capture		BRCA - Breast invasive adenocarcinoma(108;0.0718)	Missense_Mutation	SNP	100037390	100037390	17640	6	G	A	A	44	44	USP45	A	2	2
HIST1H2BA	255626	broad.mit.edu	36	6	25835464	25835464	+	Missense_Mutation	SNP	A	G	G			TCGA-14-1034-01	TCGA-14-1034-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr6:25835464A>G	uc003nfd.1	+	c.349A>G	c.(349-351)ACC>GCC	p.T117A	HIST1H2AA_uc003nfc.1_5'Flank	NM_170610	NP_733759	Q96A08	H2B1A_HUMAN	histone cluster 1, H2ba	117					nucleosome assembly	nucleosome|nucleus	DNA binding			kidney(1)	1														0.216667	27.696013	32.202555	13	47	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	25835464	25835464	7425	6	A	G	G	6	6	HIST1H2BA	G	4	4
SCAND3	114821	broad.mit.edu	36	6	28647807	28647807	+	Missense_Mutation	SNP	C	T	T			TCGA-14-1034-01	TCGA-14-1034-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr6:28647807C>T	uc003nlo.1	-	c.3838G>A	c.(3838-3840)GGA>AGA	p.G1280R		NM_052923	NP_443155	Q6R2W3	SCND3_HUMAN	SCAN domain containing 3	1280					DNA integration|regulation of transcription, DNA-dependent|viral reproduction	nucleus	DNA binding|protein dimerization activity|sequence-specific DNA binding transcription factor activity			ovary(1)	1														0.413043	176.553544	177.463865	57	81	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	28647807	28647807	14357	6	C	T	T	23	23	SCAND3	T	1	1
F13A1	2162	broad.mit.edu	36	6	6212039	6212039	+	Missense_Mutation	SNP	G	A	A			TCGA-14-1034-01	TCGA-14-1034-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr6:6212039G>A	uc003mwv.1	-	c.322C>T	c.(322-324)CGC>TGC	p.R108C		NM_000129	NP_000120	P00488	F13A_HUMAN	coagulation factor XIII A1 subunit precursor	108					peptide cross-linking|platelet activation|platelet degranulation	extracellular region|platelet alpha granule lumen	acyltransferase activity|metal ion binding|protein-glutamine gamma-glutamyltransferase activity			ovary(2)|central_nervous_system(1)|pancreas(1)	4	Ovarian(93;0.0816)	all_hematologic(90;0.152)			L-Glutamine(DB00130)									0.286885	177.835763	187.78869	70	174	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	6212039	6212039	5534	6	G	A	A	37	37	F13A1	A	1	1
C6orf165	154313	broad.mit.edu	36	6	88197587	88197587	+	Missense_Mutation	SNP	C	T	T			TCGA-14-1034-01	TCGA-14-1034-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr6:88197587C>T	uc003plv.1	+	c.1277C>T	c.(1276-1278)GCA>GTA	p.A426V	C6orf165_uc003plw.1_Missense_Mutation_p.A238V|C6orf165_uc010kbv.1_Non-coding_Transcript|C6orf165_uc003plu.1_Missense_Mutation_p.A426V	NM_001031743	NP_001026913	Q8IYR0	CF165_HUMAN	hypothetical protein LOC154313 isoform 1	426										central_nervous_system(1)	1		all_cancers(76;3.93e-06)|Acute lymphoblastic leukemia(125;3.55e-10)|Prostate(29;3.51e-09)|all_hematologic(105;3.29e-06)|all_epithelial(107;0.00575)												0.275	104.682388	112.015857	44	116	CC		KEEP	---	---	---	---	capture		BRCA - Breast invasive adenocarcinoma(108;0.0419)	Missense_Mutation	SNP	88197587	88197587	2446	6	C	T	T	25	25	C6orf165	T	2	2
GRM8	2918	broad.mit.edu	36	7	125961089	125961089	+	Missense_Mutation	SNP	G	A	A			TCGA-14-1034-01	TCGA-14-1034-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr7:125961089G>A	uc003vlr.2	-	c.1583C>T	c.(1582-1584)ACG>ATG	p.T528M	GRM8_uc003vls.2_3'UTR|GRM8_uc003vlt.2_Missense_Mutation_p.T528M|GRM8_uc010lkz.1_Non-coding_Transcript	NM_000845	NP_000836	O00222	GRM8_HUMAN	glutamate receptor, metabotropic 8 isoform a	528	Extracellular (Potential).				negative regulation of cAMP biosynthetic process|sensory perception of smell|visual perception	integral to plasma membrane				ovary(5)|pancreas(1)	6		Prostate(267;0.186)			L-Glutamic Acid(DB00142)									0.255814	129.391373	141.050817	55	160	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	125961089	125961089	7082	7	G	A	A	40	40	GRM8	A	1	1
TAS2R41	259287	broad.mit.edu	36	7	142885331	142885331	+	Nonsense_Mutation	SNP	C	T	T			TCGA-14-1034-01	TCGA-14-1034-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr7:142885331C>T	uc003wdc.1	+	c.244C>T	c.(244-246)CGA>TGA	p.R82*		NM_176883	NP_795364	P59536	T2R41_HUMAN	taste receptor, type 2, member 41	82	Extracellular (Potential).				sensory perception of taste	integral to membrane	G-protein coupled receptor activity			pancreas(1)	1	Melanoma(164;0.15)													0.287234	150.435219	158.031764	54	134	CC		KEEP	---	---	---	---	capture			Nonsense_Mutation	SNP	142885331	142885331	16101	7	C	T	T	23	23	TAS2R41	T	5	1
ZNF862	643641	broad.mit.edu	36	7	149188740	149188740	+	Nonsense_Mutation	SNP	G	T	T			TCGA-14-1034-01	TCGA-14-1034-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr7:149188740G>T	uc010lpn.1	+	c.1558G>T	c.(1558-1560)GAA>TAA	p.E520*	ZNF862_uc003wgm.2_Non-coding_Transcript	NM_001099220	NP_001092690	O60290	ZN862_HUMAN	zinc finger protein 862	520	TTF-type 2.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	metal ion binding|nucleic acid binding|protein dimerization activity			skin(1)	1														0.225	81.509474	92.632231	36	124	GG		KEEP	---	---	---	---	capture			Nonsense_Mutation	SNP	149188740	149188740	18798	7	G	T	T	45	45	ZNF862	T	5	3
DNAH11	8701	broad.mit.edu	36	7	21607230	21607230	+	Silent	SNP	G	A	A			TCGA-14-1034-01	TCGA-14-1034-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr7:21607230G>A	uc003svc.1	+	c.3333G>A	c.(3331-3333)GTG>GTA	p.V1111V		NM_003777	NP_003768	Q96DT5	DYH11_HUMAN	dynein, axonemal, heavy chain 11	1111	Stem (By similarity).				microtubule-based movement	axonemal dynein complex|cilium axoneme|cytoplasm|microtubule	ATP binding|ATPase activity|microtubule motor activity			ovary(8)|large_intestine(3)|pancreas(3)|central_nervous_system(1)	15														0.283465	96.942585	102.292858	36	91	GG		KEEP	---	---	---	---	capture			Silent	SNP	21607230	21607230	4781	7	G	A	A	47	47	DNAH11	A	2	2
AVL9	23080	broad.mit.edu	36	7	32586998	32586998	+	Missense_Mutation	SNP	G	C	C			TCGA-14-1034-01	TCGA-14-1034-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr7:32586998G>C	uc003tcv.1	+	c.1802G>C	c.(1801-1803)CGG>CCG	p.R601P	AVL9_uc010kwj.1_Missense_Mutation_p.G385R	NM_015060	NP_055875	Q8NBF6	AVL9_HUMAN	AVL9 homolog (S. cerevisiase)	601						integral to membrane					0														0.203125	27.334926	32.579456	13	51	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	32586998	32586998	1249	7	G	C	C	39	39	AVL9	C	3	3
EGFR	1956	broad.mit.edu	36	7	55177571	55177571	+	Missense_Mutation	SNP	G	A	A			TCGA-14-1034-01	TCGA-14-1034-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr7:55177571G>A	uc003tqk.1	+	c.187G>A	c.(187-189)GGG>AGG	p.G63R	EGFR_uc003tqh.1_Missense_Mutation_p.G63R|EGFR_uc003tqi.1_Missense_Mutation_p.G63R|EGFR_uc003tqj.1_Missense_Mutation_p.G63R|EGFR_uc010kzg.1_Missense_Mutation_p.G63R	NM_005228	NP_005219	P00533	EGFR_HUMAN	epidermal growth factor receptor isoform a	63	Extracellular (Potential).				activation of phospholipase A2 activity by calcium-mediated signaling|activation of phospholipase C activity|axon guidance|cell proliferation|cell-cell adhesion|negative regulation of apoptosis|negative regulation of epidermal growth factor receptor signaling pathway|ossification|positive regulation of catenin import into nucleus|positive regulation of cell migration|positive regulation of cyclin-dependent protein kinase activity involved in G1/S|positive regulation of epithelial cell proliferation|positive regulation of MAP kinase activity|positive regulation of nitric oxide biosynthetic process|positive regulation of phosphorylation|positive regulation of protein kinase B signaling cascade|protein autophosphorylation|protein insertion into membrane|regulation of nitric-oxide synthase activity|regulation of peptidyl-tyrosine phosphorylation|response to stress|response to UV-A	basolateral plasma membrane|endoplasmic reticulum membrane|endosome|extracellular space|Golgi membrane|integral to membrane|nuclear membrane|Shc-EGFR complex	actin filament binding|ATP binding|double-stranded DNA binding|epidermal growth factor receptor activity|identical protein binding|MAP/ERK kinase kinase activity|protein heterodimerization activity|protein phosphatase binding|receptor signaling protein tyrosine kinase activity	p.V30_R297>G(5)|p.G63R(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)			0.173913	97.32012	125.030199	48	228	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	55177571	55177571	5156	7	G	A	A	47	47	EGFR	A	2	2
TG	7038	broad.mit.edu	36	8	133949572	133949572	+	Missense_Mutation	SNP	C	T	T			TCGA-14-1034-01	TCGA-14-1034-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr8:133949572C>T	uc003ytw.1	+	c.98C>T	c.(97-99)CCC>CTC	p.P33L		NM_003235	NP_003226	P01266	THYG_HUMAN	thyroglobulin	33	Thyroglobulin type-1 1.				hormone biosynthetic process|regulation of synaptic transmission|signal transduction		carboxylesterase activity|hormone activity			ovary(8)|breast(4)|pancreas(1)	13	Ovarian(258;0.00438)|Acute lymphoblastic leukemia(118;0.155)	Myeloproliferative disorder(644;0.00878)|Acute lymphoblastic leukemia(644;0.0559)|Breast(495;0.0735)								1778				0.333333	76.025177	77.943438	26	52	CC		KEEP	---	---	---	---	capture	BRCA - Breast invasive adenocarcinoma(115;0.000701)	KIRC - Kidney renal clear cell carcinoma(542;0.0546)	Missense_Mutation	SNP	133949572	133949572	16341	8	C	T	T	22	22	TG	T	2	2
CYC1	1537	broad.mit.edu	36	8	145223560	145223560	+	Missense_Mutation	SNP	T	A	A			TCGA-14-1034-01	TCGA-14-1034-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr8:145223560T>A	uc003zaz.2	+	c.697T>A	c.(697-699)TTC>ATC	p.F233I	CYC1_uc003zay.1_Missense_Mutation_p.F174I	NM_001916	NP_001907	P08574	CY1_HUMAN	cytochrome c-1	233					respiratory electron transport chain|transport	cell junction|integral to membrane|mitochondrial inner membrane|respiratory chain	electron transporter, transferring electrons from CoQH2-cytochrome c reductase complex and cytochrome c oxidase complex activity|heme binding				0	all_cancers(97;2.87e-11)|all_epithelial(106;2.16e-09)|Lung NSC(106;5.89e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)													0.432203	147.697997	148.17227	51	67	TT		KEEP	---	---	---	---	capture	OV - Ovarian serous cystadenocarcinoma(54;3.38e-41)|Epithelial(56;8.71e-40)|all cancers(56;3e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.105)		Missense_Mutation	SNP	145223560	145223560	4300	8	T	A	A	56	56	CYC1	A	4	4
SFTPC	6440	broad.mit.edu	36	8	22076092	22076092	+	Missense_Mutation	SNP	C	T	T			TCGA-14-1034-01	TCGA-14-1034-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr8:22076092C>T	uc003xaw.2	+	c.250C>T	c.(250-252)CGC>TGC	p.R84C	SFTPC_uc003xax.2_Missense_Mutation_p.R35C|SFTPC_uc003xaz.2_Missense_Mutation_p.R35C|SFTPC_uc003xay.2_Missense_Mutation_p.R35C|BMP1_uc003xba.1_5'Flank|BMP1_uc003xbb.1_5'Flank|BMP1_uc003xbc.1_5'Flank|BMP1_uc003xbd.1_5'Flank|BMP1_uc003xbf.1_5'Flank|BMP1_uc003xbe.1_5'Flank|BMP1_uc003xbh.1_5'Flank|BMP1_uc003xbg.1_5'Flank	NM_003018	NP_003009	P11686	PSPC_HUMAN	surfactant, pulmonary-associated protein C	35					respiratory gaseous exchange	extracellular space					0														0.381818	179.386833	181.40712	63	102	CC		KEEP	---	---	---	---	capture		Colorectal(74;0.00191)|COAD - Colon adenocarcinoma(73;0.0615)|READ - Rectum adenocarcinoma(644;0.1)	Missense_Mutation	SNP	22076092	22076092	14683	8	C	T	T	19	19	SFTPC	T	1	1
ADAM28	10863	broad.mit.edu	36	8	24255119	24255119	+	Silent	SNP	G	T	T			TCGA-14-1034-01	TCGA-14-1034-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr8:24255119G>T	uc003xdy.1	+	c.1734G>T	c.(1732-1734)CGG>CGT	p.R578R	ADAM28_uc010lua.1_Silent_p.R265R	NM_014265	NP_055080	Q9UKQ2	ADA28_HUMAN	ADAM metallopeptidase domain 28 isoform 1	578	Extracellular (Potential).|Cys-rich.				proteolysis|spermatogenesis	extracellular region|integral to membrane|plasma membrane	metalloendopeptidase activity|zinc ion binding	p.R578R(1)		skin(2)|lung(1)|central_nervous_system(1)	4		Prostate(55;0.0959)				NSCLC(193;488 2149 22258 34798 40734)				410				0.349754	187.80072	191.8272	71	132	GG		KEEP	---	---	---	---	capture		Colorectal(74;0.0129)|COAD - Colon adenocarcinoma(73;0.0434)|BRCA - Breast invasive adenocarcinoma(99;0.175)	Silent	SNP	24255119	24255119	247	8	G	T	T	41	41	ADAM28	T	3	3
UBE2W	55284	broad.mit.edu	36	8	74885262	74885263	+	Splice_Site_DNP	DNP	CC	AA	AA			TCGA-14-1034-01	TCGA-14-1034-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:74885262_74885263CC>AA	uc003xzu.1	-	c.399_splice	c.e5+1	p.K133_splice	UBE2W_uc003xzt.2_Splice_Site_DNP_p.K122_splice|UBE2W_uc003xzv.1_Splice_Site_DNP_p.K122_splice|UBE2W_uc003xzw.1_Splice_Site_DNP	NM_001001481	NP_001001481			ubiquitin-conjugating enzyme E2W (putative)						post-translational protein modification|protein K11-linked ubiquitination|protein monoubiquitination		ATP binding|protein binding|ubiquitin-protein ligase activity				0	Breast(64;0.0311)					Pancreas(14;490 592 20090 21022 23311)								0.142857	28.022308	41.790412	16	96	CC		KEEP	---	---	---	---	capture	Epithelial(68;0.0235)|all cancers(69;0.0687)|BRCA - Breast invasive adenocarcinoma(89;0.069)		Splice_Site_DNP	DNP	74885262	74885263	17435	8	CC	AA	AA	18	18	UBE2W	AA	5	3
DENND1A	57706	broad.mit.edu	36	9	125259458	125259458	+	Silent	SNP	G	A	A			TCGA-14-1034-01	TCGA-14-1034-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr9:125259458G>A	uc004bnz.1	-	c.1176C>T	c.(1174-1176)GGC>GGT	p.G392G	DENND1A_uc004bny.1_Intron|DENND1A_uc004boa.1_Silent_p.G392G|DENND1A_uc004bob.1_Silent_p.G362G|DENND1A_uc004boc.2_Silent_p.G360G	NM_020946	NP_065997	Q8TEH3	DEN1A_HUMAN	DENN/MADD domain containing 1A isoform 1	392						cell junction|clathrin coated vesicle membrane|presynaptic membrane	guanyl-nucleotide exchange factor activity			ovary(2)	2														0.356322	258.000104	262.746911	93	168	GG		KEEP	---	---	---	---	capture			Silent	SNP	125259458	125259458	4605	9	G	A	A	38	38	DENND1A	A	1	1
APBA1	320	broad.mit.edu	36	9	71321180	71321180	+	Missense_Mutation	SNP	G	A	A			TCGA-14-1034-01	TCGA-14-1034-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr9:71321180G>A	uc004ahh.1	-	c.767C>T	c.(766-768)GCG>GTG	p.A256V		NM_001163	NP_001154	Q02410	APBA1_HUMAN	amyloid beta A4 precursor protein-binding,	256	Munc-18-1 binding.				axon cargo transport|cell adhesion|intracellular protein transport|nervous system development|protein complex assembly|synaptic transmission	synaptic vesicle				lung(1)	1														0.23913	26.320287	29.166228	11	35	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	71321180	71321180	766	9	G	A	A	38	38	APBA1	A	1	1
ZCCHC12	170261	broad.mit.edu	36	X	117843288	117843288	+	Missense_Mutation	SNP	T	G	G			TCGA-14-1034-01	TCGA-14-1034-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chrX:117843288T>G	uc004equ.1	+	c.53T>G	c.(52-54)TTG>TGG	p.L18W	ZCCHC12_uc010nqj.1_Missense_Mutation_p.L18W	NM_173798	NP_776159	Q6PEW1	ZCH12_HUMAN	zinc finger, CCHC domain containing 12	18					regulation of transcription, DNA-dependent|transcription, DNA-dependent		nucleic acid binding|zinc ion binding			ovary(1)	1														0.347107	129.740737	132.271335	42	79	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	117843288	117843288	18169	23	T	G	G	63	63	ZCCHC12	G	4	4
KIAA1210	57481	broad.mit.edu	36	X	118134632	118134632	+	Missense_Mutation	SNP	C	A	A			TCGA-14-1034-01	TCGA-14-1034-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chrX:118134632C>A	uc004era.2	-	c.505G>T	c.(505-507)GCC>TCC	p.A169S		NM_020721	NP_065772	Q9ULL0	K1210_HUMAN	hypothetical protein LOC57481	169										ovary(4)|skin(1)	5														0.325581	38.533936	39.695227	14	29	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	118134632	118134632	8522	23	C	A	A	28	28	KIAA1210	A	3	3
GPR112	139378	broad.mit.edu	36	X	135282864	135282864	+	Missense_Mutation	SNP	C	A	A			TCGA-14-1034-01	TCGA-14-1034-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chrX:135282864C>A	uc004ezu.1	+	c.7751C>A	c.(7750-7752)TCC>TAC	p.S2584Y	GPR112_uc010nsb.1_Missense_Mutation_p.S2379Y	NM_153834	NP_722576	Q8IZF6	GP112_HUMAN	G-protein coupled receptor 112	2584	Extracellular (Potential).				neuropeptide signaling pathway	integral to membrane|plasma membrane	G-protein coupled receptor activity			ovary(5)|large_intestine(2)|lung(1)|breast(1)|skin(1)|pancreas(1)	11	Acute lymphoblastic leukemia(192;0.000127)									487				0.318182	381.16103	394.737372	147	315	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	135282864	135282864	6903	23	C	A	A	30	30	GPR112	A	3	3
PPEF1	5475	broad.mit.edu	36	X	18755326	18755326	+	Missense_Mutation	SNP	G	A	A			TCGA-14-1034-01	TCGA-14-1034-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chrX:18755326G>A	uc004cyq.1	+	c.1762G>A	c.(1762-1764)GTG>ATG	p.V588M	PPEF1_uc004cyp.1_Missense_Mutation_p.V560M|PPEF1_uc004cyr.1_Missense_Mutation_p.V526M|PPEF1_uc004cys.1_Missense_Mutation_p.V588M	NM_006240	NP_006231	O14829	PPE1_HUMAN	protein phosphatase with EF hand calcium-binding	588	EF-hand 2.|1 (Potential).				detection of stimulus involved in sensory perception|protein dephosphorylation		calcium ion binding|iron ion binding|manganese ion binding|protein binding|protein serine/threonine phosphatase activity				0	Hepatocellular(33;0.183)													0.352113	214.572251	218.675759	75	138	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	18755326	18755326	12737	23	G	A	A	40	40	PPEF1	A	1	1
ARSD	414	broad.mit.edu	36	X	2850042	2850042	+	Missense_Mutation	SNP	G	C	C			TCGA-14-1034-01	TCGA-14-1034-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chrX:2850042G>C	uc004cqy.1	-	c.218C>G	c.(217-219)GCA>GGA	p.A73G	ARSD_uc004cqz.1_Intron|ARSD_uc004cra.1_Missense_Mutation_p.A73G|ARSD_uc004crb.2_Missense_Mutation_p.A73G	NM_001669	NP_001660	P51689	ARSD_HUMAN	arylsulfatase D isoform a precursor	73						lysosome	arylsulfatase activity|metal ion binding				0		all_cancers(21;4.28e-07)|all_epithelial(21;2.07e-08)|all_lung(23;2.81e-05)|Lung NSC(23;0.000693)|Lung SC(21;0.122)												0.35	65.009175	66.221457	21	39	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	2850042	2850042	1007	23	G	C	C	46	46	ARSD	C	3	3
CCDC22	28952	broad.mit.edu	36	X	48980643	48980643	+	Missense_Mutation	SNP	G	A	A			TCGA-14-1034-01	TCGA-14-1034-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chrX:48980643G>A	uc004dnd.1	+	c.197G>A	c.(196-198)CGC>CAC	p.R66H	CCDC22_uc004dnc.1_Non-coding_Transcript	NM_014008	NP_054727	O60826	CCD22_HUMAN	coiled-coil domain containing 22	66										central_nervous_system(1)	1														0.333333	88.945754	91.440346	34	68	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	48980643	48980643	2919	23	G	A	A	38	38	CCDC22	A	1	1
GPR174	84636	broad.mit.edu	36	X	78313742	78313742	+	Missense_Mutation	SNP	T	A	A			TCGA-14-1034-01	TCGA-14-1034-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chrX:78313742T>A	uc004edg.1	+	c.582T>A	c.(580-582)TTT>TTA	p.F194L		NM_032553	NP_115942	Q9BXC1	GP174_HUMAN	putative purinergic receptor FKSG79	194	Helical; Name=5; (Potential).					integral to membrane|plasma membrane	purinergic nucleotide receptor activity, G-protein coupled			lung(1)|central_nervous_system(1)	2														0.318841	179.873748	185.913169	66	141	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	78313742	78313742	6947	23	T	A	A	63	63	GPR174	A	4	4
SYTL4	94121	broad.mit.edu	36	X	99843255	99843255	+	Missense_Mutation	SNP	G	A	A			TCGA-14-1034-01	TCGA-14-1034-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chrX:99843255G>A	uc004egd.2	-	c.181C>T	c.(181-183)CGG>TGG	p.R61W	SYTL4_uc010nnc.1_Missense_Mutation_p.R61W|SYTL4_uc004ege.2_Missense_Mutation_p.R61W|SYTL4_uc004egf.2_Missense_Mutation_p.R61W|SYTL4_uc004egg.2_Missense_Mutation_p.R61W	NM_080737	NP_542775	Q96C24	SYTL4_HUMAN	synaptotagmin-like 4	61	RabBD.				exocytosis|intracellular protein transport	extrinsic to membrane|plasma membrane|synaptic vesicle|transport vesicle membrane	neurexin binding|phospholipid binding|Rab GTPase binding|transporter activity|zinc ion binding			ovary(2)	2					Insulin Glargine recombinant(DB00047)|Insulin Lyspro recombinant(DB00046)|Insulin recombinant(DB00030)|Insulin, porcine(DB00071)									0.188235	64.302992	79.768866	32	138	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	99843255	99843255	16006	23	G	A	A	37	37	SYTL4	A	1	1
TOP3A	7156	broad.mit.edu	36	17	18150970	18150971	+	Frame_Shift_Del	DEL	TC	-	-			TCGA-14-1034-01	TCGA-14-1034-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:18150970_18150971delTC	uc002gsx.1	-	c.349_350delGA	c.(349-351)GAAfs	p.E117fs	TOP3A_uc002gsw.1_5'UTR|TOP3A_uc010cqa.1_Non-coding_Transcript	NM_004618	NP_004609	Q13472	TOP3A_HUMAN	topoisomerase (DNA) III alpha	117	Toprim.				DNA topological change|DNA unwinding involved in replication|meiosis	chromosome|PML body	ATP binding|DNA topoisomerase type I activity|protein binding|zinc ion binding			skin(2)	2														0.32			29	61				---	---	---	---	capture_indel			Frame_Shift_Del	DEL	18150970	18150971	16909	17	TC	-	-	62	62	TOP3A	-	5	5
NF1	4763	broad.mit.edu	36	17	26709623	26709623	+	Splice_Site_Del	DEL	G	-	-			TCGA-14-1034-01	TCGA-14-1034-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:26709623_26709623delG	uc002hgg.1	+	c.e55_splice_site			NF1_uc002hgh.1_Splice_Site_Del|NF1_uc010cso.1_Splice_Site_Del	NM_001042492	NP_001035957			neurofibromin isoform 1						actin cytoskeleton organization|adrenal gland development|artery morphogenesis|camera-type eye morphogenesis|cerebral cortex development|collagen fibril organization|forebrain astrocyte development|forebrain morphogenesis|heart development|liver development|MAPKKK cascade|metanephros development|myelination in peripheral nervous system|negative regulation of cell migration|negative regulation of endothelial cell proliferation|negative regulation of MAP kinase activity|negative regulation of MAPKKK cascade|negative regulation of neuroblast proliferation|negative regulation of oligodendrocyte differentiation|negative regulation of transcription factor import into nucleus|osteoblast differentiation|phosphatidylinositol 3-kinase cascade|pigmentation|positive regulation of adenylate cyclase activity|positive regulation of neuron apoptosis|Ras protein signal transduction|regulation of blood vessel endothelial cell migration|regulation of bone resorption|response to hypoxia|smooth muscle tissue development|spinal cord development|sympathetic nervous system development|visual learning|wound healing	axon|cytoplasm|dendrite|intrinsic to internal side of plasma membrane|nucleus	protein binding|Ras GTPase activator activity	p.?(1)		soft_tissue(155)|central_nervous_system(56)|large_intestine(27)|lung(19)|haematopoietic_and_lymphoid_tissue(13)|ovary(12)|autonomic_ganglia(7)|skin(3)|stomach(2)|breast(2)|thyroid(1)|prostate(1)|kidney(1)|pancreas(1)	300		all_cancers(10;1.29e-12)|all_epithelial(10;0.00347)|all_hematologic(16;0.00556)|Acute lymphoblastic leukemia(14;0.00593)|Breast(31;0.014)|Myeloproliferative disorder(56;0.0255)|all_lung(9;0.0321)|Lung NSC(157;0.0659)		UCEC - Uterine corpus endometrioid carcinoma (4;4.38e-05)|all cancers(4;1.64e-26)|Epithelial(4;9.15e-23)|OV - Ovarian serous cystadenocarcinoma(4;3.58e-21)|GBM - Glioblastoma multiforme(4;0.00146)						847	TCGA GBM(6;<1E-8)|TSP Lung(7;0.0071)|TCGA Ovarian(3;0.0088)			0.51			28	27				---	---	---	---	capture_indel			Splice_Site_Del	DEL	26709623	26709623	10756	17	G	-	-	35	35	NF1	-	5	5
KRT23	25984	broad.mit.edu	36	17	36341159	36341159	+	Frame_Shift_Del	DEL	G	-	-			TCGA-14-1034-01	TCGA-14-1034-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:36341159_36341159delG	uc002hvm.1	-	c.471_471delC	c.(469-471)TTCfs	p.F157fs	KRT23_uc010cxf.1_5'UTR|KRT23_uc010cxg.1_Frame_Shift_Del_p.F157fs|KRT23_uc002hvn.1_Frame_Shift_Del_p.F157fs	NM_015515	NP_056330	Q9C075	K1C23_HUMAN	keratin 23	157	Rod.|Coil 1B.					intermediate filament	structural molecule activity			ovary(1)	1		Breast(137;0.000301)|Ovarian(249;0.15)												0.31			37	83				---	---	---	---	capture_indel			Frame_Shift_Del	DEL	36341159	36341159	8775	17	G	-	-	45	45	KRT23	-	5	5
KCNC4	3749	broad.mit.edu	36	1	110555924	110555926	+	In_Frame_Del	DEL	TTC	-	-			TCGA-14-1034-01	TCGA-14-1034-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:110555924_110555926delTTC	uc009wfr.1	+	c.280_282delTTC	c.(280-282)TTCdel	p.F96del	KCNC4_uc001dzf.1_In_Frame_Del_p.F96del|KCNC4_uc001dzg.1_In_Frame_Del_p.F96del|KCNC4_uc001dzh.1_In_Frame_Del_p.F96del|KCNC4_uc001dzi.1_Non-coding_Transcript	NM_001039574	NP_001034663	Q03721	KCNC4_HUMAN	Shaw-related voltage-gated potassium channel	96	Cytoplasmic (Potential).				synaptic transmission	voltage-gated potassium channel complex	voltage-gated potassium channel activity			large_intestine(1)|ovary(1)|central_nervous_system(1)	3		all_cancers(81;9.88e-06)|all_epithelial(167;3.23e-06)|all_lung(203;0.000116)|Lung NSC(277;0.000233)		Lung(183;0.0238)|all cancers(265;0.0693)|Epithelial(280;0.0748)|Colorectal(144;0.112)|LUSC - Lung squamous cell carcinoma(189;0.135)										0.37			10	17				---	---	---	---	capture_indel			In_Frame_Del	DEL	110555924	110555926	8322	1	TTC	-	-	60	60	KCNC4	-	5	5
HOOK3	84376	broad.mit.edu	36	8	42961022	42961023	+	Frame_Shift_Ins	INS	-	A	A			TCGA-14-1034-01	TCGA-14-1034-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:42961022_42961023insA	uc003xpr.1	+	c.1459_1460insA	c.(1459-1461)GAAfs	p.E487fs	HOOK3_uc010lxq.1_Frame_Shift_Ins_p.E487fs	NM_032410	NP_115786	Q86VS8	HOOK3_HUMAN	golgi-associated microtubule-binding protein	487	Potential.				cytoplasmic microtubule organization|early endosome to late endosome transport|endosome organization|endosome to lysosome transport|Golgi localization|interkinetic nuclear migration|lysosome organization|microtubule anchoring|negative regulation of neurogenesis|protein localization to centrosome|protein transport	cis-Golgi network|FHF complex|microtubule|pericentriolar material	identical protein binding|microtubule binding			ovary(1)|breast(1)	2	Ovarian(28;0.01)|Prostate(17;0.0119)|Lung SC(25;0.184)	all_lung(54;0.000105)|Lung NSC(58;0.000419)|Hepatocellular(245;0.0524)|Renal(179;0.0822)|Esophageal squamous(32;0.129)	Lung(22;0.048)|LUSC - Lung squamous cell carcinoma(45;0.114)											0.35			56	105				---	---	---	---	capture_indel			Frame_Shift_Ins	INS	42961022	42961023	7576	8	-	A	A	45	45	HOOK3	A	5	5
