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
SEC23IP	11196	broad.mit.edu	36	10	121658618	121658618	+	Missense_Mutation	SNP	A	G	G			TCGA-16-0846-01	TCGA-16-0846-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr10:121658618A>G	uc001leu.1	+	c.1177A>G	c.(1177-1179)ATG>GTG	p.M393V		NM_007190	NP_009121	Q9Y6Y8	S23IP_HUMAN	Sec23-interacting protein p125	393					Golgi organization|intracellular protein transport	endoplasmic reticulum|ER to Golgi transport vesicle membrane|ER-Golgi intermediate compartment	metal ion binding			ovary(3)	3		Lung NSC(174;0.109)|all_lung(145;0.142)|all_neural(114;0.234)												0.763889	197.363868	201.950042	55	17	AA		KEEP	---	---	---	---	capture		all cancers(201;0.00515)	Missense_Mutation	SNP	121658618	121658618	14479	10	A	G	G	16	16	SEC23IP	G	4	4
FAM53B	9679	broad.mit.edu	36	10	126302091	126302091	+	Missense_Mutation	SNP	C	G	G			TCGA-16-0846-01	TCGA-16-0846-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr10:126302091C>G	uc001lhv.1	-	c.979G>C	c.(979-981)GCC>CCC	p.A327P	FAM53B_uc001lhu.1_Intron	NM_014661	NP_055476	Q14153	FA53B_HUMAN	hypothetical protein LOC9679	327										ovary(1)|pancreas(1)	2		all_lung(145;0.0191)|Lung NSC(174;0.0301)|Colorectal(57;0.106)|all_neural(114;0.117)												0.571429	10.597043	10.627828	4	3	CC		KEEP	---	---	---	---	capture		COAD - Colon adenocarcinoma(40;0.141)|Colorectal(40;0.15)	Missense_Mutation	SNP	126302091	126302091	5802	10	C	G	G	27	27	FAM53B	G	3	3
PITRM1	10531	broad.mit.edu	36	10	3190333	3190333	+	Nonsense_Mutation	SNP	G	T	T			TCGA-16-0846-01	TCGA-16-0846-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr10:3190333G>T	uc001igt.1	-	c.1149C>A	c.(1147-1149)TAC>TAA	p.Y383*	PITRM1_uc001igr.1_Nonsense_Mutation_p.Y383*|PITRM1_uc009xhv.1_5'Flank|PITRM1_uc001igu.1_Nonsense_Mutation_p.Y375*|PITRM1_uc001igw.1_Nonsense_Mutation_p.Y383*	NM_014889	NP_055704	Q5JRX3	PREP_HUMAN	metalloprotease 1	383					proteolysis	mitochondrial matrix|nucleus	enzyme activator activity|metalloendopeptidase activity|protein binding|zinc ion binding			pancreas(1)	1														0.206897	7.0651	9.368167	6	23	GG		KEEP	---	---	---	---	capture			Nonsense_Mutation	SNP	3190333	3190333	12377	10	G	T	T	48	48	PITRM1	T	5	3
VDAC2	7417	broad.mit.edu	36	10	76640932	76640932	+	Missense_Mutation	SNP	C	T	T			TCGA-16-0846-01	TCGA-16-0846-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr10:76640932C>T	uc001jwz.1	+	c.10C>T	c.(10-12)CAC>TAC	p.H4Y	VDAC2_uc001jxa.1_5'UTR	NM_003375	NP_003366	P45880	VDAC2_HUMAN	voltage-dependent anion channel 2	4						mitochondrial nucleoid|mitochondrial outer membrane|pore complex	nucleotide binding|porin activity|protein binding|voltage-gated anion channel activity			pancreas(2)|ovary(1)	3	all_cancers(46;0.0642)|all_epithelial(25;0.00604)|Prostate(51;0.0112)|Ovarian(15;0.183)				Dihydroxyaluminium(DB01375)									0.875	45.459435	47.65607	14	2	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	76640932	76640932	17714	10	C	T	T	21	21	VDAC2	T	2	2
PTEN	5728	broad.mit.edu	36	10	89680826	89680826	+	Missense_Mutation	SNP	G	T	T			TCGA-16-0846-01	TCGA-16-0846-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr10:89680826G>T	uc001kfb.1	+	c.253G>T	c.(253-255)GTT>TTT	p.V85F		NM_000314	NP_000305	P60484	PTEN_HUMAN	phosphatase and tensin homolog	85	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.V85A(2)|p.C71fs*6(2)|p.L70fs*7(2)|p.Y27_N212>Y(2)|p.?(1)|p.N82_P95del(1)|p.F56fs*2(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	(NCIH446-Tumor)	264	TCGA GBM(2;<1E-8)|TSP Lung(26;0.18)			0.595745	87.505344	87.881218	28	19	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	89680826	89680826	13192	10	G	T	T	35	35	PTEN	T	3	3
NAV2	89797	broad.mit.edu	36	11	19917854	19917854	+	Missense_Mutation	SNP	A	G	G			TCGA-16-0846-01	TCGA-16-0846-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr11:19917854A>G	uc009yhw.1	+	c.2174A>G	c.(2173-2175)CAC>CGC	p.H725R	NAV2_uc001mpp.1_Missense_Mutation_p.H638R|NAV2_uc001mpr.2_Missense_Mutation_p.H702R	NM_182964	NP_892009	Q8IVL1	NAV2_HUMAN	neuron navigator 2 isoform 1	725						nucleus	ATP binding|helicase activity			ovary(1)|pancreas(1)	2														0.176471	19.346911	24.375207	9	42	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	19917854	19917854	10580	11	A	G	G	6	6	NAV2	G	4	4
LRP4	4038	broad.mit.edu	36	11	46853199	46853199	+	Silent	SNP	G	C	C			TCGA-16-0846-01	TCGA-16-0846-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr11:46853199G>C	uc001ndn.2	-	c.3957C>G	c.(3955-3957)GGC>GGG	p.G1319G		NM_002334	NP_002325	O75096	LRP4_HUMAN	low density lipoprotein receptor-related protein	1319	Extracellular (Potential).				endocytosis|negative regulation of canonical Wnt receptor signaling pathway|Wnt receptor signaling pathway	integral to membrane	calcium ion binding|receptor activity			ovary(1)	1														0.266667	6.887968	7.630217	4	11	GG		KEEP	---	---	---	---	capture		Lung(87;0.159)	Silent	SNP	46853199	46853199	9332	11	G	C	C	34	34	LRP4	C	3	3
OR51A4	401666	broad.mit.edu	36	11	4924497	4924497	+	Missense_Mutation	SNP	A	G	G			TCGA-16-0846-01	TCGA-16-0846-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr11:4924497A>G	uc001lzt.1	-	c.410T>C	c.(409-411)ATC>ACC	p.I137T		NM_001005329	NP_001005329	Q8NGJ6	O51A4_HUMAN	olfactory receptor, family 51, subfamily A,	137	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(2)	2		Medulloblastoma(188;0.0075)|all_neural(188;0.0577)|Breast(177;0.086)												0.316562	457.464456	471.732449	151	326	AA		KEEP	---	---	---	---	capture		Epithelial(150;3.22e-11)|BRCA - Breast invasive adenocarcinoma(625;0.0284)|LUSC - Lung squamous cell carcinoma(625;0.19)	Missense_Mutation	SNP	4924497	4924497	11497	11	A	G	G	12	12	OR51A4	G	4	4
SPRYD5	84767	broad.mit.edu	36	11	55412167	55412167	+	Missense_Mutation	SNP	C	A	A			TCGA-16-0846-01	TCGA-16-0846-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr11:55412167C>A	uc001nia.1	+	c.114C>A	c.(112-114)CAC>CAA	p.H38Q		NM_032681	NP_116070	Q9BSJ1	SPRY5_HUMAN	SPRY domain containing 5	197						intracellular	zinc ion binding				0		all_epithelial(135;0.226)												0.2	23.895017	28.498072	11	44	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	55412167	55412167	15625	11	C	A	A	20	20	SPRYD5	A	3	3
SERPING1	710	broad.mit.edu	36	11	57138446	57138446	+	Missense_Mutation	SNP	C	T	T			TCGA-16-0846-01	TCGA-16-0846-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr11:57138446C>T	uc009ymi.1	+	c.1346C>T	c.(1345-1347)GCG>GTG	p.A449V	SERPING1_uc001nkp.1_Missense_Mutation_p.A440V|SERPING1_uc001nkq.1_Missense_Mutation_p.A403V|SERPING1_uc001nkr.1_Missense_Mutation_p.A440V|SERPING1_uc009ymj.1_3'UTR|SERPING1_uc001nks.1_Missense_Mutation_p.A131V	NM_001032295	NP_001027466	P05155	IC1_HUMAN	serpin peptidase inhibitor, clade G, member 1	440					blood circulation|blood coagulation, intrinsic pathway|complement activation, classical pathway|innate immune response|negative regulation of complement activation, lectin pathway|platelet activation|platelet degranulation	extracellular space|platelet alpha granule lumen	protein binding|serine-type endopeptidase inhibitor activity			central_nervous_system(1)	1														0.133929	17.858923	32.418554	15	97	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	57138446	57138446	14604	11	C	T	T	27	27	SERPING1	T	1	1
SLCO2B1	11309	broad.mit.edu	36	11	74582230	74582230	+	Missense_Mutation	SNP	C	G	G			TCGA-16-0846-01	TCGA-16-0846-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr11:74582230C>G	uc001owb.1	+	c.1395C>G	c.(1393-1395)TGC>TGG	p.C465W	SLCO2B1_uc001owc.1_Missense_Mutation_p.C238W|SLCO2B1_uc001owd.1_Missense_Mutation_p.C443W	NM_007256	NP_009187	O94956	SO2B1_HUMAN	solute carrier organic anion transporter family,	465	Extracellular (Potential).				sodium-independent organic anion transport	integral to membrane	sodium-independent organic anion transmembrane transporter activity			ovary(1)|breast(1)	2					Ergoloid mesylate(DB01049)									0.210526	6.385787	7.864021	4	15	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	74582230	74582230	15224	11	C	G	G	28	28	SLCO2B1	G	3	3
TBX5	6910	broad.mit.edu	36	12	113288448	113288448	+	Missense_Mutation	SNP	C	A	A			TCGA-16-0846-01	TCGA-16-0846-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr12:113288448C>A	uc001tvo.1	-	c.887G>T	c.(886-888)GGT>GTT	p.G296V	TBX5_uc001tvp.1_Missense_Mutation_p.G296V|TBX5_uc001tvq.1_Missense_Mutation_p.G246V|TBX5_uc001tvr.1_Missense_Mutation_p.G296V	NM_181486	NP_542448	Q99593	TBX5_HUMAN	T-box 5 isoform 1	296					cardiac left ventricle formation|cell migration involved in coronary vasculogenesis|cell-cell signaling|embryonic arm morphogenesis|induction of apoptosis|negative regulation of cardiac muscle cell proliferation|negative regulation of cell migration|negative regulation of epithelial to mesenchymal transition|pericardium development|positive regulation of cardioblast differentiation|positive regulation of gene-specific transcription from RNA polymerase II promoter|ventricular septum development	cytoplasm|nucleus	protein binding|RNA polymerase II transcription factor activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription factor binding			ovary(6)|pancreas(1)	7	Medulloblastoma(191;0.163)|all_neural(191;0.178)					NSCLC(152;1358 1980 4050 23898 40356)								0.378641	109.599964	110.93064	39	64	CC		KEEP	---	---	---	---	capture		BRCA - Breast invasive adenocarcinoma(302;0.0893)	Missense_Mutation	SNP	113288448	113288448	16187	12	C	A	A	18	18	TBX5	A	3	3
BIN2	51411	broad.mit.edu	36	12	49983137	49983137	+	Splice_Site_SNP	SNP	C	T	T			TCGA-16-0846-01	TCGA-16-0846-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr12:49983137C>T	uc001ryg.1	-	c.217_splice	c.e3+1	p.V73_splice	BIN2_uc009zlz.1_Splice_Site_SNP_p.V73_splice|BIN2_uc001ryh.1_Splice_Site_SNP	NM_016293	NP_057377			bridging integrator 2							cytoplasm	protein binding			ovary(1)	1														0.337349	156.146267	160.031695	56	110	CC		KEEP	---	---	---	---	capture			Splice_Site_SNP	SNP	49983137	49983137	1458	12	C	T	T	18	18	BIN2	T	5	2
OR6C75	390323	broad.mit.edu	36	12	54045667	54045667	+	Missense_Mutation	SNP	C	G	G			TCGA-16-0846-01	TCGA-16-0846-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr12:54045667C>G	uc001sgw.1	+	c.506C>G	c.(505-507)TCC>TGC	p.S169C		NM_001005497	NP_001005497	A6NL08	O6C75_HUMAN	olfactory receptor, family 6, subfamily C,	169	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			large_intestine(1)|ovary(1)	2														0.302158	130.599704	135.45528	42	97	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	54045667	54045667	11609	12	C	G	G	30	30	OR6C75	G	3	3
LRRIQ1	84125	broad.mit.edu	36	12	84147479	84147479	+	Missense_Mutation	SNP	C	T	T	rs1395676	by-cluster,by-frequency,by-hapmap	TCGA-16-0846-01	TCGA-16-0846-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr12:84147479C>T	uc001tac.1	+	c.4876C>T	c.(4876-4878)CGG>TGG	p.R1626W		NM_001079910	NP_001073379	Q96JM4	LRIQ1_HUMAN	leucine-rich repeats and IQ motif containing 1	1626										ovary(4)|central_nervous_system(1)	5														0.37234	197.608667	200.296941	70	118	CC		KEEP	---	---	---	---	capture		GBM - Glioblastoma multiforme(134;0.212)	Missense_Mutation	SNP	84147479	84147479	9405	12	C	T	T	19	19	LRRIQ1	T	1	1
FGD6	55785	broad.mit.edu	36	12	94128312	94128312	+	Silent	SNP	T	C	C			TCGA-16-0846-01	TCGA-16-0846-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr12:94128312T>C	uc001tdp.2	-	c.879A>G	c.(877-879)TCA>TCG	p.S293S	FGD6_uc009zsx.1_Intron	NM_018351	NP_060821	Q6ZV73	FGD6_HUMAN	FYVE, RhoGEF and PH domain containing 6	293					actin cytoskeleton organization|filopodium assembly|regulation of Cdc42 GTPase activity|regulation of cell shape	cytoskeleton|Golgi apparatus|lamellipodium|ruffle	metal ion binding|Rho guanyl-nucleotide exchange factor activity|small GTPase binding			ovary(2)|breast(1)	3														0.40113	212.080445	213.595595	71	106	TT		KEEP	---	---	---	---	capture			Silent	SNP	94128312	94128312	6074	12	T	C	C	55	55	FGD6	C	4	4
FAM124A	220108	broad.mit.edu	36	13	50723706	50723706	+	Missense_Mutation	SNP	G	A	A			TCGA-16-0846-01	TCGA-16-0846-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr13:50723706G>A	uc001vff.1	+	c.310G>A	c.(310-312)GTC>ATC	p.V104I	FAM124A_uc001vfe.2_Missense_Mutation_p.V68I|FAM124A_uc001vfg.1_Missense_Mutation_p.V68I	NM_145019	NP_659456	Q86V42	F124A_HUMAN	hypothetical protein LOC220108	68										central_nervous_system(1)	1		Acute lymphoblastic leukemia(7;0.000334)|Breast(56;0.00156)|Prostate(109;0.00538)|Lung NSC(96;0.0216)|Hepatocellular(98;0.152)|Glioma(44;0.236)												0.255319	28.078516	30.631079	12	35	GG		KEEP	---	---	---	---	capture		GBM - Glioblastoma multiforme(99;4.25e-07)	Missense_Mutation	SNP	50723706	50723706	5622	13	G	A	A	40	40	FAM124A	A	1	1
FOXA1	3169	broad.mit.edu	36	14	37131655	37131655	+	Missense_Mutation	SNP	C	T	T			TCGA-16-0846-01	TCGA-16-0846-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr14:37131655C>T	uc001wuf.1	-	c.85G>A	c.(85-87)GTC>ATC	p.V29I		NM_004496	NP_004487	P55317	FOXA1_HUMAN	forkhead box A1	29					chromatin remodeling|embryo development|epithelial cell maturation involved in prostate gland development|epithelial tube branching involved in lung morphogenesis|epithelial-mesenchymal signaling involved in prostate gland development|glucose homeostasis|lung epithelial cell differentiation|negative regulation of gene-specific transcription from RNA polymerase II promoter|negative regulation of survival gene product expression|neuron fate specification|pattern specification process|positive regulation of estrogen receptor signaling pathway|positive regulation of gene-specific transcription from RNA polymerase II promoter|positive regulation of mitotic cell cycle|positive regulation of neuron differentiation|positive regulation of sequence-specific DNA binding transcription factor activity|prostate gland epithelium morphogenesis|prostate gland stromal morphogenesis|response to estradiol stimulus|secretory columnal luminar epithelial cell differentiation involved in prostate glandular acinus development	transcription factor complex	DNA bending activity|double-stranded DNA binding|promoter binding|protein domain specific binding|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription|sequence-specific enhancer binding RNA polymerase II transcription factor activity|specific RNA polymerase II transcription factor activity|specific transcriptional repressor activity|transcription activator activity|transcription factor binding				0	Breast(36;0.0954)|Esophageal squamous(585;0.164)|Hepatocellular(127;0.213)													0.353448	106.561262	108.791561	41	75	CC		KEEP	---	---	---	---	capture	Lung(238;5.41e-07)|LUAD - Lung adenocarcinoma(48;2.48e-05)|Epithelial(34;0.0454)|LUSC - Lung squamous cell carcinoma(13;0.0917)|all cancers(34;0.0925)|BRCA - Breast invasive adenocarcinoma(188;0.239)	GBM - Glioblastoma multiforme(112;0.0222)	Missense_Mutation	SNP	37131655	37131655	6231	14	C	T	T	19	19	FOXA1	T	1	1
UNC13C	440279	broad.mit.edu	36	15	52343684	52343684	+	Missense_Mutation	SNP	G	A	A			TCGA-16-0846-01	TCGA-16-0846-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr15:52343684G>A	uc002ack.1	+	c.3475G>A	c.(3475-3477)GGT>AGT	p.G1159S	UNC13C_uc002acl.2_5'UTR	NM_001080534	NP_001074003	Q8NB66	UN13C_HUMAN	unc-13 homolog C	1159					exocytosis|intracellular signal transduction	cell junction|cytoplasm|presynaptic membrane	metal ion binding			ovary(5)|pancreas(2)	7										2691				0.6	18.250785	18.337994	6	4	GG		KEEP	---	---	---	---	capture		GBM - Glioblastoma multiforme(80;0.0789)|all cancers(107;0.124)	Missense_Mutation	SNP	52343684	52343684	17544	15	G	A	A	47	47	UNC13C	A	2	2
SLC28A1	9154	broad.mit.edu	36	15	83249824	83249824	+	Silent	SNP	A	T	T			TCGA-16-0846-01	TCGA-16-0846-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr15:83249824A>T	uc002blg.1	+	c.654A>T	c.(652-654)GGA>GGT	p.G218G	SLC28A1_uc010bnb.1_Silent_p.G218G	NM_004213	NP_004204	O00337	S28A1_HUMAN	solute carrier family 28 (sodium-coupled	218	Helical; (Potential).				nucleobase, nucleoside and nucleotide metabolic process	integral to plasma membrane|membrane fraction	nucleoside binding			ovary(1)	1														0.115942	8.355682	18.371706	8	61	AA		KEEP	---	---	---	---	capture	BRCA - Breast invasive adenocarcinoma(143;0.0587)		Silent	SNP	83249824	83249824	15028	15	A	T	T	10	10	SLC28A1	T	4	4
IL4R	3566	broad.mit.edu	36	16	27265427	27265427	+	Missense_Mutation	SNP	A	T	T			TCGA-16-0846-01	TCGA-16-0846-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr16:27265427A>T	uc002don.1	+	c.500A>T	c.(499-501)AAC>ATC	p.N167I	IL4R_uc002dom.1_Missense_Mutation_p.N167I|IL4R_uc010bxy.1_Missense_Mutation_p.N167I|IL4R_uc002doo.1_Missense_Mutation_p.T9S	NM_000418	NP_000409	P24394	IL4RA_HUMAN	interleukin 4 receptor alpha chain isoform a	167	Extracellular (Potential).|Fibronectin type-III.				immune response|production of molecular mediator involved in inflammatory response	integral to plasma membrane	identical protein binding|interleukin-4 receptor activity|receptor signaling protein activity			ovary(1)|skin(1)	2														0.325926	118.654462	122.283244	44	91	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	27265427	27265427	7999	16	A	T	T	2	2	IL4R	T	4	4
ZNF319	57567	broad.mit.edu	36	16	56588434	56588434	+	Missense_Mutation	SNP	C	T	T			TCGA-16-0846-01	TCGA-16-0846-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr16:56588434C>T	uc002emx.1	-	c.1237G>A	c.(1237-1239)GAG>AAG	p.E413K	ZNF319_uc010cdi.1_Missense_Mutation_p.E413K	NM_020807	NP_065858	Q9P2F9	ZN319_HUMAN	zinc finger protein 319	413	C2H2-type 11; degenerate.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0														0.411111	102.250825	102.873221	37	53	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	56588434	56588434	18429	16	C	T	T	31	31	ZNF319	T	1	1
MYOCD	93649	broad.mit.edu	36	17	12596788	12596788	+	Silent	SNP	G	A	A			TCGA-16-0846-01	TCGA-16-0846-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr17:12596788G>A	uc002gno.1	+	c.1458G>A	c.(1456-1458)CCG>CCA	p.P486P	MYOCD_uc002gnn.1_Silent_p.P486P|MYOCD_uc002gnp.1_Silent_p.P390P|MYOCD_uc002gnq.1_Silent_p.P205P	NM_153604	NP_705832	Q8IZQ8	MYCD_HUMAN	myocardin	486	Ser-rich.				cardiac cell differentiation|positive regulation of gene-specific transcription from RNA polymerase II promoter|positive regulation of smooth muscle contraction|regulation of smooth muscle cell differentiation|transcription, DNA-dependent	nucleus	nucleic acid binding|transcription factor binding			central_nervous_system(2)|ovary(1)	3														0.537037	84.574286	84.63866	29	25	GG		KEEP	---	---	---	---	capture		UCEC - Uterine corpus endometrioid carcinoma (92;0.0969)	Silent	SNP	12596788	12596788	10482	17	G	A	A	40	40	MYOCD	A	1	1
MYBBP1A	10514	broad.mit.edu	36	17	4395891	4395891	+	Missense_Mutation	SNP	G	C	C			TCGA-16-0846-01	TCGA-16-0846-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr17:4395891G>C	uc002fxz.2	-	c.1920C>G	c.(1918-1920)ATC>ATG	p.I640M	MYBBP1A_uc002fyb.2_Missense_Mutation_p.I640M	NM_001105538	NP_001099008	Q9BQG0	MBB1A_HUMAN	MYB binding protein 1a isoform 1	640					nucleocytoplasmic transport|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|NLS-dependent protein nuclear import complex|nucleolus	DNA binding|DNA-directed DNA polymerase activity|transcription factor binding			ovary(1)|skin(1)	2														0.666667	49.357501	49.874991	14	7	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	4395891	4395891	10403	17	G	C	C	37	37	MYBBP1A	C	3	3
TP53	7157	broad.mit.edu	36	17	7519120	7519120	+	Missense_Mutation	SNP	G	A	A			TCGA-16-0846-01	TCGA-16-0846-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr17:7519120G>A	uc002gim.2	-	c.535C>T	c.(535-537)CAT>TAT	p.H179Y	TP53_uc002gig.1_Missense_Mutation_p.H179Y|TP53_uc002gih.1_Missense_Mutation_p.H179Y|TP53_uc010cne.1_5'Flank|TP53_uc010cnf.1_Missense_Mutation_p.H47Y|TP53_uc010cng.1_Missense_Mutation_p.H47Y|TP53_uc002gii.1_Missense_Mutation_p.H47Y|TP53_uc010cnh.1_Missense_Mutation_p.H179Y|TP53_uc010cni.1_Missense_Mutation_p.H179Y|TP53_uc002gij.2_Missense_Mutation_p.H179Y|TP53_uc010cnj.1_Non-coding_Transcript|TP53_uc002gin.2_Missense_Mutation_p.H86Y|TP53_uc002gio.2_Missense_Mutation_p.H47Y	NM_001126112	NP_001119584	P04637	P53_HUMAN	tumor protein p53 isoform a	179	Required for interaction with FBXO42.||Interaction with HIPK1 (By similarity).|Interaction with AXIN1 (By similarity).	Zinc.	H -> Q (in sporadic cancers; somatic mutation).|H -> N (in sporadic cancers; somatic mutation).|H -> R (in sporadic cancers; somatic mutation).|HH -> QS (in a sporadic cancer; somatic mutation).|H -> L (in sporadic cancers; somatic mutation).|H -> D (in sporadic cancers; somatic mutation).|H -> P (in sporadic cancers; somatic mutation).|H -> Y (in LFS; germline mutation and 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.H179Y(72)|p.H179N(13)|p.H179D(10)|p.P177_C182delPHHERC(7)|p.0?(6)|p.C176_R181delCPHHER(3)|p.R175_E180delRCPHHE(3)|p.P177fs*3(2)|p.V173fs*59(2)|p.R174fs*1(2)|p.H179fs*68(1)|p.C176fs*65(1)|p.C176fs*68(1)|p.P177_H179delPHH(1)|p.V173fs*23(1)|p.V172_E180delVVRRCPHHE(1)|p.R174_H179delRRCPHH(1)|p.E171fs*1(1)|p.H179del(1)|p.E171_H179delEVVRRCPHH(1)|p.R174_E180>K(1)|p.P177_E180delPHHE(1)|p.H179R(1)|p.R174fs*3(1)|p.H178_H179>QY(1)|p.E171fs*61(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	p.R174fs(THP1-Tumor)|p.H179D(FUOV1-Tumor)	690	TCGA GBM(1;<1E-8)|TSP Lung(2;<1E-8)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)			0.567164	112.958979	113.223837	38	29	GG		KEEP	---	---	---	---	capture		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Missense_Mutation	SNP	7519120	7519120	16923	17	G	A	A	47	47	TP53	A	2	2
SERPINB11	89778	broad.mit.edu	36	18	59528503	59528503	+	Silent	SNP	G	A	A			TCGA-16-0846-01	TCGA-16-0846-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr18:59528503G>A	uc002ljk.2	+	c.96G>A	c.(94-96)TCG>TCA	p.S32S	SERPINB11_uc010dqd.1_5'UTR|SERPINB11_uc002ljj.2_5'UTR|SERPINB11_uc010dqe.1_5'UTR|SERPINB11_uc010dqf.1_Silent_p.S32S	NM_080475	NP_536723	Q96P15	SPB11_HUMAN	serpin peptidase inhibitor, clade B, member 11	32					regulation of proteolysis	cytoplasm	serine-type endopeptidase inhibitor activity			breast(1)	1		Esophageal squamous(42;0.129)				Ovarian(27;496 784 5942 8975 23930)								0.175439	19.217916	24.878376	10	47	GG		KEEP	---	---	---	---	capture			Silent	SNP	59528503	59528503	14586	18	G	A	A	38	38	SERPINB11	A	1	1
LRRC30	339291	broad.mit.edu	36	18	7221554	7221554	+	Nonsense_Mutation	SNP	C	T	T			TCGA-16-0846-01	TCGA-16-0846-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr18:7221554C>T	uc010dku.1	+	c.418C>T	c.(418-420)CGA>TGA	p.R140*		NM_001105581	NP_001099051	A6NM36	LRC30_HUMAN	leucine rich repeat containing 30	140										ovary(1)|liver(1)	2														0.263889	50.622379	54.232417	19	53	CC		KEEP	---	---	---	---	capture			Nonsense_Mutation	SNP	7221554	7221554	9360	18	C	T	T	23	23	LRRC30	T	5	1
SALL3	27164	broad.mit.edu	36	18	74854181	74854181	+	Missense_Mutation	SNP	C	T	T			TCGA-16-0846-01	TCGA-16-0846-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr18:74854181C>T	uc002lmt.1	+	c.1202C>T	c.(1201-1203)CCG>CTG	p.P401L	SALL3_uc010dra.1_Missense_Mutation_p.P8L	NM_171999	NP_741996	Q9BXA9	SALL3_HUMAN	sal-like 3	401					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			large_intestine(1)|ovary(1)|central_nervous_system(1)	3		Esophageal squamous(42;0.129)|Melanoma(33;0.16)|Prostate(75;0.167)												0.5	33.423927	33.423927	11	11	CC		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(15;4.69e-06)|BRCA - Breast invasive adenocarcinoma(31;0.0256)	Missense_Mutation	SNP	74854181	74854181	14292	18	C	T	T	23	23	SALL3	T	1	1
ILF3	3609	broad.mit.edu	36	19	10655068	10655068	+	Silent	SNP	A	G	G			TCGA-16-0846-01	TCGA-16-0846-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr19:10655068A>G	uc002mpo.1	+	c.1713A>G	c.(1711-1713)CAA>CAG	p.Q571Q	ILF3_uc002mpk.1_Silent_p.Q567Q|ILF3_uc002mpl.1_Silent_p.Q567Q|ILF3_uc002mpm.1_Silent_p.Q571Q|ILF3_uc002mpn.1_Silent_p.Q567Q|ILF3_uc002mpp.2_Silent_p.Q392Q|ILF3_uc002mpq.1_5'Flank	NM_012218	NP_036350	Q12906	ILF3_HUMAN	interleukin enhancer binding factor 3 isoform a	567	DRBM 2.				M phase|negative regulation of transcription, DNA-dependent|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	mitochondrion|nucleolus|ribonucleoprotein complex	DNA binding|double-stranded RNA binding|protein binding|protein binding|transcription activator activity|transcription repressor activity			ovary(3)	3														0.409091	114.584288	115.219369	36	52	AA		KEEP	---	---	---	---	capture	Epithelial(33;6.86e-06)|all cancers(31;1.65e-05)		Silent	SNP	10655068	10655068	8013	19	A	G	G	3	3	ILF3	G	4	4
CACNA1A	773	broad.mit.edu	36	19	13270825	13270825	+	Silent	SNP	C	G	G			TCGA-16-0846-01	TCGA-16-0846-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr19:13270825C>G	uc010dzd.1	-	c.2634G>C	c.(2632-2634)TCG>TCC	p.S878S	CACNA1A_uc010dzc.1_Silent_p.S400S|CACNA1A_uc002mwz.2_Silent_p.S878S|CACNA1A_uc002mwy.2_Silent_p.S874S|CACNA1A_uc010dze.1_Silent_p.S875S	NM_023035	NP_075461	O00555	CAC1A_HUMAN	Voltage-dependent P/Q-type calcium channel subunit alpha-1A (Voltage- gated calcium channel subunit alpha Cav2.1) (Calcium channel, L type, alpha-1 polypeptide isoform 4) (Brain calcium channel I) (BI).	875	Cytoplasmic (Potential).				cell death|elevation of cytosolic calcium ion concentration|energy reserve metabolic process|membrane depolarization|regulation of insulin secretion	cytoplasm|nucleus	syntaxin binding			large_intestine(2)	2					Bepridil(DB01244)|Cinnarizine(DB00568)|Loperamide(DB00836)|Nisoldipine(DB00401)|Pregabalin(DB00230)									0.25	7.086578	8.001304	4	12	CC		KEEP	---	---	---	---	capture	OV - Ovarian serous cystadenocarcinoma(19;5.07e-21)		Silent	SNP	13270825	13270825	2654	19	C	G	G	23	23	CACNA1A	G	3	3
OR10H5	284433	broad.mit.edu	36	19	15766136	15766136	+	Missense_Mutation	SNP	C	T	T			TCGA-16-0846-01	TCGA-16-0846-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr19:15766136C>T	uc002nbp.1	+	c.278C>T	c.(277-279)GCC>GTC	p.A93V		NM_001004466	NP_001004466	Q8NGA6	O10H5_HUMAN	olfactory receptor, family 10, subfamily H,	93	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)	1														0.201342	59.471452	71.824902	30	119	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	15766136	15766136	11315	19	C	T	T	26	26	OR10H5	T	2	2
MYO9B	4650	broad.mit.edu	36	19	17173748	17173748	+	Missense_Mutation	SNP	G	A	A			TCGA-16-0846-01	TCGA-16-0846-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr19:17173748G>A	uc010eak.1	+	c.4577G>A	c.(4576-4578)CGT>CAT	p.R1526H	MYO9B_uc002nfi.1_Missense_Mutation_p.R1526H|MYO9B_uc002nfj.1_Missense_Mutation_p.R1526H|MYO9B_uc002nfk.1_Missense_Mutation_p.R1526H|MYO9B_uc002nfl.1_Missense_Mutation_p.R75H	NM_004145	NP_004136	Q13459	MYO9B_HUMAN	myosin IXB isoform 1	1526	Tail.				actin filament-based movement|Rho protein signal transduction	cell cortex|cytosol|filamentous actin|myosin complex|perinuclear region of cytoplasm	actin binding|ADP binding|ATP binding|ATPase activity|calmodulin binding|metal ion binding|microfilament motor activity|Rho GTPase activator activity			breast(1)	1														0.173913	7.890408	10.195239	4	19	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	17173748	17173748	10480	19	G	A	A	40	40	MYO9B	A	1	1
PIK3R2	5296	broad.mit.edu	36	19	18141016	18141016	+	Missense_Mutation	SNP	C	T	T			TCGA-16-0846-01	TCGA-16-0846-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr19:18141016C>T	uc002nia.1	+	c.2099C>T	c.(2098-2100)TCG>TTG	p.S700L	PIK3R2_uc002nib.1_Non-coding_Transcript|PIK3R2_uc010ebi.1_Non-coding_Transcript	NM_005027	NP_005018	O00459	P85B_HUMAN	phosphoinositide-3-kinase, regulatory subunit 2	700	SH2 2.				fibroblast growth factor receptor signaling pathway|insulin receptor signaling pathway|leukocyte migration|negative regulation of anti-apoptosis|nerve growth factor receptor signaling pathway|phosphatidylinositol-mediated signaling|platelet activation|regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction|T cell costimulation|T cell receptor signaling pathway	phosphatidylinositol 3-kinase complex	GTPase activator activity|phosphatidylinositol 3-kinase regulator activity|protein binding			lung(2)|central_nervous_system(1)|pancreas(1)	4										186				0.381818	59.465482	60.137748	21	34	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	18141016	18141016	12343	19	C	T	T	31	31	PIK3R2	T	1	1
ADAT3	113179	broad.mit.edu	36	19	1863807	1863807	+	Missense_Mutation	SNP	G	T	T			TCGA-16-0846-01	TCGA-16-0846-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr19:1863807G>T	uc002luh.1	+	c.713G>T	c.(712-714)CGC>CTC	p.R238L	SCAMP4_uc002lui.1_Intron|SCAMP4_uc002luj.1_Intron|SCAMP4_uc002luk.1_Intron|SCAMP4_uc010dss.1_Intron|ADAT3_uc010dst.1_Missense_Mutation_p.R238L	NM_138422	NP_612431	Q96EY9	ADAT3_HUMAN	tRNA-specific adenosine deaminase 3	238					tRNA processing		hydrolase activity|zinc ion binding			breast(1)	1		Ovarian(11;2.11e-07)|Hepatocellular(1079;0.137)												0.307692	22.497237	23.350515	8	18	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	1863807	1863807	287	19	G	T	T	38	38	ADAT3	T	3	3
SLC7A10	56301	broad.mit.edu	36	19	38398537	38398537	+	Missense_Mutation	SNP	C	T	T			TCGA-16-0846-01	TCGA-16-0846-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr19:38398537C>T	uc002num.1	-	c.334G>A	c.(334-336)GAG>AAG	p.E112K	SLC7A10_uc010edi.1_Intron	NM_019849	NP_062823	Q9NS82	AAA1_HUMAN	solute carrier family 7, member 10	112			E -> D (in a family with cystinuria).		blood coagulation|cellular nitrogen compound metabolic process|ion transport|leukocyte migration	integral to plasma membrane	L-serine transmembrane transporter activity			ovary(1)|central_nervous_system(1)	2	Esophageal squamous(110;0.137)													0.333333	8.121699	8.343255	3	6	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	38398537	38398537	15190	19	C	T	T	32	32	SLC7A10	T	2	2
VANGL1	81839	broad.mit.edu	36	1	116028153	116028153	+	Missense_Mutation	SNP	T	A	A			TCGA-16-0846-01	TCGA-16-0846-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr1:116028153T>A	uc001efv.1	+	c.1012T>A	c.(1012-1014)TCA>ACA	p.S338T	VANGL1_uc009wgy.1_Missense_Mutation_p.S336T	NM_138959	NP_620409	Q8TAA9	VANG1_HUMAN	vang-like 1	338	Cytoplasmic (Potential).				multicellular organismal development	integral to membrane	protein binding			central_nervous_system(1)	1	Lung SC(450;0.211)	all_cancers(81;1.24e-06)|all_epithelial(167;1.02e-06)|all_lung(203;7.95e-06)|Lung NSC(69;4.97e-05)												0.142857	6.999509	11.262745	5	30	TT		KEEP	---	---	---	---	capture		Lung(183;0.0171)|Colorectal(144;0.0686)|LUSC - Lung squamous cell carcinoma(189;0.0903)|all cancers(265;0.108)|COAD - Colon adenocarcinoma(174;0.111)|Epithelial(280;0.12)	Missense_Mutation	SNP	116028153	116028153	17684	1	T	A	A	54	54	VANGL1	A	4	4
YY1AP1	55249	broad.mit.edu	36	1	153896595	153896595	+	Missense_Mutation	SNP	A	T	T			TCGA-16-0846-01	TCGA-16-0846-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr1:153896595A>T	uc001flh.1	-	c.2084T>A	c.(2083-2085)GTC>GAC	p.V695D	YY1AP1_uc001flg.1_Missense_Mutation_p.V362D|YY1AP1_uc009wqt.1_Missense_Mutation_p.V546D|YY1AP1_uc009wqu.1_Missense_Mutation_p.V410D|YY1AP1_uc001fll.1_Missense_Mutation_p.V577D|YY1AP1_uc009wqv.1_Missense_Mutation_p.V294D|YY1AP1_uc001flm.1_Missense_Mutation_p.V566D|YY1AP1_uc001fli.1_Missense_Mutation_p.V577D|YY1AP1_uc009wqw.1_Missense_Mutation_p.V546D|YY1AP1_uc001flj.1_Missense_Mutation_p.V557D|YY1AP1_uc001flk.1_Missense_Mutation_p.V566D|YY1AP1_uc001flo.1_Missense_Mutation_p.V511D|YY1AP1_uc001flp.1_Missense_Mutation_p.V577D|YY1AP1_uc001fln.1_Missense_Mutation_p.V623D	NM_139118	NP_620829	Q9H869	YYAP1_HUMAN	YY1-associated protein isoform 2	623					regulation of cell cycle|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	protein binding			ovary(2)	2	Hepatocellular(266;0.0997)|all_hematologic(923;0.145)													0.36	70.501306	71.796508	27	48	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	153896595	153896595	18091	1	A	T	T	10	10	YY1AP1	T	4	4
OLFML2B	25903	broad.mit.edu	36	1	160253921	160253921	+	Missense_Mutation	SNP	G	A	A			TCGA-16-0846-01	TCGA-16-0846-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:160253921G>A	uc001gbu.1	-	c.439C>T	c.(439-441)CTC>TTC	p.L147F		NM_015441	NP_056256	Q68BL8	OLM2B_HUMAN	olfactomedin-like 2B	147											0	all_hematologic(112;0.156)													0.319588	81.112295	83.906578	31	66	GG		KEEP	---	---	---	---	capture	BRCA - Breast invasive adenocarcinoma(70;0.0172)		Missense_Mutation	SNP	160253921	160253921	11263	1	G	A	A	34	34	OLFML2B	A	2	2
SERINC2	347735	broad.mit.edu	36	1	31678447	31678447	+	Missense_Mutation	SNP	G	A	A			TCGA-16-0846-01	TCGA-16-0846-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:31678447G>A	uc001bst.1	+	c.1060G>A	c.(1060-1062)GAG>AAG	p.E354K	SERINC2_uc001bsu.1_Missense_Mutation_p.E299K|SERINC2_uc001bsv.1_Missense_Mutation_p.E299K	NM_178865	NP_849196	Q96SA4	SERC2_HUMAN	tumor differentially expressed 2-like	354						integral to membrane					0		Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0308)|all_neural(195;0.0629)|Breast(348;0.0707)|Medulloblastoma(700;0.123)												0.432432	44.992569	45.139931	16	21	GG		KEEP	---	---	---	---	capture		STAD - Stomach adenocarcinoma(196;0.0541)|READ - Rectum adenocarcinoma(331;0.151)	Missense_Mutation	SNP	31678447	31678447	14568	1	G	A	A	37	37	SERINC2	A	1	1
MFSD2A	84879	broad.mit.edu	36	1	40205120	40205120	+	Missense_Mutation	SNP	C	T	T			TCGA-16-0846-01	TCGA-16-0846-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr1:40205120C>T	uc001cev.1	+	c.895C>T	c.(895-897)CGG>TGG	p.R299W	MFSD2A_uc001ceu.1_Missense_Mutation_p.R286W|MFSD2A_uc009vvy.1_Non-coding_Transcript|MFSD2A_uc001cex.1_5'Flank	NM_032793	NP_116182	Q8NA29	MFS2A_HUMAN	major facilitator superfamily domain containing	299					transmembrane transport	endoplasmic reticulum membrane|integral to membrane				ovary(1)|pancreas(1)	2										141				0.255	122.741821	133.627094	51	149	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	40205120	40205120	9920	1	C	T	T	19	19	MFSD2A	T	1	1
FAM151A	338094	broad.mit.edu	36	1	54850956	54850956	+	Silent	SNP	G	T	T			TCGA-16-0846-01	TCGA-16-0846-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:54850956G>T	uc001cxn.1	-	c.591C>A	c.(589-591)GTC>GTA	p.V197V	ACOT11_uc001cxm.1_Intron	NM_176782	NP_788954	Q8WW52	F151A_HUMAN	hypothetical protein LOC338094	197						integral to membrane					0														0.4	107.27113	108.147841	40	60	GG		KEEP	---	---	---	---	capture			Silent	SNP	54850956	54850956	5656	1	G	T	T	41	41	FAM151A	T	3	3
TM2D1	83941	broad.mit.edu	36	1	61963293	61963293	+	Missense_Mutation	SNP	T	A	A			TCGA-16-0846-01	TCGA-16-0846-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr1:61963293T>A	uc001czz.1	-	c.88A>T	c.(88-90)ACA>TCA	p.T30S		NM_032027	NP_114416	Q9BX74	TM2D1_HUMAN	beta-amyloid binding protein precursor	30					apoptosis					ovary(1)	1														0.307692	61.77535	64.344514	24	54	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	61963293	61963293	16493	1	T	A	A	57	57	TM2D1	A	4	4
SEL1L2	80343	broad.mit.edu	36	20	13778942	13778942	+	Missense_Mutation	SNP	C	A	A			TCGA-16-0846-01	TCGA-16-0846-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr20:13778942C>A	uc010gcf.1	-	c.1842G>T	c.(1840-1842)TTG>TTT	p.L614F	SEL1L2_uc002woq.2_Missense_Mutation_p.L475F|SEL1L2_uc002wor.1_Non-coding_Transcript	NM_025229	NP_079505	Q5TEA6	SE1L2_HUMAN	sel-1 suppressor of lin-12-like 2	614	Extracellular (Potential).|Sel1-like 11.					integral to membrane	binding			ovary(1)	1														0.109756	8.310506	20.678895	9	73	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	13778942	13778942	14497	20	C	A	A	17	17	SEL1L2	A	3	3
KCNB1	3745	broad.mit.edu	36	20	47532251	47532251	+	Silent	SNP	G	C	C			TCGA-16-0846-01	TCGA-16-0846-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr20:47532251G>C	uc002xur.1	-	c.174C>G	c.(172-174)GGC>GGG	p.G58G	KCNB1_uc002xus.1_Silent_p.G58G	NM_004975	NP_004966	Q14721	KCNB1_HUMAN	potassium voltage-gated channel, Shab-related	58	Cytoplasmic (Potential).				energy reserve metabolic process|regulation of insulin secretion	voltage-gated potassium channel complex	protein binding|voltage-gated potassium channel activity			pancreas(1)	1														0.235294	6.993635	8.08288	4	13	GG		KEEP	---	---	---	---	capture	BRCA - Breast invasive adenocarcinoma(12;0.000405)|COAD - Colon adenocarcinoma(4;0.14)|Colorectal(8;0.166)		Silent	SNP	47532251	47532251	8317	20	G	C	C	46	46	KCNB1	C	3	3
ZBP1	81030	broad.mit.edu	36	20	55623995	55623995	+	Missense_Mutation	SNP	G	A	A			TCGA-16-0846-01	TCGA-16-0846-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr20:55623995G>A	uc002xyo.1	-	c.307C>T	c.(307-309)CCT>TCT	p.P103S	ZBP1_uc010gjm.1_Missense_Mutation_p.P103S|ZBP1_uc002xyp.1_Missense_Mutation_p.P28S	NM_030776	NP_110403	Q9H171	ZBP1_HUMAN	Z-DNA binding protein 1	103	DRADA 2.						double-stranded RNA adenosine deaminase activity|left-handed Z-DNA binding|RNA binding			ovary(2)	2	Lung NSC(12;0.000545)|all_lung(29;0.00195)|Melanoma(10;0.242)													0.307692	88.806141	92.210301	32	72	GG		KEEP	---	---	---	---	capture	BRCA - Breast invasive adenocarcinoma(13;7.87e-13)|Epithelial(14;3.26e-09)|all cancers(14;3.62e-08)		Missense_Mutation	SNP	55623995	55623995	18107	20	G	A	A	43	43	ZBP1	A	2	2
SRMS	6725	broad.mit.edu	36	20	61643387	61643387	+	Missense_Mutation	SNP	G	A	A			TCGA-16-0846-01	TCGA-16-0846-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr20:61643387G>A	uc002yfi.1	-	c.977C>T	c.(976-978)CCA>CTA	p.P326L		NM_080823	NP_543013	Q9H3Y6	SRMS_HUMAN	src-related kinase lacking C-terminal regulatory	326	Protein kinase.				protein phosphorylation		ATP binding|non-membrane spanning protein tyrosine kinase activity			lung(1)	1	all_cancers(38;2.51e-11)|all_epithelial(29;8.27e-13)									557				0.294118	11.663558	12.311751	5	12	GG		KEEP	---	---	---	---	capture	Epithelial(9;9.69e-09)|all cancers(9;5.84e-08)|BRCA - Breast invasive adenocarcinoma(10;3.63e-06)		Missense_Mutation	SNP	61643387	61643387	15666	20	G	A	A	47	47	SRMS	A	2	2
DNMT3L	29947	broad.mit.edu	36	21	44493352	44493352	+	Missense_Mutation	SNP	A	G	G			TCGA-16-0846-01	TCGA-16-0846-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr21:44493352A>G	uc002zeh.1	-	c.980T>C	c.(979-981)ATC>ACC	p.I327T	DNMT3L_uc002zeg.1_Missense_Mutation_p.I327T	NM_013369	NP_037501	Q9UJW3	DNM3L_HUMAN	cytosine-5-methyltransferase 3-like protein	327					DNA methylation|regulation of gene expression by genetic imprinting|spermatogenesis	cytosol	enzyme activator activity|enzyme binding|transcription repressor activity|zinc ion binding				0														0.4	9.69631	9.784153	4	6	AA		KEEP	---	---	---	---	capture		Colorectal(79;0.0165)|READ - Rectum adenocarcinoma(84;0.0781)	Missense_Mutation	SNP	44493352	44493352	4861	21	A	G	G	12	12	DNMT3L	G	4	4
C1QTNF6	114904	broad.mit.edu	36	22	35908252	35908252	+	Silent	SNP	G	A	A			TCGA-16-0846-01	TCGA-16-0846-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr22:35908252G>A	uc003aqx.1	-	c.759C>T	c.(757-759)CGC>CGT	p.R253R	C1QTNF6_uc003aqy.1_Silent_p.R253R|C1QTNF6_uc003aqz.1_Non-coding_Transcript|C1QTNF6_uc003aqw.1_Silent_p.R234R	NM_182486	NP_872292	Q9BXI9	C1QT6_HUMAN	C1q and tumor necrosis factor related protein 6	234	C1q.					collagen					0														0.438596	66.590302	66.771741	25	32	GG		KEEP	---	---	---	---	capture			Silent	SNP	35908252	35908252	2034	22	G	A	A	38	38	C1QTNF6	A	1	1
SH3BP1	23616	broad.mit.edu	36	22	36376168	36376168	+	Silent	SNP	G	A	A			TCGA-16-0846-01	TCGA-16-0846-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr22:36376168G>A	uc003ati.1	+	c.1380G>A	c.(1378-1380)GCG>GCA	p.A460A	SH3BP1_uc003atg.1_Non-coding_Transcript|SH3BP1_uc003ath.1_Silent_p.A460A|SH3BP1_uc003atj.1_Silent_p.A396A|SH3BP1_uc003atk.1_Silent_p.A374A	NM_018957	NP_061830	Q9Y3L3	3BP1_HUMAN	SH3-domain binding protein 1	460	Rho-GAP.				signal transduction	cytoplasm	GTPase activator activity|SH3 domain binding			central_nervous_system(1)	1	Melanoma(58;0.0574)													0.351852	49.408356	50.453799	19	35	GG		KEEP	---	---	---	---	capture			Silent	SNP	36376168	36376168	14735	22	G	A	A	38	38	SH3BP1	A	1	1
SMC1B	27127	broad.mit.edu	36	22	44133332	44133332	+	Missense_Mutation	SNP	G	A	A			TCGA-16-0846-01	TCGA-16-0846-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr22:44133332G>A	uc003bgc.1	-	c.2870C>T	c.(2869-2871)ACT>ATT	p.T957I	SMC1B_uc003bgd.1_Missense_Mutation_p.T957I	NM_148674	NP_683515	Q8NDV3	SMC1B_HUMAN	SMC1 structural maintenance of chromosomes	957					chromosome organization|meiosis	chromosome, centromeric region|cytoplasm|meiotic cohesin complex|nucleus	ATP binding			ovary(2)	2		Ovarian(80;0.00965)|all_neural(38;0.0416)												0.377049	128.715891	130.335928	46	76	GG		KEEP	---	---	---	---	capture		UCEC - Uterine corpus endometrioid carcinoma (28;0.0182)	Missense_Mutation	SNP	44133332	44133332	15280	22	G	A	A	36	36	SMC1B	A	2	2
MYO7B	4648	broad.mit.edu	36	2	128086608	128086608	+	Missense_Mutation	SNP	C	T	T			TCGA-16-0846-01	TCGA-16-0846-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr2:128086608C>T	uc002top.1	+	c.3280C>T	c.(3280-3282)CAC>TAC	p.H1094Y		NM_001080527	NP_001073996	Q6PIF6	MYO7B_HUMAN	myosin VIIB	1094	MyTH4 1.					apical plasma membrane|myosin complex	actin binding|ATP binding|motor activity			ovary(1)|pancreas(1)	2	Colorectal(110;0.1)													0.2	9.761076	11.854015	5	20	CC		KEEP	---	---	---	---	capture		BRCA - Breast invasive adenocarcinoma(221;0.0753)	Missense_Mutation	SNP	128086608	128086608	10478	2	C	T	T	25	25	MYO7B	T	2	2
SCN9A	6335	broad.mit.edu	36	2	166764492	166764492	+	Missense_Mutation	SNP	A	T	T			TCGA-16-0846-01	TCGA-16-0846-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr2:166764492A>T	uc002udq.2	-	c.4870T>A	c.(4870-4872)TTT>ATT	p.F1624I		NM_002977	NP_002968	Q15858	SCN9A_HUMAN	sodium channel, voltage-gated, type IX, alpha	1635	IV.					voltage-gated sodium channel complex	voltage-gated sodium channel activity			ovary(6)|central_nervous_system(5)	11					Lamotrigine(DB00555)|Lidocaine(DB00281)									0.524229	355.317538	355.432593	119	108	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	166764492	166764492	14407	2	A	T	T	3	3	SCN9A	T	4	4
HOXD4	3233	broad.mit.edu	36	2	176725588	176725588	+	Missense_Mutation	SNP	C	T	T			TCGA-16-0846-01	TCGA-16-0846-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr2:176725588C>T	uc002uks.1	+	c.440C>T	c.(439-441)CCC>CTC	p.P147L		NM_014621	NP_055436	P09016	HXD4_HUMAN	homeobox D4	147					regulation of transcription, DNA-dependent	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription regulator activity			pancreas(1)	1														0.232877	42.838862	47.606683	17	56	CC		KEEP	---	---	---	---	capture	OV - Ovarian serous cystadenocarcinoma(117;0.00765)|Epithelial(96;0.105)	Colorectal(32;0.0224)|READ - Rectum adenocarcinoma(9;0.0556)	Missense_Mutation	SNP	176725588	176725588	7616	2	C	T	T	22	22	HOXD4	T	2	2
COL3A1	1281	broad.mit.edu	36	2	189567048	189567048	+	Missense_Mutation	SNP	G	A	A			TCGA-16-0846-01	TCGA-16-0846-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr2:189567048G>A	uc002uqj.1	+	c.1189G>A	c.(1189-1191)GAA>AAA	p.E397K	COL3A1_uc010frw.1_Non-coding_Transcript	NM_000090	NP_000081	P02461	CO3A1_HUMAN	collagen type III alpha 1 preproprotein	397	Triple-helical region.				axon guidance|cell-matrix adhesion|collagen biosynthetic process|collagen fibril organization|fibril organization|heart development|integrin-mediated signaling pathway|negative regulation of immune response|peptide cross-linking|platelet activation|response to cytokine stimulus|response to radiation|skin development|transforming growth factor beta receptor signaling pathway	collagen type III|extracellular space	extracellular matrix structural constituent|integrin binding|platelet-derived growth factor binding			central_nervous_system(7)|ovary(4)|large_intestine(2)	13					Collagenase(DB00048)|Palifermin(DB00039)					1079				0.506173	125.257194	125.259669	41	40	GG		KEEP	---	---	---	---	capture	OV - Ovarian serous cystadenocarcinoma(117;0.0106)|Epithelial(96;0.141)		Missense_Mutation	SNP	189567048	189567048	3826	2	G	A	A	37	37	COL3A1	A	1	1
APOB	338	broad.mit.edu	36	2	21103333	21103333	+	Missense_Mutation	SNP	C	A	A			TCGA-16-0846-01	TCGA-16-0846-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr2:21103333C>A	uc002red.1	-	c.2076G>T	c.(2074-2076)TTG>TTT	p.L692F		NM_000384	NP_000375	P04114	APOB_HUMAN	apolipoprotein B precursor	692					cholesterol homeostasis|cholesterol metabolic process|leukocyte migration|low-density lipoprotein particle clearance|low-density lipoprotein particle remodeling|platelet activation|positive regulation of cholesterol storage|positive regulation of macrophage derived foam cell differentiation|receptor-mediated endocytosis|response to virus|very-low-density lipoprotein particle assembly	chylomicron remnant|clathrin-coated endocytic vesicle membrane|endoplasmic reticulum lumen|endoplasmic reticulum membrane|endosome lumen|endosome membrane|intermediate-density lipoprotein particle|low-density lipoprotein particle|mature chylomicron|microsome|plasma membrane|very-low-density lipoprotein particle	cholesterol transporter activity|enzyme binding|heparin binding|low-density lipoprotein particle receptor binding|phospholipid binding|protein heterodimerization activity			ovary(11)|central_nervous_system(3)|large_intestine(2)|pancreas(1)|skin(1)	18	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)				Atorvastatin(DB01076)									0.196078	10.289919	14.738055	10	41	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	21103333	21103333	796	2	C	A	A	21	21	APOB	A	3	3
GRM7	2917	broad.mit.edu	36	3	6878256	6878256	+	Missense_Mutation	SNP	G	T	T			TCGA-16-0846-01	TCGA-16-0846-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr3:6878256G>T	uc003bql.1	+	c.181G>T	c.(181-183)GGT>TGT	p.G61C	GRM7_uc010hcf.1_Non-coding_Transcript|GRM7_uc010hcg.1_Missense_Mutation_p.G61C|GRM7_uc003bqm.1_Missense_Mutation_p.G61C	NM_181874	NP_870989	Q14831	GRM7_HUMAN	glutamate receptor, metabotropic 7 isoform b	61	Extracellular (Potential).				negative regulation of adenylate cyclase activity|negative regulation of cAMP biosynthetic process|negative regulation of glutamate secretion|sensory perception of smell|sensory perception of sound|synaptic transmission	asymmetric synapse|axon|cell cortex|dendritic shaft|integral to plasma membrane|postsynaptic membrane|presynaptic active zone	adenylate cyclase inhibitor activity|calcium ion binding|glutamate binding|group III metabotropic glutamate receptor activity|PDZ domain binding|serine binding			ovary(4)	4					L-Glutamic Acid(DB00142)									0.3	22.566133	23.636743	9	21	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	6878256	6878256	7081	3	G	T	T	43	43	GRM7	T	3	3
GALNT7	51809	broad.mit.edu	36	4	174455901	174455901	+	Silent	SNP	C	T	T			TCGA-16-0846-01	TCGA-16-0846-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr4:174455901C>T	uc003isz.2	+	c.1026C>T	c.(1024-1026)CCC>CCT	p.P342P		NM_017423	NP_059119	Q86SF2	GALT7_HUMAN	polypeptide N-acetylgalactosaminyltransferase 7	342	Lumenal (Potential).				protein O-linked glycosylation	Golgi membrane|integral to membrane	polypeptide N-acetylgalactosaminyltransferase activity|sugar binding			central_nervous_system(1)	1		Prostate(90;0.0132)|Renal(120;0.0183)|Melanoma(52;0.0749)|all_hematologic(60;0.107)|all_neural(102;0.122)												0.525773	160.424506	160.480228	51	46	CC		KEEP	---	---	---	---	capture		all cancers(43;1.87e-18)|Epithelial(43;3.44e-17)|OV - Ovarian serous cystadenocarcinoma(60;2.48e-09)|STAD - Stomach adenocarcinoma(60;0.0019)|GBM - Glioblastoma multiforme(59;0.0119)|LUSC - Lung squamous cell carcinoma(193;0.0199)	Silent	SNP	174455901	174455901	6482	4	C	T	T	22	22	GALNT7	T	2	2
GUF1	60558	broad.mit.edu	36	4	44375448	44375448	+	Missense_Mutation	SNP	C	G	G			TCGA-16-0846-01	TCGA-16-0846-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr4:44375448C>G	uc003gww.2	+	c.52C>G	c.(52-54)CGA>GGA	p.R18G	GUF1_uc010ifz.1_Non-coding_Transcript	NM_021927	NP_068746	Q8N442	GUF1_HUMAN	GUF1 GTPase homolog	18					translation	mitochondrial inner membrane	GTP binding|GTPase activity				0														0.222222	8.994145	10.269452	4	14	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	44375448	44375448	7179	4	C	G	G	19	19	GUF1	G	3	3
SH3TC2	79628	broad.mit.edu	36	5	148407733	148407733	+	Missense_Mutation	SNP	G	C	C			TCGA-16-0846-01	TCGA-16-0846-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr5:148407733G>C	uc003lpu.1	-	c.164C>G	c.(163-165)TCC>TGC	p.S55C	SH3TC2_uc003lpp.1_Non-coding_Transcript|SH3TC2_uc003lpt.1_5'UTR|SH3TC2_uc010jgx.1_Missense_Mutation_p.S55C|SH3TC2_uc003lpv.1_5'UTR|SH3TC2_uc003lpw.1_Missense_Mutation_p.S55C	NM_024577	NP_078853	Q8TF17	S3TC2_HUMAN	SH3 domain and tetratricopeptide repeats 2	55							binding			ovary(2)	2														0.432836	298.203765	298.992907	87	114	GG		KEEP	---	---	---	---	capture	KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)		Missense_Mutation	SNP	148407733	148407733	14754	5	G	C	C	41	41	SH3TC2	C	3	3
C9	735	broad.mit.edu	36	5	39351849	39351849	+	Missense_Mutation	SNP	C	G	G			TCGA-16-0846-01	TCGA-16-0846-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr5:39351849C>G	uc003jlv.2	-	c.655G>C	c.(655-657)GAA>CAA	p.E219Q		NM_001737	NP_001728	P02748	CO9_HUMAN	complement component 9 precursor	219	MACPF.				complement activation, alternative pathway|complement activation, classical pathway|cytolysis|hemolysis by symbiont of host erythrocytes	extracellular region|membrane attack complex					0	all_lung(31;0.000197)	all_neural(839;7.57e-10)|Lung NSC(810;2.62e-08)|Ovarian(839;0.00384)|Breast(839;0.0184)|Myeloproliferative disorder(839;0.0511)												0.246753	52.492761	56.98353	19	58	CC		KEEP	---	---	---	---	capture	Epithelial(62;0.158)		Missense_Mutation	SNP	39351849	39351849	2556	5	C	G	G	32	32	C9	G	3	3
HEATR7B2	133558	broad.mit.edu	36	5	41097581	41097581	+	Missense_Mutation	SNP	G	T	T			TCGA-16-0846-01	TCGA-16-0846-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr5:41097581G>T	uc003jmj.2	-	c.463C>A	c.(463-465)CTT>ATT	p.L155I		NM_173489	NP_775760	Q7Z745	HTRB2_HUMAN	HEAT repeat family member 7B2	155							binding			ovary(6)|central_nervous_system(2)	8														0.416667	117.581539	118.163891	40	56	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	41097581	41097581	7318	5	G	T	T	35	35	HEATR7B2	T	3	3
POLR3G	10622	broad.mit.edu	36	5	89838209	89838209	+	Missense_Mutation	SNP	G	A	A			TCGA-16-0846-01	TCGA-16-0846-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr5:89838209G>A	uc003kjq.1	+	c.547G>A	c.(547-549)GCA>ACA	p.A183T		NM_006467	NP_006458	O15318	RPC7_HUMAN	polymerase (RNA) III (DNA directed) polypeptide	183	Glu-rich.				innate immune response|positive regulation of innate immune response|positive regulation of interferon-beta production|regulation of transcription from RNA polymerase III promoter|response to virus	DNA-directed RNA polymerase III complex	DNA-directed RNA polymerase activity				0		all_cancers(142;5.03e-09)|all_epithelial(76;1.23e-11)|Lung NSC(167;2.46e-05)|all_lung(232;3.25e-05)|Ovarian(174;0.00832)|Colorectal(57;0.122)|Breast(839;0.198)												0.402174	107.579377	108.341729	37	55	GG		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(54;2.74e-31)|Epithelial(54;8.2e-26)|all cancers(79;3.86e-22)	Missense_Mutation	SNP	89838209	89838209	12662	5	G	A	A	38	38	POLR3G	A	1	1
KIAA0319	9856	broad.mit.edu	36	6	24671607	24671607	+	Silent	SNP	C	T	T			TCGA-16-0846-01	TCGA-16-0846-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr6:24671607C>T	uc003neh.1	-	c.2550G>A	c.(2548-2550)TCG>TCA	p.S850S	KIAA0319_uc010jpt.1_Silent_p.S261S	NM_014809	NP_055624	Q5VV43	K0319_HUMAN	KIAA0319	850	Extracellular (Potential).				negative regulation of dendrite development|neuron migration	early endosome membrane|integral to membrane|plasma membrane	protein binding			ovary(1)	1														0.561644	123.662758	123.902966	41	32	CC		KEEP	---	---	---	---	capture			Silent	SNP	24671607	24671607	8475	6	C	T	T	23	23	KIAA0319	T	1	1
ZAN	7455	broad.mit.edu	36	7	100215097	100215097	+	Silent	SNP	G	A	A			TCGA-16-0846-01	TCGA-16-0846-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr7:100215097G>A	uc003uwj.1	+	c.6411G>A	c.(6409-6411)GCG>GCA	p.A2137A	ZAN_uc003uwk.1_Silent_p.A2137A|ZAN_uc003uwl.1_Non-coding_Transcript|ZAN_uc010lhh.1_Non-coding_Transcript|ZAN_uc010lhi.1_Non-coding_Transcript	NM_003386	NP_003377	Q9Y493	ZAN_HUMAN	zonadhesin isoform 3	2137	Extracellular (Potential).|VWFD 3.				binding of sperm to zona pellucida|cell-cell adhesion	integral to membrane|plasma membrane				ovary(4)|large_intestine(3)|central_nervous_system(2)|pancreas(2)	11	Lung NSC(181;0.041)|all_lung(186;0.0581)													0.342105	33.861089	34.699257	13	25	GG		KEEP	---	---	---	---	capture	STAD - Stomach adenocarcinoma(171;0.19)		Silent	SNP	100215097	100215097	18096	7	G	A	A	38	38	ZAN	A	1	1
MUC17	140453	broad.mit.edu	36	7	100461646	100461646	+	Missense_Mutation	SNP	G	A	A			TCGA-16-0846-01	TCGA-16-0846-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr7:100461646G>A	uc003uxp.1	+	c.229G>A	c.(229-231)GTG>ATG	p.V77M	MUC17_uc010lho.1_Non-coding_Transcript	NM_001040105	NP_001035194	Q685J3	MUC17_HUMAN	mucin 17	77	Extracellular (Potential).					extracellular region|integral to membrane|plasma membrane	extracellular matrix constituent, lubricant activity			ovary(14)|breast(3)|lung(2)	19	Lung NSC(181;0.136)|all_lung(186;0.182)													0.196581	48.760904	58.795253	23	94	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	100461646	100461646	10368	7	G	A	A	40	40	MUC17	A	1	1
RELN	5649	broad.mit.edu	36	7	102911416	102911416	+	Silent	SNP	G	A	A			TCGA-16-0846-01	TCGA-16-0846-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr7:102911416G>A	uc003vca.1	-	c.10101C>T	c.(10099-10101)AAC>AAT	p.N3367N	RELN_uc010liz.1_Silent_p.N3367N	NM_005045	NP_005036	P78509	RELN_HUMAN	reelin isoform a	3367	BNR 16.				axon guidance|cell adhesion|cerebral cortex tangential migration|glial cell differentiation|neuron migration|peptidyl-tyrosine phosphorylation|positive regulation of protein kinase activity|positive regulation of small GTPase mediated signal transduction|response to pain|spinal cord patterning	cytoplasm|dendrite|extracellular space|proteinaceous extracellular matrix	metal ion binding|protein serine/threonine/tyrosine kinase activity|serine-type peptidase activity			ovary(8)|large_intestine(2)|central_nervous_system(2)|pancreas(1)|skin(1)	14						NSCLC(146;835 1944 15585 22231 52158)								0.102473	18.337331	62.850424	29	254	GG		KEEP	---	---	---	---	capture		COAD - Colon adenocarcinoma(1;8.98e-05)|Colorectal(1;0.00184)	Silent	SNP	102911416	102911416	13689	7	G	A	A	40	40	RELN	A	1	1
PUS7	54517	broad.mit.edu	36	7	104898406	104898406	+	Missense_Mutation	SNP	A	C	C			TCGA-16-0846-01	TCGA-16-0846-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr7:104898406A>C	uc010lji.1	-	c.1381T>G	c.(1381-1383)TAT>GAT	p.Y461D	PUS7_uc003vcx.1_Missense_Mutation_p.Y455D|PUS7_uc003vcy.1_Missense_Mutation_p.Y455D|PUS7_uc003vcz.1_Missense_Mutation_p.Y455D	NM_019042	NP_061915	Q96PZ0	PUS7_HUMAN	pseudouridylate synthase 7 homolog	455	TRUD.				pseudouridine synthesis|tRNA processing		pseudouridine synthase activity|RNA binding			breast(1)	1						Colon(138;2387 3051 17860)								0.263158	189.407563	201.908243	65	182	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	104898406	104898406	13291	7	A	C	C	16	16	PUS7	C	4	4
CPA4	51200	broad.mit.edu	36	7	129732917	129732917	+	Missense_Mutation	SNP	G	A	A			TCGA-16-0846-01	TCGA-16-0846-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr7:129732917G>A	uc003vpr.1	+	c.512G>A	c.(511-513)CGG>CAG	p.R171Q		NM_016352	NP_057436	Q9UI42	CBPA4_HUMAN	carboxypeptidase A4 preproprotein	171					histone acetylation|proteolysis	extracellular region	metallocarboxypeptidase activity|zinc ion binding			ovary(1)	1	Melanoma(18;0.0435)													0.208	57.293652	67.157799	26	99	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	129732917	129732917	3930	7	G	A	A	39	39	CPA4	A	1	1
SSPO	23145	broad.mit.edu	36	7	149115567	149115567	+	Missense_Mutation	SNP	A	C	C			TCGA-16-0846-01	TCGA-16-0846-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr7:149115567A>C	uc010lpk.1	+	c.3557A>C	c.(3556-3558)GAC>GCC	p.D1186A		NM_198455	NP_940857	A2VEC9	SSPO_HUMAN	SCO-spondin	1186	VWFD 3.				cell adhesion	extracellular space	peptidase inhibitor activity				0	Melanoma(164;0.165)|Ovarian(565;0.177)													0.428571	15.145747	15.208311	6	8	AA		KEEP	---	---	---	---	capture	OV - Ovarian serous cystadenocarcinoma(82;0.00625)		Missense_Mutation	SNP	149115567	149115567	15705	7	A	C	C	10	10	SSPO	C	4	4
GIMAP7	168537	broad.mit.edu	36	7	149848029	149848029	+	Missense_Mutation	SNP	G	A	A			TCGA-16-0846-01	TCGA-16-0846-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr7:149848029G>A	uc003whk.1	+	c.34G>A	c.(34-36)GTT>ATT	p.V12I	GIMAP7_uc010lpt.1_Missense_Mutation_p.V12I	NM_153236	NP_694968	Q8NHV1	GIMA7_HUMAN	GTPase, IMAP family member 7	12							GTP binding			pancreas(1)	1														0.298246	86.904282	91.053295	34	80	GG		KEEP	---	---	---	---	capture	OV - Ovarian serous cystadenocarcinoma(82;0.0218)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)	Missense_Mutation	SNP	149848029	149848029	6652	7	G	A	A	40	40	GIMAP7	A	1	1
CPVL	54504	broad.mit.edu	36	7	29127101	29127101	+	Silent	SNP	T	C	C			TCGA-16-0846-01	TCGA-16-0846-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr7:29127101T>C	uc003szv.1	-	c.102A>G	c.(100-102)CCA>CCG	p.P34P	CPVL_uc003szw.1_Silent_p.P34P|CPVL_uc003szx.1_Silent_p.P34P	NM_031311	NP_112601	Q9H3G5	CPVL_HUMAN	serine carboxypeptidase vitellogenic-like	34					proteolysis		protein binding|serine-type carboxypeptidase activity			ovary(2)	2														0.349206	113.424847	115.969298	44	82	TT		KEEP	---	---	---	---	capture			Silent	SNP	29127101	29127101	3974	7	T	C	C	59	59	CPVL	C	4	4
AEBP1	165	broad.mit.edu	36	7	44115061	44115061	+	Missense_Mutation	SNP	G	A	A			TCGA-16-0846-01	TCGA-16-0846-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr7:44115061G>A	uc003tkb.1	+	c.979G>A	c.(979-981)GAT>AAT	p.D327N	AEBP1_uc003tkc.2_5'Flank|AEBP1_uc003tkd.1_5'Flank	NM_001129	NP_001120	Q8IUX7	AEBP1_HUMAN	adipocyte enhancer binding protein 1 precursor	327					cell adhesion|muscle organ development|proteolysis|regulation of transcription, DNA-dependent|skeletal system development	cytoplasm|extracellular space|nucleus	DNA binding|metallocarboxypeptidase activity|sequence-specific DNA binding transcription factor activity|zinc ion binding				0														0.347826	22.393735	22.863517	8	15	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	44115061	44115061	350	7	G	A	A	37	37	AEBP1	A	1	1
ZNF680	340252	broad.mit.edu	36	7	63641534	63641534	+	Missense_Mutation	SNP	A	G	G			TCGA-16-0846-01	TCGA-16-0846-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr7:63641534A>G	uc003tta.1	-	c.239T>C	c.(238-240)GTA>GCA	p.V80A	ZNF680_uc010kzr.1_Intron|ZNF680_uc003ttb.1_Missense_Mutation_p.V80A	NM_178558	NP_848653	Q8NEM1	ZN680_HUMAN	zinc finger protein 680 isoform 1	80	KRAB.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1		Lung NSC(55;0.118)|all_lung(88;0.243)												0.212903	88.301656	100.09646	33	122	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	63641534	63641534	18682	7	A	G	G	14	14	ZNF680	G	4	4
EEF1D	1936	broad.mit.edu	36	8	144742691	144742691	+	Missense_Mutation	SNP	T	C	C			TCGA-16-0846-01	TCGA-16-0846-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr8:144742691T>C	uc003yyq.1	-	c.854A>G	c.(853-855)GAG>GGG	p.E285G	EEF1D_uc003yyp.1_Missense_Mutation_p.E235G|EEF1D_uc003yyr.1_Missense_Mutation_p.E235G|EEF1D_uc003yys.1_Intron|EEF1D_uc003yyt.1_Missense_Mutation_p.E235G|EEF1D_uc003yyu.1_Intron|EEF1D_uc003yyv.1_Intron	NM_032378	NP_115754	P29692	EF1D_HUMAN	eukaryotic translation elongation factor 1 delta	14					positive regulation of I-kappaB kinase/NF-kappaB cascade	cytosol|eukaryotic translation elongation factor 1 complex	protein binding|signal transducer activity|translation elongation factor activity			ovary(1)|kidney(1)|skin(1)	3	all_cancers(97;3.74e-11)|all_epithelial(106;2.62e-09)|Lung NSC(106;0.00013)|all_lung(105;0.000374)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)									610				0.6	6.621934	6.66522	3	2	TT		KEEP	---	---	---	---	capture	Colorectal(110;0.134)|BRCA - Breast invasive adenocarcinoma(115;0.239)		Missense_Mutation	SNP	144742691	144742691	5113	8	T	C	C	54	54	EEF1D	C	4	4
MAPK15	225689	broad.mit.edu	36	8	144873295	144873295	+	Missense_Mutation	SNP	G	T	T			TCGA-16-0846-01	TCGA-16-0846-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr8:144873295G>T	uc003yzj.1	+	c.562G>T	c.(562-564)GTG>TTG	p.V188L		NM_139021	NP_620590	Q8TD08	MK15_HUMAN	mitogen-activated protein kinase 15	188	Protein kinase.				protein autophosphorylation	extracellular region	ATP binding|MAP kinase activity|SH3 domain binding			lung(2)	2	all_cancers(97;3.74e-11)|all_epithelial(106;2.62e-09)|Lung NSC(106;0.00013)|all_lung(105;0.000374)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)									103				0.583333	22.629302	22.703073	7	5	GG		KEEP	---	---	---	---	capture	OV - Ovarian serous cystadenocarcinoma(54;3.38e-41)|Epithelial(56;6.8e-40)|all cancers(56;6.43e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.146)		Missense_Mutation	SNP	144873295	144873295	9660	8	G	T	T	44	44	MAPK15	T	3	3
INTS9	55756	broad.mit.edu	36	8	28683445	28683445	+	Silent	SNP	G	T	T			TCGA-16-0846-01	TCGA-16-0846-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr8:28683445G>T	uc003xha.1	-	c.1680C>A	c.(1678-1680)GCC>GCA	p.A560A	INTS9_uc010lvc.1_Non-coding_Transcript	NM_018250	NP_060720	Q9NV88	INT9_HUMAN	integrator complex subunit 9 isoform 1	560					snRNA processing	integrator complex	protein binding			central_nervous_system(1)|pancreas(1)	2		Ovarian(32;0.0439)										OREG0018682	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	0.483333	82.169242	82.18375	29	31	GG		KEEP	---	---	---	---	capture		KIRC - Kidney renal clear cell carcinoma(542;0.127)|Kidney(114;0.152)	Silent	SNP	28683445	28683445	8086	8	G	T	T	43	43	INTS9	T	3	3
PRKDC	5591	broad.mit.edu	36	8	48934808	48934808	+	Nonsense_Mutation	SNP	G	A	A			TCGA-16-0846-01	TCGA-16-0846-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr8:48934808G>A	uc003xqi.1	-	c.6124C>T	c.(6124-6126)CAA>TAA	p.Q2042*	PRKDC_uc003xqj.1_Nonsense_Mutation_p.Q2042*	NM_006904	NP_008835	P78527	PRKDC_HUMAN	protein kinase, DNA-activated, catalytic	2042					cellular response to insulin stimulus|double-strand break repair via nonhomologous end joining|peptidyl-serine phosphorylation|positive regulation of gene-specific transcription from RNA polymerase II promoter	DNA-dependent protein kinase-DNA ligase 4 complex|transcription factor complex	ATP binding|DNA binding|DNA-dependent protein kinase activity|transcription factor binding			lung(12)|central_nervous_system(9)|ovary(6)|skin(4)|large_intestine(3)	34		all_cancers(86;0.0336)|all_epithelial(80;0.00111)|Lung NSC(129;0.00363)|all_lung(136;0.00391)				Esophageal Squamous(79;1091 1253 12329 31680 40677)				1566				0.242647	76.001014	84.219328	33	103	GG		KEEP	---	---	---	---	capture			Nonsense_Mutation	SNP	48934808	48934808	12964	8	G	A	A	45	45	PRKDC	A	5	2
RP1	6101	broad.mit.edu	36	8	55703485	55703485	+	Missense_Mutation	SNP	A	T	T			TCGA-16-0846-01	TCGA-16-0846-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr8:55703485A>T	uc003xsd.1	+	c.4490A>T	c.(4489-4491)GAG>GTG	p.E1497V	RP1_uc003xse.1_Intron	NM_006269	NP_006260	P56715	RP1_HUMAN	retinitis pigmentosa RP1 protein	1497					cell projection organization|intracellular signal transduction|phototransduction, visible light|visual perception	cilium axoneme|cytoplasm|microtubule|photoreceptor connecting cilium|photoreceptor outer segment				ovary(4)|pancreas(1)	5		all_lung(136;0.0831)|Lung NSC(129;0.109)|all_epithelial(80;0.123)				Colon(91;1014 1389 7634 14542 40420)								0.470588	116.78454	116.848856	40	45	AA		KEEP	---	---	---	---	capture	OV - Ovarian serous cystadenocarcinoma(7;4.4e-07)|Epithelial(17;3.37e-05)|all cancers(17;0.000285)		Missense_Mutation	SNP	55703485	55703485	14011	8	A	T	T	11	11	RP1	T	4	4
TRPA1	8989	broad.mit.edu	36	8	73136534	73136534	+	Missense_Mutation	SNP	G	A	A			TCGA-16-0846-01	TCGA-16-0846-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr8:73136534G>A	uc003xza.1	-	c.824C>T	c.(823-825)GCC>GTC	p.A275V		NM_007332	NP_015628	O75762	TRPA1_HUMAN	ankyrin-like protein 1	275	Cytoplasmic (Potential).|ANK 7.					integral to plasma membrane				ovary(4)|lung(1)|kidney(1)	6					Menthol(DB00825)									0.25	44.584949	48.905543	19	57	GG		KEEP	---	---	---	---	capture	Epithelial(68;0.223)		Missense_Mutation	SNP	73136534	73136534	17128	8	G	A	A	42	42	TRPA1	A	2	2
GTF3C5	9328	broad.mit.edu	36	9	134916102	134916102	+	Missense_Mutation	SNP	G	C	C			TCGA-16-0846-01	TCGA-16-0846-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr9:134916102G>C	uc004ccj.2	+	c.684G>C	c.(682-684)AAG>AAC	p.K228N	GTF3C5_uc010mzz.1_Missense_Mutation_p.K103N|GTF3C5_uc004cci.2_Missense_Mutation_p.K228N	NM_001122823	NP_001116295	Q9Y5Q8	TF3C5_HUMAN	general transcription factor IIIC, polypeptide 5	228					5S class rRNA transcription from RNA polymerase III type 1 promoter|tRNA transcription from RNA polymerase III promoter	transcription factor TFIIIC complex	DNA binding|protein binding				0														0.222222	6.810728	8.07531	4	14	GG		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(145;4.01e-06)|Epithelial(140;4e-05)	Missense_Mutation	SNP	134916102	134916102	7156	9	G	C	C	34	34	GTF3C5	C	3	3
FUT7	2529	broad.mit.edu	36	9	139045459	139045459	+	Missense_Mutation	SNP	G	C	C			TCGA-16-0846-01	TCGA-16-0846-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr9:139045459G>C	uc004ckq.2	-	c.553C>G	c.(553-555)CTG>GTG	p.L185V	ABCA2_uc010nby.1_5'Flank|ABCA2_uc010nbz.1_5'Flank|ABCA2_uc004ckl.1_5'Flank|ABCA2_uc004ckm.1_5'Flank|C9orf139_uc004ckp.1_Intron	NM_004479	NP_004470	Q11130	FUT7_HUMAN	fucosyltransferase 7	185	Lumenal (Potential).				L-fucose catabolic process|protein glycosylation	Golgi cisterna membrane|integral to membrane	alpha(1,3)-fucosyltransferase activity				0	all_cancers(76;0.0893)	Myeloproliferative disorder(178;0.0511)												0.285714	20.35787	22.107611	12	30	GG		KEEP	---	---	---	---	capture	STAD - Stomach adenocarcinoma(284;0.123)	OV - Ovarian serous cystadenocarcinoma(145;2.96e-05)|Epithelial(140;0.000486)	Missense_Mutation	SNP	139045459	139045459	6360	9	G	C	C	34	34	FUT7	C	3	3
GABRE	2564	broad.mit.edu	36	X	150874658	150874658	+	Silent	SNP	G	T	T			TCGA-16-0846-01	TCGA-16-0846-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chrX:150874658G>T	uc004ffi.1	-	c.975C>A	c.(973-975)ACC>ACA	p.T325T	GABRE_uc004ffg.1_Silent_p.T180T|GABRE_uc004fff.1_Silent_p.T212T|GABRE_uc004ffh.1_Silent_p.T212T	NM_004961	NP_068830	P78334	GBRE_HUMAN	gamma-aminobutyric acid (GABA) A receptor,	325					gamma-aminobutyric acid signaling pathway	cell junction|chloride channel complex|integral to plasma membrane|postsynaptic membrane	chloride channel activity|extracellular ligand-gated ion channel activity|GABA-A receptor activity			ovary(2)	2	Acute lymphoblastic leukemia(192;6.56e-05)													0.702703	80.357708	81.714664	26	11	GG		KEEP	---	---	---	---	capture			Silent	SNP	150874658	150874658	6421	23	G	T	T	35	35	GABRE	T	3	3
DMD	1756	broad.mit.edu	36	X	32339853	32339853	+	Missense_Mutation	SNP	G	C	C			TCGA-16-0846-01	TCGA-16-0846-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chrX:32339853G>C	uc004dda.1	-	c.4170C>G	c.(4168-4170)GAC>GAG	p.D1390E	DMD_uc004dcw.2_Missense_Mutation_p.D46E|DMD_uc004dcx.2_Missense_Mutation_p.D49E|DMD_uc004dcz.2_Missense_Mutation_p.D1267E|DMD_uc004dcy.1_Missense_Mutation_p.D1386E|DMD_uc004ddb.1_Missense_Mutation_p.D1382E|DMD_uc010ngo.1_Intron	NM_004006	NP_004001	P11532	DMD_HUMAN	dystrophin Dp427m isoform	1390					muscle filament sliding|peptide biosynthetic process	cell surface|costamere|cytoskeleton|cytosol|dystrophin-associated glycoprotein complex|sarcolemma	actin binding|dystroglycan binding|nitric-oxide synthase binding|protein binding|structural constituent of cytoskeleton|structural constituent of muscle|zinc ion binding			ovary(3)|pancreas(2)|large_intestine(1)	6		all_cancers(2;1.22e-16)|Acute lymphoblastic leukemia(2;4.65e-06)|all_hematologic(2;0.00108)|all_epithelial(3;0.00626)|all_neural(2;0.0189)|all_lung(315;0.182)|Glioma(3;0.203)												0.792453	150.47863	154.67744	42	11	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	32339853	32339853	4760	23	G	C	C	48	48	DMD	C	3	3
EDA	1896	broad.mit.edu	36	X	68752966	68752966	+	Missense_Mutation	SNP	C	G	G			TCGA-16-0846-01	TCGA-16-0846-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chrX:68752966C>G	uc004dxs.1	+	c.89C>G	c.(88-90)GCC>GGC	p.A30G	EDA_uc004dxn.1_Missense_Mutation_p.A30G|EDA_uc004dxm.1_Missense_Mutation_p.A30G|EDA_uc004dxp.1_Missense_Mutation_p.A30G|EDA_uc004dxq.1_Missense_Mutation_p.A30G|EDA_uc004dxr.1_Missense_Mutation_p.A30G|EDA_uc004dxl.1_Missense_Mutation_p.A30G	NM_001399	NP_001390	Q92838	EDA_HUMAN	ectodysplasin A isoform EDA-A1	30	Cytoplasmic (Potential).				cell differentiation|ectoderm development|immune response|positive regulation of NF-kappaB transcription factor activity|signal transduction	collagen|cytoskeleton|membrane fraction	tumor necrosis factor receptor binding			ovary(2)|large_intestine(1)	3														0.4	6.7765	6.922453	6	9	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	68752966	68752966	5090	23	C	G	G	26	26	EDA	G	3	3
CXCR3	2833	broad.mit.edu	36	X	70753277	70753277	+	Missense_Mutation	SNP	A	C	C			TCGA-16-0846-01	TCGA-16-0846-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chrX:70753277A>C	uc004eaf.1	-	c.770T>G	c.(769-771)GTG>GGG	p.V257G		NM_001504	NP_001495	P49682	CXCR3_HUMAN	chemokine (C-X-C motif) receptor 3 isoform A	257	Helical; Name=6; (Potential).				cell adhesion|cellular component movement|chemotaxis|elevation of cytosolic calcium ion concentration	cytoplasm|integral to plasma membrane	C-X-C chemokine receptor activity			ovary(2)|central_nervous_system(1)	3	Renal(35;0.156)													0.538462	8.872474	8.877972	7	6	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	70753277	70753277	4252	23	A	C	C	6	6	CXCR3	C	4	4
PCDH11X	27328	broad.mit.edu	36	X	91020182	91020182	+	Missense_Mutation	SNP	T	A	A			TCGA-16-0846-01	TCGA-16-0846-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chrX:91020182T>A	uc004efk.1	+	c.2287T>A	c.(2287-2289)TTC>ATC	p.F763I	PCDH11X_uc004efl.1_Missense_Mutation_p.F763I|PCDH11X_uc004efn.1_Missense_Mutation_p.F763I|PCDH11X_uc004efo.1_Missense_Mutation_p.F763I|PCDH11X_uc010nmv.1_Missense_Mutation_p.F763I|PCDH11X_uc004efm.1_Missense_Mutation_p.F763I|PCDH11X_uc004efh.1_Missense_Mutation_p.F763I|PCDH11X_uc004efj.1_Missense_Mutation_p.F763I	NM_032968	NP_116750	Q9BZA7	PC11X_HUMAN	protocadherin 11 X-linked isoform c	763	Cadherin 7.|Extracellular (Potential).				homophilic cell adhesion	integral to plasma membrane	calcium ion binding			large_intestine(2)	2						NSCLC(38;925 1092 2571 38200 45895)								0.797297	192.662626	198.735259	59	15	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	91020182	91020182	11928	23	T	A	A	56	56	PCDH11X	A	4	4
FOXG1	2290	broad.mit.edu	36	14	28306375	28306377	+	In_Frame_Del	DEL	CAC	-	-			TCGA-16-0846-01	TCGA-16-0846-01										Phase_I	Unspecified				Illumina GAIIx	g.chr14:28306375_28306377delCAC	uc001wqe.1	+	c.139_141delCAC	c.(139-141)CACdel	p.H57del		NM_005249	NP_005240	P55316	FOXG1_HUMAN	forkhead box G1	57	His-rich.				axon midline choice point recognition|central nervous system neuron development|dorsal/ventral pattern formation|embryo development ending in birth or egg hatching|hindbrain development|inner ear morphogenesis|negative regulation of gene-specific transcription from RNA polymerase II promoter|negative regulation of neuron differentiation|nose development|positive regulation of cell cycle|positive regulation of neuroblast proliferation|positive regulation of transcription from RNA polymerase II promoter|regulation of mitotic cell cycle|regulation of sequence-specific DNA binding transcription factor activity|sensory cilium assembly|tissue development	transcription factor complex	DNA bending activity|double-stranded DNA binding|promoter binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|specific RNA polymerase II transcription factor activity|specific transcriptional repressor activity|transcription activator activity|transcription factor binding			ovary(2)|lung(1)	3			LUAD - Lung adenocarcinoma(48;0.011)|Lung(238;0.0575)	GBM - Glioblastoma multiforme(265;0.00413)										0.33			2	4				---	---	---	---	capture_indel			In_Frame_Del	DEL	28306375	28306377	6252	14	CAC	-	-	25	25	FOXG1	-	5	5
