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
KNDC1	85442	broad.mit.edu	36	10	134861870	134861870	+	Missense_Mutation	SNP	T	G	G			TCGA-06-0210-01	TCGA-06-0210-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr10:134861870T>G	uc001llz.1	+	c.1946T>G	c.(1945-1947)GTG>GGG	p.V649G	KNDC1_uc001lma.1_Missense_Mutation_p.V584G|KNDC1_uc001lmb.1_Missense_Mutation_p.V61G	NM_152643	NP_689856	Q76NI1	VKIND_HUMAN	kinase non-catalytic C-lobe domain (KIND)	649					regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction					ovary(1)	1		all_cancers(35;4.16e-10)|all_epithelial(44;2.07e-08)|Lung NSC(174;0.000845)|all_lung(145;0.00145)|all_neural(114;0.0299)|Melanoma(40;0.123)|Colorectal(31;0.173)|Glioma(114;0.203)												0.454545	6.425252	6.461151	5	6	TT		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(35;8.77e-06)|Epithelial(32;1.13e-05)|all cancers(32;1.51e-05)	Missense_Mutation	SNP	134861870	134861870	8740	10	T	G	G	59	59	KNDC1	G	4	4
MPZL2	10205	broad.mit.edu	36	11	117638383	117638383	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0210-01	TCGA-06-0210-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr11:117638383C>T	uc001psn.1	-	c.416G>A	c.(415-417)CGG>CAG	p.R139Q	MPZL2_uc001pso.1_Missense_Mutation_p.R139Q|MPZL2_uc001psp.1_Missense_Mutation_p.R139Q	NM_005797	NP_658911	O60487	MPZL2_HUMAN	myelin protein zero-like 2 precursor	139	Extracellular (Potential).|Ig-like V-type.				anatomical structure morphogenesis|homophilic cell adhesion	cytoskeleton|integral to membrane					0	all_hematologic(175;0.046)	Medulloblastoma(222;0.0425)|Breast(348;0.181)|all_hematologic(192;0.196)|all_neural(223;0.234)												0.198675	70.660643	83.422453	30	121	CC		KEEP	---	---	---	---	capture		BRCA - Breast invasive adenocarcinoma(274;3.04e-05)	Missense_Mutation	SNP	117638383	117638383	10142	11	C	T	T	23	23	MPZL2	T	1	1
FLI1	2313	broad.mit.edu	36	11	128133396	128133396	+	Silent	SNP	C	T	T			TCGA-06-0210-01	TCGA-06-0210-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr11:128133396C>T	uc001qem.1	+	c.195C>T	c.(193-195)AAC>AAT	p.N65N	FLI1_uc009zci.1_De_novo_Start_OutOfFrame|FLI1_uc001qen.2_Silent_p.N32N	NM_002017	NP_002008	Q01543	FLI1_HUMAN	Friend leukemia virus integration 1	65					hemostasis|organ morphogenesis|regulation of transcription, DNA-dependent	nucleus	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity		EWSR1/FLI1(2262)	bone(2208)|soft_tissue(46)|autonomic_ganglia(4)|central_nervous_system(4)|ovary(2)|pancreas(2)|lung(1)	2267	all_hematologic(175;0.0641)	Lung NSC(97;0.00588)|all_lung(97;0.00764)|Breast(109;0.0115)|Medulloblastoma(222;0.0523)|all_neural(223;0.0862)|all_hematologic(192;0.182)							(639V-Tumor)	400				0.243902	23.728547	26.179999	10	31	CC		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(99;0.01)|LUSC - Lung squamous cell carcinoma(976;0.0324)|Lung(977;0.0327)	Silent	SNP	128133396	128133396	6162	11	C	T	T	19	19	FLI1	T	1	1
ARFGAP2	84364	broad.mit.edu	36	11	47153400	47153400	+	Missense_Mutation	SNP	G	C	C			TCGA-06-0210-01	TCGA-06-0210-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr11:47153400G>C	uc001ndt.1	-	c.305C>G	c.(304-306)GCC>GGC	p.A102G	ARFGAP2_uc001ndu.1_Intron|ARFGAP2_uc001ndv.1_3'UTR	NM_032389	NP_115765	Q8N6H7	ARFG2_HUMAN	ADP-ribosylation factor GTPase activating	102	Required for interaction with coatomer.|Arf-GAP.				protein transport|regulation of ARF GTPase activity|vesicle-mediated transport	Golgi membrane|nucleolus|plasma membrane	ARF GTPase activator activity|zinc ion binding			ovary(1)	1														0.197568	153.919391	182.079898	65	264	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	47153400	47153400	861	11	G	C	C	42	42	ARFGAP2	C	3	3
OR52R1	119695	broad.mit.edu	36	11	4781523	4781523	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0210-01	TCGA-06-0210-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr11:4781523C>T	uc001lzm.1	-	c.901G>A	c.(901-903)GTG>ATG	p.V301M		NM_001005177	NP_001005177	Q8NGF1	O52R1_HUMAN	olfactory receptor, family 52, subfamily R,	222	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0		Medulloblastoma(188;0.0025)|Breast(177;0.0184)|all_neural(188;0.0227)												0.218182	50.842288	58.895134	24	86	CC		KEEP	---	---	---	---	capture		Epithelial(150;4.77e-12)|BRCA - Breast invasive adenocarcinoma(625;0.00435)|LUSC - Lung squamous cell carcinoma(625;0.19)	Missense_Mutation	SNP	4781523	4781523	11541	11	C	T	T	19	19	OR52R1	T	1	1
MS4A1	931	broad.mit.edu	36	11	59990202	59990202	+	Missense_Mutation	SNP	T	A	A			TCGA-06-0210-01	TCGA-06-0210-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr11:59990202T>A	uc001npp.1	+	c.569T>A	c.(568-570)TTC>TAC	p.F190Y	MS4A1_uc001npq.1_Missense_Mutation_p.F190Y|MS4A1_uc009ymz.1_Missense_Mutation_p.F190Y|MS4A1_uc009yna.1_Missense_Mutation_p.F190Y	NM_152866	NP_690605	P11836	CD20_HUMAN	membrane-spanning 4-domains, subfamily A, member	190	Helical; (Potential).				B cell activation|immune response	integral to plasma membrane				ovary(3)	3					Ibritumomab(DB00078)|Rituximab(DB00073)|Tositumomab(DB00081)									0.241935	100.586111	111.883411	45	141	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	59990202	59990202	10247	11	T	A	A	62	62	MS4A1	A	4	4
PCNXL3	399909	broad.mit.edu	36	11	65160356	65160356	+	Splice_Site_SNP	SNP	T	G	G			TCGA-06-0210-01	TCGA-06-0210-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr11:65160356T>G	uc001oey.2	+	c.5593_splice	c.e33+2	p.G1865_splice	PCNXL3_uc001oez.2_Splice_Site_SNP_p.G752_splice|SIPA1_uc009yqo.1_5'Flank|SIPA1_uc001ofb.1_5'Flank	NM_032223	NP_115599			pecanex-like 3							integral to membrane					0														0.242424	6.664577	8.89912	8	25	TT		KEEP	---	---	---	---	capture			Splice_Site_SNP	SNP	65160356	65160356	12013	11	T	G	G	59	59	PCNXL3	G	5	4
GPR81	27198	broad.mit.edu	36	12	121780456	121780456	+	Silent	SNP	G	A	A			TCGA-06-0210-01	TCGA-06-0210-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr12:121780456G>A	uc001ucz.1	-	c.384C>T	c.(382-384)TCC>TCT	p.S128S	GPR81_uc001ucw.1_Non-coding_Transcript	NM_032554	NP_115943	Q9BXC0	GPR81_HUMAN	G protein-coupled receptor 81	128	Cytoplasmic (Potential).				response to estradiol stimulus	integral to membrane|plasma membrane	G-protein coupled receptor activity			breast(2)|ovary(1)|pancreas(1)	4	all_neural(191;0.0837)|Medulloblastoma(191;0.163)													0.225681	137.227547	154.983743	58	199	GG		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(86;2.14e-05)|Epithelial(86;3.25e-05)|BRCA - Breast invasive adenocarcinoma(302;0.197)	Silent	SNP	121780456	121780456	6986	12	G	A	A	47	47	GPR81	A	2	2
CPNE8	144402	broad.mit.edu	36	12	37410360	37410360	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0210-01	TCGA-06-0210-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr12:37410360C>T	uc001rls.1	-	c.790G>A	c.(790-792)GTA>ATA	p.V264I		NM_153634	NP_705898	Q86YQ8	CPNE8_HUMAN	copine VIII	264										pancreas(1)	1	Esophageal squamous(101;0.187)	Lung NSC(34;0.137)|Melanoma(24;0.152)|all_lung(34;0.157)												0.195402	36.121901	43.650136	17	70	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	37410360	37410360	3956	12	C	T	T	19	19	CPNE8	T	1	1
RNF17	56163	broad.mit.edu	36	13	24340748	24340748	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0210-01	TCGA-06-0210-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr13:24340748C>T	uc001upr.1	+	c.4172C>T	c.(4171-4173)TCG>TTG	p.S1391L	RNF17_uc010aab.1_Non-coding_Transcript|RNF17_uc001ups.1_Missense_Mutation_p.S1330L|RNF17_uc010aac.1_Missense_Mutation_p.S583L|RNF17_uc010aad.1_Missense_Mutation_p.S401L	NM_031277	NP_112567	Q9BXT8	RNF17_HUMAN	ring finger protein 17	1391					multicellular organismal development	cytoplasm|nucleus	hydrolase activity, acting on ester bonds|nucleic acid binding|zinc ion binding			ovary(1)	1		Lung SC(185;0.0225)|Breast(139;0.077)												0.2	70.316348	84.979012	35	140	CC		KEEP	---	---	---	---	capture		all cancers(112;0.0114)|OV - Ovarian serous cystadenocarcinoma(117;0.0311)|Epithelial(112;0.0524)	Missense_Mutation	SNP	24340748	24340748	13938	13	C	T	T	31	31	RNF17	T	1	1
KIF26A	26153	broad.mit.edu	36	14	103712762	103712762	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0210-01	TCGA-06-0210-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr14:103712762G>A	uc001yos.2	+	c.3884G>A	c.(3883-3885)CGC>CAC	p.R1295H		NM_015656	NP_056471	Q9ULI4	KI26A_HUMAN	kinesin family member 26A	1295					blood coagulation|enteric nervous system development|microtubule-based movement|negative regulation of signal transduction|regulation of cell growth by extracellular stimulus	cytosol|microtubule	ATP binding|microtubule binding|microtubule motor activity			pancreas(1)	1		all_cancers(154;0.109)|Melanoma(154;0.0525)|all_epithelial(191;0.0767)												0.142857	7.821818	12.985873	6	36	GG		KEEP	---	---	---	---	capture	Epithelial(46;0.152)	Epithelial(152;0.161)	Missense_Mutation	SNP	103712762	103712762	8605	14	G	A	A	38	38	KIF26A	A	1	1
SERPINA3	12	broad.mit.edu	36	14	94159851	94159851	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0210-01	TCGA-06-0210-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr14:94159851G>A	uc001ydo.2	+	c.1294G>A	c.(1294-1296)GAC>AAC	p.D432N	SERPINA3_uc001ydr.1_Non-coding_Transcript|SERPINA3_uc001ydq.1_Missense_Mutation_p.D407N|SERPINA3_uc001ydp.1_Missense_Mutation_p.D407N|SERPINA3_uc001yds.1_Missense_Mutation_p.D407N|SERPINA3_uc010avg.1_Missense_Mutation_p.D407N	NM_001085	NP_001076	P01011	AACT_HUMAN	serpin peptidase inhibitor, clade A, member 3	407					acute-phase response|maintenance of gastrointestinal epithelium|regulation of lipid metabolic process|regulation of proteolysis	extracellular region|nucleus	DNA binding|protein binding|serine-type endopeptidase inhibitor activity	p.D407N(1)		ovary(2)|central_nervous_system(2)|large_intestine(1)	5		all_cancers(154;0.0525)|all_epithelial(191;0.179)												0.155102	69.077273	96.937302	38	207	GG		KEEP	---	---	---	---	capture		COAD - Colon adenocarcinoma(157;0.212)|Epithelial(152;0.228)	Missense_Mutation	SNP	94159851	94159851	14578	14	G	A	A	33	33	SERPINA3	A	2	2
HEXA	3073	broad.mit.edu	36	15	70432524	70432524	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0210-01	TCGA-06-0210-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr15:70432524C>T	uc002aun.2	-	c.509G>A	c.(508-510)CGG>CAG	p.R170Q	CELF6_uc002auk.2_Intron|HEXA_uc002auo.2_Missense_Mutation_p.R33Q|HEXA_uc010bix.1_Missense_Mutation_p.R170Q|HEXA_uc010biy.1_Missense_Mutation_p.R33Q|HEXA_uc010biz.1_Non-coding_Transcript	NM_000520	NP_000511	P06865	HEXA_HUMAN	hexosaminidase A preproprotein	170			R -> W (in GM2G1; infantile).|R -> Q (in GM2G1; infantile; inactive or unstable protein).			lysosome	beta-N-acetylhexosaminidase activity|cation binding|protein heterodimerization activity			ovary(3)	3														0.175824	30.649228	39.662191	16	75	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	70432524	70432524	7356	15	C	T	T	23	23	HEXA	T	1	1
CDH1	999	broad.mit.edu	36	16	67413594	67413594	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0210-01	TCGA-06-0210-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr16:67413594C>T	uc002ewg.1	+	c.1901C>T	c.(1900-1902)GCG>GTG	p.A634V	CDH1_uc010cfg.1_Missense_Mutation_p.A573V	NM_004360	NP_004351	P12830	CADH1_HUMAN	cadherin 1, type 1 preproprotein	634	Cadherin 5.|Extracellular (Potential).		A -> V (found in a gastric cancer sample; cells exhibited decreased aggregation increased invasiveness and non-uniform migration in vitro compared to cells transfected with wild-type sequence).	ASA -> RVP (in Ref. 3; AAA61259).	adherens junction organization|cellular component disassembly involved in apoptosis|cellular response to indole-3-methanol|cellular response to lithium ion|homophilic cell adhesion|negative regulation of cell-cell adhesion|positive regulation of transcription factor import into nucleus|regulation of immune response	actin cytoskeleton|aggresome|apical junction complex|catenin complex|cell-cell adherens junction|focal adhesion|integral to membrane|lateral plasma membrane|perinuclear region of cytoplasm	cell adhesion molecule binding|gamma-catenin binding|transcription activator activity	p.A634V(3)		breast(136)|stomach(71)|biliary_tract(8)|endometrium(3)|soft_tissue(2)|large_intestine(2)|urinary_tract(2)|oesophagus(2)|ovary(2)|thyroid(1)|central_nervous_system(1)|lung(1)	231		all_neural(199;0.0189)|Ovarian(137;0.0563)								231				0.172414	44.690033	59.39032	25	120	CC		KEEP	---	---	---	---	capture		Epithelial(162;8.44e-05)|all cancers(182;0.000404)|OV - Ovarian serous cystadenocarcinoma(108;0.000426)|BRCA - Breast invasive adenocarcinoma(181;0.0261)	Missense_Mutation	SNP	67413594	67413594	3224	16	C	T	T	27	27	CDH1	T	1	1
NF1	4763	broad.mit.edu	36	17	26521129	26521129	+	Nonsense_Mutation	SNP	C	T	T			TCGA-06-0210-01	TCGA-06-0210-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr17:26521129C>T	uc002hgg.1	+	c.574C>T	c.(574-576)CGA>TGA	p.R192*	NF1_uc002hge.1_Nonsense_Mutation_p.R192*|NF1_uc002hgf.1_Nonsense_Mutation_p.R192*|NF1_uc002hgh.1_Nonsense_Mutation_p.R192*|NF1_uc010csn.1_Intron	NM_001042492	NP_001035957	P21359	NF1_HUMAN	neurofibromin isoform 1	192					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.?(2)|p.R192*(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)							p.R192*(JHUEM1-Tumor)|p.R192*(KS1-Tumor)	847	TCGA GBM(6;<1E-8)|TSP Lung(7;0.0071)|TCGA Ovarian(3;0.0088)			0.157143	19.080969	26.931034	11	59	CC		KEEP	---	---	---	---	capture		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)	Nonsense_Mutation	SNP	26521129	26521129	10756	17	C	T	T	19	19	NF1	T	5	1
EVPL	2125	broad.mit.edu	36	17	71517526	71517526	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0210-01	TCGA-06-0210-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr17:71517526G>A	uc002jqi.2	-	c.3355C>T	c.(3355-3357)CGC>TGC	p.R1119C		NM_001988	NP_001979	Q92817	EVPL_HUMAN	envoplakin	1119	Central fibrous rod domain.|Potential.				keratinization|peptide cross-linking	cornified envelope|cytoplasm|desmosome	protein binding, bridging|structural molecule activity			pancreas(2)|central_nervous_system(1)	3														0.195946	58.609653	71.349581	29	119	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	71517526	71517526	5485	17	G	A	A	37	37	EVPL	A	1	1
TP53	7157	broad.mit.edu	36	17	7518263	7518263	+	Missense_Mutation	SNP	C	T	T	rs11540652	by-hapmap	TCGA-06-0210-01	TCGA-06-0210-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr17:7518263C>T	uc002gim.2	-	c.743G>A	c.(742-744)CGG>CAG	p.R248Q	TP53_uc002gig.1_Missense_Mutation_p.R248Q|TP53_uc002gih.1_Missense_Mutation_p.R248Q|TP53_uc010cne.1_5'Flank|TP53_uc010cnf.1_Missense_Mutation_p.R116Q|TP53_uc010cng.1_Missense_Mutation_p.R116Q|TP53_uc002gii.1_Missense_Mutation_p.R116Q|TP53_uc010cnh.1_Missense_Mutation_p.R248Q|TP53_uc010cni.1_Missense_Mutation_p.R248Q|TP53_uc002gij.2_Missense_Mutation_p.R248Q|TP53_uc010cnj.1_Non-coding_Transcript|TP53_uc002gin.2_Missense_Mutation_p.R155Q|TP53_uc002gio.2_Missense_Mutation_p.R116Q	NM_001126112	NP_001119584	P04637	P53_HUMAN	tumor protein p53 isoform a	248	|Interaction with HIPK1 (By similarity).|Interacts with the 53BP2 SH3 domain.|Interaction with AXIN1 (By similarity).		R -> W (in LFS; germline mutation and in sporadic cancers; somatic mutation).|R -> P (in sporadic cancers; somatic mutation).|R -> G (in sporadic cancers; somatic mutation).|R -> L (in sporadic cancers; somatic mutation).|NR -> KW (in sporadic cancers; somatic mutation).|R -> C (in a sporadic cancer; somatic mutation).|NR -> IP (in a sporadic cancer; 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.R248Q(503)|p.R248L(63)|p.R248P(11)|p.0?(6)|p.N247_R248delNR(2)|p.M246_P250delMNRRP(2)|p.R248_P250delRRP(1)|p.N247_R249delNRR(1)|p.N247_P250delNRRP(1)|p.R249fs*96(1)|p.R248C(1)|p.G245fs*14(1)|p.N247_R248>IP(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)	R248Q(KASUMI1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(HS683_CENTRAL_NERVOUS_SYSTEM)|R248Q(NAMALWA_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(HCC1143_BREAST)|R248Q(BL41_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(SKUT1_SOFT_TISSUE)|R248Q(HSC4_UPPER_AERODIGESTIVE_TRACT)|R248Q(HEC1A_ENDOMETRIUM)|R248Q(SF295_CENTRAL_NERVOUS_SYSTEM)|R248Q(KOPN8_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(NUDHL1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(WSUDLCL2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(NCIN87_STOMACH)|R248Q(P12ICHIKAWA_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(DB_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(RT112_URINARY_TRACT)|R248Q(PF382_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(PANC0203_PANCREAS)|R248Q(EM2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(SEM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(CI1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(MOLM6_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(NIHOVCAR3_OVARY)|R248Q(CA46_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(SUPT1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(SW1463_LARGE_INTESTINE)|R248Q(HCC70_BREAST)|R248Q(KYSE150_OESOPHAGUS)|R248Q(NB4_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(NCIH211_LUNG)|R248Q(KYO1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(PC14_LUNG)	111	p.R248L(NCIH211-Tumor)|p.R248L(NB4-Tumor)|p.R248L(PC14-Tumor)|p.R248L(KYO1-Tumor)|p.R248L(PCM6-Tumor)|p.R248L(NUDHL1-Tumor)|p.R248L(BL41-Tumor)|p.R248Q(FADU-Tumor)|p.R248L(CI1-Tumor)|p.R248L(SW1463-Tumor)|p.R248L(COLO699-Tumor)|p.R248L(HS683-Tumor)|p.R248*(DB-Tumor)|p.R248L(HCC1143-Tumor)|p.R248L(NCIN87-Tumor)|p.R248A(SF126-Tumor)|p.R248L(PANC02.03-Tumor)|p.R248L(HEC1B-Tumor)|p.R248L(PECAPJ15-Tumor)|p.R248L(LNCAPCLONEFGC-Tumor)|p.R248L(NIHOVCAR3-Tumor)|p.R248L(NUDUL1-Tumor)|p.R248L(ONCODG1-Tumor)|p.R248L(RT112-Tumor)|p.R248L(SF295-Tumor)|p.R248L(P12ICHIKAWA-Tumor)|p.R248L(DND41-Tumor)|p.R248Q(SBC5-Tumor)|p.R248L(KOPN8-Tumor)|p.R248L(KASUMI1-Tumor)|p.R248L(EM2-Tumor)|p.R248L(SKUT1-Tumor)|p.R248L(NCCSTCK140-Tumor)|p.R248L(TE6-Tumor)|p.R248L(MOLM6-Tumor)|p.R248L(SEM-Tumor)|p.R248L(NAMALWA-Tumor)|p.R248L(CA46-Tumor)|p.R248L(639V-Tumor)|p.R248L(SKM1-Tumor)|p.R248Q(NCIH1573-Tumor)|p.R248Q(NCIH1618-Tumor)|p.R248L(HCC70-Tumor)|p.R248L(WSUDLCL2-Tumor)|p.R248L(HEC1A-Tumor)|p.R248L(KYSE150-Tumor)|p.R248L(HSC4-Tumor)|p.R248L(CL40-Tumor)	690	TCGA GBM(1;<1E-8)|TSP Lung(2;<1E-8)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)			0.172131	43.299211	55.693895	21	101	CC		KEEP	---	---	---	---	capture		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Missense_Mutation	SNP	7518263	7518263	16923	17	C	T	T	23	23	TP53	T	1	1
RYR1	6261	broad.mit.edu	36	19	43768613	43768613	+	Missense_Mutation	SNP	A	G	G			TCGA-06-0210-01	TCGA-06-0210-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr19:43768613A>G	uc002oit.1	+	c.14911A>G	c.(14911-14913)ACG>GCG	p.T4971A	RYR1_uc002oiu.1_Missense_Mutation_p.T4966A	NM_000540	NP_000531	P21817	RYR1_HUMAN	skeletal muscle ryanodine receptor isoform 1	4971					muscle contraction|release of sequestered calcium ion into cytosol|response to caffeine|response to hypoxia	cell cortex|I band|integral to plasma membrane|junctional sarcoplasmic reticulum membrane|smooth endoplasmic reticulum|terminal cisterna	calcium ion binding|calmodulin binding|receptor activity|ryanodine-sensitive calcium-release channel activity			ovary(7)|pancreas(2)|breast(1)	10	all_cancers(60;7.91e-06)				Dantrolene(DB01219)									0.158879	37.324265	49.172863	17	90	AA		KEEP	---	---	---	---	capture	Lung(45;0.00172)|LUSC - Lung squamous cell carcinoma(53;0.00272)		Missense_Mutation	SNP	43768613	43768613	14248	19	A	G	G	14	14	RYR1	G	4	4
CYP2F1	1572	broad.mit.edu	36	19	46322516	46322516	+	Silent	SNP	G	A	A			TCGA-06-0210-01	TCGA-06-0210-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr19:46322516G>A	uc002opu.1	+	c.1017G>A	c.(1015-1017)GCG>GCA	p.A339A	CYP2F1_uc002opv.1_Non-coding_Transcript	NM_000774	NP_000765	P24903	CP2F1_HUMAN	cytochrome P450, family 2, subfamily F,	339					naphthalene metabolic process|oxidation-reduction process|xenobiotic metabolic process	endoplasmic reticulum membrane|microsome	aromatase activity|electron carrier activity|heme binding|oxygen binding				0														0.162791	10.697558	15.34728	7	36	GG		KEEP	---	---	---	---	capture			Silent	SNP	46322516	46322516	4336	19	G	A	A	38	38	CYP2F1	A	1	1
MEGF8	1954	broad.mit.edu	36	19	47547683	47547683	+	Missense_Mutation	SNP	A	C	C			TCGA-06-0210-01	TCGA-06-0210-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr19:47547683A>C	uc002otl.2	+	c.2830A>C	c.(2830-2832)ACC>CCC	p.T944P	MEGF8_uc002otm.2_Missense_Mutation_p.T552P	NM_001410	NP_001401	Q7Z7M0	MEGF8_HUMAN	multiple EGF-like-domains 8	1011	Extracellular (Potential).					integral to membrane	calcium ion binding|structural molecule activity			ovary(1)	1		Prostate(69;0.00682)												0.272727	7.119849	7.632425	3	8	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	47547683	47547683	9852	19	A	C	C	10	10	MEGF8	C	4	4
CCDC155	147872	broad.mit.edu	36	19	54592764	54592764	+	Missense_Mutation	SNP	G	T	T			TCGA-06-0210-01	TCGA-06-0210-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr19:54592764G>T	uc002pnm.1	+	c.445G>T	c.(445-447)GGC>TGC	p.G149C	CCDC155_uc002pnl.1_Missense_Mutation_p.G149C|CCDC155_uc010emx.1_Missense_Mutation_p.G122C	NM_144688	NP_653289	Q8N6L0	CC155_HUMAN	coiled-coil domain containing 155	149						integral to membrane	calcium ion binding			ovary(1)	1														0.194853	109.612688	133.239699	53	219	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	54592764	54592764	2910	19	G	T	T	35	35	CCDC155	T	3	3
TMC4	147798	broad.mit.edu	36	19	59359327	59359327	+	Missense_Mutation	SNP	C	A	A			TCGA-06-0210-01	TCGA-06-0210-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr19:59359327C>A	uc010erf.1	-	c.1236G>T	c.(1234-1236)AAG>AAT	p.K412N	TMC4_uc002qdn.1_Missense_Mutation_p.A103S|TMC4_uc002qdo.1_Missense_Mutation_p.K406N	NM_144686	NP_653287	Q7Z404	TMC4_HUMAN	transmembrane channel-like 4 isoform 2	412	Helical; (Potential).					integral to membrane				pancreas(1)	1	all_cancers(19;0.0065)|all_epithelial(19;0.00348)|all_lung(19;0.0175)|Lung NSC(19;0.0325)|Ovarian(34;0.19)											OREG0003641	type=REGULATORY REGION|Gene=AK124406|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay	0.198113	86.851762	104.824726	42	170	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	59359327	59359327	16517	19	C	A	A	28	28	TMC4	A	3	3
ACTL9	284382	broad.mit.edu	36	19	8668914	8668914	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0210-01	TCGA-06-0210-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr19:8668914C>T	uc002mkl.1	-	c.1138G>A	c.(1138-1140)GTA>ATA	p.V380I		NM_178525	NP_848620	Q8TC94	ACTL9_HUMAN	hypothetical protein LOC284382	380						cytoplasm|cytoskeleton				large_intestine(2)|pancreas(1)	3														0.261261	68.24042	73.957046	29	82	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	8668914	8668914	204	19	C	T	T	19	19	ACTL9	T	1	1
SPTA1	6708	broad.mit.edu	36	1	156884992	156884992	+	Silent	SNP	C	G	G			TCGA-06-0210-01	TCGA-06-0210-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr1:156884992C>G	uc001fst.1	-	c.3645G>C	c.(3643-3645)CTG>CTC	p.L1215L		NM_003126	NP_003117	P02549	SPTA1_HUMAN	spectrin, alpha, erythrocytic 1	1215	Spectrin 12.				actin filament capping|actin filament organization|axon guidance|regulation of cell shape	cytosol|intrinsic to internal side of plasma membrane|spectrin|spectrin-associated cytoskeleton	actin filament binding|calcium ion binding|structural constituent of cytoskeleton			ovary(4)|breast(1)	5	all_hematologic(112;0.0378)													0.155844	82.072679	108.17578	36	195	CC		KEEP	---	---	---	---	capture			Silent	SNP	156884992	156884992	15630	1	C	G	G	17	17	SPTA1	G	3	3
SPTA1	6708	broad.mit.edu	36	1	156894025	156894025	+	Nonsense_Mutation	SNP	G	A	A			TCGA-06-0210-01	TCGA-06-0210-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:156894025G>A	uc001fst.1	-	c.2671C>T	c.(2671-2673)CGA>TGA	p.R891*		NM_003126	NP_003117	P02549	SPTA1_HUMAN	spectrin, alpha, erythrocytic 1	891	Spectrin 9.				actin filament capping|actin filament organization|axon guidance|regulation of cell shape	cytosol|intrinsic to internal side of plasma membrane|spectrin|spectrin-associated cytoskeleton	actin filament binding|calcium ion binding|structural constituent of cytoskeleton			ovary(4)|breast(1)	5	all_hematologic(112;0.0378)													0.2	127.284483	154.902668	66	264	GG		KEEP	---	---	---	---	capture			Nonsense_Mutation	SNP	156894025	156894025	15630	1	G	A	A	38	38	SPTA1	A	5	1
F5	2153	broad.mit.edu	36	1	167778978	167778978	+	Splice_Site_SNP	SNP	T	G	G			TCGA-06-0210-01	TCGA-06-0210-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr1:167778978T>G	uc001ggg.1	-	c.1976_splice	c.e13-1	p.G659_splice		NM_000130	NP_000121			coagulation factor V precursor						cell adhesion|oxidation-reduction process|platelet activation|platelet degranulation	plasma membrane|platelet alpha granule lumen	copper ion binding|oxidoreductase activity			ovary(3)|large_intestine(1)|central_nervous_system(1)	5	all_hematologic(923;0.208)				Drotrecogin alfa(DB00055)									0.206897	47.007783	53.928963	18	69	TT		KEEP	---	---	---	---	capture			Splice_Site_SNP	SNP	167778978	167778978	5542	1	T	G	G	53	53	F5	G	5	4
TNN	63923	broad.mit.edu	36	1	173315310	173315310	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0210-01	TCGA-06-0210-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:173315310G>A	uc001gkl.1	+	c.628G>A	c.(628-630)GGC>AGC	p.G210S		NM_022093	NP_071376	Q9UQP3	TENN_HUMAN	tenascin N	210	EGF-like 2.				cell growth|cell migration|signal transduction	extracellular space|proteinaceous extracellular matrix				large_intestine(5)|ovary(3)|central_nervous_system(1)	9		Breast(1374;0.000962)								470				0.352941	15.546534	15.86995	6	11	GG		KEEP	---	---	---	---	capture		KIRC - Kidney renal clear cell carcinoma(1967;0.00198)	Missense_Mutation	SNP	173315310	173315310	16864	1	G	A	A	39	39	TNN	A	1	1
CAMSAP1L1	23271	broad.mit.edu	36	1	199051366	199051366	+	Missense_Mutation	SNP	C	G	G			TCGA-06-0210-01	TCGA-06-0210-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr1:199051366C>G	uc001gvl.1	+	c.616C>G	c.(616-618)CAC>GAC	p.H206D	CAMSAP1L1_uc001gvk.1_Missense_Mutation_p.H206D|CAMSAP1L1_uc001gvm.1_Missense_Mutation_p.H206D	NM_203459	NP_982284	Q08AD1	CAMP2_HUMAN	calmodulin regulated spectrin-associated protein	206						cytoplasm|microtubule	protein binding			ovary(2)|large_intestine(1)|pancreas(1)	4														0.275862	25.787217	27.098866	8	21	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	199051366	199051366	2729	1	C	G	G	29	29	CAMSAP1L1	G	3	3
CD46	4179	broad.mit.edu	36	1	205997572	205997572	+	Silent	SNP	C	T	T			TCGA-06-0210-01	TCGA-06-0210-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr1:205997572C>T	uc001hgj.1	+	c.351C>T	c.(349-351)TAC>TAT	p.Y117Y	CD46_uc001hgc.1_Silent_p.Y117Y|CD46_uc001hgd.1_Silent_p.Y117Y|CD46_uc001hge.1_Silent_p.Y117Y|CD46_uc001hgf.1_Silent_p.Y117Y|CD46_uc001hgg.1_Silent_p.Y117Y|CD46_uc001hgh.1_Silent_p.Y117Y|CD46_uc001hgi.1_Silent_p.Y117Y|CD46_uc001hgk.1_Silent_p.Y117Y|CD46_uc001hgm.1_Silent_p.Y117Y|CD46_uc001hgl.1_Silent_p.Y117Y|CD46_uc001hgn.1_Silent_p.Y117Y|CD46_uc001hgo.1_Silent_p.Y117Y|CD46_uc001hgp.1_Silent_p.Y117Y	NM_172359	NP_758869	P15529	MCP_HUMAN	CD46 antigen, complement regulatory protein	117	Extracellular (Potential).|Sushi 2.				complement activation, classical pathway|innate immune response|interspecies interaction between organisms|single fertilization	inner acrosomal membrane|integral to plasma membrane	receptor activity			large_intestine(2)|central_nervous_system(1)	3														0.177778	15.3719	19.772626	8	37	CC		KEEP	---	---	---	---	capture			Silent	SNP	205997572	205997572	3146	1	C	T	T	19	19	CD46	T	1	1
LCK	3932	broad.mit.edu	36	1	32514106	32514106	+	Silent	SNP	G	A	A	rs1126767	unknown	TCGA-06-0210-01	TCGA-06-0210-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:32514106G>A	uc001buz.1	+	c.486G>A	c.(484-486)TCG>TCA	p.S162S	LCK_uc001bux.1_Silent_p.S162S|LCK_uc001buy.1_Silent_p.S162S|LCK_uc001bva.1_Silent_p.S220S	NM_005356	NP_005347	P06239	LCK_HUMAN	lymphocyte-specific protein tyrosine kinase	162	SH2.|Interaction with PTPRH.				activation of caspase activity|cellular zinc ion homeostasis|induction of apoptosis|interspecies interaction between organisms|leukocyte migration|platelet activation|positive regulation of T cell receptor signaling pathway|regulation of defense response to virus by virus|release of sequestered calcium ion into cytosol|response to drug|T cell costimulation|T cell differentiation|T cell receptor signaling pathway|viral reproduction	cytosol|Golgi apparatus|membrane raft|pericentriolar material|plasma membrane	ATP binding|ATPase binding|CD4 receptor binding|CD8 receptor binding|glycoprotein binding|non-membrane spanning protein tyrosine kinase activity|phosphatidylinositol 3-kinase binding|protein C-terminus binding|protein kinase binding|protein serine/threonine phosphatase activity|SH2 domain binding	p.S162S(1)		central_nervous_system(2)|ovary(1)|lung(1)	4		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0837)|Ovarian(437;0.101)|Breast(348;0.212)			Dasatinib(DB01254)					146				0.259259	68.469274	74.126622	28	80	GG		KEEP	---	---	---	---	capture			Silent	SNP	32514106	32514106	9000	1	G	A	A	40	40	LCK	A	1	1
PRPF38A	84950	broad.mit.edu	36	1	52653076	52653076	+	Missense_Mutation	SNP	C	G	G			TCGA-06-0210-01	TCGA-06-0210-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr1:52653076C>G	uc001ctv.2	+	c.804C>G	c.(802-804)AGC>AGG	p.S268R	PRPF38A_uc001ctw.2_Missense_Mutation_p.A79G	NM_032864	NP_116253	Q8NAV1	PR38A_HUMAN	PRP38 pre-mRNA processing factor 38 (yeast)	268	Arg-rich.				mRNA processing|RNA splicing	spliceosomal complex					0														0.173516	90.997555	113.058412	38	181	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	52653076	52653076	13010	1	C	G	G	25	25	PRPF38A	G	3	3
CHD5	26038	broad.mit.edu	36	1	6111646	6111646	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0210-01	TCGA-06-0210-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:6111646G>A	uc001amb.1	-	c.3458C>T	c.(3457-3459)TCG>TTG	p.S1153L	CHD5_uc001alz.1_Missense_Mutation_p.S10L|CHD5_uc001ama.1_Non-coding_Transcript|CHD5_uc001amc.1_Non-coding_Transcript|CHD5_uc009vlx.1_Non-coding_Transcript	NM_015557	NP_056372	Q8TDI0	CHD5_HUMAN	chromodomain helicase DNA binding protein 5	1153	Helicase C-terminal.				chromatin assembly or disassembly|chromatin modification|regulation of transcription, DNA-dependent|transcription, DNA-dependent	chromatin|nucleus	ATP binding|ATP-dependent helicase activity|chromatin binding|DNA binding|zinc ion binding	p.S1153L(1)		breast(3)|central_nervous_system(3)|ovary(1)|lung(1)|pancreas(1)	9	Ovarian(185;0.0634)	all_cancers(23;5.36e-32)|all_epithelial(116;2.32e-17)|all_neural(13;3.68e-06)|all_lung(118;3.94e-06)|all_hematologic(16;2.39e-05)|Lung NSC(185;5.33e-05)|Acute lymphoblastic leukemia(12;0.000372)|Glioma(11;0.00127)|Renal(390;0.00188)|Colorectal(325;0.00342)|Breast(487;0.00373)|Hepatocellular(190;0.0218)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.15)								2304				0.239437	80.179315	88.981389	34	108	GG		KEEP	---	---	---	---	capture		Epithelial(90;3.08e-37)|GBM - Glioblastoma multiforme(13;1.36e-31)|OV - Ovarian serous cystadenocarcinoma(86;7.7e-19)|Colorectal(212;9.97e-08)|COAD - Colon adenocarcinoma(227;1.07e-05)|Kidney(185;6.16e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.00109)|BRCA - Breast invasive adenocarcinoma(365;0.0012)|STAD - Stomach adenocarcinoma(132;0.00346)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.193)	Missense_Mutation	SNP	6111646	6111646	3462	1	G	A	A	37	37	CHD5	A	1	1
DNAJC6	9829	broad.mit.edu	36	1	65625091	65625091	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0210-01	TCGA-06-0210-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:65625091G>A	uc001dce.1	+	c.1004G>A	c.(1003-1005)CGT>CAT	p.R335H	DNAJC6_uc001dcc.1_Missense_Mutation_p.R309H|DNAJC6_uc001dcd.1_Missense_Mutation_p.R278H	NM_014787	NP_055602	O75061	AUXI_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 6	278	C2 tensin-type.				cellular membrane organization|post-Golgi vesicle-mediated transport	cytosol	heat shock protein binding|protein tyrosine phosphatase activity|SH3 domain binding			large_intestine(1)|lung(1)|ovary(1)	3														0.198413	52.315722	62.975013	25	101	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	65625091	65625091	4836	1	G	A	A	40	40	DNAJC6	A	1	1
PCSK2	5126	broad.mit.edu	36	20	17155991	17155991	+	Missense_Mutation	SNP	G	T	T			TCGA-06-0210-01	TCGA-06-0210-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr20:17155991G>T	uc002wpm.1	+	c.41G>T	c.(40-42)GGG>GTG	p.G14V	PCSK2_uc002wpl.1_5'UTR	NM_002594	NP_002585	P16519	NEC2_HUMAN	proprotein convertase subtilisin/kexin type 2	14					enkephalin processing|insulin processing|islet amyloid polypeptide processing	extracellular space|membrane|soluble fraction|transport vesicle	serine-type endopeptidase activity			ovary(3)|central_nervous_system(2)|large_intestine(1)|pancreas(1)	7					Insulin Glargine recombinant(DB00047)|Insulin Lyspro recombinant(DB00046)|Insulin recombinant(DB00030)|Insulin, porcine(DB00071)									0.20904	80.181718	94.057988	37	140	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	17155991	17155991	12022	20	G	T	T	43	43	PCSK2	T	3	3
BFSP1	631	broad.mit.edu	36	20	17437628	17437628	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0210-01	TCGA-06-0210-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr20:17437628G>A	uc002wpo.1	-	c.641C>T	c.(640-642)ACG>ATG	p.T214M	BFSP1_uc002wpp.1_Missense_Mutation_p.T89M	NM_001195	NP_001186	Q12934	BFSP1_HUMAN	filensin	214	Rod.|Coil 2.					cytoplasm|intermediate filament|membrane	structural constituent of cytoskeleton|structural constituent of eye lens			central_nervous_system(1)	1														0.294118	24.939159	26.227566	10	24	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	17437628	17437628	1439	20	G	A	A	40	40	BFSP1	A	1	1
SBF1	6305	broad.mit.edu	36	22	49251694	49251694	+	Missense_Mutation	SNP	C	G	G			TCGA-06-0210-01	TCGA-06-0210-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr22:49251694C>G	uc003blh.1	-	c.739G>C	c.(739-741)GCC>CCC	p.A247P	SBF1_uc003blg.1_Missense_Mutation_p.A247P|SBF1_uc003bli.1_Missense_Mutation_p.A248P	NM_002972	NP_002963	O95248	MTMR5_HUMAN	SET binding factor 1 isoform a	247	DENN.				protein dephosphorylation	integral to membrane|nucleus	protein tyrosine/serine/threonine phosphatase activity				0		all_cancers(38;5.78e-13)|all_epithelial(38;1.71e-11)|all_lung(38;3.89e-05)|Breast(42;0.000523)|Lung NSC(38;0.000992)|Ovarian(80;0.0221)|Hepatocellular(38;0.0691)|Lung SC(80;0.113)												0.571429	8.62216	8.643064	4	3	CC		KEEP	---	---	---	---	capture		BRCA - Breast invasive adenocarcinoma(115;0.206)|LUAD - Lung adenocarcinoma(64;0.247)	Missense_Mutation	SNP	49251694	49251694	14339	22	C	G	G	27	27	SBF1	G	3	3
PSD4	23550	broad.mit.edu	36	2	113659049	113659049	+	Silent	SNP	C	T	T			TCGA-06-0210-01	TCGA-06-0210-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr2:113659049C>T	uc002tjc.1	+	c.1101C>T	c.(1099-1101)GAC>GAT	p.D367D	PSD4_uc002tjd.1_De_novo_Start_InFrame|PSD4_uc002tje.1_Silent_p.D366D|PSD4_uc002tjf.1_De_novo_Start_OutOfFrame	NM_012455	NP_036587	Q8NDX1	PSD4_HUMAN	pleckstrin and Sec7 domain containing 4	367					regulation of ARF protein signal transduction	cytoplasm|plasma membrane	ARF guanyl-nucleotide exchange factor activity			ovary(2)	2														0.184307	199.853524	251.099553	101	447	CC		KEEP	---	---	---	---	capture			Silent	SNP	113659049	113659049	13102	2	C	T	T	19	19	PSD4	T	1	1
SLC30A3	7781	broad.mit.edu	36	2	27334538	27334538	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0210-01	TCGA-06-0210-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr2:27334538C>T	uc002rjk.1	-	c.419G>A	c.(418-420)CGT>CAT	p.R140H	SLC30A3_uc002rjj.1_5'UTR	NM_003459	NP_003450	Q99726	ZNT3_HUMAN	solute carrier family 30 (zinc transporter),	140	Cytoplasmic (Potential).				regulation of sequestering of zinc ion	cell junction|integral to plasma membrane|late endosome|membrane fraction|synaptic vesicle membrane	zinc transporting ATPase activity				0	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)													0.184	87.835226	111.236474	46	204	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	27334538	27334538	15053	2	C	T	T	19	19	SLC30A3	T	1	1
CTNNA2	1496	broad.mit.edu	36	2	79825121	79825121	+	Missense_Mutation	SNP	C	G	G			TCGA-06-0210-01	TCGA-06-0210-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr2:79825121C>G	uc002soi.1	+	c.203C>G	c.(202-204)ACT>AGT	p.T68S	CTNNA2_uc002sog.1_Missense_Mutation_p.T68S|CTNNA2_uc002soh.1_Missense_Mutation_p.T68S	NM_004389	NP_004380	P26232	CTNA2_HUMAN	catenin, alpha 2	68					axonogenesis|brain morphogenesis|cell-cell adhesion|dendrite morphogenesis|muscle cell differentiation|positive regulation of muscle cell differentiation|prepulse inhibition|radial glia guided migration of Purkinje cell|regulation of synapse structural plasticity	actin cytoskeleton|axon|cytosol	cadherin binding|structural constituent of cytoskeleton			pancreas(4)|lung(3)|breast(1)	8										489				0.216867	47.903895	54.040444	18	65	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	79825121	79825121	4172	2	C	G	G	20	20	CTNNA2	G	3	3
STXBP5L	9515	broad.mit.edu	36	3	122458710	122458710	+	Nonsense_Mutation	SNP	C	T	T			TCGA-06-0210-01	TCGA-06-0210-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr3:122458710C>T	uc003eec.2	+	c.1672C>T	c.(1672-1674)CGA>TGA	p.R558*		NM_014980	NP_055795	Q9Y2K9	STB5L_HUMAN	syntaxin binding protein 5-like	558	WD 9.				exocytosis|protein transport	cytoplasm|integral to membrane|plasma membrane				ovary(7)	7														0.124138	18.623481	38.712823	18	127	CC		KEEP	---	---	---	---	capture		GBM - Glioblastoma multiforme(114;0.0694)	Nonsense_Mutation	SNP	122458710	122458710	15877	3	C	T	T	19	19	STXBP5L	T	5	1
PIK3CA	5290	broad.mit.edu	36	3	180418785	180418785	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0210-01	TCGA-06-0210-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr3:180418785G>A	uc003fjk.1	+	c.1633G>A	c.(1633-1635)GAG>AAG	p.E545K		NM_006218	NP_006209	P42336	PK3CA_HUMAN	phosphoinositide-3-kinase, catalytic, alpha	545			E -> G (in KERSEB).|E -> A (in cancer).|E -> K (in KERSEB; shows an increase in lipid kinase activity; oncogenic in vivo).		epidermal growth factor receptor signaling pathway|fibroblast growth factor receptor signaling pathway|insulin receptor signaling pathway|leukocyte migration|nerve growth factor receptor signaling pathway|phosphatidylinositol-mediated signaling|platelet activation|T cell costimulation|T cell receptor signaling pathway		1-phosphatidylinositol-3-kinase activity|ATP binding|phosphatidylinositol-4,5-bisphosphate 3-kinase activity	p.E545K(713)|p.E545?(19)|p.E545Q(11)|p.E545D(1)|p.E545G(1)|p.E545A(1)		breast(1506)|large_intestine(749)|endometrium(244)|urinary_tract(195)|ovary(136)|skin(112)|stomach(89)|thyroid(77)|central_nervous_system(69)|lung(61)|upper_aerodigestive_tract(48)|haematopoietic_and_lymphoid_tissue(27)|cervix(25)|biliary_tract(22)|liver(20)|oesophagus(17)|pancreas(11)|penis(8)|pituitary(8)|autonomic_ganglia(4)|kidney(2)|prostate(2)|meninges(1)|eye(1)|NS(1)|soft_tissue(1)|bone(1)	3437	all_cancers(143;1.19e-17)|Ovarian(172;0.00769)|Breast(254;0.155)					Colon(199;1504 1750 3362 26421 31210 32040)	E545K(RERFLCSQ1_LUNG)|E545K(KYSE510_OESOPHAGUS)|E545K(NCIH508_LARGE_INTESTINE)|E545K(HCC202_BREAST)|E545K(BFTC909_KIDNEY)|E545K(HCT15_LARGE_INTESTINE)|E545K(NCIH596_LUNG)|E545K(L363_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|E545K(DLD1_LARGE_INTESTINE)|E545K(ESS1_ENDOMETRIUM)|E545K(MDAMB361_BREAST)|E545K(MKN1_STOMACH)|E545K(MCF7_BREAST)|E545K(NCIH460_LUNG)|E545K(TCCSUP_URINARY_TRACT)|E545K(HSC4_UPPER_AERODIGESTIVE_TRACT)|E545K(BC3C_URINARY_TRACT)|E545K(HUH28_BILIARY_TRACT)|E545K(HT1197_URINARY_TRACT)|E545K(TE5_OESOPHAGUS)	57	p.E545K(NCIH508-Tumor)|p.E545K(L363-Tumor)|p.E545K(KYSE510-Tumor)|p.E545K(MKN1-Tumor)|p.E545K(BFTC909-Tumor)|p.E545K(NCIH460-Tumor)|p.E545K(HCC202-Tumor)|p.E545K(KPL1-Tumor)|p.E545K(NCIH596-Tumor)|p.E545K(HUH28-Tumor)|p.E545K(MDAMB361-Tumor)|p.E545K(ESS1-Tumor)|p.E545K(TE5-Tumor)|p.E545K(HSC4-Tumor)|p.E545K(RERFLCSQ1-Tumor)	621	TCGA GBM(8;5.49e-07)			0.225806	15.606469	17.749023	7	24	GG		KEEP	---	---	---	---	capture	OV - Ovarian serous cystadenocarcinoma(80;9.59e-28)|GBM - Glioblastoma multiforme(14;0.003)|BRCA - Breast invasive adenocarcinoma(182;0.0282)		Missense_Mutation	SNP	180418785	180418785	12337	3	G	A	A	45	45	PIK3CA	A	2	2
MOBP	4336	broad.mit.edu	36	3	39518754	39518754	+	Missense_Mutation	SNP	G	C	C			TCGA-06-0210-01	TCGA-06-0210-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr3:39518754G>C	uc003cjv.1	+	c.190G>C	c.(190-192)GCC>CCC	p.A64P	MOBP_uc003cju.1_Missense_Mutation_p.A64P|MOBP_uc003cjw.1_Non-coding_Transcript|MOBP_uc010hht.1_Missense_Mutation_p.A64P|MOBP_uc003cjx.1_Non-coding_Transcript|MOBP_uc003cjy.1_Non-coding_Transcript	NM_182935	NP_891980	Q13875	MOBP_HUMAN	myelin-associated oligodendrocyte basic protein	64					nervous system development	nucleolus|perinuclear region of cytoplasm|soluble fraction				ovary(1)|central_nervous_system(1)	2														0.232558	7.97556	10.997217	10	33	GG		KEEP	---	---	---	---	capture		KIRC - Kidney renal clear cell carcinoma(284;0.082)|Kidney(284;0.0998)	Missense_Mutation	SNP	39518754	39518754	10079	3	G	C	C	38	38	MOBP	C	3	3
SEMA3F	6405	broad.mit.edu	36	3	50186756	50186756	+	Missense_Mutation	SNP	G	T	T			TCGA-06-0210-01	TCGA-06-0210-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr3:50186756G>T	uc003cyj.1	+	c.425G>T	c.(424-426)TGC>TTC	p.C142F	SEMA3F_uc003cyk.1_Missense_Mutation_p.C142F	NM_004186	NP_004177	Q13275	SEM3F_HUMAN	semaphorin 3F	142	Sema.				axon guidance	extracellular space|membrane	chemorepellent activity|receptor activity			lung(1)	1														0.182836	90.278584	115.567885	49	219	GG		KEEP	---	---	---	---	capture		BRCA - Breast invasive adenocarcinoma(193;0.00013)|KIRC - Kidney renal clear cell carcinoma(197;0.00599)|Kidney(197;0.00688)	Missense_Mutation	SNP	50186756	50186756	14515	3	G	T	T	46	46	SEMA3F	T	3	3
STAB1	23166	broad.mit.edu	36	3	52527005	52527005	+	Silent	SNP	C	T	T			TCGA-06-0210-01	TCGA-06-0210-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr3:52527005C>T	uc003dej.1	+	c.4707C>T	c.(4705-4707)TGC>TGT	p.C1569C	STAB1_uc003dek.1_5'Flank	NM_015136	NP_055951	Q9NY15	STAB1_HUMAN	stabilin 1 precursor	1569	Extracellular (Potential).|EGF-like 13.				cell adhesion|cell-cell signaling|defense response to bacterium|inflammatory response|negative regulation of angiogenesis|receptor-mediated endocytosis	integral to plasma membrane	bacterial cell surface binding|hyaluronic acid binding|low-density lipoprotein receptor activity|protein disulfide oxidoreductase activity|scavenger receptor activity			large_intestine(3)|pancreas(1)|breast(1)|central_nervous_system(1)|skin(1)	7														0.187879	57.120456	72.180347	31	134	CC		KEEP	---	---	---	---	capture		BRCA - Breast invasive adenocarcinoma(193;1.73e-05)|Kidney(197;0.00182)|KIRC - Kidney renal clear cell carcinoma(197;0.00205)|OV - Ovarian serous cystadenocarcinoma(275;0.0482)	Silent	SNP	52527005	52527005	15755	3	C	T	T	27	27	STAB1	T	1	1
CPZ	8532	broad.mit.edu	36	4	8656753	8656753	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0210-01	TCGA-06-0210-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr4:8656753G>A	uc003glm.1	+	c.647G>A	c.(646-648)AGC>AAC	p.S216N	CPZ_uc003gll.1_Non-coding_Transcript|CPZ_uc003glo.1_Missense_Mutation_p.S205N|CPZ_uc003gln.1_Missense_Mutation_p.S79N|CPZ_uc003glp.1_Non-coding_Transcript	NM_001014447	NP_001014448	Q66K79	CBPZ_HUMAN	carboxypeptidase Z isoform 1	216					proteolysis|Wnt receptor signaling pathway	proteinaceous extracellular matrix	metallocarboxypeptidase activity|zinc ion binding			ovary(2)|pancreas(1)	3														0.25	12.536069	13.901898	6	18	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	8656753	8656753	3978	4	G	A	A	34	34	CPZ	A	2	2
PDHA2	5161	broad.mit.edu	36	4	96980347	96980347	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0210-01	TCGA-06-0210-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr4:96980347G>A	uc003htr.2	+	c.23G>A	c.(22-24)CGC>CAC	p.R8H		NM_005390	NP_005381	P29803	ODPAT_HUMAN	pyruvate dehydrogenase (lipoamide) alpha 2	8					glycolysis|oxidation-reduction process	mitochondrial matrix	pyruvate dehydrogenase (acetyl-transferring) activity			central_nervous_system(1)	1		Hepatocellular(203;0.114)			NADH(DB00157)									0.206349	28.140898	33.177079	13	50	GG		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(123;1.23e-06)	Missense_Mutation	SNP	96980347	96980347	12086	4	G	A	A	38	38	PDHA2	A	1	1
PCDHGB3	56102	broad.mit.edu	36	5	140730447	140730447	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0210-01	TCGA-06-0210-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr5:140730447C>T	uc003ljw.1	+	c.302C>T	c.(301-303)ACG>ATG	p.T101M	PCDHGA1_uc003lji.1_Intron|PCDHGA2_uc003ljk.1_Intron|PCDHGA3_uc010jfx.1_Intron|PCDHGA3_uc003ljm.1_Intron|PCDHGB1_uc003ljo.1_Intron|PCDHGA4_uc003ljq.1_Intron|PCDHGB2_uc003ljs.1_Intron|PCDHGA5_uc003lju.1_Intron|PCDHGB3_uc003ljv.1_Missense_Mutation_p.T101M	NM_018924	NP_061747	Q9Y5G1	PCDGF_HUMAN	protocadherin gamma subfamily B, 3 isoform 1	101	Extracellular (Potential).|Cadherin 1.				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding				0														0.223077	194.121113	221.624771	87	303	CC		KEEP	---	---	---	---	capture	KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)		Missense_Mutation	SNP	140730447	140730447	11984	5	C	T	T	19	19	PCDHGB3	T	1	1
PRDM9	56979	broad.mit.edu	36	5	23563437	23563437	+	Missense_Mutation	SNP	G	T	T			TCGA-06-0210-01	TCGA-06-0210-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr5:23563437G>T	uc003jgo.1	+	c.2483G>T	c.(2482-2484)GGG>GTG	p.G828V		NM_020227	NP_064612	Q9NQV7	PRDM9_HUMAN	PR domain containing 9	828					meiosis|regulation of transcription, DNA-dependent|transcription, DNA-dependent	chromosome|nucleoplasm	histone-lysine N-methyltransferase activity|nucleic acid binding|zinc ion binding			ovary(3)|large_intestine(2)|pancreas(1)	6														0.128319	30.098049	60.56983	29	197	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	23563437	23563437	12906	5	G	T	T	43	43	PRDM9	T	3	3
RGNEF	64283	broad.mit.edu	36	5	73125985	73125985	+	Missense_Mutation	SNP	A	G	G			TCGA-06-0210-01	TCGA-06-0210-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr5:73125985A>G	uc010izf.1	+	c.913A>G	c.(913-915)ATT>GTT	p.I305V	RGNEF_uc003kcx.1_Missense_Mutation_p.I305V|RGNEF_uc003kcy.1_Missense_Mutation_p.I305V	NM_001080479	NP_001073948	Q8N1W1	RGNEF_HUMAN	Rho-guanine nucleotide exchange factor	305					cell differentiation|intracellular signal transduction|regulation of Rho protein signal transduction	cytoplasm|plasma membrane	metal ion binding|Rho guanyl-nucleotide exchange factor activity|RNA binding				0		Lung NSC(167;0.0378)|all_lung(232;0.04)|Ovarian(174;0.0798)												0.25	11.592539	12.501319	4	12	AA		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(47;1.25e-51)	Missense_Mutation	SNP	73125985	73125985	13756	5	A	G	G	12	12	RGNEF	G	4	4
KIF13A	63971	broad.mit.edu	36	6	17912709	17912709	+	Silent	SNP	G	T	T			TCGA-06-0210-01	TCGA-06-0210-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr6:17912709G>T	uc003ncg.2	-	c.2316C>A	c.(2314-2316)CTC>CTA	p.L772L	KIF13A_uc003ncf.2_Silent_p.L772L|KIF13A_uc003nch.2_Silent_p.L772L|KIF13A_uc003nci.2_Silent_p.L772L	NM_022113	NP_071396	Q9H1H9	KI13A_HUMAN	kinesin family member 13A isoform a	772	Potential.				cargo loading into vesicle|cell cycle|cytokinesis|endosome to lysosome transport|Golgi to plasma membrane protein transport|melanosome organization|plus-end-directed vesicle transport along microtubule	centrosome|endosome membrane|microtubule|midbody|trans-Golgi network membrane	ATP binding|microtubule motor activity|protein binding			large_intestine(2)|ovary(2)	4	Breast(50;0.0107)|Ovarian(93;0.016)	all_hematologic(90;0.125)												0.333333	10.495661	10.791038	4	8	GG		KEEP	---	---	---	---	capture	all cancers(50;0.0865)|Epithelial(50;0.0974)		Silent	SNP	17912709	17912709	8585	6	G	T	T	33	33	KIF13A	T	3	3
PRSS35	167681	broad.mit.edu	36	6	84291091	84291091	+	Silent	SNP	C	T	T			TCGA-06-0210-01	TCGA-06-0210-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr6:84291091C>T	uc003pjz.1	+	c.1212C>T	c.(1210-1212)CAC>CAT	p.H404H	PRSS35_uc010kbm.1_Silent_p.H404H|PRSS35_uc010kbn.1_Silent_p.H404H	NM_153362	NP_699193	Q8N3Z0	PRS35_HUMAN	protease, serine, 35	404	Peptidase S1.				proteolysis	extracellular region	serine-type endopeptidase activity			ovary(1)	1		all_cancers(76;0.000113)|Acute lymphoblastic leukemia(125;1.09e-08)|all_hematologic(105;3.12e-05)|all_epithelial(107;0.0575)												0.304878	65.342985	68.128872	25	57	CC		KEEP	---	---	---	---	capture		BRCA - Breast invasive adenocarcinoma(397;0.0768)	Silent	SNP	84291091	84291091	13074	6	C	T	T	19	19	PRSS35	T	1	1
LRWD1	222229	broad.mit.edu	36	7	101893699	101893699	+	Silent	SNP	C	T	T			TCGA-06-0210-01	TCGA-06-0210-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr7:101893699C>T	uc003uzn.1	+	c.409C>T	c.(409-411)CTG>TTG	p.L137L	ALKBH4_uc003uzl.1_5'Flank|ALKBH4_uc003uzm.1_5'Flank|LRWD1_uc003uzo.1_5'UTR	NM_152892	NP_690852	Q9UFC0	LRWD1_HUMAN	leucine-rich repeats and WD repeat domain	137					chromatin modification|DNA-dependent DNA replication initiation|establishment of protein localization to chromatin|G1 phase of mitotic cell cycle	centromeric heterochromatin|nuclear origin of replication recognition complex|telomeric heterochromatin	chromatin binding|methyl-CpG binding|methylated histone residue binding				0														0.156977	52.809988	72.122594	27	145	CC		KEEP	---	---	---	---	capture			Silent	SNP	101893699	101893699	9423	7	C	T	T	24	24	LRWD1	T	2	2
THSD7A	221981	broad.mit.edu	36	7	11452352	11452352	+	Silent	SNP	T	A	A			TCGA-06-0210-01	TCGA-06-0210-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr7:11452352T>A	uc003ssf.2	-	c.2925A>T	c.(2923-2925)CCA>CCT	p.P975P		NM_015204	NP_056019	Q9UPZ6	THS7A_HUMAN	thrombospondin, type I, domain containing 7A	975	TSP type-1 10.|Extracellular (Potential).					integral to membrane				ovary(3)	3														0.190311	120.455232	146.369831	55	234	TT		KEEP	---	---	---	---	capture		UCEC - Uterine corpus endometrioid carcinoma (126;0.163)	Silent	SNP	11452352	11452352	16407	7	T	A	A	55	55	THSD7A	A	4	4
REPIN1	29803	broad.mit.edu	36	7	149700729	149700729	+	Missense_Mutation	SNP	G	T	T			TCGA-06-0210-01	TCGA-06-0210-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr7:149700729G>T	uc010lpr.1	+	c.1637G>T	c.(1636-1638)TGC>TTC	p.C546F	REPIN1_uc003whd.2_Missense_Mutation_p.C478F|REPIN1_uc010lpq.1_Missense_Mutation_p.C489F|REPIN1_uc003whc.2_Missense_Mutation_p.C489F|REPIN1_uc003whe.2_Missense_Mutation_p.C489F	NM_001099695	NP_001093165	Q9BWE0	REPI1_HUMAN	replication initiator 1 isoform 3	489	C2H2-type 13.				DNA replication	nuclear origin of replication recognition complex	DNA binding|zinc ion binding			pancreas(1)	1	Ovarian(565;0.183)|Melanoma(164;0.226)													0.197368	56.356788	69.33906	30	122	GG		KEEP	---	---	---	---	capture	OV - Ovarian serous cystadenocarcinoma(82;0.011)		Missense_Mutation	SNP	149700729	149700729	13696	7	G	T	T	46	46	REPIN1	T	3	3
INHBA	3624	broad.mit.edu	36	7	41695924	41695924	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0210-01	TCGA-06-0210-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr7:41695924C>T	uc003thq.1	-	c.1130G>A	c.(1129-1131)CGC>CAC	p.R377H	INHBA_uc003thr.1_Missense_Mutation_p.R377H	NM_002192	NP_002183	P08476	INHBA_HUMAN	inhibin beta A precursor	377				RMR -> AC (in Ref. 7; CAA51163).	cell cycle arrest|cell surface receptor linked signaling pathway|defense response|erythrocyte differentiation|eyelid development in camera-type eye|G1/S transition of mitotic cell cycle|growth|hair follicle development|hemoglobin biosynthetic process|hemopoietic progenitor cell differentiation|induction of apoptosis|male gonad development|negative regulation of B cell differentiation|negative regulation of cell growth|negative regulation of cell proliferation|negative regulation of follicle-stimulating hormone secretion|negative regulation of interferon-gamma biosynthetic process|negative regulation of macrophage differentiation|negative regulation of phosphorylation|nervous system development|odontogenesis|ovarian follicle development|palate development|positive regulation of erythrocyte differentiation|positive regulation of follicle-stimulating hormone secretion|positive regulation of ovulation|positive regulation of transcription from RNA polymerase II promoter|progesterone secretion|regulation of activin receptor signaling pathway|regulation of gene-specific transcription from RNA polymerase II promoter	activin A complex|inhibin A complex	cytokine activity|follistatin binding|growth factor activity|hormone activity|identical protein binding|signal transducer activity|transcription activator activity			lung(5)|ovary(1)	6									p.R377H(NCIH727-Tumor)	102	TSP Lung(11;0.080)			0.120155	29.242926	65.783893	31	227	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	41695924	41695924	8042	7	C	T	T	27	27	INHBA	T	1	1
GCK	2645	broad.mit.edu	36	7	44152644	44152644	+	Missense_Mutation	SNP	G	C	C			TCGA-06-0210-01	TCGA-06-0210-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr7:44152644G>C	uc003tkk.1	-	c.965C>G	c.(964-966)TCC>TGC	p.S322C	GCK_uc003tkl.2_Missense_Mutation_p.S321C|GCK_uc003tkh.1_5'Flank|GCK_uc003tki.1_5'Flank|GCK_uc003tkj.1_Missense_Mutation_p.S320C	NM_033507	NP_277042	P35557	HXK4_HUMAN	glucokinase isoform 2	321					cellular response to insulin stimulus|cellular response to leptin stimulus|detection of glucose|endocrine pancreas development|glucose homeostasis|glucose transport|glycolysis|negative regulation of gluconeogenesis|positive regulation of glycogen biosynthetic process|positive regulation of insulin secretion|regulation of glucose transport|regulation of glycolysis|transmembrane transport	cytosol|nucleoplasm	ATP binding|glucokinase activity|glucose binding|protein binding			lung(1)|skin(1)	2										356				0.173913	81.411253	102.154293	36	171	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	44152644	44152644	6559	7	G	C	C	41	41	GCK	C	3	3
ADCY1	107	broad.mit.edu	36	7	45685846	45685846	+	Missense_Mutation	SNP	C	G	G			TCGA-06-0210-01	TCGA-06-0210-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr7:45685846C>G	uc003tne.2	+	c.1912C>G	c.(1912-1914)CTG>GTG	p.L638V		NM_021116	NP_066939	Q08828	ADCY1_HUMAN	brain adenylate cyclase 1	638	Helical; (Potential).				activation of adenylate cyclase activity by G-protein signaling pathway|activation of phospholipase C activity|activation of protein kinase A activity|cellular response to glucagon stimulus|energy reserve metabolic process|inhibition of adenylate cyclase activity by G-protein signaling pathway|nerve growth factor receptor signaling pathway|synaptic transmission|transmembrane transport|water transport	integral to membrane|plasma membrane	ATP binding|calcium- and calmodulin-responsive adenylate cyclase activity|calmodulin binding|metal ion binding			ovary(3)|central_nervous_system(1)	4					Adenosine(DB00640)|Adenosine monophosphate(DB00131)|Adenosine triphosphate(DB00171)									0.142105	39.084818	62.567006	27	163	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	45685846	45685846	293	7	C	G	G	24	24	ADCY1	G	3	3
WBSCR17	64409	broad.mit.edu	36	7	70813811	70813811	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0210-01	TCGA-06-0210-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr7:70813811G>A	uc003tvy.1	+	c.1630G>A	c.(1630-1632)GTC>ATC	p.V544I	WBSCR17_uc003tvz.1_Missense_Mutation_p.V243I	NM_022479	NP_071924	Q6IS24	GLTL3_HUMAN	UDP-GalNAc:polypeptide	544	Ricin B-type lectin.|Lumenal (Potential).					Golgi membrane|integral to membrane	polypeptide N-acetylgalactosaminyltransferase activity|sugar binding			ovary(1)|central_nervous_system(1)|pancreas(1)	3		all_cancers(73;0.2)|Lung NSC(55;0.094)|all_lung(88;0.125)												0.170455	23.506259	32.522948	15	73	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	70813811	70813811	17836	7	G	A	A	44	44	WBSCR17	A	2	2
FKBP6	8468	broad.mit.edu	36	7	72392684	72392684	+	Missense_Mutation	SNP	G	C	C			TCGA-06-0210-01	TCGA-06-0210-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr7:72392684G>C	uc003tya.2	+	c.697G>C	c.(697-699)GAC>CAC	p.D233H	FKBP6_uc003twz.2_Missense_Mutation_p.D203H|FKBP6_uc010lbe.1_Non-coding_Transcript	NM_003602	NP_003593	O75344	FKBP6_HUMAN	FK506 binding protein 6 isoform a	233	TPR 2.				protein folding	membrane	FK506 binding|peptidyl-prolyl cis-trans isomerase activity				0		Lung NSC(55;0.0908)|all_lung(88;0.198)												0.223404	116.1499	129.37242	42	146	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	72392684	72392684	6150	7	G	C	C	33	33	FKBP6	C	3	3
CCDC132	55610	broad.mit.edu	36	7	92724693	92724693	+	Missense_Mutation	SNP	A	G	G			TCGA-06-0210-01	TCGA-06-0210-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr7:92724693A>G	uc003umo.1	+	c.403A>G	c.(403-405)ATC>GTC	p.I135V	CCDC132_uc003ump.1_Missense_Mutation_p.I105V|CCDC132_uc003umq.1_Non-coding_Transcript|CCDC132_uc003umr.1_Non-coding_Transcript|CCDC132_uc003umn.1_Missense_Mutation_p.I135V	NM_017667	NP_060137	Q96JG6	CC132_HUMAN	coiled-coil domain containing 132 isoform a	135											0	all_cancers(62;2.64e-11)|all_epithelial(64;1.4e-10)|Breast(17;0.000675)|Lung NSC(181;0.0618)|all_lung(186;0.0837)													0.176471	22.246303	27.274252	9	42	AA		KEEP	---	---	---	---	capture	STAD - Stomach adenocarcinoma(171;0.000302)		Missense_Mutation	SNP	92724693	92724693	2887	7	A	G	G	16	16	CCDC132	G	4	4
PPP1R3B	79660	broad.mit.edu	36	8	9036077	9036077	+	Silent	SNP	C	T	T			TCGA-06-0210-01	TCGA-06-0210-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr8:9036077C>T	uc003wsn.2	-	c.495G>A	c.(493-495)ACG>ACA	p.T165T	PPP1R3B_uc003wso.2_Silent_p.T164T|PPP1R3B_uc010lrr.1_Silent_p.T165T	NM_024607	NP_078883	Q86XI6	PPR3B_HUMAN	protein phosphatase 1, regulatory (inhibitor)	165	CBM21.				glycogen metabolic process					ovary(1)	1														0.193798	103.101939	125.675816	50	208	CC		KEEP	---	---	---	---	capture		COAD - Colon adenocarcinoma(149;0.0717)|READ - Rectum adenocarcinoma(644;0.241)	Silent	SNP	9036077	9036077	12807	8	C	T	T	19	19	PPP1R3B	T	1	1
ZNF483	158399	broad.mit.edu	36	9	113344049	113344049	+	Missense_Mutation	SNP	C	G	G			TCGA-06-0210-01	TCGA-06-0210-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr9:113344049C>G	uc004bff.2	+	c.1013C>G	c.(1012-1014)CCC>CGC	p.P338R	ZNF483_uc004bfg.2_Intron	NM_133464	NP_597721	Q8TF39	ZN483_HUMAN	zinc finger protein 483 isoform a	338					regulation of transcription, DNA-dependent|viral reproduction	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding				0														0.27027	138.708867	147.491252	50	135	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	113344049	113344049	18530	9	C	G	G	22	22	ZNF483	G	3	3
ATP2B3	492	broad.mit.edu	36	X	152460543	152460543	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0210-01	TCGA-06-0210-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chrX:152460543C>T	uc004fht.1	+	c.629C>T	c.(628-630)GCG>GTG	p.A210V	ATP2B3_uc004fhs.1_Missense_Mutation_p.A210V	NM_001001344	NP_001001344	Q16720	AT2B3_HUMAN	plasma membrane calcium ATPase 3 isoform 3b	210	Cytoplasmic (Potential).				ATP biosynthetic process|platelet activation	integral to membrane|plasma membrane	ATP binding|calcium-transporting ATPase activity|calmodulin binding|metal ion binding			pancreas(1)	1	all_hematologic(71;4.25e-06)|Acute lymphoblastic leukemia(192;6.56e-05)													0.214035	131.327735	152.860952	61	224	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	152460543	152460543	1160	23	C	T	T	27	27	ATP2B3	T	1	1
CASK	8573	broad.mit.edu	36	X	41667180	41667180	+	Silent	SNP	G	A	A			TCGA-06-0210-01	TCGA-06-0210-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chrX:41667180G>A	uc004dfl.2	-	c.6C>T	c.(4-6)GCC>GCT	p.A2A	CASK_uc004dfm.2_Silent_p.A2A|CASK_uc004dfn.2_Silent_p.A2A	NM_003688	NP_003679	O14936	CSKP_HUMAN	calcium/calmodulin-dependent serine protein	2					cell adhesion|protein phosphorylation	actin cytoskeleton|cytoplasm|nucleus|plasma membrane	ATP binding|calmodulin binding|guanylate kinase activity|protein serine/threonine kinase activity			ovary(3)|lung(2)|stomach(1)	6						NSCLC(42;104 1086 3090 27189 35040)				254				0.3	104.973932	109.620387	39	91	GG		KEEP	---	---	---	---	capture			Silent	SNP	41667180	41667180	2784	23	G	A	A	39	39	CASK	A	1	1
FGD1	2245	broad.mit.edu	36	X	54514531	54514531	+	Missense_Mutation	SNP	G	T	T			TCGA-06-0210-01	TCGA-06-0210-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chrX:54514531G>T	uc004dtg.1	-	c.422C>A	c.(421-423)ACT>AAT	p.T141N		NM_004463	NP_004454	P98174	FGD1_HUMAN	faciogenital dysplasia protein	141	Pro-rich.				actin cytoskeleton organization|apoptosis|filopodium assembly|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|organ morphogenesis|regulation of Cdc42 GTPase activity|regulation of cell shape|small GTPase mediated signal transduction	cytoskeleton|cytosol|Golgi apparatus|lamellipodium|nucleus|plasma membrane|ruffle	Rho guanyl-nucleotide exchange factor activity|small GTPase binding|zinc ion binding			ovary(3)|skin(2)|central_nervous_system(1)	6														0.190045	93.432276	113.276443	42	179	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	54514531	54514531	6069	23	G	T	T	36	36	FGD1	T	3	3
CASKIN2	57513	broad.mit.edu	36	17	71010395	71010396	+	Frame_Shift_Ins	INS	-	G	G			TCGA-06-0210-01	TCGA-06-0210-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:71010395_71010396insG	uc002joc.1	-	c.2354_2355insC	c.(2353-2355)CCTfs	p.P785fs		NM_020753	NP_065804	Q8WXE0	CSKI2_HUMAN	cask-interacting protein 2 isoform a	785	Pro-rich.					cytoplasm				pancreas(1)	1	all_cancers(13;3.15e-09)|all_epithelial(9;5.78e-10)|Breast(9;5.8e-10)|all_lung(278;0.246)		all cancers(21;4.57e-07)|Epithelial(20;2.92e-06)|Lung(188;0.0809)|LUSC - Lung squamous cell carcinoma(166;0.154)											0.31			16	36				---	---	---	---	capture_indel			Frame_Shift_Ins	INS	71010395	71010396	2786	17	-	G	G	7	7	CASKIN2	G	5	5
