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
A1CF	29974	broad.mit.edu	36	10	52239778	52239778	+	Silent	SNP	G	T	T			TCGA-16-0850-01	TCGA-16-0850-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr10:52239778G>T	uc001jjj.1	-	c.1515C>A	c.(1513-1515)GCC>GCA	p.A505A	A1CF_uc001jji.1_Silent_p.A497A|A1CF_uc001jjh.1_Silent_p.A505A|A1CF_uc009xov.1_Silent_p.A497A	NM_138932	NP_620310	Q9NQ94	A1CF_HUMAN	apobec-1 complementation factor isoform 2	505					cytidine to uridine editing|mRNA modification|mRNA processing|protein stabilization	apolipoprotein B mRNA editing enzyme complex|endoplasmic reticulum|nucleoplasm	nucleotide binding|protein binding|single-stranded RNA binding			central_nervous_system(1)	1														0.371429	39.465471	39.973965	13	22	GG		KEEP	---	---	---	---	capture			Silent	SNP	52239778	52239778	2	10	G	T	T	35	35	A1CF	T	3	3
TMEM26	219623	broad.mit.edu	36	10	62840109	62840109	+	Missense_Mutation	SNP	C	T	T			TCGA-16-0850-01	TCGA-16-0850-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr10:62840109C>T	uc001jlo.1	-	c.1084G>A	c.(1084-1086)GAC>AAC	p.D362N	TMEM26_uc001jlp.1_Non-coding_Transcript	NM_178505	NP_848600	Q6ZUK4	TMM26_HUMAN	transmembrane protein 26	362						integral to membrane					0	Prostate(12;0.0112)													0.333333	9.222053	9.443432	3	6	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	62840109	62840109	16690	10	C	T	T	31	31	TMEM26	T	1	1
CCDC153	283152	broad.mit.edu	36	11	118566297	118566297	+	Silent	SNP	G	A	A			TCGA-16-0850-01	TCGA-16-0850-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr11:118566297G>A	uc001pwc.1	-	c.297C>T	c.(295-297)CAC>CAT	p.H99H	CCDC153_uc001pwd.1_Silent_p.H99H	NM_001033658	NP_001028830	Q494R4	CC153_HUMAN	coiled-coil domain containing 153	185											0														0.3	122.316148	127.677661	45	105	GG		KEEP	---	---	---	---	capture			Silent	SNP	118566297	118566297	2908	11	G	A	A	40	40	CCDC153	A	1	1
DGAT2	84649	broad.mit.edu	36	11	75189173	75189173	+	Missense_Mutation	SNP	C	T	T			TCGA-16-0850-01	TCGA-16-0850-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr11:75189173C>T	uc001oxa.2	+	c.1139C>T	c.(1138-1140)CCG>CTG	p.P380L	DGAT2_uc001oxb.2_Missense_Mutation_p.P337L	NM_032564	NP_115953	Q96PD7	DGAT2_HUMAN	diacylglycerol O-acyltransferase homolog 2	380	Cytoplasmic (Potential).				glycerol metabolic process|triglyceride biosynthetic process	endoplasmic reticulum membrane|integral to membrane	diacylglycerol O-acyltransferase activity				0	Ovarian(111;0.103)					Melanoma(35;811 1096 8354 24009 39363)								0.296053	234.021666	245.281823	90	214	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	75189173	75189173	4637	11	C	T	T	23	23	DGAT2	T	1	1
KDM2B	84678	broad.mit.edu	36	12	120366428	120366428	+	Missense_Mutation	SNP	A	G	G			TCGA-16-0850-01	TCGA-16-0850-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr12:120366428A>G	uc001uat.1	-	c.2221T>C	c.(2221-2223)TCC>CCC	p.S741P	KDM2B_uc001uas.1_Missense_Mutation_p.S710P|KDM2B_uc009zxe.1_Missense_Mutation_p.S710P|KDM2B_uc001uau.1_Intron|KDM2B_uc009zxf.1_Missense_Mutation_p.S741P|KDM2B_uc001uao.1_5'UTR|KDM2B_uc001uap.1_Non-coding_Transcript|KDM2B_uc001uaq.1_Missense_Mutation_p.S181P|KDM2B_uc001uar.1_Missense_Mutation_p.S332P	NM_032590	NP_115979	Q8NHM5	KDM2B_HUMAN	F-box and leucine-rich repeat protein 10 isoform	741					oxidation-reduction process|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleolus	DNA binding|histone demethylase activity (H3-K36 specific)|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|protein binding|rRNA binding|zinc ion binding			ovary(1)	1												OREG0022201	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	0.135135	6.946152	11.72862	5	32	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	120366428	120366428	8431	12	A	G	G	11	11	KDM2B	G	4	4
DNAJC22	79962	broad.mit.edu	36	12	48029391	48029391	+	Missense_Mutation	SNP	G	A	A			TCGA-16-0850-01	TCGA-16-0850-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr12:48029391G>A	uc001rua.1	+	c.469G>A	c.(469-471)GTG>ATG	p.V157M	DNAJC22_uc001rub.1_Missense_Mutation_p.V157M	NM_024902	NP_079178	Q8N4W6	DJC22_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 22	157	Helical; (Potential).				protein folding	integral to membrane	heat shock protein binding|unfolded protein binding			ovary(1)	1														0.279412	51.295619	54.271691	19	49	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	48029391	48029391	4824	12	G	A	A	40	40	DNAJC22	A	1	1
TSFM	10102	broad.mit.edu	36	12	56463249	56463249	+	Silent	SNP	C	T	T			TCGA-16-0850-01	TCGA-16-0850-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr12:56463249C>T	uc001sqh.2	+	c.147C>T	c.(145-147)CTC>CTT	p.L49L	TSFM_uc001sqi.2_Silent_p.L49L	NM_005726	NP_005717	P43897	EFTS_HUMAN	Ts translation elongation factor, mitochondrial	49						mitochondrion|nucleus	transcription elongation regulator activity|translation elongation factor activity				0	all_cancers(7;6.31e-80)|Glioma(12;6.95e-05)|all_neural(12;0.00016)|Melanoma(17;0.122)											OREG0021954	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	0.149438	199.645166	304.493359	133	757	CC		KEEP	---	---	---	---	capture			Silent	SNP	56463249	56463249	17166	12	C	T	T	30	30	TSFM	T	2	2
CAND1	55832	broad.mit.edu	36	12	65982532	65982532	+	Missense_Mutation	SNP	A	G	G			TCGA-16-0850-01	TCGA-16-0850-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr12:65982532A>G	uc001stn.2	+	c.1163A>G	c.(1162-1164)GAG>GGG	p.E388G	CAND1_uc001sto.2_Missense_Mutation_p.E66G	NM_018448	NP_060918	Q86VP6	CAND1_HUMAN	TIP120 protein	388	HEAT 9.				cell differentiation|negative regulation of catalytic activity|protein ubiquitination|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus|ubiquitin ligase complex	protein binding			central_nervous_system(1)	1			GBM - Glioblastoma multiforme(1;1.13e-10)|Lung(24;0.000342)|LUSC - Lung squamous cell carcinoma(43;0.196)	GBM - Glioblastoma multiforme(28;0.0279)										0.232432	118.934106	131.058303	43	142	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	65982532	65982532	2732	12	A	G	G	11	11	CAND1	G	4	4
ISM2	145501	broad.mit.edu	36	14	77014687	77014687	+	Missense_Mutation	SNP	G	T	T			TCGA-16-0850-01	TCGA-16-0850-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr14:77014687G>T	uc001xtz.1	-	c.1098C>A	c.(1096-1098)GAC>GAA	p.D366E	ISM2_uc001xty.1_Missense_Mutation_p.D278E|ISM2_uc001xua.1_Missense_Mutation_p.T251N	NM_199296	NP_954874	Q6H9L7	ISM2_HUMAN	isthmin 2 homolog isoform 1	366	TSP type-1.					extracellular region					0														0.258621	37.096677	40.160014	15	43	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	77014687	77014687	8165	14	G	T	T	44	44	ISM2	T	3	3
CA12	771	broad.mit.edu	36	15	61424842	61424842	+	Missense_Mutation	SNP	T	A	A			TCGA-16-0850-01	TCGA-16-0850-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr15:61424842T>A	uc002amc.1	-	c.316A>T	c.(316-318)ATC>TTC	p.I106F	CA12_uc002amd.1_Missense_Mutation_p.I106F|CA12_uc002ame.1_Missense_Mutation_p.I46F	NM_001218	NP_001209	O43570	CAH12_HUMAN	carbonic anhydrase XII isoform 1 precursor	106	Extracellular (Potential).				one-carbon metabolic process	integral to membrane	carbonate dehydratase activity|zinc ion binding			ovary(1)	1					Acetazolamide(DB00819)									0.24424	130.175339	143.107175	53	164	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	61424842	61424842	2629	15	T	A	A	51	51	CA12	A	4	4
POLR3E	55718	broad.mit.edu	36	16	22244929	22244929	+	Silent	SNP	C	T	T			TCGA-16-0850-01	TCGA-16-0850-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr16:22244929C>T	uc002dkk.1	+	c.1695C>T	c.(1693-1695)TTC>TTT	p.F565F	POLR3E_uc002dkj.1_Silent_p.F565F|POLR3E_uc002dkl.1_Silent_p.F565F|POLR3E_uc002dkm.1_Silent_p.F529F	NM_018119	NP_060589	Q9NVU0	RPC5_HUMAN	polymerase (RNA) III (DNA directed) polypeptide	565					innate immune response|response to virus|termination of RNA polymerase III transcription|transcription elongation from RNA polymerase III promoter	nucleoplasm	DNA-directed RNA polymerase activity			ovary(1)|central_nervous_system(1)	2				GBM - Glioblastoma multiforme(48;0.012)										0.621951	157.924124	158.993797	51	31	CC		KEEP	---	---	---	---	capture			Silent	SNP	22244929	22244929	12660	16	C	T	T	31	31	POLR3E	T	1	1
IL21R	50615	broad.mit.edu	36	16	27348905	27348905	+	Silent	SNP	C	G	G			TCGA-16-0850-01	TCGA-16-0850-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr16:27348905C>G	uc002doq.1	+	c.12C>G	c.(10-12)GGC>GGG	p.G4G	IL21R_uc002dor.1_Silent_p.G4G|IL21R_uc002dos.1_Silent_p.G4G	NM_181078	NP_851565	Q9HBE5	IL21R_HUMAN	interleukin 21 receptor precursor	4					natural killer cell activation	integral to membrane	interleukin-21 receptor activity			ovary(2)	2										423				0.168	41.547644	54.564386	21	104	CC		KEEP	---	---	---	---	capture			Silent	SNP	27348905	27348905	7972	16	C	G	G	28	28	IL21R	G	3	3
RPGRIP1L	23322	broad.mit.edu	36	16	52227862	52227862	+	Missense_Mutation	SNP	T	G	G			TCGA-16-0850-01	TCGA-16-0850-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr16:52227862T>G	uc002ehp.1	-	c.3284A>C	c.(3283-3285)AAT>ACT	p.N1095T	RPGRIP1L_uc002ehn.1_Missense_Mutation_p.N510T|RPGRIP1L_uc002eho.2_Missense_Mutation_p.N1061T|RPGRIP1L_uc010cbx.1_Missense_Mutation_p.N1061T	NM_015272	NP_056087	Q68CZ1	FTM_HUMAN	RPGRIP1-like isoform a	1095					negative regulation of G-protein coupled receptor protein signaling pathway	centrosome|cilium axoneme|microtubule basal body	thromboxane A2 receptor binding			ovary(1)	1		all_cancers(37;0.0973)												0.128205	16.293402	26.801325	10	68	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	52227862	52227862	14029	16	T	G	G	52	52	RPGRIP1L	G	4	4
FAM65A	79567	broad.mit.edu	36	16	66130122	66130122	+	Missense_Mutation	SNP	G	A	A			TCGA-16-0850-01	TCGA-16-0850-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr16:66130122G>A	uc010cej.1	+	c.160G>A	c.(160-162)GCG>ACG	p.A54T	FAM65A_uc010cei.1_5'UTR|FAM65A_uc002eth.1_Missense_Mutation_p.A51T|FAM65A_uc002eti.1_Intron|FAM65A_uc002etj.1_Missense_Mutation_p.A50T|FAM65A_uc002etk.1_Missense_Mutation_p.A50T	NM_024519	NP_078795	Q6ZS17	FA65A_HUMAN	hypothetical protein LOC79567	55						cytoplasm	binding			ovary(2)|central_nervous_system(1)	3		Acute lymphoblastic leukemia(13;3.76e-06)|all_hematologic(13;0.000303)|Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0474)|Epithelial(162;0.117)										0.194805	28.375842	35.083501	15	62	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	66130122	66130122	5822	16	G	A	A	38	38	FAM65A	A	1	1
KRT19	3880	broad.mit.edu	36	17	36935002	36935002	+	Missense_Mutation	SNP	T	C	C			TCGA-16-0850-01	TCGA-16-0850-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr17:36935002T>C	uc002hxd.2	-	c.470A>G	c.(469-471)AAT>AGT	p.N157S		NM_002276	NP_002267	P08727	K1C19_HUMAN	keratin 19	157	Coil 1B.|Rod.				interspecies interaction between organisms|response to estrogen stimulus|sarcomere organization	costamere|intermediate filament	protein binding|structural constituent of cytoskeleton|structural constituent of muscle				0		Breast(137;0.00038)												0.302326	113.780069	118.277843	39	90	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	36935002	36935002	8771	17	T	C	C	52	52	KRT19	C	4	4
TP53	7157	broad.mit.edu	36	17	7518284	7518284	+	Missense_Mutation	SNP	G	T	T	rs28934573	unknown	TCGA-16-0850-01	TCGA-16-0850-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr17:7518284G>T	uc002gim.2	-	c.722C>A	c.(721-723)TCC>TAC	p.S241Y	TP53_uc002gig.1_Missense_Mutation_p.S241Y|TP53_uc002gih.1_Missense_Mutation_p.S241Y|TP53_uc010cne.1_5'Flank|TP53_uc010cnf.1_Missense_Mutation_p.S109Y|TP53_uc010cng.1_Missense_Mutation_p.S109Y|TP53_uc002gii.1_Missense_Mutation_p.S109Y|TP53_uc010cnh.1_Missense_Mutation_p.S241Y|TP53_uc010cni.1_Missense_Mutation_p.S241Y|TP53_uc002gij.2_Missense_Mutation_p.S241Y|TP53_uc010cnj.1_Non-coding_Transcript|TP53_uc002gin.2_Missense_Mutation_p.S148Y|TP53_uc002gio.2_Missense_Mutation_p.S109Y	NM_001126112	NP_001119584	P04637	P53_HUMAN	tumor protein p53 isoform a	241	|Interaction with HIPK1 (By similarity).|Interacts with the 53BP2 SH3 domain.|Interaction with AXIN1 (By similarity).		S -> A (in sporadic cancers; somatic mutation).|S -> P (in sporadic cancers; somatic mutation).|S -> C (in sporadic cancers; somatic mutation).|S -> Y (in sporadic cancers; somatic mutation).|S -> T (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.S241F(72)|p.S241C(24)|p.S241Y(7)|p.0?(6)|p.C242fs*5(6)|p.S241del(5)|p.N239_C242delNSSC(3)|p.N239_C242>S(1)|p.C238fs*21(1)|p.S241fs*22(1)|p.N239_C242del(1)|p.Y236_M243delYMCNSSCM(1)|p.S241_G245delSCMGG(1)|p.N239fs*4(1)|p.C238_M246delCNSSCMGGM(1)|p.H233_C242del10(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)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)		Pancreas(47;798 1329 9957 10801)		111	p.S241Y(DMS53-Tumor)|p.S241Y(KMM1-Tumor)|p.S241Y(KALS1-Tumor)|p.S241C(EVSAT-Tumor)|p.S241C(BFTC909-Tumor)|p.S241Y(HCC78-Tumor)|p.S241Y(ES2-Tumor)|p.S241Y(HCT15-Tumor)|p.C238fs(SW1417-Tumor)|p.S241F(HEC251-Tumor)	690	TCGA GBM(1;<1E-8)|TSP Lung(2;<1E-8)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)			0.967448	2652.053783	2708.147529	743	25	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	7518284	7518284	16923	17	G	T	T	41	41	TP53	T	3	3
CD226	10666	broad.mit.edu	36	18	65682626	65682626	+	Silent	SNP	A	G	G			TCGA-16-0850-01	TCGA-16-0850-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr18:65682626A>G	uc010dqo.1	-	c.915T>C	c.(913-915)TCT>TCC	p.S305S	CD226_uc002lkm.2_Silent_p.S305S	NM_006566	NP_006557	Q15762	CD226_HUMAN	CD226 molecule precursor	305	Cytoplasmic (Potential).				cell adhesion|cell recognition|positive regulation of Fc receptor mediated stimulatory signaling pathway|positive regulation of immunoglobulin mediated immune response|positive regulation of mast cell activation|positive regulation of natural killer cell mediated cytotoxicity directed against tumor cell target	cell surface|integral to plasma membrane|membrane raft	cell adhesion molecule binding|integrin binding|protein kinase binding|receptor activity				0		Esophageal squamous(42;0.129)				NSCLC(184;838 2130 8673 21498 50749)								0.257576	143.440122	153.981756	51	147	AA		KEEP	---	---	---	---	capture			Silent	SNP	65682626	65682626	3113	18	A	G	G	15	15	CD226	G	4	4
ATP4A	495	broad.mit.edu	36	19	40733621	40733621	+	Missense_Mutation	SNP	C	G	G			TCGA-16-0850-01	TCGA-16-0850-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr19:40733621C>G	uc002oal.1	-	c.3034G>C	c.(3034-3036)GTC>CTC	p.V1012L	ATP4A_uc010eee.1_Missense_Mutation_p.V170L	NM_000704	NP_000695	P20648	ATP4A_HUMAN	hydrogen/potassium-exchanging ATPase 4A	1012	Helical; (Potential).				ATP biosynthetic process|ATP hydrolysis coupled proton transport	integral to plasma membrane	ATP binding|hydrogen:potassium-exchanging ATPase activity|magnesium ion binding				0	all_lung(56;1.05e-07)|Lung NSC(56;1.63e-07)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0724)		Esomeprazole(DB00736)|Lansoprazole(DB00448)|Omeprazole(DB00338)|Pantoprazole(DB00213)|Rabeprazole(DB01129)|Trifluoperazine(DB00831)									0.560976	363.862573	364.523123	115	90	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	40733621	40733621	1164	19	C	G	G	19	19	ATP4A	G	3	3
LILRB2	10288	broad.mit.edu	36	19	59475967	59475967	+	Splice_Site_SNP	SNP	C	T	T			TCGA-16-0850-01	TCGA-16-0850-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr19:59475967C>T	uc002qfb.1	-	c.e3_splice_site			LILRA6_uc002qew.1_Intron|LILRB2_uc010eri.1_Splice_Site_SNP|LILRB2_uc010erj.1_Splice_Site_SNP|LILRB2_uc002qfc.1_Splice_Site_SNP	NM_005874	NP_005865			leukocyte immunoglobulin-like receptor,						cell surface receptor linked signaling pathway|cell-cell signaling|cellular defense response|immune response|regulation of immune response	integral to plasma membrane|membrane fraction	receptor activity				0	Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.105)										0.612903	64.23143	64.578049	19	12	CC		KEEP	---	---	---	---	capture			Splice_Site_SNP	SNP	59475967	59475967	9117	19	C	T	T	24	24	LILRB2	T	5	2
NCR1	9437	broad.mit.edu	36	19	60113191	60113191	+	Silent	SNP	C	A	A			TCGA-16-0850-01	TCGA-16-0850-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr19:60113191C>A	uc002qib.1	+	c.636C>A	c.(634-636)GGC>GGA	p.G212G	NCR1_uc002qic.1_Silent_p.G212G|NCR1_uc002qid.1_Silent_p.G117G|NCR1_uc002qie.1_Silent_p.G212G|NCR1_uc010esj.1_Silent_p.G105G|NCR1_uc002qif.1_Silent_p.G117G	NM_004829	NP_004820	O76036	NCTR1_HUMAN	natural cytotoxicity triggering receptor 1	212	Extracellular (Potential).				cellular defense response|natural killer cell activation|regulation of natural killer cell mediated cytotoxicity	integral to plasma membrane|SWI/SNF complex	receptor activity|receptor signaling protein activity			large_intestine(1)|ovary(1)	2				GBM - Glioblastoma multiforme(193;0.0449)										0.583333	1437.18795	1441.996521	462	330	CC		KEEP	---	---	---	---	capture			Silent	SNP	60113191	60113191	10636	19	C	A	A	27	27	NCR1	A	3	3
SLC22A15	55356	broad.mit.edu	36	1	116410662	116410662	+	Splice_Site_SNP	SNP	A	C	C			TCGA-16-0850-01	TCGA-16-0850-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr1:116410662A>C	uc001egb.2	+	c.e11_splice_site				NM_018420	NP_060890			solute carrier family 22, member 15						ion transport|transmembrane transport	integral to membrane	transporter activity			large_intestine(2)	2	Lung SC(450;0.184)	all_cancers(81;3.17e-06)|all_epithelial(167;2.32e-06)|all_lung(203;9.81e-06)|Lung NSC(69;5.94e-05)		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)						219				0.514019	330.93283	330.969019	110	104	AA		KEEP	---	---	---	---	capture			Splice_Site_SNP	SNP	116410662	116410662	14942	1	A	C	C	7	7	SLC22A15	C	5	4
IGSF3	3321	broad.mit.edu	36	1	116952240	116952240	+	Missense_Mutation	SNP	T	C	C			TCGA-16-0850-01	TCGA-16-0850-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr1:116952240T>C	uc001egq.1	-	c.1069A>G	c.(1069-1071)AGT>GGT	p.S357G	IGSF3_uc001egr.1_Missense_Mutation_p.S357G|IGSF3_uc001egs.1_Missense_Mutation_p.S30G	NM_001542	NP_001533	O75054	IGSF3_HUMAN	immunoglobulin superfamily, member 3 isoform 1	357	Ig-like C2-type 3.|Extracellular (Potential).					integral to membrane				ovary(2)	2	Lung SC(450;0.225)	all_cancers(81;1.24e-06)|all_epithelial(167;4.85e-07)|all_lung(203;1.66e-06)|Lung NSC(69;1.11e-05)		Lung(183;0.0142)|Colorectal(144;0.0929)|LUSC - Lung squamous cell carcinoma(189;0.108)|COAD - Colon adenocarcinoma(174;0.139)|all cancers(265;0.159)|Epithelial(280;0.166)										0.225989	104.005993	116.211442	40	137	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	116952240	116952240	7902	1	T	C	C	55	55	IGSF3	C	4	4
TCHHL1	126637	broad.mit.edu	36	1	150325219	150325219	+	Missense_Mutation	SNP	G	T	T			TCGA-16-0850-01	TCGA-16-0850-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:150325219G>T	uc001ezo.1	-	c.1563C>A	c.(1561-1563)GAC>GAA	p.D521E		NM_001008536	NP_001008536	Q5QJ38	TCHL1_HUMAN	trichohyalin-like 1	521							calcium ion binding			ovary(1)	1	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.246)											0.217726	255.985402	294.128156	113	406	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	150325219	150325219	16227	1	G	T	T	44	44	TCHHL1	T	3	3
KPRP	448834	broad.mit.edu	36	1	150999883	150999883	+	Missense_Mutation	SNP	T	C	C			TCGA-16-0850-01	TCGA-16-0850-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr1:150999883T>C	uc001fal.1	+	c.1195T>C	c.(1195-1197)TGT>CGT	p.C399R	KPRP_uc009wnn.1_Missense_Mutation_p.C399R	NM_001025231	NP_001020402	Q5T749	KPRP_HUMAN	keratinocyte proline-rich protein	399	Pro-rich.					cytoplasm				ovary(4)|pancreas(1)	5	Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.206)											0.508197	102.018101	102.021572	31	30	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	150999883	150999883	8751	1	T	C	C	51	51	KPRP	C	4	4
KLHDC8A	55220	broad.mit.edu	36	1	203575067	203575067	+	Missense_Mutation	SNP	C	T	T			TCGA-16-0850-01	TCGA-16-0850-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr1:203575067C>T	uc001hcf.1	-	c.635G>A	c.(634-636)CGG>CAG	p.R212Q	KLHDC8A_uc001hcg.1_Missense_Mutation_p.R212Q	NM_018203	NP_060673	Q8IYD2	KLD8A_HUMAN	kelch domain containing 8A	212	Kelch 5.									ovary(1)	1	Breast(84;0.23)		BRCA - Breast invasive adenocarcinoma(75;0.117)											0.189333	309.984485	377.651281	142	608	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	203575067	203575067	8674	1	C	T	T	23	23	KLHDC8A	T	1	1
PRPF6	24148	broad.mit.edu	36	20	62127766	62127766	+	Missense_Mutation	SNP	G	A	A			TCGA-16-0850-01	TCGA-16-0850-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr20:62127766G>A	uc002yho.1	+	c.1939G>A	c.(1939-1941)GCA>ACA	p.A647T	PRPF6_uc002yhp.1_Intron	NM_012469	NP_036601	O94906	PRP6_HUMAN	PRP6 pre-mRNA processing factor 6 homolog	647	HAT 6.				assembly of spliceosomal tri-snRNP|positive regulation of transcription from RNA polymerase II promoter|spliceosome assembly	catalytic step 2 spliceosome|nucleoplasm|U4/U6 snRNP|U4/U6 x U5 tri-snRNP complex|U5 snRNP	androgen receptor binding|ribonucleoprotein binding|transcription coactivator activity			ovary(2)	2	all_cancers(38;6.47e-12)|all_epithelial(29;1.26e-13)|Lung NSC(23;9.37e-10)|all_lung(23;3.23e-09)													0.692308	27.176096	27.603836	9	4	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	62127766	62127766	13017	20	G	A	A	42	42	PRPF6	A	2	2
MMP11	4320	broad.mit.edu	36	22	22454555	22454555	+	Silent	SNP	G	A	A			TCGA-16-0850-01	TCGA-16-0850-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr22:22454555G>A	uc002zxx.1	+	c.1218G>A	c.(1216-1218)AGG>AGA	p.R406R	MMP11_uc002zxy.1_Non-coding_Transcript|MMP11_uc002zxz.1_Non-coding_Transcript	NM_005940	NP_005931	P24347	MMP11_HUMAN	matrix metalloproteinase 11 preproprotein	406	Hemopexin-like 3.				collagen catabolic process|multicellular organismal development|proteolysis	proteinaceous extracellular matrix	calcium ion binding|metalloendopeptidase activity|zinc ion binding			large_intestine(1)	1		Medulloblastoma(6;9.86e-08)|all_neural(6;0.000318)												0.232227	117.238904	131.04808	49	162	GG		KEEP	---	---	---	---	capture			Silent	SNP	22454555	22454555	10040	22	G	A	A	43	43	MMP11	A	2	2
ADAM23	8745	broad.mit.edu	36	2	207134125	207134125	+	Missense_Mutation	SNP	A	T	T			TCGA-16-0850-01	TCGA-16-0850-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr2:207134125A>T	uc002vbq.1	+	c.1198A>T	c.(1198-1200)AGT>TGT	p.S400C		NM_003812	NP_003803	O75077	ADA23_HUMAN	ADAM metallopeptidase domain 23 preproprotein	400	Peptidase M12B.|Extracellular (Potential).				cell adhesion|central nervous system development|proteolysis	extracellular region|integral to plasma membrane	integrin binding|metalloendopeptidase activity|zinc ion binding			ovary(1)|skin(1)	2				LUSC - Lung squamous cell carcinoma(261;0.0961)|Lung(261;0.182)|Epithelial(149;0.205)		Melanoma(194;1127 2130 19620 24042 27855)								0.218182	30.470114	34.496627	12	43	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	207134125	207134125	246	2	A	T	T	7	7	ADAM23	T	4	4
IDH1	3417	broad.mit.edu	36	2	208821357	208821357	+	Missense_Mutation	SNP	C	T	T			TCGA-16-0850-01	TCGA-16-0850-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr2:208821357C>T	uc002vcs.1	-	c.395G>A	c.(394-396)CGT>CAT	p.R132H	IDH1_uc002vct.1_Missense_Mutation_p.R132H|IDH1_uc002vcu.1_Missense_Mutation_p.R132H	NM_005896	NP_005887	O75874	IDHC_HUMAN	isocitrate dehydrogenase 1 (NADP+), soluble	132		Substrate.	R -> G (in a glioma sample; glioblastoma multiforme; somatic mutation).|R -> L (in a glioma sample; glioblastoma multiforme; somatic mutation; abolishes magnesium binding and alters enzyme activity so that isocitrate is no longer converted to alpha-ketoglutarate but instead alpha-ketoglutarate is converted to R(-)-2-hydroxyglutarate).|R -> S (in a glioma sample; glioblastoma multiforme; somatic mutation; abolishes magnesium binding and alters enzyme activity so that isocitrate is no longer converted to alpha-ketoglutarate but instead alpha-ketoglutarate is converted to R(-)-2-hydroxyglutarate).|R -> H (in a glioma sample; glioblastoma multiforme; somatic mutation; abolishes magnesium binding and alters enzyme activity so that isocitrate is no longer converted to alpha-ketoglutarate but instead alpha-ketoglutarate is converted to R(-)-2-hydroxyglutarate).|R -> C (in colorectal cancer and glioma samples; glioblastoma multiforme; somatic mutation; abolishes magnesium binding and alters enzyme activity so that isocitrate is no longer converted to alpha- ketoglutarate but instead alpha- ketoglutarate is converted to R(-)-2- hydroxyglutarate).		2-oxoglutarate metabolic process|cellular lipid metabolic process|glyoxylate cycle|isocitrate metabolic process|NADPH regeneration|tricarboxylic acid cycle	cytosol|peroxisomal matrix	isocitrate dehydrogenase (NADP+) activity|magnesium ion binding|NAD binding|protein homodimerization activity	p.R132H(1725)|p.R132?(210)|p.R132C(92)|p.R132L(48)|p.R132G(26)|p.R132S(11)|p.R132V(1)|p.G131_R132>VL(1)		central_nervous_system(1848)|haematopoietic_and_lymphoid_tissue(593)|large_intestine(4)|skin(2)|prostate(2)|autonomic_ganglia(1)|soft_tissue(1)	2451				Epithelial(149;0.0322)|LUSC - Lung squamous cell carcinoma(261;0.0711)|Lung(261;0.136)		Pancreas(158;264 1958 3300 35450 36047)				134				0.610698	1303.637373	1310.840009	411	262	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	208821357	208821357	7794	2	C	T	T	19	19	IDH1	T	1	1
OTX1	5013	broad.mit.edu	36	2	63136929	63136929	+	Missense_Mutation	SNP	G	A	A			TCGA-16-0850-01	TCGA-16-0850-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr2:63136929G>A	uc002scd.1	+	c.1039G>A	c.(1039-1041)GCC>ACC	p.A347T		NM_014562	NP_055377	P32242	OTX1_HUMAN	orthodenticle homeobox 1	347						nucleus	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			pancreas(2)	2	Lung NSC(7;0.121)|all_lung(7;0.211)													0.210526	19.877825	22.824408	8	30	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	63136929	63136929	11733	2	G	A	A	34	34	OTX1	A	2	2
PIK3R4	30849	broad.mit.edu	36	3	131885834	131885834	+	Missense_Mutation	SNP	C	T	T			TCGA-16-0850-01	TCGA-16-0850-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr3:131885834C>T	uc003enj.1	-	c.3557G>A	c.(3556-3558)CGA>CAA	p.R1186Q		NM_014602	NP_055417	Q99570	PI3R4_HUMAN	phosphoinositide-3-kinase, regulatory subunit 4,	1186	WD 5.				fibroblast growth factor receptor signaling pathway|innate immune response|insulin receptor signaling pathway|protein phosphorylation	cytosol	ATP binding|protein binding|protein serine/threonine kinase activity			ovary(3)|kidney(1)|breast(1)|central_nervous_system(1)	6										587				0.192698	205.456393	248.920704	95	398	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	131885834	131885834	12345	3	C	T	T	31	31	PIK3R4	T	1	1
LPP	4026	broad.mit.edu	36	3	190074832	190074832	+	Splice_Site_SNP	SNP	G	A	A			TCGA-16-0850-01	TCGA-16-0850-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr3:190074832G>A	uc003frs.1	+	c.e11_splice_site				NM_005578	NP_005569			LIM domain containing preferred translocation						cell adhesion	cytoplasm|focal adhesion|nucleus	protein binding|zinc ion binding		HMGA2/LPP(161)	soft_tissue(134)|bone(27)|ovary(1)	162	all_cancers(143;1.37e-09)|all_hematologic(3;0.0429)|Ovarian(172;0.088)	all_lung(153;0.00139)|Lung NSC(153;0.00202)		GBM - Glioblastoma multiforme(93;0.00602)						184				0.176101	113.722267	145.166057	56	262	GG		KEEP	---	---	---	---	capture			Splice_Site_SNP	SNP	190074832	190074832	9296	3	G	A	A	35	35	LPP	A	5	2
KIAA1109	84162	broad.mit.edu	36	4	123360154	123360154	+	Silent	SNP	T	G	G			TCGA-16-0850-01	TCGA-16-0850-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr4:123360154T>G	uc003ieh.1	+	c.2457T>G	c.(2455-2457)GTT>GTG	p.V819V	KIAA1109_uc003iei.1_Silent_p.V573V|KIAA1109_uc010ins.1_Silent_p.V163V|KIAA1109_uc003iej.1_Silent_p.V204V	NM_015312	NP_056127	Q2LD37	K1109_HUMAN	hypothetical protein LOC84162	819					regulation of cell growth|regulation of epithelial cell differentiation	integral to membrane|nucleus				ovary(7)|central_nervous_system(1)|pancreas(1)	9														0.175676	29.728317	37.068433	13	61	TT		KEEP	---	---	---	---	capture			Silent	SNP	123360154	123360154	8516	4	T	G	G	62	62	KIAA1109	G	4	4
VEGFC	7424	broad.mit.edu	36	4	177846064	177846064	+	Missense_Mutation	SNP	G	A	A			TCGA-16-0850-01	TCGA-16-0850-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr4:177846064G>A	uc003ius.1	-	c.716C>T	c.(715-717)GCG>GTG	p.A239V		NM_005429	NP_005420	P49767	VEGFC_HUMAN	vascular endothelial growth factor C	239					angiogenesis|induction of positive chemotaxis|platelet activation|platelet degranulation|positive regulation of cell division|positive regulation of mast cell chemotaxis|substrate-dependent cell migration|vascular endothelial growth factor receptor signaling pathway	membrane|platelet alpha granule lumen	chemoattractant activity|growth factor activity			lung(2)	2		Breast(14;0.000223)|Renal(120;0.00988)|Prostate(90;0.00996)|Melanoma(52;0.0101)|all_hematologic(60;0.107)|all_neural(102;0.164)		all cancers(43;1.59e-18)|Epithelial(43;3.68e-16)|OV - Ovarian serous cystadenocarcinoma(60;8.52e-09)|GBM - Glioblastoma multiforme(59;0.000546)|STAD - Stomach adenocarcinoma(60;0.00308)|Colorectal(24;0.025)|COAD - Colon adenocarcinoma(29;0.0359)|LUSC - Lung squamous cell carcinoma(193;0.0397)						148				0.240481	272.305517	302.954416	120	379	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	177846064	177846064	17719	4	G	A	A	38	38	VEGFC	A	1	1
TRIML2	205860	broad.mit.edu	36	4	189249641	189249641	+	Silent	SNP	G	A	A			TCGA-16-0850-01	TCGA-16-0850-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr4:189249641G>A	uc003izl.1	-	c.1044C>T	c.(1042-1044)TGC>TGT	p.C348C	TRIML2_uc003izj.1_Silent_p.C176C|TRIML2_uc003izk.1_Silent_p.C156C	NM_173553	NP_775824	Q8N7C3	TRIMM_HUMAN	tripartite motif family-like 2	348	B30.2/SPRY.						ligase activity			central_nervous_system(2)	2		all_cancers(14;3.11e-44)|all_epithelial(14;7.86e-31)|all_lung(41;4.3e-13)|Lung NSC(41;9.69e-13)|Melanoma(20;7.86e-05)|Breast(6;0.000148)|all_hematologic(60;0.0202)|Hepatocellular(41;0.0218)|Renal(120;0.0376)|Prostate(90;0.0513)		OV - Ovarian serous cystadenocarcinoma(60;1.79e-11)|BRCA - Breast invasive adenocarcinoma(30;4.52e-06)|GBM - Glioblastoma multiforme(59;1.62e-05)|STAD - Stomach adenocarcinoma(60;0.000279)|LUSC - Lung squamous cell carcinoma(40;0.0091)|READ - Rectum adenocarcinoma(43;0.163)										0.242187	153.628582	169.144423	62	194	GG		KEEP	---	---	---	---	capture			Silent	SNP	189249641	189249641	17101	4	G	A	A	38	38	TRIML2	A	1	1
PDE6B	5158	broad.mit.edu	36	4	646323	646323	+	Missense_Mutation	SNP	C	T	T			TCGA-16-0850-01	TCGA-16-0850-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr4:646323C>T	uc003gap.1	+	c.1748C>T	c.(1747-1749)ACG>ATG	p.T583M	PDE6B_uc003gao.2_Missense_Mutation_p.T583M	NM_000283	NP_000274	P35913	PDE6B_HUMAN	rod cGMP-phosphodiesterase beta-subunit isoform	583					cytosolic calcium ion homeostasis|GMP metabolic process|phototransduction, visible light|platelet activation|visual perception	cytosol|membrane	3',5'-cyclic-GMP phosphodiesterase activity|metal ion binding				0						GBM(71;463 1194 9848 25922 46834)								0.333333	24.492877	25.082854	8	16	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	646323	646323	12067	4	C	T	T	19	19	PDE6B	T	1	1
UGT2B4	7363	broad.mit.edu	36	4	70386916	70386916	+	Missense_Mutation	SNP	C	T	T			TCGA-16-0850-01	TCGA-16-0850-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr4:70386916C>T	uc003hek.2	-	c.1090G>A	c.(1090-1092)GGT>AGT	p.G364S	UGT2B4_uc003hel.2_Missense_Mutation_p.D364N	NM_021139	NP_066962	P06133	UD2B4_HUMAN	UDP glucuronosyltransferase 2 family,	364					estrogen catabolic process|xenobiotic metabolic process	endoplasmic reticulum membrane|integral to membrane|microsome	glucuronosyltransferase activity				0														0.352459	250.182496	254.863871	86	158	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	70386916	70386916	17519	4	C	T	T	21	21	UGT2B4	T	2	2
PCDHA3	56145	broad.mit.edu	36	5	140162321	140162321	+	Missense_Mutation	SNP	C	T	T			TCGA-16-0850-01	TCGA-16-0850-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr5:140162321C>T	uc003lhf.1	+	c.1355C>T	c.(1354-1356)GCG>GTG	p.A452V	PCDHA1_uc003lha.1_Intron|PCDHA1_uc003lhb.1_Intron|PCDHA2_uc003lhd.1_Intron|PCDHA3_uc003lhe.1_Missense_Mutation_p.A452V	NM_018906	NP_061729	Q9Y5H8	PCDA3_HUMAN	protocadherin alpha 3 isoform 1 precursor	452	Cadherin 4.|Extracellular (Potential).				homophilic cell adhesion|nervous system development	integral to plasma membrane	calcium ion binding|protein binding			ovary(5)	5			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)											0.470588	25.499242	25.511974	8	9	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	140162321	140162321	11945	5	C	T	T	27	27	PCDHA3	T	1	1
ADAMTS12	81792	broad.mit.edu	36	5	33612200	33612200	+	Missense_Mutation	SNP	C	T	T			TCGA-16-0850-01	TCGA-16-0850-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr5:33612200C>T	uc003jia.1	-	c.3688G>A	c.(3688-3690)GAA>AAA	p.E1230K	ADAMTS12_uc010iuq.1_Missense_Mutation_p.E1145K	NM_030955	NP_112217	P58397	ATS12_HUMAN	ADAM metallopeptidase with thrombospondin type 1	1230	Spacer 2.				proteolysis	proteinaceous extracellular matrix	metalloendopeptidase activity|zinc ion binding			ovary(4)|lung(1)|kidney(1)|skin(1)	7														0.383562	387.043505	391.368633	140	225	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	33612200	33612200	258	5	C	T	T	31	31	ADAMTS12	T	1	1
SEMA5A	9037	broad.mit.edu	36	5	9116082	9116082	+	Missense_Mutation	SNP	T	C	C			TCGA-16-0850-01	TCGA-16-0850-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr5:9116082T>C	uc003jek.2	-	c.2435A>G	c.(2434-2436)AAC>AGC	p.N812S		NM_003966	NP_003957	Q13591	SEM5A_HUMAN	semaphorin 5A	812	TSP type-1 5.|Extracellular (Potential).				cell adhesion|cell-cell signaling	integral to membrane|plasma membrane				ovary(1)|central_nervous_system(1)	2														0.285714	28.836365	30.278015	10	25	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	9116082	9116082	14523	5	T	C	C	60	60	SEMA5A	C	4	4
RTN4IP1	84816	broad.mit.edu	36	6	107126668	107126668	+	Missense_Mutation	SNP	G	A	A			TCGA-16-0850-01	TCGA-16-0850-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr6:107126668G>A	uc003prj.1	-	c.1087C>T	c.(1087-1089)CGG>TGG	p.R363W	RTN4IP1_uc010kdd.1_3'UTR|RTN4IP1_uc003prk.1_Missense_Mutation_p.R263W	NM_032730	NP_116119	Q8WWV3	RT4I1_HUMAN	reticulon 4 interacting protein 1 precursor	363					oxidation-reduction process	mitochondrion	oxidoreductase activity|zinc ion binding				0	Breast(9;0.0107)|all_epithelial(6;0.14)	all_cancers(87;9.45e-05)|Acute lymphoblastic leukemia(125;2.13e-07)|all_hematologic(75;5.28e-06)|all_epithelial(87;0.0144)	Epithelial(6;0.000873)|all cancers(7;0.00363)|BRCA - Breast invasive adenocarcinoma(8;0.00721)|OV - Ovarian serous cystadenocarcinoma(5;0.0394)	all cancers(137;0.113)|BRCA - Breast invasive adenocarcinoma(108;0.127)|Epithelial(106;0.144)										0.327273	53.930269	55.386057	18	37	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	107126668	107126668	14209	6	G	A	A	39	39	RTN4IP1	A	1	1
PKHD1	5314	broad.mit.edu	36	6	51859976	51859976	+	Silent	SNP	A	G	G			TCGA-16-0850-01	TCGA-16-0850-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr6:51859976A>G	uc003pah.1	-	c.7023T>C	c.(7021-7023)TAT>TAC	p.Y2341Y	PKHD1_uc010jzn.1_Silent_p.Y324Y|PKHD1_uc003pai.1_Silent_p.Y2341Y	NM_138694	NP_619639	P08F94	PKHD1_HUMAN	fibrocystin isoform 1	2341	PbH1 4.|Extracellular (Potential).				cell-cell adhesion|cilium assembly|homeostatic process|kidney development|negative regulation of cellular component movement	anchored to external side of plasma membrane|apical plasma membrane|integral to membrane|microtubule basal body	protein binding|receptor activity			ovary(12)|large_intestine(5)|central_nervous_system(3)	20	Lung NSC(77;0.0605)									1537				0.220779	161.734015	183.870463	68	240	AA		KEEP	---	---	---	---	capture			Silent	SNP	51859976	51859976	12396	6	A	G	G	8	8	PKHD1	G	4	4
MUC17	140453	broad.mit.edu	36	7	100462370	100462370	+	Missense_Mutation	SNP	C	T	T			TCGA-16-0850-01	TCGA-16-0850-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr7:100462370C>T	uc003uxp.1	+	c.953C>T	c.(952-954)ACG>ATG	p.T318M	MUC17_uc010lho.1_Non-coding_Transcript	NM_001040105	NP_001035194	Q685J3	MUC17_HUMAN	mucin 17	318	Extracellular (Potential).|Ser-rich.|3.|59 X approximate tandem repeats.					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)													0.1875	85.911094	104.927625	39	169	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	100462370	100462370	10368	7	C	T	T	19	19	MUC17	T	1	1
DNAH11	8701	broad.mit.edu	36	7	21607578	21607578	+	Silent	SNP	C	T	T			TCGA-16-0850-01	TCGA-16-0850-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr7:21607578C>T	uc003svc.1	+	c.3465C>T	c.(3463-3465)TCC>TCT	p.S1155S		NM_003777	NP_003768	Q96DT5	DYH11_HUMAN	dynein, axonemal, heavy chain 11	1155	Stem (By similarity).				microtubule-based movement	axonemal dynein complex|cilium axoneme|cytoplasm|microtubule	ATP binding|ATPase activity|microtubule motor activity			ovary(8)|large_intestine(3)|pancreas(3)|central_nervous_system(1)	15														0.235532	433.992275	481.502668	175	568	CC		KEEP	---	---	---	---	capture			Silent	SNP	21607578	21607578	4781	7	C	T	T	23	23	DNAH11	T	1	1
HOXA10	3206	broad.mit.edu	36	7	27179944	27179944	+	Nonsense_Mutation	SNP	G	C	C			TCGA-16-0850-01	TCGA-16-0850-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr7:27179944G>C	uc003syv.1	-	c.456C>G	c.(454-456)TAC>TAG	p.Y152*	HOXA10_uc003syw.2_Intron	NM_018951	NP_061824	P31260	HXA10_HUMAN	homeobox A10 isoform a	169					regulation of transcription, DNA-dependent|spermatogenesis		protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription regulator activity				0														0.184211	17.003395	20.557156	7	31	GG		KEEP	---	---	---	---	capture			Nonsense_Mutation	SNP	27179944	27179944	7581	7	G	C	C	36	36	HOXA10	C	5	3
HGSNAT	138050	broad.mit.edu	36	8	43165815	43165815	+	Nonsense_Mutation	SNP	G	A	A			TCGA-16-0850-01	TCGA-16-0850-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr8:43165815G>A	uc003xpx.2	+	c.1170G>A	c.(1168-1170)TGG>TGA	p.W390*		NM_152419	NP_689632	Q68CP4	HGNAT_HUMAN	heparan-alpha-glucosaminide N-acetyltransferase	418	Cytoplasmic (Potential).				lysosomal transport|protein oligomerization	integral to membrane|lysosomal membrane	heparan-alpha-glucosaminide N-acetyltransferase activity				0	Prostate(17;0.0119)|Ovarian(28;0.0172)|Lung SC(25;0.184)	all_cancers(86;0.000223)|all_epithelial(80;1.61e-07)|all_lung(54;0.00021)|Lung NSC(58;0.000778)|Hepatocellular(245;0.0524)|Renal(179;0.0822)|Esophageal squamous(32;0.129)	Lung(22;0.0777)|LUSC - Lung squamous cell carcinoma(45;0.17)											0.434211	96.061661	96.348517	33	43	GG		KEEP	---	---	---	---	capture			Nonsense_Mutation	SNP	43165815	43165815	7372	8	G	A	A	42	42	HGSNAT	A	5	2
RGS3	5998	broad.mit.edu	36	9	115310659	115310659	+	Silent	SNP	C	T	T			TCGA-16-0850-01	TCGA-16-0850-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr9:115310659C>T	uc004bhq.1	+	c.1455C>T	c.(1453-1455)TAC>TAT	p.Y485Y	RGS3_uc004bhr.1_Silent_p.Y373Y|RGS3_uc004bhs.1_Silent_p.Y375Y|RGS3_uc004bht.1_Silent_p.Y204Y|RGS3_uc010muy.1_Silent_p.Y204Y|RGS3_uc004bhu.1_Silent_p.Y111Y	NM_144488	NP_652759	P49796	RGS3_HUMAN	regulator of G-protein signalling 3 isoform 6	485					inactivation of MAPK activity|negative regulation of signal transduction|regulation of G-protein coupled receptor protein signaling pathway	cytosol|nucleus|plasma membrane	GTPase activator activity|signal transducer activity			ovary(1)|lung(1)|skin(1)	3														0.114754	8.679336	17.602688	7	54	CC		KEEP	---	---	---	---	capture			Silent	SNP	115310659	115310659	13780	9	C	T	T	18	18	RGS3	T	2	2
RABGAP1	23637	broad.mit.edu	36	9	124791550	124791550	+	Missense_Mutation	SNP	C	G	G			TCGA-16-0850-01	TCGA-16-0850-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr9:124791550C>G	uc010mwf.1	+	c.528C>G	c.(526-528)TTC>TTG	p.F176L	RABGAP1_uc004bnl.2_Non-coding_Transcript|RABGAP1_uc004bnm.1_Missense_Mutation_p.F248L	NM_012197	NP_036329	Q9Y3P9	RBGP1_HUMAN	RAB GTPase activating protein 1	248	PID.				cell cycle	centrosome|cytosol|microtubule associated complex	Rab GTPase activator activity|tubulin binding			ovary(3)|kidney(2)	5														0.182353	62.83429	78.943081	31	139	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	124791550	124791550	13423	9	C	G	G	30	30	RABGAP1	G	3	3
IFNA7	3444	broad.mit.edu	36	9	21191717	21191717	+	Missense_Mutation	SNP	T	C	C			TCGA-16-0850-01	TCGA-16-0850-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr9:21191717T>C	uc003zop.1	-	c.448A>G	c.(448-450)ATC>GTC	p.I150V	IFNA14_uc003zoo.1_Intron	NM_021057	NP_066401	P01567	IFNA7_HUMAN	interferon, alpha 7	150					blood coagulation|cell-cell signaling|regulation of type I interferon-mediated signaling pathway|response to virus|type I interferon-mediated signaling pathway	extracellular space	cytokine activity|interferon-alpha/beta receptor binding				0				GBM - Glioblastoma multiforme(5;4.75e-197)|Lung(24;1.26e-23)|LUSC - Lung squamous cell carcinoma(38;1.4e-13)										0.22291	355.370055	400.983749	144	502	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	21191717	21191717	7843	9	T	C	C	52	52	IFNA7	C	4	4
CUL4B	8450	broad.mit.edu	36	X	119562428	119562428	+	Missense_Mutation	SNP	C	G	G			TCGA-16-0850-01	TCGA-16-0850-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chrX:119562428C>G	uc004esw.1	-	c.1073G>C	c.(1072-1074)AGG>ACG	p.R358T	CUL4B_uc010nqq.1_Missense_Mutation_p.R57T|CUL4B_uc004esv.1_Missense_Mutation_p.R340T	NM_003588	NP_003579	Q13620	CUL4B_HUMAN	cullin 4B isoform 1	358					cell cycle|DNA repair|ubiquitin-dependent protein catabolic process	Cul4B-RING ubiquitin ligase complex|nucleus	protein binding|ubiquitin protein ligase binding			lung(1)|central_nervous_system(1)|pancreas(1)	3														0.260274	325.014182	351.628825	133	378	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	119562428	119562428	4218	23	C	G	G	24	24	CUL4B	G	3	3
DUSP9	1852	broad.mit.edu	36	X	152568899	152568899	+	Missense_Mutation	SNP	C	G	G			TCGA-16-0850-01	TCGA-16-0850-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chrX:152568899C>G	uc004fhx.2	+	c.1100C>G	c.(1099-1101)CCC>CGC	p.P367R	DUSP9_uc004fhy.2_Missense_Mutation_p.P367R	NM_001395	NP_001386	Q99956	DUS9_HUMAN	dual specificity phosphatase 9	367	Tyrosine-protein phosphatase.				inactivation of MAPK activity|JNK cascade	cytosol|endoplasmic reticulum|nucleus	MAP kinase tyrosine/serine/threonine phosphatase activity|protein tyrosine phosphatase activity			ovary(2)	2	all_hematologic(71;4.25e-06)|Acute lymphoblastic leukemia(192;6.56e-05)													0.52	33.267776	33.272136	13	12	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	152568899	152568899	5017	23	C	G	G	22	22	DUSP9	G	3	3
RP2	6102	broad.mit.edu	36	X	46598110	46598110	+	Nonsense_Mutation	SNP	C	T	T			TCGA-16-0850-01	TCGA-16-0850-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chrX:46598110C>T	uc004dgw.2	+	c.358C>T	c.(358-360)CGA>TGA	p.R120*		NM_006915	NP_008846	O75695	XRP2_HUMAN	XRP2 protein	120	C-CAP/cofactor C-like.			R->H: Reduces affinity for mouse ARL3; when associated with S-121.	cell morphogenesis|CTP biosynthetic process|GTP biosynthetic process|protein folding|response to stimulus|UTP biosynthetic process|visual perception	cytoplasm|plasma membrane	ATP binding|GTP binding|GTPase activator activity|nucleoside diphosphate kinase activity|unfolded protein binding				0														0.446328	249.610689	250.053208	79	98	CC		KEEP	---	---	---	---	capture			Nonsense_Mutation	SNP	46598110	46598110	14013	23	C	T	T	27	27	RP2	T	5	1
HUWE1	10075	broad.mit.edu	36	X	53581346	53581346	+	Silent	SNP	C	T	T			TCGA-16-0850-01	TCGA-16-0850-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chrX:53581346C>T	uc004dso.1	-	c.12033G>A	c.(12031-12033)GGG>GGA	p.G4011G	HUWE1_uc004dsn.1_Silent_p.G2819G|HUWE1_uc004dsp.1_Silent_p.G4011G|HUWE1_uc004dsq.1_Silent_p.G311G	NM_031407	NP_113584	Q7Z6Z7	HUWE1_HUMAN	HECT, UBA and WWE domain containing 1	4011					base-excision repair|cell differentiation|histone ubiquitination|protein monoubiquitination|protein polyubiquitination|protein ubiquitination involved in ubiquitin-dependent protein catabolic process	cytoplasm|nucleus	DNA binding|protein binding|ubiquitin-protein ligase activity			ovary(8)|large_intestine(4)|breast(4)|kidney(1)	17														0.20462	398.722695	472.277782	186	723	CC		KEEP	---	---	---	---	capture			Silent	SNP	53581346	53581346	7761	23	C	T	T	26	26	HUWE1	T	2	2
CCDC88B	283234	broad.mit.edu	36	11	63866091	63866102	+	In_Frame_Del	DEL	AGGCTCCCTCTA	-	-			TCGA-16-0850-01	TCGA-16-0850-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:63866091_63866102delAGGCTCCCTCTA	uc001nzy.1	+	c.725_736delAGGCTCCCTCTA	c.(724-738)GAGGCTCCCTCTAGG>GGG	p.242_246EAPSR>G	CCDC88B_uc009ypo.1_In_Frame_Del_p.239_243EAPSR>G|CCDC88B_uc001nzz.1_5'Flank	NM_032251	NP_115627	A6NC98	CC88B_HUMAN	coiled-coil domain containing 88	242_246					microtubule cytoskeleton organization	cytoplasm	microtubule binding			ovary(3)	3														0.33			2	4				---	---	---	---	capture_indel			In_Frame_Del	DEL	63866091	63866102	2989	11	AGGCTCCCTCTA	-	-	11	11	CCDC88B	-	5	5
CLSTN3	9746	broad.mit.edu	36	12	7201924	7201925	+	Frame_Shift_Ins	INS	-	C	C			TCGA-16-0850-01	TCGA-16-0850-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:7201924_7201925insC	uc001qss.1	+	c.2887_2888insC	c.(2887-2889)ACCfs	p.T963fs	CLSTN3_uc001qsr.1_Frame_Shift_Ins_p.T951fs|CLSTN3_uc001qst.1_3'UTR	NM_014718	NP_055533	Q9BQT9	CSTN3_HUMAN	calsyntenin 3	951	Cytoplasmic (Potential).				homophilic cell adhesion	endoplasmic reticulum membrane|Golgi membrane|integral to membrane|plasma membrane	calcium ion binding			large_intestine(1)	1														0.33			2	4				---	---	---	---	capture_indel			Frame_Shift_Ins	INS	7201924	7201925	3701	12	-	C	C	10	10	CLSTN3	C	5	5
MPRIP	23164	broad.mit.edu	36	17	16987610	16987611	+	Frame_Shift_Ins	INS	-	C	C			TCGA-16-0850-01	TCGA-16-0850-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:16987610_16987611insC	uc002gqv.1	+	c.1051_1052insC	c.(1051-1053)GCCfs	p.A351fs	MPRIP_uc002gqu.1_Frame_Shift_Ins_p.A351fs|MPRIP_uc002gqw.1_Intron	NM_015134	NP_055949	Q6WCQ1	MPRIP_HUMAN	myosin phosphatase-Rho interacting protein	351	Interaction with F-actin (By similarity).					cytoplasm|cytoskeleton	actin binding				0														0.31			5	11				---	---	---	---	capture_indel			Frame_Shift_Ins	INS	16987610	16987611	10135	17	-	C	C	34	34	MPRIP	C	5	5
HEXDC	284004	broad.mit.edu	36	17	77993586	77993587	+	Frame_Shift_Ins	INS	-	G	G			TCGA-16-0850-01	TCGA-16-0850-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:77993586_77993587insG	uc002kev.2	+	c.1587_1588insG	c.(1585-1590)GCTGGGfs	p.A529fs	HEXDC_uc010diq.1_Frame_Shift_Ins_p.L502fs|HEXDC_uc002kew.1_3'UTR	NM_173620	NP_775891	Q8WVB3	HEXDC_HUMAN	hexosaminidase (glycosyl hydrolase family 20,	89_90					carbohydrate metabolic process	cytoplasm|nucleus	beta-N-acetylhexosaminidase activity|cation binding			ovary(1)	1	Breast(20;0.00106)|all_neural(118;0.0804)		OV - Ovarian serous cystadenocarcinoma(97;0.0143)|BRCA - Breast invasive adenocarcinoma(99;0.0369)											0.33			2	4				---	---	---	---	capture_indel			Frame_Shift_Ins	INS	77993586	77993587	7358	17	-	G	G	55	55	HEXDC	G	5	5
FAM187B	148109	broad.mit.edu	36	19	40407923	40407924	+	Frame_Shift_Ins	INS	-	GG	GG			TCGA-16-0850-01	TCGA-16-0850-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:40407923_40407924insGG	uc002nyk.1	-	c.754_755insCC	c.(754-756)CTGfs	p.L252fs		NM_152481	NP_689694	Q17R55	F187B_HUMAN	family with sequence similarity 187, member B	252	Extracellular (Potential).					integral to membrane				ovary(2)	2														0.33			2	4				---	---	---	---	capture_indel			Frame_Shift_Ins	INS	40407923	40407924	5723	19	-	GG	GG	7	7	FAM187B	GG	5	5
