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
SUPV3L1	6832	broad.mit.edu	36	10	70624962	70624962	+	Missense_Mutation	SNP	T	G	G			TCGA-12-1599-01	TCGA-12-1599-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr10:70624962T>G	uc001jpe.1	+	c.866T>G	c.(865-867)GTA>GGA	p.V289G		NM_003171	NP_003162	Q8IYB8	SUV3_HUMAN	suppressor of var1, 3-like 1	289	Helicase ATP-binding.				DNA duplex unwinding	mitochondrial nucleoid|nucleus	ATP binding|DNA binding|DNA helicase activity|RNA binding			urinary_tract(1)|ovary(1)	2														0.294118	7.849609	8.508735	5	12	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	70624962	70624962	15922	10	T	G	G	57	57	SUPV3L1	G	4	4
PGR	5241	broad.mit.edu	36	11	100417937	100417937	+	Silent	SNP	C	T	T			TCGA-12-1599-01	TCGA-12-1599-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr11:100417937C>T	uc001pgh.2	-	c.2595G>A	c.(2593-2595)TCG>TCA	p.S865S	PGR_uc001pgg.2_Silent_p.S246S|PGR_uc001pgi.2_Silent_p.S763S|PGR_uc009yww.1_Non-coding_Transcript|PGR_uc001pgj.2_Non-coding_Transcript|PGR_uc009ywx.1_Non-coding_Transcript	NM_000926	NP_000917	P06401	PRGR_HUMAN	progesterone receptor	865	Steroid-binding.				cell-cell signaling|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor	cytoplasm|nucleoplasm	enzyme binding|receptor binding|sequence-specific DNA binding transcription factor activity|steroid binding|steroid hormone receptor activity|zinc ion binding			lung(1)|liver(1)|central_nervous_system(1)|pancreas(1)	4		Acute lymphoblastic leukemia(157;0.000885)|all_hematologic(158;0.014)		LUSC - Lung squamous cell carcinoma(1;0.0387)|BRCA - Breast invasive adenocarcinoma(274;0.124)|OV - Ovarian serous cystadenocarcinoma(223;0.148)|Lung(307;0.164)	Desogestrel(DB00304)|Drospirenone(DB01395)|Dydrogesterone(DB00378)|Ethynodiol Diacetate(DB00823)|Etonogestrel(DB00294)|Levonorgestrel(DB00367)|Medroxyprogesterone(DB00603)|Megestrol(DB00351)|Mifepristone(DB00834)|Norethindrone(DB00717)|Norgestimate(DB00957)|Norgestrel(DB00506)|Progesterone(DB00396)	Pancreas(124;2271 2354 21954 22882)				429				0.321429	103.750546	106.928238	36	76	CC		KEEP	---	---	---	---	capture			Silent	SNP	100417937	100417937	12228	11	C	T	T	31	31	PGR	T	1	1
MRGPRX1	259249	broad.mit.edu	36	11	18912364	18912364	+	Missense_Mutation	SNP	C	T	T			TCGA-12-1599-01	TCGA-12-1599-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr11:18912364C>T	uc001mpg.1	-	c.544G>A	c.(544-546)GCG>ACG	p.A182T		NM_147199	NP_671732	Q96LB2	MRGX1_HUMAN	MAS-related GPR, member X1	182	Helical; Name=5; (Potential).				acute-phase response	integral to membrane|plasma membrane	G-protein coupled receptor activity			pancreas(2)|central_nervous_system(1)	3														0.381356	129.330545	130.792253	45	73	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	18912364	18912364	10159	11	C	T	T	27	27	MRGPRX1	T	1	1
GAS2	2620	broad.mit.edu	36	11	22704422	22704422	+	Silent	SNP	G	A	A			TCGA-12-1599-01	TCGA-12-1599-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr11:22704422G>A	uc009yie.1	+	c.276G>A	c.(274-276)CCG>CCA	p.P92P	GAS2_uc001mqm.1_Silent_p.P92P|GAS2_uc001mqn.1_Non-coding_Transcript|GAS2_uc001mqo.1_Silent_p.P92P	NM_177553	NP_808221	O43903	GAS2_HUMAN	growth arrest-specific 2	92	CH.				cell cycle arrest|cellular component disassembly involved in apoptosis|regulation of cell shape	actin filament|cytosol|membrane				ovary(1)	1														0.329843	187.2658	192.164621	63	128	GG		KEEP	---	---	---	---	capture			Silent	SNP	22704422	22704422	6509	11	G	A	A	40	40	GAS2	A	1	1
IFFO1	25900	broad.mit.edu	36	12	6528157	6528157	+	Silent	SNP	C	G	G			TCGA-12-1599-01	TCGA-12-1599-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr12:6528157C>G	uc001qpc.1	-	c.1176G>C	c.(1174-1176)GGG>GGC	p.G392G	IFFO1_uc001qoy.2_Non-coding_Transcript|IFFO1_uc001qpa.1_Silent_p.G29G|IFFO1_uc001qpb.1_Silent_p.G66G|IFFO1_uc001qpe.1_Non-coding_Transcript|IFFO1_uc001qpf.1_Silent_p.G392G|IFFO1_uc001qoz.1_Silent_p.G29G|IFFO1_uc001qpd.1_Silent_p.G389G|IFFO1_uc001qpg.2_Silent_p.G29G	NM_001039670	NP_001034759	Q0D2I5	IFFO1_HUMAN	intermediate filament family orphan isoform 4	389						intermediate filament					0														0.30303	26.344037	27.483249	10	23	CC		KEEP	---	---	---	---	capture			Silent	SNP	6528157	6528157	7810	12	C	G	G	22	22	IFFO1	G	3	3
SLC6A15	55117	broad.mit.edu	36	12	83779721	83779721	+	Missense_Mutation	SNP	C	T	T			TCGA-12-1599-01	TCGA-12-1599-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr12:83779721C>T	uc001szv.1	-	c.2014G>A	c.(2014-2016)GAT>AAT	p.D672N	SLC6A15_uc001szw.1_3'UTR	NM_182767	NP_877499	Q9H2J7	S6A15_HUMAN	solute carrier family 6, member 15 isoform 1	672	Cytoplasmic (Potential).				cellular nitrogen compound metabolic process|leucine transport|proline transport	integral to plasma membrane	amino acid transmembrane transporter activity|neurotransmitter:sodium symporter activity			pancreas(2)|ovary(1)	3														0.268293	127.13345	135.077019	44	120	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	83779721	83779721	15175	12	C	T	T	31	31	SLC6A15	T	1	1
SERPINA1	5265	broad.mit.edu	36	14	93915590	93915590	+	Silent	SNP	G	A	A			TCGA-12-1599-01	TCGA-12-1599-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr14:93915590G>A	uc001ycx.2	-	c.1029C>T	c.(1027-1029)TCC>TCT	p.S343S	SERPINA1_uc001ycw.2_Non-coding_Transcript|SERPINA1_uc010auw.1_Silent_p.S343S|SERPINA1_uc010aux.1_Silent_p.S343S|SERPINA1_uc001ycy.2_Silent_p.S343S|SERPINA1_uc010auy.1_Silent_p.S343S|SERPINA1_uc001ycz.2_Silent_p.S343S|SERPINA1_uc010auz.1_Silent_p.S343S|SERPINA1_uc010ava.1_Silent_p.S343S|SERPINA1_uc001ydb.2_Silent_p.S343S|SERPINA1_uc010avb.1_Silent_p.S343S|SERPINA1_uc001ydc.2_Silent_p.S343S|SERPINA1_uc001yda.1_Silent_p.S343S	NM_000295	NP_001121179	P01009	A1AT_HUMAN	serine proteinase inhibitor, clade A, member 1	343					acute-phase response|platelet activation|platelet degranulation|regulation of proteolysis	extracellular space|platelet alpha granule lumen|proteinaceous extracellular matrix	protease binding|serine-type endopeptidase inhibitor activity			skin(1)	1		all_cancers(154;0.0649)|all_epithelial(191;0.223)		Epithelial(152;0.135)|COAD - Colon adenocarcinoma(157;0.207)|all cancers(159;0.221)	Alpha-1-proteinase inhibitor(DB00058)									0.380952	104.485155	105.527512	32	52	GG		KEEP	---	---	---	---	capture			Silent	SNP	93915590	93915590	14574	14	G	A	A	39	39	SERPINA1	A	1	1
ZC3H18	124245	broad.mit.edu	36	16	87216188	87216188	+	Missense_Mutation	SNP	C	T	T			TCGA-12-1599-01	TCGA-12-1599-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr16:87216188C>T	uc002fky.1	+	c.1558C>T	c.(1558-1560)CGC>TGC	p.R520C	ZC3H18_uc010chw.1_Non-coding_Transcript	NM_144604	NP_653205	Q86VM9	ZCH18_HUMAN	zinc finger CCCH-type containing 18	520						nucleus	nucleic acid binding|zinc ion binding				0				BRCA - Breast invasive adenocarcinoma(80;0.0542)		Ovarian(121;375 2276 20373 38669)								0.2	7.31869	8.572474	3	12	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	87216188	87216188	18156	16	C	T	T	27	27	ZC3H18	T	1	1
NF1	4763	broad.mit.edu	36	17	26611527	26611527	+	Missense_Mutation	SNP	T	C	C			TCGA-12-1599-01	TCGA-12-1599-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr17:26611527T>C	uc002hgg.1	+	c.4445T>C	c.(4444-4446)ATA>ACA	p.I1482T	NF1_uc002hgh.1_Missense_Mutation_p.I1461T|NF1_uc002hgi.1_Missense_Mutation_p.I494T	NM_001042492	NP_001035957	P21359	NF1_HUMAN	neurofibromin isoform 1	1482					actin cytoskeleton organization|adrenal gland development|artery morphogenesis|camera-type eye morphogenesis|cerebral cortex development|collagen fibril organization|forebrain astrocyte development|forebrain morphogenesis|heart development|liver development|MAPKKK cascade|metanephros development|myelination in peripheral nervous system|negative regulation of cell migration|negative regulation of endothelial cell proliferation|negative regulation of MAP kinase activity|negative regulation of MAPKKK cascade|negative regulation of neuroblast proliferation|negative regulation of oligodendrocyte differentiation|negative regulation of transcription factor import into nucleus|osteoblast differentiation|phosphatidylinositol 3-kinase cascade|pigmentation|positive regulation of adenylate cyclase activity|positive regulation of neuron apoptosis|Ras protein signal transduction|regulation of blood vessel endothelial cell migration|regulation of bone resorption|response to hypoxia|smooth muscle tissue development|spinal cord development|sympathetic nervous system development|visual learning|wound healing	axon|cytoplasm|dendrite|intrinsic to internal side of plasma membrane|nucleus	protein binding|Ras GTPase activator activity	p.?(1)		soft_tissue(155)|central_nervous_system(56)|large_intestine(27)|lung(19)|haematopoietic_and_lymphoid_tissue(13)|ovary(12)|autonomic_ganglia(7)|skin(3)|stomach(2)|breast(2)|thyroid(1)|prostate(1)|kidney(1)|pancreas(1)	300		all_cancers(10;1.29e-12)|all_epithelial(10;0.00347)|all_hematologic(16;0.00556)|Acute lymphoblastic leukemia(14;0.00593)|Breast(31;0.014)|Myeloproliferative disorder(56;0.0255)|all_lung(9;0.0321)|Lung NSC(157;0.0659)		UCEC - Uterine corpus endometrioid carcinoma (4;4.38e-05)|all cancers(4;1.64e-26)|Epithelial(4;9.15e-23)|OV - Ovarian serous cystadenocarcinoma(4;3.58e-21)|GBM - Glioblastoma multiforme(4;0.00146)					p.I1482T(RERFLCSQ1-Tumor)	847	TCGA GBM(6;<1E-8)|TSP Lung(7;0.0071)|TCGA Ovarian(3;0.0088)			0.241071	151.740646	165.44055	54	170	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	26611527	26611527	10756	17	T	C	C	49	49	NF1	C	4	4
SGCA	6442	broad.mit.edu	36	17	45600870	45600870	+	Silent	SNP	C	T	T			TCGA-12-1599-01	TCGA-12-1599-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr17:45600870C>T	uc002iqi.1	+	c.522C>T	c.(520-522)AAC>AAT	p.N174N	SGCA_uc002iqj.1_Silent_p.N174N	NM_000023	NP_000014	Q16586	SGCA_HUMAN	sarcoglycan, alpha isoform 1 precursor	174	Extracellular (Potential).				muscle contraction|muscle organ development	cytoplasm|cytoskeleton|integral to membrane|sarcoglycan complex|sarcolemma	calcium ion binding			ovary(2)	2														0.272727	8.820396	9.332314	3	8	CC		KEEP	---	---	---	---	capture			Silent	SNP	45600870	45600870	14690	17	C	T	T	19	19	SGCA	T	1	1
DNAH2	146754	broad.mit.edu	36	17	7631014	7631014	+	Missense_Mutation	SNP	G	A	A			TCGA-12-1599-01	TCGA-12-1599-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr17:7631014G>A	uc002giu.1	+	c.6541G>A	c.(6541-6543)GTC>ATC	p.V2181I		NM_020877	NP_065928	Q9P225	DYH2_HUMAN	dynein heavy chain domain 3	2181	AAA 2 (By similarity).				ciliary or flagellar motility|microtubule-based movement	axonemal dynein complex|cilium axoneme|cytoplasm|microtubule	ATP binding|ATPase activity|microtubule motor activity			ovary(6)|central_nervous_system(1)	7		all_cancers(10;4.66e-07)|Prostate(122;0.081)												0.371622	164.688922	166.830831	55	93	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	7631014	7631014	4785	17	G	A	A	40	40	DNAH2	A	1	1
FAM38B	63895	broad.mit.edu	36	18	10662764	10662764	+	Silent	SNP	C	T	T			TCGA-12-1599-01	TCGA-12-1599-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr18:10662764C>T	uc002koq.1	-	c.1305G>A	c.(1303-1305)CCG>CCA	p.P435P		NM_022068	NP_071351	Q9H5I5	PIEZ2_HUMAN	hypothetical protein LOC63895	2643						integral to membrane	ion channel activity			ovary(1)	1														0.329609	178.875123	183.476161	59	120	CC		KEEP	---	---	---	---	capture			Silent	SNP	10662764	10662764	5776	18	C	T	T	31	31	FAM38B	T	1	1
MAPK4	5596	broad.mit.edu	36	18	46444687	46444687	+	Silent	SNP	C	T	T			TCGA-12-1599-01	TCGA-12-1599-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr18:46444687C>T	uc002lev.1	+	c.361C>T	c.(361-363)CTG>TTG	p.L121L	MAPK4_uc010doz.1_Silent_p.L121L	NM_002747	NP_002738	P31152	MK04_HUMAN	mitogen-activated protein kinase 4	121	Protein kinase.				cell cycle|protein phosphorylation		ATP binding|MAP kinase activity			lung(2)	2		Colorectal(6;0.0297)		Colorectal(21;0.156)						110				0.373494	92.506286	93.671672	31	52	CC		KEEP	---	---	---	---	capture			Silent	SNP	46444687	46444687	9663	18	C	T	T	28	28	MAPK4	T	2	2
PTPRH	5794	broad.mit.edu	36	19	60388815	60388815	+	Missense_Mutation	SNP	G	A	A			TCGA-12-1599-01	TCGA-12-1599-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr19:60388815G>A	uc002qjq.1	-	c.2929C>T	c.(2929-2931)CGC>TGC	p.R977C	PTPRH_uc010esv.1_Missense_Mutation_p.R799C	NM_002842	NP_002833	Q9HD43	PTPRH_HUMAN	protein tyrosine phosphatase, receptor type, H	977	Cytoplasmic (Potential).|Tyrosine-protein phosphatase.				apoptosis	cytoplasm|integral to plasma membrane	protein binding|transmembrane receptor protein tyrosine phosphatase activity			ovary(2)|large_intestine(1)	3		Renal(1328;0.245)	BRCA - Breast invasive adenocarcinoma(297;0.209)	GBM - Glioblastoma multiforme(193;0.0479)										0.409091	24.068862	24.228141	9	13	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	60388815	60388815	13260	19	G	A	A	38	38	PTPRH	A	1	1
NLRP13	126204	broad.mit.edu	36	19	61115666	61115666	+	Silent	SNP	G	A	A			TCGA-12-1599-01	TCGA-12-1599-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr19:61115666G>A	uc002qmg.1	-	c.1329C>T	c.(1327-1329)TAC>TAT	p.Y443Y		NM_176810	NP_789780	Q86W25	NAL13_HUMAN	NACHT, leucine rich repeat and PYD containing	443	NACHT.						ATP binding			ovary(3)|skin(2)|pancreas(1)|lung(1)	7		Colorectal(82;3.48e-05)|Ovarian(87;0.0481)|Renal(1328;0.218)		GBM - Glioblastoma multiforme(193;0.0642)										0.227848	86.016881	96.757136	36	122	GG		KEEP	---	---	---	---	capture			Silent	SNP	61115666	61115666	10878	19	G	A	A	40	40	NLRP13	A	1	1
HMCN1	83872	broad.mit.edu	36	1	184348587	184348587	+	Silent	SNP	C	A	A			TCGA-12-1599-01	TCGA-12-1599-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr1:184348587C>A	uc001grq.1	+	c.11010C>A	c.(11008-11010)ATC>ATA	p.I3670I		NM_031935	NP_114141	Q96RW7	HMCN1_HUMAN	hemicentin 1	3670	Ig-like C2-type 35.				bioluminescence|protein-chromophore linkage|response to stimulus|visual perception	basement membrane	calcium ion binding			ovary(22)	22														0.235	122.831489	135.672016	47	153	CC		KEEP	---	---	---	---	capture			Silent	SNP	184348587	184348587	7511	1	C	A	A	30	30	HMCN1	A	3	3
UBR4	23352	broad.mit.edu	36	1	19367184	19367184	+	Missense_Mutation	SNP	T	C	C			TCGA-12-1599-01	TCGA-12-1599-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr1:19367184T>C	uc001bbi.1	-	c.3823A>G	c.(3823-3825)AGC>GGC	p.S1275G	UBR4_uc001bbm.1_Missense_Mutation_p.S486G	NM_020765	NP_065816	Q5T4S7	UBR4_HUMAN	retinoblastoma-associated factor 600	1275					interspecies interaction between organisms	cytoplasm|cytoskeleton|integral to membrane|nucleus	calmodulin binding|ubiquitin-protein ligase activity|zinc ion binding			kidney(10)|ovary(7)|breast(4)|pancreas(2)	23		Colorectal(325;3.46e-05)|Renal(390;0.000147)|all_lung(284;0.000328)|Lung NSC(340;0.000406)|Breast(348;0.000814)|Ovarian(437;0.00774)|Myeloproliferative disorder(586;0.0256)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00674)|BRCA - Breast invasive adenocarcinoma(304;5.43e-05)|Kidney(64;0.000337)|KIRC - Kidney renal clear cell carcinoma(64;0.00426)|STAD - Stomach adenocarcinoma(196;0.00715)|READ - Rectum adenocarcinoma(331;0.0816)										0.315217	82.140595	84.9358	29	63	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	19367184	19367184	17462	1	T	C	C	53	53	UBR4	C	4	4
CACNA1S	779	broad.mit.edu	36	1	199325119	199325119	+	Missense_Mutation	SNP	C	T	T			TCGA-12-1599-01	TCGA-12-1599-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr1:199325119C>T	uc001gvv.1	-	c.790G>A	c.(790-792)GGC>AGC	p.G264S		NM_000069	NP_000060	Q13698	CAC1S_HUMAN	calcium channel, voltage-dependent, L type,	264	Extracellular (Potential).|I.				axon guidance	I band|T-tubule|voltage-gated calcium channel complex	high voltage-gated calcium channel activity			ovary(3)|central_nervous_system(1)	4					Magnesium Sulfate(DB00653)|Verapamil(DB00661)									0.538462	42.248013	42.281381	14	12	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	199325119	199325119	2663	1	C	T	T	23	23	CACNA1S	T	1	1
PLXNA2	5362	broad.mit.edu	36	1	206300654	206300654	+	Missense_Mutation	SNP	T	C	C			TCGA-12-1599-01	TCGA-12-1599-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr1:206300654T>C	uc001hgz.1	-	c.2738A>G	c.(2737-2739)CAG>CGG	p.Q913R		NM_025179	NP_079455	O75051	PLXA2_HUMAN	plexin A2	913	Extracellular (Potential).|IPT/TIG 1.				axon guidance	integral to membrane|intracellular|plasma membrane				ovary(2)	2				OV - Ovarian serous cystadenocarcinoma(81;0.199)										0.305556	57.199437	59.642698	22	50	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	206300654	206300654	12546	1	T	C	C	55	55	PLXNA2	C	4	4
PTPRU	10076	broad.mit.edu	36	1	29502967	29502967	+	Silent	SNP	C	T	T			TCGA-12-1599-01	TCGA-12-1599-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr1:29502967C>T	uc001bru.1	+	c.2520C>T	c.(2518-2520)AGC>AGT	p.S840S	PTPRU_uc001brv.1_Silent_p.S830S|PTPRU_uc001brw.1_Silent_p.S830S|PTPRU_uc009vtq.1_Silent_p.S830S|PTPRU_uc009vtr.1_Silent_p.S830S	NM_005704	NP_005695	Q92729	PTPRU_HUMAN	protein tyrosine phosphatase, receptor type, U	840	Mediates interaction with CTNNB1 (By similarity).|Cytoplasmic (Potential).			SG -> GW (in Ref. 4; AAC51938).	canonical Wnt receptor signaling pathway|cell differentiation|negative regulation of cell migration|negative regulation of cell proliferation|negative regulation of transcription, DNA-dependent|protein localization at cell surface|transmembrane receptor protein tyrosine phosphatase signaling pathway	cell-cell junction|integral to plasma membrane	beta-catenin binding|transmembrane receptor protein tyrosine phosphatase activity			large_intestine(3)|ovary(1)|kidney(1)|central_nervous_system(1)	6		Colorectal(325;0.000399)|Lung NSC(340;0.00953)|all_lung(284;0.0112)|Breast(348;0.0126)|all_neural(195;0.0199)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0563)|Medulloblastoma(700;0.123)		Colorectal(126;6.99e-07)|COAD - Colon adenocarcinoma(152;3.18e-05)|STAD - Stomach adenocarcinoma(196;0.0234)|READ - Rectum adenocarcinoma(331;0.0686)|BRCA - Breast invasive adenocarcinoma(304;0.0871)						874				0.40678	68.376715	68.827102	24	35	CC		KEEP	---	---	---	---	capture			Silent	SNP	29502967	29502967	13271	1	C	T	T	27	27	PTPRU	T	1	1
WDR63	126820	broad.mit.edu	36	1	85319678	85319678	+	Missense_Mutation	SNP	A	G	G			TCGA-12-1599-01	TCGA-12-1599-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr1:85319678A>G	uc001dkt.1	+	c.277A>G	c.(277-279)ATT>GTT	p.I93V	WDR63_uc009wcl.1_Missense_Mutation_p.I93V	NM_145172	NP_660155	Q8IWG1	WDR63_HUMAN	WD repeat domain 63	93										ovary(2)	2				all cancers(265;0.00391)|Epithelial(280;0.00922)|Colorectal(170;0.166)										0.399123	306.579899	308.609185	91	137	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	85319678	85319678	17887	1	A	G	G	4	4	WDR63	G	4	4
RALGAPB	57148	broad.mit.edu	36	20	36636272	36636272	+	Missense_Mutation	SNP	G	A	A			TCGA-12-1599-01	TCGA-12-1599-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr20:36636272G>A	uc002xiw.1	+	c.4208G>A	c.(4207-4209)CGG>CAG	p.R1403Q	RALGAPB_uc002xix.1_Missense_Mutation_p.R1400Q|RALGAPB_uc002xiy.1_Intron|RALGAPB_uc002xiz.1_Missense_Mutation_p.R1182Q	NM_020336	NP_065069	Q86X10	RLGPB_HUMAN	hypothetical protein LOC57148	1403					activation of Ral GTPase activity	intracellular	protein heterodimerization activity|Ral GTPase activator activity			pancreas(1)	1														0.345679	85.875711	87.578897	28	53	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	36636272	36636272	13475	20	G	A	A	39	39	RALGAPB	A	1	1
PRIC285	85441	broad.mit.edu	36	20	61662462	61662462	+	Silent	SNP	C	T	T			TCGA-12-1599-01	TCGA-12-1599-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr20:61662462C>T	uc002yfm.2	-	c.7314G>A	c.(7312-7314)GCG>GCA	p.A2438A	PRIC285_uc002yfl.1_Silent_p.A1869A	NM_001037335	NP_001032412	Q9BYK8	PR285_HUMAN	PPAR-alpha interacting complex protein 285	2438					cellular lipid metabolic process|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleoplasm	ATP binding|DNA binding|helicase activity|ribonuclease activity|RNA binding|transcription coactivator activity|zinc ion binding			central_nervous_system(2)	2	all_cancers(38;2.51e-11)|all_epithelial(29;8.27e-13)		Epithelial(9;1.27e-08)|all cancers(9;7.32e-08)|BRCA - Breast invasive adenocarcinoma(10;5.15e-06)											0.2	9.789968	11.462887	4	16	CC		KEEP	---	---	---	---	capture			Silent	SNP	61662462	61662462	12928	20	C	T	T	19	19	PRIC285	T	1	1
BACH1	571	broad.mit.edu	36	21	29615666	29615666	+	Missense_Mutation	SNP	G	A	A			TCGA-12-1599-01	TCGA-12-1599-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr21:29615666G>A	uc002ynj.1	+	c.194G>A	c.(193-195)GGC>GAC	p.G65D	BACH1_uc002ynk.1_Missense_Mutation_p.G65D|BACH1_uc002ynl.1_Missense_Mutation_p.G65D	NM_001186	NP_996749	O14867	BACH1_HUMAN	BTB and CNC homology 1 isoform a	65	BTB.				regulation of transcription, DNA-dependent	nucleus	protein dimerization activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			ovary(1)|liver(1)	2														0.244444	23.997515	26.680699	11	34	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	29615666	29615666	1304	21	G	A	A	42	42	BACH1	A	2	2
SFRS15	57466	broad.mit.edu	36	21	31997993	31997993	+	Missense_Mutation	SNP	T	G	G			TCGA-12-1599-01	TCGA-12-1599-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr21:31997993T>G	uc002ypd.1	-	c.277A>C	c.(277-279)ACT>CCT	p.T93P	SFRS15_uc002ype.1_Missense_Mutation_p.T93P|SFRS15_uc010glu.1_Missense_Mutation_p.T78P|SFRS15_uc002ypf.1_5'Flank|SFRS15_uc002ypg.1_Missense_Mutation_p.T93P	NM_020706	NP_065757	O95104	SFR15_HUMAN	splicing factor, arginine/serine-rich 15 isoform	93	CID.					nucleus	nucleotide binding|RNA binding				0														0.148148	6.794497	9.993465	4	23	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	31997993	31997993	14661	21	T	G	G	60	60	SFRS15	G	4	4
IL1R2	7850	broad.mit.edu	36	2	101992568	101992568	+	Silent	SNP	T	G	G			TCGA-12-1599-01	TCGA-12-1599-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr2:101992568T>G	uc002tbm.1	+	c.180T>G	c.(178-180)TCT>TCG	p.S60S	IL1R2_uc002tbn.1_Silent_p.S60S|IL1R2_uc002tbo.1_Silent_p.S60S	NM_004633	NP_775465	P27930	IL1R2_HUMAN	interleukin 1 receptor, type II precursor	60	Extracellular (Potential).|Ig-like C2-type 1.				immune response	integral to membrane|plasma membrane	interleukin-1, Type II, blocking receptor activity				0					Anakinra(DB00026)	Pancreas(106;189 1628 2302 5133 12295)				365				0.232558	43.750391	49.391777	20	66	TT		KEEP	---	---	---	---	capture			Silent	SNP	101992568	101992568	7960	2	T	G	G	55	55	IL1R2	G	4	4
SLC9A2	6549	broad.mit.edu	36	2	102666294	102666294	+	Missense_Mutation	SNP	G	A	A			TCGA-12-1599-01	TCGA-12-1599-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr2:102666294G>A	uc002tca.1	+	c.1147G>A	c.(1147-1149)GTG>ATG	p.V383M		NM_003048	NP_003039	Q9UBY0	SL9A2_HUMAN	solute carrier family 9 (sodium/hydrogen	383	Cytoplasmic (Potential).					integral to membrane|plasma membrane	sodium:hydrogen antiporter activity	p.V383M(1)		central_nervous_system(3)|breast(2)	5														0.380952	251.552501	254.161476	80	130	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	102666294	102666294	15209	2	G	A	A	40	40	SLC9A2	A	1	1
TTN	7273	broad.mit.edu	36	2	179349233	179349233	+	Missense_Mutation	SNP	G	A	A			TCGA-12-1599-01	TCGA-12-1599-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr2:179349233G>A	uc002umr.1	-	c.5603C>T	c.(5602-5604)CCT>CTT	p.P1868L	TTN_uc002ums.1_Missense_Mutation_p.P1822L|TTN_uc010frc.1_Missense_Mutation_p.P1822L|TTN_uc010frd.1_Missense_Mutation_p.P1822L|TTN_uc002unb.1_Missense_Mutation_p.P1868L	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	1868								p.A1868V(1)		ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1)	153			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)							8722				0.375566	524.752157	530.755894	166	276	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	179349233	179349233	17290	2	G	A	A	35	35	TTN	A	2	2
SLC23A3	151295	broad.mit.edu	36	2	219736367	219736367	+	Silent	SNP	G	T	T			TCGA-12-1599-01	TCGA-12-1599-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr2:219736367G>T	uc010fwb.1	-	c.1077C>A	c.(1075-1077)GTC>GTA	p.V359V	NHEJ1_uc002vjp.2_5'Flank|NHEJ1_uc002vjq.2_Non-coding_Transcript	NM_144712	NP_653313	Q6PIS1	S23A3_HUMAN	solute carrier family 23 (nucleobase	476	Extracellular (Potential).				transmembrane transport	integral to membrane	protein binding|transporter activity				0		Renal(207;0.0474)		Epithelial(149;9.27e-07)|all cancers(144;0.000156)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)										0.3	23.961714	25.034891	9	21	GG		KEEP	---	---	---	---	capture			Silent	SNP	219736367	219736367	14961	2	G	T	T	41	41	SLC23A3	T	3	3
TMPRSS7	344805	broad.mit.edu	36	3	113249402	113249402	+	Missense_Mutation	SNP	G	A	A			TCGA-12-1599-01	TCGA-12-1599-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr3:113249402G>A	uc010hqb.1	+	c.479G>A	c.(478-480)CGT>CAT	p.R160H	TMPRSS7_uc003dyp.1_Missense_Mutation_p.R15H	NM_001042575	NP_001036040	Q7RTY8	TMPS7_HUMAN	transmembrane protease, serine 7	286	Extracellular (Potential).|CUB 1.				proteolysis	integral to membrane|plasma membrane	serine-type endopeptidase activity			ovary(1)|kidney(1)	2														0.297297	60.825786	63.541759	22	52	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	113249402	113249402	16793	3	G	A	A	40	40	TMPRSS7	A	1	1
GPR160	26996	broad.mit.edu	36	3	171285010	171285010	+	Missense_Mutation	SNP	T	G	G			TCGA-12-1599-01	TCGA-12-1599-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr3:171285010T>G	uc010hwq.1	+	c.556T>G	c.(556-558)TCA>GCA	p.S186A	GPR160_uc003fgi.1_Missense_Mutation_p.S186A|GPR160_uc003fgj.1_Missense_Mutation_p.S186A|GPR160_uc010hwr.1_Missense_Mutation_p.S186A	NM_014373	NP_055188	Q9UJ42	GP160_HUMAN	G protein-coupled receptor 160	186	Helical; Name=5; (Potential).					integral to membrane|plasma membrane	G-protein coupled receptor activity				0	all_cancers(22;3.26e-22)|all_epithelial(15;5.71e-27)|all_lung(20;8.41e-17)|Lung NSC(18;3.49e-16)|Ovarian(172;0.000337)|Breast(254;0.169)		Lung(28;2.71e-13)|STAD - Stomach adenocarcinoma(35;0.0655)											0.307692	6.330487	6.800712	4	9	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	171285010	171285010	6939	3	T	G	G	58	58	GPR160	G	4	4
DSE	29940	broad.mit.edu	36	6	116854553	116854553	+	Silent	SNP	G	A	A			TCGA-12-1599-01	TCGA-12-1599-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr6:116854553G>A	uc003pws.1	+	c.540G>A	c.(538-540)GTG>GTA	p.V180V	DSE_uc003pwt.1_Silent_p.V180V	NM_001080976	NP_037484	Q9UL01	DSE_HUMAN	dermatan sulfate epimerase precursor	180					dermatan sulfate biosynthetic process	endoplasmic reticulum|Golgi apparatus|integral to membrane	chondroitin-glucuronate 5-epimerase activity			ovary(1)	1		all_cancers(87;0.00019)|all_epithelial(87;0.000416)|Ovarian(999;0.133)|Colorectal(196;0.234)		Epithelial(106;0.00915)|OV - Ovarian serous cystadenocarcinoma(136;0.0149)|GBM - Glioblastoma multiforme(226;0.0189)|all cancers(137;0.0262)										0.28972	176.856426	185.341168	62	152	GG		KEEP	---	---	---	---	capture			Silent	SNP	116854553	116854553	4958	6	G	A	A	45	45	DSE	A	2	2
JARID2	3720	broad.mit.edu	36	6	15612788	15612788	+	Missense_Mutation	SNP	C	G	G			TCGA-12-1599-01	TCGA-12-1599-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr6:15612788C>G	uc003nbj.1	+	c.2527C>G	c.(2527-2529)CCA>GCA	p.P843A		NM_004973	NP_004964	Q92833	JARD2_HUMAN	jumonji, AT rich interactive domain 2 protein	843					central nervous system development|chromatin modification|negative regulation of histone methylation|positive regulation of histone H3-K9 methylation|stem cell differentiation|transcription, DNA-dependent		chromatin binding			ovary(2)|lung(1)|pancreas(1)	4	Breast(50;0.0142)|Ovarian(93;0.103)	all_hematologic(90;0.00612)								694				0.25	8.919573	9.600984	3	9	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	15612788	15612788	8249	6	C	G	G	22	22	JARID2	G	3	3
C6orf89	221477	broad.mit.edu	36	6	36990394	36990394	+	Silent	SNP	C	T	T			TCGA-12-1599-01	TCGA-12-1599-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr6:36990394C>T	uc003omw.1	+	c.663C>T	c.(661-663)TTC>TTT	p.F221F	C6orf89_uc003omv.1_Silent_p.F108F|C6orf89_uc003omx.1_Silent_p.F214F|C6orf89_uc003omy.1_Silent_p.F48F	NM_152734	NP_689947	Q6UWU4	CF089_HUMAN	hypothetical protein LOC221477	214						integral to membrane				ovary(1)	1														0.356021	213.049814	216.536609	68	123	CC		KEEP	---	---	---	---	capture			Silent	SNP	36990394	36990394	2479	6	C	T	T	31	31	C6orf89	T	1	1
PPP1R3A	5506	broad.mit.edu	36	7	113305558	113305558	+	Missense_Mutation	SNP	G	C	C			TCGA-12-1599-01	TCGA-12-1599-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr7:113305558G>C	uc010ljy.1	-	c.2825C>G	c.(2824-2826)GCT>GGT	p.A942G		NM_002711	NP_002702	Q16821	PPR3A_HUMAN	protein phosphatase 1, regulatory (inhibitor)	942					glycogen metabolic process	integral to membrane				ovary(9)|pancreas(7)|skin(2)|breast(2)|lung(1)	21										235				0.24826	288.410175	313.261665	107	324	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	113305558	113305558	12806	7	G	C	C	34	34	PPP1R3A	C	3	3
CFTR	1080	broad.mit.edu	36	7	117069753	117069753	+	Nonsense_Mutation	SNP	C	A	A			TCGA-12-1599-01	TCGA-12-1599-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr7:117069753C>A	uc003vjd.1	+	c.3743C>A	c.(3742-3744)TCA>TAA	p.S1248*		NM_000492	NP_000483	P13569	CFTR_HUMAN	cystic fibrosis transmembrane conductance	1248	Cytoplasmic (Potential).|ABC transporter 2.|ATP 2 (Potential).				respiratory gaseous exchange	apical plasma membrane|basolateral plasma membrane|chloride channel complex|early endosome membrane	ATP binding|ATP-binding and phosphorylation-dependent chloride channel activity|channel-conductance-controlling ATPase activity|chloride channel regulator activity|enzyme binding|PDZ domain binding			central_nervous_system(2)|ovary(1)	3	Lung NSC(10;0.00148)|all_lung(10;0.00171)		STAD - Stomach adenocarcinoma(10;0.000534)		Bumetanide(DB00887)|Glibenclamide(DB01016)									0.227612	154.426732	172.680466	61	207	CC		KEEP	---	---	---	---	capture			Nonsense_Mutation	SNP	117069753	117069753	3427	7	C	A	A	29	29	CFTR	A	5	3
KEL	3792	broad.mit.edu	36	7	142353447	142353447	+	Missense_Mutation	SNP	C	T	T			TCGA-12-1599-01	TCGA-12-1599-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr7:142353447C>T	uc003wcb.1	-	c.1283G>A	c.(1282-1284)CGT>CAT	p.R428H		NM_000420	NP_000411	P23276	KELL_HUMAN	Kell blood group, metallo-endopeptidase	428	Extracellular (Potential).				proteolysis|vasoconstriction	integral to membrane|plasma membrane	metal ion binding|metalloendopeptidase activity|protein binding			ovary(3)|central_nervous_system(1)	4	Melanoma(164;0.059)													0.166667	59.946187	78.902761	30	150	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	142353447	142353447	8448	7	C	T	T	19	19	KEL	T	1	1
TG	7038	broad.mit.edu	36	8	134054067	134054067	+	Missense_Mutation	SNP	A	T	T			TCGA-12-1599-01	TCGA-12-1599-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr8:134054067A>T	uc003ytw.1	+	c.6098A>T	c.(6097-6099)CAG>CTG	p.Q2033L	TG_uc010mdw.1_Missense_Mutation_p.Q792L	NM_003235	NP_003226	P01266	THYG_HUMAN	thyroglobulin	2033	Type IIIB.				hormone biosynthetic process|regulation of synaptic transmission|signal transduction		carboxylesterase activity|hormone activity			ovary(8)|breast(4)|pancreas(1)	13	Ovarian(258;0.00438)|Acute lymphoblastic leukemia(118;0.155)	Myeloproliferative disorder(644;0.00878)|Acute lymphoblastic leukemia(644;0.0559)|Breast(495;0.0735)	BRCA - Breast invasive adenocarcinoma(115;0.000701)	KIRC - Kidney renal clear cell carcinoma(542;0.0546)						1778				0.323529	32.303275	33.248595	11	23	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	134054067	134054067	16341	8	A	T	T	7	7	TG	T	4	4
CDCA2	157313	broad.mit.edu	36	8	25381669	25381669	+	Silent	SNP	C	T	T			TCGA-12-1599-01	TCGA-12-1599-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr8:25381669C>T	uc003xep.1	+	c.558C>T	c.(556-558)AGC>AGT	p.S186S	PPP2R2A_uc003xek.1_Intron|CDCA2_uc003xeq.1_Silent_p.S171S|CDCA2_uc003xer.1_5'UTR	NM_152562	NP_689775	Q69YH5	CDCA2_HUMAN	cell division cycle associated 2	186					cell division|mitosis	cytoplasm|nucleus					0		all_cancers(63;0.0378)|Ovarian(32;0.000878)|all_epithelial(46;0.0162)|Breast(100;0.0164)|Prostate(55;0.191)		UCEC - Uterine corpus endometrioid carcinoma (27;0.022)|Epithelial(17;1.37e-11)|Colorectal(74;0.0129)|COAD - Colon adenocarcinoma(73;0.0443)										0.416667	28.542918	28.689028	10	14	CC		KEEP	---	---	---	---	capture			Silent	SNP	25381669	25381669	3215	8	C	T	T	27	27	CDCA2	T	1	1
POTEA	340441	broad.mit.edu	36	8	43331175	43331175	+	Missense_Mutation	SNP	G	T	T			TCGA-12-1599-01	TCGA-12-1599-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr8:43331175G>T	uc003xpz.1	+	c.1477G>T	c.(1477-1479)GTT>TTT	p.V493F	POTEA_uc003xqa.1_Missense_Mutation_p.V447F	NM_001005365	NP_001005365	Q6S8J7	POTEA_HUMAN	POTE ankyrin domain family, member A isoform 2	493	Potential.									ovary(1)	1														0.34375	101.648532	103.717533	33	63	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	43331175	43331175	12690	8	G	T	T	44	44	POTEA	T	3	3
IMPA1	3612	broad.mit.edu	36	8	82755484	82755484	+	Missense_Mutation	SNP	T	G	G			TCGA-12-1599-01	TCGA-12-1599-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr8:82755484T>G	uc003ych.1	-	c.153A>C	c.(151-153)GAA>GAC	p.E51D		NM_005536	NP_005527	P29218	IMPA1_HUMAN	inositol(myo)-1(or 4)-monophosphatase 1 isoform	51					inositol phosphate dephosphorylation|phosphatidylinositol biosynthetic process|signal transduction	cytoplasm	inositol-1(or 4)-monophosphatase activity|metal ion binding|protein homodimerization activity			skin(1)	1					Lithium(DB01356)									0.340426	52.384415	53.442849	16	31	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	82755484	82755484	8023	8	T	G	G	64	64	IMPA1	G	4	4
FBP2	8789	broad.mit.edu	36	9	96373602	96373603	+	Missense_Mutation	DNP	GA	AC	AC			TCGA-12-1599-01	TCGA-12-1599-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:96373602_96373603GA>AC	uc004auv.1	-	c.529_530TC>GT	c.(529-531)TCC>GTC	p.S177V		NM_003837	NP_003828	O00757	F16P2_HUMAN	fructose-1,6-bisphosphatase 2	177					fructose metabolic process|gluconeogenesis	cytosol	fructose 1,6-bisphosphate 1-phosphatase activity|fructose-2,6-bisphosphate 2-phosphatase activity|metal ion binding				0		Acute lymphoblastic leukemia(62;0.136)												0.307229	137.74259	143.199348	51	115	GG		KEEP	---	---	---	---	capture			Missense_Mutation	DNP	96373602	96373603	5942	9	GA	AC	AC	41	41	FBP2	AC	2	2
GPR101	83550	broad.mit.edu	36	X	135941247	135941247	+	Missense_Mutation	SNP	C	A	A			TCGA-12-1599-01	TCGA-12-1599-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chrX:135941247C>A	uc004faj.1	-	c.253G>T	c.(253-255)GCC>TCC	p.A85S		NM_054021	NP_473362	Q96P66	GP101_HUMAN	G protein-coupled receptor 101	85	Helical; Name=2; (Potential).					integral to membrane|plasma membrane	G-protein coupled receptor activity			ovary(3)|lung(1)	4	Acute lymphoblastic leukemia(192;0.000127)													0.416667	40.124829	40.340945	15	21	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	135941247	135941247	6896	23	C	A	A	26	26	GPR101	A	3	3
SPANXN2	494119	broad.mit.edu	36	X	142623068	142623068	+	Silent	SNP	A	T	T			TCGA-12-1599-01	TCGA-12-1599-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chrX:142623068A>T	uc004fbz.1	-	c.276T>A	c.(274-276)GCT>GCA	p.A92A		NM_001009615	NP_001009615	Q5MJ10	SPXN2_HUMAN	SPANX-N2 protein	92										ovary(1)	1	Acute lymphoblastic leukemia(192;6.56e-05)													0.332918	815.363233	835.190337	267	535	AA		KEEP	---	---	---	---	capture			Silent	SNP	142623068	142623068	15499	23	A	T	T	7	7	SPANXN2	T	4	4
L1CAM	3897	broad.mit.edu	36	X	152781497	152781497	+	Missense_Mutation	SNP	C	T	T			TCGA-12-1599-01	TCGA-12-1599-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chrX:152781497C>T	uc004fjb.1	-	c.3589G>A	c.(3589-3591)GGG>AGG	p.G1197R	L1CAM_uc004fjc.1_Missense_Mutation_p.G1193R	NM_000425	NP_000416	P32004	L1CAM_HUMAN	L1 cell adhesion molecule isoform 1 precursor	1197	Cytoplasmic (Potential).				axon guidance|blood coagulation|cell death|leukocyte migration	integral to membrane				ovary(8)|central_nervous_system(1)	9	all_cancers(53;6.72e-15)|all_epithelial(53;3.19e-09)|all_lung(58;3.39e-06)|all_hematologic(71;4.25e-06)|Lung NSC(58;4.7e-06)|Acute lymphoblastic leukemia(192;6.56e-05)													0.333333	7.722228	7.94352	3	6	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	152781497	152781497	8911	23	C	T	T	23	23	L1CAM	T	1	1
PTEN	5728	broad.mit.edu	36	10	89710779	89710782	+	Frame_Shift_Del	DEL	TACT	-	-			TCGA-12-1599-01	TCGA-12-1599-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:89710779_89710782delTACT	uc001kfb.1	+	c.950_953delTACT	c.(949-954)GTACTTfs	p.V317fs		NM_000314	NP_000305	P60484	PTEN_HUMAN	phosphatase and tensin homolog	317_318	C2 tensin-type.				apoptosis|canonical Wnt receptor signaling pathway|cell proliferation|central nervous system development|induction of apoptosis|inositol phosphate dephosphorylation|negative regulation of cell migration|negative regulation of focal adhesion assembly|negative regulation of protein kinase B signaling cascade|negative regulation of protein phosphorylation|nerve growth factor receptor signaling pathway|phosphatidylinositol dephosphorylation|phosphatidylinositol-mediated signaling|positive regulation of sequence-specific DNA binding transcription factor activity|protein stabilization|regulation of cyclin-dependent protein kinase activity|regulation of neuron projection development|T cell receptor signaling pathway	cytosol|internal side of plasma membrane|PML body	enzyme binding|inositol-1,3,4,5-tetrakisphosphate 3-phosphatase activity|lipid binding|magnesium ion binding|PDZ domain binding|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity|phosphatidylinositol-3,4-bisphosphate 3-phosphatase activity|phosphatidylinositol-3-phosphatase activity|protein serine/threonine phosphatase activity|protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity	p.L318fs*2(16)|p.V317fs*3(16)|p.V317fs*6(2)|p.G165_K342del(1)|p.G165_*404del(1)|p.L316fs*1(1)|p.V317_K322del(1)|p.W274_F341del(1)|p.L318F(1)|p.T318fs*2(1)		endometrium(831)|central_nervous_system(654)|skin(119)|haematopoietic_and_lymphoid_tissue(101)|prostate(97)|large_intestine(90)|breast(67)|lung(63)|ovary(58)|thyroid(29)|stomach(29)|upper_aerodigestive_tract(25)|cervix(21)|liver(20)|vulva(17)|kidney(15)|NS(14)|soft_tissue(12)|urinary_tract(12)|eye(8)|pancreas(6)|salivary_gland(5)|bone(5)|biliary_tract(4)|autonomic_ganglia(2)|meninges(2)|testis(1)|oesophagus(1)	2308		all_cancers(4;3.61e-31)|all_epithelial(4;3.96e-23)|Prostate(4;8.12e-23)|Breast(4;0.000111)|Melanoma(5;0.00146)|all_hematologic(4;0.00227)|Colorectal(252;0.00494)|all_neural(4;0.00513)|Acute lymphoblastic leukemia(4;0.0116)|Glioma(4;0.0274)|all_lung(38;0.132)	KIRC - Kidney renal clear cell carcinoma(1;0.214)	UCEC - Uterine corpus endometrioid carcinoma (6;0.000228)|all cancers(1;4.16e-84)|GBM - Glioblastoma multiforme(1;7.77e-49)|Epithelial(1;7.67e-41)|OV - Ovarian serous cystadenocarcinoma(1;6.22e-15)|BRCA - Breast invasive adenocarcinoma(1;1.1e-06)|Lung(2;3.18e-06)|Colorectal(12;4.88e-06)|LUSC - Lung squamous cell carcinoma(2;4.97e-06)|COAD - Colon adenocarcinoma(12;1.13e-05)|Kidney(1;0.000288)|KIRC - Kidney renal clear cell carcinoma(1;0.00037)|STAD - Stomach adenocarcinoma(243;0.218)			V317fs*3(SKUT1_SOFT_TISSUE)|V317fs*3(EVSAT_BREAST)|V317fs*3(IGROV1_OVARY)|V317fs*3(ISHIKAWAHERAKLIO02ER_ENDOMETRIUM)	31	p.L318fs(JHOM1-Tumor)|p.V317fs(SKUT1-Tumor)|p.V317fs(EVSAT-Tumor)|p.V317fs(ISHIKAWAHERAKLIO02ER-Tumor)	264	TCGA GBM(2;<1E-8)|TSP Lung(26;0.18)			0.33			62	125				---	---	---	---	capture_indel			Frame_Shift_Del	DEL	89710779	89710782	13192	10	TACT	-	-	57	57	PTEN	-	5	5
FN3KRP	79672	broad.mit.edu	36	17	78267979	78267980	+	Frame_Shift_Ins	INS	-	G	G			TCGA-12-1599-01	TCGA-12-1599-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:78267979_78267980insG	uc002kfu.1	+	c.59_60insG	c.(58-60)TCGfs	p.S20fs		NM_024619	NP_078895	Q9HA64	KT3K_HUMAN	fructosamine 3 kinase related protein	20							kinase activity				0	Breast(20;0.000523)|all_neural(118;0.0952)		BRCA - Breast invasive adenocarcinoma(99;0.0344)|OV - Ovarian serous cystadenocarcinoma(97;0.061)											0.36			4	7				---	---	---	---	capture_indel			Frame_Shift_Ins	INS	78267979	78267980	6206	17	-	G	G	31	31	FN3KRP	G	5	5
