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
VAX1	11023	broad.mit.edu	36	10	118886040	118886040	+	Missense_Mutation	SNP	C	G	G			TCGA-06-0216-01	TCGA-06-0216-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr10:118886040C>G	uc009xyx.1	-	c.362G>C	c.(361-363)CGC>CCC	p.R121P	VAX1_uc001ldb.1_Missense_Mutation_p.R121P	NM_001112704	NP_001106175	Q5SQQ9	VAX1_HUMAN	ventral anterior homeobox 1 isoform a	121	Homeobox.					nucleus	sequence-specific DNA binding|transcription regulator activity			ovary(2)	2														0.368421	7.985804	8.364267	7	12	CC		KEEP	---	---	---	---	capture		all cancers(201;0.0108)	Missense_Mutation	SNP	118886040	118886040	17699	10	C	G	G	27	27	VAX1	G	3	3
BNIP3	664	broad.mit.edu	36	10	133637367	133637367	+	Nonsense_Mutation	SNP	A	T	T			TCGA-06-0216-01	TCGA-06-0216-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr10:133637367A>T	uc001lkv.1	-	c.117T>A	c.(115-117)TAT>TAA	p.Y39*		NM_004052	NP_004043	Q12983	BNIP3_HUMAN	BCL2/adenovirus E1B 19kD-interacting protein 3	39					cellular response to cobalt ion|cellular response to hypoxia|cellular response to mechanical stimulus|chromatin remodeling|defense response to virus|DNA fragmentation involved in apoptotic nuclear change|induction of apoptosis|interspecies interaction between organisms|mitochondrial fragmentation involved in apoptosis|negative regulation of membrane potential|negative regulation of mitochondrial fusion|negative regulation of survival gene product expression|neuron apoptosis|positive regulation of mitochondrial fission|positive regulation of protein complex disassembly|positive regulation of release of cytochrome c from mitochondria|reactive oxygen species metabolic process|regulation of mitochondrial membrane permeability	dendrite|integral to mitochondrial outer membrane|nuclear envelope|nucleoplasm	GTPase binding|protein heterodimerization activity|protein homodimerization activity			lung(1)|skin(1)	2		all_cancers(35;4e-11)|all_epithelial(44;5.07e-08)|Ovarian(717;2.61e-05)|Lung NSC(174;0.00237)|all_lung(145;0.00354)|Breast(234;0.023)|all_neural(114;0.0299)|Colorectal(31;0.109)|Melanoma(40;0.123)|Glioma(114;0.203)								137				0.567797	211.640273	212.113804	67	51	AA		KEEP	---	---	---	---	capture		Epithelial(32;1.59e-12)|all cancers(32;3.75e-11)|OV - Ovarian serous cystadenocarcinoma(35;2.57e-08)|BRCA - Breast invasive adenocarcinoma(275;0.208)	Nonsense_Mutation	SNP	133637367	133637367	1503	10	A	T	T	16	16	BNIP3	T	5	4
PTEN	5728	broad.mit.edu	36	10	89682815	89682815	+	Missense_Mutation	SNP	G	C	C	rs57374291	unknown	TCGA-06-0216-01	TCGA-06-0216-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr10:89682815G>C	uc001kfb.1	+	c.319G>C	c.(319-321)GAT>CAT	p.D107H		NM_000314	NP_000305	P60484	PTEN_HUMAN	phosphatase and tensin homolog	107	Phosphatase tensin-type.		D -> Y (in BZS and glioblastoma; loss of phosphatase activity towards Ins(1,3,4,5)P4).		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.D107Y(3)|p.Y27_N212>Y(2)|p.F56fs*2(1)|p.P103fs*3(1)|p.D107N(1)		endometrium(831)|central_nervous_system(654)|skin(119)|haematopoietic_and_lymphoid_tissue(101)|prostate(97)|large_intestine(90)|breast(67)|lung(63)|ovary(58)|thyroid(29)|stomach(29)|upper_aerodigestive_tract(25)|cervix(21)|liver(20)|vulva(17)|kidney(15)|NS(14)|soft_tissue(12)|urinary_tract(12)|eye(8)|pancreas(6)|salivary_gland(5)|bone(5)|biliary_tract(4)|autonomic_ganglia(2)|meninges(2)|testis(1)|oesophagus(1)	2308		all_cancers(4;3.61e-31)|all_epithelial(4;3.96e-23)|Prostate(4;8.12e-23)|Breast(4;0.000111)|Melanoma(5;0.00146)|all_hematologic(4;0.00227)|Colorectal(252;0.00494)|all_neural(4;0.00513)|Acute lymphoblastic leukemia(4;0.0116)|Glioma(4;0.0274)|all_lung(38;0.132)						31		264	TCGA GBM(2;<1E-8)|TSP Lung(26;0.18)			0.810811	102.770807	106.113972	30	7	GG		KEEP	---	---	---	---	capture	KIRC - Kidney renal clear cell carcinoma(1;0.214)	UCEC - Uterine corpus endometrioid carcinoma (6;0.000228)|all cancers(1;4.16e-84)|GBM - Glioblastoma multiforme(1;7.77e-49)|Epithelial(1;7.67e-41)|OV - Ovarian serous cystadenocarcinoma(1;6.22e-15)|BRCA - Breast invasive adenocarcinoma(1;1.1e-06)|Lung(2;3.18e-06)|Colorectal(12;4.88e-06)|LUSC - Lung squamous cell carcinoma(2;4.97e-06)|COAD - Colon adenocarcinoma(12;1.13e-05)|Kidney(1;0.000288)|KIRC - Kidney renal clear cell carcinoma(1;0.00037)|STAD - Stomach adenocarcinoma(243;0.218)	Missense_Mutation	SNP	89682815	89682815	13192	10	G	C	C	33	33	PTEN	C	3	3
MRGPRX4	117196	broad.mit.edu	36	11	18152076	18152076	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0216-01	TCGA-06-0216-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr11:18152076G>A	uc001mnv.1	+	c.697G>A	c.(697-699)GGC>AGC	p.G233S		NM_054032	NP_473373	Q96LA9	MRGX4_HUMAN	MAS-related GPR, member X4	233	Helical; Name=6; (Potential).					integral to membrane|plasma membrane	G-protein coupled receptor activity				0														0.460177	158.497801	158.652396	52	61	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	18152076	18152076	10162	11	G	A	A	39	39	MRGPRX4	A	1	1
LRRC4C	57689	broad.mit.edu	36	11	40093768	40093768	+	Silent	SNP	C	T	T			TCGA-06-0216-01	TCGA-06-0216-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr11:40093768C>T	uc001mxa.1	-	c.651G>A	c.(649-651)CCG>CCA	p.P217P	LRRC4C_uc001mxc.1_Silent_p.P213P|LRRC4C_uc001mxd.1_Silent_p.P213P|LRRC4C_uc001mxb.1_Silent_p.P213P|LRRC4C_uc009ykn.1_Silent_p.P217P	NM_020929	NP_065980	Q9HCJ2	LRC4C_HUMAN	netrin-G1 ligand	217	LRR 6.				regulation of axonogenesis	integral to membrane	protein binding			ovary(4)|central_nervous_system(1)	5		all_lung(304;0.0575)|Lung NSC(402;0.138)												0.273585	69.349339	74.233607	29	77	CC		KEEP	---	---	---	---	capture			Silent	SNP	40093768	40093768	9383	11	C	T	T	27	27	LRRC4C	T	1	1
LRRC55	219527	broad.mit.edu	36	11	56706660	56706660	+	Missense_Mutation	SNP	T	A	A			TCGA-06-0216-01	TCGA-06-0216-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr11:56706660T>A	uc001njl.1	+	c.717T>A	c.(715-717)AAT>AAA	p.N239K		NM_001005210	NP_001005210	Q6ZSA7	LRC55_HUMAN	leucine rich repeat containing 55	209	LRRCT.					integral to membrane					0														0.439189	183.142168	183.619947	65	83	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	56706660	56706660	9386	11	T	A	A	50	50	LRRC55	A	4	4
DAGLA	747	broad.mit.edu	36	11	61268434	61268434	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0216-01	TCGA-06-0216-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr11:61268434G>A	uc001nsa.1	+	c.3026G>A	c.(3025-3027)AGT>AAT	p.S1009N		NM_006133	NP_006124	Q9Y4D2	DGLA_HUMAN	neural stem cell-derived dendrite regulator	1009	Cytoplasmic (Potential).				lipid catabolic process|platelet activation	integral to membrane|plasma membrane	acylglycerol lipase activity|metal ion binding|triglyceride lipase activity			ovary(2)|central_nervous_system(1)	3														0.316239	91.850887	95.3555	37	80	GG		KEEP	---	---	---	---	capture		READ - Rectum adenocarcinoma(4;0.219)	Missense_Mutation	SNP	61268434	61268434	4393	11	G	A	A	36	36	DAGLA	A	2	2
NUMA1	4926	broad.mit.edu	36	11	71394919	71394919	+	Silent	SNP	C	T	T			TCGA-06-0216-01	TCGA-06-0216-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr11:71394919C>T	uc001orl.1	-	c.5502G>A	c.(5500-5502)TCG>TCA	p.S1834S	NUMA1_uc001ork.1_Silent_p.S698S|NUMA1_uc001orm.1_Silent_p.S1820S|NUMA1_uc001orj.2_Silent_p.S16S|NUMA1_uc009ysw.1_Silent_p.S1401S	NM_006185	NP_006176	Q14980	NUMA1_HUMAN	nuclear mitotic apparatus protein 1	1834					G2/M transition of mitotic cell cycle|mitotic anaphase|nucleus organization	chromosome|cytosol|nucleoplasm|spindle microtubule|spindle pole	protein binding|structural molecule activity			ovary(3)|lung(2)|skin(2)|central_nervous_system(1)	8										525				0.423077	94.268844	94.669448	33	45	CC		KEEP	---	---	---	---	capture			Silent	SNP	71394919	71394919	11155	11	C	T	T	19	19	NUMA1	T	1	1
LMO1	4004	broad.mit.edu	36	11	8205120	8205120	+	Missense_Mutation	SNP	C	G	G			TCGA-06-0216-01	TCGA-06-0216-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr11:8205120C>G	uc001mgg.1	-	c.343G>C	c.(343-345)GCC>CCC	p.A115P	LMO1_uc009yfo.1_Non-coding_Transcript|LMO1_uc001mgh.1_Missense_Mutation_p.A114P	NM_002315	NP_002306	P25800	RBTN1_HUMAN	LIM domain only 1	115	LIM zinc-binding 2.				cell proliferation|multicellular organismal development|positive regulation of gene-specific transcription from RNA polymerase II promoter	nucleus	sequence-specific DNA binding transcription factor activity|zinc ion binding				0										78				0.25	7.568694	8.709105	5	15	CC		KEEP	---	---	---	---	capture		Epithelial(150;1.59e-07)|BRCA - Breast invasive adenocarcinoma(625;0.203)	Missense_Mutation	SNP	8205120	8205120	9180	11	C	G	G	27	27	LMO1	G	3	3
FOLR4	390243	broad.mit.edu	36	11	93680494	93680494	+	Silent	SNP	G	A	A			TCGA-06-0216-01	TCGA-06-0216-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr11:93680494G>A	uc001pes.1	+	c.720G>A	c.(718-720)CCG>CCA	p.P240P		NM_001080486	NP_001073955	A6ND01	FOLR4_HUMAN	folate receptor 4 (delta) homolog	247						extracellular region	folic acid binding|receptor activity			ovary(1)	1														0.5	458.921785	458.921785	155	155	GG		KEEP	---	---	---	---	capture			Silent	SNP	93680494	93680494	6226	11	G	A	A	40	40	FOLR4	A	1	1
CIT	11113	broad.mit.edu	36	12	118626581	118626581	+	Silent	SNP	G	A	A			TCGA-06-0216-01	TCGA-06-0216-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr12:118626581G>A	uc001txj.1	-	c.5274C>T	c.(5272-5274)AAC>AAT	p.N1758N	CIT_uc001txh.1_Silent_p.N1235N|CIT_uc001txi.1_Silent_p.N1716N	NM_007174	NP_009105	O14578	CTRO_HUMAN	citron	1716	CNH.				intracellular signal transduction|protein phosphorylation		ATP binding|metal ion binding|protein serine/threonine kinase activity|SH3 domain binding|small GTPase regulator activity			ovary(6)|urinary_tract(1)|lung(1)|breast(1)|skin(1)	10	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)	Myeloproliferative disorder(1001;0.0255)							p.N1758N(NCIH1793-Tumor)	1263				0.394737	82.537731	83.273118	30	46	GG		KEEP	---	---	---	---	capture		BRCA - Breast invasive adenocarcinoma(302;0.211)	Silent	SNP	118626581	118626581	3573	12	G	A	A	40	40	CIT	A	1	1
AACS	65985	broad.mit.edu	36	12	124187210	124187210	+	Silent	SNP	C	T	T			TCGA-06-0216-01	TCGA-06-0216-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr12:124187210C>T	uc001uhc.1	+	c.1728C>T	c.(1726-1728)AAC>AAT	p.N576N	AACS_uc001uhd.1_Intron|AACS_uc009zyh.1_Non-coding_Transcript|AACS_uc009zyi.1_Silent_p.N174N	NM_023928	NP_076417	Q86V21	AACS_HUMAN	acetoacetyl-CoA synthetase	576					fatty acid metabolic process	cytosol	acetoacetate-CoA ligase activity|ATP binding			ovary(1)|liver(1)|central_nervous_system(1)	3	all_neural(191;0.101)|Medulloblastoma(191;0.163)													0.378151	120.641149	122.193051	45	74	CC		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(86;9.82e-05)|Epithelial(86;0.000642)|all cancers(50;0.00843)	Silent	SNP	124187210	124187210	10	12	C	T	T	17	17	AACS	T	2	2
GALNT9	50614	broad.mit.edu	36	12	131254082	131254082	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0216-01	TCGA-06-0216-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr12:131254082C>T	uc001ukc.2	-	c.1184G>A	c.(1183-1185)CGC>CAC	p.R395H	GALNT9_uc009zyr.1_Missense_Mutation_p.R169H|GALNT9_uc001ukb.1_Missense_Mutation_p.R252H|GALNT9_uc001uka.1_Missense_Mutation_p.R29H	NM_001122636	NP_001116108	Q9HCQ5	GALT9_HUMAN	UDP-N-acetyl-alpha-D-galactosamine:polypeptide	395	Lumenal (Potential).				protein O-linked glycosylation	Golgi membrane|integral to membrane	polypeptide N-acetylgalactosaminyltransferase activity|sugar binding				0	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_epithelial(31;0.241)				Colon(186;2147 2752 13553 41466)								0.468085	184.337623	184.462045	66	75	CC		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(86;7.49e-08)|Epithelial(86;3.55e-07)|all cancers(50;2.09e-05)	Missense_Mutation	SNP	131254082	131254082	6484	12	C	T	T	27	27	GALNT9	T	1	1
BCAT1	586	broad.mit.edu	36	12	24938593	24938593	+	Silent	SNP	C	T	T			TCGA-06-0216-01	TCGA-06-0216-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr12:24938593C>T	uc001rgd.2	-	c.162G>A	c.(160-162)ACG>ACA	p.T54T	BCAT1_uc001rgc.1_Silent_p.T53T|BCAT1_uc001rge.2_Silent_p.T30T	NM_005504	NP_005495	P54687	BCAT1_HUMAN	branched chain aminotransferase 1, cytosolic	54					branched chain family amino acid biosynthetic process|branched chain family amino acid catabolic process|cell proliferation|G1/S transition of mitotic cell cycle	cytosol	L-isoleucine transaminase activity|L-leucine transaminase activity|L-valine transaminase activity				0	Acute lymphoblastic leukemia(6;0.00112)|all_hematologic(7;0.00152)|Ovarian(17;0.107)|Colorectal(261;0.196)				Gabapentin(DB00996)|L-Glutamic Acid(DB00142)|L-Isoleucine(DB00167)|L-Leucine(DB00149)|L-Valine(DB00161)|Pyridoxal Phosphate(DB00114)									0.545455	54.952215	55.011729	18	15	CC		KEEP	---	---	---	---	capture			Silent	SNP	24938593	24938593	1375	12	C	T	T	23	23	BCAT1	T	1	1
SMARCC2	6601	broad.mit.edu	36	12	54845541	54845541	+	Silent	SNP	A	G	G			TCGA-06-0216-01	TCGA-06-0216-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr12:54845541A>G	uc001skb.1	-	c.2967T>C	c.(2965-2967)GCT>GCC	p.A989A	SMARCC2_uc001ska.1_Silent_p.A1020A|SMARCC2_uc001skc.1_Silent_p.A1019A|SMARCC2_uc001skd.1_Silent_p.A1020A	NM_003075	NP_003066	Q8TAQ2	SMRC2_HUMAN	SWI/SNF-related matrix-associated	989	Pro-rich.				chromatin assembly or disassembly|chromatin remodeling|negative regulation of transcription, DNA-dependent|nervous system development|positive regulation of transcription, DNA-dependent|regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	chromatin|nBAF complex|npBAF complex|nucleoplasm|SWI/SNF complex	chromatin binding|DNA binding|protein binding|transcription coactivator activity			lung(2)|central_nervous_system(2)|ovary(1)|skin(1)	6														0.321429	10.190072	11.083179	9	19	AA		KEEP	---	---	---	---	capture	OV - Ovarian serous cystadenocarcinoma(18;0.123)		Silent	SNP	54845541	54845541	15274	12	A	G	G	11	11	SMARCC2	G	4	4
HTR2A	3356	broad.mit.edu	36	13	46364571	46364571	+	Missense_Mutation	SNP	T	C	C			TCGA-06-0216-01	TCGA-06-0216-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr13:46364571T>C	uc001vbq.2	-	c.568A>G	c.(568-570)ACT>GCT	p.T190A	HTR2A_uc001vbr.1_Missense_Mutation_p.T106A|HTR2A_uc010acr.1_Missense_Mutation_p.T190A	NM_000621	NP_000612	P28223	5HT2A_HUMAN	5-hydroxytryptamine (serotonin) receptor 2A	190	Cytoplasmic (By similarity).				ERK1 and ERK2 cascade|phosphatidylinositol 3-kinase cascade|phosphatidylinositol biosynthetic process|release of sequestered calcium ion into cytosol|response to drug|synaptic transmission	integral to plasma membrane	1-(4-iodo-2,5-dimethoxyphenyl)propan-2-amine binding|drug binding|phosphatidylinositol phospholipase C activity|serotonin binding|serotonin receptor activity			ovary(3)|central_nervous_system(1)	4		all_lung(13;7.2e-10)|Lung NSC(96;3.77e-07)|Breast(56;2.06e-05)|Prostate(109;0.00116)|Hepatocellular(98;0.0207)|Lung SC(185;0.0262)|Myeloproliferative disorder(33;0.0333)			Aripiprazole(DB01238)|Chlorpromazine(DB00477)|Chlorprothixene(DB01239)|Cisapride(DB00604)|Clomipramine(DB01242)|Clozapine(DB00363)|Cyclobenzaprine(DB00924)|Cyproheptadine(DB00434)|Dihydroergotamine(DB00320)|Donepezil(DB00843)|Epinastine(DB00751)|Ergotamine(DB00696)|Fluvoxamine(DB00176)|Mesoridazine(DB00933)|Methysergide(DB00247)|Mianserin(DB06148)|Minaprine(DB00805)|Mirtazapine(DB00370)|Nefazodone(DB01149)|Olanzapine(DB00334)|Paliperidone(DB01267)|Paroxetine(DB00715)|Prochlorperazine(DB00433)|Promazine(DB00420)|Promethazine(DB01069)|Propiomazine(DB00777)|Quetiapine(DB01224)|Risperidone(DB00734)|Sertindole(DB06144)|Thiethylperazine(DB00372)|Thioridazine(DB00679)|Tranylcypromine(DB00752)|Trazodone(DB00656)|Venlafaxine(DB00285)|Ziprasidone(DB00246)									0.33871	446.906572	456.882429	147	287	TT		KEEP	---	---	---	---	capture		GBM - Glioblastoma multiforme(144;4.67e-05)|COAD - Colon adenocarcinoma(199;0.224)	Missense_Mutation	SNP	46364571	46364571	7741	13	T	C	C	60	60	HTR2A	C	4	4
DIS3	22894	broad.mit.edu	36	13	72253006	72253006	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0216-01	TCGA-06-0216-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr13:72253006G>A	uc001vix.2	-	c.365C>T	c.(364-366)ACT>ATT	p.T122I	PIBF1_uc010aeo.1_5'Flank|PIBF1_uc001vjb.2_5'Flank|PIBF1_uc001vjc.1_5'Flank|PIBF1_uc010aep.1_5'Flank|DIS3_uc001viy.2_Intron|DIS3_uc001viz.2_Non-coding_Transcript|PIBF1_uc001vja.1_5'Flank	NM_014953	NP_055768	Q9Y2L1	RRP44_HUMAN	DIS3 mitotic control isoform b	122	PINc.				CUT catabolic process|exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay|rRNA catabolic process|rRNA processing	cytosol|exosome (RNase complex)|nucleolus|nucleoplasm	3'-5'-exoribonuclease activity|endonuclease activity|guanyl-nucleotide exchange factor activity|protein binding|RNA binding				0		Breast(118;0.0074)|Acute lymphoblastic leukemia(28;0.0195)									Multiple Myeloma(4;0.011)			0.52381	235.677151	235.749523	77	70	GG		KEEP	---	---	---	---	capture		GBM - Glioblastoma multiforme(99;0.000181)	Missense_Mutation	SNP	72253006	72253006	4714	13	G	A	A	36	36	DIS3	A	2	2
KIAA0430	9665	broad.mit.edu	36	16	15600269	15600269	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0216-01	TCGA-06-0216-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr16:15600269C>T	uc002ddr.1	-	c.4927G>A	c.(4927-4929)GTT>ATT	p.V1643I	KIAA0430_uc002ddq.1_Missense_Mutation_p.V1477I	NM_014647	NP_055462	Q9Y4F3	LKAP_HUMAN	limkain b1	1642						peroxisome	nucleotide binding|RNA binding				0														0.262295	38.877449	41.992609	16	45	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	15600269	15600269	8484	16	C	T	T	19	19	KIAA0430	T	1	1
VPS35	55737	broad.mit.edu	36	16	45251927	45251927	+	Silent	SNP	T	G	G			TCGA-06-0216-01	TCGA-06-0216-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr16:45251927T>G	uc002eef.2	-	c.2349A>C	c.(2347-2349)TCA>TCC	p.S783S	VPS35_uc002eed.1_3'UTR|VPS35_uc002eee.1_Silent_p.S744S	NM_018206	NP_060676	Q96QK1	VPS35_HUMAN	vacuolar protein sorting 35	783					protein transport|retrograde transport, endosome to Golgi	cytosol|endosome|membrane	protein binding				0		all_cancers(37;7.65e-05)|all_epithelial(9;0.000154)|all_lung(18;0.00585)|Lung NSC(13;0.0496)|Breast(268;0.116)												0.433333	77.856325	78.084768	26	34	TT		KEEP	---	---	---	---	capture			Silent	SNP	45251927	45251927	17770	16	T	G	G	59	59	VPS35	G	4	4
ABCC11	85320	broad.mit.edu	36	16	46804886	46804886	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0216-01	TCGA-06-0216-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr16:46804886G>A	uc002eff.1	-	c.1325C>T	c.(1324-1326)ACG>ATG	p.T442M	ABCC11_uc002efg.1_Missense_Mutation_p.T442M|ABCC11_uc002efh.1_Missense_Mutation_p.T442M	NM_033151	NP_149163	Q96J66	ABCCB_HUMAN	ATP-binding cassette, sub-family C, member 11	442	Cytoplasmic (Potential).|ABC transmembrane type-1 1.					integral to membrane	ATP binding|ATPase activity, coupled to transmembrane movement of substances			ovary(3)|central_nervous_system(1)	4		all_cancers(37;0.127)|all_lung(18;0.132)|Breast(268;0.166)												0.516129	97.011237	97.025974	32	30	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	46804886	46804886	52	16	G	A	A	40	40	ABCC11	A	1	1
CNGB1	1258	broad.mit.edu	36	16	56551427	56551427	+	Silent	SNP	G	A	A			TCGA-06-0216-01	TCGA-06-0216-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr16:56551427G>A	uc002emt.1	-	c.627C>T	c.(625-627)GCC>GCT	p.A209A	CNGB1_uc010cdh.1_Silent_p.A203A|CNGB1_uc002emu.1_Silent_p.A209A	NM_001297	NP_001288	Q14028	CNGB1_HUMAN	cyclic nucleotide gated channel beta 1 isoform	209	Pro-rich.				sensory perception of smell	intracellular cyclic nucleotide activated cation channel complex	cAMP binding|intracellular cAMP activated cation channel activity			breast(3)|pancreas(1)	4						Colon(156;1293 1853 16336 28962 38659)								0.5	17.248748	17.248748	6	6	GG		KEEP	---	---	---	---	capture			Silent	SNP	56551427	56551427	3738	16	G	A	A	43	43	CNGB1	A	2	2
MYH2	4620	broad.mit.edu	36	17	10369864	10369864	+	Silent	SNP	G	A	A			TCGA-06-0216-01	TCGA-06-0216-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr17:10369864G>A	uc010coi.1	-	c.4242C>T	c.(4240-4242)AAC>AAT	p.N1414N	MYH2_uc002gmp.2_Silent_p.N1414N|MYH2_uc010coj.1_Intron	NM_001100112	NP_060004	Q9UKX2	MYH2_HUMAN	myosin, heavy chain 2, skeletal muscle, adult	1414	Potential.				muscle filament sliding	muscle myosin complex|myosin filament|sarcomere	actin binding|ATP binding|calmodulin binding|microfilament motor activity|structural constituent of muscle			ovary(5)|pancreas(4)|lung(1)|kidney(1)	11														0.455556	111.381643	111.532886	41	49	GG		KEEP	---	---	---	---	capture			Silent	SNP	10369864	10369864	10430	17	G	A	A	40	40	MYH2	A	1	1
HAP1	9001	broad.mit.edu	36	17	37137573	37137573	+	Silent	SNP	C	T	T			TCGA-06-0216-01	TCGA-06-0216-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr17:37137573C>T	uc002hxm.1	-	c.1242G>A	c.(1240-1242)TCG>TCA	p.S414S	HAP1_uc002hxn.1_Silent_p.S414S|HAP1_uc002hxo.1_Intron|HAP1_uc002hxp.1_Intron	NM_003949	NP_003940	P54257	HAP1_HUMAN	Huntingtin-associated protein 1 (HAP-1) (Neuroan 1).	414	Glu-rich.|HAP1 N-terminal.				brain development|protein localization|synaptic transmission	actin cytoskeleton	protein binding			ovary(2)	2		Breast(137;0.000162)												0.484375	91.150925	91.162373	31	33	CC		KEEP	---	---	---	---	capture	BRCA - Breast invasive adenocarcinoma(4;0.0677)		Silent	SNP	37137573	37137573	7235	17	C	T	T	23	23	HAP1	T	1	1
GLTSCR2	29997	broad.mit.edu	36	19	52951660	52951660	+	Nonsense_Mutation	SNP	C	T	T			TCGA-06-0216-01	TCGA-06-0216-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr19:52951660C>T	uc002phm.1	+	c.1360C>T	c.(1360-1362)CGA>TGA	p.R454*	GLTSCR2_uc010elk.1_Non-coding_Transcript|GLTSCR2_uc002phk.1_3'UTR|GLTSCR2_uc002phl.1_Nonsense_Mutation_p.R454*|GLTSCR2_uc010elj.1_Intron	NM_015710	NP_056525	Q9NZM5	GSCR2_HUMAN	glioma tumor suppressor candidate region gene 2	454				EGNILRDRFKSFQRRNMIEPRERAKFKRKYKVKLVEKRAFR EIQL -> RGQHSFETGSRAFRGGI (in Ref. 3; AAG30413).|PEGNILRDRFKSFQRRNMIEPRERAKFKRKYKVKLVEKRAF REIQ -> VLTVSCRGAPCPVMTPSLLPVPPRGYGRHHGCP WAGPVGPMPRG (in Ref. 5).		nucleolus				central_nervous_system(1)	1		all_cancers(25;1.47e-06)|all_lung(116;6.89e-05)|all_epithelial(76;0.000108)|Lung NSC(112;0.000117)|all_neural(266;0.0332)|Ovarian(192;0.086)				Colon(58;613 1041 9473 10089 15241)								0.413333	87.109232	87.601403	31	44	CC		KEEP	---	---	---	---	capture		all cancers(93;0.000301)|OV - Ovarian serous cystadenocarcinoma(262;0.00031)|Epithelial(262;0.0149)|GBM - Glioblastoma multiforme(486;0.0278)	Nonsense_Mutation	SNP	52951660	52951660	6743	19	C	T	T	31	31	GLTSCR2	T	5	1
NLRP12	91662	broad.mit.edu	36	19	58996441	58996441	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0216-01	TCGA-06-0216-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr19:58996441C>T	uc002qcj.2	-	c.2611G>A	c.(2611-2613)GCT>ACT	p.A871T	NLRP12_uc010eqw.1_Missense_Mutation_p.A153T|NLRP12_uc002qch.2_Missense_Mutation_p.A870T|NLRP12_uc002qci.2_Missense_Mutation_p.A870T|NLRP12_uc002qck.2_Intron|NLRP12_uc010eqx.1_Intron	NM_144687	NP_653288	P59046	NAL12_HUMAN	NLR family, pyrin domain containing 12 isoform	870	LRR 2.				activation of caspase activity|negative regulation of I-kappaB kinase/NF-kappaB cascade|negative regulation of interleukin-1 secretion|negative regulation of interleukin-6 biosynthetic process|negative regulation of protein autophosphorylation|negative regulation of Toll signaling pathway|positive regulation of inflammatory response|positive regulation of interleukin-1 beta secretion|regulation of interleukin-18 biosynthetic process|release of cytoplasmic sequestered NF-kappaB	cytoplasm	ATP binding|caspase activator activity|protein binding			ovary(4)|lung(1)	5	Ovarian(34;0.19)													0.306452	45.796881	47.871001	19	43	CC		KEEP	---	---	---	---	capture		GBM - Glioblastoma multiforme(134;0.026)	Missense_Mutation	SNP	58996441	58996441	10877	19	C	T	T	25	25	NLRP12	T	2	2
PNPLA6	10908	broad.mit.edu	36	19	7532431	7532431	+	Missense_Mutation	SNP	T	C	C			TCGA-06-0216-01	TCGA-06-0216-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr19:7532431T>C	uc002mgq.1	+	c.3967T>C	c.(3967-3969)TCA>CCA	p.S1323P	PNPLA6_uc002mgr.1_Missense_Mutation_p.S1323P|PNPLA6_uc002mgs.1_Missense_Mutation_p.S1309P|PNPLA6_uc002mgt.1_Non-coding_Transcript	NM_006702	NP_006693	Q8IY17	PLPL6_HUMAN	neuropathy target esterase	1362	Cytoplasmic (Potential).				cell death|lipid catabolic process|phosphatidylcholine metabolic process	endoplasmic reticulum membrane|integral to membrane	lysophospholipase activity			ovary(3)	3														0.285714	6.33824	7.684704	8	20	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	7532431	7532431	12596	19	T	C	C	54	54	PNPLA6	C	4	4
MUC16	94025	broad.mit.edu	36	19	8932728	8932728	+	Missense_Mutation	SNP	T	C	C			TCGA-06-0216-01	TCGA-06-0216-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr19:8932728T>C	uc002mkp.1	-	c.15718A>G	c.(15718-15720)AAG>GAG	p.K5240E		NM_024690	NP_078966	Q8WXI7	MUC16_HUMAN	mucin 16	5242	Thr-rich.|Extracellular (Potential).				cell adhesion	extracellular space|extrinsic to membrane|integral to membrane|plasma membrane	protein binding			ovary(15)|large_intestine(1)|pancreas(1)|breast(1)|skin(1)	19														0.428571	275.10609	276.006356	87	116	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	8932728	8932728	10367	19	T	C	C	61	61	MUC16	C	4	4
APITD1	378708	broad.mit.edu	36	1	10434203	10434203	+	Missense_Mutation	SNP	G	T	T			TCGA-06-0216-01	TCGA-06-0216-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:10434203G>T	uc001arf.1	+	c.459G>T	c.(457-459)AGG>AGT	p.R153S	APITD1_uc001arg.1_3'UTR|CORT_uc001ari.1_Missense_Mutation_p.R144S	NM_198544	NP_940946	Q8N2Z9	CENPS_HUMAN	apoptosis-inducing, TAF9-like domain 1 isoform	Error:Variant_position_missing_in_Q8N2Z9_after_alignment					DNA repair|mitotic prometaphase|transcription initiation, DNA-dependent	chromosome, centromeric region|cytosol|Fanconi anaemia nuclear complex	chromatin binding|DNA binding|protein binding			ovary(1)	1	Ovarian(185;0.203)	all_lung(284;1.31e-05)|Lung NSC(185;2.19e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Hepatocellular(190;0.00913)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)												0.454545	54.895589	54.974445	20	24	GG		KEEP	---	---	---	---	capture		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;3.31e-07)|COAD - Colon adenocarcinoma(227;7.32e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000297)|Kidney(185;0.000747)|KIRC - Kidney renal clear cell carcinoma(229;0.00258)|STAD - Stomach adenocarcinoma(132;0.0167)|READ - Rectum adenocarcinoma(331;0.0487)	Missense_Mutation	SNP	10434203	10434203	785	1	G	T	T	41	41	APITD1	T	3	3
HIPK1	204851	broad.mit.edu	36	1	114317300	114317300	+	Silent	SNP	G	T	T			TCGA-06-0216-01	TCGA-06-0216-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:114317300G>T	uc001eem.1	+	c.3276G>T	c.(3274-3276)TCG>TCT	p.S1092S	HIPK1_uc001een.1_Silent_p.S1092S|HIPK1_uc001eeo.1_Silent_p.S718S|HIPK1_uc001eep.1_Silent_p.S698S|HIPK1_uc001eeq.1_Silent_p.S384S	NM_198268	NP_938010	Q86Z02	HIPK1_HUMAN	homeodomain-interacting protein kinase 1 isoform	1092	Interaction with TP53.				protein phosphorylation|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	ATP binding|protein binding|protein serine/threonine kinase activity			ovary(4)	4	Lung SC(450;0.184)	all_cancers(81;4.5e-08)|all_epithelial(167;1.09e-07)|all_lung(203;1.53e-05)|Lung NSC(69;2.76e-05)							p.S1092S(MFE319-Tumor)	365				0.42439	238.488552	239.509508	87	118	GG		KEEP	---	---	---	---	capture		Lung(183;0.0234)|Colorectal(144;0.0686)|all cancers(265;0.0792)|Epithelial(280;0.0866)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)	Silent	SNP	114317300	114317300	7401	1	G	T	T	37	37	HIPK1	T	3	3
CD2	914	broad.mit.edu	36	1	117112787	117112787	+	Silent	SNP	G	A	A			TCGA-06-0216-01	TCGA-06-0216-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:117112787G>A	uc001egu.2	+	c.915G>A	c.(913-915)CAG>CAA	p.Q305Q		NM_001767	NP_001758	P06729	CD2_HUMAN	CD2 molecule	305	Cytoplasmic (Potential).|Pro-rich.				blood coagulation|cell surface receptor linked signaling pathway|cell-cell adhesion|induction of apoptosis|leukocyte migration|membrane raft polarization|natural killer cell activation|positive regulation of myeloid dendritic cell activation|regulation of T cell differentiation|T cell activation	integral to plasma membrane	receptor activity			breast(1)	1	Lung SC(450;0.225)	all_cancers(81;3.15e-06)|Acute lymphoblastic leukemia(138;1.7e-08)|all_epithelial(167;8.38e-07)|all_lung(203;3.37e-06)|Lung NSC(69;2.31e-05)			Alefacept(DB00092)	NSCLC(14;263 555 26380 43512 51332)								0.446429	223.927951	224.34309	75	93	GG		KEEP	---	---	---	---	capture		Epithelial(280;6.71e-26)|OV - Ovarian serous cystadenocarcinoma(397;4.74e-24)|all cancers(265;1.93e-22)|Lung(183;0.0543)|Kidney(133;0.0813)|Colorectal(144;0.174)|KIRC - Kidney renal clear cell carcinoma(1967;0.176)|LUSC - Lung squamous cell carcinoma(189;0.189)|BRCA - Breast invasive adenocarcinoma(282;0.201)	Silent	SNP	117112787	117112787	3106	1	G	A	A	34	34	CD2	A	2	2
TCHH	7062	broad.mit.edu	36	1	150351619	150351619	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0216-01	TCGA-06-0216-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr1:150351619C>T	uc001ezp.2	-	c.698G>A	c.(697-699)CGG>CAG	p.R233Q	TCHH_uc009wne.1_Missense_Mutation_p.R233Q	NM_007113	NP_009044	Q07283	TRHY_HUMAN	trichohyalin	233					keratinization	cytoskeleton	calcium ion binding			ovary(3)|kidney(1)|central_nervous_system(1)	5	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)													0.470356	363.921608	364.113178	119	134	CC		KEEP	---	---	---	---	capture	LUSC - Lung squamous cell carcinoma(543;0.206)		Missense_Mutation	SNP	150351619	150351619	16226	1	C	T	T	23	23	TCHH	T	1	1
NPR1	4881	broad.mit.edu	36	1	151918882	151918882	+	Missense_Mutation	SNP	T	C	C			TCGA-06-0216-01	TCGA-06-0216-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr1:151918882T>C	uc001fcs.2	+	c.674T>C	c.(673-675)CTC>CCC	p.L225P		NM_000906	NP_000897	P16066	ANPRA_HUMAN	natriuretic peptide receptor 1	225	Extracellular (Potential).				diuresis|intracellular signal transduction|natriuresis|negative regulation of angiogenesis|negative regulation of cell growth|protein phosphorylation|receptor guanylyl cyclase signaling pathway|regulation of blood pressure|regulation of blood vessel size|regulation of vascular permeability|regulation of vasodilation	integral to plasma membrane	ATP binding|GTP binding|guanylate cyclase activity|natriuretic peptide receptor activity|peptide receptor activity, G-protein coupled|protein kinase activity			ovary(3)|lung(2)|breast(1)	6	all_lung(78;3.75e-32)|Lung NSC(65;1.37e-30)|Hepatocellular(266;0.0877)|Melanoma(130;0.199)				Erythrityl Tetranitrate(DB01613)|Isosorbide Dinitrate(DB00883)|Isosorbide Mononitrate(DB01020)|Nesiritide(DB04899)|Nitric Oxide(DB00435)|Nitroglycerin(DB00727)|Nitroprusside(DB00325)	Pancreas(141;1349 1870 15144 15830 40702)				382				0.571429	12.830626	12.885505	8	6	TT		KEEP	---	---	---	---	capture	LUSC - Lung squamous cell carcinoma(543;0.151)		Missense_Mutation	SNP	151918882	151918882	10999	1	T	C	C	54	54	NPR1	C	4	4
PAPPA2	60676	broad.mit.edu	36	1	174792784	174792784	+	Missense_Mutation	SNP	C	A	A			TCGA-06-0216-01	TCGA-06-0216-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr1:174792784C>A	uc001gkz.1	+	c.703C>A	c.(703-705)CCA>ACA	p.P235T	PAPPA2_uc001gky.1_Missense_Mutation_p.P235T|PAPPA2_uc009www.1_Non-coding_Transcript	NM_020318	NP_064714	Q9BXP8	PAPP2_HUMAN	pappalysin 2 isoform 1	235					cell differentiation|proteolysis|regulation of cell growth	extracellular region|intracellular|membrane	metalloendopeptidase activity|zinc ion binding			ovary(7)|central_nervous_system(5)|lung(1)|breast(1)	14														0.420765	206.936926	207.939942	77	106	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	174792784	174792784	11850	1	C	A	A	30	30	PAPPA2	A	3	3
OR11L1	391189	broad.mit.edu	36	1	246070927	246070927	+	Nonsense_Mutation	SNP	C	A	A			TCGA-06-0216-01	TCGA-06-0216-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr1:246070927C>A	uc001idn.1	-	c.895G>T	c.(895-897)GAA>TAA	p.E299*		NM_001001959	NP_001001959	Q8NGX0	O11L1_HUMAN	olfactory receptor, family 11, subfamily L,	299	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)|pancreas(1)	2	all_cancers(71;8.78e-05)|all_epithelial(71;9.15e-06)|Breast(184;0.0117)|Ovarian(71;0.0377)|all_lung(81;0.0786)|Lung NSC(105;0.0858)													0.530612	227.143424	227.262225	78	69	CC		KEEP	---	---	---	---	capture	OV - Ovarian serous cystadenocarcinoma(106;0.0319)		Nonsense_Mutation	SNP	246070927	246070927	11336	1	C	A	A	32	32	OR11L1	A	5	3
RSPO1	284654	broad.mit.edu	36	1	37854927	37854927	+	Silent	SNP	G	A	A			TCGA-06-0216-01	TCGA-06-0216-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:37854927G>A	uc001cbl.1	-	c.102C>T	c.(100-102)GCC>GCT	p.A34A	RSPO1_uc009vvf.1_Silent_p.A7A|RSPO1_uc001cbm.1_Silent_p.A34A|RSPO1_uc009vvg.1_Silent_p.A34A	NM_001038633	NP_001033722	Q2MKA7	RSPO1_HUMAN	R-spondin1	34	FU 1.				positive regulation of canonical Wnt receptor signaling pathway|regulation of receptor internalization		heparin binding				0		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.164)				GBM(122;680 2230 27822 42821)								0.452703	204.007168	204.295513	67	81	GG		KEEP	---	---	---	---	capture			Silent	SNP	37854927	37854927	14189	1	G	A	A	39	39	RSPO1	A	1	1
KIF2C	11004	broad.mit.edu	36	1	45005103	45005103	+	Nonsense_Mutation	SNP	G	T	T			TCGA-06-0216-01	TCGA-06-0216-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:45005103G>T	uc001cmg.2	+	c.1990G>T	c.(1990-1992)GAG>TAG	p.E664*	KIF2C_uc001cmh.2_Nonsense_Mutation_p.E610*	NM_006845	NP_006836	Q99661	KIF2C_HUMAN	kinesin family member 2C	664					blood coagulation|cell division|cell proliferation|chromosome segregation|establishment or maintenance of microtubule cytoskeleton polarity|microtubule depolymerization|microtubule-based movement|mitotic prometaphase|regulation of chromosome segregation	condensed chromosome kinetochore|cytosol|kinesin complex|microtubule|nucleus	ATP binding|centromeric DNA binding|microtubule motor activity|microtubule plus-end binding			ovary(1)	1	Acute lymphoblastic leukemia(166;0.155)													0.333333	14.967749	15.682972	9	18	GG		KEEP	---	---	---	---	capture			Nonsense_Mutation	SNP	45005103	45005103	8610	1	G	T	T	45	45	KIF2C	T	5	3
WFDC13	164237	broad.mit.edu	36	20	43767939	43767939	+	Missense_Mutation	SNP	T	C	C			TCGA-06-0216-01	TCGA-06-0216-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr20:43767939T>C	uc002xpd.1	+	c.263T>C	c.(262-264)GTC>GCC	p.V88A	WFDC10B_uc002xpb.1_5'Flank|WFDC10B_uc002xpc.1_5'Flank	NM_172005	NP_742002	Q8IUB5	WFD13_HUMAN	WAP four-disulfide core domain 13 precursor	88						extracellular region	peptidase inhibitor activity				0		Myeloproliferative disorder(115;0.0122)												0.352273	95.303791	96.995212	31	57	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	43767939	43767939	17925	20	T	C	C	58	58	WFDC13	C	4	4
TTN	7273	broad.mit.edu	36	2	179302365	179302365	+	Missense_Mutation	SNP	T	A	A			TCGA-06-0216-01	TCGA-06-0216-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr2:179302365T>A	uc002umr.1	-	c.15031A>T	c.(15031-15033)AAC>TAC	p.N5011Y	TTN_uc002ums.1_Intron|TTN_uc010frc.1_Intron|TTN_uc010frd.1_Intron|TTN_uc002umz.1_Missense_Mutation_p.N1672Y	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	5938										ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1)	153										8722				0.360215	167.080223	170.233149	67	119	TT		KEEP	---	---	---	---	capture	OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)		Missense_Mutation	SNP	179302365	179302365	17290	2	T	A	A	61	61	TTN	A	4	4
INPP5D	3635	broad.mit.edu	36	2	233652302	233652302	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0216-01	TCGA-06-0216-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr2:233652302G>A	uc002vtv.1	+	c.148G>A	c.(148-150)GTT>ATT	p.V50I	INPP5D_uc002vtw.1_Missense_Mutation_p.V50I	NM_001017915	NP_001017915	Q92835	SHIP1_HUMAN	SH2 containing inositol phosphatase isoform a	50	SH2.				apoptosis|blood coagulation|leukocyte migration|T cell receptor signaling pathway	cytosol	inositol-polyphosphate 5-phosphatase activity|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity|SH3 domain binding			ovary(1)|central_nervous_system(1)	2		Breast(86;0.0013)|Renal(207;0.00339)|all_hematologic(139;0.0116)|all_lung(227;0.0273)|Acute lymphoblastic leukemia(138;0.0328)|Lung NSC(271;0.0843)				NSCLC(82;1215 1426 16163 20348 41018)				816				0.53125	103.453314	103.507841	34	30	GG		KEEP	---	---	---	---	capture		Epithelial(121;1.16e-17)|BRCA - Breast invasive adenocarcinoma(100;0.000479)|LUSC - Lung squamous cell carcinoma(224;0.00655)|Lung(119;0.00802)|GBM - Glioblastoma multiforme(43;0.0185)	Missense_Mutation	SNP	233652302	233652302	8057	2	G	A	A	40	40	INPP5D	A	1	1
SMEK2	57223	broad.mit.edu	36	2	55644972	55644972	+	Silent	SNP	C	T	T			TCGA-06-0216-01	TCGA-06-0216-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr2:55644972C>T	uc002rzc.1	-	c.2241G>A	c.(2239-2241)AAG>AAA	p.K747K	SMEK2_uc002ryz.1_Silent_p.K174K|SMEK2_uc002rza.1_Silent_p.K531K|SMEK2_uc002rzb.1_Silent_p.K662K|SMEK2_uc002rzd.1_Silent_p.K715K	NM_001122964	NP_001116436	Q5MIZ7	P4R3B_HUMAN	SMEK homolog 2, suppressor of mek1 isoform 1	747						microtubule organizing center|nucleus	protein binding				0														0.32	41.480285	42.920786	16	34	CC		KEEP	---	---	---	---	capture	LUSC - Lung squamous cell carcinoma(58;0.127)|Lung(47;0.132)		Silent	SNP	55644972	55644972	15292	2	C	T	T	20	20	SMEK2	T	2	2
TMEM45A	55076	broad.mit.edu	36	3	101758306	101758306	+	Missense_Mutation	SNP	A	G	G			TCGA-06-0216-01	TCGA-06-0216-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr3:101758306A>G	uc003dua.1	+	c.251A>G	c.(250-252)GAG>GGG	p.E84G	TMEM45A_uc003dtz.1_Missense_Mutation_p.E68G	NM_018004	NP_060474	Q9NWC5	TM45A_HUMAN	transmembrane protein 45A	68	Helical; (Potential).					integral to membrane				ovary(1)	1														0.333333	9.171185	9.539623	5	10	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	101758306	101758306	16708	3	A	G	G	11	11	TMEM45A	G	4	4
IMPG2	50939	broad.mit.edu	36	3	102434374	102434374	+	Silent	SNP	A	G	G			TCGA-06-0216-01	TCGA-06-0216-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr3:102434374A>G	uc003duq.1	-	c.3174T>C	c.(3172-3174)CCT>CCC	p.P1058P	IMPG2_uc010hpj.1_Non-coding_Transcript	NM_016247	NP_057331	Q9BZV3	IMPG2_HUMAN	interphotoreceptor matrix proteoglycan 2	1058	Extracellular (Potential).|EGF-like 2.				visual perception	integral to membrane|proteinaceous extracellular matrix	extracellular matrix structural constituent|heparin binding|hyaluronic acid binding|receptor activity			ovary(2)|haematopoietic_and_lymphoid_tissue(1)	3														0.321429	46.927811	48.515253	18	38	AA		KEEP	---	---	---	---	capture			Silent	SNP	102434374	102434374	8030	3	A	G	G	7	7	IMPG2	G	4	4
DZIP3	9666	broad.mit.edu	36	3	109836409	109836409	+	Missense_Mutation	SNP	G	T	T			TCGA-06-0216-01	TCGA-06-0216-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr3:109836409G>T	uc003dxd.1	+	c.818G>T	c.(817-819)GGA>GTA	p.G273V	DZIP3_uc003dxe.1_Missense_Mutation_p.G273V|DZIP3_uc003dxf.1_Missense_Mutation_p.G273V|DZIP3_uc003dxg.1_5'UTR	NM_014648	NP_055463	Q86Y13	DZIP3_HUMAN	DAZ interacting protein 3, zinc finger	273					protein polyubiquitination	cytoplasm	polyubiquitin binding|RNA binding|ubiquitin-protein ligase activity|zinc ion binding			ovary(1)|central_nervous_system(1)	2														0.592593	45.298925	45.500188	16	11	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	109836409	109836409	5051	3	G	T	T	41	41	DZIP3	T	3	3
DIRC2	84925	broad.mit.edu	36	3	123996984	123996984	+	Silent	SNP	C	T	T			TCGA-06-0216-01	TCGA-06-0216-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr3:123996984C>T	uc003efw.2	+	c.255C>T	c.(253-255)TTC>TTT	p.F85F	HSPBAP1_uc003efu.1_5'Flank|HSPBAP1_uc003efv.1_5'Flank|DIRC2_uc010hrl.1_Non-coding_Transcript|DIRC2_uc010hrm.1_5'UTR	NM_032839	NP_116228	Q96SL1	DIRC2_HUMAN	disrupted in renal carcinoma 2	85					transport	integral to membrane					0														0.192308	6.857088	9.168866	5	21	CC		KEEP	---	---	---	---	capture		GBM - Glioblastoma multiforme(114;0.0614)	Silent	SNP	123996984	123996984	4713	3	C	T	T	32	32	DIRC2	T	2	2
ALG1L	200810	broad.mit.edu	36	3	127132089	127132089	+	Splice_Site_SNP	SNP	C	A	A			TCGA-06-0216-01	TCGA-06-0216-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr3:127132089C>A	uc003eig.1	-	c.348_splice	c.e5+1	p.Q116_splice		NM_001015050	NP_001015050			hypothetical protein LOC200810								transferase activity, transferring glycosyl groups				0														0.25	6.667824	7.807967	5	15	CC		KEEP	---	---	---	---	capture			Splice_Site_SNP	SNP	127132089	127132089	520	3	C	A	A	18	18	ALG1L	A	5	3
CEP70	80321	broad.mit.edu	36	3	139772578	139772578	+	Missense_Mutation	SNP	T	C	C			TCGA-06-0216-01	TCGA-06-0216-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr3:139772578T>C	uc003esl.1	-	c.272A>G	c.(271-273)AAT>AGT	p.N91S	CEP70_uc003esm.2_Missense_Mutation_p.N91S|CEP70_uc003esn.2_Missense_Mutation_p.N91S	NM_024491	NP_077817	Q8NHQ1	CEP70_HUMAN	centrosomal protein 70 kDa	91	Potential.				G2/M transition of mitotic cell cycle	cytosol|microtubule organizing center	protein binding				0														0.42	65.568227	65.84708	21	29	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	139772578	139772578	3392	3	T	C	C	52	52	CEP70	C	4	4
FNDC3B	64778	broad.mit.edu	36	3	173578837	173578837	+	Missense_Mutation	SNP	A	G	G			TCGA-06-0216-01	TCGA-06-0216-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr3:173578837A>G	uc010hwt.1	+	c.3092A>G	c.(3091-3093)CAG>CGG	p.Q1031R	FNDC3B_uc003fhy.1_Missense_Mutation_p.Q1027R|FNDC3B_uc003fhz.2_Missense_Mutation_p.Q1027R	NM_022763	NP_073600	Q53EP0	FND3B_HUMAN	fibronectin type III domain containing 3B	1031	Fibronectin type-III 8.					endoplasmic reticulum|integral to membrane				ovary(1)|breast(1)	2	all_cancers(22;1.01e-18)|Ovarian(172;0.00167)|Breast(254;0.165)													0.304348	75.265447	78.407772	28	64	AA		KEEP	---	---	---	---	capture	LUSC - Lung squamous cell carcinoma(14;3.57e-14)|Lung(28;9.39e-14)	GBM - Glioblastoma multiforme(1;0.0494)	Missense_Mutation	SNP	173578837	173578837	6212	3	A	G	G	7	7	FNDC3B	G	4	4
LRRC3B	116135	broad.mit.edu	36	3	26726915	26726915	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0216-01	TCGA-06-0216-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr3:26726915G>A	uc003cdp.1	+	c.748G>A	c.(748-750)GAT>AAT	p.D250N	LRRC3B_uc003cdq.1_Missense_Mutation_p.D250N|LRRC3B_uc010hfi.1_Missense_Mutation_p.D250N	NM_052953	NP_443185	Q96PB8	LRC3B_HUMAN	leucine rich repeat containing 3B	250						integral to membrane				pancreas(2)|ovary(1)	3														0.409836	72.962736	73.396157	25	36	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	26726915	26726915	9371	3	G	A	A	33	33	LRRC3B	A	2	2
AZI2	64343	broad.mit.edu	36	3	28356962	28356962	+	Nonsense_Mutation	SNP	G	A	A			TCGA-06-0216-01	TCGA-06-0216-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr3:28356962G>A	uc003ceb.1	-	c.151C>T	c.(151-153)CGA>TGA	p.R51*	AZI2_uc003cec.1_De_novo_Start_OutOfFrame|AZI2_uc003ced.1_Nonsense_Mutation_p.R51*|AZI2_uc003cee.2_Nonsense_Mutation_p.R51*|AZI2_uc003cef.1_Nonsense_Mutation_p.R51*|AZI2_uc003ceg.1_Nonsense_Mutation_p.R51*	NM_022461	NP_071906	Q9H6S1	AZI2_HUMAN	5-azacytidine induced 2 isoform a	51	Potential.					mitochondrion|plasma membrane				ovary(2)	2														0.16129	6.850074	10.250049	5	26	GG		KEEP	---	---	---	---	capture			Nonsense_Mutation	SNP	28356962	28356962	1262	3	G	A	A	40	40	AZI2	A	5	1
OTUD4	54726	broad.mit.edu	36	4	146296568	146296568	+	Silent	SNP	C	T	T			TCGA-06-0216-01	TCGA-06-0216-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr4:146296568C>T	uc003ika.2	-	c.465G>A	c.(463-465)GTG>GTA	p.V155V	OTUD4_uc003ijz.2_Silent_p.V155V	NM_001102653	NP_001096123	Q01804	OTUD4_HUMAN	OTU domain containing 4 protein isoform 3	220							protein binding			ovary(2)|breast(1)	3	all_hematologic(180;0.151)													0.522727	60.971299	60.988566	23	21	CC		KEEP	---	---	---	---	capture			Silent	SNP	146296568	146296568	11727	4	C	T	T	29	29	OTUD4	T	2	2
KIAA1211	57482	broad.mit.edu	36	4	56876505	56876505	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0216-01	TCGA-06-0216-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr4:56876505G>A	uc003hbk.2	+	c.2080G>A	c.(2080-2082)GGT>AGT	p.G694S	KIAA1211_uc010iha.1_Missense_Mutation_p.G687S|KIAA1211_uc003hbm.1_Missense_Mutation_p.G580S	NM_020722	NP_065773	Q6ZU35	K1211_HUMAN	hypothetical protein LOC57482	694										ovary(1)|skin(1)	2	Glioma(25;0.08)|all_neural(26;0.101)													0.572414	261.544404	262.208901	83	62	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	56876505	56876505	8523	4	G	A	A	39	39	KIAA1211	A	1	1
SH3TC1	54436	broad.mit.edu	36	4	8280489	8280489	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0216-01	TCGA-06-0216-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr4:8280489C>T	uc003gkv.2	+	c.2168C>T	c.(2167-2169)CCC>CTC	p.P723L	SH3TC1_uc003gkw.2_Missense_Mutation_p.P647L|SH3TC1_uc003gkx.2_Non-coding_Transcript|SH3TC1_uc003gky.1_5'Flank	NM_018986	NP_061859	Q8TE82	S3TC1_HUMAN	SH3 domain and tetratricopeptide repeats 1	723							binding			large_intestine(2)|pancreas(1)	3						NSCLC(145;2298 2623 35616 37297)								0.557692	176.619691	176.917032	58	46	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	8280489	8280489	14753	4	C	T	T	22	22	SH3TC1	T	2	2
DRD5	1816	broad.mit.edu	36	4	9394035	9394035	+	Silent	SNP	C	T	T			TCGA-06-0216-01	TCGA-06-0216-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr4:9394035C>T	uc003gmb.2	+	c.1284C>T	c.(1282-1284)GAC>GAT	p.D428D		NM_000798	NP_000789	P21918	DRD5_HUMAN	dopamine receptor D5	428	Cytoplasmic (Potential).				activation of adenylate cyclase activity by dopamine receptor signaling pathway|activation of phospholipase C activity by dopamine receptor signaling pathway|cellular calcium ion homeostasis|negative regulation of NAD(P)H oxidase activity|reactive oxygen species metabolic process|synaptic transmission, dopaminergic	integral to plasma membrane					0					Apomorphine(DB00714)|Carphenazine(DB01038)|Fenoldopam(DB00800)|Zuclopenthixol(DB01624)									0.527273	171.651237	171.72249	58	52	CC		KEEP	---	---	---	---	capture			Silent	SNP	9394035	9394035	4944	4	C	T	T	19	19	DRD5	T	1	1
EFNA5	1946	broad.mit.edu	36	5	106790835	106790835	+	Nonsense_Mutation	SNP	G	A	A			TCGA-06-0216-01	TCGA-06-0216-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr5:106790835G>A	uc003kol.1	-	c.400C>T	c.(400-402)CGA>TGA	p.R134*	EFNA5_uc010jbr.1_Nonsense_Mutation_p.R134*	NM_001962	NP_001953	P52803	EFNA5_HUMAN	ephrin-A5	134					cell-cell signaling	anchored to plasma membrane|caveola|extracellular space	ephrin receptor binding				0		all_cancers(142;5.15e-06)|all_epithelial(76;4.39e-07)|Prostate(80;0.00726)|Lung NSC(167;0.0736)|Ovarian(225;0.0797)|all_lung(232;0.0854)|Colorectal(57;0.241)												0.441176	90.052373	90.254904	30	38	GG		KEEP	---	---	---	---	capture		Epithelial(69;1.25e-12)|OV - Ovarian serous cystadenocarcinoma(64;1.32e-11)|BRCA - Breast invasive adenocarcinoma(61;0.0376)|COAD - Colon adenocarcinoma(37;0.109)	Nonsense_Mutation	SNP	106790835	106790835	5142	5	G	A	A	39	39	EFNA5	A	5	1
CTNNA1	1495	broad.mit.edu	36	5	138288271	138288271	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0216-01	TCGA-06-0216-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr5:138288271G>A	uc003ldh.1	+	c.1720G>A	c.(1720-1722)GAA>AAA	p.E574K	CTNNA1_uc003ldi.1_Missense_Mutation_p.E272K|CTNNA1_uc003ldj.1_Missense_Mutation_p.E574K|CTNNA1_uc003ldl.1_Missense_Mutation_p.E204K	NM_001903	NP_001894	P35221	CTNA1_HUMAN	catenin, alpha 1	574					adherens junction organization|apical junction assembly|cell adhesion|cellular response to indole-3-methanol|muscle cell differentiation|positive regulation of muscle cell differentiation	actin cytoskeleton|catenin complex|cytosol	beta-catenin binding|cadherin binding|gamma-catenin binding|structural molecule activity|vinculin binding			breast(6)|ovary(2)|large_intestine(2)|kidney(1)	11														0.625	6.301901	6.373748	5	3	GG		KEEP	---	---	---	---	capture	KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00325)		Missense_Mutation	SNP	138288271	138288271	4171	5	G	A	A	41	41	CTNNA1	A	2	2
DND1	373863	broad.mit.edu	36	5	140031270	140031270	+	Nonsense_Mutation	SNP	C	T	T			TCGA-06-0216-01	TCGA-06-0216-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr5:140031270C>T	uc003lgt.1	-	c.854G>A	c.(853-855)TGG>TAG	p.W285*		NM_194249	NP_919225	Q8IYX4	DND1_HUMAN	dead end homolog 1	285					multicellular organismal development|negative regulation of gene silencing by miRNA	cytoplasm|nucleus	AU-rich element binding|nucleotide binding				0														0.25	14.809736	16.402387	7	21	CC		KEEP	---	---	---	---	capture	KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)		Nonsense_Mutation	SNP	140031270	140031270	4849	5	C	T	T	21	21	DND1	T	5	2
TBC1D9B	23061	broad.mit.edu	36	5	179247740	179247740	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0216-01	TCGA-06-0216-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr5:179247740C>T	uc003mlh.1	-	c.1223G>A	c.(1222-1224)AGG>AAG	p.R408K	TBC1D9B_uc003mli.1_Missense_Mutation_p.R408K|TBC1D9B_uc003mlj.1_Missense_Mutation_p.R408K	NM_198868	NP_942568	Q66K14	TBC9B_HUMAN	TBC1 domain family, member 9B (with GRAM domain)	408						integral to membrane|intracellular	calcium ion binding|Rab GTPase activator activity			breast(1)	1	all_cancers(89;0.000197)|all_epithelial(37;6.84e-05)|Renal(175;0.000159)|Lung NSC(126;0.00136)|all_lung(126;0.00243)	all_cancers(40;0.0236)|Medulloblastoma(196;0.00498)|all_neural(177;0.0138)												0.322727	201.549598	207.687294	71	149	CC		KEEP	---	---	---	---	capture	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)		Missense_Mutation	SNP	179247740	179247740	16154	5	C	T	T	24	24	TBC1D9B	T	2	2
KHDRBS2	202559	broad.mit.edu	36	6	62662592	62662592	+	Silent	SNP	T	A	A			TCGA-06-0216-01	TCGA-06-0216-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr6:62662592T>A	uc003peg.2	-	c.717A>T	c.(715-717)GCA>GCT	p.A239A		NM_152688	NP_689901	Q5VWX1	KHDR2_HUMAN	KH domain-containing, RNA-binding, signal	239	Pro-rich.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	SH3 domain binding			ovary(3)|liver(1)|skin(1)	5														0.375	101.074705	102.391968	36	60	TT		KEEP	---	---	---	---	capture		BRCA - Breast invasive adenocarcinoma(397;0.149)	Silent	SNP	62662592	62662592	8453	6	T	A	A	63	63	KHDRBS2	A	4	4
GIMAP6	474344	broad.mit.edu	36	7	149956314	149956314	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0216-01	TCGA-06-0216-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr7:149956314G>A	uc003whn.1	-	c.305C>T	c.(304-306)CCC>CTC	p.P102L	GIMAP6_uc003whm.1_Intron	NM_024711	NP_078987	Q6P9H5	GIMA6_HUMAN	GTPase, IMAP family member 6	102							GTP binding			ovary(1)	1														0.190265	88.294914	108.566152	43	183	GG		KEEP	---	---	---	---	capture	OV - Ovarian serous cystadenocarcinoma(82;0.0145)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)	Missense_Mutation	SNP	149956314	149956314	6651	7	G	A	A	43	43	GIMAP6	A	2	2
ABP1	26	broad.mit.edu	36	7	150185353	150185353	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0216-01	TCGA-06-0216-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr7:150185353C>T	uc003wia.1	+	c.862C>T	c.(862-864)CGC>TGC	p.R288C	ABP1_uc003why.1_Missense_Mutation_p.R288C|ABP1_uc003whz.1_Missense_Mutation_p.R288C	NM_001091	NP_001082	P19801	ABP1_HUMAN	amiloride binding protein 1 precursor	288					amine metabolic process|oxidation-reduction process	extracellular space|peroxisome	copper ion binding|diamine oxidase activity|heparin binding|histamine oxidase activity|methylputrescine oxidase activity|primary amine oxidase activity|propane-1,3-diamine oxidase activity|quinone binding			ovary(2)|breast(2)	4	all_neural(206;0.219)				Amiloride(DB00594)|Spermine(DB00127)	Pancreas(195;1227 3054 24912 28503)								0.313725	42.385881	43.958437	16	35	CC		KEEP	---	---	---	---	capture	OV - Ovarian serous cystadenocarcinoma(82;0.0121)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)	Missense_Mutation	SNP	150185353	150185353	99	7	C	T	T	23	23	ABP1	T	1	1
SRRM3	222183	broad.mit.edu	36	7	75732674	75732674	+	Missense_Mutation	SNP	A	C	C			TCGA-06-0216-01	TCGA-06-0216-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr7:75732674A>C	uc003uer.2	+	c.782A>C	c.(781-783)CAC>CCC	p.H261P		NM_001110199	NP_001103669			hypothetical protein LOC222183												0														0.282051	6.655087	8.598604	11	28	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	75732674	75732674	15684	7	A	C	C	6	6	SRRM3	C	4	4
CPA6	57094	broad.mit.edu	36	8	68581678	68581678	+	Splice_Site_SNP	SNP	C	G	G			TCGA-06-0216-01	TCGA-06-0216-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr8:68581678C>G	uc003xxq.2	-	c.535_splice	c.e6-1	p.L179_splice	CPA6_uc003xxr.2_Splice_Site_SNP_p.L31_splice|CPA6_uc003xxs.2_Splice_Site_SNP_p.L179_splice	NM_020361	NP_065094			carboxypeptidase B isoform 1 precursor						proteolysis	proteinaceous extracellular matrix	metallocarboxypeptidase activity|zinc ion binding			ovary(2)	2														0.4	41.543372	41.849332	14	21	CC		KEEP	---	---	---	---	capture	Epithelial(68;0.04)|OV - Ovarian serous cystadenocarcinoma(28;0.0593)|all cancers(69;0.136)		Splice_Site_SNP	SNP	68581678	68581678	3932	8	C	G	G	28	28	CPA6	G	5	3
PTGS1	5742	broad.mit.edu	36	9	124185835	124185835	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0216-01	TCGA-06-0216-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr9:124185835C>T	uc004bmg.1	+	c.989C>T	c.(988-990)ACG>ATG	p.T330M	PTGS1_uc010mwb.1_Missense_Mutation_p.T221M|PTGS1_uc004bmf.1_Missense_Mutation_p.T330M|PTGS1_uc004bmh.1_Missense_Mutation_p.T221M	NM_000962	NP_000953	P23219	PGH1_HUMAN	prostaglandin-endoperoxide synthase 1 isoform 1	330					cyclooxygenase pathway|hormone biosynthetic process|oxidation-reduction process|regulation of blood pressure|response to oxidative stress|xenobiotic metabolic process	endoplasmic reticulum membrane|Golgi apparatus|microsome|plasma membrane	heme binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|peroxidase activity|prostaglandin-endoperoxide synthase activity			ovary(1)	1					Acetaminophen(DB00316)|Aspirin(DB00945)|Balsalazide(DB01014)|Bromfenac(DB00963)|Ciclopirox(DB01188)|Diclofenac(DB00586)|Diflunisal(DB00861)|Dipyrone(DB04817)|Etodolac(DB00749)|Fenoprofen(DB00573)|Flurbiprofen(DB00712)|gamma-Homolinolenic acid(DB00154)|Ibuprofen(DB01050)|Icosapent(DB00159)|Indomethacin(DB00328)|Ketoprofen(DB01009)|Ketorolac(DB00465)|Lumiracoxib(DB01283)|Meclofenamic acid(DB00939)|Mefenamic acid(DB00784)|Mesalazine(DB00244)|Minoxidil(DB00350)|Nabumetone(DB00461)|Naproxen(DB00788)|Phenacetin(DB03783)|Piroxicam(DB00554)|Rofecoxib(DB00533)|Salicyclic acid(DB00936)|Salsalate(DB01399)|Sulindac(DB00605)|Suprofen(DB00870)|Tenoxicam(DB00469)|Tolmetin(DB00500)									0.370968	62.018851	62.921615	23	39	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	124185835	124185835	13210	9	C	T	T	19	19	PTGS1	T	1	1
COQ4	51117	broad.mit.edu	36	9	130127890	130127890	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0216-01	TCGA-06-0216-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr9:130127890G>A	uc004bur.2	+	c.311G>A	c.(310-312)CGG>CAG	p.R104Q	COQ4_uc004bus.1_Missense_Mutation_p.R80Q|COQ4_uc010mxy.1_Missense_Mutation_p.R80Q	NM_016035	NP_057119	Q9Y3A0	COQ4_HUMAN	coenzyme Q4 homolog	104					ubiquinone biosynthetic process	mitochondrial inner membrane					0														0.441667	151.983745	152.34933	53	67	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	130127890	130127890	3885	9	G	A	A	39	39	COQ4	A	1	1
SHB	6461	broad.mit.edu	36	9	37938668	37938668	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0216-01	TCGA-06-0216-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr9:37938668C>T	uc004aax.1	-	c.1310G>A	c.(1309-1311)AGC>AAC	p.S437N		NM_003028	NP_003019	Q15464	SHB_HUMAN	Src homology 2 domain containing adaptor protein	437	SH2.				angiogenesis|apoptosis|cell differentiation|signal transduction	cytoplasm|plasma membrane	SH3/SH2 adaptor activity			central_nervous_system(2)	2		all_epithelial(88;0.122)												0.462264	142.974523	143.104338	49	57	CC		KEEP	---	---	---	---	capture		GBM - Glioblastoma multiforme(29;3.27e-05)|Lung(182;0.0658)	Missense_Mutation	SNP	37938668	37938668	14760	9	C	T	T	28	28	SHB	T	2	2
CAPN6	827	broad.mit.edu	36	X	110380803	110380803	+	Missense_Mutation	SNP	G	T	T			TCGA-06-0216-01	TCGA-06-0216-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chrX:110380803G>T	uc004epc.1	-	c.1156C>A	c.(1156-1158)CAG>AAG	p.Q386K		NM_014289	NP_055104	Q9Y6Q1	CAN6_HUMAN	calpain 6	386	Domain III.				microtubule bundle formation|proteolysis|regulation of cytoskeleton organization	perinuclear region of cytoplasm|spindle microtubule	calcium-dependent cysteine-type endopeptidase activity|microtubule binding			ovary(2)|upper_aerodigestive_tract(1)|large_intestine(1)|lung(1)|skin(1)	6														0.356707	319.470463	325.408323	117	211	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	110380803	110380803	2748	23	G	T	T	47	47	CAPN6	T	3	3
DDX26B	203522	broad.mit.edu	36	X	134541747	134541747	+	Missense_Mutation	SNP	G	C	C			TCGA-06-0216-01	TCGA-06-0216-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chrX:134541747G>C	uc004eyw.2	+	c.2377G>C	c.(2377-2379)GGT>CGT	p.G793R	DDX26B_uc004eyx.2_Missense_Mutation_p.G394R	NM_182540	NP_872346	Q5JSJ4	DX26B_HUMAN	DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide	793											0	Acute lymphoblastic leukemia(192;6.56e-05)													0.546667	119.072216	119.213537	41	34	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	134541747	134541747	4524	23	G	C	C	47	47	DDX26B	C	3	3
SOX3	6658	broad.mit.edu	36	X	139414729	139414729	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0216-01	TCGA-06-0216-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chrX:139414729C>T	uc004fbd.1	-	c.163G>A	c.(163-165)GCT>ACT	p.A55T		NM_005634	NP_005625	P41225	SOX3_HUMAN	SRY (sex determining region Y)-box 3	55					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding			pancreas(1)	1	Acute lymphoblastic leukemia(192;7.65e-05)													0.3	7.320878	7.678476	3	7	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	139414729	139414729	15451	23	C	T	T	27	27	SOX3	T	1	1
SLITRK2	84631	broad.mit.edu	36	X	144713731	144713731	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0216-01	TCGA-06-0216-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chrX:144713731C>T	uc004fcc.1	+	c.2096C>T	c.(2095-2097)CCC>CTC	p.P699L	SLITRK2_uc010nso.1_Missense_Mutation_p.P699L|SLITRK2_uc004fcd.1_Missense_Mutation_p.P699L|SLITRK2_uc004fce.1_Missense_Mutation_p.P699L|SLITRK2_uc004fcg.1_Missense_Mutation_p.P699L|SLITRK2_uc010nsp.1_Missense_Mutation_p.P699L|CXorf1_uc004fch.1_5'Flank	NM_032539	NP_115928	Q9H156	SLIK2_HUMAN	SLIT and NTRK-like family, member 2	699	Cytoplasmic (Potential).					integral to membrane				ovary(4)|pancreas(1)	5	Acute lymphoblastic leukemia(192;6.56e-05)													0.326667	133.824771	137.821683	49	101	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	144713731	144713731	15241	23	C	T	T	22	22	SLITRK2	T	2	2
GPR50	9248	broad.mit.edu	36	X	150098936	150098936	+	Missense_Mutation	SNP	A	G	G			TCGA-06-0216-01	TCGA-06-0216-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chrX:150098936A>G	uc010ntg.1	+	c.223A>G	c.(223-225)ATG>GTG	p.M75V		NM_004224	NP_004215	Q13585	MTR1L_HUMAN	G protein-coupled receptor 50	75	Helical; Name=2; (Potential).				cell-cell signaling	integral to plasma membrane	melatonin receptor activity			large_intestine(1)|lung(1)|ovary(1)|pancreas(1)	4	Acute lymphoblastic leukemia(192;6.56e-05)													0.30303	473.499524	492.891924	170	391	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	150098936	150098936	6972	23	A	G	G	16	16	GPR50	G	4	4
FGD1	2245	broad.mit.edu	36	X	54513246	54513246	+	Silent	SNP	G	A	A			TCGA-06-0216-01	TCGA-06-0216-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chrX:54513246G>A	uc004dtg.1	-	c.1029C>T	c.(1027-1029)GAC>GAT	p.D343D		NM_004463	NP_004454	P98174	FGD1_HUMAN	faciogenital dysplasia protein	343					actin cytoskeleton organization|apoptosis|filopodium assembly|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|organ morphogenesis|regulation of Cdc42 GTPase activity|regulation of cell shape|small GTPase mediated signal transduction	cytoskeleton|cytosol|Golgi apparatus|lamellipodium|nucleus|plasma membrane|ruffle	Rho guanyl-nucleotide exchange factor activity|small GTPase binding|zinc ion binding			ovary(3)|skin(2)|central_nervous_system(1)	6														0.348837	39.322104	40.184456	15	28	GG		KEEP	---	---	---	---	capture			Silent	SNP	54513246	54513246	6069	23	G	A	A	40	40	FGD1	A	1	1
ZMYM3	9203	broad.mit.edu	36	X	70384015	70384015	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0216-01	TCGA-06-0216-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chrX:70384015C>T	uc004dzh.1	-	c.2219G>A	c.(2218-2220)CGT>CAT	p.R740H	ZMYM3_uc004dzi.1_Missense_Mutation_p.R740H|ZMYM3_uc004dzj.1_Missense_Mutation_p.R740H	NM_201599	NP_963893	Q14202	ZMYM3_HUMAN	zinc finger protein 261	740					multicellular organismal development	nucleus	DNA binding|zinc ion binding			ovary(1)	1	Renal(35;0.156)													0.296296	19.190153	20.191931	8	19	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	70384015	70384015	18292	23	C	T	T	19	19	ZMYM3	T	1	1
FAM174B	400451	broad.mit.edu	36	15	90999683	90999688	+	In_Frame_Del	DEL	TGGAGC	-	-			TCGA-06-0216-01	TCGA-06-0216-01										Phase_I	Unspecified				Illumina GAIIx	g.chr15:90999683_90999688delTGGAGC	uc010boe.1	-	c.206_211delGCTCCA	c.(205-213)AGCTCCAAC>AAC	p.SS69del	FAM174B_uc002bsl.2_Intron	NM_207446	NP_997329	Q3ZCQ3	F174B_HUMAN	hypothetical protein LOC400451	69_70	Extracellular (Potential).					integral to membrane					0														0.33			2	4				---	---	---	---	capture_indel			In_Frame_Del	DEL	90999683	90999688	5702	15	TGGAGC	-	-	63	63	FAM174B	-	5	5
CD22	933	broad.mit.edu	36	19	40524124	40524125	+	Frame_Shift_Ins	INS	-	T	T			TCGA-06-0216-01	TCGA-06-0216-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:40524124_40524125insT	uc010edt.1	+	c.1546_1547insT	c.(1546-1548)CTTfs	p.L516fs	CD22_uc010edu.1_Frame_Shift_Ins_p.L428fs|CD22_uc010edv.1_Frame_Shift_Ins_p.L516fs|CD22_uc002nzb.2_Frame_Shift_Ins_p.L339fs|CD22_uc010edw.1_Frame_Shift_Ins_p.L344fs|CD22_uc010edx.1_Non-coding_Transcript	NM_001771	NP_001762	P20273	CD22_HUMAN	CD22 molecule	516	Extracellular (Potential).|Ig-like C2-type 5.				cell adhesion		protein binding|sugar binding			ovary(4)	4	all_lung(56;9.78e-09)|Lung NSC(56;1.46e-08)|Esophageal squamous(110;0.162)		Epithelial(14;5.83e-19)|OV - Ovarian serous cystadenocarcinoma(14;3.19e-18)|all cancers(14;3.41e-16)|LUSC - Lung squamous cell carcinoma(66;0.0417)		OspA lipoprotein(DB00045)	Ovarian(42;1009 1133 23674 26041)								0.45			40	48				---	---	---	---	capture_indel			Frame_Shift_Ins	INS	40524124	40524125	3112	19	-	T	T	24	24	CD22	T	5	5
RPL5	6125	broad.mit.edu	36	1	93074485	93074486	+	Frame_Shift_Ins	INS	-	T	T			TCGA-06-0216-01	TCGA-06-0216-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:93074485_93074486insT	uc001doz.1	+	c.475_476insT	c.(475-477)GTTfs	p.V159fs	FAM69A_uc001dpc.2_Intron|RPL5_uc001dpa.1_Non-coding_Transcript|RPL5_uc001dpb.1_Frame_Shift_Ins_p.V109fs|RPL5_uc001dpd.1_5'UTR|SNORD21_uc001dpe.2_5'Flank	NM_000969	NP_000960	P46777	RL5_HUMAN	ribosomal protein L5	159					endocrine pancreas development|ribosomal large subunit biogenesis|rRNA processing|translational elongation|translational termination|viral transcription	cytosolic large ribosomal subunit|nucleolus	5S rRNA binding|protein binding|structural constituent of ribosome				0		all_lung(203;0.00265)|Lung NSC(277;0.0056)|all_neural(321;0.185)|Melanoma(281;0.192)|Glioma(108;0.203)		GBM - Glioblastoma multiforme(16;0.000305)|all cancers(265;0.000343)|Epithelial(280;0.0927)										0.46			74	87				---	---	---	---	capture_indel			Frame_Shift_Ins	INS	93074485	93074486	14076	1	-	T	T	36	36	RPL5	T	5	5
