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
VENTX	27287	broad.mit.edu	36	10	134903289	134903289	+	Missense_Mutation	SNP	C	T	T			TCGA-28-2509-01	TCGA-28-2509-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr10:134903289C>T	uc001lmd.1	+	c.361C>T	c.(361-363)CGG>TGG	p.R121W		NM_014468	NP_055283	O95231	VENTX_HUMAN	VENT homeobox	121	Homeobox.				multicellular organismal development|regulation of transcription, DNA-dependent	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription regulator activity				0		all_cancers(35;4.15e-10)|all_epithelial(44;2.07e-08)|Lung NSC(174;0.000845)|all_lung(145;0.00144)|all_neural(114;0.0299)|Melanoma(40;0.123)|Colorectal(31;0.172)|Glioma(114;0.203)												0.771429	87.635434	90.001268	27	8	CC		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(35;7.8e-06)|Epithelial(32;9.31e-06)|all cancers(32;1.19e-05)	Missense_Mutation	SNP	134903289	134903289	17720	10	C	T	T	27	27	VENTX	T	1	1
USP28	57646	broad.mit.edu	36	11	113177469	113177469	+	Missense_Mutation	SNP	C	T	T			TCGA-28-2509-01	TCGA-28-2509-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr11:113177469C>T	uc001poh.1	-	c.3004G>A	c.(3004-3006)GCC>ACC	p.A1002T	USP28_uc001poi.1_Missense_Mutation_p.A325T|USP28_uc001pog.1_Missense_Mutation_p.A678T	NM_020886	NP_065937	Q96RU2	UBP28_HUMAN	ubiquitin specific protease 28	1002					cell proliferation|DNA damage checkpoint|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|DNA repair|protein deubiquitination|response to ionizing radiation|ubiquitin-dependent protein catabolic process	nucleolus|nucleoplasm	protein binding|ubiquitin thiolesterase activity|ubiquitin-specific protease activity			breast(2)|ovary(1)|large_intestine(1)|kidney(1)	5		all_cancers(61;3.74e-18)|all_epithelial(67;3.75e-11)|Melanoma(852;1.46e-05)|all_hematologic(158;4.65e-05)|Acute lymphoblastic leukemia(157;0.000967)|Breast(348;0.0101)|Prostate(24;0.0153)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)				Melanoma(4;162 555 7664)|GBM(79;500 2010 17506)|Esophageal Squamous(9;463 924 15765)								0.311475	98.81052	102.669045	38	84	CC		KEEP	---	---	---	---	capture		BRCA - Breast invasive adenocarcinoma(274;3.93e-06)|Epithelial(105;0.000122)|all cancers(92;0.00104)	Missense_Mutation	SNP	113177469	113177469	17622	11	C	T	T	25	25	USP28	T	2	2
DDX25	29118	broad.mit.edu	36	11	125293759	125293759	+	Silent	SNP	C	T	T			TCGA-28-2509-01	TCGA-28-2509-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr11:125293759C>T	uc001qcz.2	+	c.1065C>T	c.(1063-1065)ACC>ACT	p.T355T		NM_013264	NP_037396	Q9UHL0	DDX25_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 25	355	Helicase C-terminal.				mRNA export from nucleus|multicellular organismal development|regulation of translation|spermatid development	chromatoid body|nucleus	ATP binding|ATP-dependent RNA helicase activity|RNA binding			ovary(1)	1	all_hematologic(175;0.177)	Breast(109;0.0021)|all_lung(97;0.0203)|Lung NSC(97;0.0203)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)												0.375	62.763585	63.530774	21	35	CC		KEEP	---	---	---	---	capture		BRCA - Breast invasive adenocarcinoma(274;1.14e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.046)	Silent	SNP	125293759	125293759	4523	11	C	T	T	23	23	DDX25	T	1	1
OR4A47	403253	broad.mit.edu	36	11	48467236	48467236	+	Missense_Mutation	SNP	G	A	A			TCGA-28-2509-01	TCGA-28-2509-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr11:48467236G>A	uc001ngw.1	+	c.316G>A	c.(316-318)GGT>AGT	p.G106S		NM_001005512	NP_001005512	Q6IF82	O4A47_HUMAN	olfactory receptor, family 4, subfamily A,	106	Helical; Name=3; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)	1														0.357143	216.034279	219.5406	70	126	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	48467236	48467236	11448	11	G	A	A	39	39	OR4A47	A	1	1
OR5W2	390148	broad.mit.edu	36	11	55438327	55438327	+	Missense_Mutation	SNP	A	G	G			TCGA-28-2509-01	TCGA-28-2509-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr11:55438327A>G	uc001nib.1	-	c.308T>C	c.(307-309)GTC>GCC	p.V103A		NM_001001960	NP_001001960	Q8NH69	OR5W2_HUMAN	olfactory receptor, family 5, subfamily W,	103	Helical; Name=3; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)	1						Melanoma(48;171 1190 15239 43886 49348)								0.403226	161.717833	162.734582	50	74	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	55438327	55438327	11595	11	A	G	G	10	10	OR5W2	G	4	4
GANAB	23193	broad.mit.edu	36	11	62157311	62157311	+	Silent	SNP	C	T	T			TCGA-28-2509-01	TCGA-28-2509-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr11:62157311C>T	uc001nua.1	-	c.705G>A	c.(703-705)GAG>GAA	p.E235E	GANAB_uc001nub.1_Silent_p.E213E|GANAB_uc001nuc.1_Silent_p.E116E	NM_198335	NP_938149	Q14697	GANAB_HUMAN	alpha glucosidase II alpha subunit isoform 3	213					post-translational protein modification|protein folding|protein N-linked glycosylation via asparagine	endoplasmic reticulum lumen|Golgi apparatus|melanosome	carbohydrate binding|glucan 1,3-alpha-glucosidase activity|protein binding			ovary(3)|central_nervous_system(1)	4						Melanoma(23;1005 1074 15747 18937)								0.447489	310.536079	311.059589	98	121	CC		KEEP	---	---	---	---	capture			Silent	SNP	62157311	62157311	6497	11	C	T	T	32	32	GANAB	T	2	2
FXC1	26515	broad.mit.edu	36	11	6460024	6460024	+	Silent	SNP	C	T	T			TCGA-28-2509-01	TCGA-28-2509-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr11:6460024C>T	uc001mdn.2	+	c.309C>T	c.(307-309)AGC>AGT	p.S103S	ARFIP2_uc001mdk.1_5'Flank|ARFIP2_uc001mdl.1_5'Flank|ARFIP2_uc001mdm.1_5'Flank|ARFIP2_uc009yfe.1_5'Flank|FXC1_uc001mdo.2_Non-coding_Transcript	NM_012192	NP_036324	Q9Y5J6	TIM9B_HUMAN	fractured callus expressed transcript 1	103					cell-matrix adhesion|protein import into mitochondrial inner membrane|transmembrane transport	mitochondrial inner membrane|mitochondrial intermembrane space protein transporter complex	metal ion binding				0		Medulloblastoma(188;0.00263)|all_neural(188;0.026)|Breast(177;0.029)												0.266667	7.57839	8.329159	4	11	CC		KEEP	---	---	---	---	capture		Epithelial(150;3.26e-08)|BRCA - Breast invasive adenocarcinoma(625;0.189)	Silent	SNP	6460024	6460024	6364	11	C	T	T	28	28	FXC1	T	2	2
SLC24A6	80024	broad.mit.edu	36	12	112222124	112222124	+	Silent	SNP	G	A	A			TCGA-28-2509-01	TCGA-28-2509-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr12:112222124G>A	uc001tvc.1	-	c.1596C>T	c.(1594-1596)GGC>GGT	p.G532G	SLC24A6_uc001tuz.1_Silent_p.G237G|SLC24A6_uc001tva.1_Non-coding_Transcript|SLC24A6_uc001tvb.1_Silent_p.G270G	NM_024959	NP_079235	Q6J4K2	NCKX6_HUMAN	solute carrier family 24 member 6	532	Helical; Name=12; (Potential).				response to stimulus|sodium ion transport	integral to membrane|plasma membrane	calcium:cation antiporter activity			central_nervous_system(1)	1														0.383333	55.438336	56.142798	23	37	GG		KEEP	---	---	---	---	capture			Silent	SNP	112222124	112222124	14967	12	G	A	A	38	38	SLC24A6	A	1	1
KSR2	283455	broad.mit.edu	36	12	116589737	116589737	+	Missense_Mutation	SNP	G	A	A			TCGA-28-2509-01	TCGA-28-2509-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr12:116589737G>A	uc001two.2	-	c.1009C>T	c.(1009-1011)CGC>TGC	p.R337C		NM_173598	NP_775869	Q6VAB6	KSR2_HUMAN	kinase suppressor of ras 2	366					intracellular signal transduction|protein phosphorylation	cytoplasm|membrane	ATP binding|metal ion binding|protein serine/threonine kinase activity			lung(7)|central_nervous_system(2)|large_intestine(1)	10	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)									623				0.181818	12.230553	15.369448	6	27	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	116589737	116589737	8905	12	G	A	A	39	39	KSR2	A	1	1
GCN1L1	10985	broad.mit.edu	36	12	119112484	119112484	+	Missense_Mutation	SNP	C	T	T			TCGA-28-2509-01	TCGA-28-2509-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr12:119112484C>T	uc001txo.1	-	c.121G>A	c.(121-123)GAT>AAT	p.D41N		NM_006836	NP_006827	Q92616	GCN1L_HUMAN	GCN1 general control of amino-acid synthesis	41					regulation of translation	ribosome	protein binding|translation factor activity, nucleic acid binding			ovary(3)	3	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)													0.489051	225.928115	225.94216	67	70	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	119112484	119112484	6565	12	C	T	T	24	24	GCN1L1	T	2	2
PDZRN4	29951	broad.mit.edu	36	12	40118033	40118033	+	Missense_Mutation	SNP	C	T	T			TCGA-28-2509-01	TCGA-28-2509-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr12:40118033C>T	uc001rmq.2	+	c.20C>T	c.(19-21)ACT>ATT	p.T7I	PDZRN4_uc009zjz.1_5'UTR	NM_013377	NP_037509	Q6ZMN7	PZRN4_HUMAN	PDZ domain containing RING finger 4	Error:Variant_position_missing_in_Q6ZMN7_after_alignment							ubiquitin-protein ligase activity|zinc ion binding			lung(3)|ovary(2)|large_intestine(1)|kidney(1)|pancreas(1)	8	all_cancers(12;0.000673)	Lung NSC(34;0.0205)|all_lung(34;0.0264)								467				0.486631	582.101391	582.160206	182	192	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	40118033	40118033	12131	12	C	T	T	20	20	PDZRN4	T	2	2
PTPRB	5787	broad.mit.edu	36	12	69214901	69214901	+	Silent	SNP	G	A	A			TCGA-28-2509-01	TCGA-28-2509-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr12:69214901G>A	uc001swc.2	-	c.6183C>T	c.(6181-6183)ATC>ATT	p.I2061I	PTPRB_uc001swb.2_Silent_p.I1843I|PTPRB_uc001swa.2_Silent_p.I1973I	NM_001109754	NP_001103224	P23467	PTPRB_HUMAN	protein tyrosine phosphatase, receptor type, B	1843	Cytoplasmic (Potential).|Tyrosine-protein phosphatase.				angiogenesis	integral to plasma membrane	protein binding|transmembrane receptor protein tyrosine phosphatase activity			lung(2)|skin(1)	3	Renal(347;0.236)													0.518072	135.625912	135.649396	43	40	GG		KEEP	---	---	---	---	capture	GBM - Glioblastoma multiforme(2;2.17e-05)|Lung(24;0.000636)|OV - Ovarian serous cystadenocarcinoma(12;0.00306)|STAD - Stomach adenocarcinoma(21;0.149)		Silent	SNP	69214901	69214901	13253	12	G	A	A	41	41	PTPRB	A	2	2
NEK3	4752	broad.mit.edu	36	13	51626303	51626303	+	Missense_Mutation	SNP	A	G	G			TCGA-28-2509-01	TCGA-28-2509-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr13:51626303A>G	uc001vgh.1	-	c.187T>C	c.(187-189)TCT>CCT	p.S63P	NEK3_uc001vgg.1_Intron|NEK3_uc001vgi.1_Missense_Mutation_p.S42P|NEK3_uc001vgj.1_Missense_Mutation_p.S42P	NM_002498	NP_002489	P51956	NEK3_HUMAN	NIMA-related kinase 3	42	Protein kinase.				cell division|mitosis|protein phosphorylation	nucleus	ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity			ovary(1)	1		Breast(56;0.000207)|Lung NSC(96;0.00145)|Prostate(109;0.034)|Hepatocellular(98;0.065)|all_neural(104;0.173)								244				0.84375	97.720232	101.319052	27	5	AA		KEEP	---	---	---	---	capture		GBM - Glioblastoma multiforme(99;2.81e-08)	Missense_Mutation	SNP	51626303	51626303	10724	13	A	G	G	11	11	NEK3	G	4	4
SEMA7A	8482	broad.mit.edu	36	15	72495214	72495214	+	Missense_Mutation	SNP	C	T	T			TCGA-28-2509-01	TCGA-28-2509-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr15:72495214C>T	uc002axv.1	-	c.967G>A	c.(967-969)GGT>AGT	p.G323S		NM_003612	NP_003603	O75326	SEM7A_HUMAN	semaphorin 7A	323	Sema.				axon guidance|immune response|inflammatory response|integrin-mediated signaling pathway|positive regulation of axon extension|positive regulation of ERK1 and ERK2 cascade|positive regulation of macrophage cytokine production|regulation of inflammatory response	anchored to membrane|external side of plasma membrane	receptor activity			breast(1)|central_nervous_system(1)	2														0.448276	84.778572	84.907339	26	32	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	72495214	72495214	14529	15	C	T	T	21	21	SEMA7A	T	2	2
DNAH3	55567	broad.mit.edu	36	16	20988334	20988334	+	Missense_Mutation	SNP	G	A	A			TCGA-28-2509-01	TCGA-28-2509-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr16:20988334G>A	uc002did.1	-	c.3284C>T	c.(3283-3285)CCA>CTA	p.P1095L		NM_017539	NP_060009	Q8TD57	DYH3_HUMAN	dynein, axonemal, heavy chain 3	1095	Stem (By similarity).				ciliary or flagellar motility|microtubule-based movement	axonemal dynein complex|cilium axoneme|cytoplasm|microtubule	ATP binding|ATPase activity|microtubule motor activity			ovary(10)|large_intestine(2)|central_nervous_system(2)	14														0.594262	484.918969	486.816538	145	99	GG		KEEP	---	---	---	---	capture		GBM - Glioblastoma multiforme(48;0.207)	Missense_Mutation	SNP	20988334	20988334	4786	16	G	A	A	47	47	DNAH3	A	2	2
RLTPR	146206	broad.mit.edu	36	16	66240969	66240969	+	Missense_Mutation	SNP	G	A	A			TCGA-28-2509-01	TCGA-28-2509-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr16:66240969G>A	uc002etn.1	+	c.1865G>A	c.(1864-1866)GGG>GAG	p.G622E	RLTPR_uc010cel.1_Missense_Mutation_p.G615E	NM_001013838	NP_001013860	Q6F5E8	LR16C_HUMAN	RGD motif, leucine rich repeats, tropomodulin	622	Tropomodulin-like.|LRR 14.									breast(1)	1		Acute lymphoblastic leukemia(13;3.23e-05)|all_hematologic(13;0.00251)|Ovarian(137;0.192)												0.267857	39.6984	42.424443	15	41	GG		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(108;0.0146)|Epithelial(162;0.0481)|all cancers(182;0.232)	Missense_Mutation	SNP	66240969	66240969	13871	16	G	A	A	43	43	RLTPR	A	2	2
SLC47A2	146802	broad.mit.edu	36	17	19522805	19522805	+	Missense_Mutation	SNP	G	T	T			TCGA-28-2509-01	TCGA-28-2509-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr17:19522805G>T	uc002gwe.2	-	c.1595C>A	c.(1594-1596)ACA>AAA	p.T532K	SLC47A2_uc002gwg.2_Missense_Mutation_p.T496K|SLC47A2_uc002gwf.2_Missense_Mutation_p.T510K|SLC47A2_uc002gwh.2_Non-coding_Transcript|SLC47A2_uc002gwi.1_Non-coding_Transcript	NM_152908	NP_690872	Q86VL8	S47A2_HUMAN	solute carrier family 47, member 2 isoform 1	532	Cytoplasmic (Potential).					integral to membrane|plasma membrane	drug:hydrogen antiporter activity				0	all_cancers(12;2.3e-05)|all_epithelial(12;0.0024)|Breast(13;0.245)													0.333333	7.88634	8.186418	4	8	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	19522805	19522805	15145	17	G	T	T	48	48	SLC47A2	T	3	3
CLDN7	1366	broad.mit.edu	36	17	7104543	7104543	+	Silent	SNP	T	C	C			TCGA-28-2509-01	TCGA-28-2509-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr17:7104543T>C	uc002gfm.2	-	c.510A>G	c.(508-510)GCA>GCG	p.A170A	CLDN7_uc010cmc.1_Missense_Mutation_p.Q142R|CLDN7_uc002gfn.2_Silent_p.A170A	NM_001307	NP_001298	O95471	CLD7_HUMAN	claudin 7	170	Helical; (Potential).				calcium-independent cell-cell adhesion	integral to membrane|lateral plasma membrane|tight junction	identical protein binding|structural molecule activity			ovary(1)	1														0.225806	10.212639	12.361609	7	24	TT		KEEP	---	---	---	---	capture			Silent	SNP	7104543	7104543	3627	17	T	C	C	55	55	CLDN7	C	4	4
TP53	7157	broad.mit.edu	36	17	7518281	7518281	+	Missense_Mutation	SNP	C	T	T			TCGA-28-2509-01	TCGA-28-2509-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr17:7518281C>T	uc002gim.2	-	c.725G>A	c.(724-726)TGC>TAC	p.C242Y	TP53_uc002gig.1_Missense_Mutation_p.C242Y|TP53_uc002gih.1_Missense_Mutation_p.C242Y|TP53_uc010cne.1_5'Flank|TP53_uc010cnf.1_Missense_Mutation_p.C110Y|TP53_uc010cng.1_Missense_Mutation_p.C110Y|TP53_uc002gii.1_Missense_Mutation_p.C110Y|TP53_uc010cnh.1_Missense_Mutation_p.C242Y|TP53_uc010cni.1_Missense_Mutation_p.C242Y|TP53_uc002gij.2_Missense_Mutation_p.C242Y|TP53_uc010cnj.1_Non-coding_Transcript|TP53_uc002gin.2_Missense_Mutation_p.C149Y|TP53_uc002gio.2_Missense_Mutation_p.C110Y	NM_001126112	NP_001119584	P04637	P53_HUMAN	tumor protein p53 isoform a	242	|Interaction with HIPK1 (By similarity).|Interacts with the 53BP2 SH3 domain.|Interaction with AXIN1 (By similarity).	Zinc.	C -> F (in sporadic cancers; somatic mutation).|C -> G (in sporadic cancers; somatic mutation).|C -> S (in sporadic cancers; somatic mutation).|C -> R (in sporadic cancers; somatic mutation).|C -> W (in sporadic cancers; somatic mutation).|C -> Y (in a familial cancer not matching LFS; germline mutation and in sporadic cancers; somatic mutation).		activation of caspase activity by cytochrome c|base-excision repair|blood coagulation|cell cycle arrest|cell differentiation|cell proliferation|cellular protein localization|cellular response to drug|cellular response to glucose starvation|cellular response to hypoxia|cellular response to ionizing radiation|cellular response to UV|determination of adult lifespan|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator|ER overload response|interspecies interaction between organisms|negative regulation of apoptosis|negative regulation of cell growth|negative regulation of cell proliferation|negative regulation of gene-specific transcription from RNA polymerase II promoter|negative regulation of helicase activity|negative regulation of transcription from RNA polymerase II promoter|nucleotide-excision repair|oxidative stress-induced premature senescence|positive regulation of gene-specific transcription from RNA polymerase II promoter|positive regulation of histone deacetylation|positive regulation of neuron apoptosis|positive regulation of peptidyl-tyrosine phosphorylation|positive regulation of reactive oxygen species metabolic process|positive regulation of thymocyte apoptosis|positive regulation of transcription from RNA polymerase II promoter|protein localization|protein tetramerization|Ras protein signal transduction|regulation of mitochondrial membrane permeability|replicative senescence|response to antibiotic|response to gamma radiation|response to X-ray	chromatin|cytoplasm|cytosol|endoplasmic reticulum|insoluble fraction|mitochondrion|nuclear matrix|nucleolus|nucleus|PML body|protein complex|replication fork	ATP binding|chaperone binding|chromatin binding|copper ion binding|damaged DNA binding|DNA strand annealing activity|histone acetyltransferase binding|p53 binding|promoter binding|promoter binding|protease binding|protein heterodimerization activity|protein kinase binding|protein N-terminus binding|protein phosphatase 2A binding|sequence-specific DNA binding transcription factor activity|specific transcriptional repressor activity|transcription activator activity|transcription factor binding|ubiquitin protein ligase binding|zinc ion binding	p.C242F(62)|p.C242Y(37)|p.C242S(15)|p.0?(6)|p.N239_C242delNSSC(3)|p.C238fs*21(1)|p.C242fs*20(1)|p.Y236_M243delYMCNSSCM(1)|p.S241_G245delSCMGG(1)|p.C242fs*98(1)|p.C242_M246>L(1)|p.N239fs*4(1)|p.C238_M246delCNSSCMGGM(1)|p.H233_C242del10(1)|p.N239_C242del(1)		large_intestine(4614)|breast(2344)|upper_aerodigestive_tract(2150)|lung(1958)|ovary(1559)|oesophagus(1462)|haematopoietic_and_lymphoid_tissue(1212)|stomach(1127)|urinary_tract(1113)|central_nervous_system(1072)|liver(805)|skin(693)|pancreas(370)|biliary_tract(247)|soft_tissue(209)|prostate(192)|endometrium(150)|bone(102)|vulva(79)|kidney(79)|cervix(68)|thyroid(54)|salivary_gland(41)|adrenal_gland(37)|peritoneum(33)|eye(24)|thymus(21)|genital_tract(16)|autonomic_ganglia(16)|small_intestine(14)|testis(11)|penis(10)|vagina(6)|meninges(5)|pituitary(4)|pleura(3)|gastrointestinal_tract_(site_indeterminate)(1)|NS(1)|Fallopian tube(1)|placenta(1)	21904		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)				Pancreas(47;798 1329 9957 10801)		111	p.C242F(DAOY-Tumor)|p.C242S(NCIH889-Tumor)|p.C238fs(SW1417-Tumor)|p.C242Y(HCC33-Tumor)|p.C242Y(TE10-Tumor)|p.C242S(NCIH841-Tumor)	690	TCGA GBM(1;<1E-8)|TSP Lung(2;<1E-8)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)			0.802817	181.406165	187.465364	57	14	CC		KEEP	---	---	---	---	capture		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Missense_Mutation	SNP	7518281	7518281	16923	17	C	T	T	25	25	TP53	T	2	2
NTN1	9423	broad.mit.edu	36	17	9083769	9083769	+	Missense_Mutation	SNP	C	G	G			TCGA-28-2509-01	TCGA-28-2509-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr17:9083769C>G	uc002glw.2	+	c.1574C>G	c.(1573-1575)ACG>AGG	p.T525R		NM_004822	NP_004813	O95631	NET1_HUMAN	netrin 1	525	NTR.				apoptosis|axon guidance		protein binding				0														0.166667	6.687558	9.215094	4	20	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	9083769	9083769	11105	17	C	G	G	19	19	NTN1	G	3	3
CNDP1	84735	broad.mit.edu	36	18	70377656	70377656	+	Missense_Mutation	SNP	G	A	A			TCGA-28-2509-01	TCGA-28-2509-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr18:70377656G>A	uc002llq.1	+	c.272G>A	c.(271-273)CGT>CAT	p.R91H		NM_032649	NP_116038	Q96KN2	CNDP1_HUMAN	carnosinase 1	91					proteolysis	extracellular region	carboxypeptidase activity|dipeptidase activity|metal ion binding|metallopeptidase activity|tripeptidase activity				0		Esophageal squamous(42;0.129)|Prostate(75;0.157)|Melanoma(33;0.211)				Melanoma(32;1029 1042 25286 38395 44237)								0.296296	75.711413	79.75252	32	76	GG		KEEP	---	---	---	---	capture		BRCA - Breast invasive adenocarcinoma(31;0.109)	Missense_Mutation	SNP	70377656	70377656	3731	18	G	A	A	40	40	CNDP1	A	1	1
MAST1	22983	broad.mit.edu	36	19	12840571	12840571	+	Missense_Mutation	SNP	G	A	A			TCGA-28-2509-01	TCGA-28-2509-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr19:12840571G>A	uc002mvm.1	+	c.2681G>A	c.(2680-2682)GGG>GAG	p.G894E		NM_014975	NP_055790	Q9Y2H9	MAST1_HUMAN	microtubule associated serine/threonine kinase	894					cytoskeleton organization|intracellular protein kinase cascade|protein phosphorylation	cytoplasm|cytoskeleton|plasma membrane	ATP binding|magnesium ion binding|protein serine/threonine kinase activity			ovary(3)|lung(2)|large_intestine(1)|skin(1)	7										239				0.57619	404.266492	405.323982	121	89	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	12840571	12840571	9708	19	G	A	A	43	43	MAST1	A	2	2
APC2	10297	broad.mit.edu	36	19	1416159	1416159	+	Missense_Mutation	SNP	T	G	G			TCGA-28-2509-01	TCGA-28-2509-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr19:1416159T>G	uc002lsr.1	+	c.1859T>G	c.(1858-1860)GTG>GGG	p.V620G	APC2_uc002lss.1_Missense_Mutation_p.V202G|APC2_uc002lst.1_Missense_Mutation_p.V620G|APC2_uc002lsu.1_Missense_Mutation_p.V619G	NM_005883	NP_005874	O95996	APC2_HUMAN	adenomatosis polyposis coli 2	620	ARM 5.				negative regulation of canonical Wnt receptor signaling pathway|negative regulation of catenin import into nucleus|Wnt receptor signaling pathway	actin filament|catenin complex|cytoplasmic microtubule|Golgi membrane|lamellipodium membrane|perinuclear region of cytoplasm	beta-catenin binding|microtubule binding			breast(3)|pancreas(1)	4		Acute lymphoblastic leukemia(61;3.02e-13)|all_hematologic(61;4.32e-09)|Hepatocellular(1079;0.137)												0.555556	8.473426	8.486766	5	4	TT		KEEP	---	---	---	---	capture		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)	Missense_Mutation	SNP	1416159	1416159	774	19	T	G	G	59	59	APC2	G	4	4
ZNF626	199777	broad.mit.edu	36	19	20599918	20599918	+	Missense_Mutation	SNP	T	A	A			TCGA-28-2509-01	TCGA-28-2509-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr19:20599918T>A	uc002npb.1	-	c.605A>T	c.(604-606)AAA>ATA	p.K202I	ZNF626_uc002npc.1_Missense_Mutation_p.K126I	NM_001076675	NP_001070143	Q68DY1	ZN626_HUMAN	zinc finger protein 626 isoform 1	202	C2H2-type 2.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0														0.456	164.455296	164.666623	57	68	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	20599918	20599918	18645	19	T	A	A	64	64	ZNF626	A	4	4
FKRP	79147	broad.mit.edu	36	19	51950657	51950657	+	Missense_Mutation	SNP	G	A	A			TCGA-28-2509-01	TCGA-28-2509-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr19:51950657G>A	uc002pfn.1	+	c.110G>A	c.(109-111)CGG>CAG	p.R37Q	FKRP_uc002pfo.1_Missense_Mutation_p.R37Q|FKRP_uc002pfp.1_Missense_Mutation_p.R37Q|FKRP_uc010eku.1_Missense_Mutation_p.R37Q	NM_024301	NP_077277	Q9H9S5	FKRP_HUMAN	fukutin-related protein	37						extracellular space|Golgi apparatus|rough endoplasmic reticulum|sarcolemma	transferase activity			pancreas(1)	1		all_epithelial(76;5.08e-05)|Ovarian(192;0.0129)|all_neural(266;0.0459)|Breast(70;0.212)												0.611111	36.129381	36.32448	11	7	GG		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(262;0.000541)|all cancers(93;0.00128)|Epithelial(262;0.0207)|GBM - Glioblastoma multiforme(486;0.0336)	Missense_Mutation	SNP	51950657	51950657	6155	19	G	A	A	39	39	FKRP	A	1	1
TMEM146	257062	broad.mit.edu	36	19	5727309	5727309	+	Silent	SNP	C	T	T			TCGA-28-2509-01	TCGA-28-2509-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr19:5727309C>T	uc002mda.1	+	c.2079C>T	c.(2077-2079)ATC>ATT	p.I693I		NM_152784	NP_689997	Q86XM0	TM146_HUMAN	transmembrane protein 146	693	Extracellular (Potential).					integral to membrane				ovary(1)|central_nervous_system(1)|pancreas(1)	3														0.557377	109.858572	110.034064	34	27	CC		KEEP	---	---	---	---	capture			Silent	SNP	5727309	5727309	16592	19	C	T	T	31	31	TMEM146	T	1	1
LILRB3	11025	broad.mit.edu	36	19	59416296	59416296	+	Missense_Mutation	SNP	G	A	A			TCGA-28-2509-01	TCGA-28-2509-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr19:59416296G>A	uc010erh.1	-	c.1172C>T	c.(1171-1173)GCG>GTG	p.A391V	LILRB3_uc002qee.1_Missense_Mutation_p.A391V|LILRB3_uc002qef.1_Missense_Mutation_p.A391V|LILRB3_uc002qes.1_Missense_Mutation_p.A391V|LILRB3_uc002qeg.1_Non-coding_Transcript|LILRB3_uc002qeh.1_Missense_Mutation_p.A391V|LILRB3_uc002qei.1_Missense_Mutation_p.A391V|LILRB3_uc002qej.1_Non-coding_Transcript|LILRA6_uc002qek.1_Intron|LILRA6_uc002qel.1_Intron|LILRA6_uc002qem.1_Intron|LILRB3_uc002qen.1_Intron|LILRB3_uc002qeo.1_Missense_Mutation_p.A391V|LILRB3_uc002qep.1_Missense_Mutation_p.A391V|LILRB3_uc002qeq.1_Missense_Mutation_p.A391V|LILRB3_uc002qer.1_Non-coding_Transcript	NM_006864	NP_006855	O75022	LIRB3_HUMAN	leukocyte immunoglobulin-like receptor,	391	Extracellular (Potential).|Ig-like C2-type 4.				cell surface receptor linked signaling pathway|defense response	integral to plasma membrane	transmembrane receptor activity			ovary(1)	1	all_cancers(19;0.00723)|all_epithelial(19;0.00389)|all_lung(19;0.0175)|Lung NSC(19;0.0325)|Ovarian(34;0.19)													0.129412	14.675561	26.033213	11	74	GG		KEEP	---	---	---	---	capture		GBM - Glioblastoma multiforme(193;0.105)	Missense_Mutation	SNP	59416296	59416296	9118	19	G	A	A	38	38	LILRB3	A	1	1
MUC16	94025	broad.mit.edu	36	19	8951864	8951864	+	Silent	SNP	G	A	A			TCGA-28-2509-01	TCGA-28-2509-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr19:8951864G>A	uc002mkp.1	-	c.951C>T	c.(949-951)GCC>GCT	p.A317A		NM_024690	NP_078966	Q8WXI7	MUC16_HUMAN	mucin 16	317	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														0.50655	348.695354	348.703887	116	113	GG		KEEP	---	---	---	---	capture			Silent	SNP	8951864	8951864	10367	19	G	A	A	47	47	MUC16	A	2	2
DARC	2532	broad.mit.edu	36	1	157442119	157442119	+	Missense_Mutation	SNP	G	A	A			TCGA-28-2509-01	TCGA-28-2509-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:157442119G>A	uc001ftp.2	+	c.272G>A	c.(271-273)CGC>CAC	p.R91H	DARC_uc001fto.1_Missense_Mutation_p.R89H	NM_001122951	NP_001116423	Q16570	DUFFY_HUMAN	Duffy blood group antigen isoform a	89	Cytoplasmic (Potential).				defense response	integral to membrane|plasma membrane	C-C chemokine binding|chemokine receptor activity			ovary(1)|lung(1)	2	all_hematologic(112;0.0429)													0.538043	624.175292	624.63954	198	170	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	157442119	157442119	4407	1	G	A	A	38	38	DARC	A	1	1
OBSCN	84033	broad.mit.edu	36	1	226595939	226595939	+	Splice_Site_SNP	SNP	G	A	A			TCGA-28-2509-01	TCGA-28-2509-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:226595939G>A	uc009xez.1	+	c.18034_splice	c.e74+1	p.R6012_splice	OBSCN_uc001hsn.1_Splice_Site_SNP_p.R6012_splice|OBSCN_uc001hsr.1_Splice_Site_SNP_p.R641_splice	NM_001098623	NP_001092093			obscurin, cytoskeletal calmodulin and						apoptosis|cell differentiation|induction of apoptosis by extracellular signals|multicellular organismal development|nerve growth factor receptor signaling pathway|protein phosphorylation|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol|M band|Z disc	ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity|protein tyrosine kinase activity|Rho guanyl-nucleotide exchange factor activity|structural constituent of muscle|titin binding			large_intestine(7)|breast(5)|ovary(4)|skin(2)|stomach(1)|central_nervous_system(1)|pancreas(1)	21		Prostate(94;0.0405)								4006				0.342857	32.089881	32.85317	12	23	GG		KEEP	---	---	---	---	capture			Splice_Site_SNP	SNP	226595939	226595939	11217	1	G	A	A	40	40	OBSCN	A	5	1
SH3BP5L	80851	broad.mit.edu	36	1	247073921	247073921	+	Missense_Mutation	SNP	A	C	C			TCGA-28-2509-01	TCGA-28-2509-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr1:247073921A>C	uc001iew.1	-	c.601T>G	c.(601-603)TGC>GGC	p.C201G	SH3BP5L_uc001iev.1_Missense_Mutation_p.C82G	NM_030645	NP_085148	Q7L8J4	3BP5L_HUMAN	SH3-binding domain protein 5-like	201	Potential.										0	all_cancers(71;3.33e-06)|all_epithelial(71;2.41e-06)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.0458)|Lung NSC(105;0.0494)|Melanoma(84;0.199)	all_cancers(173;0.19)												0.257143	7.220054	9.322812	9	26	AA		KEEP	---	---	---	---	capture	OV - Ovarian serous cystadenocarcinoma(106;0.00805)		Missense_Mutation	SNP	247073921	247073921	14739	1	A	C	C	6	6	SH3BP5L	C	4	4
ERG	2078	broad.mit.edu	36	21	38686182	38686182	+	Missense_Mutation	SNP	G	A	A			TCGA-28-2509-01	TCGA-28-2509-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr21:38686182G>A	uc010gnw.1	-	c.821C>T	c.(820-822)ACG>ATG	p.T274M	ERG_uc002ywz.1_Missense_Mutation_p.T274M|ERG_uc010gnv.1_Missense_Mutation_p.T151M|ERG_uc010gnx.1_Missense_Mutation_p.T250M|ERG_uc002yxb.1_Missense_Mutation_p.T250M|ERG_uc002yxa.1_Missense_Mutation_p.T267M|ERG_uc010gny.1_Non-coding_Transcript	NM_182918	NP_891548	P11308	ERG_HUMAN	ets-related isoform 1	274					cell proliferation|multicellular organismal development|protein phosphorylation|regulation of transcription, DNA-dependent	cytoplasm|nucleus|ribonucleoprotein complex	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|signal transducer activity		TMPRSS2/ERG(2058)|FUS/ERG(163)|EWSR1/ERG(162)	prostate(2058)|bone(167)|haematopoietic_and_lymphoid_tissue(153)|soft_tissue(5)|lung(2)|ovary(1)	2386		Prostate(19;3.6e-06)				Esophageal Squamous(130;336 1700 3010 3083 40589)				177				0.611111	34.528414	34.723242	11	7	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	38686182	38686182	5415	21	G	A	A	40	40	ERG	A	1	1
GALNT3	2591	broad.mit.edu	36	2	166319476	166319476	+	Silent	SNP	G	A	A			TCGA-28-2509-01	TCGA-28-2509-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr2:166319476G>A	uc010fph.1	-	c.1533C>T	c.(1531-1533)AGC>AGT	p.S511S		NM_004482	NP_004473	Q14435	GALT3_HUMAN	polypeptide N-acetylgalactosaminyltransferase 3	511	Ricin B-type lectin.|Lumenal (Potential).				protein O-linked glycosylation via serine|protein O-linked glycosylation via threonine	Golgi cisterna membrane|integral to membrane|membrane fraction|nucleus|perinuclear region of cytoplasm	calcium ion binding|manganese ion binding|polypeptide N-acetylgalactosaminyltransferase activity|sugar binding			central_nervous_system(2)|ovary(1)	3														0.413043	52.912202	53.216923	19	27	GG		KEEP	---	---	---	---	capture			Silent	SNP	166319476	166319476	6478	2	G	A	A	38	38	GALNT3	A	1	1
ABCG5	64240	broad.mit.edu	36	2	43912443	43912443	+	Missense_Mutation	SNP	C	T	T			TCGA-28-2509-01	TCGA-28-2509-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr2:43912443C>T	uc002rtn.1	-	c.470G>A	c.(469-471)CGC>CAC	p.R157H	ABCG5_uc002rto.1_Missense_Mutation_p.R76H|ABCG5_uc002rtp.1_5'UTR	NM_022436	NP_071881	Q9H222	ABCG5_HUMAN	ATP-binding cassette sub-family G member 5	157	ABC transporter.|Cytoplasmic (Potential).				cholesterol efflux|cholesterol homeostasis|excretion|intestinal cholesterol absorption|lipid metabolic process|negative regulation of intestinal cholesterol absorption|negative regulation of intestinal phytosterol absorption	apical plasma membrane|integral to membrane	ATP binding|ATPase activity|protein heterodimerization activity			ovary(1)	1		all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.175)												0.333333	8.221989	8.4434	3	6	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	43912443	43912443	72	2	C	T	T	27	27	ABCG5	T	1	1
TRAT1	50852	broad.mit.edu	36	3	110055292	110055292	+	Missense_Mutation	SNP	G	A	A			TCGA-28-2509-01	TCGA-28-2509-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr3:110055292G>A	uc003dxi.1	+	c.439G>A	c.(439-441)GTT>ATT	p.V147I	TRAT1_uc010hpx.1_Missense_Mutation_p.V110I	NM_016388	NP_057472	Q6PIZ9	TRAT1_HUMAN	T-cell receptor interacting molecule	147	Cytoplasmic (Potential).				cellular defense response|negative regulation of receptor recycling|negative regulation of transport|positive regulation of calcium-mediated signaling|positive regulation of T cell receptor signaling pathway|T cell receptor signaling pathway	integral to plasma membrane|T cell receptor complex	phosphatidylinositol-4,5-bisphosphate 3-kinase activity|transmembrane receptor protein tyrosine kinase adaptor activity				0														0.338129	132.789881	136.006907	47	92	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	110055292	110055292	17010	3	G	A	A	40	40	TRAT1	A	1	1
BOC	91653	broad.mit.edu	36	3	114452364	114452364	+	Silent	SNP	C	T	T			TCGA-28-2509-01	TCGA-28-2509-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr3:114452364C>T	uc003dzz.1	+	c.370C>T	c.(370-372)CTA>TTA	p.L124L	BOC_uc003dzw.1_Silent_p.L124L|BOC_uc003dzx.1_Silent_p.L124L|BOC_uc010hqi.1_Silent_p.L124L|BOC_uc003dzy.1_Silent_p.L124L|BOC_uc003eaa.1_Silent_p.L124L	NM_033254	NP_150279	Q9BWV1	BOC_HUMAN	brother of CDO	124	Extracellular (Potential).				cell adhesion|muscle cell differentiation|positive regulation of myoblast differentiation	integral to membrane|plasma membrane	protein binding			ovary(3)|breast(1)|central_nervous_system(1)|pancreas(1)	6														0.173913	6.703509	9.000025	4	19	CC		KEEP	---	---	---	---	capture	Epithelial(53;0.227)		Silent	SNP	114452364	114452364	1506	3	C	T	T	20	20	BOC	T	2	2
PARP9	83666	broad.mit.edu	36	3	123757603	123757603	+	Missense_Mutation	SNP	G	C	C			TCGA-28-2509-01	TCGA-28-2509-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr3:123757603G>C	uc010hri.1	-	c.210C>G	c.(208-210)GAC>GAG	p.D70E	PARP9_uc003eff.2_Missense_Mutation_p.D35E|PARP9_uc003efg.1_Intron|PARP9_uc003efh.1_Missense_Mutation_p.D70E|PARP9_uc003efi.1_Missense_Mutation_p.D35E|PARP9_uc003efj.1_Missense_Mutation_p.D35E	NM_031458	NP_113646	Q8IXQ6	PARP9_HUMAN	poly (ADP-ribose) polymerase family, member 9	70					cell migration	cytosol|nucleus	NAD+ ADP-ribosyltransferase activity|protein binding			ovary(1)|pancreas(1)	2										175				0.557971	283.690967	284.094533	77	61	GG		KEEP	---	---	---	---	capture		GBM - Glioblastoma multiforme(114;0.0519)	Missense_Mutation	SNP	123757603	123757603	11883	3	G	C	C	36	36	PARP9	C	3	3
SULT1B1	27284	broad.mit.edu	36	4	70627472	70627472	+	Missense_Mutation	SNP	C	T	T			TCGA-28-2509-01	TCGA-28-2509-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr4:70627472C>T	uc003hen.1	-	c.814G>A	c.(814-816)GCC>ACC	p.A272T		NM_014465	NP_055280	O43704	ST1B1_HUMAN	sulfotransferase family, cytosolic, 1B, member	272					3'-phosphoadenosine 5'-phosphosulfate metabolic process|cellular biogenic amine metabolic process|flavonoid metabolic process|steroid metabolic process|sulfation|thyroid hormone metabolic process|xenobiotic metabolic process	cytosol					0														0.205357	49.667106	58.682929	23	89	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	70627472	70627472	15896	4	C	T	T	26	26	SULT1B1	T	2	2
FRAS1	80144	broad.mit.edu	36	4	79666750	79666750	+	Missense_Mutation	SNP	C	G	G			TCGA-28-2509-01	TCGA-28-2509-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr4:79666750C>G	uc003hkx.2	+	c.10837C>G	c.(10837-10839)CTG>GTG	p.L3613V	FRAS1_uc003hlb.1_Missense_Mutation_p.L1835V	NM_025074	NP_079350	Q86XX4	FRAS1_HUMAN	Fraser syndrome 1	3609	Extracellular (Potential).				cell communication	integral to membrane|plasma membrane	metal ion binding			large_intestine(5)	5														0.730769	61.93488	63.183514	19	7	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	79666750	79666750	6288	4	C	G	G	24	24	FRAS1	G	3	3
PCDHB7	56129	broad.mit.edu	36	5	140533714	140533714	+	Missense_Mutation	SNP	G	C	C			TCGA-28-2509-01	TCGA-28-2509-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr5:140533714G>C	uc003lit.1	+	c.1114G>C	c.(1114-1116)GAC>CAC	p.D372H		NM_018940	NP_061763	Q9Y5E2	PCDB7_HUMAN	protocadherin beta 7 precursor	372	Extracellular (Potential).|Cadherin 4.				calcium-dependent cell-cell adhesion|homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(3)|central_nervous_system(1)	4														0.47561	129.718363	129.760878	39	43	GG		KEEP	---	---	---	---	capture	KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)		Missense_Mutation	SNP	140533714	140533714	11967	5	G	C	C	33	33	PCDHB7	C	3	3
GM2A	2760	broad.mit.edu	36	5	150619604	150619604	+	Silent	SNP	C	T	T			TCGA-28-2509-01	TCGA-28-2509-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr5:150619604C>T	uc003ltr.2	+	c.177C>T	c.(175-177)ATC>ATT	p.I59I	GM2A_uc003ltt.1_5'UTR	NM_000405	NP_000396	P17900	SAP3_HUMAN	GM2 ganglioside activator precursor	59						lysosome|nucleolus	sphingolipid activator protein activity				0		Medulloblastoma(196;0.091)|all_hematologic(541;0.207)												0.41791	81.887036	82.281295	28	39	CC		KEEP	---	---	---	---	capture	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)		Silent	SNP	150619604	150619604	6753	5	C	T	T	31	31	GM2A	T	1	1
FAT2	2196	broad.mit.edu	36	5	150902723	150902723	+	Missense_Mutation	SNP	C	G	G			TCGA-28-2509-01	TCGA-28-2509-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr5:150902723C>G	uc003lue.2	-	c.8158G>C	c.(8158-8160)GAT>CAT	p.D2720H		NM_001447	NP_001438	Q9NYQ8	FAT2_HUMAN	FAT tumor suppressor 2 precursor	2720	Cadherin 24.|Extracellular (Potential).				epithelial cell migration|homophilic cell adhesion	cell-cell adherens junction|integral to membrane|nucleus	calcium ion binding			ovary(4)	4		Medulloblastoma(196;0.0912)|all_hematologic(541;0.104)												0.314516	122.090289	125.880798	39	85	CC		KEEP	---	---	---	---	capture	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)		Missense_Mutation	SNP	150902723	150902723	5926	5	C	G	G	32	32	FAT2	G	3	3
SLIT3	6586	broad.mit.edu	36	5	168166152	168166152	+	Missense_Mutation	SNP	G	T	T			TCGA-28-2509-01	TCGA-28-2509-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr5:168166152G>T	uc010jjg.1	-	c.812C>A	c.(811-813)CCA>CAA	p.P271Q	SLIT3_uc003mab.1_Missense_Mutation_p.P271Q|SLIT3_uc003mac.1_Missense_Mutation_p.P68Q|SLIT3_uc010jji.1_Missense_Mutation_p.P271Q	NM_003062	NP_003053	O75094	SLIT3_HUMAN	slit homolog 3	271	LRRNT 2.				apoptosis involved in luteolysis|axon extension involved in axon guidance|cellular response to hormone stimulus|negative chemotaxis|negative regulation of cell growth|negative regulation of chemokine-mediated signaling pathway|response to cortisol stimulus|Roundabout signaling pathway	extracellular space|mitochondrion	calcium ion binding|Roundabout binding			ovary(3)	3	Renal(175;0.000159)|Lung NSC(126;0.0174)|all_lung(126;0.0392)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)				Ovarian(29;311 847 10864 17279 24903)								0.478632	165.100273	165.145812	56	61	GG		KEEP	---	---	---	---	capture	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)		Missense_Mutation	SNP	168166152	168166152	15239	5	G	T	T	47	47	SLIT3	T	3	3
FOXI1	2299	broad.mit.edu	36	5	169467693	169467693	+	Missense_Mutation	SNP	C	T	T			TCGA-28-2509-01	TCGA-28-2509-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr5:169467693C>T	uc003mai.2	+	c.637C>T	c.(637-639)CGC>TGC	p.R213C	FOXI1_uc003maj.2_Intron	NM_012188	NP_036320	Q12951	FOXI1_HUMAN	forkhead box I1 isoform a	213	Fork-head.				epidermal cell fate specification|negative regulation of gene-specific transcription from RNA polymerase II promoter|otic placode formation|pattern specification process|positive regulation of gene-specific transcription from RNA polymerase II promoter|regulation of sequence-specific DNA binding transcription factor activity	transcription factor complex	DNA bending activity|double-stranded DNA binding|promoter binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|specific RNA polymerase II transcription factor activity|specific transcriptional repressor activity|transcription activator activity|transcription factor binding			breast(3)|central_nervous_system(1)	4	Renal(175;0.000159)|Lung NSC(126;0.0267)|all_lung(126;0.04)	Medulloblastoma(196;0.0109)|all_neural(177;0.0298)												0.333333	155.025302	158.935151	53	106	CC		KEEP	---	---	---	---	capture	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)		Missense_Mutation	SNP	169467693	169467693	6254	5	C	T	T	23	23	FOXI1	T	1	1
RELN	5649	broad.mit.edu	36	7	102913960	102913960	+	Silent	SNP	G	A	A	rs73714404	unknown	TCGA-28-2509-01	TCGA-28-2509-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr7:102913960G>A	uc003vca.1	-	c.9903C>T	c.(9901-9903)TAC>TAT	p.Y3301Y	RELN_uc010liz.1_Silent_p.Y3301Y	NM_005045	NP_005036	P78509	RELN_HUMAN	reelin isoform a	3301					axon guidance|cell adhesion|cerebral cortex tangential migration|glial cell differentiation|neuron migration|peptidyl-tyrosine phosphorylation|positive regulation of protein kinase activity|positive regulation of small GTPase mediated signal transduction|response to pain|spinal cord patterning	cytoplasm|dendrite|extracellular space|proteinaceous extracellular matrix	metal ion binding|protein serine/threonine/tyrosine kinase activity|serine-type peptidase activity			ovary(8)|large_intestine(2)|central_nervous_system(2)|pancreas(1)|skin(1)	14						NSCLC(146;835 1944 15585 22231 52158)								0.35	192.395347	196.362639	70	130	GG		KEEP	---	---	---	---	capture		COAD - Colon adenocarcinoma(1;8.98e-05)|Colorectal(1;0.00184)	Silent	SNP	102913960	102913960	13689	7	G	A	A	40	40	RELN	A	1	1
GCC1	79571	broad.mit.edu	36	7	127010222	127010222	+	Silent	SNP	A	G	G			TCGA-28-2509-01	TCGA-28-2509-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr7:127010222A>G	uc003vma.1	-	c.1410T>C	c.(1408-1410)GCT>GCC	p.A470A		NM_024523	NP_078799	Q96CN9	GCC1_HUMAN	Golgi coiled-coil protein 1	470	Potential.					Golgi membrane|plasma membrane	protein binding			ovary(2)	2														0.315136	362.334287	374.613388	127	276	AA		KEEP	---	---	---	---	capture			Silent	SNP	127010222	127010222	6551	7	A	G	G	7	7	GCC1	G	4	4
MICALL2	79778	broad.mit.edu	36	7	1451075	1451075	+	Missense_Mutation	SNP	G	C	C			TCGA-28-2509-01	TCGA-28-2509-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr7:1451075G>C	uc003skj.2	-	c.1157C>G	c.(1156-1158)GCT>GGT	p.A386G	MICALL2_uc003ski.2_5'Flank	NM_182924	NP_891554	Q8IY33	MILK2_HUMAN	MICAL-like 2 isoform 1	386						cytoplasm|cytoskeleton	zinc ion binding			central_nervous_system(1)	1		Ovarian(82;0.0253)												0.375	7.041719	7.143995	3	5	GG		KEEP	---	---	---	---	capture		UCEC - Uterine corpus endometrioid carcinoma (27;0.0178)|OV - Ovarian serous cystadenocarcinoma(56;6.01e-15)	Missense_Mutation	SNP	1451075	1451075	9964	7	G	C	C	34	34	MICALL2	C	3	3
SSPO	23145	broad.mit.edu	36	7	149110321	149110321	+	Splice_Site_SNP	SNP	G	T	T			TCGA-28-2509-01	TCGA-28-2509-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr7:149110321G>T	uc010lpk.1	+	c.1900_splice	c.e14+1	p.G634_splice	SSPO_uc010lpl.1_Splice_Site_SNP_p.Q27_splice	NM_198455	NP_940857			SCO-spondin						cell adhesion	extracellular space	peptidase inhibitor activity				0	Melanoma(164;0.165)|Ovarian(565;0.177)													0.225806	8.313914	10.58225	7	24	GG		KEEP	---	---	---	---	capture	OV - Ovarian serous cystadenocarcinoma(82;0.00625)		Splice_Site_SNP	SNP	149110321	149110321	15705	7	G	T	T	44	44	SSPO	T	5	3
ABCB8	11194	broad.mit.edu	36	7	150368643	150368643	+	Missense_Mutation	SNP	C	G	G			TCGA-28-2509-01	TCGA-28-2509-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr7:150368643C>G	uc003wil.2	+	c.1428C>G	c.(1426-1428)AAC>AAG	p.N476K	ABCB8_uc010lpw.1_Missense_Mutation_p.N348K|ABCB8_uc010lpx.1_Missense_Mutation_p.N459K|ABCB8_uc003wim.2_Missense_Mutation_p.N254K|ABCB8_uc003wik.2_Missense_Mutation_p.N459K	NM_007188	NP_009119	Q9NUT2	ABCB8_HUMAN	ATP-binding cassette, sub-family B, member 8	476	ABC transporter.					ATP-binding cassette (ABC) transporter complex|integral to membrane|membrane fraction|mitochondrial inner membrane	ATP binding|ATPase activity, coupled to transmembrane movement of substances			breast(2)	2														0.166144	117.791165	151.50376	53	266	CC		KEEP	---	---	---	---	capture	OV - Ovarian serous cystadenocarcinoma(82;0.0121)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)	Missense_Mutation	SNP	150368643	150368643	48	7	C	G	G	19	19	ABCB8	G	3	3
TSNARE1	203062	broad.mit.edu	36	8	143423547	143423547	+	Silent	SNP	G	A	A			TCGA-28-2509-01	TCGA-28-2509-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr8:143423547G>A	uc003ywj.1	-	c.432C>T	c.(430-432)CAC>CAT	p.H144H	TSNARE1_uc003ywk.1_Silent_p.H144H|TSNARE1_uc003ywl.2_Intron	NM_145003	NP_659440	Q96NA8	TSNA1_HUMAN	t-SNARE domain containing 1	144					vesicle-mediated transport	integral to membrane					0	all_cancers(97;7.39e-11)|all_epithelial(106;8.98e-09)|Lung NSC(106;0.000167)|all_lung(105;0.000332)|Ovarian(258;0.0315)|Acute lymphoblastic leukemia(118;0.155)													0.46	67.020162	67.089657	23	27	GG		KEEP	---	---	---	---	capture			Silent	SNP	143423547	143423547	17181	8	G	A	A	44	44	TSNARE1	A	2	2
SGK223	157285	broad.mit.edu	36	8	8272883	8272883	+	Missense_Mutation	SNP	G	T	T			TCGA-28-2509-01	TCGA-28-2509-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr8:8272883G>T	uc003wsh.2	-	c.446C>A	c.(445-447)CCT>CAT	p.P149H		NM_001080826	NP_001074295	Q86YV5	SG223_HUMAN	pragmin	149					protein phosphorylation		ATP binding|non-membrane spanning protein tyrosine kinase activity				0						GBM(34;731 755 10259 33573 33867)				135				0.179641	59.043055	75.171802	30	137	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	8272883	8272883	14701	8	G	T	T	35	35	SGK223	T	3	3
C9orf140	89958	broad.mit.edu	36	9	139079024	139079024	+	Missense_Mutation	SNP	C	T	T			TCGA-28-2509-01	TCGA-28-2509-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr9:139079024C>T	uc004cky.2	-	c.1078G>A	c.(1078-1080)GAG>AAG	p.E360K		NM_178448	NP_848543	Q86UD0	CI140_HUMAN	tumor specificity and mitosis phase-dependent	365	Potential.					cytoplasm|nucleus					0	all_cancers(76;0.0926)	Myeloproliferative disorder(178;0.0821)										OREG0019628	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	0.333333	16.812933	17.332092	7	14	CC		KEEP	---	---	---	---	capture	STAD - Stomach adenocarcinoma(284;0.123)	OV - Ovarian serous cystadenocarcinoma(145;3.02e-05)|Epithelial(140;0.000499)	Missense_Mutation	SNP	139079024	139079024	2573	9	C	T	T	30	30	C9orf140	T	2	2
ZNF658	26149	broad.mit.edu	36	9	40762759	40762759	+	Missense_Mutation	SNP	G	A	A			TCGA-28-2509-01	TCGA-28-2509-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr9:40762759G>A	uc004abs.2	-	c.2516C>T	c.(2515-2517)ACA>ATA	p.T839I	ZNF658_uc010mmm.1_Intron|ZNF658_uc010mmn.1_Missense_Mutation_p.T839I	NM_033160	NP_149350	Q5TYW1	ZN658_HUMAN	zinc finger protein 658	839	C2H2-type 17.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1														0.429936	385.655287	387.003297	135	179	GG		KEEP	---	---	---	---	capture		GBM - Glioblastoma multiforme(29;0.02)|Lung(182;0.0681)	Missense_Mutation	SNP	40762759	40762759	18664	9	G	A	A	48	48	ZNF658	A	2	2
MORF4L2	9643	broad.mit.edu	36	X	102818427	102818427	+	Missense_Mutation	SNP	C	T	T			TCGA-28-2509-01	TCGA-28-2509-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chrX:102818427C>T	uc004ekw.1	-	c.185G>A	c.(184-186)CGC>CAC	p.R62H	MORF4L2_uc004ekx.1_Missense_Mutation_p.R62H|MORF4L2_uc004eky.1_Missense_Mutation_p.R62H|MORF4L2_uc004ekz.1_Missense_Mutation_p.R62H|MORF4L2_uc004ela.1_Missense_Mutation_p.R62H|MORF4L2_uc004elb.1_Missense_Mutation_p.R62H|MORF4L2_uc004elf.1_Missense_Mutation_p.R62H|MORF4L2_uc004elc.1_Missense_Mutation_p.R62H|MORF4L2_uc004eld.1_Missense_Mutation_p.R62H|MORF4L2_uc004ele.1_Missense_Mutation_p.R62H|MORF4L2_uc010nos.1_Missense_Mutation_p.R62H	NM_012286	NP_036418	Q15014	MO4L2_HUMAN	mortality factor 4 like 2	62					chromatin modification|DNA repair|regulation of cell growth|transcription, DNA-dependent	nucleolus	protein binding				0														0.34	184.540183	189.065333	68	132	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	102818427	102818427	10098	23	C	T	T	27	27	MORF4L2	T	1	1
MID2	11043	broad.mit.edu	36	X	106970785	106970785	+	Silent	SNP	C	T	T			TCGA-28-2509-01	TCGA-28-2509-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chrX:106970785C>T	uc004enl.1	+	c.174C>T	c.(172-174)ACC>ACT	p.T58T	MID2_uc004enk.1_Silent_p.T58T	NM_012216	NP_036348	Q9UJV3	TRIM1_HUMAN	midline 2 isoform 1	78	RING-type.					centrosome|microtubule	ligase activity|zinc ion binding			ovary(1)	1														0.597222	733.844596	736.809867	215	145	CC		KEEP	---	---	---	---	capture			Silent	SNP	106970785	106970785	9968	23	C	T	T	24	24	MID2	T	2	2
HCCS	3052	broad.mit.edu	36	X	11049838	11049838	+	Missense_Mutation	SNP	G	A	A			TCGA-28-2509-01	TCGA-28-2509-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chrX:11049838G>A	uc004cuk.2	+	c.794G>A	c.(793-795)CGT>CAT	p.R265H	HCCS_uc004cuj.2_Missense_Mutation_p.R265H|HCCS_uc004cul.1_Missense_Mutation_p.R265H	NM_005333	NP_005324	P53701	CCHL_HUMAN	holocytochrome c synthase (cytochrome c	265					organ morphogenesis|oxidation-reduction process	mitochondrial inner membrane	holocytochrome-c synthase activity|metal ion binding				0						Ovarian(86;1338 1347 1462 10340 37882)								0.336066	113.135056	116.036813	41	81	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	11049838	11049838	7272	23	G	A	A	40	40	HCCS	A	1	1
IGSF1	3547	broad.mit.edu	36	X	130244315	130244315	+	Nonsense_Mutation	SNP	G	A	A			TCGA-28-2509-01	TCGA-28-2509-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chrX:130244315G>A	uc004ewd.1	-	c.1030C>T	c.(1030-1032)CGA>TGA	p.R344*	IGSF1_uc004ewf.1_Nonsense_Mutation_p.R324*|IGSF1_uc010nri.1_Nonsense_Mutation_p.R333*|IGSF1_uc004ewe.2_Nonsense_Mutation_p.R333*	NM_001555	NP_001546	Q8N6C5	IGSF1_HUMAN	immunoglobulin superfamily, member 1 isoform 1	344	Ig-like C2-type 4.|Extracellular (Potential).				regulation of transcription, DNA-dependent	extracellular region|integral to membrane	inhibin beta-A binding|inhibin beta-B binding			ovary(3)|lung(1)|central_nervous_system(1)	5														0.291845	183.116686	192.15245	68	165	GG		KEEP	---	---	---	---	capture			Nonsense_Mutation	SNP	130244315	130244315	7897	23	G	A	A	37	37	IGSF1	A	5	1
DDX26B	203522	broad.mit.edu	36	X	134482837	134482837	+	Silent	SNP	C	T	T			TCGA-28-2509-01	TCGA-28-2509-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chrX:134482837C>T	uc004eyw.2	+	c.117C>T	c.(115-117)CGC>CGT	p.R39R		NM_182540	NP_872346	Q5JSJ4	DX26B_HUMAN	DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide	39	VWFA.										0	Acute lymphoblastic leukemia(192;6.56e-05)													0.269231	16.914086	18.163359	7	19	CC		KEEP	---	---	---	---	capture			Silent	SNP	134482837	134482837	4524	23	C	T	T	27	27	DDX26B	T	1	1
MAGEB6	158809	broad.mit.edu	36	X	26122553	26122553	+	Silent	SNP	G	A	A			TCGA-28-2509-01	TCGA-28-2509-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chrX:26122553G>A	uc004dbr.1	+	c.669G>A	c.(667-669)AAG>AAA	p.K223K	MAGEB6_uc010ngc.1_Silent_p.K3K|MAGEB6_uc010ngd.1_Silent_p.K223K	NM_173523	NP_775794	Q8N7X4	MAGB6_HUMAN	melanoma antigen family B, 6	223	MAGE.									ovary(3)	3														0.588957	315.834259	316.964467	96	67	GG		KEEP	---	---	---	---	capture			Silent	SNP	26122553	26122553	9560	23	G	A	A	36	36	MAGEB6	A	2	2
ZNF157	7712	broad.mit.edu	36	X	47157234	47157234	+	Missense_Mutation	SNP	C	T	T			TCGA-28-2509-01	TCGA-28-2509-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chrX:47157234C>T	uc004dhr.1	+	c.818C>T	c.(817-819)CCC>CTC	p.P273L		NM_003446	NP_003437	P51786	ZN157_HUMAN	zinc finger protein 157	273					negative regulation of transcription from RNA polymerase II promoter	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding				0														0.333333	93.265501	95.628415	32	64	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	47157234	47157234	18328	23	C	T	T	22	22	ZNF157	T	2	2
MICALCL	84953	broad.mit.edu	36	11	12272960	12272965	+	In_Frame_Del	DEL	CTCCTA	-	-			TCGA-28-2509-01	TCGA-28-2509-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:12272960_12272965delCTCCTA	uc001mkg.1	+	c.1406_1411delCTCCTA	c.(1405-1413)CCTCCTACA>CCA	p.PT470del		NM_032867	NP_116256	Q6ZW33	MICLK_HUMAN	MICAL C-terminal like	470_471					cell differentiation|multicellular organismal development|spermatogenesis	cytoplasm	mitogen-activated protein kinase binding				0				Epithelial(150;0.00177)										0.31			4	9				---	---	---	---	capture_indel			In_Frame_Del	DEL	12272960	12272965	9962	11	CTCCTA	-	-	24	24	MICALCL	-	5	5
LRRK2	120892	broad.mit.edu	36	12	38905260	38905263	+	Frame_Shift_Del	DEL	AGTC	-	-			TCGA-28-2509-01	TCGA-28-2509-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:38905260_38905263delAGTC	uc001rmg.2	+	c.60_63delAGTC	c.(58-63)ATAGTCfs	p.I20fs		NM_198578	NP_940980	Q5S007	LRRK2_HUMAN	leucine-rich repeat kinase 2	20_21					activation of MAPKK activity|determination of adult lifespan|intracellular distribution of mitochondria|negative regulation of branching morphogenesis of a nerve|negative regulation of dendritic spine morphogenesis|negative regulation of neuroblast proliferation|negative regulation of neuron maturation|neuromuscular junction development|neuron death|peptidyl-serine phosphorylation|positive regulation of autophagy|positive regulation of programmed cell death|positive regulation of proteasomal ubiquitin-dependent protein catabolic process|positive regulation of protein ubiquitination|protein autophosphorylation|regulation of kidney size|regulation of locomotion|regulation of membrane potential|response to oxidative stress|small GTPase mediated signal transduction|tangential migration from the subventricular zone to the olfactory bulb	external side of mitochondrial outer membrane	ATP binding|GTP binding|GTP-dependent protein kinase activity|GTPase activator activity|MAP kinase kinase activity|protein homodimerization activity|tubulin binding			ovary(11)|lung(2)|upper_aerodigestive_tract(1)|large_intestine(1)|stomach(1)|urinary_tract(1)|pancreas(1)	18	all_cancers(12;0.00108)|Breast(8;0.218)	Lung NSC(34;0.0942)|all_lung(34;0.11)								1771				0.41			25	36				---	---	---	---	capture_indel			Frame_Shift_Del	DEL	38905260	38905263	9409	12	AGTC	-	-	15	15	LRRK2	-	5	5
SRCAP	10847	broad.mit.edu	36	16	30656843	30656843	+	Frame_Shift_Del	DEL	G	-	-			TCGA-28-2509-01	TCGA-28-2509-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:30656843_30656843delG	uc002dze.1	+	c.7981_7981delG	c.(7981-7983)GATfs	p.D2661fs	SRCAP_uc002dzf.2_Non-coding_Transcript|SRCAP_uc002dzg.1_Frame_Shift_Del_p.D2456fs	NM_006662	NP_006653	Q6ZRS2	SRCAP_HUMAN	Snf2-related CBP activator protein	2661	Pro-rich.				interspecies interaction between organisms|regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	Golgi apparatus|nucleus|protein complex	ATP binding|DNA binding|helicase activity|histone acetyltransferase activity|transcription coactivator activity			ovary(3)	3			Colorectal(24;0.198)											0.55			47	38				---	---	---	---	capture_indel			Frame_Shift_Del	DEL	30656843	30656843	15649	16	G	-	-	45	45	SRCAP	-	5	5
SP100	6672	broad.mit.edu	36	2	231037030	231037030	+	Frame_Shift_Del	DEL	C	-	-			TCGA-28-2509-01	TCGA-28-2509-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:231037030_231037030delC	uc002vqu.1	+	c.1062_1062delC	c.(1060-1062)ATCfs	p.I354fs	SP100_uc002vqs.2_Frame_Shift_Del_p.I354fs|SP100_uc002vqt.1_Frame_Shift_Del_p.I354fs|SP100_uc002vqq.1_Frame_Shift_Del_p.I354fs|SP100_uc002vqr.1_Frame_Shift_Del_p.I329fs|SP100_uc002vqv.1_Frame_Shift_Del_p.I318fs	NM_001080391	NP_001073860	P23497	SP100_HUMAN	nuclear antigen Sp100 isoform 1	354					DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator|interferon-gamma-mediated signaling pathway|interspecies interaction between organisms|negative regulation of cellular component movement|negative regulation of DNA binding|negative regulation of sequence-specific DNA binding transcription factor activity|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transcription, DNA-dependent|negative regulation of viral transcription|positive regulation of sequence-specific DNA binding transcription factor activity|positive regulation of transcription, DNA-dependent|positive regulation of transcription, DNA-dependent|response to cytokine stimulus|response to retinoic acid|response to type I interferon|retinoic acid receptor signaling pathway|type I interferon-mediated signaling pathway	cytoplasm|nuclear periphery|nucleolus|PML body	chromo shadow domain binding|DNA binding|general transcriptional repressor activity|identical protein binding|kinase binding|protein homodimerization activity|transcription coactivator activity|transcription corepressor activity|transcription factor binding			ovary(4)|central_nervous_system(1)	5		Renal(207;0.0112)|all_lung(227;0.0335)|all_hematologic(139;0.0749)|Lung NSC(271;0.142)|Acute lymphoblastic leukemia(138;0.167)		Epithelial(121;1.13e-12)|all cancers(144;2.71e-10)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(119;0.00942)										0.47			27	31				---	---	---	---	capture_indel			Frame_Shift_Del	DEL	231037030	231037030	15460	2	C	-	-	29	29	SP100	-	5	5
STAG3L2	442582	broad.mit.edu	36	7	73938493	73938500	+	Frame_Shift_Del	DEL	AGAGCTCC	-	-			TCGA-28-2509-01	TCGA-28-2509-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:73938493_73938500delAGAGCTCC	uc003ubj.2	-	c.243_250delGGAGCTCT	c.(241-252)CTGGAGCTCTTCfs	p.L81fs	STAG3L2_uc010lbv.1_Non-coding_Transcript|STAG3L2_uc003ubi.2_Non-coding_Transcript	NM_001025202	NP_001020373	P0CL84	ST3L2_HUMAN	STAG3-like	81_84	SCD.					nucleus					0														0.38			11	18				---	---	---	---	capture_indel			Frame_Shift_Del	DEL	73938493	73938500	15764	7	AGAGCTCC	-	-	3	3	STAG3L2	-	5	5
