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
BTRC	8945	broad.mit.edu	36	10	103180187	103180187	+	Silent	SNP	C	T	T			TCGA-28-5209-01	TCGA-28-5209-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr10:103180187C>T	uc001kta.1	+	c.144C>T	c.(142-144)CTC>CTT	p.L48L	BTRC_uc001ksz.1_Intron|BTRC_uc001ktb.1_Intron|BTRC_uc001ktc.1_Silent_p.L48L	NM_033637	NP_378663	Q9Y297	FBW1A_HUMAN	beta-transducin repeat containing protein	48					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|interspecies interaction between organisms|negative regulation of gene-specific transcription|positive regulation of proteolysis|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|protein destabilization|viral reproduction|Wnt receptor signaling pathway	cytosol|nucleus|SCF ubiquitin ligase complex	specific transcriptional repressor activity			ovary(1)	1		Colorectal(252;0.234)								243				0.753247	183.079327	187.570465	58	19	CC		KEEP	---	---	---	---	capture		Epithelial(162;1.05e-08)|all cancers(201;6.59e-07)	Silent	SNP	103180187	103180187	1603	10	C	T	T	29	29	BTRC	T	2	2
ARMC4	55130	broad.mit.edu	36	10	28268849	28268849	+	Missense_Mutation	SNP	C	T	T			TCGA-28-5209-01	TCGA-28-5209-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr10:28268849C>T	uc009xky.1	-	c.2080G>A	c.(2080-2082)GCC>ACC	p.A694T	ARMC4_uc001itz.1_Missense_Mutation_p.A694T	NM_018076	NP_060546	Q5T2S8	ARMC4_HUMAN	armadillo repeat containing 4	694	ARM 4.|HEAT.						binding			ovary(4)	4														0.918033	176.844321	187.681474	56	5	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	28268849	28268849	971	10	C	T	T	27	27	ARMC4	T	1	1
PI4K2A	55361	broad.mit.edu	36	10	99416244	99416244	+	Missense_Mutation	SNP	G	T	T			TCGA-28-5209-01	TCGA-28-5209-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr10:99416244G>T	uc001kog.1	+	c.1144G>T	c.(1144-1146)GAT>TAT	p.D382Y	PI4K2A_uc009xvw.1_Intron	NM_018425	NP_060895	Q9BTU6	P4K2A_HUMAN	phosphatidylinositol 4-kinase type 2 alpha	382	PI3K/PI4K.				phosphatidylinositol biosynthetic process	cytoplasm|integral to plasma membrane|membrane raft	1-phosphatidylinositol 4-kinase activity|ATP binding|magnesium ion binding			lung(1)|skin(1)	2		Colorectal(252;0.162)								218				0.876712	205.043	215.172904	64	9	GG		KEEP	---	---	---	---	capture		Epithelial(162;1.24e-10)|all cancers(201;1.2e-08)	Missense_Mutation	SNP	99416244	99416244	12295	10	G	T	T	33	33	PI4K2A	T	3	3
MMP27	64066	broad.mit.edu	36	11	102078760	102078760	+	Missense_Mutation	SNP	G	A	A			TCGA-28-5209-01	TCGA-28-5209-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr11:102078760G>A	uc001phd.1	-	c.553C>T	c.(553-555)CCT>TCT	p.P185S		NM_022122	NP_071405	Q9H306	MMP27_HUMAN	matrix metalloproteinase 27	185					collagen catabolic process|proteolysis	proteinaceous extracellular matrix	calcium ion binding|metalloendopeptidase activity|zinc ion binding			ovary(2)	2	all_cancers(8;0.000843)|all_epithelial(12;0.00362)|Lung NSC(15;0.21)	all_hematologic(158;0.00092)|Acute lymphoblastic leukemia(157;0.000967)												0.472789	424.995274	425.185455	139	155	GG		KEEP	---	---	---	---	capture	Epithelial(9;0.0509)|Lung(13;0.0696)|LUSC - Lung squamous cell carcinoma(19;0.13)|all cancers(10;0.176)	BRCA - Breast invasive adenocarcinoma(274;0.0151)	Missense_Mutation	SNP	102078760	102078760	10055	11	G	A	A	41	41	MMP27	A	2	2
DSCAML1	57453	broad.mit.edu	36	11	116847838	116847838	+	Missense_Mutation	SNP	C	T	T			TCGA-28-5209-01	TCGA-28-5209-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr11:116847838C>T	uc001prh.1	-	c.3089G>A	c.(3088-3090)CGC>CAC	p.R1030H		NM_020693	NP_065744	Q8TD84	DSCL1_HUMAN	Down syndrome cell adhesion molecule like 1	970	Extracellular (Potential).|Fibronectin type-III 1.				axonogenesis|brain development|cell fate determination|dorsal/ventral pattern formation|embryonic skeletal system morphogenesis|homophilic cell adhesion	cell surface|integral to membrane|plasma membrane	protein homodimerization activity			ovary(3)|large_intestine(2)	5	all_hematologic(175;0.0487)	Breast(348;0.0424)|Medulloblastoma(222;0.0523)|all_hematologic(192;0.232)												0.467391	250.228497	250.399	86	98	CC		KEEP	---	---	---	---	capture		BRCA - Breast invasive adenocarcinoma(274;9.12e-06)|Epithelial(105;0.00172)	Missense_Mutation	SNP	116847838	116847838	4953	11	C	T	T	27	27	DSCAML1	T	1	1
COPB1	1315	broad.mit.edu	36	11	14455062	14455062	+	Missense_Mutation	SNP	C	A	A			TCGA-28-5209-01	TCGA-28-5209-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr11:14455062C>A	uc001mlg.1	-	c.1434G>T	c.(1432-1434)GAG>GAT	p.E478D	COPB1_uc001mlh.1_Missense_Mutation_p.E478D|COPB1_uc001mli.1_Missense_Mutation_p.E478D	NM_016451	NP_057535	P53618	COPB_HUMAN	coatomer protein complex, subunit beta 1	478					COPI coating of Golgi vesicle|interspecies interaction between organisms|intra-Golgi vesicle-mediated transport|intracellular protein transport|retrograde vesicle-mediated transport, Golgi to ER	COPI vesicle coat|cytosol	protein binding|structural molecule activity			ovary(1)|central_nervous_system(1)	2														0.460993	366.798963	367.174744	130	152	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	14455062	14455062	3866	11	C	A	A	32	32	COPB1	A	3	3
KCNA4	3739	broad.mit.edu	36	11	29989754	29989754	+	Missense_Mutation	SNP	A	T	T			TCGA-28-5209-01	TCGA-28-5209-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr11:29989754A>T	uc001msk.1	-	c.1048T>A	c.(1048-1050)TTG>ATG	p.L350M	KCNA4_uc009yjh.1_Missense_Mutation_p.L350M	NM_002233	NP_002224	P22459	KCNA4_HUMAN	potassium voltage-gated channel, shaker-related	350						voltage-gated potassium channel complex	potassium ion binding|protein binding|voltage-gated potassium channel activity			ovary(2)|central_nervous_system(1)|pancreas(1)	4														0.52973	259.889867	260.017404	98	87	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	29989754	29989754	8310	11	A	T	T	2	2	KCNA4	T	4	4
LRP4	4038	broad.mit.edu	36	11	46857381	46857381	+	Missense_Mutation	SNP	T	C	C			TCGA-28-5209-01	TCGA-28-5209-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr11:46857381T>C	uc001ndn.2	-	c.2876A>G	c.(2875-2877)TAT>TGT	p.Y959C		NM_002334	NP_002325	O75096	LRP4_HUMAN	low density lipoprotein receptor-related protein	959	Extracellular (Potential).|LDL-receptor class B 10.				endocytosis|negative regulation of canonical Wnt receptor signaling pathway|Wnt receptor signaling pathway	integral to membrane	calcium ion binding|receptor activity			ovary(1)	1														0.488789	394.896153	394.919487	109	114	TT		KEEP	---	---	---	---	capture		Lung(87;0.159)	Missense_Mutation	SNP	46857381	46857381	9332	11	T	C	C	49	49	LRP4	C	4	4
TRIM6-TRIM34	445372	broad.mit.edu	36	11	5582425	5582425	+	Missense_Mutation	SNP	C	A	A			TCGA-28-5209-01	TCGA-28-5209-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr11:5582425C>A	uc001mbf.1	+	c.593C>A	c.(592-594)ACA>AAA	p.T198K	HBG2_uc001mak.1_Intron|TRIM6_uc001mbc.1_Missense_Mutation_p.T170K|TRIM6_uc009yeo.1_Missense_Mutation_p.T144K|TRIM6_uc001mbe.1_5'UTR|TRIM6_uc001mbd.1_Missense_Mutation_p.T198K|TRIM6_uc001mbg.1_5'Flank|TRIM6_uc009yep.1_5'Flank	NM_001003819	NP_067629	B2RNG4	B2RNG4_HUMAN	tripartite motif-containing 6 and tripartite	198						intracellular	zinc ion binding			ovary(1)	1		Medulloblastoma(188;0.00225)|Breast(177;0.0204)|all_neural(188;0.0212)												0.456522	253.471122	253.7751	84	100	CC		KEEP	---	---	---	---	capture		Epithelial(150;1.01e-08)|BRCA - Breast invasive adenocarcinoma(625;0.145)	Missense_Mutation	SNP	5582425	5582425	17080	11	C	A	A	17	17	TRIM6-TRIM34	A	3	3
MS4A15	219995	broad.mit.edu	36	11	60287797	60287797	+	Silent	SNP	C	T	T			TCGA-28-5209-01	TCGA-28-5209-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr11:60287797C>T	uc009ynf.1	+	c.15C>T	c.(13-15)CCC>CCT	p.P5P	MS4A15_uc001npx.2_Intron|MS4A15_uc001npy.2_Non-coding_Transcript|MS4A15_uc009yng.1_Silent_p.P5P	NM_001098835	NP_001092305	Q8N5U1	M4A15_HUMAN	membrane-spanning 4-domains, subfamily A, member	5						integral to membrane	receptor activity			lung(1)	1														0.452297	412.136666	412.686217	128	155	CC		KEEP	---	---	---	---	capture			Silent	SNP	60287797	60287797	10252	11	C	T	T	23	23	MS4A15	T	1	1
SLC22A20	440044	broad.mit.edu	36	11	64738062	64738062	+	Missense_Mutation	SNP	C	A	A			TCGA-28-5209-01	TCGA-28-5209-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr11:64738062C>A	uc009yqe.1	+	c.143C>A	c.(142-144)CCC>CAC	p.P48H		NM_001004326	NP_001004326	A6NK97	S22AK_HUMAN	solute carrier family 22, member 20	46	Extracellular (Potential).				ion transport|transmembrane transport	integral to membrane	transporter activity			central_nervous_system(1)	1														0.538462	16.915155	16.931085	7	6	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	64738062	64738062	14948	11	C	A	A	22	22	SLC22A20	A	3	3
MTERFD3	80298	broad.mit.edu	36	12	105895466	105895466	+	Silent	SNP	C	T	T			TCGA-28-5209-01	TCGA-28-5209-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr12:105895466C>T	uc001tme.1	-	c.1157G>A	c.(1156-1158)TGA>TAA	p.*386*	MTERFD3_uc001tmf.1_Silent_p.*386*|MTERFD3_uc001tmg.1_Silent_p.*386*|MTERFD3_uc009zus.1_Silent_p.*386*|MTERFD3_uc001tmh.1_3'UTR	NM_025198	NP_079474	Q49AM1	MTER3_HUMAN	transcription termination factor-like protein	386					regulation of transcription, DNA-dependent|transcription, DNA-dependent	mitochondrial nucleoid	promoter binding|transcription regulator activity				0														0.39899	229.275736	231.045539	79	119	CC		KEEP	---	---	---	---	capture			Silent	SNP	105895466	105895466	10314	12	C	T	T	29	29	MTERFD3	T	2	2
WSCD2	9671	broad.mit.edu	36	12	107128116	107128116	+	Missense_Mutation	SNP	G	A	A			TCGA-28-5209-01	TCGA-28-5209-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr12:107128116G>A	uc001tms.1	+	c.586G>A	c.(586-588)GAC>AAC	p.D196N	WSCD2_uc001tmt.1_Missense_Mutation_p.D196N	NM_014653	NP_055468	Q2TBF2	WSCD2_HUMAN	WSC domain containing 2	196	WSC 1.					integral to membrane				ovary(1)|large_intestine(1)|breast(1)	3														0.470588	69.204115	69.241294	24	27	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	107128116	107128116	17981	12	G	A	A	37	37	WSCD2	A	1	1
ABCC9	10060	broad.mit.edu	36	12	21882288	21882288	+	Missense_Mutation	SNP	C	T	T			TCGA-28-5209-01	TCGA-28-5209-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr12:21882288C>T	uc001rfh.1	-	c.3557G>A	c.(3556-3558)CGG>CAG	p.R1186Q	ABCC9_uc001rfi.1_Missense_Mutation_p.R1186Q|ABCC9_uc001rfj.1_Missense_Mutation_p.R1150Q	NM_020297	NP_064693	O60706	ABCC9_HUMAN	ATP-binding cassette, sub-family C, member 9	1186	Extracellular (Potential).|ABC transmembrane type-1 2.				defense response to virus|potassium ion import	ATP-sensitive potassium channel complex	ATP binding|ATPase activity, coupled to transmembrane movement of substances|potassium channel regulator activity|sulfonylurea receptor activity			ovary(4)	4					Adenosine triphosphate(DB00171)|Glibenclamide(DB01016)									0.42623	168.181523	168.760603	52	70	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	21882288	21882288	60	12	C	T	T	23	23	ABCC9	T	1	1
ADCY6	112	broad.mit.edu	36	12	47450859	47450859	+	Silent	SNP	C	T	T			TCGA-28-5209-01	TCGA-28-5209-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr12:47450859C>T	uc001rsh.2	-	c.3213G>A	c.(3211-3213)AAG>AAA	p.K1071K	ADCY6_uc001rsj.2_Silent_p.K1071K|ADCY6_uc001rsi.2_Silent_p.K1018K	NM_015270	NP_056085	O43306	ADCY6_HUMAN	adenylate cyclase 6 isoform a	1071	Cytoplasmic (Potential).				activation of adenylate cyclase activity by G-protein signaling pathway|activation of phospholipase C activity|activation of protein kinase A activity|cellular response to glucagon stimulus|energy reserve metabolic process|inhibition of adenylate cyclase activity by G-protein signaling pathway|nerve growth factor receptor signaling pathway|synaptic transmission|transmembrane transport|water transport	integral to membrane	ATP binding|metal ion binding				0														0.810013	2157.815855	2227.867373	631	148	CC		KEEP	---	---	---	---	capture			Silent	SNP	47450859	47450859	299	12	C	T	T	28	28	ADCY6	T	2	2
TRHDE	29953	broad.mit.edu	36	12	71333085	71333085	+	Missense_Mutation	SNP	T	A	A			TCGA-28-5209-01	TCGA-28-5209-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr12:71333085T>A	uc001sxa.1	+	c.2731T>A	c.(2731-2733)TCT>ACT	p.S911T		NM_013381	NP_037513	Q9UKU6	TRHDE_HUMAN	thyrotropin-releasing hormone degrading enzyme	911	Extracellular (Potential).				cell-cell signaling|proteolysis|signal transduction	integral to plasma membrane	aminopeptidase activity|metallopeptidase activity|zinc ion binding			ovary(2)	2														0.438889	222.593615	223.180102	79	101	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	71333085	71333085	17023	12	T	A	A	62	62	TRHDE	A	4	4
DPPA3	359787	broad.mit.edu	36	12	7760869	7760869	+	Missense_Mutation	SNP	G	A	A			TCGA-28-5209-01	TCGA-28-5209-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr12:7760869G>A	uc001qtf.1	+	c.409G>A	c.(409-411)GTG>ATG	p.V137M		NM_199286	NP_954980	Q6W0C5	DPPA3_HUMAN	stella	137						cytoplasm|nucleus					0														0.408889	271.659199	273.290386	92	133	GG		KEEP	---	---	---	---	capture		Kidney(36;0.0887)	Missense_Mutation	SNP	7760869	7760869	4919	12	G	A	A	40	40	DPPA3	A	1	1
CLEC4E	26253	broad.mit.edu	36	12	8581045	8581045	+	Missense_Mutation	SNP	G	A	A			TCGA-28-5209-01	TCGA-28-5209-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr12:8581045G>A	uc001quo.1	-	c.305C>T	c.(304-306)GCG>GTG	p.A102V		NM_014358	NP_055173	Q9ULY5	CLC4E_HUMAN	C-type lectin domain family 4, member E	102	C-type lectin.|Extracellular (Potential).					integral to membrane	sugar binding			central_nervous_system(1)	1	Lung SC(5;0.184)													0.434286	216.488628	217.143357	76	99	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	8581045	8581045	3653	12	G	A	A	38	38	CLEC4E	A	1	1
TUBA3C	7278	broad.mit.edu	36	13	18650451	18650451	+	Missense_Mutation	SNP	C	T	T			TCGA-28-5209-01	TCGA-28-5209-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr13:18650451C>T	uc009zzj.1	-	c.310G>A	c.(310-312)GCC>ACC	p.A104T		NM_006001	NP_525125	Q13748	TBA3C_HUMAN	tubulin, alpha 3c	104					'de novo' posttranslational protein folding|microtubule-based movement|protein polymerization	cytoplasm|microtubule	GTP binding|GTPase activity|protein binding|structural molecule activity			ovary(3)	3		all_cancers(29;1.31e-20)|all_epithelial(30;1.59e-20)|all_lung(29;6.91e-20)|Lung NSC(5;9.25e-17)|Hepatocellular(1;0.0207)|Lung SC(185;0.0262)|Ovarian(182;0.162)												0.445783	319.504422	320.138931	111	138	CC		KEEP	---	---	---	---	capture		all cancers(112;6.78e-06)|Epithelial(112;3.79e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00172)|Lung(94;0.0186)|LUSC - Lung squamous cell carcinoma(192;0.108)	Missense_Mutation	SNP	18650451	18650451	17301	13	C	T	T	27	27	TUBA3C	T	1	1
FLT3	2322	broad.mit.edu	36	13	27534176	27534176	+	Missense_Mutation	SNP	C	T	T			TCGA-28-5209-01	TCGA-28-5209-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr13:27534176C>T	uc001urw.1	-	c.196G>A	c.(196-198)GCG>ACG	p.A66T	FLT3_uc010aao.1_Non-coding_Transcript	NM_004119	NP_004110	P36888	FLT3_HUMAN	fms-related tyrosine kinase 3	66	Extracellular (Potential).				positive regulation of cell proliferation	integral to plasma membrane	ATP binding|vascular endothelial growth factor receptor activity	p.599_560>LTGSSDNEYFYVDFREYEY(1)		haematopoietic_and_lymphoid_tissue(8072)|ovary(2)|lung(1)|central_nervous_system(1)	8076	Acute lymphoblastic leukemia(6;0.04)	Lung SC(185;0.0156)|Ovarian(182;0.0392)			Sorafenib(DB00398)|Sunitinib(DB01268)					630				0.388889	149.853645	151.415242	56	88	CC		KEEP	---	---	---	---	capture	Colorectal(13;0.000157)|READ - Rectum adenocarcinoma(15;0.105)	OV - Ovarian serous cystadenocarcinoma(117;0.00154)|all cancers(112;0.00459)|GBM - Glioblastoma multiforme(144;0.00562)|Epithelial(112;0.0959)|Lung(94;0.212)	Missense_Mutation	SNP	27534176	27534176	6184	13	C	T	T	25	25	FLT3	T	2	2
SUCLA2	8803	broad.mit.edu	36	13	47469117	47469117	+	Missense_Mutation	SNP	C	T	T			TCGA-28-5209-01	TCGA-28-5209-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr13:47469117C>T	uc001vbs.1	-	c.133G>A	c.(133-135)GTA>ATA	p.V45I	SUCLA2_uc001vbt.1_Non-coding_Transcript|SUCLA2_uc001vbu.1_Missense_Mutation_p.V45I	NM_003850	NP_003841	Q9P2R7	SUCB1_HUMAN	succinate-CoA ligase, ADP-forming, beta subunit	45					succinyl-CoA pathway|tricarboxylic acid cycle	mitochondrial matrix	ATP binding|protein binding|succinate-CoA ligase (ADP-forming) activity			central_nervous_system(1)	1		all_cancers(8;1.13e-24)|all_epithelial(8;1.78e-13)|all_lung(13;2.85e-06)|Breast(56;0.000141)|Lung NSC(96;0.000226)|all_hematologic(8;0.000885)|Prostate(109;0.00132)|Acute lymphoblastic leukemia(8;0.0167)|Myeloproliferative disorder(33;0.039)|Hepatocellular(98;0.0556)|Lung SC(185;0.102)|Glioma(44;0.236)			Succinic acid(DB00139)									0.425	213.778409	214.56241	68	92	CC		KEEP	---	---	---	---	capture		GBM - Glioblastoma multiforme(144;2.1e-06)	Missense_Mutation	SNP	47469117	47469117	15883	13	C	T	T	20	20	SUCLA2	T	2	2
KLF5	688	broad.mit.edu	36	13	72534602	72534602	+	Missense_Mutation	SNP	G	A	A			TCGA-28-5209-01	TCGA-28-5209-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr13:72534602G>A	uc001vje.1	+	c.864G>A	c.(862-864)ATG>ATA	p.M288I	KLF5_uc001vjd.1_Missense_Mutation_p.M197I	NM_001730	NP_001721	Q13887	KLF5_HUMAN	Kruppel-like factor 5	288					regulation of transcription, DNA-dependent|transcription from RNA polymerase II promoter	nucleus	DNA binding|RNA polymerase II transcription factor activity|zinc ion binding			large_intestine(1)|ovary(1)|pancreas(1)	3		Prostate(6;0.00187)|Breast(118;0.0735)												0.478261	182.078904	182.138712	66	72	GG		KEEP	---	---	---	---	capture		GBM - Glioblastoma multiforme(99;0.0011)	Missense_Mutation	SNP	72534602	72534602	8661	13	G	A	A	46	46	KLF5	A	2	2
KIF26A	26153	broad.mit.edu	36	14	103711483	103711483	+	Missense_Mutation	SNP	G	A	A			TCGA-28-5209-01	TCGA-28-5209-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr14:103711483G>A	uc001yos.2	+	c.2605G>A	c.(2605-2607)GCC>ACC	p.A869T		NM_015656	NP_056471	Q9ULI4	KI26A_HUMAN	kinesin family member 26A	869					blood coagulation|enteric nervous system development|microtubule-based movement|negative regulation of signal transduction|regulation of cell growth by extracellular stimulus	cytosol|microtubule	ATP binding|microtubule binding|microtubule motor activity			pancreas(1)	1		all_cancers(154;0.109)|Melanoma(154;0.0525)|all_epithelial(191;0.0767)												0.416667	13.371334	13.444416	5	7	GG		KEEP	---	---	---	---	capture	Epithelial(46;0.152)	Epithelial(152;0.161)	Missense_Mutation	SNP	103711483	103711483	8605	14	G	A	A	42	42	KIF26A	A	2	2
AHNAK2	113146	broad.mit.edu	36	14	104484921	104484921	+	Missense_Mutation	SNP	C	T	T			TCGA-28-5209-01	TCGA-28-5209-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr14:104484921C>T	uc010axc.1	-	c.7912G>A	c.(7912-7914)GAC>AAC	p.D2638N	AHNAK2_uc001ypx.2_Missense_Mutation_p.D2538N	NM_138420	NP_612429	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	2638						nucleus				ovary(1)	1		all_cancers(154;0.115)|Melanoma(154;0.155)|all_epithelial(191;0.183)												0.492201	852.516523	852.545605	284	293	CC		KEEP	---	---	---	---	capture	all cancers(16;0.000479)|OV - Ovarian serous cystadenocarcinoma(23;0.00659)|Epithelial(46;0.0151)|GBM - Glioblastoma multiforme(11;0.116)		Missense_Mutation	SNP	104484921	104484921	418	14	C	T	T	31	31	AHNAK2	T	1	1
FOXG1	2290	broad.mit.edu	36	14	28306936	28306936	+	Missense_Mutation	SNP	T	G	G			TCGA-28-5209-01	TCGA-28-5209-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr14:28306936T>G	uc001wqe.1	+	c.700T>G	c.(700-702)TCC>GCC	p.S234A		NM_005249	NP_005240	P55316	FOXG1_HUMAN	forkhead box G1	234	Fork-head.				axon midline choice point recognition|central nervous system neuron development|dorsal/ventral pattern formation|embryo development ending in birth or egg hatching|hindbrain development|inner ear morphogenesis|negative regulation of gene-specific transcription from RNA polymerase II promoter|negative regulation of neuron differentiation|nose development|positive regulation of cell cycle|positive regulation of neuroblast proliferation|positive regulation of transcription from RNA polymerase II promoter|regulation of mitotic cell cycle|regulation of sequence-specific DNA binding transcription factor activity|sensory cilium assembly|tissue development	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			ovary(2)|lung(1)	3														0.402299	112.516855	113.240038	35	52	TT		KEEP	---	---	---	---	capture	LUAD - Lung adenocarcinoma(48;0.011)|Lung(238;0.0575)	GBM - Glioblastoma multiforme(265;0.00413)	Missense_Mutation	SNP	28306936	28306936	6252	14	T	G	G	58	58	FOXG1	G	4	4
SPG11	80208	broad.mit.edu	36	15	42645487	42645487	+	Nonsense_Mutation	SNP	G	A	A			TCGA-28-5209-01	TCGA-28-5209-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr15:42645487G>A	uc001ztx.1	-	c.6856C>T	c.(6856-6858)CGA>TGA	p.R2286*	SPG11_uc010bdw.1_Nonsense_Mutation_p.R416*	NM_025137	NP_079413	Q96JI7	SPTCS_HUMAN	spastic paraplegia 11 (autosomal recessive)	2286	Extracellular (Potential).				cell death	cytosol|integral to membrane|nucleus	protein binding			ovary(4)	4		all_cancers(109;1.29e-14)|all_epithelial(112;1.26e-12)|Lung NSC(122;1.34e-07)|all_lung(180;1.21e-06)|Melanoma(134;0.0122)												0.394366	80.383505	81.077273	28	43	GG		KEEP	---	---	---	---	capture		all cancers(107;2.93e-22)|GBM - Glioblastoma multiforme(94;1.55e-06)|COAD - Colon adenocarcinoma(120;0.0432)|Colorectal(105;0.0484)|Lung(196;0.104)|LUSC - Lung squamous cell carcinoma(244;0.214)	Nonsense_Mutation	SNP	42645487	42645487	15553	15	G	A	A	38	38	SPG11	A	5	1
ACSM2A	123876	broad.mit.edu	36	16	20399704	20399704	+	Missense_Mutation	SNP	A	T	T			TCGA-28-5209-01	TCGA-28-5209-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr16:20399704A>T	uc010bwe.1	+	c.1469A>T	c.(1468-1470)GAG>GTG	p.E490V	ACSM2A_uc002dhf.2_Missense_Mutation_p.E490V|ACSM2A_uc002dhg.2_Missense_Mutation_p.E490V|ACSM2A_uc002dhh.2_Missense_Mutation_p.E120V	NM_001010845	NP_001010845	Q08AH3	ACS2A_HUMAN	acyl-CoA synthetase medium-chain family member	490					fatty acid metabolic process	mitochondrial matrix	ATP binding|butyrate-CoA ligase activity|metal ion binding			breast(1)	1														0.409639	192.668628	193.852213	68	98	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	20399704	20399704	184	16	A	T	T	11	11	ACSM2A	T	4	4
CHP2	63928	broad.mit.edu	36	16	23676083	23676083	+	Missense_Mutation	SNP	C	T	T			TCGA-28-5209-01	TCGA-28-5209-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr16:23676083C>T	uc002dmb.1	+	c.475C>T	c.(475-477)CGC>TGC	p.R159C		NM_022097	NP_071380	O43745	CHP2_HUMAN	hepatocellular carcinoma antigen gene 520	159	EF-hand 4.						calcium ion binding			central_nervous_system(1)	1														0.430894	158.954521	159.466358	53	70	CC		KEEP	---	---	---	---	capture		GBM - Glioblastoma multiforme(48;0.0144)	Missense_Mutation	SNP	23676083	23676083	3501	16	C	T	T	23	23	CHP2	T	1	1
SLC38A7	55238	broad.mit.edu	36	16	57267438	57267438	+	Missense_Mutation	SNP	C	T	T			TCGA-28-5209-01	TCGA-28-5209-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr16:57267438C>T	uc002eod.1	-	c.790G>A	c.(790-792)GTC>ATC	p.V264I	SLC38A7_uc002eob.1_Intron|SLC38A7_uc002eoc.1_Missense_Mutation_p.V264I|SLC38A7_uc002eoe.1_Missense_Mutation_p.V264I	NM_018231	NP_060701	Q9NVC3	S38A7_HUMAN	solute carrier family 38, member 7	264					amino acid transport|sodium ion transport	integral to membrane				ovary(1)	1														0.438596	72.069551	72.256104	25	32	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	57267438	57267438	15106	16	C	T	T	19	19	SLC38A7	T	1	1
ATP2A3	489	broad.mit.edu	36	17	3787469	3787469	+	Missense_Mutation	SNP	C	T	T			TCGA-28-5209-01	TCGA-28-5209-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr17:3787469C>T	uc002fwy.1	-	c.2311G>A	c.(2311-2313)GAG>AAG	p.E771K	ATP2A3_uc002fwx.1_Missense_Mutation_p.E771K|ATP2A3_uc002fwz.1_Missense_Mutation_p.E771K|ATP2A3_uc002fxa.1_Missense_Mutation_p.E771K|ATP2A3_uc002fxb.1_Missense_Mutation_p.E771K|ATP2A3_uc002fxc.1_Missense_Mutation_p.E771K|ATP2A3_uc002fxd.1_Missense_Mutation_p.E771K	NM_174953	NP_777613	Q93084	AT2A3_HUMAN	ATPase, Ca++ transporting, ubiquitous isoform e	771	Helical; Name=5; (By similarity).	Calcium 1 (By similarity).			ATP biosynthetic process|platelet activation	integral to membrane|nuclear membrane|platelet dense tubular network membrane|sarcoplasmic reticulum membrane	ATP binding|calcium-transporting ATPase activity|metal ion binding|protein binding			ovary(3)|breast(1)|central_nervous_system(1)	5						GBM(32;29 774 15719 37967)								0.290323	45.525611	47.96788	18	44	CC		KEEP	---	---	---	---	capture		LUAD - Lung adenocarcinoma(1115;0.000692)|Lung(3;0.0766)	Missense_Mutation	SNP	3787469	3787469	1157	17	C	T	T	31	31	ATP2A3	T	1	1
C17orf59	54785	broad.mit.edu	36	17	8033369	8033370	+	Missense_Mutation	DNP	CC	AA	AA			TCGA-28-5209-01	TCGA-28-5209-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:8033369_8033370CC>AA	uc002gkl.2	-	c.412_413GG>TT	c.(412-414)GGA>TTA	p.G138L		NM_017622	NP_060092	Q96GS4	CQ059_HUMAN	hypothetical protein LOC54785	272											0														0.441176	43.318757	43.421517	15	19	CC		KEEP	---	---	---	---	capture			Missense_Mutation	DNP	8033369	8033370	1924	17	CC	AA	AA	30	30	C17orf59	AA	3	3
AFG3L2	10939	broad.mit.edu	36	18	12341333	12341333	+	Silent	SNP	C	T	T			TCGA-28-5209-01	TCGA-28-5209-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr18:12341333C>T	uc002kqz.1	-	c.1398G>A	c.(1396-1398)CCG>CCA	p.P466P		NM_006796	NP_006787	Q9Y4W6	AFG32_HUMAN	AFG3 ATPase family gene 3-like 2	466					cell death|protein catabolic process|proteolysis	integral to membrane	ATP binding|metalloendopeptidase activity|nucleoside-triphosphatase activity|unfolded protein binding|zinc ion binding				0					Adenosine triphosphate(DB00171)									0.363636	173.455836	176.154123	60	105	CC		KEEP	---	---	---	---	capture			Silent	SNP	12341333	12341333	361	18	C	T	T	23	23	AFG3L2	T	1	1
LAMA1	284217	broad.mit.edu	36	18	6955403	6955403	+	Missense_Mutation	SNP	C	A	A			TCGA-28-5209-01	TCGA-28-5209-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr18:6955403C>A	uc002knm.1	-	c.7079G>T	c.(7078-7080)CGT>CTT	p.R2360L	LAMA1_uc002knl.1_5'UTR	NM_005559	NP_005550	P25391	LAMA1_HUMAN	laminin, alpha 1 precursor	2360	Laminin G-like 2.				axon guidance|cell adhesion|cell surface receptor linked signaling pathway|regulation of cell adhesion|regulation of cell migration|regulation of embryonic development	extracellular space|laminin-1 complex|laminin-3 complex	extracellular matrix structural constituent|receptor binding			ovary(8)|large_intestine(4)|breast(2)|pancreas(2)|central_nervous_system(1)	17		Colorectal(10;0.172)			Alteplase(DB00009)|Anistreplase(DB00029)|Reteplase(DB00015)|Tenecteplase(DB00031)					1597				0.463054	311.17807	311.41336	94	109	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	6955403	6955403	8928	18	C	A	A	19	19	LAMA1	A	3	3
ICAM1	3383	broad.mit.edu	36	19	10255191	10255191	+	Silent	SNP	C	T	T			TCGA-28-5209-01	TCGA-28-5209-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr19:10255191C>T	uc002mnq.2	+	c.366C>T	c.(364-366)CCC>CCT	p.P122P		NM_000201	NP_000192	P05362	ICAM1_HUMAN	intercellular adhesion molecule 1 precursor	122	Extracellular (Potential).				adhesion to symbiont|heterophilic cell-cell adhesion|interferon-gamma-mediated signaling pathway|leukocyte cell-cell adhesion|leukocyte migration|membrane to membrane docking|positive regulation of cellular extravasation|regulation of immune response|regulation of leukocyte mediated cytotoxicity|T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell|virion attachment, binding of host cell surface receptor	extracellular space|integral to plasma membrane	integrin binding|transmembrane receptor activity			ovary(1)	1					Natalizumab(DB00108)|Simvastatin(DB00641)					72				0.321875	285.789446	294.819579	103	217	CC		KEEP	---	---	---	---	capture	OV - Ovarian serous cystadenocarcinoma(20;1.39e-09)|Epithelial(33;2.81e-06)|all cancers(31;6.56e-06)		Silent	SNP	10255191	10255191	7779	19	C	T	T	24	24	ICAM1	T	2	2
MAN2B1	4125	broad.mit.edu	36	19	12620205	12620205	+	Missense_Mutation	SNP	C	G	G			TCGA-28-5209-01	TCGA-28-5209-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr19:12620205C>G	uc002mub.2	-	c.2448G>C	c.(2446-2448)AGG>AGC	p.R816S	MAN2B1_uc010dyv.1_Missense_Mutation_p.R815S	NM_000528	NP_000519	O00754	MA2B1_HUMAN	mannosidase, alpha, class 2B, member 1	816					protein deglycosylation	lysosome	alpha-mannosidase activity|zinc ion binding			ovary(4)|central_nervous_system(2)	6														0.338235	73.222412	74.78704	23	45	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	12620205	12620205	9599	19	C	G	G	26	26	MAN2B1	G	3	3
EMR2	30817	broad.mit.edu	36	19	14726775	14726775	+	Silent	SNP	G	A	A			TCGA-28-5209-01	TCGA-28-5209-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr19:14726775G>A	uc002mzp.1	-	c.1581C>T	c.(1579-1581)TAC>TAT	p.Y527Y	EMR2_uc010dzs.1_Intron|EMR2_uc002mzo.1_Silent_p.Y516Y|EMR2_uc002mzq.1_Silent_p.Y467Y|EMR2_uc002mzr.1_Silent_p.Y478Y|EMR2_uc002mzs.1_Silent_p.Y385Y|EMR2_uc002mzt.1_Silent_p.Y423Y|EMR2_uc002mzu.1_Silent_p.Y434Y	NM_013447	NP_038475	Q9UHX3	EMR2_HUMAN	egf-like module containing, mucin-like, hormone	527	Extracellular (Potential).|GPS.				cell adhesion|neuropeptide signaling pathway	integral to membrane|plasma membrane	calcium ion binding|G-protein coupled receptor activity			ovary(1)	1														0.325103	218.75863	225.345365	79	164	GG		KEEP	---	---	---	---	capture			Silent	SNP	14726775	14726775	5298	19	G	A	A	40	40	EMR2	A	1	1
ZNF98	148198	broad.mit.edu	36	19	22367562	22367562	+	Silent	SNP	T	C	C			TCGA-28-5209-01	TCGA-28-5209-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr19:22367562T>C	uc002nqt.2	-	c.315A>G	c.(313-315)CAA>CAG	p.Q105Q		NM_001098626	NP_001092096	A6NK75	ZNF98_HUMAN	zinc finger protein 98	105					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1		all_cancers(12;0.0536)|all_lung(12;0.00187)|Lung NSC(12;0.0019)|all_epithelial(12;0.00542)|Hepatocellular(1079;0.244)												0.235955	61.43015	67.102848	21	68	TT		KEEP	---	---	---	---	capture			Silent	SNP	22367562	22367562	18807	19	T	C	C	64	64	ZNF98	C	4	4
GPATCH1	55094	broad.mit.edu	36	19	38276933	38276933	+	Silent	SNP	C	T	T			TCGA-28-5209-01	TCGA-28-5209-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr19:38276933C>T	uc002nug.1	+	c.471C>T	c.(469-471)TTC>TTT	p.F157F		NM_018025	NP_060495	Q9BRR8	GPTC1_HUMAN	G patch domain containing 1	157	G-patch.				nuclear mRNA splicing, via spliceosome	catalytic step 2 spliceosome	nucleic acid binding				0	Esophageal squamous(110;0.137)					Pancreas(67;88 1713 4567 18227)								0.353211	218.903144	223.04805	77	141	CC		KEEP	---	---	---	---	capture			Silent	SNP	38276933	38276933	6864	19	C	T	T	31	31	GPATCH1	T	1	1
SLC7A10	56301	broad.mit.edu	36	19	38398703	38398703	+	Silent	SNP	C	G	G			TCGA-28-5209-01	TCGA-28-5209-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr19:38398703C>G	uc002num.1	-	c.168G>C	c.(166-168)TCG>TCC	p.S56S	SLC7A10_uc010edi.1_Intron	NM_019849	NP_062823	Q9NS82	AAA1_HUMAN	solute carrier family 7, member 10	56	Helical; (Potential).				blood coagulation|cellular nitrogen compound metabolic process|ion transport|leukocyte migration	integral to plasma membrane	L-serine transmembrane transporter activity			ovary(1)|central_nervous_system(1)	2	Esophageal squamous(110;0.137)													0.3	7.969441	8.73449	6	14	CC		KEEP	---	---	---	---	capture			Silent	SNP	38398703	38398703	15190	19	C	G	G	23	23	SLC7A10	G	3	3
NPHS1	4868	broad.mit.edu	36	19	41028493	41028493	+	Missense_Mutation	SNP	G	A	A			TCGA-28-5209-01	TCGA-28-5209-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr19:41028493G>A	uc002oby.2	-	c.1675C>T	c.(1675-1677)CCG>TCG	p.P559S		NM_004646	NP_004637	O60500	NPHN_HUMAN	nephrin precursor	559	Ig-like C2-type 6.|Extracellular (Potential).				cell adhesion|excretion|muscle organ development	integral to plasma membrane				ovary(4)	4	all_lung(56;7.14e-07)|Lung NSC(56;1.12e-06)|Esophageal squamous(110;0.162)													0.268817	64.630441	69.118832	25	68	GG		KEEP	---	---	---	---	capture	LUSC - Lung squamous cell carcinoma(66;0.0515)		Missense_Mutation	SNP	41028493	41028493	10986	19	G	A	A	43	43	NPHS1	A	2	2
C5AR1	728	broad.mit.edu	36	19	52515137	52515137	+	Missense_Mutation	SNP	C	T	T			TCGA-28-5209-01	TCGA-28-5209-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr19:52515137C>T	uc002pgj.1	+	c.263C>T	c.(262-264)GCG>GTG	p.A88V		NM_001736	NP_001727	P21730	C5AR_HUMAN	complement component 5 receptor 1	88	Helical; Name=2; (Potential).				activation of MAPK activity|activation of phospholipase C activity|cellular defense response|elevation of cytosolic calcium ion concentration|immune response|sensory perception of chemical stimulus	integral to plasma membrane	C5a anaphylatoxin receptor activity			ovary(2)|central_nervous_system(1)	3		all_cancers(25;2e-09)|all_epithelial(76;9.95e-08)|all_lung(116;7.27e-07)|Lung NSC(112;1.6e-06)|Ovarian(192;0.0139)|all_neural(266;0.026)|Breast(70;0.0503)												0.27193	149.345643	160.042698	62	166	CC		KEEP	---	---	---	---	capture		all cancers(93;0.000267)|OV - Ovarian serous cystadenocarcinoma(262;0.000618)|Epithelial(262;0.0142)|GBM - Glioblastoma multiforme(486;0.0242)	Missense_Mutation	SNP	52515137	52515137	2379	19	C	T	T	27	27	C5AR1	T	1	1
CD33	945	broad.mit.edu	36	19	56421101	56421101	+	Missense_Mutation	SNP	G	A	A			TCGA-28-5209-01	TCGA-28-5209-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr19:56421101G>A	uc002pwa.2	+	c.649G>A	c.(649-651)GCT>ACT	p.A217T	CD33_uc010eos.1_Missense_Mutation_p.A217T|CD33_uc010eot.1_Missense_Mutation_p.A90T|CD33_uc010eou.1_Non-coding_Transcript	NM_001772	NP_001763	P20138	CD33_HUMAN	CD33 antigen isoform 1 precursor	217	Extracellular (Potential).|Ig-like C2-type.				cell adhesion|cell-cell signaling|negative regulation of cell proliferation	integral to plasma membrane	receptor activity|sugar binding				0		all_neural(266;0.0199)			Gemtuzumab ozogamicin(DB00056)									0.293413	120.393186	126.784221	49	118	GG		KEEP	---	---	---	---	capture		GBM - Glioblastoma multiforme(134;0.000224)|OV - Ovarian serous cystadenocarcinoma(262;0.00468)	Missense_Mutation	SNP	56421101	56421101	3133	19	G	A	A	38	38	CD33	A	1	1
DUS3L	56931	broad.mit.edu	36	19	5740592	5740592	+	Missense_Mutation	SNP	T	G	G			TCGA-28-5209-01	TCGA-28-5209-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr19:5740592T>G	uc002mdc.1	-	c.526A>C	c.(526-528)ACC>CCC	p.T176P	DUS3L_uc002mdd.1_Intron|DUS3L_uc010duk.1_5'UTR	NM_020175	NP_064560	Q96G46	DUS3L_HUMAN	dihydrouridine synthase 3-like	176	C3H1-type 2.				oxidation-reduction process|tRNA processing		flavin adenine dinucleotide binding|nucleic acid binding|tRNA dihydrouridine synthase activity|zinc ion binding				0														0.214286	6.817722	7.872942	3	11	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	5740592	5740592	4992	19	T	G	G	58	58	DUS3L	G	4	4
PEG3	5178	broad.mit.edu	36	19	62018285	62018285	+	Missense_Mutation	SNP	C	T	T			TCGA-28-5209-01	TCGA-28-5209-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr19:62018285C>T	uc002qnu.1	-	c.3337G>A	c.(3337-3339)GGC>AGC	p.G1113S	ZIM2_uc010etp.1_Intron|ZIM2_uc002qnq.1_Intron|ZIM2_uc002qnr.1_Intron|PEG3_uc010etq.1_5'Flank|PEG3_uc002qnt.1_Missense_Mutation_p.G1084S|PEG3_uc002qnv.1_Missense_Mutation_p.G1113S|PEG3_uc010etr.1_Missense_Mutation_p.G1113S|PEG3_uc002qnw.1_Missense_Mutation_p.G989S|PEG3_uc002qnx.1_Missense_Mutation_p.G987S	NM_006210	NP_006201	Q9GZU2	PEG3_HUMAN	paternally expressed 3	1113	C2H2-type 6.				apoptosis|regulation of transcription, DNA-dependent|viral reproduction	cytoplasm|nucleus	nucleic acid binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(7)|large_intestine(1)|pancreas(1)	9		Colorectal(82;0.000256)|all_neural(62;0.103)|Ovarian(87;0.243)												0.251121	271.730407	296.881862	112	334	CC		KEEP	---	---	---	---	capture		GBM - Glioblastoma multiforme(193;0.0269)	Missense_Mutation	SNP	62018285	62018285	12141	19	C	T	T	21	21	PEG3	T	2	2
ZNF543	125919	broad.mit.edu	36	19	62531465	62531465	+	Missense_Mutation	SNP	C	T	T			TCGA-28-5209-01	TCGA-28-5209-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr19:62531465C>T	uc002qoi.1	+	c.823C>T	c.(823-825)CGG>TGG	p.R275W		NM_213598	NP_998763	Q08ER8	ZN543_HUMAN	zinc finger protein 543	275	C2H2-type 3.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			skin(1)|pancreas(1)	2		Colorectal(82;0.000256)|all_neural(62;0.0577)|Ovarian(87;0.221)												0.279762	117.956557	125.282273	47	121	CC		KEEP	---	---	---	---	capture		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0257)	Missense_Mutation	SNP	62531465	62531465	18571	19	C	T	T	27	27	ZNF543	T	1	1
SPAG17	200162	broad.mit.edu	36	1	118375951	118375951	+	Missense_Mutation	SNP	C	A	A			TCGA-28-5209-01	TCGA-28-5209-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr1:118375951C>A	uc001ehk.1	-	c.3496G>T	c.(3496-3498)GTT>TTT	p.V1166F		NM_206996	NP_996879	Q6Q759	SPG17_HUMAN	sperm associated antigen 17	1166						cilium|flagellar axoneme|microtubule				ovary(2)|large_intestine(1)	3	Esophageal squamous(2;0.0106)	all_cancers(81;0.0204)|all_lung(203;9.46e-05)|Lung NSC(69;0.000675)|all_epithelial(167;0.01)												0.390977	301.040986	303.80946	104	162	CC		KEEP	---	---	---	---	capture		Lung(183;0.0858)	Missense_Mutation	SNP	118375951	118375951	15482	1	C	A	A	18	18	SPAG17	A	3	3
FCER1A	2205	broad.mit.edu	36	1	157539279	157539279	+	Missense_Mutation	SNP	G	A	A			TCGA-28-5209-01	TCGA-28-5209-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:157539279G>A	uc001ftq.1	+	c.67G>A	c.(67-69)GTG>ATG	p.V23M		NM_002001	NP_001992	P12319	FCERA_HUMAN	Fc fragment of IgE, high affinity I, receptor	23						integral to plasma membrane					0	all_hematologic(112;0.0429)				Benzylpenicilloyl Polylysine(DB00895)|Omalizumab(DB00043)									0.441758	599.810918	601.155902	201	254	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	157539279	157539279	6011	1	G	A	A	40	40	FCER1A	A	1	1
PLA2G4A	5321	broad.mit.edu	36	1	185129889	185129889	+	Missense_Mutation	SNP	A	T	T			TCGA-28-5209-01	TCGA-28-5209-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr1:185129889A>T	uc001gsc.1	+	c.301A>T	c.(301-303)ACT>TCT	p.T101S		NM_024420	NP_077734	P47712	PA24A_HUMAN	cytosolic phospholipase A2, group IVA	101	C2.|Phospholipid binding (Probable).				phospholipid catabolic process|platelet activating factor biosynthetic process|platelet activation	cytosol|endoplasmic reticulum membrane	calcium ion binding|calcium-dependent phospholipid binding|lysophospholipase activity			breast(1)	1					Flunisolide(DB00180)|Fluocinolone Acetonide(DB00591)|Fluocinonide(DB01047)|Fluorometholone(DB00324)|Flurandrenolide(DB00846)|Fluticasone Propionate(DB00588)|Medrysone(DB00253)|Quinacrine(DB01103)									0.386364	189.74788	191.743059	68	108	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	185129889	185129889	12427	1	A	T	T	2	2	PLA2G4A	T	4	4
ODF2L	57489	broad.mit.edu	36	1	86610725	86610725	+	Missense_Mutation	SNP	T	A	A			TCGA-28-5209-01	TCGA-28-5209-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr1:86610725T>A	uc001dln.1	-	c.897A>T	c.(895-897)GAA>GAT	p.E299D	ODF2L_uc001dll.1_Missense_Mutation_p.E299D|ODF2L_uc001dlm.1_Missense_Mutation_p.E299D|ODF2L_uc001dlo.1_Missense_Mutation_p.E168D|ODF2L_uc001dlp.1_Missense_Mutation_p.E299D|ODF2L_uc001dlq.1_Missense_Mutation_p.E129D|ODF2L_uc009wcr.1_Missense_Mutation_p.E168D	NM_020729	NP_001007023	Q9ULJ1	ODF2L_HUMAN	outer dense fiber of sperm tails 2-like isoform	299	Potential.									ovary(1)	1														0.285714	16.4413	17.306608	6	15	TT		KEEP	---	---	---	---	capture		all cancers(265;0.0313)|Epithelial(280;0.0611)	Missense_Mutation	SNP	86610725	86610725	11233	1	T	A	A	56	56	ODF2L	A	4	4
PCSK2	5126	broad.mit.edu	36	20	17382533	17382533	+	Silent	SNP	C	T	T			TCGA-28-5209-01	TCGA-28-5209-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr20:17382533C>T	uc002wpm.1	+	c.1032C>T	c.(1030-1032)GAC>GAT	p.D344D	PCSK2_uc002wpl.1_Silent_p.D325D	NM_002594	NP_002585	P16519	NEC2_HUMAN	proprotein convertase subtilisin/kexin type 2	344	Catalytic.				enkephalin processing|insulin processing|islet amyloid polypeptide processing	extracellular space|membrane|soluble fraction|transport vesicle	serine-type endopeptidase activity			ovary(3)|central_nervous_system(2)|large_intestine(1)|pancreas(1)	7					Insulin Glargine recombinant(DB00047)|Insulin Lyspro recombinant(DB00046)|Insulin recombinant(DB00030)|Insulin, porcine(DB00071)									0.429577	177.553443	178.166729	61	81	CC		KEEP	---	---	---	---	capture			Silent	SNP	17382533	17382533	12022	20	C	T	T	19	19	PCSK2	T	1	1
PROKR2	128674	broad.mit.edu	36	20	5231318	5231318	+	Missense_Mutation	SNP	C	T	T			TCGA-28-5209-01	TCGA-28-5209-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr20:5231318C>T	uc002wlx.2	-	c.523G>A	c.(523-525)GCC>ACC	p.A175T	PROKR2_uc010gbj.1_Missense_Mutation_p.A175T|PROKR2_uc010gbk.1_Missense_Mutation_p.A175T	NM_144773	NP_658986	Q8NFJ6	PKR2_HUMAN	prokineticin receptor 2	175	Helical; Name=4; (Potential).					integral to membrane|plasma membrane	neuropeptide Y receptor activity			ovary(3)|central_nervous_system(1)|pancreas(1)	5														0.350515	274.658926	280.396866	102	189	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	5231318	5231318	12996	20	C	T	T	27	27	PROKR2	T	1	1
PROKR2	128674	broad.mit.edu	36	20	5242853	5242853	+	Missense_Mutation	SNP	C	T	T			TCGA-28-5209-01	TCGA-28-5209-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr20:5242853C>T	uc002wlx.2	-	c.163G>A	c.(163-165)GTC>ATC	p.V55I	PROKR2_uc010gbj.1_Missense_Mutation_p.V55I|PROKR2_uc010gbk.1_Missense_Mutation_p.V55I	NM_144773	NP_658986	Q8NFJ6	PKR2_HUMAN	prokineticin receptor 2	55	Helical; Name=1; (Potential).					integral to membrane|plasma membrane	neuropeptide Y receptor activity			ovary(3)|central_nervous_system(1)|pancreas(1)	5														0.395604	200.654764	202.39223	72	110	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	5242853	5242853	12996	20	C	T	T	19	19	PROKR2	T	1	1
ITGB2	3689	broad.mit.edu	36	21	45144744	45144744	+	Silent	SNP	G	A	A			TCGA-28-5209-01	TCGA-28-5209-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr21:45144744G>A	uc002zgd.1	-	c.816C>T	c.(814-816)GAC>GAT	p.D272D	ITGB2_uc002zge.1_Silent_p.D272D|ITGB2_uc002zgf.2_Silent_p.D272D|ITGB2_uc010gpw.1_Silent_p.D215D|ITGB2_uc002zgg.1_Silent_p.D272D	NM_001127491	NP_001120963	P05107	ITB2_HUMAN	integrin, beta 2 precursor	272	Extracellular (Potential).|VWFA.				apoptosis|blood coagulation|cell-cell signaling|cell-matrix adhesion|inflammatory response|integrin-mediated signaling pathway|leukocyte cell-cell adhesion|multicellular organismal development|neutrophil chemotaxis|regulation of cell shape|regulation of immune response|regulation of peptidyl-tyrosine phosphorylation	integrin complex	glycoprotein binding|protein kinase binding|receptor activity			ovary(3)|central_nervous_system(3)|breast(2)	8					Simvastatin(DB00641)									0.424242	150.173537	150.834296	56	76	GG		KEEP	---	---	---	---	capture		Colorectal(79;0.0669)	Silent	SNP	45144744	45144744	8198	21	G	A	A	40	40	ITGB2	A	1	1
TPTE	7179	broad.mit.edu	36	21	9973203	9973203	+	Missense_Mutation	SNP	C	T	T			TCGA-28-5209-01	TCGA-28-5209-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr21:9973203C>T	uc002yip.1	-	c.380G>A	c.(379-381)CGT>CAT	p.R127H	TPTE_uc002yiq.1_Missense_Mutation_p.R109H|TPTE_uc002yir.1_Missense_Mutation_p.R89H|TPTE_uc010gkv.1_5'UTR|TPTE_uc002yis.1_Non-coding_Transcript	NM_199261	NP_954870	P56180	TPTE_HUMAN	transmembrane phosphatase with tensin homology	127					signal transduction	integral to membrane	ion channel activity|protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity			ovary(2)|lung(1)|breast(1)|skin(1)	5														0.164	72.817407	99.626204	41	209	CC		KEEP	---	---	---	---	capture	Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723)	UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247)	Missense_Mutation	SNP	9973203	9973203	16974	21	C	T	T	19	19	TPTE	T	1	1
ZNF280A	129025	broad.mit.edu	36	22	21198784	21198784	+	Missense_Mutation	SNP	C	T	T			TCGA-28-5209-01	TCGA-28-5209-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr22:21198784C>T	uc002zwe.1	-	c.1171G>A	c.(1171-1173)GAA>AAA	p.E391K	ZNF280A_uc010gtq.1_Missense_Mutation_p.E391K	NM_080740	NP_542778	P59817	Z280A_HUMAN	zinc finger protein 280A	391					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1	all_hematologic(9;0.0135)|Acute lymphoblastic leukemia(84;0.17)	all_hematologic(6;1.74e-30)|Acute lymphoblastic leukemia(6;7.75e-22)												0.306667	182.288511	189.789454	69	156	CC		KEEP	---	---	---	---	capture		READ - Rectum adenocarcinoma(21;0.145)	Missense_Mutation	SNP	21198784	21198784	18406	22	C	T	T	31	31	ZNF280A	T	1	1
TTN	7273	broad.mit.edu	36	2	179339479	179339479	+	Nonsense_Mutation	SNP	G	A	A			TCGA-28-5209-01	TCGA-28-5209-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr2:179339479G>A	uc002umr.1	-	c.9577C>T	c.(9577-9579)CGA>TGA	p.R3193*	TTN_uc002ums.1_Nonsense_Mutation_p.R3147*|TTN_uc010frc.1_Nonsense_Mutation_p.R3147*|TTN_uc010frd.1_Nonsense_Mutation_p.R3147*|TTN_uc002umz.1_5'Flank|TTN_uc002unb.1_Nonsense_Mutation_p.R3193*	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	3193										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				0.413146	254.861751	256.264424	88	125	GG		KEEP	---	---	---	---	capture	OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)		Nonsense_Mutation	SNP	179339479	179339479	17290	2	G	A	A	40	40	TTN	A	5	1
SIDT1	54847	broad.mit.edu	36	3	114734763	114734763	+	Missense_Mutation	SNP	A	C	C			TCGA-28-5209-01	TCGA-28-5209-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr3:114734763A>C	uc003eak.1	+	c.205A>C	c.(205-207)ACC>CCC	p.T69P	SIDT1_uc003eaj.1_Missense_Mutation_p.T69P	NM_017699	NP_060169	Q9NXL6	SIDT1_HUMAN	SID1 transmembrane family, member 1	69	Extracellular (Potential).					integral to membrane				ovary(3)|pancreas(1)|skin(1)	5														0.3	7.38011	8.206041	6	14	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	114734763	114734763	14797	3	A	C	C	6	6	SIDT1	C	4	4
UROC1	131669	broad.mit.edu	36	3	127719194	127719194	+	Missense_Mutation	SNP	C	T	T			TCGA-28-5209-01	TCGA-28-5209-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr3:127719194C>T	uc010hsi.1	-	c.59G>A	c.(58-60)CGG>CAG	p.R20Q	UROC1_uc003eiz.1_Missense_Mutation_p.R20Q	NM_144639	NP_653240	Q96N76	HUTU_HUMAN	urocanase domain containing 1	20					histidine catabolic process	cytosol	urocanate hydratase activity			ovary(1)	1														0.477273	62.573742	62.593325	21	23	CC		KEEP	---	---	---	---	capture		GBM - Glioblastoma multiforme(114;0.17)	Missense_Mutation	SNP	127719194	127719194	17590	3	C	T	T	23	23	UROC1	T	1	1
ACAD11	84129	broad.mit.edu	36	3	133843645	133843645	+	Missense_Mutation	SNP	G	C	C			TCGA-28-5209-01	TCGA-28-5209-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr3:133843645G>C	uc003eov.2	-	c.398C>G	c.(397-399)ACA>AGA	p.T133R	ACAD11_uc003eoy.2_Missense_Mutation_p.T133R	NM_032169	NP_115545	Q709F0	ACD11_HUMAN	putative acyl-CoA dehydrogenase	133					oxidation-reduction process	peroxisome	acyl-CoA dehydrogenase activity|flavin adenine dinucleotide binding			ovary(1)	1														0.354067	251.691459	255.614226	74	135	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	133843645	133843645	110	3	G	C	C	48	48	ACAD11	C	3	3
MST1R	4486	broad.mit.edu	36	3	49915352	49915352	+	Missense_Mutation	SNP	A	T	T			TCGA-28-5209-01	TCGA-28-5209-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr3:49915352A>T	uc003cxy.2	-	c.695T>A	c.(694-696)TTT>TAT	p.F232Y		NM_002447	NP_002438	Q04912	RON_HUMAN	macrophage stimulating 1 receptor precursor	232	Extracellular (Potential).|Sema.				cellular component movement|defense response|multicellular organismal development|positive regulation of cell proliferation|protein phosphorylation|single fertilization|transmembrane receptor protein tyrosine kinase signaling pathway	integral to plasma membrane	ATP binding|macrophage colony-stimulating factor receptor activity|protein binding			ovary(5)|lung(1)	6										205				0.454545	111.184732	111.343531	40	48	AA		KEEP	---	---	---	---	capture		BRCA - Breast invasive adenocarcinoma(193;4.65e-05)|KIRC - Kidney renal clear cell carcinoma(197;0.00553)|Kidney(197;0.00625)	Missense_Mutation	SNP	49915352	49915352	10284	3	A	T	T	1	1	MST1R	T	4	4
CACNA1D	776	broad.mit.edu	36	3	53812589	53812589	+	Nonsense_Mutation	SNP	T	G	G			TCGA-28-5209-01	TCGA-28-5209-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr3:53812589T>G	uc003dgu.2	+	c.5595T>G	c.(5593-5595)TAT>TAG	p.Y1865*	CACNA1D_uc003dgv.2_Nonsense_Mutation_p.Y1845*|CACNA1D_uc003dgy.2_Nonsense_Mutation_p.Y1821*|CACNA1D_uc003dgw.2_Nonsense_Mutation_p.Y1512*	NM_000720	NP_000711	Q01668	CAC1D_HUMAN	calcium channel, voltage-dependent, L type,	1845	Cytoplasmic (Potential).				axon guidance|energy reserve metabolic process|regulation of insulin secretion	voltage-gated calcium channel complex	voltage-gated calcium channel activity			ovary(6)|liver(1)	7					Verapamil(DB00661)									0.481579	633.228345	633.339059	183	197	TT		KEEP	---	---	---	---	capture		BRCA - Breast invasive adenocarcinoma(193;0.00029)|KIRC - Kidney renal clear cell carcinoma(284;0.0145)|Kidney(284;0.0175)|OV - Ovarian serous cystadenocarcinoma(275;0.0613)	Nonsense_Mutation	SNP	53812589	53812589	2657	3	T	G	G	52	52	CACNA1D	G	5	4
ADAD1	132612	broad.mit.edu	36	4	123536967	123536967	+	Missense_Mutation	SNP	T	C	C			TCGA-28-5209-01	TCGA-28-5209-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr4:123536967T>C	uc003ieo.1	+	c.709T>C	c.(709-711)TTT>CTT	p.F237L	ADAD1_uc003iep.1_Missense_Mutation_p.F237L|ADAD1_uc003ieq.1_Missense_Mutation_p.F219L	NM_139243	NP_640336	Q96M93	ADAD1_HUMAN	adenosine deaminase domain containing 1	237					multicellular organismal development|RNA processing	nucleus	adenosine deaminase activity|double-stranded RNA binding				0														0.378205	208.59592	210.623543	59	97	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	123536967	123536967	232	4	T	C	C	64	64	ADAD1	C	4	4
ABCG2	9429	broad.mit.edu	36	4	89272787	89272787	+	Silent	SNP	G	A	A			TCGA-28-5209-01	TCGA-28-5209-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr4:89272787G>A	uc003hrg.1	-	c.228C>T	c.(226-228)AAC>AAT	p.N76N	ABCG2_uc003hrf.1_5'Flank|ABCG2_uc003hrh.1_Silent_p.N76N|ABCG2_uc003hri.1_Silent_p.N76N|ABCG2_uc003hrj.1_Silent_p.N76N|ABCG2_uc003hrk.1_Silent_p.N76N	NM_004827	NP_004818	Q9UNQ0	ABCG2_HUMAN	ATP-binding cassette, sub-family G, member 2	76	ABC transporter.|Cytoplasmic (Potential).				cellular iron ion homeostasis|urate metabolic process	integral to membrane|plasma membrane	ATP binding|heme transporter activity|protein homodimerization activity|xenobiotic-transporting ATPase activity			central_nervous_system(1)	1		Hepatocellular(203;0.114)			Imatinib(DB00619)|Mitoxantrone(DB01204)|Nicardipine(DB00622)|Nitrendipine(DB01054)|Rosuvastatin(DB01098)|Saquinavir(DB01232)|Topotecan(DB01030)									0.454545	279.394767	279.771479	95	114	GG		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(123;7.02e-05)	Silent	SNP	89272787	89272787	70	4	G	A	A	40	40	ABCG2	A	1	1
PDHA2	5161	broad.mit.edu	36	4	96981228	96981228	+	Nonsense_Mutation	SNP	C	T	T			TCGA-28-5209-01	TCGA-28-5209-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr4:96981228C>T	uc003htr.2	+	c.904C>T	c.(904-906)CGA>TGA	p.R302*		NM_005390	NP_005381	P29803	ODPAT_HUMAN	pyruvate dehydrogenase (lipoamide) alpha 2	302					glycolysis|oxidation-reduction process	mitochondrial matrix	pyruvate dehydrogenase (acetyl-transferring) activity			central_nervous_system(1)	1		Hepatocellular(203;0.114)			NADH(DB00157)									0.405229	180.418059	181.619609	62	91	CC		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(123;1.23e-06)	Nonsense_Mutation	SNP	96981228	96981228	12086	4	C	T	T	19	19	PDHA2	T	5	1
SLC22A5	6584	broad.mit.edu	36	5	131757822	131757822	+	Missense_Mutation	SNP	G	T	T			TCGA-28-5209-01	TCGA-28-5209-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr5:131757822G>T	uc003kwx.2	+	c.1705G>T	c.(1705-1707)GGT>TGT	p.G569C	SLC22A5_uc003kww.2_Missense_Mutation_p.G545C	NM_003060	NP_003051	O76082	S22A5_HUMAN	solute carrier family 22 member 5	545					positive regulation of intestinal epithelial structure maintenance|quorum sensing involved in interaction with host|sodium ion transport|sodium-dependent organic cation transport	apical plasma membrane|brush border membrane|integral to membrane	ATP binding|carnitine transporter activity|PDZ domain binding|symporter activity				0		all_cancers(142;0.0751)|Breast(839;0.198)			L-Carnitine(DB00583)									0.426901	219.050131	219.846392	73	98	GG		KEEP	---	---	---	---	capture	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)		Missense_Mutation	SNP	131757822	131757822	14954	5	G	T	T	47	47	SLC22A5	T	3	3
PCDHGB3	56102	broad.mit.edu	36	5	140731664	140731664	+	Missense_Mutation	SNP	G	A	A			TCGA-28-5209-01	TCGA-28-5209-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr5:140731664G>A	uc003ljw.1	+	c.1519G>A	c.(1519-1521)GTG>ATG	p.V507M	PCDHGA1_uc003lji.1_Intron|PCDHGA2_uc003ljk.1_Intron|PCDHGA3_uc010jfx.1_Intron|PCDHGA3_uc003ljm.1_Intron|PCDHGB1_uc003ljo.1_Intron|PCDHGA4_uc003ljq.1_Intron|PCDHGB2_uc003ljs.1_Intron|PCDHGA5_uc003lju.1_Intron|PCDHGA6_uc003ljy.1_5'Flank|PCDHGB3_uc003ljv.1_Missense_Mutation_p.V507M|PCDHGA6_uc003ljx.1_5'Flank	NM_018924	NP_061747	Q9Y5G1	PCDGF_HUMAN	protocadherin gamma subfamily B, 3 isoform 1	507	Extracellular (Potential).|Cadherin 5.				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding				0														0.447761	170.371927	170.691523	60	74	GG		KEEP	---	---	---	---	capture	KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)		Missense_Mutation	SNP	140731664	140731664	11984	5	G	A	A	40	40	PCDHGB3	A	1	1
GRM6	2916	broad.mit.edu	36	5	178341374	178341374	+	Missense_Mutation	SNP	C	T	T			TCGA-28-5209-01	TCGA-28-5209-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr5:178341374C>T	uc003mjr.1	-	c.2524G>A	c.(2524-2526)GTC>ATC	p.V842I	GRM6_uc003mjq.1_Missense_Mutation_p.V245I	NM_000843	NP_000834	O15303	GRM6_HUMAN	glutamate receptor, metabotropic 6 precursor	842	Helical; Name=7; (Potential).				detection of visible light|visual perception	integral to plasma membrane				ovary(2)|breast(1)|pancreas(1)	4	all_cancers(89;0.000828)|Renal(175;0.000159)|all_epithelial(37;0.000167)|Lung NSC(126;0.00199)|all_lung(126;0.00351)	all_cancers(40;0.0156)|all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)												0.515723	469.949971	470.016782	164	154	CC		KEEP	---	---	---	---	capture	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	all cancers(165;0.245)	Missense_Mutation	SNP	178341374	178341374	7080	5	C	T	T	19	19	GRM6	T	1	1
RASGRF2	5924	broad.mit.edu	36	5	80418514	80418514	+	Missense_Mutation	SNP	C	T	T			TCGA-28-5209-01	TCGA-28-5209-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr5:80418514C>T	uc003kha.1	+	c.1376C>T	c.(1375-1377)ACG>ATG	p.T459M	RASGRF2_uc003khb.1_Missense_Mutation_p.T287M	NM_006909	NP_008840	O14827	RGRF2_HUMAN	Ras protein-specific guanine	459					apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction|synaptic transmission	cytosol|endoplasmic reticulum membrane|plasma membrane	protein binding|Rho guanyl-nucleotide exchange factor activity			breast(3)|ovary(2)|large_intestine(2)|central_nervous_system(1)|skin(1)	9		Lung NSC(167;0.00498)|all_lung(232;0.00531)|Ovarian(174;0.0357)								847				0.401709	133.724974	134.705532	47	70	CC		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(54;4.22e-42)|Epithelial(54;4.04e-35)|all cancers(79;2.52e-29)	Missense_Mutation	SNP	80418514	80418514	13534	5	C	T	T	19	19	RASGRF2	T	1	1
SYNJ2	8871	broad.mit.edu	36	6	158403041	158403041	+	Silent	SNP	C	T	T			TCGA-28-5209-01	TCGA-28-5209-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr6:158403041C>T	uc003qqx.1	+	c.984C>T	c.(982-984)GGC>GGT	p.G328G	SYNJ2_uc003qqw.1_Silent_p.G328G|SYNJ2_uc003qqy.1_Silent_p.G88G|SYNJ2_uc010kjo.1_Silent_p.G277G|SYNJ2_uc003qqz.1_5'UTR	NM_003898	NP_003889	O15056	SYNJ2_HUMAN	synaptojanin 2	328	SAC.						nucleotide binding|phosphatidylinositol-4,5-bisphosphate 5-phosphatase activity|RNA binding			skin(1)	1														0.848592	761.77133	795.067503	241	43	CC		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(65;4.42e-18)|BRCA - Breast invasive adenocarcinoma(81;4.23e-05)	Silent	SNP	158403041	158403041	15974	6	C	T	T	27	27	SYNJ2	T	1	1
LRFN2	57497	broad.mit.edu	36	6	40467706	40467706	+	Missense_Mutation	SNP	C	T	T			TCGA-28-5209-01	TCGA-28-5209-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr6:40467706C>T	uc003oph.1	-	c.2324G>A	c.(2323-2325)CGG>CAG	p.R775Q		NM_020737	NP_065788	Q9ULH4	LRFN2_HUMAN	leucine rich repeat and fibronectin type III	775	Cytoplasmic (Potential).					cell junction|integral to membrane|postsynaptic membrane				ovary(2)	2	Ovarian(28;0.0418)|Colorectal(47;0.196)													0.49635	210.004062	210.005516	68	69	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	40467706	40467706	9311	6	C	T	T	23	23	LRFN2	T	1	1
DEFB114	245928	broad.mit.edu	36	6	50036091	50036091	+	Missense_Mutation	SNP	C	T	T			TCGA-28-5209-01	TCGA-28-5209-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr6:50036091C>T	uc003ozz.1	-	c.83G>A	c.(82-84)CGT>CAT	p.R28H		NM_001037499	NP_001032588	Q30KQ6	DB114_HUMAN	beta-defensin 114	28					defense response to bacterium	extracellular region				ovary(1)	1	Lung NSC(77;0.042)													0.34127	120.785758	123.591657	43	83	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	50036091	50036091	4580	6	C	T	T	19	19	DEFB114	T	1	1
SVOPL	136306	broad.mit.edu	36	7	137956413	137956413	+	Missense_Mutation	SNP	G	A	A			TCGA-28-5209-01	TCGA-28-5209-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr7:137956413G>A	uc003vue.1	-	c.815C>T	c.(814-816)CCC>CTC	p.P272L	SVOPL_uc003vud.1_Non-coding_Transcript	NM_174959	NP_777619	Q8N434	SVOPL_HUMAN	SVOP-like isoform 2	424					transmembrane transport	integral to membrane	transporter activity				0														0.267241	83.6719	89.348152	31	85	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	137956413	137956413	15944	7	G	A	A	43	43	SVOPL	A	2	2
CARD11	84433	broad.mit.edu	36	7	2919546	2919546	+	Missense_Mutation	SNP	G	A	A			TCGA-28-5209-01	TCGA-28-5209-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr7:2919546G>A	uc003smv.2	-	c.2920C>T	c.(2920-2922)CGC>TGC	p.R974C		NM_032415	NP_115791	Q9BXL7	CAR11_HUMAN	caspase recruitment domain family, member 11	974	Guanylate kinase-like.				positive regulation of cytokine production|positive regulation of NF-kappaB transcription factor activity|regulation of apoptosis|T cell costimulation|T cell receptor signaling pathway	cytosol|membrane raft|plasma membrane	CARD domain binding|guanylate kinase activity			haematopoietic_and_lymphoid_tissue(43)|ovary(2)|kidney(2)|central_nervous_system(1)	48		Ovarian(82;0.0115)								1492				0.317536	189.254843	195.497623	67	144	GG		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(56;8.44e-14)	Missense_Mutation	SNP	2919546	2919546	2764	7	G	A	A	39	39	CARD11	A	1	1
CCDC129	223075	broad.mit.edu	36	7	31649030	31649030	+	Silent	SNP	G	A	A			TCGA-28-5209-01	TCGA-28-5209-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr7:31649030G>A	uc003tcj.1	+	c.1521G>A	c.(1519-1521)CTG>CTA	p.L507L	CCDC129_uc003tci.1_Silent_p.L358L|CCDC129_uc003tck.1_Silent_p.L415L	NM_194300	NP_919276	Q6ZRS4	CC129_HUMAN	coiled-coil domain containing 129	507											0														0.297003	263.927202	277.455144	109	258	GG		KEEP	---	---	---	---	capture			Silent	SNP	31649030	31649030	2884	7	G	A	A	46	46	CCDC129	A	2	2
AEBP1	165	broad.mit.edu	36	7	44112911	44112911	+	Silent	SNP	G	A	A			TCGA-28-5209-01	TCGA-28-5209-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr7:44112911G>A	uc003tkb.1	+	c.495G>A	c.(493-495)CCG>CCA	p.P165P		NM_001129	NP_001120	Q8IUX7	AEBP1_HUMAN	adipocyte enhancer binding protein 1 precursor	165	Pro-rich.				cell adhesion|muscle organ development|proteolysis|regulation of transcription, DNA-dependent|skeletal system development	cytoplasm|extracellular space|nucleus	DNA binding|metallocarboxypeptidase activity|sequence-specific DNA binding transcription factor activity|zinc ion binding				0														0.402778	77.921261	78.525955	29	43	GG		KEEP	---	---	---	---	capture			Silent	SNP	44112911	44112911	350	7	G	A	A	40	40	AEBP1	A	1	1
EGFR	1956	broad.mit.edu	36	7	55200537	55200537	+	Missense_Mutation	SNP	G	C	C			TCGA-28-5209-01	TCGA-28-5209-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr7:55200537G>C	uc003tqk.1	+	c.1793G>C	c.(1792-1794)GGA>GCA	p.G598A	EGFR_uc003tqi.1_Missense_Mutation_p.G598A|EGFR_uc003tqj.1_Missense_Mutation_p.G598A|EGFR_uc010kzg.1_Missense_Mutation_p.G553A|EGFR_uc003tqn.1_Non-coding_Transcript	NM_005228	NP_005219	P00533	EGFR_HUMAN	epidermal growth factor receptor isoform a	598	Approximate.|Extracellular (Potential).				activation of phospholipase A2 activity by calcium-mediated signaling|activation of phospholipase C activity|axon guidance|cell proliferation|cell-cell adhesion|negative regulation of apoptosis|negative regulation of epidermal growth factor receptor signaling pathway|ossification|positive regulation of catenin import into nucleus|positive regulation of cell migration|positive regulation of cyclin-dependent protein kinase activity involved in G1/S|positive regulation of epithelial cell proliferation|positive regulation of MAP kinase activity|positive regulation of nitric oxide biosynthetic process|positive regulation of phosphorylation|positive regulation of protein kinase B signaling cascade|protein autophosphorylation|protein insertion into membrane|regulation of nitric-oxide synthase activity|regulation of peptidyl-tyrosine phosphorylation|response to stress|response to UV-A	basolateral plasma membrane|endoplasmic reticulum membrane|endosome|extracellular space|Golgi membrane|integral to membrane|nuclear membrane|Shc-EGFR complex	actin filament binding|ATP binding|double-stranded DNA binding|epidermal growth factor receptor activity|identical protein binding|MAP/ERK kinase kinase activity|protein heterodimerization activity|protein phosphatase binding|receptor signaling protein tyrosine kinase activity	p.G598V(16)		lung(8200)|central_nervous_system(103)|upper_aerodigestive_tract(37)|prostate(32)|ovary(31)|thyroid(23)|breast(11)|peritoneum(9)|oesophagus(9)|salivary_gland(9)|large_intestine(8)|stomach(6)|urinary_tract(6)|skin(5)|adrenal_gland(5)|kidney(4)|soft_tissue(4)|bone(3)|NS(2)|haematopoietic_and_lymphoid_tissue(2)|thymus(2)|liver(2)|eye(1)|pancreas(1)	8515	all_cancers(1;1.57e-46)|all_epithelial(1;5.62e-37)|Lung NSC(1;9.29e-25)|all_lung(1;4.39e-23)|Esophageal squamous(2;7.55e-08)|Breast(14;0.0318)				Cetuximab(DB00002)|Erlotinib(DB00530)|Gefitinib(DB00317)|Lapatinib(DB01259)|Lidocaine(DB00281)|Panitumumab(DB01269)|Trastuzumab(DB00072)			8		608	TCGA GBM(3;<1E-8)|TSP Lung(4;<1E-8)			0.132789	238.331258	366.501324	130	849	GG		KEEP	---	---	---	---	capture	GBM - Glioblastoma multiforme(1;0)|all cancers(1;2.19e-314)|Lung(13;4.65e-05)|LUSC - Lung squamous cell carcinoma(13;0.000168)|STAD - Stomach adenocarcinoma(5;0.00164)|Epithelial(13;0.0607)		Missense_Mutation	SNP	55200537	55200537	5156	7	G	C	C	41	41	EGFR	C	3	3
CALN1	83698	broad.mit.edu	36	7	70890791	70890791	+	Missense_Mutation	SNP	C	T	T			TCGA-28-5209-01	TCGA-28-5209-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr7:70890791C>T	uc003twb.2	-	c.691G>A	c.(691-693)GTC>ATC	p.V231I	CALN1_uc003twa.2_Missense_Mutation_p.V189I|CALN1_uc003twc.2_Missense_Mutation_p.V189I	NM_031468	NP_113656	Q9BXU9	CABP8_HUMAN	calneuron 1 isoform 1	189	Cytoplasmic (Potential).					Golgi apparatus|integral to membrane|perinuclear region of cytoplasm|plasma membrane	calcium ion binding				0		all_cancers(73;0.069)|Lung NSC(55;0.0658)|all_lung(88;0.0912)|all_epithelial(88;0.161)												0.349462	175.908956	179.632448	65	121	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	70890791	70890791	2708	7	C	T	T	19	19	CALN1	T	1	1
FZD9	8326	broad.mit.edu	36	7	72486429	72486429	+	Nonsense_Mutation	SNP	C	A	A			TCGA-28-5209-01	TCGA-28-5209-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr7:72486429C>A	uc003tyb.1	+	c.156C>A	c.(154-156)TAC>TAA	p.Y52*		NM_003508	NP_003499	O00144	FZD9_HUMAN	frizzled 9	52	FZ.|Extracellular (Potential).				B cell differentiation|brain development|canonical Wnt receptor signaling pathway|embryo development|gonad development|neuroblast proliferation|regulation of gene-specific transcription from RNA polymerase II promoter|vasculature development	cell surface|filopodium membrane|integral to membrane|perinuclear region of cytoplasm	G-protein coupled receptor activity|PDZ domain binding|protein heterodimerization activity|protein homodimerization activity|Wnt receptor activity|Wnt-protein binding			central_nervous_system(1)	1		Lung NSC(55;0.0659)|all_lung(88;0.152)				Pancreas(144;909 1878 36867 38226 39554)								0.318182	7.227318	7.926788	7	15	CC		KEEP	---	---	---	---	capture			Nonsense_Mutation	SNP	72486429	72486429	6388	7	C	A	A	17	17	FZD9	A	5	3
SEMA3E	9723	broad.mit.edu	36	7	82870018	82870018	+	Nonsense_Mutation	SNP	G	A	A			TCGA-28-5209-01	TCGA-28-5209-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr7:82870018G>A	uc003uhy.1	-	c.1009C>T	c.(1009-1011)CGA>TGA	p.R337*		NM_012431	NP_036563	O15041	SEM3E_HUMAN	semaphorin 3E	337	Sema.				axon guidance	extracellular space|membrane	receptor activity			ovary(3)	3		Medulloblastoma(109;0.109)												0.279412	98.486879	104.441246	38	98	GG		KEEP	---	---	---	---	capture			Nonsense_Mutation	SNP	82870018	82870018	14514	7	G	A	A	37	37	SEMA3E	A	5	1
ABCB4	5244	broad.mit.edu	36	7	86912140	86912140	+	Missense_Mutation	SNP	A	G	G			TCGA-28-5209-01	TCGA-28-5209-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr7:86912140A>G	uc003uiv.1	-	c.1093T>C	c.(1093-1095)TAT>CAT	p.Y365H	ABCB4_uc003uiw.1_Missense_Mutation_p.Y365H|ABCB4_uc003uix.1_Missense_Mutation_p.Y365H	NM_018849	NP_061337	P21439	MDR3_HUMAN	ATP-binding cassette, subfamily B, member 4	365	Cytoplasmic (By similarity).				cellular lipid metabolic process	apical plasma membrane|Golgi membrane|integral to plasma membrane|intercellular canaliculus|membrane fraction	ATP binding|xenobiotic-transporting ATPase activity			ovary(4)|pancreas(1)	5	Esophageal squamous(14;0.0058)|all_lung(186;0.201)|Lung NSC(181;0.203)													0.258065	75.46385	80.391164	24	69	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	86912140	86912140	44	7	A	G	G	16	16	ABCB4	G	4	4
COL1A2	1278	broad.mit.edu	36	7	93892885	93892885	+	Missense_Mutation	SNP	G	T	T	rs72659309	unknown	TCGA-28-5209-01	TCGA-28-5209-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr7:93892885G>T	uc003ung.1	+	c.2809G>T	c.(2809-2811)GGT>TGT	p.G937C		NM_000089	NP_000080	P08123	CO1A2_HUMAN	alpha 2 type I collagen	937					axon guidance|blood vessel development|collagen fibril organization|leukocyte migration|odontogenesis|platelet activation|regulation of blood pressure|Rho protein signal transduction|skeletal system development|skin morphogenesis|transforming growth factor beta receptor signaling pathway	collagen type I|extracellular space|plasma membrane	extracellular matrix structural constituent|identical protein binding|platelet-derived growth factor binding|protein binding, bridging	p.G937S(1)		central_nervous_system(3)|ovary(2)	5	all_cancers(62;2.46e-09)|all_epithelial(64;2.7e-08)				Collagenase(DB00048)									0.264	166.733452	179.325115	66	184	GG		KEEP	---	---	---	---	capture	STAD - Stomach adenocarcinoma(171;0.0031)		Missense_Mutation	SNP	93892885	93892885	3816	7	G	T	T	35	35	COL1A2	T	3	3
TMEM130	222865	broad.mit.edu	36	7	98287159	98287159	+	Missense_Mutation	SNP	C	T	T			TCGA-28-5209-01	TCGA-28-5209-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr7:98287159C>T	uc003upo.1	-	c.827G>A	c.(826-828)CGT>CAT	p.R276H	TMEM130_uc003upm.1_Missense_Mutation_p.R276H|TMEM130_uc003upn.1_Missense_Mutation_p.R174H	NM_152913	NP_690877	Q8N3G9	TM130_HUMAN	transmembrane protein 130 isoform b	276	Extracellular (Potential).					Golgi membrane|integral to membrane				ovary(1)|central_nervous_system(1)	2	all_cancers(62;4.05e-09)|all_epithelial(64;2.62e-09)|Lung NSC(181;0.01)|all_lung(186;0.0115)|Esophageal squamous(72;0.0274)													0.2625	52.248275	56.324613	21	59	CC		KEEP	---	---	---	---	capture	STAD - Stomach adenocarcinoma(171;0.215)		Missense_Mutation	SNP	98287159	98287159	16574	7	C	T	T	19	19	TMEM130	T	1	1
FAM83H	286077	broad.mit.edu	36	8	144882333	144882333	+	Missense_Mutation	SNP	A	C	C			TCGA-28-5209-01	TCGA-28-5209-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr8:144882333A>C	uc003yzk.1	-	c.1286T>G	c.(1285-1287)GTG>GGG	p.V429G	FAM83H_uc010mfk.1_Non-coding_Transcript	NM_198488	NP_940890	Q6ZRV2	FA83H_HUMAN	hypothetical protein LOC286077	429					biomineral tissue development					lung(1)|central_nervous_system(1)|pancreas(1)	3	all_cancers(97;3.74e-11)|all_epithelial(106;2.62e-09)|Lung NSC(106;0.00013)|all_lung(105;0.000374)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)													0.3125	6.375843	6.936741	5	11	AA		KEEP	---	---	---	---	capture	OV - Ovarian serous cystadenocarcinoma(54;3.38e-41)|Epithelial(56;6.8e-40)|all cancers(56;6.43e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.146)		Missense_Mutation	SNP	144882333	144882333	5866	8	A	C	C	6	6	FAM83H	C	4	4
NFKBIL2	4796	broad.mit.edu	36	8	145632452	145632452	+	Silent	SNP	T	G	G			TCGA-28-5209-01	TCGA-28-5209-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr8:145632452T>G	uc003zcu.2	-	c.1695A>C	c.(1693-1695)GCA>GCC	p.A565A		NM_013432	NP_038460	Q96HA7	TONSL_HUMAN	NF-kappa-B inhibitor-like protein 2	724					cytoplasmic sequestering of transcription factor|double-strand break repair via homologous recombination|replication fork processing	cytoplasm|nuclear replication fork	histone binding|transcription corepressor activity				0	all_cancers(97;4.61e-11)|all_epithelial(106;2.89e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)													0.291667	6.58064	7.612729	7	17	TT		KEEP	---	---	---	---	capture	OV - Ovarian serous cystadenocarcinoma(54;1.08e-41)|Epithelial(56;8.67e-41)|all cancers(56;1.1e-35)|BRCA - Breast invasive adenocarcinoma(115;0.035)|Colorectal(110;0.055)		Silent	SNP	145632452	145632452	10782	8	T	G	G	59	59	NFKBIL2	G	4	4
NRK	203447	broad.mit.edu	36	X	105043400	105043400	+	Missense_Mutation	SNP	T	G	G			TCGA-28-5209-01	TCGA-28-5209-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chrX:105043400T>G	uc004emd.1	+	c.2346T>G	c.(2344-2346)ATT>ATG	p.I782M	NRK_uc010npc.1_Missense_Mutation_p.I450M	NM_198465	NP_940867	Q7Z2Y5	NRK_HUMAN	Nik related kinase	782					protein phosphorylation		ATP binding|protein serine/threonine kinase activity|small GTPase regulator activity			breast(7)|ovary(3)|lung(2)|large_intestine(1)|central_nervous_system(1)	14										430				0.47619	36.45032	36.460576	10	11	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	105043400	105043400	11060	23	T	G	G	63	63	NRK	G	4	4
MTMR1	8776	broad.mit.edu	36	X	149649266	149649266	+	Missense_Mutation	SNP	A	G	G			TCGA-28-5209-01	TCGA-28-5209-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chrX:149649266A>G	uc004feh.1	+	c.583A>G	c.(583-585)AAA>GAA	p.K195E	MTMR1_uc004fei.1_Missense_Mutation_p.K187E|MTMR1_uc004fej.1_Non-coding_Transcript|MTMR1_uc010ntf.1_Non-coding_Transcript|MTMR1_uc004feg.1_Missense_Mutation_p.K187E	NM_003828	NP_003819	Q13613	MTMR1_HUMAN	myotubularin-related protein 1	187						plasma membrane	protein tyrosine phosphatase activity			ovary(1)	1	Acute lymphoblastic leukemia(192;6.56e-05)													0.455696	248.927314	249.18878	72	86	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	149649266	149649266	10331	23	A	G	G	13	13	MTMR1	G	4	4
PLXNB3	5365	broad.mit.edu	36	X	152686067	152686067	+	Silent	SNP	G	A	A			TCGA-28-5209-01	TCGA-28-5209-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chrX:152686067G>A	uc004fii.1	+	c.591G>A	c.(589-591)TCG>TCA	p.S197S	PLXNB3_uc010nuk.1_Silent_p.S220S	NM_005393	NP_005384	Q9ULL4	PLXB3_HUMAN	plexin B3	197	Extracellular (Potential).|Sema.				axon guidance	integral to membrane|intracellular|plasma membrane	protein binding|receptor activity			lung(1)	1	all_hematologic(71;4.25e-06)|all_lung(58;3.83e-05)|Lung NSC(58;5.54e-05)|Acute lymphoblastic leukemia(192;6.56e-05)													0.26087	14.541562	15.730937	6	17	GG		KEEP	---	---	---	---	capture			Silent	SNP	152686067	152686067	12551	23	G	A	A	39	39	PLXNB3	A	1	1
ZNF157	7712	broad.mit.edu	36	X	47157267	47157267	+	Missense_Mutation	SNP	G	A	A			TCGA-28-5209-01	TCGA-28-5209-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chrX:47157267G>A	uc004dhr.1	+	c.851G>A	c.(850-852)CGT>CAT	p.R284H		NM_003446	NP_003437	P51786	ZN157_HUMAN	zinc finger protein 157	284	C2H2-type 5.				negative regulation of transcription from RNA polymerase II promoter	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding				0														0.43038	100.237157	100.571113	34	45	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	47157267	47157267	18328	23	G	A	A	40	40	ZNF157	A	1	1
SUV39H1	6839	broad.mit.edu	36	X	48449931	48449931	+	Silent	SNP	C	T	T			TCGA-28-5209-01	TCGA-28-5209-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chrX:48449931C>T	uc004dkn.1	+	c.1074C>T	c.(1072-1074)GGC>GGT	p.G358G		NM_003173	NP_003164	O43463	SUV91_HUMAN	suppressor of variegation 3-9 homolog 1	358	Mediates interaction with MECOM (By similarity).|SET.				cell cycle|cell differentiation|chromatin assembly or disassembly|chromatin silencing at rDNA|interspecies interaction between organisms|rRNA processing|transcription, DNA-dependent	chromatin silencing complex|chromosome, centromeric region|condensed nuclear chromosome|rDNA heterochromatin	chromatin binding|histone methyltransferase activity (H3-K9 specific)|protein N-terminus binding|zinc ion binding				0														0.473684	51.345965	51.368859	18	20	CC		KEEP	---	---	---	---	capture			Silent	SNP	48449931	48449931	15932	23	C	T	T	27	27	SUV39H1	T	1	1
ZC3H12B	340554	broad.mit.edu	36	X	64638930	64638930	+	Missense_Mutation	SNP	C	A	A			TCGA-28-5209-01	TCGA-28-5209-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chrX:64638930C>A	uc010nko.1	+	c.1594C>A	c.(1594-1596)CAT>AAT	p.H532N		NM_001010888	NP_001010888	Q5HYM0	ZC12B_HUMAN	zinc finger CCCH-type containing 12B	532							endonuclease activity|nucleic acid binding|zinc ion binding			lung(1)|kidney(1)|pancreas(1)	3														0.477987	228.581679	228.649239	76	83	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	64638930	64638930	18150	23	C	A	A	21	21	ZC3H12B	A	3	3
GPR174	84636	broad.mit.edu	36	X	78313721	78313721	+	Silent	SNP	C	A	A			TCGA-28-5209-01	TCGA-28-5209-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chrX:78313721C>A	uc004edg.1	+	c.561C>A	c.(559-561)ACC>ACA	p.T187T		NM_032553	NP_115942	Q9BXC1	GP174_HUMAN	putative purinergic receptor FKSG79	187	Helical; Name=5; (Potential).					integral to membrane|plasma membrane	purinergic nucleotide receptor activity, G-protein coupled			lung(1)|central_nervous_system(1)	2														0.466387	335.049233	335.287669	111	127	CC		KEEP	---	---	---	---	capture			Silent	SNP	78313721	78313721	6947	23	C	A	A	21	21	GPR174	A	3	3
BRWD3	254065	broad.mit.edu	36	X	79846916	79846916	+	Missense_Mutation	SNP	G	A	A			TCGA-28-5209-01	TCGA-28-5209-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chrX:79846916G>A	uc004edt.2	-	c.2638C>T	c.(2638-2640)CGT>TGT	p.R880C	BRWD3_uc010nmi.1_Non-coding_Transcript|BRWD3_uc004edo.2_Missense_Mutation_p.R476C|BRWD3_uc004edp.2_Missense_Mutation_p.R709C|BRWD3_uc004edq.2_Missense_Mutation_p.R476C|BRWD3_uc010nmj.1_Missense_Mutation_p.R476C|BRWD3_uc004edr.2_Missense_Mutation_p.R550C|BRWD3_uc004eds.2_Missense_Mutation_p.R476C|BRWD3_uc004edu.2_Missense_Mutation_p.R550C|BRWD3_uc004edv.2_Missense_Mutation_p.R476C|BRWD3_uc004edw.2_Missense_Mutation_p.R476C|BRWD3_uc004edx.2_Missense_Mutation_p.R476C|BRWD3_uc004edy.2_Missense_Mutation_p.R476C|BRWD3_uc004edz.2_Missense_Mutation_p.R550C|BRWD3_uc004eea.2_Missense_Mutation_p.R550C|BRWD3_uc004eeb.2_Missense_Mutation_p.R476C	NM_153252	NP_694984	Q6RI45	BRWD3_HUMAN	bromodomain and WD repeat domain containing 3	880										ovary(4)	4														0.32	302.576609	312.652106	112	238	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	79846916	79846916	1557	23	G	A	A	40	40	BRWD3	A	1	1
PTEN	5728	broad.mit.edu	36	10	89707675	89707676	+	Frame_Shift_Ins	INS	-	T	T			TCGA-28-5209-01	TCGA-28-5209-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:89707675_89707676insT	uc001kfb.1	+	c.720_721insT	c.(718-723)TACTTTfs	p.Y240fs		NM_000314	NP_000305	P60484	PTEN_HUMAN	phosphatase and tensin homolog	240_241	C2 tensin-type.		F -> S (in MCEPHAS).		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.F241L(1)|p.F241fs*1(1)|p.G165_K342del(1)|p.G165_*404del(1)|p.R234fs*9(1)|p.F241fs*17(1)		endometrium(831)|central_nervous_system(654)|skin(119)|haematopoietic_and_lymphoid_tissue(101)|prostate(97)|large_intestine(90)|breast(67)|lung(63)|ovary(58)|thyroid(29)|stomach(29)|upper_aerodigestive_tract(25)|cervix(21)|liver(20)|vulva(17)|kidney(15)|NS(14)|soft_tissue(12)|urinary_tract(12)|eye(8)|pancreas(6)|salivary_gland(5)|bone(5)|biliary_tract(4)|autonomic_ganglia(2)|meninges(2)|testis(1)|oesophagus(1)	2308		all_cancers(4;3.61e-31)|all_epithelial(4;3.96e-23)|Prostate(4;8.12e-23)|Breast(4;0.000111)|Melanoma(5;0.00146)|all_hematologic(4;0.00227)|Colorectal(252;0.00494)|all_neural(4;0.00513)|Acute lymphoblastic leukemia(4;0.0116)|Glioma(4;0.0274)|all_lung(38;0.132)	KIRC - Kidney renal clear cell carcinoma(1;0.214)	UCEC - Uterine corpus endometrioid carcinoma (6;0.000228)|all cancers(1;4.16e-84)|GBM - Glioblastoma multiforme(1;7.77e-49)|Epithelial(1;7.67e-41)|OV - Ovarian serous cystadenocarcinoma(1;6.22e-15)|BRCA - Breast invasive adenocarcinoma(1;1.1e-06)|Lung(2;3.18e-06)|Colorectal(12;4.88e-06)|LUSC - Lung squamous cell carcinoma(2;4.97e-06)|COAD - Colon adenocarcinoma(12;1.13e-05)|Kidney(1;0.000288)|KIRC - Kidney renal clear cell carcinoma(1;0.00037)|STAD - Stomach adenocarcinoma(243;0.218)				31	p.F241L(SNU449-Tumor)	264	TCGA GBM(2;<1E-8)|TSP Lung(26;0.18)			0.76			108	35				---	---	---	---	capture_indel			Frame_Shift_Ins	INS	89707675	89707676	13192	10	-	T	T	20	20	PTEN	T	5	5
COX16	51241	broad.mit.edu	36	14	69862769	69862769	+	Splice_Site_Del	DEL	A	-	-	rs71744102	unknown	TCGA-28-5209-01	TCGA-28-5209-01										Phase_I	Unspecified				Illumina GAIIx	g.chr14:69862769_69862769delA	uc001xmb.1	-	c.e4_splice_site				NM_016468	NP_057552			COX16 cytochrome c oxidase assembly homolog							integral to membrane|mitochondrial membrane					0														0.36			4	7				---	---	---	---	capture_indel			Splice_Site_Del	DEL	69862769	69862769	3903	14	A	-	-	13	13	COX16	-	5	5
TAOK1	57551	broad.mit.edu	36	17	24802707	24802719	+	Frame_Shift_Del	DEL	CAGAGCAGGCAGC	-	-			TCGA-28-5209-01	TCGA-28-5209-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:24802707_24802719delCAGAGCAGGCAGC	uc002hdz.1	+	c.15_27delCAGAGCAGGCAGC	c.(13-27)AACAGAGCAGGCAGCfs	p.N5fs		NM_020791	NP_065842	Q7L7X3	TAOK1_HUMAN	TAO kinase 1	5_9					mitotic prometaphase|protein phosphorylation	cytosol|intracellular membrane-bounded organelle	ATP binding|protein serine/threonine kinase activity			upper_aerodigestive_tract(1)|lung(1)|central_nervous_system(1)|skin(1)	4			Colorectal(6;0.198)							290				0.35			35	65				---	---	---	---	capture_indel			Frame_Shift_Del	DEL	24802707	24802719	16068	17	CAGAGCAGGCAGC	-	-	17	17	TAOK1	-	5	5
AKR7A3	22977	broad.mit.edu	36	1	19483832	19483832	+	Frame_Shift_Del	DEL	G	-	-			TCGA-28-5209-01	TCGA-28-5209-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:19483832_19483832delG	uc001bbv.1	-	c.639_639delC	c.(637-639)GACfs	p.D213fs		NM_012067	NP_036199	O95154	ARK73_HUMAN	aldo-keto reductase family 7, member A3	213					cellular aldehyde metabolic process|oxidation-reduction process	cytosol	aldo-keto reductase (NADP) activity|electron carrier activity				0		Colorectal(325;3.46e-05)|Renal(390;0.000147)|all_lung(284;0.000321)|Lung NSC(340;0.000398)|Breast(348;0.00049)|Ovarian(437;0.00764)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00459)|BRCA - Breast invasive adenocarcinoma(304;1.78e-05)|Kidney(64;0.00016)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|GBM - Glioblastoma multiforme(114;0.00276)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)										0.37			112	193				---	---	---	---	capture_indel			Frame_Shift_Del	DEL	19483832	19483832	479	1	G	-	-	48	48	AKR7A3	-	5	5
PODXL	5420	broad.mit.edu	36	7	130891570	130891575	+	In_Frame_Del	DEL	GGCGAC	-	-			TCGA-28-5209-01	TCGA-28-5209-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:130891570_130891575delGGCGAC	uc003vqw.2	-	c.84_89delGTCGCC	c.(82-90)CCGTCGCCC>CCC	p.28_30PSP>P	PODXL_uc003vqx.2_In_Frame_Del_p.28_30PSP>P	NM_001018111	NP_001018121	O00592	PODXL_HUMAN	podocalyxin-like isoform 1 precursor	28_30	Extracellular (Potential).				cell adhesion|epithelial tube formation|negative regulation of cell-cell adhesion|positive regulation of cell migration|positive regulation of cell-cell adhesion mediated by integrin|regulation of microvillus assembly	actin cytoskeleton|apical plasma membrane|centrosome|filopodium|integral to plasma membrane|lamellipodium|membrane raft|microvillus membrane|nucleolus|ruffle				breast(2)|pancreas(1)	3	Melanoma(18;0.162)													0.43			3	4				---	---	---	---	capture_indel			In_Frame_Del	DEL	130891570	130891575	12608	7	GGCGAC	-	-	43	43	PODXL	-	5	5
DOCK11	139818	broad.mit.edu	36	X	117632751	117632751	+	Frame_Shift_Del	DEL	C	-	-			TCGA-28-5209-01	TCGA-28-5209-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:117632751_117632751delC	uc004eqp.2	+	c.3165_3165delC	c.(3163-3165)AGCfs	p.S1055fs	DOCK11_uc004eqq.2_Frame_Shift_Del_p.S821fs	NM_144658	NP_653259	Q5JSL3	DOC11_HUMAN	dedicator of cytokinesis 11	1055					blood coagulation	cytosol	GTP binding			ovary(3)	3														0.72			124	48				---	---	---	---	capture_indel			Frame_Shift_Del	DEL	117632751	117632751	4870	23	C	-	-	26	26	DOCK11	-	5	5
