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	Tumor_Sample_UUID	Matched_Norm_Sample_UUID	Genome_Change	Annotation_Transcript	Transcript_Strand	Transcript_Exon	Transcript_Position	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	TCGAscape_Amplification_Peaks	TCGAscape_Deletion_Peaks	DrugBank	ref_context	gc_content	CCLE_ONCOMAP_overlapping_mutations	CCLE_ONCOMAP_total_mutations_in_gene	CGC_Mutation_Type	CGC_Translocation_Partner	CGC_Tumor_Types_Somatic	CGC_Tumor_Types_Germline	CGC_Other_Diseases	DNARepairGenes_Role	FamilialCancerDatabase_Syndromes	MUTSIG_Published_Results	OREGANNO_ID	OREGANNO_Values	t_alt_count	t_ref_count	validation_status	validation_method	validation_tumor_sample	validation_alt_allele	pox	qox	pox_cutoff	isArtifactMode	oxoGCut
MEGF6	1953	broad.mit.edu	37	1	3427403	3427403	+	Missense_Mutation	SNP	T	C	C			TCGA-ET-A39M-01A-11D-A19J-08	TCGA-ET-A39M-10A-01D-A19M-08									Somatic	Phase_I	Capture				Illumina GAIIx	39c627f7-225b-4a78-a589-e3228fed1d6e	cfdd0348-3531-4c23-bc2f-963173dfd77e	g.chr1:3427403T>C	uc001akl.2	-	10	1405	c.1178A>G	c.(1177-1179)TAC>TGC	p.Y393C	MEGF6_uc001akk.2_Missense_Mutation_p.Y288C	NM_001409	NP_001400	O75095	MEGF6_HUMAN	EGF-like-domain, multiple 3 precursor	393	EGF-like 7.					extracellular region	calcium ion binding			large_intestine(1)	1	all_cancers(77;0.00681)|all_epithelial(69;0.00301)|Ovarian(185;0.0634)|Lung NSC(156;0.0969)|all_lung(157;0.105)	all_epithelial(116;7.41e-22)|all_lung(118;8.3e-09)|Lung NSC(185;3.55e-06)|Breast(487;0.000659)|Renal(390;0.00121)|Hepatocellular(190;0.00308)|Myeloproliferative disorder(586;0.0255)|Lung SC(97;0.0262)|Ovarian(437;0.0308)|Medulloblastoma(700;0.211)		Epithelial(90;3.78e-37)|OV - Ovarian serous cystadenocarcinoma(86;6.86e-22)|GBM - Glioblastoma multiforme(42;1.96e-12)|Colorectal(212;6.15e-05)|COAD - Colon adenocarcinoma(227;0.000241)|Kidney(185;0.000448)|BRCA - Breast invasive adenocarcinoma(365;0.000779)|KIRC - Kidney renal clear cell carcinoma(229;0.00645)|STAD - Stomach adenocarcinoma(132;0.00669)|Lung(427;0.213)		GCCGCACTCGTACCCGCCAGG	0.687													4	100	---	---	---	---	0	0	0.014758	0	0
TMCO4	255104	broad.mit.edu	37	1	20009578	20009578	+	Silent	SNP	G	A	A			TCGA-ET-A39M-01A-11D-A19J-08	TCGA-ET-A39M-10A-01D-A19M-08									Somatic	Phase_I	Capture				Illumina GAIIx	39c627f7-225b-4a78-a589-e3228fed1d6e	cfdd0348-3531-4c23-bc2f-963173dfd77e	g.chr1:20009578G>A	uc001bcn.2	-	16	2102	c.1860C>T	c.(1858-1860)CCC>CCT	p.P620P	TMCO4_uc001bcm.2_Silent_p.P451P|TMCO4_uc001bco.1_Intron|TMCO4_uc001bcp.1_Intron	NM_181719	NP_859070	Q5TGY1	TMCO4_HUMAN	transmembrane and coiled-coil domains 4	620						integral to membrane					0		Colorectal(325;0.000147)|Renal(390;0.000469)|all_lung(284;0.00519)|Breast(348;0.00526)|Lung NSC(340;0.00544)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0439)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00708)|COAD - Colon adenocarcinoma(152;2.28e-05)|BRCA - Breast invasive adenocarcinoma(304;5.8e-05)|Kidney(64;0.000367)|GBM - Glioblastoma multiforme(114;0.000377)|KIRC - Kidney renal clear cell carcinoma(64;0.00459)|STAD - Stomach adenocarcinoma(196;0.0072)|READ - Rectum adenocarcinoma(331;0.0862)|Lung(427;0.223)		AGGCACAATCGGGGCAGCCCA	0.652													52	167	---	---	---	---	0	0	0.048971	0	0
MYBPHL	343263	broad.mit.edu	37	1	109839501	109839501	+	Missense_Mutation	SNP	C	T	T	rs140827712		TCGA-ET-A39M-01A-11D-A19J-08	TCGA-ET-A39M-10A-01D-A19M-08									Somatic	Phase_I	Capture				Illumina GAIIx	39c627f7-225b-4a78-a589-e3228fed1d6e	cfdd0348-3531-4c23-bc2f-963173dfd77e	g.chr1:109839501C>T	uc001dxk.1	-	5	684	c.634G>A	c.(634-636)GGC>AGC	p.G212S	MYBPHL_uc010ovh.1_Missense_Mutation_p.G189S|MYBPHL_uc001dxl.2_Intron	NM_001010985	NP_001010985	A2RUH7	MBPHL_HUMAN	myosin binding protein H-like	212	Fibronectin type-III.									ovary(1)|central_nervous_system(1)|pancreas(1)	3		all_lung(203;0.00519)|all_epithelial(167;0.00575)|Lung NSC(277;0.00822)		Colorectal(144;0.0306)|Lung(183;0.0681)|COAD - Colon adenocarcinoma(174;0.117)|Epithelial(280;0.197)|all cancers(265;0.225)		TAGGAGTTGCCGATGATGAGG	0.567													6	134	---	---	---	---	0	0	0.021553	0	0
OBSCN	84033	broad.mit.edu	37	1	228437749	228437749	+	Missense_Mutation	SNP	G	A	A			TCGA-ET-A39M-01A-11D-A19J-08	TCGA-ET-A39M-10A-01D-A19M-08									Somatic	Phase_I	Capture				Illumina GAIIx	39c627f7-225b-4a78-a589-e3228fed1d6e	cfdd0348-3531-4c23-bc2f-963173dfd77e	g.chr1:228437749G>A	uc009xez.1	+	14	4161	c.4117G>A	c.(4117-4119)GAG>AAG	p.E1373K	OBSCN_uc001hsn.2_Missense_Mutation_p.E1373K	NM_001098623	NP_001092093	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and	1373	Ig-like 14.				apoptosis|cell differentiation|induction of apoptosis by extracellular signals|multicellular organismal development|nerve growth factor receptor signaling pathway|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			stomach(8)|large_intestine(7)|breast(5)|ovary(4)|skin(2)|central_nervous_system(1)|pancreas(1)	28		Prostate(94;0.0405)				GCTGAGCTGCGAGGTGGCCCA	0.637													6	193	---	---	---	---	0	0	0.021553	0	0
KIF26B	55083	broad.mit.edu	37	1	245850296	245850296	+	Silent	SNP	C	T	T	rs114792430	by1000genomes	TCGA-ET-A39M-01A-11D-A19J-08	TCGA-ET-A39M-10A-01D-A19M-08									Somatic	Phase_I	Capture				Illumina GAIIx	39c627f7-225b-4a78-a589-e3228fed1d6e	cfdd0348-3531-4c23-bc2f-963173dfd77e	g.chr1:245850296C>T	uc001ibf.1	+	12	4451	c.4011C>T	c.(4009-4011)CCC>CCT	p.P1337P	KIF26B_uc001ibg.1_Silent_p.P955P|KIF26B_uc001ibh.1_Silent_p.P579P	NM_018012	NP_060482	Q2KJY2	KI26B_HUMAN	kinesin family member 26B	1337					microtubule-based movement	cytoplasm|microtubule	ATP binding|microtubule motor activity			ovary(3)	3	all_cancers(71;3.86e-05)|all_epithelial(71;0.000121)|Ovarian(71;0.0412)|all_lung(81;0.0498)|Lung NSC(105;0.0708)|Breast(184;0.127)		OV - Ovarian serous cystadenocarcinoma(106;0.022)			AGGCCAGCCCCGACAACTTGC	0.562													5	55	---	---	---	---	0	0	0.014758	0	0
LDB3	11155	broad.mit.edu	37	10	88441336	88441336	+	Silent	SNP	C	T	T	rs45516997	byFrequency	TCGA-ET-A39M-01A-11D-A19J-08	TCGA-ET-A39M-10A-01D-A19M-08									Somatic	Phase_I	Capture				Illumina GAIIx	39c627f7-225b-4a78-a589-e3228fed1d6e	cfdd0348-3531-4c23-bc2f-963173dfd77e	g.chr10:88441336C>T	uc001kdv.2	+	4	488	c.465C>T	c.(463-465)CTC>CTT	p.L155L	LDB3_uc010qml.1_Silent_p.L155L|LDB3_uc010qmm.1_Silent_p.L155L|LDB3_uc001kdu.2_Intron|LDB3_uc009xsz.2_Intron|LDB3_uc001kdr.2_Intron|LDB3_uc009xsy.2_Silent_p.L155L|LDB3_uc001kds.2_Silent_p.L155L|LDB3_uc001kdt.2_RNA	NM_007078	NP_009009	O75112	LDB3_HUMAN	LIM domain binding 3 isoform 1	155						cytoskeleton|perinuclear region of cytoplasm|pseudopodium	zinc ion binding			ovary(1)	1						TCTCCTCACTCGCCGAGGCCT	0.736													5	72	---	---	---	---	0	0	0.014758	0	0
FLJ46111	283102	broad.mit.edu	37	11	9116358	9116358	+	RNA	SNP	G	A	A	rs11042176	by1000genomes	TCGA-ET-A39M-01A-11D-A19J-08	TCGA-ET-A39M-10A-01D-A19M-08									Somatic	Phase_I	Capture				Illumina GAIIx	39c627f7-225b-4a78-a589-e3228fed1d6e	cfdd0348-3531-4c23-bc2f-963173dfd77e	g.chr11:9116358G>A	uc010rbv.1	+	1		c.449G>A				NR_027713				Homo sapiens cDNA FLJ46111 fis, clone TESTI2034913, moderately similar to Keratin, type II cytoskeletal 8.												0						CTCCTTCATCGAGAAGGTGCG	0.562													6	176	---	---	---	---	0	0	0.021553	0	0
DAGLA	747	broad.mit.edu	37	11	61511242	61511242	+	Missense_Mutation	SNP	C	T	T			TCGA-ET-A39M-01A-11D-A19J-08	TCGA-ET-A39M-10A-01D-A19M-08									Somatic	Phase_I	Capture				Illumina GAIIx	39c627f7-225b-4a78-a589-e3228fed1d6e	cfdd0348-3531-4c23-bc2f-963173dfd77e	g.chr11:61511242C>T	uc001nsa.2	+	20	2521	c.2410C>T	c.(2410-2412)CGG>TGG	p.R804W		NM_006133	NP_006124	Q9Y4D2	DGLA_HUMAN	neural stem cell-derived dendrite regulator	804	Cytoplasmic (Potential).				cell death|lipid catabolic process|platelet activation	integral to membrane|plasma membrane	acylglycerol lipase activity|metal ion binding|triglyceride lipase activity			ovary(2)|central_nervous_system(1)	3				READ - Rectum adenocarcinoma(4;0.219)		CCGCAGCATCCGGGGCTCCCC	0.662													14	286	---	---	---	---	0	0	0.105934	0	0
P2RY2	5029	broad.mit.edu	37	11	72945651	72945651	+	Silent	SNP	C	T	T	rs147817701	byFrequency	TCGA-ET-A39M-01A-11D-A19J-08	TCGA-ET-A39M-10A-01D-A19M-08									Somatic	Phase_I	Capture				Illumina GAIIx	39c627f7-225b-4a78-a589-e3228fed1d6e	cfdd0348-3531-4c23-bc2f-963173dfd77e	g.chr11:72945651C>T	uc001otj.2	+	3	780	c.447C>T	c.(445-447)TAC>TAT	p.Y149Y	P2RY2_uc001otk.2_Silent_p.Y149Y|P2RY2_uc001otl.2_Silent_p.Y149Y	NM_002564	NP_002555	P41231	P2RY2_HUMAN	purinergic receptor P2Y2	149	Cytoplasmic (Potential).				activation of phospholipase C activity by G-protein coupled receptor protein signaling pathway coupled to IP3 second messenger	integral to plasma membrane	purinergic nucleotide receptor activity, G-protein coupled			ovary(2)|lung(1)|skin(1)	4					Suramin(DB04786)	GGGCCCGCTACGCTCGCCGGG	0.697													9	168	---	---	---	---	0	0	0.047766	0	0
RPL13AP20	387841	broad.mit.edu	37	12	13028751	13028751	+	Missense_Mutation	SNP	G	C	C			TCGA-ET-A39M-01A-11D-A19J-08	TCGA-ET-A39M-10A-01D-A19M-08									Somatic	Phase_I	Capture				Illumina GAIIx	39c627f7-225b-4a78-a589-e3228fed1d6e	cfdd0348-3531-4c23-bc2f-963173dfd77e	g.chr12:13028751G>C	uc010sho.1	+	1	341	c.319G>C	c.(319-321)GGC>CGC	p.G107R		NR_003932				SubName: Full=Ribosomal protein L13a variant; Flags: Fragment;												0						GGTGTTTGACGGCATCCCACC	0.612													4	25	---	---	---	---	0	0	0.029380	0	0
PCK2	5106	broad.mit.edu	37	14	24568395	24568395	+	Missense_Mutation	SNP	A	G	G	rs146890792	byFrequency	TCGA-ET-A39M-01A-11D-A19J-08	TCGA-ET-A39M-10A-01D-A19M-08									Somatic	Phase_I	Capture				Illumina GAIIx	39c627f7-225b-4a78-a589-e3228fed1d6e	cfdd0348-3531-4c23-bc2f-963173dfd77e	g.chr14:24568395A>G	uc001wlt.2	+	5	934	c.802A>G	c.(802-804)ATC>GTC	p.I268V	NRL_uc001wlq.2_Intron|PCK2_uc001wlr.1_Missense_Mutation_p.I280V|PCK2_uc001wls.2_Missense_Mutation_p.I268V|PCK2_uc010tnw.1_Missense_Mutation_p.I134V|PCK2_uc010ald.2_Missense_Mutation_p.I120V|PCK2_uc010ale.2_Intron|PCK2_uc010tnx.1_Missense_Mutation_p.I134V|PCK2_uc001wlu.3_Missense_Mutation_p.I134V	NM_004563	NP_004554	Q16822	PCKGM_HUMAN	mitochondrial phosphoenolpyruvate carboxykinase	268					gluconeogenesis	mitochondrial matrix	GTP binding|metal ion binding|phosphoenolpyruvate carboxykinase (GTP) activity			ovary(1)	1				GBM - Glioblastoma multiforme(265;0.0184)		TGCCCTACGCATCGCCTCTCG	0.662													5	91	---	---	---	---	0	0	0.014758	0	0
Unknown	0	broad.mit.edu	37	15	20193342	20193342	+	RNA	SNP	A	G	G			TCGA-ET-A39M-01A-11D-A19J-08	TCGA-ET-A39M-10A-01D-A19M-08									Somatic	Phase_I	Capture				Illumina GAIIx	39c627f7-225b-4a78-a589-e3228fed1d6e	cfdd0348-3531-4c23-bc2f-963173dfd77e	g.chr15:20193342A>G	uc010tyv.1	-	1		c.31T>C								Homo sapiens immunoglobulin heavy chain leader and variable region mRNA, partial cds.																		AATAGCAACAAGGAAAACCCA	0.478													10	436	---	---	---	---	0	0	0.058154	0	0
GOLGA8DP	100132979	broad.mit.edu	37	15	22709152	22709152	+	Missense_Mutation	SNP	G	T	T			TCGA-ET-A39M-01A-11D-A19J-08	TCGA-ET-A39M-10A-01D-A19M-08									Somatic	Phase_I	Capture				Illumina GAIIx	39c627f7-225b-4a78-a589-e3228fed1d6e	cfdd0348-3531-4c23-bc2f-963173dfd77e	g.chr15:22709152G>T	uc010axw.2	-	11	1245	c.347C>A	c.(346-348)GCG>GAG	p.A116E	GOLGA8DP_uc010axx.2_Missense_Mutation_p.A116E|uc010tzw.1_5'Flank	NM_001012423	NP_001012423			golgi autoantigen, golgin subfamily a, 8E												0						GGCCTGGAGCGCTCCTGCCAC	0.607													4	84	---	---	---	---	0.00024832	0.000257449	0.009096	1	0
GOLGA6L5	374650	broad.mit.edu	37	15	85053142	85053142	+	RNA	SNP	C	T	T			TCGA-ET-A39M-01A-11D-A19J-08	TCGA-ET-A39M-10A-01D-A19M-08									Somatic	Phase_I	Capture				Illumina GAIIx	39c627f7-225b-4a78-a589-e3228fed1d6e	cfdd0348-3531-4c23-bc2f-963173dfd77e	g.chr15:85053142C>T	uc002bkm.2	-	9		c.1905G>A			uc002bkl.1_5'Flank	NR_003246				Homo sapiens cDNA FLJ33459 fis, clone BRAMY2000585.												0						TTTTTCAATTCCTTGACCCGC	0.393													15	24	---	---	---	---	0	0	0.033300	0	0
KREMEN2	79412	broad.mit.edu	37	16	3016732	3016732	+	Silent	SNP	C	T	T			TCGA-ET-A39M-01A-11D-A19J-08	TCGA-ET-A39M-10A-01D-A19M-08									Somatic	Phase_I	Capture				Illumina GAIIx	39c627f7-225b-4a78-a589-e3228fed1d6e	cfdd0348-3531-4c23-bc2f-963173dfd77e	g.chr16:3016732C>T	uc002csg.2	+	5	881	c.576C>T	c.(574-576)GAC>GAT	p.D192D	KREMEN2_uc010bsw.1_Silent_p.D192D|KREMEN2_uc002csh.2_Silent_p.D192D|KREMEN2_uc010uwl.1_Intron|KREMEN2_uc010bsx.2_Intron|KREMEN2_uc002csi.2_Silent_p.D192D|PAQR4_uc002csj.3_5'Flank|PAQR4_uc002csk.3_5'Flank|PAQR4_uc002csl.3_5'Flank	NM_172229	NP_757384	Q8NCW0	KREM2_HUMAN	kringle-containing transmembrane protein 2	192	Extracellular (Potential).|WSC.			Missing (in Ref. 2; BAC11365).	Wnt receptor signaling pathway	integral to membrane				central_nervous_system(2)	2						CCGACTGTGACCAGATCTGTT	0.706													5	60	---	---	---	---	0	0	0.021553	0	0
SEZ6L2	26470	broad.mit.edu	37	16	29897052	29897052	+	Silent	SNP	C	T	T	rs150650092	byFrequency	TCGA-ET-A39M-01A-11D-A19J-08	TCGA-ET-A39M-10A-01D-A19M-08									Somatic	Phase_I	Capture				Illumina GAIIx	39c627f7-225b-4a78-a589-e3228fed1d6e	cfdd0348-3531-4c23-bc2f-963173dfd77e	g.chr16:29897052C>T	uc002duq.3	-	8	1467	c.1227G>A	c.(1225-1227)GGG>GGA	p.G409G	uc002dtf.2_Intron|BOLA2_uc010bzb.1_Intron|SEZ6L2_uc002dup.3_Silent_p.G339G|SEZ6L2_uc002dur.3_Silent_p.G339G|SEZ6L2_uc002dus.3_Silent_p.G295G|SEZ6L2_uc010vec.1_Silent_p.G409G|SEZ6L2_uc010ved.1_Silent_p.G365G	NM_201575	NP_963869	Q6UXD5	SE6L2_HUMAN	seizure related 6 homolog (mouse)-like 2 isoform	409	CUB 2.|Extracellular (Potential).					endoplasmic reticulum membrane|integral to membrane|plasma membrane				ovary(1)|skin(1)	2						GGGGGCTGCCCCCTGAGCGCA	0.582													4	73	---	---	---	---	0	0	0.009096	0	0
MYBBP1A	10514	broad.mit.edu	37	17	4453510	4453510	+	Missense_Mutation	SNP	T	G	G			TCGA-ET-A39M-01A-11D-A19J-08	TCGA-ET-A39M-10A-01D-A19M-08									Somatic	Phase_I	Capture				Illumina GAIIx	39c627f7-225b-4a78-a589-e3228fed1d6e	cfdd0348-3531-4c23-bc2f-963173dfd77e	g.chr17:4453510T>G	uc002fyb.3	-	9	1224	c.1162A>C	c.(1162-1164)ACG>CCG	p.T388P	MYBBP1A_uc002fxz.3_Missense_Mutation_p.T388P	NM_014520	NP_055335	Q9BQG0	MBB1A_HUMAN	MYB binding protein 1a isoform 2	388	Interaction with MYB (By similarity).				nucleocytoplasmic transport|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|NLS-dependent protein nuclear import complex|nucleolus	DNA binding|DNA-directed DNA polymerase activity|transcription factor binding			ovary(1)|skin(1)	2						AAAGTAGGCGTGACAGGGAGG	0.642													10	271	---	---	---	---	0	0	0.080935	0	0
Unknown	0	broad.mit.edu	37	17	16725554	16725554	+	RNA	SNP	C	T	T			TCGA-ET-A39M-01A-11D-A19J-08	TCGA-ET-A39M-10A-01D-A19M-08									Somatic	Phase_I	Capture				Illumina GAIIx	39c627f7-225b-4a78-a589-e3228fed1d6e	cfdd0348-3531-4c23-bc2f-963173dfd77e	g.chr17:16725554C>T	uc002gqq.1	-	1		c.340G>A								full-length cDNA clone CS0DI013YN06 of Placenta Cot 25-normalized of Homo sapiens (human).																		ccatatcctcctccaaagcca	0.363													4	102	---	---	---	---	0	0	0.009096	0	0
Unknown	0	broad.mit.edu	37	17	18333915	18333915	+	RNA	SNP	C	T	T	rs148961204	by1000genomes	TCGA-ET-A39M-01A-11D-A19J-08	TCGA-ET-A39M-10A-01D-A19M-08									Somatic	Phase_I	Capture				Illumina GAIIx	39c627f7-225b-4a78-a589-e3228fed1d6e	cfdd0348-3531-4c23-bc2f-963173dfd77e	g.chr17:18333915C>T	uc010vxz.1	+	6		c.1148C>T								Homo sapiens cDNA FLJ61294 complete cds, highly similar to Keratin, type I cytoskeletal 17.																		CAGAGAACCGCTACTGCATGC	0.612													3	28	---	---	---	---	0	0	0.004672	0	0
FLJ36000	284124	broad.mit.edu	37	17	21904193	21904193	+	RNA	SNP	C	G	G	rs9904221	by1000genomes	TCGA-ET-A39M-01A-11D-A19J-08	TCGA-ET-A39M-10A-01D-A19M-08									Somatic	Phase_I	Capture				Illumina GAIIx	39c627f7-225b-4a78-a589-e3228fed1d6e	cfdd0348-3531-4c23-bc2f-963173dfd77e	g.chr17:21904193C>G	uc002gza.2	+	1		c.132C>G				NR_027084				Homo sapiens cDNA FLJ36000 fis, clone TESTI2015180.												0						cagcctcaggcctgccaggac	0													8	158	---	---	---	---	0	0	0.038147	0	0
FLJ36000	284124	broad.mit.edu	37	17	21904197	21904197	+	RNA	SNP	C	T	T	rs9904223	by1000genomes	TCGA-ET-A39M-01A-11D-A19J-08	TCGA-ET-A39M-10A-01D-A19M-08									Somatic	Phase_I	Capture				Illumina GAIIx	39c627f7-225b-4a78-a589-e3228fed1d6e	cfdd0348-3531-4c23-bc2f-963173dfd77e	g.chr17:21904197C>T	uc002gza.2	+	1		c.136C>T				NR_027084				Homo sapiens cDNA FLJ36000 fis, clone TESTI2015180.												0						ctcaggcctgccaggacggtg	0													8	149	---	---	---	---	0	0	0.038147	0	0
EVPL	2125	broad.mit.edu	37	17	74005040	74005040	+	Missense_Mutation	SNP	C	T	T	rs140832012		TCGA-ET-A39M-01A-11D-A19J-08	TCGA-ET-A39M-10A-01D-A19M-08									Somatic	Phase_I	Capture				Illumina GAIIx	39c627f7-225b-4a78-a589-e3228fed1d6e	cfdd0348-3531-4c23-bc2f-963173dfd77e	g.chr17:74005040C>T	uc002jqi.2	-	22	4474	c.4246G>A	c.(4246-4248)GTG>ATG	p.V1416M	EVPL_uc010wss.1_Missense_Mutation_p.V1438M|EVPL_uc010wst.1_Missense_Mutation_p.V886M	NM_001988	NP_001979	Q92817	EVPL_HUMAN	envoplakin	1416	Central fibrous rod domain.				keratinization|peptide cross-linking	cornified envelope|cytoplasm|desmosome	protein binding, bridging|structural molecule activity			pancreas(2)|central_nervous_system(1)|skin(1)	4						TGCTCCTCCACGCCGGCCCGC	0.692													6	166	---	---	---	---	0	0	0.021553	0	0
GPS1	2873	broad.mit.edu	37	17	80012657	80012657	+	Missense_Mutation	SNP	G	A	A	rs149095451		TCGA-ET-A39M-01A-11D-A19J-08	TCGA-ET-A39M-10A-01D-A19M-08									Somatic	Phase_I	Capture				Illumina GAIIx	39c627f7-225b-4a78-a589-e3228fed1d6e	cfdd0348-3531-4c23-bc2f-963173dfd77e	g.chr17:80012657G>A	uc002kdl.1	+	4	637	c.592G>A	c.(592-594)GTC>ATC	p.V198I	GPS1_uc002kdk.1_Missense_Mutation_p.V234I|GPS1_uc010dij.1_Missense_Mutation_p.V234I|GPS1_uc002kdm.1_Missense_Mutation_p.V178I|GPS1_uc002kdn.1_Missense_Mutation_p.V194I|GPS1_uc002kdo.1_Missense_Mutation_p.V198I|GPS1_uc010wvh.1_Missense_Mutation_p.V190I	NM_004127	NP_004118	Q13098	CSN1_HUMAN	G protein pathway suppressor 1 isoform 2	198					cell cycle|cullin deneddylation|inactivation of MAPK activity|JNK cascade	cytoplasm|signalosome	GTPase inhibitor activity|protein binding			central_nervous_system(1)	1	all_neural(118;0.0878)|Ovarian(332;0.227)|all_lung(278;0.246)		BRCA - Breast invasive adenocarcinoma(99;0.0114)|OV - Ovarian serous cystadenocarcinoma(97;0.0211)			CGCCAAACACGTCATCAACAT	0.662													4	78	---	---	---	---	0	0	0.009096	0	0
COLEC11	78989	broad.mit.edu	37	2	3691640	3691640	+	Missense_Mutation	SNP	G	A	A			TCGA-ET-A39M-01A-11D-A19J-08	TCGA-ET-A39M-10A-01D-A19M-08									Somatic	Phase_I	Capture				Illumina GAIIx	39c627f7-225b-4a78-a589-e3228fed1d6e	cfdd0348-3531-4c23-bc2f-963173dfd77e	g.chr2:3691640G>A	uc002qya.2	+	7	896	c.748G>A	c.(748-750)GGC>AGC	p.G250S	COLEC11_uc002qxz.2_Missense_Mutation_p.G247S|COLEC11_uc002qyb.2_Missense_Mutation_p.G226S|COLEC11_uc002qyc.2_Missense_Mutation_p.G226S|COLEC11_uc010ewo.2_Missense_Mutation_p.G202S|COLEC11_uc010ewp.2_Missense_Mutation_p.G224S|COLEC11_uc010ewq.2_Missense_Mutation_p.G200S|COLEC11_uc010ewr.2_Missense_Mutation_p.G200S|COLEC11_uc010ews.2_Missense_Mutation_p.G176S	NM_024027	NP_076932	Q9BWP8	COL11_HUMAN	collectin sub-family member 11 isoform a	250	C-type lectin.					collagen	mannose binding				0	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.093)			OV - Ovarian serous cystadenocarcinoma(76;0.127)		GGCCTCGGGCGGCTGGAACGA	0.622													5	111	---	---	---	---	0	0	0.014758	0	0
LOC401010	401010	broad.mit.edu	37	2	132201582	132201582	+	Silent	SNP	A	G	G	rs1806886	by1000genomes	TCGA-ET-A39M-01A-11D-A19J-08	TCGA-ET-A39M-10A-01D-A19M-08									Somatic	Phase_I	Capture				Illumina GAIIx	39c627f7-225b-4a78-a589-e3228fed1d6e	cfdd0348-3531-4c23-bc2f-963173dfd77e	g.chr2:132201582A>G	uc002tst.2	-	1	886	c.420T>C	c.(418-420)CGT>CGC	p.R140R		NR_002826				SubName: Full=cDNA FLJ12694 fis, clone NT2RP1000358, highly similar to Homo sapiens mRNA; cDNA DKFZp564C186 (from clone DKFZp564C186);												0						TAAGCAGCATACGGCACTGCT	0.602													4	67	---	---	---	---	0	0	0.009096	0	0
IL17RA	23765	broad.mit.edu	37	22	17583105	17583105	+	Silent	SNP	C	T	T			TCGA-ET-A39M-01A-11D-A19J-08	TCGA-ET-A39M-10A-01D-A19M-08									Somatic	Phase_I	Capture				Illumina GAIIx	39c627f7-225b-4a78-a589-e3228fed1d6e	cfdd0348-3531-4c23-bc2f-963173dfd77e	g.chr22:17583105C>T	uc002zly.2	+	7	808	c.675C>T	c.(673-675)AAC>AAT	p.N225N	IL17RA_uc010gqt.2_Silent_p.N225N	NM_014339	NP_055154	Q96F46	I17RA_HUMAN	interleukin 17A receptor precursor	225	Extracellular (Potential).				fibroblast activation|positive regulation of interleukin-23 production	integral to plasma membrane	interleukin-17 receptor activity			skin(2)	2		all_epithelial(15;0.0181)|Lung NSC(13;0.109)|all_lung(157;0.132)		Colorectal(9;0.241)		CCCTGTGGAACGAATCTACCC	0.572													7	159	---	---	---	---	0	0	0.038147	0	0
Unknown	0	broad.mit.edu	37	22	20295420	20295420	+	RNA	SNP	G	T	T	rs4425183	by1000genomes	TCGA-ET-A39M-01A-11D-A19J-08	TCGA-ET-A39M-10A-01D-A19M-08									Somatic	Phase_I	Capture				Illumina GAIIx	39c627f7-225b-4a78-a589-e3228fed1d6e	cfdd0348-3531-4c23-bc2f-963173dfd77e	g.chr22:20295420G>T	uc002zrw.1	+	2		c.2900G>T								Homo sapiens mRNA for KIAA1653 protein, partial cds.																		AGCCTGTGCAGCAGAGATCGG	0.627													8	58	---	---	---	---	0.000157383	0.000164378	0.038147	1	0
MMP11	4320	broad.mit.edu	37	22	24123183	24123183	+	Missense_Mutation	SNP	G	A	A			TCGA-ET-A39M-01A-11D-A19J-08	TCGA-ET-A39M-10A-01D-A19M-08									Somatic	Phase_I	Capture				Illumina GAIIx	39c627f7-225b-4a78-a589-e3228fed1d6e	cfdd0348-3531-4c23-bc2f-963173dfd77e	g.chr22:24123183G>A	uc002zxx.2	+	5	776	c.754G>A	c.(754-756)GGC>AGC	p.G252S	MMP11_uc002zxy.2_RNA|MMP11_uc002zxz.2_5'Flank	NM_005940	NP_005931	P24347	MMP11_HUMAN	matrix metalloproteinase 11 preproprotein	252					collagen catabolic process|multicellular organismal development|proteolysis	proteinaceous extracellular matrix	calcium ion binding|metalloendopeptidase activity|zinc ion binding			skin(2)|large_intestine(1)	3		Medulloblastoma(6;9.86e-08)|all_neural(6;0.000318)				TGACTGCAGGGGCGTTCAACA	0.622													5	98	---	---	---	---	0	0	0.014758	0	0
PANX2	56666	broad.mit.edu	37	22	50617591	50617591	+	Missense_Mutation	SNP	G	A	A			TCGA-ET-A39M-01A-11D-A19J-08	TCGA-ET-A39M-10A-01D-A19M-08									Somatic	Phase_I	Capture				Illumina GAIIx	39c627f7-225b-4a78-a589-e3228fed1d6e	cfdd0348-3531-4c23-bc2f-963173dfd77e	g.chr22:50617591G>A	uc003bjn.3	+	3	1919	c.1919G>A	c.(1918-1920)GGG>GAG	p.G640E	PANX2_uc003bjp.3_Intron|PANX2_uc003bjo.3_Intron	NM_052839	NP_443071	Q96RD6	PANX2_HUMAN	pannexin 2 isoform 1	640	Cytoplasmic (Potential).				protein hexamerization|synaptic transmission	gap junction|integral to membrane	gap junction hemi-channel activity|ion channel activity			breast(1)	1		all_cancers(38;1.14e-10)|all_epithelial(38;2.12e-09)|all_lung(38;7.01e-05)|Breast(42;0.000523)|Lung NSC(38;0.0018)|Ovarian(80;0.0365)|Lung SC(80;0.113)		LUAD - Lung adenocarcinoma(64;0.105)		GAGGAGGACGGGGGCCCCCGC	0.682													3	35	---	---	---	---	0	0	0.004672	0	0
FGD5	152273	broad.mit.edu	37	3	14861538	14861538	+	Silent	SNP	C	T	T			TCGA-ET-A39M-01A-11D-A19J-08	TCGA-ET-A39M-10A-01D-A19M-08									Somatic	Phase_I	Capture				Illumina GAIIx	39c627f7-225b-4a78-a589-e3228fed1d6e	cfdd0348-3531-4c23-bc2f-963173dfd77e	g.chr3:14861538C>T	uc003bzc.2	+	1	1070	c.960C>T	c.(958-960)TCC>TCT	p.S320S	FGD5_uc011avk.1_Silent_p.S320S	NM_152536	NP_689749	Q6ZNL6	FGD5_HUMAN	FYVE, RhoGEF and PH domain containing 5	320	Glu-rich.				actin cytoskeleton organization|filopodium assembly|regulation of Cdc42 GTPase activity|regulation of cell shape	cytoskeleton|Golgi apparatus|lamellipodium|ruffle	metal ion binding|Rho guanyl-nucleotide exchange factor activity|small GTPase binding			ovary(3)|kidney(1)|pancreas(1)	5						AGGATGAGTCCGCCGAGGAGA	0.552													15	166	---	---	---	---	0	0	0.024245	0	0
SCN5A	6331	broad.mit.edu	37	3	38651442	38651442	+	Silent	SNP	G	A	A	rs41285129		TCGA-ET-A39M-01A-11D-A19J-08	TCGA-ET-A39M-10A-01D-A19M-08									Somatic	Phase_I	Capture				Illumina GAIIx	39c627f7-225b-4a78-a589-e3228fed1d6e	cfdd0348-3531-4c23-bc2f-963173dfd77e	g.chr3:38651442G>A	uc003cio.2	-	7	911	c.717C>T	c.(715-717)ATC>ATT	p.I239I	SCN5A_uc003cin.2_Silent_p.I239I|SCN5A_uc003cil.3_Silent_p.I239I|SCN5A_uc010hhi.2_Silent_p.I239I|SCN5A_uc010hhk.2_Silent_p.I239I|SCN5A_uc011ayr.1_Silent_p.I239I|SCN5A_uc010hhl.1_Silent_p.I62I	NM_198056	NP_932173	Q14524	SCN5A_HUMAN	voltage-gated sodium channel type V alpha	239					blood circulation|cellular response to calcium ion|muscle contraction|regulation of heart contraction	sarcolemma|voltage-gated sodium channel complex	protein binding|voltage-gated sodium channel activity			ovary(4)|pancreas(2)|skin(2)|central_nervous_system(1)	9	Medulloblastoma(35;0.163)			KIRC - Kidney renal clear cell carcinoma(284;0.0822)|Kidney(284;0.1)	Benzonatate(DB00868)|Bepridil(DB01244)|Carbamazepine(DB00564)|Cocaine(DB00907)|Dibucaine(DB00527)|Disopyramide(DB00280)|Encainide(DB01228)|Ethotoin(DB00754)|Flecainide(DB01195)|Fosphenytoin(DB01320)|Hexylcaine(DB00473)|Indecainide(DB00192)|Lamotrigine(DB00555)|Lidocaine(DB00281)|Mephenytoin(DB00532)|Mexiletine(DB00379)|Mibefradil(DB01388)|Moricizine(DB00680)|Oxcarbazepine(DB00776)|Phenytoin(DB00252)|Prilocaine(DB00750)|Procainamide(DB01035)|Propafenone(DB01182)|Quinidine(DB00908)|Riluzole(DB00740)|Tocainide(DB01056)|Verapamil(DB00661)	GGGCCCCCACGATGGTCTTCA	0.617													5	153	---	---	---	---	0	0	0.014758	0	0
NISCH	11188	broad.mit.edu	37	3	52526279	52526279	+	Silent	SNP	C	T	T	rs61737697	byFrequency	TCGA-ET-A39M-01A-11D-A19J-08	TCGA-ET-A39M-10A-01D-A19M-08									Somatic	Phase_I	Capture				Illumina GAIIx	39c627f7-225b-4a78-a589-e3228fed1d6e	cfdd0348-3531-4c23-bc2f-963173dfd77e	g.chr3:52526279C>T	uc011beg.1	+	22	4368	c.4296C>T	c.(4294-4296)CTC>CTT	p.L1432L	NISCH_uc003ded.3_Silent_p.L1432L|NISCH_uc003dee.3_Silent_p.L921L|NISCH_uc003deg.1_Intron|NISCH_uc003deh.3_Silent_p.L181L	NM_007184	NP_009115	Q9Y2I1	NISCH_HUMAN	nischarin	1432					apoptosis|cell communication	cytosol|early endosome|plasma membrane|recycling endosome	phosphatidylinositol binding|receptor activity			ovary(3)|central_nervous_system(1)	4				BRCA - Breast invasive adenocarcinoma(193;1.93e-05)|Kidney(197;0.00216)|KIRC - Kidney renal clear cell carcinoma(197;0.00244)|OV - Ovarian serous cystadenocarcinoma(275;0.0577)		CCCTCACCCTCGTCTTCGATG	0.672													14	371	---	---	---	---	0	0	0.020292	0	0
PDZRN3	23024	broad.mit.edu	37	3	73433272	73433272	+	Silent	SNP	G	A	A	rs61739225	byFrequency	TCGA-ET-A39M-01A-11D-A19J-08	TCGA-ET-A39M-10A-01D-A19M-08									Somatic	Phase_I	Capture				Illumina GAIIx	39c627f7-225b-4a78-a589-e3228fed1d6e	cfdd0348-3531-4c23-bc2f-963173dfd77e	g.chr3:73433272G>A	uc003dpl.1	-	10	2541	c.2445C>T	c.(2443-2445)CCC>CCT	p.P815P	PDZRN3_uc011bgh.1_Silent_p.P472P|PDZRN3_uc010hoe.1_Silent_p.P513P|PDZRN3_uc011bgf.1_Silent_p.P532P|PDZRN3_uc011bgg.1_Silent_p.P535P	NM_015009	NP_055824	Q9UPQ7	PZRN3_HUMAN	PDZ domain containing ring finger 3	815							ubiquitin-protein ligase activity|zinc ion binding			pancreas(2)|ovary(2)|skin(2)|large_intestine(1)	7		Prostate(10;0.114)|Lung NSC(201;0.187)|Lung SC(41;0.236)		BRCA - Breast invasive adenocarcinoma(55;0.00041)|Epithelial(33;0.0023)|LUSC - Lung squamous cell carcinoma(21;0.0048)|Lung(16;0.0105)|KIRC - Kidney renal clear cell carcinoma(39;0.111)|Kidney(39;0.134)		TGCCCACTTCGGGATCTTCCG	0.662													10	159	---	---	---	---	0	0	0.069234	0	0
BBX	56987	broad.mit.edu	37	3	107492013	107492013	+	Missense_Mutation	SNP	A	G	G			TCGA-ET-A39M-01A-11D-A19J-08	TCGA-ET-A39M-10A-01D-A19M-08									Somatic	Phase_I	Capture				Illumina GAIIx	39c627f7-225b-4a78-a589-e3228fed1d6e	cfdd0348-3531-4c23-bc2f-963173dfd77e	g.chr3:107492013A>G	uc010hpr.2	+	11	1772	c.1445A>G	c.(1444-1446)GAC>GGC	p.D482G	BBX_uc003dwk.3_Missense_Mutation_p.D482G|BBX_uc003dwl.3_Intron|BBX_uc010hps.1_Missense_Mutation_p.D503G|BBX_uc003dwm.3_Missense_Mutation_p.D482G|BBX_uc003dwo.3_5'Flank	NM_001142568	NP_001136040	Q8WY36	BBX_HUMAN	HMG-BOX transcription factor BBX isoform 1	482	Lys-rich.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding			ovary(3)|skin(1)	4			OV - Ovarian serous cystadenocarcinoma(3;0.112)			TCGGAATCTGACATTGAGAGC	0.433													6	234	---	---	---	---	0	0	0.021553	0	0
PDS5A	23244	broad.mit.edu	37	4	39918684	39918684	+	Missense_Mutation	SNP	A	G	G			TCGA-ET-A39M-01A-11D-A19J-08	TCGA-ET-A39M-10A-01D-A19M-08									Somatic	Phase_I	Capture				Illumina GAIIx	39c627f7-225b-4a78-a589-e3228fed1d6e	cfdd0348-3531-4c23-bc2f-963173dfd77e	g.chr4:39918684A>G	uc003guv.3	-	8	1400	c.860T>C	c.(859-861)CTT>CCT	p.L287P	PDS5A_uc010ifo.2_Missense_Mutation_p.L247P|PDS5A_uc003guw.3_Missense_Mutation_p.L287P	NM_001100399	NP_001093869	Q29RF7	PDS5A_HUMAN	PDS5, regulator of cohesion maintenance, homolog	287					cell division|mitosis|negative regulation of DNA replication	chromatin|nucleus	identical protein binding				0						TTTGAATTCAAGCTGTGGCAT	0.313													3	24	---	---	---	---	0	0	0.004672	0	0
PCDHB16	57717	broad.mit.edu	37	5	140563385	140563385	+	Silent	SNP	T	C	C	rs115003049	byFrequency	TCGA-ET-A39M-01A-11D-A19J-08	TCGA-ET-A39M-10A-01D-A19M-08									Somatic	Phase_I	Capture				Illumina GAIIx	39c627f7-225b-4a78-a589-e3228fed1d6e	cfdd0348-3531-4c23-bc2f-963173dfd77e	g.chr5:140563385T>C	uc003liv.2	+	1	2406	c.1251T>C	c.(1249-1251)TAT>TAC	p.Y417Y	PCDHB16_uc010jfw.1_Silent_p.Y89Y	NM_020957	NP_066008	Q9NRJ7	PCDBG_HUMAN	protocadherin beta 16 precursor	417	Extracellular (Potential).|Cadherin 4.				calcium-dependent cell-cell adhesion|homophilic cell adhesion|synapse assembly|synaptic transmission	integral to membrane|plasma membrane	calcium ion binding			ovary(1)|pancreas(1)	2			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			GAGCTGAATATAATATCACCC	0.458													10	215	---	---	---	---	0	0	0.058154	0	0
PCDHB9	56127	broad.mit.edu	37	5	140568475	140568475	+	Missense_Mutation	SNP	C	G	G	rs17844529		TCGA-ET-A39M-01A-11D-A19J-08	TCGA-ET-A39M-10A-01D-A19M-08									Somatic	Phase_I	Capture				Illumina GAIIx	39c627f7-225b-4a78-a589-e3228fed1d6e	cfdd0348-3531-4c23-bc2f-963173dfd77e	g.chr5:140568475C>G	uc003liw.1	+	3	1584	c.1584C>G	c.(1582-1584)GAC>GAG	p.D528E		NM_019119	NP_061992	Q9Y5E1	PCDB9_HUMAN	protocadherin beta 9 precursor	528	Extracellular (Potential).|Cadherin 5.				calcium-dependent cell-cell adhesion|homophilic cell adhesion|synapse assembly|synaptic transmission	integral to membrane|plasma membrane	calcium ion binding				0			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			AGGCTTTCGACTTCCGCGTGG	0.672													11	292	---	---	---	---	0	0	0.069234	0	0
TCTE1	202500	broad.mit.edu	37	6	44250215	44250215	+	Missense_Mutation	SNP	C	T	T	rs146833594	byFrequency	TCGA-ET-A39M-01A-11D-A19J-08	TCGA-ET-A39M-10A-01D-A19M-08									Somatic	Phase_I	Capture				Illumina GAIIx	39c627f7-225b-4a78-a589-e3228fed1d6e	cfdd0348-3531-4c23-bc2f-963173dfd77e	g.chr6:44250215C>T	uc003oxi.2	-	4	1084	c.928G>A	c.(928-930)GAG>AAG	p.E310K	SPATS1_uc003oxg.2_Intron|TMEM151B_uc003oxf.2_Intron	NM_182539	NP_872345	Q5JU00	TCTE1_HUMAN	t-complex-associated testis expressed 1	310	LRR 1.									ovary(2)|skin(2)	4	Hepatocellular(11;0.00908)|all_lung(25;0.0101)|Ovarian(13;0.0273)		Colorectal(64;0.00337)|COAD - Colon adenocarcinoma(64;0.00536)			TCCAGCTCCTCGAGGACTGGG	0.572													7	168	---	---	---	---	0	0	0.029380	0	0
C6orf174	387104	broad.mit.edu	37	6	127837687	127837687	+	Missense_Mutation	SNP	C	T	T			TCGA-ET-A39M-01A-11D-A19J-08	TCGA-ET-A39M-10A-01D-A19M-08									Somatic	Phase_I	Capture				Illumina GAIIx	39c627f7-225b-4a78-a589-e3228fed1d6e	cfdd0348-3531-4c23-bc2f-963173dfd77e	g.chr6:127837687C>T	uc003qbd.2	-	2	938	c.73G>A	c.(73-75)GCT>ACT	p.A25T		NM_001012279	NP_001012279	Q5TF21	CF174_HUMAN	hypothetical protein LOC387104 precursor	25						integral to membrane				breast(3)|ovary(2)|skin(1)	6				GBM - Glioblastoma multiforme(226;0.026)|all cancers(137;0.161)		TGCAGACGAGCCTCAGTGGCT	0.647													4	27	---	---	---	---	0	0	0.009096	0	0
PMS2CL	441194	broad.mit.edu	37	7	6786731	6786731	+	RNA	SNP	C	T	T	rs111706670	by1000genomes	TCGA-ET-A39M-01A-11D-A19J-08	TCGA-ET-A39M-10A-01D-A19M-08									Somatic	Phase_I	Capture				Illumina GAIIx	39c627f7-225b-4a78-a589-e3228fed1d6e	cfdd0348-3531-4c23-bc2f-963173dfd77e	g.chr7:6786731C>T	uc003squ.2	+	12		c.2030C>T			PMS2CL_uc003sqv.1_RNA					Homo sapiens PMS2CL mRNA for PMS2-C terminal -like, complete cds.												0						CCTTCGGACCCCAGGACGTCG	0.502													6	170	---	---	---	---	0	0	0.038147	0	0
TRIM56	81844	broad.mit.edu	37	7	100732226	100732226	+	Missense_Mutation	SNP	C	T	T	rs111572673		TCGA-ET-A39M-01A-11D-A19J-08	TCGA-ET-A39M-10A-01D-A19M-08									Somatic	Phase_I	Capture				Illumina GAIIx	39c627f7-225b-4a78-a589-e3228fed1d6e	cfdd0348-3531-4c23-bc2f-963173dfd77e	g.chr7:100732226C>T	uc003uxq.2	+	3	1864	c.1633C>T	c.(1633-1635)CCG>TCG	p.P545S	TRIM56_uc003uxr.2_Intron	NM_030961	NP_112223	Q9BRZ2	TRI56_HUMAN	tripartite motif-containing 56	545					defense response to virus|interferon-beta production|protein K63-linked ubiquitination|response to type I interferon	cytoplasm	ubiquitin-protein ligase activity|zinc ion binding			kidney(1)|central_nervous_system(1)|skin(1)	3	Lung NSC(181;0.136)|all_lung(186;0.182)					GGGCACCGTGCCGGTCCCTGA	0.672													6	174	---	---	---	---	0	0	0.021553	0	0
LRWD1	222229	broad.mit.edu	37	7	102110079	102110079	+	Silent	SNP	C	T	T	rs142392925	byFrequency	TCGA-ET-A39M-01A-11D-A19J-08	TCGA-ET-A39M-10A-01D-A19M-08									Somatic	Phase_I	Capture				Illumina GAIIx	39c627f7-225b-4a78-a589-e3228fed1d6e	cfdd0348-3531-4c23-bc2f-963173dfd77e	g.chr7:102110079C>T	uc003uzn.2	+	10	1425	c.1287C>T	c.(1285-1287)TAC>TAT	p.Y429Y	LRWD1_uc003uzo.2_Silent_p.Y277Y	NM_152892	NP_690852	Q9UFC0	LRWD1_HUMAN	leucine-rich repeats and WD repeat domain	429	WD 1.				chromatin modification|DNA-dependent DNA replication initiation|establishment of protein localization to chromatin|G1 phase of mitotic cell cycle	centromeric heterochromatin|nuclear origin of replication recognition complex|telomeric heterochromatin	chromatin binding|methyl-CpG binding|methylated histone residue binding			skin(1)	1						ACCAGGACTACGAATTCCAGG	0.632													7	144	---	---	---	---	0	0	0.029380	0	0
LAMB4	22798	broad.mit.edu	37	7	107752270	107752270	+	Nonsense_Mutation	SNP	C	T	T			TCGA-ET-A39M-01A-11D-A19J-08	TCGA-ET-A39M-10A-01D-A19M-08									Somatic	Phase_I	Capture				Illumina GAIIx	39c627f7-225b-4a78-a589-e3228fed1d6e	cfdd0348-3531-4c23-bc2f-963173dfd77e	g.chr7:107752270C>T	uc010ljo.1	-	4	398	c.314G>A	c.(313-315)TGG>TAG	p.W105*	LAMB4_uc003vey.2_Nonsense_Mutation_p.W105*	NM_007356	NP_031382	A4D0S4	LAMB4_HUMAN	laminin, beta 4 precursor	105	Laminin N-terminal.				cell adhesion	basement membrane				ovary(4)|breast(2)|large_intestine(1)|skin(1)	8						TTCAGATTGCCACCATTTCTT	0.348													12	219	---	---	---	---	0	0	0.093190	0	0
Unknown	0	broad.mit.edu	37	7	121081135	121081135	+	IGR	SNP	C	A	A			TCGA-ET-A39M-01A-11D-A19J-08	TCGA-ET-A39M-10A-01D-A19M-08									Somatic	Phase_I	Capture				Illumina GAIIx	39c627f7-225b-4a78-a589-e3228fed1d6e	cfdd0348-3531-4c23-bc2f-963173dfd77e	g.chr7:121081135C>A								FAM3C (44713 upstream) : PTPRZ1 (432024 downstream)																							GCGGGCCCGGCTGGTCACGCC	0.617													52	123	---	---	---	---	1.08114e-33	1.15485e-33	0.048971	1	0
BRAF	673	broad.mit.edu	37	7	140453136	140453136	+	Missense_Mutation	SNP	A	T	T			TCGA-ET-A39M-01A-11D-A19J-08	TCGA-ET-A39M-10A-01D-A19M-08									Somatic	Phase_I	Capture				Illumina GAIIx	39c627f7-225b-4a78-a589-e3228fed1d6e	cfdd0348-3531-4c23-bc2f-963173dfd77e	g.chr7:140453136A>T	uc003vwc.3	-	15	1860	c.1799T>A	c.(1798-1800)GTG>GAG	p.V600E		NM_004333	NP_004324	P15056	BRAF_HUMAN	B-Raf	600	Protein kinase.		V -> D (in a melanoma cell line; requires 2 nucleotide substitutions).|V -> E (in sarcoma, colorectal adenocarcinoma, metastatic melanoma, ovarian serous carcinoma, pilocytic astrocytoma; somatic mutation; most common mutation; constitutive and elevated kinase activity; efficiently induces cell transformation; suppression of mutation in melanoma causes growth arrest and promotes apoptosis).		activation of MAPKK activity|anti-apoptosis|nerve growth factor receptor signaling pathway|organ morphogenesis|positive regulation of peptidyl-serine phosphorylation|small GTPase mediated signal transduction|synaptic transmission	cytosol|nucleus|plasma membrane	ATP binding|metal ion binding	p.V600E(16892)|p.V600?(325)|p.V600K(176)|p.V600R(36)|p.V600M(25)|p.V600A(23)|p.V600D(21)|p.V600G(11)|p.V600_K601>E(8)|p.T599_V600insTT(3)|p.T599_R603>I(2)|p.T599_V600>IAL(2)|p.V600L(2)|p.T599_V600insT(2)|p.V600_W604del(1)|p.V600_S605>DV(1)|p.V600_S605>D(1)|p.T599_V600insV(1)|p.T599_V600insDFGLAT(1)	KIAA1549/BRAF(229)|AKAP9_ENST00000356239/BRAF(10)|AGTRAP/BRAF(2)|FCHSD1/BRAF(2)|SLC45A3/BRAF(2)	thyroid(8166)|large_intestine(5052)|skin(3798)|NS(368)|central_nervous_system(284)|ovary(236)|lung(78)|eye(53)|prostate(44)|endometrium(30)|biliary_tract(28)|soft_tissue(27)|haematopoietic_and_lymphoid_tissue(22)|breast(18)|upper_aerodigestive_tract(13)|stomach(13)|pancreas(10)|small_intestine(10)|testis(7)|bone(6)|cervix(5)|genital_tract(4)|oesophagus(3)|urinary_tract(3)|adrenal_gland(3)|gastrointestinal_tract_(site_indeterminate)(2)|liver(2)|meninges(1)|kidney(1)|autonomic_ganglia(1)|pituitary(1)|salivary_gland(1)	18290	Melanoma(164;0.00956)				Sorafenib(DB00398)	TCGAGATTTCACTGTAGCTAG	0.368	V600E(UACC257_SKIN)|V600D(K029AX_SKIN)|V600E(HS695T_SKIN)|V600E(COLO679_SKIN)|V600E(BT474_BREAST)|V600E(IGR39_SKIN)|V600E(A101D_SKIN)|V600E(COLO783_SKIN)|V600E(IGR37_SKIN)|V600E(A375_SKIN)|V600E(WM793_SKIN)|V600E(COLO818_SKIN)|V600E(HS294T_SKIN)|V600E(SKMEL28_SKIN)|V600E(DU4475_BREAST)|V600E(SIGM5_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|V600E(IGR1_SKIN)|V600E(SKHEP1_LIVER)|V600E(WM983B_SKIN)|V600E(GCT_SOFT_TISSUE)|V600E(RVH421_SKIN)|V600D(WM2664_SKIN)|V600E(CL34_LARGE_INTESTINE)|V600E(SKMEL24_SKIN)|V600D(WM115_SKIN)|V600E(MALME3M_SKIN)|V600E(A673_BONE)|V600E(C32_SKIN)|V600E(DBTRG05MG_CENTRAL_NERVOUS_SYSTEM)|V600E(COLO800_SKIN)|V600E(COLO741_SKIN)|V600E(HS939T_SKIN)|V600E(COLO205_LARGE_INTESTINE)|V600E(K029AX_SKIN)|V600E(AM38_CENTRAL_NERVOUS_SYSTEM)|V600E(SH4_SKIN)|V600E(WM88_SKIN)|V600E(KG1C_CENTRAL_NERVOUS_SYSTEM)|V600E(COLO849_SKIN)|V600E(MELHO_SKIN)|V600E(BHT101_THYROID)|V600E(G361_SKIN)|V600E(UACC62_SKIN)|V600E(BCPAP_THYROID)|V600E(8505C_THYROID)|V600E(SW1417_LARGE_INTESTINE)|V600E(COLO829_SKIN)|V600E(RKO_LARGE_INTESTINE)|V600E(A2058_SKIN)|V600E(RPMI7951_SKIN)|V600E(OUMS23_LARGE_INTESTINE)|V600E(SKMEL5_SKIN)|V600E(ES2_OVARY)|V600E(LOXIMVI_SKIN)	61	Mis|T|O	AKAP9|KIAA1549	melanoma|colorectal|papillary thyroid|borderline ov|Non small-cell lung cancer (NSCLC)|cholangiocarcinoma|pilocytic astrocytoma		Cardio-facio-cutaneous syndrome		Cardiofaciocutaneous_syndrome				51	174	---	---	---	---	0	0	0.048971	0	0
ZNF212	7988	broad.mit.edu	37	7	148947484	148947484	+	Missense_Mutation	SNP	G	A	A			TCGA-ET-A39M-01A-11D-A19J-08	TCGA-ET-A39M-10A-01D-A19M-08									Somatic	Phase_I	Capture				Illumina GAIIx	39c627f7-225b-4a78-a589-e3228fed1d6e	cfdd0348-3531-4c23-bc2f-963173dfd77e	g.chr7:148947484G>A	uc003wfp.2	+	2	355	c.259G>A	c.(259-261)GGG>AGG	p.G87R		NM_012256	NP_036388	Q9UDV6	ZN212_HUMAN	zinc finger protein 212	87					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|identical protein binding|zinc ion binding			ovary(1)	1	Melanoma(164;0.15)		OV - Ovarian serous cystadenocarcinoma(82;0.00171)			CGTGGAGTTCGGGAACCAGCT	0.652													8	236	---	---	---	---	0	0	0.038147	0	0
GPIHBP1	338328	broad.mit.edu	37	8	144296991	144296991	+	Silent	SNP	C	T	T	rs138215873	byFrequency	TCGA-ET-A39M-01A-11D-A19J-08	TCGA-ET-A39M-10A-01D-A19M-08									Somatic	Phase_I	Capture				Illumina GAIIx	39c627f7-225b-4a78-a589-e3228fed1d6e	cfdd0348-3531-4c23-bc2f-963173dfd77e	g.chr8:144296991C>T	uc003yxu.1	+	3	360	c.285C>T	c.(283-285)CAC>CAT	p.H95H		NM_178172	NP_835466	Q8IV16	HDBP1_HUMAN	glycosylphosphatidylinositol anchored high	95	UPAR/Ly6.				cholesterol homeostasis|intracellular protein transport|positive regulation of chylomicron remnant clearance|positive regulation of lipoprotein lipase activity|protein import|protein localization at cell surface|protein stabilization|response to heparin|triglyceride homeostasis	anchored to external side of plasma membrane|apical plasma membrane|basolateral plasma membrane|high-density lipoprotein particle|integral to membrane|intracellular	apolipoprotein binding|chylomicron binding|lipase binding|lipid binding|protein transmembrane transporter activity				0	all_cancers(97;6.49e-11)|all_epithelial(106;2.77e-09)|Lung NSC(106;0.000167)|all_lung(105;0.000459)|Ovarian(258;0.0254)|Acute lymphoblastic leukemia(118;0.155)					TCATTGCCCACGGGAACACCG	0.667													5	57	---	---	---	---	0	0	0.014758	0	0
GPR172A	79581	broad.mit.edu	37	8	145583505	145583505	+	Missense_Mutation	SNP	C	A	A	rs117500243	byFrequency	TCGA-ET-A39M-01A-11D-A19J-08	TCGA-ET-A39M-10A-01D-A19M-08									Somatic	Phase_I	Capture				Illumina GAIIx	39c627f7-225b-4a78-a589-e3228fed1d6e	cfdd0348-3531-4c23-bc2f-963173dfd77e	g.chr8:145583505C>A	uc003zcc.1	+	3	510	c.353C>A	c.(352-354)GCC>GAC	p.A118D	FBXL6_uc003zbz.2_5'Flank|FBXL6_uc003zca.2_5'Flank|FBXL6_uc003zcb.2_5'Flank|FBXL6_uc010mfx.2_5'Flank|GPR172A_uc003zcd.1_Missense_Mutation_p.A118D|GPR172A_uc003zce.1_Missense_Mutation_p.A118D|GPR172A_uc010mfy.1_Missense_Mutation_p.A118D|GPR172A_uc003zcf.1_Missense_Mutation_p.A118D|GPR172A_uc011llc.1_Missense_Mutation_p.A30D	NM_024531	NP_078807	Q9HAB3	RFT3_HUMAN	G protein-coupled receptor 172A precursor	118	Helical; (Potential).					integral to plasma membrane	receptor activity|riboflavin transporter activity				0	all_cancers(97;6.64e-12)|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)		OV - Ovarian serous cystadenocarcinoma(54;4.43e-40)|Epithelial(56;1.48e-39)|all cancers(56;1.49e-34)|BRCA - Breast invasive adenocarcinoma(115;0.0441)|Colorectal(110;0.055)			TTAGCACTGGCCTTTGTGCTG	0.592													10	256	---	---	---	---	2.17888e-05	2.2927e-05	0.058154	1	0
C9orf50	375759	broad.mit.edu	37	9	132375757	132375757	+	Missense_Mutation	SNP	C	T	T			TCGA-ET-A39M-01A-11D-A19J-08	TCGA-ET-A39M-10A-01D-A19M-08									Somatic	Phase_I	Capture				Illumina GAIIx	39c627f7-225b-4a78-a589-e3228fed1d6e	cfdd0348-3531-4c23-bc2f-963173dfd77e	g.chr9:132375757C>T	uc004byc.3	-	5	1202	c.1000G>A	c.(1000-1002)GAG>AAG	p.E334K	C9orf50_uc004byb.3_RNA	NM_199350	NP_955382	Q5SZB4	CI050_HUMAN	hypothetical protein LOC375759	334										ovary(1)|central_nervous_system(1)	2		Ovarian(14;0.00556)				AGGGTCTCCTCCTTGGCCCCA	0.662													8	100	---	---	---	---	0	0	0.038147	0	0
PNMA5	114824	broad.mit.edu	37	X	152159280	152159280	+	Missense_Mutation	SNP	C	T	T			TCGA-ET-A39M-01A-11D-A19J-08	TCGA-ET-A39M-10A-01D-A19M-08									Somatic	Phase_I	Capture				Illumina GAIIx	39c627f7-225b-4a78-a589-e3228fed1d6e	cfdd0348-3531-4c23-bc2f-963173dfd77e	g.chrX:152159280C>T	uc010ntw.2	-	3	1202	c.863G>A	c.(862-864)CGT>CAT	p.R288H	PNMA5_uc004fha.3_Missense_Mutation_p.R288H|PNMA5_uc010ntx.2_Missense_Mutation_p.R288H|PNMA5_uc004fgy.3_Missense_Mutation_p.R288H	NM_001103151	NP_001096621	Q96PV4	PNMA5_HUMAN	paraneoplastic antigen like 5	288					apoptosis					ovary(1)|skin(1)	2	Acute lymphoblastic leukemia(192;6.56e-05)					ATGTTTCAGACGAATCATGTC	0.562													44	50	---	---	---	---	0	0	0.111260	0	0
ZBTB40	9923	broad.mit.edu	37	1	22838561	22838563	+	In_Frame_Del	DEL	AAG	-	-			TCGA-ET-A39M-01A-11D-A19J-08	TCGA-ET-A39M-10A-01D-A19M-08									Somatic	Phase_I	Capture				Illumina GAIIx	39c627f7-225b-4a78-a589-e3228fed1d6e	cfdd0348-3531-4c23-bc2f-963173dfd77e	g.chr1:22838561_22838563delAAG	uc001bft.2	+	12	2906_2908	c.2395_2397delAAG	c.(2395-2397)AAGdel	p.K803del	ZBTB40_uc001bfu.2_In_Frame_Del_p.K803del|ZBTB40_uc009vqi.1_In_Frame_Del_p.K691del|ZBTB40_uc001bfv.1_In_Frame_Del_p.K432del	NM_001083621	NP_001077090	Q9NUA8	ZBT40_HUMAN	zinc finger and BTB domain containing 40	803					bone mineralization|regulation of transcription, DNA-dependent|response to DNA damage stimulus|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1		Colorectal(325;3.46e-05)|Lung NSC(340;6.55e-05)|all_lung(284;9.87e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|OV - Ovarian serous cystadenocarcinoma(117;2.86e-26)|Colorectal(126;8.55e-08)|COAD - Colon adenocarcinoma(152;4.1e-06)|GBM - Glioblastoma multiforme(114;1.39e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000712)|KIRC - Kidney renal clear cell carcinoma(1967;0.00374)|STAD - Stomach adenocarcinoma(196;0.00645)|READ - Rectum adenocarcinoma(331;0.0693)|Lung(427;0.216)		CGATGCCCCCAAGAAGAAGAAGA	0.517													9	171	---	---	---	---					
ZMYM4	9202	broad.mit.edu	37	1	35846960	35846960	+	Frame_Shift_Del	DEL	A	-	-			TCGA-ET-A39M-01A-11D-A19J-08	TCGA-ET-A39M-10A-01D-A19M-08									Somatic	Phase_I	Capture				Illumina GAIIx	39c627f7-225b-4a78-a589-e3228fed1d6e	cfdd0348-3531-4c23-bc2f-963173dfd77e	g.chr1:35846960delA	uc001byt.2	+	8	1362	c.1282delA	c.(1282-1284)AAAfs	p.K428fs	ZMYM4_uc009vuu.2_Frame_Shift_Del_p.K396fs|ZMYM4_uc001byu.2_Frame_Shift_Del_p.K104fs|ZMYM4_uc009vuv.2_Frame_Shift_Del_p.K167fs	NM_005095	NP_005086	Q5VZL5	ZMYM4_HUMAN	zinc finger protein 262	428	MYM-type 2.				multicellular organismal development		DNA binding|zinc ion binding			large_intestine(2)|ovary(1)|kidney(1)|skin(1)	5		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0887)				ATATGAACTGAAAAAAAAACC	0.338													10	235	---	---	---	---					
FLG2	388698	broad.mit.edu	37	1	152324558	152324559	+	Frame_Shift_Del	DEL	TG	-	-	rs140875805	byFrequency	TCGA-ET-A39M-01A-11D-A19J-08	TCGA-ET-A39M-10A-01D-A19M-08									Somatic	Phase_I	Capture				Illumina GAIIx	39c627f7-225b-4a78-a589-e3228fed1d6e	cfdd0348-3531-4c23-bc2f-963173dfd77e	g.chr1:152324558_152324559delTG	uc001ezw.3	-	3	5776_5777	c.5703_5704delCA	c.(5701-5706)CACAGCfs	p.H1901fs	uc001ezv.2_Intron	NM_001014342	NP_001014364	Q5D862	FILA2_HUMAN	filaggrin family member 2	1901_1902							calcium ion binding|structural molecule activity			ovary(10)|skin(5)|upper_aerodigestive_tract(1)|breast(1)	17	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			CTGGCTTGGCTGTGTGTGTGTC	0.515													7	667	---	---	---	---					
KCNN3	3782	broad.mit.edu	37	1	154680586	154680588	+	In_Frame_Del	DEL	GCT	-	-			TCGA-ET-A39M-01A-11D-A19J-08	TCGA-ET-A39M-10A-01D-A19M-08									Somatic	Phase_I	Capture				Illumina GAIIx	39c627f7-225b-4a78-a589-e3228fed1d6e	cfdd0348-3531-4c23-bc2f-963173dfd77e	g.chr1:154680586_154680588delGCT	uc001ffp.2	-	8	2374_2376	c.2060_2062delAGC	c.(2059-2064)CAGCTC>CTC	p.Q687del	KCNN3_uc001ffo.2_In_Frame_Del_p.Q382del	NM_002249	NP_002240	Q9UGI6	KCNN3_HUMAN	small conductance calcium-activated potassium	692	Poly-Gln.					integral to membrane	calmodulin binding			lung(1)	1	all_lung(78;2.29e-27)|all_hematologic(923;0.088)|Hepatocellular(266;0.108)|all_neural(408;0.245)		BRCA - Breast invasive adenocarcinoma(34;0.00819)			GCAGACAGGAGCTGCTGCTGCTG	0.640													8	276	---	---	---	---					
Unknown	0	broad.mit.edu	37	10	43063100	43063101	+	IGR	INS	-	A	A	rs34202394		TCGA-ET-A39M-01A-11D-A19J-08	TCGA-ET-A39M-10A-01D-A19M-08									Somatic	Phase_I	Capture				Illumina GAIIx	39c627f7-225b-4a78-a589-e3228fed1d6e	cfdd0348-3531-4c23-bc2f-963173dfd77e	g.chr10:43063100_43063101insA								ZNF37B (14820 upstream) : ZNF33B (6532 downstream)																							TTTGGAGCCAGAAAAAAAAAAA	0.218													9	3	---	---	---	---					
OR51A4	401666	broad.mit.edu	37	11	4968495	4968498	+	5'Flank	DEL	TGGT	-	-	rs143841512		TCGA-ET-A39M-01A-11D-A19J-08	TCGA-ET-A39M-10A-01D-A19M-08									Somatic	Phase_I	Capture				Illumina GAIIx	39c627f7-225b-4a78-a589-e3228fed1d6e	cfdd0348-3531-4c23-bc2f-963173dfd77e	g.chr11:4968495_4968498delTGGT	uc010qys.1	-							NM_001005329	NP_001005329	Q8NGJ6	O51A4_HUMAN	olfactory receptor, family 51, subfamily A,						sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(2)|skin(1)	3		Medulloblastoma(188;0.0075)|all_neural(188;0.0577)|Breast(177;0.086)		Epithelial(150;3.22e-11)|BRCA - Breast invasive adenocarcinoma(625;0.0284)|LUSC - Lung squamous cell carcinoma(625;0.19)		TGAAGAGAGATGGTTGGTTGCTGC	0.304													6	12	---	---	---	---					
Unknown	0	broad.mit.edu	37	11	89804293	89804294	+	IGR	DEL	TC	-	-			TCGA-ET-A39M-01A-11D-A19J-08	TCGA-ET-A39M-10A-01D-A19M-08									Somatic	Phase_I	Capture				Illumina GAIIx	39c627f7-225b-4a78-a589-e3228fed1d6e	cfdd0348-3531-4c23-bc2f-963173dfd77e	g.chr11:89804293_89804294delTC								TRIM64 (97055 upstream) : UBTFL1 (14824 downstream)																							GGAGTCGTTTTCTCTCTCTCTC	0.292													9	355	---	---	---	---					
Unknown	0	broad.mit.edu	37	14	19408019	19408019	+	IGR	DEL	A	-	-			TCGA-ET-A39M-01A-11D-A19J-08	TCGA-ET-A39M-10A-01D-A19M-08									Somatic	Phase_I	Capture				Illumina GAIIx	39c627f7-225b-4a78-a589-e3228fed1d6e	cfdd0348-3531-4c23-bc2f-963173dfd77e	g.chr14:19408019delA								OR11H12 (29447 upstream) : POTEG (145346 downstream)																							CTGTGGAGCCAAAAAAAAAAT	0.393													4	9	---	---	---	---					
SLTM	79811	broad.mit.edu	37	15	59182564	59182565	+	Frame_Shift_Del	DEL	CT	-	-			TCGA-ET-A39M-01A-11D-A19J-08	TCGA-ET-A39M-10A-01D-A19M-08									Somatic	Phase_I	Capture				Illumina GAIIx	39c627f7-225b-4a78-a589-e3228fed1d6e	cfdd0348-3531-4c23-bc2f-963173dfd77e	g.chr15:59182564_59182565delCT	uc002afp.2	-	15	2082_2083	c.1994_1995delAG	c.(1993-1995)GAGfs	p.E665fs	SLTM_uc002afn.2_Frame_Shift_Del_p.E207fs|SLTM_uc002afo.2_Frame_Shift_Del_p.E647fs|SLTM_uc002afq.2_Frame_Shift_Del_p.E234fs|SLTM_uc010bgd.2_Frame_Shift_Del_p.E234fs	NM_024755	NP_079031	Q9NWH9	SLTM_HUMAN	modulator of estrogen induced transcription	665	Arg/Glu-rich.|Potential.				apoptosis|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	nucleotide binding|RNA binding			ovary(1)	1						TTTCTAGGCGCTCTCTCTCTCT	0.475													8	407	---	---	---	---					
LRRC37A4	55073	broad.mit.edu	37	17	43591984	43591985	+	RNA	INS	-	G	G			TCGA-ET-A39M-01A-11D-A19J-08	TCGA-ET-A39M-10A-01D-A19M-08									Somatic	Phase_I	Capture				Illumina GAIIx	39c627f7-225b-4a78-a589-e3228fed1d6e	cfdd0348-3531-4c23-bc2f-963173dfd77e	g.chr17:43591984_43591985insG	uc002ije.2	-	1		c.538_539insC								Homo sapiens cDNA FLJ34414 fis, clone HEART2003168, highly similar to Homo sapiens c114 SLIT-like testicular protein (LOC474170), mRNA.												0						GTGGGTCATGCGGAGCGAGTTT	0.411													12	69	---	---	---	---					
VEZF1	7716	broad.mit.edu	37	17	56056605	56056607	+	In_Frame_Del	DEL	TGC	-	-	rs61731354	byFrequency	TCGA-ET-A39M-01A-11D-A19J-08	TCGA-ET-A39M-10A-01D-A19M-08									Somatic	Phase_I	Capture				Illumina GAIIx	39c627f7-225b-4a78-a589-e3228fed1d6e	cfdd0348-3531-4c23-bc2f-963173dfd77e	g.chr17:56056605_56056607delTGC	uc002ivf.1	-	5	1187_1189	c.1044_1046delGCA	c.(1042-1047)CAGCAA>CAA	p.348_349QQ>Q	VEZF1_uc010dcn.1_In_Frame_Del_p.198_199QQ>Q	NM_007146	NP_009077	Q14119	VEZF1_HUMAN	zinc finger protein 161	348_349	Poly-Gln.				cellular defense response|regulation of transcription from RNA polymerase II promoter|transcription from RNA polymerase II promoter	nucleus	DNA binding|zinc ion binding			ovary(1)|breast(1)	2						ttgttgttgttgctgctgctgct	0.305													8	577	---	---	---	---					
Unknown	0	broad.mit.edu	37	19	14991072	14991072	+	IGR	DEL	A	-	-	rs34163436		TCGA-ET-A39M-01A-11D-A19J-08	TCGA-ET-A39M-10A-01D-A19M-08									Somatic	Phase_I	Capture				Illumina GAIIx	39c627f7-225b-4a78-a589-e3228fed1d6e	cfdd0348-3531-4c23-bc2f-963173dfd77e	g.chr19:14991072delA								OR7A10 (38383 upstream) : OR7A17 (168 downstream)																							AAAGCTTTATAAAGGAATACA	0.313													4	3	---	---	---	---					
Unknown	0	broad.mit.edu	37	20	29449507	29449509	+	IGR	DEL	CAG	-	-	rs4010662	by1000genomes	TCGA-ET-A39M-01A-11D-A19J-08	TCGA-ET-A39M-10A-01D-A19M-08									Somatic	Phase_I	Capture				Illumina GAIIx	39c627f7-225b-4a78-a589-e3228fed1d6e	cfdd0348-3531-4c23-bc2f-963173dfd77e	g.chr20:29449507_29449509delCAG								None (None upstream) : FRG1B (162370 downstream)																							CAACCACCAACAGCTGTCCTCTT	0.374													7	149	---	---	---	---					
TPTE	7179	broad.mit.edu	37	21	10944697	10944697	+	Frame_Shift_Del	DEL	A	-	-			TCGA-ET-A39M-01A-11D-A19J-08	TCGA-ET-A39M-10A-01D-A19M-08									Somatic	Phase_I	Capture				Illumina GAIIx	39c627f7-225b-4a78-a589-e3228fed1d6e	cfdd0348-3531-4c23-bc2f-963173dfd77e	g.chr21:10944697delA	uc002yip.1	-	11	905	c.537delT	c.(535-537)TTTfs	p.F179fs	TPTE_uc002yis.1_RNA|TPTE_uc002yiq.1_Frame_Shift_Del_p.F161fs|TPTE_uc002yir.1_Frame_Shift_Del_p.F141fs|TPTE_uc010gkv.1_Frame_Shift_Del_p.F41fs	NM_199261	NP_954870	P56180	TPTE_HUMAN	transmembrane phosphatase with tensin homology	179	Helical; (Potential).				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			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)		ACTTAATGTCAAAAAAAATGT	0.299													9	763	---	---	---	---					
Unknown	0	broad.mit.edu	37	4	69242367	69242368	+	IGR	INS	-	A	A	rs35810847		TCGA-ET-A39M-01A-11D-A19J-08	TCGA-ET-A39M-10A-01D-A19M-08									Somatic	Phase_I	Capture				Illumina GAIIx	39c627f7-225b-4a78-a589-e3228fed1d6e	cfdd0348-3531-4c23-bc2f-963173dfd77e	g.chr4:69242367_69242368insA								YTHDC1 (26543 upstream) : UGT2B15 (269948 downstream)																							GCTTTGACTTGAAAAAAAAAAA	0.238													2	4	---	---	---	---					
PCDHGA8	9708	broad.mit.edu	37	5	140772899	140772899	+	Frame_Shift_Del	DEL	C	-	-			TCGA-ET-A39M-01A-11D-A19J-08	TCGA-ET-A39M-10A-01D-A19M-08									Somatic	Phase_I	Capture				Illumina GAIIx	39c627f7-225b-4a78-a589-e3228fed1d6e	cfdd0348-3531-4c23-bc2f-963173dfd77e	g.chr5:140772899delC	uc003lkd.1	+	1	1417	c.519delC	c.(517-519)AGCfs	p.S173fs	PCDHGA1_uc003lji.1_Intron|PCDHGA2_uc003ljk.1_Intron|PCDHGA3_uc003ljm.1_Intron|PCDHGA3_uc010jfx.1_Intron|PCDHGB1_uc003ljo.1_Intron|PCDHGA4_uc003ljq.1_Intron|PCDHGB2_uc003ljs.1_Intron|PCDHGA5_uc003lju.1_Intron|PCDHGB3_uc003ljw.1_Intron|PCDHGA6_uc003ljy.1_Intron|PCDHGA7_uc003lka.1_Intron|PCDHGB4_uc003lkc.1_Intron|PCDHGA8_uc003lkb.3_Frame_Shift_Del_p.S173fs	NM_032088	NP_114477	Q9Y5G5	PCDG8_HUMAN	protocadherin gamma subfamily A, 8 isoform 1	173	Extracellular (Potential).|Cadherin 2.				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding				0			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			ACCAGCTCAGCCCCAATCACC	0.572													7	192	---	---	---	---					
Unknown	0	broad.mit.edu	37	6	75560075	75560075	+	IGR	DEL	T	-	-			TCGA-ET-A39M-01A-11D-A19J-08	TCGA-ET-A39M-10A-01D-A19M-08									Somatic	Phase_I	Capture				Illumina GAIIx	39c627f7-225b-4a78-a589-e3228fed1d6e	cfdd0348-3531-4c23-bc2f-963173dfd77e	g.chr6:75560075delT								None (None upstream) : COL12A1 (233968 downstream)																							TACGTGTTGCTTTTTTTTTTT	0.373													4	8	---	---	---	---					
TMEM60	85025	broad.mit.edu	37	7	77423460	77423460	+	Frame_Shift_Del	DEL	T	-	-			TCGA-ET-A39M-01A-11D-A19J-08	TCGA-ET-A39M-10A-01D-A19M-08									Somatic	Phase_I	Capture				Illumina GAIIx	39c627f7-225b-4a78-a589-e3228fed1d6e	cfdd0348-3531-4c23-bc2f-963173dfd77e	g.chr7:77423460delT	uc003ugn.2	-	2	458	c.231delA	c.(229-231)AAAfs	p.K77fs		NM_032936	NP_116325	Q9H2L4	TMM60_HUMAN	transmembrane protein 60	77						integral to membrane					0						GGTACCAGGCTTTTTTTTTAA	0.408													7	359	---	---	---	---					
Unknown	0	broad.mit.edu	37	8	49826831	49826831	+	IGR	DEL	A	-	-	rs141577976		TCGA-ET-A39M-01A-11D-A19J-08	TCGA-ET-A39M-10A-01D-A19M-08									Somatic	Phase_I	Capture				Illumina GAIIx	39c627f7-225b-4a78-a589-e3228fed1d6e	cfdd0348-3531-4c23-bc2f-963173dfd77e	g.chr8:49826831delA								EFCAB1 (178961 upstream) : SNAI2 (3408 downstream)																							ggaaaaaggcaaaaaaaAAAa	0.070													6	8	---	---	---	---					
ZNF704	619279	broad.mit.edu	37	8	81733713	81733713	+	Frame_Shift_Del	DEL	T	-	-			TCGA-ET-A39M-01A-11D-A19J-08	TCGA-ET-A39M-10A-01D-A19M-08									Somatic	Phase_I	Capture				Illumina GAIIx	39c627f7-225b-4a78-a589-e3228fed1d6e	cfdd0348-3531-4c23-bc2f-963173dfd77e	g.chr8:81733713delT	uc003yby.1	-	2	349	c.117delA	c.(115-117)AAAfs	p.K39fs		NM_001033723	NP_001028895	Q6ZNC4	ZN704_HUMAN	zinc finger protein 704	39						intracellular	zinc ion binding				0	all_cancers(3;8.53e-08)|all_epithelial(4;4.59e-10)|Breast(3;2.56e-06)|Lung NSC(7;2.58e-06)|all_lung(9;9.4e-06)		BRCA - Breast invasive adenocarcinoma(6;0.00401)|Epithelial(68;0.00448)|all cancers(69;0.0277)			TCCGGCTGGCTTTTTTGGTGT	0.428													9	970	---	---	---	---					
PKHD1L1	93035	broad.mit.edu	37	8	110455173	110455174	+	Splice_Site	INS	-	G	G			TCGA-ET-A39M-01A-11D-A19J-08	TCGA-ET-A39M-10A-01D-A19M-08									Somatic	Phase_I	Capture				Illumina GAIIx	39c627f7-225b-4a78-a589-e3228fed1d6e	cfdd0348-3531-4c23-bc2f-963173dfd77e	g.chr8:110455173_110455174insG	uc003yne.2	+	36	4498	c.4394_splice	c.e36-1	p.G1465_splice		NM_177531	NP_803875	Q86WI1	PKHL1_HUMAN	fibrocystin L precursor						immune response	cytosol|extracellular space|integral to membrane	receptor activity			ovary(9)|central_nervous_system(2)|large_intestine(1)|breast(1)|pancreas(1)	14			OV - Ovarian serous cystadenocarcinoma(57;9.88e-13)			ATTTTATGGCAGGTTCATTTTC	0.322										HNSCC(38;0.096)			7	254	---	---	---	---					
FLJ43950	347127	broad.mit.edu	37	9	84528568	84528568	+	Frame_Shift_Del	DEL	A	-	-			TCGA-ET-A39M-01A-11D-A19J-08	TCGA-ET-A39M-10A-01D-A19M-08									Somatic	Phase_I	Capture				Illumina GAIIx	39c627f7-225b-4a78-a589-e3228fed1d6e	cfdd0348-3531-4c23-bc2f-963173dfd77e	g.chr9:84528568delA	uc011lst.1	+	1	217	c.116delA	c.(115-117)CAAfs	p.Q39fs		NR_026851				SubName: Full=cDNA FLJ43950 fis, clone TESTI4015293, moderately similar to FAM75-like protein;												0						AATGATATCCAAAAGGTAAGG	0.398													7	9	---	---	---	---					
C9orf43	257169	broad.mit.edu	37	9	116187646	116187648	+	In_Frame_Del	DEL	GCA	-	-			TCGA-ET-A39M-01A-11D-A19J-08	TCGA-ET-A39M-10A-01D-A19M-08									Somatic	Phase_I	Capture				Illumina GAIIx	39c627f7-225b-4a78-a589-e3228fed1d6e	cfdd0348-3531-4c23-bc2f-963173dfd77e	g.chr9:116187646_116187648delGCA	uc004bho.3	+	10	1284_1286	c.888_890delGCA	c.(886-891)CGGCAG>CGG	p.Q304del	C9orf43_uc004bhp.2_In_Frame_Del_p.Q304del	NM_152786	NP_689999	Q8TAL5	CI043_HUMAN	hypothetical protein LOC257169	304	Gln-rich.										0						agcagcagcggcagcagcagcag	0.438													8	155	---	---	---	---					
NUDT11	55190	broad.mit.edu	37	X	51239296	51239309	+	Translation_Start_Site	DEL	TCCTCGAGGCAGCC	-	-			TCGA-ET-A39M-01A-11D-A19J-08	TCGA-ET-A39M-10A-01D-A19M-08									Somatic	Phase_I	Capture				Illumina GAIIx	39c627f7-225b-4a78-a589-e3228fed1d6e	cfdd0348-3531-4c23-bc2f-963173dfd77e	g.chrX:51239296_51239309delTCCTCGAGGCAGCC	uc010njt.2	-	1						NM_018159	NP_060629	Q96G61	NUD11_HUMAN	nudix-type motif 11							cytoplasm	diphosphoinositol-polyphosphate diphosphatase activity|metal ion binding				0	Ovarian(276;0.236)					TTGCACTTCATCCTCGAGGCAGCCTCCTCGAGGC	0.584										HNSCC(48;0.14)			10	15	---	---	---	---					
