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	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	filter
PRAMEF1	65121	broad.mit.edu	37	1	12854406	12854406	+	Silent	SNP	G	A	A			TCGA-CJ-4899-01A-01D-1462-08	TCGA-CJ-4899-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:12854406G>A	uc001auj.1	+	3	733	c.630G>A	c.(628-630)CTG>CTA	p.L210L		NM_023013	NP_075389	O95521	PRAM1_HUMAN	PRAME family member 1	210											0	Ovarian(185;0.249)	Renal(390;0.000469)|Lung NSC(185;0.00143)|all_lung(284;0.00181)|Colorectal(325;0.00215)|Breast(348;0.0042)|Myeloproliferative disorder(586;0.0393)|Hepatocellular(190;0.0623)|Ovarian(437;0.0731)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00812)|Colorectal(212;4.88e-06)|Kidney(185;4.89e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.000194)|COAD - Colon adenocarcinoma(227;0.000241)|BRCA - Breast invasive adenocarcinoma(304;0.000293)|STAD - Stomach adenocarcinoma(313;0.0072)|READ - Rectum adenocarcinoma(331;0.0649)		TTCAAGAGCTGGAAATTCGCA	0.403													99	668	---	---	---	---	PASS
CROCCL2	114819	broad.mit.edu	37	1	16812113	16812113	+	RNA	SNP	G	A	A	rs142394748	by1000genomes	TCGA-CJ-4899-01A-01D-1462-08	TCGA-CJ-4899-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:16812113G>A	uc001ayt.2	-	7		c.1439C>T			CROCCL2_uc001ays.2_RNA	NR_023386				Homo sapiens mRNA for KIAA1922 protein, partial cds.												0						ATCCTTCTCCGGATTCTGCTT	0.607													3	22	---	---	---	---	PASS
ZC3H12A	80149	broad.mit.edu	37	1	37945923	37945923	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-4899-01A-01D-1462-08	TCGA-CJ-4899-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:37945923G>A	uc001cbb.3	+	3	626	c.476G>A	c.(475-477)GGC>GAC	p.G159D	ZC3H12A_uc001cbc.1_5'UTR	NM_025079	NP_079355	Q5D1E8	ZC12A_HUMAN	zinc finger CCCH-type containing 12A	159					angiogenesis|apoptosis|cell differentiation	cytoplasm|nucleus|plasma membrane	endonuclease activity|metal ion binding			ovary(2)	2		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.164)				TCCTGCCGGGGCATCCTGCTG	0.637													4	70	---	---	---	---	PASS
NOTCH2NL	388677	broad.mit.edu	37	1	145281487	145281487	+	Missense_Mutation	SNP	G	T	T			TCGA-CJ-4899-01A-01D-1462-08	TCGA-CJ-4899-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:145281487G>T	uc001emn.3	+	4	787	c.417G>T	c.(415-417)AAG>AAT	p.K139N	NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|NBPF10_uc001emp.3_5'UTR|NOTCH2NL_uc001emm.3_Missense_Mutation_p.K139N|NOTCH2NL_uc001emo.2_Missense_Mutation_p.K139N|NOTCH2NL_uc010oyh.1_RNA	NM_203458	NP_982283	Q7Z3S9	NT2NL_HUMAN	Notch homolog 2 N-terminal like protein	139	EGF-like 4.				cell differentiation|multicellular organismal development|Notch signaling pathway	cytoplasm|extracellular region	calcium ion binding			ovary(1)	1						CAGGGCAGAAGTGTGAGACTG	0.557													21	545	---	---	---	---	PASS
POGK	57645	broad.mit.edu	37	1	166816822	166816822	+	Silent	SNP	C	G	G			TCGA-CJ-4899-01A-01D-1462-08	TCGA-CJ-4899-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:166816822C>G	uc001gdt.1	+	4	471	c.351C>G	c.(349-351)ACC>ACG	p.T117T	POGK_uc010ple.1_Silent_p.T32T|POGK_uc010plf.1_Intron	NM_017542	NP_060012	Q9P215	POGK_HUMAN	pogo transposable element with KRAB domain	117	KRAB.				multicellular organismal development|regulation of transcription, DNA-dependent	nucleus	DNA binding			ovary(1)	1						AAGGAGGCACCTCTGCAGGTA	0.493													11	53	---	---	---	---	PASS
CR2	1380	broad.mit.edu	37	1	207648341	207648341	+	Silent	SNP	C	T	T	rs139322251		TCGA-CJ-4899-01A-01D-1462-08	TCGA-CJ-4899-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:207648341C>T	uc001hfw.2	+	13	2413	c.2319C>T	c.(2317-2319)AGC>AGT	p.S773S	CR2_uc001hfv.2_Silent_p.S832S|CR2_uc009xch.2_Silent_p.S773S	NM_001877	NP_001868	P20023	CR2_HUMAN	complement component (3d/Epstein Barr virus)	773	Sushi 12.|Extracellular (Potential).				complement activation, classical pathway|innate immune response	integral to membrane|plasma membrane	complement receptor activity|protein homodimerization activity			upper_aerodigestive_tract(3)|skin(3)|urinary_tract(1)|ovary(1)	8						GATCTTGGAGCGGGCCTTCCC	0.443													7	192	---	---	---	---	PASS
WNT3A	89780	broad.mit.edu	37	1	228246774	228246774	+	Missense_Mutation	SNP	G	T	T			TCGA-CJ-4899-01A-01D-1462-08	TCGA-CJ-4899-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:228246774G>T	uc001hrq.1	+	4	745	c.667G>T	c.(667-669)GAC>TAC	p.D223Y	WNT3A_uc001hrp.1_Missense_Mutation_p.D223Y	NM_033131	NP_149122	P56704	WNT3A_HUMAN	wingless-type MMTV integration site family,	223					axis specification|cell proliferation in forebrain|cell-cell signaling|cellular response to retinoic acid|convergent extension|dermatome development|dorsal/ventral neural tube patterning|embryonic pattern specification|extracellular matrix organization|hemopoietic stem cell proliferation|hippocampus development|inner ear morphogenesis|mammary gland development|midbrain-hindbrain boundary development|negative regulation of fat cell differentiation|negative regulation of heart induction by canonical Wnt receptor signaling pathway|negative regulation of neuron projection development|notochord development|palate development|paraxial mesodermal cell fate commitment|positive regulation of catenin import into nucleus|positive regulation of peptidyl-serine phosphorylation|positive regulation of protein binding|positive regulation of receptor internalization|positive regulation of transcription from RNA polymerase II promoter|signalosome assembly|tail morphogenesis|Wnt receptor signaling pathway involved in forebrain neuroblast division|Wnt receptor signaling pathway, calcium modulating pathway	cell surface|early endosome|extracellular space|late endosome|membrane raft|plasma membrane|proteinaceous extracellular matrix	extracellular matrix structural constituent|frizzled-2 binding|receptor agonist activity|signal transducer activity|transcription coactivator activity			ovary(1)	1		Prostate(94;0.0405)				GTCGCAACCCGACTTCCGCGC	0.657													8	47	---	---	---	---	PASS
ABCG5	64240	broad.mit.edu	37	2	44065669	44065669	+	Intron	SNP	G	A	A			TCGA-CJ-4899-01A-01D-1462-08	TCGA-CJ-4899-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:44065669G>A	uc002rtn.2	-						ABCG5_uc002rto.2_5'UTR|ABCG5_uc002rtp.2_5'UTR|ABCG8_uc002rtq.2_5'Flank|ABCG8_uc010yoa.1_5'Flank	NM_022436	NP_071881	Q9H222	ABCG5_HUMAN	ATP-binding cassette sub-family G member 5						cholesterol efflux|cholesterol homeostasis|excretion|lipid metabolic process|negative regulation of intestinal cholesterol absorption|negative regulation of intestinal phytosterol absorption	apical plasma membrane|integral to membrane	ATP binding|ATPase activity|protein heterodimerization activity			ovary(1)|skin(1)	2		all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.175)				CAAGGGCTCTGCCTTACCTGA	0.657													3	11	---	---	---	---	PASS
PSME4	23198	broad.mit.edu	37	2	54176396	54176396	+	Missense_Mutation	SNP	T	A	A			TCGA-CJ-4899-01A-01D-1462-08	TCGA-CJ-4899-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:54176396T>A	uc002rxp.2	-	2	323	c.267A>T	c.(265-267)AAA>AAT	p.K89N	PSME4_uc010yop.1_5'UTR|PSME4_uc010yoq.1_RNA|PSME4_uc010fbu.1_5'UTR|PSME4_uc010fbv.1_Missense_Mutation_p.N4I	NM_014614	NP_055429	Q14997	PSME4_HUMAN	proteasome (prosome, macropain) activator	89					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|apoptosis|cell differentiation|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|M/G1 transition of mitotic cell cycle|mRNA metabolic process|multicellular organismal development|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|regulation of apoptosis|regulation of cellular amino acid metabolic process|S phase of mitotic cell cycle|spermatogenesis|viral reproduction	nuclear speck|proteasome complex	binding			ovary(2)|breast(2)|pancreas(1)	5			Lung(47;0.125)|LUSC - Lung squamous cell carcinoma(58;0.181)			CTTTGCTAAATTTTCTCCCAT	0.214													14	52	---	---	---	---	PASS
MAT2A	4144	broad.mit.edu	37	2	85768975	85768975	+	Silent	SNP	T	C	C			TCGA-CJ-4899-01A-01D-1462-08	TCGA-CJ-4899-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:85768975T>C	uc002spr.2	+	5	552	c.429T>C	c.(427-429)ACT>ACC	p.T143T	MAT2A_uc010ysr.1_Silent_p.T143T|MAT2A_uc010fgk.2_Silent_p.T117T|MAT2A_uc010fgl.2_Silent_p.T80T|MAT2A_uc010fgm.1_3'UTR	NM_005911	NP_005902	P31153	METK2_HUMAN	methionine adenosyltransferase II, alpha	143					methylation|xenobiotic metabolic process	cytosol	ATP binding|metal ion binding|methionine adenosyltransferase activity				0					L-Methionine(DB00134)|S-Adenosylmethionine(DB00118)	GCTATGCCACTGATGAAACTG	0.418													47	200	---	---	---	---	PASS
FBLN7	129804	broad.mit.edu	37	2	112896287	112896287	+	Missense_Mutation	SNP	C	A	A			TCGA-CJ-4899-01A-01D-1462-08	TCGA-CJ-4899-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:112896287C>A	uc002tho.1	+	1	326	c.55C>A	c.(55-57)CCC>ACC	p.P19T	FBLN7_uc002thn.2_Missense_Mutation_p.P19T|FBLN7_uc010fki.1_Missense_Mutation_p.P19T|FBLN7_uc010fkj.1_Missense_Mutation_p.P19T	NM_153214	NP_694946	Q53RD9	FBLN7_HUMAN	fibulin 7 isoform 1	19					cell adhesion	proteinaceous extracellular matrix	calcium ion binding|heparin binding			ovary(1)|central_nervous_system(1)	2						CCTCGCCTGCCCCGAGCCGCG	0.418													3	29	---	---	---	---	PASS
MDH1B	130752	broad.mit.edu	37	2	207603138	207603138	+	3'UTR	SNP	C	A	A			TCGA-CJ-4899-01A-01D-1462-08	TCGA-CJ-4899-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:207603138C>A	uc002vbs.2	-	12					MDH1B_uc010ziw.1_Intron|MDH1B_uc010fui.2_3'UTR|MDH1B_uc010fuj.2_3'UTR|MDH1B_uc002vbt.2_RNA	NM_001039845	NP_001034934	Q5I0G3	MDH1B_HUMAN	malate dehydrogenase 1B, NAD (soluble)						carbohydrate metabolic process|malate metabolic process|tricarboxylic acid cycle		binding|malate dehydrogenase activity			ovary(3)|kidney(1)	4				LUSC - Lung squamous cell carcinoma(261;0.0763)|Epithelial(149;0.131)|Lung(261;0.145)		TAAATATAGACATTCATATAA	0.313													9	51	---	---	---	---	PASS
VIL1	7429	broad.mit.edu	37	2	219299387	219299387	+	Missense_Mutation	SNP	G	C	C			TCGA-CJ-4899-01A-01D-1462-08	TCGA-CJ-4899-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:219299387G>C	uc002via.2	+	14	1704	c.1639G>C	c.(1639-1641)GTC>CTC	p.V547L	VIL1_uc010zke.1_Missense_Mutation_p.V236L|VIL1_uc002vib.2_Missense_Mutation_p.V547L	NM_007127	NP_009058	P09327	VILI_HUMAN	villin 1	547	Gelsolin-like 5.|Core.				actin filament capping|actin filament depolymerization|actin filament polymerization|actin filament severing|apoptosis|cellular response to epidermal growth factor stimulus|cytoplasmic actin-based contraction involved in cell motility|epidermal growth factor receptor signaling pathway|positive regulation of actin filament bundle assembly|positive regulation of epithelial cell migration|regulation of actin nucleation|regulation of cell shape|regulation of lamellipodium morphogenesis|regulation of wound healing|response to bacterium	actin filament bundle|cytoplasm|filopodium tip|intracellular membrane-bounded organelle|lamellipodium|microvillus|ruffle	actin filament binding|calcium ion binding|caspase inhibitor activity|lysophosphatidic acid binding|phosphatidylinositol-4,5-bisphosphate binding|protein homodimerization activity			ovary(1)	1		Renal(207;0.0474)		Epithelial(149;6.88e-07)|all cancers(144;0.00013)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		TGATGTCTTTGTCCTCAAGAC	0.572													8	155	---	---	---	---	PASS
COL7A1	1294	broad.mit.edu	37	3	48609479	48609479	+	Splice_Site	SNP	C	T	T			TCGA-CJ-4899-01A-01D-1462-08	TCGA-CJ-4899-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:48609479C>T	uc003ctz.2	-	91	7025	c.7024_splice	c.e91-1	p.G2342_splice		NM_000094	NP_000085	Q02388	CO7A1_HUMAN	alpha 1 type VII collagen precursor						cell adhesion|epidermis development	basement membrane|collagen type VII	protein binding|serine-type endopeptidase inhibitor activity			ovary(4)|breast(3)|skin(3)|central_nervous_system(1)	11				BRCA - Breast invasive adenocarcinoma(193;0.000293)|KIRC - Kidney renal clear cell carcinoma(197;0.00558)|Kidney(197;0.00632)		CAGCTTCACCCTGCACAGAAT	0.672													3	21	---	---	---	---	PASS
STAB1	23166	broad.mit.edu	37	3	52540712	52540712	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-4899-01A-01D-1462-08	TCGA-CJ-4899-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:52540712G>A	uc003dej.2	+	18	1909	c.1835G>A	c.(1834-1836)CGC>CAC	p.R612H	STAB1_uc003dei.1_Missense_Mutation_p.R612H	NM_015136	NP_055951	Q9NY15	STAB1_HUMAN	stabilin 1 precursor	612	Extracellular (Potential).|FAS1 2.				cell adhesion|cell-cell signaling|defense response to bacterium|inflammatory response|negative regulation of angiogenesis|receptor-mediated endocytosis	integral to plasma membrane	bacterial cell surface binding|hyaluronic acid binding|low-density lipoprotein receptor activity|protein disulfide oxidoreductase activity|scavenger receptor activity			large_intestine(3)|upper_aerodigestive_tract(2)|central_nervous_system(1)|breast(1)|skin(1)|pancreas(1)	9				BRCA - Breast invasive adenocarcinoma(193;1.73e-05)|Kidney(197;0.00182)|KIRC - Kidney renal clear cell carcinoma(197;0.00205)|OV - Ovarian serous cystadenocarcinoma(275;0.0482)		CCGCAGGGGCGCATCCTGCTG	0.692													3	13	---	---	---	---	PASS
CEP135	9662	broad.mit.edu	37	4	56825852	56825852	+	Nonsense_Mutation	SNP	C	T	T			TCGA-CJ-4899-01A-01D-1462-08	TCGA-CJ-4899-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:56825852C>T	uc003hbi.2	+	6	853	c.619C>T	c.(619-621)CAA>TAA	p.Q207*	CEP135_uc003hbh.1_Nonsense_Mutation_p.Q207*|CEP135_uc010igz.1_Nonsense_Mutation_p.Q37*	NM_025009	NP_079285	Q66GS9	CP135_HUMAN	centrosome protein 4	207	Potential.				centriole replication|centriole-centriole cohesion|G2/M transition of mitotic cell cycle	centriole|cytosol	protein C-terminus binding			ovary(2)|pancreas(1)|central_nervous_system(1)|skin(1)	5	Glioma(25;0.08)|all_neural(26;0.101)					TTTCAGGATTCAAGAACTTCA	0.328													14	49	---	---	---	---	PASS
DNAH5	1767	broad.mit.edu	37	5	13708443	13708443	+	Missense_Mutation	SNP	A	C	C			TCGA-CJ-4899-01A-01D-1462-08	TCGA-CJ-4899-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:13708443A>C	uc003jfd.2	-	76	13169	c.13127T>G	c.(13126-13128)GTA>GGA	p.V4376G	DNAH5_uc003jfc.2_Missense_Mutation_p.V544G	NM_001369	NP_001360	Q8TE73	DYH5_HUMAN	dynein, axonemal, heavy chain 5	4376					microtubule-based movement	cilium axoneme|cytoplasm|microtubule	ATP binding|ATPase activity|microtubule motor activity			ovary(14)|skin(13)|upper_aerodigestive_tract(1)|central_nervous_system(1)|breast(1)|pancreas(1)	31	Lung NSC(4;0.00476)					CCTCTCTTTTACCTGCCATGG	0.473									Kartagener_syndrome				9	43	---	---	---	---	PASS
DTWD2	285605	broad.mit.edu	37	5	118280326	118280326	+	Silent	SNP	A	G	G			TCGA-CJ-4899-01A-01D-1462-08	TCGA-CJ-4899-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:118280326A>G	uc003ksa.2	-	2	271	c.237T>C	c.(235-237)TGT>TGC	p.C79C		NM_173666	NP_775937	Q8NBA8	DTWD2_HUMAN	DTW domain containing 2	79											0		all_epithelial(76;0.0982)|Prostate(80;0.121)		OV - Ovarian serous cystadenocarcinoma(64;0.000228)|Epithelial(69;0.000941)|all cancers(49;0.00939)		ATGGACACAAACACACTTTCT	0.353													16	134	---	---	---	---	PASS
TCOF1	6949	broad.mit.edu	37	5	149743741	149743741	+	Missense_Mutation	SNP	G	T	T	rs145365677		TCGA-CJ-4899-01A-01D-1462-08	TCGA-CJ-4899-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:149743741G>T	uc003lry.2	+	3	338	c.230G>T	c.(229-231)CGT>CTT	p.R77L	TCOF1_uc003lrw.2_Missense_Mutation_p.R77L|TCOF1_uc011dch.1_Missense_Mutation_p.R77L|TCOF1_uc003lrz.2_Missense_Mutation_p.R77L|TCOF1_uc003lrx.2_Missense_Mutation_p.R77L|TCOF1_uc003lsa.2_Missense_Mutation_p.R77L	NM_001135243	NP_001128715	Q13428	TCOF_HUMAN	Treacher Collins-Franceschetti syndrome 1	77					skeletal system development	nucleolus	protein binding|transporter activity			ovary(2)|large_intestine(1)	3		all_hematologic(541;0.224)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			AAGAAAACCCGTGTGTCAGAC	0.557													30	152	---	---	---	---	PASS
IGF2R	3482	broad.mit.edu	37	6	160465623	160465623	+	Missense_Mutation	SNP	T	G	G			TCGA-CJ-4899-01A-01D-1462-08	TCGA-CJ-4899-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:160465623T>G	uc003qta.2	+	13	1847	c.1699T>G	c.(1699-1701)TCA>GCA	p.S567A		NM_000876	NP_000867	P11717	MPRI_HUMAN	insulin-like growth factor 2 receptor precursor	567	4.|Lumenal (Potential).				receptor-mediated endocytosis	cell surface|endocytic vesicle|endosome|integral to plasma membrane|lysosomal membrane|trans-Golgi network transport vesicle	glycoprotein binding|insulin-like growth factor receptor activity|phosphoprotein binding|transporter activity			ovary(3)	3		Breast(66;0.000777)|Ovarian(120;0.0305)		OV - Ovarian serous cystadenocarcinoma(65;2.45e-17)|BRCA - Breast invasive adenocarcinoma(81;1.09e-05)		ACTCTCTTATTCAGATGGTGA	0.328													20	55	---	---	---	---	PASS
LOC643955	643955	broad.mit.edu	37	7	62752443	62752443	+	3'UTR	SNP	G	C	C			TCGA-CJ-4899-01A-01D-1462-08	TCGA-CJ-4899-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:62752443G>C	uc011kdj.1	-	3						NR_003952				Homo sapiens cDNA clone IMAGE:30377995, containing frame-shift errors.												0						CTTATGTCTAGTAAGGTTTGA	0.438													4	50	---	---	---	---	PASS
CHCHD3	54927	broad.mit.edu	37	7	132719639	132719639	+	Intron	SNP	G	A	A			TCGA-CJ-4899-01A-01D-1462-08	TCGA-CJ-4899-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:132719639G>A	uc003vre.2	-						CHCHD3_uc010lmi.2_Intron|CHCHD3_uc003vrf.2_Intron|CHCHD3_uc010lmj.2_Intron|CHCHD3_uc011kpn.1_Intron|uc003vrg.1_Nonsense_Mutation_p.R228*	NM_017812	NP_060282	Q9NX63	CHCH3_HUMAN	coiled-coil-helix-coiled-coil-helix domain						inner mitochondrial membrane organization|mitochondrial fusion	mitochondrial inner membrane	protein complex scaffold				0						TTGTCCAGTCGCTGGAACATT	0.512													3	23	---	---	---	---	PASS
UBN2	254048	broad.mit.edu	37	7	138958746	138958746	+	Silent	SNP	T	A	A			TCGA-CJ-4899-01A-01D-1462-08	TCGA-CJ-4899-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:138958746T>A	uc011kqr.1	+	11	1899	c.1899T>A	c.(1897-1899)TCT>TCA	p.S633S	UBN2_uc003vuv.2_Silent_p.S356S	NM_173569	NP_775840	Q6ZU65	UBN2_HUMAN	ubinuclein 2	633										ovary(1)|skin(1)	2						AAAGCCAGTCTGCTGAAGATT	0.368													19	91	---	---	---	---	PASS
SLC4A2	6522	broad.mit.edu	37	7	150772425	150772425	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-4899-01A-01D-1462-08	TCGA-CJ-4899-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:150772425G>A	uc003wit.3	+	20	3387	c.3131G>A	c.(3130-3132)GGC>GAC	p.G1044D	SLC4A2_uc011kve.1_Missense_Mutation_p.G1035D|SLC4A2_uc003wiu.3_Missense_Mutation_p.G1030D|SLC4A2_uc003wiv.3_Missense_Mutation_p.G238D|uc011kvf.1_Missense_Mutation_p.A154V	NM_003040	NP_003031	P04920	B3A2_HUMAN	solute carrier family 4, anion exchanger, member	1044	Membrane (anion exchange).|Helical; (Potential).				bicarbonate transport	integral to membrane|membrane fraction	inorganic anion exchanger activity				0			OV - Ovarian serous cystadenocarcinoma(82;0.0121)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)		GCCATGGGCGGCATCTGTGCC	0.632													4	75	---	---	---	---	PASS
CSMD1	64478	broad.mit.edu	37	8	2818703	2818703	+	Missense_Mutation	SNP	G	T	T			TCGA-CJ-4899-01A-01D-1462-08	TCGA-CJ-4899-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:2818703G>T	uc011kwk.1	-	62	10055	c.9665C>A	c.(9664-9666)ACG>AAG	p.T3222K	CSMD1_uc011kwj.1_Missense_Mutation_p.T2551K|CSMD1_uc010lrg.2_Missense_Mutation_p.T1113K	NM_033225	NP_150094	Q96PZ7	CSMD1_HUMAN	CUB and Sushi multiple domains 1 precursor	3222	Extracellular (Potential).|Sushi 27.					integral to membrane				breast(20)|large_intestine(5)	25		all_cancers(1;5.7e-41)|all_epithelial(1;2.54e-36)|Lung NSC(1;7.54e-11)|all_lung(1;3.2e-10)|Hepatocellular(1;3.78e-05)|Breast(1;0.000196)|Myeloproliferative disorder(4;0.000374)|Esophageal squamous(1;0.0157)|Ovarian(12;0.091)|Renal(68;0.144)|Colorectal(14;0.234)		all cancers(1;5.03e-41)|Epithelial(1;4.78e-31)|Lung(1;1.14e-14)|LUSC - Lung squamous cell carcinoma(1;2.34e-14)|GBM - Glioblastoma multiforme(1;4.49e-10)|Colorectal(4;1.18e-07)|OV - Ovarian serous cystadenocarcinoma(1;3.2e-07)|BRCA - Breast invasive adenocarcinoma(1;6.17e-07)|COAD - Colon adenocarcinoma(4;0.000539)|READ - Rectum adenocarcinoma(4;0.00896)|Kidney(5;0.00957)|KIRC - Kidney renal clear cell carcinoma(5;0.0689)		AAAGTGTGGCGTACCAGGGTC	0.348													15	64	---	---	---	---	PASS
NFKBIL2	4796	broad.mit.edu	37	8	145666223	145666223	+	Missense_Mutation	SNP	C	G	G			TCGA-CJ-4899-01A-01D-1462-08	TCGA-CJ-4899-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:145666223C>G	uc011llg.1	-	9	1057	c.1042G>C	c.(1042-1044)GGT>CGT	p.G348R		NM_013432	NP_038460	Q96HA7	TONSL_HUMAN	NF-kappa-B inhibitor-like protein 2	348					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)		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)			CGCTCAGCACCCGGTCTGTCC	0.657													9	53	---	---	---	---	PASS
C10orf18	54906	broad.mit.edu	37	10	5789077	5789077	+	Silent	SNP	A	C	C			TCGA-CJ-4899-01A-01D-1462-08	TCGA-CJ-4899-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:5789077A>C	uc001iij.2	+	15	4318	c.3693A>C	c.(3691-3693)TCA>TCC	p.S1231S	C10orf18_uc001iik.2_Silent_p.S75S	NM_017782	NP_060252	Q5VWN6	CJ018_HUMAN	hypothetical protein LOC54906	1231										ovary(1)|central_nervous_system(1)	2						GCCACACATCAGGTGACTCTT	0.413													12	161	---	---	---	---	PASS
LOC441666	441666	broad.mit.edu	37	10	42832147	42832147	+	RNA	SNP	G	T	T	rs144592176	by1000genomes	TCGA-CJ-4899-01A-01D-1462-08	TCGA-CJ-4899-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:42832147G>T	uc010qey.1	-	3		c.1828C>A				NR_024380				Homo sapiens noncoding mRNA sequence.												0						CACAATTGTAGGGTTTCTCTC	0.353													4	17	---	---	---	---	PASS
ERCC6	2074	broad.mit.edu	37	10	50696268	50696268	+	Intron	SNP	A	G	G			TCGA-CJ-4899-01A-01D-1462-08	TCGA-CJ-4899-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:50696268A>G	uc001jhs.3	-						ERCC6_uc010qgr.1_Intron|ERCC6_uc001jhr.3_5'UTR	NM_000124	NP_000115	Q03468	ERCC6_HUMAN	excision repair cross-complementing rodent						base-excision repair|positive regulation of transcription elongation, DNA-dependent|transcription from RNA polymerase II promoter|transcription-coupled nucleotide-excision repair	nucleolus|soluble fraction|transcription elongation factor complex	ATP binding|chromatin binding|DNA binding|DNA-dependent ATPase activity|helicase activity|protein C-terminus binding|protein complex binding|protein N-terminus binding			lung(5)|breast(5)|ovary(3)|large_intestine(2)|skin(1)	16						TGGAGGCTCAAGAGACCAATC	0.483								Direct_reversal_of_damage|NER					6	20	---	---	---	---	PASS
ERCC6	2074	broad.mit.edu	37	10	50696276	50696276	+	Intron	SNP	A	T	T			TCGA-CJ-4899-01A-01D-1462-08	TCGA-CJ-4899-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:50696276A>T	uc001jhs.3	-						ERCC6_uc010qgr.1_Intron|ERCC6_uc001jhr.3_Translation_Start_Site	NM_000124	NP_000115	Q03468	ERCC6_HUMAN	excision repair cross-complementing rodent						base-excision repair|positive regulation of transcription elongation, DNA-dependent|transcription from RNA polymerase II promoter|transcription-coupled nucleotide-excision repair	nucleolus|soluble fraction|transcription elongation factor complex	ATP binding|chromatin binding|DNA binding|DNA-dependent ATPase activity|helicase activity|protein C-terminus binding|protein complex binding|protein N-terminus binding			lung(5)|breast(5)|ovary(3)|large_intestine(2)|skin(1)	16						CAAGAGACCAATCCCTCCTAG	0.507								Direct_reversal_of_damage|NER					5	17	---	---	---	---	PASS
LOC650368	650368	broad.mit.edu	37	11	3427845	3427845	+	RNA	SNP	C	T	T			TCGA-CJ-4899-01A-01D-1462-08	TCGA-CJ-4899-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:3427845C>T	uc010qxs.1	+	9		c.838C>T			LOC650368_uc001lxx.2_RNA|LOC650368_uc001lxy.2_RNA	NR_024248				Homo sapiens cDNA FLJ41654 fis, clone FEBRA2025463, weakly  similar to Homo sapiens HMT-1 mRNA for beta-1,4 mannosyltransferase.												0						CTTCAAGTGGCAGGAGCAGAA	0.587													7	67	---	---	---	---	PASS
BBOX1	8424	broad.mit.edu	37	11	27147298	27147298	+	Missense_Mutation	SNP	G	T	T			TCGA-CJ-4899-01A-01D-1462-08	TCGA-CJ-4899-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:27147298G>T	uc001mre.1	+	8	1302	c.934G>T	c.(934-936)GCT>TCT	p.A312S	BBOX1_uc009yih.1_Missense_Mutation_p.A312S|BBOX1_uc001mrg.1_Missense_Mutation_p.A312S	NM_003986	NP_003977	O75936	BODG_HUMAN	gamma-butyrobetaine dioxygenase	312					carnitine biosynthetic process	actin cytoskeleton|cytosol|intracellular membrane-bounded organelle	gamma-butyrobetaine dioxygenase activity|iron ion binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|zinc ion binding			ovary(1)	1					Succinic acid(DB00139)|Vitamin C(DB00126)	gcctttttatgctgcTCTGAA	0.174													15	56	---	---	---	---	PASS
BBOX1	8424	broad.mit.edu	37	11	27147299	27147299	+	Missense_Mutation	SNP	C	A	A			TCGA-CJ-4899-01A-01D-1462-08	TCGA-CJ-4899-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:27147299C>A	uc001mre.1	+	8	1303	c.935C>A	c.(934-936)GCT>GAT	p.A312D	BBOX1_uc009yih.1_Missense_Mutation_p.A312D|BBOX1_uc001mrg.1_Missense_Mutation_p.A312D	NM_003986	NP_003977	O75936	BODG_HUMAN	gamma-butyrobetaine dioxygenase	312					carnitine biosynthetic process	actin cytoskeleton|cytosol|intracellular membrane-bounded organelle	gamma-butyrobetaine dioxygenase activity|iron ion binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|zinc ion binding			ovary(1)	1					Succinic acid(DB00139)|Vitamin C(DB00126)	cctttttatgctgcTCTGAAG	0.174													15	59	---	---	---	---	PASS
TSGA10IP	254187	broad.mit.edu	37	11	65714961	65714961	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-4899-01A-01D-1462-08	TCGA-CJ-4899-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:65714961C>T	uc001ogk.1	+	5	697	c.665C>T	c.(664-666)GCT>GTT	p.A222V	TSGA10IP_uc009yqw.1_RNA|TSGA10IP_uc009yqx.1_Intron	NM_152762	NP_689975	Q3SY00	T10IP_HUMAN	testis specific, 10 interacting protein	222											0						AGCCTGGGTGCTGAGGAGGCC	0.647													8	60	---	---	---	---	PASS
UBE4A	9354	broad.mit.edu	37	11	118263549	118263549	+	Missense_Mutation	SNP	G	C	C			TCGA-CJ-4899-01A-01D-1462-08	TCGA-CJ-4899-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:118263549G>C	uc001psw.2	+	19	3142	c.3013G>C	c.(3013-3015)GTG>CTG	p.V1005L	UBE4A_uc001psv.2_Missense_Mutation_p.V1012L	NM_004788	NP_004779	Q14139	UBE4A_HUMAN	ubiquitination factor E4A	1005	U-box.				ubiquitin-dependent protein catabolic process	ubiquitin ligase complex	protein binding			ovary(2)|upper_aerodigestive_tract(1)|breast(1)|kidney(1)	5	all_hematologic(175;0.046)	Medulloblastoma(222;0.0425)|Breast(348;0.181)|all_hematologic(192;0.196)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;3.28e-05)		GTGTGACCCTGTGGTGCTGCC	0.478													70	221	---	---	---	---	PASS
LRMP	4033	broad.mit.edu	37	12	25232338	25232338	+	Nonsense_Mutation	SNP	T	G	G			TCGA-CJ-4899-01A-01D-1462-08	TCGA-CJ-4899-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:25232338T>G	uc001rgh.2	+	7	1112	c.78T>G	c.(76-78)TAT>TAG	p.Y26*	LRMP_uc001rgg.1_RNA|LRMP_uc010sja.1_Nonsense_Mutation_p.Y26*|LRMP_uc010sjb.1_5'UTR|LRMP_uc001rgi.2_RNA|LRMP_uc010sjc.1_Nonsense_Mutation_p.Y26*|LRMP_uc010sjd.1_5'UTR	NM_006152	NP_006143	Q12912	LRMP_HUMAN	lymphoid-restricted membrane protein	82	Cytoplasmic (Potential).				vesicle fusion|vesicle targeting	endoplasmic reticulum membrane|integral to plasma membrane				ovary(1)|skin(1)	2	Acute lymphoblastic leukemia(6;0.00112)|all_hematologic(7;0.00152)|Colorectal(261;0.11)					GCAGGGAATATTCCTCACTAC	0.343													8	227	---	---	---	---	PASS
TARBP2	6895	broad.mit.edu	37	12	53899955	53899955	+	3'UTR	SNP	G	A	A			TCGA-CJ-4899-01A-01D-1462-08	TCGA-CJ-4899-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:53899955G>A	uc001sdo.2	+	9					TARBP2_uc001sdp.2_3'UTR|TARBP2_uc001sdq.2_3'UTR|TARBP2_uc001sdr.2_3'UTR|TARBP2_uc001sds.2_3'UTR|TARBP2_uc001sdt.2_3'UTR|TARBP2_uc001sdu.2_3'UTR|TARBP2_uc001sdv.2_RNA	NM_134323	NP_599150	Q15633	TRBP2_HUMAN	TAR RNA binding protein 2 isoform a						miRNA loading onto RISC involved in gene silencing by miRNA|negative regulation of defense response to virus by host|negative regulation of protein kinase activity|positive regulation of viral genome replication|pre-miRNA processing|production of siRNA involved in RNA interference|regulation of transcription from RNA polymerase II promoter|regulation of translation|regulation of viral transcription|targeting of mRNA for destruction involved in RNA interference	cytosol|nucleus|perinuclear region of cytoplasm|RNA-induced silencing complex	double-stranded RNA binding|protein homodimerization activity|siRNA binding			central_nervous_system(1)	1						ACTCATGGATGTGCACCCTTT	0.612													6	34	---	---	---	---	PASS
GPR137C	283554	broad.mit.edu	37	14	53020188	53020188	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-4899-01A-01D-1462-08	TCGA-CJ-4899-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:53020188G>A	uc001wzu.3	+	1	323	c.323G>A	c.(322-324)GGC>GAC	p.G108D	TXNDC16_uc010tqu.1_5'Flank|TXNDC16_uc001wzs.2_5'Flank|TXNDC16_uc010aoe.2_5'Flank|GPR137C_uc001wzt.3_Missense_Mutation_p.G108D	NM_001099652	NP_001093122	Q8N3F9	G137C_HUMAN	G protein-coupled receptor 137C	108	Extracellular (Potential).					integral to membrane					0	Breast(41;0.0716)					TCGCTCAGCGGCTCCCTGCCC	0.662													4	79	---	---	---	---	PASS
LTBP2	4053	broad.mit.edu	37	14	74972836	74972836	+	Silent	SNP	C	T	T			TCGA-CJ-4899-01A-01D-1462-08	TCGA-CJ-4899-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:74972836C>T	uc001xqa.2	-	28	4479	c.4092G>A	c.(4090-4092)GTG>GTA	p.V1364V		NM_000428	NP_000419	Q14767	LTBP2_HUMAN	latent transforming growth factor beta binding	1364	EGF-like 16; calcium-binding (Potential).|Cys-rich.				protein secretion|protein targeting|transforming growth factor beta receptor signaling pathway	extracellular space|proteinaceous extracellular matrix	calcium ion binding|growth factor binding			liver(1)|skin(1)	2				BRCA - Breast invasive adenocarcinoma(234;0.00219)|READ - Rectum adenocarcinoma(1;0.0649)		AGGAGCCCTCCACGTTCTCAC	0.637													23	129	---	---	---	---	PASS
SNORD116-4	100033416	broad.mit.edu	37	15	25333795	25333795	+	Intron	SNP	C	A	A			TCGA-CJ-4899-01A-01D-1462-08	TCGA-CJ-4899-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:25333795C>A	uc001yxh.1	+						SNORD116-4_uc001yxm.1_Intron|IPW_uc001yxn.3_Intron|SNORD116-28_uc001yxy.2_Intron|IPW_uc001yyb.3_Intron|uc001yyd.2_Intron|SNORD116-20_uc001yyf.2_RNA|SNORD116-22_uc001yyg.1_5'Flank					Homo sapiens clone kid4 SNURF-SNRPN mRNA, downstream untranslated exons, alternatively spliced.												0						TGGTGAGGGACAATTGTTACC	0.532													2	4	---	---	---	---	PASS
USP50	373509	broad.mit.edu	37	15	50835798	50835798	+	Missense_Mutation	SNP	T	A	A			TCGA-CJ-4899-01A-01D-1462-08	TCGA-CJ-4899-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:50835798T>A	uc001zyq.3	-	3	636	c.456A>T	c.(454-456)AAA>AAT	p.K152N		NM_203494	NP_987090	E9PP86	E9PP86_HUMAN	ubiquitin specific protease 50	147					ubiquitin-dependent protein catabolic process		ubiquitin thiolesterase activity			lung(1)|breast(1)	2				all cancers(107;0.000519)|GBM - Glioblastoma multiforme(94;0.00288)		TACTTACCTTTTTTAGAGCTT	0.328													6	35	---	---	---	---	PASS
TRPM7	54822	broad.mit.edu	37	15	50891464	50891464	+	Missense_Mutation	SNP	A	C	C			TCGA-CJ-4899-01A-01D-1462-08	TCGA-CJ-4899-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:50891464A>C	uc001zyt.3	-	22	3282	c.3018T>G	c.(3016-3018)ATT>ATG	p.I1006M	TRPM7_uc010bew.1_Missense_Mutation_p.I1006M	NM_017672	NP_060142	Q96QT4	TRPM7_HUMAN	transient receptor potential cation channel,	1006	Helical; (Potential).				cell death	integral to membrane	ATP binding|calcium channel activity|metal ion binding|protein serine/threonine kinase activity			ovary(4)|stomach(3)|breast(1)|central_nervous_system(1)|skin(1)	10				all cancers(107;0.000819)|GBM - Glioblastoma multiforme(94;0.0045)		CAAGAGCCATAATCACTACAA	0.338													28	170	---	---	---	---	PASS
WASH3P	374666	broad.mit.edu	37	15	102515299	102515299	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-4899-01A-01D-1462-08	TCGA-CJ-4899-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:102515299G>A	uc002cdi.2	+	9	1943	c.523G>A	c.(523-525)GGC>AGC	p.G175S	WASH3P_uc002cdl.2_Missense_Mutation_p.G175S|WASH3P_uc002cdk.2_RNA|WASH3P_uc002cdp.2_Missense_Mutation_p.G175S|WASH3P_uc010bpo.2_RNA|WASH3P_uc002cdq.2_RNA|WASH3P_uc002cdr.2_RNA	NR_003659				RecName: Full=WAS protein family homolog 2; AltName: Full=Protein FAM39B; AltName: Full=CXYorf1-like protein on chromosome 2;												0						TGGGGGCATCGGCAAGGCCAA	0.652													6	31	---	---	---	---	PASS
RNF40	9810	broad.mit.edu	37	16	30777596	30777596	+	Missense_Mutation	SNP	G	T	T			TCGA-CJ-4899-01A-01D-1462-08	TCGA-CJ-4899-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:30777596G>T	uc002dzq.2	+	9	1229	c.1106G>T	c.(1105-1107)CGC>CTC	p.R369L	RNF40_uc010caa.2_Missense_Mutation_p.R369L|RNF40_uc010cab.2_Intron|RNF40_uc010vfa.1_Intron|RNF40_uc002dzr.2_Missense_Mutation_p.R369L|RNF40_uc010vfb.1_Intron|RNF40_uc010vfc.1_5'Flank	NM_014771	NP_055586	O75150	BRE1B_HUMAN	ring finger protein 40	369	Potential.				histone H2B ubiquitination|histone monoubiquitination|ubiquitin-dependent protein catabolic process	nucleus|synaptosome|ubiquitin ligase complex	protein homodimerization activity|ubiquitin protein ligase binding|zinc ion binding			central_nervous_system(1)	1			Colorectal(24;0.198)			ACCAATGAGCGCCTCAAGGTG	0.592													40	125	---	---	---	---	PASS
ORC6L	23594	broad.mit.edu	37	16	46730054	46730054	+	Intron	SNP	G	T	T			TCGA-CJ-4899-01A-01D-1462-08	TCGA-CJ-4899-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:46730054G>T	uc002eeh.2	+						ORC6L_uc010cbe.1_3'UTR	NM_014321	NP_055136	Q9Y5N6	ORC6_HUMAN	origin recognition complex subunit 6						cell cycle checkpoint|DNA replication|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|S phase of mitotic cell cycle	nuclear origin of replication recognition complex|nucleoplasm	DNA binding|protein binding				0		all_cancers(37;0.00023)|all_epithelial(9;0.000543)|all_lung(18;0.00585)|Lung NSC(13;0.0496)|Breast(268;0.116)				ACAGCCCAGTGCTGCTCTAGC	0.433													8	30	---	---	---	---	PASS
CDRT15P	94158	broad.mit.edu	37	17	13927900	13927900	+	RNA	SNP	T	C	C			TCGA-CJ-4899-01A-01D-1462-08	TCGA-CJ-4899-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:13927900T>C	uc002god.1	+	1		c.86T>C				NR_003261				Homo sapiens CMT1A duplicated region transcript 15 pseudogene (CDRT15P), non-coding RNA.												0						GAGCCTTTTCTGACGATGCCG	0.572													3	32	---	---	---	---	PASS
SLC47A1	55244	broad.mit.edu	37	17	19470436	19470436	+	Missense_Mutation	SNP	A	G	G			TCGA-CJ-4899-01A-01D-1462-08	TCGA-CJ-4899-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:19470436A>G	uc002gvy.1	+	14	1290	c.1204A>G	c.(1204-1206)AGT>GGT	p.S402G	SLC47A1_uc002gvx.2_Missense_Mutation_p.S402G|SLC47A1_uc010vyz.1_Missense_Mutation_p.S379G|SLC47A1_uc010cqp.1_Intron|SLC47A1_uc010cqq.1_Missense_Mutation_p.S207G|SLC47A1_uc010vza.1_Missense_Mutation_p.S114G|SLC47A1_uc010vzb.1_Missense_Mutation_p.S136G|SLC47A1_uc010vzc.1_Missense_Mutation_p.S74G	NM_018242	NP_060712	Q96FL8	S47A1_HUMAN	solute carrier family 47, member 1	402	Cytoplasmic (Potential).					integral to membrane|plasma membrane	drug:hydrogen antiporter activity				0	all_cancers(12;2.49e-05)|all_epithelial(12;0.00263)|Hepatocellular(7;0.00345)					TCTGAGGGGGAGTGGAAATCA	0.537													54	255	---	---	---	---	PASS
OR4D1	26689	broad.mit.edu	37	17	56232813	56232813	+	Missense_Mutation	SNP	A	G	G			TCGA-CJ-4899-01A-01D-1462-08	TCGA-CJ-4899-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:56232813A>G	uc010wno.1	+	1	299	c.299A>G	c.(298-300)CAG>CGG	p.Q100R	MSX2P1_uc002ivn.2_5'Flank	NM_012374	NP_036506	Q15615	OR4D1_HUMAN	olfactory receptor, family 4, subfamily D,	100	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)	1						TGCATGGCCCAGATCTTCTTC	0.532													35	145	---	---	---	---	PASS
JMJD6	23210	broad.mit.edu	37	17	74721938	74721938	+	Splice_Site	SNP	C	T	T			TCGA-CJ-4899-01A-01D-1462-08	TCGA-CJ-4899-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:74721938C>T	uc002jso.2	-	2	454	c.130_splice	c.e2-1	p.D44_splice	JMJD6_uc002jsn.1_Splice_Site_p.D44_splice|JMJD6_uc010dgz.2_Splice_Site_p.D44_splice|C17orf95_uc002jsp.2_5'Flank|C17orf95_uc002jsq.2_5'Flank|C17orf95_uc002jsr.2_5'Flank|C17orf95_uc002jss.2_5'Flank|C17orf95_uc002jst.2_5'Flank|C17orf95_uc002jsu.2_5'Flank	NM_015167	NP_055982	Q6NYC1	JMJD6_HUMAN	jumonji domain containing 6 isoform 2						mRNA processing|peptidyl-lysine hydroxylation to 5-hydroxy-L-lysine|regulation of nuclear mRNA splicing, via spliceosome|regulation of transcription, DNA-dependent|RNA splicing|sprouting angiogenesis|transcription, DNA-dependent	nucleolus|nucleoplasm	histone demethylase activity (H3-R2 specific)|histone demethylase activity (H4-R3 specific)|identical protein binding|iron ion binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|peptidyl-lysine 5-dioxygenase activity|single-stranded RNA binding			skin(2)|ovary(1)	3						CCACGTTATCCTGAGGGAATT	0.443													14	87	---	---	---	---	PASS
CEP192	55125	broad.mit.edu	37	18	13056647	13056647	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-4899-01A-01D-1462-08	TCGA-CJ-4899-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:13056647G>A	uc010xac.1	+	19	4138	c.4058G>A	c.(4057-4059)GGT>GAT	p.G1353D	CEP192_uc010dlf.1_RNA|CEP192_uc010xad.1_Missense_Mutation_p.G878D|CEP192_uc002kru.2_RNA|CEP192_uc002krv.2_5'UTR|CEP192_uc002krs.1_Missense_Mutation_p.G1094D	NM_032142	NP_115518	E9PF99	E9PF99_HUMAN	centrosomal protein 192kDa	1353										ovary(4)|pancreas(1)	5						CCGTCTGTTGGTACAAACTGT	0.393													11	372	---	---	---	---	PASS
CDH2	1000	broad.mit.edu	37	18	25583110	25583110	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-4899-01A-01D-1462-08	TCGA-CJ-4899-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:25583110C>T	uc002kwg.2	-	7	1330	c.871G>A	c.(871-873)GCA>ACA	p.A291T	CDH2_uc010xbn.1_Missense_Mutation_p.A260T	NM_001792	NP_001783	P19022	CADH2_HUMAN	cadherin 2, type 1 preproprotein	291	Extracellular (Potential).|Cadherin 2.				adherens junction organization|cell junction assembly|positive regulation of muscle cell differentiation	catenin complex|integral to membrane	alpha-catenin binding|beta-catenin binding|calcium ion binding|gamma-catenin binding			ovary(3)|lung(1)	4						GCATCAATTGCTGTTACGGTC	0.433													24	97	---	---	---	---	PASS
PAF1	54623	broad.mit.edu	37	19	39880362	39880362	+	Missense_Mutation	SNP	G	C	C			TCGA-CJ-4899-01A-01D-1462-08	TCGA-CJ-4899-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:39880362G>C	uc002old.2	-	4	385	c.210C>G	c.(208-210)CAC>CAG	p.H70Q	PAF1_uc002ole.1_Missense_Mutation_p.H60Q|PAF1_uc010xuv.1_Intron|MED29_uc010xuw.1_5'Flank|MED29_uc002olf.2_5'Flank|MED29_uc010xux.1_5'Flank	NM_019088	NP_061961	Q8N7H5	PAF1_HUMAN	Paf1, RNA polymerase II associated factor,	70					histone H2B ubiquitination|histone monoubiquitination|regulation of transcription, DNA-dependent|transcription, DNA-dependent	Cdc73/Paf1 complex	protein binding			pancreas(1)	1	all_cancers(60;9.14e-07)|all_lung(34;4.03e-08)|Lung NSC(34;4.66e-08)|all_epithelial(25;1.88e-06)|Ovarian(47;0.0512)		Epithelial(26;9.6e-28)|all cancers(26;9.14e-25)|Lung(45;0.000168)|LUSC - Lung squamous cell carcinoma(53;0.000199)			GGTCATGTTTGTGCTGTTTCT	0.552													28	166	---	---	---	---	PASS
AKT1S1	84335	broad.mit.edu	37	19	50374936	50374936	+	Silent	SNP	G	A	A			TCGA-CJ-4899-01A-01D-1462-08	TCGA-CJ-4899-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:50374936G>A	uc002pql.3	-	4	1221	c.495C>T	c.(493-495)CCC>CCT	p.P165P	AKT1S1_uc002pqn.3_Silent_p.P165P|AKT1S1_uc002pqm.3_Silent_p.P165P	NM_032375	NP_115751	Q96B36	AKTS1_HUMAN	AKT1 substrate 1 (proline-rich)	165					negative regulation of cell size|negative regulation of protein kinase activity|negative regulation of TOR signaling cascade|nerve growth factor receptor signaling pathway|neuroprotection|phosphatidylinositol-mediated signaling|regulation of survival gene product expression	cytosolic part	protein binding				0		all_lung(116;3.24e-07)|Lung NSC(112;1.6e-06)|all_neural(266;0.0459)|Ovarian(192;0.0728)		GBM - Glioblastoma multiforme(134;0.0116)|OV - Ovarian serous cystadenocarcinoma(262;0.0132)		CTGAGCAGGTGGGGGGGCCGG	0.652													18	83	---	---	---	---	PASS
C20orf186	149954	broad.mit.edu	37	20	31690805	31690805	+	Missense_Mutation	SNP	C	A	A			TCGA-CJ-4899-01A-01D-1462-08	TCGA-CJ-4899-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:31690805C>A	uc010zue.1	+	13	1680	c.1665C>A	c.(1663-1665)AAC>AAA	p.N555K		NM_182519	NP_872325	P59827	LPLC4_HUMAN	antimicrobial peptide RY2G5 precursor	555						cytoplasm|extracellular region	lipid binding				0						GAACCTCAAACGTGGGCAACT	0.498													40	189	---	---	---	---	PASS
CHD6	84181	broad.mit.edu	37	20	40033900	40033900	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-4899-01A-01D-1462-08	TCGA-CJ-4899-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:40033900C>T	uc002xka.1	-	37	7659	c.7481G>A	c.(7480-7482)GGG>GAG	p.G2494E	CHD6_uc002xjz.1_Missense_Mutation_p.G31E	NM_032221	NP_115597	Q8TD26	CHD6_HUMAN	chromodomain helicase DNA binding protein 6	2494					chromatin remodeling|nervous system development|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	ATP binding|ATP-dependent helicase activity|chromatin binding|DNA binding			ovary(6)|skin(5)|lung(2)|central_nervous_system(1)	14		Myeloproliferative disorder(115;0.00425)				CCCCACCAGCCCGGTGAGGGG	0.562													21	90	---	---	---	---	PASS
SEMG1	6406	broad.mit.edu	37	20	43836172	43836172	+	Silent	SNP	G	A	A			TCGA-CJ-4899-01A-01D-1462-08	TCGA-CJ-4899-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:43836172G>A	uc002xni.2	+	2	291	c.234G>A	c.(232-234)CAG>CAA	p.Q78Q	SEMG1_uc002xnj.2_Silent_p.Q78Q|SEMG2_uc010ggz.2_Intron|SEMG1_uc002xnh.2_Silent_p.Q78Q	NM_003007	NP_002998	P04279	SEMG1_HUMAN	semenogelin I preproprotein	78					insemination|sexual reproduction	extracellular space|stored secretory granule	structural molecule activity			skin(2)	2		Myeloproliferative disorder(115;0.0122)				ATCATGACCAGTCCCGAAAAA	0.393													12	181	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	22	18846113	18846113	+	RNA	SNP	C	T	T			TCGA-CJ-4899-01A-01D-1462-08	TCGA-CJ-4899-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:18846113C>T	uc002zoe.2	+	5		c.2475C>T			uc002zof.2_5'Flank					Homo sapiens cDNA FLJ76361 complete cds.																		ATCTCCTCCACGCACTGGCGC	0.612													4	30	---	---	---	---	PASS
NHP2L1	4809	broad.mit.edu	37	22	42071041	42071041	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-4899-01A-01D-1462-08	TCGA-CJ-4899-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:42071041C>T	uc003bat.2	-	3	477	c.283G>A	c.(283-285)GTC>ATC	p.V95I	NHP2L1_uc003bau.2_Missense_Mutation_p.V95I|NHP2L1_uc003bav.2_Missense_Mutation_p.V95I|NHP2L1_uc003baw.2_Missense_Mutation_p.V95I	NM_005008	NP_004999	P55769	NH2L1_HUMAN	NHP2 non-histone chromosome protein 2-like 1	95					nuclear mRNA splicing, via spliceosome|ribosome biogenesis	box C/D snoRNP complex|nucleoplasm|spliceosomal complex	protein binding|RNA binding				0						GGCCTGGAGACCCCACAGGCT	0.552													35	101	---	---	---	---	PASS
SLC6A14	11254	broad.mit.edu	37	X	115576198	115576198	+	Nonsense_Mutation	SNP	G	T	T			TCGA-CJ-4899-01A-01D-1462-08	TCGA-CJ-4899-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:115576198G>T	uc004eqi.2	+	6	873	c.769G>T	c.(769-771)GGA>TGA	p.G257*	SLC6A14_uc011mtm.1_RNA	NM_007231	NP_009162	Q9UN76	S6A14_HUMAN	solute carrier family 6 (amino acid	257					cellular amino acid metabolic process|response to toxin	integral to membrane	amino acid transmembrane transporter activity|neurotransmitter:sodium symporter activity			ovary(2)|pancreas(1)	3					L-Proline(DB00172)	ACTATTTAAAGGAATCAAATC	0.388													9	108	---	---	---	---	PASS
GPR112	139378	broad.mit.edu	37	X	135485423	135485423	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-4899-01A-01D-1462-08	TCGA-CJ-4899-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:135485423G>A	uc004ezu.1	+	22	8887	c.8596G>A	c.(8596-8598)GCA>ACA	p.A2866T	GPR112_uc010nsb.1_Missense_Mutation_p.A2661T	NM_153834	NP_722576	Q8IZF6	GP112_HUMAN	G-protein coupled receptor 112	2866	Helical; Name=4; (Potential).				neuropeptide signaling pathway	integral to membrane|plasma membrane	G-protein coupled receptor activity			ovary(5)|large_intestine(2)|skin(2)|lung(1)|breast(1)|pancreas(1)	12	Acute lymphoblastic leukemia(192;0.000127)					TATCATGGTGGCAATCACAGT	0.488													3	37	---	---	---	---	PASS
FGF13	2258	broad.mit.edu	37	X	138286289	138286289	+	5'UTR	SNP	A	T	T			TCGA-CJ-4899-01A-01D-1462-08	TCGA-CJ-4899-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:138286289A>T	uc004faq.2	-	1					FGF13_uc004far.2_5'UTR|FGF13_uc011mwj.1_5'UTR|FGF13_uc011mwk.1_5'UTR	NM_001139502	NP_001132974	Q92913	FGF13_HUMAN	fibroblast growth factor 13 isoform 3						cell-cell signaling|MAPKKK cascade|nervous system development	cytoplasm|nucleus	growth factor activity|protein kinase activator activity			ovary(1)|large_intestine(1)|breast(1)	3	Acute lymphoblastic leukemia(192;0.000127)					CTTGCTTGACAAGGTTCGCTC	0.597													6	51	---	---	---	---	PASS
INADL	10207	broad.mit.edu	37	1	62443869	62443872	+	Intron	DEL	CTTC	-	-			TCGA-CJ-4899-01A-01D-1462-08	TCGA-CJ-4899-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:62443869_62443872delCTTC	uc001dab.2	+						INADL_uc009waf.1_Intron|INADL_uc001daa.2_Intron|INADL_uc001dad.3_Intron|INADL_uc001dac.2_Intron|INADL_uc010oot.1_Intron|INADL_uc009wag.2_Intron|INADL_uc010oou.1_Intron	NM_176877	NP_795352	Q8NI35	INADL_HUMAN	InaD-like						intracellular signal transduction|tight junction assembly	apical plasma membrane|perinuclear region of cytoplasm|tight junction	protein binding			ovary(3)|skin(1)	4						ATCTTCATATcttccttccttcct	0.147													4	4	---	---	---	---	
LRRC7	57554	broad.mit.edu	37	1	70181839	70181839	+	Intron	DEL	A	-	-			TCGA-CJ-4899-01A-01D-1462-08	TCGA-CJ-4899-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:70181839delA	uc001deo.1	+									Q96NW7	LRRC7_HUMAN	SubName: Full=Leucine rich repeat containing 7; SubName: Full=cDNA FLJ54846, highly similar to Leucine-rich repeat-containing protein 7;							centrosome|focal adhesion|nucleolus	protein binding			ovary(9)|breast(2)|central_nervous_system(2)|liver(1)	14						CCGCTACATGAAAAAAAATGC	0.279													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	116891725	116891725	+	IGR	DEL	A	-	-			TCGA-CJ-4899-01A-01D-1462-08	TCGA-CJ-4899-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:116891725delA								C1orf161 (213864 upstream) : ATP1A1 (23279 downstream)																							taaggagcttaaaaaaaaaaa	0.000													5	3	---	---	---	---	
CHD1L	9557	broad.mit.edu	37	1	146731281	146731281	+	Intron	DEL	A	-	-			TCGA-CJ-4899-01A-01D-1462-08	TCGA-CJ-4899-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:146731281delA	uc001epm.3	+						uc001epp.2_RNA|CHD1L_uc001epn.3_Intron|CHD1L_uc010ozo.1_Intron|CHD1L_uc009wjg.2_Intron|CHD1L_uc009wjh.2_Intron|CHD1L_uc010ozp.1_Intron|CHD1L_uc001epo.3_Intron	NM_004284	NP_004275	Q86WJ1	CHD1L_HUMAN	chromodomain helicase DNA binding protein						chromatin remodeling|DNA repair	cytoplasm|nucleus|plasma membrane	ATP binding|ATP-dependent DNA helicase activity|DNA binding|protein binding			ovary(3)|lung(2)|upper_aerodigestive_tract(1)	6	all_hematologic(923;0.0487)					CCATTTTGTTAAAAAAAAAAA	0.299													4	2	---	---	---	---	
SLAMF1	6504	broad.mit.edu	37	1	160582213	160582213	+	Intron	DEL	C	-	-	rs2025515	by1000genomes	TCGA-CJ-4899-01A-01D-1462-08	TCGA-CJ-4899-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:160582213delC	uc001fwl.3	-						SLAMF1_uc010pjk.1_Intron|SLAMF1_uc010pjl.1_Intron|SLAMF1_uc010pjm.1_Intron	NM_003037	NP_003028	Q13291	SLAF1_HUMAN	signaling lymphocytic activation molecule family						interspecies interaction between organisms|lymphocyte activation|positive regulation of cell proliferation	integral to membrane	antigen binding|transmembrane receptor activity			ovary(1)|breast(1)	2	all_cancers(52;4.94e-17)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.0175)			AAAAAAAAAACTTCCTCATTT	0.274													6	3	---	---	---	---	
ACBD6	84320	broad.mit.edu	37	1	180471041	180471041	+	Intron	DEL	A	-	-	rs5779061		TCGA-CJ-4899-01A-01D-1462-08	TCGA-CJ-4899-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:180471041delA	uc001gog.2	-							NM_032360	NP_115736	Q9BR61	ACBD6_HUMAN	acyl-coenzyme A binding domain containing 6							cytoplasm|nucleus	fatty-acyl-CoA binding			ovary(1)	1						GCAGATGGTCAAAAAAAAAAA	0.383													3	3	---	---	---	---	
C1orf106	55765	broad.mit.edu	37	1	200876789	200876789	+	Intron	DEL	A	-	-	rs72126102		TCGA-CJ-4899-01A-01D-1462-08	TCGA-CJ-4899-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:200876789delA	uc001gvo.2	+						C1orf106_uc010ppm.1_Intron	NM_018265	NP_060735	Q3KP66	CA106_HUMAN	hypothetical protein LOC55765 isoform 1											skin(2)|ovary(1)	3						cctgtctcttaaaaaaaaaaa	0.219													4	2	---	---	---	---	
KCTD3	51133	broad.mit.edu	37	1	215777330	215777330	+	Intron	DEL	T	-	-			TCGA-CJ-4899-01A-01D-1462-08	TCGA-CJ-4899-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:215777330delT	uc001hks.2	+						KCTD3_uc001hkt.2_Intron|KCTD3_uc010pub.1_Intron|KCTD3_uc009xdn.2_Intron	NM_016121	NP_057205	Q9Y597	KCTD3_HUMAN	potassium channel tetramerisation domain							voltage-gated potassium channel complex	protein binding|voltage-gated potassium channel activity			ovary(3)	3				all cancers(67;0.0164)|OV - Ovarian serous cystadenocarcinoma(81;0.019)|GBM - Glioblastoma multiforme(131;0.0862)|Epithelial(68;0.13)		AGTCTTAAGATTTTTTTTTTT	0.373													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	10356283	10356284	+	IGR	INS	-	GGAA	GGAA			TCGA-CJ-4899-01A-01D-1462-08	TCGA-CJ-4899-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:10356283_10356284insGGAA								C2orf48 (4427 upstream) : HPCAL1 (86756 downstream)																							gaaaaggaaagggaaggaagga	0.139													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	45224046	45224046	+	IGR	DEL	A	-	-	rs34239087		TCGA-CJ-4899-01A-01D-1462-08	TCGA-CJ-4899-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:45224046delA								SIX3 (51656 upstream) : SIX2 (8279 downstream)																							TTATTTGTTTAAAAAAAAAAA	0.224													3	4	---	---	---	---	
ATOH8	84913	broad.mit.edu	37	2	85990944	85990945	+	Intron	INS	-	GT	GT	rs138097885	by1000genomes	TCGA-CJ-4899-01A-01D-1462-08	TCGA-CJ-4899-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:85990944_85990945insGT	uc002sqn.2	+						ATOH8_uc002sqm.3_Intron	NM_032827	NP_116216	Q96SQ7	ATOH8_HUMAN	atonal homolog 8						cell differentiation|nervous system development|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding				0						GATGAGCTGACgtgtgtgtgtg	0.386													7	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	91764888	91764903	+	IGR	DEL	TGTGTGTGTGTGTGTG	-	-	rs139523492		TCGA-CJ-4899-01A-01D-1462-08	TCGA-CJ-4899-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:91764888_91764903delTGTGTGTGTGTGTGTG								None (None upstream) : LOC654342 (40289 downstream)																							tgtacgtatatgtgtgtgtgtgtgtgtgtgtgtgtg	0.000													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	227164353	227164354	+	IGR	INS	-	TTG	TTG			TCGA-CJ-4899-01A-01D-1462-08	TCGA-CJ-4899-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:227164353_227164354insTTG								KIAA1486 (568882 upstream) : IRS1 (431680 downstream)																							ttGTTGATTAAttgttgttgtt	0.015													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	232509782	232509785	+	IGR	DEL	CTTT	-	-	rs144976269		TCGA-CJ-4899-01A-01D-1462-08	TCGA-CJ-4899-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:232509782_232509785delCTTT								C2orf57 (50790 upstream) : PTMA (63450 downstream)																							ccctccctccctttctttcttttt	0.152													4	5	---	---	---	---	
IL17RB	55540	broad.mit.edu	37	3	53883546	53883547	+	Intron	INS	-	A	A	rs149695132	by1000genomes	TCGA-CJ-4899-01A-01D-1462-08	TCGA-CJ-4899-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:53883546_53883547insA	uc003dha.2	+							NM_018725	NP_061195	Q9NRM6	I17RB_HUMAN	interleukin 17B receptor precursor						defense response|regulation of cell growth	extracellular region|integral to plasma membrane	cytokine receptor activity			ovary(2)|pancreas(1)	3				BRCA - Breast invasive adenocarcinoma(193;0.000158)|KIRC - Kidney renal clear cell carcinoma(284;0.00588)|Kidney(284;0.00673)|OV - Ovarian serous cystadenocarcinoma(275;0.118)		ctacaaaaaacatttttttaat	0.208													4	2	---	---	---	---	
FAM19A1	407738	broad.mit.edu	37	3	68466755	68466755	+	Intron	DEL	T	-	-	rs34877887		TCGA-CJ-4899-01A-01D-1462-08	TCGA-CJ-4899-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:68466755delT	uc003dnd.2	+						FAM19A1_uc003dne.2_Intron|FAM19A1_uc003dng.2_Intron	NM_213609	NP_998774	Q7Z5A9	F19A1_HUMAN	family with sequence similarity 19 (chemokine							endoplasmic reticulum|extracellular region				ovary(1)	1		Lung NSC(201;0.0117)		BRCA - Breast invasive adenocarcinoma(55;7.7e-05)|Epithelial(33;0.000937)|KIRC - Kidney renal clear cell carcinoma(39;0.0579)|Kidney(39;0.0743)		tatttgaatgttttttcccca	0.174													9	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	75703977	75703978	+	IGR	INS	-	T	T			TCGA-CJ-4899-01A-01D-1462-08	TCGA-CJ-4899-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:75703977_75703978insT								MIR1324 (23968 upstream) : ZNF717 (54816 downstream)																							TCTTTTCTGAATTTTTTATTTT	0.322													5	3	---	---	---	---	
SLIT2	9353	broad.mit.edu	37	4	20584836	20584838	+	Intron	DEL	TTG	-	-			TCGA-CJ-4899-01A-01D-1462-08	TCGA-CJ-4899-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:20584836_20584838delTTG	uc003gpr.1	+						SLIT2_uc003gps.1_Intron	NM_004787	NP_004778	O94813	SLIT2_HUMAN	slit homolog 2 precursor						apoptosis involved in luteolysis|axon extension involved in axon guidance|branching morphogenesis of a tube|cell migration involved in sprouting angiogenesis|cellular response to heparin|cellular response to hormone stimulus|chemorepulsion involved in postnatal olfactory bulb interneuron migration|corticospinal neuron axon guidance through spinal cord|induction of negative chemotaxis|motor axon guidance|negative regulation of actin filament polymerization|negative regulation of cell growth|negative regulation of cellular response to growth factor stimulus|negative regulation of chemokine-mediated signaling pathway|negative regulation of endothelial cell migration|negative regulation of lamellipodium assembly|negative regulation of mononuclear cell migration|negative regulation of neutrophil chemotaxis|negative regulation of protein phosphorylation|negative regulation of retinal ganglion cell axon guidance|negative regulation of small GTPase mediated signal transduction|negative regulation of smooth muscle cell chemotaxis|negative regulation of vascular permeability|positive regulation of apoptosis|positive regulation of axonogenesis|response to cortisol stimulus|retinal ganglion cell axon guidance|Roundabout signaling pathway|ureteric bud development	cell surface|cytoplasm|extracellular space|plasma membrane	calcium ion binding|GTPase inhibitor activity|heparin binding|laminin-1 binding|protein homodimerization activity|proteoglycan binding|Roundabout binding			central_nervous_system(4)|skin(4)|ovary(3)	11						TAGGAATAGTttgttgttgttgt	0.261													4	2	---	---	---	---	
GUF1	60558	broad.mit.edu	37	4	44692171	44692173	+	Intron	DEL	GAA	-	-	rs138822277		TCGA-CJ-4899-01A-01D-1462-08	TCGA-CJ-4899-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:44692171_44692173delGAA	uc003gww.3	+							NM_021927	NP_068746	Q8N442	GUF1_HUMAN	GUF1 GTPase homolog						translation	mitochondrial inner membrane	GTP binding|GTPase activity			upper_aerodigestive_tract(1)	1						GGCTAATGATGAAGAACTTTTTT	0.261													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	53614272	53614272	+	Intron	DEL	A	-	-			TCGA-CJ-4899-01A-01D-1462-08	TCGA-CJ-4899-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:53614272delA	uc003gzr.2	-						uc003gzs.2_Intron					RecName: Full=Uncharacterized protein LP9056; Flags: Precursor;																		CAAACCCTGTAAAAAAAAAAA	0.328													4	2	---	---	---	---	
FRAS1	80144	broad.mit.edu	37	4	79371639	79371640	+	Intron	INS	-	T	T	rs138438777	by1000genomes	TCGA-CJ-4899-01A-01D-1462-08	TCGA-CJ-4899-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:79371639_79371640insT	uc003hlb.2	+							NM_025074	NP_079350	Q86XX4	FRAS1_HUMAN	Fraser syndrome 1						cell communication	integral to membrane|plasma membrane	metal ion binding			large_intestine(5)	5						ttgttttcttattttttttttc	0.277													6	3	---	---	---	---	
KIAA0922	23240	broad.mit.edu	37	4	154509194	154509194	+	Intron	DEL	T	-	-			TCGA-CJ-4899-01A-01D-1462-08	TCGA-CJ-4899-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:154509194delT	uc003inm.3	+						KIAA0922_uc010ipp.2_Intron|KIAA0922_uc010ipq.2_Intron|KIAA0922_uc010ips.1_Intron	NM_015196	NP_056011	A2VDJ0	T131L_HUMAN	hypothetical protein LOC23240 isoform 2							integral to membrane				upper_aerodigestive_tract(1)|ovary(1)	2	all_hematologic(180;0.093)	Renal(120;0.118)				TCCGCAAGGGTTTTTTTTTTT	0.333													4	3	---	---	---	---	
SLC30A5	64924	broad.mit.edu	37	5	68396440	68396441	+	Intron	DEL	AA	-	-	rs33982147		TCGA-CJ-4899-01A-01D-1462-08	TCGA-CJ-4899-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:68396440_68396441delAA	uc003jvh.2	+						SLC30A5_uc003jvg.2_Intron|SLC30A5_uc011crc.1_Intron|SLC30A5_uc003jvi.2_5'Flank	NM_022902	NP_075053	Q8TAD4	ZNT5_HUMAN	solute carrier family 30 (zinc transporter),						cellular zinc ion homeostasis|cobalt ion transport|regulation of proton transport|response to zinc ion	apical plasma membrane|Golgi apparatus|integral to plasma membrane|membrane fraction|secretory granule membrane	zinc ion binding|zinc ion transmembrane transporter activity			central_nervous_system(1)	1		Lung NSC(167;0.000986)|Prostate(74;0.00809)|Colorectal(97;0.0508)|Ovarian(174;0.16)		OV - Ovarian serous cystadenocarcinoma(47;1.24e-56)|Epithelial(20;1.12e-52)|all cancers(19;2.63e-48)|Lung(70;0.0177)		tctatgagttaaaaaaaaaaaa	0.153													6	4	---	---	---	---	
FAM172A	83989	broad.mit.edu	37	5	93152794	93152795	+	Intron	DEL	AC	-	-	rs34686494		TCGA-CJ-4899-01A-01D-1462-08	TCGA-CJ-4899-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:93152794_93152795delAC	uc010jbd.2	-						FAM172A_uc011cuf.1_Intron|FAM172A_uc011cug.1_Intron|FAM172A_uc011cuh.1_Intron|FAM172A_uc011cui.1_Intron|FAM172A_uc011cuj.1_Intron	NM_032042	NP_114431	Q8WUF8	F172A_HUMAN	hypothetical protein LOC83989 isoform 1							endoplasmic reticulum|extracellular region					0						atacacacaaacacacacacac	0.000													4	3	---	---	---	---	
SLC12A2	6558	broad.mit.edu	37	5	127487248	127487249	+	Intron	INS	-	T	T	rs146057040		TCGA-CJ-4899-01A-01D-1462-08	TCGA-CJ-4899-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:127487248_127487249insT	uc003kus.2	+						SLC12A2_uc010jdf.2_Intron|SLC12A2_uc010jdg.2_Intron	NM_001046	NP_001037	P55011	S12A2_HUMAN	solute carrier family 12						potassium ion transport|sodium ion transport|transepithelial ammonium transport|transepithelial chloride transport	integral to plasma membrane|membrane fraction	ammonia transmembrane transporter activity|sodium:potassium:chloride symporter activity			ovary(3)	3		all_cancers(142;0.0972)|Prostate(80;0.151)	KIRC - Kidney renal clear cell carcinoma(527;0.0268)|Kidney(363;0.0488)	Epithelial(69;0.0433)|OV - Ovarian serous cystadenocarcinoma(64;0.0978)	Bumetanide(DB00887)|Potassium Chloride(DB00761)	AACTCCTAAAGTTTTTTTTTTT	0.233													5	3	---	---	---	---	
C5orf15	56951	broad.mit.edu	37	5	133304077	133304078	+	Intron	INS	-	C	C			TCGA-CJ-4899-01A-01D-1462-08	TCGA-CJ-4899-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:133304077_133304078insC	uc003kyo.2	-							NM_020199	NP_064584	Q8NC54	KCT2_HUMAN	keratinocytes associated transmembrane protein 2							integral to membrane					0			KIRC - Kidney renal clear cell carcinoma(527;0.00806)|Kidney(363;0.02)			CCGGCCTGTCTCCTGCCCTGCG	0.668													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	180708776	180708777	+	IGR	INS	-	G	G	rs140221514		TCGA-CJ-4899-01A-01D-1462-08	TCGA-CJ-4899-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:180708776_180708777insG								TRIM52 (20657 upstream) : None (None downstream)																							gggcggtaggagggggctggag	0.144													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	14151723	14151730	+	IGR	DEL	CCTTCCTT	-	-	rs35401522		TCGA-CJ-4899-01A-01D-1462-08	TCGA-CJ-4899-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:14151723_14151730delCCTTCCTT								CD83 (14577 upstream) : None (None downstream)																							TTTTTCTTTCccttccttccttccttcc	0.192													6	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	73308509	73308510	+	IGR	INS	-	G	G			TCGA-CJ-4899-01A-01D-1462-08	TCGA-CJ-4899-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:73308509_73308510insG								RIMS1 (196002 upstream) : KCNQ5 (23061 downstream)																							CAGAAAATCGAGGGTTTTTTTT	0.366													10	5	---	---	---	---	
C6orf167	253714	broad.mit.edu	37	6	97654259	97654260	+	Intron	DEL	AC	-	-	rs150210793		TCGA-CJ-4899-01A-01D-1462-08	TCGA-CJ-4899-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:97654259_97654260delAC	uc003ppb.2	-						C6orf167_uc011eaf.1_Intron	NM_198468	NP_940870	Q6ZRQ5	MMS22_HUMAN	hypothetical protein LOC253714						double-strand break repair via homologous recombination|replication fork processing	nuclear replication fork	protein binding				0		all_cancers(76;0.000243)|Acute lymphoblastic leukemia(125;7.02e-10)|all_hematologic(75;1.23e-06)|all_epithelial(107;0.148)|Colorectal(196;0.198)		BRCA - Breast invasive adenocarcinoma(108;0.0457)		CCTCGCATGTacacacacacac	0.257													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	139094629	139094630	+	Intron	INS	-	G	G	rs143951524	by1000genomes	TCGA-CJ-4899-01A-01D-1462-08	TCGA-CJ-4899-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:139094629_139094630insG	uc003qid.1	-						CCDC28A_uc003qie.2_5'Flank					Homo sapiens cDNA FLJ35273 fis, clone PROST2006020.																		AATTGTAGTTCGGGGGGGGAAT	0.554													5	3	---	---	---	---	
MLXIPL	51085	broad.mit.edu	37	7	73008884	73008884	+	Intron	DEL	T	-	-			TCGA-CJ-4899-01A-01D-1462-08	TCGA-CJ-4899-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:73008884delT	uc003tyn.1	-						MLXIPL_uc003tyj.1_Intron|MLXIPL_uc003tyk.1_Intron|MLXIPL_uc003tyl.1_Intron|MLXIPL_uc003tym.1_Intron|MLXIPL_uc003tyo.1_Intron|MLXIPL_uc003typ.1_Intron	NM_032951	NP_116569	Q9NP71	WBS14_HUMAN	Williams Beuren syndrome chromosome region 14						anatomical structure morphogenesis|energy reserve metabolic process|glucose mediated signaling pathway|intracellular protein kinase cascade|negative regulation of cell cycle arrest|negative regulation of oxidative phosphorylation|negative regulation of peptidyl-serine phosphorylation|positive regulation of cell proliferation|positive regulation of fatty acid biosynthetic process|positive regulation of glycolysis|positive regulation of transcription from RNA polymerase II promoter|triglyceride homeostasis	cytosol|transcription factor complex	carbohydrate response element binding|protein heterodimerization activity|sequence-specific DNA binding transcription factor activity|transcription factor binding			pancreas(1)	1		Lung NSC(55;0.0659)|all_lung(88;0.152)				CTACttcttcttttttttttt	0.259													4	2	---	---	---	---	
ADCY8	114	broad.mit.edu	37	8	131859133	131859134	+	Intron	DEL	CT	-	-	rs71878573		TCGA-CJ-4899-01A-01D-1462-08	TCGA-CJ-4899-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:131859133_131859134delCT	uc003ytd.3	-						ADCY8_uc010mds.2_Intron	NM_001115	NP_001106	P40145	ADCY8_HUMAN	adenylate cyclase 8						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|membrane fraction|plasma membrane	ATP binding|calcium- and calmodulin-responsive adenylate cyclase activity|metal ion binding			skin(4)|large_intestine(1)|central_nervous_system(1)	6	Esophageal squamous(12;0.00693)|Ovarian(258;0.00707)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.000538)			cttcccttccctttccttcctt	0.079										HNSCC(32;0.087)			2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	22697343	22697344	+	Intron	INS	-	CTCT	CTCT	rs139803209	by1000genomes	TCGA-CJ-4899-01A-01D-1462-08	TCGA-CJ-4899-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:22697343_22697344insCTCT	uc003zpq.1	+											Homo sapiens cDNA FLJ35282 fis, clone PROST2007328.																		gtgtgtgtgCACTATTTCTGGT	0.292													4	2	---	---	---	---	
DDX58	23586	broad.mit.edu	37	9	32481587	32481587	+	Intron	DEL	T	-	-			TCGA-CJ-4899-01A-01D-1462-08	TCGA-CJ-4899-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:32481587delT	uc003zra.2	-						DDX58_uc010mjj.2_Intron|DDX58_uc010mjk.1_Intron|DDX58_uc011lnr.1_Intron|DDX58_uc010mji.2_Intron	NM_014314	NP_055129	O95786	DDX58_HUMAN	DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide						detection of virus|innate immune response|negative regulation of type I interferon production|positive regulation of defense response to virus by host|positive regulation of interferon-alpha production|positive regulation of interferon-beta production|positive regulation of transcription factor import into nucleus|positive regulation of transcription from RNA polymerase II promoter	cytosol	ATP binding|ATP-dependent helicase activity|double-stranded RNA binding|protein binding|zinc ion binding			ovary(2)|liver(1)|pancreas(1)	4			LUSC - Lung squamous cell carcinoma(29;0.00813)	GBM - Glioblastoma multiforme(74;0.00056)		tttctttttcttttttttttt	0.134													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	44084401	44084402	+	IGR	INS	-	ATCTT	ATCTT			TCGA-CJ-4899-01A-01D-1462-08	TCGA-CJ-4899-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:44084401_44084402insATCTT								FAM75A6 (453671 upstream) : FAM27C (905834 downstream)																							TAAAGACTATATATAAAAATAA	0.277													5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	69876385	69876386	+	IGR	INS	-	TCT	TCT			TCGA-CJ-4899-01A-01D-1462-08	TCGA-CJ-4899-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:69876385_69876386insTCT								LOC100133920 (211436 upstream) : FOXD4L5 (299323 downstream)																							TTCTTCTCTTCTCTTCTTGTTT	0.277													4	2	---	---	---	---	
TMEM38B	55151	broad.mit.edu	37	9	108468184	108468184	+	Intron	DEL	T	-	-	rs75898442		TCGA-CJ-4899-01A-01D-1462-08	TCGA-CJ-4899-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:108468184delT	uc004bcu.1	+						TMEM38B_uc010mtn.1_Intron	NM_018112	NP_060582	Q9NVV0	TM38B_HUMAN	transmembrane protein 38B							integral to membrane|nuclear membrane|sarcoplasmic reticulum membrane	potassium channel activity			ovary(1)|skin(1)	2						TGCTAAGGGGttttttttttt	0.149													6	3	---	---	---	---	
TNFSF8	944	broad.mit.edu	37	9	117692255	117692256	+	Intron	INS	-	AGAG	AGAG	rs10982457		TCGA-CJ-4899-01A-01D-1462-08	TCGA-CJ-4899-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:117692255_117692256insAGAG	uc004bji.1	-							NM_001244	NP_001235	P32971	TNFL8_HUMAN	tumor necrosis factor (ligand) superfamily,						cell proliferation|cell-cell signaling|immune response|induction of apoptosis|signal transduction	extracellular space|integral to plasma membrane	cytokine activity|tumor necrosis factor receptor binding			lung(3)|skin(2)|ovary(1)	6						tatatatatatataGAGAGAGA	0.168													4	2	---	---	---	---	
SPTAN1	6709	broad.mit.edu	37	9	131340165	131340166	+	Intron	INS	-	G	G	rs146851621	by1000genomes	TCGA-CJ-4899-01A-01D-1462-08	TCGA-CJ-4899-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:131340165_131340166insG	uc004bvl.3	+						SPTAN1_uc011mbg.1_Intron|SPTAN1_uc011mbh.1_Intron|SPTAN1_uc004bvm.3_Intron|SPTAN1_uc004bvn.3_Intron	NM_003127	NP_003118	Q13813	SPTA2_HUMAN	spectrin, alpha, non-erythrocytic 1						actin filament capping|axon guidance|cellular component disassembly involved in apoptosis	cytosol|intracellular membrane-bounded organelle|membrane fraction|microtubule cytoskeleton|spectrin	actin binding|calcium ion binding|calmodulin binding|structural constituent of cytoskeleton			breast(5)|ovary(4)|pancreas(1)	10						GGGACAGGATTGGGGCATTATA	0.386													3	3	---	---	---	---	
PFKFB3	5209	broad.mit.edu	37	10	6257402	6257403	+	Intron	INS	-	GGGCTGCG	GGGCTGCG	rs148095189	by1000genomes	TCGA-CJ-4899-01A-01D-1462-08	TCGA-CJ-4899-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:6257402_6257403insGGGCTGCG	uc001ije.2	+						PFKFB3_uc001ijd.2_Intron|PFKFB3_uc009xii.2_Intron|PFKFB3_uc010qaw.1_Intron|PFKFB3_uc001ijf.2_Intron	NM_004566	NP_004557	Q16875	F263_HUMAN	6-phosphofructo-2-kinase/fructose-2,						fructose 2,6-bisphosphate metabolic process|glycolysis	cytosol	6-phosphofructo-2-kinase activity|ATP binding|fructose-2,6-bisphosphate 2-phosphatase activity|identical protein binding			ovary(2)|central_nervous_system(1)	3						ggaataaggctgggctgcgggg	0.173													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	34220055	34220056	+	IGR	INS	-	TTCCTTCCTTCC	TTCCTTCCTTCC			TCGA-CJ-4899-01A-01D-1462-08	TCGA-CJ-4899-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:34220055_34220056insTTCCTTCCTTCC								NRP1 (596049 upstream) : PARD3 (180042 downstream)																							AGATAAGTGGAttccttccttc	0.188													8	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	37691031	37691032	+	IGR	INS	-	CCTT	CCTT			TCGA-CJ-4899-01A-01D-1462-08	TCGA-CJ-4899-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:37691031_37691032insCCTT								ANKRD30A (169536 upstream) : ZNF248 (399415 downstream)																							ccctttctttcccttccttcct	0.000													4	2	---	---	---	---	
MIR606	693191	broad.mit.edu	37	10	77312183	77312184	+	5'Flank	DEL	TC	-	-	rs1367290		TCGA-CJ-4899-01A-01D-1462-08	TCGA-CJ-4899-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:77312183_77312184delTC	hsa-mir-606|MI0003619	+																							0						tttttttttttcccccccctct	0.000													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	99068827	99068828	+	IGR	INS	-	AAAA	AAAA	rs140674552	by1000genomes	TCGA-CJ-4899-01A-01D-1462-08	TCGA-CJ-4899-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:99068827_99068828insAAAA								ARHGAP19 (16414 upstream) : FRAT1 (10194 downstream)																							cacgcccagccAAAAAAAGTTT	0.149													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	37121367	37121367	+	IGR	DEL	T	-	-			TCGA-CJ-4899-01A-01D-1462-08	TCGA-CJ-4899-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:37121367delT								C11orf74 (424977 upstream) : None (None downstream)																							ccttccttccttccttccttc	0.090													8	5	---	---	---	---	
GRIA4	2893	broad.mit.edu	37	11	105505081	105505081	+	Intron	DEL	A	-	-			TCGA-CJ-4899-01A-01D-1462-08	TCGA-CJ-4899-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:105505081delA	uc001pix.2	+						GRIA4_uc001piu.1_Intron|GRIA4_uc001piw.2_Intron|GRIA4_uc001piv.2_Intron|GRIA4_uc009yxk.1_Intron	NM_000829	NP_000820	P48058	GRIA4_HUMAN	glutamate receptor, ionotrophic, AMPA 4 isoform						glutamate signaling pathway|synaptic transmission	cell junction|endocytic vesicle membrane|integral to membrane|postsynaptic membrane	alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity			ovary(3)|skin(3)|lung(1)|central_nervous_system(1)	8		Melanoma(852;0.000902)|Acute lymphoblastic leukemia(157;0.000994)|all_hematologic(158;0.0017)|Breast(348;0.0323)		BRCA - Breast invasive adenocarcinoma(274;0.000147)|Epithelial(105;0.0291)|all cancers(92;0.0899)	L-Glutamic Acid(DB00142)	ctccgtctccaaaaaaaaaaa	0.000													5	3	---	---	---	---	
TMPRSS13	84000	broad.mit.edu	37	11	117772787	117772788	+	3'UTR	INS	-	CA	CA	rs138699837	by1000genomes	TCGA-CJ-4899-01A-01D-1462-08	TCGA-CJ-4899-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:117772787_117772788insCA	uc001prs.1	-	13					TMPRSS13_uc009yzr.1_3'UTR	NM_001077263	NP_001070731	Q9BYE2	TMPSD_HUMAN	transmembrane protease, serine 13						proteolysis	integral to membrane	scavenger receptor activity|serine-type endopeptidase activity			pancreas(1)	1	all_hematologic(175;0.0487)	Medulloblastoma(222;0.0425)|all_hematologic(192;0.196)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;1.78e-05)|Epithelial(105;0.00106)		Gcacacatatgcacacacacac	0.421													4	3	---	---	---	---	
GPRC5D	55507	broad.mit.edu	37	12	13099300	13099300	+	Intron	DEL	T	-	-	rs55785207		TCGA-CJ-4899-01A-01D-1462-08	TCGA-CJ-4899-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:13099300delT	uc010shp.1	-							NM_018654	NP_061124	Q9NZD1	GPC5D_HUMAN	G protein-coupled receptor, family C, group 5,							integral to membrane|plasma membrane	G-protein coupled receptor activity				0		Prostate(47;0.183)		BRCA - Breast invasive adenocarcinoma(232;0.15)		tctttctttcttttctttctt	0.000													6	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	58065357	58065358	+	IGR	INS	-	AAAG	AAAG	rs150140755		TCGA-CJ-4899-01A-01D-1462-08	TCGA-CJ-4899-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:58065357_58065358insAAAG								B4GALNT1 (38372 upstream) : OS9 (22528 downstream)																							gtctcaagagaaaagaaagaga	0.064													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	61263464	61263487	+	IGR	DEL	TTCCTTCCTTCCTTCCTTCCTTCC	-	-	rs72204013	by1000genomes	TCGA-CJ-4899-01A-01D-1462-08	TCGA-CJ-4899-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:61263464_61263487delTTCCTTCCTTCCTTCCTTCCTTCC								None (None upstream) : FAM19A2 (838556 downstream)																							TTGATtttctttccttccttccttccttccttccttccttcctt	0.138													4	4	---	---	---	---	
FOXN4	121643	broad.mit.edu	37	12	109723077	109723078	+	Intron	INS	-	GC	GC	rs34524845		TCGA-CJ-4899-01A-01D-1462-08	TCGA-CJ-4899-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:109723077_109723078insGC	uc001toe.3	-						FOXN4_uc009zvg.2_Intron|FOXN4_uc001tof.3_Intron	NM_213596	NP_998761	Q96NZ1	FOXN4_HUMAN	forkhead box N4						axon extension|embryo development|organ development|pattern specification process|regulation of heart contraction|regulation of sequence-specific DNA binding transcription factor activity|tissue development	transcription factor complex	DNA bending activity|double-stranded DNA binding|promoter binding|sequence-specific DNA 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(1)|lung(1)	2						tgtgtgtgtgtgtgCGCGCACT	0.495													4	2	---	---	---	---	
KSR2	283455	broad.mit.edu	37	12	117965130	117965131	+	Intron	DEL	AG	-	-	rs58270726		TCGA-CJ-4899-01A-01D-1462-08	TCGA-CJ-4899-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:117965130_117965131delAG	uc001two.2	-							NM_173598	NP_775869	Q6VAB6	KSR2_HUMAN	kinase suppressor of ras 2						intracellular signal transduction	cytoplasm|membrane	ATP binding|metal ion binding|protein serine/threonine kinase activity			lung(10)|central_nervous_system(2)|stomach(1)|large_intestine(1)|breast(1)	15	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)					acacacacacagacacacacac	0.228													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	119145437	119145442	+	IGR	DEL	TGATGA	-	-	rs28756141		TCGA-CJ-4899-01A-01D-1462-08	TCGA-CJ-4899-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:119145437_119145442delTGATGA								SUDS3 (289598 upstream) : SRRM4 (273954 downstream)																							atggtggtggtgatgatgatggtggt	0.000													6	3	---	---	---	---	
NBEA	26960	broad.mit.edu	37	13	36003970	36003971	+	Intron	INS	-	TGTA	TGTA	rs77962246	by1000genomes	TCGA-CJ-4899-01A-01D-1462-08	TCGA-CJ-4899-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:36003970_36003971insTGTA	uc001uvb.2	+						NBEA_uc010abi.2_Intron	NM_015678	NP_056493	Q8NFP9	NBEA_HUMAN	neurobeachin							cytosol|endomembrane system|plasma membrane|trans-Golgi network	protein binding			ovary(9)|large_intestine(2)	11		Breast(139;0.0141)|Lung SC(185;0.0548)|Prostate(109;0.207)		all cancers(112;1.93e-08)|Epithelial(112;1.62e-07)|BRCA - Breast invasive adenocarcinoma(63;0.00033)|OV - Ovarian serous cystadenocarcinoma(117;0.00109)|KIRC - Kidney renal clear cell carcinoma(186;0.00575)|Kidney(163;0.00656)|GBM - Glioblastoma multiforme(144;0.191)|Lung(94;0.199)		gtgtgtgtgtgtACAcacattt	0.010													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	23154909	23154909	+	IGR	DEL	A	-	-			TCGA-CJ-4899-01A-01D-1462-08	TCGA-CJ-4899-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:23154909delA								ABHD4 (73652 upstream) : OXA1L (80822 downstream)																							TCTTCTTGGGAAAAAAAAAAA	0.264													7	5	---	---	---	---	
MED6	10001	broad.mit.edu	37	14	71067484	71067504	+	5'Flank	DEL	GGCAGGAGAGAGGCAGGGGGT	-	-			TCGA-CJ-4899-01A-01D-1462-08	TCGA-CJ-4899-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:71067484_71067504delGGCAGGAGAGAGGCAGGGGGT	uc001xmf.2	-						MED6_uc010tth.1_5'Flank|MED6_uc010tti.1_5'Flank|MED6_uc001xmg.1_5'Flank|MED6_uc010ttj.1_5'Flank	NM_005466	NP_005457	O75586	MED6_HUMAN	mediator of RNA polymerase II transcription,						positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	mediator complex	transcription coactivator activity				0				all cancers(60;0.00315)|BRCA - Breast invasive adenocarcinoma(234;0.00685)|OV - Ovarian serous cystadenocarcinoma(108;0.0352)		gggcggggcgggcaggagagaggcagggggtggaggtgcgg	0.167													6	3	---	---	---	---	
DAPK2	23604	broad.mit.edu	37	15	64286703	64286704	+	Intron	INS	-	CTT	CTT	rs139129405	by1000genomes	TCGA-CJ-4899-01A-01D-1462-08	TCGA-CJ-4899-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:64286703_64286704insCTT	uc002amr.2	-						DAPK2_uc010uim.1_Intron|DAPK2_uc010bgu.1_Intron	NM_014326	NP_055141	Q9UIK4	DAPK2_HUMAN	death-associated kinase 2						apoptosis|induction of apoptosis|intracellular protein kinase cascade	cytoplasm	ATP binding|calmodulin binding|calmodulin-dependent protein kinase activity|identical protein binding			stomach(1)|central_nervous_system(1)	2				LUAD - Lung adenocarcinoma(2;0.215)		gttccttagtcccacctttcta	0.025													4	2	---	---	---	---	
SV2B	9899	broad.mit.edu	37	15	91764923	91764924	+	Intron	INS	-	CA	CA	rs71880791		TCGA-CJ-4899-01A-01D-1462-08	TCGA-CJ-4899-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:91764923_91764924insCA	uc010uqv.1	+						SV2B_uc002bqt.2_Intron|SV2B_uc002bqu.3_Intron	NM_014848	NP_055663	Q7L1I2	SV2B_HUMAN	synaptic vesicle protein 2B homolog						neurotransmitter transport	acrosomal vesicle|cell junction|integral to membrane|synaptic vesicle membrane	transmembrane transporter activity			ovary(3)|central_nervous_system(2)|skin(2)|upper_aerodigestive_tract(1)	8	Lung NSC(78;0.0987)|all_lung(78;0.172)		BRCA - Breast invasive adenocarcinoma(143;0.0895)			AAGCATGTGCGcacacacacac	0.416													4	2	---	---	---	---	
USP6	9098	broad.mit.edu	37	17	5036584	5036585	+	Intron	DEL	TT	-	-			TCGA-CJ-4899-01A-01D-1462-08	TCGA-CJ-4899-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:5036584_5036585delTT	uc002gau.1	+						USP6_uc002gav.1_Intron|USP6_uc010ckz.1_Intron|USP6_uc002gaw.2_Intron|uc002gay.1_5'Flank	NM_004505	NP_004496	P35125	UBP6_HUMAN	ubiquitin specific protease 6						protein deubiquitination|regulation of vesicle-mediated transport|ubiquitin-dependent protein catabolic process	lysosome|plasma membrane|recycling endosome	calmodulin binding|cysteine-type endopeptidase activity|nucleic acid binding|protein binding|Rab GTPase activator activity|ubiquitin thiolesterase activity|ubiquitin-specific protease activity			skin(2)|upper_aerodigestive_tract(1)|lung(1)|breast(1)	5						CCATCCACTCTTTCAGTCCTGG	0.554			T	COL1A1|CDH11|ZNF9|OMD	aneurysmal bone cysts								6	4	---	---	---	---	
TNFSF12-TNFSF13	407977	broad.mit.edu	37	17	7451454	7451455	+	5'Flank	INS	-	TCCGTCCTTCCT	TCCGTCCTTCCT			TCGA-CJ-4899-01A-01D-1462-08	TCGA-CJ-4899-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:7451454_7451455insTCCGTCCTTCCT	uc002ghi.1	+						TNFSF12_uc002ghg.2_5'Flank|TNFSF12_uc002ghh.2_5'Flank	NM_172089	NP_742086	Q8IZK7	Q8IZK7_HUMAN	TNFSF12-TNFSF13 protein						immune response	extracellular space|membrane	cytokine activity|tumor necrosis factor receptor binding				0		Prostate(122;0.157)				gccAATTTTGGtccttccttcc	0.010													4	5	---	---	---	---	
TBC1D29	26083	broad.mit.edu	37	17	28885450	28885451	+	5'Flank	INS	-	T	T			TCGA-CJ-4899-01A-01D-1462-08	TCGA-CJ-4899-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:28885450_28885451insT	uc002hfh.2	+						uc002hfg.1_5'Flank|TBC1D29_uc002hfi.2_5'Flank	NM_015594	NP_056409	Q9UFV1	TBC29_HUMAN	TBC1 domain family, member 29							intracellular	Rab GTPase activator activity				0		Myeloproliferative disorder(56;0.0255)				TGGCATAAACCTCCAGCAAGGG	0.540													6	4	---	---	---	---	
INTS2	57508	broad.mit.edu	37	17	59946936	59946936	+	Intron	DEL	A	-	-			TCGA-CJ-4899-01A-01D-1462-08	TCGA-CJ-4899-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:59946936delA	uc002izn.2	-						INTS2_uc002izm.2_Intron	NM_020748	NP_065799	Q9H0H0	INT2_HUMAN	integrator complex subunit 2						snRNA processing	integral to membrane|integrator complex|nuclear membrane	protein binding			ovary(1)|lung(1)|pancreas(1)	3						TCATTAGGTTAAAAAAAAAAA	0.328													9	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	65243822	65243823	+	IGR	DEL	AA	-	-			TCGA-CJ-4899-01A-01D-1462-08	TCGA-CJ-4899-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:65243822_65243823delAA								DSEL (59855 upstream) : None (None downstream)																							agaaagaaagaaagagagagag	0.040													4	2	---	---	---	---	
ARHGEF18	23370	broad.mit.edu	37	19	7515307	7515307	+	Intron	DEL	C	-	-			TCGA-CJ-4899-01A-01D-1462-08	TCGA-CJ-4899-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:7515307delC	uc002mgi.2	+						ARHGEF18_uc010xjm.1_Intron|ARHGEF18_uc002mgh.2_Intron|ARHGEF18_uc002mgj.1_Intron	NM_001130955	NP_001124427	Q6ZSZ5	ARHGI_HUMAN	Rho/Rac guanine nucleotide exchange factor 18						actin cytoskeleton organization|apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of cell shape|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol	Rho guanyl-nucleotide exchange factor activity			ovary(1)	1		Renal(5;0.0902)				GATGTTAATGCGGGATCTTGC	0.448													4	2	---	---	---	---	
ARRDC2	27106	broad.mit.edu	37	19	18111475	18111476	+	5'Flank	INS	-	GGAA	GGAA	rs141584055	by1000genomes	TCGA-CJ-4899-01A-01D-1462-08	TCGA-CJ-4899-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:18111475_18111476insGGAA	uc002nhu.2	+							NM_001025604	NP_001020775	Q8TBH0	ARRD2_HUMAN	arrestin domain containing 2 isoform 2											pancreas(1)	1						agaggaaggagggaaggaagga	0.223													7	8	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	53703995	53703995	+	IGR	DEL	T	-	-	rs113703393		TCGA-CJ-4899-01A-01D-1462-08	TCGA-CJ-4899-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:53703995delT								ZNF665 (7376 upstream) : ZNF677 (34643 downstream)																							TGTTTCCCCCttttttttttt	0.229													9	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	44621932	44621936	+	IGR	DEL	AGGAG	-	-			TCGA-CJ-4899-01A-01D-1462-08	TCGA-CJ-4899-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:44621932_44621936delAGGAG								ZNF335 (21099 upstream) : MMP9 (15611 downstream)																							ggaaaaagaaaggagaggagaggag	0.102													4	2	---	---	---	---	
NKAIN4	128414	broad.mit.edu	37	20	61874138	61874139	+	Intron	INS	-	G	G	rs147746767	by1000genomes	TCGA-CJ-4899-01A-01D-1462-08	TCGA-CJ-4899-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:61874138_61874139insG	uc002yek.2	-							NM_152864	NP_690603	Q8IVV8	NKAI4_HUMAN	Na+/K+ transporting ATPase interacting 4							integral to membrane|plasma membrane					0	all_cancers(38;2.72e-09)					CCTGGGGGGACGGGGGGGGTGG	0.673													5	3	---	---	---	---	
C22orf43	51233	broad.mit.edu	37	22	23973867	23973868	+	Intron	INS	-	C	C	rs141675360	by1000genomes	TCGA-CJ-4899-01A-01D-1462-08	TCGA-CJ-4899-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:23973867_23973868insC	uc002zxf.2	-							NM_016449	NP_057533	Q6PGQ1	CV043_HUMAN	hypothetical protein LOC51233											skin(1)	1						TGTCCCCCATGCCCAGACCTGG	0.535													4	2	---	---	---	---	
ARSH	347527	broad.mit.edu	37	X	2942330	2942330	+	Intron	DEL	A	-	-			TCGA-CJ-4899-01A-01D-1462-08	TCGA-CJ-4899-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:2942330delA	uc011mhj.1	+							NM_001011719	NP_001011719	Q5FYA8	ARSH_HUMAN	arylsulfatase family, member H							integral to membrane	arylsulfatase activity|metal ion binding			lung(1)	1		all_cancers(21;9e-05)|all_epithelial(21;6.22e-06)|all_lung(23;0.000597)|Lung NSC(23;0.00901)|Lung SC(21;0.186)				AGCTAGACCGAAAAAAAAAAA	0.373													6	3	---	---	---	---	
TSPAN6	7105	broad.mit.edu	37	X	99887402	99887403	+	Intron	INS	-	A	A			TCGA-CJ-4899-01A-01D-1462-08	TCGA-CJ-4899-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:99887402_99887403insA	uc004ega.1	-						TSPAN6_uc010nna.1_Intron	NM_003270	NP_003261	O43657	TSN6_HUMAN	transmembrane 4 superfamily member 6						positive regulation of I-kappaB kinase/NF-kappaB cascade	integral to membrane	signal transducer activity			ovary(1)	1						gactccatctcaaaaaaaaaaa	0.158													4	3	---	---	---	---	
IDS	3423	broad.mit.edu	37	X	148577954	148577954	+	Frame_Shift_Del	DEL	T	-	-			TCGA-CJ-4899-01A-01D-1462-08	TCGA-CJ-4899-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:148577954delT	uc011mxe.1	-	6	1000	c.802delA	c.(802-804)ATGfs	p.M268fs	IDS_uc011mxf.1_Frame_Shift_Del_p.M178fs|IDS_uc011mxg.1_Frame_Shift_Del_p.M57fs|IDS_uc010nsu.1_Intron|IDS_uc004fcw.3_Frame_Shift_Del_p.M57fs|IDS_uc011mxh.1_Frame_Shift_Del_p.M268fs|IDS_uc011mxi.1_RNA	NM_000202	NP_000193	P22304	IDS_HUMAN	iduronate-2-sulfatase isoform a precursor	268						lysosome	iduronate-2-sulfatase activity|metal ion binding				0	Acute lymphoblastic leukemia(192;6.56e-05)|Colorectal(9;0.0662)					CTGATGTCCATCCAGGGGTTG	0.542													129	93	---	---	---	---	
