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
CROCCL1	84809	broad.mit.edu	37	1	16956555	16956555	+	Intron	SNP	C	T	T	rs9329440	by1000genomes	TCGA-BP-4970-01A-01D-1462-08	TCGA-BP-4970-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:16956555C>T	uc009vov.1	-						CROCCL1_uc001aze.2_Intron|CROCCL1_uc001azf.2_Intron|CROCCL1_uc001azg.1_Intron|CROCCL1_uc001azi.1_RNA	NR_026752				Homo sapiens mRNA for FLJ00313 protein.												0						CTCTAGGGCCCGCCGCTCACT	0.502													8	29	---	---	---	---	PASS
EPHA8	2046	broad.mit.edu	37	1	22902833	22902833	+	Missense_Mutation	SNP	C	T	T			TCGA-BP-4970-01A-01D-1462-08	TCGA-BP-4970-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:22902833C>T	uc001bfx.1	+	3	408	c.283C>T	c.(283-285)CGG>TGG	p.R95W	EPHA8_uc001bfw.2_Missense_Mutation_p.R95W	NM_020526	NP_065387	P29322	EPHA8_HUMAN	ephrin receptor EphA8 isoform 1 precursor	95	Extracellular (Potential).					integral to plasma membrane	ATP binding|ephrin receptor activity			central_nervous_system(5)|breast(3)|lung(2)|large_intestine(1)|stomach(1)|skin(1)	13		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;0.0227)|OV - Ovarian serous cystadenocarcinoma(117;7.29e-27)|Colorectal(126;1.61e-07)|COAD - Colon adenocarcinoma(152;1.14e-05)|GBM - Glioblastoma multiforme(114;1.74e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000554)|KIRC - Kidney renal clear cell carcinoma(1967;0.00272)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.199)		AGACGGCGCCCGGCGCGTCTA	0.607													5	58	---	---	---	---	PASS
LOC728989	728989	broad.mit.edu	37	1	146494537	146494537	+	Silent	SNP	C	T	T			TCGA-BP-4970-01A-01D-1462-08	TCGA-BP-4970-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:146494537C>T	uc001epd.2	-	4	536	c.462G>A	c.(460-462)GCG>GCA	p.A154A		NR_024442				SubName: Full=cDNA FLJ59595, highly similar to Homo sapiens phosphodiesterase 4D interacting protein, transcript variant 1, mRNA;												0						TTGGCAGGGCCGCTCTCCAGA	0.567													4	33	---	---	---	---	PASS
POGZ	23126	broad.mit.edu	37	1	151380970	151380970	+	Missense_Mutation	SNP	G	T	T			TCGA-BP-4970-01A-01D-1462-08	TCGA-BP-4970-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:151380970G>T	uc001eyd.1	-	14	2455	c.2149C>A	c.(2149-2151)CCG>ACG	p.P717T	POGZ_uc001eye.1_Missense_Mutation_p.P664T|POGZ_uc010pdb.1_Missense_Mutation_p.P708T|POGZ_uc001eyf.1_Missense_Mutation_p.P673T|POGZ_uc010pdc.1_Missense_Mutation_p.P655T|POGZ_uc009wmv.1_Missense_Mutation_p.P622T|POGZ_uc010pdd.1_Missense_Mutation_p.P208T	NM_015100	NP_055915	Q7Z3K3	POGZ_HUMAN	pogo transposable element with ZNF domain	717					cell division|kinetochore assembly|mitotic sister chromatid cohesion|regulation of transcription, DNA-dependent	cytoplasm|nuclear chromatin	DNA binding|protein binding|zinc ion binding			ovary(3)	3	Lung SC(34;0.00471)|Ovarian(49;0.00672)|Hepatocellular(266;0.0997)|all_hematologic(923;0.127)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.112)|LUSC - Lung squamous cell carcinoma(543;0.181)			GAGGTCAGCGGTGCTGCCTCC	0.567													9	71	---	---	---	---	PASS
NT5C1B	93034	broad.mit.edu	37	2	18757590	18757590	+	Missense_Mutation	SNP	A	G	G			TCGA-BP-4970-01A-01D-1462-08	TCGA-BP-4970-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:18757590A>G	uc002rcz.2	-	9	1473	c.1369T>C	c.(1369-1371)TAC>CAC	p.Y457H	NT5C1B_uc002rcy.2_Missense_Mutation_p.Y457H|NT5C1B_uc010exr.2_Missense_Mutation_p.Y399H|NT5C1B_uc010yju.1_Missense_Mutation_p.Y397H|NT5C1B_uc002rda.2_Missense_Mutation_p.Y397H|NT5C1B_uc010yjv.1_Missense_Mutation_p.Y474H|NT5C1B_uc010yjw.1_Missense_Mutation_p.Y440H|NT5C1B_uc010exs.2_Missense_Mutation_p.Y459H	NM_001002006	NP_001002006	Q96P26	5NT1B_HUMAN	5' nucleotidase, cytosolic IB isoform 1	457					purine base metabolic process|purine nucleotide catabolic process	cytosol	5'-nucleotidase activity|magnesium ion binding|nucleotide binding			skin(2)|ovary(1)	3	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.177)	Ovarian(717;0.208)				GTGTCACAGTAAGCCATGTCT	0.433													11	34	---	---	---	---	PASS
VHL	7428	broad.mit.edu	37	3	10188321	10188321	+	Splice_Site	SNP	G	T	T	rs5030814		TCGA-BP-4970-01A-01D-1462-08	TCGA-BP-4970-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:10188321G>T	uc003bvc.2	+	2	676	c.463_splice	c.e2+1	p.V155_splice	VHL_uc003bvd.2_Intron	NM_000551	NP_000542	P40337	VHL_HUMAN	von Hippel-Lindau tumor suppressor isoform 1						anti-apoptosis|cell morphogenesis|negative regulation of cell proliferation|negative regulation of transcription from RNA polymerase II promoter|positive regulation of cell differentiation|positive regulation of transcription, DNA-dependent|protein stabilization|protein ubiquitination|proteolysis	cytosol|endoplasmic reticulum|membrane|mitochondrion|nucleus	protein binding|transcription factor binding	p.?(9)		kidney(1273)|soft_tissue(24)|adrenal_gland(15)|large_intestine(13)|pancreas(5)|endometrium(4)|thyroid(3)|upper_aerodigestive_tract(3)|central_nervous_system(2)|lung(2)|pleura(1)|paratesticular_tissues(1)	1346				Kidney(1;0.000404)|KIRC - Kidney renal clear cell carcinoma(1;0.000569)		ACACTGCCAGGTACTGACGTT	0.403		1	D|Mis|N|F|S		renal|hemangioma|pheochromocytoma	renal|hemangioma|pheochromocytoma			von_Hippel-Lindau_disease|Chuvash_Polycythemia_|Pheochromocytoma_(Adrenal)_Familial				20	112	---	---	---	---	PASS
ZBTB38	253461	broad.mit.edu	37	3	141161609	141161609	+	Missense_Mutation	SNP	T	C	C			TCGA-BP-4970-01A-01D-1462-08	TCGA-BP-4970-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:141161609T>C	uc003etw.2	+	8	1361	c.379T>C	c.(379-381)TTC>CTC	p.F127L	ZBTB38_uc010hun.2_Missense_Mutation_p.F124L|ZBTB38_uc010huo.2_Missense_Mutation_p.F127L|ZBTB38_uc003ety.2_Missense_Mutation_p.F127L|ZBTB38_uc010hup.2_Missense_Mutation_p.F128L	NM_001080412	NP_001073881	Q8NAP3	ZBT38_HUMAN	zinc finger and BTB domain containing 38	127					positive regulation of transcription from RNA polymerase II promoter	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(3)	3						TGATCGCAACTTCTCAAATTC	0.423													13	54	---	---	---	---	PASS
LRRC15	131578	broad.mit.edu	37	3	194081603	194081603	+	Missense_Mutation	SNP	C	A	A			TCGA-BP-4970-01A-01D-1462-08	TCGA-BP-4970-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:194081603C>A	uc003ftu.2	-	2	256	c.170G>T	c.(169-171)AGC>ATC	p.S57I	LRRC15_uc003ftt.2_Missense_Mutation_p.S63I	NM_130830	NP_570843	Q8TF66	LRC15_HUMAN	leucine rich repeat containing 15 isoform b	57	LRR 1.|Extracellular (Potential).					integral to membrane				ovary(3)	3	all_cancers(143;5.31e-09)|Ovarian(172;0.0634)		OV - Ovarian serous cystadenocarcinoma(49;2.2e-17)|LUSC - Lung squamous cell carcinoma(58;3.55e-06)|Lung(62;4.19e-06)	GBM - Glioblastoma multiforme(46;4.94e-05)		GATCTGCAGGCTCATGGCGTT	0.602													3	39	---	---	---	---	PASS
PROM1	8842	broad.mit.edu	37	4	16020105	16020105	+	Silent	SNP	G	A	A			TCGA-BP-4970-01A-01D-1462-08	TCGA-BP-4970-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:16020105G>A	uc003goo.2	-	8	1055	c.843C>T	c.(841-843)CAC>CAT	p.H281H	PROM1_uc003gor.2_Silent_p.H281H|PROM1_uc003gos.2_Silent_p.H272H|PROM1_uc003got.2_Silent_p.H281H|PROM1_uc003gou.2_Silent_p.H272H|PROM1_uc003gop.2_Silent_p.H272H|PROM1_uc003goq.3_Silent_p.H272H|PROM1_uc010iec.1_Silent_p.H159H	NM_006017	NP_006008	O43490	PROM1_HUMAN	prominin 1 isoform 1	281	Extracellular (Potential).				camera-type eye photoreceptor cell differentiation|photoreceptor cell maintenance|retina layer formation	apical plasma membrane|cell surface|integral to plasma membrane|microvillus membrane|photoreceptor outer segment membrane|plasma membrane	beta-actinin binding|cadherin binding			ovary(3)|upper_aerodigestive_tract(1)|lung(1)|kidney(1)|central_nervous_system(1)	7						TACTTTGTTGGTGCAAGCTCT	0.502													3	19	---	---	---	---	PASS
PCDHA2	56146	broad.mit.edu	37	5	140176057	140176057	+	Missense_Mutation	SNP	C	T	T			TCGA-BP-4970-01A-01D-1462-08	TCGA-BP-4970-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140176057C>T	uc003lhd.2	+	1	1614	c.1508C>T	c.(1507-1509)GCG>GTG	p.A503V	PCDHA1_uc003lha.2_Intron|PCDHA1_uc003lhb.2_Intron|PCDHA2_uc003lhc.1_Missense_Mutation_p.A503V|PCDHA2_uc011czy.1_Missense_Mutation_p.A503V	NM_018905	NP_061728	Q9Y5H9	PCDA2_HUMAN	protocadherin alpha 2 isoform 1 precursor	503	Cadherin 5.|Extracellular (Potential).				homophilic cell adhesion|nervous system development	integral to plasma membrane	calcium ion binding|protein binding			ovary(4)	4			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GGCGAGCGCGCGTTGTCGAGC	0.677													6	39	---	---	---	---	PASS
HSD17B8	7923	broad.mit.edu	37	6	33173664	33173664	+	Missense_Mutation	SNP	A	G	G			TCGA-BP-4970-01A-01D-1462-08	TCGA-BP-4970-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:33173664A>G	uc003odi.1	+	6	653	c.626A>G	c.(625-627)AAA>AGA	p.K209R	uc003odj.1_5'Flank|MIR219-1_hsa-mir-219-1|MI0000296_5'Flank|RING1_uc011dqw.1_5'Flank|RING1_uc011dqx.1_5'Flank|RING1_uc003odk.2_5'Flank	NM_014234	NP_055049	Q92506	DHB8_HUMAN	estradiol 17 beta-dehydrogenase 8	209					estrogen biosynthetic process|fatty acid biosynthetic process	mitochondrial matrix	3-hydroxyacyl-CoA dehydrogenase activity|estradiol 17-beta-dehydrogenase activity|protein binding|testosterone 17-beta-dehydrogenase (NAD+) activity			breast(1)|central_nervous_system(1)	2					NADH(DB00157)	ATGACACAGAAAGTGCCACAG	0.502													10	74	---	---	---	---	PASS
COL19A1	1310	broad.mit.edu	37	6	70733567	70733567	+	Nonsense_Mutation	SNP	G	T	T			TCGA-BP-4970-01A-01D-1462-08	TCGA-BP-4970-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:70733567G>T	uc003pfc.1	+	12	1192	c.1075G>T	c.(1075-1077)GAA>TAA	p.E359*	COL19A1_uc010kam.1_Nonsense_Mutation_p.E255*	NM_001858	NP_001849	Q14993	COJA1_HUMAN	alpha 1 type XIX collagen precursor	359					cell differentiation|cell-cell adhesion|extracellular matrix organization|skeletal system development	collagen	extracellular matrix structural constituent|protein binding, bridging			ovary(2)|breast(2)	4						CCTTAATGGAGAAAATGTAAG	0.338													14	45	---	---	---	---	PASS
EXOC4	60412	broad.mit.edu	37	7	133059626	133059626	+	Missense_Mutation	SNP	C	A	A			TCGA-BP-4970-01A-01D-1462-08	TCGA-BP-4970-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:133059626C>A	uc003vrk.2	+	7	1087	c.1052C>A	c.(1051-1053)GCT>GAT	p.A351D	EXOC4_uc011kpo.1_Missense_Mutation_p.A250D|EXOC4_uc003vri.2_Missense_Mutation_p.A351D|EXOC4_uc003vrj.2_Missense_Mutation_p.A351D	NM_021807	NP_068579	Q96A65	EXOC4_HUMAN	SEC8 protein isoform a	351					vesicle docking involved in exocytosis	exocyst	protein N-terminus binding			ovary(4)|large_intestine(3)|upper_aerodigestive_tract(1)|skin(1)	9		Esophageal squamous(399;0.129)				AAGTTTAATGCTGTAGCCGCT	0.433													20	67	---	---	---	---	PASS
UBE3C	9690	broad.mit.edu	37	7	156967613	156967613	+	Missense_Mutation	SNP	A	G	G			TCGA-BP-4970-01A-01D-1462-08	TCGA-BP-4970-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:156967613A>G	uc010lqs.2	+	5	655	c.343A>G	c.(343-345)ATA>GTA	p.I115V	UBE3C_uc003wnf.2_Missense_Mutation_p.I72V|UBE3C_uc003wng.2_Missense_Mutation_p.I115V	NM_014671	NP_055486	Q15386	UBE3C_HUMAN	ubiquitin protein ligase E3C	115					protein polyubiquitination|protein ubiquitination involved in ubiquitin-dependent protein catabolic process	nucleus|proteasome complex	protein binding|ubiquitin-protein ligase activity			ovary(2)|lung(2)|large_intestine(1)	5		all_hematologic(28;0.0185)|all_epithelial(9;0.0664)	OV - Ovarian serous cystadenocarcinoma(82;0.00448)	UCEC - Uterine corpus endometrioid carcinoma (81;0.19)		GCTGTTTCAGATATGGCTGTA	0.313													11	39	---	---	---	---	PASS
PPP3CC	5533	broad.mit.edu	37	8	22370886	22370886	+	Missense_Mutation	SNP	T	G	G			TCGA-BP-4970-01A-01D-1462-08	TCGA-BP-4970-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:22370886T>G	uc003xbs.2	+	6	1038	c.711T>G	c.(709-711)AAT>AAG	p.N237K	PPP3CC_uc003xbr.1_Missense_Mutation_p.N237K|PPP3CC_uc011kzi.1_Missense_Mutation_p.N237K|PPP3CC_uc003xbt.2_Missense_Mutation_p.N237K	NM_005605	NP_005596	P48454	PP2BC_HUMAN	protein phosphatase 3, catalytic subunit, gamma	237					activation of pro-apoptotic gene products|induction of apoptosis by intracellular signals	cytosol	calmodulin binding|metal ion binding|phosphoprotein phosphatase activity			ovary(1)	1		Prostate(55;0.104)		BRCA - Breast invasive adenocarcinoma(99;0.00756)|Colorectal(74;0.0238)|COAD - Colon adenocarcinoma(73;0.0835)		ATTATGGCAATGAGAAGACCT	0.473													49	92	---	---	---	---	PASS
MTDH	92140	broad.mit.edu	37	8	98703207	98703207	+	Missense_Mutation	SNP	C	G	G			TCGA-BP-4970-01A-01D-1462-08	TCGA-BP-4970-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:98703207C>G	uc003yhz.2	+	6	1167	c.839C>G	c.(838-840)ACT>AGT	p.T280S	MTDH_uc010mbf.2_RNA	NM_178812	NP_848927	Q86UE4	LYRIC_HUMAN	metadherin	280	Cytoplasmic (Potential).				lipopolysaccharide-mediated signaling pathway|negative regulation of apoptosis|negative regulation of transcription from RNA polymerase II promoter|positive regulation of angiogenesis|positive regulation of autophagy|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of NF-kappaB transcription factor activity|positive regulation of protein kinase B signaling cascade	apical plasma membrane|endoplasmic reticulum membrane|integral to membrane|intercellular canaliculus|nuclear body|nuclear membrane|nucleolus|perinuclear region of cytoplasm|tight junction	NF-kappaB binding|RNA polymerase II transcription factor binding|transcription coactivator activity			liver(1)|central_nervous_system(1)	2	Breast(36;2.56e-06)		OV - Ovarian serous cystadenocarcinoma(57;0.178)			GAAAACCTCACTGTCAATGGA	0.383													10	36	---	---	---	---	PASS
CSTF2T	23283	broad.mit.edu	37	10	53458229	53458229	+	Missense_Mutation	SNP	C	T	T			TCGA-BP-4970-01A-01D-1462-08	TCGA-BP-4970-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:53458229C>T	uc001jjp.2	-	1	1127	c.1081G>A	c.(1081-1083)GGT>AGT	p.G361S	PRKG1_uc001jjm.2_Intron|PRKG1_uc001jjn.2_Intron|PRKG1_uc001jjo.2_Intron	NM_015235	NP_056050	Q9H0L4	CSTFT_HUMAN	cleavage stimulation factor, 3' pre-RNA, subunit	361	Gly-rich.				mRNA processing	nucleus	nucleotide binding|RNA binding			ovary(1)	1				COAD - Colon adenocarcinoma(2;0.00736)|Colorectal(2;0.00898)|all cancers(4;0.0188)|GBM - Glioblastoma multiforme(4;0.0778)|Epithelial(53;0.122)		ATGGGGGGACCCTGATGGGGT	0.552													14	72	---	---	---	---	PASS
TRIM5	85363	broad.mit.edu	37	11	5687233	5687233	+	Silent	SNP	T	C	C			TCGA-BP-4970-01A-01D-1462-08	TCGA-BP-4970-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:5687233T>C	uc001mbm.1	-	6	1103	c.846A>G	c.(844-846)AAA>AAG	p.K282K	TRIM78P_uc009yer.2_RNA|TRIM5_uc001mbl.1_RNA|TRIM5_uc001mbn.2_Silent_p.K282K|TRIM5_uc001mbo.2_Silent_p.K282K|TRIM5_uc001mbp.2_Silent_p.K282K	NM_033034	NP_149023	Q9C035	TRIM5_HUMAN	tripartite motif protein TRIM5 isoform alpha	282	B30.2/SPRY.				interspecies interaction between organisms|protein trimerization|response to virus	cytoplasm|cytoplasmic mRNA processing body	ligase activity|protein binding|protein homodimerization activity|zinc ion binding			ovary(1)	1		Medulloblastoma(188;0.00225)|Breast(177;0.0204)|all_neural(188;0.0212)|Lung NSC(207;0.138)|all_lung(207;0.221)		Epithelial(150;7.21e-09)|BRCA - Breast invasive adenocarcinoma(625;0.139)		CTAGCATTCCTTTCAGATCAG	0.403													34	90	---	---	---	---	PASS
SF3B2	10992	broad.mit.edu	37	11	65822560	65822560	+	Missense_Mutation	SNP	C	A	A			TCGA-BP-4970-01A-01D-1462-08	TCGA-BP-4970-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:65822560C>A	uc001ogy.1	+	4	312	c.272C>A	c.(271-273)CCC>CAC	p.P91H	SF3B2_uc001ogx.1_Missense_Mutation_p.P91H	NM_006842	NP_006833	Q13435	SF3B2_HUMAN	splicing factor 3B subunit 2	91	Poly-Pro.				interspecies interaction between organisms	catalytic step 2 spliceosome|nucleoplasm|U12-type spliceosomal complex	nucleic acid binding|protein binding			ovary(2)|breast(1)	3						CCTGGAATTCCCATGCCACCA	0.433													25	84	---	---	---	---	PASS
DDN	23109	broad.mit.edu	37	12	49390707	49390707	+	Missense_Mutation	SNP	G	A	A			TCGA-BP-4970-01A-01D-1462-08	TCGA-BP-4970-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:49390707G>A	uc001rsv.1	-	2	1970	c.1952C>T	c.(1951-1953)GCC>GTC	p.A651V	uc001rsw.2_5'Flank	NM_015086	NP_055901	O94850	DEND_HUMAN	dendrin	651	Interaction with CD2AP and NPHS1 (By similarity).					dendritic spine membrane|endoplasmic reticulum membrane|nucleus|perikaryon				large_intestine(1)	1						CCGCCAGGAGGCGCCCGGGGC	0.627											OREG0021778	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	3	8	---	---	---	---	PASS
PRKAG1	5571	broad.mit.edu	37	12	49396983	49396983	+	Missense_Mutation	SNP	T	G	G			TCGA-BP-4970-01A-01D-1462-08	TCGA-BP-4970-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:49396983T>G	uc001rsy.2	-	11	901	c.832A>C	c.(832-834)AAG>CAG	p.K278Q	uc001rsw.2_Intron|PRKAG1_uc010smd.1_Missense_Mutation_p.K246Q|PRKAG1_uc001rsx.2_Missense_Mutation_p.K194Q|PRKAG1_uc001rsz.2_Missense_Mutation_p.K287Q|PRKAG1_uc009zlb.2_Missense_Mutation_p.K90Q	NM_002733	NP_002724	P54619	AAKG1_HUMAN	AMP-activated protein kinase, noncatalytic	278	CBS 4.				cell cycle arrest|fatty acid biosynthetic process|insulin receptor signaling pathway|positive regulation of protein kinase activity|regulation of fatty acid oxidation|regulation of glycolysis|spermatogenesis	cytosol	cAMP-dependent protein kinase activity|cAMP-dependent protein kinase regulator activity|protein kinase binding			kidney(1)	1						AGGTAGCACTTGAGAACACCC	0.502													73	307	---	---	---	---	PASS
C13orf26	122046	broad.mit.edu	37	13	31526903	31526903	+	Missense_Mutation	SNP	G	T	T			TCGA-BP-4970-01A-01D-1462-08	TCGA-BP-4970-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:31526903G>T	uc001uti.2	+	3	272	c.253G>T	c.(253-255)GAT>TAT	p.D85Y		NM_152325	NP_689538	Q8N6G2	CM026_HUMAN	hypothetical protein LOC122046	85										ovary(2)|skin(1)	3		Lung SC(185;0.0281)		all cancers(112;0.0176)|Epithelial(112;0.0768)|OV - Ovarian serous cystadenocarcinoma(117;0.0852)		CTCTAAAGAAGATTTGATCAA	0.328													25	126	---	---	---	---	PASS
FSCB	84075	broad.mit.edu	37	14	44975908	44975908	+	Missense_Mutation	SNP	C	T	T			TCGA-BP-4970-01A-01D-1462-08	TCGA-BP-4970-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:44975908C>T	uc001wvn.2	-	1	592	c.283G>A	c.(283-285)GAA>AAA	p.E95K		NM_032135	NP_115511	Q5H9T9	FSCB_HUMAN	fibrous sheath CABYR binding protein	95						cilium				lung(3)|breast(3)|ovary(2)|central_nervous_system(1)	9				GBM - Glioblastoma multiforme(112;0.128)		GACTTTTCTTCAGGTACCACG	0.398													51	222	---	---	---	---	PASS
TAF1C	9013	broad.mit.edu	37	16	84215586	84215586	+	Missense_Mutation	SNP	G	A	A			TCGA-BP-4970-01A-01D-1462-08	TCGA-BP-4970-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:84215586G>A	uc002fhn.2	-	8	1028	c.800C>T	c.(799-801)CCT>CTT	p.P267L	TAF1C_uc002fhm.2_Missense_Mutation_p.P200L|TAF1C_uc010vnx.1_Missense_Mutation_p.P267L|TAF1C_uc010vny.1_5'UTR|TAF1C_uc010vnz.1_5'UTR|TAF1C_uc002fho.2_5'UTR|TAF1C_uc010voa.1_5'UTR|TAF1C_uc002fhp.1_RNA|TAF1C_uc010vob.1_Missense_Mutation_p.P267L	NM_005679	NP_005670	Q15572	TAF1C_HUMAN	TBP-associated factor 1C isoform 1	267					regulation of transcription, DNA-dependent|termination of RNA polymerase I transcription|transcription elongation from RNA polymerase I promoter|transcription from RNA polymerase II promoter|transcription initiation from RNA polymerase I promoter	nucleoplasm	DNA binding			ovary(1)	1						TTGCCGGACAGGTCCCTGGAG	0.562													33	109	---	---	---	---	PASS
C17orf66	256957	broad.mit.edu	37	17	34182253	34182253	+	Silent	SNP	T	C	C			TCGA-BP-4970-01A-01D-1462-08	TCGA-BP-4970-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:34182253T>C	uc002hke.1	-	15	1676	c.1527A>G	c.(1525-1527)CAA>CAG	p.Q509Q	C17orf66_uc010wck.1_RNA|C17orf66_uc010wcl.1_Silent_p.Q469Q	NM_152781	NP_689994	A2RTY3	CQ066_HUMAN	hypothetical protein LOC256957	509							binding			breast(2)|skin(1)	3		Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0184)		GTCGAAAGTCTTGAATAGTTA	0.468													50	139	---	---	---	---	PASS
OSBPL7	114881	broad.mit.edu	37	17	45894652	45894652	+	Silent	SNP	G	A	A			TCGA-BP-4970-01A-01D-1462-08	TCGA-BP-4970-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:45894652G>A	uc002ilx.1	-	8	875	c.672C>T	c.(670-672)ATC>ATT	p.I224I	OSBPL7_uc002ilw.1_5'Flank	NM_145798	NP_665741	Q9BZF2	OSBL7_HUMAN	oxysterol-binding protein-like protein 7	224					lipid transport		lipid binding				0						GGGCTGAGGGGATTCGGTGCA	0.587													6	45	---	---	---	---	PASS
ACSF2	80221	broad.mit.edu	37	17	48539834	48539834	+	Missense_Mutation	SNP	T	C	C			TCGA-BP-4970-01A-01D-1462-08	TCGA-BP-4970-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:48539834T>C	uc002iqu.2	+	6	784	c.680T>C	c.(679-681)CTG>CCG	p.L227P	ACSF2_uc010wml.1_Missense_Mutation_p.L184P|ACSF2_uc010wmm.1_Missense_Mutation_p.L252P|ACSF2_uc010wmn.1_Missense_Mutation_p.L214P|ACSF2_uc010wmo.1_Missense_Mutation_p.L67P	NM_025149	NP_079425	Q96CM8	ACSF2_HUMAN	acyl-CoA synthetase family member 2 precursor	227					fatty acid metabolic process	mitochondrion	ATP binding|ligase activity				0	Breast(11;1.93e-18)		BRCA - Breast invasive adenocarcinoma(22;1.55e-09)			CCGGGGACCCTGCTCCTGGAT	0.622													9	51	---	---	---	---	PASS
MKS1	54903	broad.mit.edu	37	17	56283522	56283522	+	Missense_Mutation	SNP	C	T	T			TCGA-BP-4970-01A-01D-1462-08	TCGA-BP-4970-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:56283522C>T	uc002ivr.1	-	18	1673	c.1598G>A	c.(1597-1599)CGT>CAT	p.R533H	MKS1_uc010wnq.1_Missense_Mutation_p.R330H|MKS1_uc002ivs.1_3'UTR	NM_017777	NP_060247	Q9NXB0	MKS1_HUMAN	Meckel syndrome type 1 protein isoform 1	533					cilium assembly	centrosome|cilium|microtubule basal body	protein binding			ovary(1)	1						CCGGGCTCGACGGAAGGCCTC	0.612													5	24	---	---	---	---	PASS
B3GNT3	10331	broad.mit.edu	37	19	17918663	17918663	+	Missense_Mutation	SNP	C	A	A			TCGA-BP-4970-01A-01D-1462-08	TCGA-BP-4970-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:17918663C>A	uc002nhk.1	+	2	132	c.47C>A	c.(46-48)GCC>GAC	p.A16D	B3GNT3_uc002nhl.1_Missense_Mutation_p.A16D|B3GNT3_uc010ebd.1_Missense_Mutation_p.A16D|B3GNT3_uc010ebe.1_Missense_Mutation_p.A16D	NM_014256	NP_055071	Q9Y2A9	B3GN3_HUMAN	UDP-GlcNAc:betaGal	16	Helical; Signal-anchor for type II membrane protein; (Potential).				protein glycosylation	Golgi membrane|integral to plasma membrane	galactosyltransferase activity			upper_aerodigestive_tract(1)	1						CTCATTCTGGCCATCGGCGCT	0.667													3	33	---	---	---	---	PASS
DMKN	93099	broad.mit.edu	37	19	36003526	36003526	+	Missense_Mutation	SNP	T	G	G			TCGA-BP-4970-01A-01D-1462-08	TCGA-BP-4970-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:36003526T>G	uc002nzm.3	-	2	776	c.593A>C	c.(592-594)AAT>ACT	p.N198T	DMKN_uc002nzj.2_5'Flank|DMKN_uc002nzk.3_5'Flank|DMKN_uc002nzl.3_5'Flank|DMKN_uc002nzo.3_Missense_Mutation_p.N198T|DMKN_uc002nzn.3_Missense_Mutation_p.N198T|DMKN_uc002nzw.2_5'Flank|DMKN_uc002nzr.2_5'Flank|DMKN_uc002nzp.2_5'Flank|DMKN_uc002nzq.2_5'Flank|DMKN_uc002nzt.2_5'Flank|DMKN_uc002nzs.2_5'Flank|DMKN_uc002nzu.2_5'Flank|DMKN_uc002nzv.2_5'Flank|DMKN_uc010xsv.1_5'Flank|DMKN_uc010xsw.1_5'Flank|DMKN_uc002nzx.3_5'Flank|DMKN_uc002nzy.3_5'Flank|DMKN_uc002nzz.2_5'Flank|DMKN_uc002oac.3_Missense_Mutation_p.N198T|DMKN_uc010eeb.2_Missense_Mutation_p.N198T|DMKN_uc002oaa.3_Missense_Mutation_p.N198T|DMKN_uc002oab.3_Missense_Mutation_p.N198T	NM_033317	NP_201574	Q6E0U4	DMKN_HUMAN	dermokine isoform 2 precursor	198	Gly-rich.			N -> D (in Ref. 3; ABN11273).		extracellular region				large_intestine(1)|ovary(1)|skin(1)	3	all_lung(56;1.89e-08)|Lung NSC(56;2.9e-08)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0724)			TGGCCCTCCATTGCCTCCTTG	0.617													18	70	---	---	---	---	PASS
ZNF614	80110	broad.mit.edu	37	19	52519644	52519644	+	Missense_Mutation	SNP	C	T	T			TCGA-BP-4970-01A-01D-1462-08	TCGA-BP-4970-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:52519644C>T	uc002pyj.2	-	5	1609	c.1207G>A	c.(1207-1209)GAA>AAA	p.E403K	ZNF614_uc002pyi.3_Intron|ZNF614_uc010epj.2_Missense_Mutation_p.E106K	NM_025040	NP_079316	Q8N883	ZN614_HUMAN	zinc finger protein 614	403	C2H2-type 7.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(2)|upper_aerodigestive_tract(1)|pancreas(1)|skin(1)	5		all_neural(266;0.0505)		GBM - Glioblastoma multiforme(134;0.00513)|OV - Ovarian serous cystadenocarcinoma(262;0.0177)		TTTCCACATTCGCTGCATATG	0.423													15	228	---	---	---	---	PASS
TRIM28	10155	broad.mit.edu	37	19	59060112	59060112	+	Missense_Mutation	SNP	G	A	A			TCGA-BP-4970-01A-01D-1462-08	TCGA-BP-4970-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:59060112G>A	uc002qtg.1	+	10	1618	c.1329G>A	c.(1327-1329)ATG>ATA	p.M443I	TRIM28_uc010eut.1_Missense_Mutation_p.M361I|TRIM28_uc002qth.1_Missense_Mutation_p.M66I	NM_005762	NP_005753	Q13263	TIF1B_HUMAN	tripartite motif-containing 28 protein	443					epithelial to mesenchymal transition|positive regulation of transcription, DNA-dependent	nucleoplasm	chromo shadow domain binding|ligase activity|transcription corepressor activity|zinc ion binding			ovary(1)|lung(1)|breast(1)	3		all_cancers(17;4.4e-22)|all_epithelial(17;2.15e-16)|Lung NSC(17;1.24e-06)|all_lung(17;5.41e-06)|Colorectal(82;3.46e-05)|Renal(17;0.00179)|all_neural(62;0.00607)|Ovarian(87;0.0443)|Breast(46;0.0928)|Medulloblastoma(540;0.184)		UCEC - Uterine corpus endometrioid carcinoma (67;0.0434)|all cancers(4;1.39e-13)|Epithelial(4;1.01e-10)|OV - Ovarian serous cystadenocarcinoma(4;2.34e-09)|GBM - Glioblastoma multiforme(193;0.0102)|Lung(386;0.179)		CACAGCCCATGGAGGTGCAGG	0.617													4	25	---	---	---	---	PASS
PIGU	128869	broad.mit.edu	37	20	33225754	33225754	+	Silent	SNP	C	T	T			TCGA-BP-4970-01A-01D-1462-08	TCGA-BP-4970-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:33225754C>T	uc002xas.2	-	5	554	c.354G>A	c.(352-354)CAG>CAA	p.Q118Q	PIGU_uc010zul.1_Silent_p.Q118Q|PIGU_uc002xat.2_Silent_p.Q98Q|PIGU_uc010gev.1_RNA	NM_080476	NP_536724	Q9H490	PIGU_HUMAN	phosphatidylinositol glycan anchor biosynthesis,	118					attachment of GPI anchor to protein|C-terminal protein lipidation|regulation of JAK-STAT cascade	GPI-anchor transamidase complex|plasma membrane					0						CTGGGGCATACTGGTCCAGTT	0.373													9	59	---	---	---	---	PASS
ACOT8	10005	broad.mit.edu	37	20	44477168	44477168	+	Missense_Mutation	SNP	G	T	T			TCGA-BP-4970-01A-01D-1462-08	TCGA-BP-4970-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:44477168G>T	uc002xqa.1	-	3	490	c.409C>A	c.(409-411)CAG>AAG	p.Q137K	ACOT8_uc010zxe.1_Missense_Mutation_p.Q137K|ACOT8_uc002xqc.1_Missense_Mutation_p.Q84K|ACOT8_uc010zxf.1_Intron	NM_005469	NP_005460	O14734	ACOT8_HUMAN	peroxisomal acyl-CoA thioesterase 1 isoform a	137					bile acid biosynthetic process|fatty acid beta-oxidation using acyl-CoA oxidase|interspecies interaction between organisms|peroxisome organization	peroxisomal matrix	acetyl-CoA hydrolase activity|acyl-CoA thioesterase activity|carboxylesterase activity|choloyl-CoA hydrolase activity|protein binding			skin(1)	1		Myeloproliferative disorder(115;0.0122)				AACTGGTGCTGCATGGGGCTG	0.592													40	141	---	---	---	---	PASS
SLC12A5	57468	broad.mit.edu	37	20	44669098	44669098	+	Silent	SNP	C	T	T			TCGA-BP-4970-01A-01D-1462-08	TCGA-BP-4970-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:44669098C>T	uc010zxl.1	+	7	844	c.768C>T	c.(766-768)TAC>TAT	p.Y256Y	SLC12A5_uc002xra.2_Silent_p.Y233Y|SLC12A5_uc010zxm.1_Intron|SLC12A5_uc002xrb.2_Silent_p.Y233Y	NM_001134771	NP_001128243	Q9H2X9	S12A5_HUMAN	solute carrier family 12 (potassium-chloride	256	Helical; (Potential).				potassium ion transport|sodium ion transport	integral to membrane	potassium:chloride symporter activity			ovary(2)|large_intestine(1)|central_nervous_system(1)|skin(1)	5		Myeloproliferative disorder(115;0.0122)			Bumetanide(DB00887)|Potassium Chloride(DB00761)	TGCGTGTTTACGGCACCTGTG	0.547													19	69	---	---	---	---	PASS
INPP5J	27124	broad.mit.edu	37	22	31520974	31520974	+	Silent	SNP	A	T	T			TCGA-BP-4970-01A-01D-1462-08	TCGA-BP-4970-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:31520974A>T	uc003aju.3	+	2	341	c.249A>T	c.(247-249)CGA>CGT	p.R83R	INPP5J_uc010gwf.2_Silent_p.R83R|INPP5J_uc003ajv.3_Intron|INPP5J_uc003ajs.3_Intron|INPP5J_uc011alk.1_Silent_p.R16R|INPP5J_uc010gwg.2_Intron|INPP5J_uc003ajw.2_Intron|INPP5J_uc003ajt.3_Intron|INPP5J_uc003ajx.2_5'Flank|INPP5J_uc003ajy.2_5'Flank|INPP5J_uc003ajz.2_5'Flank	NM_001002837	NP_001002837	Q15735	PI5PA_HUMAN	phosphatidylinositol (4,5) bisphosphate	83						cytoplasm|ruffle	inositol 1,3,4,5-tetrakisphosphate 5-phosphatase activity|inositol-1,4,5-trisphosphate 5-phosphatase activity|inositol-polyphosphate 5-phosphatase activity|SH3 domain binding			skin(1)	1						CATCTCCCCGACCAATCCTGG	0.622													6	9	---	---	---	---	PASS
NBPF10	100132406	broad.mit.edu	37	1	145298606	145298607	+	Intron	INS	-	A	A			TCGA-BP-4970-01A-01D-1462-08	TCGA-BP-4970-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:145298606_145298607insA	uc001end.3	+						NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|NBPF10_uc001emp.3_Intron|NBPF10_uc001emq.1_Intron	NM_001039703	NP_001034792	A6NDV3	A6NDV3_HUMAN	hypothetical protein LOC100132406												0	all_hematologic(923;0.032)			Colorectal(1306;1.36e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.00258)		acaaagaatacaaaaaattagg	0.054													4	3	---	---	---	---	
NBPF10	100132406	broad.mit.edu	37	1	146227920	146227920	+	Intron	DEL	A	-	-			TCGA-BP-4970-01A-01D-1462-08	TCGA-BP-4970-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:146227920delA	uc001emp.3	+							NM_017940	NP_060410	A6NDV3	A6NDV3_HUMAN	hypothetical protein LOC55672												0	all_hematologic(923;0.032)			Colorectal(1306;1.36e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.00258)		CTGAGCCTGGAAAAGTGGGAA	0.458													5	3	---	---	---	---	
ANP32E	81611	broad.mit.edu	37	1	150199259	150199259	+	Intron	DEL	T	-	-			TCGA-BP-4970-01A-01D-1462-08	TCGA-BP-4970-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:150199259delT	uc001etw.2	-						ANP32E_uc010pbt.1_5'Flank|ANP32E_uc010pbu.1_Intron|ANP32E_uc010pbv.1_Intron|ANP32E_uc001etv.3_Intron|ANP32E_uc010pbw.1_Intron	NM_030920	NP_112182	Q9BTT0	AN32E_HUMAN	acidic (leucine-rich) nuclear phosphoprotein 32							cytoplasmic membrane-bounded vesicle|nucleus	phosphatase inhibitor activity				0	Lung NSC(24;7.29e-29)|Breast(34;0.00211)|Ovarian(49;0.0167)|all_hematologic(923;0.0597)|Hepatocellular(266;0.161)|Colorectal(459;0.171)		LUSC - Lung squamous cell carcinoma(543;0.171)			ACAGCGATACTTTTTTTTTTT	0.348													4	2	---	---	---	---	
INTS3	65123	broad.mit.edu	37	1	153742536	153742536	+	Intron	DEL	T	-	-	rs111972686		TCGA-BP-4970-01A-01D-1462-08	TCGA-BP-4970-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:153742536delT	uc009wom.2	+						INTS3_uc001fct.2_Intron|INTS3_uc001fcu.2_Intron|INTS3_uc001fcv.2_Intron|INTS3_uc010peb.1_Intron|INTS3_uc001fcw.2_Intron|INTS3_uc010pec.1_Intron|INTS3_uc001fcy.2_Intron|INTS3_uc001fcx.2_Intron	NM_023015	NP_075391	Q68E01	INT3_HUMAN	integrator complex subunit 3						DNA repair|G2/M transition checkpoint|response to ionizing radiation|snRNA processing	integrator complex|SOSS complex	protein binding			ovary(2)|upper_aerodigestive_tract(1)	3	all_lung(78;3.75e-32)|Lung NSC(65;1.37e-30)|Hepatocellular(266;0.0877)|Melanoma(130;0.199)		LUSC - Lung squamous cell carcinoma(543;0.151)			TGGATTGGGgtgtgtgtgtgt	0.438													10	6	---	---	---	---	
LEFTY1	10637	broad.mit.edu	37	1	226075411	226075411	+	Intron	DEL	C	-	-			TCGA-BP-4970-01A-01D-1462-08	TCGA-BP-4970-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:226075411delC	uc001hpo.2	-						LEFTY1_uc010pvj.1_Intron|LEFTY1_uc009xej.1_3'UTR	NM_020997	NP_066277	O75610	LFTY1_HUMAN	left-right determination, factor B						cell growth|multicellular organismal development|transforming growth factor beta receptor signaling pathway	extracellular space	cytokine activity|growth factor activity|transforming growth factor beta receptor binding				0	Breast(184;0.197)					CCCCGCACCGCCCCCCCGCGT	0.751													4	2	---	---	---	---	
MYO3B	140469	broad.mit.edu	37	2	171258312	171258312	+	Intron	DEL	C	-	-	rs78393302		TCGA-BP-4970-01A-01D-1462-08	TCGA-BP-4970-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:171258312delC	uc002ufy.2	+						MYO3B_uc002ufv.2_Intron|MYO3B_uc010fqb.1_Intron|MYO3B_uc002ufz.2_Intron|MYO3B_uc002ufw.2_Intron|MYO3B_uc002ufx.2_Intron|MYO3B_uc002ugb.2_Intron	NM_138995	NP_620482	Q8WXR4	MYO3B_HUMAN	myosin IIIB isoform 2						response to stimulus|visual perception	cytoplasm|myosin complex	actin binding|ATP binding|motor activity|protein serine/threonine kinase activity			lung(8)|ovary(6)|skin(4)|central_nervous_system(1)	19						ctttctttttctttttttttt	0.234													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	5550718	5550721	+	IGR	DEL	TCCC	-	-			TCGA-BP-4970-01A-01D-1462-08	TCGA-BP-4970-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:5550718_5550721delTCCC								C4orf6 (21193 upstream) : EVC2 (13433 downstream)																							ctttcttccgtccctccctccctc	0.157													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	16972708	16972708	+	IGR	DEL	A	-	-			TCGA-BP-4970-01A-01D-1462-08	TCGA-BP-4970-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:16972708delA								ATXN1 (210987 upstream) : RBM24 (309101 downstream)																							ggaaggaaggaaggaaggaag	0.020													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	17162942	17162943	+	IGR	INS	-	A	A			TCGA-BP-4970-01A-01D-1462-08	TCGA-BP-4970-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:17162942_17162943insA								ATXN1 (401221 upstream) : RBM24 (118866 downstream)																							cagagcaagacaaaaaaaaaaa	0.000													4	2	---	---	---	---	
ISPD	729920	broad.mit.edu	37	7	16298499	16298500	+	Intron	DEL	AT	-	-	rs34926669		TCGA-BP-4970-01A-01D-1462-08	TCGA-BP-4970-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:16298499_16298500delAT	uc010ktx.2	-						ISPD_uc010kty.2_Intron|uc003stf.2_Intron	NM_001101426	NP_001094896	A4D126	ISPD_HUMAN	notch1-induced protein isoform a						isoprenoid biosynthetic process		nucleotidyltransferase activity			ovary(1)	1						TCTCTTCCACATTTGTTCATAT	0.277										Multiple Myeloma(15;0.18)			5	13	---	---	---	---	
CCL26	10344	broad.mit.edu	37	7	75401042	75401043	+	Intron	INS	-	A	A			TCGA-BP-4970-01A-01D-1462-08	TCGA-BP-4970-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:75401042_75401043insA	uc003udt.1	-							NM_006072	NP_006063	Q9Y258	CCL26_HUMAN	chemokine (C-C motif) ligand 26 precursor						cell-cell signaling|chemotaxis|immune response|inflammatory response|positive regulation of actin filament polymerization|positive regulation of cell migration|positive regulation of endothelial cell proliferation|positive regulation of Rac GTPase activity|signal transduction	extracellular space	chemokine activity				0						ctcaaaaagagaaaaaaaaaGT	0.252													4	2	---	---	---	---	
ANKIB1	54467	broad.mit.edu	37	7	91936976	91936976	+	Intron	DEL	T	-	-			TCGA-BP-4970-01A-01D-1462-08	TCGA-BP-4970-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:91936976delT	uc003ulw.2	+							NM_019004	NP_061877	Q9P2G1	AKIB1_HUMAN	ankyrin repeat and IBR domain containing 1								protein binding|zinc ion binding			lung(1)	1	all_cancers(62;2.06e-09)|all_epithelial(64;9.24e-09)|Breast(17;0.0034)|all_lung(186;0.0509)|Lung NSC(181;0.0692)		STAD - Stomach adenocarcinoma(171;6.16e-05)|all cancers(6;0.00183)|Lung(22;0.123)|LUSC - Lung squamous cell carcinoma(200;0.225)			TAGAGGtaaattttttttttt	0.328													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	99738338	99738338	+	IGR	DEL	T	-	-	rs140959495		TCGA-BP-4970-01A-01D-1462-08	TCGA-BP-4970-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:99738338delT								MBLAC1 (12219 upstream) : C7orf59 (8192 downstream)																							CATAGGTCACttttttttttt	0.224													6	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	142750405	142750406	+	IGR	INS	-	C	C	rs151002851	by1000genomes	TCGA-BP-4970-01A-01D-1462-08	TCGA-BP-4970-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:142750405_142750406insC								OR6V1 (27 upstream) : OR6W1P (8975 downstream)																							GGGGAACCTGGCCTGCCTCCAT	0.515													5	3	---	---	---	---	
MSR1	4481	broad.mit.edu	37	8	15978192	15978192	+	Intron	DEL	T	-	-	rs35356880		TCGA-BP-4970-01A-01D-1462-08	TCGA-BP-4970-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:15978192delT	uc003wwz.2	-						MSR1_uc010lsu.2_Intron|MSR1_uc003wxa.2_Intron	NM_138715	NP_619729	P21757	MSRE_HUMAN	macrophage scavenger receptor 1 isoform type 1						cholesterol transport|plasma lipoprotein particle clearance|positive regulation of cholesterol storage|positive regulation of macrophage derived foam cell differentiation|receptor-mediated endocytosis	collagen|integral to plasma membrane|low-density lipoprotein particle	low-density lipoprotein particle binding|protein binding|scavenger receptor activity			ovary(1)	1				Colorectal(111;0.00475)|COAD - Colon adenocarcinoma(73;0.0164)		TTTACAGCACTTTTTTTTTAA	0.279													3	6	---	---	---	---	
CHD7	55636	broad.mit.edu	37	8	61714076	61714076	+	Intron	DEL	T	-	-			TCGA-BP-4970-01A-01D-1462-08	TCGA-BP-4970-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:61714076delT	uc003xue.2	+							NM_017780	NP_060250	Q9P2D1	CHD7_HUMAN	chromodomain helicase DNA binding protein 7						central nervous system development|chromatin modification|cognition|cranial nerve development|face development|heart morphogenesis|in utero embryonic development|inner ear morphogenesis|nose development|palate development|regulation of growth hormone secretion|regulation of transcription, DNA-dependent|retina development in camera-type eye|skeletal system development|T cell differentiation|transcription, DNA-dependent	nucleus	ATP binding|chromatin binding|DNA binding|helicase activity	p.556_871dup(1)		ovary(4)|large_intestine(1)|central_nervous_system(1)|lung(1)|breast(1)|pancreas(1)	9		all_cancers(86;0.2)|all_lung(136;0.0402)|Lung NSC(129;0.0459)|all_epithelial(80;0.0477)	BRCA - Breast invasive adenocarcinoma(89;0.143)			TGCACATGCCTTTTTTTTTAG	0.403													4	2	---	---	---	---	
PRDM14	63978	broad.mit.edu	37	8	70967742	70967744	+	Intron	DEL	TTC	-	-			TCGA-BP-4970-01A-01D-1462-08	TCGA-BP-4970-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:70967742_70967744delTTC	uc003xym.2	-							NM_024504	NP_078780	Q9GZV8	PRD14_HUMAN	PR domain containing 14						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(3)	3	Breast(64;0.193)		Epithelial(68;0.00508)|all cancers(69;0.0259)|OV - Ovarian serous cystadenocarcinoma(28;0.0405)			TCCAAtttttttctttttttttt	0.172													4	2	---	---	---	---	
PVT1	5820	broad.mit.edu	37	8	129015214	129015215	+	Intron	INS	-	CTTC	CTTC			TCGA-BP-4970-01A-01D-1462-08	TCGA-BP-4970-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:129015214_129015215insCTTC	uc010mdq.2	+						PVT1_uc003ysl.2_Intron	NR_003367				Homo sapiens Pvt1 oncogene (non-protein coding), mRNA (cDNA clone IMAGE:5517530), with apparent retained intron.												0						cctccctccctcttccttcctt	0.000													3	3	---	---	---	---	
TOP1MT	116447	broad.mit.edu	37	8	144403622	144403634	+	Intron	DEL	CACACACGCACGC	-	-	rs62524730	by1000genomes	TCGA-BP-4970-01A-01D-1462-08	TCGA-BP-4970-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:144403622_144403634delCACACACGCACGC	uc003yxz.2	-						TOP1MT_uc011lkd.1_Intron|TOP1MT_uc011lke.1_Intron|TOP1MT_uc010mfb.2_Intron|TOP1MT_uc011lkf.1_Intron|TOP1MT_uc010mfd.1_Intron	NM_052963	NP_443195	Q969P6	TOP1M_HUMAN	mitochondrial topoisomerase I precursor						DNA topological change	chromosome|mitochondrial nucleoid	ATP binding|chromatin DNA binding|DNA topoisomerase (ATP-hydrolyzing) activity|DNA topoisomerase type I activity			ovary(1)	1	all_cancers(97;1.01e-10)|all_epithelial(106;4.86e-09)|Lung NSC(106;0.000167)|all_lung(105;0.000459)|Ovarian(258;0.0212)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.156)|Colorectal(110;0.173)		Irinotecan(DB00762)|Topotecan(DB01030)	acgcacgccacacacacgcacgccacacacgca	0.235													6	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	44084399	44084400	+	IGR	INS	-	TAATC	TAATC			TCGA-BP-4970-01A-01D-1462-08	TCGA-BP-4970-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:44084399_44084400insTAATC								FAM75A6 (453669 upstream) : FAM27C (905836 downstream)																							GATAAAGACTATATATAAAAAT	0.277													12	10	---	---	---	---	
KCNT1	57582	broad.mit.edu	37	9	138606581	138606582	+	Intron	INS	-	GG	GG	rs141291153	by1000genomes	TCGA-BP-4970-01A-01D-1462-08	TCGA-BP-4970-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:138606581_138606582insGG	uc011mdq.1	+						KCNT1_uc011mdr.1_Intron|KCNT1_uc010nbf.2_Intron	NM_020822	NP_065873	Q5JUK3	KCNT1_HUMAN	potassium channel, subfamily T, member 1							membrane	binding|calcium-activated potassium channel activity			large_intestine(2)|ovary(1)|pancreas(1)	4		Myeloproliferative disorder(178;0.0821)		OV - Ovarian serous cystadenocarcinoma(145;2.11e-07)|Epithelial(140;1.57e-06)|all cancers(34;9.22e-05)		GGACCGGGCGCGGGGTGGGGGC	0.614													3	3	---	---	---	---	
FRMD4A	55691	broad.mit.edu	37	10	13743623	13743624	+	Intron	DEL	AC	-	-			TCGA-BP-4970-01A-01D-1462-08	TCGA-BP-4970-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:13743623_13743624delAC	uc001ims.2	-						FRMD4A_uc009xjf.1_Intron|FRMD4A_uc001imt.1_Intron|FRMD4A_uc001imu.1_Intron	NM_018027	NP_060497	Q9P2Q2	FRM4A_HUMAN	FERM domain containing 4A							cytoplasm|cytoskeleton	binding			ovary(1)|skin(1)|pancreas(1)	3						ACCTAGGCGTACACACACACAC	0.495													4	2	---	---	---	---	
HNRNPH3	3189	broad.mit.edu	37	10	70097830	70097831	+	Intron	INS	-	T	T	rs141809609	by1000genomes	TCGA-BP-4970-01A-01D-1462-08	TCGA-BP-4970-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:70097830_70097831insT	uc001jnw.3	+						HNRNPH3_uc001jnx.3_Intron|HNRNPH3_uc009xpu.2_5'UTR|HNRNPH3_uc010qiv.1_Intron|HNRNPH3_uc001jny.3_Intron	NM_012207	NP_036339	P31942	HNRH3_HUMAN	heterogeneous nuclear ribonucleoprotein H3						nuclear mRNA splicing, via spliceosome	heterogeneous nuclear ribonucleoprotein complex	nucleotide binding|protein binding|RNA binding			ovary(2)	2						AAATGGGGGGGTAGCCATAACA	0.371													8	5	---	---	---	---	
TCF7L2	6934	broad.mit.edu	37	10	114918647	114918647	+	Intron	DEL	T	-	-			TCGA-BP-4970-01A-01D-1462-08	TCGA-BP-4970-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:114918647delT	uc001lae.3	+						TCF7L2_uc001lac.3_Intron|TCF7L2_uc010qrk.1_Intron|TCF7L2_uc010qrl.1_Intron|TCF7L2_uc010qrm.1_Intron|TCF7L2_uc010qrn.1_Intron|TCF7L2_uc001lad.3_Intron|TCF7L2_uc001lag.3_Intron|TCF7L2_uc001laf.3_Intron|TCF7L2_uc010qro.1_Intron|TCF7L2_uc001lah.2_Intron|TCF7L2_uc010qrp.1_Intron|TCF7L2_uc010qrq.1_Intron|TCF7L2_uc010qrr.1_Intron|TCF7L2_uc010qrs.1_Intron|TCF7L2_uc010qrt.1_Intron|TCF7L2_uc010qru.1_Intron|TCF7L2_uc010qrv.1_Intron|TCF7L2_uc010qrw.1_Intron|TCF7L2_uc010qrx.1_Intron	NM_001146274	NP_001139746	Q9NQB0	TF7L2_HUMAN	transcription factor 7-like 2 isoform 1						anti-apoptosis|blood vessel development|canonical Wnt receptor signaling pathway involved in positive regulation of epithelial to mesenchymal transition|cell cycle arrest|cell proliferation|fat cell differentiation|glucose homeostasis|maintenance of DNA repeat elements|myoblast cell fate commitment|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of sequence-specific DNA binding transcription factor activity|negative regulation of transcription from RNA polymerase II promoter|pancreas development|positive regulation of heparan sulfate proteoglycan biosynthetic process|positive regulation of insulin secretion|positive regulation of protein binding|positive regulation of protein export from nucleus|positive regulation of protein kinase B signaling cascade|positive regulation of transcription from RNA polymerase II promoter|regulation of hormone metabolic process|regulation of smooth muscle cell proliferation|response to glucose stimulus	beta-catenin-TCF7L2 complex|PML body|protein-DNA complex	armadillo repeat domain binding|beta-catenin binding|gamma-catenin binding|nuclear hormone receptor binding|protein kinase binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription factor binding|transcription regulatory region DNA binding			large_intestine(3)|ovary(1)	4		Breast(234;0.058)|Colorectal(252;0.0615)		Epithelial(162;0.00554)|all cancers(201;0.02)		gttgcttctgttttttttttt	0.224													4	2	---	---	---	---	
SBF2	81846	broad.mit.edu	37	11	9861385	9861386	+	Intron	INS	-	T	T			TCGA-BP-4970-01A-01D-1462-08	TCGA-BP-4970-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:9861385_9861386insT	uc001mib.2	-						SBF2_uc001mif.3_Intron|uc001mig.2_Intron	NM_030962	NP_112224	Q86WG5	MTMRD_HUMAN	SET binding factor 2						myelination	cytoplasm|membrane	phosphatase activity|protein binding			upper_aerodigestive_tract(1)|ovary(1)|skin(1)	3				all cancers(16;2.88e-11)|Epithelial(150;3.61e-10)|BRCA - Breast invasive adenocarcinoma(625;0.00887)		GCTCAAAGCAATTGAGGCCTTC	0.441													11	6	---	---	---	---	
STAT6	6778	broad.mit.edu	37	12	57496760	57496761	+	Intron	INS	-	CC	CC			TCGA-BP-4970-01A-01D-1462-08	TCGA-BP-4970-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:57496760_57496761insCC	uc009zpe.2	-						STAT6_uc009zpf.2_Intron|STAT6_uc001sna.2_Intron|STAT6_uc010srb.1_Intron|STAT6_uc010src.1_Intron|STAT6_uc010srd.1_Intron|STAT6_uc009zpg.2_Intron	NM_003153	NP_003144	P42226	STAT6_HUMAN	signal transducer and activator of transcription						regulation of transcription from RNA polymerase II promoter	cytosol|nucleus	calcium ion binding|DNA binding|protein binding|sequence-specific DNA binding transcription factor activity|signal transducer activity			ovary(2)|lung(1)|skin(1)	4						tttttttttttttttttttttt	0.208													4	2	---	---	---	---	
TMPO	7112	broad.mit.edu	37	12	98925325	98925326	+	Intron	INS	-	T	T			TCGA-BP-4970-01A-01D-1462-08	TCGA-BP-4970-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:98925325_98925326insT	uc001tfj.2	+						TMPO_uc001tfi.1_Intron|TMPO_uc001tfk.2_Intron|TMPO_uc001tfl.2_Intron|TMPO_uc001tfh.1_Intron	NM_001032283	NP_001027454	P42167	LAP2B_HUMAN	thymopoietin isoform beta							integral to membrane|nuclear inner membrane	DNA binding|lamin binding			ovary(2)	2						ATTATATGGTATTTTTTTTTTT	0.163													4	2	---	---	---	---	
CHPT1	56994	broad.mit.edu	37	12	102113732	102113733	+	Intron	INS	-	TAAA	TAAA	rs143042949	by1000genomes	TCGA-BP-4970-01A-01D-1462-08	TCGA-BP-4970-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:102113732_102113733insTAAA	uc001tin.2	+						CHPT1_uc001tio.2_Intron|CHPT1_uc001tip.1_Intron	NM_020244	NP_064629	Q8WUD6	CHPT1_HUMAN	choline phosphotransferase 1						platelet activating factor biosynthetic process|regulation of cell growth	Golgi membrane|integral to membrane|microsome	diacylglycerol binding|diacylglycerol cholinephosphotransferase activity|metal ion binding				0						aaaaaaaaagttaaaaaaaagt	0.139													6	3	---	---	---	---	
TUBGCP4	27229	broad.mit.edu	37	15	43690581	43690582	+	Intron	DEL	AA	-	-	rs150462033		TCGA-BP-4970-01A-01D-1462-08	TCGA-BP-4970-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:43690581_43690582delAA	uc001zro.2	+						TUBGCP4_uc001zrn.2_Intron|TUBGCP4_uc010bdh.2_Intron	NM_014444	NP_055259	Q9UGJ1	GCP4_HUMAN	tubulin, gamma complex associated protein 4						G2/M transition of mitotic cell cycle|microtubule nucleation|protein complex assembly	centrosome|cytosol|gamma-tubulin ring complex|microtubule|spindle pole	structural constituent of cytoskeleton			ovary(3)	3		all_cancers(109;1.27e-10)|all_epithelial(112;4.82e-09)|Lung NSC(122;1.72e-06)|all_lung(180;1.59e-05)|Melanoma(134;0.0728)		GBM - Glioblastoma multiforme(94;3.53e-07)		cccatctcataaaaaaaaaaaa	0.089													6	3	---	---	---	---	
OTOA	146183	broad.mit.edu	37	16	21725621	21725622	+	Intron	INS	-	CTTCCTTC	CTTCCTTC	rs34598445		TCGA-BP-4970-01A-01D-1462-08	TCGA-BP-4970-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:21725621_21725622insCTTCCTTC	uc002djh.2	+						uc002diq.3_Intron|OTOA_uc010vbj.1_Intron|OTOA_uc002dji.2_Intron|OTOA_uc010vbk.1_Intron	NM_144672	NP_653273	Q7RTW8	OTOAN_HUMAN	otoancorin isoform 1						sensory perception of sound	anchored to membrane|apical plasma membrane|proteinaceous extracellular matrix				ovary(1)|central_nervous_system(1)|skin(1)	3				GBM - Glioblastoma multiforme(48;0.0414)		tcttttcctttcttccttcctt	0.000													6	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	32399771	32399772	+	IGR	DEL	TG	-	-			TCGA-BP-4970-01A-01D-1462-08	TCGA-BP-4970-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:32399771_32399772delTG								HERC2P4 (235897 upstream) : TP53TG3B (285069 downstream)																							atttgctgtatgtgtgtgtgtg	0.193													13	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	33942128	33942129	+	IGR	INS	-	T	T	rs76660512	by1000genomes	TCGA-BP-4970-01A-01D-1462-08	TCGA-BP-4970-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:33942128_33942129insT								None (None upstream) : MIR1826 (23379 downstream)																							TGGAAAAAATACCACTTGTTAC	0.267													4	3	---	---	---	---	
ATP6V0A1	535	broad.mit.edu	37	17	40647391	40647391	+	Intron	DEL	T	-	-			TCGA-BP-4970-01A-01D-1462-08	TCGA-BP-4970-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:40647391delT	uc002hzr.2	+						ATP6V0A1_uc002hzq.2_Intron|ATP6V0A1_uc002hzs.2_Intron|ATP6V0A1_uc010wgj.1_Intron|ATP6V0A1_uc010wgk.1_Intron|ATP6V0A1_uc010cyg.2_Intron|ATP6V0A1_uc010wgl.1_Intron	NM_001130021	NP_001123493	Q93050	VPP1_HUMAN	ATPase, H+ transporting, lysosomal V0 subunit a1						ATP hydrolysis coupled proton transport|cellular iron ion homeostasis|insulin receptor signaling pathway|transferrin transport	cytoplasmic vesicle membrane|endosome membrane|Golgi apparatus|integral to membrane|melanosome|nucleus|plasma membrane|proton-transporting two-sector ATPase complex, proton-transporting domain	ATPase binding|hydrogen ion transmembrane transporter activity			pancreas(1)	1		all_cancers(22;1.18e-05)|Breast(137;0.000105)|all_epithelial(22;0.000254)		BRCA - Breast invasive adenocarcinoma(366;0.137)		TTAGAAATGATTTTTTTTTTT	0.363													6	4	---	---	---	---	
HDAC5	10014	broad.mit.edu	37	17	42165217	42165217	+	Intron	DEL	T	-	-			TCGA-BP-4970-01A-01D-1462-08	TCGA-BP-4970-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:42165217delT	uc002ifd.1	-						HDAC5_uc002ife.1_Intron|HDAC5_uc002iff.1_Intron|HDAC5_uc010czp.1_Intron|HDAC5_uc002ifg.1_5'Flank|HDAC5_uc002ifh.2_Intron	NM_005474	NP_005465	Q9UQL6	HDAC5_HUMAN	histone deacetylase 5 isoform 1						B cell differentiation|cellular response to insulin stimulus|chromatin remodeling|chromatin silencing|inflammatory response|negative regulation of cell migration involved in sprouting angiogenesis|negative regulation of myotube differentiation|negative regulation of transcription from RNA polymerase II promoter|positive regulation of sequence-specific DNA binding transcription factor activity|positive regulation of transcription from RNA polymerase II promoter|regulation of protein binding|transcription, DNA-dependent	cytoplasm|histone deacetylase complex	histone deacetylase activity (H3-K16 specific)|NAD-dependent histone deacetylase activity (H3-K14 specific)|NAD-dependent histone deacetylase activity (H3-K9 specific)|NAD-dependent histone deacetylase activity (H4-K16 specific)|protein kinase C binding|repressing transcription factor binding			ovary(1)	1		Breast(137;0.00637)|Prostate(33;0.0313)		BRCA - Breast invasive adenocarcinoma(366;0.118)		CTGAGAGGACttttttttttt	0.239													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	110425	110425	+	Intron	DEL	G	-	-	rs28886940		TCGA-BP-4970-01A-01D-1462-08	TCGA-BP-4970-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:110425delG	uc002kke.2	+											Homo sapiens Rho-associated, coiled-coil containing protein kinase 1, mRNA (cDNA clone IMAGE:5269982), complete cds.																		tgtaactcttgtctaggctct	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	63778855	63778858	+	IGR	DEL	GAAG	-	-			TCGA-BP-4970-01A-01D-1462-08	TCGA-BP-4970-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:63778855_63778858delGAAG								CDH7 (230681 upstream) : CDH19 (392463 downstream)																							aaggaagaaagaaggaaggaagga	0.000													8	9	---	---	---	---	
CCDC102B	79839	broad.mit.edu	37	18	66503861	66503862	+	Intron	INS	-	A	A	rs149330255	by1000genomes	TCGA-BP-4970-01A-01D-1462-08	TCGA-BP-4970-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:66503861_66503862insA	uc002lkk.2	+						CCDC102B_uc002lki.2_Intron|CCDC102B_uc002lkj.1_Intron	NM_001093729	NP_001087198	Q68D86	C102B_HUMAN	coiled-coil domain containing 102B											ovary(1)|lung(1)|skin(1)	3		Esophageal squamous(42;0.0559)|Colorectal(73;0.0604)				aagactctgtcaaaaataaaaa	0.119													4	3	---	---	---	---	
BSG	682	broad.mit.edu	37	19	580992	581005	+	Intron	DEL	CCCGGACCCAGCCC	-	-	rs12977361		TCGA-BP-4970-01A-01D-1462-08	TCGA-BP-4970-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:580992_581005delCCCGGACCCAGCCC	uc002loz.2	+						BSG_uc002loy.2_Intron|BSG_uc002lpa.2_Intron|BSG_uc002lpb.2_Intron|BSG_uc010drr.2_Intron|BSG_uc002lpc.2_Intron|BSG_uc002lpd.2_5'Flank	NM_001728	NP_001719	P35613	BASI_HUMAN	basigin isoform 1 precursor						blood coagulation|cell surface receptor linked signaling pathway|leukocyte migration|pyruvate metabolic process	Golgi membrane|integral to membrane|melanosome	lactate transmembrane transporter activity|mannose binding|protein binding				0		all_epithelial(18;2.78e-22)|Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;3.55e-06)|all_lung(49;5.41e-06)|Breast(49;4.08e-05)|Hepatocellular(1079;0.137)|Renal(1328;0.228)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		GACTGGGGGTCCCGGACCCAGCCCTCCGGACTGG	0.729													4	3	---	---	---	---	
TYK2	7297	broad.mit.edu	37	19	10477410	10477411	+	Intron	DEL	AA	-	-			TCGA-BP-4970-01A-01D-1462-08	TCGA-BP-4970-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:10477410_10477411delAA	uc002moc.3	-						TYK2_uc010dxe.2_Intron|TYK2_uc002mod.2_Intron	NM_003331	NP_003322	P29597	TYK2_HUMAN	tyrosine kinase 2						intracellular protein kinase cascade|regulation of type I interferon-mediated signaling pathway|type I interferon-mediated signaling pathway	cytoskeleton|cytosol|membrane|nucleus	ATP binding|growth hormone receptor binding|non-membrane spanning protein tyrosine kinase activity			lung(5)|large_intestine(2)|ovary(1)|breast(1)	9			OV - Ovarian serous cystadenocarcinoma(20;1.77e-09)|Epithelial(33;3.92e-06)|all cancers(31;8.95e-06)			ctgatgagctaaaaaaaaaaaa	0.015													3	3	---	---	---	---	
CIB3	117286	broad.mit.edu	37	19	16283777	16283780	+	Intron	DEL	GAAG	-	-	rs3076228		TCGA-BP-4970-01A-01D-1462-08	TCGA-BP-4970-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:16283777_16283780delGAAG	uc002nds.2	-						CIB3_uc010eae.2_Intron|CIB3_uc010eaf.2_Intron|CIB3_uc010eag.2_Intron	NM_054113	NP_473454	Q96Q77	CIB3_HUMAN	DNA-dependent protein kinase catalytic								calcium ion binding			ovary(1)	1						aaaaagaaaagaaggaaggaagga	0.020													4	4	---	---	---	---	
SPHK2	56848	broad.mit.edu	37	19	49133064	49133085	+	3'UTR	DEL	GCCTACATTCCAATGGGGCGGA	-	-			TCGA-BP-4970-01A-01D-1462-08	TCGA-BP-4970-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:49133064_49133085delGCCTACATTCCAATGGGGCGGA	uc002pjr.2	+	7					SPHK2_uc010xzt.1_3'UTR|SPHK2_uc002pjs.2_3'UTR|SPHK2_uc002pjt.2_3'UTR|SPHK2_uc002pju.2_Intron|SPHK2_uc002pjv.2_3'UTR|SPHK2_uc002pjw.2_Intron	NM_020126	NP_064511	Q9NRA0	SPHK2_HUMAN	sphingosine kinase 2						activation of protein kinase C activity by G-protein coupled receptor protein signaling pathway|anti-apoptosis|cell proliferation|sphinganine-1-phosphate biosynthetic process	cytosol|lysosomal membrane|membrane fraction	ATP binding|D-erythro-sphingosine kinase activity|diacylglycerol kinase activity|Ras GTPase binding|sphinganine kinase activity			lung(1)	1		all_lung(116;0.000125)|Lung NSC(112;0.000202)|all_epithelial(76;0.000283)|all_neural(266;0.0506)|Ovarian(192;0.113)		OV - Ovarian serous cystadenocarcinoma(262;0.000102)|all cancers(93;0.000117)|GBM - Glioblastoma multiforme(486;0.00627)|Epithelial(262;0.0158)		CGGGGGCGGGGCCTACATTCCAATGGGGCGGAGCCTGAGCTA	0.653													8	7	---	---	---	---	
TNNT1	7138	broad.mit.edu	37	19	55646746	55646749	+	Intron	DEL	TTCC	-	-			TCGA-BP-4970-01A-01D-1462-08	TCGA-BP-4970-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:55646746_55646749delTTCC	uc002qjb.3	-						TNNT1_uc002qiz.3_Intron|TNNT1_uc002qja.3_Intron|TNNT1_uc002qjc.3_Intron|TNNT1_uc002qje.3_Intron|TNNT1_uc002qjd.3_Intron	NM_003283	NP_003274	P13805	TNNT1_HUMAN	troponin T1, skeletal, slow isoform a						muscle filament sliding|negative regulation of muscle contraction	cytosol|troponin complex	tropomyosin binding			ovary(1)	1			BRCA - Breast invasive adenocarcinoma(297;0.209)	GBM - Glioblastoma multiforme(193;0.047)		aaacctacctttccttccttcctt	0.000													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	2056532	2056532	+	IGR	DEL	A	-	-			TCGA-BP-4970-01A-01D-1462-08	TCGA-BP-4970-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:2056532delA								PDYN (81829 upstream) : STK35 (25996 downstream)																							TCTCAAACGGAAAAAAAAAAA	0.209													6	3	---	---	---	---	
NCRNA00176	284739	broad.mit.edu	37	20	62669916	62669917	+	Intron	INS	-	CCGGG	CCGGG			TCGA-BP-4970-01A-01D-1462-08	TCGA-BP-4970-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:62669916_62669917insCCGGG	uc002yhq.2	+						NCRNA00176_uc011abq.1_RNA|NCRNA00176_uc010gko.2_Intron	NR_027686				Homo sapiens cDNA FLJ27267 fis, clone TMS00367.												0						CGTCTCCCTTcccgggccgggc	0.644													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	33157638	33157640	+	IGR	DEL	CAT	-	-	rs112554433	by1000genomes	TCGA-BP-4970-01A-01D-1462-08	TCGA-BP-4970-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:33157638_33157640delCAT								SFRS15 (53207 upstream) : HUNK (87988 downstream)																							ccaccaccaccatcaccatcacc	0.000													3	3	---	---	---	---	
PKNOX1	5316	broad.mit.edu	37	21	44424347	44424348	+	Intron	INS	-	A	A			TCGA-BP-4970-01A-01D-1462-08	TCGA-BP-4970-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:44424347_44424348insA	uc002zcq.1	+						PKNOX1_uc002zcp.1_Intron|PKNOX1_uc011aex.1_Intron|PKNOX1_uc002zcr.2_5'Flank	NM_004571	NP_004562	P55347	PKNX1_HUMAN	PBX/knotted 1 homeobox 1								sequence-specific DNA binding			large_intestine(2)	2						aactcggtctcaaaaaaaaaaa	0.163													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	29263225	29263228	+	IGR	DEL	GAAA	-	-	rs59295229		TCGA-BP-4970-01A-01D-1462-08	TCGA-BP-4970-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:29263225_29263228delGAAA								XBP1 (66665 upstream) : ZNRF3 (16662 downstream)																							aggaaggaaggaaagaaagaaaga	0.093													3	4	---	---	---	---	
XG	7499	broad.mit.edu	37	X	2683418	2683425	+	Intron	DEL	GGAAGGAA	-	-			TCGA-BP-4970-01A-01D-1462-08	TCGA-BP-4970-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:2683418_2683425delGGAAGGAA	uc011mhg.1	+						XG_uc010ndb.2_Intron|XG_uc004cqp.2_Intron	NM_175569	NP_780778	P55808	XG_HUMAN	XG glycoprotein isoform 1 precursor							integral to membrane|plasma membrane				ovary(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)				agggagggagggaaggaaggaaggaagg	0.135													6	3	---	---	---	---	
TSPAN6	7105	broad.mit.edu	37	X	99887403	99887403	+	Intron	DEL	A	-	-			TCGA-BP-4970-01A-01D-1462-08	TCGA-BP-4970-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:99887403delA	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						actccatctcaaaaaaaaaaa	0.159													4	2	---	---	---	---	
ZDHHC9	51114	broad.mit.edu	37	X	128948898	128948898	+	Intron	DEL	T	-	-			TCGA-BP-4970-01A-01D-1462-08	TCGA-BP-4970-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:128948898delT	uc004euv.2	-						ZDHHC9_uc004euw.2_Intron|ZDHHC9_uc004eux.1_Intron|ZDHHC9_uc004euy.1_Intron	NM_001008222	NP_001008223	Q9Y397	ZDHC9_HUMAN	zinc finger, DHHC domain containing 9							endoplasmic reticulum membrane|Golgi membrane|integral to membrane	acyltransferase activity|zinc ion binding			ovary(1)	1						AAATATAGGGTTTTTTTTTTT	0.189													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	Y	3720516	3720517	+	IGR	INS	-	T	T	rs35895769		TCGA-BP-4970-01A-01D-1462-08	TCGA-BP-4970-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:3720516_3720517insT								TGIF2LY (272436 upstream) : None (None downstream)																							TTTTTTTCCCATTTTTTCTCTT	0.347													5	3	---	---	---	---	
