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	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	validation_status	validation_method	validation_tumor_sample	validation_alt_allele
KIAA1751	85452	broad.mit.edu	37	1	1896229	1896229	+	Intron	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:1896229delA	uc001aim.1	-						KIAA1751_uc009vkz.1_Intron	NM_001080484	NP_001073953			hypothetical protein LOC85452											pancreas(1)	1	all_cancers(77;0.000708)|all_epithelial(69;0.000943)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;6.04e-15)|all_lung(118;9.67e-07)|Lung NSC(185;5.59e-05)|Renal(390;0.00571)|Breast(487;0.0183)|Hepatocellular(190;0.0268)|Myeloproliferative disorder(586;0.028)|Ovarian(437;0.127)|Medulloblastoma(700;0.151)|Lung SC(97;0.217)		Epithelial(90;8.79e-39)|OV - Ovarian serous cystadenocarcinoma(86;9.61e-25)|GBM - Glioblastoma multiforme(42;1.2e-07)|Colorectal(212;4.84e-05)|COAD - Colon adenocarcinoma(227;0.000214)|Kidney(185;0.00254)|BRCA - Breast invasive adenocarcinoma(365;0.00461)|STAD - Stomach adenocarcinoma(132;0.00645)|KIRC - Kidney renal clear cell carcinoma(229;0.037)|Lung(427;0.205)														---	---	---	---
TNFRSF1B	7133	broad.mit.edu	37	1	12251283	12251284	+	Intron	INS	-	A	A			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:12251283_12251284insA	uc001att.2	+						TNFRSF1B_uc001atu.2_Intron|TNFRSF1B_uc009vnk.2_Intron	NM_001066	NP_001057			tumor necrosis factor receptor 2 precursor						apoptosis	extracellular region|integral to membrane|membrane raft|plasma membrane	tumor necrosis factor receptor activity			liver(1)|central_nervous_system(1)|skin(1)	3	Ovarian(185;0.249)	Lung NSC(185;8.72e-05)|all_lung(284;9.92e-05)|Renal(390;0.000147)|Colorectal(325;0.000584)|Breast(348;0.00093)|Ovarian(437;0.00965)|Hepatocellular(190;0.0202)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0234)|Colorectal(212;5.52e-07)|COAD - Colon adenocarcinoma(227;0.000345)|BRCA - Breast invasive adenocarcinoma(304;0.000353)|Kidney(185;0.00102)|KIRC - Kidney renal clear cell carcinoma(229;0.00302)|STAD - Stomach adenocarcinoma(313;0.00815)|READ - Rectum adenocarcinoma(331;0.0284)	Etanercept(DB00005)|Infliximab(DB00065)													---	---	---	---
CLCNKA	1187	broad.mit.edu	37	1	16355578	16355578	+	Intron	DEL	G	-	-	rs71774158		TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:16355578delG	uc001axu.2	+						CLCNKA_uc001axt.2_Intron|CLCNKA_uc001axv.2_Intron|CLCNKA_uc010obw.1_Intron|CLCNKB_uc001axw.3_Intron|CLCNKA_uc010obx.1_Intron|CLCNKA_uc010oby.1_Intron	NM_004070	NP_004061			chloride channel Ka isoform 1						excretion	chloride channel complex|integral to plasma membrane	voltage-gated chloride channel activity			ovary(1)	1		Colorectal(325;3.46e-05)|Breast(348;0.000278)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.000567)|Ovarian(437;0.0221)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|Colorectal(212;8.04e-08)|COAD - Colon adenocarcinoma(227;5.46e-06)|BRCA - Breast invasive adenocarcinoma(304;9.02e-05)|Kidney(64;0.00016)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(313;0.00655)|READ - Rectum adenocarcinoma(331;0.0649)	Niflumic Acid(DB04552)													---	---	---	---
EPHA8	2046	broad.mit.edu	37	1	22928009	22928009	+	Intron	DEL	G	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:22928009delG	uc001bfx.1	+							NM_020526	NP_065387			ephrin receptor EphA8 isoform 1 precursor							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)														---	---	---	---
RPS6KA1	6195	broad.mit.edu	37	1	26900934	26900934	+	3'UTR	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:26900934delA	uc001bmr.1	+	22					RPS6KA1_uc010ofe.1_3'UTR|RPS6KA1_uc001bms.1_3'UTR|RPS6KA1_uc009vsl.1_3'UTR	NM_002953	NP_002944			ribosomal protein S6 kinase, 90kDa, polypeptide						axon guidance|innate immune response|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|nerve growth factor receptor signaling pathway|stress-activated MAPK cascade|synaptic transmission|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway	cytosol|nucleoplasm	ATP binding|caspase inhibitor activity|magnesium ion binding|protein binding|protein serine/threonine kinase activity			lung(1)	1		all_cancers(24;2.49e-24)|Colorectal(325;3.46e-05)|all_lung(284;4.76e-05)|Lung NSC(340;5.83e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Breast(348;0.00571)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|Epithelial(14;1.12e-50)|OV - Ovarian serous cystadenocarcinoma(117;2.89e-29)|Colorectal(126;1.4e-08)|COAD - Colon adenocarcinoma(152;9.31e-07)|BRCA - Breast invasive adenocarcinoma(304;0.000537)|KIRC - Kidney renal clear cell carcinoma(1967;0.000759)|STAD - Stomach adenocarcinoma(196;0.00151)|GBM - Glioblastoma multiforme(114;0.0361)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.161)|LUSC - Lung squamous cell carcinoma(448;0.234)														---	---	---	---
PHACTR4	65979	broad.mit.edu	37	1	28817356	28817356	+	Intron	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:28817356delA	uc001bpw.2	+						PHACTR4_uc001bpv.1_Intron|PHACTR4_uc001bpx.2_Intron|PHACTR4_uc001bpy.2_Intron|PHACTR4_uc001bpz.2_5'Flank	NM_001048183	NP_001041648			phosphatase and actin regulator 4 isoform 1								actin binding|protein phosphatase inhibitor activity				0		Colorectal(325;3.46e-05)|Lung NSC(340;4.37e-05)|all_lung(284;7.01e-05)|Renal(390;0.00121)|Breast(348;0.00345)|all_neural(195;0.0208)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0261)		OV - Ovarian serous cystadenocarcinoma(117;1.35e-21)|Colorectal(126;2.96e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|KIRC - Kidney renal clear cell carcinoma(1967;0.00273)|STAD - Stomach adenocarcinoma(196;0.00299)|BRCA - Breast invasive adenocarcinoma(304;0.0144)|READ - Rectum adenocarcinoma(331;0.0649)														---	---	---	---
EPB41	2035	broad.mit.edu	37	1	29320170	29320170	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:29320170delT	uc001brm.1	+						EPB41_uc001brg.1_Intron|EPB41_uc001brh.1_Intron|EPB41_uc001bri.1_Intron|EPB41_uc001brj.1_Intron|EPB41_uc009vtk.1_Intron|EPB41_uc001brk.2_Intron|EPB41_uc001brl.1_Intron|EPB41_uc009vtl.1_Intron|EPB41_uc009vtm.1_Intron	NM_203342	NP_976217			erythrocyte membrane protein band 4.1						blood circulation|cortical actin cytoskeleton organization|positive regulation of protein binding	extrinsic to membrane|Golgi apparatus|nucleus|plasma membrane|protein complex|spectrin|spectrin-associated cytoskeleton	1-phosphatidylinositol binding|actin binding|spectrin binding|structural constituent of cytoskeleton			ovary(1)	1		Colorectal(325;3.46e-05)|Prostate(1639;0.000244)|Lung NSC(340;0.00328)|all_lung(284;0.00412)|Breast(348;0.00765)|all_neural(195;0.0199)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)|Medulloblastoma(700;0.123)		Colorectal(126;3.12e-07)|COAD - Colon adenocarcinoma(152;1.21e-05)|STAD - Stomach adenocarcinoma(196;0.00395)|KIRC - Kidney renal clear cell carcinoma(1967;0.0249)|BRCA - Breast invasive adenocarcinoma(304;0.0289)|READ - Rectum adenocarcinoma(331;0.0757)														---	---	---	---
CDCA8	55143	broad.mit.edu	37	1	38170966	38170966	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:38170966delT	uc001cbr.2	+						CDCA8_uc001cbs.2_Intron|CDCA8_uc010oih.1_Intron	NM_018101	NP_060571			cell division cycle associated 8						cell division|chromosome organization|mitotic metaphase|mitotic prometaphase	chromosome passenger complex|chromosome, centromeric region|cytosol|nucleolus|spindle	protein binding			central_nervous_system(1)	1		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.164)																---	---	---	---
MED8	112950	broad.mit.edu	37	1	43850143	43850143	+	Frame_Shift_Del	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:43850143delT	uc001cje.1	-	8	932	c.884delA	c.(883-885)AATfs	p.N295fs		NM_052877	NP_443109	Q96G25	MED8_HUMAN	mediator complex subunit 8 isoform 3	Error:Variant_position_missing_in_Q96G25_after_alignment					regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	mediator complex					0	all_hematologic(146;0.0958)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0333)																---	---	---	---
ST3GAL3	6487	broad.mit.edu	37	1	44360318	44360318	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:44360318delT	uc001ckc.2	+						ST3GAL3_uc010okj.1_Intron|ST3GAL3_uc001cjz.2_Intron|ST3GAL3_uc001cka.2_Intron|ST3GAL3_uc001ckb.2_Intron|ST3GAL3_uc001ckd.2_Intron|ST3GAL3_uc001cke.2_Intron|ST3GAL3_uc001ckf.2_Intron|ST3GAL3_uc001ckg.2_Intron|ST3GAL3_uc001ckh.2_Intron|ST3GAL3_uc001cki.2_Intron|ST3GAL3_uc009vwv.2_Intron|ST3GAL3_uc001ckj.2_Intron|ST3GAL3_uc009vww.2_Intron|ST3GAL3_uc001ckk.2_Intron|ST3GAL3_uc009vwy.2_Intron|ST3GAL3_uc009vwx.2_Intron|ST3GAL3_uc001ckm.2_Intron|ST3GAL3_uc001ckl.2_Intron|ST3GAL3_uc009vwz.2_Intron|ST3GAL3_uc001ckn.2_Intron|ST3GAL3_uc001ckp.2_Intron|ST3GAL3_uc001cko.2_Intron|ST3GAL3_uc009vxa.2_Intron|ST3GAL3_uc001ckq.2_Intron|ST3GAL3_uc001ckr.2_Intron|ST3GAL3_uc009vxb.2_Intron	NM_006279	NP_006270			sialyltransferase 6 isoform j						protein glycosylation	extracellular region|Golgi cisterna membrane|integral to Golgi membrane	N-acetyllactosaminide alpha-2,3-sialyltransferase activity			ovary(3)	3	Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0518)																---	---	---	---
CYP4Z2P	163720	broad.mit.edu	37	1	47339125	47339125	+	Intron	DEL	C	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:47339125delC	uc001cqo.1	-						CYP4Z2P_uc009vyn.1_Intron	NR_002788				Homo sapiens cDNA FLJ40054 fis, clone TBAES2000315, weakly similar to CYTOCHROME P450 4A1 (EC 1.14.15.3).												0																		---	---	---	---
DAB1	1600	broad.mit.edu	37	1	57498845	57498846	+	Intron	DEL	AC	-	-	rs66580844		TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:57498845_57498846delAC	uc001cys.1	-						DAB1_uc001cyt.1_Intron|DAB1_uc001cyq.1_Intron|DAB1_uc001cyr.1_Intron|DAB1_uc009vzw.1_Intron|DAB1_uc009vzx.1_Intron	NM_021080	NP_066566			disabled homolog 1						cell differentiation|nervous system development					skin(2)|ovary(1)	3																		---	---	---	---
CTH	1491	broad.mit.edu	37	1	70895655	70895655	+	Intron	DEL	A	-	-	rs144207053		TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:70895655delA	uc001dfd.2	+						CTH_uc009wbl.1_Intron|CTH_uc001dfe.2_Intron|CTH_uc010oqq.1_Intron	NM_001902	NP_001893			cystathionase isoform 1						cysteine biosynthetic process|hydrogen sulfide biosynthetic process|protein homotetramerization|protein-pyridoxal-5-phosphate linkage via peptidyl-N6-pyridoxal phosphate-L-lysine	cytoplasm|nucleus	cystathionine gamma-lyase activity|L-cysteine desulfhydrase activity|pyridoxal phosphate binding			lung(1)	1					L-Cysteine(DB00151)|Pyridoxal Phosphate(DB00114)													---	---	---	---
Unknown	0	broad.mit.edu	37	1	78240627	78240627	+	IGR	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:78240627delT								USP33 (15090 upstream) : FAM73A (4682 downstream)																																			---	---	---	---
CCDC18	343099	broad.mit.edu	37	1	93692050	93692050	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:93692050delT	uc001dpq.2	+						CCDC18_uc009wdl.1_Intron	NM_206886	NP_996769			sarcoma antigen NY-SAR-41											ovary(2)|breast(2)|pancreas(1)	5		all_lung(203;0.00196)|Lung NSC(277;0.00903)|Melanoma(281;0.099)|all_neural(321;0.185)|Glioma(108;0.203)		all cancers(265;0.00166)|GBM - Glioblastoma multiforme(16;0.00551)|Epithelial(280;0.0967)														---	---	---	---
SASS6	163786	broad.mit.edu	37	1	100572825	100572825	+	Intron	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:100572825delA	uc001dsu.2	-						SASS6_uc009wdz.2_Intron	NM_194292	NP_919268			spindle assembly abnormal protein 6						centriole replication	centriole				upper_aerodigestive_tract(1)|ovary(1)	2		all_epithelial(167;4.58e-06)|all_lung(203;0.00125)|Lung NSC(277;0.00131)		Epithelial(280;0.085)|all cancers(265;0.139)|COAD - Colon adenocarcinoma(174;0.15)|Lung(183;0.197)														---	---	---	---
MOV10	4343	broad.mit.edu	37	1	113238691	113238691	+	Intron	DEL	G	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:113238691delG	uc001eck.2	+						MOV10_uc001ecl.2_Intron|MOV10_uc001ecn.2_Intron|MOV10_uc001ecm.2_Intron|MOV10_uc009wgj.1_Intron	NM_001130079	NP_001123551			Mov10, Moloney leukemia virus 10, homolog						mRNA cleavage involved in gene silencing by miRNA|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasmic mRNA processing body	ATP binding|helicase activity|protein binding|RNA binding			ovary(4)|skin(1)	5	Lung SC(450;0.246)	all_cancers(81;3.31e-11)|all_epithelial(167;5.69e-10)|all_lung(203;3.73e-05)|Breast(1374;0.000525)|Lung NSC(69;0.000954)|Ovarian(761;0.0367)|Lung SC(238;0.114)		OV - Ovarian serous cystadenocarcinoma(397;3.99e-67)|all cancers(265;1e-62)|Epithelial(280;4.78e-61)|Lung(183;0.0234)|Colorectal(144;0.0686)|READ - Rectum adenocarcinoma(129;0.0929)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)|BRCA - Breast invasive adenocarcinoma(282;0.24)														---	---	---	---
LRIG2	9860	broad.mit.edu	37	1	113635953	113635953	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:113635953delT	uc001edf.1	+						LRIG2_uc009wgn.1_Intron	NM_014813	NP_055628			leucine-rich repeats and immunoglobulin-like							cytoplasm|integral to membrane|plasma membrane				ovary(3)	3	Lung SC(450;0.246)	all_cancers(81;1.56e-05)|all_epithelial(167;2.62e-05)|all_lung(203;0.000665)|Lung NSC(69;0.000986)		Lung(183;0.0279)|Colorectal(144;0.0885)|COAD - Colon adenocarcinoma(174;0.134)|all cancers(265;0.139)|Epithelial(280;0.143)|LUSC - Lung squamous cell carcinoma(189;0.15)														---	---	---	---
PHTF1	10745	broad.mit.edu	37	1	114281008	114281008	+	Intron	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:114281008delA	uc009wgp.1	-						PHTF1_uc001edn.2_Intron|PHTF1_uc010own.1_Intron|PHTF1_uc001edp.2_Intron	NM_006608	NP_006599			putative homeodomain transcription factor 1							nucleus	DNA binding|sequence-specific DNA binding transcription factor activity			ovary(1)	1	Lung SC(450;0.184)	all_cancers(81;3.78e-08)|all_epithelial(167;5.56e-08)|all_lung(203;6.97e-06)|Lung NSC(69;1.18e-05)		Lung(183;0.0234)|Colorectal(144;0.0686)|all cancers(265;0.0792)|Epithelial(280;0.0866)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)														---	---	---	---
WDR3	10885	broad.mit.edu	37	1	118502088	118502088	+	3'UTR	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:118502088delT	uc010oxe.1	+	27					WDR3_uc001ehi.2_Intron|SPAG17_uc001ehk.2_Intron	NM_006784	NP_006775			WD repeat-containing protein 3							nuclear membrane|nucleolus				upper_aerodigestive_tract(1)	1	Esophageal squamous(2;0.162)	all_cancers(81;2.72e-05)|Acute lymphoblastic leukemia(138;1e-08)|all_epithelial(167;4.4e-07)|all_lung(203;1.7e-06)|Lung NSC(69;1.98e-05)|Prostate(1639;0.00955)|Breast(1374;0.244)		OV - Ovarian serous cystadenocarcinoma(397;1.39e-08)|Epithelial(280;1.82e-07)|all cancers(265;2.04e-05)|Lung(183;0.0525)|BRCA - Breast invasive adenocarcinoma(282;0.0695)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.185)														---	---	---	---
NBPF10	100132406	broad.mit.edu	37	1	145818587	145818587	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:145818587delT	uc001emp.3	+						GPR89A_uc010ozb.1_Intron|GPR89A_uc001eos.2_Intron|GPR89A_uc001eot.2_Intron|GPR89A_uc010ozc.1_Intron|GPR89A_uc010ozd.1_Intron|GPR89A_uc010oze.1_Intron	NM_017940	NP_060410			hypothetical protein LOC55672												0	all_hematologic(923;0.032)			Colorectal(1306;1.36e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.00258)														---	---	---	---
ANP32E	81611	broad.mit.edu	37	1	150199259	150199259	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									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			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)															---	---	---	---
THEM4	117145	broad.mit.edu	37	1	151849315	151849315	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:151849315delT	uc001ezj.1	-						THEM4_uc001ezk.1_Intron	NM_053055	NP_444283			thioesterase superfamily member 4						insulin receptor signaling pathway|nerve growth factor receptor signaling pathway|phosphatidylinositol-mediated signaling	cytosol|ruffle membrane					0	Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.14)		LUSC - Lung squamous cell carcinoma(543;0.181)															---	---	---	---
NUP210L	91181	broad.mit.edu	37	1	154090061	154090061	+	Intron	DEL	A	-	-	rs79748906		TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:154090061delA	uc001fdw.2	-						NUP210L_uc009woq.2_Intron|NUP210L_uc010peh.1_Intron	NM_207308	NP_997191			nucleoporin 210kDa-like isoform 1							integral to membrane				skin(5)|ovary(4)|large_intestine(1)|central_nervous_system(1)	11	all_lung(78;9.35e-31)|Lung NSC(65;1.33e-28)|Hepatocellular(266;0.0877)|Melanoma(130;0.128)		LUSC - Lung squamous cell carcinoma(543;0.151)|Colorectal(543;0.198)															---	---	---	---
CHRNB2	1141	broad.mit.edu	37	1	154543476	154543476	+	Intron	DEL	C	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:154543476delC	uc001ffg.2	+							NM_000748	NP_000739			neuronal nicotinic acetylcholine receptor beta 2						B cell activation|behavioral response to nicotine|calcium ion transport|central nervous system projection neuron axonogenesis|lateral geniculate nucleus development|locomotory behavior|membrane depolarization|memory|negative regulation of action potential|optic nerve morphogenesis|positive regulation of B cell proliferation|positive regulation of dopamine secretion|regulation of circadian sleep/wake cycle, REM sleep|regulation of dendrite morphogenesis|regulation of dopamine metabolic process|regulation of synaptogenesis|response to cocaine|response to ethanol|response to hypoxia|sensory perception of pain|sensory perception of sound|smooth muscle contraction|social behavior|synaptic transmission involved in micturition|synaptic transmission, cholinergic|vestibulocochlear nerve development|visual learning|visual perception	cell junction|external side of plasma membrane|nicotinic acetylcholine-gated receptor-channel complex|postsynaptic membrane	acetylcholine receptor activity|nicotinic acetylcholine-activated cation-selective channel activity				0	all_lung(78;2.22e-29)|Lung NSC(65;3.66e-27)|Hepatocellular(266;0.0877)|all_hematologic(923;0.088)		LUSC - Lung squamous cell carcinoma(543;0.185)		Nicotine(DB00184)													---	---	---	---
Unknown	0	broad.mit.edu	37	1	155556427	155556427	+	IGR	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:155556427delT								LOC645676 (22695 upstream) : MSTO1 (23580 downstream)																																			---	---	---	---
GON4L	54856	broad.mit.edu	37	1	155785777	155785777	+	Intron	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:155785777delA	uc001flz.2	-						GON4L_uc001fly.1_Intron|GON4L_uc009wrh.1_Intron|GON4L_uc001fma.1_Intron|GON4L_uc001fmc.2_Intron|GON4L_uc001fmd.3_Intron|GON4L_uc009wri.2_5'UTR|GON4L_uc001fme.2_Intron|GON4L_uc001fmf.2_Intron	NM_001037533	NP_001032622			gon-4-like isoform a						regulation of transcription, DNA-dependent	cytoplasm|nucleus	DNA binding			ovary(3)	3	Hepatocellular(266;0.0997)|all_hematologic(923;0.145)|all_neural(408;0.195)																	---	---	---	---
C1orf66	51093	broad.mit.edu	37	1	156702951	156702951	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:156702951delT	uc001fpu.2	+						C1orf66_uc001fpv.2_Intron	NM_015997	NP_057081			hypothetical protein LOC51093 isoform 1							integral to membrane	rRNA (adenine-N6,N6-)-dimethyltransferase activity				0	all_hematologic(923;0.088)|Hepatocellular(266;0.158)																	---	---	---	---
C1orf66	51093	broad.mit.edu	37	1	156703374	156703375	+	Intron	DEL	CA	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:156703374_156703375delCA	uc001fpu.2	+						C1orf66_uc001fpv.2_Intron	NM_015997	NP_057081			hypothetical protein LOC51093 isoform 1							integral to membrane	rRNA (adenine-N6,N6-)-dimethyltransferase activity				0	all_hematologic(923;0.088)|Hepatocellular(266;0.158)																	---	---	---	---
RABGAP1L	9910	broad.mit.edu	37	1	174210540	174210540	+	Intron	DEL	A	-	-	rs61628461	by1000genomes	TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:174210540delA	uc001gjx.2	+						RABGAP1L_uc009wwq.1_Intron|RABGAP1L_uc001gjw.2_Intron	NM_014857	NP_055672			RAB GTPase activating protein 1-like isoform A						regulation of protein localization	early endosome|Golgi apparatus|nucleus	Rab GTPase activator activity			ovary(2)|lung(1)|kidney(1)	4																		---	---	---	---
CDC73	79577	broad.mit.edu	37	1	193121497	193121497	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:193121497delT	uc001gtb.2	+							NM_024529	NP_078805			parafibromin						cell cycle|histone H2B ubiquitination|histone monoubiquitination|transcription, DNA-dependent	Cdc73/Paf1 complex	protein binding			parathyroid(46)|ovary(1)|breast(1)|pancreas(1)	49														Hyperparathyroidism_Familial_Isolated|Hyperparathyroidism-Jaw_Tumor_Syndrome				---	---	---	---
KCNT2	343450	broad.mit.edu	37	1	196438097	196438097	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:196438097delT	uc001gtd.1	-						KCNT2_uc009wyt.1_5'Flank|KCNT2_uc001gte.1_Intron|KCNT2_uc001gtf.1_Intron|KCNT2_uc001gtg.1_Intron|KCNT2_uc009wyu.2_Intron|KCNT2_uc009wyv.1_Intron	NM_198503	NP_940905			potassium channel, subfamily T, member 2							voltage-gated potassium channel complex	ATP binding|calcium-activated potassium channel activity|voltage-gated potassium channel activity			ovary(5)|breast(1)|skin(1)	7																		---	---	---	---
SYT2	127833	broad.mit.edu	37	1	202573400	202573400	+	Intron	DEL	C	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:202573400delC	uc001gye.2	-						SYT2_uc010pqb.1_Intron|SYT2_uc009xaf.2_Intron	NM_001136504	NP_001129976			synaptotagmin II						neurotransmitter secretion	cell junction|chromaffin granule membrane|endocytic vesicle membrane|integral to membrane|synaptic vesicle membrane	protein binding|transporter activity			ovary(2)|skin(1)	3			BRCA - Breast invasive adenocarcinoma(75;0.169)		Botulinum Toxin Type B(DB00042)													---	---	---	---
RPS6KC1	26750	broad.mit.edu	37	1	213290877	213290877	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:213290877delT	uc010ptr.1	+						RPS6KC1_uc001hkd.2_Intron|RPS6KC1_uc010pts.1_Intron|RPS6KC1_uc010ptt.1_Intron|RPS6KC1_uc010ptu.1_Intron|RPS6KC1_uc010ptv.1_Intron|RPS6KC1_uc001hke.2_Intron	NM_012424	NP_036556			ribosomal protein S6 kinase, 52kDa, polypeptide						cell communication|signal transduction	early endosome|membrane	ATP binding|phosphatidylinositol binding|protein binding|protein serine/threonine kinase activity			lung(4)|ovary(3)|breast(1)	8				OV - Ovarian serous cystadenocarcinoma(81;0.00705)|all cancers(67;0.016)|GBM - Glioblastoma multiforme(131;0.0663)|Epithelial(68;0.145)														---	---	---	---
RPS6KC1	26750	broad.mit.edu	37	1	213434712	213434712	+	Intron	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:213434712delA	uc010ptr.1	+						RPS6KC1_uc001hkd.2_Intron|RPS6KC1_uc010pts.1_Intron|RPS6KC1_uc010ptt.1_Intron|RPS6KC1_uc010ptu.1_Intron|RPS6KC1_uc010ptv.1_Intron|RPS6KC1_uc001hke.2_Intron	NM_012424	NP_036556			ribosomal protein S6 kinase, 52kDa, polypeptide						cell communication|signal transduction	early endosome|membrane	ATP binding|phosphatidylinositol binding|protein binding|protein serine/threonine kinase activity			lung(4)|ovary(3)|breast(1)	8				OV - Ovarian serous cystadenocarcinoma(81;0.00705)|all cancers(67;0.016)|GBM - Glioblastoma multiforme(131;0.0663)|Epithelial(68;0.145)														---	---	---	---
KCTD3	51133	broad.mit.edu	37	1	215777330	215777330	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									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			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)														---	---	---	---
NUP133	55746	broad.mit.edu	37	1	229631436	229631436	+	Intron	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:229631436delA	uc001htn.2	-							NM_018230	NP_060700			nucleoporin 133kDa						carbohydrate metabolic process|glucose transport|mitotic prometaphase|mRNA export from nucleus|nuclear pore organization|protein transport|regulation of glucose transport|transmembrane transport|viral reproduction	condensed chromosome kinetochore|cytosol|Nup107-160 complex	nucleocytoplasmic transporter activity|protein binding			breast(4)|skin(2)|ovary(1)	7	Breast(184;0.104)|Ovarian(103;0.249)	Prostate(94;0.167)																---	---	---	---
PCNXL2	80003	broad.mit.edu	37	1	233270662	233270662	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:233270662delT	uc001hvl.2	-						PCNXL2_uc001hvm.1_Intron|PCNXL2_uc009xfu.2_Intron|PCNXL2_uc001hvp.1_Intron|PCNXL2_uc009xfv.1_Intron	NM_014801	NP_055616			pecanex-like 2							integral to membrane				central_nervous_system(1)|pancreas(1)	2		all_cancers(173;0.0347)|Prostate(94;0.137)																---	---	---	---
PPPDE1	51029	broad.mit.edu	37	1	244857682	244857682	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:244857682delT	uc001iao.2	+						PPPDE1_uc001iap.2_Intron	NM_016076	NP_057160			PPPDE peptidase domain containing 1											breast(3)	3																		---	---	---	---
SMYD3	64754	broad.mit.edu	37	1	246093029	246093029	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:246093029delT	uc001ibl.2	-						SMYD3_uc001ibk.2_Intron|SMYD3_uc001ibi.2_Intron|SMYD3_uc001ibj.2_Intron	NM_022743	NP_073580			SET and MYND domain containing 3							cytoplasm|nucleus	histone-lysine N-methyltransferase activity|protein binding|zinc ion binding				0	all_cancers(71;0.000291)|all_epithelial(71;0.000174)|Ovarian(71;0.0377)|all_lung(81;0.0568)|Lung NSC(105;0.0804)|Breast(184;0.173)|Melanoma(84;0.242)	all_cancers(173;0.0496)|Acute lymphoblastic leukemia(190;0.164)	OV - Ovarian serous cystadenocarcinoma(106;0.0129)	all cancers(4;0.028)|GBM - Glioblastoma multiforme(49;0.0537)														---	---	---	---
MYT1L	23040	broad.mit.edu	37	2	1890247	1890247	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:1890247delT	uc002qxe.2	-						MYT1L_uc002qxd.2_Intron|MYT1L_uc010ewl.1_Intron	NM_015025	NP_055840			myelin transcription factor 1-like						cell differentiation|nervous system development	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(5)|central_nervous_system(1)	6	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.0797)	all_cancers(51;0.037)|all_epithelial(98;0.241)		OV - Ovarian serous cystadenocarcinoma(76;0.169)|all cancers(51;0.244)														---	---	---	---
RNASEH1	246243	broad.mit.edu	37	2	3596130	3596130	+	Intron	DEL	C	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:3596130delC	uc002qxt.2	-						RNASEH1_uc002qxs.2_Intron	NM_002936	NP_002927			ribonuclease H1						RNA catabolic process	cytoplasm	magnesium ion binding|ribonuclease H activity|RNA binding			ovary(1)	1	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.093)			OV - Ovarian serous cystadenocarcinoma(76;0.0713)|Epithelial(75;0.167)|all cancers(51;0.22)														---	---	---	---
CPSF3	51692	broad.mit.edu	37	2	9611343	9611343	+	Intron	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:9611343delA	uc002qzo.1	+						CPSF3_uc002qzp.1_Intron|CPSF3_uc002qzq.1_Intron	NM_016207	NP_057291			cleavage and polyadenylation specific factor 3,						histone mRNA 3'-end processing|mRNA cleavage|mRNA export from nucleus|mRNA polyadenylation|nuclear mRNA splicing, via spliceosome|termination of RNA polymerase II transcription	mRNA cleavage and polyadenylation specificity factor complex|ribonucleoprotein complex	5'-3' exonuclease activity|endoribonuclease activity|metal ion binding|protein binding|RNA binding			breast(2)	2	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)	all_cancers(51;2.39e-25)|all_epithelial(98;8.75e-19)|Lung NSC(108;2.38e-06)|Ovarian(717;0.0308)		all cancers(51;2.2e-40)|Epithelial(75;6.71e-35)|OV - Ovarian serous cystadenocarcinoma(76;4.35e-21)|STAD - Stomach adenocarcinoma(1183;0.00644)														---	---	---	---
SMC6	79677	broad.mit.edu	37	2	17888597	17888597	+	Frame_Shift_Del	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:17888597delT	uc002rco.2	-	18	2191	c.1895delA	c.(1894-1896)AATfs	p.N632fs	SMC6_uc010exo.2_Frame_Shift_Del_p.N632fs|SMC6_uc002rcn.2_Frame_Shift_Del_p.N632fs|SMC6_uc002rcp.1_Frame_Shift_Del_p.N658fs|SMC6_uc002rcq.2_Frame_Shift_Del_p.N658fs	NM_001142286	NP_001135758	Q96SB8	SMC6_HUMAN	SMC6 protein	632	Flexible hinge.				DNA recombination|DNA repair	chromosome|nucleus	ATP binding			breast(4)|upper_aerodigestive_tract(1)|kidney(1)	6	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.158)																	---	---	---	---
WDR35	57539	broad.mit.edu	37	2	20130442	20130442	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:20130442delT	uc002rdi.2	-						WDR35_uc002rdj.2_Intron|WDR35_uc010ext.2_Intron|WDR35_uc002rdh.2_Intron	NM_001006657	NP_001006658			WD repeat domain 35 isoform 1											ovary(1)	1	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)																	---	---	---	---
PUM2	23369	broad.mit.edu	37	2	20454512	20454512	+	Intron	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:20454512delA	uc002rds.1	-						PUM2_uc002rdq.1_Intron|PUM2_uc002rdt.1_Intron|PUM2_uc002rdr.2_Intron|PUM2_uc010yjy.1_Intron|PUM2_uc002rdu.1_Intron|PUM2_uc010yjz.1_Intron	NM_015317	NP_056132			pumilio homolog 2						regulation of translation	perinuclear region of cytoplasm|stress granule	protein binding|RNA binding			ovary(1)	1	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)																	---	---	---	---
Unknown	0	broad.mit.edu	37	2	26363043	26363043	+	IGR	DEL	A	-	-	rs112696641		TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:26363043delA								RAB10 (2721 upstream) : HADHA (50462 downstream)																																			---	---	---	---
KRTCAP3	200634	broad.mit.edu	37	2	27666755	27666755	+	Intron	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:27666755delA	uc002rks.2	+						KRTCAP3_uc010ylr.1_Intron|KRTCAP3_uc002rkt.2_Intron	NM_173853	NP_776252			keratinocyte associated protein 3							integral to membrane					0	Acute lymphoblastic leukemia(172;0.155)																	---	---	---	---
BRE	9577	broad.mit.edu	37	2	28464370	28464372	+	Intron	DEL	TTT	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:28464370_28464372delTTT	uc002rlr.2	+						BRE_uc002rlp.1_Intron|BRE_uc002rlq.2_Intron|BRE_uc002rls.2_Intron|BRE_uc002rlt.2_Intron|BRE_uc002rlu.2_Intron|BRE_uc002rlv.2_Intron	NM_199194	NP_954664			brain and reproductive organ-expressed (TNFRSF1A						apoptosis|chromatin modification|double-strand break repair|G2/M transition DNA damage checkpoint|positive regulation of anti-apoptosis|positive regulation of DNA repair|response to ionizing radiation|signal transduction	BRCA1-A complex|BRISC complex|cytoplasm|nuclear ubiquitin ligase complex	peroxisome targeting sequence binding|polyubiquitin binding|tumor necrosis factor receptor binding			lung(1)|kidney(1)|skin(1)	3	Acute lymphoblastic leukemia(172;0.155)																	---	---	---	---
WDR43	23160	broad.mit.edu	37	2	29158318	29158318	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:29158318delT	uc002rmo.2	+							NM_015131	NP_055946			WD repeat domain 43							nucleolus				ovary(1)	1	Acute lymphoblastic leukemia(172;0.155)																	---	---	---	---
SLC30A6	55676	broad.mit.edu	37	2	32400336	32400336	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:32400336delT	uc002roe.1	+						SLC30A6_uc002rof.1_Intron|SLC30A6_uc010ymw.1_Intron|SLC30A6_uc010ezr.1_Intron|SLC30A6_uc002rog.1_Intron|SLC30A6_uc010ezs.1_Intron|SLC30A6_uc002roh.1_Intron	NM_017964	NP_060434			solute carrier family 30 (zinc transporter),							Golgi membrane|integral to membrane	zinc ion transmembrane transporter activity				0	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.208)																	---	---	---	---
BIRC6	57448	broad.mit.edu	37	2	32820253	32820253	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:32820253delT	uc010ezu.2	+							NM_016252	NP_057336			baculoviral IAP repeat-containing 6						anti-apoptosis|apoptosis	intracellular	acid-amino acid ligase activity|cysteine-type endopeptidase inhibitor activity|protein binding			ovary(5)|skin(4)|lung(2)|central_nervous_system(1)|breast(1)|pancreas(1)	14	Acute lymphoblastic leukemia(172;0.155)																	---	---	---	---
MSH2	4436	broad.mit.edu	37	2	47643365	47643365	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:47643365delT	uc002rvy.1	+						MSH2_uc010yoh.1_Intron|MSH2_uc002rvz.2_Intron|MSH2_uc010fbg.2_Intron	NM_000251	NP_000242			mutS homolog 2						B cell differentiation|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|double-strand break repair|intra-S DNA damage checkpoint|isotype switching|maintenance of DNA repeat elements|male gonad development|meiotic gene conversion|meiotic mismatch repair|negative regulation of neuron apoptosis|negative regulation of reciprocal meiotic recombination|positive regulation of helicase activity|postreplication repair|response to UV-B|response to X-ray|somatic hypermutation of immunoglobulin genes	MutSalpha complex|MutSbeta complex|nuclear chromosome	ATP binding|DNA-dependent ATPase activity|double-strand/single-strand DNA junction binding|guanine/thymine mispair binding|loop DNA binding|protein C-terminus binding|protein homodimerization activity|protein kinase binding|Y-form DNA binding			large_intestine(33)|haematopoietic_and_lymphoid_tissue(6)|endometrium(4)|ovary(3)|cervix(2)|central_nervous_system(2)|stomach(1)|small_intestine(1)|breast(1)|skin(1)|prostate(1)	55		all_hematologic(82;0.0359)|Acute lymphoblastic leukemia(82;0.175)	Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151)					D|Mis|N|F|S		colorectal|endometrial|ovarian	colorectal|endometrial|ovarian		MMR	Lynch_syndrome|Muir-Torre_syndrome|Turcot_syndrome|Constitutional_Mismatch_Repair_Deficiency_Syndrome				---	---	---	---
LHCGR	3973	broad.mit.edu	37	2	48914783	48914783	+	3'UTR	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:48914783delT	uc002rwu.3	-	11					GTF2A1L_uc002rwt.2_Intron	NM_000233	NP_000224			luteinizing hormone/choriogonadotropin receptor						male genitalia development|male gonad development	endosome|integral to plasma membrane	luteinizing hormone receptor activity			ovary(3)|lung(2)|breast(2)|skin(1)	8		all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.176)	Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151)		Cetrorelix(DB00050)|Choriogonadotropin alfa(DB00097)|Goserelin(DB00014)|Lutropin alfa(DB00044)|Menotropins(DB00032)									Familial_Male-Limited_Precocious_Puberty				---	---	---	---
VPS54	51542	broad.mit.edu	37	2	64193106	64193106	+	Intron	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:64193106delA	uc002scq.2	-						VPS54_uc002scp.2_Intron|VPS54_uc010fct.2_Intron	NM_016516	NP_057600			vacuolar protein sorting 54 isoform 1						protein transport|retrograde transport, endosome to Golgi						0																		---	---	---	---
GMCL1	64395	broad.mit.edu	37	2	70096843	70096843	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:70096843delT	uc002sfu.2	+							NM_178439	NP_848526			germ cell-less						cell differentiation|multicellular organismal development|spermatogenesis	nuclear matrix				ovary(3)	3																		---	---	---	---
RTKN	6242	broad.mit.edu	37	2	74653450	74653450	+	Frame_Shift_Del	DEL	G	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:74653450delG	uc002sle.2	-	12	1729	c.1612delC	c.(1612-1614)CTCfs	p.L538fs	RTKN_uc002slc.2_Frame_Shift_Del_p.L525fs|RTKN_uc002sld.2_Frame_Shift_Del_p.L488fs	NM_001015055	NP_001015055	Q9BST9	RTKN_HUMAN	rhotekin isoform a	538	Pro-rich.				apoptosis|regulation of anti-apoptosis|Rho protein signal transduction	intracellular	GTP binding|GTP-Rho binding|GTPase inhibitor activity			skin(1)	1																		---	---	---	---
HK2	3099	broad.mit.edu	37	2	75094527	75094527	+	Intron	DEL	A	-	-	rs151230031		TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:75094527delA	uc002snd.2	+							NM_000189	NP_000180			hexokinase 2						apoptotic mitochondrial changes|glucose transport|glycolysis|transmembrane transport	cytosol|mitochondrial outer membrane	ATP binding|glucokinase activity			ovary(1)|lung(1)	2																		---	---	---	---
C2orf3	6936	broad.mit.edu	37	2	75928421	75928421	+	Intron	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:75928421delA	uc002sno.2	-						C2orf3_uc010ffs.2_5'UTR|C2orf3_uc002snn.2_Intron|C2orf3_uc010fft.2_Intron	NM_003203	NP_003194			hypothetical protein LOC6936						negative regulation of transcription, DNA-dependent	nucleus	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity			ovary(1)|central_nervous_system(1)	2																		---	---	---	---
PROM2	150696	broad.mit.edu	37	2	95943601	95943601	+	Intron	DEL	C	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:95943601delC	uc002suh.1	+						PROM2_uc002sui.2_Intron|PROM2_uc002suj.2_Intron|PROM2_uc002suk.2_Intron|PROM2_uc002sul.2_Intron	NM_144707	NP_653308			prominin 2 precursor							apical plasma membrane|basolateral plasma membrane|cilium membrane|integral to membrane|microvillus membrane				ovary(1)	1																		---	---	---	---
MRPL30	51263	broad.mit.edu	37	2	99811772	99811772	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:99811772delT	uc002szu.2	+						MRPL30_uc002szl.1_Intron|MRPL30_uc002szt.1_Intron|MRPL30_uc002szv.2_Intron	NM_145213	NP_660214			RecName: Full=39S ribosomal protein L30, mitochondrial;          Short=L30mt; AltName: Full=MRP-L30; AltName: Full=MRP-L28; Flags: Precursor;						translation	mitochondrion|ribosome	structural constituent of ribosome			ovary(1)	1																		---	---	---	---
REV1	51455	broad.mit.edu	37	2	100017907	100017908	+	Intron	DEL	AA	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:100017907_100017908delAA	uc002tad.2	-						REV1_uc002tac.2_Intron	NM_016316	NP_057400			REV1-like isoform 1						DNA replication|error-prone translesion synthesis|response to UV	nucleoplasm	damaged DNA binding|DNA-directed DNA polymerase activity|magnesium ion binding|protein binding			ovary(2)	2													DNA_polymerases_(catalytic_subunits)|Direct_reversal_of_damage					---	---	---	---
IL1RL2	8808	broad.mit.edu	37	2	102851247	102851247	+	Intron	DEL	A	-	-	rs72526182		TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:102851247delA	uc002tbs.2	+						IL1RL2_uc002tbt.2_Intron	NM_003854	NP_003845			interleukin 1 receptor-like 2 precursor						cellular defense response|innate immune response	integral to plasma membrane	interleukin-1, Type I, activating receptor activity			ovary(2)	2																		---	---	---	---
TGFBRAP1	9392	broad.mit.edu	37	2	105913017	105913017	+	Intron	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:105913017delA	uc002tcq.2	-						TGFBRAP1_uc010fjc.2_Intron|TGFBRAP1_uc002tcr.3_Intron	NM_004257	NP_004248			transforming growth factor, beta receptor						regulation of transcription, DNA-dependent|transforming growth factor beta receptor signaling pathway	cytoplasm|membrane	SMAD binding|small GTPase regulator activity|transforming growth factor beta receptor binding			central_nervous_system(1)|skin(1)	2																		---	---	---	---
ZC3H6	376940	broad.mit.edu	37	2	113043561	113043562	+	Intron	INS	-	TGT	TGT			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:113043561_113043562insTGT	uc002thq.1	+							NM_198581	NP_940983			zinc finger CCCH-type domain containing 6								nucleic acid binding|zinc ion binding			ovary(3)|central_nervous_system(1)	4																		---	---	---	---
CLASP1	23332	broad.mit.edu	37	2	122216728	122216728	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:122216728delT	uc002tnc.2	-						CLASP1_uc002tna.2_5'Flank|CLASP1_uc010yyw.1_Intron|CLASP1_uc002tnb.2_Intron|CLASP1_uc010yyx.1_Intron|CLASP1_uc010yyy.1_Intron|CLASP1_uc010yyz.1_Intron|CLASP1_uc010yza.1_Intron|CLASP1_uc010yzb.1_Intron|CLASP1_uc010yzc.1_Intron|CLASP1_uc002tng.1_Intron	NM_015282	NP_056097			CLIP-associating protein 1 isoform 1						axon guidance|cell division|establishment or maintenance of cell polarity|exit from mitosis|G2/M transition of mitotic cell cycle|microtubule anchoring|microtubule bundle formation|microtubule nucleation|microtubule organizing center organization|mitotic prometaphase|negative regulation of microtubule depolymerization	centrosomal corona|condensed chromosome kinetochore|cortical microtubule cytoskeleton|cytoplasmic microtubule|cytosol|Golgi apparatus|kinetochore microtubule	kinetochore binding|microtubule plus-end binding			ovary(1)|central_nervous_system(1)	2	Renal(3;0.0496)																	---	---	---	---
Unknown	0	broad.mit.edu	37	2	128825103	128825103	+	IGR	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:128825103delA								SAP130 (39470 upstream) : UGGT1 (23651 downstream)																																			---	---	---	---
NCKAP5	344148	broad.mit.edu	37	2	133887625	133887625	+	Frame_Shift_Del	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:133887625delT	uc002ttp.2	-	6	640	c.266delA	c.(265-267)AAGfs	p.K89fs	NCKAP5_uc002ttq.2_Frame_Shift_Del_p.K89fs|NCKAP5_uc002ttt.1_Frame_Shift_Del_p.K89fs|NCKAP5_uc002tts.1_Frame_Shift_Del_p.K64fs	NM_207363	NP_997246	O14513	NCKP5_HUMAN	Nck-associated protein 5 isoform 1	89	Potential.						protein binding				0																		---	---	---	---
ZRANB3	84083	broad.mit.edu	37	2	136103039	136103039	+	Intron	DEL	A	-	-	rs113439308		TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:136103039delA	uc002tum.2	-						ZRANB3_uc002tuk.2_Intron|ZRANB3_uc002tul.2_Intron|ZRANB3_uc002tun.1_Intron	NM_032143	NP_115519			zinc finger, RAN-binding domain containing 3							intracellular	ATP binding|DNA binding|endonuclease activity|helicase activity|zinc ion binding			lung(2)	2				BRCA - Breast invasive adenocarcinoma(221;0.135)														---	---	---	---
R3HDM1	23518	broad.mit.edu	37	2	136472952	136472952	+	Intron	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:136472952delA	uc002tuo.2	+						R3HDM1_uc010fni.2_Intron|R3HDM1_uc002tup.2_Intron|R3HDM1_uc010zbh.1_Intron	NM_015361	NP_056176			R3H domain containing 1								nucleic acid binding			skin(1)	1				BRCA - Breast invasive adenocarcinoma(221;0.127)														---	---	---	---
CXCR4	7852	broad.mit.edu	37	2	136872415	136872415	+	3'UTR	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:136872415delA	uc002tuz.2	-	2					CXCR4_uc002tuy.2_3'UTR|CXCR4_uc010fnk.2_3'UTR	NM_003467	NP_003458			chemokine (C-X-C motif) receptor 4 isoform b						activation of MAPK activity|apoptosis|dendritic cell chemotaxis|elevation of cytosolic calcium ion concentration|entry into host cell|inflammatory response|initiation of viral infection|regulation of chemotaxis|response to hypoxia|response to virus	cell leading edge|cell surface|cytoplasmic membrane-bounded vesicle|integral to membrane|plasma membrane	actin binding|C-X-C chemokine receptor activity|coreceptor activity|myosin light chain binding|ubiquitin binding|ubiquitin protein ligase binding			upper_aerodigestive_tract(1)|large_intestine(1)|lung(1)	3				BRCA - Breast invasive adenocarcinoma(221;0.155)	Framycetin(DB00452)													---	---	---	---
ARHGAP15	55843	broad.mit.edu	37	2	144313915	144313915	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:144313915delT	uc002tvm.3	+						ARHGAP15_uc002tvn.2_Intron	NM_018460	NP_060930			ARHGAP15						regulation of cell shape|small GTPase mediated signal transduction	cytosol|membrane	protein binding|Rac GTPase activator activity			ovary(1)|skin(1)	2				BRCA - Breast invasive adenocarcinoma(221;0.151)														---	---	---	---
ARHGAP15	55843	broad.mit.edu	37	2	144525481	144525481	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:144525481delT	uc002tvm.3	+						ARHGAP15_uc002tvn.2_Intron	NM_018460	NP_060930			ARHGAP15						regulation of cell shape|small GTPase mediated signal transduction	cytosol|membrane	protein binding|Rac GTPase activator activity			ovary(1)|skin(1)	2				BRCA - Breast invasive adenocarcinoma(221;0.151)														---	---	---	---
ACVR2A	92	broad.mit.edu	37	2	148683686	148683686	+	Frame_Shift_Del	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:148683686delA	uc002twg.2	+	11	1572	c.1303delA	c.(1303-1305)AAAfs	p.K435fs	ACVR2A_uc010zbn.1_Frame_Shift_Del_p.K327fs|ACVR2A_uc002twh.2_Frame_Shift_Del_p.K435fs	NM_001616	NP_001607	P27037	AVR2A_HUMAN	activin A receptor, type IIA precursor	435	Cytoplasmic (Potential).|Protein kinase.				activin receptor signaling pathway|BMP signaling pathway|positive regulation of activin receptor signaling pathway|positive regulation of bone mineralization|positive regulation of erythrocyte differentiation|positive regulation of osteoblast differentiation|positive regulation of protein phosphorylation	cytoplasm|inhibin-betaglycan-ActRII complex|integral to plasma membrane	ATP binding|coreceptor activity|inhibin beta-A binding|metal ion binding|receptor signaling protein serine/threonine kinase activity|transforming growth factor beta receptor activity			stomach(8)|large_intestine(2)|lung(1)|breast(1)|kidney(1)	13				BRCA - Breast invasive adenocarcinoma(221;0.0969)														---	---	---	---
Unknown	0	broad.mit.edu	37	2	149627550	149627550	+	IGR	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:149627550delT								EPC2 (82415 upstream) : KIF5C (5269 downstream)																																			---	---	---	---
RIF1	55183	broad.mit.edu	37	2	152331352	152331352	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:152331352delT	uc002txm.2	+						RIF1_uc002txl.2_Intron|RIF1_uc002txn.2_Intron|RIF1_uc002txo.2_Intron|RIF1_uc002txp.2_Intron|uc010fnw.1_5'Flank	NM_018151	NP_060621			RAP1 interacting factor 1						cell cycle|response to DNA damage stimulus	chromosome, telomeric region|cytoplasm|nucleus|spindle	binding			ovary(5)|breast(4)|skin(3)|lung(2)|kidney(1)	15				BRCA - Breast invasive adenocarcinoma(221;0.0429)														---	---	---	---
CACNB4	785	broad.mit.edu	37	2	152695482	152695482	+	3'UTR	DEL	T	-	-	rs111950042		TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:152695482delT	uc002tya.2	-	14					CACNB4_uc002txy.2_3'UTR|CACNB4_uc002txz.2_3'UTR|CACNB4_uc010fnz.2_3'UTR	NM_000726	NP_000717			calcium channel, voltage-dependent, beta 4						axon guidance|membrane depolarization|synaptic transmission	cytosol|internal side of plasma membrane|plasma membrane|synapse|voltage-gated calcium channel complex	protein binding|voltage-gated calcium channel activity			ovary(2)	2				BRCA - Breast invasive adenocarcinoma(221;0.156)	Verapamil(DB00661)													---	---	---	---
ACVR1C	130399	broad.mit.edu	37	2	158406602	158406602	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:158406602delT	uc002tzk.3	-						ACVR1C_uc002tzl.3_Intron|ACVR1C_uc010fof.2_Intron|ACVR1C_uc010foe.2_Intron	NM_145259	NP_660302			activin A receptor, type IC isoform 1						apoptosis|cell differentiation|regulation of apoptosis	activin receptor complex	activin receptor activity, type I|ATP binding|transforming growth factor beta receptor activity			lung(3)|ovary(2)|skin(2)	7																		---	---	---	---
DPP4	1803	broad.mit.edu	37	2	162903784	162903784	+	Intron	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:162903784delA	uc002ubz.2	-						DPP4_uc010fpb.2_Intron|DPP4_uc002uca.1_Intron|DPP4_uc002ucb.1_Intron	NM_001935	NP_001926			dipeptidylpeptidase IV						cell adhesion|endothelial cell migration|negative regulation of extracellular matrix disassembly|positive regulation of cell proliferation|proteolysis|regulation of cell-cell adhesion mediated by integrin|response to hypoxia|T cell activation|T cell costimulation	apical plasma membrane|cell surface|endocytic vesicle|extracellular region|integral to membrane|invadopodium membrane|lamellipodium membrane|membrane raft	aminopeptidase activity|dipeptidyl-peptidase activity|protease binding|protein homodimerization activity|receptor activity|receptor binding|serine-type endopeptidase activity			ovary(3)	3					Sitagliptin(DB01261)													---	---	---	---
LRP2	4036	broad.mit.edu	37	2	170060794	170060794	+	Intron	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:170060794delA	uc002ues.2	-							NM_004525	NP_004516			low density lipoprotein-related protein 2						hormone biosynthetic process|protein glycosylation|receptor-mediated endocytosis|vitamin D metabolic process	coated pit|integral to membrane|lysosome	calcium ion binding|receptor activity|SH3 domain binding			ovary(13)|skin(6)|central_nervous_system(4)|large_intestine(3)|kidney(2)|pancreas(1)	29				STAD - Stomach adenocarcinoma(1183;0.000766)|COAD - Colon adenocarcinoma(177;0.0101)	Gentamicin(DB00798)|Insulin Glargine recombinant(DB00047)|Insulin Lyspro recombinant(DB00046)|Insulin recombinant(DB00030)|Insulin, porcine(DB00071)|Urokinase(DB00013)													---	---	---	---
ITGAV	3685	broad.mit.edu	37	2	187501040	187501041	+	Intron	INS	-	T	T			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:187501040_187501041insT	uc002upq.2	+						ITGAV_uc010frs.2_Intron|ITGAV_uc010zfv.1_Intron	NM_002210	NP_002201			integrin alpha-V isoform 1 precursor						angiogenesis|axon guidance|blood coagulation|cell-matrix adhesion|entry of bacterium into host cell|entry of symbiont into host cell by promotion of host phagocytosis|entry of virus into host cell|ERK1 and ERK2 cascade|integrin-mediated signaling pathway|leukocyte migration|negative regulation of apoptosis|negative regulation of lipid storage|negative regulation of lipid transport|negative regulation of lipoprotein metabolic process|negative regulation of low-density lipoprotein particle receptor biosynthetic process|negative regulation of macrophage derived foam cell differentiation|positive regulation of cell adhesion|positive regulation of cell proliferation|regulation of apoptotic cell clearance	integrin complex	receptor activity|transforming growth factor beta binding			ovary(2)|kidney(1)|skin(1)	4			OV - Ovarian serous cystadenocarcinoma(117;0.0185)|Epithelial(96;0.072)|all cancers(119;0.189)	STAD - Stomach adenocarcinoma(3;0.106)|COAD - Colon adenocarcinoma(31;0.108)														---	---	---	---
GULP1	51454	broad.mit.edu	37	2	189434251	189434251	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:189434251delT	uc010fru.2	+						GULP1_uc002uqd.2_Intron|GULP1_uc010zfw.1_Intron|GULP1_uc002uqf.2_Intron|GULP1_uc002uqg.2_Intron|GULP1_uc002uqh.1_5'Flank	NM_016315	NP_057399			GULP, engulfment adaptor PTB domain containing						apoptosis|lipid transport|phagocytosis, engulfment	cytoplasm|intracellular membrane-bounded organelle	signal transducer activity			ovary(1)	1			OV - Ovarian serous cystadenocarcinoma(117;0.0423)|Epithelial(96;0.158)															---	---	---	---
GLS	2744	broad.mit.edu	37	2	191769683	191769683	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:191769683delT	uc002usf.2	+						GLS_uc002use.2_Intron	NM_014905	NP_055720			glutaminase precursor						cellular amino acid biosynthetic process|glutamate secretion|glutamine catabolic process|neurotransmitter secretion	mitochondrial matrix	glutaminase activity			ovary(1)|skin(1)	2			OV - Ovarian serous cystadenocarcinoma(117;0.00625)|Epithelial(96;0.0744)|all cancers(119;0.181)		L-Glutamic Acid(DB00142)|L-Glutamine(DB00130)													---	---	---	---
PGAP1	80055	broad.mit.edu	37	2	197755382	197755382	+	Intron	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:197755382delA	uc002utw.2	-						PGAP1_uc002utx.2_Intron|PGAP1_uc002uty.1_Intron|PGAP1_uc010zgv.1_Intron	NM_024989	NP_079265			GPI deacylase						attachment of GPI anchor to protein|C-terminal protein lipidation|intracellular protein transport|myo-inositol transport	integral to membrane|intrinsic to endoplasmic reticulum membrane	nuclease activity|phosphoric ester hydrolase activity			ovary(3)|central_nervous_system(1)	4																		---	---	---	---
COQ10B	80219	broad.mit.edu	37	2	198318518	198318518	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:198318518delT	uc002uuh.1	+						COQ10B_uc010fsl.1_5'Flank	NM_025147	NP_079423			coenzyme Q10 homolog B precursor							mitochondrial inner membrane					0			Epithelial(96;0.231)|OV - Ovarian serous cystadenocarcinoma(117;0.246)															---	---	---	---
RFTN2	130132	broad.mit.edu	37	2	198540350	198540354	+	5'UTR	DEL	AAAAC	-	-	rs148812496		TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:198540350_198540354delAAAAC	uc002uuo.3	-	1						NM_144629	NP_653230			raftlin family member 2							plasma membrane					0																		---	---	---	---
FAM126B	285172	broad.mit.edu	37	2	201931967	201931967	+	Intron	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:201931967delA	uc002uws.3	-						FAM126B_uc002uwu.2_Intron|FAM126B_uc002uwv.2_Intron|FAM126B_uc002uww.1_Intron	NM_173822	NP_776183			hypothetical protein LOC285172							intracellular				ovary(1)	1																		---	---	---	---
SUMO1	7341	broad.mit.edu	37	2	203079026	203079027	+	Intron	DEL	AA	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:203079026_203079027delAA	uc002uyz.1	-						SUMO1_uc002uza.1_Intron	NM_001005781	NP_001005781			SMT3 suppressor of mif two 3 homolog 1 isoform a						DNA repair|interferon-gamma-mediated signaling pathway|negative regulation of DNA binding|negative regulation of sequence-specific DNA binding transcription factor activity|negative regulation of transcription, DNA-dependent|palate development|positive regulation of proteasomal ubiquitin-dependent protein catabolic process|positive regulation of protein complex assembly|protein sumoylation|regulation of interferon-gamma-mediated signaling pathway|regulation of protein localization	cytoplasm|nuclear membrane|nuclear pore|nuclear speck	ubiquitin protein ligase binding				0																		---	---	---	---
ABI2	10152	broad.mit.edu	37	2	204231587	204231587	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:204231587delT	uc002vaa.2	+						ABI2_uc010zig.1_Intron|ABI2_uc002uzz.2_Intron|ABI2_uc010zih.1_Intron|ABI2_uc010zii.1_Intron|ABI2_uc010zij.1_Intron|ABI2_uc002vab.2_5'Flank	NM_005759	NP_005750			abl interactor 2						actin polymerization or depolymerization|cell migration|peptidyl-tyrosine phosphorylation	cytoskeleton|cytosol|filopodium|lamellipodium	cytoskeletal adaptor activity|DNA binding|kinase binding|proline-rich region binding|SH3 domain binding|ubiquitin protein ligase binding				0																		---	---	---	---
CD28	940	broad.mit.edu	37	2	204591340	204591340	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:204591340delT	uc002vah.3	+						CD28_uc002vag.1_Intron|CD28_uc010zio.1_Intron|CD28_uc010ftx.2_Intron|CD28_uc002vaj.3_Intron	NM_006139	NP_006130			CD28 antigen precursor						cell surface receptor linked signaling pathway|cytokine biosynthetic process|humoral immune response|positive regulation of anti-apoptosis|positive regulation of interleukin-2 biosynthetic process|positive regulation of mitosis|positive regulation of translation|positive regulation of viral genome replication|regulation of defense response to virus by virus|regulatory T cell differentiation|T cell costimulation|viral reproduction	cytosol|external side of plasma membrane|integral to plasma membrane	coreceptor activity|protease binding|SH3/SH2 adaptor activity				0																		---	---	---	---
NDUFS1	4719	broad.mit.edu	37	2	207018409	207018409	+	Intron	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:207018409delA	uc002vbe.2	-						NDUFS1_uc010ziq.1_Intron|NDUFS1_uc010zir.1_Intron|NDUFS1_uc010zis.1_Intron|NDUFS1_uc010zit.1_Intron|NDUFS1_uc010ziu.1_Intron	NM_005006	NP_004997			NADH dehydrogenase (ubiquinone) Fe-S protein 1,						apoptosis|ATP metabolic process|mitochondrial electron transport, NADH to ubiquinone|reactive oxygen species metabolic process|regulation of mitochondrial membrane potential|transport	mitochondrial intermembrane space|mitochondrial respiratory chain complex I	2 iron, 2 sulfur cluster binding|4 iron, 4 sulfur cluster binding|electron carrier activity|metal ion binding|NADH dehydrogenase (ubiquinone) activity|protein binding			ovary(1)	1					NADH(DB00157)													---	---	---	---
KLF7	8609	broad.mit.edu	37	2	208030440	208030440	+	5'UTR	DEL	A	-	-	rs71412410		TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:208030440delA	uc002vbz.1	-	1					KLF7_uc002vca.1_Intron	NM_003709	NP_003700			Kruppel-like factor 7 (ubiquitous)						regulation of transcription from RNA polymerase II promoter	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|transcription coactivator activity|zinc ion binding			central_nervous_system(1)|skin(1)	2				LUSC - Lung squamous cell carcinoma(261;0.0856)|Lung(261;0.166)|Epithelial(149;0.173)														---	---	---	---
FN1	2335	broad.mit.edu	37	2	216251710	216251710	+	Intron	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:216251710delA	uc002vfa.2	-						FN1_uc002vfb.2_Intron|FN1_uc002vfc.2_Intron|FN1_uc002vfd.2_Intron|FN1_uc002vfe.2_Intron|FN1_uc002vff.2_Intron|FN1_uc002vfg.2_Intron|FN1_uc002vfh.2_Intron|FN1_uc002vfi.2_Intron|FN1_uc002vfj.2_Intron|FN1_uc002vez.2_Intron|FN1_uc010zjp.1_Intron	NM_212482	NP_997647			fibronectin 1 isoform 1 preproprotein						acute-phase response|angiogenesis|leukocyte migration|peptide cross-linking|platelet activation|platelet degranulation|regulation of cell shape|substrate adhesion-dependent cell spreading	ER-Golgi intermediate compartment|fibrinogen complex|platelet alpha granule lumen|proteinaceous extracellular matrix	collagen binding|extracellular matrix structural constituent|heparin binding			central_nervous_system(7)|large_intestine(2)|breast(2)|ovary(1)|pancreas(1)	13		Renal(323;0.127)		Epithelial(149;9.59e-07)|all cancers(144;0.000174)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00948)	Alteplase(DB00009)|Anistreplase(DB00029)|Reteplase(DB00015)|Tenecteplase(DB00031)													---	---	---	---
STK36	27148	broad.mit.edu	37	2	219562025	219562026	+	Intron	INS	-	T	T			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:219562025_219562026insT	uc002viu.2	+						STK36_uc002viv.2_Intron|STK36_uc002viw.2_Intron|STK36_uc002vix.2_Intron	NM_015690	NP_056505			serine/threonine kinase 36						cilium assembly|positive regulation of hh target transcription factor activity|positive regulation of smoothened signaling pathway|post-embryonic development	aggresome|cytoplasm|focal adhesion|intermediate filament cytoskeleton|nucleus	ATP binding|protein serine/threonine kinase activity|transcription factor binding			ovary(4)|stomach(2)|lung(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)|breast(1)	11		Renal(207;0.0915)		Epithelial(149;9.65e-07)|all cancers(144;0.000174)|LUSC - Lung squamous cell carcinoma(224;0.00813)|Lung(261;0.00984)														---	---	---	---
MOGAT1	116255	broad.mit.edu	37	2	223562598	223562598	+	Intron	DEL	T	-	-	rs79429686		TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:223562598delT	uc010fws.1	+						MOGAT1_uc010fwt.1_Intron	NM_058165	NP_477513			monoacylglycerol O-acyltransferase 1						glycerol metabolic process	endoplasmic reticulum membrane|integral to membrane	2-acylglycerol O-acyltransferase activity			breast(1)	1		Renal(207;0.0183)		Epithelial(121;4.13e-10)|all cancers(144;2.06e-07)|LUSC - Lung squamous cell carcinoma(224;0.00829)|Lung(261;0.0105)														---	---	---	---
COL4A4	1286	broad.mit.edu	37	2	227916908	227916908	+	Intron	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:227916908delA	uc010zlt.1	-							NM_000092	NP_000083			alpha 4 type IV collagen precursor						axon guidance|glomerular basement membrane development	basal lamina|collagen type IV	extracellular matrix structural constituent|protein binding			ovary(5)|central_nervous_system(3)|pancreas(1)|breast(1)|skin(1)	11		Renal(207;0.00844)|all_lung(227;0.0187)|Lung NSC(271;0.0879)|all_hematologic(139;0.21)|Esophageal squamous(248;0.242)		Epithelial(121;6.7e-11)|all cancers(144;5.39e-08)|Lung(261;0.0132)|LUSC - Lung squamous cell carcinoma(224;0.0181)														---	---	---	---
TRIP12	9320	broad.mit.edu	37	2	230672689	230672690	+	Intron	DEL	TT	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:230672689_230672690delTT	uc002vpw.1	-						TRIP12_uc002vpx.1_Intron|TRIP12_uc002vpy.1_Intron|TRIP12_uc010zlz.1_Intron|TRIP12_uc010fxh.1_Intron	NM_004238	NP_004229			thyroid hormone receptor interactor 12						protein ubiquitination involved in ubiquitin-dependent protein catabolic process	proteasome complex	thyroid hormone receptor binding|ubiquitin-protein ligase activity			ovary(4)|lung(2)|breast(1)|central_nervous_system(1)|skin(1)	9		Renal(207;0.025)|all_hematologic(139;0.122)|all_lung(227;0.126)|Acute lymphoblastic leukemia(138;0.164)		Epithelial(121;4.76e-13)|all cancers(144;4.34e-10)|LUSC - Lung squamous cell carcinoma(224;0.00864)|Lung(119;0.0116)														---	---	---	---
SP140L	93349	broad.mit.edu	37	2	231266129	231266129	+	Frame_Shift_Del	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:231266129delT	uc010fxm.1	+	17	1562	c.1471delT	c.(1471-1473)TTTfs	p.F491fs	SP140L_uc010fxo.1_3'UTR	NM_138402	NP_612411	Q9H930	LY10L_HUMAN	SP140 nuclear body protein-like	Error:Variant_position_missing_in_Q9H930_after_alignment						nucleus	DNA binding|metal ion binding			central_nervous_system(1)	1																		---	---	---	---
INPP5D	3635	broad.mit.edu	37	2	234104167	234104167	+	Intron	DEL	G	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:234104167delG	uc010zmo.1	+						INPP5D_uc010zmp.1_Intron	NM_001017915	NP_001017915			SH2 containing inositol phosphatase isoform a						apoptosis|blood coagulation|leukocyte migration|T cell receptor signaling pathway	cytosol	inositol-polyphosphate 5-phosphatase activity|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity|SH3 domain binding			ovary(1)|central_nervous_system(1)	2		Breast(86;0.0013)|Renal(207;0.00339)|all_hematologic(139;0.0116)|all_lung(227;0.0273)|Acute lymphoblastic leukemia(138;0.0328)|Lung NSC(271;0.0843)		Epithelial(121;1.16e-17)|BRCA - Breast invasive adenocarcinoma(100;0.000479)|LUSC - Lung squamous cell carcinoma(224;0.00655)|Lung(119;0.00802)|GBM - Glioblastoma multiforme(43;0.0185)														---	---	---	---
COL6A3	1293	broad.mit.edu	37	2	238234469	238234469	+	Intron	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:238234469delA	uc002vwl.2	-						COL6A3_uc002vwo.2_Intron|COL6A3_uc010znj.1_Intron|COL6A3_uc002vwj.2_Intron	NM_004369	NP_004360			alpha 3 type VI collagen isoform 1 precursor						axon guidance|cell adhesion|muscle organ development	collagen type VI|extracellular space	serine-type endopeptidase inhibitor activity			ovary(8)|central_nervous_system(6)|skin(2)|upper_aerodigestive_tract(1)|pancreas(1)	18		Breast(86;0.000301)|Renal(207;0.000966)|all_hematologic(139;0.067)|Ovarian(221;0.0694)|all_lung(227;0.0943)|Melanoma(123;0.203)		Epithelial(121;1.23e-21)|OV - Ovarian serous cystadenocarcinoma(60;1.34e-10)|Kidney(56;5.71e-09)|KIRC - Kidney renal clear cell carcinoma(57;1.51e-07)|BRCA - Breast invasive adenocarcinoma(100;0.00025)|Lung(119;0.0142)|LUSC - Lung squamous cell carcinoma(224;0.034)														---	---	---	---
SCLY	51540	broad.mit.edu	37	2	238925156	238925156	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:238925156delT	uc002vxm.3	+						UBE2F_uc010znn.1_Intron|UBE2F_uc002vxk.2_Intron|UBE2F_uc002vxl.2_Intron|UBE2F_uc010zno.1_Intron|UBE2F_uc010znp.1_Intron	NM_016510	NP_057594			selenocysteine lyase						cellular amino acid metabolic process	cytosol	pyridoxal phosphate binding|selenocysteine lyase activity|transferase activity			ovary(2)	2		Breast(86;7.61e-05)|Renal(207;0.00183)|Ovarian(221;0.0481)|all_hematologic(139;0.158)|all_lung(227;0.198)|Melanoma(123;0.203)|Hepatocellular(293;0.244)		Epithelial(121;1.37e-23)|OV - Ovarian serous cystadenocarcinoma(60;4.6e-12)|Kidney(56;3.21e-09)|KIRC - Kidney renal clear cell carcinoma(57;8.25e-08)|BRCA - Breast invasive adenocarcinoma(100;0.000128)|Lung(119;0.0118)|LUSC - Lung squamous cell carcinoma(224;0.0285)														---	---	---	---
Unknown	0	broad.mit.edu	37	3	5125122	5125122	+	IGR	DEL	C	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:5125122delC								BHLHE40 (98259 upstream) : ARL8B (38808 downstream)																																			---	---	---	---
SETD5	55209	broad.mit.edu	37	3	9516725	9516725	+	Intron	DEL	T	-	-	rs113358265		TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:9516725delT	uc003brt.2	+						SETD5_uc003bru.2_Intron|SETD5_uc003brv.2_Intron|SETD5_uc010hck.2_Intron|SETD5_uc003brx.2_Intron	NM_001080517	NP_001073986			SET domain containing 5											ovary(2)	2	Medulloblastoma(99;0.227)			OV - Ovarian serous cystadenocarcinoma(96;0.112)														---	---	---	---
TTLL3	26140	broad.mit.edu	37	3	9869089	9869089	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:9869089delT	uc003btg.2	+						ARPC4_uc003btc.1_Intron|TTLL3_uc003btd.3_Intron|TTLL3_uc003btf.3_Intron|TTLL3_uc010hco.1_Intron|TTLL3_uc003bth.3_Intron|TTLL3_uc011atj.1_Intron|TTLL3_uc003btj.3_Intron|TTLL3_uc003bti.3_Intron|TTLL3_uc003btk.2_3'UTR	NM_001025930	NP_001021100			tubulin tyrosine ligase-like family, member 3						axoneme assembly|cilium assembly|protein polyglycylation	cilium axoneme|cytoplasm|microtubule	protein-glycine ligase activity, initiating|tubulin-tyrosine ligase activity			large_intestine(2)	2	Medulloblastoma(99;0.227)																	---	---	---	---
CAPN7	23473	broad.mit.edu	37	3	15282164	15282164	+	Intron	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:15282164delA	uc003bzn.2	+							NM_014296	NP_055111			calpain 7						proteolysis	nucleus	calcium-dependent cysteine-type endopeptidase activity			ovary(1)	1																		---	---	---	---
TBC1D5	9779	broad.mit.edu	37	3	17300086	17300086	+	Intron	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:17300086delA	uc003cbf.2	-						TBC1D5_uc010heu.2_Intron|TBC1D5_uc010hev.2_Intron|TBC1D5_uc003cbe.2_Intron|TBC1D5_uc010hew.1_Intron	NM_014744	NP_055559			TBC1 domain family, member 5 isoform b							intracellular	protein binding|Rab GTPase activator activity			ovary(1)	1																		---	---	---	---
TOP2B	7155	broad.mit.edu	37	3	25646157	25646158	+	Intron	INS	-	A	A			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:25646157_25646158insA	uc003cdj.2	-						TOP2B_uc011awm.1_Intron|TOP2B_uc010hff.1_Intron	NM_001068	NP_001059			DNA topoisomerase II, beta isozyme						DNA topological change|DNA-dependent DNA replication|mitotic cell cycle G2/M transition decatenation checkpoint|mitotic recombination|resolution of meiotic recombination intermediates|sister chromatid segregation	cytosol|DNA topoisomerase complex (ATP-hydrolyzing)|nucleolus|nucleoplasm|synaptonemal complex|WINAC complex	ATP binding|chromatin binding|DNA topoisomerase (ATP-hydrolyzing) activity|DNA-dependent ATPase activity|histone deacetylase binding|protein C-terminus binding|protein heterodimerization activity|protein kinase C binding|sequence-specific DNA binding transcription factor activity			breast(2)|ovary(1)|lung(1)|skin(1)	5																		---	---	---	---
KIF15	56992	broad.mit.edu	37	3	44868019	44868019	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:44868019delT	uc003cnx.3	+						KIF15_uc010hiq.2_Intron|KIF15_uc010hir.2_Intron	NM_020242	NP_064627			kinesin family member 15						blood coagulation|cell proliferation|microtubule-based movement|mitosis	centrosome|cytosol|microtubule|plus-end kinesin complex|spindle	ATP binding|DNA binding|microtubule motor activity			ovary(1)	1				BRCA - Breast invasive adenocarcinoma(193;0.0099)|KIRC - Kidney renal clear cell carcinoma(197;0.0564)|Kidney(197;0.0707)														---	---	---	---
LARS2	23395	broad.mit.edu	37	3	45561625	45561625	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:45561625delT	uc003cop.1	+						LARS2_uc010hit.1_Intron	NM_015340	NP_056155			leucyl-tRNA synthetase 2, mitochondrial						leucyl-tRNA aminoacylation	mitochondrial matrix	ATP binding|leucine-tRNA ligase activity			upper_aerodigestive_tract(1)|ovary(1)	2				BRCA - Breast invasive adenocarcinoma(193;0.0122)|KIRC - Kidney renal clear cell carcinoma(197;0.0313)|Kidney(197;0.0372)	L-Leucine(DB00149)													---	---	---	---
DOCK3	1795	broad.mit.edu	37	3	51266881	51266881	+	Intron	DEL	A	-	-	rs113104131		TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:51266881delA	uc011bds.1	+							NM_004947	NP_004938			dedicator of cytokinesis 3							cytoplasm	GTP binding|GTPase binding|guanyl-nucleotide exchange factor activity|SH3 domain binding				0				BRCA - Breast invasive adenocarcinoma(193;0.00105)|KIRC - Kidney renal clear cell carcinoma(197;0.00449)|Kidney(197;0.00518)														---	---	---	---
CACNA1D	776	broad.mit.edu	37	3	53529004	53529004	+	5'Flank	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:53529004delT	uc003dgv.3	+						CACNA1D_uc003dgu.3_5'Flank|CACNA1D_uc003dgy.3_5'Flank	NM_001128840	NP_001122312			calcium channel, voltage-dependent, L type,						axon guidance|energy reserve metabolic process|regulation of insulin secretion	voltage-gated calcium channel complex	voltage-gated calcium channel activity			ovary(6)|upper_aerodigestive_tract(2)|liver(1)|central_nervous_system(1)|skin(1)	11				BRCA - Breast invasive adenocarcinoma(193;0.00029)|KIRC - Kidney renal clear cell carcinoma(284;0.0145)|Kidney(284;0.0175)|OV - Ovarian serous cystadenocarcinoma(275;0.0613)	Verapamil(DB00661)													---	---	---	---
TOMM70A	9868	broad.mit.edu	37	3	100086754	100086754	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:100086754delT	uc003dtw.2	-							NM_014820	NP_055635			translocase of outer mitochondrial membrane 70						protein targeting to mitochondrion	integral to membrane|mitochondrial outer membrane translocase complex	protein binding|protein transmembrane transporter activity			ovary(1)	1																		---	---	---	---
LOC100302640	100302640	broad.mit.edu	37	3	106567681	106567682	+	Intron	INS	-	T	T			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:106567681_106567682insT	uc003dwf.3	-											Homo sapiens cDNA clone IMAGE:5284861.												0																		---	---	---	---
MORC1	27136	broad.mit.edu	37	3	108818455	108818456	+	Intron	DEL	TT	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:108818455_108818456delTT	uc003dxl.2	-						MORC1_uc011bhn.1_Intron	NM_014429	NP_055244			MORC family CW-type zinc finger 1						cell differentiation|multicellular organismal development|spermatogenesis	nucleus	ATP binding|zinc ion binding			ovary(3)|skin(3)|breast(2)	8																		---	---	---	---
Unknown	0	broad.mit.edu	37	3	110401053	110401054	+	IGR	INS	-	T	T	rs113398685		TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:110401053_110401054insT								None (None upstream) : PVRL3 (389811 downstream)																																			---	---	---	---
TMPRSS7	344805	broad.mit.edu	37	3	111775808	111775808	+	Intron	DEL	G	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:111775808delG	uc010hqb.2	+						TMPRSS7_uc011bhr.1_Intron	NM_001042575	NP_001036040			transmembrane protease, serine 7						proteolysis	integral to membrane|plasma membrane	serine-type endopeptidase activity			ovary(1)|kidney(1)	2																		---	---	---	---
RPN1	6184	broad.mit.edu	37	3	128350619	128350620	+	Intron	INS	-	G	G			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:128350619_128350620insG	uc003ekr.1	-						RPN1_uc011bkq.1_Intron	NM_002950	NP_002941			ribophorin I precursor						post-translational protein modification|protein N-linked glycosylation via asparagine	integral to membrane|melanosome|oligosaccharyltransferase complex|rough microsome	dolichyl-diphosphooligosaccharide-protein glycotransferase activity|protein binding			ovary(2)|central_nervous_system(1)	3				GBM - Glioblastoma multiforme(114;0.189)				T	EVI1	AML								---	---	---	---
IFT122	55764	broad.mit.edu	37	3	129183764	129183764	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:129183764delT	uc003emm.2	+						IFT122_uc003eml.2_Intron|IFT122_uc003emn.2_Intron|IFT122_uc003emo.2_Intron|IFT122_uc003emp.2_Intron|IFT122_uc010htc.2_Intron|IFT122_uc011bky.1_Intron|IFT122_uc003emq.2_Intron|IFT122_uc003emr.2_Intron|IFT122_uc011bla.1_Intron|IFT122_uc011bkx.1_Intron|IFT122_uc011bkz.1_Intron	NM_052989	NP_443715			WD repeat domain 10 isoform 2						camera-type eye morphogenesis|cilium morphogenesis|embryonic body morphogenesis|embryonic heart tube development|limb development|neural tube closure	microtubule basal body|photoreceptor connecting cilium				ovary(1)|skin(1)	2																		---	---	---	---
TMEM108	66000	broad.mit.edu	37	3	133114515	133114516	+	Intron	DEL	AC	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:133114515_133114516delAC	uc003eph.2	+						TMEM108_uc003epi.2_Intron|TMEM108_uc003epk.2_Intron|TMEM108_uc003epm.2_Intron	NM_023943	NP_076432			transmembrane protein 108 precursor							integral to membrane				ovary(2)|skin(2)	4																		---	---	---	---
NMNAT3	349565	broad.mit.edu	37	3	139301744	139301745	+	Intron	DEL	AA	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:139301744_139301745delAA	uc003etj.2	-						NMNAT3_uc003etk.2_Intron|NMNAT3_uc003etl.2_Intron|NMNAT3_uc010hul.2_Intron	NM_178177	NP_835471			nicotinamide mononucleotide adenylyltransferase						water-soluble vitamin metabolic process	cytosol|mitochondrion	ATP binding|nicotinamide-nucleotide adenylyltransferase activity|nicotinate-nucleotide adenylyltransferase activity				0																		---	---	---	---
NMD3	51068	broad.mit.edu	37	3	160960578	160960578	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:160960578delT	uc003feb.1	+						NMD3_uc003fec.2_Intron|NMD3_uc003fed.1_Intron|NMD3_uc010hwh.2_Intron	NM_015938	NP_057022			NMD3 homolog						protein transport	cytoplasm|nucleolus|nucleoplasm				ovary(1)	1			Lung(72;0.00111)|LUSC - Lung squamous cell carcinoma(72;0.00156)															---	---	---	---
TNIK	23043	broad.mit.edu	37	3	170802258	170802258	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:170802258delT	uc003fhh.2	-						TNIK_uc003fhi.2_Intron|TNIK_uc003fhj.2_Intron|TNIK_uc003fhk.2_Intron|TNIK_uc003fhl.2_Intron|TNIK_uc003fhm.2_Intron|TNIK_uc003fhn.2_Intron|TNIK_uc003fho.2_Intron|TNIK_uc003fhg.2_Intron|TNIK_uc003fhp.2_5'Flank	NM_015028	NP_055843			TRAF2 and NCK interacting kinase isoform 1						actin cytoskeleton reorganization|activation of JNKK activity|protein autophosphorylation|regulation of dendrite morphogenesis|Wnt receptor signaling pathway	cytoskeleton|nucleus|recycling endosome	ATP binding|protein binding|protein serine/threonine kinase activity|small GTPase regulator activity			ovary(4)|large_intestine(1)	5	all_cancers(22;2.55e-19)|all_lung(20;2.22e-14)|Ovarian(172;0.00197)|Breast(254;0.122)		LUSC - Lung squamous cell carcinoma(14;3.57e-14)|Lung(28;9.39e-14)															---	---	---	---
ACTL6A	86	broad.mit.edu	37	3	179305643	179305643	+	Intron	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:179305643delA	uc003fjw.2	+						ACTL6A_uc003fjx.2_Intron|ACTL6A_uc003fjy.2_Intron	NM_004301	NP_004292			actin-like 6A isoform 1						chromatin remodeling|DNA recombination|DNA repair|histone H2A acetylation|histone H4 acetylation|nervous system development|regulation of growth|regulation of transcription, DNA-dependent|signal transduction|transcription, DNA-dependent	Ino80 complex|npBAF complex|NuA4 histone acetyltransferase complex|plasma membrane|SWI/SNF complex	ATP binding|chromatin binding			ovary(1)	1	all_cancers(143;3.94e-16)|Ovarian(172;0.0172)|Breast(254;0.191)		OV - Ovarian serous cystadenocarcinoma(80;5.98e-26)|GBM - Glioblastoma multiforme(14;0.0169)															---	---	---	---
USP13	8975	broad.mit.edu	37	3	179479203	179479203	+	Intron	DEL	T	-	-	rs74695249		TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:179479203delT	uc003fkh.2	+							NM_003940	NP_003931			ubiquitin thiolesterase 13						ubiquitin-dependent protein catabolic process		cysteine-type endopeptidase activity|omega peptidase activity|protein binding|ubiquitin thiolesterase activity|ubiquitin-specific protease activity|zinc ion binding			ovary(1)	1	all_cancers(143;7.79e-15)|Ovarian(172;0.0338)|Breast(254;0.148)		OV - Ovarian serous cystadenocarcinoma(80;1e-25)|GBM - Glioblastoma multiforme(14;0.0169)															---	---	---	---
UTS2D	257313	broad.mit.edu	37	3	190986180	190986180	+	3'UTR	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:190986180delT	uc003fsu.2	-	9						NM_198152	NP_937795			urotensin 2 domain containing precursor							extracellular region	hormone activity				0	all_cancers(143;1.77e-09)|Ovarian(172;0.103)		LUSC - Lung squamous cell carcinoma(58;2.42e-06)|Lung(62;2.86e-06)	GBM - Glioblastoma multiforme(46;0.000214)														---	---	---	---
GAK	2580	broad.mit.edu	37	4	887514	887514	+	Intron	DEL	C	-	-	rs76878427		TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:887514delC	uc003gbm.3	-						GAK_uc003gbn.3_Intron|GAK_uc010ibk.1_Intron|GAK_uc003gbl.3_Intron	NM_005255	NP_005246			cyclin G associated kinase						cell cycle	focal adhesion|Golgi apparatus|perinuclear region of cytoplasm	ATP binding|heat shock protein binding|protein serine/threonine kinase activity			lung(2)|central_nervous_system(1)|skin(1)	4				Colorectal(103;0.219)														---	---	---	---
Unknown	0	broad.mit.edu	37	4	3923361	3923361	+	IGR	DEL	G	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:3923361delG								ADRA2C (153110 upstream) : LOC348926 (20309 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	10412981	10412982	+	IGR	INS	-	CT	CT	rs143148489		TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:10412981_10412982insCT								WDR1 (294408 upstream) : ZNF518B (28523 downstream)																																			---	---	---	---
ANAPC4	29945	broad.mit.edu	37	4	25411236	25411236	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:25411236delT	uc003gro.2	+						ANAPC4_uc003grp.2_Intron	NM_013367	NP_037499			anaphase-promoting complex subunit 4						anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|cell division|G2/M transition of mitotic cell cycle|mitotic anaphase|mitotic cell cycle spindle assembly checkpoint|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|protein K11-linked ubiquitination	anaphase-promoting complex|cytosol|nucleoplasm	protein phosphatase binding|ubiquitin-protein ligase activity			ovary(2)|large_intestine(1)|pancreas(1)|skin(1)	5		Breast(46;0.0503)																---	---	---	---
SEL1L3	23231	broad.mit.edu	37	4	25804213	25804213	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:25804213delT	uc003gru.3	-						SEL1L3_uc003grv.2_Intron	NM_015187	NP_056002			sel-1 suppressor of lin-12-like 3							integral to membrane	binding				0																		---	---	---	---
LIAS	11019	broad.mit.edu	37	4	39478849	39478849	+	3'UTR	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:39478849delA	uc003guf.2	+	11					LIAS_uc003gug.2_3'UTR|LIAS_uc003guh.2_3'UTR	NM_006859	NP_006850			lipoic acid synthetase isoform 1 precursor						inflammatory response|response to lipopolysaccharide|response to oxidative stress	mitochondrion	4 iron, 4 sulfur cluster binding|lipoate synthase activity|metal ion binding				0					Lipoic Acid(DB00166)													---	---	---	---
SLC30A9	10463	broad.mit.edu	37	4	42037517	42037518	+	Intron	DEL	TT	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:42037517_42037518delTT	uc003gwl.2	+						SLC30A9_uc011byx.1_Intron	NM_006345	NP_006336			solute carrier family 30 (zinc transporter),						nucleotide-excision repair|zinc ion transport	cytoskeleton|integral to membrane|nucleus	cation transmembrane transporter activity|nucleotide binding|sequence-specific DNA binding transcription factor activity			central_nervous_system(2)|ovary(1)	3																		---	---	---	---
CORIN	10699	broad.mit.edu	37	4	47625086	47625087	+	Intron	INS	-	CTCTCTCT	CTCTCTCT	rs35531403		TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:47625086_47625087insCTCTCTCT	uc003gxm.2	-						CORIN_uc011bzf.1_Intron|CORIN_uc011bzg.1_Intron	NM_006587	NP_006578			corin						peptide hormone processing|regulation of systemic arterial blood pressure by atrial natriuretic peptide	integral to membrane|plasma membrane	scavenger receptor activity|serine-type endopeptidase activity|serine-type exopeptidase activity			ovary(1)|central_nervous_system(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	4	70267902	70267902	+	IGR	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:70267902delA								UGT2B28 (107135 upstream) : UGT2B4 (77982 downstream)																																			---	---	---	---
HTN1	3346	broad.mit.edu	37	4	70921372	70921372	+	Intron	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:70921372delA	uc003hex.2	+							NM_002159	NP_002150			histatin 1 precursor						biomineral tissue development|defense response to bacterium|defense response to fungus|killing of cells of other organism	extracellular region	protein binding			skin(1)	1																		---	---	---	---
DCK	1633	broad.mit.edu	37	4	71889230	71889231	+	Intron	INS	-	T	T	rs3833976		TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:71889230_71889231insT	uc003hfx.2	+						DCK_uc011cbb.1_Intron	NM_000788	NP_000779			deoxycytidine kinase						purine base metabolic process|purine-containing compound salvage|pyrimidine base metabolic process|pyrimidine nucleoside salvage|pyrimidine nucleotide metabolic process	cytosol|nucleus	ATP binding|deoxycytidine kinase activity|drug binding|phosphotransferase activity, alcohol group as acceptor|protein homodimerization activity			ovary(1)	1			Lung(101;0.235)		Cladribine(DB00242)|Clofarabine(DB00631)|Decitabine(DB01262)|Fludarabine(DB01073)|Gemcitabine(DB00441)|Pemetrexed(DB00642)|Zalcitabine(DB00943)													---	---	---	---
RASSF6	166824	broad.mit.edu	37	4	74441817	74441817	+	3'UTR	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:74441817delT	uc003hhd.1	-	11					RASSF6_uc003hhc.1_3'UTR|RASSF6_uc010iik.1_3'UTR|RASSF6_uc010iil.1_3'UTR	NM_201431	NP_958834			Ras association (RalGDS/AF-6) domain family 6						apoptosis|signal transduction		protein binding			pancreas(2)	2	Breast(15;0.00102)		all cancers(17;0.00104)|Lung(101;0.128)|LUSC - Lung squamous cell carcinoma(112;0.187)															---	---	---	---
FRAS1	80144	broad.mit.edu	37	4	79328730	79328730	+	Intron	DEL	A	-	-	rs34880017		TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:79328730delA	uc003hlb.2	+						FRAS1_uc003hkw.2_Intron	NM_025074	NP_079350			Fraser syndrome 1						cell communication	integral to membrane|plasma membrane	metal ion binding			large_intestine(5)	5																		---	---	---	---
SEC31A	22872	broad.mit.edu	37	4	83740164	83740164	+	3'UTR	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:83740164delT	uc003hnf.2	-	27					SEC31A_uc003hnd.2_3'UTR|SEC31A_uc003hne.2_3'UTR|SEC31A_uc011ccl.1_3'UTR|SEC31A_uc003hnl.2_3'UTR|SEC31A_uc003hng.2_3'UTR|SEC31A_uc003hnh.2_3'UTR|SEC31A_uc003hni.2_3'UTR|SEC31A_uc003hnj.2_3'UTR|SEC31A_uc011ccm.1_3'UTR|SEC31A_uc011ccn.1_3'UTR|SEC31A_uc003hnk.2_3'UTR|SEC31A_uc003hnm.2_3'UTR	NM_001077207	NP_001070675			SEC31 homolog A isoform 1						COPII vesicle coating|post-translational protein modification|protein N-linked glycosylation via asparagine|protein transport|response to calcium ion	COPII vesicle coat|cytosol|endoplasmic reticulum membrane|perinuclear region of cytoplasm	calcium-dependent protein binding		SEC31A/JAK2(4)|SEC31A/ALK(3)	haematopoietic_and_lymphoid_tissue(4)|soft_tissue(3)|breast(1)	8		Hepatocellular(203;0.114)																---	---	---	---
RPL34	6164	broad.mit.edu	37	4	109546421	109546421	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:109546421delT	uc003hyz.2	+						RPL34_uc003hza.2_Intron	NM_000995	NP_000986			ribosomal protein L34						endocrine pancreas development|translational elongation|translational termination|viral transcription	cytosolic large ribosomal subunit	protein binding|RNA binding|structural constituent of ribosome				0		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;0.000286)														---	---	---	---
AP1AR	55435	broad.mit.edu	37	4	113186056	113186056	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:113186056delT	uc003iaj.3	+						AP1AR_uc010imm.1_Intron|AP1AR_uc003iak.3_Intron	NM_018569	NP_061039			adaptor-related protein complex 1 associated						protein transport	early endosome|Golgi apparatus|late endosome|transport vesicle					0																		---	---	---	---
UGT8	7368	broad.mit.edu	37	4	115585067	115585067	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:115585067delT	uc003ibs.2	+						UGT8_uc003ibt.2_Intron|UGT8_uc011cge.1_Intron	NM_001128174	NP_001121646			UDP-galactose-ceramide galactosyltransferase 8						central nervous system development|peripheral nervous system development	integral to membrane	2-hydroxyacylsphingosine 1-beta-galactosyltransferase activity|UDP-galactose:glucosylceramide beta-1,4-galactosyltransferase activity			ovary(1)|skin(1)	2		Ovarian(17;0.156)		OV - Ovarian serous cystadenocarcinoma(123;0.000632)														---	---	---	---
ELMOD2	255520	broad.mit.edu	37	4	141448706	141448706	+	Intron	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:141448706delA	uc003iik.2	+							NM_153702	NP_714913			ELMO/CED-12 domain containing 2						phagocytosis|regulation of defense response to virus|response to virus	cytoskeleton	GTPase activator activity			ovary(1)	1	all_hematologic(180;0.162)																	---	---	---	---
USP38	84640	broad.mit.edu	37	4	144108896	144108896	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:144108896delT	uc003ijb.2	+						USP38_uc003ija.3_Intron|USP38_uc003ijc.2_Intron	NM_032557	NP_115946			ubiquitin specific peptidase 38						ubiquitin-dependent protein catabolic process		cysteine-type peptidase activity|ubiquitin thiolesterase activity			lung(2)|ovary(1)|breast(1)|pancreas(1)	5	all_hematologic(180;0.158)																	---	---	---	---
ABCE1	6059	broad.mit.edu	37	4	146041224	146041224	+	Frame_Shift_Del	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:146041224delA	uc003ijx.2	+	11	1503	c.1063delA	c.(1063-1065)AAAfs	p.K355fs	ABCE1_uc003ijy.2_Frame_Shift_Del_p.K355fs|ABCE1_uc010iot.2_RNA	NM_001040876	NP_001035809	P61221	ABCE1_HUMAN	ATP-binding cassette, sub-family E, member 1	355	ABC transporter 2.				interspecies interaction between organisms|response to virus|RNA catabolic process	mitochondrion	ATP binding|ATPase activity|electron carrier activity|iron-sulfur cluster binding|ribonuclease inhibitor activity			skin(1)	1	all_hematologic(180;0.151)																	---	---	---	---
Unknown	0	broad.mit.edu	37	4	153849441	153849442	+	IGR	INS	-	A	A			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:153849441_153849442insA								ARFIP1 (16380 upstream) : FHDC1 (14693 downstream)																																			---	---	---	---
ACCN5	51802	broad.mit.edu	37	4	156773541	156773541	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:156773541delT	uc003ipe.1	-							NM_017419	NP_059115			amiloride-sensitive cation channel 5,							integral to membrane|plasma membrane				ovary(2)|skin(1)	3	all_hematologic(180;0.24)	Renal(120;0.0458)		KIRC - Kidney renal clear cell carcinoma(143;0.0464)|Kidney(143;0.058)|COAD - Colon adenocarcinoma(41;0.141)														---	---	---	---
GLRB	2743	broad.mit.edu	37	4	158059927	158059927	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:158059927delT	uc003ipj.2	+							NM_000824	NP_000815			glycine receptor, beta isoform A precursor						nervous system development|neuropeptide signaling pathway|startle response	cell junction|chloride channel complex|integral to plasma membrane|postsynaptic membrane	extracellular-glycine-gated chloride channel activity|protein binding|receptor activity			skin(2)	2	all_hematologic(180;0.24)	Renal(120;0.0458)		KIRC - Kidney renal clear cell carcinoma(143;0.0564)|COAD - Colon adenocarcinoma(41;0.0642)|Kidney(143;0.0707)	Glycine(DB00145)													---	---	---	---
RAPGEF2	9693	broad.mit.edu	37	4	160251796	160251797	+	Intron	INS	-	A	A	rs78225051		TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:160251796_160251797insA	uc003iqg.3	+							NM_014247	NP_055062			Rap guanine nucleotide exchange factor 2						cAMP-mediated signaling|MAPKKK cascade|small GTPase mediated signal transduction	integral to plasma membrane|intracellular	calcium ion binding|diacylglycerol binding|Rap GTPase activator activity|Rap guanyl-nucleotide exchange factor activity|signal transducer activity			lung(2)|upper_aerodigestive_tract(1)|skin(1)	4	all_hematologic(180;0.24)			COAD - Colon adenocarcinoma(41;0.0817)														---	---	---	---
SEMA5A	9037	broad.mit.edu	37	5	9201932	9201932	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:9201932delT	uc003jek.2	-							NM_003966	NP_003957			semaphorin 5A precursor						cell adhesion|cell-cell signaling	integral to membrane|plasma membrane				ovary(1)|central_nervous_system(1)	2																		---	---	---	---
GUSBP1	728411	broad.mit.edu	37	5	21459960	21459960	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:21459960delT	uc010iub.2	+						GUSBP1_uc011cnn.1_Intron|GUSBP1_uc003jgh.3_Intron|GUSBP1_uc003jgf.3_Intron|GUSBP1_uc003jgg.3_Intron	NR_027028				SubName: Full=Putative uncharacterized protein GUSBL2;												0																OREG0016459	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
C5orf22	55322	broad.mit.edu	37	5	31541526	31541526	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:31541526delT	uc003jhj.3	+						C5orf22_uc011cnw.1_Intron|C5orf22_uc003jhk.3_Intron	NM_018356	NP_060826			hypothetical protein LOC55322											ovary(2)	2																		---	---	---	---
NPR3	4883	broad.mit.edu	37	5	32786466	32786466	+	3'UTR	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:32786466delT	uc003jhv.2	+	8					NPR3_uc011cnz.1_3'UTR|NPR3_uc003jhu.2_3'UTR|C5orf23_uc003jhw.1_5'Flank	NM_000908	NP_000899			natriuretic peptide receptor C/guanylate cyclase						osteoclast proliferation|positive regulation of urine volume|regulation of blood pressure|regulation of osteoblast proliferation|skeletal system development	integral to membrane	hormone binding|natriuretic peptide receptor activity			ovary(1)|central_nervous_system(1)	2					Nesiritide(DB04899)													---	---	---	---
C5orf42	65250	broad.mit.edu	37	5	37120153	37120153	+	Intron	DEL	A	-	-	rs75040582	by1000genomes	TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:37120153delA	uc011cpa.1	-						C5orf42_uc003jko.1_Intron|C5orf42_uc003jkp.1_Intron|C5orf42_uc011coy.1_Intron|C5orf42_uc003jks.2_Intron|C5orf42_uc011coz.1_Intron	NM_023073	NP_075561			hypothetical protein LOC65250											ovary(4)|breast(2)|skin(1)	7	all_lung(31;0.000616)		COAD - Colon adenocarcinoma(61;0.14)|Epithelial(62;0.177)|Colorectal(62;0.202)															---	---	---	---
WDR70	55100	broad.mit.edu	37	5	37697601	37697601	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:37697601delT	uc003jkv.2	+						WDR70_uc010iva.1_Intron	NM_018034	NP_060504			WD repeat domain 70											ovary(1)|central_nervous_system(1)	2	all_lung(31;0.000285)		COAD - Colon adenocarcinoma(61;0.14)|Colorectal(62;0.202)															---	---	---	---
KIF2A	3796	broad.mit.edu	37	5	61662224	61662224	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:61662224delT	uc003jsy.3	+						KIF2A_uc003jsz.3_Intron|KIF2A_uc010iwp.2_Intron|KIF2A_uc003jsx.3_Intron|KIF2A_uc010iwq.2_Intron	NM_004520	NP_004511			kinesin heavy chain member 2 isoform 1						blood coagulation|cell differentiation|cell division|microtubule-based movement|mitotic prometaphase|mitotic spindle organization|nervous system development	centrosome|cytosol|microtubule|spindle pole	ATP binding|microtubule motor activity|protein binding				0		Lung NSC(810;8.94e-06)|Prostate(74;0.0132)|Ovarian(174;0.051)|Breast(144;0.077)		Lung(70;0.14)														---	---	---	---
GTF2H2B	653238	broad.mit.edu	37	5	69717511	69717512	+	Intron	INS	-	G	G			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:69717511_69717512insG	uc003jzb.3	+						uc011crh.1_Intron|uc011crl.1_Intron|LOC100170939_uc010ixu.2_Intron|uc003jyr.1_Intron|LOC100170939_uc003jys.2_Intron|LOC100170939_uc011crn.1_Intron|uc011cro.1_Intron|GTF2H2B_uc011crp.1_Intron|GTF2H2B_uc003jza.3_Intron|GTF2H2B_uc003jzd.1_5'Flank	NM_001098729	NP_001092199			general transcription factor IIH, polypeptide												0																		---	---	---	---
RPS23	6228	broad.mit.edu	37	5	81571879	81571879	+	3'UTR	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:81571879delT	uc003khu.2	-	4						NM_001025	NP_001016			ribosomal protein S23						endocrine pancreas development|translational elongation|translational termination|viral transcription	cytosolic small ribosomal subunit	protein binding|structural constituent of ribosome				0		Lung NSC(167;0.0025)|all_lung(232;0.00278)|Ovarian(174;0.0336)		OV - Ovarian serous cystadenocarcinoma(54;1.94e-42)|Epithelial(54;8.38e-37)|all cancers(79;1.42e-31)														---	---	---	---
TMEM161B	153396	broad.mit.edu	37	5	87492365	87492365	+	Intron	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:87492365delA	uc003kjc.2	-						TMEM161B_uc011cty.1_Intron|TMEM161B_uc010jax.2_Intron|TMEM161B_uc011ctx.1_Intron	NM_153354	NP_699185			transmembrane protein 161B							integral to membrane				skin(2)	2		all_cancers(142;0.000275)|Lung NSC(167;0.00901)|all_lung(232;0.0111)|Colorectal(57;0.0959)|Ovarian(174;0.1)		OV - Ovarian serous cystadenocarcinoma(54;6.24e-36)|Epithelial(54;6.8e-31)|all cancers(79;1.07e-26)														---	---	---	---
PAM	5066	broad.mit.edu	37	5	102355717	102355717	+	Intron	DEL	T	-	-	rs3215069		TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:102355717delT	uc003knw.2	+						PAM_uc003kns.2_Intron|PAM_uc003knt.2_Intron|PAM_uc003knu.2_Intron|PAM_uc003knv.2_Intron|PAM_uc011cuz.1_Intron|PAM_uc003knz.2_Intron	NM_000919	NP_000910			peptidylglycine alpha-amidating monooxygenase						peptide metabolic process|protein modification process	extracellular region|integral to membrane|stored secretory granule	L-ascorbic acid binding|peptidylamidoglycolate lyase activity|peptidylglycine monooxygenase activity|protein binding				0		all_cancers(142;3.12e-07)|all_epithelial(76;3.48e-10)|Prostate(80;0.00914)|Lung NSC(167;0.0213)|Ovarian(225;0.024)|Colorectal(57;0.0251)|all_lung(232;0.0284)		Epithelial(69;1.1e-13)|COAD - Colon adenocarcinoma(37;0.0127)	Vitamin C(DB00126)													---	---	---	---
Unknown	0	broad.mit.edu	37	5	117115221	117115221	+	IGR	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:117115221delT								None (None upstream) : None (None downstream)																																			---	---	---	---
MYOT	9499	broad.mit.edu	37	5	137217571	137217571	+	Intron	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:137217571delA	uc011cye.1	+						MYOT_uc003lbv.2_Intron|MYOT_uc011cyg.1_Intron|MYOT_uc011cyh.1_Intron	NM_001135940	NP_001129412			myotilin isoform b						muscle contraction	actin cytoskeleton|sarcolemma|sarcomere	actin binding|structural constituent of muscle			large_intestine(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0109)															---	---	---	---
Unknown	0	broad.mit.edu	37	5	147517869	147517869	+	IGR	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:147517869delT								SPINK5 (944 upstream) : SPINK14 (31427 downstream)																																			---	---	---	---
COL23A1	91522	broad.mit.edu	37	5	177673154	177673171	+	Intron	DEL	GTGCAGGGACCCAGTGAG	-	-	rs35716676		TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:177673154_177673171delGTGCAGGGACCCAGTGAG	uc003mje.2	-						COL23A1_uc010jkt.2_Intron	NM_173465	NP_775736			collagen, type XXIII, alpha 1							collagen|integral to membrane|plasma membrane	protein binding			central_nervous_system(1)|skin(1)	2	all_cancers(89;0.00188)|Renal(175;0.000159)|Lung NSC(126;0.00814)|all_lung(126;0.0129)	all_neural(177;0.00802)|Medulloblastoma(196;0.0145)|all_hematologic(541;0.248)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	OV - Ovarian serous cystadenocarcinoma(192;0.153)|all cancers(165;0.172)														---	---	---	---
MAPK9	5601	broad.mit.edu	37	5	179707339	179707339	+	Intron	DEL	T	-	-	rs138341304	by1000genomes	TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:179707339delT	uc003mls.3	-						MAPK9_uc003mlt.3_Intron|MAPK9_uc010jlc.2_Intron|MAPK9_uc003mlv.3_Intron|MAPK9_uc011dgx.1_Intron	NM_002752	NP_002743			mitogen-activated protein kinase 9 isoform JNK2						innate immune response|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|positive regulation of gene expression|positive regulation of macrophage derived foam cell differentiation|regulation of sequence-specific DNA binding transcription factor activity|stress-activated MAPK cascade|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway	cytosol|nucleoplasm	ATP binding|JUN kinase activity|protein binding|protein binding			central_nervous_system(2)|upper_aerodigestive_tract(1)|large_intestine(1)	4	all_cancers(89;6.54e-05)|all_epithelial(37;1.22e-05)|Renal(175;0.000269)|Lung NSC(126;0.00199)|all_lung(126;0.00351)|Breast(19;0.137)	all_cancers(40;0.0236)|Medulloblastoma(196;0.0133)|all_neural(177;0.0199)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)															---	---	---	---
SIRT5	23408	broad.mit.edu	37	6	13584591	13584591	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:13584591delT	uc003nay.2	+						SIRT5_uc003naw.2_Intron|SIRT5_uc003nax.2_Intron|SIRT5_uc011dit.1_Intron	NM_012241	NP_036373			sirtuin 5 isoform 1						chromatin silencing|protein ADP-ribosylation|protein deacetylation	mitochondrial intermembrane space|mitochondrial matrix	hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides|NAD+ ADP-ribosyltransferase activity|NAD+ binding|zinc ion binding			skin(2)|upper_aerodigestive_tract(1)	3	Breast(50;0.00669)|Ovarian(93;0.0634)	all_hematologic(90;0.117)	Epithelial(50;0.176)		Suramin(DB04786)													---	---	---	---
MYLIP	29116	broad.mit.edu	37	6	16141709	16141709	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:16141709delT	uc003nbq.2	+						MYLIP_uc003nbr.2_Intron	NM_013262	NP_037394			myosin regulatory light chain interacting						cellular component movement|nervous system development	cytoplasm|cytoskeleton|extrinsic to membrane	cytoskeletal protein binding|ubiquitin-protein ligase activity|zinc ion binding			pancreas(1)	1	Breast(50;0.0799)|Ovarian(93;0.103)	all_hematologic(90;0.0895)	Epithelial(50;0.241)															---	---	---	---
CDKAL1	54901	broad.mit.edu	37	6	20955922	20955922	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:20955922delT	uc003ndc.1	+						CDKAL1_uc003ndd.1_Intron|CDKAL1_uc003nde.1_Intron	NM_017774	NP_060244			CDK5 regulatory subunit associated protein						RNA modification	integral to membrane	4 iron, 4 sulfur cluster binding|metal ion binding|transferase activity			ovary(2)	2	all_epithelial(95;0.0708)|Breast(50;0.131)|Ovarian(93;0.227)		OV - Ovarian serous cystadenocarcinoma(7;0.0241)|all cancers(50;0.123)|Epithelial(50;0.248)															---	---	---	---
NFYA	4800	broad.mit.edu	37	6	41057863	41057863	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:41057863delT	uc003opo.2	+						NFYA_uc003opp.2_Intron|NFYA_uc003opq.2_Intron	NM_002505	NP_002496			nuclear transcription factor Y, alpha isoform 1						transcription from RNA polymerase II promoter	CCAAT-binding factor complex	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity				0	Ovarian(28;0.0418)|Colorectal(47;0.196)																	---	---	---	---
PGM3	5238	broad.mit.edu	37	6	83900377	83900377	+	Intron	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:83900377delA	uc003pjv.2	-						PGM3_uc003pjw.2_Intron|PGM3_uc011dyz.1_Intron|RWDD2A_uc003pjx.3_5'Flank|RWDD2A_uc011dza.1_5'Flank	NM_015599	NP_056414			phosphoglucomutase 3						dolichol-linked oligosaccharide biosynthetic process|embryo development ending in birth or egg hatching|glucose 1-phosphate metabolic process|hemopoiesis|post-translational protein modification|protein N-linked glycosylation via asparagine|UDP-N-acetylglucosamine biosynthetic process	cytosol	magnesium ion binding|phosphoacetylglucosamine mutase activity|phosphoglucomutase activity				0		all_cancers(76;0.000504)|Acute lymphoblastic leukemia(125;3.85e-06)|all_hematologic(105;0.0017)|all_epithelial(107;0.068)		BRCA - Breast invasive adenocarcinoma(397;0.0478)														---	---	---	---
CYB5R4	51167	broad.mit.edu	37	6	84624111	84624111	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:84624111delT	uc003pkf.2	+							NM_016230	NP_057314			cytochrome b5 reductase 4						cell development|detection of oxygen|generation of precursor metabolites and energy|glucose homeostasis|insulin secretion|response to antibiotic|superoxide metabolic process	endoplasmic reticulum|perinuclear region of cytoplasm	cytochrome-b5 reductase activity|heme binding|NAD(P)H oxidase activity			breast(2)	2		all_cancers(76;7e-07)|Acute lymphoblastic leukemia(125;2.69e-07)|all_hematologic(105;0.000151)|all_epithelial(107;0.00128)		BRCA - Breast invasive adenocarcinoma(397;0.0871)														---	---	---	---
ZNF292	23036	broad.mit.edu	37	6	87969484	87969484	+	Frame_Shift_Del	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:87969484delA	uc003plm.3	+	8	6178	c.6137delA	c.(6136-6138)GAAfs	p.E2046fs		NM_015021	NP_055836	O60281	ZN292_HUMAN	zinc finger protein 292	2046					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(4)	4		all_cancers(76;3.82e-09)|Prostate(29;1.34e-10)|Acute lymphoblastic leukemia(125;2.17e-10)|all_hematologic(105;1.08e-06)|all_epithelial(107;5.31e-05)		BRCA - Breast invasive adenocarcinoma(108;0.0199)														---	---	---	---
RRAGD	58528	broad.mit.edu	37	6	90087542	90087542	+	Intron	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:90087542delA	uc003pnd.3	-						RRAGD_uc010kcc.2_Intron	NM_021244	NP_067067			Ras-related GTP binding D						cellular protein localization|cellular response to amino acid stimulus|positive regulation of TOR signaling cascade	lysosome|nucleus	GTP binding|protein heterodimerization activity			ovary(2)|central_nervous_system(1)	3		all_cancers(76;7.01e-07)|Acute lymphoblastic leukemia(125;2.23e-10)|Prostate(29;5.55e-10)|all_hematologic(105;2.42e-06)|all_epithelial(107;0.00139)		BRCA - Breast invasive adenocarcinoma(108;0.0144)														---	---	---	---
MDN1	23195	broad.mit.edu	37	6	90409616	90409616	+	Intron	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:90409616delA	uc003pnn.1	-							NM_014611	NP_055426			MDN1, midasin homolog						protein complex assembly|regulation of protein complex assembly	nucleus	ATP binding|ATPase activity|unfolded protein binding			ovary(8)|skin(2)	10		all_cancers(76;1.47e-06)|Acute lymphoblastic leukemia(125;2.23e-10)|Prostate(29;5.55e-10)|all_hematologic(105;2.42e-06)|all_epithelial(107;0.00246)		BRCA - Breast invasive adenocarcinoma(108;0.0193)														---	---	---	---
SOBP	55084	broad.mit.edu	37	6	107956280	107956282	+	In_Frame_Del	DEL	GCC	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:107956280_107956282delGCC	uc003prx.2	+	6	2736_2738	c.2232_2234delGCC	c.(2230-2235)CAGCCG>CAG	p.P751del		NM_018013	NP_060483	A7XYQ1	SOBP_HUMAN	sine oculis binding protein homolog	751	Pro-rich.						metal ion binding			ovary(1)	1		all_cancers(87;5.26e-06)|Acute lymphoblastic leukemia(125;2.87e-08)|all_hematologic(75;1.14e-06)|all_epithelial(87;0.00193)|Colorectal(196;0.156)		BRCA - Breast invasive adenocarcinoma(108;0.026)|all cancers(137;0.087)|Epithelial(106;0.104)|OV - Ovarian serous cystadenocarcinoma(136;0.154)														---	---	---	---
SCML4	256380	broad.mit.edu	37	6	108076968	108076968	+	Intron	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:108076968delA	uc010kdf.2	-						SCML4_uc003prz.3_Intron|SCML4_uc011eam.1_Intron|SCML4_uc003psa.3_Intron	NM_198081	NP_932347			sex comb on midleg-like 4						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding			ovary(1)	1		all_cancers(87;3.26e-06)|Acute lymphoblastic leukemia(125;3.08e-08)|all_hematologic(75;1.15e-06)|all_epithelial(87;0.00142)|Colorectal(196;0.0316)		BRCA - Breast invasive adenocarcinoma(108;0.01)|Epithelial(106;0.0509)|all cancers(137;0.0586)|OV - Ovarian serous cystadenocarcinoma(136;0.0758)														---	---	---	---
TRDN	10345	broad.mit.edu	37	6	123786155	123786156	+	Intron	DEL	AA	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:123786155_123786156delAA	uc003pzj.1	-						TRDN_uc003pzk.1_Intron|TRDN_uc003pzl.1_Intron|TRDN_uc010ken.2_Intron|uc003pzm.1_Intron	NM_006073	NP_006064			triadin						muscle contraction	integral to membrane|plasma membrane|sarcoplasmic reticulum membrane	receptor binding			ovary(1)	1				GBM - Glioblastoma multiforme(226;0.184)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	127683600	127683600	+	IGR	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:127683600delA								ECHDC1 (18846 upstream) : C6orf174 (75952 downstream)																																			---	---	---	---
FAM54A	113115	broad.mit.edu	37	6	136566111	136566111	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:136566111delT	uc010kgp.1	-						FAM54A_uc003qgt.1_Intron|FAM54A_uc003qgu.1_Intron	NM_001099286	NP_001092756			DUF729 domain containing 1											skin(1)	1	Colorectal(23;0.24)			GBM - Glioblastoma multiforme(68;0.00228)|OV - Ovarian serous cystadenocarcinoma(155;0.00504)														---	---	---	---
UTRN	7402	broad.mit.edu	37	6	144796037	144796037	+	Intron	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:144796037delA	uc003qkt.2	+						UTRN_uc010khq.1_Intron	NM_007124	NP_009055			utrophin						muscle contraction|muscle organ development|positive regulation of cell-matrix adhesion	cell junction|cytoplasm|cytoskeleton|membrane fraction|nucleus|postsynaptic membrane	actin binding|calcium ion binding|zinc ion binding			ovary(4)|pancreas(1)	5		Ovarian(120;0.218)		OV - Ovarian serous cystadenocarcinoma(155;5.72e-07)|GBM - Glioblastoma multiforme(68;4.9e-05)|Colorectal(48;0.213)														---	---	---	---
C6orf97	80129	broad.mit.edu	37	6	151917439	151917439	+	Intron	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:151917439delA	uc003qol.2	+							NM_025059	NP_079335			hypothetical protein LOC80129												0		Ovarian(120;0.126)	BRCA - Breast invasive adenocarcinoma(37;0.111)	OV - Ovarian serous cystadenocarcinoma(155;1.48e-10)														---	---	---	---
IPCEF1	26034	broad.mit.edu	37	6	154568731	154568731	+	Intron	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:154568731delA	uc003qpx.2	-						IPCEF1_uc003qpw.2_Intron|IPCEF1_uc010kjh.2_Intron	NM_015553	NP_056368			phosphoinositide-binding protein PIP3-E isoform						response to oxidative stress	cytoplasm|plasma membrane	oxygen transporter activity|peroxidase activity				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	6	155028499	155028499	+	IGR	DEL	A	-	-	rs147940473		TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:155028499delA								CNKSR3 (196746 upstream) : RBM16 (26013 downstream)																																			---	---	---	---
CCR6	1235	broad.mit.edu	37	6	167416821	167416821	+	5'UTR	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:167416821delT	uc003qvl.2	+	3					FGFR1OP_uc011egp.1_Intron|FGFR1OP_uc003qvj.2_Intron|FGFR1OP_uc003qvk.2_Intron	NM_031409	NP_113597			chemokine (C-C motif) receptor 6						cellular defense response|dendritic cell chemotaxis|elevation of cytosolic calcium ion concentration|humoral immune response	integral to plasma membrane	C-C chemokine receptor activity			ovary(1)	1		Breast(66;1.53e-05)|Ovarian(120;0.0606)		OV - Ovarian serous cystadenocarcinoma(33;8.21e-20)|BRCA - Breast invasive adenocarcinoma(81;4.55e-06)|GBM - Glioblastoma multiforme(31;0.00507)														---	---	---	---
ACTB	60	broad.mit.edu	37	7	5568135	5568137	+	In_Frame_Del	DEL	GAG	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:5568135_5568137delGAG	uc003sos.3	-	3	613_615	c.577_579delCTC	c.(577-579)CTCdel	p.L193del	ACTB_uc003sor.3_In_Frame_Del_p.L71del|ACTB_uc003sot.3_In_Frame_Del_p.L193del|ACTB_uc003soq.3_In_Frame_Del_p.L71del|ACTB_uc010ksy.2_In_Frame_Del_p.L71del	NM_001101	NP_001092	P60709	ACTB_HUMAN	beta actin	193					'de novo' posttranslational protein folding|adherens junction organization|axon guidance|blood coagulation|cell junction assembly|cellular component movement	cytoskeleton|cytosol|MLL5-L complex|NuA4 histone acetyltransferase complex|ribonucleoprotein complex	ATP binding|kinesin binding|nitric-oxide synthase binding|structural constituent of cytoskeleton				0		Ovarian(82;0.0606)		UCEC - Uterine corpus endometrioid carcinoma (126;0.175)|OV - Ovarian serous cystadenocarcinoma(56;4.24e-37)														---	---	---	---
C7orf26	79034	broad.mit.edu	37	7	6633948	6633948	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:6633948delT	uc003sqo.1	+						C7orf26_uc003sqp.1_Intron|C7orf26_uc003sqq.1_Intron	NM_024067	NP_076972			hypothetical protein LOC79034											ovary(1)	1		Ovarian(82;0.232)		UCEC - Uterine corpus endometrioid carcinoma (126;0.0986)														---	---	---	---
HDAC9	9734	broad.mit.edu	37	7	18988718	18988719	+	Intron	INS	-	T	T			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:18988718_18988719insT	uc003suh.2	+						HDAC9_uc003sue.2_Intron|HDAC9_uc003sui.2_Intron|HDAC9_uc003suj.2_Intron|HDAC9_uc003suk.2_Intron	NM_058176	NP_478056			histone deacetylase 9 isoform 1						B cell differentiation|cellular response to insulin stimulus|heart development|histone H3 deacetylation|histone H4 deacetylation|inflammatory response|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transcription, DNA-dependent|peptidyl-lysine deacetylation|positive regulation of cell migration involved in sprouting angiogenesis|regulation of skeletal muscle fiber development|transcription, DNA-dependent	cytoplasm|histone deacetylase complex|histone methyltransferase complex|transcription factor complex	histone deacetylase activity (H3-K16 specific)|histone deacetylase binding|histone deacetylase binding|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 binding|protein kinase C binding|repressing transcription factor binding|transcription corepressor activity			lung(2)|central_nervous_system(2)|kidney(1)	5	all_lung(11;0.187)				Valproic Acid(DB00313)													---	---	---	---
CDCA7L	55536	broad.mit.edu	37	7	21956150	21956157	+	Intron	DEL	AAAAAAAG	-	-	rs144020292		TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:21956150_21956157delAAAAAAAG	uc010kuk.2	-						CDCA7L_uc003sve.3_Intron|CDCA7L_uc010kul.2_Intron|CDCA7L_uc003svf.3_Intron|CDCA7L_uc011jyk.1_Intron	NM_018719	NP_061189			cell division cycle associated 7-like isoform 1						positive regulation of cell proliferation|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleolus					0																		---	---	---	---
GARS	2617	broad.mit.edu	37	7	30662267	30662267	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:30662267delT	uc003tbm.2	+							NM_002047	NP_002038			glycyl-tRNA synthetase						cell death|diadenosine tetraphosphate biosynthetic process|glycyl-tRNA aminoacylation	cytosol|mitochondrial matrix|soluble fraction	ATP binding|glycine-tRNA ligase activity|protein dimerization activity			ovary(1)	1					Glycine(DB00145)													---	---	---	---
POLD2	5425	broad.mit.edu	37	7	44155940	44155940	+	Intron	DEL	C	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:44155940delC	uc010kxz.2	-						POLD2_uc003tke.3_Intron|POLD2_uc010kya.2_Intron|POLD2_uc003tkf.3_Intron	NM_006230	NP_006221			DNA-directed DNA polymerase delta 2						base-excision repair|DNA strand elongation involved in DNA replication|nucleotide-excision repair, DNA gap filling|S phase of mitotic cell cycle|telomere maintenance via recombination|telomere maintenance via semi-conservative replication|transcription-coupled nucleotide-excision repair	nucleoplasm	DNA binding|DNA-directed DNA polymerase activity|protein binding			ovary(2)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	53256452	53256452	+	IGR	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:53256452delA								POM121L12 (151835 upstream) : None (None downstream)																																			---	---	---	---
CCT6A	908	broad.mit.edu	37	7	56126037	56126037	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:56126037delT	uc003trl.1	+						PSPH_uc003trj.2_Intron|CCT6A_uc003trm.1_Intron|CCT6A_uc011kcu.1_Intron|SNORA15_uc003trn.1_5'Flank	NM_001762	NP_001753			chaperonin containing TCP1, subunit 6A isoform						'de novo' posttranslational protein folding	cytosol	ATP binding|unfolded protein binding			upper_aerodigestive_tract(1)	1	Breast(14;0.214)		Lung(13;0.00024)|LUSC - Lung squamous cell carcinoma(13;0.00099)															---	---	---	---
Unknown	0	broad.mit.edu	37	7	56635559	56635559	+	IGR	DEL	G	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:56635559delG								DKFZp434L192 (70582 upstream) : ZNF479 (551769 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	57216044	57216044	+	IGR	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:57216044delT								ZNF479 (8473 upstream) : ZNF716 (293839 downstream)																																			---	---	---	---
ZNF679	168417	broad.mit.edu	37	7	63721435	63721435	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:63721435delT	uc003tsx.2	+							NM_153363	NP_699194			zinc finger protein 679						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			skin(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	65222951	65222952	+	Intron	DEL	TT	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:65222951_65222952delTT	uc003tud.1	-						CCT6P1_uc003tug.2_Intron|CCT6P1_uc003tuh.2_Intron|CCT6P1_uc003tui.2_Intron|uc003tuk.1_5'Flank					Homo sapiens hypothetical LOC441242, mRNA (cDNA clone MGC:87648 IMAGE:5267764), complete cds.																														---	---	---	---
SBDSP1	155370	broad.mit.edu	37	7	72304617	72304618	+	Intron	INS	-	T	T			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:72304617_72304618insT	uc003twg.2	+						SBDSP1_uc003twh.2_Intron|SBDSP1_uc003twe.2_Intron	NR_024110				Homo sapiens Shwachman-Bodian-Diamond syndrome pseudogene, mRNA (cDNA clone IMAGE:4329436).												0																		---	---	---	---
SPDYE7P	441251	broad.mit.edu	37	7	72341012	72341012	+	5'Flank	DEL	G	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:72341012delG	uc010lal.1	-							NR_003666				Homo sapiens speedy homolog E7 (Xenopus laevis), pseudogene (SPDYE7P), non-coding RNA.												0																		---	---	---	---
CLIP2	7461	broad.mit.edu	37	7	73803287	73803287	+	Intron	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:73803287delA	uc003uam.2	+						CLIP2_uc003uan.2_Intron	NM_003388	NP_003379			CAP-GLY domain containing linker protein 2							microtubule associated complex				skin(3)	3																		---	---	---	---
PMS2L11	441263	broad.mit.edu	37	7	76610356	76610356	+	RNA	DEL	C	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:76610356delC	uc003ufw.3	+	1		c.218delC			PMS2L11_uc011kgn.1_RNA	NR_023383				Homo sapiens cDNA FLJ59034 complete cds, moderately similar to Protein deltex-2.												0																		---	---	---	---
HGF	3082	broad.mit.edu	37	7	81381622	81381622	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:81381622delT	uc003uhl.2	-						HGF_uc003uhm.2_Intron|HGF_uc003uhn.1_Intron|HGF_uc003uho.1_Intron|HGF_uc003uhp.2_Intron	NM_000601	NP_000592			hepatocyte growth factor isoform 1						epithelial to mesenchymal transition|mitosis|platelet activation|platelet degranulation|proteolysis|regulation of branching involved in salivary gland morphogenesis by mesenchymal-epithelial signaling	platelet alpha granule lumen	growth factor activity|serine-type endopeptidase activity			ovary(2)|central_nervous_system(2)	4																		---	---	---	---
CACNA2D1	781	broad.mit.edu	37	7	81614084	81614084	+	Intron	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:81614084delA	uc003uhr.1	-							NM_000722	NP_000713			calcium channel, voltage-dependent, alpha							voltage-gated calcium channel complex	metal ion binding			ovary(5)|pancreas(1)	6					Felodipine(DB01023)|Gabapentin(DB00996)|Ibutilide(DB00308)|Isradipine(DB00270)|Magnesium Sulfate(DB00653)|Nifedipine(DB01115)													---	---	---	---
ANKIB1	54467	broad.mit.edu	37	7	91936976	91936976	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:91936976delT	uc003ulw.2	+							NM_019004	NP_061877			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)															---	---	---	---
FAM133B	257415	broad.mit.edu	37	7	92208639	92208639	+	Frame_Shift_Del	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:92208639delT	uc003umc.2	-	3	294	c.193delA	c.(193-195)ATGfs	p.M65fs	FAM133B_uc003umb.2_Frame_Shift_Del_p.M55fs|FAM133B_uc003umd.2_RNA	NM_152789	NP_690002	Q5BKY9	F133B_HUMAN	hypothetical protein LOC257415 isoform 1	65	Lys-rich.									ovary(1)	1	all_cancers(62;7.39e-11)|all_epithelial(64;7.03e-10)|Breast(17;0.00201)|all_lung(186;0.0384)|Lung NSC(181;0.053)|all_hematologic(106;0.237)		STAD - Stomach adenocarcinoma(4;6.16e-07)|GBM - Glioblastoma multiforme(5;9.78e-06)|all cancers(6;1.67e-05)|Epithelial(20;0.113)|LUSC - Lung squamous cell carcinoma(200;0.225)|Lung(22;0.23)															---	---	---	---
CCDC132	55610	broad.mit.edu	37	7	92883251	92883251	+	Intron	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:92883251delA	uc003umo.2	+						CCDC132_uc003umq.2_Intron|CCDC132_uc003ump.2_Intron|CCDC132_uc003umr.2_Intron|CCDC132_uc011khz.1_Intron|CCDC132_uc003umn.2_Intron	NM_017667	NP_060137			coiled-coil domain containing 132 isoform a												0	all_cancers(62;2.64e-11)|all_epithelial(64;1.4e-10)|Breast(17;0.000675)|Lung NSC(181;0.0618)|all_lung(186;0.0837)		STAD - Stomach adenocarcinoma(171;0.000302)															---	---	---	---
TRRAP	8295	broad.mit.edu	37	7	98491664	98491664	+	Intron	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:98491664delA	uc003upp.2	+						TRRAP_uc011kis.1_Intron	NM_003496	NP_003487			transformation/transcription domain-associated						histone deubiquitination|histone H2A acetylation|histone H4 acetylation|regulation of transcription, DNA-dependent|transcription, DNA-dependent	NuA4 histone acetyltransferase complex|PCAF complex|STAGA complex|transcription factor TFTC complex	phosphotransferase activity, alcohol group as acceptor|protein binding|transcription cofactor activity			ovary(9)|large_intestine(8)|central_nervous_system(6)|skin(6)|stomach(5)|upper_aerodigestive_tract(1)|lung(1)|liver(1)	37	all_cancers(62;6.96e-09)|all_epithelial(64;4.86e-09)|Lung NSC(181;0.01)|all_lung(186;0.016)|Esophageal squamous(72;0.0274)		STAD - Stomach adenocarcinoma(171;0.215)															---	---	---	---
TRRAP	8295	broad.mit.edu	37	7	98513649	98513649	+	Intron	DEL	C	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:98513649delC	uc003upp.2	+						TRRAP_uc011kis.1_Intron|TRRAP_uc003upr.2_Intron	NM_003496	NP_003487			transformation/transcription domain-associated						histone deubiquitination|histone H2A acetylation|histone H4 acetylation|regulation of transcription, DNA-dependent|transcription, DNA-dependent	NuA4 histone acetyltransferase complex|PCAF complex|STAGA complex|transcription factor TFTC complex	phosphotransferase activity, alcohol group as acceptor|protein binding|transcription cofactor activity			ovary(9)|large_intestine(8)|central_nervous_system(6)|skin(6)|stomach(5)|upper_aerodigestive_tract(1)|lung(1)|liver(1)	37	all_cancers(62;6.96e-09)|all_epithelial(64;4.86e-09)|Lung NSC(181;0.01)|all_lung(186;0.016)|Esophageal squamous(72;0.0274)		STAD - Stomach adenocarcinoma(171;0.215)															---	---	---	---
TRRAP	8295	broad.mit.edu	37	7	98533362	98533362	+	Intron	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:98533362delA	uc003upp.2	+						TRRAP_uc011kis.1_Intron|TRRAP_uc003upr.2_Intron	NM_003496	NP_003487			transformation/transcription domain-associated						histone deubiquitination|histone H2A acetylation|histone H4 acetylation|regulation of transcription, DNA-dependent|transcription, DNA-dependent	NuA4 histone acetyltransferase complex|PCAF complex|STAGA complex|transcription factor TFTC complex	phosphotransferase activity, alcohol group as acceptor|protein binding|transcription cofactor activity			ovary(9)|large_intestine(8)|central_nervous_system(6)|skin(6)|stomach(5)|upper_aerodigestive_tract(1)|lung(1)|liver(1)	37	all_cancers(62;6.96e-09)|all_epithelial(64;4.86e-09)|Lung NSC(181;0.01)|all_lung(186;0.016)|Esophageal squamous(72;0.0274)		STAD - Stomach adenocarcinoma(171;0.215)															---	---	---	---
ARPC1A	10552	broad.mit.edu	37	7	98951411	98951411	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:98951411delT	uc003upx.1	+						ARPC1A_uc010lfu.1_Intron|ARPC1A_uc003upy.1_Intron|ARPC1A_uc011kit.1_Intron	NM_006409	NP_006400			actin related protein 2/3 complex subunit 1A						actin cytoskeleton organization|regulation of actin filament polymerization	actin cytoskeleton|cytoplasm	actin binding			ovary(1)	1	all_cancers(62;4.46e-09)|all_epithelial(64;3.44e-10)|Lung NSC(181;0.0053)|all_lung(186;0.00895)|Esophageal squamous(72;0.0258)		STAD - Stomach adenocarcinoma(171;0.215)															---	---	---	---
AGFG2	3268	broad.mit.edu	37	7	100146315	100146315	+	Intron	DEL	G	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:100146315delG	uc003uvf.2	+						AGFG2_uc003uvg.1_Intron|AGFG2_uc010lgy.2_5'Flank	NM_006076	NP_006067			ArfGAP with FG repeats 2						regulation of ARF GTPase activity		ARF GTPase activator activity|zinc ion binding			central_nervous_system(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	101967964	101967964	+	IGR	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:101967964delA								SH2B2 (5787 upstream) : SPDYE6 (18229 downstream)																																			---	---	---	---
LAMB4	22798	broad.mit.edu	37	7	107749452	107749452	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:107749452delT	uc010ljo.1	-						LAMB4_uc003vey.2_Intron	NM_007356	NP_031382			laminin, beta 4 precursor						cell adhesion	basement membrane				ovary(4)|breast(2)|large_intestine(1)|skin(1)	8																		---	---	---	---
IFRD1	3475	broad.mit.edu	37	7	112112570	112112570	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:112112570delT	uc003vgh.2	+						IFRD1_uc011kmn.1_Intron|IFRD1_uc003vgj.2_Intron|IFRD1_uc011kmo.1_Intron|IFRD1_uc011kmp.1_Intron|IFRD1_uc003vgk.2_Intron	NM_001007245	NP_001007246			interferon-related developmental regulator 1						multicellular organismal development|myoblast cell fate determination		binding			kidney(1)|central_nervous_system(1)	2																		---	---	---	---
FAM3C	10447	broad.mit.edu	37	7	121022812	121022812	+	Intron	DEL	A	-	-	rs77488516		TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:121022812delA	uc003vjx.2	-						FAM3C_uc010lkm.2_Intron	NM_014888	NP_055703			family with sequence similarity 3, member C						multicellular organismal development	cytoplasmic membrane-bounded vesicle|extracellular region	cytokine activity				0	all_neural(327;0.117)																	---	---	---	---
AASS	10157	broad.mit.edu	37	7	121738971	121738971	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:121738971delT	uc003vka.2	-						AASS_uc011knu.1_Intron|AASS_uc011knv.1_Intron|AASS_uc003vkb.2_Intron|AASS_uc011knw.1_Intron	NM_005763	NP_005754			aminoadipate-semialdehyde synthase precursor						protein tetramerization	mitochondrial matrix	binding|saccharopine dehydrogenase (NAD+, L-glutamate-forming) activity|saccharopine dehydrogenase (NADP+, L-lysine-forming) activity			upper_aerodigestive_tract(1)|ovary(1)	2					L-Glutamic Acid(DB00142)|NADH(DB00157)													---	---	---	---
SLC13A1	6561	broad.mit.edu	37	7	122811637	122811637	+	Intron	DEL	T	-	-	rs147641390	by1000genomes	TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:122811637delT	uc003vkm.2	-						SLC13A1_uc010lks.2_Intron	NM_022444	NP_071889			solute carrier family 13 (sodium/sulfate							integral to membrane|plasma membrane	sodium:sulfate symporter activity			ovary(2)	2					Succinic acid(DB00139)													---	---	---	---
CPA2	1358	broad.mit.edu	37	7	129922051	129922052	+	Intron	INS	-	T	T			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:129922051_129922052insT	uc003vpq.2	+							NM_001869	NP_001860			carboxypeptidase A2 (pancreatic) precursor						proteolysis|vacuolar protein catabolic process	extracellular region|vacuole	metallocarboxypeptidase activity|zinc ion binding			ovary(1)	1	Melanoma(18;0.0435)																	---	---	---	---
NUP205	23165	broad.mit.edu	37	7	135307420	135307420	+	Intron	DEL	T	-	-	rs113426605		TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:135307420delT	uc003vsw.2	+						NUP205_uc003vsx.2_Intron	NM_015135	NP_055950			nucleoporin 205kDa						carbohydrate metabolic process|glucose transport|mRNA transport|protein import into nucleus, docking|regulation of glucose transport|transmembrane transport|viral reproduction	nuclear pore	protein binding			ovary(3)|breast(1)|central_nervous_system(1)|skin(1)	6																		---	---	---	---
DGKI	9162	broad.mit.edu	37	7	137341101	137341101	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:137341101delT	uc003vtt.2	-						DGKI_uc003vtu.2_Intron	NM_004717	NP_004708			diacylglycerol kinase, iota						activation of protein kinase C activity by G-protein coupled receptor protein signaling pathway|intracellular signal transduction|platelet activation	nucleus|plasma membrane	ATP binding|diacylglycerol kinase activity|metal ion binding			ovary(1)|kidney(1)|skin(1)	3																OREG0018350	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
DENND2A	27147	broad.mit.edu	37	7	140273441	140273441	+	Intron	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:140273441delA	uc010lnj.2	-						DENND2A_uc011kre.1_Intron|DENND2A_uc010lnk.2_Intron|DENND2A_uc003vvw.2_Intron|DENND2A_uc003vvx.2_Intron	NM_015689	NP_056504			DENN/MADD domain containing 2A											ovary(3)|breast(1)	4	Melanoma(164;0.00956)																	---	---	---	---
CUL1	8454	broad.mit.edu	37	7	148486619	148486620	+	Intron	DEL	CT	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:148486619_148486620delCT	uc010lpg.2	+						CUL1_uc003wey.2_Intron|CUL1_uc003wez.2_Intron|CUL1_uc003wfa.2_Intron	NM_003592	NP_003583			cullin 1						anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|cell cycle arrest|G1/S transition of mitotic cell cycle|induction of apoptosis by intracellular signals|interspecies interaction between organisms|negative regulation of cell proliferation|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|protein ubiquitination|S phase of mitotic cell cycle|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process	cytosol|nucleoplasm|SCF ubiquitin ligase complex	ubiquitin protein ligase binding			lung(1)	1	Melanoma(164;0.15)		OV - Ovarian serous cystadenocarcinoma(82;0.00291)															---	---	---	---
Unknown	0	broad.mit.edu	37	7	152445928	152445929	+	IGR	DEL	AA	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:152445928_152445929delAA								XRCC2 (72678 upstream) : ACTR3B (10922 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	7217563	7217563	+	IGR	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:7217563delA								LOC349196 (4689 upstream) : DEFB103B (68928 downstream)																																			---	---	---	---
C8orf80	389643	broad.mit.edu	37	8	27884280	27884282	+	Intron	DEL	TCA	-	-	rs142016219		TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:27884280_27884282delTCA	uc003xgm.3	-							NM_001010906	NP_001010906			speckled-like pattern in the germinal center							nucleus	GTP binding|GTPase activity			ovary(1)|central_nervous_system(1)	2		Ovarian(32;0.0218)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0228)|KIRC - Kidney renal clear cell carcinoma(542;0.126)|Kidney(114;0.15)|Colorectal(74;0.181)														---	---	---	---
MYST3	7994	broad.mit.edu	37	8	41806989	41806989	+	Intron	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:41806989delA	uc010lxb.2	-						MYST3_uc010lxc.2_Intron|MYST3_uc003xon.3_Intron|MYST3_uc010lxd.2_Intron	NM_001099412	NP_001092882			MYST histone acetyltransferase (monocytic						histone H3 acetylation|myeloid cell differentiation|negative regulation of transcription, DNA-dependent|nucleosome assembly|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	MOZ/MORF histone acetyltransferase complex|nucleosome	DNA binding|histone acetyltransferase activity|transcription coactivator activity|transcription factor binding|zinc ion binding			ovary(4)|pancreas(1)|central_nervous_system(1)|skin(1)	7	all_epithelial(6;1.12e-27)|all_lung(13;3.94e-12)|Lung NSC(13;6.54e-11)|Ovarian(28;0.00744)|Prostate(17;0.0119)|Colorectal(14;0.0221)|Lung SC(25;0.211)	all_lung(54;0.000294)|Lung NSC(58;0.00105)|Hepatocellular(245;0.0524)|Esophageal squamous(32;0.0954)|Renal(179;0.0983)	Epithelial(1;2.82e-19)|all cancers(1;1.15e-16)|BRCA - Breast invasive adenocarcinoma(8;9.17e-11)|OV - Ovarian serous cystadenocarcinoma(14;9.4e-05)|Colorectal(10;0.000728)|Lung(22;0.00153)|LUSC - Lung squamous cell carcinoma(45;0.00741)|COAD - Colon adenocarcinoma(11;0.0171)															---	---	---	---
CYP7B1	9420	broad.mit.edu	37	8	65528843	65528843	+	Intron	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:65528843delA	uc003xvj.2	-							NM_004820	NP_004811			cytochrome P450, family 7, subfamily B,						bile acid biosynthetic process|cell death|cholesterol metabolic process|xenobiotic metabolic process	endoplasmic reticulum membrane|microsome	25-hydroxycholesterol 7alpha-hydroxylase activity|electron carrier activity|heme binding|oxysterol 7-alpha-hydroxylase activity			ovary(3)	3		all_cancers(86;0.217)|Lung NSC(129;0.0521)|all_lung(136;0.0906)|all_epithelial(80;0.215)																---	---	---	---
ARFGEF1	10565	broad.mit.edu	37	8	68189370	68189370	+	Intron	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:68189370delA	uc003xxo.1	-							NM_006421	NP_006412			brefeldin A-inhibited guanine						exocytosis|regulation of ARF protein signal transduction	cytoplasm	ARF guanyl-nucleotide exchange factor activity|myosin binding			ovary(4)|upper_aerodigestive_tract(1)|large_intestine(1)|lung(1)|kidney(1)	8	Breast(64;0.214)	Lung NSC(129;0.0908)|all_lung(136;0.152)	Epithelial(68;0.0043)|OV - Ovarian serous cystadenocarcinoma(28;0.00578)|all cancers(69;0.0173)|BRCA - Breast invasive adenocarcinoma(89;0.206)															---	---	---	---
TMEM64	169200	broad.mit.edu	37	8	91637754	91637755	+	3'UTR	DEL	AA	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:91637754_91637755delAA	uc003yen.2	-	3					TMEM64_uc003yeo.2_3'UTR|TMEM64_uc011lgf.1_3'UTR	NM_001008495	NP_001008495			transmembrane protein 64 isoform 1							integral to membrane					0			BRCA - Breast invasive adenocarcinoma(11;0.0598)															---	---	---	---
RBM12B	389677	broad.mit.edu	37	8	94745548	94745548	+	3'UTR	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:94745548delA	uc003yfz.2	-	3						NM_203390	NP_976324			RNA binding motif protein 12B								nucleotide binding|RNA binding				0	Breast(36;4.14e-07)		BRCA - Breast invasive adenocarcinoma(8;0.0168)															---	---	---	---
KIAA1429	25962	broad.mit.edu	37	8	95504678	95504679	+	Intron	INS	-	T	T			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:95504678_95504679insT	uc003ygo.1	-						KIAA1429_uc010maz.1_Intron	NM_015496	NP_056311			hypothetical protein LOC25962 isoform 1						mRNA processing|RNA splicing	nucleus				ovary(1)|skin(1)	2	Breast(36;3.29e-05)		BRCA - Breast invasive adenocarcinoma(8;0.00185)															---	---	---	---
TP53INP1	94241	broad.mit.edu	37	8	95942503	95942503	+	3'UTR	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:95942503delA	uc003yhg.2	-	4					C8orf38_uc003yhe.1_Intron|C8orf38_uc003yhf.2_Intron|TP53INP1_uc003yhh.2_3'UTR	NM_033285	NP_150601			tumor protein p53 inducible nuclear protein 1						apoptosis	PML body					0	Breast(36;8.75e-07)																	---	---	---	---
OXR1	55074	broad.mit.edu	37	8	107704922	107704922	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:107704922delT	uc011lht.1	+						OXR1_uc003ymf.2_Intron|OXR1_uc011lhu.1_Intron|OXR1_uc010mcg.2_Intron|OXR1_uc003ymg.1_Intron|OXR1_uc003ymi.1_Intron	NM_018002	NP_060472			oxidation resistance 1 isoform 1						cell wall macromolecule catabolic process|response to oxidative stress	mitochondrion					0			OV - Ovarian serous cystadenocarcinoma(57;1.81e-09)															---	---	---	---
TATDN1	83940	broad.mit.edu	37	8	125507787	125507787	+	Intron	DEL	A	-	-	rs35308504		TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:125507787delA	uc003yrd.2	-						TATDN1_uc003yre.2_Intron|TATDN1_uc010mdm.2_Intron|TATDN1_uc003yrf.2_Intron	NM_032026	NP_114415			TatD DNase domain containing 1 isoform a							nucleus	endodeoxyribonuclease activity, producing 5'-phosphomonoesters|metal ion binding				0	Ovarian(258;0.00438)|all_neural(195;0.0779)|Hepatocellular(40;0.108)		STAD - Stomach adenocarcinoma(47;0.00288)															---	---	---	---
EEF1D	1936	broad.mit.edu	37	8	144668488	144668488	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:144668488delT	uc011lki.1	-						EEF1D_uc003yyp.1_Intron|EEF1D_uc003yyq.1_Intron|EEF1D_uc011lkj.1_Intron|EEF1D_uc003yyr.2_Intron|EEF1D_uc003yyt.2_Intron|EEF1D_uc011lkk.1_Intron|EEF1D_uc003yys.2_Intron|EEF1D_uc003yyv.2_Intron|EEF1D_uc003yyu.2_Intron|EEF1D_uc011lkl.1_Intron	NM_001130057	NP_001123529			eukaryotic translation elongation factor 1 delta						positive regulation of I-kappaB kinase/NF-kappaB cascade	cytosol|eukaryotic translation elongation factor 1 complex	protein binding|signal transducer activity|translation elongation factor activity			ovary(1)|kidney(1)|skin(1)	3	all_cancers(97;3.74e-11)|all_epithelial(106;2.62e-09)|Lung NSC(106;0.00013)|all_lung(105;0.000374)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		Colorectal(110;0.134)|BRCA - Breast invasive adenocarcinoma(115;0.239)															---	---	---	---
GLDC	2731	broad.mit.edu	37	9	6553326	6553326	+	Intron	DEL	C	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:6553326delC	uc003zkc.2	-							NM_000170	NP_000161			glycine dehydrogenase (decarboxylating)						glycine catabolic process	mitochondrion	electron carrier activity|glycine dehydrogenase (decarboxylating) activity|lyase activity|pyridoxal phosphate binding			ovary(2)	2		Acute lymphoblastic leukemia(23;0.161)		GBM - Glioblastoma multiforme(50;0.0421)|Lung(218;0.134)	Glycine(DB00145)|Pyridoxal Phosphate(DB00114)													---	---	---	---
IFNA14	3448	broad.mit.edu	37	9	21217459	21217459	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:21217459delT	uc003zoo.1	-						IFNA16_uc003zor.1_5'Flank	NM_002172				interferon, alpha 14 precursor						blood coagulation|regulation of type I interferon-mediated signaling pathway|response to virus|type I interferon-mediated signaling pathway	extracellular space	cytokine activity|cytokine receptor binding				0				Lung(24;2.12e-22)|LUSC - Lung squamous cell carcinoma(38;1.4e-13)														---	---	---	---
DNAJB5	25822	broad.mit.edu	37	9	34997369	34997369	+	3'UTR	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:34997369delA	uc003zvt.2	+	4					DNAJB5_uc003zvs.2_3'UTR|DNAJB5_uc011los.1_3'UTR	NM_012266	NP_036398			DnaJ (Hsp40) homolog, subfamily B, member 5						protein folding|response to unfolded protein		heat shock protein binding|unfolded protein binding				0			LUSC - Lung squamous cell carcinoma(32;0.00575)															---	---	---	---
ALDH1A1	216	broad.mit.edu	37	9	75533865	75533865	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:75533865delT	uc004ajd.2	-						ALDH1A1_uc011lsh.1_Intron|ALDH1A1_uc011lsg.1_Intron	NM_000689	NP_000680			aldehyde dehydrogenase 1A1						cellular aldehyde metabolic process|ethanol oxidation|xenobiotic metabolic process	cytosol	aldehyde dehydrogenase (NAD) activity|androgen binding|Ras GTPase activator activity|retinal dehydrogenase activity			ovary(3)|lung(1)	4					NADH(DB00157)|Tretinoin(DB00755)|Vitamin A(DB00162)													---	---	---	---
PCSK5	5125	broad.mit.edu	37	9	78794417	78794417	+	Intron	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:78794417delA	uc004ajz.2	+						PCSK5_uc004aka.2_Intron|PCSK5_uc004akb.2_5'Flank	NM_006200	NP_006191			proprotein convertase subtilisin/kexin type 5						anterior/posterior pattern formation|cell-cell signaling|cytokine biosynthetic process|embryo implantation|embryonic digestive tract development|embryonic skeletal system development|heart development|kidney development|limb morphogenesis|nerve growth factor processing|nerve growth factor receptor signaling pathway|peptide biosynthetic process|renin secretion into blood stream|respiratory tube development|signal peptide processing|viral assembly, maturation, egress, and release	extracellular space|Golgi lumen|stored secretory granule	peptide binding|serine-type endopeptidase activity			ovary(2)|skin(1)	3																		---	---	---	---
C5	727	broad.mit.edu	37	9	123751833	123751833	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:123751833delT	uc004bkv.2	-							NM_001735	NP_001726			complement component 5 preproprotein						activation of MAPK activity|chemotaxis|complement activation, alternative pathway|complement activation, classical pathway|cytolysis|G-protein coupled receptor protein signaling pathway|inflammatory response|negative regulation of macrophage chemotaxis|positive regulation of chemokine secretion|positive regulation vascular endothelial growth factor production	extracellular space|membrane attack complex	chemokine activity|endopeptidase inhibitor activity			ovary(2)	2				OV - Ovarian serous cystadenocarcinoma(323;4.98e-53)|GBM - Glioblastoma multiforme(294;0.0242)	Eculizumab(DB01257)													---	---	---	---
CERCAM	51148	broad.mit.edu	37	9	131187045	131187046	+	Intron	DEL	TT	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:131187045_131187046delTT	uc004buz.3	+						CERCAM_uc004buy.1_Intron|CERCAM_uc010mxz.2_Intron|CERCAM_uc010mya.1_Intron	NM_016174	NP_057258			cerebral endothelial cell adhesion molecule 1						cellular component movement|leukocyte cell-cell adhesion|lipopolysaccharide biosynthetic process	endoplasmic reticulum lumen|plasma membrane				pancreas(1)	1																		---	---	---	---
PKN3	29941	broad.mit.edu	37	9	131478876	131478878	+	Intron	DEL	CAA	-	-	rs10819432	by1000genomes	TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:131478876_131478878delCAA	uc004bvw.2	+						PKN3_uc010myh.2_Intron|PKN3_uc011mbk.1_Intron	NM_013355	NP_037487			protein kinase PKNbeta						signal transduction	Golgi apparatus|nucleus|perinuclear region of cytoplasm	ATP binding|protein binding|protein kinase C activity			stomach(2)|lung(2)	4																		---	---	---	---
BAT2L1	84726	broad.mit.edu	37	9	134322056	134322056	+	Intron	DEL	C	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:134322056delC	uc004can.3	+						BAT2L1_uc010mzj.1_5'Flank|BAT2L1_uc004cam.1_Intron	NM_013318	NP_037450			HLA-B associated transcript 2-like								protein binding				0																		---	---	---	---
WDR85	92715	broad.mit.edu	37	9	140468517	140468517	+	Intron	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:140468517delA	uc004cnk.1	-						WDR85_uc004cnl.1_Intron|WDR85_uc004cnm.1_Intron|WDR85_uc004cnn.1_Intron	NM_138778	NP_620133			WD repeat domain 85						peptidyl-diphthamide biosynthetic process from peptidyl-histidine						0	all_cancers(76;0.106)			OV - Ovarian serous cystadenocarcinoma(145;0.00029)|Epithelial(140;0.000509)														---	---	---	---
KIN	22944	broad.mit.edu	37	10	7816627	7816627	+	Intron	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:7816627delA	uc001ijt.2	-						KIN_uc010qaz.1_Intron|KIN_uc009xip.2_Intron|KIN_uc010qba.1_Intron	NM_012311	NP_036443			HsKin17 protein						DNA recombination|DNA repair|DNA replication|interspecies interaction between organisms|mRNA processing	cytoplasm|nuclear matrix	double-stranded DNA binding|RNA binding|zinc ion binding			ovary(1)|pancreas(1)|skin(1)	3																		---	---	---	---
DCLRE1C	64421	broad.mit.edu	37	10	14950368	14950368	+	3'UTR	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:14950368delT	uc001inn.2	-	14					DCLRE1C_uc010qbx.1_Intron|DCLRE1C_uc001ink.2_3'UTR|DCLRE1C_uc001inl.2_3'UTR|DCLRE1C_uc009xji.2_3'UTR|DCLRE1C_uc001inm.2_3'UTR|DCLRE1C_uc001ino.2_3'UTR|DCLRE1C_uc009xjh.2_RNA|DCLRE1C_uc001inp.2_3'UTR|DCLRE1C_uc001inq.2_3'UTR|DCLRE1C_uc001inr.2_3'UTR	NM_001033855	NP_001029027			artemis protein isoform a						DNA recombination	nucleus	5'-3' exonuclease activity|single-stranded DNA specific endodeoxyribonuclease activity			ovary(1)	1													Involved_in_tolerance_or_repair_of_DNA_crosslinks|NHEJ					---	---	---	---
ITGA8	8516	broad.mit.edu	37	10	15719443	15719443	+	Intron	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:15719443delA	uc001ioc.1	-						ITGA8_uc010qcb.1_Intron	NM_003638	NP_003629			integrin, alpha 8 precursor						cell differentiation|cell-cell adhesion|cell-matrix adhesion|integrin-mediated signaling pathway|nervous system development	integrin complex	receptor activity			ovary(3)|lung(3)	6																		---	---	---	---
Unknown	0	broad.mit.edu	37	10	19341155	19341155	+	IGR	DEL	C	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:19341155delC								ARL5B (374215 upstream) : PLXDC2 (764217 downstream)																																			---	---	---	---
BMI1	648	broad.mit.edu	37	10	22607161	22607161	+	5'Flank	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:22607161delT	uc001irh.2	+						COMMD3_uc001ire.2_Intron|COMMD3_uc001irf.2_Intron|COMMD3_uc001irg.2_Intron|BMI1_uc009xkg.2_Intron	NM_005180	NP_005171			BMI1 polycomb ring finger oncogene						hemopoiesis|negative regulation of transcription from RNA polymerase II promoter|positive regulation of fibroblast proliferation|positive regulation of ubiquitin-protein ligase activity|segment specification|transcription, DNA-dependent	cytoplasm|nucleolus|PcG protein complex|ubiquitin ligase complex	RING-like zinc finger domain binding|zinc ion binding			ovary(1)|skin(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	10	42924610	42924610	+	Intron	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:42924610delA	uc001izx.2	-											Homo sapiens cyclin Y-like 2, mRNA (cDNA clone IMAGE:4704933), with apparent retained intron.																														---	---	---	---
CCAR1	55749	broad.mit.edu	37	10	70515996	70515996	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:70515996delT	uc001joo.2	+						CCAR1_uc001jol.1_Intron|CCAR1_uc001jom.1_Intron|CCAR1_uc009xpx.1_Intron|CCAR1_uc001jon.1_Intron|CCAR1_uc010qiz.1_Intron|CCAR1_uc010qja.1_Intron|CCAR1_uc010qjb.1_Intron	NM_018237	NP_060707			cell-cycle and apoptosis regulatory protein 1						apoptosis|cell cycle|nuclear mRNA splicing, via spliceosome|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleoplasm|perinuclear region of cytoplasm	calcium ion binding|nucleic acid binding|protein binding			ovary(6)|large_intestine(1)	7																		---	---	---	---
SUPV3L1	6832	broad.mit.edu	37	10	70962150	70962150	+	Intron	DEL	A	-	-	rs112179393		TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:70962150delA	uc001jpe.1	+						SUPV3L1_uc010qjd.1_Intron	NM_003171	NP_003162			suppressor of var1, 3-like 1 precursor						DNA duplex unwinding	mitochondrial nucleoid|nucleus	ATP binding|DNA binding|DNA helicase activity|RNA binding			urinary_tract(1)|ovary(1)	2																		---	---	---	---
ASCC1	51008	broad.mit.edu	37	10	73887716	73887716	+	Intron	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:73887716delA	uc001jst.1	-						ASCC1_uc001jsr.1_Intron|ASCC1_uc001jss.1_Intron|ASCC1_uc001jsu.1_Intron|ASCC1_uc010qju.1_Intron					RecName: Full=Activating signal cointegrator 1 complex subunit 1; AltName: Full=ASC-1 complex subunit p50; AltName: Full=Trip4 complex subunit p50;						regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|transcription factor complex	RNA binding				0																		---	---	---	---
STAMBPL1	57559	broad.mit.edu	37	10	90672691	90672691	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:90672691delT	uc001kfk.2	+						STAMBPL1_uc010qmx.1_Intron|STAMBPL1_uc009xto.2_Intron|STAMBPL1_uc001kfl.2_Intron|STAMBPL1_uc001kfn.2_5'UTR	NM_020799	NP_065850			STAM binding protein-like 1								metal ion binding|metallopeptidase activity|protein binding			ovary(1)	1		Colorectal(252;0.0381)		Colorectal(12;6.38e-05)|COAD - Colon adenocarcinoma(12;7.75e-05)														---	---	---	---
KIF20B	9585	broad.mit.edu	37	10	91483917	91483917	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:91483917delT	uc001kgs.1	+						KIF20B_uc001kgr.1_Intron|KIF20B_uc001kgt.1_Intron	NM_016195	NP_057279			M-phase phosphoprotein 1						cell cycle arrest|cell division|microtubule-based movement|mitosis|regulation of mitosis	centrosome|microtubule|nucleolus|nucleoplasm|spindle	ATP binding|ATPase activity|microtubule motor activity|WW domain binding			ovary(1)|pancreas(1)|skin(1)	3																		---	---	---	---
BTAF1	9044	broad.mit.edu	37	10	93741213	93741213	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:93741213delT	uc001khr.2	+						BTAF1_uc001khs.1_Intron|BTAF1_uc001kht.1_Intron	NM_003972	NP_003963			BTAF1 RNA polymerase II, B-TFIID transcription						negative regulation of transcription, DNA-dependent	nucleus	ATP binding|DNA binding|helicase activity|sequence-specific DNA binding transcription factor activity			ovary(1)|central_nervous_system(1)|skin(1)	3		Colorectal(252;0.0846)																---	---	---	---
KIF11	3832	broad.mit.edu	37	10	94396790	94396793	+	Intron	DEL	AAAA	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:94396790_94396793delAAAA	uc001kic.2	+						KIF11_uc010qnq.1_Intron	NM_004523	NP_004514			kinesin family member 11						blood coagulation|cell division|microtubule-based movement|spindle assembly involved in mitosis	chromatin remodeling complex|cytosol|kinesin complex|microtubule|spindle pole	ATP binding|microtubule motor activity|protein kinase binding			skin(1)	1																		---	---	---	---
SORBS1	10580	broad.mit.edu	37	10	97127476	97127476	+	Intron	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:97127476delA	uc001kkp.2	-						SORBS1_uc001kkk.2_Intron|SORBS1_uc001kkl.2_Intron|SORBS1_uc001kkn.2_Intron|SORBS1_uc001kkm.2_Intron|SORBS1_uc001kko.2_Intron|SORBS1_uc001kkq.2_Intron|SORBS1_uc001kkr.2_Intron|SORBS1_uc001kks.2_Intron|SORBS1_uc001kkt.2_Intron|SORBS1_uc001kku.2_Intron|SORBS1_uc001kkv.2_Intron|SORBS1_uc001kkw.2_Intron|SORBS1_uc010qoe.1_Intron|SORBS1_uc010qof.1_Intron	NM_001034954	NP_001030126			sorbin and SH3 domain containing 1 isoform 3						focal adhesion assembly|glucose transport|insulin receptor signaling pathway|muscle contraction|positive regulation of establishment of protein localization in plasma membrane|positive regulation of glucose import|positive regulation of glycogen biosynthetic process|positive regulation of lipid biosynthetic process|stress fiber assembly	centrosome|cytosol|focal adhesion|membrane raft|nucleus|stress fiber|zonula adherens	actin binding|insulin receptor binding|SH3/SH2 adaptor activity			breast(1)	1		Colorectal(252;0.0429)		Epithelial(162;1.7e-06)|all cancers(201;6.52e-05)														---	---	---	---
SORBS1	10580	broad.mit.edu	37	10	97131604	97131604	+	Intron	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:97131604delA	uc001kkp.2	-						SORBS1_uc001kkk.2_Intron|SORBS1_uc001kkl.2_Intron|SORBS1_uc001kkn.2_Intron|SORBS1_uc001kkm.2_Intron|SORBS1_uc001kko.2_Intron|SORBS1_uc001kkq.2_Intron|SORBS1_uc001kkr.2_Intron|SORBS1_uc001kks.2_Intron|SORBS1_uc001kkt.2_Intron|SORBS1_uc001kku.2_Intron|SORBS1_uc001kkv.2_Intron|SORBS1_uc001kkw.2_Intron|SORBS1_uc010qoe.1_Intron|SORBS1_uc010qof.1_Intron	NM_001034954	NP_001030126			sorbin and SH3 domain containing 1 isoform 3						focal adhesion assembly|glucose transport|insulin receptor signaling pathway|muscle contraction|positive regulation of establishment of protein localization in plasma membrane|positive regulation of glucose import|positive regulation of glycogen biosynthetic process|positive regulation of lipid biosynthetic process|stress fiber assembly	centrosome|cytosol|focal adhesion|membrane raft|nucleus|stress fiber|zonula adherens	actin binding|insulin receptor binding|SH3/SH2 adaptor activity			breast(1)	1		Colorectal(252;0.0429)		Epithelial(162;1.7e-06)|all cancers(201;6.52e-05)														---	---	---	---
ENTPD7	57089	broad.mit.edu	37	10	101462505	101462505	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:101462505delT	uc001kqa.3	+						ENTPD7_uc009xwl.2_Intron	NM_020354	NP_065087			ectonucleoside triphosphate diphosphohydrolase							cytoplasmic vesicle membrane|integral to membrane	hydrolase activity			ovary(1)	1		Colorectal(252;0.234)		Epithelial(162;4.72e-10)|all cancers(201;3.75e-08)														---	---	---	---
HIF1AN	55662	broad.mit.edu	37	10	102305592	102305592	+	Intron	DEL	T	-	-	rs11817143	by1000genomes	TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:102305592delT	uc001krj.3	+							NM_017902	NP_060372			hypoxia-inducible factor 1, alpha subunit						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	metal ion binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|peptide-aspartate beta-dioxygenase activity|protein binding				0		Colorectal(252;0.234)		Epithelial(162;6.75e-10)|all cancers(201;4.88e-08)														---	---	---	---
SORCS3	22986	broad.mit.edu	37	10	106982853	106982853	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:106982853delT	uc001kyi.1	+						SORCS3_uc010qqz.1_Intron	NM_014978	NP_055793			VPS10 domain receptor protein SORCS 3 precursor							integral to membrane	neuropeptide receptor activity			ovary(6)|skin(3)|central_nervous_system(1)	10		Colorectal(252;0.134)|Breast(234;0.142)|Lung NSC(174;0.191)		Epithelial(162;1.58e-07)|all cancers(201;1.02e-05)|BRCA - Breast invasive adenocarcinoma(275;0.0628)														---	---	---	---
Unknown	0	broad.mit.edu	37	10	111440917	111440917	+	IGR	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:111440917delA								None (None upstream) : XPNPEP1 (183607 downstream)																																			---	---	---	---
BTBD16	118663	broad.mit.edu	37	10	124057386	124057387	+	Intron	INS	-	G	G			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:124057386_124057387insG	uc001lgc.1	+						BTBD16_uc001lgd.1_Intron	NM_144587	NP_653188			BTB (POZ) domain containing 16											skin(1)	1		all_neural(114;0.107)|Lung NSC(174;0.175)|all_lung(145;0.222)|Breast(234;0.238)																---	---	---	---
B4GALNT4	338707	broad.mit.edu	37	11	379842	379842	+	Intron	DEL	C	-	-	rs72431160		TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:379842delC	uc001lpb.2	+							NM_178537	NP_848632			beta							Golgi cisterna membrane|integral to membrane	N-acetyl-beta-glucosaminyl-glycoprotein 4-beta-N-acetylgalactosaminyltransferase activity			pancreas(1)	1		all_cancers(49;1.59e-06)|all_epithelial(84;0.000256)|Breast(177;0.00122)|Ovarian(85;0.0228)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762)		all cancers(45;1.56e-27)|Epithelial(43;9.31e-27)|OV - Ovarian serous cystadenocarcinoma(40;1.11e-20)|BRCA - Breast invasive adenocarcinoma(625;3.56e-05)|Lung(200;0.0182)|LUSC - Lung squamous cell carcinoma(625;0.0703)														---	---	---	---
IRF7	3665	broad.mit.edu	37	11	613181	613181	+	Intron	DEL	C	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:613181delC	uc001lqh.2	-						IRF7_uc009ycb.2_Intron|IRF7_uc010qwf.1_Intron|IRF7_uc001lqf.2_Intron|IRF7_uc010qwg.1_Intron|IRF7_uc001lqg.2_Intron|IRF7_uc001lqi.2_Intron|IRF7_uc010qwh.1_Intron	NM_001572	NP_001563			interferon regulatory factor 7 isoform a						interferon-gamma-mediated signaling pathway|interspecies interaction between organisms|MyD88-independent toll-like receptor signaling pathway|negative regulation of transcription from RNA polymerase II promoter|positive regulation of interferon-alpha production|positive regulation of transcription from RNA polymerase II promoter|response to virus|Toll signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway|transcription from RNA polymerase II promoter|type I interferon-mediated signaling pathway	cytosol|endosome membrane|nucleoplasm|plasma membrane	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity				0		all_cancers(49;1.69e-08)|all_epithelial(84;1.65e-05)|Breast(177;0.000231)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.106)|all_lung(207;0.136)		all cancers(45;7.68e-28)|Epithelial(43;7.44e-27)|OV - Ovarian serous cystadenocarcinoma(40;3.53e-21)|BRCA - Breast invasive adenocarcinoma(625;6.96e-05)|Lung(200;0.0375)|LUSC - Lung squamous cell carcinoma(625;0.0703)														---	---	---	---
TSPAN4	7106	broad.mit.edu	37	11	865495	865495	+	Intron	DEL	C	-	-	rs61614113	by1000genomes	TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:865495delC	uc001lsd.1	+						TSPAN4_uc001lse.1_Intron|TSPAN4_uc001lsf.1_Intron|TSPAN4_uc001lsg.1_Intron|TSPAN4_uc001lsh.1_Intron|TSPAN4_uc001lsi.1_Intron|TSPAN4_uc001lsj.1_Intron	NM_003271	NP_003262			tetraspanin 4 isoform a						protein complex assembly	integral to plasma membrane				breast(1)	1		all_cancers(49;2.64e-08)|all_epithelial(84;4.17e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.191)|all_lung(207;0.24)		all cancers(45;4.32e-25)|Epithelial(43;3.29e-24)|BRCA - Breast invasive adenocarcinoma(625;4.23e-05)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)														---	---	---	---
RRM1	6240	broad.mit.edu	37	11	4141256	4141256	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:4141256delT	uc001lyw.3	+						RRM1_uc009yej.2_Intron|RRM1_uc009yei.2_Intron|RRM1_uc010qyc.1_Intron|RRM1_uc010qyd.1_Intron	NM_001033	NP_001024			ribonucleoside-diphosphate reductase M1 chain						deoxyribonucleotide biosynthetic process|DNA replication|nucleobase, nucleoside and nucleotide interconversion	cytosol|nucleoplasm|ribonucleoside-diphosphate reductase complex	ATP binding|ribonucleoside-diphosphate reductase activity			skin(1)	1		Medulloblastoma(188;0.0025)|Breast(177;0.00502)|all_neural(188;0.0227)		BRCA - Breast invasive adenocarcinoma(625;0.0848)|LUSC - Lung squamous cell carcinoma(625;0.205)	Clofarabine(DB00631)|Fludarabine(DB01073)|Gemcitabine(DB00441)|Hydroxyurea(DB01005)													---	---	---	---
OR56A1	120796	broad.mit.edu	37	11	6049169	6049170	+	5'Flank	DEL	AA	-	-	rs111685831		TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:6049169_6049170delAA	uc010qzw.1	-							NM_001001917	NP_001001917			olfactory receptor, family 56, subfamily A,						sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(2)|breast(1)	3		Medulloblastoma(188;0.00776)|all_neural(188;0.0652)|Breast(177;0.114)		Epithelial(150;7.01e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)														---	---	---	---
PRRG4	79056	broad.mit.edu	37	11	32852020	32852020	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:32852020delT	uc001mtx.2	+							NM_024081	NP_076986			proline rich Gla (G-carboxyglutamic acid) 4							extracellular region|Golgi apparatus|integral to membrane	calcium ion binding				0	Breast(20;0.206)																	---	---	---	---
KIAA0652	9776	broad.mit.edu	37	11	46666873	46666873	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:46666873delT	uc009yld.2	+						KIAA0652_uc001nda.2_Intron|KIAA0652_uc001ndb.2_Intron|KIAA0652_uc001ncz.2_Intron|KIAA0652_uc001ndc.2_Intron|KIAA0652_uc010rgv.1_Intron	NM_001142673	NP_001136145			autophagy-related protein 13 isoform 1						autophagic vacuole assembly	cytosol|pre-autophagosomal structure|ULK1-ATG13-FIP200 complex	protein binding				0				GBM - Glioblastoma multiforme(35;0.226)														---	---	---	---
MTCH2	23788	broad.mit.edu	37	11	47657242	47657242	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:47657242delT	uc010rho.1	-						MTCH2_uc001nge.2_Intron|MTCH2_uc010rhp.1_Intron	NM_014342	NP_055157			mitochondrial carrier 2						transport	integral to membrane|mitochondrial inner membrane					0																		---	---	---	---
Unknown	0	broad.mit.edu	37	11	55607259	55607259	+	IGR	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:55607259delA								OR5D16 (47 upstream) : SPRYD5 (43514 downstream)																																			---	---	---	---
SLC43A1	8501	broad.mit.edu	37	11	57281506	57281508	+	In_Frame_Del	DEL	AGA	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:57281506_57281508delAGA	uc001nkk.2	-	2	195_197	c.77_79delTCT	c.(76-81)TTCTCT>TCT	p.F26del	SLC43A1_uc001nkl.2_In_Frame_Del_p.F26del	NM_003627	NP_003618	O75387	LAT3_HUMAN	solute carrier family 43, member 1	26	Helical; (Potential).				cellular nitrogen compound metabolic process|ion transport	integral to plasma membrane	neutral amino acid transmembrane transporter activity				0																		---	---	---	---
CTNND1	1500	broad.mit.edu	37	11	57571337	57571337	+	Intron	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:57571337delA	uc001nmc.3	+						CTNND1_uc001nlh.1_Intron|CTNND1_uc001nlu.3_Intron|CTNND1_uc001nlt.3_Intron|CTNND1_uc001nls.3_Intron|CTNND1_uc001nlw.3_Intron|CTNND1_uc001nmf.3_Intron|CTNND1_uc001nmd.3_Intron|CTNND1_uc001nlk.3_Intron|CTNND1_uc001nme.3_Intron|CTNND1_uc001nll.3_Intron|CTNND1_uc001nmg.3_Intron|CTNND1_uc001nlj.3_Intron|CTNND1_uc001nlr.3_Intron|CTNND1_uc001nlp.3_Intron|CTNND1_uc001nlx.3_Intron|CTNND1_uc001nlz.3_Intron|CTNND1_uc009ymn.2_Intron|CTNND1_uc001nlm.3_Intron|CTNND1_uc001nly.3_Intron|CTNND1_uc001nmb.3_Intron|CTNND1_uc001nma.3_Intron|CTNND1_uc001nmi.3_Intron|CTNND1_uc001nmh.3_Intron|CTNND1_uc001nlq.3_Intron|CTNND1_uc001nln.3_Intron|CTNND1_uc001nli.3_Intron|CTNND1_uc001nlo.3_Intron|CTNND1_uc001nlv.3_Intron	NM_001085458	NP_001078927			catenin, delta 1 isoform 1ABC						adherens junction organization|cell junction assembly|negative regulation of canonical Wnt receptor signaling pathway|regulation of transcription, DNA-dependent|transcription, DNA-dependent|Wnt receptor signaling pathway	cytosol|midbody|nucleus	cadherin binding|protein binding|receptor binding			breast(4)|ovary(1)|kidney(1)	6		all_epithelial(135;0.155)																---	---	---	---
CTNND1	1500	broad.mit.edu	37	11	57582848	57582848	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:57582848delT	uc001nmc.3	+						CTNND1_uc001nlh.1_Intron|CTNND1_uc001nlu.3_Intron|CTNND1_uc001nlt.3_Intron|CTNND1_uc001nls.3_Intron|CTNND1_uc001nlw.3_Intron|CTNND1_uc001nmf.3_Intron|CTNND1_uc001nmd.3_Intron|CTNND1_uc001nlk.3_Intron|CTNND1_uc001nme.3_Intron|CTNND1_uc001nll.3_Intron|CTNND1_uc001nmg.3_Intron|CTNND1_uc001nlj.3_Intron|CTNND1_uc001nlr.3_Intron|CTNND1_uc001nlp.3_Intron|CTNND1_uc001nlx.3_Intron|CTNND1_uc001nlz.3_Intron|CTNND1_uc009ymn.2_Intron|CTNND1_uc001nlm.3_Intron|CTNND1_uc001nly.3_Intron|CTNND1_uc001nmb.3_Intron|CTNND1_uc001nma.3_Intron|CTNND1_uc001nmi.3_Intron|CTNND1_uc001nmh.3_Intron|CTNND1_uc001nlq.3_Intron|CTNND1_uc001nln.3_Intron|CTNND1_uc001nli.3_Intron|CTNND1_uc001nlo.3_Intron|CTNND1_uc001nlv.3_Intron	NM_001085458	NP_001078927			catenin, delta 1 isoform 1ABC						adherens junction organization|cell junction assembly|negative regulation of canonical Wnt receptor signaling pathway|regulation of transcription, DNA-dependent|transcription, DNA-dependent|Wnt receptor signaling pathway	cytosol|midbody|nucleus	cadherin binding|protein binding|receptor binding			breast(4)|ovary(1)|kidney(1)	6		all_epithelial(135;0.155)																---	---	---	---
HNRNPUL2	221092	broad.mit.edu	37	11	62489135	62489135	+	Intron	DEL	A	-	-	rs77636809		TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:62489135delA	uc001nuw.2	-						HNRNPUL2_uc001nuu.1_Intron	NM_001079559	NP_001073027			heterogeneous nuclear ribonucleoprotein U-like						cell killing	nucleus	ATP binding|nucleic acid binding				0																		---	---	---	---
PLCB3	5331	broad.mit.edu	37	11	64032517	64032517	+	Frame_Shift_Del	DEL	C	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:64032517delC	uc001nzb.2	+	23	2747	c.2747delC	c.(2746-2748)TCCfs	p.S916fs	PLCB3_uc009ypg.1_Frame_Shift_Del_p.S916fs|PLCB3_uc009yph.1_Frame_Shift_Del_p.S849fs|PLCB3_uc009ypi.2_Frame_Shift_Del_p.S916fs	NM_000932	NP_000923	Q01970	PLCB3_HUMAN	phospholipase C beta 3	916					intracellular signal transduction|lipid catabolic process|synaptic transmission	cytosol	calcium ion binding|calmodulin binding|phosphatidylinositol phospholipase C activity|signal transducer activity			ovary(1)|pancreas(1)	2																		---	---	---	---
RPS6KA4	8986	broad.mit.edu	37	11	64138941	64138941	+	Frame_Shift_Del	DEL	C	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:64138941delC	uc001oae.2	+	17	2391	c.2308delC	c.(2308-2310)CCCfs	p.P770fs	RPS6KA4_uc001oad.2_Frame_Shift_Del_p.P764fs|RPS6KA4_uc010rnl.1_Frame_Shift_Del_p.P707fs|RPS6KA4_uc001oaf.2_Frame_Shift_Del_p.P763fs|RPS6KA4_uc009ypp.2_Frame_Shift_Del_p.P522fs	NM_003942	NP_003933	O75676	KS6A4_HUMAN	ribosomal protein S6 kinase, 90kDa, polypeptide	770					axon guidance|histone phosphorylation|interleukin-1-mediated signaling pathway|intracellular protein kinase cascade|positive regulation of histone acetylation|positive regulation of histone phosphorylation|positive regulation of transcription from RNA polymerase II promoter	cytoplasm|nucleus	ATP binding|magnesium ion binding|mitogen-activated protein kinase p38 binding|ribosomal protein S6 kinase activity			lung(3)|ovary(1)|breast(1)	5																		---	---	---	---
MALAT1	378938	broad.mit.edu	37	11	65269498	65269498	+	RNA	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:65269498delT	uc010roh.1	+	1		c.4266delT			uc001ody.2_RNA|MALAT1_uc001odz.2_5'Flank	NR_002819				Homo sapiens clone alpha1 mRNA sequence.												0																		---	---	---	---
SF3B2	10992	broad.mit.edu	37	11	65835245	65835245	+	Intron	DEL	C	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:65835245delC	uc001ogy.1	+						PACS1_uc001ogz.1_5'Flank|PACS1_uc001oha.1_5'Flank	NM_006842	NP_006833			splicing factor 3B subunit 2						interspecies interaction between organisms	catalytic step 2 spliceosome|nucleoplasm|U12-type spliceosomal complex	nucleic acid binding|protein binding			ovary(2)|breast(1)	3																OREG0021094	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
ARHGEF17	9828	broad.mit.edu	37	11	73057889	73057889	+	Intron	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:73057889delA	uc001otu.2	+							NM_014786	NP_055601			Rho guanine nucleotide exchange factor (GEF) 17						actin cytoskeleton organization|apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol	Rho guanyl-nucleotide exchange factor activity				0																		---	---	---	---
TRIM49	57093	broad.mit.edu	37	11	89536750	89536750	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:89536750delT	uc001pdb.2	-							NM_020358	NP_065091			ring finger protein 18							intracellular	zinc ion binding				0		Acute lymphoblastic leukemia(157;2.31e-05)|all_hematologic(158;0.00556)																---	---	---	---
CEP57	9702	broad.mit.edu	37	11	95564074	95564075	+	Intron	INS	-	TGAG	TGAG	rs147497264	by1000genomes	TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:95564074_95564075insTGAG	uc001pfp.1	+						CEP57_uc010ruh.1_Intron|CEP57_uc010rui.1_Intron|CEP57_uc009ywn.1_Intron|CEP57_uc001pfq.1_Intron|CEP57_uc001pfr.1_Intron	NM_014679	NP_055494			translokin						fibroblast growth factor receptor signaling pathway|G2/M transition of mitotic cell cycle|protein import into nucleus, translocation|spermatid development	centrosome|cytosol|Golgi apparatus|microtubule|nucleus	fibroblast growth factor binding|protein homodimerization activity			ovary(1)	1		Acute lymphoblastic leukemia(157;2.31e-05)|all_hematologic(158;0.00824)												Mosaic_Variegated_Aneuploidy_Syndrome				---	---	---	---
MMP12	4321	broad.mit.edu	37	11	102737945	102737945	+	Intron	DEL	A	-	-	rs28381681		TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:102737945delA	uc001phk.2	-							NM_002426	NP_002417			matrix metalloproteinase 12 preproprotein						positive regulation of epithelial cell proliferation involved in wound healing|proteolysis|wound healing, spreading of epidermal cells	proteinaceous extracellular matrix	calcium ion binding|metalloendopeptidase activity|zinc ion binding				0		all_hematologic(158;0.00092)|Acute lymphoblastic leukemia(157;0.000967)		BRCA - Breast invasive adenocarcinoma(274;0.014)	Acetohydroxamic Acid(DB00551)													---	---	---	---
EXPH5	23086	broad.mit.edu	37	11	108412614	108412614	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:108412614delT	uc001pkk.2	-						EXPH5_uc010rwa.1_Intron	NM_015065	NP_055880			exophilin 5 isoform a						intracellular protein transport		Rab GTPase binding			skin(3)|ovary(2)	5		all_cancers(61;3.99e-08)|Acute lymphoblastic leukemia(157;3.97e-05)|Melanoma(852;4.04e-05)|all_epithelial(67;0.000116)|all_hematologic(158;0.000315)|Breast(348;0.104)|all_neural(303;0.16)		Epithelial(105;8.1e-06)|BRCA - Breast invasive adenocarcinoma(274;1.22e-05)|all cancers(92;0.000129)|OV - Ovarian serous cystadenocarcinoma(223;0.11)|Colorectal(284;0.184)														---	---	---	---
DDX10	1662	broad.mit.edu	37	11	108548163	108548163	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:108548163delT	uc001pkm.2	+						DDX10_uc001pkl.1_Intron	NM_004398	NP_004389			DEAD (Asp-Glu-Ala-Asp) box polypeptide 10								ATP binding|ATP-dependent helicase activity|RNA binding|RNA helicase activity			breast(2)|lung(1)|prostate(1)	4		all_cancers(61;1.29e-11)|all_epithelial(67;2.96e-07)|Melanoma(852;1.54e-05)|Acute lymphoblastic leukemia(157;4.24e-05)|all_hematologic(158;0.000141)|Breast(348;0.026)|all_neural(223;0.0729)		BRCA - Breast invasive adenocarcinoma(274;2.48e-05)|Epithelial(105;4.35e-05)|all cancers(92;0.000609)|OV - Ovarian serous cystadenocarcinoma(223;0.133)				T	NUP98	AML*								---	---	---	---
CRTAM	56253	broad.mit.edu	37	11	122741787	122741787	+	Intron	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:122741787delA	uc001pyj.2	+						CRTAM_uc001pyk.2_Intron	NM_019604	NP_062550			class-I MHC-restricted T cell associated						cell recognition|detection of tumor cell|positive regulation of cytokine secretion|positive regulation of natural killer cell mediated cytotoxicity directed against tumor cell target	integral to membrane|plasma membrane	receptor binding			ovary(1)	1		Breast(109;0.00249)|Lung NSC(97;0.0177)|all_lung(97;0.0179)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;5.28e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0308)														---	---	---	---
KDM5A	5927	broad.mit.edu	37	12	463406	463406	+	Intron	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:463406delA	uc001qif.1	-						KDM5A_uc001qie.1_Intron|KDM5A_uc010sdn.1_Intron|KDM5A_uc010sdo.1_Intron	NM_001042603	NP_001036068			retinoblastoma binding protein 2 isoform 1						chromatin modification|multicellular organismal development|positive regulation of transcription, DNA-dependent|transcription from RNA polymerase II promoter	cytoplasm|nucleolus	DNA binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|sequence-specific DNA binding transcription factor activity|zinc ion binding			skin(2)|ovary(1)	3								T 	NUP98	AML								---	---	---	---
ADIPOR2	79602	broad.mit.edu	37	12	1863751	1863751	+	Intron	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:1863751delA	uc001qjm.2	+						ADIPOR2_uc001qjn.2_Intron	NM_024551	NP_078827			adiponectin receptor 2						fatty acid oxidation|hormone-mediated signaling pathway	integral to membrane	hormone binding|receptor activity				0	Ovarian(42;0.107)		OV - Ovarian serous cystadenocarcinoma(31;0.000382)															---	---	---	---
TULP3	7289	broad.mit.edu	37	12	3046966	3046967	+	Intron	DEL	AA	-	-	rs3742080	by1000genomes	TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:3046966_3046967delAA	uc010seh.1	+						TULP3_uc009zec.1_Intron|TULP3_uc010seg.1_Intron|TULP3_uc001qlj.2_Intron|TULP3_uc010sei.1_Intron	NM_003324	NP_003315			tubby like protein 3 isoform 1						G-protein coupled receptor protein signaling pathway|regulation of transcription, DNA-dependent	cytoplasm|extracellular region|nucleus|plasma membrane	phosphatidylinositol-4,5-bisphosphate binding				0			OV - Ovarian serous cystadenocarcinoma(31;0.000818)															---	---	---	---
IFFO1	25900	broad.mit.edu	37	12	6658357	6658357	+	Intron	DEL	A	-	-	rs72489368		TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:6658357delA	uc001qpd.1	-						IFFO1_uc001qoy.2_Intron|IFFO1_uc001qpa.1_5'Flank|IFFO1_uc001qpb.1_Intron|IFFO1_uc001qpe.1_Intron|IFFO1_uc010sfe.1_Intron|IFFO1_uc001qpf.1_Intron|IFFO1_uc001qoz.1_5'Flank|IFFO1_uc001qpc.1_Intron|IFFO1_uc001qpg.2_5'Flank	NM_080730	NP_542768			intermediate filament family orphan isoform 2							intermediate filament					0																		---	---	---	---
Unknown	0	broad.mit.edu	37	12	7338794	7338794	+	IGR	DEL	G	-	-	rs113717305		TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:7338794delG								CLSTN3 (27266 upstream) : PEX5 (2965 downstream)																																			---	---	---	---
ATF7IP	55729	broad.mit.edu	37	12	14590987	14590987	+	Intron	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:14590987delA	uc001rbw.2	+						ATF7IP_uc010shs.1_Intron|ATF7IP_uc001rbu.2_Intron|ATF7IP_uc001rbv.1_Intron|ATF7IP_uc001rbx.2_Intron|ATF7IP_uc010sht.1_Intron|ATF7IP_uc001rby.3_Intron|ATF7IP_uc001rca.2_Intron	NM_018179	NP_060649			activating transcription factor 7 interacting						DNA methylation|interspecies interaction between organisms|positive regulation of transcription, DNA-dependent|regulation of RNA polymerase II transcriptional preinitiation complex assembly|transcription, DNA-dependent		protein binding			lung(3)|ovary(1)|skin(1)	5																		---	---	---	---
PIK3C2G	5288	broad.mit.edu	37	12	18690984	18690984	+	Intron	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:18690984delA	uc001rdt.2	+						PIK3C2G_uc010sia.1_Intron|PIK3C2G_uc010sib.1_Intron|PIK3C2G_uc010sic.1_Intron	NM_004570	NP_004561			phosphoinositide-3-kinase, class 2 gamma						cell communication|phosphatidylinositol-mediated signaling	membrane|phosphatidylinositol 3-kinase complex	1-phosphatidylinositol-3-kinase activity|ATP binding|phosphatidylinositol binding|phosphatidylinositol-4-phosphate 3-kinase activity			lung(8)|central_nervous_system(6)|breast(3)|stomach(2)|ovary(2)	21		Hepatocellular(102;0.194)																---	---	---	---
PLEKHA5	54477	broad.mit.edu	37	12	19406761	19406761	+	Intron	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:19406761delA	uc001reb.2	+						PLEKHA5_uc010sie.1_Intron|PLEKHA5_uc001rea.2_Intron|PLEKHA5_uc009zin.2_Intron|PLEKHA5_uc010sif.1_Intron|PLEKHA5_uc010sig.1_Intron|PLEKHA5_uc010sih.1_Intron	NM_019012	NP_061885			pleckstrin homology domain containing, family A								1-phosphatidylinositol binding|protein binding			ovary(1)|kidney(1)|skin(1)	3	Acute lymphoblastic leukemia(4;0.000455)|all_hematologic(4;0.00804)																	---	---	---	---
ITPR2	3709	broad.mit.edu	37	12	26877744	26877744	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:26877744delT	uc001rhg.2	-						ITPR2_uc001rhh.1_Intron|ITPR2_uc001rhi.1_Intron	NM_002223	NP_002214			inositol 1,4,5-triphosphate receptor, type 2						activation of phospholipase C activity|energy reserve metabolic process|nerve growth factor receptor signaling pathway|platelet activation|regulation of insulin secretion|response to hypoxia	integral to membrane|plasma membrane enriched fraction|platelet dense tubular network membrane|sarcoplasmic reticulum membrane	calcium ion transmembrane transporter activity|inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity			kidney(6)|ovary(4)|skin(2)|upper_aerodigestive_tract(1)|lung(1)	14	Colorectal(261;0.0847)																	---	---	---	---
DENND5B	160518	broad.mit.edu	37	12	31630952	31630952	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:31630952delT	uc001rki.1	-						DENND5B_uc001rkh.1_Intron|DENND5B_uc009zjq.1_Intron|DENND5B_uc001rkj.2_Intron|DENND5B_uc001rkk.1_Intron	NM_144973	NP_659410			DENN/MADD domain containing 5B							integral to membrane				ovary(1)|central_nervous_system(1)	2																		---	---	---	---
ADAMTS20	80070	broad.mit.edu	37	12	43820983	43820983	+	Intron	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:43820983delA	uc010skx.1	-						ADAMTS20_uc001rno.1_Intron	NM_025003	NP_079279			a disintegrin-like and metalloprotease with							proteinaceous extracellular matrix	zinc ion binding			central_nervous_system(5)|ovary(4)|lung(3)|large_intestine(2)|skin(2)|urinary_tract(1)|kidney(1)|pancreas(1)	19	all_cancers(12;2.6e-05)|Lung SC(27;0.184)	Lung NSC(34;0.0569)|all_lung(34;0.129)		GBM - Glioblastoma multiforme(48;0.0473)														---	---	---	---
ADAMTS20	80070	broad.mit.edu	37	12	43833279	43833279	+	Intron	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:43833279delA	uc010skx.1	-						ADAMTS20_uc001rno.1_Intron|ADAMTS20_uc001rnp.1_Intron	NM_025003	NP_079279			a disintegrin-like and metalloprotease with							proteinaceous extracellular matrix	zinc ion binding			central_nervous_system(5)|ovary(4)|lung(3)|large_intestine(2)|skin(2)|urinary_tract(1)|kidney(1)|pancreas(1)	19	all_cancers(12;2.6e-05)|Lung SC(27;0.184)	Lung NSC(34;0.0569)|all_lung(34;0.129)		GBM - Glioblastoma multiforme(48;0.0473)														---	---	---	---
CCNT1	904	broad.mit.edu	37	12	49086775	49086775	+	3'UTR	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:49086775delT	uc001rse.1	-	9					LOC144438_uc001rsd.3_5'Flank|CCNT1_uc009zkz.1_3'UTR	NM_001240	NP_001231			cyclin T1						cell cycle|cell division|interspecies interaction between organisms|positive regulation of viral transcription|protein phosphorylation|regulation of cyclin-dependent protein kinase activity|regulation of transcription, DNA-dependent|transcription elongation from RNA polymerase II promoter|viral reproduction	nucleoplasm	DNA binding|protein kinase binding			ovary(3)|lung(1)|breast(1)|skin(1)	6																		---	---	---	---
FKBP11	51303	broad.mit.edu	37	12	49318789	49318789	+	Intron	DEL	C	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:49318789delC	uc001rsp.2	-						FKBP11_uc010sma.1_5'Flank|FKBP11_uc001rsq.3_Intron|FKBP11_uc010smb.1_Intron	NM_016594	NP_057678			FK506 binding protein 11 isoform 1 precursor						protein folding	integral to membrane	FK506 binding|peptidyl-prolyl cis-trans isomerase activity				0																		---	---	---	---
LARP4	113251	broad.mit.edu	37	12	50869285	50869285	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:50869285delT	uc001rwp.1	+						LARP4_uc001rwo.1_Intron|LARP4_uc001rwq.1_Intron|LARP4_uc001rwr.1_Intron|LARP4_uc001rws.1_Intron|LARP4_uc009zlr.1_Intron|LARP4_uc001rwt.1_Intron	NM_052879	NP_443111			c-Mpl binding protein isoform a								nucleotide binding|RNA binding			ovary(1)	1																		---	---	---	---
MUCL1	118430	broad.mit.edu	37	12	55251961	55251961	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:55251961delT	uc001sgk.2	+							NM_058173	NP_477521			small breast epithelial mucin precursor							extracellular region|membrane					0																		---	---	---	---
TSPAN8	7103	broad.mit.edu	37	12	71523013	71523013	+	Intron	DEL	T	-	-	rs112700480		TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:71523013delT	uc009zrt.1	-						TSPAN8_uc001swk.1_Intron|TSPAN8_uc001swj.1_Intron	NM_004616	NP_004607			transmembrane 4 superfamily member 3						protein glycosylation	integral to membrane|lysosome	signal transducer activity			skin(2)|lung(1)|central_nervous_system(1)	4			LUSC - Lung squamous cell carcinoma(43;0.24)|OV - Ovarian serous cystadenocarcinoma(12;0.244)															---	---	---	---
CEP290	80184	broad.mit.edu	37	12	88515039	88515039	+	Intron	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:88515039delA	uc001tar.2	-						CEP290_uc001tat.2_Intron|CEP290_uc009zsl.1_Intron	NM_025114	NP_079390			centrosomal protein 290kDa						cilium assembly|eye photoreceptor cell development|G2/M transition of mitotic cell cycle|hindbrain development|otic vesicle formation|positive regulation of transcription, DNA-dependent|pronephros development|protein transport	cell surface|centrosome|cytosol|nucleus|photoreceptor connecting cilium	protein binding			ovary(5)|breast(1)|pancreas(1)	7																		---	---	---	---
GALNT4	8693	broad.mit.edu	37	12	89919639	89919639	+	5'Flank	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:89919639delA	uc001tbd.2	-						POC1B_uc001tba.2_5'Flank|POC1B_uc001tbb.2_5'Flank|POC1B_uc001tbc.2_Intron|POC1B_uc010sun.1_Intron|GALNT4_uc001tbe.2_Intron|GALNT4_uc010suo.1_Intron	NM_003774	NP_003765			polypeptide N-acetylgalactosaminyltransferase 4						carbohydrate metabolic process	Golgi membrane|integral to membrane|perinuclear region of cytoplasm	polypeptide N-acetylgalactosaminyltransferase activity|sugar binding				0																		---	---	---	---
CCDC41	51134	broad.mit.edu	37	12	94729387	94729387	+	Frame_Shift_Del	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:94729387delT	uc001tdd.2	-	12	1983	c.1397delA	c.(1396-1398)AATfs	p.N466fs	CCDC41_uc001tde.2_Frame_Shift_Del_p.N466fs|CCDC41_uc009zsw.1_RNA	NM_016122	NP_057206	Q9Y592	CCD41_HUMAN	NY-REN-58 antigen	458	Potential.										0																		---	---	---	---
NR2C1	7181	broad.mit.edu	37	12	95442823	95442823	+	Intron	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:95442823delA	uc001tdm.3	-						NR2C1_uc010suu.1_Intron|NR2C1_uc001tdo.3_Intron|NR2C1_uc001tdn.3_Intron	NM_003297	NP_003288			nuclear receptor subfamily 2, group C, member 1						regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor	PML body	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|steroid hormone receptor activity|zinc ion binding			ovary(1)	1																		---	---	---	---
SLC41A2	84102	broad.mit.edu	37	12	105199286	105199286	+	Intron	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:105199286delA	uc001tla.2	-							NM_032148	NP_115524			solute carrier family 41, member 2							integral to membrane|plasma membrane	magnesium ion transmembrane transporter activity			ovary(1)|skin(1)	2																		---	---	---	---
IFT81	28981	broad.mit.edu	37	12	110570466	110570466	+	Intron	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:110570466delA	uc001tqi.2	+						IFT81_uc001tqh.2_Intron|IFT81_uc001tqj.2_Intron|IFT81_uc001tqg.2_Intron	NM_001143779	NP_001137251			intraflagellar transport 81-like isoform 1						cell differentiation|multicellular organismal development|spermatogenesis	intraflagellar transport particle B|microtubule-based flagellum				ovary(1)	1																		---	---	---	---
C12orf24	29902	broad.mit.edu	37	12	110911025	110911025	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:110911025delT	uc001tqu.3	+						C12orf24_uc010sxz.1_Intron|C12orf24_uc009zvo.2_Intron|C12orf24_uc001tqt.2_Intron|C12orf24_uc001tqv.3_Intron	NM_013300	NP_037432			hypothetical protein LOC29902												0																		---	---	---	---
SLC24A6	80024	broad.mit.edu	37	12	113748006	113748006	+	Intron	DEL	C	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:113748006delC	uc001tvc.2	-						SLC24A6_uc001tuz.2_Intron|SLC24A6_uc001tva.2_Intron|SLC24A6_uc001tvb.2_Intron	NM_024959	NP_079235			solute carrier family 24 member 6 precursor						response to stimulus|sodium ion transport	integral to membrane|plasma membrane	calcium:cation antiporter activity			central_nervous_system(1)	1																		---	---	---	---
CIT	11113	broad.mit.edu	37	12	120194922	120194922	+	Intron	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:120194922delA	uc001txi.1	-						CIT_uc001txh.1_Intron|CIT_uc001txj.1_Intron	NM_007174	NP_009105			citron						intracellular signal transduction		ATP binding|metal ion binding|protein serine/threonine kinase activity|SH3 domain binding|small GTPase regulator activity			ovary(6)|urinary_tract(1)|lung(1)|breast(1)|skin(1)	10	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)	Myeloproliferative disorder(1001;0.0255)		BRCA - Breast invasive adenocarcinoma(302;0.211)														---	---	---	---
CCDC64	92558	broad.mit.edu	37	12	120510172	120510172	+	Intron	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:120510172delA	uc001txl.1	+						CCDC64_uc001txk.2_Intron|CCDC64_uc009zwv.1_Intron|CCDC64_uc010sze.1_Intron|CCDC64_uc010szf.1_Intron	NM_207311	NP_997194			coiled-coil domain containing 64						Golgi to secretory granule transport|neuron projection development	centrosome	dynactin binding|Rab GTPase binding			ovary(2)	2	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)																	---	---	---	---
P2RX4	5025	broad.mit.edu	37	12	121660179	121660179	+	Intron	DEL	G	-	-	rs11065488		TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:121660179delG	uc001tzr.2	+						P2RX4_uc010szr.1_Intron|P2RX4_uc010szs.1_Intron|P2RX4_uc009zxc.2_Intron|P2RX4_uc001tzs.2_Intron|P2RX4_uc009zxb.2_Intron|P2RX4_uc010szt.1_Intron	NM_002560	NP_002551			purinergic receptor P2X4						endothelial cell activation|negative regulation of cardiac muscle hypertrophy|positive regulation of calcium ion transport into cytosol|positive regulation of calcium-mediated signaling|positive regulation of nitric oxide biosynthetic process|positive regulation of prostaglandin secretion|regulation of apoptosis|regulation of blood pressure|regulation of sodium ion transport|relaxation of cardiac muscle|response to ATP|response to fluid shear stress|sensory perception of pain|tissue homeostasis	cell junction|perinuclear region of cytoplasm	cadherin binding|copper ion binding|extracellular ATP-gated cation channel activity|protein homodimerization activity|purinergic nucleotide receptor activity|receptor binding|zinc ion binding				0	all_neural(191;0.0684)|Medulloblastoma(191;0.0922)																	---	---	---	---
KNTC1	9735	broad.mit.edu	37	12	123067170	123067170	+	Intron	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:123067170delA	uc001ucv.2	+						KNTC1_uc010taf.1_Intron	NM_014708	NP_055523			Rough Deal homolog, centromere/kinetochore						cell division|mitotic cell cycle checkpoint|mitotic prometaphase|protein complex assembly|regulation of exit from mitosis	condensed chromosome kinetochore|cytosol|kinetochore microtubule|nucleus|spindle pole	protein binding			ovary(5)|kidney(3)|lung(1)|central_nervous_system(1)	10	all_neural(191;0.0837)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;7.21e-05)|Epithelial(86;0.000178)|BRCA - Breast invasive adenocarcinoma(302;0.217)														---	---	---	---
DNAH10	196385	broad.mit.edu	37	12	124315343	124315343	+	Intron	DEL	T	-	-	rs7976816		TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:124315343delT	uc001uft.3	+							NM_207437	NP_997320			dynein, axonemal, heavy chain 10						microtubule-based movement	cilium axoneme|cytoplasm|dynein complex|microtubule	ATP binding|ATPase activity|microtubule motor activity			ovary(3)|skin(2)|central_nervous_system(1)	6	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000207)|Epithelial(86;0.000556)|all cancers(50;0.00346)														---	---	---	---
DNAH10	196385	broad.mit.edu	37	12	124358316	124358317	+	Intron	INS	-	GT	GT			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:124358316_124358317insGT	uc001uft.3	+							NM_207437	NP_997320			dynein, axonemal, heavy chain 10						microtubule-based movement	cilium axoneme|cytoplasm|dynein complex|microtubule	ATP binding|ATPase activity|microtubule motor activity			ovary(3)|skin(2)|central_nervous_system(1)	6	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000207)|Epithelial(86;0.000556)|all cancers(50;0.00346)														---	---	---	---
Unknown	0	broad.mit.edu	37	13	19700978	19700978	+	IGR	DEL	A	-	-	rs9511728	by1000genomes	TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:19700978delA								DKFZp686A1627 (8555 upstream) : TUBA3C (46942 downstream)																																			---	---	---	---
TPTE2	93492	broad.mit.edu	37	13	19997315	19997315	+	Intron	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:19997315delA	uc001umd.2	-						TPTE2_uc009zzk.2_Intron|TPTE2_uc009zzl.2_Intron|TPTE2_uc001ume.2_Intron|TPTE2_uc009zzm.2_Intron|TPTE2_uc010tcm.1_Intron|TPTE2_uc010tcl.1_Intron	NM_199254	NP_954863			TPTE and PTEN homologous inositol lipid							endoplasmic reticulum membrane|integral to membrane	ion channel activity|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity|protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity				0		all_cancers(29;1.23e-20)|all_lung(29;1.97e-20)|all_epithelial(30;5.86e-20)|Lung NSC(5;3.36e-17)|Lung SC(185;0.0262)|Ovarian(182;0.162)		all cancers(112;1.73e-05)|Epithelial(112;7.42e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.000785)|Lung(94;0.0176)|LUSC - Lung squamous cell carcinoma(192;0.089)														---	---	---	---
CRYL1	51084	broad.mit.edu	37	13	21013654	21013654	+	Intron	DEL	A	-	-	rs67005224		TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:21013654delA	uc001une.2	-						CRYL1_uc001unf.2_Intron|CRYL1_uc001ung.2_Intron|CRYL1_uc010tcp.1_Intron	NM_015974	NP_057058			lambda-crystallin						fatty acid metabolic process	cytosol	3-hydroxyacyl-CoA dehydrogenase activity|L-gulonate 3-dehydrogenase activity|NAD+ binding|protein homodimerization activity				0		all_cancers(29;2.27e-23)|all_epithelial(30;1.69e-19)|all_lung(29;8.29e-18)|Lung SC(185;0.0262)|Ovarian(182;0.0827)|Hepatocellular(188;0.244)		all cancers(112;6.6e-05)|Epithelial(112;0.00178)|OV - Ovarian serous cystadenocarcinoma(117;0.0169)|Lung(94;0.0215)|GBM - Glioblastoma multiforme(144;0.0402)|LUSC - Lung squamous cell carcinoma(192;0.061)														---	---	---	---
FLT1	2321	broad.mit.edu	37	13	28886057	28886057	+	Intron	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:28886057delA	uc001usb.3	-						FLT1_uc010aap.2_Intron|FLT1_uc010aaq.2_Intron|FLT1_uc001usa.3_Intron	NM_002019	NP_002010			fms-related tyrosine kinase 1 isoform 1						cell differentiation|female pregnancy|positive regulation of vascular endothelial growth factor receptor signaling pathway	extracellular space|Golgi apparatus|integral to plasma membrane|nucleus	ATP binding|growth factor binding|vascular endothelial growth factor receptor activity			lung(10)|central_nervous_system(5)|ovary(3)|stomach(2)|skin(2)|urinary_tract(1)|breast(1)	24	Acute lymphoblastic leukemia(6;0.04)	Lung SC(185;0.0262)|Breast(139;0.188)	Colorectal(13;0.000674)	all cancers(112;0.0301)|Epithelial(112;0.155)|GBM - Glioblastoma multiforme(144;0.184)|OV - Ovarian serous cystadenocarcinoma(117;0.205)|Lung(94;0.207)	Sunitinib(DB01268)													---	---	---	---
FRY	10129	broad.mit.edu	37	13	32836660	32836660	+	Intron	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:32836660delA	uc001utx.2	+						FRY_uc010tdw.1_Intron|FRY_uc001uty.2_Intron|FRY_uc001utz.2_Intron|FRY_uc010tdx.1_5'Flank	NM_023037	NP_075463			furry homolog						regulation of transcription, DNA-dependent|transcription, DNA-dependent	integral to membrane				ovary(5)|large_intestine(1)|skin(1)	7		Lung SC(185;0.0271)		all cancers(112;4.81e-05)|Epithelial(112;0.000656)|OV - Ovarian serous cystadenocarcinoma(117;0.0123)|BRCA - Breast invasive adenocarcinoma(63;0.0295)|GBM - Glioblastoma multiforme(144;0.104)														---	---	---	---
FRY	10129	broad.mit.edu	37	13	32868431	32868431	+	Intron	DEL	T	-	-	rs11400232		TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:32868431delT	uc001utx.2	+						FRY_uc010tdw.1_Intron|FRY_uc001utz.2_Intron|FRY_uc010tdx.1_Intron	NM_023037	NP_075463			furry homolog						regulation of transcription, DNA-dependent|transcription, DNA-dependent	integral to membrane				ovary(5)|large_intestine(1)|skin(1)	7		Lung SC(185;0.0271)		all cancers(112;4.81e-05)|Epithelial(112;0.000656)|OV - Ovarian serous cystadenocarcinoma(117;0.0123)|BRCA - Breast invasive adenocarcinoma(63;0.0295)|GBM - Glioblastoma multiforme(144;0.104)														---	---	---	---
FAM48A	55578	broad.mit.edu	37	13	37600969	37600970	+	Intron	INS	-	A	A			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:37600969_37600970insA	uc001uwg.2	-						FAM48A_uc010abt.2_Intron|FAM48A_uc001uwh.2_Intron|FAM48A_uc001uwi.2_Intron|FAM48A_uc001uwj.2_Intron|FAM48A_uc001uwk.2_Intron|FAM48A_uc010tes.1_Intron|FAM48A_uc001uwl.1_Intron|FAM48A_uc001uwe.2_5'Flank|FAM48A_uc001uwf.2_5'Flank	NM_001014286	NP_001014308			family with sequence similarity 48, member A						autophagy|gastrulation	SAGA-type complex	protein binding				0		Lung NSC(96;2.09e-06)|Breast(139;0.014)|Lung SC(185;0.0548)|Prostate(109;0.0959)		all cancers(112;6.06e-07)|Epithelial(112;1.87e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00794)|BRCA - Breast invasive adenocarcinoma(63;0.0128)|GBM - Glioblastoma multiforme(144;0.0477)														---	---	---	---
FREM2	341640	broad.mit.edu	37	13	39447134	39447134	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:39447134delT	uc001uwv.2	+							NM_207361	NP_997244			FRAS1-related extracellular matrix protein 2						cell communication|homophilic cell adhesion|multicellular organismal development	integral to membrane|plasma membrane	calcium ion binding			ovary(7)|pancreas(1)|haematopoietic_and_lymphoid_tissue(1)|central_nervous_system(1)|skin(1)	11		Lung NSC(96;1.04e-07)|Prostate(109;0.00384)|Breast(139;0.00396)|Lung SC(185;0.0565)|Hepatocellular(188;0.114)		all cancers(112;3.32e-07)|Epithelial(112;1.66e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00154)|BRCA - Breast invasive adenocarcinoma(63;0.00631)|GBM - Glioblastoma multiforme(144;0.0312)														---	---	---	---
ELF1	1997	broad.mit.edu	37	13	41517026	41517026	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:41517026delT	uc001uxs.2	-						ELF1_uc010tfc.1_Intron|ELF1_uc010acd.2_Intron	NM_172373	NP_758961			E74-like factor 1 (ets domain transcription						positive regulation of transcription from RNA polymerase II promoter	cytoplasm|nucleus	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			ovary(1)	1		Lung NSC(96;8.3e-05)|Prostate(109;0.0233)|Breast(139;0.0296)|Lung SC(185;0.0367)		all cancers(112;1.87e-08)|Epithelial(112;8.45e-06)|OV - Ovarian serous cystadenocarcinoma(117;0.000202)|GBM - Glioblastoma multiforme(144;0.00266)|BRCA - Breast invasive adenocarcinoma(63;0.072)														---	---	---	---
CPB2	1361	broad.mit.edu	37	13	46630052	46630052	+	Intron	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:46630052delA	uc001vaw.2	-						uc001vau.1_Intron|uc001vav.1_Intron|CPB2_uc001vax.2_Intron	NM_001872	NP_001863			plasma carboxypeptidase B2 isoform a						blood coagulation|fibrinolysis|proteolysis	extracellular space	metallocarboxypeptidase activity|zinc ion binding			ovary(1)|skin(1)	2		Lung NSC(96;4.21e-05)|Breast(56;0.000118)|Prostate(109;0.00217)|Hepatocellular(98;0.0207)|Lung SC(185;0.0262)|all_neural(104;0.235)	KIRC - Kidney renal clear cell carcinoma(16;0.234)	GBM - Glioblastoma multiforme(144;5.44e-05)														---	---	---	---
LCP1	3936	broad.mit.edu	37	13	46716269	46716269	+	Intron	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:46716269delA	uc001vaz.3	-						LCP1_uc010ack.2_Intron|LCP1_uc001vay.3_Intron|LCP1_uc001vba.3_Intron	NM_002298	NP_002289			L-plastin						regulation of intracellular protein transport|T cell activation involved in immune response	cell junction|cytosol|ruffle membrane	calcium ion binding			lung(4)|ovary(3)	7		Lung NSC(96;1.27e-05)|Breast(56;8.04e-05)|Prostate(109;0.00217)|Hepatocellular(98;0.0207)|Lung SC(185;0.0262)	KIRC - Kidney renal clear cell carcinoma(16;0.234)	GBM - Glioblastoma multiforme(144;5.39e-05)				T	BCL6	NHL 								---	---	---	---
FNDC3A	22862	broad.mit.edu	37	13	49742591	49742591	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:49742591delT	uc001vcm.2	+						FNDC3A_uc001vcn.2_Intron|FNDC3A_uc001vco.2_Intron|FNDC3A_uc001vcp.1_Intron|FNDC3A_uc001vcq.2_Intron	NM_001079673	NP_001073141			fibronectin type III domain containing 3A							Golgi membrane|integral to membrane				lung(2)	2		all_lung(13;7.44e-08)|Lung NSC(96;4.08e-06)|Breast(56;0.000111)|Prostate(109;0.00174)|Myeloproliferative disorder(33;0.0179)|Hepatocellular(98;0.0207)|Lung SC(185;0.187)|all_neural(104;0.19)	KIRC - Kidney renal clear cell carcinoma(9;0.206)	GBM - Glioblastoma multiforme(99;2.94e-09)														---	---	---	---
INTS6	26512	broad.mit.edu	37	13	51936274	51936274	+	3'UTR	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:51936274delT	uc001vfk.2	-	18					SERPINE3_uc010tgp.1_Intron|INTS6_uc001vfi.2_3'UTR|INTS6_uc001vfj.2_3'UTR|INTS6_uc001vfl.2_3'UTR	NM_012141	NP_036273			integrator complex subunit 6 isoform a						snRNA processing	actin cytoskeleton|integrator complex	protein binding|transmembrane receptor activity			ovary(1)|lung(1)	2		Breast(56;0.000286)|Lung NSC(96;0.00145)|Prostate(109;0.00403)|Hepatocellular(98;0.065)|Myeloproliferative disorder(33;0.163)|all_neural(104;0.19)		GBM - Glioblastoma multiforme(99;7.7e-08)														---	---	---	---
TDRD3	81550	broad.mit.edu	37	13	61057789	61057789	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:61057789delT	uc001via.2	+						TDRD3_uc010aef.2_Intron|TDRD3_uc001vhz.3_Intron|TDRD3_uc010aeg.2_Intron|TDRD3_uc001vib.3_Intron	NM_030794	NP_110421			tudor domain containing 3 isoform 2						chromatin modification	cytoplasm|nucleus	chromatin binding|methylated histone residue binding|nucleic acid binding|transcription coactivator activity			upper_aerodigestive_tract(1)|skin(1)	2		Prostate(109;0.173)|Breast(118;0.174)		GBM - Glioblastoma multiforme(99;0.000291)														---	---	---	---
Unknown	0	broad.mit.edu	37	13	67840882	67840882	+	IGR	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:67840882delT								PCDH9 (36414 upstream) : None (None downstream)																																			---	---	---	---
COMMD6	170622	broad.mit.edu	37	13	76112127	76112127	+	5'Flank	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:76112127delA	uc001vjo.1	-						COMMD6_uc001vjn.1_5'Flank|COMMD6_uc010aet.1_5'Flank|COMMD6_uc001vjp.1_Intron	NM_203495	NP_987091			COMM domain containing 6 isoform b							cytoplasm|nucleus	protein binding				0		Breast(118;0.0979)|Prostate(6;0.122)		GBM - Glioblastoma multiforme(99;0.0104)														---	---	---	---
DNAJC3	5611	broad.mit.edu	37	13	96395171	96395171	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:96395171delT	uc001vmq.2	+						DNAJC3_uc001vmp.2_Frame_Shift_Del_p.I226fs|DNAJC3_uc001vmr.2_Intron	NM_006260	NP_006251			DnaJ (Hsp40) homolog, subfamily C, member 3						protein folding|response to unfolded protein|response to virus		heat shock protein binding|protein kinase inhibitor activity|unfolded protein binding				0	all_neural(89;0.0878)|Breast(111;0.148)|Medulloblastoma(90;0.163)		BRCA - Breast invasive adenocarcinoma(86;0.126)															---	---	---	---
MYO16	23026	broad.mit.edu	37	13	109858929	109858930	+	Intron	INS	-	T	T			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:109858929_109858930insT	uc001vqt.1	+						MYO16_uc010agk.1_Intron	NM_015011	NP_055826			myosin heavy chain Myr 8						cerebellum development|negative regulation of cell proliferation|negative regulation of S phase of mitotic cell cycle	myosin complex|nucleoplasm|perinuclear region of cytoplasm|plasma membrane	actin filament binding|ATP binding|motor activity			ovary(6)|large_intestine(1)|kidney(1)|breast(1)|central_nervous_system(1)	10	all_lung(23;0.000332)|all_neural(89;0.00294)|Medulloblastoma(90;0.00596)|Lung NSC(43;0.00751)|Lung SC(71;0.104)		BRCA - Breast invasive adenocarcinoma(86;0.19)|all cancers(43;0.201)															---	---	---	---
Unknown	0	broad.mit.edu	37	14	19339542	19339542	+	IGR	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:19339542delA								None (None upstream) : OR11H12 (38052 downstream)																																			---	---	---	---
PSMB5	5693	broad.mit.edu	37	14	23502434	23502434	+	Intron	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:23502434delA	uc001wii.2	-						PSMB5_uc001wij.2_Intron|PSMB5_uc010tni.1_Intron	NM_002797	NP_002788			proteasome beta 5 subunit isoform 1						anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|G1/S transition of mitotic cell cycle|interspecies interaction between organisms|M/G1 transition of mitotic cell cycle|mRNA metabolic process|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|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|viral reproduction	cytoplasm|nucleus	protein binding|threonine-type endopeptidase activity			ovary(1)	1	all_cancers(95;3.3e-05)			GBM - Glioblastoma multiforme(265;0.0121)	Bortezomib(DB00188)													---	---	---	---
HECTD1	25831	broad.mit.edu	37	14	31583617	31583617	+	Intron	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:31583617delA	uc001wrc.1	-						HECTD1_uc001wra.1_Intron|HECTD1_uc001wrb.1_Intron|HECTD1_uc001wrd.1_Intron	NM_015382	NP_056197			HECT domain containing 1						protein ubiquitination involved in ubiquitin-dependent protein catabolic process	intracellular	metal ion binding|protein binding|ubiquitin-protein ligase activity			ovary(3)|large_intestine(1)|lung(1)	5	Hepatocellular(127;0.0877)|Breast(36;0.176)		LUAD - Lung adenocarcinoma(48;0.00292)|Lung(238;0.0164)|BRCA - Breast invasive adenocarcinoma(188;0.111)|STAD - Stomach adenocarcinoma(7;0.173)	GBM - Glioblastoma multiforme(265;0.00617)														---	---	---	---
KCNH5	27133	broad.mit.edu	37	14	63417320	63417321	+	Intron	DEL	AA	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:63417320_63417321delAA	uc001xfx.2	-						KCNH5_uc001xfy.2_Intron|KCNH5_uc001xfz.1_Intron|KCNH5_uc001xga.2_Intron	NM_139318	NP_647479			potassium voltage-gated channel, subfamily H,						regulation of transcription, DNA-dependent	integral to membrane	calmodulin binding|two-component sensor activity|voltage-gated potassium channel activity			ovary(4)|skin(4)|central_nervous_system(1)	9				OV - Ovarian serous cystadenocarcinoma(108;0.00958)|BRCA - Breast invasive adenocarcinoma(234;0.168)														---	---	---	---
Unknown	0	broad.mit.edu	37	14	73428538	73428539	+	IGR	DEL	CT	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:73428538_73428539delCT								DCAF4 (2182 upstream) : ZFYVE1 (7621 downstream)																																			---	---	---	---
ALDH6A1	4329	broad.mit.edu	37	14	74533914	74533915	+	Intron	INS	-	A	A			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:74533914_74533915insA	uc001xpo.2	-						C14orf45_uc001xpm.1_Intron|ALDH6A1_uc010asa.2_Intron|ALDH6A1_uc010tuq.1_Intron	NM_005589	NP_005580			aldehyde dehydrogenase 6A1 precursor							mitochondrial matrix|nucleus	fatty-acyl-CoA binding|malonate-semialdehyde dehydrogenase (acetylating) activity|methylmalonate-semialdehyde dehydrogenase (acylating) activity				0				BRCA - Breast invasive adenocarcinoma(234;0.00354)	NADH(DB00157)													---	---	---	---
AHSA1	10598	broad.mit.edu	37	14	77934395	77934399	+	Intron	DEL	TTTTT	-	-	rs35071844		TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:77934395_77934399delTTTTT	uc001xtw.2	+						AHSA1_uc010tvk.1_Intron	NM_012111	NP_036243			activator of heat shock 90kDa protein ATPase						protein folding|response to stress	cytosol|endoplasmic reticulum	ATPase activator activity|chaperone binding				0			Kidney(204;0.164)	BRCA - Breast invasive adenocarcinoma(234;0.0281)														---	---	---	---
CATSPERB	79820	broad.mit.edu	37	14	92176040	92176041	+	Intron	DEL	AC	-	-	rs12882622		TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:92176040_92176041delAC	uc001xzs.1	-							NM_024764	NP_079040			cation channel, sperm-associated, beta						cell differentiation|multicellular organismal development|spermatogenesis	integral to membrane				breast(2)|skin(2)|ovary(1)	5		all_cancers(154;0.0663)|all_epithelial(191;0.236)																---	---	---	---
TRIP11	9321	broad.mit.edu	37	14	92493257	92493257	+	Intron	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:92493257delA	uc001xzy.2	-							NM_004239	NP_004230			thyroid hormone receptor interactor 11						transcription from RNA polymerase II promoter	cytoskeleton|Golgi apparatus|membrane|nucleus	protein binding|transcription coactivator activity			ovary(6)|skin(2)|kidney(2)|central_nervous_system(1)|lung(1)|breast(1)	13				COAD - Colon adenocarcinoma(157;0.223)				T	PDGFRB	AML								---	---	---	---
CPSF2	53981	broad.mit.edu	37	14	92623949	92623949	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:92623949delT	uc001yah.1	+							NM_017437	NP_059133			cleavage and polyadenylation specific factor 2						histone mRNA 3'-end processing|mRNA export from nucleus|nuclear mRNA splicing, via spliceosome|termination of RNA polymerase II transcription	mRNA cleavage and polyadenylation specificity factor complex	hydrolase activity|protein binding|RNA binding			ovary(2)	2		all_cancers(154;0.0766)		COAD - Colon adenocarcinoma(157;0.222)														---	---	---	---
CPSF2	53981	broad.mit.edu	37	14	92625696	92625696	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:92625696delT	uc001yah.1	+							NM_017437	NP_059133			cleavage and polyadenylation specific factor 2						histone mRNA 3'-end processing|mRNA export from nucleus|nuclear mRNA splicing, via spliceosome|termination of RNA polymerase II transcription	mRNA cleavage and polyadenylation specificity factor complex	hydrolase activity|protein binding|RNA binding			ovary(2)	2		all_cancers(154;0.0766)		COAD - Colon adenocarcinoma(157;0.222)														---	---	---	---
NF1P1	440225	broad.mit.edu	37	15	21136692	21136693	+	5'Flank	DEL	CA	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:21136692_21136693delCA	uc001ytv.1	-											Human NF1-related locus DNA in A9 mouse DNA background.												0																		---	---	---	---
UBE3A	7337	broad.mit.edu	37	15	25650459	25650459	+	Intron	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:25650459delA	uc001zaq.2	-						UBE3A_uc001zar.2_Intron|UBE3A_uc001zas.2_Intron|UBE3A_uc001zat.2_Intron	NM_000462	NP_000453			ubiquitin protein ligase E3A isoform 2						brain development|interspecies interaction between organisms|protein K48-linked ubiquitination|protein ubiquitination involved in ubiquitin-dependent protein catabolic process	nucleus|proteasome complex	protein binding|ubiquitin-protein ligase activity			upper_aerodigestive_tract(1)|ovary(1)|breast(1)	3		all_cancers(20;3.47e-21)|Breast(32;0.00123)		all cancers(64;2.78e-08)|Epithelial(43;8.85e-08)|BRCA - Breast invasive adenocarcinoma(123;0.0155)|Lung(196;0.0616)														---	---	---	---
HERC2	8924	broad.mit.edu	37	15	28388214	28388214	+	Intron	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:28388214delA	uc001zbj.2	-							NM_004667	NP_004658			hect domain and RLD 2						DNA repair|intracellular protein transport|protein ubiquitination involved in ubiquitin-dependent protein catabolic process	nucleus	guanyl-nucleotide exchange factor activity|heme binding|protein binding|ubiquitin-protein ligase activity|zinc ion binding			ovary(4)|lung(4)|skin(3)|upper_aerodigestive_tract(1)|central_nervous_system(1)	13		all_lung(180;1.3e-11)|Breast(32;0.000194)|Colorectal(260;0.227)		all cancers(64;3.93e-09)|Epithelial(43;9.99e-08)|BRCA - Breast invasive adenocarcinoma(123;0.0271)|GBM - Glioblastoma multiforme(186;0.0497)|Lung(196;0.199)														---	---	---	---
RYR3	6263	broad.mit.edu	37	15	33923503	33923503	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:33923503delT	uc001zhi.2	+						RYR3_uc010bar.2_Intron	NM_001036	NP_001027			ryanodine receptor 3						cellular calcium ion homeostasis	integral to membrane	calcium ion binding|receptor activity|ryanodine-sensitive calcium-release channel activity			ovary(5)|central_nervous_system(4)|lung(1)	10		all_lung(180;7.18e-09)		all cancers(64;8.95e-12)|GBM - Glioblastoma multiforme(186;0.00109)|BRCA - Breast invasive adenocarcinoma(123;0.0363)														---	---	---	---
LPCAT4	254531	broad.mit.edu	37	15	34656628	34656628	+	Intron	DEL	T	-	-	rs10718217		TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:34656628delT	uc001zig.2	-						LPCAT4_uc010bav.1_Intron	NM_153613	NP_705841			lysophosphatidylcholine acyltransferase 4						phospholipid biosynthetic process	endoplasmic reticulum membrane|integral to membrane	acyltransferase activity|calcium ion binding				0																		---	---	---	---
USP50	373509	broad.mit.edu	37	15	50833546	50833546	+	Intron	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:50833546delA	uc001zyq.3	-							NM_203494	NP_987090			ubiquitin specific protease 50						ubiquitin-dependent protein catabolic process		ubiquitin thiolesterase activity			lung(1)|breast(1)	2				all cancers(107;0.000519)|GBM - Glioblastoma multiforme(94;0.00288)														---	---	---	---
GTF2A2	2958	broad.mit.edu	37	15	59942804	59942804	+	Intron	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:59942804delA	uc002agg.2	-							NM_004492	NP_004483			general transcription factor IIA, 2, 12kDa						interspecies interaction between organisms|positive regulation of sequence-specific DNA binding transcription factor activity|positive regulation of transcription from RNA polymerase II promoter|RNA polymerase II transcriptional preinitiation complex assembly|transcription elongation from RNA polymerase II promoter|viral reproduction	transcription factor TFIIA complex	protein heterodimerization activity|protein homodimerization activity|TBP-class protein binding|transcription coactivator activity			central_nervous_system(2)	2																		---	---	---	---
VPS13C	54832	broad.mit.edu	37	15	62284070	62284070	+	Intron	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:62284070delA	uc002agz.2	-						VPS13C_uc002aha.2_Intron|VPS13C_uc002ahb.1_Intron|VPS13C_uc002ahc.1_Intron	NM_020821	NP_065872			vacuolar protein sorting 13C protein isoform 2A						protein localization					ovary(2)	2																		---	---	---	---
DAPK2	23604	broad.mit.edu	37	15	64231579	64231581	+	Intron	DEL	AAA	-	-	rs75862994		TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:64231579_64231581delAAA	uc002amr.2	-						DAPK2_uc010uim.1_Intron|DAPK2_uc010bgu.1_Intron	NM_014326	NP_055141			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)														---	---	---	---
FAM96A	84191	broad.mit.edu	37	15	64367853	64367853	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:64367853delT	uc002amt.1	-						FAM96A_uc002amu.1_Intron|FAM96A_uc010uin.1_Intron	NM_032231	NP_115607			family with sequence similarity 96, member A						chromosome segregation						0																		---	---	---	---
Unknown	0	broad.mit.edu	37	15	75541371	75541372	+	IGR	DEL	TT	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:75541371_75541372delTT								C15orf39 (36863 upstream) : GOLGA6C (9527 downstream)																																			---	---	---	---
WDR61	80349	broad.mit.edu	37	15	78575973	78575973	+	Intron	DEL	G	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:78575973delG	uc002bdn.2	-						WDR61_uc002bdo.2_Intron	NM_025234	NP_079510			WD repeat domain 61								protein binding			ovary(1)|skin(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	15	79156196	79156196	+	IGR	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:79156196delA								ADAMTS7 (52423 upstream) : MORF4L1 (8976 downstream)																																			---	---	---	---
BLM	641	broad.mit.edu	37	15	91308328	91308328	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:91308328delT	uc002bpr.2	+						BLM_uc010uqh.1_Intron|BLM_uc010uqi.1_Intron|BLM_uc010bnx.2_Intron|BLM_uc002bps.1_Intron	NM_000057	NP_000048			Bloom syndrome protein						double-strand break repair via homologous recombination|G2 phase of mitotic cell cycle|G2/M transition DNA damage checkpoint|negative regulation of cell division|positive regulation of transcription, DNA-dependent|protein oligomerization|regulation of cyclin-dependent protein kinase activity|replication fork processing|replication fork protection|response to X-ray	cytoplasm|lateral element|nuclear matrix|nucleolus|PML body	ATP binding|bubble DNA binding|DNA strand annealing activity|four-way junction helicase activity|G-quadruplex DNA binding|p53 binding			ovary(3)|skin(2)|breast(1)	6	Lung NSC(78;0.0875)|all_lung(78;0.109)		Lung(145;0.189)					Mis|N|F			leukemia|lymphoma|skin squamous cell |other cancers		Genes_defective_in_diseases_associated_with_sensitivity_to_DNA_damaging_agents	Bloom_syndrome				---	---	---	---
PGPEP1L	145814	broad.mit.edu	37	15	99514430	99514440	+	Intron	DEL	GGGGGGGGGGT	-	-	rs72362970		TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:99514430_99514440delGGGGGGGGGGT	uc002bum.2	-						PGPEP1L_uc010bop.2_Intron|PGPEP1L_uc002bun.2_Intron	NM_001102612	NP_001096082			pyroglutamyl-peptidase 1-like protein						proteolysis		cysteine-type peptidase activity				0																		---	---	---	---
C16orf90	646174	broad.mit.edu	37	16	3546140	3546141	+	5'Flank	INS	-	A	A			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:3546140_3546141insA	uc002cvi.2	-							NM_001080524	NP_001073993			hypothetical protein LOC646174												0																		---	---	---	---
ADCY9	115	broad.mit.edu	37	16	4027728	4027728	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:4027728delT	uc002cvx.2	-							NM_001116	NP_001107			adenylate cyclase 9						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 plasma membrane	adenylate cyclase activity|ATP binding|metal ion binding			ovary(4)|large_intestine(1)|central_nervous_system(1)	6																		---	---	---	---
PARN	5073	broad.mit.edu	37	16	14674917	14674917	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:14674917delT	uc010uzd.1	-						PARN_uc010uzc.1_Intron|PARN_uc010uze.1_Intron|PARN_uc010uzf.1_Intron	NM_002582	NP_002573			poly(A)-specific ribonuclease (deadenylation						female gamete generation|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay|nuclear-transcribed mRNA poly(A) tail shortening|RNA modification	cytosol|nucleolus	metal ion binding|mRNA 3'-UTR binding|nucleotide binding|poly(A)-specific ribonuclease activity|protein binding			ovary(2)	2																		---	---	---	---
PDZD9	255762	broad.mit.edu	37	16	22009713	22009714	+	Intron	INS	-	A	A			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:22009713_22009714insA	uc002dka.1	-							NM_173806	NP_776167			hypothetical protein LOC255762											pancreas(1)	1																		---	---	---	---
COG7	91949	broad.mit.edu	37	16	23445141	23445142	+	Intron	DEL	AA	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:23445141_23445142delAA	uc002dlo.2	-							NM_153603	NP_705831			component of oligomeric golgi complex 7						intracellular protein transport|protein glycosylation|protein localization in Golgi apparatus|protein stabilization|retrograde vesicle-mediated transport, Golgi to ER	Golgi membrane|Golgi transport complex	protein binding				0				GBM - Glioblastoma multiforme(48;0.0401)												OREG0023684	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
Unknown	0	broad.mit.edu	37	16	29437102	29437102	+	IGR	DEL	G	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:29437102delG								RUNDC2C (18753 upstream) : LOC440354 (17124 downstream)																																			---	---	---	---
LOC595101	595101	broad.mit.edu	37	16	30291742	30291742	+	Intron	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:30291742delA	uc002dxp.1	-							NR_002453				Homo sapiens cDNA FLJ39663 fis, clone SMINT2007187.												0																		---	---	---	---
SETD1A	9739	broad.mit.edu	37	16	30995407	30995407	+	3'UTR	DEL	C	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:30995407delC	uc002ead.1	+	19					HSD3B7_uc002eaf.2_5'Flank|HSD3B7_uc010cac.2_5'Flank|HSD3B7_uc002eag.2_5'Flank|HSD3B7_uc002eah.2_5'Flank	NM_014712	NP_055527			SET domain containing 1A						regulation of transcription, DNA-dependent|transcription, DNA-dependent	chromosome|nuclear speck|Set1C/COMPASS complex	histone-lysine N-methyltransferase activity|nucleotide binding|protein binding|RNA binding			ovary(2)|skin(1)	3																		---	---	---	---
ITFG1	81533	broad.mit.edu	37	16	47292700	47292700	+	Intron	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:47292700delA	uc002eet.2	-						ITFG1_uc010vgg.1_Intron|ITFG1_uc010vgh.1_Intron	NM_030790	NP_110417			integrin alpha FG-GAP repeat containing 1							extracellular region|integral to membrane				ovary(1)|central_nervous_system(1)	2		all_cancers(37;0.0613)|all_lung(18;0.0543)|Lung NSC(13;0.227)																---	---	---	---
CLEC18C	283971	broad.mit.edu	37	16	70066043	70066043	+	Intron	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:70066043delA	uc002exy.2	+						PDXDC2_uc002eyb.2_Intron|PDXDC2_uc002eyc.2_Intron	NM_182619	NP_872425			secretory protein LOC348174 precursor							extracellular region	sugar binding				0																		---	---	---	---
GLG1	2734	broad.mit.edu	37	16	74542594	74542594	+	Intron	DEL	C	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:74542594delC	uc002fcy.3	-						GLG1_uc002fcx.2_Intron|GLG1_uc002fcw.3_Intron|GLG1_uc002fcz.3_Intron	NM_001145667	NP_001139139			golgi apparatus protein 1 isoform 3							Golgi membrane|integral to membrane	receptor binding			ovary(1)|breast(1)	2																		---	---	---	---
CENPN	55839	broad.mit.edu	37	16	81051516	81051516	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:81051516delT	uc002ffx.2	+						CENPN_uc002ffw.3_Intron|CENPN_uc010vnl.1_Intron|CENPN_uc010vnm.1_Intron|CENPN_uc002ffy.3_Intron	NM_001100624	NP_001094094			centromere protein N isoform 2						CenH3-containing nucleosome assembly at centromere|mitotic prometaphase	condensed chromosome kinetochore|cytosol|nucleoplasm					0																		---	---	---	---
C17orf68	80169	broad.mit.edu	37	17	8134459	8134459	+	Intron	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:8134459delA	uc002gkq.3	-						C17orf68_uc010cnv.2_Intron	NM_025099	NP_079375			alpha accessory factor 132						positive regulation of DNA replication|telomere maintenance	Stn1-Ten1 complex	protein binding|single-stranded DNA binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	17	14608988	14608989	+	IGR	DEL	TT	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:14608988_14608989delTT								HS3ST3B1 (359496 upstream) : PMP22 (524108 downstream)																																			---	---	---	---
DRG2	1819	broad.mit.edu	37	17	17996994	17996994	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:17996994delT	uc002gsh.1	+						DRG2_uc010vxg.1_Intron|DRG2_uc002gsi.1_Intron|DRG2_uc002gsj.1_Intron	NM_001388	NP_001379			developmentally regulated GTP binding protein 2						signal transduction		GTP binding			ovary(1)	1	all_neural(463;0.228)																	---	---	---	---
CYTSB	92521	broad.mit.edu	37	17	20150446	20150446	+	Intron	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:20150446delA	uc002gwq.2	+						CYTSB_uc002gws.2_Intron|CYTSB_uc002gwv.2_Intron|CYTSB_uc010vzf.1_Intron|CYTSB_uc002gww.2_Intron	NM_001033553	NP_001028725			spectrin domain with coiled-coils 1 NSP5b3b							nucleus					0																		---	---	---	---
Unknown	0	broad.mit.edu	37	17	29349140	29349141	+	5'Flank	INS	-	AT	AT			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:29349140_29349141insAT	uc002hgd.1	+											Homo sapiens full length insert cDNA clone ZD88F12.									p.?(1)																					---	---	---	---
NF1	4763	broad.mit.edu	37	17	29575850	29575851	+	Intron	DEL	TT	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:29575850_29575851delTT	uc002hgg.2	+						NF1_uc002hgh.2_Intron|NF1_uc010csn.1_Intron|NF1_uc002hgi.1_Intron	NM_001042492	NP_001035957			neurofibromin isoform 1						actin cytoskeleton organization|adrenal gland development|artery morphogenesis|camera-type eye morphogenesis|cerebral cortex development|collagen fibril organization|forebrain astrocyte development|forebrain morphogenesis|heart development|liver development|MAPKKK cascade|metanephros development|myelination in peripheral nervous system|negative regulation of cell migration|negative regulation of endothelial cell proliferation|negative regulation of MAP kinase activity|negative regulation of MAPKKK cascade|negative regulation of neuroblast proliferation|negative regulation of oligodendrocyte differentiation|negative regulation of transcription factor import into nucleus|osteoblast differentiation|phosphatidylinositol 3-kinase cascade|pigmentation|positive regulation of adenylate cyclase activity|positive regulation of neuron apoptosis|Ras protein signal transduction|regulation of blood vessel endothelial cell migration|regulation of bone resorption|response to hypoxia|smooth muscle tissue development|spinal cord development|sympathetic nervous system development|visual learning|wound healing	axon|cytoplasm|dendrite|intrinsic to internal side of plasma membrane|nucleus	protein binding|Ras GTPase activator activity	p.?(2)		soft_tissue(159)|central_nervous_system(56)|lung(28)|large_intestine(27)|haematopoietic_and_lymphoid_tissue(18)|ovary(18)|autonomic_ganglia(12)|breast(3)|skin(3)|stomach(2)|thyroid(1)|prostate(1)|kidney(1)|pancreas(1)	330		all_cancers(10;1.29e-12)|all_epithelial(10;0.00347)|all_hematologic(16;0.00556)|Acute lymphoblastic leukemia(14;0.00593)|Breast(31;0.014)|Myeloproliferative disorder(56;0.0255)|all_lung(9;0.0321)|Lung NSC(157;0.0659)		UCEC - Uterine corpus endometrioid carcinoma (4;4.38e-05)|all cancers(4;1.64e-26)|Epithelial(4;9.15e-23)|OV - Ovarian serous cystadenocarcinoma(4;3.58e-21)|GBM - Glioblastoma multiforme(4;0.00146)				D|Mis|N|F|S|O		neurofibroma|glioma	neurofibroma|glioma			Neurofibromatosis_type_1	TCGA GBM(6;<1E-08)|TSP Lung(7;0.0071)|TCGA Ovarian(3;0.0088)			---	---	---	---
LRRC37B	114659	broad.mit.edu	37	17	30375152	30375152	+	Intron	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:30375152delA	uc002hgu.2	+						LRRC37B_uc010wbx.1_Intron|LRRC37B_uc010csu.2_Intron	NM_052888	NP_443120			leucine rich repeat containing 37B precursor							integral to membrane				upper_aerodigestive_tract(1)|ovary(1)	2		Myeloproliferative disorder(56;0.0255)|all_hematologic(16;0.111)|Ovarian(249;0.182)|Breast(31;0.244)																---	---	---	---
DDX52	11056	broad.mit.edu	37	17	35985898	35985898	+	Intron	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:35985898delA	uc002hoi.1	-						DDX52_uc002hoh.1_Intron	NM_007010	NP_008941			ATP-dependent RNA helicase ROK1 isoform a							nucleolus	ATP binding|ATP-dependent helicase activity|RNA binding			ovary(1)|skin(1)	2		Breast(25;0.00637)|Ovarian(249;0.15)																---	---	---	---
KRT40	125115	broad.mit.edu	37	17	39139511	39139511	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:39139511delT	uc010cxh.1	-						KRT40_uc002hvq.1_Intron	NM_182497	NP_872303			type I hair keratin KA36							intermediate filament	structural molecule activity				0		Breast(137;0.00043)																---	---	---	---
CCDC43	124808	broad.mit.edu	37	17	42756533	42756533	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:42756533delT	uc002ihc.2	-						CCDC43_uc010czw.1_Intron	NM_144609	NP_653210			coiled-coil domain containing 43 isoform 1												0		Prostate(33;0.0322)																---	---	---	---
ABI3	51225	broad.mit.edu	37	17	47295005	47295005	+	Intron	DEL	C	-	-	rs113223751		TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:47295005delC	uc002iop.1	+						ABI3_uc002ioq.1_Intron	NM_016428	NP_057512			NESH protein isoform 1						cellular component movement|regulation of cell migration	cytoplasm|lamellipodium	protein binding				0			Epithelial(5;6.37e-06)|all cancers(6;6.36e-05)												HNSCC(55;0.14)			---	---	---	---
TUBD1	51174	broad.mit.edu	37	17	57963684	57963684	+	Intron	DEL	A	-	-	rs113094238		TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:57963684delA	uc002ixw.1	-						TUBD1_uc010ddf.1_Intron|TUBD1_uc010ddg.1_Intron|TUBD1_uc010ddh.1_Intron|TUBD1_uc010wok.1_Intron|TUBD1_uc002ixx.1_Intron|TUBD1_uc010wol.1_Intron|TUBD1_uc010ddi.1_Intron	NM_016261	NP_057345			delta-tubulin						cell differentiation|microtubule-based movement|multicellular organismal development|protein polymerization|spermatogenesis	centriole|microtubule|nucleus	GTP binding|GTPase activity|structural molecule activity			ovary(1)	1	all_cancers(5;3.18e-13)|Breast(5;2.91e-25)|all_neural(34;0.0878)|Medulloblastoma(34;0.0922)		Epithelial(12;9.34e-13)|all cancers(12;1.91e-11)															---	---	---	---
HEATR6	63897	broad.mit.edu	37	17	58136999	58136999	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:58136999delT	uc002iyk.1	-						HEATR6_uc010ddk.1_Intron|HEATR6_uc010wos.1_Intron	NM_022070	NP_071353			HEAT repeat containing 6								binding			ovary(1)|skin(1)	2	all_cancers(5;2.25e-13)|Breast(5;4.84e-25)|all_neural(34;0.0878)|Medulloblastoma(34;0.0922)		BRCA - Breast invasive adenocarcinoma(1;5.93e-19)|Epithelial(12;7.59e-12)|all cancers(12;1.26e-10)															---	---	---	---
TBX2	6909	broad.mit.edu	37	17	59482166	59482166	+	Intron	DEL	C	-	-	rs66504335		TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:59482166delC	uc010wox.1	+						TBX2_uc002ize.2_Frame_Shift_Del_p.R353fs|TBX2_uc002izg.2_Intron	NM_005994	NP_005985			T-box 2						cell aging|positive regulation of cell proliferation		sequence-specific DNA binding				0																		---	---	---	---
LOC146880	146880	broad.mit.edu	37	17	62750914	62750914	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:62750914delT	uc010wqc.1	-							NR_026899				Homo sapiens cDNA FLJ30780 fis, clone FEBRA2000856.												0																		---	---	---	---
CYTH1	9267	broad.mit.edu	37	17	76696603	76696603	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:76696603delT	uc002jvw.2	-						CYTH1_uc010wtw.1_Intron|CYTH1_uc010wtx.1_Intron	NM_017456	NP_059430			cytohesin 1 isoform 2						regulation of ARF protein signal transduction|regulation of cell adhesion|vesicle-mediated transport	cytoplasm|plasma membrane	ARF guanyl-nucleotide exchange factor activity|protein binding			ovary(1)	1																		---	---	---	---
MYL12B	103910	broad.mit.edu	37	18	3273141	3273142	+	Intron	INS	-	T	T			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:3273141_3273142insT	uc010dkl.2	+						MYL12B_uc002klt.3_Intron|MYL12B_uc010wyv.1_Intron	NM_001144944	NP_001138416			myosin regulatory light chain MRCL2 isoform A						axon guidance|muscle contraction	cytosol|myosin complex	calcium ion binding				0																		---	---	---	---
NAPG	8774	broad.mit.edu	37	18	10548537	10548539	+	Intron	DEL	TTT	-	-	rs1662154		TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:10548537_10548539delTTT	uc002kon.2	+						NAPG_uc010wzr.1_Intron|NAPG_uc002koo.2_Intron|NAPG_uc002kop.2_Intron	NM_003826	NP_003817			N-ethylmaleimide-sensitive factor attachment						cellular membrane fusion|intra-Golgi vesicle-mediated transport|intracellular protein transport|protein complex assembly|protein stabilization	membrane|membrane fraction|mitochondrion	protein binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	18	14225639	14225639	+	IGR	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:14225639delA								ZNF519 (93210 upstream) : LOC284233 (111783 downstream)																																			---	---	---	---
NPC1	4864	broad.mit.edu	37	18	21120909	21120909	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:21120909delT	uc002kum.3	-						NPC1_uc010xaz.1_Intron|NPC1_uc010xba.1_Intron	NM_000271	NP_000262			Niemann-Pick disease, type C1 precursor						autophagy|bile acid metabolic process|cholesterol efflux|cholesterol homeostasis|lysosomal transport	endoplasmic reticulum|integral to plasma membrane|late endosome membrane|lysosomal membrane|nuclear envelope|perinuclear region of cytoplasm	hedgehog receptor activity|protein binding|sterol transporter activity			ovary(2)	2	all_cancers(21;0.000106)|all_epithelial(16;6.57e-07)|Lung NSC(20;0.00166)|all_lung(20;0.00536)|Colorectal(14;0.0202)|Ovarian(20;0.127)																	---	---	---	---
CDH2	1000	broad.mit.edu	37	18	25593923	25593923	+	Intron	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:25593923delA	uc002kwg.2	-						CDH2_uc010xbn.1_Intron	NM_001792	NP_001783			cadherin 2, type 1 preproprotein						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																		---	---	---	---
DSG1	1828	broad.mit.edu	37	18	28923779	28923779	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:28923779delT	uc002kwp.2	+						DSG1_uc010xbp.1_5'UTR	NM_001942	NP_001933			desmoglein 1 preproprotein						calcium-dependent cell-cell adhesion|cell-cell junction assembly|cellular component disassembly involved in apoptosis|homophilic cell adhesion|protein stabilization	cytosol|desmosome|integral to membrane|internal side of plasma membrane	calcium ion binding|gamma-catenin binding|toxin binding			skin(3)|ovary(2)|central_nervous_system(2)	7			OV - Ovarian serous cystadenocarcinoma(10;0.00559)															---	---	---	---
PRSSL1	400668	broad.mit.edu	37	19	691213	691213	+	Intron	DEL	A	-	-	rs147436553		TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:691213delA	uc002lpl.1	-						PRSSL1_uc010xfs.1_Intron	NM_214710	NP_999875			protease, serine-like 1 precursor						proteolysis	extracellular region	serine-type endopeptidase activity				0		all_epithelial(18;2.19e-21)|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)														---	---	---	---
GRIN3B	116444	broad.mit.edu	37	19	1008813	1008813	+	Intron	DEL	C	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:1008813delC	uc002lqo.1	+						uc002lqp.1_RNA	NM_138690	NP_619635			glutamate receptor, ionotropic,						ionotropic glutamate receptor signaling pathway|protein insertion into membrane|regulation of calcium ion transport	cell junction|N-methyl-D-aspartate selective glutamate receptor complex|neuronal cell body|outer membrane-bounded periplasmic space|postsynaptic membrane	extracellular-glutamate-gated ion channel activity|glycine binding|ionotropic glutamate receptor activity|neurotransmitter receptor activity				0		Acute lymphoblastic leukemia(61;4.36e-14)|all_hematologic(61;4.84e-09)|Lung NSC(49;0.000226)|all_lung(49;0.000353)|Breast(49;0.00066)		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)	Glycine(DB00145)|L-Glutamic Acid(DB00142)|Orphenadrine(DB01173)													---	---	---	---
KHSRP	8570	broad.mit.edu	37	19	6414223	6414223	+	Intron	DEL	G	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:6414223delG	uc002mer.3	-							NM_003685	NP_003676			KH-type splicing regulatory protein						mRNA processing|mRNA transport|regulation of transcription, DNA-dependent|RNA splicing, via transesterification reactions|transcription, DNA-dependent	cytosol|nucleus	DNA binding|protein binding|RNA binding			skin(1)	1																		---	---	---	---
SLC25A41	284427	broad.mit.edu	37	19	6432329	6432330	+	Intron	INS	-	T	T			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:6432329_6432330insT	uc010dus.2	-						SLC25A41_uc010dut.2_Intron	NM_173637	NP_775908			solute carrier family 25, member 41						transmembrane transport	integral to membrane|mitochondrial inner membrane	binding				0																		---	---	---	---
EMR1	2015	broad.mit.edu	37	19	6896646	6896647	+	Intron	INS	-	T	T			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:6896646_6896647insT	uc002mfw.2	+						EMR1_uc010dvc.2_Intron|EMR1_uc010dvb.2_Intron|EMR1_uc010xji.1_Intron|EMR1_uc010xjj.1_Intron	NM_001974	NP_001965			egf-like module containing, mucin-like, hormone						cell adhesion|neuropeptide signaling pathway	integral to plasma membrane	calcium ion binding|G-protein coupled receptor activity			ovary(3)|lung(1)|skin(1)	5	all_hematologic(4;0.166)																	---	---	---	---
FBN3	84467	broad.mit.edu	37	19	8188240	8188240	+	Intron	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:8188240delA	uc002mjf.2	-							NM_032447	NP_115823			fibrillin 3 precursor							proteinaceous extracellular matrix	calcium ion binding|extracellular matrix structural constituent			ovary(6)|skin(3)|pancreas(1)|central_nervous_system(1)	11																		---	---	---	---
RGL3	57139	broad.mit.edu	37	19	11495174	11495174	+	3'UTR	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:11495174delT	uc002mrn.2	-	19					EPOR_uc002mri.2_5'Flank|EPOR_uc002mrk.1_5'Flank|EPOR_uc002mrl.1_5'Flank|EPOR_uc002mrj.1_5'Flank|EPOR_uc010xlx.1_5'Flank|EPOR_uc010xly.1_5'Flank|RGL3_uc002mrm.2_3'UTR					SubName: Full=FLJ00153 protein; Flags: Fragment;						regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	intracellular				ovary(1)	1																		---	---	---	---
UNC13A	23025	broad.mit.edu	37	19	17750846	17750846	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:17750846delT	uc002nhd.2	-							NM_001080421	NP_001073890			unc-13 homolog A						exocytosis|intracellular signal transduction	cell junction|cytoplasm|presynaptic membrane	metal ion binding			ovary(3)	3																		---	---	---	---
ZNF430	80264	broad.mit.edu	37	19	21217112	21217112	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:21217112delT	uc002npj.2	+						ZNF430_uc002npk.2_Intron	NM_025189	NP_079465			zinc finger protein 430						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			skin(2)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	19	22500220	22500220	+	IGR	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:22500220delT								ZNF676 (120467 upstream) : ZNF98 (73679 downstream)																																			---	---	---	---
ZNF681	148213	broad.mit.edu	37	19	23938518	23938518	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:23938518delT	uc002nrk.3	-						ZNF681_uc002nrl.3_Intron|ZNF681_uc002nrj.3_Intron|ZNF681_uc002nrm.1_5'Flank	NM_138286	NP_612143			zinc finger protein 681						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0		all_lung(12;0.11)|Lung NSC(12;0.163)|all_epithelial(12;0.206)																---	---	---	---
C19orf2	8725	broad.mit.edu	37	19	30462218	30462219	+	Intron	DEL	GT	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:30462218_30462219delGT	uc002nsr.2	+						C19orf2_uc002nsq.2_Intron|C19orf2_uc002nss.2_Intron	NM_003796	NP_003787			RPB5-mediating protein isoform a						protein folding|regulation of transcription from RNA polymerase II promoter|response to virus	DNA-directed RNA polymerase II, core complex|prefoldin complex	transcription corepressor activity|unfolded protein binding			ovary(1)|kidney(1)	2	Ovarian(5;0.000902)|Breast(6;0.0203)|Esophageal squamous(110;0.195)	Hepatocellular(1079;0.137)|Renal(1328;0.228)	STAD - Stomach adenocarcinoma(5;5.36e-06)|Lung(7;0.0144)|LUAD - Lung adenocarcinoma(5;0.115)	STAD - Stomach adenocarcinoma(1328;0.18)														---	---	---	---
GPATCH1	55094	broad.mit.edu	37	19	33587442	33587442	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:33587442delT	uc002nug.1	+							NM_018025	NP_060495			G patch domain containing 1							catalytic step 2 spliceosome	nucleic acid binding			skin(1)	1	Esophageal squamous(110;0.137)																	---	---	---	---
ZNF790	388536	broad.mit.edu	37	19	37314514	37314514	+	Intron	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:37314514delA	uc002oew.2	-						uc002oev.1_Intron	NM_206894	NP_996777			zinc finger protein 790						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			upper_aerodigestive_tract(1)|skin(1)	2	Esophageal squamous(110;0.183)		COAD - Colon adenocarcinoma(19;0.0454)|Colorectal(19;0.065)															---	---	---	---
BCKDHA	593	broad.mit.edu	37	19	41929040	41929042	+	In_Frame_Del	DEL	AGG	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:41929040_41929042delAGG	uc002oqq.2	+	8	1162_1164	c.1133_1135delAGG	c.(1132-1137)CAGGAG>CAG	p.E379del	CYP2F1_uc010xvw.1_Intron|BCKDHA_uc002oqm.3_In_Frame_Del_p.E413del|BCKDHA_uc002oqr.2_In_Frame_Del_p.E378del|BCKDHA_uc010xvz.1_In_Frame_Del_p.E382del	NM_000709	NP_000700	P12694	ODBA_HUMAN	branched chain keto acid dehydrogenase E1, alpha	379					branched chain family amino acid catabolic process	mitochondrial alpha-ketoglutarate dehydrogenase complex	3-methyl-2-oxobutanoate dehydrogenase (2-methylpropanoyl-transferring) activity|alpha-ketoacid dehydrogenase activity|carboxy-lyase activity|metal ion binding|protein binding				0																		---	---	---	---
SLC8A2	6543	broad.mit.edu	37	19	47941333	47941335	+	Intron	DEL	CTC	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:47941333_47941335delCTC	uc002pgx.2	-						SLC8A2_uc010xyq.1_Intron|SLC8A2_uc010xyr.1_Intron|SLC8A2_uc010ele.2_Intron	NM_015063	NP_055878			solute carrier family 8 member 2 precursor						cell communication|platelet activation	integral to membrane|plasma membrane	calcium:sodium antiporter activity|calmodulin binding			skin(3)|ovary(1)	4		all_cancers(25;3.05e-07)|all_lung(116;4.19e-06)|Lung NSC(112;7.16e-06)|all_epithelial(76;7.65e-06)|all_neural(266;0.0652)|Ovarian(192;0.086)|Breast(70;0.173)		OV - Ovarian serous cystadenocarcinoma(262;0.000501)|all cancers(93;0.00058)|Epithelial(262;0.0181)|GBM - Glioblastoma multiforme(486;0.0457)														---	---	---	---
PPFIA3	8541	broad.mit.edu	37	19	49641825	49641826	+	Intron	DEL	AA	-	-	rs3032696		TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:49641825_49641826delAA	uc002pmr.2	+						PPFIA3_uc010yai.1_Intron|PPFIA3_uc010yaj.1_Intron|PPFIA3_uc002pms.2_Intron	NM_003660	NP_003651			PTPRF interacting protein alpha 3							cell surface|cytoplasm	protein binding			lung(1)	1		all_lung(116;3.16e-06)|Lung NSC(112;6.25e-06)|all_neural(266;0.0189)|Ovarian(192;0.0392)		all cancers(93;2.36e-05)|OV - Ovarian serous cystadenocarcinoma(262;0.000203)|GBM - Glioblastoma multiforme(486;0.00307)|Epithelial(262;0.00677)														---	---	---	---
PTPRH	5794	broad.mit.edu	37	19	55698755	55698755	+	Intron	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:55698755delA	uc002qjq.2	-						PTPRH_uc010esv.2_Intron|uc002qjr.2_5'Flank	NM_002842	NP_002833			protein tyrosine phosphatase, receptor type, H						apoptosis	cytoplasm|integral to plasma membrane	protein binding|transmembrane receptor protein tyrosine phosphatase activity			ovary(2)|large_intestine(1)|skin(1)	4		Renal(1328;0.245)	BRCA - Breast invasive adenocarcinoma(297;0.209)	GBM - Glioblastoma multiforme(193;0.0479)														---	---	---	---
ZIM2	23619	broad.mit.edu	37	19	57287026	57287027	+	Intron	DEL	AA	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:57287026_57287027delAA	uc002qnr.2	-						uc010ygp.1_Intron|uc002qnp.1_Intron|ZIM2_uc010ygq.1_Intron|ZIM2_uc010ygr.1_Intron|ZIM2_uc002qnq.2_Intron|ZIM2_uc010etp.2_Intron|ZIM2_uc010ygs.1_Intron	NM_015363	NP_056178			zinc finger, imprinted 2						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(3)	3		Colorectal(82;0.000256)|all_neural(62;0.103)|Ovarian(87;0.243)		GBM - Glioblastoma multiforme(193;0.0314)														---	---	---	---
NOP56	10528	broad.mit.edu	37	20	2633378	2633379	+	Intron	INS	-	GAGCCTGGGCCT	GAGCCTGGGCCT	rs149713688	by1000genomes	TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:2633378_2633379insGAGCCTGGGCCT	uc002wgh.2	+						NOP56_uc010zpy.1_Intron|MIR1292_hsa-mir-1292|MI0006433_5'Flank|NOP56_uc002wgi.2_5'Flank|SNORD110_uc002wgj.2_5'Flank|SNORA51_uc002wgk.1_5'Flank|NOP56_uc002wgm.1_5'Flank	NM_006392	NP_006383			nucleolar protein 5A						rRNA processing	box C/D snoRNP complex|pre-snoRNP complex	protein binding|snoRNA binding			ovary(1)|pancreas(1)	2																		---	---	---	---
C20orf194	25943	broad.mit.edu	37	20	3298752	3298753	+	Intron	DEL	TT	-	-	rs118050597	by1000genomes	TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:3298752_3298753delTT	uc002wii.2	-						C20orf194_uc002wij.3_Intron|C20orf194_uc002wik.2_Intron	NM_001009984	NP_001009984			hypothetical protein LOC25943												0																		---	---	---	---
PLK1S1	55857	broad.mit.edu	37	20	21196192	21196192	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:21196192delT	uc002wsb.2	+						PLK1S1_uc010zsh.1_Intron|PLK1S1_uc010zsi.1_Intron|PLK1S1_uc010zsj.1_Intron|uc002wsc.2_Intron|PLK1S1_uc002wsd.2_Intron|uc002wse.2_Intron	NM_018474	NP_060944			polo-like kinase 1 substrate 1 isoform 1						spindle organization	centrosome	protein kinase binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	20	29930733	29930733	+	IGR	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:29930733delT								DEFB116 (34345 upstream) : DEFB118 (25695 downstream)																																			---	---	---	---
PIGU	128869	broad.mit.edu	37	20	33222326	33222327	+	Intron	INS	-	A	A	rs140906518	by1000genomes	TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:33222326_33222327insA	uc002xas.2	-						PIGU_uc010zul.1_Intron|PIGU_uc002xat.2_Intron|PIGU_uc010gev.1_Intron	NM_080476	NP_536724			phosphatidylinositol glycan anchor biosynthesis,						attachment of GPI anchor to protein|C-terminal protein lipidation|regulation of JAK-STAT cascade	GPI-anchor transamidase complex|plasma membrane					0																		---	---	---	---
RBM12	10137	broad.mit.edu	37	20	34240428	34240428	+	3'UTR	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:34240428delA	uc002xdq.2	-	3					CPNE1_uc010zvj.1_Intron|CPNE1_uc002xde.2_Intron|CPNE1_uc002xdf.2_Intron|CPNE1_uc002xdg.2_Intron|CPNE1_uc010gfi.2_Intron|CPNE1_uc010gfj.2_Intron|CPNE1_uc002xdh.2_Intron|CPNE1_uc002xdi.2_Intron|CPNE1_uc002xdj.2_Intron|CPNE1_uc002xdk.2_Intron|CPNE1_uc002xdl.2_Intron|CPNE1_uc002xdm.2_Intron|CPNE1_uc010gfk.1_Intron|CPNE1_uc002xdn.1_Intron|CPNE1_uc002xdo.1_Intron|CPNE1_uc002xdp.1_Intron|RBM12_uc002xdr.2_3'UTR|RBM12_uc002xds.2_3'UTR	NM_152838	NP_690051			RNA binding motif protein 12							nucleus	nucleotide binding|protein binding|RNA binding			ovary(3)	3	Lung NSC(9;0.00608)|all_lung(11;0.00918)		BRCA - Breast invasive adenocarcinoma(18;0.00953)															---	---	---	---
PHF20	51230	broad.mit.edu	37	20	34519091	34519093	+	Intron	DEL	ATG	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:34519091_34519093delATG	uc002xek.1	+							NM_016436	NP_057520			PHD finger protein 20						regulation of transcription, DNA-dependent|transcription, DNA-dependent	MLL1 complex	DNA binding|zinc ion binding			ovary(1)	1	Breast(12;0.00631)|all_lung(11;0.0145)																	---	---	---	---
SAMHD1	25939	broad.mit.edu	37	20	35526445	35526446	+	Intron	INS	-	T	T			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:35526445_35526446insT	uc002xgh.1	-						SAMHD1_uc010gft.1_Intron	NM_015474	NP_056289			SAM domain- and HD domain-containing protein 1						defense response to virus|innate immune response|regulation of innate immune response	nucleus	metal ion binding|phosphoric diester hydrolase activity				0		Myeloproliferative disorder(115;0.00878)																---	---	---	---
FAM83D	81610	broad.mit.edu	37	20	37555035	37555035	+	Frame_Shift_Del	DEL	C	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:37555035delC	uc002xjg.2	+	1	81	c.40delC	c.(40-42)CGGfs	p.R14fs	FAM83D_uc002xjf.2_Frame_Shift_Del_p.R14fs	NM_030919	NP_112181	Q9H4H8	FA83D_HUMAN	hypothetical protein LOC81610	Error:Variant_position_missing_in_Q9H4H8_after_alignment					cell division|mitosis	cytoplasm|spindle pole				ovary(3)	3		Myeloproliferative disorder(115;0.00878)																---	---	---	---
PCIF1	63935	broad.mit.edu	37	20	44567581	44567581	+	Intron	DEL	G	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:44567581delG	uc002xqs.2	+							NM_022104	NP_071387			phosphorylated CTD interacting factor 1							nucleus				skin(1)	1																		---	---	---	---
PREX1	57580	broad.mit.edu	37	20	47244216	47244216	+	Intron	DEL	G	-	-	rs80011299	byFrequency;by1000genomes	TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:47244216delG	uc002xtw.1	-						PREX1_uc002xtv.1_Intron	NM_020820	NP_065871			phosphatidylinositol-3,4,						actin filament polymerization|apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|neutrophil activation|small GTPase mediated signal transduction|superoxide metabolic process	cytosol|plasma membrane	enzyme binding|phospholipid binding|Rho GTPase activator activity|Rho guanyl-nucleotide exchange factor activity			lung(3)|ovary(2)|pancreas(1)	6			BRCA - Breast invasive adenocarcinoma(12;0.0135)|Colorectal(8;0.198)															---	---	---	---
C20orf106	200232	broad.mit.edu	37	20	55100911	55100911	+	Frame_Shift_Del	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:55100911delA	uc002xxx.2	+	2	381	c.301delA	c.(301-303)AAAfs	p.K101fs	GCNT7_uc010zzg.1_5'UTR|C20orf107_uc010zzh.1_Intron	NM_001012971	NP_001012989	Q5JX71	CT106_HUMAN	hypothetical protein LOC200232 precursor	101	Cytoplasmic (Potential).					integral to membrane					0			Colorectal(105;0.202)															---	---	---	---
NKAIN4	128414	broad.mit.edu	37	20	61874139	61874139	+	Intron	DEL	G	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:61874139delG	uc002yek.2	-							NM_152864	NP_690603			Na+/K+ transporting ATPase interacting 4							integral to membrane|plasma membrane					0	all_cancers(38;2.72e-09)																	---	---	---	---
Unknown	0	broad.mit.edu	37	21	9483288	9483288	+	IGR	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:9483288delA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	21112407	21112408	+	IGR	DEL	GA	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:21112407_21112408delGA								None (None upstream) : None (None downstream)																																			---	---	---	---
GCFC1	94104	broad.mit.edu	37	21	34116927	34116927	+	Intron	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:34116927delA	uc002yqn.2	-						GCFC1_uc002yql.2_Intron|GCFC1_uc002yqm.2_Intron|GCFC1_uc002yqo.2_Intron|GCFC1_uc002yqp.2_Intron	NM_016631	NP_057715			GC-rich sequence DNA-binding factor candidate							cytosol|nucleus	DNA binding|sequence-specific DNA binding transcription factor activity			ovary(2)	2																		---	---	---	---
GCFC1	94104	broad.mit.edu	37	21	34133214	34133215	+	Intron	DEL	GT	-	-	rs71981845		TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:34133214_34133215delGT	uc002yqn.2	-						GCFC1_uc002yqo.2_Intron|GCFC1_uc002yqp.2_Intron|GCFC1_uc002yqr.2_Intron	NM_016631	NP_057715			GC-rich sequence DNA-binding factor candidate							cytosol|nucleus	DNA binding|sequence-specific DNA binding transcription factor activity			ovary(2)	2																		---	---	---	---
ITSN1	6453	broad.mit.edu	37	21	35231209	35231209	+	Intron	DEL	T	-	-	rs5843624		TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:35231209delT	uc002yta.1	+						DONSON_uc002ysn.1_Intron|ITSN1_uc002ytb.1_Intron|ITSN1_uc002ytj.2_Intron|ITSN1_uc010gmm.1_Intron	NM_003024	NP_003015			intersectin 1 isoform ITSN-l						apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction|synaptic vesicle endocytosis	cell junction|coated pit|cytosol|lamellipodium|synapse|synaptosome	calcium ion binding|proline-rich region binding|protein complex scaffold|Rho guanyl-nucleotide exchange factor activity			ovary(3)|skin(1)	4																		---	---	---	---
BRWD1	54014	broad.mit.edu	37	21	40684718	40684718	+	Intron	DEL	G	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:40684718delG	uc002yxk.1	-						BRWD1_uc002yxl.2_Intron|BRWD1_uc002yxm.2_Intron	NM_018963	NP_061836			bromodomain and WD repeat domain containing 1						regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus				skin(3)|ovary(1)	4		Prostate(19;8.44e-08)|all_epithelial(19;0.223)																---	---	---	---
DSCAM	1826	broad.mit.edu	37	21	41741250	41741250	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:41741250delT	uc002yyq.1	-						DSCAM_uc002yyr.1_Intron	NM_001389	NP_001380			Down syndrome cell adhesion molecule isoform						cell adhesion|dendrite self-avoidance|negative regulation of cell adhesion|positive regulation of axon extension involved in axon guidance|positive regulation of phosphorylation	axon|extracellular region|growth cone|integral to plasma membrane|membrane fraction	protein binding			ovary(6)|skin(4)|upper_aerodigestive_tract(1)	11		all_cancers(19;0.186)|Prostate(19;1.15e-05)|all_epithelial(19;0.0103)																---	---	---	---
BACE2	25825	broad.mit.edu	37	21	42609816	42609816	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:42609816delT	uc002yyw.2	+						BACE2_uc002yyx.2_Intron|BACE2_uc002yyy.2_Intron	NM_012105	NP_036237			beta-site APP-cleaving enzyme 2 isoform A						membrane protein ectodomain proteolysis|negative regulation of amyloid precursor protein biosynthetic process|peptide hormone processing	cell surface|endoplasmic reticulum|endosome|Golgi apparatus|integral to membrane	aspartic-type endopeptidase activity			ovary(2)	2		Prostate(19;1.57e-07)|all_epithelial(19;0.0251)																---	---	---	---
SIK1	150094	broad.mit.edu	37	21	44836942	44836942	+	Frame_Shift_Del	DEL	G	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:44836942delG	uc002zdf.2	-	14	2159	c.2032delC	c.(2032-2034)CAGfs	p.Q678fs		NM_173354	NP_775490	P57059	SIK1_HUMAN	salt-inducible kinase 1	678					anoikis|cell cycle|cell differentiation|intracellular protein kinase cascade|multicellular organismal development|regulation of cell differentiation|regulation of mitotic cell cycle	nucleus	ATP binding|magnesium ion binding|protein binding|protein serine/threonine kinase activity			lung(2)|testis(2)|ovary(1)|central_nervous_system(1)|skin(1)	7																		---	---	---	---
MYH9	4627	broad.mit.edu	37	22	36744899	36744899	+	Intron	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:36744899delA	uc003apg.2	-						MYH9_uc003api.1_Intron	NM_002473	NP_002464			myosin, heavy polypeptide 9, non-muscle						actin cytoskeleton reorganization|actin filament-based movement|angiogenesis|axon guidance|blood vessel endothelial cell migration|cytokinesis|integrin-mediated signaling pathway|leukocyte migration|membrane protein ectodomain proteolysis|monocyte differentiation|platelet formation|protein transport|regulation of cell shape	actomyosin contractile ring|cleavage furrow|cytosol|myosin complex|nucleus|ruffle|stress fiber|uropod	actin filament binding|actin-dependent ATPase activity|ADP binding|ATP binding|calmodulin binding|microfilament motor activity|protein anchor|protein homodimerization activity			breast(3)|ovary(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)|lung(1)|skin(1)|kidney(1)|pancreas(1)	11								T	ALK	ALCL		Deafness|autosomal dominant 17|Epstein syndrome|Fechtner syndrome|May-Hegglin anomaly|Sebastian syndrome		Hereditary_Macrothrombocytopenia_MYH9-associated				---	---	---	---
ELFN2	114794	broad.mit.edu	37	22	37769104	37769104	+	3'UTR	DEL	G	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:37769104delG	uc003asq.3	-	3						NM_052906	NP_443138			leucine rich repeat containing 62							cell surface|integral to membrane				upper_aerodigestive_tract(1)|ovary(1)	2	Melanoma(58;0.0574)																	---	---	---	---
SHANK3	85358	broad.mit.edu	37	22	51159932	51159933	+	Frame_Shift_Ins	INS	-	G	G			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:51159932_51159933insG	uc003bne.1	+	22	3719_3720	c.3719_3720insG	c.(3718-3720)CTGfs	p.L1240fs	SHANK3_uc003bnf.1_Frame_Shift_Ins_p.L687fs|SHANK3_uc010hbg.1_Frame_Shift_Ins_p.L422fs	NM_001080420	NP_001073889	F2Z3L0	F2Z3L0_HUMAN	SH3 and multiple ankyrin repeat domains 3	1240										central_nervous_system(1)	1		all_cancers(38;3.75e-11)|all_epithelial(38;1.82e-09)|Breast(42;0.000448)|all_lung(38;0.000665)|Lung NSC(38;0.0104)|Ovarian(80;0.104)|Lung SC(80;0.162)|Hepatocellular(38;0.178)		BRCA - Breast invasive adenocarcinoma(115;0.22)														---	---	---	---
ASB9	140462	broad.mit.edu	37	X	15273107	15273107	+	Intron	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:15273107delA	uc004cwl.2	-						ASB9_uc004cwk.2_Intron|ASB9_uc004cwm.2_Intron|ASB9_uc010ner.2_Intron|ASB9_uc004cwn.2_Intron	NM_001031739	NP_001026909			ankyrin repeat and SOCS box-containing 9 isoform						intracellular signal transduction						0	Hepatocellular(33;0.183)																	---	---	---	---
PHEX	5251	broad.mit.edu	37	X	22196328	22196328	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:22196328delT	uc004dah.2	+						PHEX_uc011mjr.1_Intron|PHEX_uc011mjs.1_Intron	NM_000444	NP_000435			phosphate-regulating neutral endopeptidase						biomineral tissue development|cell-cell signaling|protein modification process|proteolysis|skeletal system development	integral to plasma membrane	aminopeptidase activity|metalloendopeptidase activity|zinc ion binding			ovary(2)|lung(1)	3																		---	---	---	---
ARHGEF9	23229	broad.mit.edu	37	X	62944292	62944293	+	Intron	INS	-	A	A			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:62944292_62944293insA	uc004dvl.2	-						ARHGEF9_uc004dvj.1_Intron|ARHGEF9_uc004dvk.1_Intron|ARHGEF9_uc011mos.1_Intron|ARHGEF9_uc004dvm.1_Intron|ARHGEF9_uc011mot.1_Intron|ARHGEF9_uc004dvn.2_Intron	NM_015185	NP_056000			Cdc42 guanine exchange factor 9						apoptosis|induction of apoptosis by extracellular signals|ion transmembrane transport|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction|synaptic transmission	cytosol	Rho guanyl-nucleotide exchange factor activity			ovary(5)|large_intestine(1)|central_nervous_system(1)|pancreas(1)	8																		---	---	---	---
APOOL	139322	broad.mit.edu	37	X	84309335	84309335	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:84309335delT	uc004eem.2	+						APOOL_uc010nmp.2_Intron	NM_198450	NP_940852			apolipoprotein O-like precursor							extracellular region					0																		---	---	---	---
PLS3	5358	broad.mit.edu	37	X	114877477	114877477	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:114877477delT	uc004eqd.2	+						PLS3_uc010nqg.2_Intron|PLS3_uc011mtf.1_Intron|PLS3_uc004eqe.2_Intron|PLS3_uc011mtg.1_Intron|PLS3_uc011mth.1_Intron|PLS3_uc011mti.1_Intron|PLS3_uc011mtj.1_Intron|PLS3_uc011mtk.1_5'Flank|PLS3_uc011mtl.1_5'Flank	NM_005032	NP_005023			plastin 3							cytoplasm	actin binding|calcium ion binding			lung(1)|breast(1)	2																		---	---	---	---
DOCK11	139818	broad.mit.edu	37	X	117761299	117761299	+	Intron	DEL	T	-	-	rs78788801		TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:117761299delT	uc004eqp.2	+						DOCK11_uc004eqq.2_Intron	NM_144658	NP_653259			dedicator of cytokinesis 11						blood coagulation	cytosol	GTP binding			ovary(3)	3																		---	---	---	---
ODZ1	10178	broad.mit.edu	37	X	123517275	123517275	+	Intron	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:123517275delA	uc004euj.2	-						ODZ1_uc011muj.1_Intron|ODZ1_uc010nqy.2_Intron	NM_014253	NP_055068			odz, odd Oz/ten-m homolog 1 isoform 3						immune response|negative regulation of cell proliferation|nervous system development|signal transduction	extracellular region	heparin binding			ovary(11)|breast(4)|large_intestine(2)|skin(2)|pancreas(2)|upper_aerodigestive_tract(1)|lung(1)	23																		---	---	---	---
ODZ1	10178	broad.mit.edu	37	X	124028293	124028293	+	Intron	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:124028293delA	uc004euj.2	-						ODZ1_uc011muj.1_Intron|ODZ1_uc010nqy.2_Intron	NM_014253	NP_055068			odz, odd Oz/ten-m homolog 1 isoform 3						immune response|negative regulation of cell proliferation|nervous system development|signal transduction	extracellular region	heparin binding			ovary(11)|breast(4)|large_intestine(2)|skin(2)|pancreas(2)|upper_aerodigestive_tract(1)|lung(1)	23																		---	---	---	---
Unknown	0	broad.mit.edu	37	X	136065450	136065450	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-10A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:136065450delT	uc004fai.1	+											Homo sapiens cDNA FLJ31132 fis, clone IMR322000953.																														---	---	---	---
KIAA1751	85452	broad.mit.edu	37	1	1896229	1896229	+	Intron	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:1896229delA	uc001aim.1	-						KIAA1751_uc009vkz.1_Intron	NM_001080484	NP_001073953			hypothetical protein LOC85452											pancreas(1)	1	all_cancers(77;0.000708)|all_epithelial(69;0.000943)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;6.04e-15)|all_lung(118;9.67e-07)|Lung NSC(185;5.59e-05)|Renal(390;0.00571)|Breast(487;0.0183)|Hepatocellular(190;0.0268)|Myeloproliferative disorder(586;0.028)|Ovarian(437;0.127)|Medulloblastoma(700;0.151)|Lung SC(97;0.217)		Epithelial(90;8.79e-39)|OV - Ovarian serous cystadenocarcinoma(86;9.61e-25)|GBM - Glioblastoma multiforme(42;1.2e-07)|Colorectal(212;4.84e-05)|COAD - Colon adenocarcinoma(227;0.000214)|Kidney(185;0.00254)|BRCA - Breast invasive adenocarcinoma(365;0.00461)|STAD - Stomach adenocarcinoma(132;0.00645)|KIRC - Kidney renal clear cell carcinoma(229;0.037)|Lung(427;0.205)														---	---	---	---
CHD5	26038	broad.mit.edu	37	1	6170301	6170303	+	Intron	DEL	ACT	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:6170301_6170303delACT	uc001amb.1	-						CHD5_uc001alz.1_Intron|CHD5_uc001ama.1_Intron	NM_015557	NP_056372			chromodomain helicase DNA binding protein 5						chromatin modification|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	ATP binding|ATP-dependent helicase activity|DNA binding|zinc ion binding			central_nervous_system(3)|breast(3)|ovary(2)|upper_aerodigestive_tract(1)|lung(1)|skin(1)|pancreas(1)	12	Ovarian(185;0.0634)	all_cancers(23;5.36e-32)|all_epithelial(116;2.32e-17)|all_neural(13;3.68e-06)|all_lung(118;3.94e-06)|all_hematologic(16;2.39e-05)|Lung NSC(185;5.33e-05)|Acute lymphoblastic leukemia(12;0.000372)|Glioma(11;0.00127)|Renal(390;0.00188)|Colorectal(325;0.00342)|Breast(487;0.00373)|Hepatocellular(190;0.0218)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.15)		Epithelial(90;3.08e-37)|GBM - Glioblastoma multiforme(13;1.36e-31)|OV - Ovarian serous cystadenocarcinoma(86;7.7e-19)|Colorectal(212;9.97e-08)|COAD - Colon adenocarcinoma(227;1.07e-05)|Kidney(185;6.16e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.00109)|BRCA - Breast invasive adenocarcinoma(365;0.0012)|STAD - Stomach adenocarcinoma(132;0.00346)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.193)														---	---	---	---
TNFRSF1B	7133	broad.mit.edu	37	1	12251283	12251284	+	Intron	INS	-	A	A			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:12251283_12251284insA	uc001att.2	+						TNFRSF1B_uc001atu.2_Intron|TNFRSF1B_uc009vnk.2_Intron	NM_001066	NP_001057			tumor necrosis factor receptor 2 precursor						apoptosis	extracellular region|integral to membrane|membrane raft|plasma membrane	tumor necrosis factor receptor activity			liver(1)|central_nervous_system(1)|skin(1)	3	Ovarian(185;0.249)	Lung NSC(185;8.72e-05)|all_lung(284;9.92e-05)|Renal(390;0.000147)|Colorectal(325;0.000584)|Breast(348;0.00093)|Ovarian(437;0.00965)|Hepatocellular(190;0.0202)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0234)|Colorectal(212;5.52e-07)|COAD - Colon adenocarcinoma(227;0.000345)|BRCA - Breast invasive adenocarcinoma(304;0.000353)|Kidney(185;0.00102)|KIRC - Kidney renal clear cell carcinoma(229;0.00302)|STAD - Stomach adenocarcinoma(313;0.00815)|READ - Rectum adenocarcinoma(331;0.0284)	Etanercept(DB00005)|Infliximab(DB00065)													---	---	---	---
PRAMEF17	391004	broad.mit.edu	37	1	13719052	13719052	+	3'UTR	DEL	T	-	-	rs141370897	by1000genomes	TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:13719052delT	uc009vnz.1	+	3						NM_001099851	NP_001093321			PRAME family member 17												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;0.00224)|Myeloproliferative disorder(586;0.0393)|Hepatocellular(190;0.0623)|Ovarian(437;0.0731)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00812)|Colorectal(212;9.86e-06)|Kidney(185;4.89e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.000194)|BRCA - Breast invasive adenocarcinoma(304;0.000293)|COAD - Colon adenocarcinoma(227;0.000502)|STAD - Stomach adenocarcinoma(313;0.0072)|READ - Rectum adenocarcinoma(331;0.0649)														---	---	---	---
DNAJC16	23341	broad.mit.edu	37	1	15863352	15863352	+	Intron	DEL	T	-	-	rs112015425		TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:15863352delT	uc001aws.2	+						DNAJC16_uc001awr.1_Intron|DNAJC16_uc001awt.2_Intron	NM_015291	NP_056106			DnaJ (Hsp40) homolog, subfamily C, member 16						cell redox homeostasis|protein folding	integral to membrane	heat shock protein binding|unfolded protein binding			urinary_tract(1)|lung(1)|kidney(1)	3		Colorectal(325;0.00108)|Renal(390;0.00145)|Breast(348;0.00173)|all_lung(284;0.00459)|Lung NSC(340;0.00499)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0798)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;9.18e-07)|COAD - Colon adenocarcinoma(227;4.5e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000133)|KIRC - Kidney renal clear cell carcinoma(229;0.00262)|STAD - Stomach adenocarcinoma(313;0.00774)|READ - Rectum adenocarcinoma(331;0.0657)														---	---	---	---
CLCNKA	1187	broad.mit.edu	37	1	16355578	16355578	+	Intron	DEL	G	-	-	rs71774158		TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:16355578delG	uc001axu.2	+						CLCNKA_uc001axt.2_Intron|CLCNKA_uc001axv.2_Intron|CLCNKA_uc010obw.1_Intron|CLCNKB_uc001axw.3_Intron|CLCNKA_uc010obx.1_Intron|CLCNKA_uc010oby.1_Intron	NM_004070	NP_004061			chloride channel Ka isoform 1						excretion	chloride channel complex|integral to plasma membrane	voltage-gated chloride channel activity			ovary(1)	1		Colorectal(325;3.46e-05)|Breast(348;0.000278)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.000567)|Ovarian(437;0.0221)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|Colorectal(212;8.04e-08)|COAD - Colon adenocarcinoma(227;5.46e-06)|BRCA - Breast invasive adenocarcinoma(304;9.02e-05)|Kidney(64;0.00016)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(313;0.00655)|READ - Rectum adenocarcinoma(331;0.0649)	Niflumic Acid(DB04552)													---	---	---	---
MRTO4	51154	broad.mit.edu	37	1	19581443	19581443	+	Intron	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:19581443delA	uc001bbs.2	+							NM_016183	NP_057267			mRNA turnover 4 homolog						ribosome biogenesis	nuclear membrane|nucleolus					0		Colorectal(325;3.46e-05)|Renal(390;0.000147)|all_lung(284;0.000321)|Lung NSC(340;0.000398)|Breast(348;0.00049)|Ovarian(437;0.00764)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00462)|BRCA - Breast invasive adenocarcinoma(304;1.87e-05)|Kidney(64;0.000171)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|GBM - Glioblastoma multiforme(114;0.00301)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)														---	---	---	---
RPS6KA1	6195	broad.mit.edu	37	1	26900934	26900934	+	3'UTR	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:26900934delA	uc001bmr.1	+	22					RPS6KA1_uc010ofe.1_3'UTR|RPS6KA1_uc001bms.1_3'UTR|RPS6KA1_uc009vsl.1_3'UTR	NM_002953	NP_002944			ribosomal protein S6 kinase, 90kDa, polypeptide						axon guidance|innate immune response|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|nerve growth factor receptor signaling pathway|stress-activated MAPK cascade|synaptic transmission|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway	cytosol|nucleoplasm	ATP binding|caspase inhibitor activity|magnesium ion binding|protein binding|protein serine/threonine kinase activity			lung(1)	1		all_cancers(24;2.49e-24)|Colorectal(325;3.46e-05)|all_lung(284;4.76e-05)|Lung NSC(340;5.83e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Breast(348;0.00571)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|Epithelial(14;1.12e-50)|OV - Ovarian serous cystadenocarcinoma(117;2.89e-29)|Colorectal(126;1.4e-08)|COAD - Colon adenocarcinoma(152;9.31e-07)|BRCA - Breast invasive adenocarcinoma(304;0.000537)|KIRC - Kidney renal clear cell carcinoma(1967;0.000759)|STAD - Stomach adenocarcinoma(196;0.00151)|GBM - Glioblastoma multiforme(114;0.0361)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.161)|LUSC - Lung squamous cell carcinoma(448;0.234)														---	---	---	---
MED8	112950	broad.mit.edu	37	1	43850143	43850143	+	Frame_Shift_Del	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:43850143delT	uc001cje.1	-	8	932	c.884delA	c.(883-885)AATfs	p.N295fs		NM_052877	NP_443109	Q96G25	MED8_HUMAN	mediator complex subunit 8 isoform 3	Error:Variant_position_missing_in_Q96G25_after_alignment					regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	mediator complex					0	all_hematologic(146;0.0958)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0333)																---	---	---	---
CYP4Z2P	163720	broad.mit.edu	37	1	47339125	47339125	+	Intron	DEL	C	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:47339125delC	uc001cqo.1	-						CYP4Z2P_uc009vyn.1_Intron	NR_002788				Homo sapiens cDNA FLJ40054 fis, clone TBAES2000315, weakly similar to CYTOCHROME P450 4A1 (EC 1.14.15.3).												0																		---	---	---	---
RPE65	6121	broad.mit.edu	37	1	68917241	68917241	+	5'Flank	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:68917241delT	uc001dei.1	-							NM_000329	NP_000320			retinal pigment epithelium-specific protein						visual perception	cytoplasm|plasma membrane	all-trans-retinyl-palmitate hydrolase activity|metal ion binding|retinol isomerase activity			ovary(1)	1																		---	---	---	---
CTH	1491	broad.mit.edu	37	1	70895655	70895655	+	Intron	DEL	A	-	-	rs144207053		TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:70895655delA	uc001dfd.2	+						CTH_uc009wbl.1_Intron|CTH_uc001dfe.2_Intron|CTH_uc010oqq.1_Intron	NM_001902	NP_001893			cystathionase isoform 1						cysteine biosynthetic process|hydrogen sulfide biosynthetic process|protein homotetramerization|protein-pyridoxal-5-phosphate linkage via peptidyl-N6-pyridoxal phosphate-L-lysine	cytoplasm|nucleus	cystathionine gamma-lyase activity|L-cysteine desulfhydrase activity|pyridoxal phosphate binding			lung(1)	1					L-Cysteine(DB00151)|Pyridoxal Phosphate(DB00114)													---	---	---	---
Unknown	0	broad.mit.edu	37	1	78240627	78240627	+	IGR	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:78240627delT								USP33 (15090 upstream) : FAM73A (4682 downstream)																																			---	---	---	---
GIPC2	54810	broad.mit.edu	37	1	78509970	78509970	+	5'Flank	DEL	T	-	-	rs112459517		TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:78509970delT	uc001dik.2	+							NM_017655	NP_060125			PDZ domain protein GIPC2							cytoplasm				ovary(1)	1																		---	---	---	---
GBP7	388646	broad.mit.edu	37	1	89614951	89614951	+	Intron	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:89614951delA	uc001dna.2	-						GBP2_uc001dmy.1_Intron	NM_207398	NP_997281			guanylate binding protein 4-like							integral to membrane	GTP binding|GTPase activity			ovary(1)|skin(1)	2		Lung NSC(277;0.0908)		all cancers(265;0.00835)|Epithelial(280;0.0322)														---	---	---	---
BARHL2	343472	broad.mit.edu	37	1	91182861	91182861	+	5'Flank	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:91182861delA	uc001dns.2	-							NM_020063	NP_064447			BarH-like homeobox 2							nucleus	sequence-specific DNA binding			ovary(1)	1		all_lung(203;0.0263)|Lung SC(238;0.128)		all cancers(265;0.000897)|Epithelial(280;0.00516)|OV - Ovarian serous cystadenocarcinoma(397;0.211)														---	---	---	---
MOV10	4343	broad.mit.edu	37	1	113238691	113238691	+	Intron	DEL	G	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:113238691delG	uc001eck.2	+						MOV10_uc001ecl.2_Intron|MOV10_uc001ecn.2_Intron|MOV10_uc001ecm.2_Intron|MOV10_uc009wgj.1_Intron	NM_001130079	NP_001123551			Mov10, Moloney leukemia virus 10, homolog						mRNA cleavage involved in gene silencing by miRNA|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasmic mRNA processing body	ATP binding|helicase activity|protein binding|RNA binding			ovary(4)|skin(1)	5	Lung SC(450;0.246)	all_cancers(81;3.31e-11)|all_epithelial(167;5.69e-10)|all_lung(203;3.73e-05)|Breast(1374;0.000525)|Lung NSC(69;0.000954)|Ovarian(761;0.0367)|Lung SC(238;0.114)		OV - Ovarian serous cystadenocarcinoma(397;3.99e-67)|all cancers(265;1e-62)|Epithelial(280;4.78e-61)|Lung(183;0.0234)|Colorectal(144;0.0686)|READ - Rectum adenocarcinoma(129;0.0929)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)|BRCA - Breast invasive adenocarcinoma(282;0.24)														---	---	---	---
PHTF1	10745	broad.mit.edu	37	1	114281008	114281008	+	Intron	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:114281008delA	uc009wgp.1	-						PHTF1_uc001edn.2_Intron|PHTF1_uc010own.1_Intron|PHTF1_uc001edp.2_Intron	NM_006608	NP_006599			putative homeodomain transcription factor 1							nucleus	DNA binding|sequence-specific DNA binding transcription factor activity			ovary(1)	1	Lung SC(450;0.184)	all_cancers(81;3.78e-08)|all_epithelial(167;5.56e-08)|all_lung(203;6.97e-06)|Lung NSC(69;1.18e-05)		Lung(183;0.0234)|Colorectal(144;0.0686)|all cancers(265;0.0792)|Epithelial(280;0.0866)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)														---	---	---	---
FAM63A	55793	broad.mit.edu	37	1	150972560	150972560	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:150972560delT	uc001ewf.2	-						FAM63A_uc001ewc.2_Intron|FAM63A_uc010pcm.1_Intron|FAM63A_uc001ewd.2_Intron|FAM63A_uc001ewe.2_Intron|FAM63A_uc010pcn.1_Intron|FAM63A_uc001ewg.2_Intron	NM_018379	NP_001156731			hypothetical protein LOC55793 isoform 1								protein binding			ovary(1)	1	all_lung(15;1.09e-34)|Lung NSC(24;1.1e-30)|Lung SC(34;0.00202)|Ovarian(49;0.0167)|all_hematologic(923;0.0597)|Hepatocellular(266;0.0997)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.0486)|LUSC - Lung squamous cell carcinoma(543;0.211)															---	---	---	---
THEM4	117145	broad.mit.edu	37	1	151849315	151849315	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:151849315delT	uc001ezj.1	-						THEM4_uc001ezk.1_Intron	NM_053055	NP_444283			thioesterase superfamily member 4						insulin receptor signaling pathway|nerve growth factor receptor signaling pathway|phosphatidylinositol-mediated signaling	cytosol|ruffle membrane					0	Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.14)		LUSC - Lung squamous cell carcinoma(543;0.181)															---	---	---	---
NUP210L	91181	broad.mit.edu	37	1	154090061	154090061	+	Intron	DEL	A	-	-	rs79748906		TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:154090061delA	uc001fdw.2	-						NUP210L_uc009woq.2_Intron|NUP210L_uc010peh.1_Intron	NM_207308	NP_997191			nucleoporin 210kDa-like isoform 1							integral to membrane				skin(5)|ovary(4)|large_intestine(1)|central_nervous_system(1)	11	all_lung(78;9.35e-31)|Lung NSC(65;1.33e-28)|Hepatocellular(266;0.0877)|Melanoma(130;0.128)		LUSC - Lung squamous cell carcinoma(543;0.151)|Colorectal(543;0.198)															---	---	---	---
CHRNB2	1141	broad.mit.edu	37	1	154543476	154543476	+	Intron	DEL	C	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:154543476delC	uc001ffg.2	+							NM_000748	NP_000739			neuronal nicotinic acetylcholine receptor beta 2						B cell activation|behavioral response to nicotine|calcium ion transport|central nervous system projection neuron axonogenesis|lateral geniculate nucleus development|locomotory behavior|membrane depolarization|memory|negative regulation of action potential|optic nerve morphogenesis|positive regulation of B cell proliferation|positive regulation of dopamine secretion|regulation of circadian sleep/wake cycle, REM sleep|regulation of dendrite morphogenesis|regulation of dopamine metabolic process|regulation of synaptogenesis|response to cocaine|response to ethanol|response to hypoxia|sensory perception of pain|sensory perception of sound|smooth muscle contraction|social behavior|synaptic transmission involved in micturition|synaptic transmission, cholinergic|vestibulocochlear nerve development|visual learning|visual perception	cell junction|external side of plasma membrane|nicotinic acetylcholine-gated receptor-channel complex|postsynaptic membrane	acetylcholine receptor activity|nicotinic acetylcholine-activated cation-selective channel activity				0	all_lung(78;2.22e-29)|Lung NSC(65;3.66e-27)|Hepatocellular(266;0.0877)|all_hematologic(923;0.088)		LUSC - Lung squamous cell carcinoma(543;0.185)		Nicotine(DB00184)													---	---	---	---
GON4L	54856	broad.mit.edu	37	1	155822905	155822905	+	Intron	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:155822905delA	uc001flz.2	-						GON4L_uc001fly.1_Intron|GON4L_uc009wrh.1_Intron|GON4L_uc001fma.1_Intron|GON4L_uc001fmc.2_Intron|GON4L_uc001fmd.3_Intron|GON4L_uc009wri.2_Intron	NM_001037533	NP_001032622			gon-4-like isoform a						regulation of transcription, DNA-dependent	cytoplasm|nucleus	DNA binding			ovary(3)	3	Hepatocellular(266;0.0997)|all_hematologic(923;0.145)|all_neural(408;0.195)																	---	---	---	---
C1orf66	51093	broad.mit.edu	37	1	156702951	156702951	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:156702951delT	uc001fpu.2	+						C1orf66_uc001fpv.2_Intron	NM_015997	NP_057081			hypothetical protein LOC51093 isoform 1							integral to membrane	rRNA (adenine-N6,N6-)-dimethyltransferase activity				0	all_hematologic(923;0.088)|Hepatocellular(266;0.158)																	---	---	---	---
C1orf66	51093	broad.mit.edu	37	1	156703374	156703375	+	Intron	DEL	CA	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:156703374_156703375delCA	uc001fpu.2	+						C1orf66_uc001fpv.2_Intron	NM_015997	NP_057081			hypothetical protein LOC51093 isoform 1							integral to membrane	rRNA (adenine-N6,N6-)-dimethyltransferase activity				0	all_hematologic(923;0.088)|Hepatocellular(266;0.158)																	---	---	---	---
TPR	7175	broad.mit.edu	37	1	186300536	186300536	+	Intron	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:186300536delA	uc001grv.2	-							NM_003292	NP_003283			nuclear pore complex-associated protein TPR						carbohydrate metabolic process|glucose transport|mitotic cell cycle spindle assembly checkpoint|mRNA transport|protein import into nucleus|regulation of glucose transport|seryl-tRNA aminoacylation|transmembrane transport|viral reproduction	condensed chromosome kinetochore|cytoplasm|nuclear membrane|nuclear pore|nucleoplasm	ATP binding|protein binding|serine-tRNA ligase activity			ovary(2)|lung(2)|urinary_tract(1)|central_nervous_system(1)|skin(1)	7		Breast(1374;0.000659)|Lung SC(1967;0.0262)|Prostate(1639;0.157)		Colorectal(1306;1.12e-05)|KIRC - Kidney renal clear cell carcinoma(1967;0.00553)				T	NTRK1	papillary thyroid								---	---	---	---
CDC73	79577	broad.mit.edu	37	1	193121497	193121497	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:193121497delT	uc001gtb.2	+							NM_024529	NP_078805			parafibromin						cell cycle|histone H2B ubiquitination|histone monoubiquitination|transcription, DNA-dependent	Cdc73/Paf1 complex	protein binding			parathyroid(46)|ovary(1)|breast(1)|pancreas(1)	49														Hyperparathyroidism_Familial_Isolated|Hyperparathyroidism-Jaw_Tumor_Syndrome				---	---	---	---
KCNT2	343450	broad.mit.edu	37	1	196438097	196438097	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:196438097delT	uc001gtd.1	-						KCNT2_uc009wyt.1_5'Flank|KCNT2_uc001gte.1_Intron|KCNT2_uc001gtf.1_Intron|KCNT2_uc001gtg.1_Intron|KCNT2_uc009wyu.2_Intron|KCNT2_uc009wyv.1_Intron	NM_198503	NP_940905			potassium channel, subfamily T, member 2							voltage-gated potassium channel complex	ATP binding|calcium-activated potassium channel activity|voltage-gated potassium channel activity			ovary(5)|breast(1)|skin(1)	7																		---	---	---	---
SYT2	127833	broad.mit.edu	37	1	202573400	202573400	+	Intron	DEL	C	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:202573400delC	uc001gye.2	-						SYT2_uc010pqb.1_Intron|SYT2_uc009xaf.2_Intron	NM_001136504	NP_001129976			synaptotagmin II						neurotransmitter secretion	cell junction|chromaffin granule membrane|endocytic vesicle membrane|integral to membrane|synaptic vesicle membrane	protein binding|transporter activity			ovary(2)|skin(1)	3			BRCA - Breast invasive adenocarcinoma(75;0.169)		Botulinum Toxin Type B(DB00042)													---	---	---	---
TMEM183A	92703	broad.mit.edu	37	1	202991831	202991831	+	Intron	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:202991831delA	uc001gyu.1	+						TMEM183A_uc001gyv.1_Intron|TMEM183A_uc001gyw.1_Intron|TMEM183A_uc001gyx.1_Intron|TMEM183A_uc001gyy.2_5'Flank	NM_001079809	NP_001073277			transmembrane protein 183B							integral to membrane					0			BRCA - Breast invasive adenocarcinoma(75;0.18)															---	---	---	---
RPS6KC1	26750	broad.mit.edu	37	1	213290877	213290877	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:213290877delT	uc010ptr.1	+						RPS6KC1_uc001hkd.2_Intron|RPS6KC1_uc010pts.1_Intron|RPS6KC1_uc010ptt.1_Intron|RPS6KC1_uc010ptu.1_Intron|RPS6KC1_uc010ptv.1_Intron|RPS6KC1_uc001hke.2_Intron	NM_012424	NP_036556			ribosomal protein S6 kinase, 52kDa, polypeptide						cell communication|signal transduction	early endosome|membrane	ATP binding|phosphatidylinositol binding|protein binding|protein serine/threonine kinase activity			lung(4)|ovary(3)|breast(1)	8				OV - Ovarian serous cystadenocarcinoma(81;0.00705)|all cancers(67;0.016)|GBM - Glioblastoma multiforme(131;0.0663)|Epithelial(68;0.145)														---	---	---	---
RPS6KC1	26750	broad.mit.edu	37	1	213434712	213434712	+	Intron	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:213434712delA	uc010ptr.1	+						RPS6KC1_uc001hkd.2_Intron|RPS6KC1_uc010pts.1_Intron|RPS6KC1_uc010ptt.1_Intron|RPS6KC1_uc010ptu.1_Intron|RPS6KC1_uc010ptv.1_Intron|RPS6KC1_uc001hke.2_Intron	NM_012424	NP_036556			ribosomal protein S6 kinase, 52kDa, polypeptide						cell communication|signal transduction	early endosome|membrane	ATP binding|phosphatidylinositol binding|protein binding|protein serine/threonine kinase activity			lung(4)|ovary(3)|breast(1)	8				OV - Ovarian serous cystadenocarcinoma(81;0.00705)|all cancers(67;0.016)|GBM - Glioblastoma multiforme(131;0.0663)|Epithelial(68;0.145)														---	---	---	---
KCTD3	51133	broad.mit.edu	37	1	215777330	215777330	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									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			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)														---	---	---	---
PCNXL2	80003	broad.mit.edu	37	1	233270662	233270662	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:233270662delT	uc001hvl.2	-						PCNXL2_uc001hvm.1_Intron|PCNXL2_uc009xfu.2_Intron|PCNXL2_uc001hvp.1_Intron|PCNXL2_uc009xfv.1_Intron	NM_014801	NP_055616			pecanex-like 2							integral to membrane				central_nervous_system(1)|pancreas(1)	2		all_cancers(173;0.0347)|Prostate(94;0.137)																---	---	---	---
EDARADD	128178	broad.mit.edu	37	1	236577755	236577755	+	Intron	DEL	T	-	-	rs34360581		TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:236577755delT	uc001hxu.1	+						EDARADD_uc001hxv.1_Intron	NM_145861	NP_665860			EDAR-associated death domain isoform A						cell differentiation|signal transduction	cytoplasm					0	Ovarian(103;0.0634)|Breast(184;0.247)	all_cancers(173;0.0232)|Prostate(94;0.174)	OV - Ovarian serous cystadenocarcinoma(106;0.00117)															---	---	---	---
MYT1L	23040	broad.mit.edu	37	2	1890247	1890247	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:1890247delT	uc002qxe.2	-						MYT1L_uc002qxd.2_Intron|MYT1L_uc010ewl.1_Intron	NM_015025	NP_055840			myelin transcription factor 1-like						cell differentiation|nervous system development	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(5)|central_nervous_system(1)	6	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.0797)	all_cancers(51;0.037)|all_epithelial(98;0.241)		OV - Ovarian serous cystadenocarcinoma(76;0.169)|all cancers(51;0.244)														---	---	---	---
RNASEH1	246243	broad.mit.edu	37	2	3596130	3596130	+	Intron	DEL	C	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:3596130delC	uc002qxt.2	-						RNASEH1_uc002qxs.2_Intron	NM_002936	NP_002927			ribonuclease H1						RNA catabolic process	cytoplasm	magnesium ion binding|ribonuclease H activity|RNA binding			ovary(1)	1	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.093)			OV - Ovarian serous cystadenocarcinoma(76;0.0713)|Epithelial(75;0.167)|all cancers(51;0.22)														---	---	---	---
SMC6	79677	broad.mit.edu	37	2	17888597	17888597	+	Frame_Shift_Del	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:17888597delT	uc002rco.2	-	18	2191	c.1895delA	c.(1894-1896)AATfs	p.N632fs	SMC6_uc010exo.2_Frame_Shift_Del_p.N632fs|SMC6_uc002rcn.2_Frame_Shift_Del_p.N632fs|SMC6_uc002rcp.1_Frame_Shift_Del_p.N658fs|SMC6_uc002rcq.2_Frame_Shift_Del_p.N658fs	NM_001142286	NP_001135758	Q96SB8	SMC6_HUMAN	SMC6 protein	632	Flexible hinge.				DNA recombination|DNA repair	chromosome|nucleus	ATP binding			breast(4)|upper_aerodigestive_tract(1)|kidney(1)	6	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.158)																	---	---	---	---
WDR35	57539	broad.mit.edu	37	2	20130442	20130442	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:20130442delT	uc002rdi.2	-						WDR35_uc002rdj.2_Intron|WDR35_uc010ext.2_Intron|WDR35_uc002rdh.2_Intron	NM_001006657	NP_001006658			WD repeat domain 35 isoform 1											ovary(1)	1	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)																	---	---	---	---
KRTCAP3	200634	broad.mit.edu	37	2	27666755	27666755	+	Intron	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:27666755delA	uc002rks.2	+						KRTCAP3_uc010ylr.1_Intron|KRTCAP3_uc002rkt.2_Intron	NM_173853	NP_776252			keratinocyte associated protein 3							integral to membrane					0	Acute lymphoblastic leukemia(172;0.155)																	---	---	---	---
GPN1	11321	broad.mit.edu	37	2	27852150	27852151	+	Intron	INS	-	G	G	rs146892484	by1000genomes	TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:27852150_27852151insG	uc010ymc.1	+						ZNF512_uc010yly.1_Intron|CCDC121_uc010eze.2_5'Flank|CCDC121_uc002rld.2_5'Flank|CCDC121_uc002rle.2_5'Flank|GPN1_uc010ezf.2_Intron|GPN1_uc010yma.1_Intron|GPN1_uc010ymb.1_Intron|GPN1_uc010ymd.1_Intron|GPN1_uc010yme.1_Intron|GPN1_uc010ezg.1_5'UTR	NM_007266	NP_009197			GPN-loop GTPase 1 isoform a							cytoplasm	GTP binding|nucleoside-triphosphatase activity|protein binding				0																		---	---	---	---
BRE	9577	broad.mit.edu	37	2	28464370	28464372	+	Intron	DEL	TTT	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:28464370_28464372delTTT	uc002rlr.2	+						BRE_uc002rlp.1_Intron|BRE_uc002rlq.2_Intron|BRE_uc002rls.2_Intron|BRE_uc002rlt.2_Intron|BRE_uc002rlu.2_Intron|BRE_uc002rlv.2_Intron	NM_199194	NP_954664			brain and reproductive organ-expressed (TNFRSF1A						apoptosis|chromatin modification|double-strand break repair|G2/M transition DNA damage checkpoint|positive regulation of anti-apoptosis|positive regulation of DNA repair|response to ionizing radiation|signal transduction	BRCA1-A complex|BRISC complex|cytoplasm|nuclear ubiquitin ligase complex	peroxisome targeting sequence binding|polyubiquitin binding|tumor necrosis factor receptor binding			lung(1)|kidney(1)|skin(1)	3	Acute lymphoblastic leukemia(172;0.155)																	---	---	---	---
SLC30A6	55676	broad.mit.edu	37	2	32400336	32400336	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:32400336delT	uc002roe.1	+						SLC30A6_uc002rof.1_Intron|SLC30A6_uc010ymw.1_Intron|SLC30A6_uc010ezr.1_Intron|SLC30A6_uc002rog.1_Intron|SLC30A6_uc010ezs.1_Intron|SLC30A6_uc002roh.1_Intron	NM_017964	NP_060434			solute carrier family 30 (zinc transporter),							Golgi membrane|integral to membrane	zinc ion transmembrane transporter activity				0	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.208)																	---	---	---	---
BIRC6	57448	broad.mit.edu	37	2	32820253	32820253	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:32820253delT	uc010ezu.2	+							NM_016252	NP_057336			baculoviral IAP repeat-containing 6						anti-apoptosis|apoptosis	intracellular	acid-amino acid ligase activity|cysteine-type endopeptidase inhibitor activity|protein binding			ovary(5)|skin(4)|lung(2)|central_nervous_system(1)|breast(1)|pancreas(1)	14	Acute lymphoblastic leukemia(172;0.155)																	---	---	---	---
SOS1	6654	broad.mit.edu	37	2	39294567	39294567	+	Intron	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:39294567delA	uc002rrk.3	-						SOS1_uc010ynr.1_Intron	NM_005633	NP_005624			son of sevenless homolog 1						apoptosis|axon guidance|blood coagulation|epidermal growth factor receptor signaling pathway|fibroblast growth factor receptor signaling pathway|induction of apoptosis by extracellular signals|insulin receptor signaling pathway|leukocyte migration|nerve growth factor receptor signaling pathway|Ras protein signal transduction	cytosol	DNA binding|protein binding|Rho GTPase activator activity|Rho guanyl-nucleotide exchange factor activity			ovary(4)|breast(3)|lung(2)|central_nervous_system(1)	10		all_hematologic(82;0.21)												Noonan_syndrome				---	---	---	---
THUMPD2	80745	broad.mit.edu	37	2	39964207	39964207	+	Intron	DEL	A	-	-	rs75145165		TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:39964207delA	uc002rru.2	-						THUMPD2_uc002rrv.2_Intron|THUMPD2_uc010ynt.1_Intron	NM_025264	NP_079540			THUMP domain containing 2								methyltransferase activity			skin(1)	1		all_hematologic(82;0.248)																---	---	---	---
ABCG8	64241	broad.mit.edu	37	2	44101418	44101418	+	Intron	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:44101418delA	uc002rtq.2	+						ABCG8_uc010yoa.1_Intron	NM_022437	NP_071882			ATP-binding cassette sub-family G member 8						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			skin(3)|ovary(1)	4		all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.175)																---	---	---	---
PREPL	9581	broad.mit.edu	37	2	44554099	44554099	+	Intron	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:44554099delA	uc002ruf.2	-						PREPL_uc002rug.2_Intron|PREPL_uc002ruh.2_Intron|PREPL_uc010fax.2_Intron|PREPL_uc002rui.3_Intron|PREPL_uc002ruj.1_Intron|PREPL_uc002ruk.1_Intron	NM_006036	NP_006027			prolyl endopeptidase-like isoform C						proteolysis	cytosol	serine-type endopeptidase activity			ovary(1)	1		all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.175)																---	---	---	---
MSH2	4436	broad.mit.edu	37	2	47643365	47643365	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:47643365delT	uc002rvy.1	+						MSH2_uc010yoh.1_Intron|MSH2_uc002rvz.2_Intron|MSH2_uc010fbg.2_Intron	NM_000251	NP_000242			mutS homolog 2						B cell differentiation|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|double-strand break repair|intra-S DNA damage checkpoint|isotype switching|maintenance of DNA repeat elements|male gonad development|meiotic gene conversion|meiotic mismatch repair|negative regulation of neuron apoptosis|negative regulation of reciprocal meiotic recombination|positive regulation of helicase activity|postreplication repair|response to UV-B|response to X-ray|somatic hypermutation of immunoglobulin genes	MutSalpha complex|MutSbeta complex|nuclear chromosome	ATP binding|DNA-dependent ATPase activity|double-strand/single-strand DNA junction binding|guanine/thymine mispair binding|loop DNA binding|protein C-terminus binding|protein homodimerization activity|protein kinase binding|Y-form DNA binding			large_intestine(33)|haematopoietic_and_lymphoid_tissue(6)|endometrium(4)|ovary(3)|cervix(2)|central_nervous_system(2)|stomach(1)|small_intestine(1)|breast(1)|skin(1)|prostate(1)	55		all_hematologic(82;0.0359)|Acute lymphoblastic leukemia(82;0.175)	Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151)					D|Mis|N|F|S		colorectal|endometrial|ovarian	colorectal|endometrial|ovarian		MMR	Lynch_syndrome|Muir-Torre_syndrome|Turcot_syndrome|Constitutional_Mismatch_Repair_Deficiency_Syndrome				---	---	---	---
LHCGR	3973	broad.mit.edu	37	2	48914783	48914783	+	3'UTR	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:48914783delT	uc002rwu.3	-	11					GTF2A1L_uc002rwt.2_Intron	NM_000233	NP_000224			luteinizing hormone/choriogonadotropin receptor						male genitalia development|male gonad development	endosome|integral to plasma membrane	luteinizing hormone receptor activity			ovary(3)|lung(2)|breast(2)|skin(1)	8		all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.176)	Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151)		Cetrorelix(DB00050)|Choriogonadotropin alfa(DB00097)|Goserelin(DB00014)|Lutropin alfa(DB00044)|Menotropins(DB00032)									Familial_Male-Limited_Precocious_Puberty				---	---	---	---
ASB3	51130	broad.mit.edu	37	2	54028522	54028522	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:54028522delT	uc002rxi.3	-						ERLEC1_uc002rxl.2_Intron|ERLEC1_uc002rxm.2_Intron|ERLEC1_uc002rxn.2_Intron	NM_001164165	NP_001157637			hypothetical protein LOC100302652						intracellular signal transduction					ovary(1)|kidney(1)	2			Lung(47;0.125)|LUSC - Lung squamous cell carcinoma(58;0.181)															---	---	---	---
VPS54	51542	broad.mit.edu	37	2	64193106	64193106	+	Intron	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:64193106delA	uc002scq.2	-						VPS54_uc002scp.2_Intron|VPS54_uc010fct.2_Intron	NM_016516	NP_057600			vacuolar protein sorting 54 isoform 1						protein transport|retrograde transport, endosome to Golgi						0																		---	---	---	---
GMCL1	64395	broad.mit.edu	37	2	70096843	70096843	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:70096843delT	uc002sfu.2	+							NM_178439	NP_848526			germ cell-less						cell differentiation|multicellular organismal development|spermatogenesis	nuclear matrix				ovary(3)	3																		---	---	---	---
RTKN	6242	broad.mit.edu	37	2	74653450	74653450	+	Frame_Shift_Del	DEL	G	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:74653450delG	uc002sle.2	-	12	1729	c.1612delC	c.(1612-1614)CTCfs	p.L538fs	RTKN_uc002slc.2_Frame_Shift_Del_p.L525fs|RTKN_uc002sld.2_Frame_Shift_Del_p.L488fs	NM_001015055	NP_001015055	Q9BST9	RTKN_HUMAN	rhotekin isoform a	538	Pro-rich.				apoptosis|regulation of anti-apoptosis|Rho protein signal transduction	intracellular	GTP binding|GTP-Rho binding|GTPase inhibitor activity			skin(1)	1																		---	---	---	---
HK2	3099	broad.mit.edu	37	2	75094527	75094527	+	Intron	DEL	A	-	-	rs151230031		TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:75094527delA	uc002snd.2	+							NM_000189	NP_000180			hexokinase 2						apoptotic mitochondrial changes|glucose transport|glycolysis|transmembrane transport	cytosol|mitochondrial outer membrane	ATP binding|glucokinase activity			ovary(1)|lung(1)	2																		---	---	---	---
C2orf3	6936	broad.mit.edu	37	2	75928421	75928421	+	Intron	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:75928421delA	uc002sno.2	-						C2orf3_uc010ffs.2_5'UTR|C2orf3_uc002snn.2_Intron|C2orf3_uc010fft.2_Intron	NM_003203	NP_003194			hypothetical protein LOC6936						negative regulation of transcription, DNA-dependent	nucleus	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity			ovary(1)|central_nervous_system(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	85143886	85143887	+	IGR	INS	-	A	A			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:85143886_85143887insA								TMSB10 (10087 upstream) : KCMF1 (54344 downstream)																																			---	---	---	---
KDM3A	55818	broad.mit.edu	37	2	86701787	86701789	+	Intron	DEL	AAA	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:86701787_86701789delAAA	uc002sri.3	+						KDM3A_uc010ytj.1_Intron|KDM3A_uc010ytk.1_Intron	NM_018433	NP_060903			jumonji domain containing 1A						androgen receptor signaling pathway|cell differentiation|formaldehyde biosynthetic process|histone H3-K9 demethylation|hormone-mediated signaling pathway|positive regulation of transcription, DNA-dependent|spermatogenesis|transcription, DNA-dependent	cytoplasm|nucleus	androgen receptor binding|iron ion binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen			breast(2)|ovary(1)|central_nervous_system(1)|skin(1)	5																		---	---	---	---
RMND5A	64795	broad.mit.edu	37	2	87954896	87954896	+	Intron	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:87954896delA	uc002srs.3	+											SubName: Full=cDNA FLJ10361 fis, clone NT2RM2001256, highly similar to Anaphase-promoting complex subunit 1;											ovary(1)|skin(1)	2																		---	---	---	---
PROM2	150696	broad.mit.edu	37	2	95943601	95943601	+	Intron	DEL	C	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:95943601delC	uc002suh.1	+						PROM2_uc002sui.2_Intron|PROM2_uc002suj.2_Intron|PROM2_uc002suk.2_Intron|PROM2_uc002sul.2_Intron	NM_144707	NP_653308			prominin 2 precursor							apical plasma membrane|basolateral plasma membrane|cilium membrane|integral to membrane|microvillus membrane				ovary(1)	1																		---	---	---	---
MRPL30	51263	broad.mit.edu	37	2	99811772	99811772	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:99811772delT	uc002szu.2	+						MRPL30_uc002szl.1_Intron|MRPL30_uc002szt.1_Intron|MRPL30_uc002szv.2_Intron	NM_145213	NP_660214			RecName: Full=39S ribosomal protein L30, mitochondrial;          Short=L30mt; AltName: Full=MRP-L30; AltName: Full=MRP-L28; Flags: Precursor;						translation	mitochondrion|ribosome	structural constituent of ribosome			ovary(1)	1																		---	---	---	---
TGFBRAP1	9392	broad.mit.edu	37	2	105913017	105913017	+	Intron	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:105913017delA	uc002tcq.2	-						TGFBRAP1_uc010fjc.2_Intron|TGFBRAP1_uc002tcr.3_Intron	NM_004257	NP_004248			transforming growth factor, beta receptor						regulation of transcription, DNA-dependent|transforming growth factor beta receptor signaling pathway	cytoplasm|membrane	SMAD binding|small GTPase regulator activity|transforming growth factor beta receptor binding			central_nervous_system(1)|skin(1)	2																		---	---	---	---
ZC3H6	376940	broad.mit.edu	37	2	113043561	113043562	+	Intron	INS	-	TGT	TGT			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:113043561_113043562insTGT	uc002thq.1	+							NM_198581	NP_940983			zinc finger CCCH-type domain containing 6								nucleic acid binding|zinc ion binding			ovary(3)|central_nervous_system(1)	4																		---	---	---	---
CLASP1	23332	broad.mit.edu	37	2	122216728	122216728	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:122216728delT	uc002tnc.2	-						CLASP1_uc002tna.2_5'Flank|CLASP1_uc010yyw.1_Intron|CLASP1_uc002tnb.2_Intron|CLASP1_uc010yyx.1_Intron|CLASP1_uc010yyy.1_Intron|CLASP1_uc010yyz.1_Intron|CLASP1_uc010yza.1_Intron|CLASP1_uc010yzb.1_Intron|CLASP1_uc010yzc.1_Intron|CLASP1_uc002tng.1_Intron	NM_015282	NP_056097			CLIP-associating protein 1 isoform 1						axon guidance|cell division|establishment or maintenance of cell polarity|exit from mitosis|G2/M transition of mitotic cell cycle|microtubule anchoring|microtubule bundle formation|microtubule nucleation|microtubule organizing center organization|mitotic prometaphase|negative regulation of microtubule depolymerization	centrosomal corona|condensed chromosome kinetochore|cortical microtubule cytoskeleton|cytoplasmic microtubule|cytosol|Golgi apparatus|kinetochore microtubule	kinetochore binding|microtubule plus-end binding			ovary(1)|central_nervous_system(1)	2	Renal(3;0.0496)																	---	---	---	---
NCKAP5	344148	broad.mit.edu	37	2	133887625	133887625	+	Frame_Shift_Del	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:133887625delT	uc002ttp.2	-	6	640	c.266delA	c.(265-267)AAGfs	p.K89fs	NCKAP5_uc002ttq.2_Frame_Shift_Del_p.K89fs|NCKAP5_uc002ttt.1_Frame_Shift_Del_p.K89fs|NCKAP5_uc002tts.1_Frame_Shift_Del_p.K64fs	NM_207363	NP_997246	O14513	NCKP5_HUMAN	Nck-associated protein 5 isoform 1	89	Potential.						protein binding				0																		---	---	---	---
R3HDM1	23518	broad.mit.edu	37	2	136472952	136472952	+	Intron	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:136472952delA	uc002tuo.2	+						R3HDM1_uc010fni.2_Intron|R3HDM1_uc002tup.2_Intron|R3HDM1_uc010zbh.1_Intron	NM_015361	NP_056176			R3H domain containing 1								nucleic acid binding			skin(1)	1				BRCA - Breast invasive adenocarcinoma(221;0.127)														---	---	---	---
CXCR4	7852	broad.mit.edu	37	2	136872415	136872415	+	3'UTR	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:136872415delA	uc002tuz.2	-	2					CXCR4_uc002tuy.2_3'UTR|CXCR4_uc010fnk.2_3'UTR	NM_003467	NP_003458			chemokine (C-X-C motif) receptor 4 isoform b						activation of MAPK activity|apoptosis|dendritic cell chemotaxis|elevation of cytosolic calcium ion concentration|entry into host cell|inflammatory response|initiation of viral infection|regulation of chemotaxis|response to hypoxia|response to virus	cell leading edge|cell surface|cytoplasmic membrane-bounded vesicle|integral to membrane|plasma membrane	actin binding|C-X-C chemokine receptor activity|coreceptor activity|myosin light chain binding|ubiquitin binding|ubiquitin protein ligase binding			upper_aerodigestive_tract(1)|large_intestine(1)|lung(1)	3				BRCA - Breast invasive adenocarcinoma(221;0.155)	Framycetin(DB00452)													---	---	---	---
ARHGAP15	55843	broad.mit.edu	37	2	144313915	144313915	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:144313915delT	uc002tvm.3	+						ARHGAP15_uc002tvn.2_Intron	NM_018460	NP_060930			ARHGAP15						regulation of cell shape|small GTPase mediated signal transduction	cytosol|membrane	protein binding|Rac GTPase activator activity			ovary(1)|skin(1)	2				BRCA - Breast invasive adenocarcinoma(221;0.151)														---	---	---	---
ARHGAP15	55843	broad.mit.edu	37	2	144525481	144525481	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:144525481delT	uc002tvm.3	+						ARHGAP15_uc002tvn.2_Intron	NM_018460	NP_060930			ARHGAP15						regulation of cell shape|small GTPase mediated signal transduction	cytosol|membrane	protein binding|Rac GTPase activator activity			ovary(1)|skin(1)	2				BRCA - Breast invasive adenocarcinoma(221;0.151)														---	---	---	---
Unknown	0	broad.mit.edu	37	2	149627550	149627550	+	IGR	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:149627550delT								EPC2 (82415 upstream) : KIF5C (5269 downstream)																																			---	---	---	---
CACNB4	785	broad.mit.edu	37	2	152695482	152695482	+	3'UTR	DEL	T	-	-	rs111950042		TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:152695482delT	uc002tya.2	-	14					CACNB4_uc002txy.2_3'UTR|CACNB4_uc002txz.2_3'UTR|CACNB4_uc010fnz.2_3'UTR	NM_000726	NP_000717			calcium channel, voltage-dependent, beta 4						axon guidance|membrane depolarization|synaptic transmission	cytosol|internal side of plasma membrane|plasma membrane|synapse|voltage-gated calcium channel complex	protein binding|voltage-gated calcium channel activity			ovary(2)	2				BRCA - Breast invasive adenocarcinoma(221;0.156)	Verapamil(DB00661)													---	---	---	---
ACVR1C	130399	broad.mit.edu	37	2	158406602	158406602	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:158406602delT	uc002tzk.3	-						ACVR1C_uc002tzl.3_Intron|ACVR1C_uc010fof.2_Intron|ACVR1C_uc010foe.2_Intron	NM_145259	NP_660302			activin A receptor, type IC isoform 1						apoptosis|cell differentiation|regulation of apoptosis	activin receptor complex	activin receptor activity, type I|ATP binding|transforming growth factor beta receptor activity			lung(3)|ovary(2)|skin(2)	7																		---	---	---	---
HAT1	8520	broad.mit.edu	37	2	172809273	172809273	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:172809273delT	uc002uhi.2	+						HAT1_uc010fqi.2_Intron|HAT1_uc002uhj.2_Intron	NM_003642	NP_003633			histone acetyltransferase 1						chromatin silencing at telomere|DNA packaging	cytoplasm|nuclear matrix|nucleoplasm	histone acetyltransferase activity|protein binding			large_intestine(1)|ovary(1)	2			OV - Ovarian serous cystadenocarcinoma(117;0.216)															---	---	---	---
HAT1	8520	broad.mit.edu	37	2	172823128	172823128	+	Intron	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:172823128delA	uc002uhi.2	+						HAT1_uc010fqi.2_Intron|HAT1_uc002uhj.2_Intron	NM_003642	NP_003633			histone acetyltransferase 1						chromatin silencing at telomere|DNA packaging	cytoplasm|nuclear matrix|nucleoplasm	histone acetyltransferase activity|protein binding			large_intestine(1)|ovary(1)	2			OV - Ovarian serous cystadenocarcinoma(117;0.216)															---	---	---	---
ITGAV	3685	broad.mit.edu	37	2	187501040	187501041	+	Intron	INS	-	T	T			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:187501040_187501041insT	uc002upq.2	+						ITGAV_uc010frs.2_Intron|ITGAV_uc010zfv.1_Intron	NM_002210	NP_002201			integrin alpha-V isoform 1 precursor						angiogenesis|axon guidance|blood coagulation|cell-matrix adhesion|entry of bacterium into host cell|entry of symbiont into host cell by promotion of host phagocytosis|entry of virus into host cell|ERK1 and ERK2 cascade|integrin-mediated signaling pathway|leukocyte migration|negative regulation of apoptosis|negative regulation of lipid storage|negative regulation of lipid transport|negative regulation of lipoprotein metabolic process|negative regulation of low-density lipoprotein particle receptor biosynthetic process|negative regulation of macrophage derived foam cell differentiation|positive regulation of cell adhesion|positive regulation of cell proliferation|regulation of apoptotic cell clearance	integrin complex	receptor activity|transforming growth factor beta binding			ovary(2)|kidney(1)|skin(1)	4			OV - Ovarian serous cystadenocarcinoma(117;0.0185)|Epithelial(96;0.072)|all cancers(119;0.189)	STAD - Stomach adenocarcinoma(3;0.106)|COAD - Colon adenocarcinoma(31;0.108)														---	---	---	---
GLS	2744	broad.mit.edu	37	2	191769683	191769683	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:191769683delT	uc002usf.2	+						GLS_uc002use.2_Intron	NM_014905	NP_055720			glutaminase precursor						cellular amino acid biosynthetic process|glutamate secretion|glutamine catabolic process|neurotransmitter secretion	mitochondrial matrix	glutaminase activity			ovary(1)|skin(1)	2			OV - Ovarian serous cystadenocarcinoma(117;0.00625)|Epithelial(96;0.0744)|all cancers(119;0.181)		L-Glutamic Acid(DB00142)|L-Glutamine(DB00130)													---	---	---	---
PGAP1	80055	broad.mit.edu	37	2	197755382	197755382	+	Intron	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:197755382delA	uc002utw.2	-						PGAP1_uc002utx.2_Intron|PGAP1_uc002uty.1_Intron|PGAP1_uc010zgv.1_Intron	NM_024989	NP_079265			GPI deacylase						attachment of GPI anchor to protein|C-terminal protein lipidation|intracellular protein transport|myo-inositol transport	integral to membrane|intrinsic to endoplasmic reticulum membrane	nuclease activity|phosphoric ester hydrolase activity			ovary(3)|central_nervous_system(1)	4																		---	---	---	---
COQ10B	80219	broad.mit.edu	37	2	198318518	198318518	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:198318518delT	uc002uuh.1	+						COQ10B_uc010fsl.1_5'Flank	NM_025147	NP_079423			coenzyme Q10 homolog B precursor							mitochondrial inner membrane					0			Epithelial(96;0.231)|OV - Ovarian serous cystadenocarcinoma(117;0.246)															---	---	---	---
RFTN2	130132	broad.mit.edu	37	2	198540350	198540354	+	5'UTR	DEL	AAAAC	-	-	rs148812496		TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:198540350_198540354delAAAAC	uc002uuo.3	-	1						NM_144629	NP_653230			raftlin family member 2							plasma membrane					0																		---	---	---	---
CLK1	1195	broad.mit.edu	37	2	201719893	201719894	+	Intron	DEL	AA	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:201719893_201719894delAA	uc002uwe.2	-						CLK1_uc002uwd.2_Intron|CLK1_uc010zhi.1_Intron|CLK1_uc002uwf.2_Intron|CLK1_uc002uwg.2_Intron|CLK1_uc010fsv.2_Intron	NM_004071	NP_004062			CDC-like kinase 1 isoform 1						cell proliferation	nucleus	ATP binding|non-membrane spanning protein tyrosine kinase activity|protein serine/threonine kinase activity			pancreas(2)	2																		---	---	---	---
ABI2	10152	broad.mit.edu	37	2	204231587	204231587	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:204231587delT	uc002vaa.2	+						ABI2_uc010zig.1_Intron|ABI2_uc002uzz.2_Intron|ABI2_uc010zih.1_Intron|ABI2_uc010zii.1_Intron|ABI2_uc010zij.1_Intron|ABI2_uc002vab.2_5'Flank	NM_005759	NP_005750			abl interactor 2						actin polymerization or depolymerization|cell migration|peptidyl-tyrosine phosphorylation	cytoskeleton|cytosol|filopodium|lamellipodium	cytoskeletal adaptor activity|DNA binding|kinase binding|proline-rich region binding|SH3 domain binding|ubiquitin protein ligase binding				0																		---	---	---	---
NDUFS1	4719	broad.mit.edu	37	2	207018409	207018409	+	Intron	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:207018409delA	uc002vbe.2	-						NDUFS1_uc010ziq.1_Intron|NDUFS1_uc010zir.1_Intron|NDUFS1_uc010zis.1_Intron|NDUFS1_uc010zit.1_Intron|NDUFS1_uc010ziu.1_Intron	NM_005006	NP_004997			NADH dehydrogenase (ubiquinone) Fe-S protein 1,						apoptosis|ATP metabolic process|mitochondrial electron transport, NADH to ubiquinone|reactive oxygen species metabolic process|regulation of mitochondrial membrane potential|transport	mitochondrial intermembrane space|mitochondrial respiratory chain complex I	2 iron, 2 sulfur cluster binding|4 iron, 4 sulfur cluster binding|electron carrier activity|metal ion binding|NADH dehydrogenase (ubiquinone) activity|protein binding			ovary(1)	1					NADH(DB00157)													---	---	---	---
KLF7	8609	broad.mit.edu	37	2	208030440	208030440	+	5'UTR	DEL	A	-	-	rs71412410		TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:208030440delA	uc002vbz.1	-	1					KLF7_uc002vca.1_Intron	NM_003709	NP_003700			Kruppel-like factor 7 (ubiquitous)						regulation of transcription from RNA polymerase II promoter	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|transcription coactivator activity|zinc ion binding			central_nervous_system(1)|skin(1)	2				LUSC - Lung squamous cell carcinoma(261;0.0856)|Lung(261;0.166)|Epithelial(149;0.173)														---	---	---	---
FN1	2335	broad.mit.edu	37	2	216251710	216251710	+	Intron	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:216251710delA	uc002vfa.2	-						FN1_uc002vfb.2_Intron|FN1_uc002vfc.2_Intron|FN1_uc002vfd.2_Intron|FN1_uc002vfe.2_Intron|FN1_uc002vff.2_Intron|FN1_uc002vfg.2_Intron|FN1_uc002vfh.2_Intron|FN1_uc002vfi.2_Intron|FN1_uc002vfj.2_Intron|FN1_uc002vez.2_Intron|FN1_uc010zjp.1_Intron	NM_212482	NP_997647			fibronectin 1 isoform 1 preproprotein						acute-phase response|angiogenesis|leukocyte migration|peptide cross-linking|platelet activation|platelet degranulation|regulation of cell shape|substrate adhesion-dependent cell spreading	ER-Golgi intermediate compartment|fibrinogen complex|platelet alpha granule lumen|proteinaceous extracellular matrix	collagen binding|extracellular matrix structural constituent|heparin binding			central_nervous_system(7)|large_intestine(2)|breast(2)|ovary(1)|pancreas(1)	13		Renal(323;0.127)		Epithelial(149;9.59e-07)|all cancers(144;0.000174)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00948)	Alteplase(DB00009)|Anistreplase(DB00029)|Reteplase(DB00015)|Tenecteplase(DB00031)													---	---	---	---
STK36	27148	broad.mit.edu	37	2	219562025	219562026	+	Intron	INS	-	T	T			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:219562025_219562026insT	uc002viu.2	+						STK36_uc002viv.2_Intron|STK36_uc002viw.2_Intron|STK36_uc002vix.2_Intron	NM_015690	NP_056505			serine/threonine kinase 36						cilium assembly|positive regulation of hh target transcription factor activity|positive regulation of smoothened signaling pathway|post-embryonic development	aggresome|cytoplasm|focal adhesion|intermediate filament cytoskeleton|nucleus	ATP binding|protein serine/threonine kinase activity|transcription factor binding			ovary(4)|stomach(2)|lung(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)|breast(1)	11		Renal(207;0.0915)		Epithelial(149;9.65e-07)|all cancers(144;0.000174)|LUSC - Lung squamous cell carcinoma(224;0.00813)|Lung(261;0.00984)														---	---	---	---
SP140L	93349	broad.mit.edu	37	2	231266129	231266129	+	Frame_Shift_Del	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:231266129delT	uc010fxm.1	+	17	1562	c.1471delT	c.(1471-1473)TTTfs	p.F491fs	SP140L_uc010fxo.1_3'UTR	NM_138402	NP_612411	Q9H930	LY10L_HUMAN	SP140 nuclear body protein-like	Error:Variant_position_missing_in_Q9H930_after_alignment						nucleus	DNA binding|metal ion binding			central_nervous_system(1)	1																		---	---	---	---
INPP5D	3635	broad.mit.edu	37	2	234104167	234104167	+	Intron	DEL	G	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:234104167delG	uc010zmo.1	+						INPP5D_uc010zmp.1_Intron	NM_001017915	NP_001017915			SH2 containing inositol phosphatase isoform a						apoptosis|blood coagulation|leukocyte migration|T cell receptor signaling pathway	cytosol	inositol-polyphosphate 5-phosphatase activity|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity|SH3 domain binding			ovary(1)|central_nervous_system(1)	2		Breast(86;0.0013)|Renal(207;0.00339)|all_hematologic(139;0.0116)|all_lung(227;0.0273)|Acute lymphoblastic leukemia(138;0.0328)|Lung NSC(271;0.0843)		Epithelial(121;1.16e-17)|BRCA - Breast invasive adenocarcinoma(100;0.000479)|LUSC - Lung squamous cell carcinoma(224;0.00655)|Lung(119;0.00802)|GBM - Glioblastoma multiforme(43;0.0185)														---	---	---	---
PASK	23178	broad.mit.edu	37	2	242075147	242075148	+	Intron	INS	-	C	C	rs140491962	by1000genomes	TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:242075147_242075148insC	uc002wao.1	-						PASK_uc010zol.1_Intron|PASK_uc010zom.1_Intron|PASK_uc010fzl.1_Intron|PASK_uc010zon.1_Intron|PASK_uc002wap.2_5'Flank|PASK_uc002waq.2_Intron	NM_015148	NP_055963			PAS domain containing serine/threonine kinase						regulation of transcription, DNA-dependent	Golgi apparatus	ATP binding|identical protein binding|protein serine/threonine kinase activity|signal transducer activity			ovary(4)|lung(1)|skin(1)	6		all_cancers(19;4.46e-39)|all_epithelial(40;1.34e-17)|Breast(86;1.53e-05)|Renal(207;0.00179)|all_lung(227;0.00481)|Lung NSC(271;0.017)|Ovarian(221;0.0228)|Esophageal squamous(248;0.129)|all_hematologic(139;0.158)|Melanoma(123;0.16)|all_neural(83;0.243)|Hepatocellular(293;0.244)		Epithelial(32;1.34e-31)|all cancers(36;1e-28)|OV - Ovarian serous cystadenocarcinoma(60;3.53e-14)|Kidney(56;4.31e-09)|KIRC - Kidney renal clear cell carcinoma(57;4.35e-08)|BRCA - Breast invasive adenocarcinoma(100;5.64e-06)|Lung(119;0.000596)|LUSC - Lung squamous cell carcinoma(224;0.00481)|Colorectal(34;0.014)|COAD - Colon adenocarcinoma(134;0.0968)														---	---	---	---
Unknown	0	broad.mit.edu	37	3	5125122	5125122	+	IGR	DEL	C	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:5125122delC								BHLHE40 (98259 upstream) : ARL8B (38808 downstream)																																			---	---	---	---
SETD5	55209	broad.mit.edu	37	3	9516725	9516725	+	Intron	DEL	T	-	-	rs113358265		TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:9516725delT	uc003brt.2	+						SETD5_uc003bru.2_Intron|SETD5_uc003brv.2_Intron|SETD5_uc010hck.2_Intron|SETD5_uc003brx.2_Intron	NM_001080517	NP_001073986			SET domain containing 5											ovary(2)	2	Medulloblastoma(99;0.227)			OV - Ovarian serous cystadenocarcinoma(96;0.112)														---	---	---	---
CAPN7	23473	broad.mit.edu	37	3	15282164	15282164	+	Intron	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:15282164delA	uc003bzn.2	+							NM_014296	NP_055111			calpain 7						proteolysis	nucleus	calcium-dependent cysteine-type endopeptidase activity			ovary(1)	1																		---	---	---	---
CAPN7	23473	broad.mit.edu	37	3	15288743	15288744	+	Intron	DEL	TT	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:15288743_15288744delTT	uc003bzn.2	+							NM_014296	NP_055111			calpain 7						proteolysis	nucleus	calcium-dependent cysteine-type endopeptidase activity			ovary(1)	1																		---	---	---	---
TBC1D5	9779	broad.mit.edu	37	3	17300086	17300086	+	Intron	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:17300086delA	uc003cbf.2	-						TBC1D5_uc010heu.2_Intron|TBC1D5_uc010hev.2_Intron|TBC1D5_uc003cbe.2_Intron|TBC1D5_uc010hew.1_Intron	NM_014744	NP_055559			TBC1 domain family, member 5 isoform b							intracellular	protein binding|Rab GTPase activator activity			ovary(1)	1																		---	---	---	---
TOP2B	7155	broad.mit.edu	37	3	25646157	25646158	+	Intron	INS	-	A	A			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:25646157_25646158insA	uc003cdj.2	-						TOP2B_uc011awm.1_Intron|TOP2B_uc010hff.1_Intron	NM_001068	NP_001059			DNA topoisomerase II, beta isozyme						DNA topological change|DNA-dependent DNA replication|mitotic cell cycle G2/M transition decatenation checkpoint|mitotic recombination|resolution of meiotic recombination intermediates|sister chromatid segregation	cytosol|DNA topoisomerase complex (ATP-hydrolyzing)|nucleolus|nucleoplasm|synaptonemal complex|WINAC complex	ATP binding|chromatin binding|DNA topoisomerase (ATP-hydrolyzing) activity|DNA-dependent ATPase activity|histone deacetylase binding|protein C-terminus binding|protein heterodimerization activity|protein kinase C binding|sequence-specific DNA binding transcription factor activity			breast(2)|ovary(1)|lung(1)|skin(1)	5																		---	---	---	---
KIF15	56992	broad.mit.edu	37	3	44868019	44868019	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:44868019delT	uc003cnx.3	+						KIF15_uc010hiq.2_Intron|KIF15_uc010hir.2_Intron	NM_020242	NP_064627			kinesin family member 15						blood coagulation|cell proliferation|microtubule-based movement|mitosis	centrosome|cytosol|microtubule|plus-end kinesin complex|spindle	ATP binding|DNA binding|microtubule motor activity			ovary(1)	1				BRCA - Breast invasive adenocarcinoma(193;0.0099)|KIRC - Kidney renal clear cell carcinoma(197;0.0564)|Kidney(197;0.0707)														---	---	---	---
LARS2	23395	broad.mit.edu	37	3	45561625	45561625	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:45561625delT	uc003cop.1	+						LARS2_uc010hit.1_Intron	NM_015340	NP_056155			leucyl-tRNA synthetase 2, mitochondrial						leucyl-tRNA aminoacylation	mitochondrial matrix	ATP binding|leucine-tRNA ligase activity			upper_aerodigestive_tract(1)|ovary(1)	2				BRCA - Breast invasive adenocarcinoma(193;0.0122)|KIRC - Kidney renal clear cell carcinoma(197;0.0313)|Kidney(197;0.0372)	L-Leucine(DB00149)													---	---	---	---
TOMM70A	9868	broad.mit.edu	37	3	100086754	100086754	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:100086754delT	uc003dtw.2	-							NM_014820	NP_055635			translocase of outer mitochondrial membrane 70						protein targeting to mitochondrion	integral to membrane|mitochondrial outer membrane translocase complex	protein binding|protein transmembrane transporter activity			ovary(1)	1																		---	---	---	---
LOC100302640	100302640	broad.mit.edu	37	3	106567681	106567682	+	Intron	INS	-	T	T			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:106567681_106567682insT	uc003dwf.3	-											Homo sapiens cDNA clone IMAGE:5284861.												0																		---	---	---	---
TMPRSS7	344805	broad.mit.edu	37	3	111775808	111775808	+	Intron	DEL	G	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:111775808delG	uc010hqb.2	+						TMPRSS7_uc011bhr.1_Intron	NM_001042575	NP_001036040			transmembrane protease, serine 7						proteolysis	integral to membrane|plasma membrane	serine-type endopeptidase activity			ovary(1)|kidney(1)	2																		---	---	---	---
RPN1	6184	broad.mit.edu	37	3	128350619	128350620	+	Intron	INS	-	G	G			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:128350619_128350620insG	uc003ekr.1	-						RPN1_uc011bkq.1_Intron	NM_002950	NP_002941			ribophorin I precursor						post-translational protein modification|protein N-linked glycosylation via asparagine	integral to membrane|melanosome|oligosaccharyltransferase complex|rough microsome	dolichyl-diphosphooligosaccharide-protein glycotransferase activity|protein binding			ovary(2)|central_nervous_system(1)	3				GBM - Glioblastoma multiforme(114;0.189)				T	EVI1	AML								---	---	---	---
Unknown	0	broad.mit.edu	37	3	142895155	142895155	+	IGR	DEL	C	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:142895155delC								CHST2 (53345 upstream) : SLC9A9 (88910 downstream)																																			---	---	---	---
GYG1	2992	broad.mit.edu	37	3	148711907	148711907	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:148711907delT	uc003ewn.2	+						GYG1_uc011bnp.1_Intron|GYG1_uc003ewo.2_Intron|GYG1_uc003ewp.2_Intron	NM_004130	NP_004121			glycogenin 1						glucose metabolic process|glycogen biosynthetic process|glycogen catabolic process	cytosol	glycogenin glucosyltransferase activity|metal ion binding|protein binding			ovary(1)	1			LUSC - Lung squamous cell carcinoma(72;0.0473)|Lung(72;0.0607)															---	---	---	---
TNIK	23043	broad.mit.edu	37	3	170802258	170802258	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:170802258delT	uc003fhh.2	-						TNIK_uc003fhi.2_Intron|TNIK_uc003fhj.2_Intron|TNIK_uc003fhk.2_Intron|TNIK_uc003fhl.2_Intron|TNIK_uc003fhm.2_Intron|TNIK_uc003fhn.2_Intron|TNIK_uc003fho.2_Intron|TNIK_uc003fhg.2_Intron|TNIK_uc003fhp.2_5'Flank	NM_015028	NP_055843			TRAF2 and NCK interacting kinase isoform 1						actin cytoskeleton reorganization|activation of JNKK activity|protein autophosphorylation|regulation of dendrite morphogenesis|Wnt receptor signaling pathway	cytoskeleton|nucleus|recycling endosome	ATP binding|protein binding|protein serine/threonine kinase activity|small GTPase regulator activity			ovary(4)|large_intestine(1)	5	all_cancers(22;2.55e-19)|all_lung(20;2.22e-14)|Ovarian(172;0.00197)|Breast(254;0.122)		LUSC - Lung squamous cell carcinoma(14;3.57e-14)|Lung(28;9.39e-14)															---	---	---	---
DGKG	1608	broad.mit.edu	37	3	185985707	185985708	+	Intron	DEL	GT	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:185985707_185985708delGT	uc003fqa.2	-						DGKG_uc003fqb.2_Intron|DGKG_uc003fqc.2_Intron|DGKG_uc011brx.1_Intron	NM_001346	NP_001337			diacylglycerol kinase gamma isoform 1						activation of protein kinase C activity by G-protein coupled receptor protein signaling pathway|intracellular signal transduction|platelet activation	cytoplasm|plasma membrane	ATP binding|calcium ion binding|diacylglycerol kinase activity			breast(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)|skin(1)	5	all_cancers(143;3.26e-12)|Ovarian(172;0.0315)|Breast(254;0.247)		OV - Ovarian serous cystadenocarcinoma(80;1.93e-20)	GBM - Glioblastoma multiforme(93;0.0657)	Phosphatidylserine(DB00144)													---	---	---	---
UTS2D	257313	broad.mit.edu	37	3	190986180	190986180	+	3'UTR	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:190986180delT	uc003fsu.2	-	9						NM_198152	NP_937795			urotensin 2 domain containing precursor							extracellular region	hormone activity				0	all_cancers(143;1.77e-09)|Ovarian(172;0.103)		LUSC - Lung squamous cell carcinoma(58;2.42e-06)|Lung(62;2.86e-06)	GBM - Glioblastoma multiforme(46;0.000214)														---	---	---	---
FYTTD1	84248	broad.mit.edu	37	3	197508915	197508915	+	3'UTR	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:197508915delT	uc003fyi.2	+	9					FYTTD1_uc011bui.1_3'UTR|FYTTD1_uc011buj.1_RNA|FYTTD1_uc011buk.1_3'UTR	NM_032288	NP_115664			forty-two-three domain containing 1 isoform 1						mRNA export from nucleus	nuclear speck	mRNA binding|protein binding				0	all_cancers(143;1.15e-09)|Ovarian(172;0.0418)|Breast(254;0.0976)	Lung NSC(153;0.132)	Epithelial(36;2.19e-23)|all cancers(36;1.39e-21)|OV - Ovarian serous cystadenocarcinoma(49;1.21e-18)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(93;0.175)														---	---	---	---
Unknown	0	broad.mit.edu	37	4	1389815	1389815	+	IGR	DEL	G	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:1389815delG								CRIPAK (33 upstream) : FAM53A (251794 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	3923361	3923361	+	IGR	DEL	G	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:3923361delG								ADRA2C (153110 upstream) : LOC348926 (20309 downstream)																																			---	---	---	---
ANAPC4	29945	broad.mit.edu	37	4	25411236	25411236	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:25411236delT	uc003gro.2	+						ANAPC4_uc003grp.2_Intron	NM_013367	NP_037499			anaphase-promoting complex subunit 4						anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|cell division|G2/M transition of mitotic cell cycle|mitotic anaphase|mitotic cell cycle spindle assembly checkpoint|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|protein K11-linked ubiquitination	anaphase-promoting complex|cytosol|nucleoplasm	protein phosphatase binding|ubiquitin-protein ligase activity			ovary(2)|large_intestine(1)|pancreas(1)|skin(1)	5		Breast(46;0.0503)																---	---	---	---
SEL1L3	23231	broad.mit.edu	37	4	25804213	25804213	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:25804213delT	uc003gru.3	-						SEL1L3_uc003grv.2_Intron	NM_015187	NP_056002			sel-1 suppressor of lin-12-like 3							integral to membrane	binding				0																		---	---	---	---
ARAP2	116984	broad.mit.edu	37	4	36230062	36230062	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:36230062delT	uc003gsq.1	-						ARAP2_uc003gsr.1_Intron	NM_015230	NP_056045			ArfGAP with RhoGAP domain, ankyrin repeat and PH						regulation of ARF GTPase activity|small GTPase mediated signal transduction	cytosol	ARF GTPase activator activity|phosphatidylinositol-3,4,5-trisphosphate binding|zinc ion binding			ovary(1)|pancreas(1)|skin(1)	3																		---	---	---	---
LIAS	11019	broad.mit.edu	37	4	39478849	39478849	+	3'UTR	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:39478849delA	uc003guf.2	+	11					LIAS_uc003gug.2_3'UTR|LIAS_uc003guh.2_3'UTR	NM_006859	NP_006850			lipoic acid synthetase isoform 1 precursor						inflammatory response|response to lipopolysaccharide|response to oxidative stress	mitochondrion	4 iron, 4 sulfur cluster binding|lipoate synthase activity|metal ion binding				0					Lipoic Acid(DB00166)													---	---	---	---
SLC30A9	10463	broad.mit.edu	37	4	42037517	42037518	+	Intron	DEL	TT	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:42037517_42037518delTT	uc003gwl.2	+						SLC30A9_uc011byx.1_Intron	NM_006345	NP_006336			solute carrier family 30 (zinc transporter),						nucleotide-excision repair|zinc ion transport	cytoskeleton|integral to membrane|nucleus	cation transmembrane transporter activity|nucleotide binding|sequence-specific DNA binding transcription factor activity			central_nervous_system(2)|ovary(1)	3																		---	---	---	---
C4orf14	84273	broad.mit.edu	37	4	57839652	57839652	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:57839652delT	uc003hck.2	-							NM_032313	NP_115689			hypothetical protein LOC84273								GTP binding			ovary(1)|breast(1)	2	Glioma(25;0.08)|all_neural(26;0.181)																	---	---	---	---
Unknown	0	broad.mit.edu	37	4	70267902	70267902	+	IGR	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:70267902delA								UGT2B28 (107135 upstream) : UGT2B4 (77982 downstream)																																			---	---	---	---
DCK	1633	broad.mit.edu	37	4	71889230	71889231	+	Intron	INS	-	T	T	rs3833976		TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:71889230_71889231insT	uc003hfx.2	+						DCK_uc011cbb.1_Intron	NM_000788	NP_000779			deoxycytidine kinase						purine base metabolic process|purine-containing compound salvage|pyrimidine base metabolic process|pyrimidine nucleoside salvage|pyrimidine nucleotide metabolic process	cytosol|nucleus	ATP binding|deoxycytidine kinase activity|drug binding|phosphotransferase activity, alcohol group as acceptor|protein homodimerization activity			ovary(1)	1			Lung(101;0.235)		Cladribine(DB00242)|Clofarabine(DB00631)|Decitabine(DB01262)|Fludarabine(DB01073)|Gemcitabine(DB00441)|Pemetrexed(DB00642)|Zalcitabine(DB00943)													---	---	---	---
RASSF6	166824	broad.mit.edu	37	4	74441817	74441817	+	3'UTR	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:74441817delT	uc003hhd.1	-	11					RASSF6_uc003hhc.1_3'UTR|RASSF6_uc010iik.1_3'UTR|RASSF6_uc010iil.1_3'UTR	NM_201431	NP_958834			Ras association (RalGDS/AF-6) domain family 6						apoptosis|signal transduction		protein binding			pancreas(2)	2	Breast(15;0.00102)		all cancers(17;0.00104)|Lung(101;0.128)|LUSC - Lung squamous cell carcinoma(112;0.187)															---	---	---	---
SEC31A	22872	broad.mit.edu	37	4	83740164	83740164	+	3'UTR	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:83740164delT	uc003hnf.2	-	27					SEC31A_uc003hnd.2_3'UTR|SEC31A_uc003hne.2_3'UTR|SEC31A_uc011ccl.1_3'UTR|SEC31A_uc003hnl.2_3'UTR|SEC31A_uc003hng.2_3'UTR|SEC31A_uc003hnh.2_3'UTR|SEC31A_uc003hni.2_3'UTR|SEC31A_uc003hnj.2_3'UTR|SEC31A_uc011ccm.1_3'UTR|SEC31A_uc011ccn.1_3'UTR|SEC31A_uc003hnk.2_3'UTR|SEC31A_uc003hnm.2_3'UTR	NM_001077207	NP_001070675			SEC31 homolog A isoform 1						COPII vesicle coating|post-translational protein modification|protein N-linked glycosylation via asparagine|protein transport|response to calcium ion	COPII vesicle coat|cytosol|endoplasmic reticulum membrane|perinuclear region of cytoplasm	calcium-dependent protein binding		SEC31A/JAK2(4)|SEC31A/ALK(3)	haematopoietic_and_lymphoid_tissue(4)|soft_tissue(3)|breast(1)	8		Hepatocellular(203;0.114)																---	---	---	---
CENPE	1062	broad.mit.edu	37	4	104072322	104072322	+	Intron	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:104072322delA	uc003hxb.1	-						CENPE_uc003hxc.1_Intron	NM_001813	NP_001804			centromere protein E						blood coagulation|cell division|kinetochore assembly|microtubule-based movement|mitotic chromosome movement towards spindle pole|mitotic metaphase|mitotic metaphase plate congression|mitotic prometaphase|multicellular organismal development|positive regulation of protein kinase activity	condensed chromosome kinetochore|cytosol|microtubule|nucleus|spindle	ATP binding|kinetochore binding|microtubule motor activity			ovary(5)|breast(4)	9				OV - Ovarian serous cystadenocarcinoma(123;2.95e-08)														---	---	---	---
TBCK	93627	broad.mit.edu	37	4	107037270	107037270	+	Intron	DEL	T	-	-	rs79018134		TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:107037270delT	uc010ilv.2	-						TBCK_uc003hyb.2_Intron|TBCK_uc003hye.2_Intron|TBCK_uc003hyc.2_Intron|TBCK_uc003hyd.2_Intron|TBCK_uc003hyf.2_Intron	NM_001163435	NP_001156907			TBC domain-containing protein kinase-like							intracellular	Rab GTPase activator activity			large_intestine(2)|upper_aerodigestive_tract(1)|stomach(1)|ovary(1)	5																		---	---	---	---
RPL34	6164	broad.mit.edu	37	4	109546421	109546421	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:109546421delT	uc003hyz.2	+						RPL34_uc003hza.2_Intron	NM_000995	NP_000986			ribosomal protein L34						endocrine pancreas development|translational elongation|translational termination|viral transcription	cytosolic large ribosomal subunit	protein binding|RNA binding|structural constituent of ribosome				0		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;0.000286)														---	---	---	---
UGT8	7368	broad.mit.edu	37	4	115585067	115585067	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:115585067delT	uc003ibs.2	+						UGT8_uc003ibt.2_Intron|UGT8_uc011cge.1_Intron	NM_001128174	NP_001121646			UDP-galactose-ceramide galactosyltransferase 8						central nervous system development|peripheral nervous system development	integral to membrane	2-hydroxyacylsphingosine 1-beta-galactosyltransferase activity|UDP-galactose:glucosylceramide beta-1,4-galactosyltransferase activity			ovary(1)|skin(1)	2		Ovarian(17;0.156)		OV - Ovarian serous cystadenocarcinoma(123;0.000632)														---	---	---	---
NDST3	9348	broad.mit.edu	37	4	119163441	119163441	+	Intron	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:119163441delA	uc003ibx.2	+							NM_004784	NP_004775			N-deacetylase/N-sulfotransferase (heparan							Golgi membrane|integral to membrane	[heparan sulfate]-glucosamine N-sulfotransferase activity|hydrolase activity			large_intestine(1)	1																		---	---	---	---
ELMOD2	255520	broad.mit.edu	37	4	141448706	141448706	+	Intron	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:141448706delA	uc003iik.2	+							NM_153702	NP_714913			ELMO/CED-12 domain containing 2						phagocytosis|regulation of defense response to virus|response to virus	cytoskeleton	GTPase activator activity			ovary(1)	1	all_hematologic(180;0.162)																	---	---	---	---
USP38	84640	broad.mit.edu	37	4	144130643	144130644	+	Intron	DEL	AA	-	-	rs111830994		TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:144130643_144130644delAA	uc003ijb.2	+						USP38_uc003ija.3_Intron|USP38_uc003ijc.2_Intron	NM_032557	NP_115946			ubiquitin specific peptidase 38						ubiquitin-dependent protein catabolic process		cysteine-type peptidase activity|ubiquitin thiolesterase activity			lung(2)|ovary(1)|breast(1)|pancreas(1)	5	all_hematologic(180;0.158)																	---	---	---	---
ABCE1	6059	broad.mit.edu	37	4	146041224	146041224	+	Frame_Shift_Del	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:146041224delA	uc003ijx.2	+	11	1503	c.1063delA	c.(1063-1065)AAAfs	p.K355fs	ABCE1_uc003ijy.2_Frame_Shift_Del_p.K355fs|ABCE1_uc010iot.2_RNA	NM_001040876	NP_001035809	P61221	ABCE1_HUMAN	ATP-binding cassette, sub-family E, member 1	355	ABC transporter 2.				interspecies interaction between organisms|response to virus|RNA catabolic process	mitochondrion	ATP binding|ATPase activity|electron carrier activity|iron-sulfur cluster binding|ribonuclease inhibitor activity			skin(1)	1	all_hematologic(180;0.151)																	---	---	---	---
ZNF827	152485	broad.mit.edu	37	4	146770908	146770908	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:146770908delT	uc003ikn.2	-						ZNF827_uc003ikm.2_Intron|ZNF827_uc010iox.2_Intron	NM_178835	NP_849157			zinc finger protein 827						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0	all_hematologic(180;0.151)																	---	---	---	---
ACCN5	51802	broad.mit.edu	37	4	156773541	156773541	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:156773541delT	uc003ipe.1	-							NM_017419	NP_059115			amiloride-sensitive cation channel 5,							integral to membrane|plasma membrane				ovary(2)|skin(1)	3	all_hematologic(180;0.24)	Renal(120;0.0458)		KIRC - Kidney renal clear cell carcinoma(143;0.0464)|Kidney(143;0.058)|COAD - Colon adenocarcinoma(41;0.141)														---	---	---	---
GLRB	2743	broad.mit.edu	37	4	158059927	158059927	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:158059927delT	uc003ipj.2	+							NM_000824	NP_000815			glycine receptor, beta isoform A precursor						nervous system development|neuropeptide signaling pathway|startle response	cell junction|chloride channel complex|integral to plasma membrane|postsynaptic membrane	extracellular-glycine-gated chloride channel activity|protein binding|receptor activity			skin(2)	2	all_hematologic(180;0.24)	Renal(120;0.0458)		KIRC - Kidney renal clear cell carcinoma(143;0.0564)|COAD - Colon adenocarcinoma(41;0.0642)|Kidney(143;0.0707)	Glycine(DB00145)													---	---	---	---
RAPGEF2	9693	broad.mit.edu	37	4	160251796	160251797	+	Intron	INS	-	A	A	rs78225051		TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:160251796_160251797insA	uc003iqg.3	+							NM_014247	NP_055062			Rap guanine nucleotide exchange factor 2						cAMP-mediated signaling|MAPKKK cascade|small GTPase mediated signal transduction	integral to plasma membrane|intracellular	calcium ion binding|diacylglycerol binding|Rap GTPase activator activity|Rap guanyl-nucleotide exchange factor activity|signal transducer activity			lung(2)|upper_aerodigestive_tract(1)|skin(1)	4	all_hematologic(180;0.24)			COAD - Colon adenocarcinoma(41;0.0817)														---	---	---	---
AGA	175	broad.mit.edu	37	4	178361260	178361260	+	Intron	DEL	T	-	-	rs75220849		TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:178361260delT	uc003iuu.1	-						AGA_uc003iuv.1_5'Flank|AGA_uc003iuw.2_5'Flank	NM_000027	NP_000018			aspartylglucosaminidase precursor						asparagine catabolic process via L-aspartate|protein deglycosylation|protein maturation	endoplasmic reticulum|intermediate filament cytoskeleton|lysosome|microtubule cytoskeleton	N4-(beta-N-acetylglucosaminyl)-L-asparaginase activity				0		all_lung(41;1.27e-09)|Lung NSC(41;1.1e-08)|Breast(14;6.27e-05)|Melanoma(52;0.00102)|Renal(120;0.00988)|Prostate(90;0.00996)|all_hematologic(60;0.014)|Hepatocellular(41;0.148)|all_neural(102;0.164)|Colorectal(36;0.245)		all cancers(43;1.37e-22)|Epithelial(43;3.86e-20)|OV - Ovarian serous cystadenocarcinoma(60;3.8e-11)|Colorectal(24;6.98e-05)|GBM - Glioblastoma multiforme(59;0.000362)|COAD - Colon adenocarcinoma(29;0.000462)|STAD - Stomach adenocarcinoma(60;0.0029)|LUSC - Lung squamous cell carcinoma(193;0.0328)|READ - Rectum adenocarcinoma(43;0.163)														---	---	---	---
SEMA5A	9037	broad.mit.edu	37	5	9201932	9201932	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:9201932delT	uc003jek.2	-							NM_003966	NP_003957			semaphorin 5A precursor						cell adhesion|cell-cell signaling	integral to membrane|plasma membrane				ovary(1)|central_nervous_system(1)	2																		---	---	---	---
GUSBP1	728411	broad.mit.edu	37	5	21459960	21459960	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:21459960delT	uc010iub.2	+						GUSBP1_uc011cnn.1_Intron|GUSBP1_uc003jgh.3_Intron|GUSBP1_uc003jgf.3_Intron|GUSBP1_uc003jgg.3_Intron	NR_027028				SubName: Full=Putative uncharacterized protein GUSBL2;												0																OREG0016459	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
C5orf22	55322	broad.mit.edu	37	5	31541526	31541526	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:31541526delT	uc003jhj.3	+						C5orf22_uc011cnw.1_Intron|C5orf22_uc003jhk.3_Intron	NM_018356	NP_060826			hypothetical protein LOC55322											ovary(2)	2																		---	---	---	---
C5orf42	65250	broad.mit.edu	37	5	37120153	37120153	+	Intron	DEL	A	-	-	rs75040582	by1000genomes	TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:37120153delA	uc011cpa.1	-						C5orf42_uc003jko.1_Intron|C5orf42_uc003jkp.1_Intron|C5orf42_uc011coy.1_Intron|C5orf42_uc003jks.2_Intron|C5orf42_uc011coz.1_Intron	NM_023073	NP_075561			hypothetical protein LOC65250											ovary(4)|breast(2)|skin(1)	7	all_lung(31;0.000616)		COAD - Colon adenocarcinoma(61;0.14)|Epithelial(62;0.177)|Colorectal(62;0.202)															---	---	---	---
C5orf42	65250	broad.mit.edu	37	5	37162787	37162788	+	Intron	DEL	TT	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:37162787_37162788delTT	uc011cpa.1	-						C5orf42_uc011coy.1_Intron|C5orf42_uc003jks.2_Intron|C5orf42_uc011coz.1_Intron	NM_023073	NP_075561			hypothetical protein LOC65250											ovary(4)|breast(2)|skin(1)	7	all_lung(31;0.000616)		COAD - Colon adenocarcinoma(61;0.14)|Epithelial(62;0.177)|Colorectal(62;0.202)															---	---	---	---
WDR70	55100	broad.mit.edu	37	5	37697601	37697601	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:37697601delT	uc003jkv.2	+						WDR70_uc010iva.1_Intron	NM_018034	NP_060504			WD repeat domain 70											ovary(1)|central_nervous_system(1)	2	all_lung(31;0.000285)		COAD - Colon adenocarcinoma(61;0.14)|Colorectal(62;0.202)															---	---	---	---
KIF2A	3796	broad.mit.edu	37	5	61662224	61662224	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:61662224delT	uc003jsy.3	+						KIF2A_uc003jsz.3_Intron|KIF2A_uc010iwp.2_Intron|KIF2A_uc003jsx.3_Intron|KIF2A_uc010iwq.2_Intron	NM_004520	NP_004511			kinesin heavy chain member 2 isoform 1						blood coagulation|cell differentiation|cell division|microtubule-based movement|mitotic prometaphase|mitotic spindle organization|nervous system development	centrosome|cytosol|microtubule|spindle pole	ATP binding|microtubule motor activity|protein binding				0		Lung NSC(810;8.94e-06)|Prostate(74;0.0132)|Ovarian(174;0.051)|Breast(144;0.077)		Lung(70;0.14)														---	---	---	---
GTF2H2B	653238	broad.mit.edu	37	5	69717511	69717512	+	Intron	INS	-	G	G			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:69717511_69717512insG	uc003jzb.3	+						uc011crh.1_Intron|uc011crl.1_Intron|LOC100170939_uc010ixu.2_Intron|uc003jyr.1_Intron|LOC100170939_uc003jys.2_Intron|LOC100170939_uc011crn.1_Intron|uc011cro.1_Intron|GTF2H2B_uc011crp.1_Intron|GTF2H2B_uc003jza.3_Intron|GTF2H2B_uc003jzd.1_5'Flank	NM_001098729	NP_001092199			general transcription factor IIH, polypeptide												0																		---	---	---	---
RPS23	6228	broad.mit.edu	37	5	81571879	81571879	+	3'UTR	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:81571879delT	uc003khu.2	-	4						NM_001025	NP_001016			ribosomal protein S23						endocrine pancreas development|translational elongation|translational termination|viral transcription	cytosolic small ribosomal subunit	protein binding|structural constituent of ribosome				0		Lung NSC(167;0.0025)|all_lung(232;0.00278)|Ovarian(174;0.0336)		OV - Ovarian serous cystadenocarcinoma(54;1.94e-42)|Epithelial(54;8.38e-37)|all cancers(79;1.42e-31)														---	---	---	---
TMEM167A	153339	broad.mit.edu	37	5	82372898	82372898	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:82372898delT	uc003khx.3	-						XRCC4_uc003kia.1_5'Flank|XRCC4_uc003kib.2_5'Flank|XRCC4_uc003kid.2_5'Flank|XRCC4_uc003kic.2_5'Flank|XRCC4_uc003kie.2_5'Flank	NM_174909	NP_777569			transmembrane protein 167A precursor							Golgi membrane|integral to membrane					0																		---	---	---	---
TMEM161B	153396	broad.mit.edu	37	5	87491918	87491918	+	3'UTR	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:87491918delT	uc003kjc.2	-	12					TMEM161B_uc011cty.1_3'UTR|TMEM161B_uc010jax.2_RNA|TMEM161B_uc011ctx.1_3'UTR	NM_153354	NP_699185			transmembrane protein 161B							integral to membrane				skin(2)	2		all_cancers(142;0.000275)|Lung NSC(167;0.00901)|all_lung(232;0.0111)|Colorectal(57;0.0959)|Ovarian(174;0.1)		OV - Ovarian serous cystadenocarcinoma(54;6.24e-36)|Epithelial(54;6.8e-31)|all cancers(79;1.07e-26)														---	---	---	---
TMEM161B	153396	broad.mit.edu	37	5	87492365	87492365	+	Intron	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:87492365delA	uc003kjc.2	-						TMEM161B_uc011cty.1_Intron|TMEM161B_uc010jax.2_Intron|TMEM161B_uc011ctx.1_Intron	NM_153354	NP_699185			transmembrane protein 161B							integral to membrane				skin(2)	2		all_cancers(142;0.000275)|Lung NSC(167;0.00901)|all_lung(232;0.0111)|Colorectal(57;0.0959)|Ovarian(174;0.1)		OV - Ovarian serous cystadenocarcinoma(54;6.24e-36)|Epithelial(54;6.8e-31)|all cancers(79;1.07e-26)														---	---	---	---
COMMD10	51397	broad.mit.edu	37	5	115553612	115553612	+	Intron	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:115553612delA	uc003krt.1	+							NM_016144	NP_057228			COMM domain containing 10								protein binding			ovary(1)	1		all_cancers(142;0.0834)|all_epithelial(76;0.00314)|Prostate(80;0.0102)|Ovarian(225;0.232)		OV - Ovarian serous cystadenocarcinoma(64;4.3e-07)|Epithelial(69;8.06e-07)|all cancers(49;4.06e-05)														---	---	---	---
PRRC1	133619	broad.mit.edu	37	5	126866120	126866121	+	Intron	DEL	TT	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:126866120_126866121delTT	uc003kuk.2	+						PRRC1_uc003kuj.3_Intron	NM_130809	NP_570721			proline-rich coiled-coil 1							Golgi apparatus					0		Prostate(80;0.165)	KIRC - Kidney renal clear cell carcinoma(527;0.0268)|Kidney(363;0.0488)	OV - Ovarian serous cystadenocarcinoma(64;0.0851)|Epithelial(69;0.113)														---	---	---	---
ISOC1	51015	broad.mit.edu	37	5	128440485	128440485	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:128440485delT	uc003kva.2	+							NM_016048	NP_057132			isochorismatase domain containing 1							peroxisome	catalytic activity				0		all_cancers(142;0.0813)|Prostate(80;0.0865)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)	Epithelial(69;0.138)|OV - Ovarian serous cystadenocarcinoma(64;0.164)														---	---	---	---
MYOT	9499	broad.mit.edu	37	5	137217571	137217571	+	Intron	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:137217571delA	uc011cye.1	+						MYOT_uc003lbv.2_Intron|MYOT_uc011cyg.1_Intron|MYOT_uc011cyh.1_Intron	NM_001135940	NP_001129412			myotilin isoform b						muscle contraction	actin cytoskeleton|sarcolemma|sarcomere	actin binding|structural constituent of muscle			large_intestine(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0109)															---	---	---	---
Unknown	0	broad.mit.edu	37	5	147517869	147517869	+	IGR	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:147517869delT								SPINK5 (944 upstream) : SPINK14 (31427 downstream)																																			---	---	---	---
ODZ2	57451	broad.mit.edu	37	5	167589926	167589926	+	Intron	DEL	A	-	-	rs111814381		TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:167589926delA	uc010jjd.2	+						ODZ2_uc003lzr.3_Intron|ODZ2_uc003lzt.3_Intron|ODZ2_uc010jje.2_Intron|uc003lzs.1_Intron	NM_001122679	NP_001116151			odz, odd Oz/ten-m homolog 2											ovary(6)|central_nervous_system(4)	10	Renal(175;0.00124)|Lung NSC(126;0.136)|all_lung(126;0.242)	Medulloblastoma(196;0.0241)|all_neural(177;0.026)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	all cancers(165;0.0444)|OV - Ovarian serous cystadenocarcinoma(192;0.0694)|Epithelial(171;0.124)														---	---	---	---
Unknown	0	broad.mit.edu	37	5	168043289	168043289	+	IGR	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:168043289delT								PANK3 (36701 upstream) : SLIT3 (49783 downstream)																																			---	---	---	---
TMEM14B	81853	broad.mit.edu	37	6	10756864	10756864	+	3'UTR	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:10756864delA	uc003mzk.3	+	6					SYCP2L_uc011dim.1_Intron|TMEM14B_uc010jor.2_3'UTR|TMEM14B_uc010jos.1_Intron	NM_030969	NP_112231			transmembrane protein 14B isoform a							integral to membrane					0	Ovarian(93;0.107)|Breast(50;0.137)	all_hematologic(90;0.135)																---	---	---	---
SIRT5	23408	broad.mit.edu	37	6	13584591	13584591	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:13584591delT	uc003nay.2	+						SIRT5_uc003naw.2_Intron|SIRT5_uc003nax.2_Intron|SIRT5_uc011dit.1_Intron	NM_012241	NP_036373			sirtuin 5 isoform 1						chromatin silencing|protein ADP-ribosylation|protein deacetylation	mitochondrial intermembrane space|mitochondrial matrix	hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides|NAD+ ADP-ribosyltransferase activity|NAD+ binding|zinc ion binding			skin(2)|upper_aerodigestive_tract(1)	3	Breast(50;0.00669)|Ovarian(93;0.0634)	all_hematologic(90;0.117)	Epithelial(50;0.176)		Suramin(DB04786)													---	---	---	---
MYLIP	29116	broad.mit.edu	37	6	16141709	16141709	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:16141709delT	uc003nbq.2	+						MYLIP_uc003nbr.2_Intron	NM_013262	NP_037394			myosin regulatory light chain interacting						cellular component movement|nervous system development	cytoplasm|cytoskeleton|extrinsic to membrane	cytoskeletal protein binding|ubiquitin-protein ligase activity|zinc ion binding			pancreas(1)	1	Breast(50;0.0799)|Ovarian(93;0.103)	all_hematologic(90;0.0895)	Epithelial(50;0.241)															---	---	---	---
CAP2	10486	broad.mit.edu	37	6	17531050	17531050	+	Intron	DEL	T	-	-	rs35589543		TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:17531050delT	uc003ncb.2	+						CAP2_uc010jpk.1_Intron|CAP2_uc011dja.1_Intron|CAP2_uc011djb.1_Intron|CAP2_uc011djc.1_Intron|CAP2_uc011djd.1_Intron	NM_006366	NP_006357			adenylyl cyclase-associated protein 2						activation of adenylate cyclase activity|axon guidance|cytoskeleton organization|establishment or maintenance of cell polarity|signal transduction	plasma membrane	actin binding			ovary(1)	1	Breast(50;0.0333)|Ovarian(93;0.0386)	all_hematologic(90;0.0466)	all cancers(50;0.194)|Epithelial(50;0.227)															---	---	---	---
KIF13A	63971	broad.mit.edu	37	6	17898424	17898424	+	Intron	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:17898424delA	uc003ncg.3	-						KIF13A_uc003ncf.2_Intron|KIF13A_uc003nch.3_Intron|KIF13A_uc003nci.3_Intron	NM_022113	NP_071396			kinesin family member 13A isoform a						cargo loading into vesicle|cell cycle|cytokinesis|endosome to lysosome transport|Golgi to plasma membrane protein transport|melanosome organization|plus-end-directed vesicle transport along microtubule	centrosome|endosome membrane|microtubule|midbody|trans-Golgi network membrane	ATP binding|microtubule motor activity|protein binding			large_intestine(2)|ovary(2)	4	Breast(50;0.0107)|Ovarian(93;0.016)	all_hematologic(90;0.125)	all cancers(50;0.0865)|Epithelial(50;0.0974)															---	---	---	---
C6orf106	64771	broad.mit.edu	37	6	34664457	34664457	+	5'UTR	DEL	G	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:34664457delG	uc003ojr.2	-	1					C6orf106_uc003ojs.2_5'UTR	NM_024294	NP_077270			chromosome 6 open reading frame 106 isoform a											skin(2)|ovary(1)	3																		---	---	---	---
NFYA	4800	broad.mit.edu	37	6	41057863	41057863	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:41057863delT	uc003opo.2	+						NFYA_uc003opp.2_Intron|NFYA_uc003opq.2_Intron	NM_002505	NP_002496			nuclear transcription factor Y, alpha isoform 1						transcription from RNA polymerase II promoter	CCAAT-binding factor complex	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity				0	Ovarian(28;0.0418)|Colorectal(47;0.196)																	---	---	---	---
HMGCLL1	54511	broad.mit.edu	37	6	55381523	55381523	+	Intron	DEL	A	-	-	rs71693355		TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:55381523delA	uc003pcn.2	-						HMGCLL1_uc003pco.2_Intron|HMGCLL1_uc010jzx.2_Intron|HMGCLL1_uc011dxc.1_Intron|HMGCLL1_uc011dxd.1_Intron|HMGCLL1_uc011dxe.1_Intron|HMGCLL1_uc003pcp.2_Intron	NM_019036	NP_061909			3-hydroxymethyl-3-methylglutaryl-Coenzyme A								hydroxymethylglutaryl-CoA lyase activity|metal ion binding			skin(2)|ovary(1)|pancreas(1)	4	Lung NSC(77;0.0875)		LUSC - Lung squamous cell carcinoma(124;0.23)															---	---	---	---
PHF3	23469	broad.mit.edu	37	6	64410483	64410483	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:64410483delT	uc003pep.1	+						PHF3_uc010kah.1_Intron|PHF3_uc003pen.2_Intron|PHF3_uc011dxs.1_Intron	NM_015153	NP_055968			PHD finger protein 3						multicellular organismal development|transcription, DNA-dependent	nucleus	zinc ion binding			ovary(3)|lung(1)|skin(1)	5	all_cancers(3;0.0241)|all_epithelial(2;0.00306)|Lung NSC(77;0.121)		LUSC - Lung squamous cell carcinoma(74;0.0644)|Lung(124;0.148)															---	---	---	---
PGM3	5238	broad.mit.edu	37	6	83900377	83900377	+	Intron	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:83900377delA	uc003pjv.2	-						PGM3_uc003pjw.2_Intron|PGM3_uc011dyz.1_Intron|RWDD2A_uc003pjx.3_5'Flank|RWDD2A_uc011dza.1_5'Flank	NM_015599	NP_056414			phosphoglucomutase 3						dolichol-linked oligosaccharide biosynthetic process|embryo development ending in birth or egg hatching|glucose 1-phosphate metabolic process|hemopoiesis|post-translational protein modification|protein N-linked glycosylation via asparagine|UDP-N-acetylglucosamine biosynthetic process	cytosol	magnesium ion binding|phosphoacetylglucosamine mutase activity|phosphoglucomutase activity				0		all_cancers(76;0.000504)|Acute lymphoblastic leukemia(125;3.85e-06)|all_hematologic(105;0.0017)|all_epithelial(107;0.068)		BRCA - Breast invasive adenocarcinoma(397;0.0478)														---	---	---	---
CYB5R4	51167	broad.mit.edu	37	6	84624111	84624111	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:84624111delT	uc003pkf.2	+							NM_016230	NP_057314			cytochrome b5 reductase 4						cell development|detection of oxygen|generation of precursor metabolites and energy|glucose homeostasis|insulin secretion|response to antibiotic|superoxide metabolic process	endoplasmic reticulum|perinuclear region of cytoplasm	cytochrome-b5 reductase activity|heme binding|NAD(P)H oxidase activity			breast(2)	2		all_cancers(76;7e-07)|Acute lymphoblastic leukemia(125;2.69e-07)|all_hematologic(105;0.000151)|all_epithelial(107;0.00128)		BRCA - Breast invasive adenocarcinoma(397;0.0871)														---	---	---	---
TBX18	9096	broad.mit.edu	37	6	85469936	85469936	+	Intron	DEL	T	-	-	rs74587058		TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:85469936delT	uc003pkl.1	-						TBX18_uc010kbq.1_Intron	NM_001080508	NP_001073977			T-box 18						multicellular organismal development	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity			ovary(2)|pancreas(2)|lung(1)	5		all_cancers(76;0.000283)|Acute lymphoblastic leukemia(125;3.66e-08)|all_hematologic(105;8.61e-05)|all_epithelial(107;0.0858)		BRCA - Breast invasive adenocarcinoma(108;0.0267)														---	---	---	---
ZNF292	23036	broad.mit.edu	37	6	87969484	87969484	+	Frame_Shift_Del	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:87969484delA	uc003plm.3	+	8	6178	c.6137delA	c.(6136-6138)GAAfs	p.E2046fs		NM_015021	NP_055836	O60281	ZN292_HUMAN	zinc finger protein 292	2046					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(4)	4		all_cancers(76;3.82e-09)|Prostate(29;1.34e-10)|Acute lymphoblastic leukemia(125;2.17e-10)|all_hematologic(105;1.08e-06)|all_epithelial(107;5.31e-05)		BRCA - Breast invasive adenocarcinoma(108;0.0199)														---	---	---	---
MDN1	23195	broad.mit.edu	37	6	90409616	90409616	+	Intron	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:90409616delA	uc003pnn.1	-							NM_014611	NP_055426			MDN1, midasin homolog						protein complex assembly|regulation of protein complex assembly	nucleus	ATP binding|ATPase activity|unfolded protein binding			ovary(8)|skin(2)	10		all_cancers(76;1.47e-06)|Acute lymphoblastic leukemia(125;2.23e-10)|Prostate(29;5.55e-10)|all_hematologic(105;2.42e-06)|all_epithelial(107;0.00246)		BRCA - Breast invasive adenocarcinoma(108;0.0193)														---	---	---	---
SCML4	256380	broad.mit.edu	37	6	108076968	108076968	+	Intron	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:108076968delA	uc010kdf.2	-						SCML4_uc003prz.3_Intron|SCML4_uc011eam.1_Intron|SCML4_uc003psa.3_Intron	NM_198081	NP_932347			sex comb on midleg-like 4						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding			ovary(1)	1		all_cancers(87;3.26e-06)|Acute lymphoblastic leukemia(125;3.08e-08)|all_hematologic(75;1.15e-06)|all_epithelial(87;0.00142)|Colorectal(196;0.0316)		BRCA - Breast invasive adenocarcinoma(108;0.01)|Epithelial(106;0.0509)|all cancers(137;0.0586)|OV - Ovarian serous cystadenocarcinoma(136;0.0758)														---	---	---	---
ROS1	6098	broad.mit.edu	37	6	117704314	117704315	+	Intron	DEL	GC	-	-	rs112993324		TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:117704314_117704315delGC	uc003pxp.1	-						ROS1_uc011ebi.1_Intron|GOPC_uc003pxq.1_Intron	NM_002944	NP_002935			proto-oncogene c-ros-1 protein precursor						transmembrane receptor protein tyrosine kinase signaling pathway	membrane fraction|sodium:potassium-exchanging ATPase complex	ATP binding|transmembrane receptor protein tyrosine kinase activity			lung(8)|ovary(6)|central_nervous_system(3)|skin(3)|stomach(2)|breast(2)|large_intestine(1)	25		all_cancers(87;0.00846)|all_epithelial(87;0.0242)		GBM - Glioblastoma multiforme(226;0.0387)|OV - Ovarian serous cystadenocarcinoma(136;0.0954)|all cancers(137;0.137)				T	GOPC|ROS1	glioblastoma|NSCLC								---	---	---	---
TRDN	10345	broad.mit.edu	37	6	123786155	123786156	+	Intron	DEL	AA	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:123786155_123786156delAA	uc003pzj.1	-						TRDN_uc003pzk.1_Intron|TRDN_uc003pzl.1_Intron|TRDN_uc010ken.2_Intron|uc003pzm.1_Intron	NM_006073	NP_006064			triadin						muscle contraction	integral to membrane|plasma membrane|sarcoplasmic reticulum membrane	receptor binding			ovary(1)	1				GBM - Glioblastoma multiforme(226;0.184)														---	---	---	---
FAM54A	113115	broad.mit.edu	37	6	136566111	136566111	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:136566111delT	uc010kgp.1	-						FAM54A_uc003qgt.1_Intron|FAM54A_uc003qgu.1_Intron	NM_001099286	NP_001092756			DUF729 domain containing 1											skin(1)	1	Colorectal(23;0.24)			GBM - Glioblastoma multiforme(68;0.00228)|OV - Ovarian serous cystadenocarcinoma(155;0.00504)														---	---	---	---
MAP3K5	4217	broad.mit.edu	37	6	136883493	136883494	+	Intron	DEL	TT	-	-	rs11322947		TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:136883493_136883494delTT	uc003qhc.2	-						MAP3K5_uc011edj.1_Intron	NM_005923	NP_005914			mitogen-activated protein kinase kinase kinase						activation of JUN kinase activity|activation of MAPKK activity|cellular response to hydrogen peroxide|induction of apoptosis by extracellular signals|interspecies interaction between organisms		ATP binding|caspase activator activity|magnesium ion binding|MAP kinase kinase kinase activity|protein homodimerization activity|protein phosphatase binding			ovary(2)|skin(2)|lung(1)	5	Colorectal(23;0.24)			GBM - Glioblastoma multiforme(68;0.00137)|OV - Ovarian serous cystadenocarcinoma(155;0.00569)														---	---	---	---
UTRN	7402	broad.mit.edu	37	6	144796037	144796037	+	Intron	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:144796037delA	uc003qkt.2	+						UTRN_uc010khq.1_Intron	NM_007124	NP_009055			utrophin						muscle contraction|muscle organ development|positive regulation of cell-matrix adhesion	cell junction|cytoplasm|cytoskeleton|membrane fraction|nucleus|postsynaptic membrane	actin binding|calcium ion binding|zinc ion binding			ovary(4)|pancreas(1)	5		Ovarian(120;0.218)		OV - Ovarian serous cystadenocarcinoma(155;5.72e-07)|GBM - Glioblastoma multiforme(68;4.9e-05)|Colorectal(48;0.213)														---	---	---	---
C6orf97	80129	broad.mit.edu	37	6	151917439	151917439	+	Intron	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:151917439delA	uc003qol.2	+							NM_025059	NP_079335			hypothetical protein LOC80129												0		Ovarian(120;0.126)	BRCA - Breast invasive adenocarcinoma(37;0.111)	OV - Ovarian serous cystadenocarcinoma(155;1.48e-10)														---	---	---	---
IPCEF1	26034	broad.mit.edu	37	6	154568731	154568731	+	Intron	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:154568731delA	uc003qpx.2	-						IPCEF1_uc003qpw.2_Intron|IPCEF1_uc010kjh.2_Intron	NM_015553	NP_056368			phosphoinositide-binding protein PIP3-E isoform						response to oxidative stress	cytoplasm|plasma membrane	oxygen transporter activity|peroxidase activity				0																		---	---	---	---
ACTB	60	broad.mit.edu	37	7	5568135	5568137	+	In_Frame_Del	DEL	GAG	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:5568135_5568137delGAG	uc003sos.3	-	3	613_615	c.577_579delCTC	c.(577-579)CTCdel	p.L193del	ACTB_uc003sor.3_In_Frame_Del_p.L71del|ACTB_uc003sot.3_In_Frame_Del_p.L193del|ACTB_uc003soq.3_In_Frame_Del_p.L71del|ACTB_uc010ksy.2_In_Frame_Del_p.L71del	NM_001101	NP_001092	P60709	ACTB_HUMAN	beta actin	193					'de novo' posttranslational protein folding|adherens junction organization|axon guidance|blood coagulation|cell junction assembly|cellular component movement	cytoskeleton|cytosol|MLL5-L complex|NuA4 histone acetyltransferase complex|ribonucleoprotein complex	ATP binding|kinesin binding|nitric-oxide synthase binding|structural constituent of cytoskeleton				0		Ovarian(82;0.0606)		UCEC - Uterine corpus endometrioid carcinoma (126;0.175)|OV - Ovarian serous cystadenocarcinoma(56;4.24e-37)														---	---	---	---
C7orf26	79034	broad.mit.edu	37	7	6633948	6633948	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:6633948delT	uc003sqo.1	+						C7orf26_uc003sqp.1_Intron|C7orf26_uc003sqq.1_Intron	NM_024067	NP_076972			hypothetical protein LOC79034											ovary(1)	1		Ovarian(82;0.232)		UCEC - Uterine corpus endometrioid carcinoma (126;0.0986)														---	---	---	---
HDAC9	9734	broad.mit.edu	37	7	18988718	18988719	+	Intron	INS	-	T	T			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:18988718_18988719insT	uc003suh.2	+						HDAC9_uc003sue.2_Intron|HDAC9_uc003sui.2_Intron|HDAC9_uc003suj.2_Intron|HDAC9_uc003suk.2_Intron	NM_058176	NP_478056			histone deacetylase 9 isoform 1						B cell differentiation|cellular response to insulin stimulus|heart development|histone H3 deacetylation|histone H4 deacetylation|inflammatory response|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transcription, DNA-dependent|peptidyl-lysine deacetylation|positive regulation of cell migration involved in sprouting angiogenesis|regulation of skeletal muscle fiber development|transcription, DNA-dependent	cytoplasm|histone deacetylase complex|histone methyltransferase complex|transcription factor complex	histone deacetylase activity (H3-K16 specific)|histone deacetylase binding|histone deacetylase binding|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 binding|protein kinase C binding|repressing transcription factor binding|transcription corepressor activity			lung(2)|central_nervous_system(2)|kidney(1)	5	all_lung(11;0.187)				Valproic Acid(DB00313)													---	---	---	---
CBX3	11335	broad.mit.edu	37	7	26251418	26251418	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:26251418delT	uc003sxt.2	+						CBX3_uc003sxu.2_Intron|CBX3_uc003sxv.2_Intron	NM_007276	NP_009207			chromobox homolog 3						chromatin remodeling|negative regulation of transcription, DNA-dependent|transcription, DNA-dependent	condensed chromosome, centromeric region|nuclear centromeric heterochromatin|nuclear euchromatin|nuclear inner membrane|spindle	enzyme binding|protein domain specific binding			ovary(1)	1																		---	---	---	---
FAM188B	84182	broad.mit.edu	37	7	30831331	30831331	+	Intron	DEL	A	-	-	rs60449260		TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:30831331delA	uc003tbt.2	+						FAM188B_uc010kwe.2_Intron	NM_032222	NP_115598			hypothetical protein LOC84182												0																		---	---	---	---
HERPUD2	64224	broad.mit.edu	37	7	35675101	35675101	+	Intron	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:35675101delA	uc003tet.2	-						HERPUD2_uc003tes.3_Intron	NM_022373	NP_071768			HERPUD family member 2						response to unfolded protein	integral to membrane				ovary(3)	3																		---	---	---	---
POLD2	5425	broad.mit.edu	37	7	44155940	44155940	+	Intron	DEL	C	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:44155940delC	uc010kxz.2	-						POLD2_uc003tke.3_Intron|POLD2_uc010kya.2_Intron|POLD2_uc003tkf.3_Intron	NM_006230	NP_006221			DNA-directed DNA polymerase delta 2						base-excision repair|DNA strand elongation involved in DNA replication|nucleotide-excision repair, DNA gap filling|S phase of mitotic cell cycle|telomere maintenance via recombination|telomere maintenance via semi-conservative replication|transcription-coupled nucleotide-excision repair	nucleoplasm	DNA binding|DNA-directed DNA polymerase activity|protein binding			ovary(2)	2																		---	---	---	---
SUN3	256979	broad.mit.edu	37	7	48045448	48045448	+	Intron	DEL	C	-	-	rs66650652		TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:48045448delC	uc003tof.2	-						SUN3_uc010kyq.2_Intron|SUN3_uc003tog.2_Intron|SUN3_uc011kcf.1_Intron	NM_152782	NP_689995			Sad1 and UNC84 domain containing 1							integral to membrane				central_nervous_system(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	53256452	53256452	+	IGR	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:53256452delA								POM121L12 (151835 upstream) : None (None downstream)																																			---	---	---	---
PSPH	5723	broad.mit.edu	37	7	56169674	56169674	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:56169674delT	uc003trj.2	-						CHCHD2_uc003tsa.2_Intron	NM_004577	NP_004568			phosphoserine phosphatase						L-serine biosynthetic process	cytoplasm	calcium ion binding|magnesium ion binding|phosphoserine phosphatase activity|protein homodimerization activity			ovary(1)|skin(1)	2	Breast(14;0.214)		Lung(13;0.00024)|LUSC - Lung squamous cell carcinoma(13;0.00099)															---	---	---	---
Unknown	0	broad.mit.edu	37	7	56635559	56635559	+	IGR	DEL	G	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:56635559delG								DKFZp434L192 (70582 upstream) : ZNF479 (551769 downstream)																																			---	---	---	---
ZNF679	168417	broad.mit.edu	37	7	63721435	63721435	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:63721435delT	uc003tsx.2	+							NM_153363	NP_699194			zinc finger protein 679						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			skin(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	65976420	65976420	+	IGR	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:65976420delA								NCRNA00174 (111025 upstream) : LOC493754 (17026 downstream)																																			---	---	---	---
SPDYE7P	441251	broad.mit.edu	37	7	72341012	72341012	+	5'Flank	DEL	G	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:72341012delG	uc010lal.1	-							NR_003666				Homo sapiens speedy homolog E7 (Xenopus laevis), pseudogene (SPDYE7P), non-coding RNA.												0																		---	---	---	---
CLIP2	7461	broad.mit.edu	37	7	73803287	73803287	+	Intron	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:73803287delA	uc003uam.2	+						CLIP2_uc003uan.2_Intron	NM_003388	NP_003379			CAP-GLY domain containing linker protein 2							microtubule associated complex				skin(3)	3																		---	---	---	---
HGF	3082	broad.mit.edu	37	7	81381622	81381622	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:81381622delT	uc003uhl.2	-						HGF_uc003uhm.2_Intron|HGF_uc003uhn.1_Intron|HGF_uc003uho.1_Intron|HGF_uc003uhp.2_Intron	NM_000601	NP_000592			hepatocyte growth factor isoform 1						epithelial to mesenchymal transition|mitosis|platelet activation|platelet degranulation|proteolysis|regulation of branching involved in salivary gland morphogenesis by mesenchymal-epithelial signaling	platelet alpha granule lumen	growth factor activity|serine-type endopeptidase activity			ovary(2)|central_nervous_system(2)	4																		---	---	---	---
CACNA2D1	781	broad.mit.edu	37	7	81614084	81614084	+	Intron	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:81614084delA	uc003uhr.1	-							NM_000722	NP_000713			calcium channel, voltage-dependent, alpha							voltage-gated calcium channel complex	metal ion binding			ovary(5)|pancreas(1)	6					Felodipine(DB01023)|Gabapentin(DB00996)|Ibutilide(DB00308)|Isradipine(DB00270)|Magnesium Sulfate(DB00653)|Nifedipine(DB01115)													---	---	---	---
Unknown	0	broad.mit.edu	37	7	88141302	88141302	+	IGR	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:88141302delT								STEAP4 (205093 upstream) : ZNF804B (247451 downstream)																																			---	---	---	---
C7orf64	84060	broad.mit.edu	37	7	92166147	92166147	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:92166147delT	uc003ulz.2	+						C7orf64_uc003uma.2_3'UTR|MGC16142_uc011khv.1_5'Flank	NM_032120	NP_115496			hypothetical protein LOC84060								nucleotide binding			ovary(2)	2																		---	---	---	---
FAM133B	257415	broad.mit.edu	37	7	92208639	92208639	+	Frame_Shift_Del	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:92208639delT	uc003umc.2	-	3	294	c.193delA	c.(193-195)ATGfs	p.M65fs	FAM133B_uc003umb.2_Frame_Shift_Del_p.M55fs|FAM133B_uc003umd.2_RNA	NM_152789	NP_690002	Q5BKY9	F133B_HUMAN	hypothetical protein LOC257415 isoform 1	65	Lys-rich.									ovary(1)	1	all_cancers(62;7.39e-11)|all_epithelial(64;7.03e-10)|Breast(17;0.00201)|all_lung(186;0.0384)|Lung NSC(181;0.053)|all_hematologic(106;0.237)		STAD - Stomach adenocarcinoma(4;6.16e-07)|GBM - Glioblastoma multiforme(5;9.78e-06)|all cancers(6;1.67e-05)|Epithelial(20;0.113)|LUSC - Lung squamous cell carcinoma(200;0.225)|Lung(22;0.23)															---	---	---	---
TRRAP	8295	broad.mit.edu	37	7	98491664	98491664	+	Intron	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:98491664delA	uc003upp.2	+						TRRAP_uc011kis.1_Intron	NM_003496	NP_003487			transformation/transcription domain-associated						histone deubiquitination|histone H2A acetylation|histone H4 acetylation|regulation of transcription, DNA-dependent|transcription, DNA-dependent	NuA4 histone acetyltransferase complex|PCAF complex|STAGA complex|transcription factor TFTC complex	phosphotransferase activity, alcohol group as acceptor|protein binding|transcription cofactor activity			ovary(9)|large_intestine(8)|central_nervous_system(6)|skin(6)|stomach(5)|upper_aerodigestive_tract(1)|lung(1)|liver(1)	37	all_cancers(62;6.96e-09)|all_epithelial(64;4.86e-09)|Lung NSC(181;0.01)|all_lung(186;0.016)|Esophageal squamous(72;0.0274)		STAD - Stomach adenocarcinoma(171;0.215)															---	---	---	---
TRRAP	8295	broad.mit.edu	37	7	98513649	98513649	+	Intron	DEL	C	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:98513649delC	uc003upp.2	+						TRRAP_uc011kis.1_Intron|TRRAP_uc003upr.2_Intron	NM_003496	NP_003487			transformation/transcription domain-associated						histone deubiquitination|histone H2A acetylation|histone H4 acetylation|regulation of transcription, DNA-dependent|transcription, DNA-dependent	NuA4 histone acetyltransferase complex|PCAF complex|STAGA complex|transcription factor TFTC complex	phosphotransferase activity, alcohol group as acceptor|protein binding|transcription cofactor activity			ovary(9)|large_intestine(8)|central_nervous_system(6)|skin(6)|stomach(5)|upper_aerodigestive_tract(1)|lung(1)|liver(1)	37	all_cancers(62;6.96e-09)|all_epithelial(64;4.86e-09)|Lung NSC(181;0.01)|all_lung(186;0.016)|Esophageal squamous(72;0.0274)		STAD - Stomach adenocarcinoma(171;0.215)															---	---	---	---
TRRAP	8295	broad.mit.edu	37	7	98533362	98533362	+	Intron	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:98533362delA	uc003upp.2	+						TRRAP_uc011kis.1_Intron|TRRAP_uc003upr.2_Intron	NM_003496	NP_003487			transformation/transcription domain-associated						histone deubiquitination|histone H2A acetylation|histone H4 acetylation|regulation of transcription, DNA-dependent|transcription, DNA-dependent	NuA4 histone acetyltransferase complex|PCAF complex|STAGA complex|transcription factor TFTC complex	phosphotransferase activity, alcohol group as acceptor|protein binding|transcription cofactor activity			ovary(9)|large_intestine(8)|central_nervous_system(6)|skin(6)|stomach(5)|upper_aerodigestive_tract(1)|lung(1)|liver(1)	37	all_cancers(62;6.96e-09)|all_epithelial(64;4.86e-09)|Lung NSC(181;0.01)|all_lung(186;0.016)|Esophageal squamous(72;0.0274)		STAD - Stomach adenocarcinoma(171;0.215)															---	---	---	---
TAF6	6878	broad.mit.edu	37	7	99710906	99710906	+	Intron	DEL	A	-	-	rs75828513		TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:99710906delA	uc003uti.2	-						TAF6_uc003utg.2_Intron|TAF6_uc003uth.2_Intron|TAF6_uc003utk.2_Intron|TAF6_uc011kji.1_Intron|TAF6_uc003utj.2_Intron|TAF6_uc003utl.2_Intron|TAF6_uc003utm.2_Intron|TAF6_uc003utn.1_Intron	NM_139315	NP_647476			TBP-associated factor 6 isoform alpha						negative regulation of cell cycle|negative regulation of cell proliferation|regulation of sequence-specific DNA binding transcription factor activity|transcription elongation from RNA polymerase II promoter|transcription initiation from RNA polymerase II promoter|viral reproduction	cytoplasm|MLL1 complex|transcription factor TFIID complex|transcription factor TFIID complex|transcription factor TFTC complex	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity			ovary(1)|central_nervous_system(1)	2	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)																	---	---	---	---
AGFG2	3268	broad.mit.edu	37	7	100146315	100146315	+	Intron	DEL	G	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:100146315delG	uc003uvf.2	+						AGFG2_uc003uvg.1_Intron|AGFG2_uc010lgy.2_5'Flank	NM_006076	NP_006067			ArfGAP with FG repeats 2						regulation of ARF GTPase activity		ARF GTPase activator activity|zinc ion binding			central_nervous_system(1)	1																		---	---	---	---
SLC26A5	375611	broad.mit.edu	37	7	103015124	103015124	+	Intron	DEL	T	-	-	rs72245175		TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:103015124delT	uc003vbz.2	-						SLC26A5_uc003vbt.1_Intron|SLC26A5_uc003vbu.1_Intron|SLC26A5_uc003vbv.1_Intron|SLC26A5_uc003vbw.2_Intron|SLC26A5_uc003vbx.2_Intron|SLC26A5_uc003vby.2_Intron|SLC26A5_uc010liy.2_Intron	NM_198999	NP_945350			prestin isoform a						regulation of cell shape|sensory perception of sound	integral to membrane	secondary active sulfate transmembrane transporter activity			ovary(1)	1																		---	---	---	---
LHFPL3	375612	broad.mit.edu	37	7	103969195	103969200	+	5'UTR	DEL	AGGAGG	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:103969195_103969200delAGGAGG	uc003vce.2	+	1					LHFPL3_uc003vcf.2_5'UTR	NM_199000	NP_945351			lipoma HMGIC fusion partner-like 3							integral to membrane					0																		---	---	---	---
CBLL1	79872	broad.mit.edu	37	7	107389307	107389307	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:107389307delT	uc003veq.2	+						CBLL1_uc011kme.1_Intron|CBLL1_uc011kmf.1_Intron	NM_024814	NP_079090			Cas-Br-M (murine) ecotropic retroviral						cell-cell adhesion|negative regulation of cell adhesion|positive regulation of cell migration|positive regulation of endocytosis		protein binding|ubiquitin-protein ligase activity|zinc ion binding			ovary(2)|skin(2)|lung(1)	5																		---	---	---	---
IFRD1	3475	broad.mit.edu	37	7	112112570	112112570	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:112112570delT	uc003vgh.2	+						IFRD1_uc011kmn.1_Intron|IFRD1_uc003vgj.2_Intron|IFRD1_uc011kmo.1_Intron|IFRD1_uc011kmp.1_Intron|IFRD1_uc003vgk.2_Intron	NM_001007245	NP_001007246			interferon-related developmental regulator 1						multicellular organismal development|myoblast cell fate determination		binding			kidney(1)|central_nervous_system(1)	2																		---	---	---	---
FAM3C	10447	broad.mit.edu	37	7	121022812	121022812	+	Intron	DEL	A	-	-	rs77488516		TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:121022812delA	uc003vjx.2	-						FAM3C_uc010lkm.2_Intron	NM_014888	NP_055703			family with sequence similarity 3, member C						multicellular organismal development	cytoplasmic membrane-bounded vesicle|extracellular region	cytokine activity				0	all_neural(327;0.117)																	---	---	---	---
AASS	10157	broad.mit.edu	37	7	121738971	121738971	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:121738971delT	uc003vka.2	-						AASS_uc011knu.1_Intron|AASS_uc011knv.1_Intron|AASS_uc003vkb.2_Intron|AASS_uc011knw.1_Intron	NM_005763	NP_005754			aminoadipate-semialdehyde synthase precursor						protein tetramerization	mitochondrial matrix	binding|saccharopine dehydrogenase (NAD+, L-glutamate-forming) activity|saccharopine dehydrogenase (NADP+, L-lysine-forming) activity			upper_aerodigestive_tract(1)|ovary(1)	2					L-Glutamic Acid(DB00142)|NADH(DB00157)													---	---	---	---
SLC13A1	6561	broad.mit.edu	37	7	122811637	122811637	+	Intron	DEL	T	-	-	rs147641390	by1000genomes	TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:122811637delT	uc003vkm.2	-						SLC13A1_uc010lks.2_Intron	NM_022444	NP_071889			solute carrier family 13 (sodium/sulfate							integral to membrane|plasma membrane	sodium:sulfate symporter activity			ovary(2)	2					Succinic acid(DB00139)													---	---	---	---
IMPDH1	3614	broad.mit.edu	37	7	128043613	128043615	+	Intron	DEL	AAA	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:128043613_128043615delAAA	uc011kol.1	-						IMPDH1_uc011kom.1_Intron|IMPDH1_uc003vmt.2_Intron|IMPDH1_uc003vmu.2_Intron|IMPDH1_uc003vmw.2_Intron|IMPDH1_uc011kon.1_Intron|IMPDH1_uc003vmv.2_Intron|IMPDH1_uc003vmx.2_Intron|IMPDH1_uc003vmy.2_Intron	NM_001142573	NP_001136045			inosine monophosphate dehydrogenase 1 isoform e						GMP biosynthetic process|purine base metabolic process	cytosol|nucleus	DNA binding|IMP dehydrogenase activity|metal ion binding			skin(2)|lung(1)|central_nervous_system(1)	4					Mycophenolate mofetil(DB00688)|Mycophenolic acid(DB01024)|NADH(DB00157)|Ribavirin(DB00811)|Thioguanine(DB00352)													---	---	---	---
CPA2	1358	broad.mit.edu	37	7	129922051	129922052	+	Intron	INS	-	T	T			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:129922051_129922052insT	uc003vpq.2	+							NM_001869	NP_001860			carboxypeptidase A2 (pancreatic) precursor						proteolysis|vacuolar protein catabolic process	extracellular region|vacuole	metallocarboxypeptidase activity|zinc ion binding			ovary(1)	1	Melanoma(18;0.0435)																	---	---	---	---
DGKI	9162	broad.mit.edu	37	7	137341101	137341101	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:137341101delT	uc003vtt.2	-						DGKI_uc003vtu.2_Intron	NM_004717	NP_004708			diacylglycerol kinase, iota						activation of protein kinase C activity by G-protein coupled receptor protein signaling pathway|intracellular signal transduction|platelet activation	nucleus|plasma membrane	ATP binding|diacylglycerol kinase activity|metal ion binding			ovary(1)|kidney(1)|skin(1)	3																OREG0018350	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
CUL1	8454	broad.mit.edu	37	7	148486619	148486620	+	Intron	DEL	CT	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:148486619_148486620delCT	uc010lpg.2	+						CUL1_uc003wey.2_Intron|CUL1_uc003wez.2_Intron|CUL1_uc003wfa.2_Intron	NM_003592	NP_003583			cullin 1						anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|cell cycle arrest|G1/S transition of mitotic cell cycle|induction of apoptosis by intracellular signals|interspecies interaction between organisms|negative regulation of cell proliferation|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|protein ubiquitination|S phase of mitotic cell cycle|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process	cytosol|nucleoplasm|SCF ubiquitin ligase complex	ubiquitin protein ligase binding			lung(1)	1	Melanoma(164;0.15)		OV - Ovarian serous cystadenocarcinoma(82;0.00291)															---	---	---	---
CSMD1	64478	broad.mit.edu	37	8	2799865	2799865	+	Intron	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:2799865delA	uc011kwk.1	-						CSMD1_uc011kwj.1_Intron|CSMD1_uc010lrg.2_Intron	NM_033225	NP_150094			CUB and Sushi multiple domains 1 precursor							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)														---	---	---	---
ADHFE1	137872	broad.mit.edu	37	8	67369551	67369552	+	Intron	INS	-	A	A	rs148427504		TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:67369551_67369552insA	uc003xwb.3	+						ADHFE1_uc003xwd.3_Intron|ADHFE1_uc003xwc.3_Intron|ADHFE1_uc003xwe.3_Intron|ADHFE1_uc003xwf.3_Intron|ADHFE1_uc011les.1_Intron	NM_144650	NP_653251			alcohol dehydrogenase, iron containing, 1						2-oxoglutarate metabolic process|molecular hydrogen transport	mitochondrial matrix	hydroxyacid-oxoacid transhydrogenase activity|metal ion binding			ovary(1)|lung(1)|breast(1)|skin(1)	4		Lung NSC(129;0.197)	Epithelial(68;0.0321)|all cancers(69;0.0751)|BRCA - Breast invasive adenocarcinoma(89;0.0855)|OV - Ovarian serous cystadenocarcinoma(28;0.226)															---	---	---	---
ARFGEF1	10565	broad.mit.edu	37	8	68189370	68189370	+	Intron	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:68189370delA	uc003xxo.1	-							NM_006421	NP_006412			brefeldin A-inhibited guanine						exocytosis|regulation of ARF protein signal transduction	cytoplasm	ARF guanyl-nucleotide exchange factor activity|myosin binding			ovary(4)|upper_aerodigestive_tract(1)|large_intestine(1)|lung(1)|kidney(1)	8	Breast(64;0.214)	Lung NSC(129;0.0908)|all_lung(136;0.152)	Epithelial(68;0.0043)|OV - Ovarian serous cystadenocarcinoma(28;0.00578)|all cancers(69;0.0173)|BRCA - Breast invasive adenocarcinoma(89;0.206)															---	---	---	---
TMEM64	169200	broad.mit.edu	37	8	91637754	91637755	+	3'UTR	DEL	AA	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:91637754_91637755delAA	uc003yen.2	-	3					TMEM64_uc003yeo.2_3'UTR|TMEM64_uc011lgf.1_3'UTR	NM_001008495	NP_001008495			transmembrane protein 64 isoform 1							integral to membrane					0			BRCA - Breast invasive adenocarcinoma(11;0.0598)															---	---	---	---
RBM12B	389677	broad.mit.edu	37	8	94745548	94745548	+	3'UTR	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:94745548delA	uc003yfz.2	-	3						NM_203390	NP_976324			RNA binding motif protein 12B								nucleotide binding|RNA binding				0	Breast(36;4.14e-07)		BRCA - Breast invasive adenocarcinoma(8;0.0168)															---	---	---	---
TMEM67	91147	broad.mit.edu	37	8	94798301	94798301	+	Intron	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:94798301delA	uc011lgk.1	+						TMEM67_uc010mat.1_Intron|TMEM67_uc010maw.2_Intron|TMEM67_uc003yga.3_Intron	NM_153704	NP_714915			meckelin isoform 1						cilium assembly|ER-associated protein catabolic process|negative regulation of centrosome duplication	centrosome|cilium membrane|cytoplasmic vesicle membrane|endoplasmic reticulum membrane|integral to membrane|microtubule basal body	unfolded protein binding			ovary(2)	2	Breast(36;4.14e-07)		BRCA - Breast invasive adenocarcinoma(8;0.00896)															---	---	---	---
TATDN1	83940	broad.mit.edu	37	8	125507787	125507787	+	Intron	DEL	A	-	-	rs35308504		TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:125507787delA	uc003yrd.2	-						TATDN1_uc003yre.2_Intron|TATDN1_uc010mdm.2_Intron|TATDN1_uc003yrf.2_Intron	NM_032026	NP_114415			TatD DNase domain containing 1 isoform a							nucleus	endodeoxyribonuclease activity, producing 5'-phosphomonoesters|metal ion binding				0	Ovarian(258;0.00438)|all_neural(195;0.0779)|Hepatocellular(40;0.108)		STAD - Stomach adenocarcinoma(47;0.00288)															---	---	---	---
EEF1D	1936	broad.mit.edu	37	8	144668488	144668488	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:144668488delT	uc011lki.1	-						EEF1D_uc003yyp.1_Intron|EEF1D_uc003yyq.1_Intron|EEF1D_uc011lkj.1_Intron|EEF1D_uc003yyr.2_Intron|EEF1D_uc003yyt.2_Intron|EEF1D_uc011lkk.1_Intron|EEF1D_uc003yys.2_Intron|EEF1D_uc003yyv.2_Intron|EEF1D_uc003yyu.2_Intron|EEF1D_uc011lkl.1_Intron	NM_001130057	NP_001123529			eukaryotic translation elongation factor 1 delta						positive regulation of I-kappaB kinase/NF-kappaB cascade	cytosol|eukaryotic translation elongation factor 1 complex	protein binding|signal transducer activity|translation elongation factor activity			ovary(1)|kidney(1)|skin(1)	3	all_cancers(97;3.74e-11)|all_epithelial(106;2.62e-09)|Lung NSC(106;0.00013)|all_lung(105;0.000374)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		Colorectal(110;0.134)|BRCA - Breast invasive adenocarcinoma(115;0.239)															---	---	---	---
GLDC	2731	broad.mit.edu	37	9	6553326	6553326	+	Intron	DEL	C	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:6553326delC	uc003zkc.2	-							NM_000170	NP_000161			glycine dehydrogenase (decarboxylating)						glycine catabolic process	mitochondrion	electron carrier activity|glycine dehydrogenase (decarboxylating) activity|lyase activity|pyridoxal phosphate binding			ovary(2)	2		Acute lymphoblastic leukemia(23;0.161)		GBM - Glioblastoma multiforme(50;0.0421)|Lung(218;0.134)	Glycine(DB00145)|Pyridoxal Phosphate(DB00114)													---	---	---	---
IFNA14	3448	broad.mit.edu	37	9	21217459	21217459	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:21217459delT	uc003zoo.1	-						IFNA16_uc003zor.1_5'Flank	NM_002172				interferon, alpha 14 precursor						blood coagulation|regulation of type I interferon-mediated signaling pathway|response to virus|type I interferon-mediated signaling pathway	extracellular space	cytokine activity|cytokine receptor binding				0				Lung(24;2.12e-22)|LUSC - Lung squamous cell carcinoma(38;1.4e-13)														---	---	---	---
TEK	7010	broad.mit.edu	37	9	27204705	27204706	+	Intron	INS	-	A	A	rs28376331	by1000genomes	TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:27204705_27204706insA	uc003zqi.3	+						TEK_uc011lno.1_Intron|TEK_uc011lnp.1_Intron|TEK_uc003zqj.1_Intron	NM_000459	NP_000450			TEK tyrosine kinase, endothelial precursor						angiogenesis|blood coagulation|cell-cell signaling|leukocyte migration|positive regulation of ERK1 and ERK2 cascade|positive regulation of protein kinase B signaling cascade|protein oligomerization|transmembrane receptor protein tyrosine kinase signaling pathway	apical plasma membrane|basolateral plasma membrane|cell surface|integral to plasma membrane|membrane raft|microvillus	ATP binding|protein binding|transmembrane receptor protein tyrosine kinase activity			ovary(3)|central_nervous_system(3)|breast(3)|lung(2)|kidney(1)	12		all_neural(11;7.57e-10)|Myeloproliferative disorder(762;0.0255)		Lung(218;4.08e-05)|LUSC - Lung squamous cell carcinoma(38;0.00027)														---	---	---	---
Unknown	0	broad.mit.edu	37	9	30774794	30774794	+	IGR	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:30774794delA								None (None upstream) : None (None downstream)																																			---	---	---	---
KIF24	347240	broad.mit.edu	37	9	34223921	34223922	+	Intron	INS	-	T	T	rs144735597	by1000genomes	TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:34223921_34223922insT	uc010mkb.2	-						UBAP1_uc010mka.1_Intron|UBAP1_uc003ztx.2_Intron|UBAP1_uc003zty.2_Intron|UBAP1_uc011loi.1_Intron|UBAP1_uc011loj.1_Intron|UBAP1_uc003ztz.2_Intron	NM_194313	NP_919289			kinesin family member 24						microtubule-based movement	cytoplasm|microtubule	ATP binding|microtubule motor activity			central_nervous_system(1)	1			LUSC - Lung squamous cell carcinoma(29;0.0107)															---	---	---	---
DNAJB5	25822	broad.mit.edu	37	9	34997369	34997369	+	3'UTR	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:34997369delA	uc003zvt.2	+	4					DNAJB5_uc003zvs.2_3'UTR|DNAJB5_uc011los.1_3'UTR	NM_012266	NP_036398			DnaJ (Hsp40) homolog, subfamily B, member 5						protein folding|response to unfolded protein		heat shock protein binding|unfolded protein binding				0			LUSC - Lung squamous cell carcinoma(32;0.00575)															---	---	---	---
Unknown	0	broad.mit.edu	37	9	69845788	69845788	+	IGR	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:69845788delT								LOC100133920 (180839 upstream) : FOXD4L5 (329921 downstream)																																			---	---	---	---
ALDH1A1	216	broad.mit.edu	37	9	75533865	75533865	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:75533865delT	uc004ajd.2	-						ALDH1A1_uc011lsh.1_Intron|ALDH1A1_uc011lsg.1_Intron	NM_000689	NP_000680			aldehyde dehydrogenase 1A1						cellular aldehyde metabolic process|ethanol oxidation|xenobiotic metabolic process	cytosol	aldehyde dehydrogenase (NAD) activity|androgen binding|Ras GTPase activator activity|retinal dehydrogenase activity			ovary(3)|lung(1)	4					NADH(DB00157)|Tretinoin(DB00755)|Vitamin A(DB00162)													---	---	---	---
PCSK5	5125	broad.mit.edu	37	9	78799576	78799576	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:78799576delT	uc004ajz.2	+						PCSK5_uc004aka.2_Intron|PCSK5_uc004akb.2_Intron	NM_006200	NP_006191			proprotein convertase subtilisin/kexin type 5						anterior/posterior pattern formation|cell-cell signaling|cytokine biosynthetic process|embryo implantation|embryonic digestive tract development|embryonic skeletal system development|heart development|kidney development|limb morphogenesis|nerve growth factor processing|nerve growth factor receptor signaling pathway|peptide biosynthetic process|renin secretion into blood stream|respiratory tube development|signal peptide processing|viral assembly, maturation, egress, and release	extracellular space|Golgi lumen|stored secretory granule	peptide binding|serine-type endopeptidase activity			ovary(2)|skin(1)	3																		---	---	---	---
HIATL2	84278	broad.mit.edu	37	9	99734982	99734983	+	Intron	DEL	AA	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:99734982_99734983delAA	uc004aws.2	-						HIATL2_uc004awr.1_Intron	NR_002894				RecName: Full=Hippocampus abundant transcript-like protein 2;												0																		---	---	---	---
PPP6C	5537	broad.mit.edu	37	9	127911822	127911822	+	3'UTR	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:127911822delA	uc004bpg.3	-	7					PPP6C_uc010mwv.2_3'UTR|PPP6C_uc010mww.2_3'UTR|PPP6C_uc011lzr.1_3'UTR	NM_002721	NP_002712			protein phosphatase 6, catalytic subunit isoform						G1/S transition of mitotic cell cycle|protein dephosphorylation	cytosol	metal ion binding|protein binding|protein serine/threonine phosphatase activity			ovary(1)|skin(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	9	127957481	127957481	+	IGR	DEL	A	-	-	rs79479616		TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:127957481delA								PPP6C (5263 upstream) : RABEPK (5336 downstream)																																			---	---	---	---
ZBTB43	23099	broad.mit.edu	37	9	129596298	129596298	+	3'UTR	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:129596298delA	uc004bql.2	+	3					ZBTB43_uc010mxf.2_3'UTR	NM_014007	NP_054726			zinc finger and BTB domain containing 43						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1																		---	---	---	---
CERCAM	51148	broad.mit.edu	37	9	131187045	131187046	+	Intron	DEL	TT	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:131187045_131187046delTT	uc004buz.3	+						CERCAM_uc004buy.1_Intron|CERCAM_uc010mxz.2_Intron|CERCAM_uc010mya.1_Intron	NM_016174	NP_057258			cerebral endothelial cell adhesion molecule 1						cellular component movement|leukocyte cell-cell adhesion|lipopolysaccharide biosynthetic process	endoplasmic reticulum lumen|plasma membrane				pancreas(1)	1																		---	---	---	---
BAT2L1	84726	broad.mit.edu	37	9	134322056	134322056	+	Intron	DEL	C	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:134322056delC	uc004can.3	+						BAT2L1_uc010mzj.1_5'Flank|BAT2L1_uc004cam.1_Intron	NM_013318	NP_037450			HLA-B associated transcript 2-like								protein binding				0																		---	---	---	---
C9orf96	169436	broad.mit.edu	37	9	136268193	136268193	+	Intron	DEL	C	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:136268193delC	uc004cdk.2	+						C9orf96_uc004cdl.2_Intron	NM_153710	NP_714921			hypothetical protein LOC169436								ATP binding|protein kinase activity			stomach(2)|central_nervous_system(2)	4				OV - Ovarian serous cystadenocarcinoma(145;1.06e-07)|Epithelial(140;1.28e-06)|all cancers(34;1.46e-05)														---	---	---	---
ITGA8	8516	broad.mit.edu	37	10	15719443	15719443	+	Intron	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:15719443delA	uc001ioc.1	-						ITGA8_uc010qcb.1_Intron	NM_003638	NP_003629			integrin, alpha 8 precursor						cell differentiation|cell-cell adhesion|cell-matrix adhesion|integrin-mediated signaling pathway|nervous system development	integrin complex	receptor activity			ovary(3)|lung(3)	6																		---	---	---	---
FAM188A	80013	broad.mit.edu	37	10	15883640	15883640	+	Intron	DEL	A	-	-	rs111629424		TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:15883640delA	uc001iod.1	-						FAM188A_uc001ioe.1_Intron|FAM188A_uc001iof.1_Intron	NM_024948	NP_079224			chromosome 10 open reading frame 97						apoptosis	nucleus	calcium ion binding			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	10	19341155	19341155	+	IGR	DEL	C	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:19341155delC								ARL5B (374215 upstream) : PLXDC2 (764217 downstream)																																			---	---	---	---
CCAR1	55749	broad.mit.edu	37	10	70515996	70515996	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:70515996delT	uc001joo.2	+						CCAR1_uc001jol.1_Intron|CCAR1_uc001jom.1_Intron|CCAR1_uc009xpx.1_Intron|CCAR1_uc001jon.1_Intron|CCAR1_uc010qiz.1_Intron|CCAR1_uc010qja.1_Intron|CCAR1_uc010qjb.1_Intron	NM_018237	NP_060707			cell-cycle and apoptosis regulatory protein 1						apoptosis|cell cycle|nuclear mRNA splicing, via spliceosome|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleoplasm|perinuclear region of cytoplasm	calcium ion binding|nucleic acid binding|protein binding			ovary(6)|large_intestine(1)	7																		---	---	---	---
ASCC1	51008	broad.mit.edu	37	10	73887716	73887716	+	Intron	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:73887716delA	uc001jst.1	-						ASCC1_uc001jsr.1_Intron|ASCC1_uc001jss.1_Intron|ASCC1_uc001jsu.1_Intron|ASCC1_uc010qju.1_Intron					RecName: Full=Activating signal cointegrator 1 complex subunit 1; AltName: Full=ASC-1 complex subunit p50; AltName: Full=Trip4 complex subunit p50;						regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|transcription factor complex	RNA binding				0																		---	---	---	---
RNLS	55328	broad.mit.edu	37	10	90034668	90034668	+	3'UTR	DEL	A	-	-	rs113106989		TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:90034668delA	uc001kfd.2	-	7					RNLS_uc010qms.1_Intron	NM_018363	NP_060833			renalase isoform 2							extracellular region	oxidoreductase activity			ovary(1)	1																		---	---	---	---
STAMBPL1	57559	broad.mit.edu	37	10	90672691	90672691	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:90672691delT	uc001kfk.2	+						STAMBPL1_uc010qmx.1_Intron|STAMBPL1_uc009xto.2_Intron|STAMBPL1_uc001kfl.2_Intron|STAMBPL1_uc001kfn.2_5'UTR	NM_020799	NP_065850			STAM binding protein-like 1								metal ion binding|metallopeptidase activity|protein binding			ovary(1)	1		Colorectal(252;0.0381)		Colorectal(12;6.38e-05)|COAD - Colon adenocarcinoma(12;7.75e-05)														---	---	---	---
BTAF1	9044	broad.mit.edu	37	10	93741213	93741213	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:93741213delT	uc001khr.2	+						BTAF1_uc001khs.1_Intron|BTAF1_uc001kht.1_Intron	NM_003972	NP_003963			BTAF1 RNA polymerase II, B-TFIID transcription						negative regulation of transcription, DNA-dependent	nucleus	ATP binding|DNA binding|helicase activity|sequence-specific DNA binding transcription factor activity			ovary(1)|central_nervous_system(1)|skin(1)	3		Colorectal(252;0.0846)																---	---	---	---
BTAF1	9044	broad.mit.edu	37	10	93741816	93741816	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:93741816delT	uc001khr.2	+						BTAF1_uc001khs.1_Intron|BTAF1_uc001kht.1_Intron	NM_003972	NP_003963			BTAF1 RNA polymerase II, B-TFIID transcription						negative regulation of transcription, DNA-dependent	nucleus	ATP binding|DNA binding|helicase activity|sequence-specific DNA binding transcription factor activity			ovary(1)|central_nervous_system(1)|skin(1)	3		Colorectal(252;0.0846)																---	---	---	---
KIF11	3832	broad.mit.edu	37	10	94396790	94396793	+	Intron	DEL	AAAA	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:94396790_94396793delAAAA	uc001kic.2	+						KIF11_uc010qnq.1_Intron	NM_004523	NP_004514			kinesin family member 11						blood coagulation|cell division|microtubule-based movement|spindle assembly involved in mitosis	chromatin remodeling complex|cytosol|kinesin complex|microtubule|spindle pole	ATP binding|microtubule motor activity|protein kinase binding			skin(1)	1																		---	---	---	---
HELLS	3070	broad.mit.edu	37	10	96313731	96313731	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:96313731delT	uc001kjt.2	+						HELLS_uc001kjs.2_Intron|HELLS_uc009xul.2_Intron|HELLS_uc009xum.2_Intron|HELLS_uc009xun.2_Intron|HELLS_uc009xuo.2_Intron|HELLS_uc001kju.2_Intron|HELLS_uc009xup.2_Intron|HELLS_uc009xuq.2_Intron|HELLS_uc009xur.2_Intron	NM_018063	NP_060533			helicase, lymphoid-specific						cell division|centromeric heterochromatin formation|lymphocyte proliferation|maintenance of DNA methylation|methylation-dependent chromatin silencing|mitosis|transcription, DNA-dependent	centromeric heterochromatin|nucleus	ATP binding|DNA binding|helicase activity			ovary(1)|kidney(1)	2		Colorectal(252;0.0429)		all cancers(201;2.13e-05)														---	---	---	---
SORBS1	10580	broad.mit.edu	37	10	97127476	97127476	+	Intron	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:97127476delA	uc001kkp.2	-						SORBS1_uc001kkk.2_Intron|SORBS1_uc001kkl.2_Intron|SORBS1_uc001kkn.2_Intron|SORBS1_uc001kkm.2_Intron|SORBS1_uc001kko.2_Intron|SORBS1_uc001kkq.2_Intron|SORBS1_uc001kkr.2_Intron|SORBS1_uc001kks.2_Intron|SORBS1_uc001kkt.2_Intron|SORBS1_uc001kku.2_Intron|SORBS1_uc001kkv.2_Intron|SORBS1_uc001kkw.2_Intron|SORBS1_uc010qoe.1_Intron|SORBS1_uc010qof.1_Intron	NM_001034954	NP_001030126			sorbin and SH3 domain containing 1 isoform 3						focal adhesion assembly|glucose transport|insulin receptor signaling pathway|muscle contraction|positive regulation of establishment of protein localization in plasma membrane|positive regulation of glucose import|positive regulation of glycogen biosynthetic process|positive regulation of lipid biosynthetic process|stress fiber assembly	centrosome|cytosol|focal adhesion|membrane raft|nucleus|stress fiber|zonula adherens	actin binding|insulin receptor binding|SH3/SH2 adaptor activity			breast(1)	1		Colorectal(252;0.0429)		Epithelial(162;1.7e-06)|all cancers(201;6.52e-05)														---	---	---	---
ENTPD7	57089	broad.mit.edu	37	10	101462505	101462505	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:101462505delT	uc001kqa.3	+						ENTPD7_uc009xwl.2_Intron	NM_020354	NP_065087			ectonucleoside triphosphate diphosphohydrolase							cytoplasmic vesicle membrane|integral to membrane	hydrolase activity			ovary(1)	1		Colorectal(252;0.234)		Epithelial(162;4.72e-10)|all cancers(201;3.75e-08)														---	---	---	---
BTBD16	118663	broad.mit.edu	37	10	124057386	124057387	+	Intron	INS	-	G	G			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:124057386_124057387insG	uc001lgc.1	+						BTBD16_uc001lgd.1_Intron	NM_144587	NP_653188			BTB (POZ) domain containing 16											skin(1)	1		all_neural(114;0.107)|Lung NSC(174;0.175)|all_lung(145;0.222)|Breast(234;0.238)																---	---	---	---
B4GALNT4	338707	broad.mit.edu	37	11	379842	379842	+	Intron	DEL	C	-	-	rs72431160		TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:379842delC	uc001lpb.2	+							NM_178537	NP_848632			beta							Golgi cisterna membrane|integral to membrane	N-acetyl-beta-glucosaminyl-glycoprotein 4-beta-N-acetylgalactosaminyltransferase activity			pancreas(1)	1		all_cancers(49;1.59e-06)|all_epithelial(84;0.000256)|Breast(177;0.00122)|Ovarian(85;0.0228)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762)		all cancers(45;1.56e-27)|Epithelial(43;9.31e-27)|OV - Ovarian serous cystadenocarcinoma(40;1.11e-20)|BRCA - Breast invasive adenocarcinoma(625;3.56e-05)|Lung(200;0.0182)|LUSC - Lung squamous cell carcinoma(625;0.0703)														---	---	---	---
IRF7	3665	broad.mit.edu	37	11	613181	613181	+	Intron	DEL	C	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:613181delC	uc001lqh.2	-						IRF7_uc009ycb.2_Intron|IRF7_uc010qwf.1_Intron|IRF7_uc001lqf.2_Intron|IRF7_uc010qwg.1_Intron|IRF7_uc001lqg.2_Intron|IRF7_uc001lqi.2_Intron|IRF7_uc010qwh.1_Intron	NM_001572	NP_001563			interferon regulatory factor 7 isoform a						interferon-gamma-mediated signaling pathway|interspecies interaction between organisms|MyD88-independent toll-like receptor signaling pathway|negative regulation of transcription from RNA polymerase II promoter|positive regulation of interferon-alpha production|positive regulation of transcription from RNA polymerase II promoter|response to virus|Toll signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway|transcription from RNA polymerase II promoter|type I interferon-mediated signaling pathway	cytosol|endosome membrane|nucleoplasm|plasma membrane	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity				0		all_cancers(49;1.69e-08)|all_epithelial(84;1.65e-05)|Breast(177;0.000231)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.106)|all_lung(207;0.136)		all cancers(45;7.68e-28)|Epithelial(43;7.44e-27)|OV - Ovarian serous cystadenocarcinoma(40;3.53e-21)|BRCA - Breast invasive adenocarcinoma(625;6.96e-05)|Lung(200;0.0375)|LUSC - Lung squamous cell carcinoma(625;0.0703)														---	---	---	---
TSPAN4	7106	broad.mit.edu	37	11	865495	865495	+	Intron	DEL	C	-	-	rs61614113	by1000genomes	TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:865495delC	uc001lsd.1	+						TSPAN4_uc001lse.1_Intron|TSPAN4_uc001lsf.1_Intron|TSPAN4_uc001lsg.1_Intron|TSPAN4_uc001lsh.1_Intron|TSPAN4_uc001lsi.1_Intron|TSPAN4_uc001lsj.1_Intron	NM_003271	NP_003262			tetraspanin 4 isoform a						protein complex assembly	integral to plasma membrane				breast(1)	1		all_cancers(49;2.64e-08)|all_epithelial(84;4.17e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.191)|all_lung(207;0.24)		all cancers(45;4.32e-25)|Epithelial(43;3.29e-24)|BRCA - Breast invasive adenocarcinoma(625;4.23e-05)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)														---	---	---	---
RRM1	6240	broad.mit.edu	37	11	4141256	4141256	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:4141256delT	uc001lyw.3	+						RRM1_uc009yej.2_Intron|RRM1_uc009yei.2_Intron|RRM1_uc010qyc.1_Intron|RRM1_uc010qyd.1_Intron	NM_001033	NP_001024			ribonucleoside-diphosphate reductase M1 chain						deoxyribonucleotide biosynthetic process|DNA replication|nucleobase, nucleoside and nucleotide interconversion	cytosol|nucleoplasm|ribonucleoside-diphosphate reductase complex	ATP binding|ribonucleoside-diphosphate reductase activity			skin(1)	1		Medulloblastoma(188;0.0025)|Breast(177;0.00502)|all_neural(188;0.0227)		BRCA - Breast invasive adenocarcinoma(625;0.0848)|LUSC - Lung squamous cell carcinoma(625;0.205)	Clofarabine(DB00631)|Fludarabine(DB01073)|Gemcitabine(DB00441)|Hydroxyurea(DB01005)													---	---	---	---
PAMR1	25891	broad.mit.edu	37	11	35462851	35462851	+	Intron	DEL	A	-	-	rs79736526		TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:35462851delA	uc001mwg.2	-						PAMR1_uc001mwf.2_Intron|PAMR1_uc010rew.1_Intron|PAMR1_uc010rex.1_Intron	NM_001001991	NP_001001991			regeneration associated muscle protease isoform						proteolysis	extracellular region	serine-type endopeptidase activity			ovary(2)	2																		---	---	---	---
MTCH2	23788	broad.mit.edu	37	11	47657242	47657242	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:47657242delT	uc010rho.1	-						MTCH2_uc001nge.2_Intron|MTCH2_uc010rhp.1_Intron	NM_014342	NP_055157			mitochondrial carrier 2						transport	integral to membrane|mitochondrial inner membrane					0																		---	---	---	---
Unknown	0	broad.mit.edu	37	11	55607259	55607259	+	IGR	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:55607259delA								OR5D16 (47 upstream) : SPRYD5 (43514 downstream)																																			---	---	---	---
SLC43A1	8501	broad.mit.edu	37	11	57281506	57281508	+	In_Frame_Del	DEL	AGA	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:57281506_57281508delAGA	uc001nkk.2	-	2	195_197	c.77_79delTCT	c.(76-81)TTCTCT>TCT	p.F26del	SLC43A1_uc001nkl.2_In_Frame_Del_p.F26del	NM_003627	NP_003618	O75387	LAT3_HUMAN	solute carrier family 43, member 1	26	Helical; (Potential).				cellular nitrogen compound metabolic process|ion transport	integral to plasma membrane	neutral amino acid transmembrane transporter activity				0																		---	---	---	---
MRPL16	54948	broad.mit.edu	37	11	59577490	59577490	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:59577490delT	uc001noh.2	-							NM_017840	NP_060310			mitochondrial ribosomal protein L16 precursor								rRNA binding			central_nervous_system(1)	1																		---	---	---	---
PLCB3	5331	broad.mit.edu	37	11	64032517	64032517	+	Frame_Shift_Del	DEL	C	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:64032517delC	uc001nzb.2	+	23	2747	c.2747delC	c.(2746-2748)TCCfs	p.S916fs	PLCB3_uc009ypg.1_Frame_Shift_Del_p.S916fs|PLCB3_uc009yph.1_Frame_Shift_Del_p.S849fs|PLCB3_uc009ypi.2_Frame_Shift_Del_p.S916fs	NM_000932	NP_000923	Q01970	PLCB3_HUMAN	phospholipase C beta 3	916					intracellular signal transduction|lipid catabolic process|synaptic transmission	cytosol	calcium ion binding|calmodulin binding|phosphatidylinositol phospholipase C activity|signal transducer activity			ovary(1)|pancreas(1)	2																		---	---	---	---
MALAT1	378938	broad.mit.edu	37	11	65269498	65269498	+	RNA	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:65269498delT	uc010roh.1	+	1		c.4266delT			uc001ody.2_RNA|MALAT1_uc001odz.2_5'Flank	NR_002819				Homo sapiens clone alpha1 mRNA sequence.												0																		---	---	---	---
ARHGEF17	9828	broad.mit.edu	37	11	73057889	73057889	+	Intron	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:73057889delA	uc001otu.2	+							NM_014786	NP_055601			Rho guanine nucleotide exchange factor (GEF) 17						actin cytoskeleton organization|apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol	Rho guanyl-nucleotide exchange factor activity				0																		---	---	---	---
MMP12	4321	broad.mit.edu	37	11	102737945	102737945	+	Intron	DEL	A	-	-	rs28381681		TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:102737945delA	uc001phk.2	-							NM_002426	NP_002417			matrix metalloproteinase 12 preproprotein						positive regulation of epithelial cell proliferation involved in wound healing|proteolysis|wound healing, spreading of epidermal cells	proteinaceous extracellular matrix	calcium ion binding|metalloendopeptidase activity|zinc ion binding				0		all_hematologic(158;0.00092)|Acute lymphoblastic leukemia(157;0.000967)		BRCA - Breast invasive adenocarcinoma(274;0.014)	Acetohydroxamic Acid(DB00551)													---	---	---	---
EXPH5	23086	broad.mit.edu	37	11	108412614	108412614	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:108412614delT	uc001pkk.2	-						EXPH5_uc010rwa.1_Intron	NM_015065	NP_055880			exophilin 5 isoform a						intracellular protein transport		Rab GTPase binding			skin(3)|ovary(2)	5		all_cancers(61;3.99e-08)|Acute lymphoblastic leukemia(157;3.97e-05)|Melanoma(852;4.04e-05)|all_epithelial(67;0.000116)|all_hematologic(158;0.000315)|Breast(348;0.104)|all_neural(303;0.16)		Epithelial(105;8.1e-06)|BRCA - Breast invasive adenocarcinoma(274;1.22e-05)|all cancers(92;0.000129)|OV - Ovarian serous cystadenocarcinoma(223;0.11)|Colorectal(284;0.184)														---	---	---	---
DDX10	1662	broad.mit.edu	37	11	108548163	108548163	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:108548163delT	uc001pkm.2	+						DDX10_uc001pkl.1_Intron	NM_004398	NP_004389			DEAD (Asp-Glu-Ala-Asp) box polypeptide 10								ATP binding|ATP-dependent helicase activity|RNA binding|RNA helicase activity			breast(2)|lung(1)|prostate(1)	4		all_cancers(61;1.29e-11)|all_epithelial(67;2.96e-07)|Melanoma(852;1.54e-05)|Acute lymphoblastic leukemia(157;4.24e-05)|all_hematologic(158;0.000141)|Breast(348;0.026)|all_neural(223;0.0729)		BRCA - Breast invasive adenocarcinoma(274;2.48e-05)|Epithelial(105;4.35e-05)|all cancers(92;0.000609)|OV - Ovarian serous cystadenocarcinoma(223;0.133)				T	NUP98	AML*								---	---	---	---
PPP2R1B	5519	broad.mit.edu	37	11	111623158	111623158	+	Intron	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:111623158delA	uc001plx.1	-						PPP2R1B_uc001plw.1_Intron|PPP2R1B_uc010rwi.1_Intron|PPP2R1B_uc010rwj.1_Intron|PPP2R1B_uc010rwk.1_Intron|PPP2R1B_uc010rwl.1_Intron	NM_002716	NP_002707			beta isoform of regulatory subunit A, protein								protein binding				0		all_cancers(61;2.34e-15)|all_epithelial(67;1.72e-09)|Melanoma(852;1.91e-06)|all_hematologic(158;0.000405)|Acute lymphoblastic leukemia(157;0.000967)|Breast(348;0.0112)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)		BRCA - Breast invasive adenocarcinoma(274;1.13e-06)|Epithelial(105;2.36e-06)|all cancers(92;3.78e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.0761)														---	---	---	---
IL18	3606	broad.mit.edu	37	11	112024223	112024223	+	Intron	DEL	T	-	-	rs78854082		TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:112024223delT	uc001pnb.1	-						IL18_uc001pna.1_5'Flank|IL18_uc009yym.1_Intron	NM_001562	NP_001553			interleukin 18 proprotein						angiogenesis|cell-cell signaling|chemokine biosynthetic process|granulocyte macrophage colony-stimulating factor biosynthetic process|interferon-gamma biosynthetic process|interleukin-13 biosynthetic process|interleukin-2 biosynthetic process|positive regulation of activated T cell proliferation|positive regulation of granulocyte macrophage colony-stimulating factor production|positive regulation of interferon-gamma production|positive regulation of interleukin-17 production|positive regulation of natural killer cell proliferation|positive regulation of NK T cell proliferation|regulation of cell adhesion|sleep|T-helper 1 type immune response|type 2 immune response	cytosol|extracellular space	cytokine activity|signal transducer activity				0		all_cancers(61;5.7e-14)|all_epithelial(67;3.4e-08)|Melanoma(852;8.81e-06)|all_hematologic(158;0.000405)|Acute lymphoblastic leukemia(157;0.000967)|Breast(348;0.0112)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)		BRCA - Breast invasive adenocarcinoma(274;6.72e-07)|Epithelial(105;8.15e-07)|all cancers(92;1.43e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.055)														---	---	---	---
PTS	5805	broad.mit.edu	37	11	112100752	112100752	+	Intron	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:112100752delA	uc001pnj.3	+						PTS_uc009yyo.2_Intron	NM_000317	NP_000308			6-pyruvoyltetrahydropterin synthase						cellular amino acid metabolic process|central nervous system development|tetrahydrobiopterin biosynthetic process	mitochondrion	6-pyruvoyltetrahydropterin synthase activity|metal ion binding				0		all_cancers(61;2.51e-14)|all_epithelial(67;1.64e-08)|Melanoma(852;8.81e-06)|all_hematologic(158;0.000405)|Acute lymphoblastic leukemia(157;0.000967)|Breast(348;0.0112)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)		Epithelial(105;1.27e-06)|BRCA - Breast invasive adenocarcinoma(274;1.43e-06)|all cancers(92;2.1e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.0519)														---	---	---	---
ARHGEF12	23365	broad.mit.edu	37	11	120338143	120338147	+	Intron	DEL	TTTTT	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:120338143_120338147delTTTTT	uc001pxl.1	+						ARHGEF12_uc009zat.2_Intron|ARHGEF12_uc010rzn.1_Intron|ARHGEF12_uc009zau.1_Intron	NM_015313	NP_056128			Rho guanine nucleotide exchange factor (GEF) 12						apoptosis|axon guidance|G-protein coupled receptor protein signaling pathway|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol|membrane	G-protein-coupled receptor binding|GTPase activator activity|Rho guanyl-nucleotide exchange factor activity			lung(2)|breast(2)|skin(2)|ovary(1)	7		Breast(109;0.000813)|Medulloblastoma(222;0.0425)|Hepatocellular(160;0.0831)|all_hematologic(192;0.107)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;4.88e-06)|OV - Ovarian serous cystadenocarcinoma(223;0.231)				T	MLL	AML								---	---	---	---
KDM5A	5927	broad.mit.edu	37	12	463406	463406	+	Intron	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:463406delA	uc001qif.1	-						KDM5A_uc001qie.1_Intron|KDM5A_uc010sdn.1_Intron|KDM5A_uc010sdo.1_Intron	NM_001042603	NP_001036068			retinoblastoma binding protein 2 isoform 1						chromatin modification|multicellular organismal development|positive regulation of transcription, DNA-dependent|transcription from RNA polymerase II promoter	cytoplasm|nucleolus	DNA binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|sequence-specific DNA binding transcription factor activity|zinc ion binding			skin(2)|ovary(1)	3								T 	NUP98	AML								---	---	---	---
ADIPOR2	79602	broad.mit.edu	37	12	1863751	1863751	+	Intron	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:1863751delA	uc001qjm.2	+						ADIPOR2_uc001qjn.2_Intron	NM_024551	NP_078827			adiponectin receptor 2						fatty acid oxidation|hormone-mediated signaling pathway	integral to membrane	hormone binding|receptor activity				0	Ovarian(42;0.107)		OV - Ovarian serous cystadenocarcinoma(31;0.000382)															---	---	---	---
TULP3	7289	broad.mit.edu	37	12	3046966	3046967	+	Intron	DEL	AA	-	-	rs3742080	by1000genomes	TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:3046966_3046967delAA	uc010seh.1	+						TULP3_uc009zec.1_Intron|TULP3_uc010seg.1_Intron|TULP3_uc001qlj.2_Intron|TULP3_uc010sei.1_Intron	NM_003324	NP_003315			tubby like protein 3 isoform 1						G-protein coupled receptor protein signaling pathway|regulation of transcription, DNA-dependent	cytoplasm|extracellular region|nucleus|plasma membrane	phosphatidylinositol-4,5-bisphosphate binding				0			OV - Ovarian serous cystadenocarcinoma(31;0.000818)															---	---	---	---
Unknown	0	broad.mit.edu	37	12	4218857	4218858	+	IGR	INS	-	T	T	rs113936230		TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:4218857_4218858insT								PARP11 (236249 upstream) : CCND2 (164044 downstream)																																			---	---	---	---
C12orf4	57102	broad.mit.edu	37	12	4626088	4626089	+	Intron	INS	-	A	A			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:4626088_4626089insA	uc001qms.2	-						C12orf4_uc001qmt.2_Intron	NM_020374	NP_065107			hypothetical protein LOC57102												0			Colorectal(7;0.00165)|COAD - Colon adenocarcinoma(12;0.0229)	BRCA - Breast invasive adenocarcinoma(232;0.0281)														---	---	---	---
IFFO1	25900	broad.mit.edu	37	12	6658357	6658357	+	Intron	DEL	A	-	-	rs72489368		TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:6658357delA	uc001qpd.1	-						IFFO1_uc001qoy.2_Intron|IFFO1_uc001qpa.1_5'Flank|IFFO1_uc001qpb.1_Intron|IFFO1_uc001qpe.1_Intron|IFFO1_uc010sfe.1_Intron|IFFO1_uc001qpf.1_Intron|IFFO1_uc001qoz.1_5'Flank|IFFO1_uc001qpc.1_Intron|IFFO1_uc001qpg.2_5'Flank	NM_080730	NP_542768			intermediate filament family orphan isoform 2							intermediate filament					0																		---	---	---	---
MIR1244	100302285	broad.mit.edu	37	12	9392182	9392183	+	5'Flank	INS	-	T	T			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:9392182_9392183insT	hsa-mir-1244-3|MI0015975	-						uc001qvm.1_5'Flank																	0																		---	---	---	---
PRR4	11272	broad.mit.edu	37	12	11000107	11000107	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:11000107delT	uc001qyz.3	-						PRR4_uc009zhp.2_Intron|PRH1_uc001qzb.3_Intron|PRR4_uc001qza.3_Intron	NM_007244	NP_009175			proline rich 4 (lacrimal) isoform 2						visual perception	extracellular space					0																		---	---	---	---
ATF7IP	55729	broad.mit.edu	37	12	14590987	14590987	+	Intron	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:14590987delA	uc001rbw.2	+						ATF7IP_uc010shs.1_Intron|ATF7IP_uc001rbu.2_Intron|ATF7IP_uc001rbv.1_Intron|ATF7IP_uc001rbx.2_Intron|ATF7IP_uc010sht.1_Intron|ATF7IP_uc001rby.3_Intron|ATF7IP_uc001rca.2_Intron	NM_018179	NP_060649			activating transcription factor 7 interacting						DNA methylation|interspecies interaction between organisms|positive regulation of transcription, DNA-dependent|regulation of RNA polymerase II transcriptional preinitiation complex assembly|transcription, DNA-dependent		protein binding			lung(3)|ovary(1)|skin(1)	5																		---	---	---	---
PLEKHA5	54477	broad.mit.edu	37	12	19406761	19406761	+	Intron	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:19406761delA	uc001reb.2	+						PLEKHA5_uc010sie.1_Intron|PLEKHA5_uc001rea.2_Intron|PLEKHA5_uc009zin.2_Intron|PLEKHA5_uc010sif.1_Intron|PLEKHA5_uc010sig.1_Intron|PLEKHA5_uc010sih.1_Intron	NM_019012	NP_061885			pleckstrin homology domain containing, family A								1-phosphatidylinositol binding|protein binding			ovary(1)|kidney(1)|skin(1)	3	Acute lymphoblastic leukemia(4;0.000455)|all_hematologic(4;0.00804)																	---	---	---	---
ITPR2	3709	broad.mit.edu	37	12	26877744	26877744	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:26877744delT	uc001rhg.2	-						ITPR2_uc001rhh.1_Intron|ITPR2_uc001rhi.1_Intron	NM_002223	NP_002214			inositol 1,4,5-triphosphate receptor, type 2						activation of phospholipase C activity|energy reserve metabolic process|nerve growth factor receptor signaling pathway|platelet activation|regulation of insulin secretion|response to hypoxia	integral to membrane|plasma membrane enriched fraction|platelet dense tubular network membrane|sarcoplasmic reticulum membrane	calcium ion transmembrane transporter activity|inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity			kidney(6)|ovary(4)|skin(2)|upper_aerodigestive_tract(1)|lung(1)	14	Colorectal(261;0.0847)																	---	---	---	---
DENND5B	160518	broad.mit.edu	37	12	31630952	31630952	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:31630952delT	uc001rki.1	-						DENND5B_uc001rkh.1_Intron|DENND5B_uc009zjq.1_Intron|DENND5B_uc001rkj.2_Intron|DENND5B_uc001rkk.1_Intron	NM_144973	NP_659410			DENN/MADD domain containing 5B							integral to membrane				ovary(1)|central_nervous_system(1)	2																		---	---	---	---
ADAMTS20	80070	broad.mit.edu	37	12	43820983	43820983	+	Intron	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:43820983delA	uc010skx.1	-						ADAMTS20_uc001rno.1_Intron	NM_025003	NP_079279			a disintegrin-like and metalloprotease with							proteinaceous extracellular matrix	zinc ion binding			central_nervous_system(5)|ovary(4)|lung(3)|large_intestine(2)|skin(2)|urinary_tract(1)|kidney(1)|pancreas(1)	19	all_cancers(12;2.6e-05)|Lung SC(27;0.184)	Lung NSC(34;0.0569)|all_lung(34;0.129)		GBM - Glioblastoma multiforme(48;0.0473)														---	---	---	---
ADAMTS20	80070	broad.mit.edu	37	12	43833279	43833279	+	Intron	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:43833279delA	uc010skx.1	-						ADAMTS20_uc001rno.1_Intron|ADAMTS20_uc001rnp.1_Intron	NM_025003	NP_079279			a disintegrin-like and metalloprotease with							proteinaceous extracellular matrix	zinc ion binding			central_nervous_system(5)|ovary(4)|lung(3)|large_intestine(2)|skin(2)|urinary_tract(1)|kidney(1)|pancreas(1)	19	all_cancers(12;2.6e-05)|Lung SC(27;0.184)	Lung NSC(34;0.0569)|all_lung(34;0.129)		GBM - Glioblastoma multiforme(48;0.0473)														---	---	---	---
CCNT1	904	broad.mit.edu	37	12	49086775	49086775	+	3'UTR	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:49086775delT	uc001rse.1	-	9					LOC144438_uc001rsd.3_5'Flank|CCNT1_uc009zkz.1_3'UTR	NM_001240	NP_001231			cyclin T1						cell cycle|cell division|interspecies interaction between organisms|positive regulation of viral transcription|protein phosphorylation|regulation of cyclin-dependent protein kinase activity|regulation of transcription, DNA-dependent|transcription elongation from RNA polymerase II promoter|viral reproduction	nucleoplasm	DNA binding|protein kinase binding			ovary(3)|lung(1)|breast(1)|skin(1)	6																		---	---	---	---
FKBP11	51303	broad.mit.edu	37	12	49318789	49318789	+	Intron	DEL	C	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:49318789delC	uc001rsp.2	-						FKBP11_uc010sma.1_5'Flank|FKBP11_uc001rsq.3_Intron|FKBP11_uc010smb.1_Intron	NM_016594	NP_057678			FK506 binding protein 11 isoform 1 precursor						protein folding	integral to membrane	FK506 binding|peptidyl-prolyl cis-trans isomerase activity				0																		---	---	---	---
MUCL1	118430	broad.mit.edu	37	12	55251961	55251961	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:55251961delT	uc001sgk.2	+							NM_058173	NP_477521			small breast epithelial mucin precursor							extracellular region|membrane					0																		---	---	---	---
KIF5A	3798	broad.mit.edu	37	12	57975862	57975862	+	Intron	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:57975862delA	uc001sor.1	+						KIF5A_uc010srr.1_Intron|uc001sos.2_5'Flank	NM_004984	NP_004975			kinesin family member 5A						blood coagulation|cell death|microtubule-based movement|synaptic transmission	cytosol|kinesin complex|membrane fraction|microtubule|perinuclear region of cytoplasm	ATP binding|microtubule motor activity			ovary(2)|skin(1)	3																		---	---	---	---
TSPAN8	7103	broad.mit.edu	37	12	71523013	71523013	+	Intron	DEL	T	-	-	rs112700480		TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:71523013delT	uc009zrt.1	-						TSPAN8_uc001swk.1_Intron|TSPAN8_uc001swj.1_Intron	NM_004616	NP_004607			transmembrane 4 superfamily member 3						protein glycosylation	integral to membrane|lysosome	signal transducer activity			skin(2)|lung(1)|central_nervous_system(1)	4			LUSC - Lung squamous cell carcinoma(43;0.24)|OV - Ovarian serous cystadenocarcinoma(12;0.244)															---	---	---	---
CEP290	80184	broad.mit.edu	37	12	88515039	88515039	+	Intron	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:88515039delA	uc001tar.2	-						CEP290_uc001tat.2_Intron|CEP290_uc009zsl.1_Intron	NM_025114	NP_079390			centrosomal protein 290kDa						cilium assembly|eye photoreceptor cell development|G2/M transition of mitotic cell cycle|hindbrain development|otic vesicle formation|positive regulation of transcription, DNA-dependent|pronephros development|protein transport	cell surface|centrosome|cytosol|nucleus|photoreceptor connecting cilium	protein binding			ovary(5)|breast(1)|pancreas(1)	7																		---	---	---	---
DCN	1634	broad.mit.edu	37	12	91558363	91558363	+	Intron	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:91558363delA	uc001tbs.2	-						DCN_uc001tbo.2_Intron|DCN_uc001tbp.2_Intron|DCN_uc001tbq.2_Intron|DCN_uc001tbr.2_Intron|DCN_uc001tbt.2_Intron|DCN_uc001tbu.2_Intron	NM_133503	NP_598010			decorin isoform a preproprotein						organ morphogenesis	extracellular space				central_nervous_system(2)|ovary(1)|lung(1)	4																		---	---	---	---
CCDC41	51134	broad.mit.edu	37	12	94729387	94729387	+	Frame_Shift_Del	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:94729387delT	uc001tdd.2	-	12	1983	c.1397delA	c.(1396-1398)AATfs	p.N466fs	CCDC41_uc001tde.2_Frame_Shift_Del_p.N466fs|CCDC41_uc009zsw.1_RNA	NM_016122	NP_057206	Q9Y592	CCD41_HUMAN	NY-REN-58 antigen	458	Potential.										0																		---	---	---	---
NR2C1	7181	broad.mit.edu	37	12	95442823	95442823	+	Intron	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:95442823delA	uc001tdm.3	-						NR2C1_uc010suu.1_Intron|NR2C1_uc001tdo.3_Intron|NR2C1_uc001tdn.3_Intron	NM_003297	NP_003288			nuclear receptor subfamily 2, group C, member 1						regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor	PML body	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|steroid hormone receptor activity|zinc ion binding			ovary(1)	1																		---	---	---	---
IFT81	28981	broad.mit.edu	37	12	110570466	110570466	+	Intron	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:110570466delA	uc001tqi.2	+						IFT81_uc001tqh.2_Intron|IFT81_uc001tqj.2_Intron|IFT81_uc001tqg.2_Intron	NM_001143779	NP_001137251			intraflagellar transport 81-like isoform 1						cell differentiation|multicellular organismal development|spermatogenesis	intraflagellar transport particle B|microtubule-based flagellum				ovary(1)	1																		---	---	---	---
C12orf24	29902	broad.mit.edu	37	12	110911025	110911025	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:110911025delT	uc001tqu.3	+						C12orf24_uc010sxz.1_Intron|C12orf24_uc009zvo.2_Intron|C12orf24_uc001tqt.2_Intron|C12orf24_uc001tqv.3_Intron	NM_013300	NP_037432			hypothetical protein LOC29902												0																		---	---	---	---
CCDC64	92558	broad.mit.edu	37	12	120510172	120510172	+	Intron	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:120510172delA	uc001txl.1	+						CCDC64_uc001txk.2_Intron|CCDC64_uc009zwv.1_Intron|CCDC64_uc010sze.1_Intron|CCDC64_uc010szf.1_Intron	NM_207311	NP_997194			coiled-coil domain containing 64						Golgi to secretory granule transport|neuron projection development	centrosome	dynactin binding|Rab GTPase binding			ovary(2)	2	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)																	---	---	---	---
KDM2B	84678	broad.mit.edu	37	12	122018158	122018158	+	Intron	DEL	G	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:122018158delG	uc001uat.2	-						KDM2B_uc001uas.2_5'UTR|KDM2B_uc001uau.2_Intron|KDM2B_uc001uav.3_Intron	NM_032590	NP_115979			F-box and leucine-rich repeat protein 10 isoform						embryonic camera-type eye morphogenesis|fourth ventricle development|histone H2A monoubiquitination|initiation of neural tube closure|lateral ventricle development|midbrain development|midbrain-hindbrain boundary morphogenesis|negative regulation of neural precursor cell proliferation|negative regulation of neuron apoptosis|negative regulation of transcription from RNA polymerase II promoter|spermatogenesis|third ventricle development|transcription, DNA-dependent	nucleolus	DNA binding|histone demethylase activity (H3-K36 specific)|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|protein binding|rRNA binding|zinc ion binding			ovary(1)|skin(1)	2																		---	---	---	---
AACS	65985	broad.mit.edu	37	12	125626402	125626402	+	Intron	DEL	A	-	-	rs35836097		TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:125626402delA	uc001uhc.2	+						AACS_uc001uhd.2_Intron|AACS_uc009zyh.2_Intron|AACS_uc009zyi.2_Intron	NM_023928	NP_076417			acetoacetyl-CoA synthetase						fatty acid metabolic process	cytosol	acetoacetate-CoA ligase activity|ATP binding			ovary(1)|liver(1)|central_nervous_system(1)	3	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;9.82e-05)|Epithelial(86;0.000642)|all cancers(50;0.00843)														---	---	---	---
Unknown	0	broad.mit.edu	37	13	19700978	19700978	+	IGR	DEL	A	-	-	rs9511728	by1000genomes	TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:19700978delA								DKFZp686A1627 (8555 upstream) : TUBA3C (46942 downstream)																																			---	---	---	---
TPTE2	93492	broad.mit.edu	37	13	19997315	19997315	+	Intron	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:19997315delA	uc001umd.2	-						TPTE2_uc009zzk.2_Intron|TPTE2_uc009zzl.2_Intron|TPTE2_uc001ume.2_Intron|TPTE2_uc009zzm.2_Intron|TPTE2_uc010tcm.1_Intron|TPTE2_uc010tcl.1_Intron	NM_199254	NP_954863			TPTE and PTEN homologous inositol lipid							endoplasmic reticulum membrane|integral to membrane	ion channel activity|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity|protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity				0		all_cancers(29;1.23e-20)|all_lung(29;1.97e-20)|all_epithelial(30;5.86e-20)|Lung NSC(5;3.36e-17)|Lung SC(185;0.0262)|Ovarian(182;0.162)		all cancers(112;1.73e-05)|Epithelial(112;7.42e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.000785)|Lung(94;0.0176)|LUSC - Lung squamous cell carcinoma(192;0.089)														---	---	---	---
HMGB1	3146	broad.mit.edu	37	13	31036852	31036852	+	Intron	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:31036852delA	uc001usw.2	-						HMGB1_uc001usz.2_Intron|HMGB1_uc001usv.2_Intron|HMGB1_uc001usx.2_Intron|HMGB1_uc001usy.2_Intron|HMGB1_uc001uta.1_Intron	NM_002128	NP_002119			high-mobility group box 1						base-excision repair, DNA ligation|dendritic cell chemotaxis|DNA fragmentation involved in apoptotic nuclear change|DNA topological change|inflammatory response to antigenic stimulus|innate immune response|myeloid dendritic cell activation|negative regulation of RNA polymerase II transcriptional preinitiation complex assembly|neuron projection development|positive regulation of apoptosis|positive regulation of caspase activity|positive regulation of DNA binding|positive regulation of transcription from RNA polymerase II promoter|V(D)J recombination	cell surface|condensed chromosome|extracellular space|nucleolus|nucleoplasm	chemoattractant activity|cytokine activity|damaged DNA binding|DNA bending activity|double-stranded DNA binding|RAGE receptor binding|repressing transcription factor binding|sequence-specific DNA binding transcription factor activity|single-stranded DNA binding			ovary(1)	1		Lung SC(185;0.0257)		all cancers(112;0.072)|OV - Ovarian serous cystadenocarcinoma(117;0.177)|Lung(94;0.216)|GBM - Glioblastoma multiforme(144;0.232)														---	---	---	---
FAM48A	55578	broad.mit.edu	37	13	37600969	37600970	+	Intron	INS	-	A	A			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:37600969_37600970insA	uc001uwg.2	-						FAM48A_uc010abt.2_Intron|FAM48A_uc001uwh.2_Intron|FAM48A_uc001uwi.2_Intron|FAM48A_uc001uwj.2_Intron|FAM48A_uc001uwk.2_Intron|FAM48A_uc010tes.1_Intron|FAM48A_uc001uwl.1_Intron|FAM48A_uc001uwe.2_5'Flank|FAM48A_uc001uwf.2_5'Flank	NM_001014286	NP_001014308			family with sequence similarity 48, member A						autophagy|gastrulation	SAGA-type complex	protein binding				0		Lung NSC(96;2.09e-06)|Breast(139;0.014)|Lung SC(185;0.0548)|Prostate(109;0.0959)		all cancers(112;6.06e-07)|Epithelial(112;1.87e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00794)|BRCA - Breast invasive adenocarcinoma(63;0.0128)|GBM - Glioblastoma multiforme(144;0.0477)														---	---	---	---
ELF1	1997	broad.mit.edu	37	13	41517026	41517026	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:41517026delT	uc001uxs.2	-						ELF1_uc010tfc.1_Intron|ELF1_uc010acd.2_Intron	NM_172373	NP_758961			E74-like factor 1 (ets domain transcription						positive regulation of transcription from RNA polymerase II promoter	cytoplasm|nucleus	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			ovary(1)	1		Lung NSC(96;8.3e-05)|Prostate(109;0.0233)|Breast(139;0.0296)|Lung SC(185;0.0367)		all cancers(112;1.87e-08)|Epithelial(112;8.45e-06)|OV - Ovarian serous cystadenocarcinoma(117;0.000202)|GBM - Glioblastoma multiforme(144;0.00266)|BRCA - Breast invasive adenocarcinoma(63;0.072)														---	---	---	---
CPB2	1361	broad.mit.edu	37	13	46630052	46630052	+	Intron	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:46630052delA	uc001vaw.2	-						uc001vau.1_Intron|uc001vav.1_Intron|CPB2_uc001vax.2_Intron	NM_001872	NP_001863			plasma carboxypeptidase B2 isoform a						blood coagulation|fibrinolysis|proteolysis	extracellular space	metallocarboxypeptidase activity|zinc ion binding			ovary(1)|skin(1)	2		Lung NSC(96;4.21e-05)|Breast(56;0.000118)|Prostate(109;0.00217)|Hepatocellular(98;0.0207)|Lung SC(185;0.0262)|all_neural(104;0.235)	KIRC - Kidney renal clear cell carcinoma(16;0.234)	GBM - Glioblastoma multiforme(144;5.44e-05)														---	---	---	---
LCP1	3936	broad.mit.edu	37	13	46716269	46716269	+	Intron	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:46716269delA	uc001vaz.3	-						LCP1_uc010ack.2_Intron|LCP1_uc001vay.3_Intron|LCP1_uc001vba.3_Intron	NM_002298	NP_002289			L-plastin						regulation of intracellular protein transport|T cell activation involved in immune response	cell junction|cytosol|ruffle membrane	calcium ion binding			lung(4)|ovary(3)	7		Lung NSC(96;1.27e-05)|Breast(56;8.04e-05)|Prostate(109;0.00217)|Hepatocellular(98;0.0207)|Lung SC(185;0.0262)	KIRC - Kidney renal clear cell carcinoma(16;0.234)	GBM - Glioblastoma multiforme(144;5.39e-05)				T	BCL6	NHL 								---	---	---	---
LRCH1	23143	broad.mit.edu	37	13	47269177	47269177	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:47269177delT	uc001vbj.2	+						LRCH1_uc010acp.2_Intron|LRCH1_uc001vbk.2_Intron|LRCH1_uc001vbl.3_Intron	NM_015116	NP_055931			leucine-rich repeats and calponin homology (CH)											ovary(1)|central_nervous_system(1)	2		all_lung(13;5.61e-07)|Lung NSC(96;0.000117)|Breast(56;0.000141)|Prostate(109;0.0029)|Lung SC(185;0.0367)|Myeloproliferative disorder(33;0.0505)|Hepatocellular(98;0.0556)	KIRC - Kidney renal clear cell carcinoma(16;0.234)	GBM - Glioblastoma multiforme(144;0.000123)														---	---	---	---
TDRD3	81550	broad.mit.edu	37	13	61057789	61057789	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:61057789delT	uc001via.2	+						TDRD3_uc010aef.2_Intron|TDRD3_uc001vhz.3_Intron|TDRD3_uc010aeg.2_Intron|TDRD3_uc001vib.3_Intron	NM_030794	NP_110421			tudor domain containing 3 isoform 2						chromatin modification	cytoplasm|nucleus	chromatin binding|methylated histone residue binding|nucleic acid binding|transcription coactivator activity			upper_aerodigestive_tract(1)|skin(1)	2		Prostate(109;0.173)|Breast(118;0.174)		GBM - Glioblastoma multiforme(99;0.000291)														---	---	---	---
Unknown	0	broad.mit.edu	37	13	67840882	67840882	+	IGR	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:67840882delT								PCDH9 (36414 upstream) : None (None downstream)																																			---	---	---	---
POU4F1	5457	broad.mit.edu	37	13	79176484	79176486	+	In_Frame_Del	DEL	TGG	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:79176484_79176486delTGG	uc001vkv.2	-	2	558_560	c.324_326delCCA	c.(322-327)CACCAG>CAG	p.H108del	uc001vku.1_Intron	NM_006237	NP_006228	Q01851	PO4F1_HUMAN	POU domain, class 4, transcription factor 1	108	Poly-His.				axonogenesis|regulation of transcription from RNA polymerase II promoter|synapse assembly	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			ovary(1)	1		Acute lymphoblastic leukemia(28;0.0279)|Breast(118;0.0848)		GBM - Glioblastoma multiforme(99;0.129)														---	---	---	---
Unknown	0	broad.mit.edu	37	13	88542299	88542299	+	IGR	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:88542299delT								SLITRK5 (210431 upstream) : None (None downstream)																																			---	---	---	---
DNAJC3	5611	broad.mit.edu	37	13	96395171	96395171	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:96395171delT	uc001vmq.2	+						DNAJC3_uc001vmp.2_Frame_Shift_Del_p.I226fs|DNAJC3_uc001vmr.2_Intron	NM_006260	NP_006251			DnaJ (Hsp40) homolog, subfamily C, member 3						protein folding|response to unfolded protein|response to virus		heat shock protein binding|protein kinase inhibitor activity|unfolded protein binding				0	all_neural(89;0.0878)|Breast(111;0.148)|Medulloblastoma(90;0.163)		BRCA - Breast invasive adenocarcinoma(86;0.126)															---	---	---	---
TM9SF2	9375	broad.mit.edu	37	13	100196011	100196011	+	Intron	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:100196011delA	uc001voj.1	+						TM9SF2_uc010afz.1_Intron	NM_004800	NP_004791			transmembrane 9 superfamily member 2 precursor						transport	endosome membrane|integral to plasma membrane				ovary(1)	1	all_neural(89;0.0837)|Medulloblastoma(90;0.18)|Lung SC(71;0.218)																	---	---	---	---
TPP2	7174	broad.mit.edu	37	13	103289645	103289645	+	Intron	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:103289645delA	uc001vpi.3	+							NM_003291	NP_003282			tripeptidyl peptidase II						proteolysis	cytoplasm|nucleus	aminopeptidase activity|serine-type endopeptidase activity|tripeptidyl-peptidase activity			upper_aerodigestive_tract(1)|ovary(1)	2	all_neural(89;0.0438)|Medulloblastoma(90;0.163)|Lung SC(71;0.184)																	---	---	---	---
MYO16	23026	broad.mit.edu	37	13	109858929	109858930	+	Intron	INS	-	T	T			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:109858929_109858930insT	uc001vqt.1	+						MYO16_uc010agk.1_Intron	NM_015011	NP_055826			myosin heavy chain Myr 8						cerebellum development|negative regulation of cell proliferation|negative regulation of S phase of mitotic cell cycle	myosin complex|nucleoplasm|perinuclear region of cytoplasm|plasma membrane	actin filament binding|ATP binding|motor activity			ovary(6)|large_intestine(1)|kidney(1)|breast(1)|central_nervous_system(1)	10	all_lung(23;0.000332)|all_neural(89;0.00294)|Medulloblastoma(90;0.00596)|Lung NSC(43;0.00751)|Lung SC(71;0.104)		BRCA - Breast invasive adenocarcinoma(86;0.19)|all cancers(43;0.201)															---	---	---	---
LAMP1	3916	broad.mit.edu	37	13	113964899	113964899	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:113964899delT	uc001vtm.1	+						LAMP1_uc010tka.1_Intron	NM_005561	NP_005552			lysosomal-associated membrane protein 1							endosome membrane|integral to plasma membrane|lysosomal membrane|membrane fraction				central_nervous_system(2)	2	Lung NSC(43;0.0161)|all_neural(89;0.0804)|Hepatocellular(20;0.0877)|Medulloblastoma(90;0.163)|Lung SC(71;0.218)	all_cancers(25;0.0482)|all_epithelial(44;0.0148)|all_lung(25;0.0271)|Lung NSC(25;0.0977)|Breast(118;0.188)	all cancers(43;0.025)|GBM - Glioblastoma multiforme(44;0.206)|Epithelial(84;0.246)															---	---	---	---
Unknown	0	broad.mit.edu	37	14	19339542	19339542	+	IGR	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:19339542delA								None (None upstream) : OR11H12 (38052 downstream)																																			---	---	---	---
MYH6	4624	broad.mit.edu	37	14	23870221	23870221	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:23870221delT	uc001wjv.2	-						MYH6_uc010akp.1_Intron	NM_002471	NP_002462			myosin heavy chain 6						adult heart development|atrial cardiac muscle tissue morphogenesis|cardiac muscle fiber development|in utero embryonic development|muscle filament sliding|regulation of ATPase activity|regulation of blood pressure|regulation of heart rate|regulation of the force of heart contraction|sarcomere organization|striated muscle contraction|ventricular cardiac muscle tissue morphogenesis|visceral muscle development	cytosol|focal adhesion|muscle myosin complex|myosin filament|nucleus|sarcomere	actin binding|actin-dependent ATPase activity|ATP binding|calmodulin binding|microfilament motor activity|protein kinase binding|structural constituent of muscle			pancreas(2)|ovary(1)|skin(1)	4	all_cancers(95;2.54e-05)			GBM - Glioblastoma multiforme(265;0.00764)|READ - Rectum adenocarcinoma(4;0.0289)|Colorectal(4;0.0441)														---	---	---	---
HECTD1	25831	broad.mit.edu	37	14	31583617	31583617	+	Intron	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:31583617delA	uc001wrc.1	-						HECTD1_uc001wra.1_Intron|HECTD1_uc001wrb.1_Intron|HECTD1_uc001wrd.1_Intron	NM_015382	NP_056197			HECT domain containing 1						protein ubiquitination involved in ubiquitin-dependent protein catabolic process	intracellular	metal ion binding|protein binding|ubiquitin-protein ligase activity			ovary(3)|large_intestine(1)|lung(1)	5	Hepatocellular(127;0.0877)|Breast(36;0.176)		LUAD - Lung adenocarcinoma(48;0.00292)|Lung(238;0.0164)|BRCA - Breast invasive adenocarcinoma(188;0.111)|STAD - Stomach adenocarcinoma(7;0.173)	GBM - Glioblastoma multiforme(265;0.00617)														---	---	---	---
JKAMP	51528	broad.mit.edu	37	14	59953379	59953379	+	Intron	DEL	A	-	-	rs1253109	by1000genomes	TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:59953379delA	uc001xei.3	+						C14orf149_uc001xee.1_5'Flank|C14orf149_uc010trx.1_5'Flank|JKAMP_uc001xef.3_Intron|JKAMP_uc001xeh.3_Intron|JKAMP_uc001xeg.3_Intron|JKAMP_uc010try.1_Intron|JKAMP_uc001xej.3_5'Flank	NM_001098625	NP_001092095			JNK1-associated membrane protein isoform 2						ER-associated protein catabolic process|response to unfolded protein	endoplasmic reticulum membrane|integral to membrane	ubiquitin protein ligase binding			breast(1)	1																		---	---	---	---
KCNH5	27133	broad.mit.edu	37	14	63417320	63417321	+	Intron	DEL	AA	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:63417320_63417321delAA	uc001xfx.2	-						KCNH5_uc001xfy.2_Intron|KCNH5_uc001xfz.1_Intron|KCNH5_uc001xga.2_Intron	NM_139318	NP_647479			potassium voltage-gated channel, subfamily H,						regulation of transcription, DNA-dependent	integral to membrane	calmodulin binding|two-component sensor activity|voltage-gated potassium channel activity			ovary(4)|skin(4)|central_nervous_system(1)	9				OV - Ovarian serous cystadenocarcinoma(108;0.00958)|BRCA - Breast invasive adenocarcinoma(234;0.168)														---	---	---	---
ATP6V1D	51382	broad.mit.edu	37	14	67809927	67809927	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:67809927delT	uc001xjf.2	-						ATP6V1D_uc001xje.2_Intron	NM_015994	NP_057078			H(+)-transporting two-sector ATPase						ATP hydrolysis coupled proton transport|cellular iron ion homeostasis|insulin receptor signaling pathway|transferrin transport	cytosol|proton-transporting two-sector ATPase complex, catalytic domain|vacuolar proton-transporting V-type ATPase complex	protein binding|proton-transporting ATPase activity, rotational mechanism			ovary(1)|lung(1)	2				all cancers(60;0.000739)|OV - Ovarian serous cystadenocarcinoma(108;0.00597)|BRCA - Breast invasive adenocarcinoma(234;0.00957)														---	---	---	---
Unknown	0	broad.mit.edu	37	14	73428538	73428539	+	IGR	DEL	CT	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:73428538_73428539delCT								DCAF4 (2182 upstream) : ZFYVE1 (7621 downstream)																																			---	---	---	---
RBM25	58517	broad.mit.edu	37	14	73563894	73563895	+	Intron	INS	-	TTTTC	TTTTC			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:73563894_73563895insTTTTC	uc001xno.2	+						RBM25_uc001xnn.3_Intron|RBM25_uc010ttu.1_Intron|RBM25_uc001xnp.2_Intron	NM_021239	NP_067062			RNA binding motif protein 25						apoptosis|mRNA processing|regulation of alternative nuclear mRNA splicing, via spliceosome|RNA splicing	cytoplasm|nuclear speck	mRNA binding|nucleotide binding|protein binding			central_nervous_system(2)|ovary(1)|breast(1)	4				BRCA - Breast invasive adenocarcinoma(234;0.00362)|OV - Ovarian serous cystadenocarcinoma(108;0.0688)														---	---	---	---
ALDH6A1	4329	broad.mit.edu	37	14	74533914	74533915	+	Intron	INS	-	A	A			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:74533914_74533915insA	uc001xpo.2	-						C14orf45_uc001xpm.1_Intron|ALDH6A1_uc010asa.2_Intron|ALDH6A1_uc010tuq.1_Intron	NM_005589	NP_005580			aldehyde dehydrogenase 6A1 precursor							mitochondrial matrix|nucleus	fatty-acyl-CoA binding|malonate-semialdehyde dehydrogenase (acetylating) activity|methylmalonate-semialdehyde dehydrogenase (acylating) activity				0				BRCA - Breast invasive adenocarcinoma(234;0.00354)	NADH(DB00157)													---	---	---	---
CATSPERB	79820	broad.mit.edu	37	14	92176040	92176041	+	Intron	DEL	AC	-	-	rs12882622		TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:92176040_92176041delAC	uc001xzs.1	-							NM_024764	NP_079040			cation channel, sperm-associated, beta						cell differentiation|multicellular organismal development|spermatogenesis	integral to membrane				breast(2)|skin(2)|ovary(1)	5		all_cancers(154;0.0663)|all_epithelial(191;0.236)																---	---	---	---
TRIP11	9321	broad.mit.edu	37	14	92493257	92493257	+	Intron	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:92493257delA	uc001xzy.2	-							NM_004239	NP_004230			thyroid hormone receptor interactor 11						transcription from RNA polymerase II promoter	cytoskeleton|Golgi apparatus|membrane|nucleus	protein binding|transcription coactivator activity			ovary(6)|skin(2)|kidney(2)|central_nervous_system(1)|lung(1)|breast(1)	13				COAD - Colon adenocarcinoma(157;0.223)				T	PDGFRB	AML								---	---	---	---
CPSF2	53981	broad.mit.edu	37	14	92625696	92625696	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:92625696delT	uc001yah.1	+							NM_017437	NP_059133			cleavage and polyadenylation specific factor 2						histone mRNA 3'-end processing|mRNA export from nucleus|nuclear mRNA splicing, via spliceosome|termination of RNA polymerase II transcription	mRNA cleavage and polyadenylation specificity factor complex	hydrolase activity|protein binding|RNA binding			ovary(2)	2		all_cancers(154;0.0766)		COAD - Colon adenocarcinoma(157;0.222)														---	---	---	---
NF1P1	440225	broad.mit.edu	37	15	21136692	21136693	+	5'Flank	DEL	CA	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:21136692_21136693delCA	uc001ytv.1	-											Human NF1-related locus DNA in A9 mouse DNA background.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	15	23610060	23610061	+	5'Flank	INS	-	G	G			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:23610060_23610061insG	uc001ywf.2	-											DQ583953																														---	---	---	---
UBE3A	7337	broad.mit.edu	37	15	25650459	25650459	+	Intron	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:25650459delA	uc001zaq.2	-						UBE3A_uc001zar.2_Intron|UBE3A_uc001zas.2_Intron|UBE3A_uc001zat.2_Intron	NM_000462	NP_000453			ubiquitin protein ligase E3A isoform 2						brain development|interspecies interaction between organisms|protein K48-linked ubiquitination|protein ubiquitination involved in ubiquitin-dependent protein catabolic process	nucleus|proteasome complex	protein binding|ubiquitin-protein ligase activity			upper_aerodigestive_tract(1)|ovary(1)|breast(1)	3		all_cancers(20;3.47e-21)|Breast(32;0.00123)		all cancers(64;2.78e-08)|Epithelial(43;8.85e-08)|BRCA - Breast invasive adenocarcinoma(123;0.0155)|Lung(196;0.0616)														---	---	---	---
RYR3	6263	broad.mit.edu	37	15	33923503	33923503	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:33923503delT	uc001zhi.2	+						RYR3_uc010bar.2_Intron	NM_001036	NP_001027			ryanodine receptor 3						cellular calcium ion homeostasis	integral to membrane	calcium ion binding|receptor activity|ryanodine-sensitive calcium-release channel activity			ovary(5)|central_nervous_system(4)|lung(1)	10		all_lung(180;7.18e-09)		all cancers(64;8.95e-12)|GBM - Glioblastoma multiforme(186;0.00109)|BRCA - Breast invasive adenocarcinoma(123;0.0363)														---	---	---	---
CATSPER2	117155	broad.mit.edu	37	15	43927354	43927354	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:43927354delT	uc001zsh.2	-						STRC_uc010udz.1_5'Flank|CATSPER2_uc010bdm.2_Intron|CATSPER2_uc001zsi.2_Intron|CATSPER2_uc001zsj.2_Intron	NM_172095	NP_742093			sperm-associated cation channel 2 isoform 2						cell differentiation|multicellular organismal development|spermatogenesis	cilium|flagellar membrane|integral to membrane	calcium channel activity|protein binding|voltage-gated ion channel activity			ovary(1)	1		all_cancers(109;3.26e-15)|all_epithelial(112;1.48e-12)|Lung NSC(122;2.76e-08)|all_lung(180;3.1e-07)|Melanoma(134;0.027)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;3.56e-07)												OREG0003957	type=REGULATORY REGION|Gene=AK093318|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay	---	---	---	---
PDIA3	2923	broad.mit.edu	37	15	44060896	44060896	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:44060896delT	uc001zsu.2	+						PDIA3_uc010bdp.2_Intron|PDIA3_uc010ued.1_Intron	NM_005313	NP_005304			protein disulfide-isomerase A3 precursor						cell redox homeostasis|glycerol ether metabolic process|post-translational protein modification|protein folding|protein import into nucleus|protein N-linked glycosylation via asparagine|protein retention in ER lumen|signal transduction	endoplasmic reticulum lumen|melanosome	cysteine-type endopeptidase activity|electron carrier activity|phospholipase C activity|protein binding|protein disulfide isomerase activity|protein disulfide oxidoreductase activity			ovary(1)|skin(1)	2		all_cancers(109;2.61e-15)|all_epithelial(112;1.12e-12)|Lung NSC(122;2.17e-08)|all_lung(180;2.45e-07)|Melanoma(134;0.027)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;9.48e-07)														---	---	---	---
CTDSPL2	51496	broad.mit.edu	37	15	44811330	44811330	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:44811330delT	uc001ztr.2	+						CTDSPL2_uc001zts.2_Intron|CTDSPL2_uc001ztt.2_Intron|CTDSPL2_uc010bdv.2_Intron	NM_016396	NP_057480			CTD (carboxy-terminal domain, RNA polymerase II,								phosphoprotein phosphatase activity				0		all_cancers(109;4.36e-14)|all_epithelial(112;9.8e-12)|Lung NSC(122;1.66e-07)|all_lung(180;1.47e-06)|Melanoma(134;0.0122)		all cancers(107;1.02e-20)|GBM - Glioblastoma multiforme(94;1.49e-06)|COAD - Colon adenocarcinoma(120;0.0857)|Colorectal(105;0.0905)														---	---	---	---
USP50	373509	broad.mit.edu	37	15	50833546	50833546	+	Intron	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:50833546delA	uc001zyq.3	-							NM_203494	NP_987090			ubiquitin specific protease 50						ubiquitin-dependent protein catabolic process		ubiquitin thiolesterase activity			lung(1)|breast(1)	2				all cancers(107;0.000519)|GBM - Glioblastoma multiforme(94;0.00288)														---	---	---	---
CCPG1	9236	broad.mit.edu	37	15	55783155	55783156	+	Intron	DEL	AA	-	-	rs74830467		TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:55783155_55783156delAA	uc002acy.2	-						DYX1C1_uc010ugh.1_Intron|DYX1C1_uc010ugi.1_Intron|DYX1C1_uc002adb.2_Intron|DYX1C1_uc002adc.2_Intron|DYX1C1_uc002add.2_Intron	NM_020739	NP_065790			cell cycle progression 1 isoform 2						cell cycle	integral to membrane				ovary(1)	1				all cancers(107;0.0354)														---	---	---	---
GTF2A2	2958	broad.mit.edu	37	15	59942804	59942804	+	Intron	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:59942804delA	uc002agg.2	-							NM_004492	NP_004483			general transcription factor IIA, 2, 12kDa						interspecies interaction between organisms|positive regulation of sequence-specific DNA binding transcription factor activity|positive regulation of transcription from RNA polymerase II promoter|RNA polymerase II transcriptional preinitiation complex assembly|transcription elongation from RNA polymerase II promoter|viral reproduction	transcription factor TFIIA complex	protein heterodimerization activity|protein homodimerization activity|TBP-class protein binding|transcription coactivator activity			central_nervous_system(2)	2																		---	---	---	---
VPS13C	54832	broad.mit.edu	37	15	62284070	62284070	+	Intron	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:62284070delA	uc002agz.2	-						VPS13C_uc002aha.2_Intron|VPS13C_uc002ahb.1_Intron|VPS13C_uc002ahc.1_Intron	NM_020821	NP_065872			vacuolar protein sorting 13C protein isoform 2A						protein localization					ovary(2)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	15	62563040	62563040	+	IGR	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:62563040delA								C2CD4B (105558 upstream) : MGC15885 (366331 downstream)																																			---	---	---	---
FAM96A	84191	broad.mit.edu	37	15	64367853	64367853	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:64367853delT	uc002amt.1	-						FAM96A_uc002amu.1_Intron|FAM96A_uc010uin.1_Intron	NM_032231	NP_115607			family with sequence similarity 96, member A						chromosome segregation						0																		---	---	---	---
PDCD7	10081	broad.mit.edu	37	15	65411613	65411613	+	Intron	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:65411613delA	uc002aol.2	-							NM_005707	NP_005698			programmed cell death 7						apoptosis|induction of apoptosis|response to glucocorticoid stimulus	U12-type spliceosomal complex					0																		---	---	---	---
BLM	641	broad.mit.edu	37	15	91308328	91308328	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:91308328delT	uc002bpr.2	+						BLM_uc010uqh.1_Intron|BLM_uc010uqi.1_Intron|BLM_uc010bnx.2_Intron|BLM_uc002bps.1_Intron	NM_000057	NP_000048			Bloom syndrome protein						double-strand break repair via homologous recombination|G2 phase of mitotic cell cycle|G2/M transition DNA damage checkpoint|negative regulation of cell division|positive regulation of transcription, DNA-dependent|protein oligomerization|regulation of cyclin-dependent protein kinase activity|replication fork processing|replication fork protection|response to X-ray	cytoplasm|lateral element|nuclear matrix|nucleolus|PML body	ATP binding|bubble DNA binding|DNA strand annealing activity|four-way junction helicase activity|G-quadruplex DNA binding|p53 binding			ovary(3)|skin(2)|breast(1)	6	Lung NSC(78;0.0875)|all_lung(78;0.109)		Lung(145;0.189)					Mis|N|F			leukemia|lymphoma|skin squamous cell |other cancers		Genes_defective_in_diseases_associated_with_sensitivity_to_DNA_damaging_agents	Bloom_syndrome				---	---	---	---
PGPEP1L	145814	broad.mit.edu	37	15	99514430	99514440	+	Intron	DEL	GGGGGGGGGGT	-	-	rs72362970		TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:99514430_99514440delGGGGGGGGGGT	uc002bum.2	-						PGPEP1L_uc010bop.2_Intron|PGPEP1L_uc002bun.2_Intron	NM_001102612	NP_001096082			pyroglutamyl-peptidase 1-like protein						proteolysis		cysteine-type peptidase activity				0																		---	---	---	---
TEKT5	146279	broad.mit.edu	37	16	10776188	10776188	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:10776188delT	uc002czz.1	-							NM_144674	NP_653275			tektin 5						microtubule cytoskeleton organization	cilium axoneme|flagellar axoneme|microtubule				ovary(2)	2																		---	---	---	---
PDXDC1	23042	broad.mit.edu	37	16	15095528	15095528	+	Intron	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:15095528delA	uc002dda.3	+						PDXDC1_uc010uzl.1_Intron|PDXDC1_uc010uzm.1_Intron|PDXDC1_uc010bvc.1_Intron|PDXDC1_uc002dcz.2_Intron|PDXDC1_uc002ddb.3_Intron|PDXDC1_uc010uzn.1_Intron|PDXDC1_uc002ddc.2_Intron	NM_015027	NP_055842			pyridoxal-dependent decarboxylase domain						carboxylic acid metabolic process		carboxy-lyase activity|protein binding|pyridoxal phosphate binding			skin(1)	1					Pyridoxal Phosphate(DB00114)													---	---	---	---
SETD1A	9739	broad.mit.edu	37	16	30995407	30995407	+	3'UTR	DEL	C	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:30995407delC	uc002ead.1	+	19					HSD3B7_uc002eaf.2_5'Flank|HSD3B7_uc010cac.2_5'Flank|HSD3B7_uc002eag.2_5'Flank|HSD3B7_uc002eah.2_5'Flank	NM_014712	NP_055527			SET domain containing 1A						regulation of transcription, DNA-dependent|transcription, DNA-dependent	chromosome|nuclear speck|Set1C/COMPASS complex	histone-lysine N-methyltransferase activity|nucleotide binding|protein binding|RNA binding			ovary(2)|skin(1)	3																		---	---	---	---
CNGB1	1258	broad.mit.edu	37	16	57951532	57951533	+	Intron	DEL	AC	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:57951532_57951533delAC	uc002emt.2	-						CNGB1_uc010cdh.2_Intron	NM_001297	NP_001288			cyclic nucleotide gated channel beta 1 isoform						sensory perception of smell	intracellular cyclic nucleotide activated cation channel complex	cAMP binding|intracellular cAMP activated cation channel activity			breast(3)|pancreas(1)	4																		---	---	---	---
CLEC18C	283971	broad.mit.edu	37	16	70066043	70066043	+	Intron	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:70066043delA	uc002exy.2	+						PDXDC2_uc002eyb.2_Intron|PDXDC2_uc002eyc.2_Intron	NM_182619	NP_872425			secretory protein LOC348174 precursor							extracellular region	sugar binding				0																		---	---	---	---
GLG1	2734	broad.mit.edu	37	16	74542594	74542594	+	Intron	DEL	C	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:74542594delC	uc002fcy.3	-						GLG1_uc002fcx.2_Intron|GLG1_uc002fcw.3_Intron|GLG1_uc002fcz.3_Intron	NM_001145667	NP_001139139			golgi apparatus protein 1 isoform 3							Golgi membrane|integral to membrane	receptor binding			ovary(1)|breast(1)	2																		---	---	---	---
CENPN	55839	broad.mit.edu	37	16	81051516	81051516	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:81051516delT	uc002ffx.2	+						CENPN_uc002ffw.3_Intron|CENPN_uc010vnl.1_Intron|CENPN_uc010vnm.1_Intron|CENPN_uc002ffy.3_Intron	NM_001100624	NP_001094094			centromere protein N isoform 2						CenH3-containing nucleosome assembly at centromere|mitotic prometaphase	condensed chromosome kinetochore|cytosol|nucleoplasm					0																		---	---	---	---
CMIP	80790	broad.mit.edu	37	16	81694337	81694337	+	Intron	DEL	T	-	-	rs66465921		TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:81694337delT	uc002fgp.2	+						CMIP_uc002fgq.1_Intron|CMIP_uc010vnq.1_Intron|CMIP_uc002fgr.1_Intron	NM_198390	NP_938204			c-Maf-inducing protein isoform C-mip							cytoplasm|nucleus					0																		---	---	---	---
RAP1GAP2	23108	broad.mit.edu	37	17	2888574	2888575	+	Intron	DEL	TT	-	-	rs71377564		TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:2888574_2888575delTT	uc010ckd.2	+						RAP1GAP2_uc010cke.2_Intron	NM_015085	NP_055900			RAP1 GTPase activating protein 2 isoform 1						regulation of small GTPase mediated signal transduction	centrosome|cytosol|perinuclear region of cytoplasm	GTPase activator activity			ovary(1)	1																		---	---	---	---
ZZEF1	23140	broad.mit.edu	37	17	3967494	3967494	+	Intron	DEL	A	-	-	rs112787658		TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:3967494delA	uc002fxe.2	-						ZZEF1_uc002fxh.2_5'Flank|ZZEF1_uc002fxi.2_Intron|ZZEF1_uc002fxj.1_Intron	NM_015113	NP_055928			zinc finger, ZZ type with EF hand domain 1								calcium ion binding|zinc ion binding			ovary(2)|central_nervous_system(1)|pancreas(1)	4																		---	---	---	---
ZZEF1	23140	broad.mit.edu	37	17	3990635	3990635	+	Intron	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:3990635delA	uc002fxe.2	-						ZZEF1_uc002fxk.1_Intron	NM_015113	NP_055928			zinc finger, ZZ type with EF hand domain 1								calcium ion binding|zinc ion binding			ovary(2)|central_nervous_system(1)|pancreas(1)	4																		---	---	---	---
C17orf68	80169	broad.mit.edu	37	17	8134459	8134459	+	Intron	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:8134459delA	uc002gkq.3	-						C17orf68_uc010cnv.2_Intron	NM_025099	NP_079375			alpha accessory factor 132						positive regulation of DNA replication|telomere maintenance	Stn1-Ten1 complex	protein binding|single-stranded DNA binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	17	20744320	20744321	+	5'Flank	INS	-	G	G	rs35847073	by1000genomes	TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:20744320_20744321insG	uc010crb.1	+											Homo sapiens cDNA clone IMAGE:6269068, partial cds.																														---	---	---	---
Unknown	0	broad.mit.edu	37	17	29349140	29349141	+	5'Flank	INS	-	AT	AT			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:29349140_29349141insAT	uc002hgd.1	+											Homo sapiens full length insert cDNA clone ZD88F12.									p.?(1)																					---	---	---	---
DDX52	11056	broad.mit.edu	37	17	35985898	35985898	+	Intron	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:35985898delA	uc002hoi.1	-						DDX52_uc002hoh.1_Intron	NM_007010	NP_008941			ATP-dependent RNA helicase ROK1 isoform a							nucleolus	ATP binding|ATP-dependent helicase activity|RNA binding			ovary(1)|skin(1)	2		Breast(25;0.00637)|Ovarian(249;0.15)																---	---	---	---
KRT40	125115	broad.mit.edu	37	17	39139511	39139511	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:39139511delT	uc010cxh.1	-						KRT40_uc002hvq.1_Intron	NM_182497	NP_872303			type I hair keratin KA36							intermediate filament	structural molecule activity				0		Breast(137;0.00043)																---	---	---	---
CCDC43	124808	broad.mit.edu	37	17	42756533	42756533	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:42756533delT	uc002ihc.2	-						CCDC43_uc010czw.1_Intron	NM_144609	NP_653210			coiled-coil domain containing 43 isoform 1												0		Prostate(33;0.0322)																---	---	---	---
ABI3	51225	broad.mit.edu	37	17	47295005	47295005	+	Intron	DEL	C	-	-	rs113223751		TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:47295005delC	uc002iop.1	+						ABI3_uc002ioq.1_Intron	NM_016428	NP_057512			NESH protein isoform 1						cellular component movement|regulation of cell migration	cytoplasm|lamellipodium	protein binding				0			Epithelial(5;6.37e-06)|all cancers(6;6.36e-05)												HNSCC(55;0.14)			---	---	---	---
CACNA1G	8913	broad.mit.edu	37	17	48639187	48639187	+	Intron	DEL	G	-	-	rs112792872		TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:48639187delG	uc002irk.1	+						uc002irh.2_Intron|CACNA1G_uc002iri.1_Intron|CACNA1G_uc002irj.1_Intron|CACNA1G_uc002irl.1_Intron|CACNA1G_uc002irm.1_Intron|CACNA1G_uc002irn.1_Intron|CACNA1G_uc002iro.1_Intron|CACNA1G_uc002irp.1_Intron|CACNA1G_uc002irq.1_Intron|CACNA1G_uc002irr.1_Intron|CACNA1G_uc002irs.1_Intron|CACNA1G_uc002irt.1_Intron|CACNA1G_uc002irv.1_Intron|CACNA1G_uc002irw.1_Intron|CACNA1G_uc002iru.1_Intron	NM_018896	NP_061496			voltage-dependent calcium channel alpha 1G						axon guidance	voltage-gated calcium channel complex	low voltage-gated calcium channel activity			breast(1)	1	Breast(11;6.7e-17)		BRCA - Breast invasive adenocarcinoma(22;7.52e-09)		Ethosuximide(DB00593)|Flunarizine(DB04841)|Levetiracetam(DB01202)|Mibefradil(DB01388)|Pimozide(DB01100)|Trimethadione(DB00347)|Verapamil(DB00661)|Zonisamide(DB00909)													---	---	---	---
TRIM37	4591	broad.mit.edu	37	17	57148100	57148101	+	Intron	DEL	AA	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:57148100_57148101delAA	uc002iwy.3	-						TRIM37_uc002iwz.3_Intron|TRIM37_uc002ixa.3_Intron|TRIM37_uc010woc.1_Intron	NM_001005207	NP_001005207			tripartite motif-containing 37 protein							perinuclear region of cytoplasm|peroxisome	ligase activity|protein binding|zinc ion binding			lung(2)|pancreas(2)|ovary(1)|skin(1)|breast(1)	7	Medulloblastoma(34;0.0922)|all_neural(34;0.101)													Mulibrey_Nanism				---	---	---	---
HEATR6	63897	broad.mit.edu	37	17	58136999	58136999	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:58136999delT	uc002iyk.1	-						HEATR6_uc010ddk.1_Intron|HEATR6_uc010wos.1_Intron	NM_022070	NP_071353			HEAT repeat containing 6								binding			ovary(1)|skin(1)	2	all_cancers(5;2.25e-13)|Breast(5;4.84e-25)|all_neural(34;0.0878)|Medulloblastoma(34;0.0922)		BRCA - Breast invasive adenocarcinoma(1;5.93e-19)|Epithelial(12;7.59e-12)|all cancers(12;1.26e-10)															---	---	---	---
BPTF	2186	broad.mit.edu	37	17	65960135	65960135	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:65960135delT	uc002jgf.2	+						BPTF_uc002jge.2_Intron|BPTF_uc002jgg.2_Intron|BPTF_uc002jgh.2_Intron	NM_182641	NP_872579			bromodomain PHD finger transcription factor						brain development|chromatin remodeling|negative regulation of transcription from RNA polymerase II promoter|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|NURF complex	sequence-specific DNA binding|transcription factor binding|zinc ion binding			ovary(2)|skin(2)	4	all_cancers(12;6e-11)		BRCA - Breast invasive adenocarcinoma(8;7.48e-08)|Colorectal(3;0.0984)|LUSC - Lung squamous cell carcinoma(166;0.24)															---	---	---	---
MYL12B	103910	broad.mit.edu	37	18	3273141	3273142	+	Intron	INS	-	T	T			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:3273141_3273142insT	uc010dkl.2	+						MYL12B_uc002klt.3_Intron|MYL12B_uc010wyv.1_Intron	NM_001144944	NP_001138416			myosin regulatory light chain MRCL2 isoform A						axon guidance|muscle contraction	cytosol|myosin complex	calcium ion binding				0																		---	---	---	---
NAPG	8774	broad.mit.edu	37	18	10548537	10548539	+	Intron	DEL	TTT	-	-	rs1662154		TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:10548537_10548539delTTT	uc002kon.2	+						NAPG_uc010wzr.1_Intron|NAPG_uc002koo.2_Intron|NAPG_uc002kop.2_Intron	NM_003826	NP_003817			N-ethylmaleimide-sensitive factor attachment						cellular membrane fusion|intra-Golgi vesicle-mediated transport|intracellular protein transport|protein complex assembly|protein stabilization	membrane|membrane fraction|mitochondrion	protein binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	18	14225639	14225639	+	IGR	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:14225639delA								ZNF519 (93210 upstream) : LOC284233 (111783 downstream)																																			---	---	---	---
CDH2	1000	broad.mit.edu	37	18	25593923	25593923	+	Intron	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:25593923delA	uc002kwg.2	-						CDH2_uc010xbn.1_Intron	NM_001792	NP_001783			cadherin 2, type 1 preproprotein						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																		---	---	---	---
DSG1	1828	broad.mit.edu	37	18	28923779	28923779	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:28923779delT	uc002kwp.2	+						DSG1_uc010xbp.1_5'UTR	NM_001942	NP_001933			desmoglein 1 preproprotein						calcium-dependent cell-cell adhesion|cell-cell junction assembly|cellular component disassembly involved in apoptosis|homophilic cell adhesion|protein stabilization	cytosol|desmosome|integral to membrane|internal side of plasma membrane	calcium ion binding|gamma-catenin binding|toxin binding			skin(3)|ovary(2)|central_nervous_system(2)	7			OV - Ovarian serous cystadenocarcinoma(10;0.00559)															---	---	---	---
SLC14A2	8170	broad.mit.edu	37	18	43216750	43216750	+	Intron	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:43216750delA	uc010dnj.2	+						SLC14A2_uc002lbb.2_Intron|SLC14A2_uc002lbe.2_Intron	NM_007163	NP_009094			solute carrier family 14 (urea transporter),							apical plasma membrane|integral to membrane|membrane fraction	protein binding|urea transmembrane transporter activity			upper_aerodigestive_tract(1)|ovary(1)|central_nervous_system(1)|skin(1)	4																		---	---	---	---
Unknown	0	broad.mit.edu	37	18	60110469	60110469	+	IGR	DEL	T	-	-	rs74413211	byFrequency;by1000genomes	TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:60110469delT								TNFRSF11A (56967 upstream) : ZCCHC2 (80189 downstream)																																			---	---	---	---
PRSSL1	400668	broad.mit.edu	37	19	691213	691213	+	Intron	DEL	A	-	-	rs147436553		TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:691213delA	uc002lpl.1	-						PRSSL1_uc010xfs.1_Intron	NM_214710	NP_999875			protease, serine-like 1 precursor						proteolysis	extracellular region	serine-type endopeptidase activity				0		all_epithelial(18;2.19e-21)|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)														---	---	---	---
GRIN3B	116444	broad.mit.edu	37	19	1008813	1008813	+	Intron	DEL	C	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:1008813delC	uc002lqo.1	+						uc002lqp.1_RNA	NM_138690	NP_619635			glutamate receptor, ionotropic,						ionotropic glutamate receptor signaling pathway|protein insertion into membrane|regulation of calcium ion transport	cell junction|N-methyl-D-aspartate selective glutamate receptor complex|neuronal cell body|outer membrane-bounded periplasmic space|postsynaptic membrane	extracellular-glutamate-gated ion channel activity|glycine binding|ionotropic glutamate receptor activity|neurotransmitter receptor activity				0		Acute lymphoblastic leukemia(61;4.36e-14)|all_hematologic(61;4.84e-09)|Lung NSC(49;0.000226)|all_lung(49;0.000353)|Breast(49;0.00066)		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)	Glycine(DB00145)|L-Glutamic Acid(DB00142)|Orphenadrine(DB01173)													---	---	---	---
KHSRP	8570	broad.mit.edu	37	19	6414223	6414223	+	Intron	DEL	G	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:6414223delG	uc002mer.3	-							NM_003685	NP_003676			KH-type splicing regulatory protein						mRNA processing|mRNA transport|regulation of transcription, DNA-dependent|RNA splicing, via transesterification reactions|transcription, DNA-dependent	cytosol|nucleus	DNA binding|protein binding|RNA binding			skin(1)	1																		---	---	---	---
EMR1	2015	broad.mit.edu	37	19	6896646	6896647	+	Intron	INS	-	T	T			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:6896646_6896647insT	uc002mfw.2	+						EMR1_uc010dvc.2_Intron|EMR1_uc010dvb.2_Intron|EMR1_uc010xji.1_Intron|EMR1_uc010xjj.1_Intron	NM_001974	NP_001965			egf-like module containing, mucin-like, hormone						cell adhesion|neuropeptide signaling pathway	integral to plasma membrane	calcium ion binding|G-protein coupled receptor activity			ovary(3)|lung(1)|skin(1)	5	all_hematologic(4;0.166)																	---	---	---	---
Unknown	0	broad.mit.edu	37	19	10377498	10377498	+	IGR	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:10377498delT								MRPL4 (6764 upstream) : ICAM1 (4019 downstream)																																			---	---	---	---
UNC13A	23025	broad.mit.edu	37	19	17750846	17750846	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:17750846delT	uc002nhd.2	-							NM_001080421	NP_001073890			unc-13 homolog A						exocytosis|intracellular signal transduction	cell junction|cytoplasm|presynaptic membrane	metal ion binding			ovary(3)	3																		---	---	---	---
ZNF430	80264	broad.mit.edu	37	19	21216110	21216111	+	Intron	DEL	AA	-	-	rs111525322		TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:21216110_21216111delAA	uc002npj.2	+						ZNF430_uc002npk.2_Intron	NM_025189	NP_079465			zinc finger protein 430						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			skin(2)	2																		---	---	---	---
ZNF430	80264	broad.mit.edu	37	19	21217112	21217112	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:21217112delT	uc002npj.2	+						ZNF430_uc002npk.2_Intron	NM_025189	NP_079465			zinc finger protein 430						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			skin(2)	2																		---	---	---	---
C19orf2	8725	broad.mit.edu	37	19	30462218	30462219	+	Intron	DEL	GT	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:30462218_30462219delGT	uc002nsr.2	+						C19orf2_uc002nsq.2_Intron|C19orf2_uc002nss.2_Intron	NM_003796	NP_003787			RPB5-mediating protein isoform a						protein folding|regulation of transcription from RNA polymerase II promoter|response to virus	DNA-directed RNA polymerase II, core complex|prefoldin complex	transcription corepressor activity|unfolded protein binding			ovary(1)|kidney(1)	2	Ovarian(5;0.000902)|Breast(6;0.0203)|Esophageal squamous(110;0.195)	Hepatocellular(1079;0.137)|Renal(1328;0.228)	STAD - Stomach adenocarcinoma(5;5.36e-06)|Lung(7;0.0144)|LUAD - Lung adenocarcinoma(5;0.115)	STAD - Stomach adenocarcinoma(1328;0.18)														---	---	---	---
GPATCH1	55094	broad.mit.edu	37	19	33587442	33587442	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:33587442delT	uc002nug.1	+							NM_018025	NP_060495			G patch domain containing 1							catalytic step 2 spliceosome	nucleic acid binding			skin(1)	1	Esophageal squamous(110;0.137)																	---	---	---	---
ZNF829	374899	broad.mit.edu	37	19	37393061	37393061	+	Intron	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:37393061delA	uc002ofa.1	-						ZNF345_uc002oez.2_Intron	NM_001037232	NP_001032309			zinc finger protein 829						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0	Esophageal squamous(110;0.183)		COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)															---	---	---	---
PLD3	23646	broad.mit.edu	37	19	40873490	40873490	+	Intron	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:40873490delA	uc002onm.3	+						PLD3_uc002onj.3_Intron|PLD3_uc002onk.3_Intron|PLD3_uc002onl.3_Intron|PLD3_uc002onn.2_Intron|PLD3_uc002ono.2_3'UTR	NM_001031696	NP_001026866			phospholipase D3						lipid catabolic process	endoplasmic reticulum membrane|integral to membrane	NAPE-specific phospholipase D activity|phospholipase D activity|protein binding			skin(2)|ovary(1)	3			Lung(22;0.000636)|LUSC - Lung squamous cell carcinoma(20;0.00248)															---	---	---	---
BCKDHA	593	broad.mit.edu	37	19	41929040	41929042	+	In_Frame_Del	DEL	AGG	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:41929040_41929042delAGG	uc002oqq.2	+	8	1162_1164	c.1133_1135delAGG	c.(1132-1137)CAGGAG>CAG	p.E379del	CYP2F1_uc010xvw.1_Intron|BCKDHA_uc002oqm.3_In_Frame_Del_p.E413del|BCKDHA_uc002oqr.2_In_Frame_Del_p.E378del|BCKDHA_uc010xvz.1_In_Frame_Del_p.E382del	NM_000709	NP_000700	P12694	ODBA_HUMAN	branched chain keto acid dehydrogenase E1, alpha	379					branched chain family amino acid catabolic process	mitochondrial alpha-ketoglutarate dehydrogenase complex	3-methyl-2-oxobutanoate dehydrogenase (2-methylpropanoyl-transferring) activity|alpha-ketoacid dehydrogenase activity|carboxy-lyase activity|metal ion binding|protein binding				0																		---	---	---	---
SLC8A2	6543	broad.mit.edu	37	19	47941333	47941335	+	Intron	DEL	CTC	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:47941333_47941335delCTC	uc002pgx.2	-						SLC8A2_uc010xyq.1_Intron|SLC8A2_uc010xyr.1_Intron|SLC8A2_uc010ele.2_Intron	NM_015063	NP_055878			solute carrier family 8 member 2 precursor						cell communication|platelet activation	integral to membrane|plasma membrane	calcium:sodium antiporter activity|calmodulin binding			skin(3)|ovary(1)	4		all_cancers(25;3.05e-07)|all_lung(116;4.19e-06)|Lung NSC(112;7.16e-06)|all_epithelial(76;7.65e-06)|all_neural(266;0.0652)|Ovarian(192;0.086)|Breast(70;0.173)		OV - Ovarian serous cystadenocarcinoma(262;0.000501)|all cancers(93;0.00058)|Epithelial(262;0.0181)|GBM - Glioblastoma multiforme(486;0.0457)														---	---	---	---
TEAD2	8463	broad.mit.edu	37	19	49845484	49845485	+	Intron	INS	-	CCACATCAGTT	CCACATCAGTT	rs149352076	by1000genomes	TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:49845484_49845485insCCACATCAGTT	uc002pnj.2	-						uc002pnb.1_5'Flank|TEAD2_uc002png.2_Intron|TEAD2_uc002pnh.2_Intron|TEAD2_uc002pni.2_Intron|TEAD2_uc010yao.1_Intron|TEAD2_uc010emw.2_Intron	NM_003598	NP_003589			TEA domain family member 2						hippo signaling cascade		DNA binding|protein binding|sequence-specific DNA binding transcription factor activity			central_nervous_system(2)|ovary(1)	3		all_lung(116;7.65e-05)|Lung NSC(112;0.000132)|all_neural(266;0.0506)|Ovarian(192;0.15)		OV - Ovarian serous cystadenocarcinoma(262;0.00093)|GBM - Glioblastoma multiforme(486;0.0467)														---	---	---	---
ZNF320	162967	broad.mit.edu	37	19	53391576	53391577	+	Intron	INS	-	GA	GA			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:53391576_53391577insGA	uc002qag.2	-						ZNF320_uc010eqi.1_Intron|ZNF320_uc002qah.2_Intron|ZNF320_uc002qai.2_Intron	NM_207333	NP_997216			zinc finger protein 320						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0				GBM - Glioblastoma multiforme(134;0.0534)														---	---	---	---
PTPRH	5794	broad.mit.edu	37	19	55698755	55698755	+	Intron	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:55698755delA	uc002qjq.2	-						PTPRH_uc010esv.2_Intron|uc002qjr.2_5'Flank	NM_002842	NP_002833			protein tyrosine phosphatase, receptor type, H						apoptosis	cytoplasm|integral to plasma membrane	protein binding|transmembrane receptor protein tyrosine phosphatase activity			ovary(2)|large_intestine(1)|skin(1)	4		Renal(1328;0.245)	BRCA - Breast invasive adenocarcinoma(297;0.209)	GBM - Glioblastoma multiforme(193;0.0479)														---	---	---	---
MCM8	84515	broad.mit.edu	37	20	5952840	5952840	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:5952840delT	uc002wmi.2	+						MCM8_uc002wmj.2_Intron|MCM8_uc002wmk.2_Intron|MCM8_uc002wml.2_Intron|MCM8_uc010gbp.2_Intron|MCM8_uc002wmm.2_5'UTR	NM_032485	NP_115874			minichromosome maintenance complex component 8						cell cycle checkpoint|DNA strand elongation involved in DNA replication|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|regulation of transcription, DNA-dependent|S phase of mitotic cell cycle|transcription, DNA-dependent	nucleoplasm	ATP binding|DNA binding|nucleoside-triphosphatase activity			skin(1)	1																		---	---	---	---
PLK1S1	55857	broad.mit.edu	37	20	21196192	21196192	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:21196192delT	uc002wsb.2	+						PLK1S1_uc010zsh.1_Intron|PLK1S1_uc010zsi.1_Intron|PLK1S1_uc010zsj.1_Intron|uc002wsc.2_Intron|PLK1S1_uc002wsd.2_Intron|uc002wse.2_Intron	NM_018474	NP_060944			polo-like kinase 1 substrate 1 isoform 1						spindle organization	centrosome	protein kinase binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	20	29930733	29930733	+	IGR	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:29930733delT								DEFB116 (34345 upstream) : DEFB118 (25695 downstream)																																			---	---	---	---
GDF5	8200	broad.mit.edu	37	20	33969913	33969913	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:33969913delT	uc010gfc.1	-						UQCC_uc010zuy.1_Intron|UQCC_uc002xcd.2_Intron|UQCC_uc010zuz.1_Intron|UQCC_uc010zva.1_Intron|UQCC_uc002xce.2_Intron|UQCC_uc002xcg.2_Intron|UQCC_uc010gfb.2_Intron|UQCC_uc010zvb.1_Intron|UQCC_uc002xcf.2_Intron|UQCC_uc002xci.1_Intron|UQCC_uc010gfd.1_Intron	NM_000557	NP_000548			growth differentiation factor 5 preproprotein						cartilage development|cell-cell signaling|growth|transforming growth factor beta receptor signaling pathway	extracellular space	cytokine activity|growth factor activity				0	Lung NSC(9;0.00642)|all_lung(11;0.0094)		BRCA - Breast invasive adenocarcinoma(18;0.00663)															---	---	---	---
RBM12	10137	broad.mit.edu	37	20	34240428	34240428	+	3'UTR	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:34240428delA	uc002xdq.2	-	3					CPNE1_uc010zvj.1_Intron|CPNE1_uc002xde.2_Intron|CPNE1_uc002xdf.2_Intron|CPNE1_uc002xdg.2_Intron|CPNE1_uc010gfi.2_Intron|CPNE1_uc010gfj.2_Intron|CPNE1_uc002xdh.2_Intron|CPNE1_uc002xdi.2_Intron|CPNE1_uc002xdj.2_Intron|CPNE1_uc002xdk.2_Intron|CPNE1_uc002xdl.2_Intron|CPNE1_uc002xdm.2_Intron|CPNE1_uc010gfk.1_Intron|CPNE1_uc002xdn.1_Intron|CPNE1_uc002xdo.1_Intron|CPNE1_uc002xdp.1_Intron|RBM12_uc002xdr.2_3'UTR|RBM12_uc002xds.2_3'UTR	NM_152838	NP_690051			RNA binding motif protein 12							nucleus	nucleotide binding|protein binding|RNA binding			ovary(3)	3	Lung NSC(9;0.00608)|all_lung(11;0.00918)		BRCA - Breast invasive adenocarcinoma(18;0.00953)															---	---	---	---
PHF20	51230	broad.mit.edu	37	20	34519091	34519093	+	Intron	DEL	ATG	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:34519091_34519093delATG	uc002xek.1	+							NM_016436	NP_057520			PHD finger protein 20						regulation of transcription, DNA-dependent|transcription, DNA-dependent	MLL1 complex	DNA binding|zinc ion binding			ovary(1)	1	Breast(12;0.00631)|all_lung(11;0.0145)																	---	---	---	---
FAM83D	81610	broad.mit.edu	37	20	37555035	37555035	+	Frame_Shift_Del	DEL	C	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:37555035delC	uc002xjg.2	+	1	81	c.40delC	c.(40-42)CGGfs	p.R14fs	FAM83D_uc002xjf.2_Frame_Shift_Del_p.R14fs	NM_030919	NP_112181	Q9H4H8	FA83D_HUMAN	hypothetical protein LOC81610	Error:Variant_position_missing_in_Q9H4H8_after_alignment					cell division|mitosis	cytoplasm|spindle pole				ovary(3)	3		Myeloproliferative disorder(115;0.00878)																---	---	---	---
PCIF1	63935	broad.mit.edu	37	20	44567581	44567581	+	Intron	DEL	G	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:44567581delG	uc002xqs.2	+							NM_022104	NP_071387			phosphorylated CTD interacting factor 1							nucleus				skin(1)	1																		---	---	---	---
PREX1	57580	broad.mit.edu	37	20	47244216	47244216	+	Intron	DEL	G	-	-	rs80011299	byFrequency;by1000genomes	TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:47244216delG	uc002xtw.1	-						PREX1_uc002xtv.1_Intron	NM_020820	NP_065871			phosphatidylinositol-3,4,						actin filament polymerization|apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|neutrophil activation|small GTPase mediated signal transduction|superoxide metabolic process	cytosol|plasma membrane	enzyme binding|phospholipid binding|Rho GTPase activator activity|Rho guanyl-nucleotide exchange factor activity			lung(3)|ovary(2)|pancreas(1)	6			BRCA - Breast invasive adenocarcinoma(12;0.0135)|Colorectal(8;0.198)															---	---	---	---
NKAIN4	128414	broad.mit.edu	37	20	61874139	61874139	+	Intron	DEL	G	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:61874139delG	uc002yek.2	-							NM_152864	NP_690603			Na+/K+ transporting ATPase interacting 4							integral to membrane|plasma membrane					0	all_cancers(38;2.72e-09)																	---	---	---	---
Unknown	0	broad.mit.edu	37	21	9483288	9483288	+	IGR	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:9483288delA								None (None upstream) : None (None downstream)																																			---	---	---	---
ITSN1	6453	broad.mit.edu	37	21	35231209	35231209	+	Intron	DEL	T	-	-	rs5843624		TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:35231209delT	uc002yta.1	+						DONSON_uc002ysn.1_Intron|ITSN1_uc002ytb.1_Intron|ITSN1_uc002ytj.2_Intron|ITSN1_uc010gmm.1_Intron	NM_003024	NP_003015			intersectin 1 isoform ITSN-l						apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction|synaptic vesicle endocytosis	cell junction|coated pit|cytosol|lamellipodium|synapse|synaptosome	calcium ion binding|proline-rich region binding|protein complex scaffold|Rho guanyl-nucleotide exchange factor activity			ovary(3)|skin(1)	4																		---	---	---	---
Unknown	0	broad.mit.edu	37	21	37518894	37518894	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:37518894delT	uc002yvc.1	-						uc002yvd.1_Intron|uc002yvf.1_Intron					Homo sapiens mRNA expressed in placenta, clone IMAGE:139776.																														---	---	---	---
BRWD1	54014	broad.mit.edu	37	21	40684718	40684718	+	Intron	DEL	G	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:40684718delG	uc002yxk.1	-						BRWD1_uc002yxl.2_Intron|BRWD1_uc002yxm.2_Intron	NM_018963	NP_061836			bromodomain and WD repeat domain containing 1						regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus				skin(3)|ovary(1)	4		Prostate(19;8.44e-08)|all_epithelial(19;0.223)																---	---	---	---
DSCAM	1826	broad.mit.edu	37	21	41741250	41741250	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:41741250delT	uc002yyq.1	-						DSCAM_uc002yyr.1_Intron	NM_001389	NP_001380			Down syndrome cell adhesion molecule isoform						cell adhesion|dendrite self-avoidance|negative regulation of cell adhesion|positive regulation of axon extension involved in axon guidance|positive regulation of phosphorylation	axon|extracellular region|growth cone|integral to plasma membrane|membrane fraction	protein binding			ovary(6)|skin(4)|upper_aerodigestive_tract(1)	11		all_cancers(19;0.186)|Prostate(19;1.15e-05)|all_epithelial(19;0.0103)																---	---	---	---
SIK1	150094	broad.mit.edu	37	21	44836942	44836942	+	Frame_Shift_Del	DEL	G	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:44836942delG	uc002zdf.2	-	14	2159	c.2032delC	c.(2032-2034)CAGfs	p.Q678fs		NM_173354	NP_775490	P57059	SIK1_HUMAN	salt-inducible kinase 1	678					anoikis|cell cycle|cell differentiation|intracellular protein kinase cascade|multicellular organismal development|regulation of cell differentiation|regulation of mitotic cell cycle	nucleus	ATP binding|magnesium ion binding|protein binding|protein serine/threonine kinase activity			lung(2)|testis(2)|ovary(1)|central_nervous_system(1)|skin(1)	7																		---	---	---	---
BCR	613	broad.mit.edu	37	22	23634615	23634615	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:23634615delT	uc002zww.2	+						BCR_uc002zwx.2_Intron|BCR_uc011aiy.1_Intron	NM_004327	NP_004318			breakpoint cluster region isoform 1						regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol	ATP binding|GTPase activator activity|protein serine/threonine kinase activity|Rho guanyl-nucleotide exchange factor activity		BCR/JAK2(6)	haematopoietic_and_lymphoid_tissue(6)|central_nervous_system(3)|urinary_tract(1)|lung(1)|skin(1)	12								T	ABL1| FGFR1|JAK2 	CML|ALL|AML								---	---	---	---
C22orf43	51233	broad.mit.edu	37	22	23973867	23973868	+	Intron	INS	-	C	C	rs141675360	by1000genomes	TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:23973867_23973868insC	uc002zxf.2	-							NM_016449	NP_057533			hypothetical protein LOC51233											skin(1)	1																		---	---	---	---
CABIN1	23523	broad.mit.edu	37	22	24480374	24480374	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:24480374delT	uc002zzi.1	+						CABIN1_uc002zzj.1_Intron|CABIN1_uc002zzl.1_Intron	NM_012295	NP_036427			calcineurin binding protein 1						cell surface receptor linked signaling pathway|chromatin modification	nucleus	protein phosphatase inhibitor activity			ovary(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)|pancreas(1)	5																		---	---	---	---
DEPDC5	9681	broad.mit.edu	37	22	32194509	32194509	+	Intron	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:32194509delA	uc003als.2	+						DEPDC5_uc011als.1_Intron|DEPDC5_uc011alu.1_Intron|DEPDC5_uc011alv.1_Intron|DEPDC5_uc003alt.2_Intron|DEPDC5_uc003alr.1_Intron|DEPDC5_uc011alt.1_Intron	NM_014662	NP_055477			DEP domain containing 5 isoform 1						intracellular signal transduction					ovary(4)|central_nervous_system(3)|pancreas(1)	8																		---	---	---	---
MYH9	4627	broad.mit.edu	37	22	36744899	36744899	+	Intron	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:36744899delA	uc003apg.2	-						MYH9_uc003api.1_Intron	NM_002473	NP_002464			myosin, heavy polypeptide 9, non-muscle						actin cytoskeleton reorganization|actin filament-based movement|angiogenesis|axon guidance|blood vessel endothelial cell migration|cytokinesis|integrin-mediated signaling pathway|leukocyte migration|membrane protein ectodomain proteolysis|monocyte differentiation|platelet formation|protein transport|regulation of cell shape	actomyosin contractile ring|cleavage furrow|cytosol|myosin complex|nucleus|ruffle|stress fiber|uropod	actin filament binding|actin-dependent ATPase activity|ADP binding|ATP binding|calmodulin binding|microfilament motor activity|protein anchor|protein homodimerization activity			breast(3)|ovary(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)|lung(1)|skin(1)|kidney(1)|pancreas(1)	11								T	ALK	ALCL		Deafness|autosomal dominant 17|Epstein syndrome|Fechtner syndrome|May-Hegglin anomaly|Sebastian syndrome		Hereditary_Macrothrombocytopenia_MYH9-associated				---	---	---	---
ELFN2	114794	broad.mit.edu	37	22	37769104	37769104	+	3'UTR	DEL	G	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:37769104delG	uc003asq.3	-	3						NM_052906	NP_443138			leucine rich repeat containing 62							cell surface|integral to membrane				upper_aerodigestive_tract(1)|ovary(1)	2	Melanoma(58;0.0574)																	---	---	---	---
TYMP	1890	broad.mit.edu	37	22	50968827	50968830	+	5'Flank	DEL	AGAG	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:50968827_50968830delAGAG	uc003bmb.3	-						TYMP_uc003bmc.3_5'Flank|TYMP_uc003bmd.3_5'Flank|TYMP_uc010hbd.2_5'Flank|TYMP_uc003bme.3_5'Flank|TYMP_uc003bmf.3_5'Flank|TYMP_uc011arz.1_5'Flank	NM_001113756	NP_001107228			endothelial cell growth factor 1						angiogenesis|cell differentiation|chemotaxis|DNA replication|mitochondrial genome maintenance|pyrimidine base metabolic process|pyrimidine nucleoside catabolic process|pyrimidine nucleoside salvage|pyrimidine nucleotide metabolic process	cytosol	growth factor activity|platelet-derived growth factor receptor binding|pyrimidine-nucleoside phosphorylase activity|thymidine phosphorylase activity			ovary(1)	1		all_cancers(38;4.58e-14)|all_epithelial(38;1.12e-12)|all_lung(38;3.07e-05)|Breast(42;6.27e-05)|Lung NSC(38;0.000813)|Ovarian(80;0.0221)|Hepatocellular(38;0.0691)|Lung SC(80;0.113)		BRCA - Breast invasive adenocarcinoma(115;0.206)|LUAD - Lung adenocarcinoma(64;0.247)	Capecitabine(DB01101)|Docetaxel(DB01248)|Floxuridine(DB00322)|Fluorouracil(DB00544)|Sulfasalazine(DB00795)|Tamoxifen(DB00675)													---	---	---	---
SHANK3	85358	broad.mit.edu	37	22	51159932	51159933	+	Frame_Shift_Ins	INS	-	G	G			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:51159932_51159933insG	uc003bne.1	+	22	3719_3720	c.3719_3720insG	c.(3718-3720)CTGfs	p.L1240fs	SHANK3_uc003bnf.1_Frame_Shift_Ins_p.L687fs|SHANK3_uc010hbg.1_Frame_Shift_Ins_p.L422fs	NM_001080420	NP_001073889	F2Z3L0	F2Z3L0_HUMAN	SH3 and multiple ankyrin repeat domains 3	1240										central_nervous_system(1)	1		all_cancers(38;3.75e-11)|all_epithelial(38;1.82e-09)|Breast(42;0.000448)|all_lung(38;0.000665)|Lung NSC(38;0.0104)|Ovarian(80;0.104)|Lung SC(80;0.162)|Hepatocellular(38;0.178)		BRCA - Breast invasive adenocarcinoma(115;0.22)														---	---	---	---
RBBP7	5931	broad.mit.edu	37	X	16867569	16867569	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:16867569delT	uc004cxt.2	-						RBBP7_uc004cxs.1_Intron|RBBP7_uc004cxu.2_Intron	NM_002893	NP_002884			retinoblastoma binding protein 7						cell proliferation|cellular heat acclimation|CenH3-containing nucleosome assembly at centromere|DNA replication|multicellular organismal development|negative regulation of cell growth|regulation of transcription, DNA-dependent|transcription, DNA-dependent	ESC/E(Z) complex|NuRD complex	protein binding			upper_aerodigestive_tract(1)|ovary(1)	2	Hepatocellular(33;0.0997)																	---	---	---	---
CDKL5	6792	broad.mit.edu	37	X	18616437	18616437	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:18616437delT	uc004cym.2	+						CDKL5_uc004cyn.2_Intron	NM_003159	NP_003150			cyclin-dependent kinase-like 5						neuron migration|positive regulation of axon extension|positive regulation of dendrite morphogenesis|positive regulation of Rac GTPase activity|protein autophosphorylation	dendrite cytoplasm|dendritic growth cone|nucleus	ATP binding|cyclin-dependent protein kinase activity|Rac GTPase binding			ovary(2)|large_intestine(1)|stomach(1)|central_nervous_system(1)|skin(1)	6	Hepatocellular(33;0.183)																	---	---	---	---
PHEX	5251	broad.mit.edu	37	X	22196328	22196328	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:22196328delT	uc004dah.2	+						PHEX_uc011mjr.1_Intron|PHEX_uc011mjs.1_Intron	NM_000444	NP_000435			phosphate-regulating neutral endopeptidase						biomineral tissue development|cell-cell signaling|protein modification process|proteolysis|skeletal system development	integral to plasma membrane	aminopeptidase activity|metalloendopeptidase activity|zinc ion binding			ovary(2)|lung(1)	3																		---	---	---	---
PLS3	5358	broad.mit.edu	37	X	114877477	114877477	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:114877477delT	uc004eqd.2	+						PLS3_uc010nqg.2_Intron|PLS3_uc011mtf.1_Intron|PLS3_uc004eqe.2_Intron|PLS3_uc011mtg.1_Intron|PLS3_uc011mth.1_Intron|PLS3_uc011mti.1_Intron|PLS3_uc011mtj.1_Intron|PLS3_uc011mtk.1_5'Flank|PLS3_uc011mtl.1_5'Flank	NM_005032	NP_005023			plastin 3							cytoplasm	actin binding|calcium ion binding			lung(1)|breast(1)	2																		---	---	---	---
DOCK11	139818	broad.mit.edu	37	X	117752829	117752829	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:117752829delT	uc004eqp.2	+						DOCK11_uc004eqq.2_Intron	NM_144658	NP_653259			dedicator of cytokinesis 11						blood coagulation	cytosol	GTP binding			ovary(3)	3																		---	---	---	---
ODZ1	10178	broad.mit.edu	37	X	123517275	123517275	+	Intron	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:123517275delA	uc004euj.2	-						ODZ1_uc011muj.1_Intron|ODZ1_uc010nqy.2_Intron	NM_014253	NP_055068			odz, odd Oz/ten-m homolog 1 isoform 3						immune response|negative regulation of cell proliferation|nervous system development|signal transduction	extracellular region	heparin binding			ovary(11)|breast(4)|large_intestine(2)|skin(2)|pancreas(2)|upper_aerodigestive_tract(1)|lung(1)	23																		---	---	---	---
ODZ1	10178	broad.mit.edu	37	X	124028293	124028293	+	Intron	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:124028293delA	uc004euj.2	-						ODZ1_uc011muj.1_Intron|ODZ1_uc010nqy.2_Intron	NM_014253	NP_055068			odz, odd Oz/ten-m homolog 1 isoform 3						immune response|negative regulation of cell proliferation|nervous system development|signal transduction	extracellular region	heparin binding			ovary(11)|breast(4)|large_intestine(2)|skin(2)|pancreas(2)|upper_aerodigestive_tract(1)|lung(1)	23																		---	---	---	---
Unknown	0	broad.mit.edu	37	X	135873660	135873660	+	IGR	DEL	G	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:135873660delG								ARHGEF6 (10157 upstream) : RBMX (77693 downstream)																																			---	---	---	---
FMR1	2332	broad.mit.edu	37	X	147018822	147018822	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:147018822delT	uc010nst.2	+						FMR1_uc004fcj.2_Intron|FMR1_uc004fck.3_Intron|FMR1_uc004fcl.3_Intron|FMR1_uc011mxa.1_Intron	NM_002024	NP_002015			fragile X mental retardation 1						mRNA transport|negative regulation of translational initiation	cytoplasm|mRNA cap binding complex|nucleolus|nucleoplasm|soluble fraction	mRNA binding|protein binding			ovary(2)|pancreas(1)	3	Acute lymphoblastic leukemia(192;6.56e-05)													Fragile_X_syndrome				---	---	---	---
MTMR1	8776	broad.mit.edu	37	X	149898766	149898767	+	Intron	DEL	TT	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:149898766_149898767delTT	uc004fei.2	+						MTMR1_uc011mya.1_Intron|MTMR1_uc004feg.1_Intron|MTMR1_uc004feh.1_Intron|MTMR1_uc004fej.2_Intron|MTMR1_uc010ntf.2_Intron	NM_003828	NP_003819			myotubularin-related protein 1							plasma membrane	protein tyrosine phosphatase activity			ovary(1)	1	Acute lymphoblastic leukemia(192;6.56e-05)																	---	---	---	---
KIAA1751	85452	broad.mit.edu	37	1	1896229	1896229	+	Intron	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:1896229delA	uc001aim.1	-						KIAA1751_uc009vkz.1_Intron	NM_001080484	NP_001073953			hypothetical protein LOC85452											pancreas(1)	1	all_cancers(77;0.000708)|all_epithelial(69;0.000943)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;6.04e-15)|all_lung(118;9.67e-07)|Lung NSC(185;5.59e-05)|Renal(390;0.00571)|Breast(487;0.0183)|Hepatocellular(190;0.0268)|Myeloproliferative disorder(586;0.028)|Ovarian(437;0.127)|Medulloblastoma(700;0.151)|Lung SC(97;0.217)		Epithelial(90;8.79e-39)|OV - Ovarian serous cystadenocarcinoma(86;9.61e-25)|GBM - Glioblastoma multiforme(42;1.2e-07)|Colorectal(212;4.84e-05)|COAD - Colon adenocarcinoma(227;0.000214)|Kidney(185;0.00254)|BRCA - Breast invasive adenocarcinoma(365;0.00461)|STAD - Stomach adenocarcinoma(132;0.00645)|KIRC - Kidney renal clear cell carcinoma(229;0.037)|Lung(427;0.205)														---	---	---	---
CHD5	26038	broad.mit.edu	37	1	6170301	6170303	+	Intron	DEL	ACT	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:6170301_6170303delACT	uc001amb.1	-						CHD5_uc001alz.1_Intron|CHD5_uc001ama.1_Intron	NM_015557	NP_056372			chromodomain helicase DNA binding protein 5						chromatin modification|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	ATP binding|ATP-dependent helicase activity|DNA binding|zinc ion binding			central_nervous_system(3)|breast(3)|ovary(2)|upper_aerodigestive_tract(1)|lung(1)|skin(1)|pancreas(1)	12	Ovarian(185;0.0634)	all_cancers(23;5.36e-32)|all_epithelial(116;2.32e-17)|all_neural(13;3.68e-06)|all_lung(118;3.94e-06)|all_hematologic(16;2.39e-05)|Lung NSC(185;5.33e-05)|Acute lymphoblastic leukemia(12;0.000372)|Glioma(11;0.00127)|Renal(390;0.00188)|Colorectal(325;0.00342)|Breast(487;0.00373)|Hepatocellular(190;0.0218)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.15)		Epithelial(90;3.08e-37)|GBM - Glioblastoma multiforme(13;1.36e-31)|OV - Ovarian serous cystadenocarcinoma(86;7.7e-19)|Colorectal(212;9.97e-08)|COAD - Colon adenocarcinoma(227;1.07e-05)|Kidney(185;6.16e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.00109)|BRCA - Breast invasive adenocarcinoma(365;0.0012)|STAD - Stomach adenocarcinoma(132;0.00346)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.193)														---	---	---	---
TNFRSF1B	7133	broad.mit.edu	37	1	12251283	12251284	+	Intron	INS	-	A	A			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:12251283_12251284insA	uc001att.2	+						TNFRSF1B_uc001atu.2_Intron|TNFRSF1B_uc009vnk.2_Intron	NM_001066	NP_001057			tumor necrosis factor receptor 2 precursor						apoptosis	extracellular region|integral to membrane|membrane raft|plasma membrane	tumor necrosis factor receptor activity			liver(1)|central_nervous_system(1)|skin(1)	3	Ovarian(185;0.249)	Lung NSC(185;8.72e-05)|all_lung(284;9.92e-05)|Renal(390;0.000147)|Colorectal(325;0.000584)|Breast(348;0.00093)|Ovarian(437;0.00965)|Hepatocellular(190;0.0202)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0234)|Colorectal(212;5.52e-07)|COAD - Colon adenocarcinoma(227;0.000345)|BRCA - Breast invasive adenocarcinoma(304;0.000353)|Kidney(185;0.00102)|KIRC - Kidney renal clear cell carcinoma(229;0.00302)|STAD - Stomach adenocarcinoma(313;0.00815)|READ - Rectum adenocarcinoma(331;0.0284)	Etanercept(DB00005)|Infliximab(DB00065)													---	---	---	---
PRAMEF17	391004	broad.mit.edu	37	1	13719052	13719052	+	3'UTR	DEL	T	-	-	rs141370897	by1000genomes	TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:13719052delT	uc009vnz.1	+	3						NM_001099851	NP_001093321			PRAME family member 17												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;0.00224)|Myeloproliferative disorder(586;0.0393)|Hepatocellular(190;0.0623)|Ovarian(437;0.0731)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00812)|Colorectal(212;9.86e-06)|Kidney(185;4.89e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.000194)|BRCA - Breast invasive adenocarcinoma(304;0.000293)|COAD - Colon adenocarcinoma(227;0.000502)|STAD - Stomach adenocarcinoma(313;0.0072)|READ - Rectum adenocarcinoma(331;0.0649)														---	---	---	---
DNAJC16	23341	broad.mit.edu	37	1	15863352	15863352	+	Intron	DEL	T	-	-	rs112015425		TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:15863352delT	uc001aws.2	+						DNAJC16_uc001awr.1_Intron|DNAJC16_uc001awt.2_Intron	NM_015291	NP_056106			DnaJ (Hsp40) homolog, subfamily C, member 16						cell redox homeostasis|protein folding	integral to membrane	heat shock protein binding|unfolded protein binding			urinary_tract(1)|lung(1)|kidney(1)	3		Colorectal(325;0.00108)|Renal(390;0.00145)|Breast(348;0.00173)|all_lung(284;0.00459)|Lung NSC(340;0.00499)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0798)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;9.18e-07)|COAD - Colon adenocarcinoma(227;4.5e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000133)|KIRC - Kidney renal clear cell carcinoma(229;0.00262)|STAD - Stomach adenocarcinoma(313;0.00774)|READ - Rectum adenocarcinoma(331;0.0657)														---	---	---	---
CLCNKA	1187	broad.mit.edu	37	1	16355578	16355578	+	Intron	DEL	G	-	-	rs71774158		TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:16355578delG	uc001axu.2	+						CLCNKA_uc001axt.2_Intron|CLCNKA_uc001axv.2_Intron|CLCNKA_uc010obw.1_Intron|CLCNKB_uc001axw.3_Intron|CLCNKA_uc010obx.1_Intron|CLCNKA_uc010oby.1_Intron	NM_004070	NP_004061			chloride channel Ka isoform 1						excretion	chloride channel complex|integral to plasma membrane	voltage-gated chloride channel activity			ovary(1)	1		Colorectal(325;3.46e-05)|Breast(348;0.000278)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.000567)|Ovarian(437;0.0221)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|Colorectal(212;8.04e-08)|COAD - Colon adenocarcinoma(227;5.46e-06)|BRCA - Breast invasive adenocarcinoma(304;9.02e-05)|Kidney(64;0.00016)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(313;0.00655)|READ - Rectum adenocarcinoma(331;0.0649)	Niflumic Acid(DB04552)													---	---	---	---
MRTO4	51154	broad.mit.edu	37	1	19581443	19581443	+	Intron	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:19581443delA	uc001bbs.2	+							NM_016183	NP_057267			mRNA turnover 4 homolog						ribosome biogenesis	nuclear membrane|nucleolus					0		Colorectal(325;3.46e-05)|Renal(390;0.000147)|all_lung(284;0.000321)|Lung NSC(340;0.000398)|Breast(348;0.00049)|Ovarian(437;0.00764)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00462)|BRCA - Breast invasive adenocarcinoma(304;1.87e-05)|Kidney(64;0.000171)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|GBM - Glioblastoma multiforme(114;0.00301)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)														---	---	---	---
RPS6KA1	6195	broad.mit.edu	37	1	26900934	26900934	+	3'UTR	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:26900934delA	uc001bmr.1	+	22					RPS6KA1_uc010ofe.1_3'UTR|RPS6KA1_uc001bms.1_3'UTR|RPS6KA1_uc009vsl.1_3'UTR	NM_002953	NP_002944			ribosomal protein S6 kinase, 90kDa, polypeptide						axon guidance|innate immune response|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|nerve growth factor receptor signaling pathway|stress-activated MAPK cascade|synaptic transmission|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway	cytosol|nucleoplasm	ATP binding|caspase inhibitor activity|magnesium ion binding|protein binding|protein serine/threonine kinase activity			lung(1)	1		all_cancers(24;2.49e-24)|Colorectal(325;3.46e-05)|all_lung(284;4.76e-05)|Lung NSC(340;5.83e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Breast(348;0.00571)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|Epithelial(14;1.12e-50)|OV - Ovarian serous cystadenocarcinoma(117;2.89e-29)|Colorectal(126;1.4e-08)|COAD - Colon adenocarcinoma(152;9.31e-07)|BRCA - Breast invasive adenocarcinoma(304;0.000537)|KIRC - Kidney renal clear cell carcinoma(1967;0.000759)|STAD - Stomach adenocarcinoma(196;0.00151)|GBM - Glioblastoma multiforme(114;0.0361)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.161)|LUSC - Lung squamous cell carcinoma(448;0.234)														---	---	---	---
MED8	112950	broad.mit.edu	37	1	43850143	43850143	+	Frame_Shift_Del	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:43850143delT	uc001cje.1	-	8	932	c.884delA	c.(883-885)AATfs	p.N295fs		NM_052877	NP_443109	Q96G25	MED8_HUMAN	mediator complex subunit 8 isoform 3	Error:Variant_position_missing_in_Q96G25_after_alignment					regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	mediator complex					0	all_hematologic(146;0.0958)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0333)																---	---	---	---
CYP4Z2P	163720	broad.mit.edu	37	1	47339125	47339125	+	Intron	DEL	C	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:47339125delC	uc001cqo.1	-						CYP4Z2P_uc009vyn.1_Intron	NR_002788				Homo sapiens cDNA FLJ40054 fis, clone TBAES2000315, weakly similar to CYTOCHROME P450 4A1 (EC 1.14.15.3).												0																		---	---	---	---
RPE65	6121	broad.mit.edu	37	1	68917241	68917241	+	5'Flank	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:68917241delT	uc001dei.1	-							NM_000329	NP_000320			retinal pigment epithelium-specific protein						visual perception	cytoplasm|plasma membrane	all-trans-retinyl-palmitate hydrolase activity|metal ion binding|retinol isomerase activity			ovary(1)	1																		---	---	---	---
CTH	1491	broad.mit.edu	37	1	70895655	70895655	+	Intron	DEL	A	-	-	rs144207053		TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:70895655delA	uc001dfd.2	+						CTH_uc009wbl.1_Intron|CTH_uc001dfe.2_Intron|CTH_uc010oqq.1_Intron	NM_001902	NP_001893			cystathionase isoform 1						cysteine biosynthetic process|hydrogen sulfide biosynthetic process|protein homotetramerization|protein-pyridoxal-5-phosphate linkage via peptidyl-N6-pyridoxal phosphate-L-lysine	cytoplasm|nucleus	cystathionine gamma-lyase activity|L-cysteine desulfhydrase activity|pyridoxal phosphate binding			lung(1)	1					L-Cysteine(DB00151)|Pyridoxal Phosphate(DB00114)													---	---	---	---
Unknown	0	broad.mit.edu	37	1	78240627	78240627	+	IGR	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:78240627delT								USP33 (15090 upstream) : FAM73A (4682 downstream)																																			---	---	---	---
GIPC2	54810	broad.mit.edu	37	1	78509970	78509970	+	5'Flank	DEL	T	-	-	rs112459517		TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:78509970delT	uc001dik.2	+							NM_017655	NP_060125			PDZ domain protein GIPC2							cytoplasm				ovary(1)	1																		---	---	---	---
GBP7	388646	broad.mit.edu	37	1	89614951	89614951	+	Intron	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:89614951delA	uc001dna.2	-						GBP2_uc001dmy.1_Intron	NM_207398	NP_997281			guanylate binding protein 4-like							integral to membrane	GTP binding|GTPase activity			ovary(1)|skin(1)	2		Lung NSC(277;0.0908)		all cancers(265;0.00835)|Epithelial(280;0.0322)														---	---	---	---
BARHL2	343472	broad.mit.edu	37	1	91182861	91182861	+	5'Flank	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:91182861delA	uc001dns.2	-							NM_020063	NP_064447			BarH-like homeobox 2							nucleus	sequence-specific DNA binding			ovary(1)	1		all_lung(203;0.0263)|Lung SC(238;0.128)		all cancers(265;0.000897)|Epithelial(280;0.00516)|OV - Ovarian serous cystadenocarcinoma(397;0.211)														---	---	---	---
MOV10	4343	broad.mit.edu	37	1	113238691	113238691	+	Intron	DEL	G	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:113238691delG	uc001eck.2	+						MOV10_uc001ecl.2_Intron|MOV10_uc001ecn.2_Intron|MOV10_uc001ecm.2_Intron|MOV10_uc009wgj.1_Intron	NM_001130079	NP_001123551			Mov10, Moloney leukemia virus 10, homolog						mRNA cleavage involved in gene silencing by miRNA|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasmic mRNA processing body	ATP binding|helicase activity|protein binding|RNA binding			ovary(4)|skin(1)	5	Lung SC(450;0.246)	all_cancers(81;3.31e-11)|all_epithelial(167;5.69e-10)|all_lung(203;3.73e-05)|Breast(1374;0.000525)|Lung NSC(69;0.000954)|Ovarian(761;0.0367)|Lung SC(238;0.114)		OV - Ovarian serous cystadenocarcinoma(397;3.99e-67)|all cancers(265;1e-62)|Epithelial(280;4.78e-61)|Lung(183;0.0234)|Colorectal(144;0.0686)|READ - Rectum adenocarcinoma(129;0.0929)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)|BRCA - Breast invasive adenocarcinoma(282;0.24)														---	---	---	---
PHTF1	10745	broad.mit.edu	37	1	114281008	114281008	+	Intron	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:114281008delA	uc009wgp.1	-						PHTF1_uc001edn.2_Intron|PHTF1_uc010own.1_Intron|PHTF1_uc001edp.2_Intron	NM_006608	NP_006599			putative homeodomain transcription factor 1							nucleus	DNA binding|sequence-specific DNA binding transcription factor activity			ovary(1)	1	Lung SC(450;0.184)	all_cancers(81;3.78e-08)|all_epithelial(167;5.56e-08)|all_lung(203;6.97e-06)|Lung NSC(69;1.18e-05)		Lung(183;0.0234)|Colorectal(144;0.0686)|all cancers(265;0.0792)|Epithelial(280;0.0866)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)														---	---	---	---
FAM63A	55793	broad.mit.edu	37	1	150972560	150972560	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:150972560delT	uc001ewf.2	-						FAM63A_uc001ewc.2_Intron|FAM63A_uc010pcm.1_Intron|FAM63A_uc001ewd.2_Intron|FAM63A_uc001ewe.2_Intron|FAM63A_uc010pcn.1_Intron|FAM63A_uc001ewg.2_Intron	NM_018379	NP_001156731			hypothetical protein LOC55793 isoform 1								protein binding			ovary(1)	1	all_lung(15;1.09e-34)|Lung NSC(24;1.1e-30)|Lung SC(34;0.00202)|Ovarian(49;0.0167)|all_hematologic(923;0.0597)|Hepatocellular(266;0.0997)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.0486)|LUSC - Lung squamous cell carcinoma(543;0.211)															---	---	---	---
THEM4	117145	broad.mit.edu	37	1	151849315	151849315	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:151849315delT	uc001ezj.1	-						THEM4_uc001ezk.1_Intron	NM_053055	NP_444283			thioesterase superfamily member 4						insulin receptor signaling pathway|nerve growth factor receptor signaling pathway|phosphatidylinositol-mediated signaling	cytosol|ruffle membrane					0	Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.14)		LUSC - Lung squamous cell carcinoma(543;0.181)															---	---	---	---
NUP210L	91181	broad.mit.edu	37	1	154090061	154090061	+	Intron	DEL	A	-	-	rs79748906		TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:154090061delA	uc001fdw.2	-						NUP210L_uc009woq.2_Intron|NUP210L_uc010peh.1_Intron	NM_207308	NP_997191			nucleoporin 210kDa-like isoform 1							integral to membrane				skin(5)|ovary(4)|large_intestine(1)|central_nervous_system(1)	11	all_lung(78;9.35e-31)|Lung NSC(65;1.33e-28)|Hepatocellular(266;0.0877)|Melanoma(130;0.128)		LUSC - Lung squamous cell carcinoma(543;0.151)|Colorectal(543;0.198)															---	---	---	---
CHRNB2	1141	broad.mit.edu	37	1	154543476	154543476	+	Intron	DEL	C	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:154543476delC	uc001ffg.2	+							NM_000748	NP_000739			neuronal nicotinic acetylcholine receptor beta 2						B cell activation|behavioral response to nicotine|calcium ion transport|central nervous system projection neuron axonogenesis|lateral geniculate nucleus development|locomotory behavior|membrane depolarization|memory|negative regulation of action potential|optic nerve morphogenesis|positive regulation of B cell proliferation|positive regulation of dopamine secretion|regulation of circadian sleep/wake cycle, REM sleep|regulation of dendrite morphogenesis|regulation of dopamine metabolic process|regulation of synaptogenesis|response to cocaine|response to ethanol|response to hypoxia|sensory perception of pain|sensory perception of sound|smooth muscle contraction|social behavior|synaptic transmission involved in micturition|synaptic transmission, cholinergic|vestibulocochlear nerve development|visual learning|visual perception	cell junction|external side of plasma membrane|nicotinic acetylcholine-gated receptor-channel complex|postsynaptic membrane	acetylcholine receptor activity|nicotinic acetylcholine-activated cation-selective channel activity				0	all_lung(78;2.22e-29)|Lung NSC(65;3.66e-27)|Hepatocellular(266;0.0877)|all_hematologic(923;0.088)		LUSC - Lung squamous cell carcinoma(543;0.185)		Nicotine(DB00184)													---	---	---	---
GON4L	54856	broad.mit.edu	37	1	155822905	155822905	+	Intron	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:155822905delA	uc001flz.2	-						GON4L_uc001fly.1_Intron|GON4L_uc009wrh.1_Intron|GON4L_uc001fma.1_Intron|GON4L_uc001fmc.2_Intron|GON4L_uc001fmd.3_Intron|GON4L_uc009wri.2_Intron	NM_001037533	NP_001032622			gon-4-like isoform a						regulation of transcription, DNA-dependent	cytoplasm|nucleus	DNA binding			ovary(3)	3	Hepatocellular(266;0.0997)|all_hematologic(923;0.145)|all_neural(408;0.195)																	---	---	---	---
C1orf66	51093	broad.mit.edu	37	1	156702951	156702951	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:156702951delT	uc001fpu.2	+						C1orf66_uc001fpv.2_Intron	NM_015997	NP_057081			hypothetical protein LOC51093 isoform 1							integral to membrane	rRNA (adenine-N6,N6-)-dimethyltransferase activity				0	all_hematologic(923;0.088)|Hepatocellular(266;0.158)																	---	---	---	---
C1orf66	51093	broad.mit.edu	37	1	156703374	156703375	+	Intron	DEL	CA	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:156703374_156703375delCA	uc001fpu.2	+						C1orf66_uc001fpv.2_Intron	NM_015997	NP_057081			hypothetical protein LOC51093 isoform 1							integral to membrane	rRNA (adenine-N6,N6-)-dimethyltransferase activity				0	all_hematologic(923;0.088)|Hepatocellular(266;0.158)																	---	---	---	---
TPR	7175	broad.mit.edu	37	1	186300536	186300536	+	Intron	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:186300536delA	uc001grv.2	-							NM_003292	NP_003283			nuclear pore complex-associated protein TPR						carbohydrate metabolic process|glucose transport|mitotic cell cycle spindle assembly checkpoint|mRNA transport|protein import into nucleus|regulation of glucose transport|seryl-tRNA aminoacylation|transmembrane transport|viral reproduction	condensed chromosome kinetochore|cytoplasm|nuclear membrane|nuclear pore|nucleoplasm	ATP binding|protein binding|serine-tRNA ligase activity			ovary(2)|lung(2)|urinary_tract(1)|central_nervous_system(1)|skin(1)	7		Breast(1374;0.000659)|Lung SC(1967;0.0262)|Prostate(1639;0.157)		Colorectal(1306;1.12e-05)|KIRC - Kidney renal clear cell carcinoma(1967;0.00553)				T	NTRK1	papillary thyroid								---	---	---	---
CDC73	79577	broad.mit.edu	37	1	193121497	193121497	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:193121497delT	uc001gtb.2	+							NM_024529	NP_078805			parafibromin						cell cycle|histone H2B ubiquitination|histone monoubiquitination|transcription, DNA-dependent	Cdc73/Paf1 complex	protein binding			parathyroid(46)|ovary(1)|breast(1)|pancreas(1)	49														Hyperparathyroidism_Familial_Isolated|Hyperparathyroidism-Jaw_Tumor_Syndrome				---	---	---	---
KCNT2	343450	broad.mit.edu	37	1	196438097	196438097	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:196438097delT	uc001gtd.1	-						KCNT2_uc009wyt.1_5'Flank|KCNT2_uc001gte.1_Intron|KCNT2_uc001gtf.1_Intron|KCNT2_uc001gtg.1_Intron|KCNT2_uc009wyu.2_Intron|KCNT2_uc009wyv.1_Intron	NM_198503	NP_940905			potassium channel, subfamily T, member 2							voltage-gated potassium channel complex	ATP binding|calcium-activated potassium channel activity|voltage-gated potassium channel activity			ovary(5)|breast(1)|skin(1)	7																		---	---	---	---
SYT2	127833	broad.mit.edu	37	1	202573400	202573400	+	Intron	DEL	C	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:202573400delC	uc001gye.2	-						SYT2_uc010pqb.1_Intron|SYT2_uc009xaf.2_Intron	NM_001136504	NP_001129976			synaptotagmin II						neurotransmitter secretion	cell junction|chromaffin granule membrane|endocytic vesicle membrane|integral to membrane|synaptic vesicle membrane	protein binding|transporter activity			ovary(2)|skin(1)	3			BRCA - Breast invasive adenocarcinoma(75;0.169)		Botulinum Toxin Type B(DB00042)													---	---	---	---
TMEM183A	92703	broad.mit.edu	37	1	202991831	202991831	+	Intron	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:202991831delA	uc001gyu.1	+						TMEM183A_uc001gyv.1_Intron|TMEM183A_uc001gyw.1_Intron|TMEM183A_uc001gyx.1_Intron|TMEM183A_uc001gyy.2_5'Flank	NM_001079809	NP_001073277			transmembrane protein 183B							integral to membrane					0			BRCA - Breast invasive adenocarcinoma(75;0.18)															---	---	---	---
RPS6KC1	26750	broad.mit.edu	37	1	213290877	213290877	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:213290877delT	uc010ptr.1	+						RPS6KC1_uc001hkd.2_Intron|RPS6KC1_uc010pts.1_Intron|RPS6KC1_uc010ptt.1_Intron|RPS6KC1_uc010ptu.1_Intron|RPS6KC1_uc010ptv.1_Intron|RPS6KC1_uc001hke.2_Intron	NM_012424	NP_036556			ribosomal protein S6 kinase, 52kDa, polypeptide						cell communication|signal transduction	early endosome|membrane	ATP binding|phosphatidylinositol binding|protein binding|protein serine/threonine kinase activity			lung(4)|ovary(3)|breast(1)	8				OV - Ovarian serous cystadenocarcinoma(81;0.00705)|all cancers(67;0.016)|GBM - Glioblastoma multiforme(131;0.0663)|Epithelial(68;0.145)														---	---	---	---
RPS6KC1	26750	broad.mit.edu	37	1	213434712	213434712	+	Intron	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:213434712delA	uc010ptr.1	+						RPS6KC1_uc001hkd.2_Intron|RPS6KC1_uc010pts.1_Intron|RPS6KC1_uc010ptt.1_Intron|RPS6KC1_uc010ptu.1_Intron|RPS6KC1_uc010ptv.1_Intron|RPS6KC1_uc001hke.2_Intron	NM_012424	NP_036556			ribosomal protein S6 kinase, 52kDa, polypeptide						cell communication|signal transduction	early endosome|membrane	ATP binding|phosphatidylinositol binding|protein binding|protein serine/threonine kinase activity			lung(4)|ovary(3)|breast(1)	8				OV - Ovarian serous cystadenocarcinoma(81;0.00705)|all cancers(67;0.016)|GBM - Glioblastoma multiforme(131;0.0663)|Epithelial(68;0.145)														---	---	---	---
KCTD3	51133	broad.mit.edu	37	1	215777330	215777330	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									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			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)														---	---	---	---
PCNXL2	80003	broad.mit.edu	37	1	233270662	233270662	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:233270662delT	uc001hvl.2	-						PCNXL2_uc001hvm.1_Intron|PCNXL2_uc009xfu.2_Intron|PCNXL2_uc001hvp.1_Intron|PCNXL2_uc009xfv.1_Intron	NM_014801	NP_055616			pecanex-like 2							integral to membrane				central_nervous_system(1)|pancreas(1)	2		all_cancers(173;0.0347)|Prostate(94;0.137)																---	---	---	---
EDARADD	128178	broad.mit.edu	37	1	236577755	236577755	+	Intron	DEL	T	-	-	rs34360581		TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:236577755delT	uc001hxu.1	+						EDARADD_uc001hxv.1_Intron	NM_145861	NP_665860			EDAR-associated death domain isoform A						cell differentiation|signal transduction	cytoplasm					0	Ovarian(103;0.0634)|Breast(184;0.247)	all_cancers(173;0.0232)|Prostate(94;0.174)	OV - Ovarian serous cystadenocarcinoma(106;0.00117)															---	---	---	---
MYT1L	23040	broad.mit.edu	37	2	1890247	1890247	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:1890247delT	uc002qxe.2	-						MYT1L_uc002qxd.2_Intron|MYT1L_uc010ewl.1_Intron	NM_015025	NP_055840			myelin transcription factor 1-like						cell differentiation|nervous system development	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(5)|central_nervous_system(1)	6	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.0797)	all_cancers(51;0.037)|all_epithelial(98;0.241)		OV - Ovarian serous cystadenocarcinoma(76;0.169)|all cancers(51;0.244)														---	---	---	---
RNASEH1	246243	broad.mit.edu	37	2	3596130	3596130	+	Intron	DEL	C	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:3596130delC	uc002qxt.2	-						RNASEH1_uc002qxs.2_Intron	NM_002936	NP_002927			ribonuclease H1						RNA catabolic process	cytoplasm	magnesium ion binding|ribonuclease H activity|RNA binding			ovary(1)	1	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.093)			OV - Ovarian serous cystadenocarcinoma(76;0.0713)|Epithelial(75;0.167)|all cancers(51;0.22)														---	---	---	---
SMC6	79677	broad.mit.edu	37	2	17888597	17888597	+	Frame_Shift_Del	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:17888597delT	uc002rco.2	-	18	2191	c.1895delA	c.(1894-1896)AATfs	p.N632fs	SMC6_uc010exo.2_Frame_Shift_Del_p.N632fs|SMC6_uc002rcn.2_Frame_Shift_Del_p.N632fs|SMC6_uc002rcp.1_Frame_Shift_Del_p.N658fs|SMC6_uc002rcq.2_Frame_Shift_Del_p.N658fs	NM_001142286	NP_001135758	Q96SB8	SMC6_HUMAN	SMC6 protein	632	Flexible hinge.				DNA recombination|DNA repair	chromosome|nucleus	ATP binding			breast(4)|upper_aerodigestive_tract(1)|kidney(1)	6	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.158)																	---	---	---	---
WDR35	57539	broad.mit.edu	37	2	20130442	20130442	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:20130442delT	uc002rdi.2	-						WDR35_uc002rdj.2_Intron|WDR35_uc010ext.2_Intron|WDR35_uc002rdh.2_Intron	NM_001006657	NP_001006658			WD repeat domain 35 isoform 1											ovary(1)	1	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)																	---	---	---	---
KRTCAP3	200634	broad.mit.edu	37	2	27666755	27666755	+	Intron	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:27666755delA	uc002rks.2	+						KRTCAP3_uc010ylr.1_Intron|KRTCAP3_uc002rkt.2_Intron	NM_173853	NP_776252			keratinocyte associated protein 3							integral to membrane					0	Acute lymphoblastic leukemia(172;0.155)																	---	---	---	---
GPN1	11321	broad.mit.edu	37	2	27852150	27852151	+	Intron	INS	-	G	G	rs146892484	by1000genomes	TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:27852150_27852151insG	uc010ymc.1	+						ZNF512_uc010yly.1_Intron|CCDC121_uc010eze.2_5'Flank|CCDC121_uc002rld.2_5'Flank|CCDC121_uc002rle.2_5'Flank|GPN1_uc010ezf.2_Intron|GPN1_uc010yma.1_Intron|GPN1_uc010ymb.1_Intron|GPN1_uc010ymd.1_Intron|GPN1_uc010yme.1_Intron|GPN1_uc010ezg.1_5'UTR	NM_007266	NP_009197			GPN-loop GTPase 1 isoform a							cytoplasm	GTP binding|nucleoside-triphosphatase activity|protein binding				0																		---	---	---	---
BRE	9577	broad.mit.edu	37	2	28464370	28464372	+	Intron	DEL	TTT	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:28464370_28464372delTTT	uc002rlr.2	+						BRE_uc002rlp.1_Intron|BRE_uc002rlq.2_Intron|BRE_uc002rls.2_Intron|BRE_uc002rlt.2_Intron|BRE_uc002rlu.2_Intron|BRE_uc002rlv.2_Intron	NM_199194	NP_954664			brain and reproductive organ-expressed (TNFRSF1A						apoptosis|chromatin modification|double-strand break repair|G2/M transition DNA damage checkpoint|positive regulation of anti-apoptosis|positive regulation of DNA repair|response to ionizing radiation|signal transduction	BRCA1-A complex|BRISC complex|cytoplasm|nuclear ubiquitin ligase complex	peroxisome targeting sequence binding|polyubiquitin binding|tumor necrosis factor receptor binding			lung(1)|kidney(1)|skin(1)	3	Acute lymphoblastic leukemia(172;0.155)																	---	---	---	---
SLC30A6	55676	broad.mit.edu	37	2	32400336	32400336	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:32400336delT	uc002roe.1	+						SLC30A6_uc002rof.1_Intron|SLC30A6_uc010ymw.1_Intron|SLC30A6_uc010ezr.1_Intron|SLC30A6_uc002rog.1_Intron|SLC30A6_uc010ezs.1_Intron|SLC30A6_uc002roh.1_Intron	NM_017964	NP_060434			solute carrier family 30 (zinc transporter),							Golgi membrane|integral to membrane	zinc ion transmembrane transporter activity				0	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.208)																	---	---	---	---
BIRC6	57448	broad.mit.edu	37	2	32820253	32820253	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:32820253delT	uc010ezu.2	+							NM_016252	NP_057336			baculoviral IAP repeat-containing 6						anti-apoptosis|apoptosis	intracellular	acid-amino acid ligase activity|cysteine-type endopeptidase inhibitor activity|protein binding			ovary(5)|skin(4)|lung(2)|central_nervous_system(1)|breast(1)|pancreas(1)	14	Acute lymphoblastic leukemia(172;0.155)																	---	---	---	---
SOS1	6654	broad.mit.edu	37	2	39294567	39294567	+	Intron	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:39294567delA	uc002rrk.3	-						SOS1_uc010ynr.1_Intron	NM_005633	NP_005624			son of sevenless homolog 1						apoptosis|axon guidance|blood coagulation|epidermal growth factor receptor signaling pathway|fibroblast growth factor receptor signaling pathway|induction of apoptosis by extracellular signals|insulin receptor signaling pathway|leukocyte migration|nerve growth factor receptor signaling pathway|Ras protein signal transduction	cytosol	DNA binding|protein binding|Rho GTPase activator activity|Rho guanyl-nucleotide exchange factor activity			ovary(4)|breast(3)|lung(2)|central_nervous_system(1)	10		all_hematologic(82;0.21)												Noonan_syndrome				---	---	---	---
THUMPD2	80745	broad.mit.edu	37	2	39964207	39964207	+	Intron	DEL	A	-	-	rs75145165		TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:39964207delA	uc002rru.2	-						THUMPD2_uc002rrv.2_Intron|THUMPD2_uc010ynt.1_Intron	NM_025264	NP_079540			THUMP domain containing 2								methyltransferase activity			skin(1)	1		all_hematologic(82;0.248)																---	---	---	---
ABCG8	64241	broad.mit.edu	37	2	44101418	44101418	+	Intron	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:44101418delA	uc002rtq.2	+						ABCG8_uc010yoa.1_Intron	NM_022437	NP_071882			ATP-binding cassette sub-family G member 8						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			skin(3)|ovary(1)	4		all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.175)																---	---	---	---
PREPL	9581	broad.mit.edu	37	2	44554099	44554099	+	Intron	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:44554099delA	uc002ruf.2	-						PREPL_uc002rug.2_Intron|PREPL_uc002ruh.2_Intron|PREPL_uc010fax.2_Intron|PREPL_uc002rui.3_Intron|PREPL_uc002ruj.1_Intron|PREPL_uc002ruk.1_Intron	NM_006036	NP_006027			prolyl endopeptidase-like isoform C						proteolysis	cytosol	serine-type endopeptidase activity			ovary(1)	1		all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.175)																---	---	---	---
MSH2	4436	broad.mit.edu	37	2	47643365	47643365	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:47643365delT	uc002rvy.1	+						MSH2_uc010yoh.1_Intron|MSH2_uc002rvz.2_Intron|MSH2_uc010fbg.2_Intron	NM_000251	NP_000242			mutS homolog 2						B cell differentiation|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|double-strand break repair|intra-S DNA damage checkpoint|isotype switching|maintenance of DNA repeat elements|male gonad development|meiotic gene conversion|meiotic mismatch repair|negative regulation of neuron apoptosis|negative regulation of reciprocal meiotic recombination|positive regulation of helicase activity|postreplication repair|response to UV-B|response to X-ray|somatic hypermutation of immunoglobulin genes	MutSalpha complex|MutSbeta complex|nuclear chromosome	ATP binding|DNA-dependent ATPase activity|double-strand/single-strand DNA junction binding|guanine/thymine mispair binding|loop DNA binding|protein C-terminus binding|protein homodimerization activity|protein kinase binding|Y-form DNA binding			large_intestine(33)|haematopoietic_and_lymphoid_tissue(6)|endometrium(4)|ovary(3)|cervix(2)|central_nervous_system(2)|stomach(1)|small_intestine(1)|breast(1)|skin(1)|prostate(1)	55		all_hematologic(82;0.0359)|Acute lymphoblastic leukemia(82;0.175)	Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151)					D|Mis|N|F|S		colorectal|endometrial|ovarian	colorectal|endometrial|ovarian		MMR	Lynch_syndrome|Muir-Torre_syndrome|Turcot_syndrome|Constitutional_Mismatch_Repair_Deficiency_Syndrome				---	---	---	---
LHCGR	3973	broad.mit.edu	37	2	48914783	48914783	+	3'UTR	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:48914783delT	uc002rwu.3	-	11					GTF2A1L_uc002rwt.2_Intron	NM_000233	NP_000224			luteinizing hormone/choriogonadotropin receptor						male genitalia development|male gonad development	endosome|integral to plasma membrane	luteinizing hormone receptor activity			ovary(3)|lung(2)|breast(2)|skin(1)	8		all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.176)	Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151)		Cetrorelix(DB00050)|Choriogonadotropin alfa(DB00097)|Goserelin(DB00014)|Lutropin alfa(DB00044)|Menotropins(DB00032)									Familial_Male-Limited_Precocious_Puberty				---	---	---	---
ASB3	51130	broad.mit.edu	37	2	54028522	54028522	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:54028522delT	uc002rxi.3	-						ERLEC1_uc002rxl.2_Intron|ERLEC1_uc002rxm.2_Intron|ERLEC1_uc002rxn.2_Intron	NM_001164165	NP_001157637			hypothetical protein LOC100302652						intracellular signal transduction					ovary(1)|kidney(1)	2			Lung(47;0.125)|LUSC - Lung squamous cell carcinoma(58;0.181)															---	---	---	---
VPS54	51542	broad.mit.edu	37	2	64193106	64193106	+	Intron	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:64193106delA	uc002scq.2	-						VPS54_uc002scp.2_Intron|VPS54_uc010fct.2_Intron	NM_016516	NP_057600			vacuolar protein sorting 54 isoform 1						protein transport|retrograde transport, endosome to Golgi						0																		---	---	---	---
GMCL1	64395	broad.mit.edu	37	2	70096843	70096843	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:70096843delT	uc002sfu.2	+							NM_178439	NP_848526			germ cell-less						cell differentiation|multicellular organismal development|spermatogenesis	nuclear matrix				ovary(3)	3																		---	---	---	---
RTKN	6242	broad.mit.edu	37	2	74653450	74653450	+	Frame_Shift_Del	DEL	G	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:74653450delG	uc002sle.2	-	12	1729	c.1612delC	c.(1612-1614)CTCfs	p.L538fs	RTKN_uc002slc.2_Frame_Shift_Del_p.L525fs|RTKN_uc002sld.2_Frame_Shift_Del_p.L488fs	NM_001015055	NP_001015055	Q9BST9	RTKN_HUMAN	rhotekin isoform a	538	Pro-rich.				apoptosis|regulation of anti-apoptosis|Rho protein signal transduction	intracellular	GTP binding|GTP-Rho binding|GTPase inhibitor activity			skin(1)	1																		---	---	---	---
HK2	3099	broad.mit.edu	37	2	75094527	75094527	+	Intron	DEL	A	-	-	rs151230031		TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:75094527delA	uc002snd.2	+							NM_000189	NP_000180			hexokinase 2						apoptotic mitochondrial changes|glucose transport|glycolysis|transmembrane transport	cytosol|mitochondrial outer membrane	ATP binding|glucokinase activity			ovary(1)|lung(1)	2																		---	---	---	---
C2orf3	6936	broad.mit.edu	37	2	75928421	75928421	+	Intron	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:75928421delA	uc002sno.2	-						C2orf3_uc010ffs.2_5'UTR|C2orf3_uc002snn.2_Intron|C2orf3_uc010fft.2_Intron	NM_003203	NP_003194			hypothetical protein LOC6936						negative regulation of transcription, DNA-dependent	nucleus	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity			ovary(1)|central_nervous_system(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	85143886	85143887	+	IGR	INS	-	A	A			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:85143886_85143887insA								TMSB10 (10087 upstream) : KCMF1 (54344 downstream)																																			---	---	---	---
KDM3A	55818	broad.mit.edu	37	2	86701787	86701789	+	Intron	DEL	AAA	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:86701787_86701789delAAA	uc002sri.3	+						KDM3A_uc010ytj.1_Intron|KDM3A_uc010ytk.1_Intron	NM_018433	NP_060903			jumonji domain containing 1A						androgen receptor signaling pathway|cell differentiation|formaldehyde biosynthetic process|histone H3-K9 demethylation|hormone-mediated signaling pathway|positive regulation of transcription, DNA-dependent|spermatogenesis|transcription, DNA-dependent	cytoplasm|nucleus	androgen receptor binding|iron ion binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen			breast(2)|ovary(1)|central_nervous_system(1)|skin(1)	5																		---	---	---	---
RMND5A	64795	broad.mit.edu	37	2	87954896	87954896	+	Intron	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:87954896delA	uc002srs.3	+											SubName: Full=cDNA FLJ10361 fis, clone NT2RM2001256, highly similar to Anaphase-promoting complex subunit 1;											ovary(1)|skin(1)	2																		---	---	---	---
PROM2	150696	broad.mit.edu	37	2	95943601	95943601	+	Intron	DEL	C	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:95943601delC	uc002suh.1	+						PROM2_uc002sui.2_Intron|PROM2_uc002suj.2_Intron|PROM2_uc002suk.2_Intron|PROM2_uc002sul.2_Intron	NM_144707	NP_653308			prominin 2 precursor							apical plasma membrane|basolateral plasma membrane|cilium membrane|integral to membrane|microvillus membrane				ovary(1)	1																		---	---	---	---
MRPL30	51263	broad.mit.edu	37	2	99811772	99811772	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:99811772delT	uc002szu.2	+						MRPL30_uc002szl.1_Intron|MRPL30_uc002szt.1_Intron|MRPL30_uc002szv.2_Intron	NM_145213	NP_660214			RecName: Full=39S ribosomal protein L30, mitochondrial;          Short=L30mt; AltName: Full=MRP-L30; AltName: Full=MRP-L28; Flags: Precursor;						translation	mitochondrion|ribosome	structural constituent of ribosome			ovary(1)	1																		---	---	---	---
TGFBRAP1	9392	broad.mit.edu	37	2	105913017	105913017	+	Intron	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:105913017delA	uc002tcq.2	-						TGFBRAP1_uc010fjc.2_Intron|TGFBRAP1_uc002tcr.3_Intron	NM_004257	NP_004248			transforming growth factor, beta receptor						regulation of transcription, DNA-dependent|transforming growth factor beta receptor signaling pathway	cytoplasm|membrane	SMAD binding|small GTPase regulator activity|transforming growth factor beta receptor binding			central_nervous_system(1)|skin(1)	2																		---	---	---	---
ZC3H6	376940	broad.mit.edu	37	2	113043561	113043562	+	Intron	INS	-	TGT	TGT			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:113043561_113043562insTGT	uc002thq.1	+							NM_198581	NP_940983			zinc finger CCCH-type domain containing 6								nucleic acid binding|zinc ion binding			ovary(3)|central_nervous_system(1)	4																		---	---	---	---
CLASP1	23332	broad.mit.edu	37	2	122216728	122216728	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:122216728delT	uc002tnc.2	-						CLASP1_uc002tna.2_5'Flank|CLASP1_uc010yyw.1_Intron|CLASP1_uc002tnb.2_Intron|CLASP1_uc010yyx.1_Intron|CLASP1_uc010yyy.1_Intron|CLASP1_uc010yyz.1_Intron|CLASP1_uc010yza.1_Intron|CLASP1_uc010yzb.1_Intron|CLASP1_uc010yzc.1_Intron|CLASP1_uc002tng.1_Intron	NM_015282	NP_056097			CLIP-associating protein 1 isoform 1						axon guidance|cell division|establishment or maintenance of cell polarity|exit from mitosis|G2/M transition of mitotic cell cycle|microtubule anchoring|microtubule bundle formation|microtubule nucleation|microtubule organizing center organization|mitotic prometaphase|negative regulation of microtubule depolymerization	centrosomal corona|condensed chromosome kinetochore|cortical microtubule cytoskeleton|cytoplasmic microtubule|cytosol|Golgi apparatus|kinetochore microtubule	kinetochore binding|microtubule plus-end binding			ovary(1)|central_nervous_system(1)	2	Renal(3;0.0496)																	---	---	---	---
NCKAP5	344148	broad.mit.edu	37	2	133887625	133887625	+	Frame_Shift_Del	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:133887625delT	uc002ttp.2	-	6	640	c.266delA	c.(265-267)AAGfs	p.K89fs	NCKAP5_uc002ttq.2_Frame_Shift_Del_p.K89fs|NCKAP5_uc002ttt.1_Frame_Shift_Del_p.K89fs|NCKAP5_uc002tts.1_Frame_Shift_Del_p.K64fs	NM_207363	NP_997246	O14513	NCKP5_HUMAN	Nck-associated protein 5 isoform 1	89	Potential.						protein binding				0																		---	---	---	---
R3HDM1	23518	broad.mit.edu	37	2	136472952	136472952	+	Intron	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:136472952delA	uc002tuo.2	+						R3HDM1_uc010fni.2_Intron|R3HDM1_uc002tup.2_Intron|R3HDM1_uc010zbh.1_Intron	NM_015361	NP_056176			R3H domain containing 1								nucleic acid binding			skin(1)	1				BRCA - Breast invasive adenocarcinoma(221;0.127)														---	---	---	---
CXCR4	7852	broad.mit.edu	37	2	136872415	136872415	+	3'UTR	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:136872415delA	uc002tuz.2	-	2					CXCR4_uc002tuy.2_3'UTR|CXCR4_uc010fnk.2_3'UTR	NM_003467	NP_003458			chemokine (C-X-C motif) receptor 4 isoform b						activation of MAPK activity|apoptosis|dendritic cell chemotaxis|elevation of cytosolic calcium ion concentration|entry into host cell|inflammatory response|initiation of viral infection|regulation of chemotaxis|response to hypoxia|response to virus	cell leading edge|cell surface|cytoplasmic membrane-bounded vesicle|integral to membrane|plasma membrane	actin binding|C-X-C chemokine receptor activity|coreceptor activity|myosin light chain binding|ubiquitin binding|ubiquitin protein ligase binding			upper_aerodigestive_tract(1)|large_intestine(1)|lung(1)	3				BRCA - Breast invasive adenocarcinoma(221;0.155)	Framycetin(DB00452)													---	---	---	---
ARHGAP15	55843	broad.mit.edu	37	2	144313915	144313915	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:144313915delT	uc002tvm.3	+						ARHGAP15_uc002tvn.2_Intron	NM_018460	NP_060930			ARHGAP15						regulation of cell shape|small GTPase mediated signal transduction	cytosol|membrane	protein binding|Rac GTPase activator activity			ovary(1)|skin(1)	2				BRCA - Breast invasive adenocarcinoma(221;0.151)														---	---	---	---
ARHGAP15	55843	broad.mit.edu	37	2	144525481	144525481	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:144525481delT	uc002tvm.3	+						ARHGAP15_uc002tvn.2_Intron	NM_018460	NP_060930			ARHGAP15						regulation of cell shape|small GTPase mediated signal transduction	cytosol|membrane	protein binding|Rac GTPase activator activity			ovary(1)|skin(1)	2				BRCA - Breast invasive adenocarcinoma(221;0.151)														---	---	---	---
Unknown	0	broad.mit.edu	37	2	149627550	149627550	+	IGR	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:149627550delT								EPC2 (82415 upstream) : KIF5C (5269 downstream)																																			---	---	---	---
CACNB4	785	broad.mit.edu	37	2	152695482	152695482	+	3'UTR	DEL	T	-	-	rs111950042		TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:152695482delT	uc002tya.2	-	14					CACNB4_uc002txy.2_3'UTR|CACNB4_uc002txz.2_3'UTR|CACNB4_uc010fnz.2_3'UTR	NM_000726	NP_000717			calcium channel, voltage-dependent, beta 4						axon guidance|membrane depolarization|synaptic transmission	cytosol|internal side of plasma membrane|plasma membrane|synapse|voltage-gated calcium channel complex	protein binding|voltage-gated calcium channel activity			ovary(2)	2				BRCA - Breast invasive adenocarcinoma(221;0.156)	Verapamil(DB00661)													---	---	---	---
ACVR1C	130399	broad.mit.edu	37	2	158406602	158406602	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:158406602delT	uc002tzk.3	-						ACVR1C_uc002tzl.3_Intron|ACVR1C_uc010fof.2_Intron|ACVR1C_uc010foe.2_Intron	NM_145259	NP_660302			activin A receptor, type IC isoform 1						apoptosis|cell differentiation|regulation of apoptosis	activin receptor complex	activin receptor activity, type I|ATP binding|transforming growth factor beta receptor activity			lung(3)|ovary(2)|skin(2)	7																		---	---	---	---
HAT1	8520	broad.mit.edu	37	2	172809273	172809273	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:172809273delT	uc002uhi.2	+						HAT1_uc010fqi.2_Intron|HAT1_uc002uhj.2_Intron	NM_003642	NP_003633			histone acetyltransferase 1						chromatin silencing at telomere|DNA packaging	cytoplasm|nuclear matrix|nucleoplasm	histone acetyltransferase activity|protein binding			large_intestine(1)|ovary(1)	2			OV - Ovarian serous cystadenocarcinoma(117;0.216)															---	---	---	---
HAT1	8520	broad.mit.edu	37	2	172823128	172823128	+	Intron	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:172823128delA	uc002uhi.2	+						HAT1_uc010fqi.2_Intron|HAT1_uc002uhj.2_Intron	NM_003642	NP_003633			histone acetyltransferase 1						chromatin silencing at telomere|DNA packaging	cytoplasm|nuclear matrix|nucleoplasm	histone acetyltransferase activity|protein binding			large_intestine(1)|ovary(1)	2			OV - Ovarian serous cystadenocarcinoma(117;0.216)															---	---	---	---
ITGAV	3685	broad.mit.edu	37	2	187501040	187501041	+	Intron	INS	-	T	T			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:187501040_187501041insT	uc002upq.2	+						ITGAV_uc010frs.2_Intron|ITGAV_uc010zfv.1_Intron	NM_002210	NP_002201			integrin alpha-V isoform 1 precursor						angiogenesis|axon guidance|blood coagulation|cell-matrix adhesion|entry of bacterium into host cell|entry of symbiont into host cell by promotion of host phagocytosis|entry of virus into host cell|ERK1 and ERK2 cascade|integrin-mediated signaling pathway|leukocyte migration|negative regulation of apoptosis|negative regulation of lipid storage|negative regulation of lipid transport|negative regulation of lipoprotein metabolic process|negative regulation of low-density lipoprotein particle receptor biosynthetic process|negative regulation of macrophage derived foam cell differentiation|positive regulation of cell adhesion|positive regulation of cell proliferation|regulation of apoptotic cell clearance	integrin complex	receptor activity|transforming growth factor beta binding			ovary(2)|kidney(1)|skin(1)	4			OV - Ovarian serous cystadenocarcinoma(117;0.0185)|Epithelial(96;0.072)|all cancers(119;0.189)	STAD - Stomach adenocarcinoma(3;0.106)|COAD - Colon adenocarcinoma(31;0.108)														---	---	---	---
GLS	2744	broad.mit.edu	37	2	191769683	191769683	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:191769683delT	uc002usf.2	+						GLS_uc002use.2_Intron	NM_014905	NP_055720			glutaminase precursor						cellular amino acid biosynthetic process|glutamate secretion|glutamine catabolic process|neurotransmitter secretion	mitochondrial matrix	glutaminase activity			ovary(1)|skin(1)	2			OV - Ovarian serous cystadenocarcinoma(117;0.00625)|Epithelial(96;0.0744)|all cancers(119;0.181)		L-Glutamic Acid(DB00142)|L-Glutamine(DB00130)													---	---	---	---
PGAP1	80055	broad.mit.edu	37	2	197755382	197755382	+	Intron	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:197755382delA	uc002utw.2	-						PGAP1_uc002utx.2_Intron|PGAP1_uc002uty.1_Intron|PGAP1_uc010zgv.1_Intron	NM_024989	NP_079265			GPI deacylase						attachment of GPI anchor to protein|C-terminal protein lipidation|intracellular protein transport|myo-inositol transport	integral to membrane|intrinsic to endoplasmic reticulum membrane	nuclease activity|phosphoric ester hydrolase activity			ovary(3)|central_nervous_system(1)	4																		---	---	---	---
COQ10B	80219	broad.mit.edu	37	2	198318518	198318518	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:198318518delT	uc002uuh.1	+						COQ10B_uc010fsl.1_5'Flank	NM_025147	NP_079423			coenzyme Q10 homolog B precursor							mitochondrial inner membrane					0			Epithelial(96;0.231)|OV - Ovarian serous cystadenocarcinoma(117;0.246)															---	---	---	---
RFTN2	130132	broad.mit.edu	37	2	198540350	198540354	+	5'UTR	DEL	AAAAC	-	-	rs148812496		TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:198540350_198540354delAAAAC	uc002uuo.3	-	1						NM_144629	NP_653230			raftlin family member 2							plasma membrane					0																		---	---	---	---
CLK1	1195	broad.mit.edu	37	2	201719893	201719894	+	Intron	DEL	AA	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:201719893_201719894delAA	uc002uwe.2	-						CLK1_uc002uwd.2_Intron|CLK1_uc010zhi.1_Intron|CLK1_uc002uwf.2_Intron|CLK1_uc002uwg.2_Intron|CLK1_uc010fsv.2_Intron	NM_004071	NP_004062			CDC-like kinase 1 isoform 1						cell proliferation	nucleus	ATP binding|non-membrane spanning protein tyrosine kinase activity|protein serine/threonine kinase activity			pancreas(2)	2																		---	---	---	---
ABI2	10152	broad.mit.edu	37	2	204231587	204231587	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:204231587delT	uc002vaa.2	+						ABI2_uc010zig.1_Intron|ABI2_uc002uzz.2_Intron|ABI2_uc010zih.1_Intron|ABI2_uc010zii.1_Intron|ABI2_uc010zij.1_Intron|ABI2_uc002vab.2_5'Flank	NM_005759	NP_005750			abl interactor 2						actin polymerization or depolymerization|cell migration|peptidyl-tyrosine phosphorylation	cytoskeleton|cytosol|filopodium|lamellipodium	cytoskeletal adaptor activity|DNA binding|kinase binding|proline-rich region binding|SH3 domain binding|ubiquitin protein ligase binding				0																		---	---	---	---
NDUFS1	4719	broad.mit.edu	37	2	207018409	207018409	+	Intron	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:207018409delA	uc002vbe.2	-						NDUFS1_uc010ziq.1_Intron|NDUFS1_uc010zir.1_Intron|NDUFS1_uc010zis.1_Intron|NDUFS1_uc010zit.1_Intron|NDUFS1_uc010ziu.1_Intron	NM_005006	NP_004997			NADH dehydrogenase (ubiquinone) Fe-S protein 1,						apoptosis|ATP metabolic process|mitochondrial electron transport, NADH to ubiquinone|reactive oxygen species metabolic process|regulation of mitochondrial membrane potential|transport	mitochondrial intermembrane space|mitochondrial respiratory chain complex I	2 iron, 2 sulfur cluster binding|4 iron, 4 sulfur cluster binding|electron carrier activity|metal ion binding|NADH dehydrogenase (ubiquinone) activity|protein binding			ovary(1)	1					NADH(DB00157)													---	---	---	---
KLF7	8609	broad.mit.edu	37	2	208030440	208030440	+	5'UTR	DEL	A	-	-	rs71412410		TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:208030440delA	uc002vbz.1	-	1					KLF7_uc002vca.1_Intron	NM_003709	NP_003700			Kruppel-like factor 7 (ubiquitous)						regulation of transcription from RNA polymerase II promoter	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|transcription coactivator activity|zinc ion binding			central_nervous_system(1)|skin(1)	2				LUSC - Lung squamous cell carcinoma(261;0.0856)|Lung(261;0.166)|Epithelial(149;0.173)														---	---	---	---
FN1	2335	broad.mit.edu	37	2	216251710	216251710	+	Intron	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:216251710delA	uc002vfa.2	-						FN1_uc002vfb.2_Intron|FN1_uc002vfc.2_Intron|FN1_uc002vfd.2_Intron|FN1_uc002vfe.2_Intron|FN1_uc002vff.2_Intron|FN1_uc002vfg.2_Intron|FN1_uc002vfh.2_Intron|FN1_uc002vfi.2_Intron|FN1_uc002vfj.2_Intron|FN1_uc002vez.2_Intron|FN1_uc010zjp.1_Intron	NM_212482	NP_997647			fibronectin 1 isoform 1 preproprotein						acute-phase response|angiogenesis|leukocyte migration|peptide cross-linking|platelet activation|platelet degranulation|regulation of cell shape|substrate adhesion-dependent cell spreading	ER-Golgi intermediate compartment|fibrinogen complex|platelet alpha granule lumen|proteinaceous extracellular matrix	collagen binding|extracellular matrix structural constituent|heparin binding			central_nervous_system(7)|large_intestine(2)|breast(2)|ovary(1)|pancreas(1)	13		Renal(323;0.127)		Epithelial(149;9.59e-07)|all cancers(144;0.000174)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00948)	Alteplase(DB00009)|Anistreplase(DB00029)|Reteplase(DB00015)|Tenecteplase(DB00031)													---	---	---	---
STK36	27148	broad.mit.edu	37	2	219562025	219562026	+	Intron	INS	-	T	T			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:219562025_219562026insT	uc002viu.2	+						STK36_uc002viv.2_Intron|STK36_uc002viw.2_Intron|STK36_uc002vix.2_Intron	NM_015690	NP_056505			serine/threonine kinase 36						cilium assembly|positive regulation of hh target transcription factor activity|positive regulation of smoothened signaling pathway|post-embryonic development	aggresome|cytoplasm|focal adhesion|intermediate filament cytoskeleton|nucleus	ATP binding|protein serine/threonine kinase activity|transcription factor binding			ovary(4)|stomach(2)|lung(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)|breast(1)	11		Renal(207;0.0915)		Epithelial(149;9.65e-07)|all cancers(144;0.000174)|LUSC - Lung squamous cell carcinoma(224;0.00813)|Lung(261;0.00984)														---	---	---	---
SP140L	93349	broad.mit.edu	37	2	231266129	231266129	+	Frame_Shift_Del	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:231266129delT	uc010fxm.1	+	17	1562	c.1471delT	c.(1471-1473)TTTfs	p.F491fs	SP140L_uc010fxo.1_3'UTR	NM_138402	NP_612411	Q9H930	LY10L_HUMAN	SP140 nuclear body protein-like	Error:Variant_position_missing_in_Q9H930_after_alignment						nucleus	DNA binding|metal ion binding			central_nervous_system(1)	1																		---	---	---	---
INPP5D	3635	broad.mit.edu	37	2	234104167	234104167	+	Intron	DEL	G	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:234104167delG	uc010zmo.1	+						INPP5D_uc010zmp.1_Intron	NM_001017915	NP_001017915			SH2 containing inositol phosphatase isoform a						apoptosis|blood coagulation|leukocyte migration|T cell receptor signaling pathway	cytosol	inositol-polyphosphate 5-phosphatase activity|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity|SH3 domain binding			ovary(1)|central_nervous_system(1)	2		Breast(86;0.0013)|Renal(207;0.00339)|all_hematologic(139;0.0116)|all_lung(227;0.0273)|Acute lymphoblastic leukemia(138;0.0328)|Lung NSC(271;0.0843)		Epithelial(121;1.16e-17)|BRCA - Breast invasive adenocarcinoma(100;0.000479)|LUSC - Lung squamous cell carcinoma(224;0.00655)|Lung(119;0.00802)|GBM - Glioblastoma multiforme(43;0.0185)														---	---	---	---
PASK	23178	broad.mit.edu	37	2	242075147	242075148	+	Intron	INS	-	C	C	rs140491962	by1000genomes	TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:242075147_242075148insC	uc002wao.1	-						PASK_uc010zol.1_Intron|PASK_uc010zom.1_Intron|PASK_uc010fzl.1_Intron|PASK_uc010zon.1_Intron|PASK_uc002wap.2_5'Flank|PASK_uc002waq.2_Intron	NM_015148	NP_055963			PAS domain containing serine/threonine kinase						regulation of transcription, DNA-dependent	Golgi apparatus	ATP binding|identical protein binding|protein serine/threonine kinase activity|signal transducer activity			ovary(4)|lung(1)|skin(1)	6		all_cancers(19;4.46e-39)|all_epithelial(40;1.34e-17)|Breast(86;1.53e-05)|Renal(207;0.00179)|all_lung(227;0.00481)|Lung NSC(271;0.017)|Ovarian(221;0.0228)|Esophageal squamous(248;0.129)|all_hematologic(139;0.158)|Melanoma(123;0.16)|all_neural(83;0.243)|Hepatocellular(293;0.244)		Epithelial(32;1.34e-31)|all cancers(36;1e-28)|OV - Ovarian serous cystadenocarcinoma(60;3.53e-14)|Kidney(56;4.31e-09)|KIRC - Kidney renal clear cell carcinoma(57;4.35e-08)|BRCA - Breast invasive adenocarcinoma(100;5.64e-06)|Lung(119;0.000596)|LUSC - Lung squamous cell carcinoma(224;0.00481)|Colorectal(34;0.014)|COAD - Colon adenocarcinoma(134;0.0968)														---	---	---	---
Unknown	0	broad.mit.edu	37	3	5125122	5125122	+	IGR	DEL	C	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:5125122delC								BHLHE40 (98259 upstream) : ARL8B (38808 downstream)																																			---	---	---	---
SETD5	55209	broad.mit.edu	37	3	9516725	9516725	+	Intron	DEL	T	-	-	rs113358265		TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:9516725delT	uc003brt.2	+						SETD5_uc003bru.2_Intron|SETD5_uc003brv.2_Intron|SETD5_uc010hck.2_Intron|SETD5_uc003brx.2_Intron	NM_001080517	NP_001073986			SET domain containing 5											ovary(2)	2	Medulloblastoma(99;0.227)			OV - Ovarian serous cystadenocarcinoma(96;0.112)														---	---	---	---
CAPN7	23473	broad.mit.edu	37	3	15282164	15282164	+	Intron	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:15282164delA	uc003bzn.2	+							NM_014296	NP_055111			calpain 7						proteolysis	nucleus	calcium-dependent cysteine-type endopeptidase activity			ovary(1)	1																		---	---	---	---
CAPN7	23473	broad.mit.edu	37	3	15288743	15288744	+	Intron	DEL	TT	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:15288743_15288744delTT	uc003bzn.2	+							NM_014296	NP_055111			calpain 7						proteolysis	nucleus	calcium-dependent cysteine-type endopeptidase activity			ovary(1)	1																		---	---	---	---
TBC1D5	9779	broad.mit.edu	37	3	17300086	17300086	+	Intron	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:17300086delA	uc003cbf.2	-						TBC1D5_uc010heu.2_Intron|TBC1D5_uc010hev.2_Intron|TBC1D5_uc003cbe.2_Intron|TBC1D5_uc010hew.1_Intron	NM_014744	NP_055559			TBC1 domain family, member 5 isoform b							intracellular	protein binding|Rab GTPase activator activity			ovary(1)	1																		---	---	---	---
TOP2B	7155	broad.mit.edu	37	3	25646157	25646158	+	Intron	INS	-	A	A			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:25646157_25646158insA	uc003cdj.2	-						TOP2B_uc011awm.1_Intron|TOP2B_uc010hff.1_Intron	NM_001068	NP_001059			DNA topoisomerase II, beta isozyme						DNA topological change|DNA-dependent DNA replication|mitotic cell cycle G2/M transition decatenation checkpoint|mitotic recombination|resolution of meiotic recombination intermediates|sister chromatid segregation	cytosol|DNA topoisomerase complex (ATP-hydrolyzing)|nucleolus|nucleoplasm|synaptonemal complex|WINAC complex	ATP binding|chromatin binding|DNA topoisomerase (ATP-hydrolyzing) activity|DNA-dependent ATPase activity|histone deacetylase binding|protein C-terminus binding|protein heterodimerization activity|protein kinase C binding|sequence-specific DNA binding transcription factor activity			breast(2)|ovary(1)|lung(1)|skin(1)	5																		---	---	---	---
KIF15	56992	broad.mit.edu	37	3	44868019	44868019	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:44868019delT	uc003cnx.3	+						KIF15_uc010hiq.2_Intron|KIF15_uc010hir.2_Intron	NM_020242	NP_064627			kinesin family member 15						blood coagulation|cell proliferation|microtubule-based movement|mitosis	centrosome|cytosol|microtubule|plus-end kinesin complex|spindle	ATP binding|DNA binding|microtubule motor activity			ovary(1)	1				BRCA - Breast invasive adenocarcinoma(193;0.0099)|KIRC - Kidney renal clear cell carcinoma(197;0.0564)|Kidney(197;0.0707)														---	---	---	---
LARS2	23395	broad.mit.edu	37	3	45561625	45561625	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:45561625delT	uc003cop.1	+						LARS2_uc010hit.1_Intron	NM_015340	NP_056155			leucyl-tRNA synthetase 2, mitochondrial						leucyl-tRNA aminoacylation	mitochondrial matrix	ATP binding|leucine-tRNA ligase activity			upper_aerodigestive_tract(1)|ovary(1)	2				BRCA - Breast invasive adenocarcinoma(193;0.0122)|KIRC - Kidney renal clear cell carcinoma(197;0.0313)|Kidney(197;0.0372)	L-Leucine(DB00149)													---	---	---	---
TOMM70A	9868	broad.mit.edu	37	3	100086754	100086754	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:100086754delT	uc003dtw.2	-							NM_014820	NP_055635			translocase of outer mitochondrial membrane 70						protein targeting to mitochondrion	integral to membrane|mitochondrial outer membrane translocase complex	protein binding|protein transmembrane transporter activity			ovary(1)	1																		---	---	---	---
LOC100302640	100302640	broad.mit.edu	37	3	106567681	106567682	+	Intron	INS	-	T	T			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:106567681_106567682insT	uc003dwf.3	-											Homo sapiens cDNA clone IMAGE:5284861.												0																		---	---	---	---
TMPRSS7	344805	broad.mit.edu	37	3	111775808	111775808	+	Intron	DEL	G	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:111775808delG	uc010hqb.2	+						TMPRSS7_uc011bhr.1_Intron	NM_001042575	NP_001036040			transmembrane protease, serine 7						proteolysis	integral to membrane|plasma membrane	serine-type endopeptidase activity			ovary(1)|kidney(1)	2																		---	---	---	---
RPN1	6184	broad.mit.edu	37	3	128350619	128350620	+	Intron	INS	-	G	G			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:128350619_128350620insG	uc003ekr.1	-						RPN1_uc011bkq.1_Intron	NM_002950	NP_002941			ribophorin I precursor						post-translational protein modification|protein N-linked glycosylation via asparagine	integral to membrane|melanosome|oligosaccharyltransferase complex|rough microsome	dolichyl-diphosphooligosaccharide-protein glycotransferase activity|protein binding			ovary(2)|central_nervous_system(1)	3				GBM - Glioblastoma multiforme(114;0.189)				T	EVI1	AML								---	---	---	---
Unknown	0	broad.mit.edu	37	3	142895155	142895155	+	IGR	DEL	C	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:142895155delC								CHST2 (53345 upstream) : SLC9A9 (88910 downstream)																																			---	---	---	---
GYG1	2992	broad.mit.edu	37	3	148711907	148711907	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:148711907delT	uc003ewn.2	+						GYG1_uc011bnp.1_Intron|GYG1_uc003ewo.2_Intron|GYG1_uc003ewp.2_Intron	NM_004130	NP_004121			glycogenin 1						glucose metabolic process|glycogen biosynthetic process|glycogen catabolic process	cytosol	glycogenin glucosyltransferase activity|metal ion binding|protein binding			ovary(1)	1			LUSC - Lung squamous cell carcinoma(72;0.0473)|Lung(72;0.0607)															---	---	---	---
TNIK	23043	broad.mit.edu	37	3	170802258	170802258	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:170802258delT	uc003fhh.2	-						TNIK_uc003fhi.2_Intron|TNIK_uc003fhj.2_Intron|TNIK_uc003fhk.2_Intron|TNIK_uc003fhl.2_Intron|TNIK_uc003fhm.2_Intron|TNIK_uc003fhn.2_Intron|TNIK_uc003fho.2_Intron|TNIK_uc003fhg.2_Intron|TNIK_uc003fhp.2_5'Flank	NM_015028	NP_055843			TRAF2 and NCK interacting kinase isoform 1						actin cytoskeleton reorganization|activation of JNKK activity|protein autophosphorylation|regulation of dendrite morphogenesis|Wnt receptor signaling pathway	cytoskeleton|nucleus|recycling endosome	ATP binding|protein binding|protein serine/threonine kinase activity|small GTPase regulator activity			ovary(4)|large_intestine(1)	5	all_cancers(22;2.55e-19)|all_lung(20;2.22e-14)|Ovarian(172;0.00197)|Breast(254;0.122)		LUSC - Lung squamous cell carcinoma(14;3.57e-14)|Lung(28;9.39e-14)															---	---	---	---
DGKG	1608	broad.mit.edu	37	3	185985707	185985708	+	Intron	DEL	GT	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:185985707_185985708delGT	uc003fqa.2	-						DGKG_uc003fqb.2_Intron|DGKG_uc003fqc.2_Intron|DGKG_uc011brx.1_Intron	NM_001346	NP_001337			diacylglycerol kinase gamma isoform 1						activation of protein kinase C activity by G-protein coupled receptor protein signaling pathway|intracellular signal transduction|platelet activation	cytoplasm|plasma membrane	ATP binding|calcium ion binding|diacylglycerol kinase activity			breast(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)|skin(1)	5	all_cancers(143;3.26e-12)|Ovarian(172;0.0315)|Breast(254;0.247)		OV - Ovarian serous cystadenocarcinoma(80;1.93e-20)	GBM - Glioblastoma multiforme(93;0.0657)	Phosphatidylserine(DB00144)													---	---	---	---
UTS2D	257313	broad.mit.edu	37	3	190986180	190986180	+	3'UTR	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:190986180delT	uc003fsu.2	-	9						NM_198152	NP_937795			urotensin 2 domain containing precursor							extracellular region	hormone activity				0	all_cancers(143;1.77e-09)|Ovarian(172;0.103)		LUSC - Lung squamous cell carcinoma(58;2.42e-06)|Lung(62;2.86e-06)	GBM - Glioblastoma multiforme(46;0.000214)														---	---	---	---
FYTTD1	84248	broad.mit.edu	37	3	197508915	197508915	+	3'UTR	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:197508915delT	uc003fyi.2	+	9					FYTTD1_uc011bui.1_3'UTR|FYTTD1_uc011buj.1_RNA|FYTTD1_uc011buk.1_3'UTR	NM_032288	NP_115664			forty-two-three domain containing 1 isoform 1						mRNA export from nucleus	nuclear speck	mRNA binding|protein binding				0	all_cancers(143;1.15e-09)|Ovarian(172;0.0418)|Breast(254;0.0976)	Lung NSC(153;0.132)	Epithelial(36;2.19e-23)|all cancers(36;1.39e-21)|OV - Ovarian serous cystadenocarcinoma(49;1.21e-18)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(93;0.175)														---	---	---	---
Unknown	0	broad.mit.edu	37	4	1389815	1389815	+	IGR	DEL	G	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:1389815delG								CRIPAK (33 upstream) : FAM53A (251794 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	3923361	3923361	+	IGR	DEL	G	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:3923361delG								ADRA2C (153110 upstream) : LOC348926 (20309 downstream)																																			---	---	---	---
ANAPC4	29945	broad.mit.edu	37	4	25411236	25411236	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:25411236delT	uc003gro.2	+						ANAPC4_uc003grp.2_Intron	NM_013367	NP_037499			anaphase-promoting complex subunit 4						anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|cell division|G2/M transition of mitotic cell cycle|mitotic anaphase|mitotic cell cycle spindle assembly checkpoint|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|protein K11-linked ubiquitination	anaphase-promoting complex|cytosol|nucleoplasm	protein phosphatase binding|ubiquitin-protein ligase activity			ovary(2)|large_intestine(1)|pancreas(1)|skin(1)	5		Breast(46;0.0503)																---	---	---	---
SEL1L3	23231	broad.mit.edu	37	4	25804213	25804213	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:25804213delT	uc003gru.3	-						SEL1L3_uc003grv.2_Intron	NM_015187	NP_056002			sel-1 suppressor of lin-12-like 3							integral to membrane	binding				0																		---	---	---	---
ARAP2	116984	broad.mit.edu	37	4	36230062	36230062	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:36230062delT	uc003gsq.1	-						ARAP2_uc003gsr.1_Intron	NM_015230	NP_056045			ArfGAP with RhoGAP domain, ankyrin repeat and PH						regulation of ARF GTPase activity|small GTPase mediated signal transduction	cytosol	ARF GTPase activator activity|phosphatidylinositol-3,4,5-trisphosphate binding|zinc ion binding			ovary(1)|pancreas(1)|skin(1)	3																		---	---	---	---
LIAS	11019	broad.mit.edu	37	4	39478849	39478849	+	3'UTR	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:39478849delA	uc003guf.2	+	11					LIAS_uc003gug.2_3'UTR|LIAS_uc003guh.2_3'UTR	NM_006859	NP_006850			lipoic acid synthetase isoform 1 precursor						inflammatory response|response to lipopolysaccharide|response to oxidative stress	mitochondrion	4 iron, 4 sulfur cluster binding|lipoate synthase activity|metal ion binding				0					Lipoic Acid(DB00166)													---	---	---	---
SLC30A9	10463	broad.mit.edu	37	4	42037517	42037518	+	Intron	DEL	TT	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:42037517_42037518delTT	uc003gwl.2	+						SLC30A9_uc011byx.1_Intron	NM_006345	NP_006336			solute carrier family 30 (zinc transporter),						nucleotide-excision repair|zinc ion transport	cytoskeleton|integral to membrane|nucleus	cation transmembrane transporter activity|nucleotide binding|sequence-specific DNA binding transcription factor activity			central_nervous_system(2)|ovary(1)	3																		---	---	---	---
C4orf14	84273	broad.mit.edu	37	4	57839652	57839652	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:57839652delT	uc003hck.2	-							NM_032313	NP_115689			hypothetical protein LOC84273								GTP binding			ovary(1)|breast(1)	2	Glioma(25;0.08)|all_neural(26;0.181)																	---	---	---	---
Unknown	0	broad.mit.edu	37	4	70267902	70267902	+	IGR	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:70267902delA								UGT2B28 (107135 upstream) : UGT2B4 (77982 downstream)																																			---	---	---	---
DCK	1633	broad.mit.edu	37	4	71889230	71889231	+	Intron	INS	-	T	T	rs3833976		TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:71889230_71889231insT	uc003hfx.2	+						DCK_uc011cbb.1_Intron	NM_000788	NP_000779			deoxycytidine kinase						purine base metabolic process|purine-containing compound salvage|pyrimidine base metabolic process|pyrimidine nucleoside salvage|pyrimidine nucleotide metabolic process	cytosol|nucleus	ATP binding|deoxycytidine kinase activity|drug binding|phosphotransferase activity, alcohol group as acceptor|protein homodimerization activity			ovary(1)	1			Lung(101;0.235)		Cladribine(DB00242)|Clofarabine(DB00631)|Decitabine(DB01262)|Fludarabine(DB01073)|Gemcitabine(DB00441)|Pemetrexed(DB00642)|Zalcitabine(DB00943)													---	---	---	---
RASSF6	166824	broad.mit.edu	37	4	74441817	74441817	+	3'UTR	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:74441817delT	uc003hhd.1	-	11					RASSF6_uc003hhc.1_3'UTR|RASSF6_uc010iik.1_3'UTR|RASSF6_uc010iil.1_3'UTR	NM_201431	NP_958834			Ras association (RalGDS/AF-6) domain family 6						apoptosis|signal transduction		protein binding			pancreas(2)	2	Breast(15;0.00102)		all cancers(17;0.00104)|Lung(101;0.128)|LUSC - Lung squamous cell carcinoma(112;0.187)															---	---	---	---
SEC31A	22872	broad.mit.edu	37	4	83740164	83740164	+	3'UTR	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:83740164delT	uc003hnf.2	-	27					SEC31A_uc003hnd.2_3'UTR|SEC31A_uc003hne.2_3'UTR|SEC31A_uc011ccl.1_3'UTR|SEC31A_uc003hnl.2_3'UTR|SEC31A_uc003hng.2_3'UTR|SEC31A_uc003hnh.2_3'UTR|SEC31A_uc003hni.2_3'UTR|SEC31A_uc003hnj.2_3'UTR|SEC31A_uc011ccm.1_3'UTR|SEC31A_uc011ccn.1_3'UTR|SEC31A_uc003hnk.2_3'UTR|SEC31A_uc003hnm.2_3'UTR	NM_001077207	NP_001070675			SEC31 homolog A isoform 1						COPII vesicle coating|post-translational protein modification|protein N-linked glycosylation via asparagine|protein transport|response to calcium ion	COPII vesicle coat|cytosol|endoplasmic reticulum membrane|perinuclear region of cytoplasm	calcium-dependent protein binding		SEC31A/JAK2(4)|SEC31A/ALK(3)	haematopoietic_and_lymphoid_tissue(4)|soft_tissue(3)|breast(1)	8		Hepatocellular(203;0.114)																---	---	---	---
CENPE	1062	broad.mit.edu	37	4	104072322	104072322	+	Intron	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:104072322delA	uc003hxb.1	-						CENPE_uc003hxc.1_Intron	NM_001813	NP_001804			centromere protein E						blood coagulation|cell division|kinetochore assembly|microtubule-based movement|mitotic chromosome movement towards spindle pole|mitotic metaphase|mitotic metaphase plate congression|mitotic prometaphase|multicellular organismal development|positive regulation of protein kinase activity	condensed chromosome kinetochore|cytosol|microtubule|nucleus|spindle	ATP binding|kinetochore binding|microtubule motor activity			ovary(5)|breast(4)	9				OV - Ovarian serous cystadenocarcinoma(123;2.95e-08)														---	---	---	---
TBCK	93627	broad.mit.edu	37	4	107037270	107037270	+	Intron	DEL	T	-	-	rs79018134		TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:107037270delT	uc010ilv.2	-						TBCK_uc003hyb.2_Intron|TBCK_uc003hye.2_Intron|TBCK_uc003hyc.2_Intron|TBCK_uc003hyd.2_Intron|TBCK_uc003hyf.2_Intron	NM_001163435	NP_001156907			TBC domain-containing protein kinase-like							intracellular	Rab GTPase activator activity			large_intestine(2)|upper_aerodigestive_tract(1)|stomach(1)|ovary(1)	5																		---	---	---	---
RPL34	6164	broad.mit.edu	37	4	109546421	109546421	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:109546421delT	uc003hyz.2	+						RPL34_uc003hza.2_Intron	NM_000995	NP_000986			ribosomal protein L34						endocrine pancreas development|translational elongation|translational termination|viral transcription	cytosolic large ribosomal subunit	protein binding|RNA binding|structural constituent of ribosome				0		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;0.000286)														---	---	---	---
UGT8	7368	broad.mit.edu	37	4	115585067	115585067	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:115585067delT	uc003ibs.2	+						UGT8_uc003ibt.2_Intron|UGT8_uc011cge.1_Intron	NM_001128174	NP_001121646			UDP-galactose-ceramide galactosyltransferase 8						central nervous system development|peripheral nervous system development	integral to membrane	2-hydroxyacylsphingosine 1-beta-galactosyltransferase activity|UDP-galactose:glucosylceramide beta-1,4-galactosyltransferase activity			ovary(1)|skin(1)	2		Ovarian(17;0.156)		OV - Ovarian serous cystadenocarcinoma(123;0.000632)														---	---	---	---
NDST3	9348	broad.mit.edu	37	4	119163441	119163441	+	Intron	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:119163441delA	uc003ibx.2	+							NM_004784	NP_004775			N-deacetylase/N-sulfotransferase (heparan							Golgi membrane|integral to membrane	[heparan sulfate]-glucosamine N-sulfotransferase activity|hydrolase activity			large_intestine(1)	1																		---	---	---	---
ELMOD2	255520	broad.mit.edu	37	4	141448706	141448706	+	Intron	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:141448706delA	uc003iik.2	+							NM_153702	NP_714913			ELMO/CED-12 domain containing 2						phagocytosis|regulation of defense response to virus|response to virus	cytoskeleton	GTPase activator activity			ovary(1)	1	all_hematologic(180;0.162)																	---	---	---	---
USP38	84640	broad.mit.edu	37	4	144130643	144130644	+	Intron	DEL	AA	-	-	rs111830994		TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:144130643_144130644delAA	uc003ijb.2	+						USP38_uc003ija.3_Intron|USP38_uc003ijc.2_Intron	NM_032557	NP_115946			ubiquitin specific peptidase 38						ubiquitin-dependent protein catabolic process		cysteine-type peptidase activity|ubiquitin thiolesterase activity			lung(2)|ovary(1)|breast(1)|pancreas(1)	5	all_hematologic(180;0.158)																	---	---	---	---
ABCE1	6059	broad.mit.edu	37	4	146041224	146041224	+	Frame_Shift_Del	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:146041224delA	uc003ijx.2	+	11	1503	c.1063delA	c.(1063-1065)AAAfs	p.K355fs	ABCE1_uc003ijy.2_Frame_Shift_Del_p.K355fs|ABCE1_uc010iot.2_RNA	NM_001040876	NP_001035809	P61221	ABCE1_HUMAN	ATP-binding cassette, sub-family E, member 1	355	ABC transporter 2.				interspecies interaction between organisms|response to virus|RNA catabolic process	mitochondrion	ATP binding|ATPase activity|electron carrier activity|iron-sulfur cluster binding|ribonuclease inhibitor activity			skin(1)	1	all_hematologic(180;0.151)																	---	---	---	---
ZNF827	152485	broad.mit.edu	37	4	146770908	146770908	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:146770908delT	uc003ikn.2	-						ZNF827_uc003ikm.2_Intron|ZNF827_uc010iox.2_Intron	NM_178835	NP_849157			zinc finger protein 827						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0	all_hematologic(180;0.151)																	---	---	---	---
ACCN5	51802	broad.mit.edu	37	4	156773541	156773541	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:156773541delT	uc003ipe.1	-							NM_017419	NP_059115			amiloride-sensitive cation channel 5,							integral to membrane|plasma membrane				ovary(2)|skin(1)	3	all_hematologic(180;0.24)	Renal(120;0.0458)		KIRC - Kidney renal clear cell carcinoma(143;0.0464)|Kidney(143;0.058)|COAD - Colon adenocarcinoma(41;0.141)														---	---	---	---
GLRB	2743	broad.mit.edu	37	4	158059927	158059927	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:158059927delT	uc003ipj.2	+							NM_000824	NP_000815			glycine receptor, beta isoform A precursor						nervous system development|neuropeptide signaling pathway|startle response	cell junction|chloride channel complex|integral to plasma membrane|postsynaptic membrane	extracellular-glycine-gated chloride channel activity|protein binding|receptor activity			skin(2)	2	all_hematologic(180;0.24)	Renal(120;0.0458)		KIRC - Kidney renal clear cell carcinoma(143;0.0564)|COAD - Colon adenocarcinoma(41;0.0642)|Kidney(143;0.0707)	Glycine(DB00145)													---	---	---	---
RAPGEF2	9693	broad.mit.edu	37	4	160251796	160251797	+	Intron	INS	-	A	A	rs78225051		TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:160251796_160251797insA	uc003iqg.3	+							NM_014247	NP_055062			Rap guanine nucleotide exchange factor 2						cAMP-mediated signaling|MAPKKK cascade|small GTPase mediated signal transduction	integral to plasma membrane|intracellular	calcium ion binding|diacylglycerol binding|Rap GTPase activator activity|Rap guanyl-nucleotide exchange factor activity|signal transducer activity			lung(2)|upper_aerodigestive_tract(1)|skin(1)	4	all_hematologic(180;0.24)			COAD - Colon adenocarcinoma(41;0.0817)														---	---	---	---
AGA	175	broad.mit.edu	37	4	178361260	178361260	+	Intron	DEL	T	-	-	rs75220849		TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:178361260delT	uc003iuu.1	-						AGA_uc003iuv.1_5'Flank|AGA_uc003iuw.2_5'Flank	NM_000027	NP_000018			aspartylglucosaminidase precursor						asparagine catabolic process via L-aspartate|protein deglycosylation|protein maturation	endoplasmic reticulum|intermediate filament cytoskeleton|lysosome|microtubule cytoskeleton	N4-(beta-N-acetylglucosaminyl)-L-asparaginase activity				0		all_lung(41;1.27e-09)|Lung NSC(41;1.1e-08)|Breast(14;6.27e-05)|Melanoma(52;0.00102)|Renal(120;0.00988)|Prostate(90;0.00996)|all_hematologic(60;0.014)|Hepatocellular(41;0.148)|all_neural(102;0.164)|Colorectal(36;0.245)		all cancers(43;1.37e-22)|Epithelial(43;3.86e-20)|OV - Ovarian serous cystadenocarcinoma(60;3.8e-11)|Colorectal(24;6.98e-05)|GBM - Glioblastoma multiforme(59;0.000362)|COAD - Colon adenocarcinoma(29;0.000462)|STAD - Stomach adenocarcinoma(60;0.0029)|LUSC - Lung squamous cell carcinoma(193;0.0328)|READ - Rectum adenocarcinoma(43;0.163)														---	---	---	---
SEMA5A	9037	broad.mit.edu	37	5	9201932	9201932	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:9201932delT	uc003jek.2	-							NM_003966	NP_003957			semaphorin 5A precursor						cell adhesion|cell-cell signaling	integral to membrane|plasma membrane				ovary(1)|central_nervous_system(1)	2																		---	---	---	---
GUSBP1	728411	broad.mit.edu	37	5	21459960	21459960	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:21459960delT	uc010iub.2	+						GUSBP1_uc011cnn.1_Intron|GUSBP1_uc003jgh.3_Intron|GUSBP1_uc003jgf.3_Intron|GUSBP1_uc003jgg.3_Intron	NR_027028				SubName: Full=Putative uncharacterized protein GUSBL2;												0																OREG0016459	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
C5orf22	55322	broad.mit.edu	37	5	31541526	31541526	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:31541526delT	uc003jhj.3	+						C5orf22_uc011cnw.1_Intron|C5orf22_uc003jhk.3_Intron	NM_018356	NP_060826			hypothetical protein LOC55322											ovary(2)	2																		---	---	---	---
C5orf42	65250	broad.mit.edu	37	5	37120153	37120153	+	Intron	DEL	A	-	-	rs75040582	by1000genomes	TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:37120153delA	uc011cpa.1	-						C5orf42_uc003jko.1_Intron|C5orf42_uc003jkp.1_Intron|C5orf42_uc011coy.1_Intron|C5orf42_uc003jks.2_Intron|C5orf42_uc011coz.1_Intron	NM_023073	NP_075561			hypothetical protein LOC65250											ovary(4)|breast(2)|skin(1)	7	all_lung(31;0.000616)		COAD - Colon adenocarcinoma(61;0.14)|Epithelial(62;0.177)|Colorectal(62;0.202)															---	---	---	---
C5orf42	65250	broad.mit.edu	37	5	37162787	37162788	+	Intron	DEL	TT	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:37162787_37162788delTT	uc011cpa.1	-						C5orf42_uc011coy.1_Intron|C5orf42_uc003jks.2_Intron|C5orf42_uc011coz.1_Intron	NM_023073	NP_075561			hypothetical protein LOC65250											ovary(4)|breast(2)|skin(1)	7	all_lung(31;0.000616)		COAD - Colon adenocarcinoma(61;0.14)|Epithelial(62;0.177)|Colorectal(62;0.202)															---	---	---	---
WDR70	55100	broad.mit.edu	37	5	37697601	37697601	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:37697601delT	uc003jkv.2	+						WDR70_uc010iva.1_Intron	NM_018034	NP_060504			WD repeat domain 70											ovary(1)|central_nervous_system(1)	2	all_lung(31;0.000285)		COAD - Colon adenocarcinoma(61;0.14)|Colorectal(62;0.202)															---	---	---	---
KIF2A	3796	broad.mit.edu	37	5	61662224	61662224	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:61662224delT	uc003jsy.3	+						KIF2A_uc003jsz.3_Intron|KIF2A_uc010iwp.2_Intron|KIF2A_uc003jsx.3_Intron|KIF2A_uc010iwq.2_Intron	NM_004520	NP_004511			kinesin heavy chain member 2 isoform 1						blood coagulation|cell differentiation|cell division|microtubule-based movement|mitotic prometaphase|mitotic spindle organization|nervous system development	centrosome|cytosol|microtubule|spindle pole	ATP binding|microtubule motor activity|protein binding				0		Lung NSC(810;8.94e-06)|Prostate(74;0.0132)|Ovarian(174;0.051)|Breast(144;0.077)		Lung(70;0.14)														---	---	---	---
GTF2H2B	653238	broad.mit.edu	37	5	69717511	69717512	+	Intron	INS	-	G	G			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:69717511_69717512insG	uc003jzb.3	+						uc011crh.1_Intron|uc011crl.1_Intron|LOC100170939_uc010ixu.2_Intron|uc003jyr.1_Intron|LOC100170939_uc003jys.2_Intron|LOC100170939_uc011crn.1_Intron|uc011cro.1_Intron|GTF2H2B_uc011crp.1_Intron|GTF2H2B_uc003jza.3_Intron|GTF2H2B_uc003jzd.1_5'Flank	NM_001098729	NP_001092199			general transcription factor IIH, polypeptide												0																		---	---	---	---
RPS23	6228	broad.mit.edu	37	5	81571879	81571879	+	3'UTR	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:81571879delT	uc003khu.2	-	4						NM_001025	NP_001016			ribosomal protein S23						endocrine pancreas development|translational elongation|translational termination|viral transcription	cytosolic small ribosomal subunit	protein binding|structural constituent of ribosome				0		Lung NSC(167;0.0025)|all_lung(232;0.00278)|Ovarian(174;0.0336)		OV - Ovarian serous cystadenocarcinoma(54;1.94e-42)|Epithelial(54;8.38e-37)|all cancers(79;1.42e-31)														---	---	---	---
TMEM167A	153339	broad.mit.edu	37	5	82372898	82372898	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:82372898delT	uc003khx.3	-						XRCC4_uc003kia.1_5'Flank|XRCC4_uc003kib.2_5'Flank|XRCC4_uc003kid.2_5'Flank|XRCC4_uc003kic.2_5'Flank|XRCC4_uc003kie.2_5'Flank	NM_174909	NP_777569			transmembrane protein 167A precursor							Golgi membrane|integral to membrane					0																		---	---	---	---
TMEM161B	153396	broad.mit.edu	37	5	87491918	87491918	+	3'UTR	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:87491918delT	uc003kjc.2	-	12					TMEM161B_uc011cty.1_3'UTR|TMEM161B_uc010jax.2_RNA|TMEM161B_uc011ctx.1_3'UTR	NM_153354	NP_699185			transmembrane protein 161B							integral to membrane				skin(2)	2		all_cancers(142;0.000275)|Lung NSC(167;0.00901)|all_lung(232;0.0111)|Colorectal(57;0.0959)|Ovarian(174;0.1)		OV - Ovarian serous cystadenocarcinoma(54;6.24e-36)|Epithelial(54;6.8e-31)|all cancers(79;1.07e-26)														---	---	---	---
TMEM161B	153396	broad.mit.edu	37	5	87492365	87492365	+	Intron	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:87492365delA	uc003kjc.2	-						TMEM161B_uc011cty.1_Intron|TMEM161B_uc010jax.2_Intron|TMEM161B_uc011ctx.1_Intron	NM_153354	NP_699185			transmembrane protein 161B							integral to membrane				skin(2)	2		all_cancers(142;0.000275)|Lung NSC(167;0.00901)|all_lung(232;0.0111)|Colorectal(57;0.0959)|Ovarian(174;0.1)		OV - Ovarian serous cystadenocarcinoma(54;6.24e-36)|Epithelial(54;6.8e-31)|all cancers(79;1.07e-26)														---	---	---	---
COMMD10	51397	broad.mit.edu	37	5	115553612	115553612	+	Intron	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:115553612delA	uc003krt.1	+							NM_016144	NP_057228			COMM domain containing 10								protein binding			ovary(1)	1		all_cancers(142;0.0834)|all_epithelial(76;0.00314)|Prostate(80;0.0102)|Ovarian(225;0.232)		OV - Ovarian serous cystadenocarcinoma(64;4.3e-07)|Epithelial(69;8.06e-07)|all cancers(49;4.06e-05)														---	---	---	---
PRRC1	133619	broad.mit.edu	37	5	126866120	126866121	+	Intron	DEL	TT	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:126866120_126866121delTT	uc003kuk.2	+						PRRC1_uc003kuj.3_Intron	NM_130809	NP_570721			proline-rich coiled-coil 1							Golgi apparatus					0		Prostate(80;0.165)	KIRC - Kidney renal clear cell carcinoma(527;0.0268)|Kidney(363;0.0488)	OV - Ovarian serous cystadenocarcinoma(64;0.0851)|Epithelial(69;0.113)														---	---	---	---
ISOC1	51015	broad.mit.edu	37	5	128440485	128440485	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:128440485delT	uc003kva.2	+							NM_016048	NP_057132			isochorismatase domain containing 1							peroxisome	catalytic activity				0		all_cancers(142;0.0813)|Prostate(80;0.0865)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)	Epithelial(69;0.138)|OV - Ovarian serous cystadenocarcinoma(64;0.164)														---	---	---	---
MYOT	9499	broad.mit.edu	37	5	137217571	137217571	+	Intron	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:137217571delA	uc011cye.1	+						MYOT_uc003lbv.2_Intron|MYOT_uc011cyg.1_Intron|MYOT_uc011cyh.1_Intron	NM_001135940	NP_001129412			myotilin isoform b						muscle contraction	actin cytoskeleton|sarcolemma|sarcomere	actin binding|structural constituent of muscle			large_intestine(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0109)															---	---	---	---
Unknown	0	broad.mit.edu	37	5	147517869	147517869	+	IGR	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:147517869delT								SPINK5 (944 upstream) : SPINK14 (31427 downstream)																																			---	---	---	---
ODZ2	57451	broad.mit.edu	37	5	167589926	167589926	+	Intron	DEL	A	-	-	rs111814381		TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:167589926delA	uc010jjd.2	+						ODZ2_uc003lzr.3_Intron|ODZ2_uc003lzt.3_Intron|ODZ2_uc010jje.2_Intron|uc003lzs.1_Intron	NM_001122679	NP_001116151			odz, odd Oz/ten-m homolog 2											ovary(6)|central_nervous_system(4)	10	Renal(175;0.00124)|Lung NSC(126;0.136)|all_lung(126;0.242)	Medulloblastoma(196;0.0241)|all_neural(177;0.026)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	all cancers(165;0.0444)|OV - Ovarian serous cystadenocarcinoma(192;0.0694)|Epithelial(171;0.124)														---	---	---	---
Unknown	0	broad.mit.edu	37	5	168043289	168043289	+	IGR	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:168043289delT								PANK3 (36701 upstream) : SLIT3 (49783 downstream)																																			---	---	---	---
TMEM14B	81853	broad.mit.edu	37	6	10756864	10756864	+	3'UTR	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:10756864delA	uc003mzk.3	+	6					SYCP2L_uc011dim.1_Intron|TMEM14B_uc010jor.2_3'UTR|TMEM14B_uc010jos.1_Intron	NM_030969	NP_112231			transmembrane protein 14B isoform a							integral to membrane					0	Ovarian(93;0.107)|Breast(50;0.137)	all_hematologic(90;0.135)																---	---	---	---
SIRT5	23408	broad.mit.edu	37	6	13584591	13584591	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:13584591delT	uc003nay.2	+						SIRT5_uc003naw.2_Intron|SIRT5_uc003nax.2_Intron|SIRT5_uc011dit.1_Intron	NM_012241	NP_036373			sirtuin 5 isoform 1						chromatin silencing|protein ADP-ribosylation|protein deacetylation	mitochondrial intermembrane space|mitochondrial matrix	hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides|NAD+ ADP-ribosyltransferase activity|NAD+ binding|zinc ion binding			skin(2)|upper_aerodigestive_tract(1)	3	Breast(50;0.00669)|Ovarian(93;0.0634)	all_hematologic(90;0.117)	Epithelial(50;0.176)		Suramin(DB04786)													---	---	---	---
MYLIP	29116	broad.mit.edu	37	6	16141709	16141709	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:16141709delT	uc003nbq.2	+						MYLIP_uc003nbr.2_Intron	NM_013262	NP_037394			myosin regulatory light chain interacting						cellular component movement|nervous system development	cytoplasm|cytoskeleton|extrinsic to membrane	cytoskeletal protein binding|ubiquitin-protein ligase activity|zinc ion binding			pancreas(1)	1	Breast(50;0.0799)|Ovarian(93;0.103)	all_hematologic(90;0.0895)	Epithelial(50;0.241)															---	---	---	---
CAP2	10486	broad.mit.edu	37	6	17531050	17531050	+	Intron	DEL	T	-	-	rs35589543		TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:17531050delT	uc003ncb.2	+						CAP2_uc010jpk.1_Intron|CAP2_uc011dja.1_Intron|CAP2_uc011djb.1_Intron|CAP2_uc011djc.1_Intron|CAP2_uc011djd.1_Intron	NM_006366	NP_006357			adenylyl cyclase-associated protein 2						activation of adenylate cyclase activity|axon guidance|cytoskeleton organization|establishment or maintenance of cell polarity|signal transduction	plasma membrane	actin binding			ovary(1)	1	Breast(50;0.0333)|Ovarian(93;0.0386)	all_hematologic(90;0.0466)	all cancers(50;0.194)|Epithelial(50;0.227)															---	---	---	---
KIF13A	63971	broad.mit.edu	37	6	17898424	17898424	+	Intron	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:17898424delA	uc003ncg.3	-						KIF13A_uc003ncf.2_Intron|KIF13A_uc003nch.3_Intron|KIF13A_uc003nci.3_Intron	NM_022113	NP_071396			kinesin family member 13A isoform a						cargo loading into vesicle|cell cycle|cytokinesis|endosome to lysosome transport|Golgi to plasma membrane protein transport|melanosome organization|plus-end-directed vesicle transport along microtubule	centrosome|endosome membrane|microtubule|midbody|trans-Golgi network membrane	ATP binding|microtubule motor activity|protein binding			large_intestine(2)|ovary(2)	4	Breast(50;0.0107)|Ovarian(93;0.016)	all_hematologic(90;0.125)	all cancers(50;0.0865)|Epithelial(50;0.0974)															---	---	---	---
C6orf106	64771	broad.mit.edu	37	6	34664457	34664457	+	5'UTR	DEL	G	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:34664457delG	uc003ojr.2	-	1					C6orf106_uc003ojs.2_5'UTR	NM_024294	NP_077270			chromosome 6 open reading frame 106 isoform a											skin(2)|ovary(1)	3																		---	---	---	---
NFYA	4800	broad.mit.edu	37	6	41057863	41057863	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:41057863delT	uc003opo.2	+						NFYA_uc003opp.2_Intron|NFYA_uc003opq.2_Intron	NM_002505	NP_002496			nuclear transcription factor Y, alpha isoform 1						transcription from RNA polymerase II promoter	CCAAT-binding factor complex	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity				0	Ovarian(28;0.0418)|Colorectal(47;0.196)																	---	---	---	---
HMGCLL1	54511	broad.mit.edu	37	6	55381523	55381523	+	Intron	DEL	A	-	-	rs71693355		TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:55381523delA	uc003pcn.2	-						HMGCLL1_uc003pco.2_Intron|HMGCLL1_uc010jzx.2_Intron|HMGCLL1_uc011dxc.1_Intron|HMGCLL1_uc011dxd.1_Intron|HMGCLL1_uc011dxe.1_Intron|HMGCLL1_uc003pcp.2_Intron	NM_019036	NP_061909			3-hydroxymethyl-3-methylglutaryl-Coenzyme A								hydroxymethylglutaryl-CoA lyase activity|metal ion binding			skin(2)|ovary(1)|pancreas(1)	4	Lung NSC(77;0.0875)		LUSC - Lung squamous cell carcinoma(124;0.23)															---	---	---	---
PHF3	23469	broad.mit.edu	37	6	64410483	64410483	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:64410483delT	uc003pep.1	+						PHF3_uc010kah.1_Intron|PHF3_uc003pen.2_Intron|PHF3_uc011dxs.1_Intron	NM_015153	NP_055968			PHD finger protein 3						multicellular organismal development|transcription, DNA-dependent	nucleus	zinc ion binding			ovary(3)|lung(1)|skin(1)	5	all_cancers(3;0.0241)|all_epithelial(2;0.00306)|Lung NSC(77;0.121)		LUSC - Lung squamous cell carcinoma(74;0.0644)|Lung(124;0.148)															---	---	---	---
PGM3	5238	broad.mit.edu	37	6	83900377	83900377	+	Intron	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:83900377delA	uc003pjv.2	-						PGM3_uc003pjw.2_Intron|PGM3_uc011dyz.1_Intron|RWDD2A_uc003pjx.3_5'Flank|RWDD2A_uc011dza.1_5'Flank	NM_015599	NP_056414			phosphoglucomutase 3						dolichol-linked oligosaccharide biosynthetic process|embryo development ending in birth or egg hatching|glucose 1-phosphate metabolic process|hemopoiesis|post-translational protein modification|protein N-linked glycosylation via asparagine|UDP-N-acetylglucosamine biosynthetic process	cytosol	magnesium ion binding|phosphoacetylglucosamine mutase activity|phosphoglucomutase activity				0		all_cancers(76;0.000504)|Acute lymphoblastic leukemia(125;3.85e-06)|all_hematologic(105;0.0017)|all_epithelial(107;0.068)		BRCA - Breast invasive adenocarcinoma(397;0.0478)														---	---	---	---
CYB5R4	51167	broad.mit.edu	37	6	84624111	84624111	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:84624111delT	uc003pkf.2	+							NM_016230	NP_057314			cytochrome b5 reductase 4						cell development|detection of oxygen|generation of precursor metabolites and energy|glucose homeostasis|insulin secretion|response to antibiotic|superoxide metabolic process	endoplasmic reticulum|perinuclear region of cytoplasm	cytochrome-b5 reductase activity|heme binding|NAD(P)H oxidase activity			breast(2)	2		all_cancers(76;7e-07)|Acute lymphoblastic leukemia(125;2.69e-07)|all_hematologic(105;0.000151)|all_epithelial(107;0.00128)		BRCA - Breast invasive adenocarcinoma(397;0.0871)														---	---	---	---
TBX18	9096	broad.mit.edu	37	6	85469936	85469936	+	Intron	DEL	T	-	-	rs74587058		TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:85469936delT	uc003pkl.1	-						TBX18_uc010kbq.1_Intron	NM_001080508	NP_001073977			T-box 18						multicellular organismal development	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity			ovary(2)|pancreas(2)|lung(1)	5		all_cancers(76;0.000283)|Acute lymphoblastic leukemia(125;3.66e-08)|all_hematologic(105;8.61e-05)|all_epithelial(107;0.0858)		BRCA - Breast invasive adenocarcinoma(108;0.0267)														---	---	---	---
ZNF292	23036	broad.mit.edu	37	6	87969484	87969484	+	Frame_Shift_Del	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:87969484delA	uc003plm.3	+	8	6178	c.6137delA	c.(6136-6138)GAAfs	p.E2046fs		NM_015021	NP_055836	O60281	ZN292_HUMAN	zinc finger protein 292	2046					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(4)	4		all_cancers(76;3.82e-09)|Prostate(29;1.34e-10)|Acute lymphoblastic leukemia(125;2.17e-10)|all_hematologic(105;1.08e-06)|all_epithelial(107;5.31e-05)		BRCA - Breast invasive adenocarcinoma(108;0.0199)														---	---	---	---
MDN1	23195	broad.mit.edu	37	6	90409616	90409616	+	Intron	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:90409616delA	uc003pnn.1	-							NM_014611	NP_055426			MDN1, midasin homolog						protein complex assembly|regulation of protein complex assembly	nucleus	ATP binding|ATPase activity|unfolded protein binding			ovary(8)|skin(2)	10		all_cancers(76;1.47e-06)|Acute lymphoblastic leukemia(125;2.23e-10)|Prostate(29;5.55e-10)|all_hematologic(105;2.42e-06)|all_epithelial(107;0.00246)		BRCA - Breast invasive adenocarcinoma(108;0.0193)														---	---	---	---
SCML4	256380	broad.mit.edu	37	6	108076968	108076968	+	Intron	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:108076968delA	uc010kdf.2	-						SCML4_uc003prz.3_Intron|SCML4_uc011eam.1_Intron|SCML4_uc003psa.3_Intron	NM_198081	NP_932347			sex comb on midleg-like 4						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding			ovary(1)	1		all_cancers(87;3.26e-06)|Acute lymphoblastic leukemia(125;3.08e-08)|all_hematologic(75;1.15e-06)|all_epithelial(87;0.00142)|Colorectal(196;0.0316)		BRCA - Breast invasive adenocarcinoma(108;0.01)|Epithelial(106;0.0509)|all cancers(137;0.0586)|OV - Ovarian serous cystadenocarcinoma(136;0.0758)														---	---	---	---
ROS1	6098	broad.mit.edu	37	6	117704314	117704315	+	Intron	DEL	GC	-	-	rs112993324		TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:117704314_117704315delGC	uc003pxp.1	-						ROS1_uc011ebi.1_Intron|GOPC_uc003pxq.1_Intron	NM_002944	NP_002935			proto-oncogene c-ros-1 protein precursor						transmembrane receptor protein tyrosine kinase signaling pathway	membrane fraction|sodium:potassium-exchanging ATPase complex	ATP binding|transmembrane receptor protein tyrosine kinase activity			lung(8)|ovary(6)|central_nervous_system(3)|skin(3)|stomach(2)|breast(2)|large_intestine(1)	25		all_cancers(87;0.00846)|all_epithelial(87;0.0242)		GBM - Glioblastoma multiforme(226;0.0387)|OV - Ovarian serous cystadenocarcinoma(136;0.0954)|all cancers(137;0.137)				T	GOPC|ROS1	glioblastoma|NSCLC								---	---	---	---
TRDN	10345	broad.mit.edu	37	6	123786155	123786156	+	Intron	DEL	AA	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:123786155_123786156delAA	uc003pzj.1	-						TRDN_uc003pzk.1_Intron|TRDN_uc003pzl.1_Intron|TRDN_uc010ken.2_Intron|uc003pzm.1_Intron	NM_006073	NP_006064			triadin						muscle contraction	integral to membrane|plasma membrane|sarcoplasmic reticulum membrane	receptor binding			ovary(1)	1				GBM - Glioblastoma multiforme(226;0.184)														---	---	---	---
FAM54A	113115	broad.mit.edu	37	6	136566111	136566111	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:136566111delT	uc010kgp.1	-						FAM54A_uc003qgt.1_Intron|FAM54A_uc003qgu.1_Intron	NM_001099286	NP_001092756			DUF729 domain containing 1											skin(1)	1	Colorectal(23;0.24)			GBM - Glioblastoma multiforme(68;0.00228)|OV - Ovarian serous cystadenocarcinoma(155;0.00504)														---	---	---	---
MAP3K5	4217	broad.mit.edu	37	6	136883493	136883494	+	Intron	DEL	TT	-	-	rs11322947		TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:136883493_136883494delTT	uc003qhc.2	-						MAP3K5_uc011edj.1_Intron	NM_005923	NP_005914			mitogen-activated protein kinase kinase kinase						activation of JUN kinase activity|activation of MAPKK activity|cellular response to hydrogen peroxide|induction of apoptosis by extracellular signals|interspecies interaction between organisms		ATP binding|caspase activator activity|magnesium ion binding|MAP kinase kinase kinase activity|protein homodimerization activity|protein phosphatase binding			ovary(2)|skin(2)|lung(1)	5	Colorectal(23;0.24)			GBM - Glioblastoma multiforme(68;0.00137)|OV - Ovarian serous cystadenocarcinoma(155;0.00569)														---	---	---	---
UTRN	7402	broad.mit.edu	37	6	144796037	144796037	+	Intron	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:144796037delA	uc003qkt.2	+						UTRN_uc010khq.1_Intron	NM_007124	NP_009055			utrophin						muscle contraction|muscle organ development|positive regulation of cell-matrix adhesion	cell junction|cytoplasm|cytoskeleton|membrane fraction|nucleus|postsynaptic membrane	actin binding|calcium ion binding|zinc ion binding			ovary(4)|pancreas(1)	5		Ovarian(120;0.218)		OV - Ovarian serous cystadenocarcinoma(155;5.72e-07)|GBM - Glioblastoma multiforme(68;4.9e-05)|Colorectal(48;0.213)														---	---	---	---
C6orf97	80129	broad.mit.edu	37	6	151917439	151917439	+	Intron	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:151917439delA	uc003qol.2	+							NM_025059	NP_079335			hypothetical protein LOC80129												0		Ovarian(120;0.126)	BRCA - Breast invasive adenocarcinoma(37;0.111)	OV - Ovarian serous cystadenocarcinoma(155;1.48e-10)														---	---	---	---
IPCEF1	26034	broad.mit.edu	37	6	154568731	154568731	+	Intron	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:154568731delA	uc003qpx.2	-						IPCEF1_uc003qpw.2_Intron|IPCEF1_uc010kjh.2_Intron	NM_015553	NP_056368			phosphoinositide-binding protein PIP3-E isoform						response to oxidative stress	cytoplasm|plasma membrane	oxygen transporter activity|peroxidase activity				0																		---	---	---	---
ACTB	60	broad.mit.edu	37	7	5568135	5568137	+	In_Frame_Del	DEL	GAG	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:5568135_5568137delGAG	uc003sos.3	-	3	613_615	c.577_579delCTC	c.(577-579)CTCdel	p.L193del	ACTB_uc003sor.3_In_Frame_Del_p.L71del|ACTB_uc003sot.3_In_Frame_Del_p.L193del|ACTB_uc003soq.3_In_Frame_Del_p.L71del|ACTB_uc010ksy.2_In_Frame_Del_p.L71del	NM_001101	NP_001092	P60709	ACTB_HUMAN	beta actin	193					'de novo' posttranslational protein folding|adherens junction organization|axon guidance|blood coagulation|cell junction assembly|cellular component movement	cytoskeleton|cytosol|MLL5-L complex|NuA4 histone acetyltransferase complex|ribonucleoprotein complex	ATP binding|kinesin binding|nitric-oxide synthase binding|structural constituent of cytoskeleton				0		Ovarian(82;0.0606)		UCEC - Uterine corpus endometrioid carcinoma (126;0.175)|OV - Ovarian serous cystadenocarcinoma(56;4.24e-37)														---	---	---	---
C7orf26	79034	broad.mit.edu	37	7	6633948	6633948	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:6633948delT	uc003sqo.1	+						C7orf26_uc003sqp.1_Intron|C7orf26_uc003sqq.1_Intron	NM_024067	NP_076972			hypothetical protein LOC79034											ovary(1)	1		Ovarian(82;0.232)		UCEC - Uterine corpus endometrioid carcinoma (126;0.0986)														---	---	---	---
HDAC9	9734	broad.mit.edu	37	7	18988718	18988719	+	Intron	INS	-	T	T			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:18988718_18988719insT	uc003suh.2	+						HDAC9_uc003sue.2_Intron|HDAC9_uc003sui.2_Intron|HDAC9_uc003suj.2_Intron|HDAC9_uc003suk.2_Intron	NM_058176	NP_478056			histone deacetylase 9 isoform 1						B cell differentiation|cellular response to insulin stimulus|heart development|histone H3 deacetylation|histone H4 deacetylation|inflammatory response|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transcription, DNA-dependent|peptidyl-lysine deacetylation|positive regulation of cell migration involved in sprouting angiogenesis|regulation of skeletal muscle fiber development|transcription, DNA-dependent	cytoplasm|histone deacetylase complex|histone methyltransferase complex|transcription factor complex	histone deacetylase activity (H3-K16 specific)|histone deacetylase binding|histone deacetylase binding|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 binding|protein kinase C binding|repressing transcription factor binding|transcription corepressor activity			lung(2)|central_nervous_system(2)|kidney(1)	5	all_lung(11;0.187)				Valproic Acid(DB00313)													---	---	---	---
CBX3	11335	broad.mit.edu	37	7	26251418	26251418	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:26251418delT	uc003sxt.2	+						CBX3_uc003sxu.2_Intron|CBX3_uc003sxv.2_Intron	NM_007276	NP_009207			chromobox homolog 3						chromatin remodeling|negative regulation of transcription, DNA-dependent|transcription, DNA-dependent	condensed chromosome, centromeric region|nuclear centromeric heterochromatin|nuclear euchromatin|nuclear inner membrane|spindle	enzyme binding|protein domain specific binding			ovary(1)	1																		---	---	---	---
FAM188B	84182	broad.mit.edu	37	7	30831331	30831331	+	Intron	DEL	A	-	-	rs60449260		TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:30831331delA	uc003tbt.2	+						FAM188B_uc010kwe.2_Intron	NM_032222	NP_115598			hypothetical protein LOC84182												0																		---	---	---	---
HERPUD2	64224	broad.mit.edu	37	7	35675101	35675101	+	Intron	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:35675101delA	uc003tet.2	-						HERPUD2_uc003tes.3_Intron	NM_022373	NP_071768			HERPUD family member 2						response to unfolded protein	integral to membrane				ovary(3)	3																		---	---	---	---
POLD2	5425	broad.mit.edu	37	7	44155940	44155940	+	Intron	DEL	C	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:44155940delC	uc010kxz.2	-						POLD2_uc003tke.3_Intron|POLD2_uc010kya.2_Intron|POLD2_uc003tkf.3_Intron	NM_006230	NP_006221			DNA-directed DNA polymerase delta 2						base-excision repair|DNA strand elongation involved in DNA replication|nucleotide-excision repair, DNA gap filling|S phase of mitotic cell cycle|telomere maintenance via recombination|telomere maintenance via semi-conservative replication|transcription-coupled nucleotide-excision repair	nucleoplasm	DNA binding|DNA-directed DNA polymerase activity|protein binding			ovary(2)	2																		---	---	---	---
SUN3	256979	broad.mit.edu	37	7	48045448	48045448	+	Intron	DEL	C	-	-	rs66650652		TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:48045448delC	uc003tof.2	-						SUN3_uc010kyq.2_Intron|SUN3_uc003tog.2_Intron|SUN3_uc011kcf.1_Intron	NM_152782	NP_689995			Sad1 and UNC84 domain containing 1							integral to membrane				central_nervous_system(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	53256452	53256452	+	IGR	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:53256452delA								POM121L12 (151835 upstream) : None (None downstream)																																			---	---	---	---
PSPH	5723	broad.mit.edu	37	7	56169674	56169674	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:56169674delT	uc003trj.2	-						CHCHD2_uc003tsa.2_Intron	NM_004577	NP_004568			phosphoserine phosphatase						L-serine biosynthetic process	cytoplasm	calcium ion binding|magnesium ion binding|phosphoserine phosphatase activity|protein homodimerization activity			ovary(1)|skin(1)	2	Breast(14;0.214)		Lung(13;0.00024)|LUSC - Lung squamous cell carcinoma(13;0.00099)															---	---	---	---
Unknown	0	broad.mit.edu	37	7	56635559	56635559	+	IGR	DEL	G	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:56635559delG								DKFZp434L192 (70582 upstream) : ZNF479 (551769 downstream)																																			---	---	---	---
ZNF679	168417	broad.mit.edu	37	7	63721435	63721435	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:63721435delT	uc003tsx.2	+							NM_153363	NP_699194			zinc finger protein 679						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			skin(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	65976420	65976420	+	IGR	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:65976420delA								NCRNA00174 (111025 upstream) : LOC493754 (17026 downstream)																																			---	---	---	---
SPDYE7P	441251	broad.mit.edu	37	7	72341012	72341012	+	5'Flank	DEL	G	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:72341012delG	uc010lal.1	-							NR_003666				Homo sapiens speedy homolog E7 (Xenopus laevis), pseudogene (SPDYE7P), non-coding RNA.												0																		---	---	---	---
CLIP2	7461	broad.mit.edu	37	7	73803287	73803287	+	Intron	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:73803287delA	uc003uam.2	+						CLIP2_uc003uan.2_Intron	NM_003388	NP_003379			CAP-GLY domain containing linker protein 2							microtubule associated complex				skin(3)	3																		---	---	---	---
HGF	3082	broad.mit.edu	37	7	81381622	81381622	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:81381622delT	uc003uhl.2	-						HGF_uc003uhm.2_Intron|HGF_uc003uhn.1_Intron|HGF_uc003uho.1_Intron|HGF_uc003uhp.2_Intron	NM_000601	NP_000592			hepatocyte growth factor isoform 1						epithelial to mesenchymal transition|mitosis|platelet activation|platelet degranulation|proteolysis|regulation of branching involved in salivary gland morphogenesis by mesenchymal-epithelial signaling	platelet alpha granule lumen	growth factor activity|serine-type endopeptidase activity			ovary(2)|central_nervous_system(2)	4																		---	---	---	---
CACNA2D1	781	broad.mit.edu	37	7	81614084	81614084	+	Intron	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:81614084delA	uc003uhr.1	-							NM_000722	NP_000713			calcium channel, voltage-dependent, alpha							voltage-gated calcium channel complex	metal ion binding			ovary(5)|pancreas(1)	6					Felodipine(DB01023)|Gabapentin(DB00996)|Ibutilide(DB00308)|Isradipine(DB00270)|Magnesium Sulfate(DB00653)|Nifedipine(DB01115)													---	---	---	---
Unknown	0	broad.mit.edu	37	7	88141302	88141302	+	IGR	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:88141302delT								STEAP4 (205093 upstream) : ZNF804B (247451 downstream)																																			---	---	---	---
C7orf64	84060	broad.mit.edu	37	7	92166147	92166147	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:92166147delT	uc003ulz.2	+						C7orf64_uc003uma.2_3'UTR|MGC16142_uc011khv.1_5'Flank	NM_032120	NP_115496			hypothetical protein LOC84060								nucleotide binding			ovary(2)	2																		---	---	---	---
FAM133B	257415	broad.mit.edu	37	7	92208639	92208639	+	Frame_Shift_Del	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:92208639delT	uc003umc.2	-	3	294	c.193delA	c.(193-195)ATGfs	p.M65fs	FAM133B_uc003umb.2_Frame_Shift_Del_p.M55fs|FAM133B_uc003umd.2_RNA	NM_152789	NP_690002	Q5BKY9	F133B_HUMAN	hypothetical protein LOC257415 isoform 1	65	Lys-rich.									ovary(1)	1	all_cancers(62;7.39e-11)|all_epithelial(64;7.03e-10)|Breast(17;0.00201)|all_lung(186;0.0384)|Lung NSC(181;0.053)|all_hematologic(106;0.237)		STAD - Stomach adenocarcinoma(4;6.16e-07)|GBM - Glioblastoma multiforme(5;9.78e-06)|all cancers(6;1.67e-05)|Epithelial(20;0.113)|LUSC - Lung squamous cell carcinoma(200;0.225)|Lung(22;0.23)															---	---	---	---
TRRAP	8295	broad.mit.edu	37	7	98491664	98491664	+	Intron	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:98491664delA	uc003upp.2	+						TRRAP_uc011kis.1_Intron	NM_003496	NP_003487			transformation/transcription domain-associated						histone deubiquitination|histone H2A acetylation|histone H4 acetylation|regulation of transcription, DNA-dependent|transcription, DNA-dependent	NuA4 histone acetyltransferase complex|PCAF complex|STAGA complex|transcription factor TFTC complex	phosphotransferase activity, alcohol group as acceptor|protein binding|transcription cofactor activity			ovary(9)|large_intestine(8)|central_nervous_system(6)|skin(6)|stomach(5)|upper_aerodigestive_tract(1)|lung(1)|liver(1)	37	all_cancers(62;6.96e-09)|all_epithelial(64;4.86e-09)|Lung NSC(181;0.01)|all_lung(186;0.016)|Esophageal squamous(72;0.0274)		STAD - Stomach adenocarcinoma(171;0.215)															---	---	---	---
TRRAP	8295	broad.mit.edu	37	7	98513649	98513649	+	Intron	DEL	C	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:98513649delC	uc003upp.2	+						TRRAP_uc011kis.1_Intron|TRRAP_uc003upr.2_Intron	NM_003496	NP_003487			transformation/transcription domain-associated						histone deubiquitination|histone H2A acetylation|histone H4 acetylation|regulation of transcription, DNA-dependent|transcription, DNA-dependent	NuA4 histone acetyltransferase complex|PCAF complex|STAGA complex|transcription factor TFTC complex	phosphotransferase activity, alcohol group as acceptor|protein binding|transcription cofactor activity			ovary(9)|large_intestine(8)|central_nervous_system(6)|skin(6)|stomach(5)|upper_aerodigestive_tract(1)|lung(1)|liver(1)	37	all_cancers(62;6.96e-09)|all_epithelial(64;4.86e-09)|Lung NSC(181;0.01)|all_lung(186;0.016)|Esophageal squamous(72;0.0274)		STAD - Stomach adenocarcinoma(171;0.215)															---	---	---	---
TRRAP	8295	broad.mit.edu	37	7	98533362	98533362	+	Intron	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:98533362delA	uc003upp.2	+						TRRAP_uc011kis.1_Intron|TRRAP_uc003upr.2_Intron	NM_003496	NP_003487			transformation/transcription domain-associated						histone deubiquitination|histone H2A acetylation|histone H4 acetylation|regulation of transcription, DNA-dependent|transcription, DNA-dependent	NuA4 histone acetyltransferase complex|PCAF complex|STAGA complex|transcription factor TFTC complex	phosphotransferase activity, alcohol group as acceptor|protein binding|transcription cofactor activity			ovary(9)|large_intestine(8)|central_nervous_system(6)|skin(6)|stomach(5)|upper_aerodigestive_tract(1)|lung(1)|liver(1)	37	all_cancers(62;6.96e-09)|all_epithelial(64;4.86e-09)|Lung NSC(181;0.01)|all_lung(186;0.016)|Esophageal squamous(72;0.0274)		STAD - Stomach adenocarcinoma(171;0.215)															---	---	---	---
TAF6	6878	broad.mit.edu	37	7	99710906	99710906	+	Intron	DEL	A	-	-	rs75828513		TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:99710906delA	uc003uti.2	-						TAF6_uc003utg.2_Intron|TAF6_uc003uth.2_Intron|TAF6_uc003utk.2_Intron|TAF6_uc011kji.1_Intron|TAF6_uc003utj.2_Intron|TAF6_uc003utl.2_Intron|TAF6_uc003utm.2_Intron|TAF6_uc003utn.1_Intron	NM_139315	NP_647476			TBP-associated factor 6 isoform alpha						negative regulation of cell cycle|negative regulation of cell proliferation|regulation of sequence-specific DNA binding transcription factor activity|transcription elongation from RNA polymerase II promoter|transcription initiation from RNA polymerase II promoter|viral reproduction	cytoplasm|MLL1 complex|transcription factor TFIID complex|transcription factor TFIID complex|transcription factor TFTC complex	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity			ovary(1)|central_nervous_system(1)	2	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)																	---	---	---	---
AGFG2	3268	broad.mit.edu	37	7	100146315	100146315	+	Intron	DEL	G	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:100146315delG	uc003uvf.2	+						AGFG2_uc003uvg.1_Intron|AGFG2_uc010lgy.2_5'Flank	NM_006076	NP_006067			ArfGAP with FG repeats 2						regulation of ARF GTPase activity		ARF GTPase activator activity|zinc ion binding			central_nervous_system(1)	1																		---	---	---	---
SLC26A5	375611	broad.mit.edu	37	7	103015124	103015124	+	Intron	DEL	T	-	-	rs72245175		TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:103015124delT	uc003vbz.2	-						SLC26A5_uc003vbt.1_Intron|SLC26A5_uc003vbu.1_Intron|SLC26A5_uc003vbv.1_Intron|SLC26A5_uc003vbw.2_Intron|SLC26A5_uc003vbx.2_Intron|SLC26A5_uc003vby.2_Intron|SLC26A5_uc010liy.2_Intron	NM_198999	NP_945350			prestin isoform a						regulation of cell shape|sensory perception of sound	integral to membrane	secondary active sulfate transmembrane transporter activity			ovary(1)	1																		---	---	---	---
LHFPL3	375612	broad.mit.edu	37	7	103969195	103969200	+	5'UTR	DEL	AGGAGG	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:103969195_103969200delAGGAGG	uc003vce.2	+	1					LHFPL3_uc003vcf.2_5'UTR	NM_199000	NP_945351			lipoma HMGIC fusion partner-like 3							integral to membrane					0																		---	---	---	---
CBLL1	79872	broad.mit.edu	37	7	107389307	107389307	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:107389307delT	uc003veq.2	+						CBLL1_uc011kme.1_Intron|CBLL1_uc011kmf.1_Intron	NM_024814	NP_079090			Cas-Br-M (murine) ecotropic retroviral						cell-cell adhesion|negative regulation of cell adhesion|positive regulation of cell migration|positive regulation of endocytosis		protein binding|ubiquitin-protein ligase activity|zinc ion binding			ovary(2)|skin(2)|lung(1)	5																		---	---	---	---
IFRD1	3475	broad.mit.edu	37	7	112112570	112112570	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:112112570delT	uc003vgh.2	+						IFRD1_uc011kmn.1_Intron|IFRD1_uc003vgj.2_Intron|IFRD1_uc011kmo.1_Intron|IFRD1_uc011kmp.1_Intron|IFRD1_uc003vgk.2_Intron	NM_001007245	NP_001007246			interferon-related developmental regulator 1						multicellular organismal development|myoblast cell fate determination		binding			kidney(1)|central_nervous_system(1)	2																		---	---	---	---
FAM3C	10447	broad.mit.edu	37	7	121022812	121022812	+	Intron	DEL	A	-	-	rs77488516		TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:121022812delA	uc003vjx.2	-						FAM3C_uc010lkm.2_Intron	NM_014888	NP_055703			family with sequence similarity 3, member C						multicellular organismal development	cytoplasmic membrane-bounded vesicle|extracellular region	cytokine activity				0	all_neural(327;0.117)																	---	---	---	---
AASS	10157	broad.mit.edu	37	7	121738971	121738971	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:121738971delT	uc003vka.2	-						AASS_uc011knu.1_Intron|AASS_uc011knv.1_Intron|AASS_uc003vkb.2_Intron|AASS_uc011knw.1_Intron	NM_005763	NP_005754			aminoadipate-semialdehyde synthase precursor						protein tetramerization	mitochondrial matrix	binding|saccharopine dehydrogenase (NAD+, L-glutamate-forming) activity|saccharopine dehydrogenase (NADP+, L-lysine-forming) activity			upper_aerodigestive_tract(1)|ovary(1)	2					L-Glutamic Acid(DB00142)|NADH(DB00157)													---	---	---	---
SLC13A1	6561	broad.mit.edu	37	7	122811637	122811637	+	Intron	DEL	T	-	-	rs147641390	by1000genomes	TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:122811637delT	uc003vkm.2	-						SLC13A1_uc010lks.2_Intron	NM_022444	NP_071889			solute carrier family 13 (sodium/sulfate							integral to membrane|plasma membrane	sodium:sulfate symporter activity			ovary(2)	2					Succinic acid(DB00139)													---	---	---	---
IMPDH1	3614	broad.mit.edu	37	7	128043613	128043615	+	Intron	DEL	AAA	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:128043613_128043615delAAA	uc011kol.1	-						IMPDH1_uc011kom.1_Intron|IMPDH1_uc003vmt.2_Intron|IMPDH1_uc003vmu.2_Intron|IMPDH1_uc003vmw.2_Intron|IMPDH1_uc011kon.1_Intron|IMPDH1_uc003vmv.2_Intron|IMPDH1_uc003vmx.2_Intron|IMPDH1_uc003vmy.2_Intron	NM_001142573	NP_001136045			inosine monophosphate dehydrogenase 1 isoform e						GMP biosynthetic process|purine base metabolic process	cytosol|nucleus	DNA binding|IMP dehydrogenase activity|metal ion binding			skin(2)|lung(1)|central_nervous_system(1)	4					Mycophenolate mofetil(DB00688)|Mycophenolic acid(DB01024)|NADH(DB00157)|Ribavirin(DB00811)|Thioguanine(DB00352)													---	---	---	---
CPA2	1358	broad.mit.edu	37	7	129922051	129922052	+	Intron	INS	-	T	T			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:129922051_129922052insT	uc003vpq.2	+							NM_001869	NP_001860			carboxypeptidase A2 (pancreatic) precursor						proteolysis|vacuolar protein catabolic process	extracellular region|vacuole	metallocarboxypeptidase activity|zinc ion binding			ovary(1)	1	Melanoma(18;0.0435)																	---	---	---	---
DGKI	9162	broad.mit.edu	37	7	137341101	137341101	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:137341101delT	uc003vtt.2	-						DGKI_uc003vtu.2_Intron	NM_004717	NP_004708			diacylglycerol kinase, iota						activation of protein kinase C activity by G-protein coupled receptor protein signaling pathway|intracellular signal transduction|platelet activation	nucleus|plasma membrane	ATP binding|diacylglycerol kinase activity|metal ion binding			ovary(1)|kidney(1)|skin(1)	3																OREG0018350	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
CUL1	8454	broad.mit.edu	37	7	148486619	148486620	+	Intron	DEL	CT	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:148486619_148486620delCT	uc010lpg.2	+						CUL1_uc003wey.2_Intron|CUL1_uc003wez.2_Intron|CUL1_uc003wfa.2_Intron	NM_003592	NP_003583			cullin 1						anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|cell cycle arrest|G1/S transition of mitotic cell cycle|induction of apoptosis by intracellular signals|interspecies interaction between organisms|negative regulation of cell proliferation|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|protein ubiquitination|S phase of mitotic cell cycle|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process	cytosol|nucleoplasm|SCF ubiquitin ligase complex	ubiquitin protein ligase binding			lung(1)	1	Melanoma(164;0.15)		OV - Ovarian serous cystadenocarcinoma(82;0.00291)															---	---	---	---
CSMD1	64478	broad.mit.edu	37	8	2799865	2799865	+	Intron	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:2799865delA	uc011kwk.1	-						CSMD1_uc011kwj.1_Intron|CSMD1_uc010lrg.2_Intron	NM_033225	NP_150094			CUB and Sushi multiple domains 1 precursor							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)														---	---	---	---
ADHFE1	137872	broad.mit.edu	37	8	67369551	67369552	+	Intron	INS	-	A	A	rs148427504		TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:67369551_67369552insA	uc003xwb.3	+						ADHFE1_uc003xwd.3_Intron|ADHFE1_uc003xwc.3_Intron|ADHFE1_uc003xwe.3_Intron|ADHFE1_uc003xwf.3_Intron|ADHFE1_uc011les.1_Intron	NM_144650	NP_653251			alcohol dehydrogenase, iron containing, 1						2-oxoglutarate metabolic process|molecular hydrogen transport	mitochondrial matrix	hydroxyacid-oxoacid transhydrogenase activity|metal ion binding			ovary(1)|lung(1)|breast(1)|skin(1)	4		Lung NSC(129;0.197)	Epithelial(68;0.0321)|all cancers(69;0.0751)|BRCA - Breast invasive adenocarcinoma(89;0.0855)|OV - Ovarian serous cystadenocarcinoma(28;0.226)															---	---	---	---
ARFGEF1	10565	broad.mit.edu	37	8	68189370	68189370	+	Intron	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:68189370delA	uc003xxo.1	-							NM_006421	NP_006412			brefeldin A-inhibited guanine						exocytosis|regulation of ARF protein signal transduction	cytoplasm	ARF guanyl-nucleotide exchange factor activity|myosin binding			ovary(4)|upper_aerodigestive_tract(1)|large_intestine(1)|lung(1)|kidney(1)	8	Breast(64;0.214)	Lung NSC(129;0.0908)|all_lung(136;0.152)	Epithelial(68;0.0043)|OV - Ovarian serous cystadenocarcinoma(28;0.00578)|all cancers(69;0.0173)|BRCA - Breast invasive adenocarcinoma(89;0.206)															---	---	---	---
TMEM64	169200	broad.mit.edu	37	8	91637754	91637755	+	3'UTR	DEL	AA	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:91637754_91637755delAA	uc003yen.2	-	3					TMEM64_uc003yeo.2_3'UTR|TMEM64_uc011lgf.1_3'UTR	NM_001008495	NP_001008495			transmembrane protein 64 isoform 1							integral to membrane					0			BRCA - Breast invasive adenocarcinoma(11;0.0598)															---	---	---	---
RBM12B	389677	broad.mit.edu	37	8	94745548	94745548	+	3'UTR	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:94745548delA	uc003yfz.2	-	3						NM_203390	NP_976324			RNA binding motif protein 12B								nucleotide binding|RNA binding				0	Breast(36;4.14e-07)		BRCA - Breast invasive adenocarcinoma(8;0.0168)															---	---	---	---
TMEM67	91147	broad.mit.edu	37	8	94798301	94798301	+	Intron	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:94798301delA	uc011lgk.1	+						TMEM67_uc010mat.1_Intron|TMEM67_uc010maw.2_Intron|TMEM67_uc003yga.3_Intron	NM_153704	NP_714915			meckelin isoform 1						cilium assembly|ER-associated protein catabolic process|negative regulation of centrosome duplication	centrosome|cilium membrane|cytoplasmic vesicle membrane|endoplasmic reticulum membrane|integral to membrane|microtubule basal body	unfolded protein binding			ovary(2)	2	Breast(36;4.14e-07)		BRCA - Breast invasive adenocarcinoma(8;0.00896)															---	---	---	---
TATDN1	83940	broad.mit.edu	37	8	125507787	125507787	+	Intron	DEL	A	-	-	rs35308504		TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:125507787delA	uc003yrd.2	-						TATDN1_uc003yre.2_Intron|TATDN1_uc010mdm.2_Intron|TATDN1_uc003yrf.2_Intron	NM_032026	NP_114415			TatD DNase domain containing 1 isoform a							nucleus	endodeoxyribonuclease activity, producing 5'-phosphomonoesters|metal ion binding				0	Ovarian(258;0.00438)|all_neural(195;0.0779)|Hepatocellular(40;0.108)		STAD - Stomach adenocarcinoma(47;0.00288)															---	---	---	---
EEF1D	1936	broad.mit.edu	37	8	144668488	144668488	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:144668488delT	uc011lki.1	-						EEF1D_uc003yyp.1_Intron|EEF1D_uc003yyq.1_Intron|EEF1D_uc011lkj.1_Intron|EEF1D_uc003yyr.2_Intron|EEF1D_uc003yyt.2_Intron|EEF1D_uc011lkk.1_Intron|EEF1D_uc003yys.2_Intron|EEF1D_uc003yyv.2_Intron|EEF1D_uc003yyu.2_Intron|EEF1D_uc011lkl.1_Intron	NM_001130057	NP_001123529			eukaryotic translation elongation factor 1 delta						positive regulation of I-kappaB kinase/NF-kappaB cascade	cytosol|eukaryotic translation elongation factor 1 complex	protein binding|signal transducer activity|translation elongation factor activity			ovary(1)|kidney(1)|skin(1)	3	all_cancers(97;3.74e-11)|all_epithelial(106;2.62e-09)|Lung NSC(106;0.00013)|all_lung(105;0.000374)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		Colorectal(110;0.134)|BRCA - Breast invasive adenocarcinoma(115;0.239)															---	---	---	---
GLDC	2731	broad.mit.edu	37	9	6553326	6553326	+	Intron	DEL	C	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:6553326delC	uc003zkc.2	-							NM_000170	NP_000161			glycine dehydrogenase (decarboxylating)						glycine catabolic process	mitochondrion	electron carrier activity|glycine dehydrogenase (decarboxylating) activity|lyase activity|pyridoxal phosphate binding			ovary(2)	2		Acute lymphoblastic leukemia(23;0.161)		GBM - Glioblastoma multiforme(50;0.0421)|Lung(218;0.134)	Glycine(DB00145)|Pyridoxal Phosphate(DB00114)													---	---	---	---
IFNA14	3448	broad.mit.edu	37	9	21217459	21217459	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:21217459delT	uc003zoo.1	-						IFNA16_uc003zor.1_5'Flank	NM_002172				interferon, alpha 14 precursor						blood coagulation|regulation of type I interferon-mediated signaling pathway|response to virus|type I interferon-mediated signaling pathway	extracellular space	cytokine activity|cytokine receptor binding				0				Lung(24;2.12e-22)|LUSC - Lung squamous cell carcinoma(38;1.4e-13)														---	---	---	---
TEK	7010	broad.mit.edu	37	9	27204705	27204706	+	Intron	INS	-	A	A	rs28376331	by1000genomes	TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:27204705_27204706insA	uc003zqi.3	+						TEK_uc011lno.1_Intron|TEK_uc011lnp.1_Intron|TEK_uc003zqj.1_Intron	NM_000459	NP_000450			TEK tyrosine kinase, endothelial precursor						angiogenesis|blood coagulation|cell-cell signaling|leukocyte migration|positive regulation of ERK1 and ERK2 cascade|positive regulation of protein kinase B signaling cascade|protein oligomerization|transmembrane receptor protein tyrosine kinase signaling pathway	apical plasma membrane|basolateral plasma membrane|cell surface|integral to plasma membrane|membrane raft|microvillus	ATP binding|protein binding|transmembrane receptor protein tyrosine kinase activity			ovary(3)|central_nervous_system(3)|breast(3)|lung(2)|kidney(1)	12		all_neural(11;7.57e-10)|Myeloproliferative disorder(762;0.0255)		Lung(218;4.08e-05)|LUSC - Lung squamous cell carcinoma(38;0.00027)														---	---	---	---
Unknown	0	broad.mit.edu	37	9	30774794	30774794	+	IGR	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:30774794delA								None (None upstream) : None (None downstream)																																			---	---	---	---
KIF24	347240	broad.mit.edu	37	9	34223921	34223922	+	Intron	INS	-	T	T	rs144735597	by1000genomes	TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:34223921_34223922insT	uc010mkb.2	-						UBAP1_uc010mka.1_Intron|UBAP1_uc003ztx.2_Intron|UBAP1_uc003zty.2_Intron|UBAP1_uc011loi.1_Intron|UBAP1_uc011loj.1_Intron|UBAP1_uc003ztz.2_Intron	NM_194313	NP_919289			kinesin family member 24						microtubule-based movement	cytoplasm|microtubule	ATP binding|microtubule motor activity			central_nervous_system(1)	1			LUSC - Lung squamous cell carcinoma(29;0.0107)															---	---	---	---
DNAJB5	25822	broad.mit.edu	37	9	34997369	34997369	+	3'UTR	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:34997369delA	uc003zvt.2	+	4					DNAJB5_uc003zvs.2_3'UTR|DNAJB5_uc011los.1_3'UTR	NM_012266	NP_036398			DnaJ (Hsp40) homolog, subfamily B, member 5						protein folding|response to unfolded protein		heat shock protein binding|unfolded protein binding				0			LUSC - Lung squamous cell carcinoma(32;0.00575)															---	---	---	---
Unknown	0	broad.mit.edu	37	9	69845788	69845788	+	IGR	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:69845788delT								LOC100133920 (180839 upstream) : FOXD4L5 (329921 downstream)																																			---	---	---	---
ALDH1A1	216	broad.mit.edu	37	9	75533865	75533865	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:75533865delT	uc004ajd.2	-						ALDH1A1_uc011lsh.1_Intron|ALDH1A1_uc011lsg.1_Intron	NM_000689	NP_000680			aldehyde dehydrogenase 1A1						cellular aldehyde metabolic process|ethanol oxidation|xenobiotic metabolic process	cytosol	aldehyde dehydrogenase (NAD) activity|androgen binding|Ras GTPase activator activity|retinal dehydrogenase activity			ovary(3)|lung(1)	4					NADH(DB00157)|Tretinoin(DB00755)|Vitamin A(DB00162)													---	---	---	---
PCSK5	5125	broad.mit.edu	37	9	78799576	78799576	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:78799576delT	uc004ajz.2	+						PCSK5_uc004aka.2_Intron|PCSK5_uc004akb.2_Intron	NM_006200	NP_006191			proprotein convertase subtilisin/kexin type 5						anterior/posterior pattern formation|cell-cell signaling|cytokine biosynthetic process|embryo implantation|embryonic digestive tract development|embryonic skeletal system development|heart development|kidney development|limb morphogenesis|nerve growth factor processing|nerve growth factor receptor signaling pathway|peptide biosynthetic process|renin secretion into blood stream|respiratory tube development|signal peptide processing|viral assembly, maturation, egress, and release	extracellular space|Golgi lumen|stored secretory granule	peptide binding|serine-type endopeptidase activity			ovary(2)|skin(1)	3																		---	---	---	---
HIATL2	84278	broad.mit.edu	37	9	99734982	99734983	+	Intron	DEL	AA	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:99734982_99734983delAA	uc004aws.2	-						HIATL2_uc004awr.1_Intron	NR_002894				RecName: Full=Hippocampus abundant transcript-like protein 2;												0																		---	---	---	---
PPP6C	5537	broad.mit.edu	37	9	127911822	127911822	+	3'UTR	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:127911822delA	uc004bpg.3	-	7					PPP6C_uc010mwv.2_3'UTR|PPP6C_uc010mww.2_3'UTR|PPP6C_uc011lzr.1_3'UTR	NM_002721	NP_002712			protein phosphatase 6, catalytic subunit isoform						G1/S transition of mitotic cell cycle|protein dephosphorylation	cytosol	metal ion binding|protein binding|protein serine/threonine phosphatase activity			ovary(1)|skin(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	9	127957481	127957481	+	IGR	DEL	A	-	-	rs79479616		TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:127957481delA								PPP6C (5263 upstream) : RABEPK (5336 downstream)																																			---	---	---	---
ZBTB43	23099	broad.mit.edu	37	9	129596298	129596298	+	3'UTR	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:129596298delA	uc004bql.2	+	3					ZBTB43_uc010mxf.2_3'UTR	NM_014007	NP_054726			zinc finger and BTB domain containing 43						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1																		---	---	---	---
CERCAM	51148	broad.mit.edu	37	9	131187045	131187046	+	Intron	DEL	TT	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:131187045_131187046delTT	uc004buz.3	+						CERCAM_uc004buy.1_Intron|CERCAM_uc010mxz.2_Intron|CERCAM_uc010mya.1_Intron	NM_016174	NP_057258			cerebral endothelial cell adhesion molecule 1						cellular component movement|leukocyte cell-cell adhesion|lipopolysaccharide biosynthetic process	endoplasmic reticulum lumen|plasma membrane				pancreas(1)	1																		---	---	---	---
BAT2L1	84726	broad.mit.edu	37	9	134322056	134322056	+	Intron	DEL	C	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:134322056delC	uc004can.3	+						BAT2L1_uc010mzj.1_5'Flank|BAT2L1_uc004cam.1_Intron	NM_013318	NP_037450			HLA-B associated transcript 2-like								protein binding				0																		---	---	---	---
C9orf96	169436	broad.mit.edu	37	9	136268193	136268193	+	Intron	DEL	C	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:136268193delC	uc004cdk.2	+						C9orf96_uc004cdl.2_Intron	NM_153710	NP_714921			hypothetical protein LOC169436								ATP binding|protein kinase activity			stomach(2)|central_nervous_system(2)	4				OV - Ovarian serous cystadenocarcinoma(145;1.06e-07)|Epithelial(140;1.28e-06)|all cancers(34;1.46e-05)														---	---	---	---
ITGA8	8516	broad.mit.edu	37	10	15719443	15719443	+	Intron	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:15719443delA	uc001ioc.1	-						ITGA8_uc010qcb.1_Intron	NM_003638	NP_003629			integrin, alpha 8 precursor						cell differentiation|cell-cell adhesion|cell-matrix adhesion|integrin-mediated signaling pathway|nervous system development	integrin complex	receptor activity			ovary(3)|lung(3)	6																		---	---	---	---
FAM188A	80013	broad.mit.edu	37	10	15883640	15883640	+	Intron	DEL	A	-	-	rs111629424		TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:15883640delA	uc001iod.1	-						FAM188A_uc001ioe.1_Intron|FAM188A_uc001iof.1_Intron	NM_024948	NP_079224			chromosome 10 open reading frame 97						apoptosis	nucleus	calcium ion binding			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	10	19341155	19341155	+	IGR	DEL	C	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:19341155delC								ARL5B (374215 upstream) : PLXDC2 (764217 downstream)																																			---	---	---	---
CCAR1	55749	broad.mit.edu	37	10	70515996	70515996	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:70515996delT	uc001joo.2	+						CCAR1_uc001jol.1_Intron|CCAR1_uc001jom.1_Intron|CCAR1_uc009xpx.1_Intron|CCAR1_uc001jon.1_Intron|CCAR1_uc010qiz.1_Intron|CCAR1_uc010qja.1_Intron|CCAR1_uc010qjb.1_Intron	NM_018237	NP_060707			cell-cycle and apoptosis regulatory protein 1						apoptosis|cell cycle|nuclear mRNA splicing, via spliceosome|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleoplasm|perinuclear region of cytoplasm	calcium ion binding|nucleic acid binding|protein binding			ovary(6)|large_intestine(1)	7																		---	---	---	---
ASCC1	51008	broad.mit.edu	37	10	73887716	73887716	+	Intron	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:73887716delA	uc001jst.1	-						ASCC1_uc001jsr.1_Intron|ASCC1_uc001jss.1_Intron|ASCC1_uc001jsu.1_Intron|ASCC1_uc010qju.1_Intron					RecName: Full=Activating signal cointegrator 1 complex subunit 1; AltName: Full=ASC-1 complex subunit p50; AltName: Full=Trip4 complex subunit p50;						regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|transcription factor complex	RNA binding				0																		---	---	---	---
RNLS	55328	broad.mit.edu	37	10	90034668	90034668	+	3'UTR	DEL	A	-	-	rs113106989		TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:90034668delA	uc001kfd.2	-	7					RNLS_uc010qms.1_Intron	NM_018363	NP_060833			renalase isoform 2							extracellular region	oxidoreductase activity			ovary(1)	1																		---	---	---	---
STAMBPL1	57559	broad.mit.edu	37	10	90672691	90672691	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:90672691delT	uc001kfk.2	+						STAMBPL1_uc010qmx.1_Intron|STAMBPL1_uc009xto.2_Intron|STAMBPL1_uc001kfl.2_Intron|STAMBPL1_uc001kfn.2_5'UTR	NM_020799	NP_065850			STAM binding protein-like 1								metal ion binding|metallopeptidase activity|protein binding			ovary(1)	1		Colorectal(252;0.0381)		Colorectal(12;6.38e-05)|COAD - Colon adenocarcinoma(12;7.75e-05)														---	---	---	---
BTAF1	9044	broad.mit.edu	37	10	93741213	93741213	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:93741213delT	uc001khr.2	+						BTAF1_uc001khs.1_Intron|BTAF1_uc001kht.1_Intron	NM_003972	NP_003963			BTAF1 RNA polymerase II, B-TFIID transcription						negative regulation of transcription, DNA-dependent	nucleus	ATP binding|DNA binding|helicase activity|sequence-specific DNA binding transcription factor activity			ovary(1)|central_nervous_system(1)|skin(1)	3		Colorectal(252;0.0846)																---	---	---	---
BTAF1	9044	broad.mit.edu	37	10	93741816	93741816	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:93741816delT	uc001khr.2	+						BTAF1_uc001khs.1_Intron|BTAF1_uc001kht.1_Intron	NM_003972	NP_003963			BTAF1 RNA polymerase II, B-TFIID transcription						negative regulation of transcription, DNA-dependent	nucleus	ATP binding|DNA binding|helicase activity|sequence-specific DNA binding transcription factor activity			ovary(1)|central_nervous_system(1)|skin(1)	3		Colorectal(252;0.0846)																---	---	---	---
KIF11	3832	broad.mit.edu	37	10	94396790	94396793	+	Intron	DEL	AAAA	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:94396790_94396793delAAAA	uc001kic.2	+						KIF11_uc010qnq.1_Intron	NM_004523	NP_004514			kinesin family member 11						blood coagulation|cell division|microtubule-based movement|spindle assembly involved in mitosis	chromatin remodeling complex|cytosol|kinesin complex|microtubule|spindle pole	ATP binding|microtubule motor activity|protein kinase binding			skin(1)	1																		---	---	---	---
HELLS	3070	broad.mit.edu	37	10	96313731	96313731	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:96313731delT	uc001kjt.2	+						HELLS_uc001kjs.2_Intron|HELLS_uc009xul.2_Intron|HELLS_uc009xum.2_Intron|HELLS_uc009xun.2_Intron|HELLS_uc009xuo.2_Intron|HELLS_uc001kju.2_Intron|HELLS_uc009xup.2_Intron|HELLS_uc009xuq.2_Intron|HELLS_uc009xur.2_Intron	NM_018063	NP_060533			helicase, lymphoid-specific						cell division|centromeric heterochromatin formation|lymphocyte proliferation|maintenance of DNA methylation|methylation-dependent chromatin silencing|mitosis|transcription, DNA-dependent	centromeric heterochromatin|nucleus	ATP binding|DNA binding|helicase activity			ovary(1)|kidney(1)	2		Colorectal(252;0.0429)		all cancers(201;2.13e-05)														---	---	---	---
SORBS1	10580	broad.mit.edu	37	10	97127476	97127476	+	Intron	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:97127476delA	uc001kkp.2	-						SORBS1_uc001kkk.2_Intron|SORBS1_uc001kkl.2_Intron|SORBS1_uc001kkn.2_Intron|SORBS1_uc001kkm.2_Intron|SORBS1_uc001kko.2_Intron|SORBS1_uc001kkq.2_Intron|SORBS1_uc001kkr.2_Intron|SORBS1_uc001kks.2_Intron|SORBS1_uc001kkt.2_Intron|SORBS1_uc001kku.2_Intron|SORBS1_uc001kkv.2_Intron|SORBS1_uc001kkw.2_Intron|SORBS1_uc010qoe.1_Intron|SORBS1_uc010qof.1_Intron	NM_001034954	NP_001030126			sorbin and SH3 domain containing 1 isoform 3						focal adhesion assembly|glucose transport|insulin receptor signaling pathway|muscle contraction|positive regulation of establishment of protein localization in plasma membrane|positive regulation of glucose import|positive regulation of glycogen biosynthetic process|positive regulation of lipid biosynthetic process|stress fiber assembly	centrosome|cytosol|focal adhesion|membrane raft|nucleus|stress fiber|zonula adherens	actin binding|insulin receptor binding|SH3/SH2 adaptor activity			breast(1)	1		Colorectal(252;0.0429)		Epithelial(162;1.7e-06)|all cancers(201;6.52e-05)														---	---	---	---
ENTPD7	57089	broad.mit.edu	37	10	101462505	101462505	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:101462505delT	uc001kqa.3	+						ENTPD7_uc009xwl.2_Intron	NM_020354	NP_065087			ectonucleoside triphosphate diphosphohydrolase							cytoplasmic vesicle membrane|integral to membrane	hydrolase activity			ovary(1)	1		Colorectal(252;0.234)		Epithelial(162;4.72e-10)|all cancers(201;3.75e-08)														---	---	---	---
BTBD16	118663	broad.mit.edu	37	10	124057386	124057387	+	Intron	INS	-	G	G			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:124057386_124057387insG	uc001lgc.1	+						BTBD16_uc001lgd.1_Intron	NM_144587	NP_653188			BTB (POZ) domain containing 16											skin(1)	1		all_neural(114;0.107)|Lung NSC(174;0.175)|all_lung(145;0.222)|Breast(234;0.238)																---	---	---	---
B4GALNT4	338707	broad.mit.edu	37	11	379842	379842	+	Intron	DEL	C	-	-	rs72431160		TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:379842delC	uc001lpb.2	+							NM_178537	NP_848632			beta							Golgi cisterna membrane|integral to membrane	N-acetyl-beta-glucosaminyl-glycoprotein 4-beta-N-acetylgalactosaminyltransferase activity			pancreas(1)	1		all_cancers(49;1.59e-06)|all_epithelial(84;0.000256)|Breast(177;0.00122)|Ovarian(85;0.0228)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762)		all cancers(45;1.56e-27)|Epithelial(43;9.31e-27)|OV - Ovarian serous cystadenocarcinoma(40;1.11e-20)|BRCA - Breast invasive adenocarcinoma(625;3.56e-05)|Lung(200;0.0182)|LUSC - Lung squamous cell carcinoma(625;0.0703)														---	---	---	---
IRF7	3665	broad.mit.edu	37	11	613181	613181	+	Intron	DEL	C	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:613181delC	uc001lqh.2	-						IRF7_uc009ycb.2_Intron|IRF7_uc010qwf.1_Intron|IRF7_uc001lqf.2_Intron|IRF7_uc010qwg.1_Intron|IRF7_uc001lqg.2_Intron|IRF7_uc001lqi.2_Intron|IRF7_uc010qwh.1_Intron	NM_001572	NP_001563			interferon regulatory factor 7 isoform a						interferon-gamma-mediated signaling pathway|interspecies interaction between organisms|MyD88-independent toll-like receptor signaling pathway|negative regulation of transcription from RNA polymerase II promoter|positive regulation of interferon-alpha production|positive regulation of transcription from RNA polymerase II promoter|response to virus|Toll signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway|transcription from RNA polymerase II promoter|type I interferon-mediated signaling pathway	cytosol|endosome membrane|nucleoplasm|plasma membrane	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity				0		all_cancers(49;1.69e-08)|all_epithelial(84;1.65e-05)|Breast(177;0.000231)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.106)|all_lung(207;0.136)		all cancers(45;7.68e-28)|Epithelial(43;7.44e-27)|OV - Ovarian serous cystadenocarcinoma(40;3.53e-21)|BRCA - Breast invasive adenocarcinoma(625;6.96e-05)|Lung(200;0.0375)|LUSC - Lung squamous cell carcinoma(625;0.0703)														---	---	---	---
TSPAN4	7106	broad.mit.edu	37	11	865495	865495	+	Intron	DEL	C	-	-	rs61614113	by1000genomes	TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:865495delC	uc001lsd.1	+						TSPAN4_uc001lse.1_Intron|TSPAN4_uc001lsf.1_Intron|TSPAN4_uc001lsg.1_Intron|TSPAN4_uc001lsh.1_Intron|TSPAN4_uc001lsi.1_Intron|TSPAN4_uc001lsj.1_Intron	NM_003271	NP_003262			tetraspanin 4 isoform a						protein complex assembly	integral to plasma membrane				breast(1)	1		all_cancers(49;2.64e-08)|all_epithelial(84;4.17e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.191)|all_lung(207;0.24)		all cancers(45;4.32e-25)|Epithelial(43;3.29e-24)|BRCA - Breast invasive adenocarcinoma(625;4.23e-05)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)														---	---	---	---
RRM1	6240	broad.mit.edu	37	11	4141256	4141256	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:4141256delT	uc001lyw.3	+						RRM1_uc009yej.2_Intron|RRM1_uc009yei.2_Intron|RRM1_uc010qyc.1_Intron|RRM1_uc010qyd.1_Intron	NM_001033	NP_001024			ribonucleoside-diphosphate reductase M1 chain						deoxyribonucleotide biosynthetic process|DNA replication|nucleobase, nucleoside and nucleotide interconversion	cytosol|nucleoplasm|ribonucleoside-diphosphate reductase complex	ATP binding|ribonucleoside-diphosphate reductase activity			skin(1)	1		Medulloblastoma(188;0.0025)|Breast(177;0.00502)|all_neural(188;0.0227)		BRCA - Breast invasive adenocarcinoma(625;0.0848)|LUSC - Lung squamous cell carcinoma(625;0.205)	Clofarabine(DB00631)|Fludarabine(DB01073)|Gemcitabine(DB00441)|Hydroxyurea(DB01005)													---	---	---	---
PAMR1	25891	broad.mit.edu	37	11	35462851	35462851	+	Intron	DEL	A	-	-	rs79736526		TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:35462851delA	uc001mwg.2	-						PAMR1_uc001mwf.2_Intron|PAMR1_uc010rew.1_Intron|PAMR1_uc010rex.1_Intron	NM_001001991	NP_001001991			regeneration associated muscle protease isoform						proteolysis	extracellular region	serine-type endopeptidase activity			ovary(2)	2																		---	---	---	---
MTCH2	23788	broad.mit.edu	37	11	47657242	47657242	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:47657242delT	uc010rho.1	-						MTCH2_uc001nge.2_Intron|MTCH2_uc010rhp.1_Intron	NM_014342	NP_055157			mitochondrial carrier 2						transport	integral to membrane|mitochondrial inner membrane					0																		---	---	---	---
Unknown	0	broad.mit.edu	37	11	55607259	55607259	+	IGR	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:55607259delA								OR5D16 (47 upstream) : SPRYD5 (43514 downstream)																																			---	---	---	---
SLC43A1	8501	broad.mit.edu	37	11	57281506	57281508	+	In_Frame_Del	DEL	AGA	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:57281506_57281508delAGA	uc001nkk.2	-	2	195_197	c.77_79delTCT	c.(76-81)TTCTCT>TCT	p.F26del	SLC43A1_uc001nkl.2_In_Frame_Del_p.F26del	NM_003627	NP_003618	O75387	LAT3_HUMAN	solute carrier family 43, member 1	26	Helical; (Potential).				cellular nitrogen compound metabolic process|ion transport	integral to plasma membrane	neutral amino acid transmembrane transporter activity				0																		---	---	---	---
MRPL16	54948	broad.mit.edu	37	11	59577490	59577490	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:59577490delT	uc001noh.2	-							NM_017840	NP_060310			mitochondrial ribosomal protein L16 precursor								rRNA binding			central_nervous_system(1)	1																		---	---	---	---
PLCB3	5331	broad.mit.edu	37	11	64032517	64032517	+	Frame_Shift_Del	DEL	C	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:64032517delC	uc001nzb.2	+	23	2747	c.2747delC	c.(2746-2748)TCCfs	p.S916fs	PLCB3_uc009ypg.1_Frame_Shift_Del_p.S916fs|PLCB3_uc009yph.1_Frame_Shift_Del_p.S849fs|PLCB3_uc009ypi.2_Frame_Shift_Del_p.S916fs	NM_000932	NP_000923	Q01970	PLCB3_HUMAN	phospholipase C beta 3	916					intracellular signal transduction|lipid catabolic process|synaptic transmission	cytosol	calcium ion binding|calmodulin binding|phosphatidylinositol phospholipase C activity|signal transducer activity			ovary(1)|pancreas(1)	2																		---	---	---	---
MALAT1	378938	broad.mit.edu	37	11	65269498	65269498	+	RNA	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:65269498delT	uc010roh.1	+	1		c.4266delT			uc001ody.2_RNA|MALAT1_uc001odz.2_5'Flank	NR_002819				Homo sapiens clone alpha1 mRNA sequence.												0																		---	---	---	---
ARHGEF17	9828	broad.mit.edu	37	11	73057889	73057889	+	Intron	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:73057889delA	uc001otu.2	+							NM_014786	NP_055601			Rho guanine nucleotide exchange factor (GEF) 17						actin cytoskeleton organization|apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol	Rho guanyl-nucleotide exchange factor activity				0																		---	---	---	---
MMP12	4321	broad.mit.edu	37	11	102737945	102737945	+	Intron	DEL	A	-	-	rs28381681		TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:102737945delA	uc001phk.2	-							NM_002426	NP_002417			matrix metalloproteinase 12 preproprotein						positive regulation of epithelial cell proliferation involved in wound healing|proteolysis|wound healing, spreading of epidermal cells	proteinaceous extracellular matrix	calcium ion binding|metalloendopeptidase activity|zinc ion binding				0		all_hematologic(158;0.00092)|Acute lymphoblastic leukemia(157;0.000967)		BRCA - Breast invasive adenocarcinoma(274;0.014)	Acetohydroxamic Acid(DB00551)													---	---	---	---
EXPH5	23086	broad.mit.edu	37	11	108412614	108412614	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:108412614delT	uc001pkk.2	-						EXPH5_uc010rwa.1_Intron	NM_015065	NP_055880			exophilin 5 isoform a						intracellular protein transport		Rab GTPase binding			skin(3)|ovary(2)	5		all_cancers(61;3.99e-08)|Acute lymphoblastic leukemia(157;3.97e-05)|Melanoma(852;4.04e-05)|all_epithelial(67;0.000116)|all_hematologic(158;0.000315)|Breast(348;0.104)|all_neural(303;0.16)		Epithelial(105;8.1e-06)|BRCA - Breast invasive adenocarcinoma(274;1.22e-05)|all cancers(92;0.000129)|OV - Ovarian serous cystadenocarcinoma(223;0.11)|Colorectal(284;0.184)														---	---	---	---
DDX10	1662	broad.mit.edu	37	11	108548163	108548163	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:108548163delT	uc001pkm.2	+						DDX10_uc001pkl.1_Intron	NM_004398	NP_004389			DEAD (Asp-Glu-Ala-Asp) box polypeptide 10								ATP binding|ATP-dependent helicase activity|RNA binding|RNA helicase activity			breast(2)|lung(1)|prostate(1)	4		all_cancers(61;1.29e-11)|all_epithelial(67;2.96e-07)|Melanoma(852;1.54e-05)|Acute lymphoblastic leukemia(157;4.24e-05)|all_hematologic(158;0.000141)|Breast(348;0.026)|all_neural(223;0.0729)		BRCA - Breast invasive adenocarcinoma(274;2.48e-05)|Epithelial(105;4.35e-05)|all cancers(92;0.000609)|OV - Ovarian serous cystadenocarcinoma(223;0.133)				T	NUP98	AML*								---	---	---	---
PPP2R1B	5519	broad.mit.edu	37	11	111623158	111623158	+	Intron	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:111623158delA	uc001plx.1	-						PPP2R1B_uc001plw.1_Intron|PPP2R1B_uc010rwi.1_Intron|PPP2R1B_uc010rwj.1_Intron|PPP2R1B_uc010rwk.1_Intron|PPP2R1B_uc010rwl.1_Intron	NM_002716	NP_002707			beta isoform of regulatory subunit A, protein								protein binding				0		all_cancers(61;2.34e-15)|all_epithelial(67;1.72e-09)|Melanoma(852;1.91e-06)|all_hematologic(158;0.000405)|Acute lymphoblastic leukemia(157;0.000967)|Breast(348;0.0112)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)		BRCA - Breast invasive adenocarcinoma(274;1.13e-06)|Epithelial(105;2.36e-06)|all cancers(92;3.78e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.0761)														---	---	---	---
IL18	3606	broad.mit.edu	37	11	112024223	112024223	+	Intron	DEL	T	-	-	rs78854082		TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:112024223delT	uc001pnb.1	-						IL18_uc001pna.1_5'Flank|IL18_uc009yym.1_Intron	NM_001562	NP_001553			interleukin 18 proprotein						angiogenesis|cell-cell signaling|chemokine biosynthetic process|granulocyte macrophage colony-stimulating factor biosynthetic process|interferon-gamma biosynthetic process|interleukin-13 biosynthetic process|interleukin-2 biosynthetic process|positive regulation of activated T cell proliferation|positive regulation of granulocyte macrophage colony-stimulating factor production|positive regulation of interferon-gamma production|positive regulation of interleukin-17 production|positive regulation of natural killer cell proliferation|positive regulation of NK T cell proliferation|regulation of cell adhesion|sleep|T-helper 1 type immune response|type 2 immune response	cytosol|extracellular space	cytokine activity|signal transducer activity				0		all_cancers(61;5.7e-14)|all_epithelial(67;3.4e-08)|Melanoma(852;8.81e-06)|all_hematologic(158;0.000405)|Acute lymphoblastic leukemia(157;0.000967)|Breast(348;0.0112)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)		BRCA - Breast invasive adenocarcinoma(274;6.72e-07)|Epithelial(105;8.15e-07)|all cancers(92;1.43e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.055)														---	---	---	---
PTS	5805	broad.mit.edu	37	11	112100752	112100752	+	Intron	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:112100752delA	uc001pnj.3	+						PTS_uc009yyo.2_Intron	NM_000317	NP_000308			6-pyruvoyltetrahydropterin synthase						cellular amino acid metabolic process|central nervous system development|tetrahydrobiopterin biosynthetic process	mitochondrion	6-pyruvoyltetrahydropterin synthase activity|metal ion binding				0		all_cancers(61;2.51e-14)|all_epithelial(67;1.64e-08)|Melanoma(852;8.81e-06)|all_hematologic(158;0.000405)|Acute lymphoblastic leukemia(157;0.000967)|Breast(348;0.0112)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)		Epithelial(105;1.27e-06)|BRCA - Breast invasive adenocarcinoma(274;1.43e-06)|all cancers(92;2.1e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.0519)														---	---	---	---
ARHGEF12	23365	broad.mit.edu	37	11	120338143	120338147	+	Intron	DEL	TTTTT	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:120338143_120338147delTTTTT	uc001pxl.1	+						ARHGEF12_uc009zat.2_Intron|ARHGEF12_uc010rzn.1_Intron|ARHGEF12_uc009zau.1_Intron	NM_015313	NP_056128			Rho guanine nucleotide exchange factor (GEF) 12						apoptosis|axon guidance|G-protein coupled receptor protein signaling pathway|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol|membrane	G-protein-coupled receptor binding|GTPase activator activity|Rho guanyl-nucleotide exchange factor activity			lung(2)|breast(2)|skin(2)|ovary(1)	7		Breast(109;0.000813)|Medulloblastoma(222;0.0425)|Hepatocellular(160;0.0831)|all_hematologic(192;0.107)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;4.88e-06)|OV - Ovarian serous cystadenocarcinoma(223;0.231)				T	MLL	AML								---	---	---	---
KDM5A	5927	broad.mit.edu	37	12	463406	463406	+	Intron	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:463406delA	uc001qif.1	-						KDM5A_uc001qie.1_Intron|KDM5A_uc010sdn.1_Intron|KDM5A_uc010sdo.1_Intron	NM_001042603	NP_001036068			retinoblastoma binding protein 2 isoform 1						chromatin modification|multicellular organismal development|positive regulation of transcription, DNA-dependent|transcription from RNA polymerase II promoter	cytoplasm|nucleolus	DNA binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|sequence-specific DNA binding transcription factor activity|zinc ion binding			skin(2)|ovary(1)	3								T 	NUP98	AML								---	---	---	---
ADIPOR2	79602	broad.mit.edu	37	12	1863751	1863751	+	Intron	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:1863751delA	uc001qjm.2	+						ADIPOR2_uc001qjn.2_Intron	NM_024551	NP_078827			adiponectin receptor 2						fatty acid oxidation|hormone-mediated signaling pathway	integral to membrane	hormone binding|receptor activity				0	Ovarian(42;0.107)		OV - Ovarian serous cystadenocarcinoma(31;0.000382)															---	---	---	---
TULP3	7289	broad.mit.edu	37	12	3046966	3046967	+	Intron	DEL	AA	-	-	rs3742080	by1000genomes	TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:3046966_3046967delAA	uc010seh.1	+						TULP3_uc009zec.1_Intron|TULP3_uc010seg.1_Intron|TULP3_uc001qlj.2_Intron|TULP3_uc010sei.1_Intron	NM_003324	NP_003315			tubby like protein 3 isoform 1						G-protein coupled receptor protein signaling pathway|regulation of transcription, DNA-dependent	cytoplasm|extracellular region|nucleus|plasma membrane	phosphatidylinositol-4,5-bisphosphate binding				0			OV - Ovarian serous cystadenocarcinoma(31;0.000818)															---	---	---	---
Unknown	0	broad.mit.edu	37	12	4218857	4218858	+	IGR	INS	-	T	T	rs113936230		TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:4218857_4218858insT								PARP11 (236249 upstream) : CCND2 (164044 downstream)																																			---	---	---	---
C12orf4	57102	broad.mit.edu	37	12	4626088	4626089	+	Intron	INS	-	A	A			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:4626088_4626089insA	uc001qms.2	-						C12orf4_uc001qmt.2_Intron	NM_020374	NP_065107			hypothetical protein LOC57102												0			Colorectal(7;0.00165)|COAD - Colon adenocarcinoma(12;0.0229)	BRCA - Breast invasive adenocarcinoma(232;0.0281)														---	---	---	---
IFFO1	25900	broad.mit.edu	37	12	6658357	6658357	+	Intron	DEL	A	-	-	rs72489368		TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:6658357delA	uc001qpd.1	-						IFFO1_uc001qoy.2_Intron|IFFO1_uc001qpa.1_5'Flank|IFFO1_uc001qpb.1_Intron|IFFO1_uc001qpe.1_Intron|IFFO1_uc010sfe.1_Intron|IFFO1_uc001qpf.1_Intron|IFFO1_uc001qoz.1_5'Flank|IFFO1_uc001qpc.1_Intron|IFFO1_uc001qpg.2_5'Flank	NM_080730	NP_542768			intermediate filament family orphan isoform 2							intermediate filament					0																		---	---	---	---
MIR1244	100302285	broad.mit.edu	37	12	9392182	9392183	+	5'Flank	INS	-	T	T			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:9392182_9392183insT	hsa-mir-1244-3|MI0015975	-						uc001qvm.1_5'Flank																	0																		---	---	---	---
PRR4	11272	broad.mit.edu	37	12	11000107	11000107	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:11000107delT	uc001qyz.3	-						PRR4_uc009zhp.2_Intron|PRH1_uc001qzb.3_Intron|PRR4_uc001qza.3_Intron	NM_007244	NP_009175			proline rich 4 (lacrimal) isoform 2						visual perception	extracellular space					0																		---	---	---	---
ATF7IP	55729	broad.mit.edu	37	12	14590987	14590987	+	Intron	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:14590987delA	uc001rbw.2	+						ATF7IP_uc010shs.1_Intron|ATF7IP_uc001rbu.2_Intron|ATF7IP_uc001rbv.1_Intron|ATF7IP_uc001rbx.2_Intron|ATF7IP_uc010sht.1_Intron|ATF7IP_uc001rby.3_Intron|ATF7IP_uc001rca.2_Intron	NM_018179	NP_060649			activating transcription factor 7 interacting						DNA methylation|interspecies interaction between organisms|positive regulation of transcription, DNA-dependent|regulation of RNA polymerase II transcriptional preinitiation complex assembly|transcription, DNA-dependent		protein binding			lung(3)|ovary(1)|skin(1)	5																		---	---	---	---
PLEKHA5	54477	broad.mit.edu	37	12	19406761	19406761	+	Intron	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:19406761delA	uc001reb.2	+						PLEKHA5_uc010sie.1_Intron|PLEKHA5_uc001rea.2_Intron|PLEKHA5_uc009zin.2_Intron|PLEKHA5_uc010sif.1_Intron|PLEKHA5_uc010sig.1_Intron|PLEKHA5_uc010sih.1_Intron	NM_019012	NP_061885			pleckstrin homology domain containing, family A								1-phosphatidylinositol binding|protein binding			ovary(1)|kidney(1)|skin(1)	3	Acute lymphoblastic leukemia(4;0.000455)|all_hematologic(4;0.00804)																	---	---	---	---
ITPR2	3709	broad.mit.edu	37	12	26877744	26877744	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:26877744delT	uc001rhg.2	-						ITPR2_uc001rhh.1_Intron|ITPR2_uc001rhi.1_Intron	NM_002223	NP_002214			inositol 1,4,5-triphosphate receptor, type 2						activation of phospholipase C activity|energy reserve metabolic process|nerve growth factor receptor signaling pathway|platelet activation|regulation of insulin secretion|response to hypoxia	integral to membrane|plasma membrane enriched fraction|platelet dense tubular network membrane|sarcoplasmic reticulum membrane	calcium ion transmembrane transporter activity|inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity			kidney(6)|ovary(4)|skin(2)|upper_aerodigestive_tract(1)|lung(1)	14	Colorectal(261;0.0847)																	---	---	---	---
DENND5B	160518	broad.mit.edu	37	12	31630952	31630952	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:31630952delT	uc001rki.1	-						DENND5B_uc001rkh.1_Intron|DENND5B_uc009zjq.1_Intron|DENND5B_uc001rkj.2_Intron|DENND5B_uc001rkk.1_Intron	NM_144973	NP_659410			DENN/MADD domain containing 5B							integral to membrane				ovary(1)|central_nervous_system(1)	2																		---	---	---	---
ADAMTS20	80070	broad.mit.edu	37	12	43820983	43820983	+	Intron	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:43820983delA	uc010skx.1	-						ADAMTS20_uc001rno.1_Intron	NM_025003	NP_079279			a disintegrin-like and metalloprotease with							proteinaceous extracellular matrix	zinc ion binding			central_nervous_system(5)|ovary(4)|lung(3)|large_intestine(2)|skin(2)|urinary_tract(1)|kidney(1)|pancreas(1)	19	all_cancers(12;2.6e-05)|Lung SC(27;0.184)	Lung NSC(34;0.0569)|all_lung(34;0.129)		GBM - Glioblastoma multiforme(48;0.0473)														---	---	---	---
ADAMTS20	80070	broad.mit.edu	37	12	43833279	43833279	+	Intron	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:43833279delA	uc010skx.1	-						ADAMTS20_uc001rno.1_Intron|ADAMTS20_uc001rnp.1_Intron	NM_025003	NP_079279			a disintegrin-like and metalloprotease with							proteinaceous extracellular matrix	zinc ion binding			central_nervous_system(5)|ovary(4)|lung(3)|large_intestine(2)|skin(2)|urinary_tract(1)|kidney(1)|pancreas(1)	19	all_cancers(12;2.6e-05)|Lung SC(27;0.184)	Lung NSC(34;0.0569)|all_lung(34;0.129)		GBM - Glioblastoma multiforme(48;0.0473)														---	---	---	---
CCNT1	904	broad.mit.edu	37	12	49086775	49086775	+	3'UTR	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:49086775delT	uc001rse.1	-	9					LOC144438_uc001rsd.3_5'Flank|CCNT1_uc009zkz.1_3'UTR	NM_001240	NP_001231			cyclin T1						cell cycle|cell division|interspecies interaction between organisms|positive regulation of viral transcription|protein phosphorylation|regulation of cyclin-dependent protein kinase activity|regulation of transcription, DNA-dependent|transcription elongation from RNA polymerase II promoter|viral reproduction	nucleoplasm	DNA binding|protein kinase binding			ovary(3)|lung(1)|breast(1)|skin(1)	6																		---	---	---	---
FKBP11	51303	broad.mit.edu	37	12	49318789	49318789	+	Intron	DEL	C	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:49318789delC	uc001rsp.2	-						FKBP11_uc010sma.1_5'Flank|FKBP11_uc001rsq.3_Intron|FKBP11_uc010smb.1_Intron	NM_016594	NP_057678			FK506 binding protein 11 isoform 1 precursor						protein folding	integral to membrane	FK506 binding|peptidyl-prolyl cis-trans isomerase activity				0																		---	---	---	---
MUCL1	118430	broad.mit.edu	37	12	55251961	55251961	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:55251961delT	uc001sgk.2	+							NM_058173	NP_477521			small breast epithelial mucin precursor							extracellular region|membrane					0																		---	---	---	---
KIF5A	3798	broad.mit.edu	37	12	57975862	57975862	+	Intron	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:57975862delA	uc001sor.1	+						KIF5A_uc010srr.1_Intron|uc001sos.2_5'Flank	NM_004984	NP_004975			kinesin family member 5A						blood coagulation|cell death|microtubule-based movement|synaptic transmission	cytosol|kinesin complex|membrane fraction|microtubule|perinuclear region of cytoplasm	ATP binding|microtubule motor activity			ovary(2)|skin(1)	3																		---	---	---	---
TSPAN8	7103	broad.mit.edu	37	12	71523013	71523013	+	Intron	DEL	T	-	-	rs112700480		TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:71523013delT	uc009zrt.1	-						TSPAN8_uc001swk.1_Intron|TSPAN8_uc001swj.1_Intron	NM_004616	NP_004607			transmembrane 4 superfamily member 3						protein glycosylation	integral to membrane|lysosome	signal transducer activity			skin(2)|lung(1)|central_nervous_system(1)	4			LUSC - Lung squamous cell carcinoma(43;0.24)|OV - Ovarian serous cystadenocarcinoma(12;0.244)															---	---	---	---
CEP290	80184	broad.mit.edu	37	12	88515039	88515039	+	Intron	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:88515039delA	uc001tar.2	-						CEP290_uc001tat.2_Intron|CEP290_uc009zsl.1_Intron	NM_025114	NP_079390			centrosomal protein 290kDa						cilium assembly|eye photoreceptor cell development|G2/M transition of mitotic cell cycle|hindbrain development|otic vesicle formation|positive regulation of transcription, DNA-dependent|pronephros development|protein transport	cell surface|centrosome|cytosol|nucleus|photoreceptor connecting cilium	protein binding			ovary(5)|breast(1)|pancreas(1)	7																		---	---	---	---
DCN	1634	broad.mit.edu	37	12	91558363	91558363	+	Intron	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:91558363delA	uc001tbs.2	-						DCN_uc001tbo.2_Intron|DCN_uc001tbp.2_Intron|DCN_uc001tbq.2_Intron|DCN_uc001tbr.2_Intron|DCN_uc001tbt.2_Intron|DCN_uc001tbu.2_Intron	NM_133503	NP_598010			decorin isoform a preproprotein						organ morphogenesis	extracellular space				central_nervous_system(2)|ovary(1)|lung(1)	4																		---	---	---	---
CCDC41	51134	broad.mit.edu	37	12	94729387	94729387	+	Frame_Shift_Del	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:94729387delT	uc001tdd.2	-	12	1983	c.1397delA	c.(1396-1398)AATfs	p.N466fs	CCDC41_uc001tde.2_Frame_Shift_Del_p.N466fs|CCDC41_uc009zsw.1_RNA	NM_016122	NP_057206	Q9Y592	CCD41_HUMAN	NY-REN-58 antigen	458	Potential.										0																		---	---	---	---
NR2C1	7181	broad.mit.edu	37	12	95442823	95442823	+	Intron	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:95442823delA	uc001tdm.3	-						NR2C1_uc010suu.1_Intron|NR2C1_uc001tdo.3_Intron|NR2C1_uc001tdn.3_Intron	NM_003297	NP_003288			nuclear receptor subfamily 2, group C, member 1						regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor	PML body	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|steroid hormone receptor activity|zinc ion binding			ovary(1)	1																		---	---	---	---
IFT81	28981	broad.mit.edu	37	12	110570466	110570466	+	Intron	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:110570466delA	uc001tqi.2	+						IFT81_uc001tqh.2_Intron|IFT81_uc001tqj.2_Intron|IFT81_uc001tqg.2_Intron	NM_001143779	NP_001137251			intraflagellar transport 81-like isoform 1						cell differentiation|multicellular organismal development|spermatogenesis	intraflagellar transport particle B|microtubule-based flagellum				ovary(1)	1																		---	---	---	---
C12orf24	29902	broad.mit.edu	37	12	110911025	110911025	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:110911025delT	uc001tqu.3	+						C12orf24_uc010sxz.1_Intron|C12orf24_uc009zvo.2_Intron|C12orf24_uc001tqt.2_Intron|C12orf24_uc001tqv.3_Intron	NM_013300	NP_037432			hypothetical protein LOC29902												0																		---	---	---	---
CCDC64	92558	broad.mit.edu	37	12	120510172	120510172	+	Intron	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:120510172delA	uc001txl.1	+						CCDC64_uc001txk.2_Intron|CCDC64_uc009zwv.1_Intron|CCDC64_uc010sze.1_Intron|CCDC64_uc010szf.1_Intron	NM_207311	NP_997194			coiled-coil domain containing 64						Golgi to secretory granule transport|neuron projection development	centrosome	dynactin binding|Rab GTPase binding			ovary(2)	2	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)																	---	---	---	---
KDM2B	84678	broad.mit.edu	37	12	122018158	122018158	+	Intron	DEL	G	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:122018158delG	uc001uat.2	-						KDM2B_uc001uas.2_5'UTR|KDM2B_uc001uau.2_Intron|KDM2B_uc001uav.3_Intron	NM_032590	NP_115979			F-box and leucine-rich repeat protein 10 isoform						embryonic camera-type eye morphogenesis|fourth ventricle development|histone H2A monoubiquitination|initiation of neural tube closure|lateral ventricle development|midbrain development|midbrain-hindbrain boundary morphogenesis|negative regulation of neural precursor cell proliferation|negative regulation of neuron apoptosis|negative regulation of transcription from RNA polymerase II promoter|spermatogenesis|third ventricle development|transcription, DNA-dependent	nucleolus	DNA binding|histone demethylase activity (H3-K36 specific)|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|protein binding|rRNA binding|zinc ion binding			ovary(1)|skin(1)	2																		---	---	---	---
AACS	65985	broad.mit.edu	37	12	125626402	125626402	+	Intron	DEL	A	-	-	rs35836097		TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:125626402delA	uc001uhc.2	+						AACS_uc001uhd.2_Intron|AACS_uc009zyh.2_Intron|AACS_uc009zyi.2_Intron	NM_023928	NP_076417			acetoacetyl-CoA synthetase						fatty acid metabolic process	cytosol	acetoacetate-CoA ligase activity|ATP binding			ovary(1)|liver(1)|central_nervous_system(1)	3	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;9.82e-05)|Epithelial(86;0.000642)|all cancers(50;0.00843)														---	---	---	---
Unknown	0	broad.mit.edu	37	13	19700978	19700978	+	IGR	DEL	A	-	-	rs9511728	by1000genomes	TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:19700978delA								DKFZp686A1627 (8555 upstream) : TUBA3C (46942 downstream)																																			---	---	---	---
TPTE2	93492	broad.mit.edu	37	13	19997315	19997315	+	Intron	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:19997315delA	uc001umd.2	-						TPTE2_uc009zzk.2_Intron|TPTE2_uc009zzl.2_Intron|TPTE2_uc001ume.2_Intron|TPTE2_uc009zzm.2_Intron|TPTE2_uc010tcm.1_Intron|TPTE2_uc010tcl.1_Intron	NM_199254	NP_954863			TPTE and PTEN homologous inositol lipid							endoplasmic reticulum membrane|integral to membrane	ion channel activity|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity|protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity				0		all_cancers(29;1.23e-20)|all_lung(29;1.97e-20)|all_epithelial(30;5.86e-20)|Lung NSC(5;3.36e-17)|Lung SC(185;0.0262)|Ovarian(182;0.162)		all cancers(112;1.73e-05)|Epithelial(112;7.42e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.000785)|Lung(94;0.0176)|LUSC - Lung squamous cell carcinoma(192;0.089)														---	---	---	---
HMGB1	3146	broad.mit.edu	37	13	31036852	31036852	+	Intron	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:31036852delA	uc001usw.2	-						HMGB1_uc001usz.2_Intron|HMGB1_uc001usv.2_Intron|HMGB1_uc001usx.2_Intron|HMGB1_uc001usy.2_Intron|HMGB1_uc001uta.1_Intron	NM_002128	NP_002119			high-mobility group box 1						base-excision repair, DNA ligation|dendritic cell chemotaxis|DNA fragmentation involved in apoptotic nuclear change|DNA topological change|inflammatory response to antigenic stimulus|innate immune response|myeloid dendritic cell activation|negative regulation of RNA polymerase II transcriptional preinitiation complex assembly|neuron projection development|positive regulation of apoptosis|positive regulation of caspase activity|positive regulation of DNA binding|positive regulation of transcription from RNA polymerase II promoter|V(D)J recombination	cell surface|condensed chromosome|extracellular space|nucleolus|nucleoplasm	chemoattractant activity|cytokine activity|damaged DNA binding|DNA bending activity|double-stranded DNA binding|RAGE receptor binding|repressing transcription factor binding|sequence-specific DNA binding transcription factor activity|single-stranded DNA binding			ovary(1)	1		Lung SC(185;0.0257)		all cancers(112;0.072)|OV - Ovarian serous cystadenocarcinoma(117;0.177)|Lung(94;0.216)|GBM - Glioblastoma multiforme(144;0.232)														---	---	---	---
FAM48A	55578	broad.mit.edu	37	13	37600969	37600970	+	Intron	INS	-	A	A			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:37600969_37600970insA	uc001uwg.2	-						FAM48A_uc010abt.2_Intron|FAM48A_uc001uwh.2_Intron|FAM48A_uc001uwi.2_Intron|FAM48A_uc001uwj.2_Intron|FAM48A_uc001uwk.2_Intron|FAM48A_uc010tes.1_Intron|FAM48A_uc001uwl.1_Intron|FAM48A_uc001uwe.2_5'Flank|FAM48A_uc001uwf.2_5'Flank	NM_001014286	NP_001014308			family with sequence similarity 48, member A						autophagy|gastrulation	SAGA-type complex	protein binding				0		Lung NSC(96;2.09e-06)|Breast(139;0.014)|Lung SC(185;0.0548)|Prostate(109;0.0959)		all cancers(112;6.06e-07)|Epithelial(112;1.87e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00794)|BRCA - Breast invasive adenocarcinoma(63;0.0128)|GBM - Glioblastoma multiforme(144;0.0477)														---	---	---	---
ELF1	1997	broad.mit.edu	37	13	41517026	41517026	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:41517026delT	uc001uxs.2	-						ELF1_uc010tfc.1_Intron|ELF1_uc010acd.2_Intron	NM_172373	NP_758961			E74-like factor 1 (ets domain transcription						positive regulation of transcription from RNA polymerase II promoter	cytoplasm|nucleus	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			ovary(1)	1		Lung NSC(96;8.3e-05)|Prostate(109;0.0233)|Breast(139;0.0296)|Lung SC(185;0.0367)		all cancers(112;1.87e-08)|Epithelial(112;8.45e-06)|OV - Ovarian serous cystadenocarcinoma(117;0.000202)|GBM - Glioblastoma multiforme(144;0.00266)|BRCA - Breast invasive adenocarcinoma(63;0.072)														---	---	---	---
CPB2	1361	broad.mit.edu	37	13	46630052	46630052	+	Intron	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:46630052delA	uc001vaw.2	-						uc001vau.1_Intron|uc001vav.1_Intron|CPB2_uc001vax.2_Intron	NM_001872	NP_001863			plasma carboxypeptidase B2 isoform a						blood coagulation|fibrinolysis|proteolysis	extracellular space	metallocarboxypeptidase activity|zinc ion binding			ovary(1)|skin(1)	2		Lung NSC(96;4.21e-05)|Breast(56;0.000118)|Prostate(109;0.00217)|Hepatocellular(98;0.0207)|Lung SC(185;0.0262)|all_neural(104;0.235)	KIRC - Kidney renal clear cell carcinoma(16;0.234)	GBM - Glioblastoma multiforme(144;5.44e-05)														---	---	---	---
LCP1	3936	broad.mit.edu	37	13	46716269	46716269	+	Intron	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:46716269delA	uc001vaz.3	-						LCP1_uc010ack.2_Intron|LCP1_uc001vay.3_Intron|LCP1_uc001vba.3_Intron	NM_002298	NP_002289			L-plastin						regulation of intracellular protein transport|T cell activation involved in immune response	cell junction|cytosol|ruffle membrane	calcium ion binding			lung(4)|ovary(3)	7		Lung NSC(96;1.27e-05)|Breast(56;8.04e-05)|Prostate(109;0.00217)|Hepatocellular(98;0.0207)|Lung SC(185;0.0262)	KIRC - Kidney renal clear cell carcinoma(16;0.234)	GBM - Glioblastoma multiforme(144;5.39e-05)				T	BCL6	NHL 								---	---	---	---
LRCH1	23143	broad.mit.edu	37	13	47269177	47269177	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:47269177delT	uc001vbj.2	+						LRCH1_uc010acp.2_Intron|LRCH1_uc001vbk.2_Intron|LRCH1_uc001vbl.3_Intron	NM_015116	NP_055931			leucine-rich repeats and calponin homology (CH)											ovary(1)|central_nervous_system(1)	2		all_lung(13;5.61e-07)|Lung NSC(96;0.000117)|Breast(56;0.000141)|Prostate(109;0.0029)|Lung SC(185;0.0367)|Myeloproliferative disorder(33;0.0505)|Hepatocellular(98;0.0556)	KIRC - Kidney renal clear cell carcinoma(16;0.234)	GBM - Glioblastoma multiforme(144;0.000123)														---	---	---	---
TDRD3	81550	broad.mit.edu	37	13	61057789	61057789	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:61057789delT	uc001via.2	+						TDRD3_uc010aef.2_Intron|TDRD3_uc001vhz.3_Intron|TDRD3_uc010aeg.2_Intron|TDRD3_uc001vib.3_Intron	NM_030794	NP_110421			tudor domain containing 3 isoform 2						chromatin modification	cytoplasm|nucleus	chromatin binding|methylated histone residue binding|nucleic acid binding|transcription coactivator activity			upper_aerodigestive_tract(1)|skin(1)	2		Prostate(109;0.173)|Breast(118;0.174)		GBM - Glioblastoma multiforme(99;0.000291)														---	---	---	---
Unknown	0	broad.mit.edu	37	13	67840882	67840882	+	IGR	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:67840882delT								PCDH9 (36414 upstream) : None (None downstream)																																			---	---	---	---
POU4F1	5457	broad.mit.edu	37	13	79176484	79176486	+	In_Frame_Del	DEL	TGG	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:79176484_79176486delTGG	uc001vkv.2	-	2	558_560	c.324_326delCCA	c.(322-327)CACCAG>CAG	p.H108del	uc001vku.1_Intron	NM_006237	NP_006228	Q01851	PO4F1_HUMAN	POU domain, class 4, transcription factor 1	108	Poly-His.				axonogenesis|regulation of transcription from RNA polymerase II promoter|synapse assembly	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			ovary(1)	1		Acute lymphoblastic leukemia(28;0.0279)|Breast(118;0.0848)		GBM - Glioblastoma multiforme(99;0.129)														---	---	---	---
Unknown	0	broad.mit.edu	37	13	88542299	88542299	+	IGR	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:88542299delT								SLITRK5 (210431 upstream) : None (None downstream)																																			---	---	---	---
DNAJC3	5611	broad.mit.edu	37	13	96395171	96395171	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:96395171delT	uc001vmq.2	+						DNAJC3_uc001vmp.2_Frame_Shift_Del_p.I226fs|DNAJC3_uc001vmr.2_Intron	NM_006260	NP_006251			DnaJ (Hsp40) homolog, subfamily C, member 3						protein folding|response to unfolded protein|response to virus		heat shock protein binding|protein kinase inhibitor activity|unfolded protein binding				0	all_neural(89;0.0878)|Breast(111;0.148)|Medulloblastoma(90;0.163)		BRCA - Breast invasive adenocarcinoma(86;0.126)															---	---	---	---
TM9SF2	9375	broad.mit.edu	37	13	100196011	100196011	+	Intron	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:100196011delA	uc001voj.1	+						TM9SF2_uc010afz.1_Intron	NM_004800	NP_004791			transmembrane 9 superfamily member 2 precursor						transport	endosome membrane|integral to plasma membrane				ovary(1)	1	all_neural(89;0.0837)|Medulloblastoma(90;0.18)|Lung SC(71;0.218)																	---	---	---	---
TPP2	7174	broad.mit.edu	37	13	103289645	103289645	+	Intron	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:103289645delA	uc001vpi.3	+							NM_003291	NP_003282			tripeptidyl peptidase II						proteolysis	cytoplasm|nucleus	aminopeptidase activity|serine-type endopeptidase activity|tripeptidyl-peptidase activity			upper_aerodigestive_tract(1)|ovary(1)	2	all_neural(89;0.0438)|Medulloblastoma(90;0.163)|Lung SC(71;0.184)																	---	---	---	---
MYO16	23026	broad.mit.edu	37	13	109858929	109858930	+	Intron	INS	-	T	T			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:109858929_109858930insT	uc001vqt.1	+						MYO16_uc010agk.1_Intron	NM_015011	NP_055826			myosin heavy chain Myr 8						cerebellum development|negative regulation of cell proliferation|negative regulation of S phase of mitotic cell cycle	myosin complex|nucleoplasm|perinuclear region of cytoplasm|plasma membrane	actin filament binding|ATP binding|motor activity			ovary(6)|large_intestine(1)|kidney(1)|breast(1)|central_nervous_system(1)	10	all_lung(23;0.000332)|all_neural(89;0.00294)|Medulloblastoma(90;0.00596)|Lung NSC(43;0.00751)|Lung SC(71;0.104)		BRCA - Breast invasive adenocarcinoma(86;0.19)|all cancers(43;0.201)															---	---	---	---
LAMP1	3916	broad.mit.edu	37	13	113964899	113964899	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:113964899delT	uc001vtm.1	+						LAMP1_uc010tka.1_Intron	NM_005561	NP_005552			lysosomal-associated membrane protein 1							endosome membrane|integral to plasma membrane|lysosomal membrane|membrane fraction				central_nervous_system(2)	2	Lung NSC(43;0.0161)|all_neural(89;0.0804)|Hepatocellular(20;0.0877)|Medulloblastoma(90;0.163)|Lung SC(71;0.218)	all_cancers(25;0.0482)|all_epithelial(44;0.0148)|all_lung(25;0.0271)|Lung NSC(25;0.0977)|Breast(118;0.188)	all cancers(43;0.025)|GBM - Glioblastoma multiforme(44;0.206)|Epithelial(84;0.246)															---	---	---	---
Unknown	0	broad.mit.edu	37	14	19339542	19339542	+	IGR	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:19339542delA								None (None upstream) : OR11H12 (38052 downstream)																																			---	---	---	---
MYH6	4624	broad.mit.edu	37	14	23870221	23870221	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:23870221delT	uc001wjv.2	-						MYH6_uc010akp.1_Intron	NM_002471	NP_002462			myosin heavy chain 6						adult heart development|atrial cardiac muscle tissue morphogenesis|cardiac muscle fiber development|in utero embryonic development|muscle filament sliding|regulation of ATPase activity|regulation of blood pressure|regulation of heart rate|regulation of the force of heart contraction|sarcomere organization|striated muscle contraction|ventricular cardiac muscle tissue morphogenesis|visceral muscle development	cytosol|focal adhesion|muscle myosin complex|myosin filament|nucleus|sarcomere	actin binding|actin-dependent ATPase activity|ATP binding|calmodulin binding|microfilament motor activity|protein kinase binding|structural constituent of muscle			pancreas(2)|ovary(1)|skin(1)	4	all_cancers(95;2.54e-05)			GBM - Glioblastoma multiforme(265;0.00764)|READ - Rectum adenocarcinoma(4;0.0289)|Colorectal(4;0.0441)														---	---	---	---
HECTD1	25831	broad.mit.edu	37	14	31583617	31583617	+	Intron	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:31583617delA	uc001wrc.1	-						HECTD1_uc001wra.1_Intron|HECTD1_uc001wrb.1_Intron|HECTD1_uc001wrd.1_Intron	NM_015382	NP_056197			HECT domain containing 1						protein ubiquitination involved in ubiquitin-dependent protein catabolic process	intracellular	metal ion binding|protein binding|ubiquitin-protein ligase activity			ovary(3)|large_intestine(1)|lung(1)	5	Hepatocellular(127;0.0877)|Breast(36;0.176)		LUAD - Lung adenocarcinoma(48;0.00292)|Lung(238;0.0164)|BRCA - Breast invasive adenocarcinoma(188;0.111)|STAD - Stomach adenocarcinoma(7;0.173)	GBM - Glioblastoma multiforme(265;0.00617)														---	---	---	---
JKAMP	51528	broad.mit.edu	37	14	59953379	59953379	+	Intron	DEL	A	-	-	rs1253109	by1000genomes	TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:59953379delA	uc001xei.3	+						C14orf149_uc001xee.1_5'Flank|C14orf149_uc010trx.1_5'Flank|JKAMP_uc001xef.3_Intron|JKAMP_uc001xeh.3_Intron|JKAMP_uc001xeg.3_Intron|JKAMP_uc010try.1_Intron|JKAMP_uc001xej.3_5'Flank	NM_001098625	NP_001092095			JNK1-associated membrane protein isoform 2						ER-associated protein catabolic process|response to unfolded protein	endoplasmic reticulum membrane|integral to membrane	ubiquitin protein ligase binding			breast(1)	1																		---	---	---	---
KCNH5	27133	broad.mit.edu	37	14	63417320	63417321	+	Intron	DEL	AA	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:63417320_63417321delAA	uc001xfx.2	-						KCNH5_uc001xfy.2_Intron|KCNH5_uc001xfz.1_Intron|KCNH5_uc001xga.2_Intron	NM_139318	NP_647479			potassium voltage-gated channel, subfamily H,						regulation of transcription, DNA-dependent	integral to membrane	calmodulin binding|two-component sensor activity|voltage-gated potassium channel activity			ovary(4)|skin(4)|central_nervous_system(1)	9				OV - Ovarian serous cystadenocarcinoma(108;0.00958)|BRCA - Breast invasive adenocarcinoma(234;0.168)														---	---	---	---
ATP6V1D	51382	broad.mit.edu	37	14	67809927	67809927	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:67809927delT	uc001xjf.2	-						ATP6V1D_uc001xje.2_Intron	NM_015994	NP_057078			H(+)-transporting two-sector ATPase						ATP hydrolysis coupled proton transport|cellular iron ion homeostasis|insulin receptor signaling pathway|transferrin transport	cytosol|proton-transporting two-sector ATPase complex, catalytic domain|vacuolar proton-transporting V-type ATPase complex	protein binding|proton-transporting ATPase activity, rotational mechanism			ovary(1)|lung(1)	2				all cancers(60;0.000739)|OV - Ovarian serous cystadenocarcinoma(108;0.00597)|BRCA - Breast invasive adenocarcinoma(234;0.00957)														---	---	---	---
Unknown	0	broad.mit.edu	37	14	73428538	73428539	+	IGR	DEL	CT	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:73428538_73428539delCT								DCAF4 (2182 upstream) : ZFYVE1 (7621 downstream)																																			---	---	---	---
RBM25	58517	broad.mit.edu	37	14	73563894	73563895	+	Intron	INS	-	TTTTC	TTTTC			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:73563894_73563895insTTTTC	uc001xno.2	+						RBM25_uc001xnn.3_Intron|RBM25_uc010ttu.1_Intron|RBM25_uc001xnp.2_Intron	NM_021239	NP_067062			RNA binding motif protein 25						apoptosis|mRNA processing|regulation of alternative nuclear mRNA splicing, via spliceosome|RNA splicing	cytoplasm|nuclear speck	mRNA binding|nucleotide binding|protein binding			central_nervous_system(2)|ovary(1)|breast(1)	4				BRCA - Breast invasive adenocarcinoma(234;0.00362)|OV - Ovarian serous cystadenocarcinoma(108;0.0688)														---	---	---	---
ALDH6A1	4329	broad.mit.edu	37	14	74533914	74533915	+	Intron	INS	-	A	A			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:74533914_74533915insA	uc001xpo.2	-						C14orf45_uc001xpm.1_Intron|ALDH6A1_uc010asa.2_Intron|ALDH6A1_uc010tuq.1_Intron	NM_005589	NP_005580			aldehyde dehydrogenase 6A1 precursor							mitochondrial matrix|nucleus	fatty-acyl-CoA binding|malonate-semialdehyde dehydrogenase (acetylating) activity|methylmalonate-semialdehyde dehydrogenase (acylating) activity				0				BRCA - Breast invasive adenocarcinoma(234;0.00354)	NADH(DB00157)													---	---	---	---
CATSPERB	79820	broad.mit.edu	37	14	92176040	92176041	+	Intron	DEL	AC	-	-	rs12882622		TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:92176040_92176041delAC	uc001xzs.1	-							NM_024764	NP_079040			cation channel, sperm-associated, beta						cell differentiation|multicellular organismal development|spermatogenesis	integral to membrane				breast(2)|skin(2)|ovary(1)	5		all_cancers(154;0.0663)|all_epithelial(191;0.236)																---	---	---	---
TRIP11	9321	broad.mit.edu	37	14	92493257	92493257	+	Intron	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:92493257delA	uc001xzy.2	-							NM_004239	NP_004230			thyroid hormone receptor interactor 11						transcription from RNA polymerase II promoter	cytoskeleton|Golgi apparatus|membrane|nucleus	protein binding|transcription coactivator activity			ovary(6)|skin(2)|kidney(2)|central_nervous_system(1)|lung(1)|breast(1)	13				COAD - Colon adenocarcinoma(157;0.223)				T	PDGFRB	AML								---	---	---	---
CPSF2	53981	broad.mit.edu	37	14	92625696	92625696	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:92625696delT	uc001yah.1	+							NM_017437	NP_059133			cleavage and polyadenylation specific factor 2						histone mRNA 3'-end processing|mRNA export from nucleus|nuclear mRNA splicing, via spliceosome|termination of RNA polymerase II transcription	mRNA cleavage and polyadenylation specificity factor complex	hydrolase activity|protein binding|RNA binding			ovary(2)	2		all_cancers(154;0.0766)		COAD - Colon adenocarcinoma(157;0.222)														---	---	---	---
NF1P1	440225	broad.mit.edu	37	15	21136692	21136693	+	5'Flank	DEL	CA	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:21136692_21136693delCA	uc001ytv.1	-											Human NF1-related locus DNA in A9 mouse DNA background.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	15	23610060	23610061	+	5'Flank	INS	-	G	G			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:23610060_23610061insG	uc001ywf.2	-											DQ583953																														---	---	---	---
UBE3A	7337	broad.mit.edu	37	15	25650459	25650459	+	Intron	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:25650459delA	uc001zaq.2	-						UBE3A_uc001zar.2_Intron|UBE3A_uc001zas.2_Intron|UBE3A_uc001zat.2_Intron	NM_000462	NP_000453			ubiquitin protein ligase E3A isoform 2						brain development|interspecies interaction between organisms|protein K48-linked ubiquitination|protein ubiquitination involved in ubiquitin-dependent protein catabolic process	nucleus|proteasome complex	protein binding|ubiquitin-protein ligase activity			upper_aerodigestive_tract(1)|ovary(1)|breast(1)	3		all_cancers(20;3.47e-21)|Breast(32;0.00123)		all cancers(64;2.78e-08)|Epithelial(43;8.85e-08)|BRCA - Breast invasive adenocarcinoma(123;0.0155)|Lung(196;0.0616)														---	---	---	---
RYR3	6263	broad.mit.edu	37	15	33923503	33923503	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:33923503delT	uc001zhi.2	+						RYR3_uc010bar.2_Intron	NM_001036	NP_001027			ryanodine receptor 3						cellular calcium ion homeostasis	integral to membrane	calcium ion binding|receptor activity|ryanodine-sensitive calcium-release channel activity			ovary(5)|central_nervous_system(4)|lung(1)	10		all_lung(180;7.18e-09)		all cancers(64;8.95e-12)|GBM - Glioblastoma multiforme(186;0.00109)|BRCA - Breast invasive adenocarcinoma(123;0.0363)														---	---	---	---
CATSPER2	117155	broad.mit.edu	37	15	43927354	43927354	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:43927354delT	uc001zsh.2	-						STRC_uc010udz.1_5'Flank|CATSPER2_uc010bdm.2_Intron|CATSPER2_uc001zsi.2_Intron|CATSPER2_uc001zsj.2_Intron	NM_172095	NP_742093			sperm-associated cation channel 2 isoform 2						cell differentiation|multicellular organismal development|spermatogenesis	cilium|flagellar membrane|integral to membrane	calcium channel activity|protein binding|voltage-gated ion channel activity			ovary(1)	1		all_cancers(109;3.26e-15)|all_epithelial(112;1.48e-12)|Lung NSC(122;2.76e-08)|all_lung(180;3.1e-07)|Melanoma(134;0.027)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;3.56e-07)												OREG0003957	type=REGULATORY REGION|Gene=AK093318|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay	---	---	---	---
PDIA3	2923	broad.mit.edu	37	15	44060896	44060896	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:44060896delT	uc001zsu.2	+						PDIA3_uc010bdp.2_Intron|PDIA3_uc010ued.1_Intron	NM_005313	NP_005304			protein disulfide-isomerase A3 precursor						cell redox homeostasis|glycerol ether metabolic process|post-translational protein modification|protein folding|protein import into nucleus|protein N-linked glycosylation via asparagine|protein retention in ER lumen|signal transduction	endoplasmic reticulum lumen|melanosome	cysteine-type endopeptidase activity|electron carrier activity|phospholipase C activity|protein binding|protein disulfide isomerase activity|protein disulfide oxidoreductase activity			ovary(1)|skin(1)	2		all_cancers(109;2.61e-15)|all_epithelial(112;1.12e-12)|Lung NSC(122;2.17e-08)|all_lung(180;2.45e-07)|Melanoma(134;0.027)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;9.48e-07)														---	---	---	---
CTDSPL2	51496	broad.mit.edu	37	15	44811330	44811330	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:44811330delT	uc001ztr.2	+						CTDSPL2_uc001zts.2_Intron|CTDSPL2_uc001ztt.2_Intron|CTDSPL2_uc010bdv.2_Intron	NM_016396	NP_057480			CTD (carboxy-terminal domain, RNA polymerase II,								phosphoprotein phosphatase activity				0		all_cancers(109;4.36e-14)|all_epithelial(112;9.8e-12)|Lung NSC(122;1.66e-07)|all_lung(180;1.47e-06)|Melanoma(134;0.0122)		all cancers(107;1.02e-20)|GBM - Glioblastoma multiforme(94;1.49e-06)|COAD - Colon adenocarcinoma(120;0.0857)|Colorectal(105;0.0905)														---	---	---	---
USP50	373509	broad.mit.edu	37	15	50833546	50833546	+	Intron	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:50833546delA	uc001zyq.3	-							NM_203494	NP_987090			ubiquitin specific protease 50						ubiquitin-dependent protein catabolic process		ubiquitin thiolesterase activity			lung(1)|breast(1)	2				all cancers(107;0.000519)|GBM - Glioblastoma multiforme(94;0.00288)														---	---	---	---
CCPG1	9236	broad.mit.edu	37	15	55783155	55783156	+	Intron	DEL	AA	-	-	rs74830467		TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:55783155_55783156delAA	uc002acy.2	-						DYX1C1_uc010ugh.1_Intron|DYX1C1_uc010ugi.1_Intron|DYX1C1_uc002adb.2_Intron|DYX1C1_uc002adc.2_Intron|DYX1C1_uc002add.2_Intron	NM_020739	NP_065790			cell cycle progression 1 isoform 2						cell cycle	integral to membrane				ovary(1)	1				all cancers(107;0.0354)														---	---	---	---
GTF2A2	2958	broad.mit.edu	37	15	59942804	59942804	+	Intron	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:59942804delA	uc002agg.2	-							NM_004492	NP_004483			general transcription factor IIA, 2, 12kDa						interspecies interaction between organisms|positive regulation of sequence-specific DNA binding transcription factor activity|positive regulation of transcription from RNA polymerase II promoter|RNA polymerase II transcriptional preinitiation complex assembly|transcription elongation from RNA polymerase II promoter|viral reproduction	transcription factor TFIIA complex	protein heterodimerization activity|protein homodimerization activity|TBP-class protein binding|transcription coactivator activity			central_nervous_system(2)	2																		---	---	---	---
VPS13C	54832	broad.mit.edu	37	15	62284070	62284070	+	Intron	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:62284070delA	uc002agz.2	-						VPS13C_uc002aha.2_Intron|VPS13C_uc002ahb.1_Intron|VPS13C_uc002ahc.1_Intron	NM_020821	NP_065872			vacuolar protein sorting 13C protein isoform 2A						protein localization					ovary(2)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	15	62563040	62563040	+	IGR	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:62563040delA								C2CD4B (105558 upstream) : MGC15885 (366331 downstream)																																			---	---	---	---
FAM96A	84191	broad.mit.edu	37	15	64367853	64367853	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:64367853delT	uc002amt.1	-						FAM96A_uc002amu.1_Intron|FAM96A_uc010uin.1_Intron	NM_032231	NP_115607			family with sequence similarity 96, member A						chromosome segregation						0																		---	---	---	---
PDCD7	10081	broad.mit.edu	37	15	65411613	65411613	+	Intron	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:65411613delA	uc002aol.2	-							NM_005707	NP_005698			programmed cell death 7						apoptosis|induction of apoptosis|response to glucocorticoid stimulus	U12-type spliceosomal complex					0																		---	---	---	---
BLM	641	broad.mit.edu	37	15	91308328	91308328	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:91308328delT	uc002bpr.2	+						BLM_uc010uqh.1_Intron|BLM_uc010uqi.1_Intron|BLM_uc010bnx.2_Intron|BLM_uc002bps.1_Intron	NM_000057	NP_000048			Bloom syndrome protein						double-strand break repair via homologous recombination|G2 phase of mitotic cell cycle|G2/M transition DNA damage checkpoint|negative regulation of cell division|positive regulation of transcription, DNA-dependent|protein oligomerization|regulation of cyclin-dependent protein kinase activity|replication fork processing|replication fork protection|response to X-ray	cytoplasm|lateral element|nuclear matrix|nucleolus|PML body	ATP binding|bubble DNA binding|DNA strand annealing activity|four-way junction helicase activity|G-quadruplex DNA binding|p53 binding			ovary(3)|skin(2)|breast(1)	6	Lung NSC(78;0.0875)|all_lung(78;0.109)		Lung(145;0.189)					Mis|N|F			leukemia|lymphoma|skin squamous cell |other cancers		Genes_defective_in_diseases_associated_with_sensitivity_to_DNA_damaging_agents	Bloom_syndrome				---	---	---	---
PGPEP1L	145814	broad.mit.edu	37	15	99514430	99514440	+	Intron	DEL	GGGGGGGGGGT	-	-	rs72362970		TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:99514430_99514440delGGGGGGGGGGT	uc002bum.2	-						PGPEP1L_uc010bop.2_Intron|PGPEP1L_uc002bun.2_Intron	NM_001102612	NP_001096082			pyroglutamyl-peptidase 1-like protein						proteolysis		cysteine-type peptidase activity				0																		---	---	---	---
TEKT5	146279	broad.mit.edu	37	16	10776188	10776188	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:10776188delT	uc002czz.1	-							NM_144674	NP_653275			tektin 5						microtubule cytoskeleton organization	cilium axoneme|flagellar axoneme|microtubule				ovary(2)	2																		---	---	---	---
PDXDC1	23042	broad.mit.edu	37	16	15095528	15095528	+	Intron	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:15095528delA	uc002dda.3	+						PDXDC1_uc010uzl.1_Intron|PDXDC1_uc010uzm.1_Intron|PDXDC1_uc010bvc.1_Intron|PDXDC1_uc002dcz.2_Intron|PDXDC1_uc002ddb.3_Intron|PDXDC1_uc010uzn.1_Intron|PDXDC1_uc002ddc.2_Intron	NM_015027	NP_055842			pyridoxal-dependent decarboxylase domain						carboxylic acid metabolic process		carboxy-lyase activity|protein binding|pyridoxal phosphate binding			skin(1)	1					Pyridoxal Phosphate(DB00114)													---	---	---	---
SETD1A	9739	broad.mit.edu	37	16	30995407	30995407	+	3'UTR	DEL	C	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:30995407delC	uc002ead.1	+	19					HSD3B7_uc002eaf.2_5'Flank|HSD3B7_uc010cac.2_5'Flank|HSD3B7_uc002eag.2_5'Flank|HSD3B7_uc002eah.2_5'Flank	NM_014712	NP_055527			SET domain containing 1A						regulation of transcription, DNA-dependent|transcription, DNA-dependent	chromosome|nuclear speck|Set1C/COMPASS complex	histone-lysine N-methyltransferase activity|nucleotide binding|protein binding|RNA binding			ovary(2)|skin(1)	3																		---	---	---	---
CNGB1	1258	broad.mit.edu	37	16	57951532	57951533	+	Intron	DEL	AC	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:57951532_57951533delAC	uc002emt.2	-						CNGB1_uc010cdh.2_Intron	NM_001297	NP_001288			cyclic nucleotide gated channel beta 1 isoform						sensory perception of smell	intracellular cyclic nucleotide activated cation channel complex	cAMP binding|intracellular cAMP activated cation channel activity			breast(3)|pancreas(1)	4																		---	---	---	---
CLEC18C	283971	broad.mit.edu	37	16	70066043	70066043	+	Intron	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:70066043delA	uc002exy.2	+						PDXDC2_uc002eyb.2_Intron|PDXDC2_uc002eyc.2_Intron	NM_182619	NP_872425			secretory protein LOC348174 precursor							extracellular region	sugar binding				0																		---	---	---	---
GLG1	2734	broad.mit.edu	37	16	74542594	74542594	+	Intron	DEL	C	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:74542594delC	uc002fcy.3	-						GLG1_uc002fcx.2_Intron|GLG1_uc002fcw.3_Intron|GLG1_uc002fcz.3_Intron	NM_001145667	NP_001139139			golgi apparatus protein 1 isoform 3							Golgi membrane|integral to membrane	receptor binding			ovary(1)|breast(1)	2																		---	---	---	---
CENPN	55839	broad.mit.edu	37	16	81051516	81051516	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:81051516delT	uc002ffx.2	+						CENPN_uc002ffw.3_Intron|CENPN_uc010vnl.1_Intron|CENPN_uc010vnm.1_Intron|CENPN_uc002ffy.3_Intron	NM_001100624	NP_001094094			centromere protein N isoform 2						CenH3-containing nucleosome assembly at centromere|mitotic prometaphase	condensed chromosome kinetochore|cytosol|nucleoplasm					0																		---	---	---	---
CMIP	80790	broad.mit.edu	37	16	81694337	81694337	+	Intron	DEL	T	-	-	rs66465921		TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:81694337delT	uc002fgp.2	+						CMIP_uc002fgq.1_Intron|CMIP_uc010vnq.1_Intron|CMIP_uc002fgr.1_Intron	NM_198390	NP_938204			c-Maf-inducing protein isoform C-mip							cytoplasm|nucleus					0																		---	---	---	---
RAP1GAP2	23108	broad.mit.edu	37	17	2888574	2888575	+	Intron	DEL	TT	-	-	rs71377564		TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:2888574_2888575delTT	uc010ckd.2	+						RAP1GAP2_uc010cke.2_Intron	NM_015085	NP_055900			RAP1 GTPase activating protein 2 isoform 1						regulation of small GTPase mediated signal transduction	centrosome|cytosol|perinuclear region of cytoplasm	GTPase activator activity			ovary(1)	1																		---	---	---	---
ZZEF1	23140	broad.mit.edu	37	17	3967494	3967494	+	Intron	DEL	A	-	-	rs112787658		TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:3967494delA	uc002fxe.2	-						ZZEF1_uc002fxh.2_5'Flank|ZZEF1_uc002fxi.2_Intron|ZZEF1_uc002fxj.1_Intron	NM_015113	NP_055928			zinc finger, ZZ type with EF hand domain 1								calcium ion binding|zinc ion binding			ovary(2)|central_nervous_system(1)|pancreas(1)	4																		---	---	---	---
ZZEF1	23140	broad.mit.edu	37	17	3990635	3990635	+	Intron	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:3990635delA	uc002fxe.2	-						ZZEF1_uc002fxk.1_Intron	NM_015113	NP_055928			zinc finger, ZZ type with EF hand domain 1								calcium ion binding|zinc ion binding			ovary(2)|central_nervous_system(1)|pancreas(1)	4																		---	---	---	---
C17orf68	80169	broad.mit.edu	37	17	8134459	8134459	+	Intron	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:8134459delA	uc002gkq.3	-						C17orf68_uc010cnv.2_Intron	NM_025099	NP_079375			alpha accessory factor 132						positive regulation of DNA replication|telomere maintenance	Stn1-Ten1 complex	protein binding|single-stranded DNA binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	17	20744320	20744321	+	5'Flank	INS	-	G	G	rs35847073	by1000genomes	TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:20744320_20744321insG	uc010crb.1	+											Homo sapiens cDNA clone IMAGE:6269068, partial cds.																														---	---	---	---
Unknown	0	broad.mit.edu	37	17	29349140	29349141	+	5'Flank	INS	-	AT	AT			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:29349140_29349141insAT	uc002hgd.1	+											Homo sapiens full length insert cDNA clone ZD88F12.									p.?(1)																					---	---	---	---
DDX52	11056	broad.mit.edu	37	17	35985898	35985898	+	Intron	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:35985898delA	uc002hoi.1	-						DDX52_uc002hoh.1_Intron	NM_007010	NP_008941			ATP-dependent RNA helicase ROK1 isoform a							nucleolus	ATP binding|ATP-dependent helicase activity|RNA binding			ovary(1)|skin(1)	2		Breast(25;0.00637)|Ovarian(249;0.15)																---	---	---	---
KRT40	125115	broad.mit.edu	37	17	39139511	39139511	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:39139511delT	uc010cxh.1	-						KRT40_uc002hvq.1_Intron	NM_182497	NP_872303			type I hair keratin KA36							intermediate filament	structural molecule activity				0		Breast(137;0.00043)																---	---	---	---
CCDC43	124808	broad.mit.edu	37	17	42756533	42756533	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:42756533delT	uc002ihc.2	-						CCDC43_uc010czw.1_Intron	NM_144609	NP_653210			coiled-coil domain containing 43 isoform 1												0		Prostate(33;0.0322)																---	---	---	---
ABI3	51225	broad.mit.edu	37	17	47295005	47295005	+	Intron	DEL	C	-	-	rs113223751		TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:47295005delC	uc002iop.1	+						ABI3_uc002ioq.1_Intron	NM_016428	NP_057512			NESH protein isoform 1						cellular component movement|regulation of cell migration	cytoplasm|lamellipodium	protein binding				0			Epithelial(5;6.37e-06)|all cancers(6;6.36e-05)												HNSCC(55;0.14)			---	---	---	---
CACNA1G	8913	broad.mit.edu	37	17	48639187	48639187	+	Intron	DEL	G	-	-	rs112792872		TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:48639187delG	uc002irk.1	+						uc002irh.2_Intron|CACNA1G_uc002iri.1_Intron|CACNA1G_uc002irj.1_Intron|CACNA1G_uc002irl.1_Intron|CACNA1G_uc002irm.1_Intron|CACNA1G_uc002irn.1_Intron|CACNA1G_uc002iro.1_Intron|CACNA1G_uc002irp.1_Intron|CACNA1G_uc002irq.1_Intron|CACNA1G_uc002irr.1_Intron|CACNA1G_uc002irs.1_Intron|CACNA1G_uc002irt.1_Intron|CACNA1G_uc002irv.1_Intron|CACNA1G_uc002irw.1_Intron|CACNA1G_uc002iru.1_Intron	NM_018896	NP_061496			voltage-dependent calcium channel alpha 1G						axon guidance	voltage-gated calcium channel complex	low voltage-gated calcium channel activity			breast(1)	1	Breast(11;6.7e-17)		BRCA - Breast invasive adenocarcinoma(22;7.52e-09)		Ethosuximide(DB00593)|Flunarizine(DB04841)|Levetiracetam(DB01202)|Mibefradil(DB01388)|Pimozide(DB01100)|Trimethadione(DB00347)|Verapamil(DB00661)|Zonisamide(DB00909)													---	---	---	---
TRIM37	4591	broad.mit.edu	37	17	57148100	57148101	+	Intron	DEL	AA	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:57148100_57148101delAA	uc002iwy.3	-						TRIM37_uc002iwz.3_Intron|TRIM37_uc002ixa.3_Intron|TRIM37_uc010woc.1_Intron	NM_001005207	NP_001005207			tripartite motif-containing 37 protein							perinuclear region of cytoplasm|peroxisome	ligase activity|protein binding|zinc ion binding			lung(2)|pancreas(2)|ovary(1)|skin(1)|breast(1)	7	Medulloblastoma(34;0.0922)|all_neural(34;0.101)													Mulibrey_Nanism				---	---	---	---
HEATR6	63897	broad.mit.edu	37	17	58136999	58136999	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:58136999delT	uc002iyk.1	-						HEATR6_uc010ddk.1_Intron|HEATR6_uc010wos.1_Intron	NM_022070	NP_071353			HEAT repeat containing 6								binding			ovary(1)|skin(1)	2	all_cancers(5;2.25e-13)|Breast(5;4.84e-25)|all_neural(34;0.0878)|Medulloblastoma(34;0.0922)		BRCA - Breast invasive adenocarcinoma(1;5.93e-19)|Epithelial(12;7.59e-12)|all cancers(12;1.26e-10)															---	---	---	---
BPTF	2186	broad.mit.edu	37	17	65960135	65960135	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:65960135delT	uc002jgf.2	+						BPTF_uc002jge.2_Intron|BPTF_uc002jgg.2_Intron|BPTF_uc002jgh.2_Intron	NM_182641	NP_872579			bromodomain PHD finger transcription factor						brain development|chromatin remodeling|negative regulation of transcription from RNA polymerase II promoter|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|NURF complex	sequence-specific DNA binding|transcription factor binding|zinc ion binding			ovary(2)|skin(2)	4	all_cancers(12;6e-11)		BRCA - Breast invasive adenocarcinoma(8;7.48e-08)|Colorectal(3;0.0984)|LUSC - Lung squamous cell carcinoma(166;0.24)															---	---	---	---
MYL12B	103910	broad.mit.edu	37	18	3273141	3273142	+	Intron	INS	-	T	T			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:3273141_3273142insT	uc010dkl.2	+						MYL12B_uc002klt.3_Intron|MYL12B_uc010wyv.1_Intron	NM_001144944	NP_001138416			myosin regulatory light chain MRCL2 isoform A						axon guidance|muscle contraction	cytosol|myosin complex	calcium ion binding				0																		---	---	---	---
NAPG	8774	broad.mit.edu	37	18	10548537	10548539	+	Intron	DEL	TTT	-	-	rs1662154		TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:10548537_10548539delTTT	uc002kon.2	+						NAPG_uc010wzr.1_Intron|NAPG_uc002koo.2_Intron|NAPG_uc002kop.2_Intron	NM_003826	NP_003817			N-ethylmaleimide-sensitive factor attachment						cellular membrane fusion|intra-Golgi vesicle-mediated transport|intracellular protein transport|protein complex assembly|protein stabilization	membrane|membrane fraction|mitochondrion	protein binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	18	14225639	14225639	+	IGR	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:14225639delA								ZNF519 (93210 upstream) : LOC284233 (111783 downstream)																																			---	---	---	---
CDH2	1000	broad.mit.edu	37	18	25593923	25593923	+	Intron	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:25593923delA	uc002kwg.2	-						CDH2_uc010xbn.1_Intron	NM_001792	NP_001783			cadherin 2, type 1 preproprotein						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																		---	---	---	---
DSG1	1828	broad.mit.edu	37	18	28923779	28923779	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:28923779delT	uc002kwp.2	+						DSG1_uc010xbp.1_5'UTR	NM_001942	NP_001933			desmoglein 1 preproprotein						calcium-dependent cell-cell adhesion|cell-cell junction assembly|cellular component disassembly involved in apoptosis|homophilic cell adhesion|protein stabilization	cytosol|desmosome|integral to membrane|internal side of plasma membrane	calcium ion binding|gamma-catenin binding|toxin binding			skin(3)|ovary(2)|central_nervous_system(2)	7			OV - Ovarian serous cystadenocarcinoma(10;0.00559)															---	---	---	---
SLC14A2	8170	broad.mit.edu	37	18	43216750	43216750	+	Intron	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:43216750delA	uc010dnj.2	+						SLC14A2_uc002lbb.2_Intron|SLC14A2_uc002lbe.2_Intron	NM_007163	NP_009094			solute carrier family 14 (urea transporter),							apical plasma membrane|integral to membrane|membrane fraction	protein binding|urea transmembrane transporter activity			upper_aerodigestive_tract(1)|ovary(1)|central_nervous_system(1)|skin(1)	4																		---	---	---	---
Unknown	0	broad.mit.edu	37	18	60110469	60110469	+	IGR	DEL	T	-	-	rs74413211	byFrequency;by1000genomes	TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:60110469delT								TNFRSF11A (56967 upstream) : ZCCHC2 (80189 downstream)																																			---	---	---	---
PRSSL1	400668	broad.mit.edu	37	19	691213	691213	+	Intron	DEL	A	-	-	rs147436553		TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:691213delA	uc002lpl.1	-						PRSSL1_uc010xfs.1_Intron	NM_214710	NP_999875			protease, serine-like 1 precursor						proteolysis	extracellular region	serine-type endopeptidase activity				0		all_epithelial(18;2.19e-21)|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)														---	---	---	---
GRIN3B	116444	broad.mit.edu	37	19	1008813	1008813	+	Intron	DEL	C	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:1008813delC	uc002lqo.1	+						uc002lqp.1_RNA	NM_138690	NP_619635			glutamate receptor, ionotropic,						ionotropic glutamate receptor signaling pathway|protein insertion into membrane|regulation of calcium ion transport	cell junction|N-methyl-D-aspartate selective glutamate receptor complex|neuronal cell body|outer membrane-bounded periplasmic space|postsynaptic membrane	extracellular-glutamate-gated ion channel activity|glycine binding|ionotropic glutamate receptor activity|neurotransmitter receptor activity				0		Acute lymphoblastic leukemia(61;4.36e-14)|all_hematologic(61;4.84e-09)|Lung NSC(49;0.000226)|all_lung(49;0.000353)|Breast(49;0.00066)		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)	Glycine(DB00145)|L-Glutamic Acid(DB00142)|Orphenadrine(DB01173)													---	---	---	---
KHSRP	8570	broad.mit.edu	37	19	6414223	6414223	+	Intron	DEL	G	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:6414223delG	uc002mer.3	-							NM_003685	NP_003676			KH-type splicing regulatory protein						mRNA processing|mRNA transport|regulation of transcription, DNA-dependent|RNA splicing, via transesterification reactions|transcription, DNA-dependent	cytosol|nucleus	DNA binding|protein binding|RNA binding			skin(1)	1																		---	---	---	---
EMR1	2015	broad.mit.edu	37	19	6896646	6896647	+	Intron	INS	-	T	T			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:6896646_6896647insT	uc002mfw.2	+						EMR1_uc010dvc.2_Intron|EMR1_uc010dvb.2_Intron|EMR1_uc010xji.1_Intron|EMR1_uc010xjj.1_Intron	NM_001974	NP_001965			egf-like module containing, mucin-like, hormone						cell adhesion|neuropeptide signaling pathway	integral to plasma membrane	calcium ion binding|G-protein coupled receptor activity			ovary(3)|lung(1)|skin(1)	5	all_hematologic(4;0.166)																	---	---	---	---
Unknown	0	broad.mit.edu	37	19	10377498	10377498	+	IGR	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:10377498delT								MRPL4 (6764 upstream) : ICAM1 (4019 downstream)																																			---	---	---	---
UNC13A	23025	broad.mit.edu	37	19	17750846	17750846	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:17750846delT	uc002nhd.2	-							NM_001080421	NP_001073890			unc-13 homolog A						exocytosis|intracellular signal transduction	cell junction|cytoplasm|presynaptic membrane	metal ion binding			ovary(3)	3																		---	---	---	---
ZNF430	80264	broad.mit.edu	37	19	21216110	21216111	+	Intron	DEL	AA	-	-	rs111525322		TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:21216110_21216111delAA	uc002npj.2	+						ZNF430_uc002npk.2_Intron	NM_025189	NP_079465			zinc finger protein 430						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			skin(2)	2																		---	---	---	---
ZNF430	80264	broad.mit.edu	37	19	21217112	21217112	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:21217112delT	uc002npj.2	+						ZNF430_uc002npk.2_Intron	NM_025189	NP_079465			zinc finger protein 430						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			skin(2)	2																		---	---	---	---
C19orf2	8725	broad.mit.edu	37	19	30462218	30462219	+	Intron	DEL	GT	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:30462218_30462219delGT	uc002nsr.2	+						C19orf2_uc002nsq.2_Intron|C19orf2_uc002nss.2_Intron	NM_003796	NP_003787			RPB5-mediating protein isoform a						protein folding|regulation of transcription from RNA polymerase II promoter|response to virus	DNA-directed RNA polymerase II, core complex|prefoldin complex	transcription corepressor activity|unfolded protein binding			ovary(1)|kidney(1)	2	Ovarian(5;0.000902)|Breast(6;0.0203)|Esophageal squamous(110;0.195)	Hepatocellular(1079;0.137)|Renal(1328;0.228)	STAD - Stomach adenocarcinoma(5;5.36e-06)|Lung(7;0.0144)|LUAD - Lung adenocarcinoma(5;0.115)	STAD - Stomach adenocarcinoma(1328;0.18)														---	---	---	---
GPATCH1	55094	broad.mit.edu	37	19	33587442	33587442	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:33587442delT	uc002nug.1	+							NM_018025	NP_060495			G patch domain containing 1							catalytic step 2 spliceosome	nucleic acid binding			skin(1)	1	Esophageal squamous(110;0.137)																	---	---	---	---
ZNF829	374899	broad.mit.edu	37	19	37393061	37393061	+	Intron	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:37393061delA	uc002ofa.1	-						ZNF345_uc002oez.2_Intron	NM_001037232	NP_001032309			zinc finger protein 829						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0	Esophageal squamous(110;0.183)		COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)															---	---	---	---
PLD3	23646	broad.mit.edu	37	19	40873490	40873490	+	Intron	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:40873490delA	uc002onm.3	+						PLD3_uc002onj.3_Intron|PLD3_uc002onk.3_Intron|PLD3_uc002onl.3_Intron|PLD3_uc002onn.2_Intron|PLD3_uc002ono.2_3'UTR	NM_001031696	NP_001026866			phospholipase D3						lipid catabolic process	endoplasmic reticulum membrane|integral to membrane	NAPE-specific phospholipase D activity|phospholipase D activity|protein binding			skin(2)|ovary(1)	3			Lung(22;0.000636)|LUSC - Lung squamous cell carcinoma(20;0.00248)															---	---	---	---
BCKDHA	593	broad.mit.edu	37	19	41929040	41929042	+	In_Frame_Del	DEL	AGG	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:41929040_41929042delAGG	uc002oqq.2	+	8	1162_1164	c.1133_1135delAGG	c.(1132-1137)CAGGAG>CAG	p.E379del	CYP2F1_uc010xvw.1_Intron|BCKDHA_uc002oqm.3_In_Frame_Del_p.E413del|BCKDHA_uc002oqr.2_In_Frame_Del_p.E378del|BCKDHA_uc010xvz.1_In_Frame_Del_p.E382del	NM_000709	NP_000700	P12694	ODBA_HUMAN	branched chain keto acid dehydrogenase E1, alpha	379					branched chain family amino acid catabolic process	mitochondrial alpha-ketoglutarate dehydrogenase complex	3-methyl-2-oxobutanoate dehydrogenase (2-methylpropanoyl-transferring) activity|alpha-ketoacid dehydrogenase activity|carboxy-lyase activity|metal ion binding|protein binding				0																		---	---	---	---
SLC8A2	6543	broad.mit.edu	37	19	47941333	47941335	+	Intron	DEL	CTC	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:47941333_47941335delCTC	uc002pgx.2	-						SLC8A2_uc010xyq.1_Intron|SLC8A2_uc010xyr.1_Intron|SLC8A2_uc010ele.2_Intron	NM_015063	NP_055878			solute carrier family 8 member 2 precursor						cell communication|platelet activation	integral to membrane|plasma membrane	calcium:sodium antiporter activity|calmodulin binding			skin(3)|ovary(1)	4		all_cancers(25;3.05e-07)|all_lung(116;4.19e-06)|Lung NSC(112;7.16e-06)|all_epithelial(76;7.65e-06)|all_neural(266;0.0652)|Ovarian(192;0.086)|Breast(70;0.173)		OV - Ovarian serous cystadenocarcinoma(262;0.000501)|all cancers(93;0.00058)|Epithelial(262;0.0181)|GBM - Glioblastoma multiforme(486;0.0457)														---	---	---	---
TEAD2	8463	broad.mit.edu	37	19	49845484	49845485	+	Intron	INS	-	CCACATCAGTT	CCACATCAGTT	rs149352076	by1000genomes	TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:49845484_49845485insCCACATCAGTT	uc002pnj.2	-						uc002pnb.1_5'Flank|TEAD2_uc002png.2_Intron|TEAD2_uc002pnh.2_Intron|TEAD2_uc002pni.2_Intron|TEAD2_uc010yao.1_Intron|TEAD2_uc010emw.2_Intron	NM_003598	NP_003589			TEA domain family member 2						hippo signaling cascade		DNA binding|protein binding|sequence-specific DNA binding transcription factor activity			central_nervous_system(2)|ovary(1)	3		all_lung(116;7.65e-05)|Lung NSC(112;0.000132)|all_neural(266;0.0506)|Ovarian(192;0.15)		OV - Ovarian serous cystadenocarcinoma(262;0.00093)|GBM - Glioblastoma multiforme(486;0.0467)														---	---	---	---
ZNF320	162967	broad.mit.edu	37	19	53391576	53391577	+	Intron	INS	-	GA	GA			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:53391576_53391577insGA	uc002qag.2	-						ZNF320_uc010eqi.1_Intron|ZNF320_uc002qah.2_Intron|ZNF320_uc002qai.2_Intron	NM_207333	NP_997216			zinc finger protein 320						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0				GBM - Glioblastoma multiforme(134;0.0534)														---	---	---	---
PTPRH	5794	broad.mit.edu	37	19	55698755	55698755	+	Intron	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:55698755delA	uc002qjq.2	-						PTPRH_uc010esv.2_Intron|uc002qjr.2_5'Flank	NM_002842	NP_002833			protein tyrosine phosphatase, receptor type, H						apoptosis	cytoplasm|integral to plasma membrane	protein binding|transmembrane receptor protein tyrosine phosphatase activity			ovary(2)|large_intestine(1)|skin(1)	4		Renal(1328;0.245)	BRCA - Breast invasive adenocarcinoma(297;0.209)	GBM - Glioblastoma multiforme(193;0.0479)														---	---	---	---
MCM8	84515	broad.mit.edu	37	20	5952840	5952840	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:5952840delT	uc002wmi.2	+						MCM8_uc002wmj.2_Intron|MCM8_uc002wmk.2_Intron|MCM8_uc002wml.2_Intron|MCM8_uc010gbp.2_Intron|MCM8_uc002wmm.2_5'UTR	NM_032485	NP_115874			minichromosome maintenance complex component 8						cell cycle checkpoint|DNA strand elongation involved in DNA replication|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|regulation of transcription, DNA-dependent|S phase of mitotic cell cycle|transcription, DNA-dependent	nucleoplasm	ATP binding|DNA binding|nucleoside-triphosphatase activity			skin(1)	1																		---	---	---	---
PLK1S1	55857	broad.mit.edu	37	20	21196192	21196192	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:21196192delT	uc002wsb.2	+						PLK1S1_uc010zsh.1_Intron|PLK1S1_uc010zsi.1_Intron|PLK1S1_uc010zsj.1_Intron|uc002wsc.2_Intron|PLK1S1_uc002wsd.2_Intron|uc002wse.2_Intron	NM_018474	NP_060944			polo-like kinase 1 substrate 1 isoform 1						spindle organization	centrosome	protein kinase binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	20	29930733	29930733	+	IGR	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:29930733delT								DEFB116 (34345 upstream) : DEFB118 (25695 downstream)																																			---	---	---	---
GDF5	8200	broad.mit.edu	37	20	33969913	33969913	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:33969913delT	uc010gfc.1	-						UQCC_uc010zuy.1_Intron|UQCC_uc002xcd.2_Intron|UQCC_uc010zuz.1_Intron|UQCC_uc010zva.1_Intron|UQCC_uc002xce.2_Intron|UQCC_uc002xcg.2_Intron|UQCC_uc010gfb.2_Intron|UQCC_uc010zvb.1_Intron|UQCC_uc002xcf.2_Intron|UQCC_uc002xci.1_Intron|UQCC_uc010gfd.1_Intron	NM_000557	NP_000548			growth differentiation factor 5 preproprotein						cartilage development|cell-cell signaling|growth|transforming growth factor beta receptor signaling pathway	extracellular space	cytokine activity|growth factor activity				0	Lung NSC(9;0.00642)|all_lung(11;0.0094)		BRCA - Breast invasive adenocarcinoma(18;0.00663)															---	---	---	---
RBM12	10137	broad.mit.edu	37	20	34240428	34240428	+	3'UTR	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:34240428delA	uc002xdq.2	-	3					CPNE1_uc010zvj.1_Intron|CPNE1_uc002xde.2_Intron|CPNE1_uc002xdf.2_Intron|CPNE1_uc002xdg.2_Intron|CPNE1_uc010gfi.2_Intron|CPNE1_uc010gfj.2_Intron|CPNE1_uc002xdh.2_Intron|CPNE1_uc002xdi.2_Intron|CPNE1_uc002xdj.2_Intron|CPNE1_uc002xdk.2_Intron|CPNE1_uc002xdl.2_Intron|CPNE1_uc002xdm.2_Intron|CPNE1_uc010gfk.1_Intron|CPNE1_uc002xdn.1_Intron|CPNE1_uc002xdo.1_Intron|CPNE1_uc002xdp.1_Intron|RBM12_uc002xdr.2_3'UTR|RBM12_uc002xds.2_3'UTR	NM_152838	NP_690051			RNA binding motif protein 12							nucleus	nucleotide binding|protein binding|RNA binding			ovary(3)	3	Lung NSC(9;0.00608)|all_lung(11;0.00918)		BRCA - Breast invasive adenocarcinoma(18;0.00953)															---	---	---	---
PHF20	51230	broad.mit.edu	37	20	34519091	34519093	+	Intron	DEL	ATG	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:34519091_34519093delATG	uc002xek.1	+							NM_016436	NP_057520			PHD finger protein 20						regulation of transcription, DNA-dependent|transcription, DNA-dependent	MLL1 complex	DNA binding|zinc ion binding			ovary(1)	1	Breast(12;0.00631)|all_lung(11;0.0145)																	---	---	---	---
FAM83D	81610	broad.mit.edu	37	20	37555035	37555035	+	Frame_Shift_Del	DEL	C	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:37555035delC	uc002xjg.2	+	1	81	c.40delC	c.(40-42)CGGfs	p.R14fs	FAM83D_uc002xjf.2_Frame_Shift_Del_p.R14fs	NM_030919	NP_112181	Q9H4H8	FA83D_HUMAN	hypothetical protein LOC81610	Error:Variant_position_missing_in_Q9H4H8_after_alignment					cell division|mitosis	cytoplasm|spindle pole				ovary(3)	3		Myeloproliferative disorder(115;0.00878)																---	---	---	---
PCIF1	63935	broad.mit.edu	37	20	44567581	44567581	+	Intron	DEL	G	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:44567581delG	uc002xqs.2	+							NM_022104	NP_071387			phosphorylated CTD interacting factor 1							nucleus				skin(1)	1																		---	---	---	---
PREX1	57580	broad.mit.edu	37	20	47244216	47244216	+	Intron	DEL	G	-	-	rs80011299	byFrequency;by1000genomes	TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:47244216delG	uc002xtw.1	-						PREX1_uc002xtv.1_Intron	NM_020820	NP_065871			phosphatidylinositol-3,4,						actin filament polymerization|apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|neutrophil activation|small GTPase mediated signal transduction|superoxide metabolic process	cytosol|plasma membrane	enzyme binding|phospholipid binding|Rho GTPase activator activity|Rho guanyl-nucleotide exchange factor activity			lung(3)|ovary(2)|pancreas(1)	6			BRCA - Breast invasive adenocarcinoma(12;0.0135)|Colorectal(8;0.198)															---	---	---	---
NKAIN4	128414	broad.mit.edu	37	20	61874139	61874139	+	Intron	DEL	G	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:61874139delG	uc002yek.2	-							NM_152864	NP_690603			Na+/K+ transporting ATPase interacting 4							integral to membrane|plasma membrane					0	all_cancers(38;2.72e-09)																	---	---	---	---
Unknown	0	broad.mit.edu	37	21	9483288	9483288	+	IGR	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:9483288delA								None (None upstream) : None (None downstream)																																			---	---	---	---
ITSN1	6453	broad.mit.edu	37	21	35231209	35231209	+	Intron	DEL	T	-	-	rs5843624		TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:35231209delT	uc002yta.1	+						DONSON_uc002ysn.1_Intron|ITSN1_uc002ytb.1_Intron|ITSN1_uc002ytj.2_Intron|ITSN1_uc010gmm.1_Intron	NM_003024	NP_003015			intersectin 1 isoform ITSN-l						apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction|synaptic vesicle endocytosis	cell junction|coated pit|cytosol|lamellipodium|synapse|synaptosome	calcium ion binding|proline-rich region binding|protein complex scaffold|Rho guanyl-nucleotide exchange factor activity			ovary(3)|skin(1)	4																		---	---	---	---
Unknown	0	broad.mit.edu	37	21	37518894	37518894	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:37518894delT	uc002yvc.1	-						uc002yvd.1_Intron|uc002yvf.1_Intron					Homo sapiens mRNA expressed in placenta, clone IMAGE:139776.																														---	---	---	---
BRWD1	54014	broad.mit.edu	37	21	40684718	40684718	+	Intron	DEL	G	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:40684718delG	uc002yxk.1	-						BRWD1_uc002yxl.2_Intron|BRWD1_uc002yxm.2_Intron	NM_018963	NP_061836			bromodomain and WD repeat domain containing 1						regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus				skin(3)|ovary(1)	4		Prostate(19;8.44e-08)|all_epithelial(19;0.223)																---	---	---	---
DSCAM	1826	broad.mit.edu	37	21	41741250	41741250	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:41741250delT	uc002yyq.1	-						DSCAM_uc002yyr.1_Intron	NM_001389	NP_001380			Down syndrome cell adhesion molecule isoform						cell adhesion|dendrite self-avoidance|negative regulation of cell adhesion|positive regulation of axon extension involved in axon guidance|positive regulation of phosphorylation	axon|extracellular region|growth cone|integral to plasma membrane|membrane fraction	protein binding			ovary(6)|skin(4)|upper_aerodigestive_tract(1)	11		all_cancers(19;0.186)|Prostate(19;1.15e-05)|all_epithelial(19;0.0103)																---	---	---	---
SIK1	150094	broad.mit.edu	37	21	44836942	44836942	+	Frame_Shift_Del	DEL	G	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:44836942delG	uc002zdf.2	-	14	2159	c.2032delC	c.(2032-2034)CAGfs	p.Q678fs		NM_173354	NP_775490	P57059	SIK1_HUMAN	salt-inducible kinase 1	678					anoikis|cell cycle|cell differentiation|intracellular protein kinase cascade|multicellular organismal development|regulation of cell differentiation|regulation of mitotic cell cycle	nucleus	ATP binding|magnesium ion binding|protein binding|protein serine/threonine kinase activity			lung(2)|testis(2)|ovary(1)|central_nervous_system(1)|skin(1)	7																		---	---	---	---
BCR	613	broad.mit.edu	37	22	23634615	23634615	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:23634615delT	uc002zww.2	+						BCR_uc002zwx.2_Intron|BCR_uc011aiy.1_Intron	NM_004327	NP_004318			breakpoint cluster region isoform 1						regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol	ATP binding|GTPase activator activity|protein serine/threonine kinase activity|Rho guanyl-nucleotide exchange factor activity		BCR/JAK2(6)	haematopoietic_and_lymphoid_tissue(6)|central_nervous_system(3)|urinary_tract(1)|lung(1)|skin(1)	12								T	ABL1| FGFR1|JAK2 	CML|ALL|AML								---	---	---	---
C22orf43	51233	broad.mit.edu	37	22	23973867	23973868	+	Intron	INS	-	C	C	rs141675360	by1000genomes	TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:23973867_23973868insC	uc002zxf.2	-							NM_016449	NP_057533			hypothetical protein LOC51233											skin(1)	1																		---	---	---	---
CABIN1	23523	broad.mit.edu	37	22	24480374	24480374	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:24480374delT	uc002zzi.1	+						CABIN1_uc002zzj.1_Intron|CABIN1_uc002zzl.1_Intron	NM_012295	NP_036427			calcineurin binding protein 1						cell surface receptor linked signaling pathway|chromatin modification	nucleus	protein phosphatase inhibitor activity			ovary(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)|pancreas(1)	5																		---	---	---	---
DEPDC5	9681	broad.mit.edu	37	22	32194509	32194509	+	Intron	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:32194509delA	uc003als.2	+						DEPDC5_uc011als.1_Intron|DEPDC5_uc011alu.1_Intron|DEPDC5_uc011alv.1_Intron|DEPDC5_uc003alt.2_Intron|DEPDC5_uc003alr.1_Intron|DEPDC5_uc011alt.1_Intron	NM_014662	NP_055477			DEP domain containing 5 isoform 1						intracellular signal transduction					ovary(4)|central_nervous_system(3)|pancreas(1)	8																		---	---	---	---
MYH9	4627	broad.mit.edu	37	22	36744899	36744899	+	Intron	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:36744899delA	uc003apg.2	-						MYH9_uc003api.1_Intron	NM_002473	NP_002464			myosin, heavy polypeptide 9, non-muscle						actin cytoskeleton reorganization|actin filament-based movement|angiogenesis|axon guidance|blood vessel endothelial cell migration|cytokinesis|integrin-mediated signaling pathway|leukocyte migration|membrane protein ectodomain proteolysis|monocyte differentiation|platelet formation|protein transport|regulation of cell shape	actomyosin contractile ring|cleavage furrow|cytosol|myosin complex|nucleus|ruffle|stress fiber|uropod	actin filament binding|actin-dependent ATPase activity|ADP binding|ATP binding|calmodulin binding|microfilament motor activity|protein anchor|protein homodimerization activity			breast(3)|ovary(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)|lung(1)|skin(1)|kidney(1)|pancreas(1)	11								T	ALK	ALCL		Deafness|autosomal dominant 17|Epstein syndrome|Fechtner syndrome|May-Hegglin anomaly|Sebastian syndrome		Hereditary_Macrothrombocytopenia_MYH9-associated				---	---	---	---
ELFN2	114794	broad.mit.edu	37	22	37769104	37769104	+	3'UTR	DEL	G	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:37769104delG	uc003asq.3	-	3						NM_052906	NP_443138			leucine rich repeat containing 62							cell surface|integral to membrane				upper_aerodigestive_tract(1)|ovary(1)	2	Melanoma(58;0.0574)																	---	---	---	---
TYMP	1890	broad.mit.edu	37	22	50968827	50968830	+	5'Flank	DEL	AGAG	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:50968827_50968830delAGAG	uc003bmb.3	-						TYMP_uc003bmc.3_5'Flank|TYMP_uc003bmd.3_5'Flank|TYMP_uc010hbd.2_5'Flank|TYMP_uc003bme.3_5'Flank|TYMP_uc003bmf.3_5'Flank|TYMP_uc011arz.1_5'Flank	NM_001113756	NP_001107228			endothelial cell growth factor 1						angiogenesis|cell differentiation|chemotaxis|DNA replication|mitochondrial genome maintenance|pyrimidine base metabolic process|pyrimidine nucleoside catabolic process|pyrimidine nucleoside salvage|pyrimidine nucleotide metabolic process	cytosol	growth factor activity|platelet-derived growth factor receptor binding|pyrimidine-nucleoside phosphorylase activity|thymidine phosphorylase activity			ovary(1)	1		all_cancers(38;4.58e-14)|all_epithelial(38;1.12e-12)|all_lung(38;3.07e-05)|Breast(42;6.27e-05)|Lung NSC(38;0.000813)|Ovarian(80;0.0221)|Hepatocellular(38;0.0691)|Lung SC(80;0.113)		BRCA - Breast invasive adenocarcinoma(115;0.206)|LUAD - Lung adenocarcinoma(64;0.247)	Capecitabine(DB01101)|Docetaxel(DB01248)|Floxuridine(DB00322)|Fluorouracil(DB00544)|Sulfasalazine(DB00795)|Tamoxifen(DB00675)													---	---	---	---
SHANK3	85358	broad.mit.edu	37	22	51159932	51159933	+	Frame_Shift_Ins	INS	-	G	G			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:51159932_51159933insG	uc003bne.1	+	22	3719_3720	c.3719_3720insG	c.(3718-3720)CTGfs	p.L1240fs	SHANK3_uc003bnf.1_Frame_Shift_Ins_p.L687fs|SHANK3_uc010hbg.1_Frame_Shift_Ins_p.L422fs	NM_001080420	NP_001073889	F2Z3L0	F2Z3L0_HUMAN	SH3 and multiple ankyrin repeat domains 3	1240										central_nervous_system(1)	1		all_cancers(38;3.75e-11)|all_epithelial(38;1.82e-09)|Breast(42;0.000448)|all_lung(38;0.000665)|Lung NSC(38;0.0104)|Ovarian(80;0.104)|Lung SC(80;0.162)|Hepatocellular(38;0.178)		BRCA - Breast invasive adenocarcinoma(115;0.22)														---	---	---	---
RBBP7	5931	broad.mit.edu	37	X	16867569	16867569	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:16867569delT	uc004cxt.2	-						RBBP7_uc004cxs.1_Intron|RBBP7_uc004cxu.2_Intron	NM_002893	NP_002884			retinoblastoma binding protein 7						cell proliferation|cellular heat acclimation|CenH3-containing nucleosome assembly at centromere|DNA replication|multicellular organismal development|negative regulation of cell growth|regulation of transcription, DNA-dependent|transcription, DNA-dependent	ESC/E(Z) complex|NuRD complex	protein binding			upper_aerodigestive_tract(1)|ovary(1)	2	Hepatocellular(33;0.0997)																	---	---	---	---
CDKL5	6792	broad.mit.edu	37	X	18616437	18616437	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:18616437delT	uc004cym.2	+						CDKL5_uc004cyn.2_Intron	NM_003159	NP_003150			cyclin-dependent kinase-like 5						neuron migration|positive regulation of axon extension|positive regulation of dendrite morphogenesis|positive regulation of Rac GTPase activity|protein autophosphorylation	dendrite cytoplasm|dendritic growth cone|nucleus	ATP binding|cyclin-dependent protein kinase activity|Rac GTPase binding			ovary(2)|large_intestine(1)|stomach(1)|central_nervous_system(1)|skin(1)	6	Hepatocellular(33;0.183)																	---	---	---	---
PHEX	5251	broad.mit.edu	37	X	22196328	22196328	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:22196328delT	uc004dah.2	+						PHEX_uc011mjr.1_Intron|PHEX_uc011mjs.1_Intron	NM_000444	NP_000435			phosphate-regulating neutral endopeptidase						biomineral tissue development|cell-cell signaling|protein modification process|proteolysis|skeletal system development	integral to plasma membrane	aminopeptidase activity|metalloendopeptidase activity|zinc ion binding			ovary(2)|lung(1)	3																		---	---	---	---
PLS3	5358	broad.mit.edu	37	X	114877477	114877477	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:114877477delT	uc004eqd.2	+						PLS3_uc010nqg.2_Intron|PLS3_uc011mtf.1_Intron|PLS3_uc004eqe.2_Intron|PLS3_uc011mtg.1_Intron|PLS3_uc011mth.1_Intron|PLS3_uc011mti.1_Intron|PLS3_uc011mtj.1_Intron|PLS3_uc011mtk.1_5'Flank|PLS3_uc011mtl.1_5'Flank	NM_005032	NP_005023			plastin 3							cytoplasm	actin binding|calcium ion binding			lung(1)|breast(1)	2																		---	---	---	---
DOCK11	139818	broad.mit.edu	37	X	117752829	117752829	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:117752829delT	uc004eqp.2	+						DOCK11_uc004eqq.2_Intron	NM_144658	NP_653259			dedicator of cytokinesis 11						blood coagulation	cytosol	GTP binding			ovary(3)	3																		---	---	---	---
ODZ1	10178	broad.mit.edu	37	X	123517275	123517275	+	Intron	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:123517275delA	uc004euj.2	-						ODZ1_uc011muj.1_Intron|ODZ1_uc010nqy.2_Intron	NM_014253	NP_055068			odz, odd Oz/ten-m homolog 1 isoform 3						immune response|negative regulation of cell proliferation|nervous system development|signal transduction	extracellular region	heparin binding			ovary(11)|breast(4)|large_intestine(2)|skin(2)|pancreas(2)|upper_aerodigestive_tract(1)|lung(1)	23																		---	---	---	---
ODZ1	10178	broad.mit.edu	37	X	124028293	124028293	+	Intron	DEL	A	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:124028293delA	uc004euj.2	-						ODZ1_uc011muj.1_Intron|ODZ1_uc010nqy.2_Intron	NM_014253	NP_055068			odz, odd Oz/ten-m homolog 1 isoform 3						immune response|negative regulation of cell proliferation|nervous system development|signal transduction	extracellular region	heparin binding			ovary(11)|breast(4)|large_intestine(2)|skin(2)|pancreas(2)|upper_aerodigestive_tract(1)|lung(1)	23																		---	---	---	---
Unknown	0	broad.mit.edu	37	X	135873660	135873660	+	IGR	DEL	G	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:135873660delG								ARHGEF6 (10157 upstream) : RBMX (77693 downstream)																																			---	---	---	---
FMR1	2332	broad.mit.edu	37	X	147018822	147018822	+	Intron	DEL	T	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:147018822delT	uc010nst.2	+						FMR1_uc004fcj.2_Intron|FMR1_uc004fck.3_Intron|FMR1_uc004fcl.3_Intron|FMR1_uc011mxa.1_Intron	NM_002024	NP_002015			fragile X mental retardation 1						mRNA transport|negative regulation of translational initiation	cytoplasm|mRNA cap binding complex|nucleolus|nucleoplasm|soluble fraction	mRNA binding|protein binding			ovary(2)|pancreas(1)	3	Acute lymphoblastic leukemia(192;6.56e-05)													Fragile_X_syndrome				---	---	---	---
MTMR1	8776	broad.mit.edu	37	X	149898766	149898767	+	Intron	DEL	TT	-	-			TCGA-BR-6566-01A-11D-1800-08	TCGA-BR-6566-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:149898766_149898767delTT	uc004fei.2	+						MTMR1_uc011mya.1_Intron|MTMR1_uc004feg.1_Intron|MTMR1_uc004feh.1_Intron|MTMR1_uc004fej.2_Intron|MTMR1_uc010ntf.2_Intron	NM_003828	NP_003819			myotubularin-related protein 1							plasma membrane	protein tyrosine phosphatase activity			ovary(1)	1	Acute lymphoblastic leukemia(192;6.56e-05)																	---	---	---	---
