Hugo_Symbol	Entrez_Gene_Id	Center	NCBI_Build	Chromosome	Start_position	End_position	Strand	Variant_Classification	Variant_Type	Reference_Allele	Tumor_Seq_Allele1	Tumor_Seq_Allele2	dbSNP_RS	dbSNP_Val_Status	Tumor_Sample_Barcode	Matched_Norm_Sample_Barcode	Match_Norm_Seq_Allele1	Match_Norm_Seq_Allele2	Tumor_Validation_Allele1	Tumor_Validation_Allele2	Match_Norm_Validation_Allele1	Match_Norm_Validation_Allele2	Verification_Status	Validation_Status	Mutation_Status	Sequencing_Phase	Sequence_Source	Validation_Method	Score	BAM_file	Sequencer	Genome_Change	Annotation_Transcript	Transcript_Strand	Transcript_Exon	Transcript_Position	cDNA_Change	Codon_Change	Protein_Change	Other_Transcripts	Refseq_mRNA_Id	Refseq_prot_Id	SwissProt_acc_Id	SwissProt_entry_Id	Description	UniProt_AApos	UniProt_Region	UniProt_Site	UniProt_Natural_Variations	UniProt_Experimental_Info	GO_Biological_Process	GO_Cellular_Component	GO_Molecular_Function	COSMIC_overlapping_mutations	COSMIC_fusion_genes	COSMIC_tissue_types_affected	COSMIC_total_alterations_in_gene	Tumorscape_Amplification_Peaks	Tumorscape_Deletion_Peaks	TCGAscape_Amplification_Peaks	TCGAscape_Deletion_Peaks	DrugBank	ref_context	gc_content	CCLE_ONCOMAP_overlapping_mutations	CCLE_ONCOMAP_total_mutations_in_gene	CGC_Mutation_Type	CGC_Translocation_Partner	CGC_Tumor_Types_Somatic	CGC_Tumor_Types_Germline	CGC_Other_Diseases	DNARepairGenes_Role	FamilialCancerDatabase_Syndromes	MUTSIG_Published_Results	OREGANNO_ID	OREGANNO_Values	t_alt_count	t_ref_count	validation_status	validation_method	validation_tumor_sample	validation_alt_allele	filter
OPRD1	4985	broad.mit.edu	37	1	29185486	29185486	+	Missense_Mutation	SNP	C	A	A			TCGA-CZ-4863-01A-01D-1501-10	TCGA-CZ-4863-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:29185486C>A	uc001brf.1	+	2	490	c.248C>A	c.(247-249)GCC>GAC	p.A83D		NM_000911	NP_000902	P41143	OPRD_HUMAN	opioid receptor, delta 1	83	Cytoplasmic (Potential).				immune response|protein import into nucleus, translocation	integral to plasma membrane	delta-opioid receptor activity|protein binding			ovary(1)|central_nervous_system(1)	2		Colorectal(325;3.46e-05)|Lung NSC(340;0.000947)|all_lung(284;0.00131)|Renal(390;0.00758)|Breast(348;0.00765)|all_neural(195;0.0199)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0563)|Medulloblastoma(700;0.123)		Colorectal(126;1.29e-07)|COAD - Colon adenocarcinoma(152;7.51e-06)|STAD - Stomach adenocarcinoma(196;0.00306)|BRCA - Breast invasive adenocarcinoma(304;0.0241)|READ - Rectum adenocarcinoma(331;0.0649)|KIRC - Kidney renal clear cell carcinoma(1967;0.147)	Butorphanol(DB00611)|Codeine(DB00318)|Fentanyl(DB00813)|Hydrocodone(DB00956)|Hydromorphone(DB00327)|Loperamide(DB00836)|Morphine(DB00295)|Nalbuphine(DB00844)|Naloxone(DB01183)|Naltrexone(DB00704)|Oxycodone(DB00497)|Pimozide(DB01100)|Propoxyphene(DB00647)	ATGAAGACGGCCACCAACATC	0.353													3	27	---	---	---	---	PASS
MYCL1	4610	broad.mit.edu	37	1	40363317	40363317	+	Missense_Mutation	SNP	A	C	C			TCGA-CZ-4863-01A-01D-1501-10	TCGA-CZ-4863-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:40363317A>C	uc001cer.1	-	3	1039	c.822T>G	c.(820-822)AGT>AGG	p.S274R	MYCL1_uc001ces.1_Missense_Mutation_p.S274R	NM_001033082	NP_001028254	P12524	MYCL1_HUMAN	l-myc-1 proto-oncogene isoform 1	274						nucleus	DNA binding|sequence-specific DNA binding transcription factor activity			lung(1)|liver(1)	2	all_cancers(7;1.73e-14)|all_lung(5;2.77e-17)|all_epithelial(6;6.81e-17)|Lung SC(1;2.85e-13)|Lung NSC(20;7.03e-07)|Ovarian(52;0.00167)|all_hematologic(146;0.0501)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;1.51e-19)|Epithelial(16;3.36e-18)|all cancers(16;8.43e-17)|LUSC - Lung squamous cell carcinoma(16;0.000261)|Lung(16;0.000457)			CAGTATCAGAACTGACAGGTT	0.547			A		small cell lung 								9	33	---	---	---	---	PASS
ORC1L	4998	broad.mit.edu	37	1	52849596	52849596	+	Missense_Mutation	SNP	T	C	C			TCGA-CZ-4863-01A-01D-1501-10	TCGA-CZ-4863-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:52849596T>C	uc001ctt.2	-	12	1988	c.1769A>G	c.(1768-1770)CAA>CGA	p.Q590R	ORC1L_uc010oni.1_Missense_Mutation_p.Q585R|ORC1L_uc001ctu.2_Missense_Mutation_p.Q590R|ORC1L_uc009vzd.2_Missense_Mutation_p.Q344R	NM_004153	NP_004144	Q13415	ORC1_HUMAN	origin recognition complex, subunit 1	590	Necessary and sufficient for ORC complex assembly.				cell cycle checkpoint|DNA-dependent DNA replication initiation|M/G1 transition of mitotic cell cycle|regulation of transcription involved in G1/S phase of mitotic cell cycle|S phase of mitotic cell cycle	cytosol|nuclear origin of replication recognition complex|nucleolus|nucleoplasm|plasma membrane	ATP binding|DNA binding|nucleoside-triphosphatase activity|protein binding				0						TGTTGCTTTTTGGCCTGTTAG	0.507													26	81	---	---	---	---	PASS
TNNI3K	51086	broad.mit.edu	37	1	74954920	74954920	+	Silent	SNP	C	G	G			TCGA-CZ-4863-01A-01D-1501-10	TCGA-CZ-4863-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:74954920C>G	uc001dgf.1	+	22	2220	c.2169C>G	c.(2167-2169)CTC>CTG	p.L723L	TNNI3K_uc001dge.1_Silent_p.L824L	NM_015978	NP_057062	Q59H18	TNI3K_HUMAN	TNNI3 interacting kinase isoform b	723	Protein kinase.					cytoplasm|nucleus	ATP binding|metal ion binding|protein C-terminus binding|protein serine/threonine kinase activity|troponin I binding			large_intestine(4)|lung(3)|ovary(2)|upper_aerodigestive_tract(1)	10						AAGAGTGTCTCTGCAACATTG	0.383													26	147	---	---	---	---	PASS
PKN2	5586	broad.mit.edu	37	1	89271212	89271212	+	Missense_Mutation	SNP	A	G	G			TCGA-CZ-4863-01A-01D-1501-10	TCGA-CZ-4863-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:89271212A>G	uc001dmn.2	+	11	1876	c.1534A>G	c.(1534-1536)ATT>GTT	p.I512V	PKN2_uc001dmm.1_Missense_Mutation_p.I512V|PKN2_uc010osp.1_Missense_Mutation_p.I496V|PKN2_uc010osq.1_Missense_Mutation_p.I355V|PKN2_uc009wcv.2_Missense_Mutation_p.I464V|PKN2_uc010osr.1_Missense_Mutation_p.I177V	NM_006256	NP_006247	Q16513	PKN2_HUMAN	protein kinase N2	512					signal transduction	cytoplasm	ATP binding|histone deacetylase binding|protein kinase C activity			large_intestine(1)|lung(1)|skin(1)	3		Lung NSC(277;0.123)		all cancers(265;0.0136)|Epithelial(280;0.0301)		TCAAATGAATATTAATATTGC	0.373													19	91	---	---	---	---	PASS
PALMD	54873	broad.mit.edu	37	1	100155420	100155420	+	Missense_Mutation	SNP	C	T	T			TCGA-CZ-4863-01A-01D-1501-10	TCGA-CZ-4863-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:100155420C>T	uc001dsg.2	+	7	2047	c.1604C>T	c.(1603-1605)TCC>TTC	p.S535F	PALMD_uc001dsf.2_Missense_Mutation_p.S535F	NM_017734	NP_060204	Q9NP74	PALMD_HUMAN	palmdelphin	535					regulation of cell shape	cytoplasm|membrane				ovary(2)|pancreas(1)	3		all_epithelial(167;0.000813)|all_lung(203;0.0214)|Lung NSC(277;0.0216)		Epithelial(280;0.067)|all cancers(265;0.117)|COAD - Colon adenocarcinoma(174;0.142)|Lung(183;0.201)		GAGGATCCATCCTTAACAGGT	0.463													3	16	---	---	---	---	PASS
ATP1A1	476	broad.mit.edu	37	1	116932958	116932958	+	Missense_Mutation	SNP	C	A	A			TCGA-CZ-4863-01A-01D-1501-10	TCGA-CZ-4863-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:116932958C>A	uc001ege.2	+	9	1486	c.1147C>A	c.(1147-1149)CAG>AAG	p.Q383K	ATP1A1_uc010owv.1_Missense_Mutation_p.Q352K|ATP1A1_uc010oww.1_Missense_Mutation_p.Q383K|ATP1A1_uc010owx.1_Missense_Mutation_p.Q352K	NM_000701	NP_000692	P05023	AT1A1_HUMAN	Na+/K+ -ATPase alpha 1 subunit isoform a	383	Cytoplasmic (Potential).				ATP biosynthetic process	melanosome|sodium:potassium-exchanging ATPase complex	ATP binding|metal ion binding|protein binding|sodium:potassium-exchanging ATPase activity			ovary(1)	1	Lung SC(450;0.225)	all_cancers(81;1.28e-06)|all_epithelial(167;3.48e-07)|all_lung(203;2.64e-06)|Lung NSC(69;1.98e-05)		Lung(183;0.0164)|LUSC - Lung squamous cell carcinoma(189;0.0548)|Colorectal(144;0.0825)|COAD - Colon adenocarcinoma(174;0.127)|all cancers(265;0.24)	Acetyldigitoxin(DB00511)|Almitrine(DB01430)|Aluminium(DB01370)|Bepridil(DB01244)|Bretylium(DB01158)|Captopril(DB01197)|Deslanoside(DB01078)|Diazoxide(DB01119)|Digitoxin(DB01396)|Digoxin(DB00390)|Esomeprazole(DB00736)|Ethacrynic acid(DB00903)|Furosemide(DB00695)|Hydroflumethiazide(DB00774)|Methyclothiazide(DB00232)|Ouabain(DB01092)|Pantoprazole(DB00213)|Trichlormethiazide(DB01021)	AACTCTGACTCAGAACCGGAT	0.378													14	50	---	---	---	---	PASS
TNR	7143	broad.mit.edu	37	1	175348829	175348829	+	Missense_Mutation	SNP	T	C	C			TCGA-CZ-4863-01A-01D-1501-10	TCGA-CZ-4863-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:175348829T>C	uc001gkp.1	-	7	1903	c.1822A>G	c.(1822-1824)ACC>GCC	p.T608A	TNR_uc009wwu.1_Missense_Mutation_p.T608A	NM_003285	NP_003276	Q92752	TENR_HUMAN	tenascin R precursor	608	Fibronectin type-III 4.				axon guidance|cell adhesion|signal transduction	proteinaceous extracellular matrix				pancreas(5)|ovary(4)|central_nervous_system(1)|skin(1)	11	Renal(580;0.146)					TCAAGGCTGGTTGCTGTGCGA	0.478													10	30	---	---	---	---	PASS
LYST	1130	broad.mit.edu	37	1	235973791	235973791	+	Silent	SNP	T	C	C			TCGA-CZ-4863-01A-01D-1501-10	TCGA-CZ-4863-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:235973791T>C	uc001hxj.2	-	5	502	c.327A>G	c.(325-327)GAA>GAG	p.E109E	LYST_uc009xgb.1_RNA|LYST_uc010pxs.1_RNA|LYST_uc001hxl.1_Silent_p.E109E	NM_000081	NP_000072	Q99698	LYST_HUMAN	lysosomal trafficking regulator	109					defense response to bacterium|defense response to protozoan|defense response to virus|endosome to lysosome transport via multivesicular body sorting pathway|leukocyte chemotaxis|mast cell secretory granule organization|melanosome organization|natural killer cell mediated cytotoxicity|protein transport	cytoplasm|microtubule cytoskeleton	protein binding			ovary(6)|breast(4)|central_nervous_system(2)	12	Ovarian(103;0.0634)|Breast(184;0.23)	all_cancers(173;0.00246)|Prostate(94;0.0771)|Acute lymphoblastic leukemia(190;0.228)	OV - Ovarian serous cystadenocarcinoma(106;0.000674)			TTGAGTTCTTTTCTTTGGTCA	0.333									Chediak-Higashi_syndrome				4	70	---	---	---	---	PASS
OR2M1P	388762	broad.mit.edu	37	1	248285714	248285714	+	Missense_Mutation	SNP	G	T	T			TCGA-CZ-4863-01A-01D-1501-10	TCGA-CZ-4863-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:248285714G>T	uc001idy.1	+	1	277	c.277G>T	c.(277-279)GTA>TTA	p.V93L		NR_002141				RecName: Full=Olfactory receptor 2M5;												0						CATTTATGCTGTAGCCACATT	0.448													5	185	---	---	---	---	PASS
SUPT7L	9913	broad.mit.edu	37	2	27885035	27885035	+	Intron	SNP	T	C	C			TCGA-CZ-4863-01A-01D-1501-10	TCGA-CZ-4863-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:27885035T>C	uc002rlh.1	-						SUPT7L_uc002rli.1_Intron|SUPT7L_uc010ymf.1_Intron|SUPT7L_uc002rlj.1_Intron|SUPT7L_uc010ezh.1_5'UTR|SLC4A1AP_uc002rlk.3_5'Flank	NM_014860	NP_055675	O94864	ST65G_HUMAN	SPTF-associated factor 65 gamma						histone H3 acetylation|maintenance of protein location in nucleus|regulation of transcription, DNA-dependent|transcription, DNA-dependent	STAGA complex	transcription coactivator activity			skin(2)	2	Acute lymphoblastic leukemia(172;0.155)					CACAATCTGGTTTCAACTCAC	0.214													6	407	---	---	---	---	PASS
SUCLG1	8802	broad.mit.edu	37	2	84660489	84660489	+	Silent	SNP	C	T	T			TCGA-CZ-4863-01A-01D-1501-10	TCGA-CZ-4863-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:84660489C>T	uc002son.2	-	6	853	c.660G>A	c.(658-660)CAG>CAA	p.Q220Q	SUCLG1_uc010ysk.1_Silent_p.Q207Q	NM_003849	NP_003840	P53597	SUCA_HUMAN	succinate-CoA ligase, GDP-forming alpha subunit	220					tricarboxylic acid cycle		ATP citrate synthase activity|GTP binding|succinate-CoA ligase (GDP-forming) activity				0					Succinic acid(DB00139)	CGCACAAAGACTGCCCCAATC	0.363													14	62	---	---	---	---	PASS
XIRP2	129446	broad.mit.edu	37	2	167992508	167992508	+	Missense_Mutation	SNP	G	C	C			TCGA-CZ-4863-01A-01D-1501-10	TCGA-CZ-4863-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:167992508G>C	uc002udx.2	+	2	516	c.498G>C	c.(496-498)AAG>AAC	p.K166N	XIRP2_uc010fpn.2_Missense_Mutation_p.K166N|XIRP2_uc010fpo.2_Missense_Mutation_p.K166N|XIRP2_uc010fpp.2_Missense_Mutation_p.K166N|XIRP2_uc002udy.2_5'UTR	NM_152381	NP_689594	A4UGR9	XIRP2_HUMAN	xin actin-binding repeat containing 2 isoform 1	Error:Variant_position_missing_in_A4UGR9_after_alignment					actin cytoskeleton organization	cell junction	actin binding			skin(7)|ovary(6)|pancreas(1)	14						ATTCAGACAAGAAAGGCAAGG	0.433													27	120	---	---	---	---	PASS
GLB1L	79411	broad.mit.edu	37	2	220101846	220101846	+	Missense_Mutation	SNP	A	G	G			TCGA-CZ-4863-01A-01D-1501-10	TCGA-CZ-4863-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:220101846A>G	uc002vkm.2	-	17	2152	c.1913T>C	c.(1912-1914)CTT>CCT	p.L638P	GLB1L_uc002vkk.2_Missense_Mutation_p.L395P|GLB1L_uc010zkx.1_Missense_Mutation_p.L548P|GLB1L_uc002vkn.2_Missense_Mutation_p.L638P	NM_024506	NP_078782	Q6UWU2	GLB1L_HUMAN	galactosidase, beta 1-like precursor	638					carbohydrate metabolic process	extracellular region	cation binding|hydrolase activity, hydrolyzing O-glycosyl compounds				0		all_lung(227;1.19e-05)|Lung NSC(271;2.76e-05)|Medulloblastoma(418;0.0208)|Esophageal squamous(248;0.0559)		Epithelial(149;1.3e-11)|all cancers(144;2.07e-10)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		ATCAGCTGAAAGGGAATTGAT	0.353													24	159	---	---	---	---	PASS
TMEM198	130612	broad.mit.edu	37	2	220413932	220413932	+	Missense_Mutation	SNP	T	G	G			TCGA-CZ-4863-01A-01D-1501-10	TCGA-CZ-4863-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:220413932T>G	uc002vme.2	+	5	1386	c.801T>G	c.(799-801)GAT>GAG	p.D267E	TMEM198_uc002vmf.2_Missense_Mutation_p.D267E|hsa-mir-3132|MI0014152_5'Flank	NM_001005209	NP_001005209	Q66K66	TM198_HUMAN	transmembrane protein 198	267	Arg-rich.					integral to membrane				ovary(1)	1		Renal(207;0.0376)		Epithelial(149;6.49e-08)|all cancers(144;6.45e-06)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00802)		AGCAGGAAGATCGCAAGGAGA	0.642													3	11	---	---	---	---	PASS
IQCF2	389123	broad.mit.edu	37	3	51897084	51897084	+	Missense_Mutation	SNP	C	A	A			TCGA-CZ-4863-01A-01D-1501-10	TCGA-CZ-4863-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:51897084C>A	uc003dbt.1	+	3	231	c.193C>A	c.(193-195)CAT>AAT	p.H65N	IQCF1_uc003dbq.3_Intron|IQCF2_uc003dbu.1_RNA	NM_203424	NP_982248	Q8IXL9	IQCF2_HUMAN	IQ motif containing F2	65	IQ 1.										0				BRCA - Breast invasive adenocarcinoma(193;8.01e-05)|Kidney(197;0.000537)|KIRC - Kidney renal clear cell carcinoma(197;0.000716)		GACACTGCTGCATGCAGCCCT	0.572													3	16	---	---	---	---	PASS
COL29A1	256076	broad.mit.edu	37	3	130098768	130098768	+	Missense_Mutation	SNP	C	T	T			TCGA-CZ-4863-01A-01D-1501-10	TCGA-CZ-4863-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:130098768C>T	uc010htj.1	+	4	1669	c.1175C>T	c.(1174-1176)ACA>ATA	p.T392I	COL29A1_uc010hti.1_RNA	NM_153264	NP_694996	A8TX70	CO6A5_HUMAN	collagen, type XXIX, alpha 1	392	VWFA 2.|Nonhelical region.				axon guidance|cell adhesion	collagen					0						CCAGAACAGACAATTTCCACG	0.413													18	52	---	---	---	---	PASS
KLHL5	51088	broad.mit.edu	37	4	39083717	39083717	+	Missense_Mutation	SNP	C	G	G			TCGA-CZ-4863-01A-01D-1501-10	TCGA-CZ-4863-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:39083717C>G	uc003gts.2	+	4	1051	c.976C>G	c.(976-978)CGT>GGT	p.R326G	KLHL5_uc003gtp.2_Missense_Mutation_p.R280G|KLHL5_uc003gtq.2_Missense_Mutation_p.R139G|KLHL5_uc003gtr.1_Missense_Mutation_p.R326G|KLHL5_uc003gtt.2_Missense_Mutation_p.R265G	NM_015990	NP_057074	Q96PQ7	KLHL5_HUMAN	kelch-like 5 isoform 1	326						cytoplasm|cytoskeleton	actin binding			ovary(1)	1						TCTTGGAATTCGTTCTTTTGC	0.393													55	268	---	---	---	---	PASS
FAT1	2195	broad.mit.edu	37	4	187629281	187629281	+	Silent	SNP	A	C	C			TCGA-CZ-4863-01A-01D-1501-10	TCGA-CZ-4863-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:187629281A>C	uc003izf.2	-	2	1889	c.1701T>G	c.(1699-1701)CCT>CCG	p.P567P	FAT1_uc010iso.1_Silent_p.P567P	NM_005245	NP_005236	Q14517	FAT1_HUMAN	FAT tumor suppressor 1 precursor	567	Extracellular (Potential).|Cadherin 4.				actin filament organization|anatomical structure morphogenesis|cell migration|cell-cell signaling|establishment or maintenance of cell polarity|homophilic cell adhesion	cell-cell junction|integral to plasma membrane|nucleus|perinuclear region of cytoplasm	calcium ion binding|protein binding			ovary(10)|central_nervous_system(1)|pancreas(1)	12						TCTCAAACAAAGGTGTGTTGT	0.443										HNSCC(5;0.00058)			13	64	---	---	---	---	PASS
ADAMTS16	170690	broad.mit.edu	37	5	5242262	5242262	+	Missense_Mutation	SNP	T	A	A			TCGA-CZ-4863-01A-01D-1501-10	TCGA-CZ-4863-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:5242262T>A	uc003jdl.2	+	17	2758	c.2620T>A	c.(2620-2622)TGG>AGG	p.W874R	ADAMTS16_uc003jdk.1_Missense_Mutation_p.W874R	NM_139056	NP_620687	Q8TE57	ATS16_HUMAN	ADAM metallopeptidase with thrombospondin type 1	874	TSP type-1 2.				proteolysis	proteinaceous extracellular matrix	metalloendopeptidase activity|zinc ion binding			ovary(3)|lung(2)|large_intestine(1)|breast(1)|pancreas(1)	8						CAGCTACACTTGGGCCATCGT	0.632													6	15	---	---	---	---	PASS
KIAA0947	23379	broad.mit.edu	37	5	5460991	5460991	+	Missense_Mutation	SNP	C	T	T			TCGA-CZ-4863-01A-01D-1501-10	TCGA-CZ-4863-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:5460991C>T	uc003jdm.3	+	13	1766	c.1544C>T	c.(1543-1545)GCC>GTC	p.A515V		NM_015325	NP_056140	Q9Y2F5	K0947_HUMAN	hypothetical protein LOC23379	515										ovary(1)|central_nervous_system(1)	2						AGATTGTCTGCCAGCCCTGCA	0.453													4	121	---	---	---	---	PASS
DMXL1	1657	broad.mit.edu	37	5	118502425	118502425	+	Silent	SNP	A	G	G			TCGA-CZ-4863-01A-01D-1501-10	TCGA-CZ-4863-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:118502425A>G	uc003ksd.2	+	22	5266	c.5085A>G	c.(5083-5085)GAA>GAG	p.E1695E	DMXL1_uc010jcl.1_Silent_p.E1695E	NM_005509	NP_005500	Q9Y485	DMXL1_HUMAN	Dmx-like 1	1695										ovary(2)	2		all_cancers(142;0.0314)|all_epithelial(76;0.00559)|Prostate(80;0.11)|Breast(839;0.231)		OV - Ovarian serous cystadenocarcinoma(64;0.000563)|Epithelial(69;0.00179)|all cancers(49;0.0243)		AAAGATTTGAACATTCTGCAG	0.353													30	212	---	---	---	---	PASS
UNC5A	90249	broad.mit.edu	37	5	176297519	176297519	+	Silent	SNP	T	C	C			TCGA-CZ-4863-01A-01D-1501-10	TCGA-CZ-4863-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:176297519T>C	uc003mey.2	+	6	1062	c.870T>C	c.(868-870)AGT>AGC	p.S290S	UNC5A_uc003mex.1_Silent_p.S290S|UNC5A_uc010jkg.1_Silent_p.S250S	NM_133369	NP_588610	Q6ZN44	UNC5A_HUMAN	netrin receptor Unc5h1 precursor	290	TSP type-1.|Extracellular (Potential).				apoptosis|axon guidance|regulation of apoptosis	integral to membrane|plasma membrane				skin(1)	1	all_cancers(89;0.000119)|Renal(175;0.000269)|Lung NSC(126;0.00696)|all_lung(126;0.0115)	Medulloblastoma(196;0.00498)|all_neural(177;0.0138)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			ACTGTACCAGTGACCTCTGTG	0.642													4	16	---	---	---	---	PASS
RNF130	55819	broad.mit.edu	37	5	179382646	179382646	+	3'UTR	SNP	T	C	C			TCGA-CZ-4863-01A-01D-1501-10	TCGA-CZ-4863-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:179382646T>C	uc003mll.1	-	9					RNF130_uc003mlm.1_3'UTR	NM_018434	NP_060904	Q86XS8	GOLI_HUMAN	ring finger protein 130 precursor						apoptosis	cytoplasm|integral to membrane|nucleus	ubiquitin-protein ligase activity|zinc ion binding			lung(2)|ovary(1)	3	all_cancers(89;5.49e-05)|all_epithelial(37;1.94e-05)|Renal(175;0.000159)|Lung NSC(126;0.00118)|all_lung(126;0.00212)	all_cancers(40;0.0294)|Medulloblastoma(196;0.00498)|all_neural(177;0.0138)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			AAGCAGGTTTTTTCTTCTTCA	0.313													6	295	---	---	---	---	PASS
HIVEP1	3096	broad.mit.edu	37	6	12121429	12121429	+	Silent	SNP	A	G	G			TCGA-CZ-4863-01A-01D-1501-10	TCGA-CZ-4863-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:12121429A>G	uc003nac.2	+	4	1580	c.1401A>G	c.(1399-1401)CAA>CAG	p.Q467Q	HIVEP1_uc011diq.1_RNA	NM_002114	NP_002105	P15822	ZEP1_HUMAN	human immunodeficiency virus type I enhancer	467					transcription, DNA-dependent	cytoplasm|nucleus	DNA binding|protein binding|zinc ion binding			ovary(3)|large_intestine(1)|central_nervous_system(1)|skin(1)	6	Breast(50;0.0639)|Ovarian(93;0.0816)	all_hematologic(90;0.117)				TTGTCTTGCAACCAGATGCTG	0.463													4	53	---	---	---	---	PASS
DNAH8	1769	broad.mit.edu	37	6	38758125	38758125	+	Missense_Mutation	SNP	A	G	G			TCGA-CZ-4863-01A-01D-1501-10	TCGA-CZ-4863-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:38758125A>G	uc003ooe.1	+	18	2674	c.2074A>G	c.(2074-2076)AGC>GGC	p.S692G		NM_001371	NP_001362			dynein, axonemal, heavy polypeptide 8											skin(8)|ovary(7)|lung(2)|large_intestine(1)|central_nervous_system(1)|kidney(1)|pancreas(1)	21						AACACTGGAAAGCTTCTTTCA	0.348													8	356	---	---	---	---	PASS
ENPP5	59084	broad.mit.edu	37	6	46133254	46133254	+	Silent	SNP	A	G	G			TCGA-CZ-4863-01A-01D-1501-10	TCGA-CZ-4863-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:46133254A>G	uc003oxz.1	-	3	1084	c.876T>C	c.(874-876)AAT>AAC	p.N292N	ENPP5_uc003oya.1_Silent_p.N292N|ENPP5_uc011dvz.1_Silent_p.N198N|ENPP5_uc010jzc.1_Silent_p.N292N	NM_021572	NP_067547	Q9UJA9	ENPP5_HUMAN	ectonucleotide pyrophosphatase/phosphodiesterase	292						extracellular region|integral to membrane	hydrolase activity				0						AAACAGTAAGATTAGGATGAG	0.408													53	269	---	---	---	---	PASS
ICA1	3382	broad.mit.edu	37	7	8272304	8272304	+	Silent	SNP	C	T	T			TCGA-CZ-4863-01A-01D-1501-10	TCGA-CZ-4863-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:8272304C>T	uc003srm.2	-	3	166	c.99G>A	c.(97-99)ACG>ACA	p.T33T	ICA1_uc010ktr.2_Silent_p.T33T|ICA1_uc003srl.2_Silent_p.T21T|ICA1_uc003srn.3_5'UTR|ICA1_uc003srp.3_Silent_p.T32T|ICA1_uc010kts.2_RNA|ICA1_uc003srq.2_Silent_p.T33T|ICA1_uc003srr.2_Silent_p.T32T|ICA1_uc003sro.3_Silent_p.T33T|ICA1_uc011jxg.1_Silent_p.T33T|ICA1_uc003srs.1_Silent_p.T33T	NM_022307	NP_071682	Q05084	ICA69_HUMAN	islet cell autoantigen 1	33					neurotransmitter transport	cell junction|cytosol|Golgi membrane|nucleus|secretory granule membrane|synaptic vesicle membrane|transport vesicle membrane				central_nervous_system(1)	1		Ovarian(82;0.0612)		UCEC - Uterine corpus endometrioid carcinoma (126;0.246)		AGGCCTGCTTCGTCTCCCAAT	0.428													5	379	---	---	---	---	PASS
KBTBD2	25948	broad.mit.edu	37	7	32909724	32909724	+	Missense_Mutation	SNP	C	T	T			TCGA-CZ-4863-01A-01D-1501-10	TCGA-CZ-4863-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:32909724C>T	uc003tdb.2	-	4	1764	c.1105G>A	c.(1105-1107)GTC>ATC	p.V369I	AVL9_uc011kai.1_Intron	NM_015483	NP_056298	Q8IY47	KBTB2_HUMAN	kelch repeat and BTB (POZ) domain containing 2	369	Kelch 1.										0			GBM - Glioblastoma multiforme(11;0.0499)			TTTATGCGGACAAAAAGCATT	0.413													55	244	---	---	---	---	PASS
SBDSP1	155370	broad.mit.edu	37	7	72307377	72307377	+	RNA	SNP	C	G	G			TCGA-CZ-4863-01A-01D-1501-10	TCGA-CZ-4863-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:72307377C>G	uc003twg.2	+	5		c.1117C>G			SBDSP1_uc003twh.2_RNA|SBDSP1_uc003twe.2_RNA	NR_024110				Homo sapiens Shwachman-Bodian-Diamond syndrome pseudogene, mRNA (cDNA clone IMAGE:4329436).												0						CTTGCTCAAACTATTTGACAT	0.363													12	73	---	---	---	---	PASS
FAM180A	389558	broad.mit.edu	37	7	135433271	135433271	+	Missense_Mutation	SNP	A	T	T			TCGA-CZ-4863-01A-01D-1501-10	TCGA-CZ-4863-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:135433271A>T	uc003vtd.2	-	1	324	c.58T>A	c.(58-60)TGC>AGC	p.C20S	FAM180A_uc010lmt.2_RNA|FAM180A_uc010lmu.2_Missense_Mutation_p.C20S	NM_205855	NP_995327	Q6UWF9	F180A_HUMAN	hypothetical protein LOC389558 precursor	20						extracellular region				ovary(2)	2						CACCTGTGGCACATAGAAGCC	0.418													21	101	---	---	---	---	PASS
FAM180A	389558	broad.mit.edu	37	7	135433272	135433272	+	Missense_Mutation	SNP	C	A	A			TCGA-CZ-4863-01A-01D-1501-10	TCGA-CZ-4863-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:135433272C>A	uc003vtd.2	-	1	323	c.57G>T	c.(55-57)ATG>ATT	p.M19I	FAM180A_uc010lmt.2_RNA|FAM180A_uc010lmu.2_Missense_Mutation_p.M19I	NM_205855	NP_995327	Q6UWF9	F180A_HUMAN	hypothetical protein LOC389558 precursor	19						extracellular region				ovary(2)	2						ACCTGTGGCACATAGAAGCCT	0.418													21	97	---	---	---	---	PASS
NOM1	64434	broad.mit.edu	37	7	156761876	156761876	+	Missense_Mutation	SNP	T	G	G			TCGA-CZ-4863-01A-01D-1501-10	TCGA-CZ-4863-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:156761876T>G	uc003wmy.2	+	10	2409	c.2394T>G	c.(2392-2394)AGT>AGG	p.S798R		NM_138400	NP_612409	Q5C9Z4	NOM1_HUMAN	nucleolar protein with MIF4G domain 1	798					RNA metabolic process	nucleolus	protein binding				0	Ovarian(565;0.218)	all_hematologic(28;0.0749)	OV - Ovarian serous cystadenocarcinoma(82;0.00301)	UCEC - Uterine corpus endometrioid carcinoma (81;0.169)		AAGACCTCAGTTTAATTTTCA	0.368													29	122	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	8	12435889	12435889	+	Intron	SNP	C	A	A	rs617055	by1000genomes	TCGA-CZ-4863-01A-01D-1501-10	TCGA-CZ-4863-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:12435889C>A	uc003wvy.3	-						uc003wwb.1_RNA					Homo sapiens cDNA FLJ42906 fis, clone BRHIP3016213.																		TAACTTCAGACTCAGCTTAGA	0.483													4	8	---	---	---	---	PASS
TUSC3	7991	broad.mit.edu	37	8	15480643	15480643	+	Missense_Mutation	SNP	A	C	C	rs11545035	byFrequency	TCGA-CZ-4863-01A-01D-1501-10	TCGA-CZ-4863-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:15480643A>C	uc003wwt.2	+	2	403	c.193A>C	c.(193-195)ATC>CTC	p.I65L	TUSC3_uc003wwr.2_Missense_Mutation_p.I65L|TUSC3_uc003wws.2_Missense_Mutation_p.I65L|TUSC3_uc003wwu.2_Missense_Mutation_p.I65L|TUSC3_uc003wwv.2_Missense_Mutation_p.I65L|TUSC3_uc003www.2_Missense_Mutation_p.I65L|TUSC3_uc003wwx.2_RNA|TUSC3_uc003wwy.2_Missense_Mutation_p.I65L	NM_006765	NP_006756	Q13454	TUSC3_HUMAN	tumor suppressor candidate 3 isoform a	65					cell redox homeostasis|post-translational protein modification|protein N-linked glycosylation via asparagine	integral to membrane|oligosaccharyltransferase complex				ovary(2)|central_nervous_system(1)	3				Colorectal(111;0.113)		CAGACGCTCAATCTTCCGAAT	0.388													27	82	---	---	---	---	PASS
CDK5RAP2	55755	broad.mit.edu	37	9	123298713	123298713	+	Missense_Mutation	SNP	G	A	A			TCGA-CZ-4863-01A-01D-1501-10	TCGA-CZ-4863-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:123298713G>A	uc004bkf.2	-	7	780	c.599C>T	c.(598-600)TCA>TTA	p.S200L	CDK5RAP2_uc004bkg.2_Missense_Mutation_p.S200L|CDK5RAP2_uc011lxw.1_5'UTR|CDK5RAP2_uc011lxx.1_RNA|CDK5RAP2_uc011lxy.1_RNA|CDK5RAP2_uc011lxz.1_5'UTR|CDK5RAP2_uc011lya.1_5'UTR|CDK5RAP2_uc004bkh.1_Missense_Mutation_p.S200L|CDK5RAP2_uc004bki.2_5'UTR	NM_018249	NP_060719	Q96SN8	CK5P2_HUMAN	CDK5 regulatory subunit associated protein 2	200					brain development|centrosome organization|chromosome segregation|G2/M transition of mitotic cell cycle|microtubule bundle formation|negative regulation of centriole replication|positive regulation of transcription, DNA-dependent|regulation of neuron differentiation|regulation of spindle checkpoint	cytosol|Golgi apparatus|microtubule|pericentriolar material|perinuclear region of cytoplasm|spindle pole	calmodulin binding|microtubule binding|neuronal Cdc2-like kinase binding|transcription regulatory region DNA binding			ovary(2)|lung(1)|skin(1)	4						CTTCATCTCTGAAAGCTTGCT	0.537													4	84	---	---	---	---	PASS
TRUB2	26995	broad.mit.edu	37	9	131083994	131083994	+	Missense_Mutation	SNP	T	C	C			TCGA-CZ-4863-01A-01D-1501-10	TCGA-CZ-4863-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:131083994T>C	uc004buq.1	-	2	135	c.125A>G	c.(124-126)AAG>AGG	p.K42R	COQ4_uc011max.1_5'Flank|COQ4_uc004bur.3_5'Flank|COQ4_uc004bus.2_5'Flank|COQ4_uc010mxy.2_5'Flank	NM_015679	NP_056494	O95900	TRUB2_HUMAN	TruB pseudouridine (psi) synthase homolog 2	42					pseudouridine synthesis|tRNA processing		pseudouridine synthase activity|RNA binding			ovary(1)	1						AGCGGGAGGCTTCCTGGCATT	0.353													4	31	---	---	---	---	PASS
PFKFB3	5209	broad.mit.edu	37	10	6268194	6268194	+	Missense_Mutation	SNP	A	T	T			TCGA-CZ-4863-01A-01D-1501-10	TCGA-CZ-4863-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:6268194A>T	uc001ije.2	+	14	1765	c.1381A>T	c.(1381-1383)AGT>TGT	p.S461C	PFKFB3_uc001ijd.2_Missense_Mutation_p.S441C|PFKFB3_uc009xii.2_RNA|PFKFB3_uc010qaw.1_Missense_Mutation_p.S475C|PFKFB3_uc001ijf.2_Missense_Mutation_p.S461C|PFKFB3_uc001ijg.2_RNA|PFKFB3_uc009xij.2_RNA|PFKFB3_uc009xik.2_RNA|PFKFB3_uc009xil.2_Intron	NM_004566	NP_004557	Q16875	F263_HUMAN	6-phosphofructo-2-kinase/fructose-2,	461	Fructose-2,6-bisphosphatase.				fructose 2,6-bisphosphate metabolic process|glycolysis	cytosol	6-phosphofructo-2-kinase activity|ATP binding|fructose-2,6-bisphosphate 2-phosphatase activity|identical protein binding			ovary(2)|central_nervous_system(1)	3						GAGACGCAATAGTGTCACCCC	0.542													6	27	---	---	---	---	PASS
FAM175B	23172	broad.mit.edu	37	10	126523420	126523420	+	Silent	SNP	T	C	C			TCGA-CZ-4863-01A-01D-1501-10	TCGA-CZ-4863-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:126523420T>C	uc001lib.3	+	9	1173	c.1128T>C	c.(1126-1128)GAT>GAC	p.D376D		NM_032182	NP_115558	Q15018	F175B_HUMAN	hypothetical protein LOC23172	376						BRISC complex	polyubiquitin binding				0						ACGACAGTGATTATGAAAATT	0.507													8	48	---	---	---	---	PASS
AHNAK	79026	broad.mit.edu	37	11	62296732	62296732	+	Missense_Mutation	SNP	C	A	A			TCGA-CZ-4863-01A-01D-1501-10	TCGA-CZ-4863-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:62296732C>A	uc001ntl.2	-	5	5457	c.5157G>T	c.(5155-5157)AAG>AAT	p.K1719N	AHNAK_uc001ntk.1_Intron	NM_001620	NP_001611	Q09666	AHNK_HUMAN	AHNAK nucleoprotein isoform 1	1719					nervous system development	nucleus	protein binding			ovary(10)|pancreas(4)|skin(4)|upper_aerodigestive_tract(1)	19		Melanoma(852;0.155)				GCATACTGAACTTGGGCATTT	0.502													21	98	---	---	---	---	PASS
EED	8726	broad.mit.edu	37	11	85966300	85966300	+	Missense_Mutation	SNP	C	T	T			TCGA-CZ-4863-01A-01D-1501-10	TCGA-CZ-4863-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:85966300C>T	uc001pbp.2	+	4	854	c.397C>T	c.(397-399)CGG>TGG	p.R133W	EED_uc010rtm.1_Missense_Mutation_p.R133W|EED_uc001pbq.2_Missense_Mutation_p.R133W|EED_uc001pbr.2_Missense_Mutation_p.R133W|EED_uc001pbs.2_Missense_Mutation_p.R133W|EED_uc010rtn.1_5'Flank	NM_003797	NP_003788	O75530	EED_HUMAN	embryonic ectoderm development isoform a	133	Interaction with EZH2 (By similarity).|WD 1.				negative regulation of transcription, DNA-dependent|transcription, DNA-dependent	ESC/E(Z) complex	histone methyltransferase activity|identical protein binding			skin(1)|pancreas(1)	2		Acute lymphoblastic leukemia(157;7.24e-07)|all_hematologic(158;0.00092)				AGGAGAAATCCGGTTGTTGCA	0.313													9	422	---	---	---	---	PASS
MIR125B1	406911	broad.mit.edu	37	11	121970479	121970479	+	RNA	SNP	C	A	A			TCGA-CZ-4863-01A-01D-1501-10	TCGA-CZ-4863-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:121970479C>A	hsa-mir-125b-1|MI0000446	-			c.74C>A			LOC399959_uc009zba.2_Intron|uc001pxz.1_Intron|LOC399959_uc001pya.3_Intron|LOC399959_uc001pyc.1_Intron|LOC399959_uc001pyd.1_Intron|uc001pye.1_5'Flank|uc010rzr.1_RNA																	0						CGACTCGCAGCTCCCAAGAGC	0.413													8	91	---	---	---	---	PASS
IFLTD1	160492	broad.mit.edu	37	12	25706102	25706102	+	5'UTR	SNP	C	T	T			TCGA-CZ-4863-01A-01D-1501-10	TCGA-CZ-4863-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:25706102C>T	uc001rgs.2	-	1					IFLTD1_uc001rgt.1_5'UTR|IFLTD1_uc010sji.1_5'UTR|IFLTD1_uc010sjj.1_Intron|IFLTD1_uc009zjc.2_5'UTR	NM_152590	NP_689803	Q8N9Z9	ILFT1_HUMAN	intermediate filament tail domain containing 1							intermediate filament	structural molecule activity			ovary(2)|central_nervous_system(1)	3	all_lung(3;2.75e-22)|Lung NSC(3;1.77e-21)|all_hematologic(7;0.00656)|Colorectal(261;0.0847)					TAAGTACCAACATAGCCAATC	0.428													23	104	---	---	---	---	PASS
C12orf11	55726	broad.mit.edu	37	12	27075598	27075598	+	Silent	SNP	A	G	G			TCGA-CZ-4863-01A-01D-1501-10	TCGA-CZ-4863-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:27075598A>G	uc001rhk.3	-	8	1377	c.840T>C	c.(838-840)GAT>GAC	p.D280D	C12orf11_uc010sjk.1_Silent_p.D179D	NM_018164	NP_060634	Q9NVM9	M89BB_HUMAN	hypothetical protein LOC55726	280					cell division|mitosis|regulation of mitotic cell cycle		protein binding			large_intestine(1)|ovary(1)|central_nervous_system(1)	3	Colorectal(261;0.0847)					GTAGCTCCACATCATAATTGG	0.289													43	249	---	---	---	---	PASS
COPZ1	22818	broad.mit.edu	37	12	54741794	54741794	+	Nonsense_Mutation	SNP	G	T	T			TCGA-CZ-4863-01A-01D-1501-10	TCGA-CZ-4863-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:54741794G>T	uc001sfs.1	+	7	443	c.406G>T	c.(406-408)GAG>TAG	p.E136*	COPZ1_uc001sft.2_Nonsense_Mutation_p.E85*|COPZ1_uc009znm.1_Nonsense_Mutation_p.E144*|COPZ1_uc010sot.1_Nonsense_Mutation_p.E113*	NM_016057	NP_057141	P61923	COPZ1_HUMAN	coatomer protein complex, subunit zeta 1	136					COPI coating of Golgi vesicle|intra-Golgi vesicle-mediated transport|intracellular protein transport|retrograde vesicle-mediated transport, Golgi to ER	COPI vesicle coat|cytosol					0						GGTGATCCTAGAGAGTGATCC	0.527													4	177	---	---	---	---	PASS
ACTR6	64431	broad.mit.edu	37	12	100594767	100594767	+	Intron	SNP	C	T	T	rs73374435	by1000genomes	TCGA-CZ-4863-01A-01D-1501-10	TCGA-CZ-4863-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:100594767C>T	uc001thb.1	+						ACTR6_uc010svh.1_Intron|ACTR6_uc001thc.1_Intron|ACTR6_uc001thd.1_Intron|ACTR6_uc009ztu.1_Intron|ACTR6_uc001the.1_5'UTR|ACTR6_uc001thf.1_5'UTR	NM_022496	NP_071941	Q9GZN1	ARP6_HUMAN	ARP6 actin-related protein 6 homolog							cytoplasm|cytoskeleton				ovary(1)	1						GTTTCATCTCCGGACATCAAT	0.488													3	48	---	---	---	---	PASS
TTC5	91875	broad.mit.edu	37	14	20760170	20760170	+	Missense_Mutation	SNP	C	T	T			TCGA-CZ-4863-01A-01D-1501-10	TCGA-CZ-4863-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:20760170C>T	uc001vwt.2	-	9	1232	c.1175G>A	c.(1174-1176)CGG>CAG	p.R392Q	TTC5_uc001vwu.2_Missense_Mutation_p.R249Q	NM_138376	NP_612385	Q8N0Z6	TTC5_HUMAN	tetratricopeptide repeat domain 5	392					DNA repair	cytoplasm|nucleus	binding			ovary(1)	1	all_cancers(95;0.00092)		Epithelial(56;1.1e-06)|all cancers(55;8.07e-06)	GBM - Glioblastoma multiforme(265;0.0106)		TCGGTGAAGCCGCAGGTTGGG	0.453													4	71	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	15	28913498	28913498	+	RNA	SNP	T	G	G			TCGA-CZ-4863-01A-01D-1501-10	TCGA-CZ-4863-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:28913498T>G	uc010azc.2	+	9		c.1488T>G			uc010uao.1_RNA					Homo sapiens I.M.A.G.E. clone 321824, mRNA sequence.																		GAGAGAATATTCAGGTGAGTA	0.403													5	45	---	---	---	---	PASS
CEP152	22995	broad.mit.edu	37	15	49048532	49048532	+	Missense_Mutation	SNP	G	C	C			TCGA-CZ-4863-01A-01D-1501-10	TCGA-CZ-4863-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:49048532G>C	uc001zwy.2	-	20	2947	c.2913C>G	c.(2911-2913)ATC>ATG	p.I971M	CEP152_uc001zwz.2_Missense_Mutation_p.I971M|CEP152_uc001zxa.1_Missense_Mutation_p.I878M	NM_014985	NP_055800	O94986	CE152_HUMAN	centrosomal protein 152kDa	971	Potential.				centrosome duplication|G2/M transition of mitotic cell cycle	centrosome|cytosol	protein kinase binding			lung(2)	2		all_lung(180;0.0428)		all cancers(107;1.08e-07)|GBM - Glioblastoma multiforme(94;2.32e-06)		TTTGTTCTTGGATTCTGTGGA	0.393													71	373	---	---	---	---	PASS
CTSH	1512	broad.mit.edu	37	15	79227327	79227327	+	Missense_Mutation	SNP	T	A	A			TCGA-CZ-4863-01A-01D-1501-10	TCGA-CZ-4863-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:79227327T>A	uc002ben.2	-	6	459	c.362A>T	c.(361-363)AAA>ATA	p.K121I	CTSH_uc010unf.1_RNA|CTSH_uc010bll.1_Intron|CTSH_uc010ung.1_Missense_Mutation_p.K133I	NM_148979	NP_683880	P09668	CATH_HUMAN	cathepsin H isoform b precursor	133					protein destabilization|proteolysis	lysosome	cysteine-type endopeptidase activity			central_nervous_system(2)|large_intestine(1)	3						TACCTGATTTTTCACAGGTGA	0.488													19	87	---	---	---	---	PASS
RRAD	6236	broad.mit.edu	37	16	66956073	66956073	+	Missense_Mutation	SNP	G	T	T			TCGA-CZ-4863-01A-01D-1501-10	TCGA-CZ-4863-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:66956073G>T	uc002eqn.2	-	5	985	c.833C>A	c.(832-834)GCG>GAG	p.A278E	RRAD_uc002eqo.2_Missense_Mutation_p.A278E	NM_001128850	NP_001122322	P55042	RAD_HUMAN	Ras-related associated with diabetes	278	Calmodulin-binding.				small GTPase mediated signal transduction	plasma membrane	calmodulin binding|GTP binding|GTPase activity				0		Ovarian(137;0.192)		OV - Ovarian serous cystadenocarcinoma(108;0.0862)|Epithelial(162;0.198)		GAAGCGCTTCGCCTTTTTGCC	0.612													4	16	---	---	---	---	PASS
GLG1	2734	broad.mit.edu	37	16	74524933	74524933	+	Missense_Mutation	SNP	T	A	A			TCGA-CZ-4863-01A-01D-1501-10	TCGA-CZ-4863-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:74524933T>A	uc002fcy.3	-	8	1465	c.1415A>T	c.(1414-1416)GAG>GTG	p.E472V	GLG1_uc002fcx.2_Missense_Mutation_p.E472V|GLG1_uc002fcw.3_Missense_Mutation_p.E461V|GLG1_uc002fcz.3_Intron	NM_001145667	NP_001139139	Q92896	GSLG1_HUMAN	golgi apparatus protein 1 isoform 3	472	Extracellular (Potential).|Cys-rich GLG1 6.					Golgi membrane|integral to membrane	receptor binding			ovary(1)|breast(1)	2						GTTCCCCTTCTCCCCTCGAAC	0.488													10	51	---	---	---	---	PASS
SLC38A8	146167	broad.mit.edu	37	16	84050801	84050801	+	Silent	SNP	C	A	A			TCGA-CZ-4863-01A-01D-1501-10	TCGA-CZ-4863-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:84050801C>A	uc002fhg.1	-	7	897	c.897G>T	c.(895-897)CGG>CGT	p.R299R		NM_001080442	NP_001073911	A6NNN8	S38A8_HUMAN	solute carrier family 38, member 8	299	Helical; (Potential).				amino acid transport|sodium ion transport	integral to membrane					0						CAAAAAGGACCCGGGCCACAA	0.547													5	37	---	---	---	---	PASS
METT10D	79066	broad.mit.edu	37	17	2323260	2323260	+	3'UTR	SNP	G	T	T			TCGA-CZ-4863-01A-01D-1501-10	TCGA-CZ-4863-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:2323260G>T	uc002fut.2	-	10					METT10D_uc002fuu.3_RNA|METT10D_uc010cka.2_RNA|METT10D_uc002fuv.2_Intron|METT10D_uc010vqx.1_RNA|METT10D_uc010vqy.1_3'UTR	NM_024086	NP_076991	Q86W50	MET16_HUMAN	methyltransferase 10 domain containing								methyltransferase activity				0						TGTGCAGGAGGTTTCTAGTTA	0.498													4	44	---	---	---	---	PASS
CDC6	990	broad.mit.edu	37	17	38457740	38457740	+	Silent	SNP	A	G	G			TCGA-CZ-4863-01A-01D-1501-10	TCGA-CZ-4863-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:38457740A>G	uc002huj.1	+	11	1683	c.1473A>G	c.(1471-1473)AAA>AAG	p.K491K		NM_001254	NP_001245	Q99741	CDC6_HUMAN	cell division cycle 6 protein	491					cell division|DNA replication|DNA replication checkpoint|M/G1 transition of mitotic cell cycle|mitosis|negative regulation of cell proliferation|negative regulation of DNA replication|positive regulation of cell cycle cytokinesis|positive regulation of chromosome segregation|regulation of cyclin-dependent protein kinase activity|regulation of mitotic anaphase|regulation of transcription involved in G1/S phase of mitotic cell cycle|S phase of mitotic cell cycle|traversing start control point of mitotic cell cycle	cytosol|nucleoplasm|spindle midzone|spindle pole	ATP binding|kinase binding|nucleoside-triphosphatase activity			ovary(2)|breast(1)	3						CCTACAGTAAAGTCTGTCGCA	0.438													5	193	---	---	---	---	PASS
CBX1	10951	broad.mit.edu	37	17	46148933	46148933	+	Missense_Mutation	SNP	G	A	A			TCGA-CZ-4863-01A-01D-1501-10	TCGA-CZ-4863-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:46148933G>A	uc002ind.3	-	5	903	c.422C>T	c.(421-423)TCT>TTT	p.S141F	CBX1_uc002ine.3_Missense_Mutation_p.S141F	NM_006807	NP_006798	P83916	CBX1_HUMAN	heterochromatin protein 1-beta	141	Chromo 2; shadow subtype.					nuclear heterochromatin|nucleoplasm|spindle	chromatin binding|enzyme binding				0						AGCCTCATCAGAGTTTTTCCT	0.488													10	43	---	---	---	---	PASS
MTMR4	9110	broad.mit.edu	37	17	56573389	56573389	+	Missense_Mutation	SNP	A	T	T			TCGA-CZ-4863-01A-01D-1501-10	TCGA-CZ-4863-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:56573389A>T	uc002iwj.2	-	16	2224	c.2114T>A	c.(2113-2115)CTT>CAT	p.L705H		NM_004687	NP_004678	Q9NYA4	MTMR4_HUMAN	myotubularin related protein 4	705						cytoplasm|membrane	metal ion binding|protein tyrosine phosphatase activity			skin(1)	1	Medulloblastoma(34;0.127)|all_neural(34;0.237)					TGCGGTATTAAGCAGTTTGTA	0.493													20	176	---	---	---	---	PASS
MUC16	94025	broad.mit.edu	37	19	9046549	9046549	+	Silent	SNP	A	G	G			TCGA-CZ-4863-01A-01D-1501-10	TCGA-CZ-4863-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:9046549A>G	uc002mkp.2	-	5	35286	c.35082T>C	c.(35080-35082)CCT>CCC	p.P11694P		NM_024690	NP_078966	Q8WXI7	MUC16_HUMAN	mucin 16	11696	Thr-rich.|Extracellular (Potential).				cell adhesion	extracellular space|extrinsic to membrane|integral to membrane|plasma membrane	protein binding			lung(30)|ovary(15)|breast(8)|large_intestine(1)|skin(1)|prostate(1)|pancreas(1)	57						TGGTCTGTGGAGGATGAGTGA	0.522													24	151	---	---	---	---	PASS
C19orf62	29086	broad.mit.edu	37	19	17387524	17387524	+	Intron	SNP	T	G	G			TCGA-CZ-4863-01A-01D-1501-10	TCGA-CZ-4863-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:17387524T>G	uc002nfu.2	+						C19orf62_uc010xpl.1_3'UTR|C19orf62_uc002nfv.2_Intron|C19orf62_uc010ean.2_Intron|C19orf62_uc002nfw.2_Intron	NM_014173	NP_054892	Q9NWV8	BABA1_HUMAN	mediator of Rap80 interactions and targeting 40						chromatin modification|double-strand break repair|G2/M transition DNA damage checkpoint|positive regulation of DNA repair|protein K63-linked deubiquitination|response to ionizing radiation	BRCA1-A complex|BRISC complex|cytoplasm	protein binding			ovary(1)|haematopoietic_and_lymphoid_tissue(1)	2						GAGGCTGGGGTGCCTAGAGGT	0.602													8	29	---	---	---	---	PASS
CRTC1	23373	broad.mit.edu	37	19	18856654	18856654	+	Silent	SNP	C	T	T			TCGA-CZ-4863-01A-01D-1501-10	TCGA-CZ-4863-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:18856654C>T	uc002nkb.3	+	3	353	c.265C>T	c.(265-267)CTG>TTG	p.L89L	CRTC1_uc010ebv.2_Silent_p.L105L|CRTC1_uc010ebw.2_5'Flank|CRTC1_uc002nkc.3_5'Flank	NM_015321	NP_056136	Q6UUV9	CRTC1_HUMAN	mucoepidermoid carcinoma translocated 1 isoform	89					interspecies interaction between organisms|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	cytoplasm|nucleus|plasma membrane	cAMP response element binding protein binding|protein binding		CRTC1/MAML2(516)	salivary_gland(474)|lung(35)|thyroid(4)|breast(3)|skin(2)|ovary(1)	519						ATCCTCGGGCCTGGACACCAG	0.667													4	13	---	---	---	---	PASS
ZNF738	148203	broad.mit.edu	37	19	21565886	21565886	+	3'UTR	SNP	A	T	T			TCGA-CZ-4863-01A-01D-1501-10	TCGA-CZ-4863-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:21565886A>T	uc002nps.3	+	5						NR_027130				SubName: Full=cDNA FLJ14673 fis, clone NT2RP2003714, moderately similar to Zinc finger protein 430;												0						TCAATGTGATAAATATGTGAA	0.284													15	61	---	---	---	---	PASS
C19orf2	8725	broad.mit.edu	37	19	30477269	30477269	+	Missense_Mutation	SNP	G	T	T			TCGA-CZ-4863-01A-01D-1501-10	TCGA-CZ-4863-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:30477269G>T	uc002nsr.2	+	4	342	c.312G>T	c.(310-312)TGG>TGT	p.W104C	C19orf2_uc002nsq.2_Missense_Mutation_p.W86C|C19orf2_uc002nss.2_Missense_Mutation_p.W64C|C19orf2_uc002nst.2_Missense_Mutation_p.W28C	NM_003796	NP_003787	O94763	RMP_HUMAN	RPB5-mediating protein isoform a	104					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)		GGGACAACTGGTTTGCAAAGT	0.398													11	225	---	---	---	---	PASS
HRC	3270	broad.mit.edu	37	19	49657913	49657913	+	Silent	SNP	C	T	T			TCGA-CZ-4863-01A-01D-1501-10	TCGA-CZ-4863-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:49657913C>T	uc002pmv.2	-	1	769	c.582G>A	c.(580-582)GAG>GAA	p.E194E		NM_002152	NP_002143	P23327	SRCH_HUMAN	histidine rich calcium binding protein	194	4 X tandem repeats, acidic.|Glu-rich (acidic).|1-1.|6 X approximate tandem repeats.				muscle contraction	sarcoplasmic reticulum lumen	calcium ion binding			ovary(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;2.01e-05)|OV - Ovarian serous cystadenocarcinoma(262;0.00019)|GBM - Glioblastoma multiforme(486;0.00279)|Epithelial(262;0.00622)		cctcctcctcctcttcTCCTT	0.443													3	40	---	---	---	---	PASS
TPTE	7179	broad.mit.edu	37	21	10906858	10906858	+	3'UTR	SNP	T	G	G			TCGA-CZ-4863-01A-01D-1501-10	TCGA-CZ-4863-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:10906858T>G	uc002yip.1	-	24					TPTE_uc002yis.1_RNA|TPTE_uc002yiq.1_3'UTR|TPTE_uc002yir.1_3'UTR|TPTE_uc010gkv.1_3'UTR	NM_199261	NP_954870	P56180	TPTE_HUMAN	transmembrane phosphatase with tensin homology						signal transduction	integral to membrane	ion channel activity|protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity			ovary(2)|lung(1)|breast(1)|skin(1)	5			Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723)	UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247)		TGTGGCAGGGTTGGAAAGAAC	0.303													18	141	---	---	---	---	PASS
MORC2	22880	broad.mit.edu	37	22	31322760	31322760	+	3'UTR	SNP	T	G	G			TCGA-CZ-4863-01A-01D-1501-10	TCGA-CZ-4863-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:31322760T>G	uc003aje.1	-	27						NM_014941	NP_055756	Q9Y6X9	MORC2_HUMAN	MORC family CW-type zinc finger 2								ATP binding|zinc ion binding			ovary(1)|pancreas(1)	2						GAGGGGCAGGTGGGCAGGGGA	0.552													7	21	---	---	---	---	PASS
NOX1	27035	broad.mit.edu	37	X	100105317	100105317	+	Missense_Mutation	SNP	A	T	T			TCGA-CZ-4863-01A-01D-1501-10	TCGA-CZ-4863-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:100105317A>T	uc004egj.2	-	9	1162	c.956T>A	c.(955-957)ATG>AAG	p.M319K	NOX1_uc004egl.3_Missense_Mutation_p.M319K|NOX1_uc010nne.2_Missense_Mutation_p.M282K	NM_007052	NP_008983	Q9Y5S8	NOX1_HUMAN	NADPH oxidase 1 isoform long	319	FAD-binding FR-type.|Extracellular (Potential).				angiogenesis|cell migration|electron transport chain|FADH2 metabolic process|hydrogen peroxide metabolic process|inflammatory response|intracellular pH elevation|positive regulation of integrin biosynthetic process|positive regulation of smooth muscle cell proliferation|positive regulation vascular endothelial growth factor production|respiratory burst|response to pH|signal transduction|superoxide anion generation	cell junction|early endosome|invadopodium membrane|NADPH oxidase complex	electron carrier activity|flavin adenine dinucleotide binding|iron ion binding|Rac GTPase binding|superoxide-generating NADPH oxidase activity|voltage-gated proton channel activity			ovary(1)	1						CCCCACTTCCATGCTGAAGCC	0.413													24	63	---	---	---	---	PASS
MTMR1	8776	broad.mit.edu	37	X	149905237	149905237	+	Nonsense_Mutation	SNP	G	A	A			TCGA-CZ-4863-01A-01D-1501-10	TCGA-CZ-4863-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:149905237G>A	uc004fei.2	+	10	1362	c.1227G>A	c.(1225-1227)TGG>TGA	p.W409*	MTMR1_uc011mya.1_Nonsense_Mutation_p.W315*|MTMR1_uc004feh.1_Nonsense_Mutation_p.W417*|MTMR1_uc004fej.2_RNA|MTMR1_uc010ntf.2_Intron	NM_003828	NP_003819	Q13613	MTMR1_HUMAN	myotubularin-related protein 1	409	Myotubularin phosphatase.					plasma membrane	protein tyrosine phosphatase activity			ovary(1)	1	Acute lymphoblastic leukemia(192;6.56e-05)					GGACGCATTGGCTGGAATATA	0.443													4	78	---	---	---	---	PASS
HAUS7	55559	broad.mit.edu	37	X	152713268	152713268	+	3'UTR	SNP	C	T	T			TCGA-CZ-4863-01A-01D-1501-10	TCGA-CZ-4863-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:152713268C>T	uc004fho.1	-	10					TREX2_uc010nud.1_5'Flank|TREX2_uc011myp.1_5'Flank|TREX2_uc010nue.1_5'UTR|HAUS7_uc004fhl.2_RNA|HAUS7_uc004fhm.2_RNA|HAUS7_uc004fhn.1_3'UTR|HAUS7_uc004fhp.1_RNA	NM_017518	NP_059988	Q99871	HAUS7_HUMAN	HAUS augmin-like complex subunit 7						cell division|centrosome organization|mitosis|spindle assembly	centrosome|HAUS complex|microtubule|nucleolus|plasma membrane|spindle	thioesterase binding				0						TCGGCCAACTCGATCTTGGGA	0.547													3	34	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	1	23878961	23878961	+	IGR	DEL	G	-	-			TCGA-CZ-4863-01A-01D-1501-10	TCGA-CZ-4863-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:23878961delG								E2F2 (21248 upstream) : ID3 (5449 downstream)																							TATGTGGGGTGGGGAATGGAG	0.498													4	2	---	---	---	---	
BAI2	576	broad.mit.edu	37	1	32201690	32201690	+	Intron	DEL	C	-	-			TCGA-CZ-4863-01A-01D-1501-10	TCGA-CZ-4863-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:32201690delC	uc001btn.2	-						BAI2_uc001btm.2_5'Flank|BAI2_uc001btp.1_Intron|BAI2_uc010ogn.1_Intron|BAI2_uc010ogo.1_Intron|BAI2_uc010ogp.1_Intron|BAI2_uc010ogq.1_Intron|BAI2_uc001bto.2_Intron	NM_001703	NP_001694	O60241	BAI2_HUMAN	brain-specific angiogenesis inhibitor 2						negative regulation of angiogenesis|neuropeptide signaling pathway	integral to membrane|plasma membrane	G-protein coupled receptor activity			lung(5)|breast(4)|ovary(2)|central_nervous_system(1)|skin(1)	13		Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0606)|all_neural(195;0.0837)|Breast(348;0.174)		STAD - Stomach adenocarcinoma(196;0.0557)		TTAGGCTCATCCCCCAGTGCT	0.408													4	2	---	---	---	---	
SFRS11	9295	broad.mit.edu	37	1	70673204	70673205	+	Intron	INS	-	T	T			TCGA-CZ-4863-01A-01D-1501-10	TCGA-CZ-4863-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:70673204_70673205insT	uc001des.2	+						LRRC40_uc001der.1_5'Flank|SFRS11_uc009wbi.2_Intron|SFRS11_uc009wbj.1_Intron|SFRS11_uc010oqo.1_Intron|SFRS11_uc001det.2_Intron	NM_004768	NP_004759	Q05519	SRS11_HUMAN	splicing factor, arginine/serine-rich 11						mRNA 3'-end processing|mRNA export from nucleus|nuclear mRNA splicing, via spliceosome|termination of RNA polymerase II transcription	nucleoplasm	nucleotide binding|protein binding|RNA binding				0						TCCCAACTTGCTTTTTTTTTTA	0.183													4	3	---	---	---	---	
NEGR1	257194	broad.mit.edu	37	1	72401208	72401209	+	Intron	DEL	GT	-	-	rs71688145		TCGA-CZ-4863-01A-01D-1501-10	TCGA-CZ-4863-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:72401208_72401209delGT	uc001dfw.2	-						NEGR1_uc001dfv.2_Intron|NEGR1_uc010oqs.1_Intron	NM_173808	NP_776169	Q7Z3B1	NEGR1_HUMAN	neuronal growth regulator 1 precursor						cell adhesion	anchored to membrane|plasma membrane				ovary(1)	1		all_cancers(4;1.26e-06)|Renal(4;1.32e-08)|all_epithelial(4;5.39e-07)|Hepatocellular(141;0.117)		KIRC - Kidney renal clear cell carcinoma(4;0.00529)|Kidney(4;0.00609)|all cancers(265;0.022)|GBM - Glioblastoma multiforme(62;0.0382)|Epithelial(280;0.242)		TAAgtgtgtagtgtgtgtgtgt	0.248													4	2	---	---	---	---	
C1orf194	127003	broad.mit.edu	37	1	109650348	109650348	+	Intron	DEL	A	-	-	rs71823454		TCGA-CZ-4863-01A-01D-1501-10	TCGA-CZ-4863-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:109650348delA	uc009wev.2	-						C1orf194_uc001dwp.3_Intron|C1orf194_uc009wew.2_Intron	NM_001122961	NP_001116433	Q5T5A4	CA194_HUMAN	hypothetical protein LOC127003											ovary(1)	1						tcatctcttcaaaaaaaaaaa	0.000													1	6	---	---	---	---	
ARNT	405	broad.mit.edu	37	1	150842351	150842351	+	Intron	DEL	T	-	-			TCGA-CZ-4863-01A-01D-1501-10	TCGA-CZ-4863-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:150842351delT	uc001evr.1	-						ARNT_uc001evs.1_Intron|ARNT_uc009wmb.1_Intron|ARNT_uc009wmc.1_Intron|ARNT_uc009wmd.1_Intron|ARNT_uc009wme.1_Intron|ARNT_uc010pcl.1_Intron	NM_001668	NP_001659	P27540	ARNT_HUMAN	aryl hydrocarbon receptor nuclear translocator						positive regulation of hormone biosynthetic process|positive regulation vascular endothelial growth factor production|regulation of transcription from RNA polymerase II promoter in response to oxidative stress|response to hypoxia		aryl hydrocarbon receptor binding|protein heterodimerization activity|sequence-specific DNA binding transcription factor activity|signal transducer activity|transcription coactivator activity			skin(4)|lung(3)|central_nervous_system(1)|kidney(1)	9	all_lung(15;9e-35)|Lung NSC(24;3.45e-31)|Lung SC(34;0.00471)|Ovarian(49;0.0167)|all_hematologic(923;0.0597)|Hepatocellular(266;0.108)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.02)|BRCA - Breast invasive adenocarcinoma(12;0.00606)|LUSC - Lung squamous cell carcinoma(543;0.211)			TTCTAGCTCCTTTTTTTAGCA	0.264			T	ETV6	AML								4	2	---	---	---	---	
THBS3	7059	broad.mit.edu	37	1	155172353	155172354	+	Intron	DEL	CT	-	-			TCGA-CZ-4863-01A-01D-1501-10	TCGA-CZ-4863-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:155172353_155172354delCT	uc001fix.2	-						RAG1AP1_uc010pey.1_Intron|THBS3_uc009wqi.2_Intron|THBS3_uc001fiz.2_Intron|THBS3_uc001fiy.2_Intron|THBS3_uc010pfu.1_Intron|THBS3_uc010pfv.1_Intron|THBS3_uc001fja.2_Intron	NM_007112	NP_009043	P49746	TSP3_HUMAN	thrombospondin 3 precursor						cell-matrix adhesion	extracellular region|perinuclear region of cytoplasm	calcium ion binding|heparin binding|structural molecule activity			breast(3)|ovary(2)	5	all_epithelial(22;5.72e-28)|all_lung(78;2.07e-24)|all_hematologic(923;0.0359)|Hepatocellular(266;0.0877)		Epithelial(20;3.72e-10)|all cancers(21;1.19e-09)|BRCA - Breast invasive adenocarcinoma(34;0.000752)|LUSC - Lung squamous cell carcinoma(543;0.193)			TCGGGGTTCCCTCTCTCCCTCC	0.609													4	2	---	---	---	---	
NOS1AP	9722	broad.mit.edu	37	1	162288356	162288357	+	Intron	INS	-	T	T			TCGA-CZ-4863-01A-01D-1501-10	TCGA-CZ-4863-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:162288356_162288357insT	uc001gbv.2	+						NOS1AP_uc010pkr.1_Intron|NOS1AP_uc010pks.1_Intron|NOS1AP_uc001gbw.2_Intron	NM_014697	NP_055512	O75052	CAPON_HUMAN	nitric oxide synthase 1 (neuronal) adaptor						regulation of apoptosis|regulation of nitric oxide biosynthetic process|regulation of nitric-oxide synthase activity		nitric-oxide synthase binding|PDZ domain binding			lung(2)|upper_aerodigestive_tract(1)	3	all_hematologic(112;0.203)		BRCA - Breast invasive adenocarcinoma(70;0.0537)			tctgctcagtatttttttttct	0.000													4	2	---	---	---	---	
POU2F1	5451	broad.mit.edu	37	1	167234461	167234461	+	Intron	DEL	G	-	-			TCGA-CZ-4863-01A-01D-1501-10	TCGA-CZ-4863-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:167234461delG	uc001gec.2	+						POU2F1_uc010plg.1_Intron|POU2F1_uc001ged.2_Intron|POU2F1_uc001gee.2_Intron|POU2F1_uc010plh.1_Intron	NM_002697	NP_002688	P14859	PO2F1_HUMAN	POU class 2 homeobox 1						negative regulation of transcription, DNA-dependent|transcription from RNA polymerase III promoter	nucleoplasm	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			central_nervous_system(2)|skin(2)|breast(1)	5						acagtttaaagggtctgagtc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	177405506	177405506	+	IGR	DEL	G	-	-			TCGA-CZ-4863-01A-01D-1501-10	TCGA-CZ-4863-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:177405506delG								FAM5B (153949 upstream) : SEC16B (491983 downstream)																							GGACCATGATGGGACTGTGAA	0.498													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	228947104	228947104	+	IGR	DEL	A	-	-			TCGA-CZ-4863-01A-01D-1501-10	TCGA-CZ-4863-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:228947104delA								RHOU (64695 upstream) : RAB4A (459775 downstream)																							TGCTTGAAACAAAAAAAGGGT	0.453													4	2	---	---	---	---	
EXO1	9156	broad.mit.edu	37	1	242016438	242016439	+	Intron	DEL	TG	-	-	rs35698447		TCGA-CZ-4863-01A-01D-1501-10	TCGA-CZ-4863-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:242016438_242016439delTG	uc001hzh.2	+						EXO1_uc001hzi.2_Intron|EXO1_uc001hzj.2_Intron|EXO1_uc009xgq.2_Intron	NM_130398	NP_569082	Q9UQ84	EXO1_HUMAN	exonuclease 1 isoform b						meiosis|mismatch repair	nucleus	double-stranded DNA specific 5'-3' exodeoxyribonuclease activity|flap endonuclease activity|metal ion binding|protein binding|protein binding|ribonuclease H activity|single-stranded DNA specific 5'-3' exodeoxyribonuclease activity			ovary(2)|lung(2)|skin(1)	5	Ovarian(103;0.103)	all_cancers(173;0.0555)	OV - Ovarian serous cystadenocarcinoma(106;0.0107)			ATGGTAATCTTGTGTGTGTGTG	0.356								Direct_reversal_of_damage|Editing_and_processing_nucleases					4	3	---	---	---	---	
NOL10	79954	broad.mit.edu	37	2	10784819	10784819	+	Intron	DEL	C	-	-			TCGA-CZ-4863-01A-01D-1501-10	TCGA-CZ-4863-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:10784819delC	uc002raq.2	-						NOL10_uc010yje.1_Intron|NOL10_uc010yjf.1_Intron|NOL10_uc002rap.2_Intron|NOL10_uc002rar.2_Intron	NM_024894	NP_079170	Q9BSC4	NOL10_HUMAN	nucleolar protein 10							nucleolus					0	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.191)			Epithelial(75;0.172)|OV - Ovarian serous cystadenocarcinoma(76;0.207)		CACAGTCACTCCCTCACAGGG	0.398													4	2	---	---	---	---	
NBAS	51594	broad.mit.edu	37	2	15608271	15608272	+	Intron	INS	-	AATA	AATA	rs139646833	by1000genomes	TCGA-CZ-4863-01A-01D-1501-10	TCGA-CZ-4863-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:15608271_15608272insAATA	uc002rcc.1	-						NBAS_uc002rcd.1_Intron	NM_015909	NP_056993	A2RRP1	NBAS_HUMAN	neuroblastoma-amplified protein											ovary(2)|liver(1)|skin(1)	4						CTTCAAATGGTAGTGTCAGTCT	0.337													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	15987530	15987531	+	IGR	INS	-	AG	AG			TCGA-CZ-4863-01A-01D-1501-10	TCGA-CZ-4863-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:15987530_15987531insAG								DDX1 (216306 upstream) : MYCNOS (92489 downstream)																							AGTCAGCAGCCAGAGAGTGTGG	0.564													4	2	---	---	---	---	
C2orf56	55471	broad.mit.edu	37	2	37462403	37462403	+	Intron	DEL	A	-	-			TCGA-CZ-4863-01A-01D-1501-10	TCGA-CZ-4863-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:37462403delA	uc002rqa.3	+						C2orf56_uc010ynj.1_Intron|C2orf56_uc002rqc.3_Intron|C2orf56_uc010ynk.1_Intron|C2orf56_uc010ynl.1_Intron	NM_144736	NP_653337	Q7L592	MIDA_HUMAN	hypothetical protein LOC55471 isoform 1						mitochondrial respiratory chain complex I assembly	mitochondrion	enzyme binding|methyltransferase activity			central_nervous_system(1)	1		all_hematologic(82;0.21)				GGCTAATAAGAAAAAAAAAAA	0.119													2	4	---	---	---	---	
NRXN1	9378	broad.mit.edu	37	2	50847549	50847549	+	Intron	DEL	A	-	-			TCGA-CZ-4863-01A-01D-1501-10	TCGA-CZ-4863-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:50847549delA	uc010fbq.2	-						NRXN1_uc002rxb.3_Intron|NRXN1_uc002rxe.3_Intron|NRXN1_uc002rxc.1_Intron	NM_001135659	NP_001129131	P58400	NRX1B_HUMAN	neurexin 1 isoform alpha2 precursor						angiogenesis|neuron cell-cell adhesion|neuronal signal transduction	cell surface|endocytic vesicle|integral to membrane|presynaptic membrane	cell adhesion molecule binding|receptor binding			ovary(2)	2		all_hematologic(82;0.152)|Acute lymphoblastic leukemia(82;0.192)	Lung(47;0.0813)|LUSC - Lung squamous cell carcinoma(58;0.116)			TAAGAGATCTAAACTAGTTAG	0.313													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	60057355	60057355	+	IGR	DEL	A	-	-			TCGA-CZ-4863-01A-01D-1501-10	TCGA-CZ-4863-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:60057355delA								None (None upstream) : BCL11A (620948 downstream)																							CCGTTGGGAGAAAAAAAAAAT	0.428													7	4	---	---	---	---	
AHSA2	130872	broad.mit.edu	37	2	61402441	61402441	+	5'Flank	DEL	A	-	-			TCGA-CZ-4863-01A-01D-1501-10	TCGA-CZ-4863-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:61402441delA	uc002sbc.1	+						AHSA2_uc002sbb.1_5'Flank	NM_152392	NP_689605	Q719I0	AHSA2_HUMAN	AHA1, activator of heat shock 90kDa protein						response to stress	cytoplasm	ATPase activator activity|chaperone binding			breast(1)	1			Epithelial(17;0.0994)			ATTTAAAGGGAAAAGGCAAAA	0.488													4	2	---	---	---	---	
GFPT1	2673	broad.mit.edu	37	2	69567201	69567201	+	Intron	DEL	A	-	-			TCGA-CZ-4863-01A-01D-1501-10	TCGA-CZ-4863-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:69567201delA	uc002sfh.2	-							NM_002056	NP_002047	Q06210	GFPT1_HUMAN	glucosamine-fructose-6-phosphate						dolichol-linked oligosaccharide biosynthetic process|energy reserve metabolic process|fructose 6-phosphate metabolic process|glutamine metabolic process|post-translational protein modification|protein N-linked glycosylation via asparagine|UDP-N-acetylglucosamine biosynthetic process	cytosol	glutamine-fructose-6-phosphate transaminase (isomerizing) activity|sugar binding			skin(1)	1						ATTTAAAAGTAATAAACCCCA	0.239													4	2	---	---	---	---	
ASPRV1	151516	broad.mit.edu	37	2	70256272	70256272	+	Intron	DEL	C	-	-			TCGA-CZ-4863-01A-01D-1501-10	TCGA-CZ-4863-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:70256272delC	uc002sga.2	-									Q53RT3	APRV1_HUMAN	Homo sapiens cDNA FLJ32260 fis, clone PROST1000334.						protein maturation by peptide bond cleavage|skin development		aspartic-type endopeptidase activity			ovary(1)	1						ATTTCTGTATCTGGGGCTTAG	0.448													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	76474442	76474442	+	IGR	DEL	A	-	-			TCGA-CZ-4863-01A-01D-1501-10	TCGA-CZ-4863-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:76474442delA								C2orf3 (536331 upstream) : LRRTM4 (500416 downstream)																							ctgcggtggcaatgggggatg	0.000													4	2	---	---	---	---	
RMND5A	64795	broad.mit.edu	37	2	87593176	87593177	+	Intron	DEL	GA	-	-			TCGA-CZ-4863-01A-01D-1501-10	TCGA-CZ-4863-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:87593176_87593177delGA	uc002srs.3	+									Q9H871	RMD5A_HUMAN	SubName: Full=cDNA FLJ10361 fis, clone NT2RM2001256, highly similar to Anaphase-promoting complex subunit 1;											ovary(1)|skin(1)	2						gaaaaatgatgagatgaaatgc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	91766185	91766187	+	IGR	DEL	ATG	-	-	rs142832221		TCGA-CZ-4863-01A-01D-1501-10	TCGA-CZ-4863-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:91766185_91766187delATG								None (None upstream) : LOC654342 (39005 downstream)																							CTTTTTTACCATGATAGTTTAGT	0.305													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	96617496	96617496	+	Intron	DEL	A	-	-	rs141504763		TCGA-CZ-4863-01A-01D-1501-10	TCGA-CZ-4863-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:96617496delA	uc010yug.1	-											Homo sapiens cDNA FLJ54441 complete cds, highly similar to Homo sapiens ankyrin repeat domain 36 (ANKRD36), mRNA.																		AACTAATAATAAAAAAAGTAA	0.249													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	96643668	96643668	+	Intron	DEL	T	-	-			TCGA-CZ-4863-01A-01D-1501-10	TCGA-CZ-4863-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:96643668delT	uc010yug.1	-											Homo sapiens cDNA FLJ54441 complete cds, highly similar to Homo sapiens ankyrin repeat domain 36 (ANKRD36), mRNA.																		taaataataatttttttCATA	0.179													4	2	---	---	---	---	
MCM6	4175	broad.mit.edu	37	2	136626526	136626526	+	Intron	DEL	A	-	-			TCGA-CZ-4863-01A-01D-1501-10	TCGA-CZ-4863-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:136626526delA	uc002tuw.2	-							NM_005915	NP_005906	Q14566	MCM6_HUMAN	minichromosome maintenance complex component 6						cell cycle checkpoint|DNA strand elongation involved in DNA replication|DNA-dependent DNA replication initiation|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|S phase of mitotic cell cycle	MCM complex	ATP binding|identical protein binding				0				BRCA - Breast invasive adenocarcinoma(221;0.166)	Atorvastatin(DB01076)	ATTTATGTTTAAAAAAAAAAT	0.299													6	3	---	---	---	---	
ABCB11	8647	broad.mit.edu	37	2	169824641	169824642	+	Intron	INS	-	TTTC	TTTC	rs10699842		TCGA-CZ-4863-01A-01D-1501-10	TCGA-CZ-4863-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:169824641_169824642insTTTC	uc002ueo.1	-						ABCB11_uc010zda.1_Intron|ABCB11_uc010zdb.1_Intron	NM_003742	NP_003733	O95342	ABCBB_HUMAN	ATP-binding cassette, sub-family B (MDR/TAP),						bile acid biosynthetic process	apical plasma membrane|Golgi membrane|integral to plasma membrane|intercellular canaliculus|membrane fraction	ATP binding|bile acid-exporting ATPase activity|canalicular bile acid transmembrane transporter activity|sodium-exporting ATPase activity, phosphorylative mechanism			ovary(2)|large_intestine(2)|breast(1)	5					Adenosine triphosphate(DB00171)|Bosentan(DB00559)|Glibenclamide(DB01016)	TAAACACAGATTTTTTTTAAAA	0.376													1	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	201068192	201068192	+	IGR	DEL	A	-	-			TCGA-CZ-4863-01A-01D-1501-10	TCGA-CZ-4863-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:201068192delA								C2orf47 (239347 upstream) : SPATS2L (102412 downstream)																							ctgaggcaggagagtaaggcc	0.000													4	2	---	---	---	---	
KCTD18	130535	broad.mit.edu	37	2	201363974	201363975	+	Intron	INS	-	T	T	rs147029988	by1000genomes	TCGA-CZ-4863-01A-01D-1501-10	TCGA-CZ-4863-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:201363974_201363975insT	uc002uvs.2	-						KCTD18_uc002uvt.2_Intron|KCTD18_uc002uvu.1_Intron	NM_152387	NP_689600	Q6PI47	KCD18_HUMAN	potassium channel tetramerization domain							voltage-gated potassium channel complex	voltage-gated potassium channel activity			ovary(1)	1						TCAAACACACATTTTTTTTAAT	0.312													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	27135969	27135969	+	IGR	DEL	A	-	-			TCGA-CZ-4863-01A-01D-1501-10	TCGA-CZ-4863-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:27135969delA								LRRC3B (383706 upstream) : NEK10 (16426 downstream)																							TTTTAACTTTAAAAAAAAAGT	0.338													4	2	---	---	---	---	
SFMBT1	51460	broad.mit.edu	37	3	52946894	52946894	+	Intron	DEL	A	-	-			TCGA-CZ-4863-01A-01D-1501-10	TCGA-CZ-4863-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:52946894delA	uc003dgf.2	-						SFMBT1_uc010hmr.2_Intron|SFMBT1_uc003dgg.2_Intron|SFMBT1_uc003dgh.2_Intron	NM_001005159	NP_001005159	Q9UHJ3	SMBT1_HUMAN	Scm-like with four mbt domains 1						regulation of transcription, DNA-dependent	nucleus				ovary(1)	1				BRCA - Breast invasive adenocarcinoma(193;9.91e-05)|Kidney(197;0.000644)|KIRC - Kidney renal clear cell carcinoma(197;0.000792)|OV - Ovarian serous cystadenocarcinoma(275;0.113)		TACGGTCAGGAAAAAAACAGG	0.239													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	66027999	66028000	+	IGR	INS	-	TTTG	TTTG	rs138396331	by1000genomes	TCGA-CZ-4863-01A-01D-1501-10	TCGA-CZ-4863-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:66027999_66028000insTTTG								MAGI1 (3490 upstream) : SLC25A26 (91285 downstream)																							tttgtttggtttttgtttgttt	0.153													4	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	89651774	89651774	+	IGR	DEL	A	-	-			TCGA-CZ-4863-01A-01D-1501-10	TCGA-CZ-4863-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:89651774delA								EPHA3 (120492 upstream) : None (None downstream)																							gatatgatgtaaaaaaagaga	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	117374777	117374778	+	IGR	INS	-	T	T	rs142479295	by1000genomes	TCGA-CZ-4863-01A-01D-1501-10	TCGA-CZ-4863-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:117374777_117374778insT								LOC285194 (938892 upstream) : None (None downstream)																							acaaattgttgtaagagtttgg	0.000													2	6	---	---	---	---	
GPR156	165829	broad.mit.edu	37	3	119942840	119942841	+	Intron	DEL	TT	-	-	rs72366973		TCGA-CZ-4863-01A-01D-1501-10	TCGA-CZ-4863-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:119942840_119942841delTT	uc011bjf.1	-						GPR156_uc011bjg.1_Intron	NM_153002	NP_694547	Q8NFN8	GP156_HUMAN	G protein-coupled receptor 156							integral to membrane|plasma membrane	G-protein coupled receptor activity|GABA-B receptor activity			ovary(1)|skin(1)	2				GBM - Glioblastoma multiforme(114;0.19)		CCTTATTCTCTTTCTTAGGTTA	0.312													4	4	---	---	---	---	
KALRN	8997	broad.mit.edu	37	3	124310037	124310038	+	Intron	DEL	TC	-	-			TCGA-CZ-4863-01A-01D-1501-10	TCGA-CZ-4863-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:124310037_124310038delTC	uc003ehg.2	+						KALRN_uc003ehi.2_Intron|KALRN_uc003ehk.2_Intron|KALRN_uc003ehj.2_Intron	NM_001024660	NP_001019831	O60229	KALRN_HUMAN	kalirin, RhoGEF kinase isoform 1						apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|nervous system development|regulation of Rho protein signal transduction|small GTPase mediated signal transduction|vesicle-mediated transport	actin cytoskeleton|cytosol	ATP binding|GTPase activator activity|metal ion binding|protein binding|protein serine/threonine kinase activity|Rho guanyl-nucleotide exchange factor activity			large_intestine(2)|ovary(2)|central_nervous_system(1)|skin(1)	6						CACCATCACATCTCTCTCTCCC	0.431													4	2	---	---	---	---	
CPNE4	131034	broad.mit.edu	37	3	131991262	131991263	+	Intron	DEL	TG	-	-	rs72012461		TCGA-CZ-4863-01A-01D-1501-10	TCGA-CZ-4863-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:131991262_131991263delTG	uc003eom.2	-							NM_130808	NP_570720	Q96A23	CPNE4_HUMAN	copine IV											upper_aerodigestive_tract(1)|central_nervous_system(1)|skin(1)	3						CAAGCTAAACTGTGGTAATTCT	0.371													5	5	---	---	---	---	
TOPBP1	11073	broad.mit.edu	37	3	133337435	133337435	+	Intron	DEL	T	-	-			TCGA-CZ-4863-01A-01D-1501-10	TCGA-CZ-4863-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:133337435delT	uc003eps.2	-						TOPBP1_uc003ept.1_Intron	NM_007027	NP_008958	Q92547	TOPB1_HUMAN	topoisomerase (DNA) II binding protein 1						DNA repair|response to ionizing radiation	microtubule organizing center|PML body|spindle pole	DNA binding|protein C-terminus binding			ovary(2)|kidney(2)|skin(1)|lung(1)|pancreas(1)	7						CCTAGGGACATTTTTTTTTTT	0.219								Other_conserved_DNA_damage_response_genes					4	2	---	---	---	---	
NMNAT3	349565	broad.mit.edu	37	3	139292815	139292815	+	Intron	DEL	A	-	-			TCGA-CZ-4863-01A-01D-1501-10	TCGA-CZ-4863-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:139292815delA	uc003etj.2	-						NMNAT3_uc003etk.2_Intron|NMNAT3_uc003etl.2_Intron|NMNAT3_uc010hul.2_Intron	NM_178177	NP_835471	Q96T66	NMNA3_HUMAN	nicotinamide mononucleotide adenylyltransferase						water-soluble vitamin metabolic process	cytosol|mitochondrion	ATP binding|nicotinamide-nucleotide adenylyltransferase activity|nicotinate-nucleotide adenylyltransferase activity				0						AATATTTCTCAAAAAAAAAAG	0.194													4	2	---	---	---	---	
PLD1	5337	broad.mit.edu	37	3	171406294	171406294	+	Intron	DEL	G	-	-			TCGA-CZ-4863-01A-01D-1501-10	TCGA-CZ-4863-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:171406294delG	uc003fhs.2	-						PLD1_uc003fht.2_Intron	NM_002662	NP_002653	Q13393	PLD1_HUMAN	phospholipase D1 isoform a						cell communication|chemotaxis|Ras protein signal transduction	endoplasmic reticulum membrane|Golgi membrane|late endosome membrane|perinuclear region of cytoplasm	NAPE-specific phospholipase D activity|phosphatidylinositol binding|phospholipase D activity			ovary(2)|lung(1)	3	all_cancers(22;4.53e-19)|Ovarian(172;0.00197)|Breast(254;0.186)		LUSC - Lung squamous cell carcinoma(14;3.57e-14)|Lung(28;9.39e-14)		Choline(DB00122)	ctagctaggtggggaagctgg	0.249													4	2	---	---	---	---	
KCNMB3	27094	broad.mit.edu	37	3	178962008	178962011	+	Intron	DEL	AAAG	-	-			TCGA-CZ-4863-01A-01D-1501-10	TCGA-CZ-4863-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:178962008_178962011delAAAG	uc003fjm.2	-						KCNMB3_uc003fjl.3_Intron|KCNMB3_uc011bqc.1_Intron|KCNMB3_uc003fjn.2_Intron|KCNMB3_uc003fjo.2_Intron|KCNMB3_uc003fjp.1_Intron	NM_014407	NP_055222	Q9NPA1	KCMB3_HUMAN	calcium-activated potassium channel beta 3						detection of calcium ion|platelet activation|regulation of action potential in neuron	voltage-gated potassium channel complex	calcium-activated potassium channel activity|potassium channel regulator activity				0	all_cancers(143;5.6e-17)|Ovarian(172;0.0172)|Breast(254;0.155)		OV - Ovarian serous cystadenocarcinoma(80;2.41e-27)|GBM - Glioblastoma multiforme(14;0.003)|BRCA - Breast invasive adenocarcinoma(182;0.03)			GGAATCTCCAAAAGAAAGACTCCC	0.363													4	3	---	---	---	---	
KCNIP4	80333	broad.mit.edu	37	4	20732212	20732212	+	Intron	DEL	G	-	-			TCGA-CZ-4863-01A-01D-1501-10	TCGA-CZ-4863-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:20732212delG	uc003gqe.2	-						KCNIP4_uc003gqf.1_Intron|KCNIP4_uc003gqg.1_Intron|KCNIP4_uc003gqh.1_Intron|KCNIP4_uc003gqi.1_Intron|PACRGL_uc003gpu.2_Intron|PACRGL_uc003gpx.3_Intron|PACRGL_uc003gpw.2_Intron|KCNIP4_uc010iel.2_Intron|KCNIP4_uc003gqd.3_Intron	NM_147182	NP_671711	Q6PIL6	KCIP4_HUMAN	Kv channel interacting protein 4 isoform 3							plasma membrane	calcium ion binding|potassium channel activity|protein binding|voltage-gated ion channel activity				0		Breast(46;0.134)				GAGGCAGGGTGGTGGATTAAG	0.443													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	28221318	28221318	+	IGR	DEL	A	-	-			TCGA-CZ-4863-01A-01D-1501-10	TCGA-CZ-4863-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:28221318delA								None (None upstream) : None (None downstream)																							GCATTTCTCTAAAAGACTTTG	0.323													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	55210764	55210764	+	IGR	DEL	T	-	-			TCGA-CZ-4863-01A-01D-1501-10	TCGA-CZ-4863-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:55210764delT								PDGFRA (46353 upstream) : KIT (313331 downstream)																							agaaaggaaataacaaaggtc	0.000													4	2	---	---	---	---	
UCP1	7350	broad.mit.edu	37	4	141486076	141486076	+	Intron	DEL	T	-	-			TCGA-CZ-4863-01A-01D-1501-10	TCGA-CZ-4863-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:141486076delT	uc011chj.1	-						UCP1_uc011chk.1_Intron	NM_021833	NP_068605	P25874	UCP1_HUMAN	uncoupling protein 1						brown fat cell differentiation|cellular lipid metabolic process|respiratory electron transport chain	integral to membrane|mitochondrial inner membrane	binding			ovary(1)	1	all_hematologic(180;0.162)					tcagagcccatttcttcctca	0.100													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	182577696	182577696	+	IGR	DEL	C	-	-			TCGA-CZ-4863-01A-01D-1501-10	TCGA-CZ-4863-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:182577696delC								None (None upstream) : MGC45800 (482463 downstream)																							TGCAGATGGGCCCAGGAGAGC	0.483													4	2	---	---	---	---	
WWC2	80014	broad.mit.edu	37	4	184148169	184148169	+	Intron	DEL	C	-	-			TCGA-CZ-4863-01A-01D-1501-10	TCGA-CZ-4863-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:184148169delC	uc010irx.2	+						WWC2_uc003ivk.3_Intron|WWC2_uc003ivl.3_Intron|WWC2_uc010iry.2_Intron	NM_024949	NP_079225	Q6AWC2	WWC2_HUMAN	WW and C2 domain containing 2											ovary(2)|lung(1)	3		all_lung(41;5.28e-14)|Lung NSC(41;1.35e-13)|Colorectal(36;0.00681)|Hepatocellular(41;0.00886)|Renal(120;0.00992)|Prostate(90;0.0237)|all_hematologic(60;0.0592)|Esophageal squamous(56;0.179)|all_neural(102;0.202)		all cancers(43;3.38e-24)|Epithelial(43;1.4e-20)|OV - Ovarian serous cystadenocarcinoma(60;1.09e-09)|GBM - Glioblastoma multiforme(59;3.33e-05)|Colorectal(24;3.58e-05)|STAD - Stomach adenocarcinoma(60;4.21e-05)|COAD - Colon adenocarcinoma(29;0.000171)|LUSC - Lung squamous cell carcinoma(40;0.0145)|READ - Rectum adenocarcinoma(43;0.242)		TGGTGACAGACCCCAGCTGCA	0.463													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	190566242	190566243	+	IGR	INS	-	T	T	rs11393860		TCGA-CZ-4863-01A-01D-1501-10	TCGA-CZ-4863-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:190566242_190566243insT								None (None upstream) : FRG1 (295731 downstream)																							TAAGGAGACGCTGCTGATTAGA	0.475													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	10143992	10143993	+	IGR	INS	-	G	G	rs150683784	by1000genomes	TCGA-CZ-4863-01A-01D-1501-10	TCGA-CZ-4863-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:10143992_10143993insG								LOC285692 (240056 upstream) : FAM173B (82445 downstream)																							CTACTTCAAAAACACTGCCCAC	0.361													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	22857260	22857261	+	IGR	INS	-	A	A	rs140911268	by1000genomes	TCGA-CZ-4863-01A-01D-1501-10	TCGA-CZ-4863-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:22857260_22857261insA								CDH12 (3529 upstream) : PRDM9 (650463 downstream)																							atttcccaagcaaaaaaaacag	0.000													1	5	---	---	---	---	
C5orf13	9315	broad.mit.edu	37	5	111032020	111032020	+	Intron	DEL	A	-	-			TCGA-CZ-4863-01A-01D-1501-10	TCGA-CZ-4863-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:111032020delA	uc003kpk.2	-									Q16612	NP311_HUMAN	Homo sapiens cDNA FLJ55239 complete cds, moderately similar to Neuronal protein 3.1.							cytoplasm				skin(1)	1		all_cancers(142;0.00597)|all_epithelial(76;0.000144)|Prostate(80;0.0115)|Colorectal(10;0.0446)|Ovarian(225;0.156)		OV - Ovarian serous cystadenocarcinoma(64;5.45e-09)|Epithelial(69;2e-08)|all cancers(49;1.9e-06)|COAD - Colon adenocarcinoma(37;0.0514)|Colorectal(14;0.0629)		TGACTGGGAGAAAAAAAATAC	0.403													2	4	---	---	---	---	
ODZ2	57451	broad.mit.edu	37	5	167550584	167550584	+	Intron	DEL	A	-	-			TCGA-CZ-4863-01A-01D-1501-10	TCGA-CZ-4863-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:167550584delA	uc010jjd.2	+						ODZ2_uc003lzr.3_Intron|ODZ2_uc003lzt.3_Intron|ODZ2_uc010jje.2_5'Flank|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)		cgtggtccataaaaacttcaa	0.119													4	2	---	---	---	---	
CANX	821	broad.mit.edu	37	5	179135792	179135792	+	Intron	DEL	T	-	-			TCGA-CZ-4863-01A-01D-1501-10	TCGA-CZ-4863-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:179135792delT	uc003mkk.2	+						CANX_uc011dgp.1_Intron|CANX_uc010jlb.1_Intron|CANX_uc003mkl.2_Intron|CANX_uc011dgq.1_Intron	NM_001746	NP_001737	P27824	CALX_HUMAN	calnexin precursor						post-translational protein modification|protein folding|protein N-linked glycosylation via asparagine|protein secretion	endoplasmic reticulum lumen|endoplasmic reticulum membrane|integral to membrane|melanosome	calcium ion binding|sugar binding|unfolded protein binding				0	all_cancers(89;0.000129)|all_epithelial(37;5.59e-05)|Renal(175;0.000159)|Lung NSC(126;0.00121)|all_lung(126;0.00218)	all_cancers(40;0.0413)|Medulloblastoma(196;0.00498)|all_neural(177;0.0138)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)		Alteplase(DB00009)|Anistreplase(DB00029)|Antihemophilic Factor(DB00025)|Reteplase(DB00015)|Tenecteplase(DB00031)	TAATGTTCaatttaattttat	0.279													45	28	---	---	---	---	
EEF1E1	9521	broad.mit.edu	37	6	8090753	8090753	+	Intron	DEL	T	-	-			TCGA-CZ-4863-01A-01D-1501-10	TCGA-CZ-4863-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:8090753delT	uc003mxz.2	-						EEF1E1_uc011dic.1_Intron	NM_004280	NP_004271	O43324	MCA3_HUMAN	eukaryotic translation elongation factor 1						negative regulation of cell proliferation|positive regulation of apoptosis|positive regulation of DNA damage response, signal transduction by p53 class mediator|tRNA aminoacylation for protein translation	cytosol|nucleus					0	Ovarian(93;0.0398)					TAGAAAATGATATTCAAAGTG	0.264													4	2	---	---	---	---	
GCNT2	2651	broad.mit.edu	37	6	10573401	10573402	+	Intron	INS	-	ATC	ATC	rs55692625		TCGA-CZ-4863-01A-01D-1501-10	TCGA-CZ-4863-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:10573401_10573402insATC	uc010joo.2	+						GCNT2_uc010jol.2_Intron|GCNT2_uc010jom.2_Intron|GCNT2_uc010jop.2_Intron|GCNT2_uc003mza.2_Intron|GCNT2_uc003mzc.3_Intron|GCNT2_uc003mzd.2_Intron	NM_145649	NP_663624	Q8N0V5	GNT2A_HUMAN	glucosaminyl (N-acetyl) transferase 2,							Golgi membrane|integral to membrane	N-acetyllactosaminide beta-1,6-N-acetylglucosaminyltransferase activity			ovary(2)	2	Ovarian(93;0.107)|Breast(50;0.148)	all_hematologic(90;0.107)		KIRC - Kidney renal clear cell carcinoma(1;0.099)|Kidney(1;0.119)		TCTAGATATGGATCTCTGGCAG	0.386													2	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	27528843	27528844	+	IGR	INS	-	T	T			TCGA-CZ-4863-01A-01D-1501-10	TCGA-CZ-4863-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:27528843_27528844insT								ZNF184 (87946 upstream) : HIST1H2BL (246414 downstream)																							tcttttctttcttttttttttt	0.119													6	3	---	---	---	---	
ZNF318	24149	broad.mit.edu	37	6	43319918	43319919	+	Intron	INS	-	CAC	CAC	rs3078977		TCGA-CZ-4863-01A-01D-1501-10	TCGA-CZ-4863-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:43319918_43319919insCAC	uc003oux.2	-						ZNF318_uc003ouw.2_Intron	NM_014345	NP_055160	Q5VUA4	ZN318_HUMAN	zinc finger protein 318						meiosis|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	nucleic acid binding|zinc ion binding			ovary(3)|breast(2)|central_nervous_system(1)|skin(1)	7			Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.0171)|OV - Ovarian serous cystadenocarcinoma(102;0.0579)			atcatcatcatcatcaccacca	0.000													6	4	---	---	---	---	
GPR116	221395	broad.mit.edu	37	6	46868031	46868031	+	Intron	DEL	T	-	-			TCGA-CZ-4863-01A-01D-1501-10	TCGA-CZ-4863-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:46868031delT	uc003oyo.3	-						GPR116_uc003oyp.3_Intron|GPR116_uc003oyq.3_Intron|GPR116_uc003oyr.2_Intron	NM_001098518	NP_001091988	Q8IZF2	GP116_HUMAN	G-protein coupled receptor 116 precursor						neuropeptide signaling pathway	integral to membrane|plasma membrane	G-protein coupled receptor activity			central_nervous_system(1)|skin(1)	2			Lung(136;0.192)			TAGGAATTCATTTTTTTTTAG	0.408													4	2	---	---	---	---	
KIAA0776	23376	broad.mit.edu	37	6	97000116	97000116	+	Intron	DEL	A	-	-			TCGA-CZ-4863-01A-01D-1501-10	TCGA-CZ-4863-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:97000116delA	uc003por.2	+						KIAA0776_uc010kck.2_Intron	NM_015323	NP_056138	O94874	UFL1_HUMAN	hypothetical protein LOC23376						negative regulation of NF-kappaB transcription factor activity|negative regulation of protein ubiquitination|protein ufmylation	endoplasmic reticulum|nucleus	protein binding|UFM1 conjugating enzyme activity			ovary(1)	1		all_cancers(76;5.83e-05)|Acute lymphoblastic leukemia(125;7.02e-10)|all_hematologic(75;1.23e-06)|all_epithelial(107;0.0604)|Colorectal(196;0.0721)		BRCA - Breast invasive adenocarcinoma(108;0.0934)		CCAGCAACTCAAAACAAAAAA	0.348													4	2	---	---	---	---	
MED23	9439	broad.mit.edu	37	6	131941559	131941559	+	Intron	DEL	G	-	-			TCGA-CZ-4863-01A-01D-1501-10	TCGA-CZ-4863-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:131941559delG	uc003qcs.1	-						MED23_uc003qcq.2_Intron|MED23_uc003qct.1_Intron|MED23_uc011ecb.1_Intron	NM_004830	NP_004821	Q9ULK4	MED23_HUMAN	mediator complex subunit 23 isoform a						regulation of transcription from RNA polymerase II promoter|transcription initiation from RNA polymerase II promoter	transcription factor complex	protein binding|transcription coactivator activity			ovary(1)|kidney(1)|central_nervous_system(1)	3	Breast(56;0.0753)			GBM - Glioblastoma multiforme(226;0.0115)|OV - Ovarian serous cystadenocarcinoma(155;0.0608)		ctgagtagctggggctatagg	0.000													4	2	---	---	---	---	
AHI1	54806	broad.mit.edu	37	6	135726363	135726364	+	Intron	INS	-	GG	GG			TCGA-CZ-4863-01A-01D-1501-10	TCGA-CZ-4863-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:135726363_135726364insGG	uc003qgi.2	-						AHI1_uc003qgf.2_Intron|AHI1_uc003qgg.2_Intron|AHI1_uc003qgh.2_Intron|AHI1_uc003qgj.2_Intron|AHI1_uc003qgk.3_Intron|AHI1_uc003qgl.3_Intron	NM_001134831	NP_001128303	Q8N157	AHI1_HUMAN	Abelson helper integration site 1 isoform a							adherens junction|cilium|microtubule basal body				ovary(1)|kidney(1)|central_nervous_system(1)	3	Breast(56;0.239)|Colorectal(23;0.24)			GBM - Glioblastoma multiforme(68;0.00904)|OV - Ovarian serous cystadenocarcinoma(155;0.00991)		GTTATCTGCCTCAAGAAAAACT	0.351													5	3	---	---	---	---	
IFNGR1	3459	broad.mit.edu	37	6	137521826	137521826	+	Intron	DEL	A	-	-	rs75396334		TCGA-CZ-4863-01A-01D-1501-10	TCGA-CZ-4863-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:137521826delA	uc003qho.2	-						IFNGR1_uc011edm.1_Intron	NM_000416	NP_000407	P15260	INGR1_HUMAN	interferon gamma receptor 1 precursor						regulation of interferon-gamma-mediated signaling pathway|response to virus	integral to plasma membrane	interferon-gamma receptor activity			upper_aerodigestive_tract(1)	1	Colorectal(23;0.24)			GBM - Glioblastoma multiforme(68;0.000829)|OV - Ovarian serous cystadenocarcinoma(155;0.00389)	Interferon gamma-1b(DB00033)	CCCTGAGAATAAAAAAAAAAA	0.209													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	145537189	145537190	+	IGR	INS	-	A	A			TCGA-CZ-4863-01A-01D-1501-10	TCGA-CZ-4863-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:145537189_145537190insA								UTRN (363021 upstream) : EPM2A (409256 downstream)																							GGAATGCATTCAAAAAAGAGTC	0.381													4	2	---	---	---	---	
SLC22A1	6580	broad.mit.edu	37	6	160550869	160550869	+	Intron	DEL	A	-	-			TCGA-CZ-4863-01A-01D-1501-10	TCGA-CZ-4863-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:160550869delA	uc003qtc.2	+						SLC22A1_uc003qtd.2_Intron	NM_003057	NP_003048	O15245	S22A1_HUMAN	solute carrier family 22 member 1 isoform a							basolateral plasma membrane|integral to plasma membrane|membrane fraction	organic cation transmembrane transporter activity|protein binding				0		Breast(66;0.000776)|Ovarian(120;0.00556)		OV - Ovarian serous cystadenocarcinoma(65;2.73e-17)|BRCA - Breast invasive adenocarcinoma(81;1.1e-06)		aattttattgaaaaaaaaaaa	0.060													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	167621962	167621962	+	IGR	DEL	A	-	-	rs10583811		TCGA-CZ-4863-01A-01D-1501-10	TCGA-CZ-4863-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:167621962delA								TCP10L2 (25567 upstream) : UNC93A (82841 downstream)																							GTTAGAATAGAAAAAAAATAC	0.338													6	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	4424235	4424235	+	IGR	DEL	G	-	-			TCGA-CZ-4863-01A-01D-1501-10	TCGA-CZ-4863-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:4424235delG								SDK1 (115606 upstream) : FOXK1 (259153 downstream)																							GAACAGTGTAGGAAGTGGAAG	0.373													4	2	---	---	---	---	
LOC646762	646762	broad.mit.edu	37	7	29699825	29699825	+	Intron	DEL	T	-	-	rs35015386		TCGA-CZ-4863-01A-01D-1501-10	TCGA-CZ-4863-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:29699825delT	uc003tad.3	-							NR_024278				Homo sapiens cDNA: FLJ23070 fis, clone LNG05629.												0						ATTATTGACCTTTTTTTTTTC	0.249													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	35807609	35807609	+	IGR	DEL	T	-	-			TCGA-CZ-4863-01A-01D-1501-10	TCGA-CZ-4863-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:35807609delT								HERPUD2 (72837 upstream) : SEPT7 (33018 downstream)																							TTAACAGTAGTTTTTTTTTCC	0.294													10	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	73065004	73065005	+	IGR	INS	-	C	C			TCGA-CZ-4863-01A-01D-1501-10	TCGA-CZ-4863-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:73065004_73065005insC								MLXIPL (26134 upstream) : VPS37D (17169 downstream)																							GCCCACTGTTTCCTGTCTTGCA	0.510													4	2	---	---	---	---	
STAG3	10734	broad.mit.edu	37	7	99787453	99787453	+	Intron	DEL	T	-	-			TCGA-CZ-4863-01A-01D-1501-10	TCGA-CZ-4863-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:99787453delT	uc003utx.1	+						STAG3_uc010lgs.1_Intron|STAG3_uc011kjk.1_Intron	NM_012447	NP_036579	Q9UJ98	STAG3_HUMAN	stromal antigen 3						chromosome segregation|synaptonemal complex assembly	chromosome, centromeric region|meiotic cohesin complex|synaptonemal complex	binding			ovary(4)|skin(2)|lung(1)|kidney(1)	8	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)					TTTTGCTCAGTTTTTTTTTTT	0.393													3	4	---	---	---	---	
SRPK2	6733	broad.mit.edu	37	7	105029853	105029853	+	Intron	DEL	G	-	-			TCGA-CZ-4863-01A-01D-1501-10	TCGA-CZ-4863-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:105029853delG	uc003vcw.1	-						SRPK2_uc003vcv.2_5'Flank	NM_182691	NP_872633	P78362	SRPK2_HUMAN	serine/arginine-rich protein-specific kinase 2						angiogenesis|cell differentiation|intracellular protein kinase cascade|negative regulation of viral genome replication|nuclear speck organization|positive regulation of cell cycle|positive regulation of cell proliferation|positive regulation of gene expression|positive regulation of neuron apoptosis|positive regulation of viral genome replication|spliceosome assembly	cytoplasm|nucleolus	14-3-3 protein binding|ATP binding|magnesium ion binding|protein serine/threonine kinase activity			central_nervous_system(3)|ovary(2)|upper_aerodigestive_tract(1)	6						GGCgtggaaagggcacacgac	0.318													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	129162762	129162762	+	IGR	DEL	T	-	-			TCGA-CZ-4863-01A-01D-1501-10	TCGA-CZ-4863-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:129162762delT								FAM40B (34525 upstream) : NRF1 (88793 downstream)																							GAGTTCTGCCTTCTGTCGGTT	0.483													4	2	---	---	---	---	
EPHB6	2051	broad.mit.edu	37	7	142562259	142562259	+	Frame_Shift_Del	DEL	C	-	-			TCGA-CZ-4863-01A-01D-1501-10	TCGA-CZ-4863-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:142562259delC	uc011kst.1	+	7	1488	c.701delC	c.(700-702)GCCfs	p.A234fs	EPHB6_uc011ksu.1_Frame_Shift_Del_p.A234fs|EPHB6_uc003wbs.2_5'UTR|EPHB6_uc003wbt.2_Intron|EPHB6_uc003wbu.2_5'UTR|EPHB6_uc003wbv.2_5'Flank	NM_004445	NP_004436	O15197	EPHB6_HUMAN	ephrin receptor EphB6 precursor	234	Extracellular (Potential).|Cys-rich.					extracellular region|integral to plasma membrane	ATP binding|ephrin receptor activity			lung(8)|large_intestine(4)|central_nervous_system(3)|stomach(1)|skin(1)|ovary(1)|pancreas(1)	19	Melanoma(164;0.059)					ACCTGCCCTGCCGTGCTCCGA	0.662													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	37538390	37538390	+	IGR	DEL	A	-	-			TCGA-CZ-4863-01A-01D-1501-10	TCGA-CZ-4863-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:37538390delA								KCNU1 (744749 upstream) : ZNF703 (14911 downstream)																							TCAGACAAAGAAAGATACATC	0.458													4	2	---	---	---	---	
POTEA	340441	broad.mit.edu	37	8	43154194	43154194	+	Intron	DEL	T	-	-			TCGA-CZ-4863-01A-01D-1501-10	TCGA-CZ-4863-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:43154194delT	uc003xpz.1	+						POTEA_uc003xqa.1_Intron	NM_001005365	NP_001005365	Q6S8J7	POTEA_HUMAN	POTE ankyrin domain family, member A isoform 2											ovary(1)	1						tctttctttctttttttcttt	0.109													5	4	---	---	---	---	
GGH	8836	broad.mit.edu	37	8	63939437	63939437	+	Intron	DEL	A	-	-			TCGA-CZ-4863-01A-01D-1501-10	TCGA-CZ-4863-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:63939437delA	uc003xuw.2	-							NM_003878	NP_003869	Q92820	GGH_HUMAN	gamma-glutamyl hydrolase precursor						glutamine metabolic process	extracellular space|lysosome|melanosome	gamma-glutamyl-peptidase activity				0	Breast(64;0.0716)	all_cancers(86;0.189)|Lung NSC(129;0.0324)|all_lung(136;0.0593)|all_epithelial(80;0.131)			Folic Acid(DB00158)|L-Glutamic Acid(DB00142)	CAATGCCCATAAAAAAAAAAT	0.388													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	75792841	75792842	+	IGR	INS	-	T	T	rs142653392	by1000genomes	TCGA-CZ-4863-01A-01D-1501-10	TCGA-CZ-4863-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:75792841_75792842insT								PI15 (25579 upstream) : CRISPLD1 (104001 downstream)																							GGTTGATTGCATTTTTTTTGGC	0.371													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	103646799	103646799	+	IGR	DEL	A	-	-			TCGA-CZ-4863-01A-01D-1501-10	TCGA-CZ-4863-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:103646799delA								ODF1 (73554 upstream) : KLF10 (14206 downstream)																							AGATGACAACAAGGCCAAGAA	0.592													4	2	---	---	---	---	
RIMS2	9699	broad.mit.edu	37	8	104781292	104781292	+	Intron	DEL	A	-	-			TCGA-CZ-4863-01A-01D-1501-10	TCGA-CZ-4863-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:104781292delA	uc003ylp.2	+							NM_001100117	NP_001093587	Q9UQ26	RIMS2_HUMAN	regulating synaptic membrane exocytosis 2						intracellular protein transport	cell junction|presynaptic membrane	metal ion binding|Rab GTPase binding			ovary(6)|lung(2)|breast(2)|skin(2)|large_intestine(1)|central_nervous_system(1)|pancreas(1)	15			OV - Ovarian serous cystadenocarcinoma(57;7.7e-07)|STAD - Stomach adenocarcinoma(118;0.229)			AGATCAGACTAAAAAAAAAAG	0.264										HNSCC(12;0.0054)			6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	116927354	116927355	+	IGR	INS	-	GAA	GAA			TCGA-CZ-4863-01A-01D-1501-10	TCGA-CZ-4863-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:116927354_116927355insGAA								TRPS1 (246126 upstream) : EIF3H (729701 downstream)																							GGGAGAGATATGAAGAAGCAGC	0.391													4	2	---	---	---	---	
KIAA1432	57589	broad.mit.edu	37	9	5756640	5756640	+	Intron	DEL	T	-	-	rs75634422		TCGA-CZ-4863-01A-01D-1501-10	TCGA-CZ-4863-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:5756640delT	uc003zji.2	+						KIAA1432_uc003zjh.2_Intron|KIAA1432_uc003zjl.3_Intron|KIAA1432_uc003zjj.1_Intron	NM_020829	NP_065880	Q4ADV7	RIC1_HUMAN	connexin 43-interacting protein 150 isoform a							integral to membrane					0		Acute lymphoblastic leukemia(23;0.154)		GBM - Glioblastoma multiforme(50;0.000525)|Lung(218;0.122)		AGATACTAAATTTTTTTTCAC	0.338													3	3	---	---	---	---	
IFNA14	3448	broad.mit.edu	37	9	21202367	21202367	+	Intron	DEL	T	-	-			TCGA-CZ-4863-01A-01D-1501-10	TCGA-CZ-4863-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:21202367delT	uc003zoo.1	-						IFNA7_uc003zop.1_5'Flank	NM_002172		P01570	IFN14_HUMAN	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)		ACgtttttcattttttttttc	0.139													6	4	---	---	---	---	
IFNA14	3448	broad.mit.edu	37	9	21207349	21207349	+	Intron	DEL	T	-	-			TCGA-CZ-4863-01A-01D-1501-10	TCGA-CZ-4863-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:21207349delT	uc003zoo.1	-						IFNA10_uc003zoq.1_5'Flank	NM_002172		P01570	IFN14_HUMAN	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)		CCTTTTATGGTTTTTTTTTAA	0.159													4	2	---	---	---	---	
MOBKL2B	79817	broad.mit.edu	37	9	27454967	27454967	+	Intron	DEL	T	-	-			TCGA-CZ-4863-01A-01D-1501-10	TCGA-CZ-4863-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:27454967delT	uc003zqn.2	-							NM_024761	NP_079037	Q86TA1	MOL2B_HUMAN	MOB1, Mps One Binder kinase activator-like 2B								metal ion binding|protein binding			ovary(1)|pleura(1)	2		all_neural(11;9.12e-11)		Lung(218;6.54e-05)|LUSC - Lung squamous cell carcinoma(38;0.000397)		gtccataaagttttttttttc	0.239													7	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	31697723	31697724	+	IGR	INS	-	A	A	rs73644282		TCGA-CZ-4863-01A-01D-1501-10	TCGA-CZ-4863-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:31697723_31697724insA								None (None upstream) : ACO1 (686877 downstream)																							AAAAAAAAAACAAAAAAAAACA	0.376													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	66481002	66481002	+	IGR	DEL	T	-	-	rs4436239	by1000genomes	TCGA-CZ-4863-01A-01D-1501-10	TCGA-CZ-4863-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:66481002delT								FAM74A4 (986616 upstream) : LOC442421 (15468 downstream)																							accatttatctttttttattg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	68417570	68417571	+	IGR	INS	-	AA	AA	rs111263548		TCGA-CZ-4863-01A-01D-1501-10	TCGA-CZ-4863-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:68417570_68417571insAA								FAM27B (623381 upstream) : MIR1299 (584668 downstream)																							AGGATAGGAATAAAACATCAGT	0.243													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	68494353	68494353	+	IGR	DEL	A	-	-			TCGA-CZ-4863-01A-01D-1501-10	TCGA-CZ-4863-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:68494353delA								FAM27B (700164 upstream) : MIR1299 (507886 downstream)																							ATTTGAGAGGAAAGCTGGTGC	0.383													4	4	---	---	---	---	
SMC5	23137	broad.mit.edu	37	9	72893797	72893797	+	Intron	DEL	A	-	-			TCGA-CZ-4863-01A-01D-1501-10	TCGA-CZ-4863-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:72893797delA	uc004ahr.2	+							NM_015110	NP_055925	Q8IY18	SMC5_HUMAN	SMC5 protein						DNA recombination|DNA repair	chromosome|nucleus	ATP binding			ovary(2)|central_nervous_system(1)	3						ACAGTATTATAAAAAAAAATT	0.164													4	2	---	---	---	---	
NTRK2	4915	broad.mit.edu	37	9	87339543	87339543	+	Intron	DEL	T	-	-			TCGA-CZ-4863-01A-01D-1501-10	TCGA-CZ-4863-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:87339543delT	uc004aoa.1	+						NTRK2_uc004anv.1_Intron|NTRK2_uc004any.1_Intron|NTRK2_uc004anz.1_Intron|NTRK2_uc011lsz.1_Intron|NTRK2_uc011lta.1_Intron|NTRK2_uc004aob.1_Intron|NTRK2_uc011ltb.1_Intron	NM_001018064	NP_001018074	Q16620	NTRK2_HUMAN	neurotrophic tyrosine kinase, receptor, type 2						activation of adenylate cyclase activity|cell differentiation|nerve growth factor receptor signaling pathway|nervous system development	integral to plasma membrane	ATP binding|neurotrophin receptor activity|transmembrane receptor protein tyrosine kinase activity			lung(11)|central_nervous_system(1)|breast(1)|skin(1)|ovary(1)|liver(1)	16						TGATAGAATATACTTTGGGCT	0.323										TSP Lung(25;0.17)			4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	88384976	88384977	+	IGR	INS	-	TG	TG	rs139915412	by1000genomes	TCGA-CZ-4863-01A-01D-1501-10	TCGA-CZ-4863-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:88384976_88384977insTG								AGTPBP1 (28032 upstream) : NAA35 (171080 downstream)																							TGTTAATCTGTtgtgtgtgtgt	0.243													6	3	---	---	---	---	
EPB41L4B	54566	broad.mit.edu	37	9	112004925	112004926	+	Intron	INS	-	T	T			TCGA-CZ-4863-01A-01D-1501-10	TCGA-CZ-4863-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:112004925_112004926insT	uc004bdz.1	-						EPB41L4B_uc004bea.2_Intron	NM_019114	NP_061987	Q9H329	E41LB_HUMAN	erythrocyte membrane protein band 4.1 like 4B							cytoplasm|cytoskeleton|extrinsic to membrane	cytoskeletal protein binding|structural constituent of cytoskeleton			ovary(1)|central_nervous_system(1)|skin(1)	3						CCCCAACAAACTTTTTTTTGGC	0.356													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	137384534	137384535	+	IGR	INS	-	G	G			TCGA-CZ-4863-01A-01D-1501-10	TCGA-CZ-4863-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:137384534_137384535insG								RXRA (52103 upstream) : COL5A1 (149117 downstream)																							gaggatacagcggggaaaaaac	0.104													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	19341286	19341287	+	IGR	INS	-	T	T			TCGA-CZ-4863-01A-01D-1501-10	TCGA-CZ-4863-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:19341286_19341287insT								ARL5B (374346 upstream) : PLXDC2 (764085 downstream)																							GTAAATGTTACTTTTTTTTGTC	0.337													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	42649215	42649215	+	IGR	DEL	T	-	-			TCGA-CZ-4863-01A-01D-1501-10	TCGA-CZ-4863-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:42649215delT								None (None upstream) : LOC441666 (178100 downstream)																							CGTATGCAACTTTCCCCTAAA	0.348													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	45569044	45569044	+	5'Flank	DEL	T	-	-			TCGA-CZ-4863-01A-01D-1501-10	TCGA-CZ-4863-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:45569044delT	uc001jbx.1	-											Homo sapiens zinc finger protein 22 (KOX 15), mRNA (cDNA clone IMAGE:4826621).																		agacatgaggttttcctatgt	0.139													4	2	---	---	---	---	
PRKG1	5592	broad.mit.edu	37	10	54053913	54053914	+	3'UTR	INS	-	G	G	rs146539098	by1000genomes	TCGA-CZ-4863-01A-01D-1501-10	TCGA-CZ-4863-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:54053913_54053914insG	uc001jjm.2	+	18					PRKG1_uc001jjo.2_3'UTR|PRKG1_uc009xow.1_3'UTR|uc001jjq.1_Intron	NM_001098512	NP_001091982	Q13976	KGP1_HUMAN	protein kinase, cGMP-dependent, type I isoform						actin cytoskeleton organization|platelet activation|signal transduction	cytosol	ATP binding|cGMP binding|cGMP-dependent protein kinase activity			lung(2)|stomach(1)|ovary(1)|central_nervous_system(1)|skin(1)	6		all_cancers(4;2.13e-08)|all_epithelial(4;2.44e-08)|all_lung(4;0.000173)		all cancers(4;1.18e-05)|GBM - Glioblastoma multiforme(4;0.000359)|Epithelial(53;0.00532)|Lung(62;0.0606)		TCACCAGTAAAAGATGTTTTCT	0.376													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	65605092	65605093	+	IGR	DEL	GT	-	-			TCGA-CZ-4863-01A-01D-1501-10	TCGA-CZ-4863-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:65605092_65605093delGT								REEP3 (223121 upstream) : ANXA2P3 (980192 downstream)																							gcagaactgggtgtgtgtgttg	0.109													4	2	---	---	---	---	
MYOF	26509	broad.mit.edu	37	10	95137468	95137468	+	Intron	DEL	A	-	-			TCGA-CZ-4863-01A-01D-1501-10	TCGA-CZ-4863-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:95137468delA	uc001kin.2	-						MYOF_uc001kio.2_Intron|MYOF_uc009xue.2_Intron	NM_013451	NP_038479	Q9NZM1	MYOF_HUMAN	myoferlin isoform a						blood circulation|muscle contraction|plasma membrane repair	caveola|cytoplasmic vesicle membrane|integral to membrane|nuclear membrane	phospholipid binding|protein binding			ovary(3)|breast(1)	4						taaaaggcagaaaaaaaaaac	0.000													4	2	---	---	---	---	
C10orf76	79591	broad.mit.edu	37	10	103789686	103789686	+	Intron	DEL	T	-	-			TCGA-CZ-4863-01A-01D-1501-10	TCGA-CZ-4863-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:103789686delT	uc009xwy.1	-						C10orf76_uc001kui.2_Intron	NM_024541	NP_078817	Q5T2E6	CJ076_HUMAN	hypothetical protein LOC79591							integral to membrane					0		Colorectal(252;0.123)		Epithelial(162;2.41e-08)|all cancers(201;6.41e-07)		tgtttgtttgttttttttttt	0.159													5	3	---	---	---	---	
DHX32	55760	broad.mit.edu	37	10	127583269	127583269	+	Intron	DEL	C	-	-	rs10709545		TCGA-CZ-4863-01A-01D-1501-10	TCGA-CZ-4863-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:127583269delC	uc001ljg.1	-						FANK1_uc010quk.1_5'Flank|FANK1_uc001ljh.3_5'Flank|FANK1_uc009yan.2_5'Flank	NM_018180	NP_060650	Q7L7V1	DHX32_HUMAN	DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 32							mitochondrion|nucleus	ATP binding|helicase activity			breast(2)|ovary(1)|lung(1)	4		all_lung(145;0.00751)|Lung NSC(174;0.0115)|Colorectal(57;0.0846)|all_neural(114;0.0936)				AATACTAATGCTAATCCTTTA	0.303													3	3	---	---	---	---	
SLC1A2	6506	broad.mit.edu	37	11	35297395	35297395	+	Intron	DEL	C	-	-			TCGA-CZ-4863-01A-01D-1501-10	TCGA-CZ-4863-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:35297395delC	uc001mwd.2	-						SLC1A2_uc001mwe.2_Intron|SLC1A2_uc010rev.1_Intron	NM_004171	NP_004162	P43004	EAA2_HUMAN	excitatory amino acid transporter 2						D-aspartate import|L-glutamate import|synaptic transmission	integral to membrane|membrane fraction	high-affinity glutamate transmembrane transporter activity|sodium:dicarboxylate symporter activity			ovary(2)|central_nervous_system(1)	3	all_lung(20;0.211)|all_epithelial(35;0.234)	all_hematologic(20;0.109)	STAD - Stomach adenocarcinoma(6;0.00731)		L-Glutamic Acid(DB00142)	GCCAGTTGCACCCCATCTCAT	0.468													4	2	---	---	---	---	
TSPAN18	90139	broad.mit.edu	37	11	44930587	44930587	+	Intron	DEL	G	-	-			TCGA-CZ-4863-01A-01D-1501-10	TCGA-CZ-4863-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:44930587delG	uc001mye.3	+						TP53I11_uc001myf.1_Intron|TSPAN18_uc001myg.2_Intron	NM_130783	NP_570139	Q96SJ8	TSN18_HUMAN	tetraspanin 18 isoform 2							integral to membrane					0						tctttccaaagATAAATAAGG	0.204													4	2	---	---	---	---	
NAALADL1	10004	broad.mit.edu	37	11	64814798	64814799	+	Intron	DEL	TG	-	-			TCGA-CZ-4863-01A-01D-1501-10	TCGA-CZ-4863-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:64814798_64814799delTG	uc001ocn.2	-						NAALADL1_uc010rnw.1_Intron|NAALADL1_uc009ypz.2_Intron	NM_005468	NP_005459	Q9UQQ1	NALDL_HUMAN	N-acetylated alpha-linked acidic						proteolysis	apical plasma membrane|integral to membrane	carboxypeptidase activity|dipeptidase activity|metal ion binding|metallopeptidase activity				0						tgtgtatttctgtgtgtgtgtg	0.198													4	2	---	---	---	---	
ETV6	2120	broad.mit.edu	37	12	11860153	11860153	+	Intron	DEL	A	-	-			TCGA-CZ-4863-01A-01D-1501-10	TCGA-CZ-4863-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:11860153delA	uc001qzz.2	+							NM_001987	NP_001978	P41212	ETV6_HUMAN	ets variant 6							cytoplasm|nucleolus	protein domain specific binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity		ETV6/NTRK3(234)|ETV6/JAK2(11)	soft_tissue(85)|kidney(66)|breast(55)|salivary_gland(26)|haematopoietic_and_lymphoid_tissue(13)|ovary(2)|upper_aerodigestive_tract(1)|skin(1)|pancreas(1)	250		all_cancers(2;1.88e-12)|Acute lymphoblastic leukemia(2;6.91e-39)|all_hematologic(2;2.7e-36)				GTTGGAGAGGAAAAAAAATCA	0.438			T	NTRK3|RUNX1|PDGFRB|ABL1|MN1|ABL2|FACL6|CHIC2|ARNT|JAK2|EVI1|CDX2|STL|HLXB9|MDS2|PER1|SYK|TTL|FGFR3|PAX5	congenital fibrosarcoma|multiple leukemia and lymphoma| secretory breast|MDS|ALL								4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	18371218	18371218	+	IGR	DEL	T	-	-			TCGA-CZ-4863-01A-01D-1501-10	TCGA-CZ-4863-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:18371218delT								RERGL (128104 upstream) : PIK3C2G (43256 downstream)																							tcattatgaatttttacaaga	0.000													4	2	---	---	---	---	
TM7SF3	51768	broad.mit.edu	37	12	27133041	27133041	+	Intron	DEL	T	-	-			TCGA-CZ-4863-01A-01D-1501-10	TCGA-CZ-4863-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:27133041delT	uc010sjl.1	-							NM_016551	NP_057635	Q9NS93	TM7S3_HUMAN	transmembrane 7 superfamily member 3 precursor							integral to membrane|plasma membrane				upper_aerodigestive_tract(2)	2	Colorectal(261;0.0847)					TAGGGAGGGGTCTGGGCTGAG	0.517													4	4	---	---	---	---	
ARID2	196528	broad.mit.edu	37	12	46232955	46232955	+	Intron	DEL	T	-	-			TCGA-CZ-4863-01A-01D-1501-10	TCGA-CZ-4863-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:46232955delT	uc001ros.1	+						ARID2_uc001ror.2_Intron|ARID2_uc009zkg.1_Intron|ARID2_uc009zkh.1_Intron|ARID2_uc001rot.1_Intron	NM_152641	NP_689854	Q68CP9	ARID2_HUMAN	AT rich interactive domain 2 (ARID, RFX-like)						chromatin modification|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|protein binding|zinc ion binding			ovary(6)|skin(3)|upper_aerodigestive_tract(1)	10	Lung SC(27;0.192)|Renal(347;0.236)	Lung NSC(34;0.106)|all_lung(34;0.22)	OV - Ovarian serous cystadenocarcinoma(5;0.00691)	GBM - Glioblastoma multiforme(48;0.0153)		cctaaaaatctttttttttaa	0.114													4	2	---	---	---	---	
PAWR	5074	broad.mit.edu	37	12	79988481	79988482	+	Intron	DEL	GT	-	-	rs111229471		TCGA-CZ-4863-01A-01D-1501-10	TCGA-CZ-4863-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:79988481_79988482delGT	uc001syx.2	-							NM_002583	NP_002574	Q96IZ0	PAWR_HUMAN	PRKC, apoptosis, WT1, regulator						actin filament bundle assembly|apoptosis|induction of apoptosis|negative regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	cytoplasm|nucleus|plasma membrane	actin binding|enzyme binding|leucine zipper domain binding|transcription corepressor activity				0						ATTTAACCTCgtgtgtgtgtgt	0.178													9	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	90393405	90393406	+	IGR	INS	-	TTC	TTC	rs148815598	by1000genomes	TCGA-CZ-4863-01A-01D-1501-10	TCGA-CZ-4863-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:90393405_90393406insTTC								LOC338758 (287677 upstream) : C12orf12 (952587 downstream)																							TTATGACAGAATTCTTTGTCAG	0.401													4	2	---	---	---	---	
CHST11	50515	broad.mit.edu	37	12	104954953	104954963	+	Intron	DEL	CAGATAGCAAT	-	-	rs145639240		TCGA-CZ-4863-01A-01D-1501-10	TCGA-CZ-4863-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:104954953_104954963delCAGATAGCAAT	uc001tkx.1	+						CHST11_uc001tky.2_Intron	NM_018413	NP_060883	Q9NPF2	CHSTB_HUMAN	carbohydrate sulfotransferase 11						chondroitin sulfate biosynthetic process	Golgi membrane|integral to membrane	chondroitin 4-sulfotransferase activity|N-acetylgalactosamine 4-O-sulfotransferase activity				0						CCATGGCAACCAGATAGCAATGGCTTTCAGA	0.218													4	3	---	---	---	---	
C12orf51	283450	broad.mit.edu	37	12	112669620	112669621	+	Intron	INS	-	T	T			TCGA-CZ-4863-01A-01D-1501-10	TCGA-CZ-4863-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:112669620_112669621insT	uc009zwc.2	-							NM_001109662	NP_001103132			chromosome 12 open reading frame 51											ovary(1)|lung(1)	2						ATCCACACTCATTTTTTTTTAA	0.361													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	119220602	119220602	+	IGR	DEL	G	-	-			TCGA-CZ-4863-01A-01D-1501-10	TCGA-CZ-4863-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:119220602delG								SUDS3 (364763 upstream) : SRRM4 (198794 downstream)																							GGGAAGCACTGGGGGGAGTAG	0.478													4	2	---	---	---	---	
FNDC3A	22862	broad.mit.edu	37	13	49748887	49748888	+	Intron	INS	-	AT	AT			TCGA-CZ-4863-01A-01D-1501-10	TCGA-CZ-4863-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:49748887_49748888insAT	uc001vcm.2	+						FNDC3A_uc001vcn.2_Intron|FNDC3A_uc001vco.2_Intron|FNDC3A_uc001vcp.1_Intron|FNDC3A_uc001vcq.2_Intron	NM_001079673	NP_001073141	Q9Y2H6	FND3A_HUMAN	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)		CACAGGAAACATTAAACTTACA	0.297													4	2	---	---	---	---	
SUGT1	10910	broad.mit.edu	37	13	53257141	53257141	+	Intron	DEL	A	-	-			TCGA-CZ-4863-01A-01D-1501-10	TCGA-CZ-4863-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:53257141delA	uc001vhc.2	+						SUGT1_uc001vhb.2_Intron|SUGT1_uc010thb.1_Intron|SUGT1_uc001vhd.2_Intron	NM_001130912	NP_001124384	Q9Y2Z0	SUGT1_HUMAN	suppressor of G2 allele of SKP1 isoform a						mitosis	kinetochore|ubiquitin ligase complex	binding				0		Lung NSC(96;0.00212)|Breast(56;0.00235)|Hepatocellular(98;0.065)|Prostate(109;0.0771)|all_neural(104;0.173)		GBM - Glioblastoma multiforme(99;3.25e-08)		tcatttttttaatgtggacaa	0.000													4	2	---	---	---	---	
LMO7	4008	broad.mit.edu	37	13	76383646	76383648	+	Intron	DEL	ACA	-	-			TCGA-CZ-4863-01A-01D-1501-10	TCGA-CZ-4863-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:76383646_76383648delACA	uc001vjv.2	+						LMO7_uc010thv.1_Intron|LMO7_uc001vjt.1_Intron|LMO7_uc010thw.1_Intron|LMO7_uc001vjw.1_Intron	NM_015842	NP_056667	Q8WWI1	LMO7_HUMAN	LIM domain only 7 isoform 2							cytoplasm|nucleus|ubiquitin ligase complex	ubiquitin-protein ligase activity|zinc ion binding			large_intestine(2)|ovary(1)|prostate(1)|skin(1)	5		Breast(118;0.0992)		GBM - Glioblastoma multiforme(99;0.0109)		TTTGGTTGCTACATAGACTAAAA	0.281													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	81291030	81291030	+	IGR	DEL	T	-	-	rs113516621		TCGA-CZ-4863-01A-01D-1501-10	TCGA-CZ-4863-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:81291030delT								SPRY2 (375944 upstream) : None (None downstream)																							tccttttctgttttttttttc	0.338													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	91104036	91104036	+	IGR	DEL	T	-	-			TCGA-CZ-4863-01A-01D-1501-10	TCGA-CZ-4863-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:91104036delT								MIR622 (220505 upstream) : LOC144776 (439172 downstream)																							tggatgcagattttcttccca	0.050													4	2	---	---	---	---	
NALCN	259232	broad.mit.edu	37	13	101737786	101737787	+	Intron	DEL	AT	-	-			TCGA-CZ-4863-01A-01D-1501-10	TCGA-CZ-4863-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:101737786_101737787delAT	uc001vox.1	-							NM_052867	NP_443099	Q8IZF0	NALCN_HUMAN	voltage gated channel like 1							integral to membrane	sodium channel activity|voltage-gated ion channel activity			ovary(8)|breast(4)|skin(2)|pancreas(1)|central_nervous_system(1)	16	all_neural(89;0.0438)|Medulloblastoma(90;0.163)|Lung SC(71;0.184)					tgattaatggatatgaaaatac	0.000													4	2	---	---	---	---	
MYO16	23026	broad.mit.edu	37	13	109517338	109517338	+	Intron	DEL	T	-	-			TCGA-CZ-4863-01A-01D-1501-10	TCGA-CZ-4863-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:109517338delT	uc001vqt.1	+						MYO16_uc010agk.1_Intron|MYO16_uc001vqu.1_Intron	NM_015011	NP_055826	Q9Y6X6	MYO16_HUMAN	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)			tataatattcttTTTTTTAAA	0.154													4	2	---	---	---	---	
FANCM	57697	broad.mit.edu	37	14	45628666	45628666	+	Intron	DEL	T	-	-			TCGA-CZ-4863-01A-01D-1501-10	TCGA-CZ-4863-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:45628666delT	uc001wwd.3	+						FANCM_uc001wwc.2_Intron|FANCM_uc010anf.2_Intron|FANCM_uc001wwe.3_Intron	NM_020937	NP_065988	Q8IYD8	FANCM_HUMAN	Fanconi anemia, complementation group M						DNA repair	Fanconi anaemia nuclear complex	ATP binding|ATP-dependent helicase activity|chromatin binding|DNA binding|nuclease activity|protein binding			ovary(3)|lung(2)|breast(2)	7						GTTTTGGAACTTTTTTTTTTT	0.139								Involved_in_tolerance_or_repair_of_DNA_crosslinks	Fanconi_Anemia				6	3	---	---	---	---	
SERPINA12	145264	broad.mit.edu	37	14	94984721	94984721	+	5'Flank	DEL	C	-	-			TCGA-CZ-4863-01A-01D-1501-10	TCGA-CZ-4863-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:94984721delC	uc001ydj.2	-							NM_173850	NP_776249	Q8IW75	SPA12_HUMAN	serine (or cysteine) proteinase inhibitor, clade						regulation of proteolysis	extracellular region	serine-type endopeptidase inhibitor activity			central_nervous_system(2)|ovary(1)|lung(1)	4				COAD - Colon adenocarcinoma(157;0.235)		ACTTCGCACACCCCACAGGAG	0.234													4	2	---	---	---	---	
HHIPL1	84439	broad.mit.edu	37	14	100123124	100123124	+	Intron	DEL	A	-	-			TCGA-CZ-4863-01A-01D-1501-10	TCGA-CZ-4863-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:100123124delA	uc010avs.2	+						HHIPL1_uc001ygl.1_Intron	NM_001127258	NP_001120730	Q96JK4	HIPL1_HUMAN	HHIP-like protein 1 isoform a						carbohydrate metabolic process	extracellular region|membrane	oxidoreductase activity, acting on the CH-OH group of donors, quinone or similar compound as acceptor|quinone binding|scavenger receptor activity			skin(2)	2		Melanoma(154;0.128)				aaaagaaaagaaaagaaagaa	0.000													5	3	---	---	---	---	
WDR25	79446	broad.mit.edu	37	14	100854481	100854481	+	Intron	DEL	T	-	-			TCGA-CZ-4863-01A-01D-1501-10	TCGA-CZ-4863-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:100854481delT	uc010avx.2	+						WDR25_uc001yhm.2_Intron|WDR25_uc001yhn.2_Intron|WDR25_uc010avy.2_Intron|WDR25_uc001yho.2_Intron	NM_001161476	NP_001154948	Q64LD2	WDR25_HUMAN	WD repeat domain 25												0		Melanoma(154;0.212)				TTGTGGAGCATTATGCAGATG	0.413													4	2	---	---	---	---	
OTUD7A	161725	broad.mit.edu	37	15	32140650	32140650	+	Intron	DEL	T	-	-	rs9806670		TCGA-CZ-4863-01A-01D-1501-10	TCGA-CZ-4863-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:32140650delT	uc001zfr.2	-						OTUD7A_uc001zfs.1_Intron|OTUD7A_uc010baa.1_Intron	NM_130901	NP_570971	Q8TE49	OTU7A_HUMAN	OTU domain containing 7A							cytoplasm|nucleus	cysteine-type peptidase activity|DNA binding|zinc ion binding			pancreas(1)|skin(1)	2		all_lung(180;1.6e-09)		all cancers(64;2.44e-19)|Epithelial(43;6.82e-14)|GBM - Glioblastoma multiforme(186;1.49e-05)|BRCA - Breast invasive adenocarcinoma(123;0.00189)|Lung(196;0.208)		GTGCTTTTTATTTTTAAAAAA	0.408													4	2	---	---	---	---	
CASC5	57082	broad.mit.edu	37	15	40894859	40894860	+	Intron	INS	-	A	A			TCGA-CZ-4863-01A-01D-1501-10	TCGA-CZ-4863-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:40894859_40894860insA	uc010bbs.1	+						CASC5_uc010ucq.1_Intron|CASC5_uc001zme.2_Intron|CASC5_uc010bbt.1_Intron	NM_170589	NP_733468	Q8NG31	CASC5_HUMAN	cancer susceptibility candidate 5 isoform 1						acrosome assembly|attachment of spindle microtubules to kinetochore|cell division|CenH3-containing nucleosome assembly at centromere|mitotic prometaphase|spindle assembly checkpoint	acrosomal vesicle|condensed chromosome kinetochore|cytosol|nucleoplasm	protein binding			breast(3)|central_nervous_system(1)|skin(1)	5		all_cancers(109;2.03e-18)|all_epithelial(112;4.26e-15)|Lung NSC(122;1.12e-10)|all_lung(180;2.59e-09)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.0946)		GBM - Glioblastoma multiforme(113;4.99e-05)|BRCA - Breast invasive adenocarcinoma(123;0.0861)|COAD - Colon adenocarcinoma(120;0.211)		taattttgtattttggtagaga	0.000													9	4	---	---	---	---	
TTBK2	146057	broad.mit.edu	37	15	43075081	43075081	+	Intron	DEL	T	-	-			TCGA-CZ-4863-01A-01D-1501-10	TCGA-CZ-4863-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:43075081delT	uc001zqo.2	-						TTBK2_uc010bcy.2_Intron|TTBK2_uc001zqp.2_Intron|TTBK2_uc010bcz.1_Intron	NM_173500	NP_775771	Q6IQ55	TTBK2_HUMAN	tau tubulin kinase 2						cell death		ATP binding|protein serine/threonine kinase activity			ovary(2)|lung(2)|stomach(1)|pancreas(1)|skin(1)	7		all_cancers(109;6.11e-16)|all_epithelial(112;5.5e-14)|Lung NSC(122;1.76e-08)|all_lung(180;6.04e-08)|Melanoma(134;0.0179)|Colorectal(260;0.216)		GBM - Glioblastoma multiforme(94;3.23e-07)		TCACTAGTGATTTTTTTTTTG	0.403													3	3	---	---	---	---	
PPIP5K1	9677	broad.mit.edu	37	15	43864900	43864900	+	Intron	DEL	T	-	-			TCGA-CZ-4863-01A-01D-1501-10	TCGA-CZ-4863-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:43864900delT	uc001zrw.2	-						PPIP5K1_uc001zrx.1_Intron|PPIP5K1_uc001zru.2_Intron|PPIP5K1_uc001zry.3_Intron|PPIP5K1_uc001zrv.2_Intron|PPIP5K1_uc001zrz.1_Intron	NM_001130858	NP_001124330	Q6PFW1	VIP1_HUMAN	histidine acid phosphatase domain containing 2A						inositol metabolic process	cytosol	acid phosphatase activity|ATP binding|diphosphoinositol-pentakisphosphate kinase activity|inositol 1,3,4,5,6-pentakisphosphate kinase activity|inositol hexakisphosphate 5-kinase activity				0						GATAAGCAAGTTTTTTTTTTT	0.428													4	2	---	---	---	---	
DENND4A	10260	broad.mit.edu	37	15	65957481	65957481	+	Intron	DEL	A	-	-			TCGA-CZ-4863-01A-01D-1501-10	TCGA-CZ-4863-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:65957481delA	uc002aph.2	-						DENND4A_uc002api.2_Intron	NM_005848	NP_005839	Q7Z401	MYCPP_HUMAN	DENN/MADD domain containing 4A isoform 2						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|protein binding			ovary(2)|haematopoietic_and_lymphoid_tissue(1)|skin(1)	4						aacaaaaaacaaaaaaAAACC	0.363													9	4	---	---	---	---	
KIF23	9493	broad.mit.edu	37	15	69737984	69737984	+	Intron	DEL	G	-	-			TCGA-CZ-4863-01A-01D-1501-10	TCGA-CZ-4863-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:69737984delG	uc002asb.2	+						KIF23_uc002asc.2_Intron|KIF23_uc010bii.2_Intron|KIF23_uc010ukc.1_Intron	NM_138555	NP_612565	Q02241	KIF23_HUMAN	kinesin family member 23 isoform 1						blood coagulation|cytokinesis|microtubule-based movement|mitosis|mitotic spindle elongation	cytosol|kinesin complex|microtubule|midbody|nucleoplasm|spindle	ATP binding|microtubule motor activity|protein binding				0						ATTTGAATATGGGCAACAGGG	0.308													4	2	---	---	---	---	
CPEB1	64506	broad.mit.edu	37	15	83221050	83221050	+	Intron	DEL	T	-	-	rs67298411		TCGA-CZ-4863-01A-01D-1501-10	TCGA-CZ-4863-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:83221050delT	uc002bit.2	-						CPEB1_uc002biq.2_Intron|CPEB1_uc002bir.2_Intron|CPEB1_uc002bis.2_Intron|CPEB1_uc010uod.1_Intron|CPEB1_uc010uoe.1_Intron|CPEB1_uc002biu.2_Intron|CPEB1_uc010uof.1_Intron|CPEB1_uc002biv.2_Intron|CPEB1_uc002bip.2_Intron	NM_001079533	NP_001073001	Q9BZB8	CPEB1_HUMAN	cytoplasmic polyadenylation element binding						mRNA processing|regulation of translation	cell junction|cytoplasmic mRNA processing body|dendrite|postsynaptic density|postsynaptic membrane	nucleotide binding|RNA binding			ovary(1)|breast(1)	2			BRCA - Breast invasive adenocarcinoma(143;0.229)			CAAAGGTTGCTTTTTTTTTTT	0.443													3	4	---	---	---	---	
ADAMTSL3	57188	broad.mit.edu	37	15	84557760	84557760	+	Intron	DEL	T	-	-			TCGA-CZ-4863-01A-01D-1501-10	TCGA-CZ-4863-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:84557760delT	uc002bjz.3	+						ADAMTSL3_uc010bmt.1_Intron|ADAMTSL3_uc010bmu.1_Intron	NM_207517	NP_997400	P82987	ATL3_HUMAN	ADAMTS-like 3 precursor							proteinaceous extracellular matrix	metallopeptidase activity|zinc ion binding			ovary(6)|central_nervous_system(5)|lung(5)|large_intestine(4)|breast(3)|skin(2)|kidney(1)|pancreas(1)	27			BRCA - Breast invasive adenocarcinoma(143;0.211)			AAAAATTACCTTTTTTTGAAA	0.348													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	84858138	84858139	+	IGR	INS	-	T	T	rs71453232		TCGA-CZ-4863-01A-01D-1501-10	TCGA-CZ-4863-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:84858138_84858139insT								ADAMTSL3 (149547 upstream) : LOC388152 (9461 downstream)																							TGGGGAGCTGGTGCAGAGGCCT	0.599													6	3	---	---	---	---	
PGP	283871	broad.mit.edu	37	16	2267605	2267605	+	5'Flank	DEL	A	-	-			TCGA-CZ-4863-01A-01D-1501-10	TCGA-CZ-4863-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:2267605delA	uc002cpk.1	-						PGP_uc010uvz.1_5'Flank	NM_001042371	NP_001035830	A6NDG6	PGP_HUMAN	phosphoglycolate phosphatase						carbohydrate metabolic process		phosphoglycolate phosphatase activity			skin(1)	1						GGCTGGGAGGAAAGTGCGCTT	0.587													4	2	---	---	---	---	
PDXDC1	23042	broad.mit.edu	37	16	15131655	15131655	+	Intron	DEL	A	-	-			TCGA-CZ-4863-01A-01D-1501-10	TCGA-CZ-4863-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:15131655delA	uc002ddc.2	+							NM_015027	NP_055842	Q6P996	PDXD1_HUMAN	pyridoxal-dependent decarboxylase domain						carboxylic acid metabolic process		carboxy-lyase activity|protein binding|pyridoxal phosphate binding			skin(1)	1					Pyridoxal Phosphate(DB00114)	ATTACCGACCAAAAAAAAAAC	0.343													7	4	---	---	---	---	
GTF3C1	2975	broad.mit.edu	37	16	27489513	27489513	+	Intron	DEL	A	-	-			TCGA-CZ-4863-01A-01D-1501-10	TCGA-CZ-4863-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:27489513delA	uc002dov.1	-						GTF3C1_uc002dou.2_Intron	NM_001520	NP_001511	Q12789	TF3C1_HUMAN	general transcription factor IIIC, polypeptide							transcription factor TFIIIC complex	DNA binding|protein binding			ovary(2)|pancreas(1)|breast(1)|skin(1)	5						aaaaggaaagaaaaaaaaaag	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	29044908	29044908	+	Intron	DEL	A	-	-			TCGA-CZ-4863-01A-01D-1501-10	TCGA-CZ-4863-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:29044908delA	uc010vct.1	-											RecName: Full=Nuclear pore complex-interacting protein-like 2; Flags: Precursor;																		agtatgaaagaaaaacggcca	0.095													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	33053545	33053545	+	IGR	DEL	A	-	-			TCGA-CZ-4863-01A-01D-1501-10	TCGA-CZ-4863-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:33053545delA								SLC6A10P (157082 upstream) : MIR1826 (911963 downstream)																							TGCACaaaataattttctaaa	0.219													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	33972256	33972256	+	IGR	DEL	C	-	-			TCGA-CZ-4863-01A-01D-1501-10	TCGA-CZ-4863-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:33972256delC								MIR1826 (6664 upstream) : UBE2MP1 (431546 downstream)																							cctttctattcattgaccagt	0.000													5	4	---	---	---	---	
DDX19A	55308	broad.mit.edu	37	16	70365382	70365383	+	Intron	INS	-	T	T			TCGA-CZ-4863-01A-01D-1501-10	TCGA-CZ-4863-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:70365382_70365383insT	uc002eys.2	+						DDX19B_uc010vly.1_Intron|DDX19B_uc010vlv.1_Intron|DDX19B_uc010vlw.1_Intron|DDX19B_uc002eyo.2_Intron|DDX19B_uc002eyp.2_Intron|DDX19B_uc002eyq.2_Intron|DDX19B_uc002eyr.2_Intron|DDX19B_uc010vlx.1_Intron|uc002eyt.2_Intron	NM_007242	NP_009173	Q9NUU7	DD19A_HUMAN	DEAD (Asp-Glu-Ala-As) box polypeptide 19 isoform						mRNA transport|protein transport|transmembrane transport	cytoplasm|nuclear membrane|nuclear pore	ATP binding|ATP-dependent helicase activity|RNA binding				0		Ovarian(137;0.221)				TGAAAGAAAAAtttttttttga	0.144													4	2	---	---	---	---	
VAC14	55697	broad.mit.edu	37	16	70765775	70765775	+	Intron	DEL	A	-	-			TCGA-CZ-4863-01A-01D-1501-10	TCGA-CZ-4863-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:70765775delA	uc002ezm.2	-						VAC14_uc010cfw.2_Intron|VAC14_uc002ezn.2_Intron|VAC14_uc002ezl.2_5'Flank|VAC14_uc010cfx.1_Intron	NM_018052	NP_060522	Q08AM6	VAC14_HUMAN	Vac14 homolog						interspecies interaction between organisms	endoplasmic reticulum|endosome membrane|microsome	protein binding|receptor activity			pancreas(1)|skin(1)	2		Ovarian(137;0.0699)				TCGTAACTTGAAAAAAAAAAA	0.403													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	12246872	12246872	+	IGR	DEL	T	-	-			TCGA-CZ-4863-01A-01D-1501-10	TCGA-CZ-4863-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:12246872delT								MAP2K4 (199822 upstream) : MYOCD (322335 downstream)																							GGCATGAAGATTTTTTTTTAC	0.418													4	2	---	---	---	---	
NF1	4763	broad.mit.edu	37	17	29456988	29456988	+	Intron	DEL	T	-	-			TCGA-CZ-4863-01A-01D-1501-10	TCGA-CZ-4863-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:29456988delT	uc002hgg.2	+						NF1_uc002hge.1_Intron|NF1_uc002hgf.1_Intron|NF1_uc002hgh.2_Intron	NM_001042492	NP_001035957	P21359	NF1_HUMAN	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.0?(5)|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)		cagtcgtttgttttagaggaa	0.000			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)			4	2	---	---	---	---	
C17orf53	78995	broad.mit.edu	37	17	42224396	42224397	+	Intron	INS	-	GT	GT	rs143062329		TCGA-CZ-4863-01A-01D-1501-10	TCGA-CZ-4863-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:42224396_42224397insGT	uc002ifi.1	+						C17orf53_uc010czq.1_Intron|C17orf53_uc002ifj.1_Intron|C17orf53_uc002ifk.1_5'Flank	NM_024032	NP_076937	Q8N3J3	CQ053_HUMAN	hypothetical protein LOC78995												0		Breast(137;0.0364)|Prostate(33;0.0376)		BRCA - Breast invasive adenocarcinoma(366;0.114)		ATCTCtgtgtagtgtgtgtgtg	0.351													6	3	---	---	---	---	
TEX14	56155	broad.mit.edu	37	17	56634637	56634637	+	Intron	DEL	T	-	-			TCGA-CZ-4863-01A-01D-1501-10	TCGA-CZ-4863-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:56634637delT	uc010dcz.1	-						TEX14_uc002iwr.1_Intron|TEX14_uc002iws.1_Intron|TEX14_uc010dda.1_Intron	NM_198393	NP_938207	Q8IWB6	TEX14_HUMAN	testis expressed sequence 14 isoform a							cytoplasm	ATP binding|protein kinase activity			stomach(4)|lung(3)|breast(3)|ovary(3)|upper_aerodigestive_tract(1)|large_intestine(1)|skin(1)|pancreas(1)	17	Medulloblastoma(34;0.127)|all_neural(34;0.237)					AAACCTGttcttttttttttt	0.194													5	4	---	---	---	---	
USP32	84669	broad.mit.edu	37	17	58367138	58367138	+	Intron	DEL	A	-	-			TCGA-CZ-4863-01A-01D-1501-10	TCGA-CZ-4863-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:58367138delA	uc002iyo.1	-						USP32_uc010wov.1_Intron	NM_032582	NP_115971	Q8NFA0	UBP32_HUMAN	ubiquitin specific protease 32						protein deubiquitination|ubiquitin-dependent protein catabolic process	Golgi apparatus|membrane	calcium ion binding|cysteine-type peptidase activity|ubiquitin thiolesterase activity			lung(2)|breast(2)|large_intestine(1)	5	all_neural(34;0.0878)|Medulloblastoma(34;0.0922)		Epithelial(12;2.02e-11)|all cancers(12;5.23e-10)|Colorectal(3;0.198)			TTTGATCAGGAAAAAAAAGAA	0.343													4	2	---	---	---	---	
MGAT5B	146664	broad.mit.edu	37	17	74944960	74944961	+	3'UTR	INS	-	G	G			TCGA-CZ-4863-01A-01D-1501-10	TCGA-CZ-4863-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:74944960_74944961insG	uc002jti.2	+	16					MGAT5B_uc002jth.2_3'UTR|MGAT5B_uc002jtj.2_3'UTR	NM_198955	NP_945193	Q3V5L5	MGT5B_HUMAN	N-acetylglucosaminyltranferase VB isoform 2							Golgi membrane|integral to membrane	alpha-1,6-mannosyl-glycoprotein 6-beta-N-acetylglucosaminyltransferase activity|metal ion binding			ovary(2)|skin(1)	3						ACGCTGGCTCTCTCCTGCCGCG	0.683													4	2	---	---	---	---	
RAB12	201475	broad.mit.edu	37	18	8621024	8621024	+	Intron	DEL	C	-	-			TCGA-CZ-4863-01A-01D-1501-10	TCGA-CZ-4863-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:8621024delC	uc002knp.2	+							NM_001025300	NP_001020471	Q6IQ22	RAB12_HUMAN	RAB12, member RAS oncogene family						protein transport|small GTPase mediated signal transduction	Golgi membrane	GTP binding				0						CAGGGACTGTCCCCATCAACA	0.468													4	2	---	---	---	---	
NAPG	8774	broad.mit.edu	37	18	10548014	10548014	+	Intron	DEL	G	-	-	rs61368477	by1000genomes	TCGA-CZ-4863-01A-01D-1501-10	TCGA-CZ-4863-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:10548014delG	uc002kon.2	+						NAPG_uc010wzr.1_Intron|NAPG_uc002koo.2_Intron|NAPG_uc002kop.2_Intron	NM_003826	NP_003817	Q99747	SNAG_HUMAN	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						Gtcaaagtgcggtccccagac	0.214													4	2	---	---	---	---	
GNAL	2774	broad.mit.edu	37	18	11745829	11745829	+	Intron	DEL	A	-	-			TCGA-CZ-4863-01A-01D-1501-10	TCGA-CZ-4863-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:11745829delA	uc002kqc.2	+							NM_182978	NP_892023	P38405	GNAL_HUMAN	guanine nucleotide binding protein (G protein),						activation of adenylate cyclase activity by dopamine receptor signaling pathway|inhibition of adenylate cyclase activity by G-protein signaling pathway|sensory perception of smell|synaptic transmission	heterotrimeric G-protein complex	adenylate cyclase activity|G-protein beta/gamma-subunit complex binding|G-protein-coupled receptor binding|GTP binding|GTPase activity|signal transducer activity			ovary(1)	1						CTACAACCACAAAAAAAAGAT	0.388													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	15028847	15028847	+	IGR	DEL	G	-	-			TCGA-CZ-4863-01A-01D-1501-10	TCGA-CZ-4863-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:15028847delG								ANKRD30B (176110 upstream) : LOC644669 (284708 downstream)																							TATAGATTCTGGAGTCAGCAA	0.269													4	2	---	---	---	---	
CHST9	83539	broad.mit.edu	37	18	24524596	24524596	+	Intron	DEL	C	-	-			TCGA-CZ-4863-01A-01D-1501-10	TCGA-CZ-4863-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:24524596delC	uc002kwd.2	-						C18orf16_uc010xbm.1_Intron|CHST9_uc002kwc.2_Intron|CHST9_uc002kwe.2_Intron	NM_031422	NP_113610	Q7L1S5	CHST9_HUMAN	GalNAc-4-sulfotransferase 2						carbohydrate biosynthetic process|glycosaminoglycan metabolic process|hormone biosynthetic process|proteoglycan biosynthetic process|sulfur compound metabolic process	extracellular region|Golgi membrane|integral to membrane	N-acetylgalactosamine 4-O-sulfotransferase activity			ovary(2)|skin(1)	3	all_lung(6;0.0145)|Ovarian(20;0.124)					ATTAAACTTTCACAGATAAAT	0.328													9	5	---	---	---	---	
KIAA1012	22878	broad.mit.edu	37	18	29438020	29438020	+	Intron	DEL	A	-	-			TCGA-CZ-4863-01A-01D-1501-10	TCGA-CZ-4863-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:29438020delA	uc002kxc.3	-						KIAA1012_uc002kxb.3_Intron|KIAA1012_uc002kxd.3_Intron	NM_014939	NP_055754	Q9Y2L5	TPPC8_HUMAN	hypothetical protein LOC22878						ER to Golgi vesicle-mediated transport	cis-Golgi network					0						ACTTTAAGACACTTTTTTTTT	0.284													5	3	---	---	---	---	
DCC	1630	broad.mit.edu	37	18	50413182	50413182	+	Intron	DEL	A	-	-			TCGA-CZ-4863-01A-01D-1501-10	TCGA-CZ-4863-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:50413182delA	uc002lfe.1	+						DCC_uc010xdr.1_Intron	NM_005215	NP_005206	P43146	DCC_HUMAN	netrin receptor DCC precursor						apoptosis|induction of apoptosis|negative regulation of collateral sprouting|negative regulation of dendrite development	cytosol|integral to membrane				skin(8)|ovary(6)|upper_aerodigestive_tract(1)|large_intestine(1)|central_nervous_system(1)	17		all_cancers(7;0.11)|all_epithelial(6;0.00126)		Colorectal(16;0.0251)|COAD - Colon adenocarcinoma(17;0.0942)		gttggttgttaaaatttggtg	0.035													2	4	---	---	---	---	
UHRF1	29128	broad.mit.edu	37	19	4941811	4941811	+	Frame_Shift_Del	DEL	G	-	-			TCGA-CZ-4863-01A-01D-1501-10	TCGA-CZ-4863-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:4941811delG	uc002mbo.2	+	7	1109	c.941delG	c.(940-942)CGGfs	p.R314fs	UHRF1_uc010xik.1_Intron|UHRF1_uc010duf.2_RNA|UHRF1_uc002mbp.2_Frame_Shift_Del_p.R327fs	NM_001048201	NP_001041666	Q96T88	UHRF1_HUMAN	ubiquitin-like with PHD and ring finger domains	314	PHD-type.				cell cycle|cell proliferation|DNA repair|regulation of transcription from RNA polymerase II promoter	nucleus	acid-amino acid ligase activity|methyl-CpG binding|methylated histone residue binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			lung(2)	2				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0276)		AGACTCTGCCGGGTCTGCGCC	0.697													4	2	---	---	---	---	
DOCK6	57572	broad.mit.edu	37	19	11357605	11357605	+	Intron	DEL	G	-	-			TCGA-CZ-4863-01A-01D-1501-10	TCGA-CZ-4863-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:11357605delG	uc002mqs.3	-							NM_020812	NP_065863	Q96HP0	DOCK6_HUMAN	dedicator of cytokinesis 6						blood coagulation	cytosol	GTP binding|GTPase binding|guanyl-nucleotide exchange factor activity			ovary(2)|skin(1)	3						cttcctcactgggtctccatg	0.134													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	1235305	1235306	+	IGR	INS	-	T	T	rs142754247	by1000genomes	TCGA-CZ-4863-01A-01D-1501-10	TCGA-CZ-4863-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:1235305_1235306insT								RAD21L1 (160 upstream) : SNPH (11654 downstream)																							ATTCTGTTTTGTTTTtttttgt	0.168													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	10607544	10607544	+	IGR	DEL	G	-	-			TCGA-CZ-4863-01A-01D-1501-10	TCGA-CZ-4863-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:10607544delG								C20orf94 (3519 upstream) : JAG1 (10788 downstream)																							GATATATCTTGGGGACCACAA	0.343													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	22362186	22362187	+	IGR	DEL	TC	-	-			TCGA-CZ-4863-01A-01D-1501-10	TCGA-CZ-4863-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:22362186_22362187delTC								PAX1 (665566 upstream) : LOC284788 (18784 downstream)																							TGCAAAGAGGtctctctctctc	0.287													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	9843312	9843313	+	IGR	DEL	AA	-	-			TCGA-CZ-4863-01A-01D-1501-10	TCGA-CZ-4863-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:9843312_9843313delAA								None (None upstream) : None (None downstream)																							AAAGAAAACCAAAAGTCATTCT	0.287													2	4	---	---	---	---	
BAGE2	85319	broad.mit.edu	37	21	11064287	11064288	+	Intron	INS	-	A	A	rs148820757		TCGA-CZ-4863-01A-01D-1501-10	TCGA-CZ-4863-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:11064287_11064288insA	uc002yit.1	-						BAGE_uc002yix.2_Intron	NM_182482	NP_872288			B melanoma antigen family, member 2 precursor												0			Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723)	UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247)		GCTTCCACAGCAATCTTTCTAA	0.327													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	23809223	23809224	+	IGR	DEL	TG	-	-			TCGA-CZ-4863-01A-01D-1501-10	TCGA-CZ-4863-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:23809223_23809224delTG								NCAM2 (898009 upstream) : None (None downstream)																							TTTTTCCCTTTGTTTTTCAACC	0.376													3	3	---	---	---	---	
BACE2	25825	broad.mit.edu	37	21	42598069	42598069	+	Intron	DEL	T	-	-	rs67925412		TCGA-CZ-4863-01A-01D-1501-10	TCGA-CZ-4863-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:42598069delT	uc002yyw.2	+						BACE2_uc002yyx.2_Intron|BACE2_uc002yyy.2_Intron	NM_012105	NP_036237	Q9Y5Z0	BACE2_HUMAN	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)				GTCAGTATACTTTTTTTTTGT	0.303													3	3	---	---	---	---	
DIP2A	23181	broad.mit.edu	37	21	47912061	47912061	+	Intron	DEL	T	-	-			TCGA-CZ-4863-01A-01D-1501-10	TCGA-CZ-4863-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:47912061delT	uc002zjo.2	+						DIP2A_uc011afy.1_Intron|DIP2A_uc011afz.1_Intron|DIP2A_uc002zjl.2_Intron|DIP2A_uc002zjm.2_Intron|DIP2A_uc010gql.2_Intron|DIP2A_uc002zjn.2_Intron	NM_015151	NP_055966	Q14689	DIP2A_HUMAN	disco-interacting protein 2A isoform a						multicellular organismal development	nucleus	catalytic activity|transcription factor binding			ovary(2)	2	Breast(49;0.0933)			Epithelial(3;3.12e-06)|OV - Ovarian serous cystadenocarcinoma(3;5.68e-06)|all cancers(3;4.08e-05)|Colorectal(79;0.0129)|COAD - Colon adenocarcinoma(84;0.0824)		gtttgtgatctttttttttag	0.000													4	2	---	---	---	---	
PITPNB	23760	broad.mit.edu	37	22	28303569	28303569	+	Intron	DEL	T	-	-			TCGA-CZ-4863-01A-01D-1501-10	TCGA-CZ-4863-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:28303569delT	uc003adk.2	-						PITPNB_uc011akh.1_Intron|PITPNB_uc003adl.2_Intron	NM_012399	NP_036531	P48739	PIPNB_HUMAN	phosphatidylinositol transfer protein, beta						lipid metabolic process|transport	Golgi apparatus	lipid binding			skin(1)	1						CCCTCTTGCCTTTTTCCCTTT	0.453													4	2	---	---	---	---	
EFCAB6	64800	broad.mit.edu	37	22	44137361	44137361	+	Intron	DEL	T	-	-			TCGA-CZ-4863-01A-01D-1501-10	TCGA-CZ-4863-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:44137361delT	uc003bdy.1	-						EFCAB6_uc003bdz.1_Intron|EFCAB6_uc010gzi.1_Intron|EFCAB6_uc011aqa.1_Intron|EFCAB6_uc003bea.1_Intron|EFCAB6_uc003beb.3_Intron	NM_022785	NP_073622	Q5THR3	EFCB6_HUMAN	CAP-binding protein complex interacting protein						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	calcium ion binding			ovary(3)|skin(2)|upper_aerodigestive_tract(1)|pancreas(1)	7		Ovarian(80;0.0247)|all_neural(38;0.025)				aaagcgcgccttcatactctg	0.040													4	2	---	---	---	---	
OFD1	8481	broad.mit.edu	37	X	13754423	13754423	+	Intron	DEL	A	-	-	rs34932784		TCGA-CZ-4863-01A-01D-1501-10	TCGA-CZ-4863-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:13754423delA	uc004cvp.3	+						OFD1_uc004cvr.3_Intron|OFD1_uc011mil.1_Intron|OFD1_uc004cvq.3_Intron|OFD1_uc010nen.2_Intron|OFD1_uc004cvs.3_Intron|OFD1_uc004cvu.3_Intron|OFD1_uc004cvv.3_Intron|TRAPPC2_uc010nek.1_5'Flank|TRAPPC2_uc010nel.1_5'Flank|TRAPPC2_uc010nem.1_5'Flank	NM_003611	NP_003602	O75665	OFD1_HUMAN	oral-facial-digital syndrome 1						cilium movement involved in determination of left/right asymmetry|G2/M transition of mitotic cell cycle	centriole|cilium|cytosol|microtubule basal body|nuclear membrane	alpha-tubulin binding|gamma-tubulin binding				0						GGGGTAAGACAAAGTGTGCAG	0.453													1	5	---	---	---	---	
BEND2	139105	broad.mit.edu	37	X	18192525	18192526	+	Intron	INS	-	T	T			TCGA-CZ-4863-01A-01D-1501-10	TCGA-CZ-4863-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:18192525_18192526insT	uc004cyj.3	-						BEND2_uc010nfb.2_Intron	NM_153346	NP_699177	Q8NDZ0	BEND2_HUMAN	BEN domain containing 2											ovary(3)|kidney(1)|central_nervous_system(1)	5						TACTGTGTGTCGCAATACTATC	0.480													4	2	---	---	---	---	
MAP3K15	389840	broad.mit.edu	37	X	19380252	19380252	+	Intron	DEL	T	-	-			TCGA-CZ-4863-01A-01D-1501-10	TCGA-CZ-4863-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:19380252delT	uc004czk.1	-						MAP3K15_uc004czj.1_Intron|MAP3K15_uc004czi.1_Intron	NM_001001671	NP_001001671	Q6ZN16	M3K15_HUMAN	mitogen-activated protein kinase kinase kinase								ATP binding|MAP kinase kinase kinase activity|metal ion binding			ovary(3)|lung(2)|stomach(1)|skin(1)	7	Hepatocellular(33;0.183)					tcatgtgccctttacaatcag	0.124													4	2	---	---	---	---	
FAAH2	158584	broad.mit.edu	37	X	57368049	57368049	+	Intron	DEL	T	-	-			TCGA-CZ-4863-01A-01D-1501-10	TCGA-CZ-4863-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:57368049delT	uc004dvc.2	+							NM_174912	NP_777572	Q6GMR7	FAAH2_HUMAN	fatty acid amide hydrolase 2							integral to membrane	carbon-nitrogen ligase activity, with glutamine as amido-N-donor|hydrolase activity			ovary(3)	3						ataatagttgttttttttttt	0.005										HNSCC(52;0.14)			5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	135063968	135063968	+	IGR	DEL	C	-	-			TCGA-CZ-4863-01A-01D-1501-10	TCGA-CZ-4863-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:135063968delC								MMGT1 (7780 upstream) : SLC9A6 (3618 downstream)																							TCCAGAAACACCCCCTTATGA	0.294													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	137564677	137564677	+	IGR	DEL	C	-	-			TCGA-CZ-4863-01A-01D-1501-10	TCGA-CZ-4863-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:137564677delC								ZIC3 (910420 upstream) : LOC158696 (132215 downstream)																							AGGCACATGTCCTCAGCTCAC	0.552													4	2	---	---	---	---	
