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
ZBTB8B	728116	broad.mit.edu	37	1	32950945	32950945	+	Missense_Mutation	SNP	G	T	T			TCGA-CZ-5460-01A-01D-1501-10	TCGA-CZ-5460-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:32950945G>T	uc001bvl.3	+	4	1504	c.1414G>T	c.(1414-1416)GAC>TAC	p.D472Y	ZBTB8A_uc001bvk.2_Intron	NM_001145720	NP_001139192	Q8NAP8	ZBT8B_HUMAN	zinc finger and BTB domain containing 8B	472					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0						TGAGGAAAATGACCCTGCTGG	0.473													43	66	---	---	---	---	PASS
ZMPSTE24	10269	broad.mit.edu	37	1	40726535	40726535	+	Missense_Mutation	SNP	C	T	T			TCGA-CZ-5460-01A-01D-1501-10	TCGA-CZ-5460-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:40726535C>T	uc001cfg.2	+	2	359	c.148C>T	c.(148-150)CAT>TAT	p.H50Y	uc001cff.2_5'Flank	NM_005857	NP_005848	O75844	FACE1_HUMAN	zinc metallopeptidase STE24	50						endoplasmic reticulum membrane|Golgi membrane|integral to membrane	metal ion binding|metalloexopeptidase activity				0	Lung NSC(20;4.38e-06)|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;6.3e-18)			AACAACAACTCATGTACCACC	0.333													50	178	---	---	---	---	PASS
LRRC40	55631	broad.mit.edu	37	1	70616870	70616870	+	Silent	SNP	A	G	G			TCGA-CZ-5460-01A-01D-1501-10	TCGA-CZ-5460-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:70616870A>G	uc001der.1	-	13	1510	c.1458T>C	c.(1456-1458)TCT>TCC	p.S486S		NM_017768	NP_060238	Q9H9A6	LRC40_HUMAN	leucine rich repeat containing 40	486	LRR 16.									ovary(1)	1						CTTCTGGCAAAGAATTTAAAA	0.269													5	98	---	---	---	---	PASS
PKN2	5586	broad.mit.edu	37	1	89236126	89236126	+	Missense_Mutation	SNP	A	T	T			TCGA-CZ-5460-01A-01D-1501-10	TCGA-CZ-5460-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:89236126A>T	uc001dmn.2	+	4	938	c.596A>T	c.(595-597)CAG>CTG	p.Q199L	PKN2_uc001dmm.1_Missense_Mutation_p.Q199L|PKN2_uc010osp.1_Missense_Mutation_p.Q199L|PKN2_uc010osq.1_Missense_Mutation_p.Q42L|PKN2_uc009wcv.2_Missense_Mutation_p.Q199L	NM_006256	NP_006247	Q16513	PKN2_HUMAN	protein kinase N2	199	REM 2.				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)		CAGGCAGTCCAGACTAATGAA	0.408													52	73	---	---	---	---	PASS
NBPF10	100132406	broad.mit.edu	37	1	145293269	145293269	+	5'Flank	SNP	G	A	A	rs61350760	by1000genomes	TCGA-CZ-5460-01A-01D-1501-10	TCGA-CZ-5460-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:145293269G>A	uc001end.3	+						NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|NBPF10_uc001emp.3_5'UTR|NOTCH2NL_uc010oyh.1_Intron|NBPF10_uc001emq.1_5'UTR	NM_001039703	NP_001034792	A6NDV3	A6NDV3_HUMAN	hypothetical protein LOC100132406												0	all_hematologic(923;0.032)			Colorectal(1306;1.36e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.00258)		TTTCACAACAGTAAGTTAAGA	0.423													4	15	---	---	---	---	PASS
QSOX1	5768	broad.mit.edu	37	1	180166433	180166433	+	3'UTR	SNP	C	A	A			TCGA-CZ-5460-01A-01D-1501-10	TCGA-CZ-5460-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:180166433C>A	uc001gnz.2	+	12					QSOX1_uc001gny.2_Intron|QSOX1_uc001goa.2_Intron|QSOX1_uc001goc.2_Intron|FLJ23867_uc001god.3_5'Flank	NM_002826	NP_002817	O00391	QSOX1_HUMAN	quiescin Q6 sulfhydryl oxidase 1 isoform a						cell redox homeostasis|protein thiol-disulfide exchange	extracellular space|integral to Golgi membrane	flavin-linked sulfhydryl oxidase activity			ovary(1)|central_nervous_system(1)	2						GCAGCTCAGTCCCTGGCCTCT	0.572													12	29	---	---	---	---	PASS
DNAH14	127602	broad.mit.edu	37	1	225266907	225266907	+	Splice_Site	SNP	A	T	T			TCGA-CZ-5460-01A-01D-1501-10	TCGA-CZ-5460-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:225266907A>T	uc001how.2	+	18	2640	c.2425_splice	c.e18-2	p.V809_splice		NM_001373	NP_001364	Q0VDD8	DYH14_HUMAN	dynein, axonemal, heavy polypeptide 14 isoform						microtubule-based movement	cilium axoneme|cytoplasm|dynein complex|microtubule	ATP binding|microtubule motor activity			central_nervous_system(1)	1						TGTTGATTTCAGGTTGTGGAA	0.299													21	54	---	---	---	---	PASS
OR2W5	441932	broad.mit.edu	37	1	247655361	247655361	+	Missense_Mutation	SNP	G	A	A			TCGA-CZ-5460-01A-01D-1501-10	TCGA-CZ-5460-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:247655361G>A	uc001icz.1	+	1	932	c.932G>A	c.(931-933)GGC>GAC	p.G311D		NM_001004698	NP_001004698	A6NFC9	OR2W5_HUMAN	olfactory receptor, family 2, subfamily W,	311					sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)|breast(1)|skin(1)	3	all_cancers(71;4.51e-05)|all_epithelial(71;1.3e-05)|Breast(184;0.0149)|Ovarian(71;0.0377)|all_lung(81;0.0662)|Lung NSC(105;0.0724)	all_cancers(173;0.222)	OV - Ovarian serous cystadenocarcinoma(106;0.0188)			GGAGAAAGGGGCTGGGGAGCC	0.488													5	4	---	---	---	---	PASS
SLC30A6	55676	broad.mit.edu	37	2	32422862	32422862	+	Missense_Mutation	SNP	C	T	T			TCGA-CZ-5460-01A-01D-1501-10	TCGA-CZ-5460-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:32422862C>T	uc002roe.1	+	10	669	c.632C>T	c.(631-633)GCT>GTT	p.A211V	SLC30A6_uc002rof.1_Missense_Mutation_p.A251V|SLC30A6_uc010ymw.1_Missense_Mutation_p.A182V|SLC30A6_uc010ezr.1_Missense_Mutation_p.A211V|SLC30A6_uc002rog.1_Missense_Mutation_p.A14V|SLC30A6_uc010ezs.1_Missense_Mutation_p.A137V|SLC30A6_uc002roh.1_Missense_Mutation_p.A14V	NM_017964	NP_060434	Q6NXT4	ZNT6_HUMAN	solute carrier family 30 (zinc transporter),	211	Helical; (Potential).					Golgi membrane|integral to membrane	zinc ion transmembrane transporter activity				0	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.208)					GGAGCATTTGCTCTTTGTATT	0.313													116	268	---	---	---	---	PASS
IL18RAP	8807	broad.mit.edu	37	2	103068553	103068553	+	Missense_Mutation	SNP	A	G	G			TCGA-CZ-5460-01A-01D-1501-10	TCGA-CZ-5460-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:103068553A>G	uc002tbx.2	+	12	2196	c.1712A>G	c.(1711-1713)CAG>CGG	p.Q571R	IL18RAP_uc010fiz.2_Missense_Mutation_p.Q429R	NM_003853	NP_003844	O95256	I18RA_HUMAN	interleukin 18 receptor accessory protein	571	Cytoplasmic (Potential).				cell surface receptor linked signaling pathway|inflammatory response|innate immune response	integral to membrane	transmembrane receptor activity			skin(3)|ovary(2)	5						ACGTGGAACCAGCTCAGAATT	0.483													29	70	---	---	---	---	PASS
POTEF	728378	broad.mit.edu	37	2	130878125	130878125	+	5'UTR	SNP	A	G	G			TCGA-CZ-5460-01A-01D-1501-10	TCGA-CZ-5460-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:130878125A>G	uc010fmh.2	-	3						NM_001099771	NP_001093241	A5A3E0	POTEF_HUMAN	prostate, ovary, testis expressed protein on							cell cortex	ATP binding			skin(3)|ovary(2)	5						GTAGTAGCCAACAGATCGCGT	0.498													4	11	---	---	---	---	PASS
NGEF	25791	broad.mit.edu	37	2	233748710	233748710	+	Missense_Mutation	SNP	T	C	C			TCGA-CZ-5460-01A-01D-1501-10	TCGA-CZ-5460-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:233748710T>C	uc002vts.2	-	11	1830	c.1582A>G	c.(1582-1584)ATC>GTC	p.I528V	NGEF_uc010zmm.1_Missense_Mutation_p.I251V|NGEF_uc010fyg.1_Missense_Mutation_p.I436V	NM_019850	NP_062824	Q8N5V2	NGEF_HUMAN	neuronal guanine nucleotide exchange factor	528	PH.				apoptosis|cell differentiation|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	cytosol|growth cone|plasma membrane	Rho guanyl-nucleotide exchange factor activity			ovary(3)|central_nervous_system(3)|skin(1)	7		Breast(86;0.00279)|Renal(207;0.00339)|all_hematologic(139;0.00793)|Acute lymphoblastic leukemia(138;0.0182)|all_lung(227;0.0271)|Lung NSC(271;0.0839)		Epithelial(121;8.65e-17)|BRCA - Breast invasive adenocarcinoma(100;0.00037)|LUSC - Lung squamous cell carcinoma(224;0.00813)|Lung(119;0.00984)|GBM - Glioblastoma multiforme(43;0.0604)		TGCCGGCAGATCACCAGCAGG	0.597													4	51	---	---	---	---	PASS
VHL	7428	broad.mit.edu	37	3	10191593	10191593	+	Nonsense_Mutation	SNP	A	T	T			TCGA-CZ-5460-01A-01D-1501-10	TCGA-CZ-5460-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:10191593A>T	uc003bvc.2	+	3	799	c.586A>T	c.(586-588)AAA>TAA	p.K196*	VHL_uc003bvd.2_Nonsense_Mutation_p.K155*	NM_000551	NP_000542	P40337	VHL_HUMAN	von Hippel-Lindau tumor suppressor isoform 1	196					anti-apoptosis|cell morphogenesis|negative regulation of cell proliferation|negative regulation of transcription from RNA polymerase II promoter|positive regulation of cell differentiation|positive regulation of transcription, DNA-dependent|protein stabilization|protein ubiquitination|proteolysis	cytosol|endoplasmic reticulum|membrane|mitochondrion|nucleus	protein binding|transcription factor binding	p.K196fs*18(2)|p.K196*(2)|p.P192fs*3(1)|p.K196fs*4(1)|p.K196fs*17(1)		kidney(1273)|soft_tissue(24)|adrenal_gland(15)|large_intestine(13)|pancreas(5)|endometrium(4)|thyroid(3)|upper_aerodigestive_tract(3)|central_nervous_system(2)|lung(2)|pleura(1)|paratesticular_tissues(1)	1346				Kidney(1;0.000404)|KIRC - Kidney renal clear cell carcinoma(1;0.000569)		AAATGTGCAGAAAGACCTGGA	0.498		1	D|Mis|N|F|S		renal|hemangioma|pheochromocytoma	renal|hemangioma|pheochromocytoma			von_Hippel-Lindau_disease|Chuvash_Polycythemia_|Pheochromocytoma_(Adrenal)_Familial				8	26	---	---	---	---	PASS
GOLGA4	2803	broad.mit.edu	37	3	37343778	37343778	+	Missense_Mutation	SNP	C	A	A			TCGA-CZ-5460-01A-01D-1501-10	TCGA-CZ-5460-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:37343778C>A	uc003cgv.2	+	10	1493	c.1189C>A	c.(1189-1191)CAG>AAG	p.Q397K	GOLGA4_uc010hgr.1_Intron|GOLGA4_uc003cgw.2_Missense_Mutation_p.Q419K|GOLGA4_uc010hgs.2_Intron|GOLGA4_uc003cgx.2_Missense_Mutation_p.Q278K	NM_002078	NP_002069	Q13439	GOGA4_HUMAN	golgi autoantigen, golgin subfamily a, 4	397	Potential.|Glu-rich.				Golgi to plasma membrane protein transport	Golgi membrane|trans-Golgi network	protein binding			ovary(2)|breast(1)|central_nervous_system(1)	4						GATGACTACCCAGGGAGAGGA	0.403													26	25	---	---	---	---	PASS
PROS1	5627	broad.mit.edu	37	3	93646183	93646183	+	Missense_Mutation	SNP	T	C	C			TCGA-CZ-5460-01A-01D-1501-10	TCGA-CZ-5460-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:93646183T>C	uc003drb.3	-	2	486	c.145A>G	c.(145-147)ACC>GCC	p.T49A	PROS1_uc010hoo.2_5'UTR|PROS1_uc003dqz.3_5'UTR	NM_000313	NP_000304	P07225	PROS_HUMAN	protein S, alpha preproprotein	49	Gla.				leukocyte migration|peptidyl-glutamic acid carboxylation|platelet activation|platelet degranulation|post-translational protein modification|proteolysis	endoplasmic reticulum membrane|extracellular region|Golgi lumen|Golgi membrane|platelet alpha granule lumen	calcium ion binding|endopeptidase inhibitor activity			large_intestine(1)	1					Antihemophilic Factor(DB00025)|Drotrecogin alfa(DB00055)|Menadione(DB00170)	CCCTGTTTGGTTTCTTCAAGT	0.388													6	233	---	---	---	---	PASS
CASR	846	broad.mit.edu	37	3	122002936	122002936	+	Missense_Mutation	SNP	C	T	T			TCGA-CZ-5460-01A-01D-1501-10	TCGA-CZ-5460-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:122002936C>T	uc003eev.3	+	7	2507	c.2135C>T	c.(2134-2136)ACC>ATC	p.T712I	CASR_uc003eew.3_Missense_Mutation_p.T722I	NM_000388	NP_000379	P41180	CASR_HUMAN	calcium-sensing receptor precursor	712	Cytoplasmic (Potential).				anatomical structure morphogenesis|calcium ion import|cellular calcium ion homeostasis|chemosensory behavior|detection of calcium ion|ossification	integral to plasma membrane	G-protein coupled receptor activity|phosphatidylinositol phospholipase C activity			ovary(4)|skin(2)|upper_aerodigestive_tract(1)	7				GBM - Glioblastoma multiforme(114;0.226)	Cinacalcet(DB01012)	AAGATCCCCACCAGCTTCCAC	0.567													9	16	---	---	---	---	PASS
RARRES1	5918	broad.mit.edu	37	3	158415586	158415586	+	Missense_Mutation	SNP	A	G	G			TCGA-CZ-5460-01A-01D-1501-10	TCGA-CZ-5460-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:158415586A>G	uc003fci.2	-	6	837	c.766T>C	c.(766-768)TGG>CGG	p.W256R		NM_206963	NP_996846	P49788	TIG1_HUMAN	retinoic acid receptor responder (tazarotene	256	Extracellular (Potential).				negative regulation of cell proliferation	integral to membrane					0			Lung(72;0.00309)|LUSC - Lung squamous cell carcinoma(72;0.0043)		Tretinoin(DB00755)	CCAGGGTACCAGACCAAGTGA	0.388													6	174	---	---	---	---	PASS
MUC4	4585	broad.mit.edu	37	3	195511888	195511888	+	Missense_Mutation	SNP	C	G	G			TCGA-CZ-5460-01A-01D-1501-10	TCGA-CZ-5460-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:195511888C>G	uc011bto.1	-	2	7023	c.6563G>C	c.(6562-6564)GGT>GCT	p.G2188A	MUC4_uc003fvo.2_Intron|MUC4_uc003fvp.2_Intron|MUC4_uc010hzu.1_Intron	NM_018406	NP_060876	Q99102	MUC4_HUMAN	mucin 4 isoform a	Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment					cell-matrix adhesion	integral to plasma membrane|proteinaceous extracellular matrix	ErbB-2 class receptor binding|extracellular matrix constituent, lubricant activity				0	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		GGTGGCGTGACCTGTGGATGC	0.597													3	10	---	---	---	---	PASS
CFI	3426	broad.mit.edu	37	4	110687728	110687728	+	Missense_Mutation	SNP	C	T	T			TCGA-CZ-5460-01A-01D-1501-10	TCGA-CZ-5460-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:110687728C>T	uc003hzr.3	-	2	518	c.310G>A	c.(310-312)GGA>AGA	p.G104R	CFI_uc011cft.1_Missense_Mutation_p.G104R|CFI_uc003hzs.3_Missense_Mutation_p.G104R	NM_000204	NP_000195	P05156	CFAI_HUMAN	complement factor I preproprotein	104	Kazal-like.				complement activation, classical pathway|innate immune response|proteolysis	extracellular space|membrane	scavenger receptor activity|serine-type endopeptidase activity				0		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;0.000331)		GTGCATGTTCCGTTATTTAAA	0.383													4	56	---	---	---	---	PASS
FAM160A1	729830	broad.mit.edu	37	4	152577469	152577469	+	Silent	SNP	T	C	C			TCGA-CZ-5460-01A-01D-1501-10	TCGA-CZ-5460-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:152577469T>C	uc003imj.2	+	12	3212	c.2637T>C	c.(2635-2637)ATT>ATC	p.I879I		NM_001109977	NP_001103447	Q05DH4	F16A1_HUMAN	hypothetical protein LOC729830	879											0						TCGGGATCATTACTCAGCTAG	0.507													22	33	---	---	---	---	PASS
FGG	2266	broad.mit.edu	37	4	155527857	155527857	+	Missense_Mutation	SNP	C	T	T			TCGA-CZ-5460-01A-01D-1501-10	TCGA-CZ-5460-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:155527857C>T	uc003ioj.2	-	8	1270	c.1129G>A	c.(1129-1131)GGT>AGT	p.G377S	FGG_uc003iog.2_Missense_Mutation_p.G377S|FGG_uc003ioh.2_Missense_Mutation_p.G385S|FGG_uc010ipx.2_Missense_Mutation_p.G205S|FGG_uc010ipy.2_Missense_Mutation_p.G88S|FGG_uc003ioi.2_Missense_Mutation_p.G88S|FGG_uc003iok.2_Missense_Mutation_p.G385S	NM_021870	NP_068656	P02679	FIBG_HUMAN	fibrinogen, gamma chain isoform gamma-B	377	Fibrinogen C-terminal.		G -> VMCGEALPMLKDPCYS (in Paris-1; impaired polymerization).		platelet activation|platelet degranulation|protein polymerization|response to calcium ion|signal transduction	external side of plasma membrane|fibrinogen complex|platelet alpha granule lumen	eukaryotic cell surface binding|protein binding, bridging|receptor binding				0	all_hematologic(180;0.215)	Renal(120;0.0458)			Sucralfate(DB00364)	GAAAACATACCTTGGTAATAA	0.323													3	13	---	---	---	---	PASS
AGA	175	broad.mit.edu	37	4	178357480	178357480	+	Silent	SNP	T	A	A			TCGA-CZ-5460-01A-01D-1501-10	TCGA-CZ-5460-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:178357480T>A	uc003iuu.1	-	6	710	c.648A>T	c.(646-648)GGA>GGT	p.G216G	AGA_uc010irt.1_5'Flank|AGA_uc003iuv.1_Intron|AGA_uc003iuw.2_Silent_p.G120G	NM_000027	NP_000018	P20933	ASPG_HUMAN	aspartylglucosaminidase precursor	216					asparagine catabolic process via L-aspartate|protein deglycosylation|protein maturation	endoplasmic reticulum|intermediate filament cytoskeleton|lysosome|microtubule cytoskeleton	N4-(beta-N-acetylglucosaminyl)-L-asparaginase activity				0		all_lung(41;1.27e-09)|Lung NSC(41;1.1e-08)|Breast(14;6.27e-05)|Melanoma(52;0.00102)|Renal(120;0.00988)|Prostate(90;0.00996)|all_hematologic(60;0.014)|Hepatocellular(41;0.148)|all_neural(102;0.164)|Colorectal(36;0.245)		all cancers(43;1.37e-22)|Epithelial(43;3.86e-20)|OV - Ovarian serous cystadenocarcinoma(60;3.8e-11)|Colorectal(24;6.98e-05)|GBM - Glioblastoma multiforme(59;0.000362)|COAD - Colon adenocarcinoma(29;0.000462)|STAD - Stomach adenocarcinoma(60;0.0029)|LUSC - Lung squamous cell carcinoma(193;0.0328)|READ - Rectum adenocarcinoma(43;0.163)		CAGCAATATGTCCTGTCTTAT	0.328													53	209	---	---	---	---	PASS
SDHA	6389	broad.mit.edu	37	5	240480	240480	+	Silent	SNP	A	G	G			TCGA-CZ-5460-01A-01D-1501-10	TCGA-CZ-5460-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:240480A>G	uc003jao.3	+	11	1555	c.1440A>G	c.(1438-1440)AAA>AAG	p.K480K	SDHA_uc011clv.1_Silent_p.K480K|SDHA_uc011clw.1_Silent_p.K432K|SDHA_uc003jap.3_Silent_p.K480K|SDHA_uc003jaq.3_Silent_p.K255K|SDHA_uc003jar.3_Silent_p.K74K	NM_004168	NP_004159	P31040	DHSA_HUMAN	succinate dehydrogenase complex, subunit A,	480					nervous system development|respiratory electron transport chain|succinate metabolic process|transport|tricarboxylic acid cycle	mitochondrial respiratory chain complex II	electron carrier activity|flavin adenine dinucleotide binding|protein binding|succinate dehydrogenase (ubiquinone) activity				0			Epithelial(17;0.0159)|all cancers(22;0.0236)|OV - Ovarian serous cystadenocarcinoma(19;0.0674)|Lung(60;0.113)		Succinic acid(DB00139)	TAGGAGATAAAGTCCCTCCAA	0.363									Familial_Paragangliomas				5	119	---	---	---	---	PASS
CWC27	10283	broad.mit.edu	37	5	64082386	64082386	+	Silent	SNP	G	A	A			TCGA-CZ-5460-01A-01D-1501-10	TCGA-CZ-5460-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:64082386G>A	uc003jtn.1	+	6	750	c.531G>A	c.(529-531)AGG>AGA	p.R177R	CWC27_uc003jtl.2_Silent_p.R177R|CWC27_uc003jtm.2_Silent_p.R177R|CWC27_uc010iwt.1_Silent_p.R177R	NM_005869	NP_005860	Q6UX04	CWC27_HUMAN	serologically defined colon cancer antigen 10	177					protein folding	catalytic step 2 spliceosome	peptidyl-prolyl cis-trans isomerase activity				0						TCATTCCAAGGGAAATTAAAA	0.313													61	110	---	---	---	---	PASS
SLC22A4	6583	broad.mit.edu	37	5	131662990	131662990	+	Missense_Mutation	SNP	G	T	T			TCGA-CZ-5460-01A-01D-1501-10	TCGA-CZ-5460-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:131662990G>T	uc003kwq.2	+	5	1010	c.845G>T	c.(844-846)CGA>CTA	p.R282L	SLC22A4_uc010jdq.1_RNA|uc003kwr.3_Intron	NM_003059	NP_003050	Q9H015	S22A4_HUMAN	solute carrier family 22 member 4	282	Cytoplasmic (Potential).				body fluid secretion|sodium ion transport	apical plasma membrane|integral to plasma membrane|mitochondrion	ATP binding|carnitine transporter activity|cation:cation antiporter activity|PDZ domain binding|secondary active organic cation transmembrane transporter activity|symporter activity				0		all_cancers(142;0.0752)|Breast(839;0.198)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)		L-Carnitine(DB00583)	GAATCTCCCCGATGGCTGATA	0.353													5	93	---	---	---	---	PASS
ABLIM3	22885	broad.mit.edu	37	5	148521634	148521634	+	5'UTR	SNP	A	G	G			TCGA-CZ-5460-01A-01D-1501-10	TCGA-CZ-5460-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:148521634A>G	uc003lpy.2	+	2					ABLIM3_uc003lpz.1_5'UTR|ABLIM3_uc003lqa.1_5'UTR|ABLIM3_uc003lqb.2_5'UTR|ABLIM3_uc003lqc.1_5'UTR|ABLIM3_uc003lqd.1_5'UTR|ABLIM3_uc003lqf.2_5'UTR|ABLIM3_uc003lqe.1_5'UTR	NM_014945	NP_055760	O94929	ABLM3_HUMAN	actin binding LIM protein family, member 3						axon guidance|cytoskeleton organization	cytoplasm	actin binding|zinc ion binding			ovary(2)|skin(1)	3			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GTATTGAATGAAAGACCCAGT	0.542													12	46	---	---	---	---	PASS
G3BP1	10146	broad.mit.edu	37	5	151179550	151179550	+	Missense_Mutation	SNP	G	A	A			TCGA-CZ-5460-01A-01D-1501-10	TCGA-CZ-5460-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:151179550G>A	uc003lun.2	+	9	1115	c.944G>A	c.(943-945)GGA>GAA	p.G315E	G3BP1_uc003lum.2_Missense_Mutation_p.G315E|G3BP1_uc011dcu.1_Missense_Mutation_p.G133E|G3BP1_uc010jhz.2_Missense_Mutation_p.G133E|G3BP1_uc003luq.2_5'UTR	NM_005754	NP_005745	Q13283	G3BP1_HUMAN	Ras-GTPase-activating protein SH3-domain-binding	315					Ras protein signal transduction|transport	cytosol|nucleus|plasma membrane	ATP binding|ATP-dependent DNA helicase activity|ATP-dependent RNA helicase activity|DNA binding|endonuclease activity|protein binding|RNA binding			skin(3)|ovary(1)	4		all_hematologic(541;0.0338)|Medulloblastoma(196;0.091)	Kidney(363;0.000171)|KIRC - Kidney renal clear cell carcinoma(527;0.000785)			CCCCAAAGGGGACCCAGACCA	0.458													21	41	---	---	---	---	PASS
C6orf62	81688	broad.mit.edu	37	6	24719011	24719011	+	5'UTR	SNP	G	T	T			TCGA-CZ-5460-01A-01D-1501-10	TCGA-CZ-5460-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:24719011G>T	uc003nel.2	-	1						NM_030939	NP_112201	Q9GZU0	CF062_HUMAN	hypothetical protein LOC81688							intracellular					0						TAATATGATTGATTAGCGAAA	0.368													11	31	---	---	---	---	PASS
GJA10	84694	broad.mit.edu	37	6	90604723	90604723	+	Missense_Mutation	SNP	A	G	G			TCGA-CZ-5460-01A-01D-1501-10	TCGA-CZ-5460-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:90604723A>G	uc011eaa.1	+	1	536	c.536A>G	c.(535-537)TAT>TGT	p.Y179C		NM_032602	NP_115991	Q969M2	CXA10_HUMAN	gap junction protein, alpha 10	179	Helical; (Potential).				synaptic transmission	connexon complex|integral to membrane	gap junction channel activity				0		all_cancers(76;5.71e-06)|Acute lymphoblastic leukemia(125;2.23e-10)|Prostate(29;5.55e-10)|all_hematologic(105;2.42e-06)|all_epithelial(107;0.00527)		BRCA - Breast invasive adenocarcinoma(108;0.0915)		TATATTCTCTATGGGTTTCAA	0.448													14	32	---	---	---	---	PASS
OCM	654231	broad.mit.edu	37	7	5925855	5925855	+	3'UTR	SNP	C	A	A			TCGA-CZ-5460-01A-01D-1501-10	TCGA-CZ-5460-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:5925855C>A	uc003spe.3	+	4						NM_001097622	NP_001091091	P0CE72	ONCO_HUMAN	oncomodulin								calcium ion binding				0		Ovarian(82;0.0694)		UCEC - Uterine corpus endometrioid carcinoma (126;0.0978)|OV - Ovarian serous cystadenocarcinoma(56;2.11e-14)		GCAGTTTGCTCATTGTTTTAG	0.488													12	23	---	---	---	---	PASS
NUB1	51667	broad.mit.edu	37	7	151057396	151057396	+	Intron	SNP	A	C	C	rs138349282	by1000genomes	TCGA-CZ-5460-01A-01D-1501-10	TCGA-CZ-5460-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:151057396A>C	uc003wjx.2	+						NUB1_uc003wjv.2_RNA|NUB1_uc003wjw.2_Intron|NUB1_uc010lqb.2_RNA|NUB1_uc003wjy.2_RNA|NUB1_uc011kvj.1_RNA|NUB1_uc010lqc.2_Intron	NM_016118	NP_057202	Q9Y5A7	NUB1_HUMAN	NEDD8 ultimate buster-1						positive regulation of proteasomal ubiquitin-dependent protein catabolic process|protein ubiquitination|response to interferon-gamma|response to tumor necrosis factor|ubiquitin-dependent protein catabolic process	nucleus	protein binding				0			OV - Ovarian serous cystadenocarcinoma(82;0.00569)	UCEC - Uterine corpus endometrioid carcinoma (81;0.172)		TATACAGAACACCCTGCCATG	0.438													12	48	---	---	---	---	PASS
MLL3	58508	broad.mit.edu	37	7	151960100	151960100	+	Splice_Site	SNP	C	T	T			TCGA-CZ-5460-01A-01D-1501-10	TCGA-CZ-5460-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:151960100C>T	uc003wla.2	-	9	1518	c.1299_splice	c.e9+1	p.K433_splice		NM_170606	NP_733751	Q8NEZ4	MLL3_HUMAN	myeloid/lymphoid or mixed-lineage leukemia 3						intracellular signal transduction|regulation of transcription, DNA-dependent|transcription, DNA-dependent		DNA binding|protein binding|zinc ion binding			large_intestine(27)|pancreas(13)|ovary(9)|central_nervous_system(8)|breast(3)|upper_aerodigestive_tract(1)|urinary_tract(1)|skin(1)	63	all_neural(206;0.187)	all_hematologic(28;0.0592)|Prostate(32;0.0906)	OV - Ovarian serous cystadenocarcinoma(82;0.00715)	UCEC - Uterine corpus endometrioid carcinoma (81;0.0597)|BRCA - Breast invasive adenocarcinoma(188;0.0462)		aaaCAACTTACTTTGCATTTC	0.343			N		medulloblastoma								25	84	---	---	---	---	PASS
IFNA1	3439	broad.mit.edu	37	9	21440985	21440985	+	Missense_Mutation	SNP	G	A	A			TCGA-CZ-5460-01A-01D-1501-10	TCGA-CZ-5460-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:21440985G>A	uc003zpd.1	+	1	546	c.479G>A	c.(478-480)AGC>AAC	p.S160N		NM_024013	NP_076918	P01562	IFNA1_HUMAN	interferon, alpha 1 precursor	160					blood coagulation|regulation of type I interferon-mediated signaling pathway|response to virus|type I interferon-mediated signaling pathway	extracellular space	cytokine activity|interferon-alpha/beta receptor binding			ovary(2)	2				Lung(24;7.66e-27)|LUSC - Lung squamous cell carcinoma(38;1.4e-13)|OV - Ovarian serous cystadenocarcinoma(39;0.0173)		AAGAAATACAGCCCTTGTGCC	0.453													9	44	---	---	---	---	PASS
FRMPD1	22844	broad.mit.edu	37	9	37744613	37744613	+	Missense_Mutation	SNP	A	T	T			TCGA-CZ-5460-01A-01D-1501-10	TCGA-CZ-5460-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:37744613A>T	uc004aag.1	+	16	2628	c.2584A>T	c.(2584-2586)AGT>TGT	p.S862C	FRMPD1_uc004aah.1_Missense_Mutation_p.S862C	NM_014907	NP_055722	Q5SYB0	FRPD1_HUMAN	FERM and PDZ domain containing 1	862						cytoskeleton|cytosol|plasma membrane				ovary(4)|central_nervous_system(2)|skin(2)|breast(1)	9				GBM - Glioblastoma multiforme(29;0.00655)		CTCCCTGGAGAGTGTAGACGA	0.562													4	17	---	---	---	---	PASS
PRUNE2	158471	broad.mit.edu	37	9	79438564	79438564	+	Missense_Mutation	SNP	A	G	G			TCGA-CZ-5460-01A-01D-1501-10	TCGA-CZ-5460-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:79438564A>G	uc010mpk.2	-	6	864	c.740T>C	c.(739-741)GTG>GCG	p.V247A	PRUNE2_uc004akn.2_Missense_Mutation_p.V247A	NM_015225	NP_056040	Q8WUY3	PRUN2_HUMAN	prune homolog 2	247					apoptosis|G1 phase|induction of apoptosis	cytoplasm	metal ion binding|pyrophosphatase activity				0						GTTCATGCTCACAGTACTAAT	0.393													22	63	---	---	---	---	PASS
PRUNE2	158471	broad.mit.edu	37	9	79438565	79438565	+	Missense_Mutation	SNP	C	G	G			TCGA-CZ-5460-01A-01D-1501-10	TCGA-CZ-5460-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:79438565C>G	uc010mpk.2	-	6	863	c.739G>C	c.(739-741)GTG>CTG	p.V247L	PRUNE2_uc004akn.2_Missense_Mutation_p.V247L	NM_015225	NP_056040	Q8WUY3	PRUN2_HUMAN	prune homolog 2	247					apoptosis|G1 phase|induction of apoptosis	cytoplasm	metal ion binding|pyrophosphatase activity				0						TTCATGCTCACAGTACTAATG	0.393													22	62	---	---	---	---	PASS
WNK2	65268	broad.mit.edu	37	9	95997112	95997112	+	Silent	SNP	C	T	T	rs113308587	byFrequency	TCGA-CZ-5460-01A-01D-1501-10	TCGA-CZ-5460-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:95997112C>T	uc004ati.1	+	4	1098	c.1098C>T	c.(1096-1098)CCC>CCT	p.P366P	WNK2_uc011lud.1_Silent_p.P366P|WNK2_uc004atj.2_Silent_p.P366P|WNK2_uc004atk.2_Silent_p.P3P|WNK2_uc010mrc.1_Silent_p.P366P|WNK2_uc010mrd.1_Silent_p.P3P	NM_006648	NP_006639	Q9Y3S1	WNK2_HUMAN	WNK lysine deficient protein kinase 2	366	Protein kinase.				intracellular protein kinase cascade		ATP binding|protein binding|protein serine/threonine kinase activity			lung(4)|stomach(3)|ovary(2)|large_intestine(1)|central_nervous_system(1)|breast(1)	12						TCATGGCGCCCGAGATGTACG	0.622													3	20	---	---	---	---	PASS
ABCA1	19	broad.mit.edu	37	9	107573110	107573110	+	Missense_Mutation	SNP	C	A	A			TCGA-CZ-5460-01A-01D-1501-10	TCGA-CZ-5460-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:107573110C>A	uc004bcl.2	-	29	4459	c.4146G>T	c.(4144-4146)TGG>TGT	p.W1382C		NM_005502	NP_005493	O95477	ABCA1_HUMAN	ATP-binding cassette, sub-family A member 1	1382	Extracellular.				Cdc42 protein signal transduction|cellular lipid metabolic process|cholesterol efflux|cholesterol homeostasis|cholesterol metabolic process|endosome transport|G-protein coupled receptor protein signaling pathway|high-density lipoprotein particle assembly|interleukin-1 beta secretion|intracellular cholesterol transport|lysosome organization|negative regulation of cholesterol storage|negative regulation of macrophage derived foam cell differentiation|phospholipid efflux|phospholipid homeostasis|platelet dense granule organization|positive regulation of cAMP biosynthetic process|reverse cholesterol transport	integral to plasma membrane|membrane fraction|membrane raft|phagocytic vesicle	anion transmembrane transporter activity|apolipoprotein A-I receptor activity|ATP binding|ATPase activity|cholesterol transporter activity|phospholipid transporter activity|small GTPase binding|syntaxin-13 binding			large_intestine(4)|lung(4)|ovary(4)|upper_aerodigestive_tract(1)|central_nervous_system(1)|breast(1)|skin(1)|pancreas(1)	17				OV - Ovarian serous cystadenocarcinoma(323;0.023)	Adenosine triphosphate(DB00171)|Glibenclamide(DB01016)	CGTTGTACATCCAGGGCTGAA	0.498													19	87	---	---	---	---	PASS
SFMBT2	57713	broad.mit.edu	37	10	7217995	7217995	+	Missense_Mutation	SNP	T	A	A			TCGA-CZ-5460-01A-01D-1501-10	TCGA-CZ-5460-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:7217995T>A	uc009xio.1	-	17	2032	c.1941A>T	c.(1939-1941)GAA>GAT	p.E647D	SFMBT2_uc001ijn.1_Missense_Mutation_p.E647D|SFMBT2_uc010qay.1_Missense_Mutation_p.E482D	NM_001029880	NP_001025051	Q5VUG0	SMBT2_HUMAN	Scm-like with four mbt domains 2	647					regulation of transcription, DNA-dependent	nucleus				ovary(4)|upper_aerodigestive_tract(2)|large_intestine(1)|central_nervous_system(1)	8						CTGGGCAGTTTTCAGATATCA	0.428													52	160	---	---	---	---	PASS
SFMBT2	57713	broad.mit.edu	37	10	7217996	7217996	+	Missense_Mutation	SNP	T	G	G			TCGA-CZ-5460-01A-01D-1501-10	TCGA-CZ-5460-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:7217996T>G	uc009xio.1	-	17	2031	c.1940A>C	c.(1939-1941)GAA>GCA	p.E647A	SFMBT2_uc001ijn.1_Missense_Mutation_p.E647A|SFMBT2_uc010qay.1_Missense_Mutation_p.E482A	NM_001029880	NP_001025051	Q5VUG0	SMBT2_HUMAN	Scm-like with four mbt domains 2	647					regulation of transcription, DNA-dependent	nucleus				ovary(4)|upper_aerodigestive_tract(2)|large_intestine(1)|central_nervous_system(1)	8						TGGGCAGTTTTCAGATATCAG	0.428													52	161	---	---	---	---	PASS
AGAP5	729092	broad.mit.edu	37	10	75451811	75451811	+	Missense_Mutation	SNP	C	T	T			TCGA-CZ-5460-01A-01D-1501-10	TCGA-CZ-5460-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:75451811C>T	uc009xri.2	-	4	427	c.386G>A	c.(385-387)TGT>TAT	p.C129Y	AGAP5_uc001juu.3_Missense_Mutation_p.C90Y	NM_001144000	NP_001137472	A6NIR3	AGAP5_HUMAN	ArfGAP with GTPase domain, ankyrin repeat and PH	129					regulation of ARF GTPase activity		ARF GTPase activator activity|zinc ion binding				0						ATGGTTTGTACAGTTGCTTCT	0.284													7	219	---	---	---	---	PASS
ANKRD1	27063	broad.mit.edu	37	10	92679944	92679944	+	Missense_Mutation	SNP	C	A	A			TCGA-CZ-5460-01A-01D-1501-10	TCGA-CZ-5460-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:92679944C>A	uc001khe.1	-	2	437	c.189G>T	c.(187-189)GAG>GAT	p.E63D		NM_014391	NP_055206	Q15327	ANKR1_HUMAN	cardiac ankyrin repeat protein	63	Potential.				cellular lipid metabolic process|defense response|signal transduction		DNA binding				0		Colorectal(252;0.0475)				CTCGTTGTTTCTCGCTTTTCC	0.512													18	46	---	---	---	---	PASS
GPAM	57678	broad.mit.edu	37	10	113932775	113932775	+	Missense_Mutation	SNP	T	C	C			TCGA-CZ-5460-01A-01D-1501-10	TCGA-CZ-5460-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:113932775T>C	uc009xxy.1	-	8	808	c.610A>G	c.(610-612)ATT>GTT	p.I204V	GPAM_uc001kzp.2_Missense_Mutation_p.I204V|GPAM_uc001kzq.1_Missense_Mutation_p.I204V	NM_020918	NP_065969	Q9HCL2	GPAT1_HUMAN	mitochondrial glycerol 3-phosphate	204				I -> F (in Ref. 1; CAD89932).	phospholipid biosynthetic process|triglyceride biosynthetic process	integral to membrane|mitochondrial outer membrane	glycerol-3-phosphate O-acyltransferase activity			ovary(1)|skin(1)	2				Epithelial(162;0.0306)|all cancers(201;0.123)		TGAATTTGAATGTTCCAAAAG	0.373													20	52	---	---	---	---	PASS
CATSPER1	117144	broad.mit.edu	37	11	65793070	65793070	+	Missense_Mutation	SNP	A	G	G			TCGA-CZ-5460-01A-01D-1501-10	TCGA-CZ-5460-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:65793070A>G	uc001ogt.2	-	1	919	c.781T>C	c.(781-783)TCT>CCT	p.S261P		NM_053054	NP_444282	Q8NEC5	CTSR1_HUMAN	sperm-associated cation channel 1	261	His-rich.|Cytoplasmic (Potential).				cell differentiation|multicellular organismal development|spermatogenesis	cilium|flagellar membrane|integral to membrane	protein binding			ovary(2)	2						tgatagtCAGATATCCCACGC	0.289													5	102	---	---	---	---	PASS
SPTBN2	6712	broad.mit.edu	37	11	66463961	66463961	+	Silent	SNP	C	A	A			TCGA-CZ-5460-01A-01D-1501-10	TCGA-CZ-5460-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:66463961C>A	uc001ojd.2	-	20	4137	c.4065G>T	c.(4063-4065)TCG>TCT	p.S1355S		NM_006946	NP_008877	O15020	SPTN2_HUMAN	spectrin, beta, non-erythrocytic 2	1355	Spectrin 10.				actin filament capping|axon guidance|cell death|vesicle-mediated transport	cytosol|spectrin	actin binding|structural constituent of cytoskeleton			large_intestine(1)|pancreas(1)|central_nervous_system(1)|skin(1)	4						TCAGCTTCTCCGACACCAGGG	0.572													3	20	---	---	---	---	PASS
CLPB	81570	broad.mit.edu	37	11	72012970	72012970	+	Silent	SNP	G	A	A			TCGA-CZ-5460-01A-01D-1501-10	TCGA-CZ-5460-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:72012970G>A	uc001osj.2	-	12	1346	c.1296C>T	c.(1294-1296)GGC>GGT	p.G432G	CLPB_uc010rqx.1_Silent_p.G387G|CLPB_uc010rqy.1_Silent_p.G373G|CLPB_uc001osk.2_Silent_p.G402G|CLPB_uc009ytg.2_RNA|CLPB_uc010rqz.1_Silent_p.G231G|CLPB_uc001osi.2_Silent_p.G40G	NM_030813	NP_110440	Q9H078	CLPB_HUMAN	caseinolytic peptidase B	432					cellular response to heat		ATP binding|nucleoside-triphosphatase activity|protein binding			pancreas(1)	1						CCTCCTCATGGCCAACGTAGC	0.522													9	23	---	---	---	---	PASS
DYNC2H1	79659	broad.mit.edu	37	11	102993704	102993704	+	Silent	SNP	T	C	C			TCGA-CZ-5460-01A-01D-1501-10	TCGA-CZ-5460-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:102993704T>C	uc001pho.2	+	11	1780	c.1636T>C	c.(1636-1638)TTA>CTA	p.L546L	DYNC2H1_uc001phn.1_Silent_p.L546L|DYNC2H1_uc009yxe.1_Silent_p.L546L	NM_001080463	NP_001073932	Q8NCM8	DYHC2_HUMAN	dynein, cytoplasmic 2, heavy chain 1	546	Stem (By similarity).				cell projection organization|Golgi organization|microtubule-based movement|multicellular organismal development	cilium axoneme|dynein complex|Golgi apparatus|microtubule|plasma membrane	ATP binding|ATPase activity|microtubule motor activity				0		Acute lymphoblastic leukemia(157;0.000966)|all_hematologic(158;0.00348)		BRCA - Breast invasive adenocarcinoma(274;0.000177)|Epithelial(105;0.0785)		TCAATCAGGTTTATCTGATTC	0.328													6	151	---	---	---	---	PASS
GLB1L3	112937	broad.mit.edu	37	11	134147161	134147161	+	Intron	SNP	C	T	T			TCGA-CZ-5460-01A-01D-1501-10	TCGA-CZ-5460-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:134147161C>T	uc009zdf.2	+						GLB1L3_uc010scs.1_Intron|GLB1L3_uc010sct.1_5'Flank	NM_001080407	NP_001073876	Q8NCI6	GLBL3_HUMAN	galactosidase, beta 1 like 3						carbohydrate metabolic process		cation binding|hydrolase activity, hydrolyzing O-glycosyl compounds			pancreas(1)	1	all_hematologic(175;0.127)	all_cancers(12;5.52e-23)|all_epithelial(12;2.15e-16)|all_lung(97;1.19e-05)|Lung NSC(97;2.76e-05)|Breast(109;0.000162)|all_neural(223;0.0182)|Medulloblastoma(222;0.0208)|Esophageal squamous(93;0.0559)		Epithelial(10;1.3e-11)|all cancers(11;2.07e-10)|BRCA - Breast invasive adenocarcinoma(10;3.09e-10)|OV - Ovarian serous cystadenocarcinoma(99;0.000873)|Lung(977;0.222)		CTTCCCGGCCCTTGCAGCCCG	0.667													3	3	---	---	---	---	PASS
CACNA1C	775	broad.mit.edu	37	12	2595320	2595320	+	Missense_Mutation	SNP	C	T	T			TCGA-CZ-5460-01A-01D-1501-10	TCGA-CZ-5460-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:2595320C>T	uc009zdu.1	+	6	1121	c.808C>T	c.(808-810)CAC>TAC	p.H270Y	CACNA1C_uc009zdv.1_Missense_Mutation_p.H270Y|CACNA1C_uc001qkb.2_Missense_Mutation_p.H270Y|CACNA1C_uc001qkc.2_Missense_Mutation_p.H270Y|CACNA1C_uc001qke.2_Missense_Mutation_p.H270Y|CACNA1C_uc001qkf.2_Missense_Mutation_p.H270Y|CACNA1C_uc001qjz.2_Missense_Mutation_p.H270Y|CACNA1C_uc001qkd.2_Missense_Mutation_p.H270Y|CACNA1C_uc001qkg.2_Missense_Mutation_p.H270Y|CACNA1C_uc009zdw.1_Missense_Mutation_p.H270Y|CACNA1C_uc001qkh.2_Missense_Mutation_p.H270Y|CACNA1C_uc001qkl.2_Missense_Mutation_p.H270Y|CACNA1C_uc001qkn.2_Missense_Mutation_p.H270Y|CACNA1C_uc001qko.2_Missense_Mutation_p.H270Y|CACNA1C_uc001qkp.2_Missense_Mutation_p.H270Y|CACNA1C_uc001qkr.2_Missense_Mutation_p.H270Y|CACNA1C_uc001qku.2_Missense_Mutation_p.H270Y|CACNA1C_uc001qkq.2_Missense_Mutation_p.H270Y|CACNA1C_uc001qks.2_Missense_Mutation_p.H270Y|CACNA1C_uc001qkt.2_Missense_Mutation_p.H270Y|CACNA1C_uc001qka.1_5'UTR|CACNA1C_uc001qki.1_Missense_Mutation_p.H6Y|CACNA1C_uc001qkj.1_Missense_Mutation_p.H6Y|CACNA1C_uc001qkk.1_Missense_Mutation_p.H6Y|CACNA1C_uc001qkm.1_Missense_Mutation_p.H6Y	NM_199460	NP_955630	Q13936	CAC1C_HUMAN	calcium channel, voltage-dependent, L type,	270	I.|Cytoplasmic (Potential).				axon guidance|calcium ion transport into cytosol|energy reserve metabolic process|regulation of insulin secretion	cytoplasm|postsynaptic density|voltage-gated calcium channel complex	calmodulin binding|voltage-gated calcium channel activity			ovary(10)|central_nervous_system(1)	11			OV - Ovarian serous cystadenocarcinoma(31;0.00256)	LUAD - Lung adenocarcinoma(1;0.134)	Ibutilide(DB00308)|Isradipine(DB00270)|Magnesium Sulfate(DB00653)|Mibefradil(DB01388)|Nicardipine(DB00622)|Verapamil(DB00661)	CCCCCTGCTGCACATCGCCCT	0.572													17	38	---	---	---	---	PASS
TAS2R50	259296	broad.mit.edu	37	12	11138584	11138584	+	Silent	SNP	C	T	T			TCGA-CZ-5460-01A-01D-1501-10	TCGA-CZ-5460-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:11138584C>T	uc001qzl.2	-	1	928	c.876G>A	c.(874-876)TTG>TTA	p.L292L	PRR4_uc009zhp.2_Intron|PRH1_uc001qzb.3_Intron|PRH1_uc001qzc.2_Intron|PRB4_uc001qzf.1_Intron|PRH1_uc001qzj.2_Intron	NM_176890	NP_795371	P59544	T2R50_HUMAN	taste receptor, type 2, member 50	292	Cytoplasmic (Potential).				sensory perception of taste	integral to membrane	G-protein coupled receptor activity			ovary(2)	2						GACACAAAATCAAAAGAAAGG	0.388													10	32	---	---	---	---	PASS
TMTC1	83857	broad.mit.edu	37	12	29908701	29908701	+	Silent	SNP	C	T	T			TCGA-CZ-5460-01A-01D-1501-10	TCGA-CZ-5460-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:29908701C>T	uc001rjb.2	-	4	822	c.348G>A	c.(346-348)ACG>ACA	p.T116T	TMTC1_uc001rjc.1_Silent_p.T116T	NM_175861	NP_787057	Q8IUR5	TMTC1_HUMAN	transmembrane and tetratricopeptide repeat	224						integral to membrane	binding				0	Lung NSC(12;7.61e-10)|Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.032)					CTCCAAACACCGTGATGCCTG	0.468													4	75	---	---	---	---	PASS
PRR13	54458	broad.mit.edu	37	12	53839947	53839947	+	3'UTR	SNP	C	T	T			TCGA-CZ-5460-01A-01D-1501-10	TCGA-CZ-5460-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:53839947C>T	uc001scz.3	+	4					PRR13_uc001scy.3_3'UTR|PCBP2_uc010soh.1_Intron|PRR13_uc001sda.3_3'UTR	NM_018457	NP_060927	Q9NZ81	PRR13_HUMAN	proline rich 13 isoform 1						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus					0						TGCTCCCCACCCCCTACCTCC	0.582													3	9	---	---	---	---	PASS
PTPRR	5801	broad.mit.edu	37	12	71033004	71033004	+	Missense_Mutation	SNP	C	T	T			TCGA-CZ-5460-01A-01D-1501-10	TCGA-CZ-5460-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:71033004C>T	uc001swi.1	-	14	2350	c.1934G>A	c.(1933-1935)TGC>TAC	p.C645Y	PTPRR_uc001swf.1_RNA|PTPRR_uc001swg.1_RNA|PTPRR_uc001swh.1_Missense_Mutation_p.C400Y|PTPRR_uc009zrs.2_Missense_Mutation_p.C494Y|PTPRR_uc010stq.1_Missense_Mutation_p.C533Y|PTPRB_uc001swc.3_5'Flank|PTPRB_uc001swa.3_5'Flank|PTPRB_uc001swd.3_5'Flank|PTPRB_uc009zrr.1_5'Flank|PTPRB_uc001swe.2_5'Flank	NM_002849	NP_002840	Q15256	PTPRR_HUMAN	protein tyrosine phosphatase, receptor type, R	645	Tyrosine-protein phosphatase.|Cytoplasmic (Potential).				in utero embryonic development	cell surface|Golgi apparatus|integral to membrane|nucleus|perinuclear region of cytoplasm|plasma membrane	protein kinase binding|transmembrane receptor protein tyrosine phosphatase activity			skin(2)|ovary(1)	3			GBM - Glioblastoma multiforme(2;5.67e-07)|Lung(24;0.00283)|OV - Ovarian serous cystadenocarcinoma(12;0.00578)|LUSC - Lung squamous cell carcinoma(43;0.132)	COAD - Colon adenocarcinoma(1;0.136)		CTCATACAGGCACAGAGCATG	0.423													13	16	---	---	---	---	PASS
WSB2	55884	broad.mit.edu	37	12	118481141	118481141	+	Missense_Mutation	SNP	T	A	A			TCGA-CZ-5460-01A-01D-1501-10	TCGA-CZ-5460-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:118481141T>A	uc001twr.2	-	3	322	c.224A>T	c.(223-225)AAT>ATT	p.N75I	WSB2_uc010sza.1_5'UTR|WSB2_uc010szb.1_Intron|WSB2_uc009zws.1_Missense_Mutation_p.N75I	NM_018639	NP_061109	Q9NYS7	WSB2_HUMAN	WD SOCS-box protein 2	75					intracellular signal transduction					ovary(1)	1	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)					TTTCGTCTCATTTTTGCTACT	0.517													17	64	---	---	---	---	PASS
WSB2	55884	broad.mit.edu	37	12	118481144	118481144	+	Missense_Mutation	SNP	T	A	A			TCGA-CZ-5460-01A-01D-1501-10	TCGA-CZ-5460-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:118481144T>A	uc001twr.2	-	3	319	c.221A>T	c.(220-222)AAA>ATA	p.K74I	WSB2_uc010sza.1_5'UTR|WSB2_uc010szb.1_Intron|WSB2_uc009zws.1_Missense_Mutation_p.K74I	NM_018639	NP_061109	Q9NYS7	WSB2_HUMAN	WD SOCS-box protein 2	74					intracellular signal transduction					ovary(1)	1	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)					CGTCTCATTTTTGCTACTTCG	0.512													16	66	---	---	---	---	PASS
OR4N2	390429	broad.mit.edu	37	14	20296164	20296164	+	Missense_Mutation	SNP	A	G	G			TCGA-CZ-5460-01A-01D-1501-10	TCGA-CZ-5460-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:20296164A>G	uc010tkv.1	+	1	557	c.557A>G	c.(556-558)AAG>AGG	p.K186R		NM_001004723	NP_001004723	Q8NGD1	OR4N2_HUMAN	olfactory receptor, family 4, subfamily N,	186	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(2)|central_nervous_system(1)|skin(1)	4	all_cancers(95;0.00108)		Epithelial(56;9.96e-07)|all cancers(55;2.95e-06)	GBM - Glioblastoma multiforme(265;0.00327)		CAGGTCATCAAGCTGGCCTGC	0.532													11	61	---	---	---	---	PASS
OSGEP	55644	broad.mit.edu	37	14	20916148	20916148	+	Silent	SNP	A	G	G			TCGA-CZ-5460-01A-01D-1501-10	TCGA-CZ-5460-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:20916148A>G	uc001vxf.2	-	8	1064	c.708T>C	c.(706-708)ACT>ACC	p.T236T		NM_017807	NP_060277	Q9NPF4	OSGEP_HUMAN	O-sialoglycoprotein endopeptidase	236					proteolysis|tRNA processing		metal ion binding|metalloendopeptidase activity|protein binding				0	all_cancers(95;0.00123)	all_lung(585;0.235)	Epithelial(56;1.09e-07)|all cancers(55;1.19e-06)	GBM - Glioblastoma multiforme(265;0.0231)|READ - Rectum adenocarcinoma(17;0.196)		TTGCAAACACAGTTTCCTGTC	0.478													14	41	---	---	---	---	PASS
RDH11	51109	broad.mit.edu	37	14	68159652	68159652	+	Silent	SNP	T	C	C			TCGA-CZ-5460-01A-01D-1501-10	TCGA-CZ-5460-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:68159652T>C	uc001xjv.3	-	2	282	c.192A>G	c.(190-192)AGA>AGG	p.R64R	RDH11_uc001xjw.3_Intron|RDH11_uc001xjx.3_Silent_p.R64R	NM_016026	NP_057110	Q8TC12	RDH11_HUMAN	retinol dehydrogenase 11	64	Cytoplasmic (Potential).				retinol metabolic process|steroid metabolic process	endoplasmic reticulum membrane|integral to membrane	binding|NADP-retinol dehydrogenase activity|retinol dehydrogenase activity			ovary(1)	1				all cancers(60;0.00047)|OV - Ovarian serous cystadenocarcinoma(108;0.00206)|BRCA - Breast invasive adenocarcinoma(234;0.00924)	Vitamin A(DB00162)	TGAACTTGCCTCTCTGAGCCA	0.453													6	117	---	---	---	---	PASS
SERPINA1	5265	broad.mit.edu	37	14	94844824	94844824	+	Missense_Mutation	SNP	G	C	C			TCGA-CZ-5460-01A-01D-1501-10	TCGA-CZ-5460-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:94844824G>C	uc001ycx.3	-	5	1480	c.1219C>G	c.(1219-1221)CTC>GTC	p.L407V	SERPINA1_uc001ycw.3_RNA|SERPINA1_uc010auw.2_Missense_Mutation_p.L407V|SERPINA1_uc010aux.2_Missense_Mutation_p.L407V|SERPINA1_uc001ycy.3_Missense_Mutation_p.L407V|SERPINA1_uc010auy.2_Missense_Mutation_p.L407V|SERPINA1_uc001ycz.3_Missense_Mutation_p.L407V|SERPINA1_uc010auz.2_Missense_Mutation_p.L407V|SERPINA1_uc010ava.2_Missense_Mutation_p.L407V|SERPINA1_uc001ydb.3_Missense_Mutation_p.L407V|SERPINA1_uc010avb.2_Missense_Mutation_p.L407V|SERPINA1_uc001ydc.3_Missense_Mutation_p.L407V	NM_000295	NP_000286	P01009	A1AT_HUMAN	serine proteinase inhibitor, clade A, member 1	407					acute-phase response|platelet activation|platelet degranulation|regulation of proteolysis	extracellular space|platelet alpha granule lumen|proteinaceous extracellular matrix	protease binding|serine-type endopeptidase inhibitor activity			skin(1)	1		all_cancers(154;0.0649)|all_epithelial(191;0.223)		Epithelial(152;0.135)|COAD - Colon adenocarcinoma(157;0.207)|all cancers(159;0.221)	Alpha-1-proteinase inhibitor(DB00058)	CCCATGAAGAGGGGAGACTTG	0.498									Alpha-1-Antitrypsin_Deficiency				53	118	---	---	---	---	PASS
TDRD9	122402	broad.mit.edu	37	14	104471683	104471683	+	Missense_Mutation	SNP	A	G	G			TCGA-CZ-5460-01A-01D-1501-10	TCGA-CZ-5460-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:104471683A>G	uc001yom.3	+	15	1684	c.1654A>G	c.(1654-1656)ACT>GCT	p.T552A	TDRD9_uc001yon.3_Missense_Mutation_p.T290A	NM_153046	NP_694591	Q8NDG6	TDRD9_HUMAN	tudor domain containing 9	552					cell differentiation|DNA methylation involved in gamete generation|fertilization|gene silencing by RNA|male meiosis|multicellular organismal development|piRNA metabolic process|spermatogenesis	nucleus|piP-body	ATP binding|ATP-dependent helicase activity|nucleic acid binding			ovary(2)|central_nervous_system(1)	3		all_cancers(154;0.109)|Melanoma(154;0.0525)|all_epithelial(191;0.0768)				TCTGCTGGCCACTGCCCTTTC	0.498													5	75	---	---	---	---	PASS
DUOX1	53905	broad.mit.edu	37	15	45434244	45434244	+	Missense_Mutation	SNP	G	A	A			TCGA-CZ-5460-01A-01D-1501-10	TCGA-CZ-5460-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:45434244G>A	uc001zus.1	+	16	2102	c.1756G>A	c.(1756-1758)GAC>AAC	p.D586N	DUOX1_uc001zut.1_Missense_Mutation_p.D586N|DUOX1_uc010bee.1_5'UTR	NM_017434	NP_059130	Q9NRD9	DUOX1_HUMAN	dual oxidase 1 precursor	586	Peroxidase-like; mediates peroxidase activity.|Extracellular (Potential).				cuticle development|cytokine-mediated signaling pathway|hormone biosynthetic process|hydrogen peroxide biosynthetic process|hydrogen peroxide catabolic process|response to cAMP|superoxide anion generation	apical plasma membrane|integral to membrane	calcium ion binding|electron carrier activity|flavin adenine dinucleotide binding|heme binding|NAD(P)H oxidase activity|NADP binding|peroxidase activity			ovary(5)|skin(2)|breast(1)	8		all_cancers(109;5.7e-11)|all_epithelial(112;4.65e-09)|Lung NSC(122;3.55e-06)|all_lung(180;2.56e-05)|Melanoma(134;0.027)		all cancers(107;5.77e-18)|GBM - Glioblastoma multiforme(94;5.11e-07)|COAD - Colon adenocarcinoma(120;0.071)|Colorectal(133;0.0717)		TGTTGTTCGTGACTATTTTGA	0.592													13	58	---	---	---	---	PASS
PYGO1	26108	broad.mit.edu	37	15	55838992	55838992	+	Silent	SNP	A	G	G			TCGA-CZ-5460-01A-01D-1501-10	TCGA-CZ-5460-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:55838992A>G	uc010bfl.1	-	3	545	c.489T>C	c.(487-489)AAT>AAC	p.N163N	PYGO1_uc002adf.1_Silent_p.N163N	NM_015617	NP_056432	Q9Y3Y4	PYGO1_HUMAN	pygopus homolog 1	163	Asn-rich.				Wnt receptor signaling pathway	nucleus	zinc ion binding			ovary(1)|skin(1)	2				all cancers(107;0.0131)|GBM - Glioblastoma multiforme(80;0.18)		GACTTAGTGCATTATTATAAG	0.373													35	67	---	---	---	---	PASS
ACSM2A	123876	broad.mit.edu	37	16	20486684	20486684	+	Missense_Mutation	SNP	A	G	G			TCGA-CZ-5460-01A-01D-1501-10	TCGA-CZ-5460-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:20486684A>G	uc010bwe.2	+	8	1134	c.895A>G	c.(895-897)ACA>GCA	p.T299A	ACSM2A_uc010bwd.1_RNA|ACSM2A_uc010vax.1_Missense_Mutation_p.T220A|ACSM2A_uc002dhf.3_Missense_Mutation_p.T299A|ACSM2A_uc002dhg.3_Missense_Mutation_p.T299A|ACSM2A_uc010vay.1_Missense_Mutation_p.T220A|ACSM2A_uc002dhh.3_5'Flank	NM_001010845	NP_001010845	Q08AH3	ACS2A_HUMAN	acyl-CoA synthetase medium-chain family member	299					fatty acid metabolic process	mitochondrial matrix	ATP binding|butyrate-CoA ligase activity|metal ion binding			skin(2)|breast(1)	3						TGTCTTCCAGACACTCTCCAG	0.478													4	42	---	---	---	---	PASS
VPS35	55737	broad.mit.edu	37	16	46695796	46695796	+	Intron	SNP	C	G	G			TCGA-CZ-5460-01A-01D-1501-10	TCGA-CZ-5460-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:46695796C>G	uc002eef.3	-						VPS35_uc002eed.2_3'UTR|VPS35_uc002eee.2_Intron	NM_018206	NP_060676	Q96QK1	VPS35_HUMAN	vacuolar protein sorting 35						protein transport|retrograde transport, endosome to Golgi	cytosol|endosome|membrane	protein binding				0		all_cancers(37;7.65e-05)|all_epithelial(9;0.000154)|all_lung(18;0.00585)|Lung NSC(13;0.0496)|Breast(268;0.116)				GGCAGGGGGACAGTGAAGAGA	0.393													5	104	---	---	---	---	PASS
NUTF2	10204	broad.mit.edu	37	16	67899046	67899046	+	Missense_Mutation	SNP	C	A	A			TCGA-CZ-5460-01A-01D-1501-10	TCGA-CZ-5460-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:67899046C>A	uc002eup.2	+	2	112	c.13C>A	c.(13-15)CCA>ACA	p.P5T	NUTF2_uc010vkf.1_Missense_Mutation_p.P5T	NM_005796	NP_005787	P61970	NTF2_HUMAN	nuclear transport factor 2	5					protein transport	cytosol|nuclear pore	protein binding|transporter activity				0		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.00443)|Epithelial(162;0.0199)|all cancers(182;0.129)		GGGAGACAAGCCAATTTGGGA	0.488													6	51	---	---	---	---	PASS
SNTB2	6645	broad.mit.edu	37	16	69294165	69294165	+	Splice_Site	SNP	T	C	C			TCGA-CZ-5460-01A-01D-1501-10	TCGA-CZ-5460-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:69294165T>C	uc002ewu.2	+	3	1025	c.1005_splice	c.e3+2	p.Q335_splice		NM_006750	NP_006741	Q13425	SNTB2_HUMAN	basic beta 2 syntrophin							cell junction|dystrophin-associated glycoprotein complex|membrane fraction|microtubule|transport vesicle membrane	actin binding|calmodulin binding|protein binding				0		Ovarian(137;0.101)		OV - Ovarian serous cystadenocarcinoma(108;0.208)		GCAGAACAGGTAGGCTGGGAG	0.517													4	48	---	---	---	---	PASS
PDPR	55066	broad.mit.edu	37	16	70180077	70180077	+	Silent	SNP	T	C	C			TCGA-CZ-5460-01A-01D-1501-10	TCGA-CZ-5460-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:70180077T>C	uc002eyf.1	+	16	2865	c.1908T>C	c.(1906-1908)TCT>TCC	p.S636S	CLEC18C_uc002exy.2_Intron|PDPR_uc010vlr.1_Silent_p.S536S|PDPR_uc002eyg.1_Silent_p.S364S|PDPR_uc002eyh.2_5'UTR|PDPR_uc010vls.1_5'UTR	NM_017990	NP_060460	Q8NCN5	PDPR_HUMAN	pyruvate dehydrogenase phosphatase regulatory	636					glycine catabolic process|pyruvate metabolic process|regulation of acetyl-CoA biosynthetic process from pyruvate	mitochondrial matrix	aminomethyltransferase activity|oxidoreductase activity			breast(1)	1				BRCA - Breast invasive adenocarcinoma(221;0.124)		ATGTGCTGTCTGAGTTGTCCT	0.473													33	58	---	---	---	---	PASS
NUDT7	283927	broad.mit.edu	37	16	77775489	77775489	+	Missense_Mutation	SNP	T	G	G			TCGA-CZ-5460-01A-01D-1501-10	TCGA-CZ-5460-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:77775489T>G	uc010chd.2	+	4	428	c.359T>G	c.(358-360)TTG>TGG	p.L120W	NUDT7_uc010vnj.1_Missense_Mutation_p.L67W	NM_001105663	NP_001099133	P0C024	NUDT7_HUMAN	nudix motif 7	120	Nudix hydrolase.				nucleoside diphosphate metabolic process	peroxisome	hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides|magnesium ion binding|manganese ion binding			ovary(1)|kidney(1)	2						ACAGATACATTGATAACTCCA	0.408													5	6	---	---	---	---	PASS
SPDYE4	388333	broad.mit.edu	37	17	8658873	8658873	+	Silent	SNP	C	T	T			TCGA-CZ-5460-01A-01D-1501-10	TCGA-CZ-5460-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:8658873C>T	uc010cnz.1	-	4	627	c.450G>A	c.(448-450)TCG>TCA	p.S150S		NM_001128076	NP_001121548	A6NLX3	SPDE4_HUMAN	speedy homolog E4	150											0						GGTATTGCCACGAGAAGAGGC	0.498													25	46	---	---	---	---	PASS
ZNF287	57336	broad.mit.edu	37	17	16456102	16456102	+	Missense_Mutation	SNP	A	T	T			TCGA-CZ-5460-01A-01D-1501-10	TCGA-CZ-5460-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:16456102A>T	uc002gqi.2	-	6	1807	c.1354T>A	c.(1354-1356)TAT>AAT	p.Y452N		NM_020653	NP_065704	Q9HBT7	ZN287_HUMAN	zinc finger protein 287	445	C2H2-type 4.				viral reproduction	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding				0				UCEC - Uterine corpus endometrioid carcinoma (92;0.083)		TCACACTTATAGGGTTTCTCT	0.443													19	31	---	---	---	---	PASS
OSBPL7	114881	broad.mit.edu	37	17	45897684	45897684	+	5'UTR	SNP	A	G	G			TCGA-CZ-5460-01A-01D-1501-10	TCGA-CZ-5460-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:45897684A>G	uc002ilx.1	-	2						NM_145798	NP_665741	Q9BZF2	OSBL7_HUMAN	oxysterol-binding protein-like protein 7						lipid transport		lipid binding				0						GATGTAGAGCAGGGAGCAGGG	0.592													3	8	---	---	---	---	PASS
TTLL6	284076	broad.mit.edu	37	17	46874444	46874444	+	Silent	SNP	G	T	T			TCGA-CZ-5460-01A-01D-1501-10	TCGA-CZ-5460-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:46874444G>T	uc010wlo.1	-	8	926	c.891C>A	c.(889-891)TCC>TCA	p.S297S	TTLL6_uc002iob.2_5'Flank|TTLL6_uc010dbi.2_5'Flank|TTLL6_uc002ioc.2_Silent_p.S50S|TTLL6_uc002iod.2_Silent_p.S144S	NM_001130918	NP_001124390	Q8N841	TTLL6_HUMAN	tubulin tyrosine ligase-like family, member 6	249	TTL.					cilium|microtubule basal body	ATP binding|tubulin binding|tubulin-tyrosine ligase activity				0						TGCAAGGGCGGGAGTAAGAGG	0.463													4	88	---	---	---	---	PASS
GDPD1	284161	broad.mit.edu	37	17	57334552	57334552	+	Missense_Mutation	SNP	C	T	T			TCGA-CZ-5460-01A-01D-1501-10	TCGA-CZ-5460-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:57334552C>T	uc002ixk.1	+	5	574	c.437C>T	c.(436-438)ACT>ATT	p.T146I	GDPD1_uc002ixj.2_Missense_Mutation_p.T146I	NM_182569	NP_872375	Q8N9F7	GDPD1_HUMAN	glycerophosphodiester phosphodiesterase domain	146	Cytoplasmic (Potential).|GDPD.				glycerol metabolic process|lipid metabolic process	cytoplasm|integral to membrane	glycerophosphodiester phosphodiesterase activity|metal ion binding				0	all_neural(34;0.0837)|Medulloblastoma(34;0.0922)					TTTCCTAACACTCCCATTAAC	0.383													67	136	---	---	---	---	PASS
LRFN1	57622	broad.mit.edu	37	19	39805558	39805558	+	Missense_Mutation	SNP	C	T	T			TCGA-CZ-5460-01A-01D-1501-10	TCGA-CZ-5460-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:39805558C>T	uc002okw.2	-	1	419	c.419G>A	c.(418-420)CGC>CAC	p.R140H		NM_020862	NP_065913	Q9P244	LRFN1_HUMAN	leucine rich repeat and fibronectin type III	140	LRR 4.|Extracellular (Potential).					cell junction|integral to membrane|postsynaptic density|postsynaptic membrane				ovary(2)	2	all_cancers(60;1.85e-07)|all_lung(34;4.03e-08)|Lung NSC(34;4.66e-08)|all_epithelial(25;6.4e-07)|Ovarian(47;0.0512)		Epithelial(26;1.96e-27)|all cancers(26;2.05e-24)|Lung(45;0.000278)|LUSC - Lung squamous cell carcinoma(53;0.000335)			GATCAGGTGGCGGAGGTTGCC	0.687													2	1	---	---	---	---	PASS
B3GNT8	374907	broad.mit.edu	37	19	41932579	41932579	+	Silent	SNP	G	A	A			TCGA-CZ-5460-01A-01D-1501-10	TCGA-CZ-5460-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:41932579G>A	uc002oqs.2	-	3	559	c.105C>T	c.(103-105)TAC>TAT	p.Y35Y	CYP2F1_uc010xvw.1_Intron|B3GNT8_uc002oqt.1_Intron	NM_198540	NP_940942	Q7Z7M8	B3GN8_HUMAN	UDP-GlcNAc:betaGal	35	Lumenal (Potential).				poly-N-acetyllactosamine biosynthetic process|protein glycosylation	Golgi membrane|integral to membrane	galactosyltransferase activity|protein N-acetylglucosaminyltransferase activity				0						GAGGGCTGGGGTAGGCCTTGC	0.667													3	4	---	---	---	---	PASS
BRWD1	54014	broad.mit.edu	37	21	40568695	40568695	+	Silent	SNP	T	C	C			TCGA-CZ-5460-01A-01D-1501-10	TCGA-CZ-5460-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:40568695T>C	uc002yxk.1	-	41	6439	c.6300A>G	c.(6298-6300)AGA>AGG	p.R2100R	BRWD1_uc010goc.1_Silent_p.R743R|BRWD1_uc002yxl.2_Silent_p.R2100R	NM_018963	NP_061836	Q9NSI6	BRWD1_HUMAN	bromodomain and WD repeat domain containing 1	2100					regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus				skin(3)|ovary(1)	4		Prostate(19;8.44e-08)|all_epithelial(19;0.223)				AGGTCCTGAGTCTTCTGCCAT	0.428													4	39	---	---	---	---	PASS
DIP2A	23181	broad.mit.edu	37	21	47983730	47983730	+	Intron	SNP	C	A	A			TCGA-CZ-5460-01A-01D-1501-10	TCGA-CZ-5460-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:47983730C>A	uc002zjo.2	+						DIP2A_uc011afz.1_Intron|DIP2A_uc002zjs.2_Intron|DIP2A_uc002zjt.2_RNA	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)		AGTCTCGTGTCATGTTTTCTT	0.512													12	58	---	---	---	---	PASS
DIP2A	23181	broad.mit.edu	37	21	47983731	47983731	+	Intron	SNP	A	T	T			TCGA-CZ-5460-01A-01D-1501-10	TCGA-CZ-5460-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:47983731A>T	uc002zjo.2	+						DIP2A_uc011afz.1_Intron|DIP2A_uc002zjs.2_Intron|DIP2A_uc002zjt.2_RNA	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)		GTCTCGTGTCATGTTTTCTTT	0.507													11	58	---	---	---	---	PASS
MID1IP1	58526	broad.mit.edu	37	X	38664279	38664279	+	Missense_Mutation	SNP	A	G	G			TCGA-CZ-5460-01A-01D-1501-10	TCGA-CZ-5460-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:38664279A>G	uc004dei.3	+	3	504	c.80A>G	c.(79-81)AAC>AGC	p.N27S	MID1IP1_uc010ngz.2_Missense_Mutation_p.N27S|MID1IP1_uc004dej.3_Missense_Mutation_p.N27S	NM_001098790	NP_001092260	Q9NPA3	M1IP1_HUMAN	MID1 interacting G12-like protein	27					lipid biosynthetic process|negative regulation of microtubule depolymerization|positive regulation of fatty acid biosynthetic process|positive regulation of ligase activity|protein polymerization	cytosol|microtubule|nucleus					0						GCCGTGAACAACATGGACCAG	0.602													3	7	---	---	---	---	PASS
MAGEA5	4104	broad.mit.edu	37	X	151283746	151283746	+	Missense_Mutation	SNP	G	T	T			TCGA-CZ-5460-01A-01D-1501-10	TCGA-CZ-5460-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:151283746G>T	uc004ffj.2	-	3	472	c.267C>A	c.(265-267)AAC>AAA	p.N89K		NM_021049	NP_066387	P43359	MAGA5_HUMAN	melanoma antigen family A, 5	89	MAGE.										0	Acute lymphoblastic leukemia(192;6.56e-05)					CCTCTTCTTGGTTGCTGGAGC	0.557													13	17	---	---	---	---	PASS
ATAD3A	55210	broad.mit.edu	37	1	1454110	1454111	+	Intron	INS	-	T	T			TCGA-CZ-5460-01A-01D-1501-10	TCGA-CZ-5460-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:1454110_1454111insT	uc001afz.1	+						ATAD3A_uc001aga.1_Intron|ATAD3A_uc001agb.1_Intron	NM_018188	NP_060658	Q9NVI7	ATD3A_HUMAN	ATPase family, AAA domain containing 3A								ATP binding|nucleoside-triphosphatase activity|protein binding			skin(1)	1	all_cancers(77;0.00164)|all_epithelial(69;0.000959)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;9.48e-15)|all_lung(118;9.67e-07)|Lung NSC(185;5.59e-05)|Renal(390;0.00571)|Breast(487;0.0183)|Hepatocellular(190;0.0268)|Myeloproliferative disorder(586;0.028)|Ovarian(437;0.127)|Lung SC(97;0.217)		Epithelial(90;1.12e-36)|OV - Ovarian serous cystadenocarcinoma(86;2.18e-22)|Colorectal(212;0.000164)|COAD - Colon adenocarcinoma(227;0.000195)|Kidney(185;0.00233)|BRCA - Breast invasive adenocarcinoma(365;0.00469)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0347)|Lung(427;0.147)		GGGCACAATCACCCCCACACAC	0.599													10	6	---	---	---	---	
KIAA1751	85452	broad.mit.edu	37	1	1890269	1890270	+	Intron	INS	-	C	C			TCGA-CZ-5460-01A-01D-1501-10	TCGA-CZ-5460-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:1890269_1890270insC	uc001aim.1	-						KIAA1751_uc009vkz.1_Intron	NM_001080484	NP_001073953	Q9C0B2	K1751_HUMAN	hypothetical protein LOC85452											pancreas(1)	1	all_cancers(77;0.000708)|all_epithelial(69;0.000943)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;6.04e-15)|all_lung(118;9.67e-07)|Lung NSC(185;5.59e-05)|Renal(390;0.00571)|Breast(487;0.0183)|Hepatocellular(190;0.0268)|Myeloproliferative disorder(586;0.028)|Ovarian(437;0.127)|Medulloblastoma(700;0.151)|Lung SC(97;0.217)		Epithelial(90;8.79e-39)|OV - Ovarian serous cystadenocarcinoma(86;9.61e-25)|GBM - Glioblastoma multiforme(42;1.2e-07)|Colorectal(212;4.84e-05)|COAD - Colon adenocarcinoma(227;0.000214)|Kidney(185;0.00254)|BRCA - Breast invasive adenocarcinoma(365;0.00461)|STAD - Stomach adenocarcinoma(132;0.00645)|KIRC - Kidney renal clear cell carcinoma(229;0.037)|Lung(427;0.205)		GCAGATGAATGTTAAGTTTTCC	0.510													9	5	---	---	---	---	
PLA2G5	5322	broad.mit.edu	37	1	20413894	20413894	+	Intron	DEL	T	-	-			TCGA-CZ-5460-01A-01D-1501-10	TCGA-CZ-5460-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:20413894delT	uc001bcy.2	+						PLA2G5_uc001bcw.2_Intron|PLA2G5_uc001bcx.2_Intron	NM_000929	NP_000920	P39877	PA2G5_HUMAN	phospholipase A2, group V precursor						lipid catabolic process	extracellular region	calcium ion binding|calcium-dependent phospholipase A2 activity			skin(1)	1		Colorectal(325;3.46e-05)|Renal(390;0.000147)|all_lung(284;0.000249)|Lung NSC(340;0.000287)|Breast(348;0.000812)|Ovarian(437;0.00328)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0182)|COAD - Colon adenocarcinoma(152;1.22e-05)|BRCA - Breast invasive adenocarcinoma(304;8.15e-05)|Kidney(64;0.000184)|GBM - Glioblastoma multiforme(114;0.00089)|KIRC - Kidney renal clear cell carcinoma(64;0.0027)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0652)		GATCATATACttttttttttt	0.025													5	3	---	---	---	---	
KDM1A	23028	broad.mit.edu	37	1	23377174	23377175	+	Intron	DEL	GT	-	-			TCGA-CZ-5460-01A-01D-1501-10	TCGA-CZ-5460-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:23377174_23377175delGT	uc001bgi.2	+						KDM1A_uc001bgj.2_Intron	NM_015013	NP_055828	O60341	KDM1A_HUMAN	lysine-specific histone demethylase 1 isoform b						blood coagulation|muscle cell development|negative regulation of apoptosis|negative regulation of DNA damage response, signal transduction by p53 class mediator|negative regulation of protein binding|negative regulation of sequence-specific DNA binding transcription factor activity|negative regulation of transcription from RNA polymerase II promoter|positive regulation of sequence-specific DNA binding transcription factor activity|positive regulation of transcription from RNA polymerase II promoter|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor	nuclear chromatin	androgen receptor binding|chromatin binding|enzyme binding|flavin adenine dinucleotide binding|histone demethylase activity (H3-dimethyl-K4 specific)|histone demethylase activity (H3-K9 specific)|ligand-dependent nuclear receptor transcription coactivator activity|MyoD binding|oxidoreductase activity|p53 binding|transcription regulatory region DNA binding			ovary(1)|lung(1)	2						tttcatttgggtatttaaaaaa	0.005													4	2	---	---	---	---	
KDM1A	23028	broad.mit.edu	37	1	23377178	23377179	+	Intron	INS	-	A	A			TCGA-CZ-5460-01A-01D-1501-10	TCGA-CZ-5460-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:23377178_23377179insA	uc001bgi.2	+						KDM1A_uc001bgj.2_Intron	NM_015013	NP_055828	O60341	KDM1A_HUMAN	lysine-specific histone demethylase 1 isoform b						blood coagulation|muscle cell development|negative regulation of apoptosis|negative regulation of DNA damage response, signal transduction by p53 class mediator|negative regulation of protein binding|negative regulation of sequence-specific DNA binding transcription factor activity|negative regulation of transcription from RNA polymerase II promoter|positive regulation of sequence-specific DNA binding transcription factor activity|positive regulation of transcription from RNA polymerase II promoter|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor	nuclear chromatin	androgen receptor binding|chromatin binding|enzyme binding|flavin adenine dinucleotide binding|histone demethylase activity (H3-dimethyl-K4 specific)|histone demethylase activity (H3-K9 specific)|ligand-dependent nuclear receptor transcription coactivator activity|MyoD binding|oxidoreductase activity|p53 binding|transcription regulatory region DNA binding			ovary(1)|lung(1)	2						atttgggtatttaaaaaatgta	0.010													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	39025381	39025381	+	IGR	DEL	G	-	-			TCGA-CZ-5460-01A-01D-1501-10	TCGA-CZ-5460-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:39025381delG								POU3F1 (512931 upstream) : RRAGC (279634 downstream)																							TGCCATCCCTGGGTCACCACT	0.537													4	2	---	---	---	---	
RIMKLA	284716	broad.mit.edu	37	1	42870005	42870006	+	Intron	INS	-	A	A			TCGA-CZ-5460-01A-01D-1501-10	TCGA-CZ-5460-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:42870005_42870006insA	uc001chi.2	+							NM_173642	NP_775913	Q8IXN7	RIMKA_HUMAN	ribosomal modification protein rimK-like family						protein modification process	cytoplasm	acid-amino acid ligase activity|ATP binding|metal ion binding				0						TTACCTCTCTGCTCCCACCTTT	0.406													8	4	---	---	---	---	
ZSWIM5	57643	broad.mit.edu	37	1	45667707	45667707	+	Intron	DEL	A	-	-			TCGA-CZ-5460-01A-01D-1501-10	TCGA-CZ-5460-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:45667707delA	uc001cnd.2	-							NM_020883	NP_065934	Q9P217	ZSWM5_HUMAN	zinc finger, SWIM domain containing 5								zinc ion binding				0	Acute lymphoblastic leukemia(166;0.155)					CATTGATCAGAAAAAAAAAAG	0.348													2	4	---	---	---	---	
CYP4Z2P	163720	broad.mit.edu	37	1	47348447	47348447	+	Intron	DEL	A	-	-			TCGA-CZ-5460-01A-01D-1501-10	TCGA-CZ-5460-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:47348447delA	uc001cqo.1	-						CYP4Z2P_uc009vyn.1_Intron	NR_002788				Homo sapiens cDNA FLJ40054 fis, clone TBAES2000315, weakly similar to CYTOCHROME P450 4A1 (EC 1.14.15.3).												0						AATACCCTCTACATAGCATTT	0.318													4	2	---	---	---	---	
LRP8	7804	broad.mit.edu	37	1	53724255	53724255	+	Intron	DEL	T	-	-			TCGA-CZ-5460-01A-01D-1501-10	TCGA-CZ-5460-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:53724255delT	uc001cvi.1	-						LRP8_uc001cvh.1_Intron|LRP8_uc001cvk.1_Intron|LRP8_uc001cvj.1_Intron|LRP8_uc001cvl.1_Intron|LRP8_uc001cvm.1_Intron	NM_004631	NP_004622	Q14114	LRP8_HUMAN	low density lipoprotein receptor-related protein						cytokine-mediated signaling pathway|endocytosis|lipid metabolic process|platelet activation|proteolysis	caveola	calcium ion binding|very-low-density lipoprotein particle receptor activity				0						TGCCCTATACTTTTTTTTTCA	0.313													4	2	---	---	---	---	
LPAR3	23566	broad.mit.edu	37	1	85304198	85304198	+	Intron	DEL	T	-	-			TCGA-CZ-5460-01A-01D-1501-10	TCGA-CZ-5460-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:85304198delT	uc001dkl.2	-						LPAR3_uc009wcj.1_Intron	NM_012152	NP_036284	Q9UBY5	LPAR3_HUMAN	lysophosphatidic acid receptor 3						G-protein signaling, coupled to cyclic nucleotide second messenger|synaptic transmission	integral to plasma membrane|intracellular membrane-bounded organelle				lung(3)|ovary(2)	5						gtaagtaccattgactctgcc	0.000													4	2	---	---	---	---	
C1orf59	113802	broad.mit.edu	37	1	109197114	109197114	+	Intron	DEL	G	-	-			TCGA-CZ-5460-01A-01D-1501-10	TCGA-CZ-5460-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:109197114delG	uc001dvt.3	-						C1orf59_uc001dvu.3_Intron|C1orf59_uc009wer.2_Intron	NM_001102592	NP_001096062	Q5T8I9	HENMT_HUMAN	hypothetical protein LOC113802						gene silencing by RNA|piRNA metabolic process	P granule	metal ion binding|O-methyltransferase activity|RNA binding|RNA methyltransferase activity				0		all_epithelial(167;0.000154)|all_lung(203;0.00026)|Lung NSC(277;0.000508)		Colorectal(144;0.0152)|Lung(183;0.0895)|COAD - Colon adenocarcinoma(174;0.114)|Epithelial(280;0.163)		TCTGGATAAAGGGGGGTATAG	0.348													4	2	---	---	---	---	
SORT1	6272	broad.mit.edu	37	1	109935815	109935815	+	Intron	DEL	C	-	-			TCGA-CZ-5460-01A-01D-1501-10	TCGA-CZ-5460-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:109935815delC	uc001dxm.1	-						SORT1_uc010ovi.1_5'UTR|SORT1_uc009wfb.2_5'UTR	NM_002959	NP_002950	Q99523	SORT_HUMAN	sortilin 1 preproprotein						endocytosis|endosome to lysosome transport|endosome transport via multivesicular body sorting pathway|glucose import|Golgi to endosome transport|induction of apoptosis by extracellular signals|myotube differentiation|negative regulation of apoptosis|negative regulation of lipoprotein lipase activity|neuropeptide signaling pathway|ossification|plasma membrane to endosome transport|regulation of gene expression|response to insulin stimulus|vesicle organization	cell surface|coated pit|early endosome|endoplasmic reticulum membrane|endosome membrane|Golgi cisterna membrane|integral to membrane|lysosomal membrane|microsome|nuclear membrane|perinuclear region of cytoplasm|plasma membrane	enzyme binding|nerve growth factor binding|nerve growth factor receptor activity|neurotensin receptor activity, non-G-protein coupled			ovary(1)	1		all_epithelial(167;4.69e-05)|all_lung(203;0.00016)|Lung NSC(277;0.000318)|Breast(1374;0.244)		Lung(183;0.0529)|Colorectal(144;0.142)|Epithelial(280;0.145)|Kidney(133;0.169)|all cancers(265;0.184)		AGAGCTGACACCCCATACAAC	0.488													4	2	---	---	---	---	
SYCP1	6847	broad.mit.edu	37	1	115456781	115456782	+	Intron	INS	-	T	T			TCGA-CZ-5460-01A-01D-1501-10	TCGA-CZ-5460-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:115456781_115456782insT	uc001efr.2	+						SYCP1_uc010owt.1_Intron|SYCP1_uc001efq.2_Intron|SYCP1_uc009wgw.2_Intron	NM_003176	NP_003167	Q15431	SYCP1_HUMAN	synaptonemal complex protein 1						cell division|reciprocal meiotic recombination|spermatogenesis|synaptonemal complex assembly		DNA binding			skin(1)	1	Lung SC(450;0.211)	all_cancers(81;8.65e-08)|all_epithelial(167;3.32e-07)|all_lung(203;6.55e-06)|Lung NSC(69;1.11e-05)|Acute lymphoblastic leukemia(138;0.221)		Lung(183;0.0234)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|all cancers(265;0.112)|Epithelial(280;0.124)|LUSC - Lung squamous cell carcinoma(189;0.133)		TATAAAGTAAAAATTAGATATA	0.238													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	121481322	121481323	+	IGR	DEL	GA	-	-	rs147513325		TCGA-CZ-5460-01A-01D-1501-10	TCGA-CZ-5460-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:121481322_121481323delGA								LOC647121 (167636 upstream) : None (None downstream)																							aggagtttctgagaatgcttct	0.000													4	2	---	---	---	---	
NBPF9	400818	broad.mit.edu	37	1	145109975	145109976	+	Intron	INS	-	C	C	rs11458983		TCGA-CZ-5460-01A-01D-1501-10	TCGA-CZ-5460-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:145109975_145109976insC	uc010oye.1	+						NBPF10_uc009wir.2_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|SEC22B_uc001eml.1_Intron			Q3BBV1	NBPFK_HUMAN	RecName: Full=Neuroblastoma breakpoint family member 8;							cytoplasm					0						CAGGAACTTTGCTAAAGATCTA	0.386													6	4	---	---	---	---	
ANP32E	81611	broad.mit.edu	37	1	150195337	150195337	+	Intron	DEL	A	-	-			TCGA-CZ-5460-01A-01D-1501-10	TCGA-CZ-5460-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:150195337delA	uc001etw.2	-						ANP32E_uc010pbt.1_Intron|ANP32E_uc010pbu.1_Intron|ANP32E_uc010pbv.1_Intron|ANP32E_uc001etv.3_Intron	NM_030920	NP_112182	Q9BTT0	AN32E_HUMAN	acidic (leucine-rich) nuclear phosphoprotein 32							cytoplasmic membrane-bounded vesicle|nucleus	phosphatase inhibitor activity				0	Lung NSC(24;7.29e-29)|Breast(34;0.00211)|Ovarian(49;0.0167)|all_hematologic(923;0.0597)|Hepatocellular(266;0.161)|Colorectal(459;0.171)		LUSC - Lung squamous cell carcinoma(543;0.171)			AATTACTCTTAAAAAAAAAAC	0.289													13	7	---	---	---	---	
CGN	57530	broad.mit.edu	37	1	151508576	151508576	+	Intron	DEL	T	-	-			TCGA-CZ-5460-01A-01D-1501-10	TCGA-CZ-5460-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:151508576delT	uc009wmw.2	+						CGN_uc010pde.1_Intron	NM_020770	NP_065821	Q9P2M7	CING_HUMAN	cingulin							myosin complex|tight junction	actin binding|motor activity			ovary(2)|pancreas(1)	3	Ovarian(49;0.0273)|Hepatocellular(266;0.0997)|all_hematologic(923;0.127)|Melanoma(130;0.185)		LUSC - Lung squamous cell carcinoma(543;0.181)			TCCCTCATTCTTTGAATCTGC	0.498													4	2	---	---	---	---	
GON4L	54856	broad.mit.edu	37	1	155722431	155722432	+	Intron	DEL	CT	-	-			TCGA-CZ-5460-01A-01D-1501-10	TCGA-CZ-5460-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:155722431_155722432delCT	uc001flz.2	-						GON4L_uc001flx.1_5'Flank|GON4L_uc009wrg.1_Intron|GON4L_uc001fly.1_Intron|GON4L_uc009wrh.1_Intron|GON4L_uc001fma.1_Intron	NM_001037533	NP_001032622	Q3T8J9	GON4L_HUMAN	gon-4-like isoform a						regulation of transcription, DNA-dependent	cytoplasm|nucleus	DNA binding			ovary(3)	3	Hepatocellular(266;0.0997)|all_hematologic(923;0.145)|all_neural(408;0.195)					CAAGATGCACCTAAGCACGAGA	0.356													4	2	---	---	---	---	
CD247	919	broad.mit.edu	37	1	167443804	167443804	+	Intron	DEL	C	-	-			TCGA-CZ-5460-01A-01D-1501-10	TCGA-CZ-5460-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:167443804delC	uc001gei.3	-						CD247_uc001gej.3_Intron|CD247_uc001gek.2_Intron	NM_198053	NP_932170	P20963	CD3Z_HUMAN	T-cell receptor zeta chain isoform 1 precursor						interspecies interaction between organisms|regulation of defense response to virus by virus|T cell costimulation|T cell receptor signaling pathway|viral reproduction	cytoplasm|integral to membrane	protein homodimerization activity|transmembrane receptor activity				0			LUSC - Lung squamous cell carcinoma(543;0.236)			actggctgagcccccggtctg	0.119													4	2	---	---	---	---	
WDR35	57539	broad.mit.edu	37	2	20138257	20138257	+	Intron	DEL	A	-	-			TCGA-CZ-5460-01A-01D-1501-10	TCGA-CZ-5460-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:20138257delA	uc002rdi.2	-						WDR35_uc002rdj.2_Intron|WDR35_uc010ext.2_Intron|WDR35_uc002rdh.2_Intron|WDR35_uc002rdk.3_Intron	NM_001006657	NP_001006658	Q9P2L0	WDR35_HUMAN	WD repeat domain 35 isoform 1											ovary(1)	1	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					ACAAAACAAGAAAAAAAACGG	0.303													4	2	---	---	---	---	
DNMT3A	1788	broad.mit.edu	37	2	25536759	25536759	+	Intron	DEL	C	-	-			TCGA-CZ-5460-01A-01D-1501-10	TCGA-CZ-5460-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:25536759delC	uc002rgc.2	-						DNMT3A_uc002rgd.2_Intron|DNMT3A_uc010eyi.2_Intron|DNMT3A_uc002rge.2_Intron|DNMT3A_uc002rgf.2_Intron	NM_022552	NP_072046	Q9Y6K1	DNM3A_HUMAN	DNA cytosine methyltransferase 3 alpha isoform						regulation of gene expression by genetic imprinting	cytoplasm|euchromatin|nuclear matrix	DNA (cytosine-5-)-methyltransferase activity|DNA binding|metal ion binding|protein binding			haematopoietic_and_lymphoid_tissue(133)|lung(4)|ovary(3)	140	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					GCCAGAGGGTCCCCAGCAGAG	0.567			Mis|F|N|S		AML								4	2	---	---	---	---	
GTF3C2	2976	broad.mit.edu	37	2	27576324	27576324	+	Intron	DEL	G	-	-			TCGA-CZ-5460-01A-01D-1501-10	TCGA-CZ-5460-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:27576324delG	uc002rjv.1	-						GTF3C2_uc002rju.1_Intron|GTF3C2_uc002rjw.1_Intron|GTF3C2_uc010eyz.1_Intron	NM_001521	NP_001512	Q8WUA4	TF3C2_HUMAN	general transcription factor IIIC, polypeptide							transcription factor TFIIIC complex				ovary(1)|skin(1)	2	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					ttgtttttttgagacagagtc	0.065													4	2	---	---	---	---	
IFT172	26160	broad.mit.edu	37	2	27669366	27669366	+	Intron	DEL	T	-	-	rs34019186		TCGA-CZ-5460-01A-01D-1501-10	TCGA-CZ-5460-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:27669366delT	uc002rku.2	-						IFT172_uc010ezb.2_Intron	NM_015662	NP_056477	Q9UG01	IF172_HUMAN	selective LIM binding factor homolog						cilium assembly	cilium	binding			large_intestine(1)|ovary(1)	2	Acute lymphoblastic leukemia(172;0.155)					TGGGTCTTAGttttttttttc	0.204													8	4	---	---	---	---	
SLC30A6	55676	broad.mit.edu	37	2	32399396	32399397	+	Intron	INS	-	G	G			TCGA-CZ-5460-01A-01D-1501-10	TCGA-CZ-5460-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:32399396_32399397insG	uc002roe.1	+						SLC30A6_uc002rof.1_Intron|SLC30A6_uc010ymw.1_Intron|SLC30A6_uc010ezr.1_Intron|SLC30A6_uc002rog.1_Intron|SLC30A6_uc010ezs.1_Intron|SLC30A6_uc002roh.1_Intron	NM_017964	NP_060434	Q6NXT4	ZNT6_HUMAN	solute carrier family 30 (zinc transporter),							Golgi membrane|integral to membrane	zinc ion transmembrane transporter activity				0	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.208)					ATTTGTTAGGATTGtaattttt	0.129													7	4	---	---	---	---	
EML4	27436	broad.mit.edu	37	2	42553087	42553087	+	Intron	DEL	A	-	-			TCGA-CZ-5460-01A-01D-1501-10	TCGA-CZ-5460-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:42553087delA	uc002rsi.2	+						EML4_uc010fap.2_Intron|EML4_uc002rsj.2_Intron|EML4_uc010faq.2_Intron|EML4_uc010ynv.1_Intron	NM_019063	NP_061936	Q9HC35	EMAL4_HUMAN	echinoderm microtubule associated protein like 4						microtubule-based process|mitosis	cytoplasm|microtubule	protein binding		EML4/ALK(246)	lung(246)|ovary(2)|central_nervous_system(1)|skin(1)	250						TTTTTAGAGGAAAAAAAAAAC	0.333			T	ALK	NSCLC								6	3	---	---	---	---	
CLEC4F	165530	broad.mit.edu	37	2	71037179	71037179	+	Intron	DEL	T	-	-			TCGA-CZ-5460-01A-01D-1501-10	TCGA-CZ-5460-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:71037179delT	uc002shf.2	-						CLEC4F_uc010yqv.1_Intron	NM_173535	NP_775806	Q8N1N0	CLC4F_HUMAN	C-type lectin, superfamily member 13						endocytosis	integral to membrane	receptor activity|sugar binding			ovary(5)	5						TACTATAGAATTTTTTAGGAT	0.289													4	2	---	---	---	---	
C2orf51	200523	broad.mit.edu	37	2	88826185	88826185	+	Intron	DEL	T	-	-	rs76507069		TCGA-CZ-5460-01A-01D-1501-10	TCGA-CZ-5460-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:88826185delT	uc002stb.1	+							NM_152670	NP_689883	Q96LM6	TSC21_HUMAN	chromosome 2 open reading frame 51							nucleus				skin(1)	1						TGTGTGTGTAttttttttttc	0.194													4	2	---	---	---	---	
ANAPC1	64682	broad.mit.edu	37	2	112552048	112552048	+	Intron	DEL	T	-	-			TCGA-CZ-5460-01A-01D-1501-10	TCGA-CZ-5460-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:112552048delT	uc002thi.2	-							NM_022662	NP_073153	Q9H1A4	APC1_HUMAN	anaphase promoting complex subunit 1						anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|cell division|mitosis|mitotic cell cycle spindle assembly checkpoint|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|protein K11-linked ubiquitination	anaphase-promoting complex|cytosol|nucleoplasm				skin(2)	2						TTTCTATGTATTTTTTTTTCA	0.343													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	133107763	133107764	+	IGR	INS	-	C	C	rs143923523	by1000genomes	TCGA-CZ-5460-01A-01D-1501-10	TCGA-CZ-5460-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:133107763_133107764insC								NCRNA00164 (92221 upstream) : GPR39 (66383 downstream)																							gatagactttttcccccacttt	0.000													4	2	---	---	---	---	
LY75	4065	broad.mit.edu	37	2	160665324	160665324	+	Intron	DEL	T	-	-			TCGA-CZ-5460-01A-01D-1501-10	TCGA-CZ-5460-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:160665324delT	uc002ubc.3	-						LY75_uc002ubb.3_Intron|LY75_uc010fos.2_Intron	NM_002349	NP_002340	O60449	LY75_HUMAN	lymphocyte antigen 75 precursor						endocytosis|immune response|inflammatory response	integral to plasma membrane	receptor activity|sugar binding				0				COAD - Colon adenocarcinoma(177;0.132)		TCTGGCAATATTTTTTTGGCC	0.209													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	166827413	166827413	+	IGR	DEL	G	-	-			TCGA-CZ-5460-01A-01D-1501-10	TCGA-CZ-5460-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:166827413delG								TTC21B (17065 upstream) : SCN1A (18258 downstream)																							tgctctgattgtttgctagtg	0.000													4	2	---	---	---	---	
PPIG	9360	broad.mit.edu	37	2	170463838	170463839	+	Intron	INS	-	A	A			TCGA-CZ-5460-01A-01D-1501-10	TCGA-CZ-5460-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:170463838_170463839insA	uc002uez.2	+						PPIG_uc010fpx.2_Intron|PPIG_uc010fpy.2_Intron|PPIG_uc002ufa.2_Intron|PPIG_uc002ufb.2_Intron|PPIG_uc002ufc.1_Intron|PPIG_uc002ufd.2_Intron	NM_004792	NP_004783	Q13427	PPIG_HUMAN	peptidylprolyl isomerase G						protein folding|RNA splicing	nuclear matrix|nuclear speck	cyclosporin A binding|peptidyl-prolyl cis-trans isomerase activity			ovary(2)|central_nervous_system(1)	3					L-Proline(DB00172)	GGTATTTTTTCTTCTTAGGACA	0.292													14	10	---	---	---	---	
SPATS2L	26010	broad.mit.edu	37	2	201342225	201342226	+	Intron	INS	-	G	G			TCGA-CZ-5460-01A-01D-1501-10	TCGA-CZ-5460-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:201342225_201342226insG	uc002uvn.3	+						SPATS2L_uc010fst.2_Intron|SPATS2L_uc002uvo.3_Intron|SPATS2L_uc002uvp.3_Intron|SPATS2L_uc002uvq.3_Intron|SPATS2L_uc002uvr.3_Intron|SPATS2L_uc010zhc.1_Intron	NM_015535	NP_056350	Q9NUQ6	SPS2L_HUMAN	SPATS2-like protein isoform a							cytoplasm|nucleolus				ovary(2)|pancreas(1)	3						TGTTTTCTGATTCTTCTGGTGT	0.337													3	3	---	---	---	---	
RAPH1	65059	broad.mit.edu	37	2	204322563	204322563	+	Intron	DEL	C	-	-			TCGA-CZ-5460-01A-01D-1501-10	TCGA-CZ-5460-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:204322563delC	uc002vad.2	-						RAPH1_uc002vae.2_Intron|RAPH1_uc002vaf.2_Intron	NM_213589	NP_998754	Q70E73	RAPH1_HUMAN	Ras association and pleckstrin homology domains						cell-matrix adhesion|signal transduction	cytoplasm|cytoskeleton|filopodium|lamellipodium|nucleus|plasma membrane				ovary(3)|breast(3)|central_nervous_system(2)|lung(1)|skin(1)	10						ACTGTCCTTACCCAGACTGTG	0.383													4	2	---	---	---	---	
UNC80	285175	broad.mit.edu	37	2	210791909	210791909	+	Intron	DEL	A	-	-			TCGA-CZ-5460-01A-01D-1501-10	TCGA-CZ-5460-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:210791909delA	uc010zjc.1	+						UNC80_uc002vdk.2_Intron	NM_032504	NP_115893	Q8N2C7	UNC80_HUMAN	chromosome 2 open reading frame 21 isoform 1							integral to membrane					0						CTTTATGGCCAAAAAAATTGC	0.363													4	2	---	---	---	---	
SGPP2	130367	broad.mit.edu	37	2	223317407	223317407	+	Intron	DEL	C	-	-			TCGA-CZ-5460-01A-01D-1501-10	TCGA-CZ-5460-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:223317407delC	uc010zlo.1	+						SGPP2_uc010zlp.1_Intron	NM_152386	NP_689599	Q8IWX5	SGPP2_HUMAN	sphingosine-1-phosphate phosphotase 2						sphingosine metabolic process	endoplasmic reticulum membrane|integral to membrane	dihydrosphingosine-1-phosphate phosphatase activity|sphingosine-1-phosphate phosphatase activity			central_nervous_system(1)|skin(1)	2		Renal(207;0.0376)		Epithelial(121;2.08e-09)|all cancers(144;9.25e-07)|LUSC - Lung squamous cell carcinoma(224;0.011)|Lung(261;0.0143)		GCTGTGGTTGCTGCAGCTTGA	0.537													4	2	---	---	---	---	
SLC16A14	151473	broad.mit.edu	37	2	230902403	230902403	+	Intron	DEL	T	-	-			TCGA-CZ-5460-01A-01D-1501-10	TCGA-CZ-5460-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:230902403delT	uc002vqd.1	-						FBXO36_uc010fxi.1_Intron	NM_152527	NP_689740	Q7RTX9	MOT14_HUMAN	solute carrier family 16 (monocarboxylic acid							integral to membrane|plasma membrane	symporter activity			ovary(4)|skin(2)	6		Renal(207;0.025)|all_hematologic(139;0.122)|all_lung(227;0.149)|Acute lymphoblastic leukemia(138;0.164)		Epithelial(121;7.31e-13)|all cancers(144;5.1e-10)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(119;0.00948)		tttcttttccttttttttttt	0.318													2	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	3556043	3556045	+	IGR	DEL	TAG	-	-	rs56740717	byFrequency	TCGA-CZ-5460-01A-01D-1501-10	TCGA-CZ-5460-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:3556043_3556045delTAG								CRBN (334653 upstream) : SUMF1 (266991 downstream)																							ctaaatagaatagtaagaaaaca	0.074													4	2	---	---	---	---	
CPNE9	151835	broad.mit.edu	37	3	9771017	9771017	+	Intron	DEL	A	-	-			TCGA-CZ-5460-01A-01D-1501-10	TCGA-CZ-5460-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:9771017delA	uc003bsd.2	+						BRPF1_uc003bse.2_5'Flank|BRPF1_uc003bsf.2_5'Flank|BRPF1_uc003bsg.2_5'Flank|BRPF1_uc011ati.1_5'Flank	NM_153635	NP_705899	Q8IYJ1	CPNE9_HUMAN	copine-like protein											ovary(2)	2	Medulloblastoma(99;0.227)					taaaaggtggaaaaaaaagtg	0.000													4	2	---	---	---	---	
IQSEC1	9922	broad.mit.edu	37	3	13104837	13104837	+	Intron	DEL	A	-	-			TCGA-CZ-5460-01A-01D-1501-10	TCGA-CZ-5460-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:13104837delA	uc011auw.1	-							NM_001134382	NP_001127854	Q6DN90	IQEC1_HUMAN	IQ motif and Sec7 domain 1 isoform a						regulation of ARF protein signal transduction	cytoplasm|nucleus	ARF guanyl-nucleotide exchange factor activity			ovary(1)	1						TCCTTCCCTTAACCTTTTAGC	0.393													4	2	---	---	---	---	
KLHL18	23276	broad.mit.edu	37	3	47338967	47338968	+	Intron	DEL	GG	-	-			TCGA-CZ-5460-01A-01D-1501-10	TCGA-CZ-5460-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:47338967_47338968delGG	uc003crd.2	+						KLHL18_uc003crc.2_Intron|KLHL18_uc011bav.1_Intron	NM_025010	NP_079286	O94889	KLH18_HUMAN	kelch-like 18												0		Acute lymphoblastic leukemia(5;0.164)		BRCA - Breast invasive adenocarcinoma(193;0.000292)|KIRC - Kidney renal clear cell carcinoma(197;0.00645)|Kidney(197;0.00741)		CTTCAGGACTGGGAATGCACTG	0.431													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	51967046	51967047	+	IGR	INS	-	C	C			TCGA-CZ-5460-01A-01D-1501-10	TCGA-CZ-5460-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:51967046_51967047insC								IQCF1 (29660 upstream) : RRP9 (399 downstream)																							CCTGACCCCCACACCTCACGGC	0.579													4	3	---	---	---	---	
PBRM1	55193	broad.mit.edu	37	3	52584765	52584766	+	Frame_Shift_Ins	INS	-	TT	TT			TCGA-CZ-5460-01A-01D-1501-10	TCGA-CZ-5460-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:52584765_52584766insTT	uc003des.2	-	28	4689_4690	c.4677_4678insAA	c.(4675-4680)CAACAGfs	p.Q1559fs	PBRM1_uc003dex.2_RNA|PBRM1_uc003deq.2_Frame_Shift_Ins_p.Q1452fs|PBRM1_uc003der.2_Frame_Shift_Ins_p.Q1472fs|PBRM1_uc003det.2_Frame_Shift_Ins_p.Q1467fs|PBRM1_uc003deu.2_Frame_Shift_Ins_p.Q1522fs|PBRM1_uc003dev.2_RNA|PBRM1_uc003dew.2_Frame_Shift_Ins_p.Q1504fs|PBRM1_uc010hmk.1_Frame_Shift_Ins_p.Q1479fs|PBRM1_uc003dey.2_Frame_Shift_Ins_p.Q1452fs	NM_181042	NP_060635	Q86U86	PB1_HUMAN	polybromo 1 isoform 4	1559_1560	Pro-rich.		Q -> H (found in an endometrial cancer cell line).		chromatin remodeling|mitosis|negative regulation of cell proliferation|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nuclear chromosome	chromatin binding|DNA binding|protein binding			kidney(136)|breast(4)	140				BRCA - Breast invasive adenocarcinoma(193;1.8e-05)|Kidney(197;0.00105)|KIRC - Kidney renal clear cell carcinoma(197;0.00122)|OV - Ovarian serous cystadenocarcinoma(275;0.0613)		AGGCTCACCTGTTGTCCATATG	0.480			Mis|N|F|S|D|O		clear cell renal carcinoma|breast								32	21	---	---	---	---	
CADPS	8618	broad.mit.edu	37	3	62431257	62431257	+	Intron	DEL	A	-	-			TCGA-CZ-5460-01A-01D-1501-10	TCGA-CZ-5460-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:62431257delA	uc003dll.2	-						CADPS_uc003dlj.1_Intron|CADPS_uc003dlk.1_Intron|CADPS_uc003dlm.2_Intron|CADPS_uc003dln.2_Intron	NM_003716	NP_003707	Q9ULU8	CAPS1_HUMAN	Ca2+-dependent secretion activator isoform 1						exocytosis|protein transport	cell junction|cytoplasmic vesicle membrane|cytosol|synapse	lipid binding|metal ion binding			central_nervous_system(2)|ovary(1)	3		Lung SC(41;0.0452)		BRCA - Breast invasive adenocarcinoma(55;5.98e-05)|KIRC - Kidney renal clear cell carcinoma(15;0.0246)|Kidney(15;0.0334)		TTCTTATCTGAAAAAAAAATT	0.358													4	2	---	---	---	---	
KIAA1524	57650	broad.mit.edu	37	3	108279408	108279408	+	Intron	DEL	G	-	-			TCGA-CZ-5460-01A-01D-1501-10	TCGA-CZ-5460-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:108279408delG	uc003dxb.3	-							NM_020890	NP_065941	Q8TCG1	CIP2A_HUMAN	p90 autoantigen							cytoplasm|integral to membrane	protein binding			ovary(2)|central_nervous_system(1)	3						AGTGAAATCTGTACCTGACAG	0.279													4	2	---	---	---	---	
ADCY5	111	broad.mit.edu	37	3	123057619	123057621	+	Intron	DEL	CCA	-	-			TCGA-CZ-5460-01A-01D-1501-10	TCGA-CZ-5460-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:123057619_123057621delCCA	uc003egh.1	-						ADCY5_uc003egg.1_Intron|ADCY5_uc003egi.1_Intron	NM_183357	NP_899200	O95622	ADCY5_HUMAN	adenylate cyclase 5						activation of phospholipase C activity|activation of protein kinase A activity|cellular response to glucagon stimulus|energy reserve metabolic process|nerve growth factor receptor signaling pathway|synaptic transmission|transmembrane transport|water transport	integral to membrane|plasma membrane	adenylate cyclase activity|ATP binding|metal ion binding			ovary(4)	4				GBM - Glioblastoma multiforme(114;0.0342)		CTTCAGCCCTCCACAGCAGCTTT	0.522													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	155779590	155779590	+	IGR	DEL	T	-	-			TCGA-CZ-5460-01A-01D-1501-10	TCGA-CZ-5460-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:155779590delT								GMPS (124072 upstream) : KCNAB1 (58747 downstream)																							acttctcttattttttatgat	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	174215425	174215426	+	Intron	INS	-	T	T	rs72585450	by1000genomes	TCGA-CZ-5460-01A-01D-1501-10	TCGA-CZ-5460-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:174215425_174215426insT	uc003fiq.1	+						uc003fir.2_Intron|uc003fis.2_Intron|uc010hwx.1_Intron					Homo sapiens NAALADL2 gene, partial 5'UTR, variant 1.																		tcataaatgtctgtcttcccta	0.099													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	184413058	184413058	+	IGR	DEL	C	-	-			TCGA-CZ-5460-01A-01D-1501-10	TCGA-CZ-5460-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:184413058delC								EPHB3 (112863 upstream) : MAGEF1 (15098 downstream)																							cataatcagtcccctcgttgt	0.020													4	2	---	---	---	---	
FYTTD1	84248	broad.mit.edu	37	3	197504101	197504101	+	Intron	DEL	G	-	-			TCGA-CZ-5460-01A-01D-1501-10	TCGA-CZ-5460-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:197504101delG	uc003fyi.2	+						FYTTD1_uc011bui.1_Intron|FYTTD1_uc011buj.1_Intron|FYTTD1_uc011buk.1_Intron	NM_032288	NP_115664	Q96QD9	UIF_HUMAN	forty-two-three domain containing 1 isoform 1						mRNA export from nucleus	nuclear speck	mRNA binding|protein binding				0	all_cancers(143;1.15e-09)|Ovarian(172;0.0418)|Breast(254;0.0976)	Lung NSC(153;0.132)	Epithelial(36;2.19e-23)|all cancers(36;1.39e-21)|OV - Ovarian serous cystadenocarcinoma(49;1.21e-18)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(93;0.175)		TGTTTTTTATGTTTTAAAAAT	0.234													7	4	---	---	---	---	
RNF4	6047	broad.mit.edu	37	4	2477681	2477681	+	Intron	DEL	G	-	-			TCGA-CZ-5460-01A-01D-1501-10	TCGA-CZ-5460-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:2477681delG	uc003gfb.2	+						RNF4_uc010ici.1_Intron|RNF4_uc010icj.2_Intron|RNF4_uc003gfc.2_Intron	NM_002938	NP_002929	P78317	RNF4_HUMAN	ring finger protein 4						androgen receptor signaling pathway|positive regulation of transcription from RNA polymerase II promoter|proteasomal ubiquitin-dependent protein catabolic process|protein autoubiquitination|protein K11-linked ubiquitination|protein K48-linked ubiquitination|protein K6-linked ubiquitination|protein K63-linked ubiquitination|regulation of kinetochore assembly|regulation of spindle assembly|response to arsenic-containing substance	cytoplasm|PML body	androgen receptor binding|DNA binding|nucleosome binding|sequence-specific DNA binding transcription factor activity|SUMO polymer binding|transcription coactivator activity|ubiquitin-protein ligase activity|zinc ion binding				0		all_epithelial(65;0.241)				TTTGTGTGGTGGGAAAGCACA	0.239													4	2	---	---	---	---	
TBC1D1	23216	broad.mit.edu	37	4	38029257	38029257	+	Intron	DEL	A	-	-	rs79921949		TCGA-CZ-5460-01A-01D-1501-10	TCGA-CZ-5460-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:38029257delA	uc003gtb.2	+						TBC1D1_uc011byd.1_Intron|TBC1D1_uc010ifd.2_Intron|TBC1D1_uc011byf.1_Intron	NM_015173	NP_055988	Q86TI0	TBCD1_HUMAN	TBC1 (tre-2/USP6, BUB2, cdc16) domain family,							nucleus	Rab GTPase activator activity			ovary(1)	1						attccatgtcaaaaaaaaaaa	0.164													6	3	---	---	---	---	
BEND4	389206	broad.mit.edu	37	4	42146104	42146104	+	Intron	DEL	A	-	-			TCGA-CZ-5460-01A-01D-1501-10	TCGA-CZ-5460-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:42146104delA	uc003gwn.2	-						BEND4_uc003gwm.2_Intron|BEND4_uc011byy.1_Intron	NM_207406	NP_997289	Q6ZU67	BEND4_HUMAN	BEN domain containing 4 isoform a												0						CAAACATGTTAAAAATATGTA	0.383													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	55618879	55618879	+	IGR	DEL	A	-	-			TCGA-CZ-5460-01A-01D-1501-10	TCGA-CZ-5460-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:55618879delA								KIT (12000 upstream) : KDR (325548 downstream)																							atccaACTGTAAGTATTTTTG	0.209													4	2	---	---	---	---	
MRPL1	65008	broad.mit.edu	37	4	78808668	78808669	+	Intron	DEL	GT	-	-	rs7692075	by1000genomes	TCGA-CZ-5460-01A-01D-1501-10	TCGA-CZ-5460-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:78808668_78808669delGT	uc003hku.2	+						MRPL1_uc010iji.1_Intron	NM_020236	NP_064621	Q9BYD6	RM01_HUMAN	mitochondrial ribosomal protein L1 precursor								RNA binding				0						tttatttggggtgtgtgtgtgt	0.129													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	118496039	118496040	+	IGR	INS	-	A	A			TCGA-CZ-5460-01A-01D-1501-10	TCGA-CZ-5460-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:118496039_118496040insA								TRAM1L1 (489303 upstream) : NDST3 (458733 downstream)																							TCTTTTTTTTTAATGGGTTAGA	0.342													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	155779298	155779298	+	IGR	DEL	T	-	-			TCGA-CZ-5460-01A-01D-1501-10	TCGA-CZ-5460-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:155779298delT								RBM46 (29334 upstream) : NPY2R (350483 downstream)																							tgggaaaggattctaagggtg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	189555086	189555087	+	IGR	DEL	TG	-	-			TCGA-CZ-5460-01A-01D-1501-10	TCGA-CZ-5460-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:189555086_189555087delTG								TRIML1 (486437 upstream) : None (None downstream)																							ccaccacacatgtagaaagctt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	190200905	190200906	+	IGR	INS	-	A	A	rs113873531		TCGA-CZ-5460-01A-01D-1501-10	TCGA-CZ-5460-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:190200905_190200906insA								None (None upstream) : FRG1 (661068 downstream)																							agcatgaacttagagtaatcaa	0.139													5	4	---	---	---	---	
NUP155	9631	broad.mit.edu	37	5	37326280	37326281	+	Intron	DEL	AA	-	-			TCGA-CZ-5460-01A-01D-1501-10	TCGA-CZ-5460-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:37326280_37326281delAA	uc003jku.1	-						NUP155_uc003jkt.1_Intron|NUP155_uc010iuz.1_Intron	NM_153485	NP_705618	O75694	NU155_HUMAN	nucleoporin 155kDa isoform 1						carbohydrate metabolic process|glucose transport|mRNA transport|nucleocytoplasmic transport|protein transport|regulation of glucose transport|transmembrane transport|viral reproduction	nuclear membrane|nuclear pore	protein binding|structural constituent of nuclear pore|transporter activity			ovary(1)	1	all_lung(31;0.000137)		COAD - Colon adenocarcinoma(61;0.14)|Colorectal(62;0.202)			AATATTACTGAAGAAAAATCAA	0.282													4	4	---	---	---	---	
SERINC5	256987	broad.mit.edu	37	5	79488426	79488427	+	Intron	DEL	CA	-	-			TCGA-CZ-5460-01A-01D-1501-10	TCGA-CZ-5460-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:79488426_79488427delCA	uc003kgj.2	-						SERINC5_uc003kgk.2_Intron|SERINC5_uc003kgl.2_Intron|SERINC5_uc003kgm.2_Intron|SERINC5_uc011ctj.1_Intron	NM_178276	NP_840060	Q86VE9	SERC5_HUMAN	developmentally regulated protein TPO1						phosphatidylserine metabolic process|phospholipid biosynthetic process|positive regulation of transferase activity	endoplasmic reticulum membrane|integral to membrane				ovary(1)	1		Lung NSC(167;0.00328)|all_lung(232;0.00356)|Ovarian(174;0.0261)		OV - Ovarian serous cystadenocarcinoma(54;2.93e-46)|Epithelial(54;5.59e-40)|all cancers(79;1.89e-34)		TCACATCTGTCACACAAACACA	0.455													4	2	---	---	---	---	
APC	324	broad.mit.edu	37	5	112127944	112127944	+	Intron	DEL	A	-	-			TCGA-CZ-5460-01A-01D-1501-10	TCGA-CZ-5460-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:112127944delA	uc010jby.2	+						APC_uc011cvt.1_Intron|APC_uc003kpz.3_Intron|APC_uc003kpy.3_Intron|APC_uc010jbz.2_Intron	NM_001127511	NP_001120983	P25054	APC_HUMAN	adenomatous polyposis coli						canonical Wnt receptor signaling pathway|cell adhesion|cell cycle arrest|cell migration|cellular component disassembly involved in apoptosis|cytokinesis after mitosis|mitotic cell cycle spindle assembly checkpoint|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of cyclin-dependent protein kinase activity|negative regulation of microtubule depolymerization|positive regulation of apoptosis|positive regulation of cell migration|positive regulation of pseudopodium assembly|protein complex assembly|regulation of attachment of spindle microtubules to kinetochore|response to DNA damage stimulus|tight junction assembly	adherens junction|APC-Axin-1-beta-catenin complex|Axin-APC-beta-catenin-GSK3B complex|beta-catenin destruction complex|centrosome|cytosol|kinetochore|lamellipodium|lateral plasma membrane|nucleus|ruffle membrane|tight junction	beta-catenin binding|gamma-catenin binding|microtubule plus-end binding|protein kinase binding|protein kinase regulator activity			large_intestine(2123)|stomach(123)|soft_tissue(55)|small_intestine(34)|breast(26)|pancreas(25)|urinary_tract(20)|lung(19)|thyroid(18)|liver(13)|central_nervous_system(10)|ovary(9)|skin(7)|upper_aerodigestive_tract(6)|adrenal_gland(6)|bone(6)|NS(5)|prostate(4)|endometrium(3)|kidney(1)|oesophagus(1)|biliary_tract(1)	2515		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		ctctgtctcgaaaaaaaaaga	0.100		12	D|Mis|N|F|S		colorectal|pancreatic|desmoid|hepatoblastoma|glioma|other CNS	colorectal|pancreatic|desmoid|hepatoblastoma|glioma|other CNS			Hereditary_Desmoid_Disease|Familial_Adenomatous_Polyposis|Turcot_syndrome	TSP Lung(16;0.13)			4	2	---	---	---	---	
ALDH7A1	501	broad.mit.edu	37	5	125911335	125911336	+	Intron	DEL	CT	-	-			TCGA-CZ-5460-01A-01D-1501-10	TCGA-CZ-5460-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:125911335_125911336delCT	uc003ktx.2	-						ALDH7A1_uc003kty.2_Intron|ALDH7A1_uc011cxa.1_Intron|ALDH7A1_uc003ktz.2_Intron	NM_001182	NP_001173	P49419	AL7A1_HUMAN	aldehyde dehydrogenase 7 family, member A1						cellular aldehyde metabolic process|lysine catabolic process|sensory perception of sound	cytosol|mitochondrial matrix|nucleus	aldehyde dehydrogenase (NAD) activity|betaine-aldehyde dehydrogenase activity|L-aminoadipate-semialdehyde dehydrogenase activity			kidney(2)|ovary(1)	3		all_cancers(142;0.24)|Prostate(80;0.081)	KIRC - Kidney renal clear cell carcinoma(527;0.0584)|Kidney(363;0.0934)	Epithelial(69;0.0417)|OV - Ovarian serous cystadenocarcinoma(64;0.068)|all cancers(49;0.109)	NADH(DB00157)|Pyridoxine(DB00165)	TCTTTGAGACCTAAGGAACAAC	0.406													4	2	---	---	---	---	
TGFBI	7045	broad.mit.edu	37	5	135396961	135396961	+	Intron	DEL	C	-	-			TCGA-CZ-5460-01A-01D-1501-10	TCGA-CZ-5460-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:135396961delC	uc003lbf.3	+						TGFBI_uc003lbg.3_Intron|TGFBI_uc003lbh.3_Intron|TGFBI_uc011cyb.1_Intron|TGFBI_uc010jed.2_Intron|TGFBI_uc010jee.2_5'Flank	NM_000358	NP_000349	Q15582	BGH3_HUMAN	transforming growth factor, beta-induced, 68kDa						angiogenesis|cell adhesion|cell proliferation|negative regulation of cell adhesion|response to stimulus|visual perception	extracellular space|proteinaceous extracellular matrix	integrin binding			breast(3)|ovary(1)	4			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)			TTCCTTGCCTCCAGTGCAGTT	0.527													4	2	---	---	---	---	
HAVCR1	26762	broad.mit.edu	37	5	156486367	156486367	+	5'Flank	DEL	T	-	-			TCGA-CZ-5460-01A-01D-1501-10	TCGA-CZ-5460-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:156486367delT	uc010jij.1	-						HAVCR1_uc003lwi.2_5'Flank|HAVCR1_uc011ddm.1_5'Flank	NM_001099414	NP_001092884	Q96D42	HAVR1_HUMAN	hepatitis A virus cellular receptor 1						interspecies interaction between organisms	integral to membrane	receptor activity			ovary(1)|skin(1)	2	Renal(175;0.00488)	Medulloblastoma(196;0.0354)|all_neural(177;0.0999)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)			GATCTCAGCATAGTGTTTTGT	0.299													4	2	---	---	---	---	
SLIT3	6586	broad.mit.edu	37	5	168264077	168264078	+	Intron	INS	-	AGG	AGG			TCGA-CZ-5460-01A-01D-1501-10	TCGA-CZ-5460-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:168264077_168264078insAGG	uc003mab.2	-						SLIT3_uc010jjg.2_Intron|SLIT3_uc010jji.2_Intron|SLIT3_uc003mac.1_Intron	NM_003062	NP_003053	O75094	SLIT3_HUMAN	slit homolog 3 precursor						apoptosis involved in luteolysis|axon extension involved in axon guidance|cellular response to hormone stimulus|negative chemotaxis|negative regulation of cell growth|negative regulation of chemokine-mediated signaling pathway|response to cortisol stimulus|Roundabout signaling pathway	extracellular space|mitochondrion	calcium ion binding|Roundabout binding			ovary(3)|skin(1)	4	Renal(175;0.000159)|Lung NSC(126;0.0174)|all_lung(126;0.0392)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			GATGACTAAGAAGGAGGTGTGT	0.411													4	2	---	---	---	---	
C5orf45	51149	broad.mit.edu	37	5	179287208	179287209	+	5'Flank	DEL	GT	-	-			TCGA-CZ-5460-01A-01D-1501-10	TCGA-CZ-5460-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:179287208_179287209delGT	uc003mky.2	-						C5orf45_uc011dgt.1_5'Flank|C5orf45_uc011dgu.1_5'Flank|C5orf45_uc003mla.2_5'Flank|C5orf45_uc003mlc.2_5'Flank|C5orf45_uc003mlb.2_5'Flank|uc003mle.2_5'UTR			Q6NTE8	CE045_HUMAN	RecName: Full=UPF0544 protein C5orf45;												0						ATTTTCTGGCGTGTGTGTGTGT	0.366													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	25272755	25272755	+	IGR	DEL	T	-	-			TCGA-CZ-5460-01A-01D-1501-10	TCGA-CZ-5460-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:25272755delT								CMAH (105962 upstream) : LRRC16A (6893 downstream)																							ccaccatcacttccaaatcca	0.040													4	2	---	---	---	---	
BCLAF1	9774	broad.mit.edu	37	6	136594194	136594194	+	Intron	DEL	A	-	-			TCGA-CZ-5460-01A-01D-1501-10	TCGA-CZ-5460-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:136594194delA	uc003qgx.1	-						BCLAF1_uc003qgw.1_Intron|BCLAF1_uc003qgy.1_Intron|BCLAF1_uc011edc.1_Intron|BCLAF1_uc011edd.1_Intron|BCLAF1_uc011ede.1_Intron	NM_014739	NP_055554	Q9NYF8	BCLF1_HUMAN	BCL2-associated transcription factor 1 isoform						induction of apoptosis|negative regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleolus	DNA binding|protein binding			ovary(1)	1	Colorectal(23;0.24)			GBM - Glioblastoma multiforme(68;0.00226)|OV - Ovarian serous cystadenocarcinoma(155;0.00331)		CAACGTTTTTATATGCCAGTT	0.353													4	2	---	---	---	---	
LTV1	84946	broad.mit.edu	37	6	144165129	144165129	+	Intron	DEL	G	-	-			TCGA-CZ-5460-01A-01D-1501-10	TCGA-CZ-5460-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:144165129delG	uc003qjs.2	+							NM_032860	NP_116249	Q96GA3	LTV1_HUMAN	LTV1 homolog											ovary(1)	1				OV - Ovarian serous cystadenocarcinoma(155;2.72e-06)|GBM - Glioblastoma multiforme(68;0.0372)		AAGAGGTGATGGATCTTATTA	0.398													4	2	---	---	---	---	
UST	10090	broad.mit.edu	37	6	149271714	149271715	+	Intron	DEL	GG	-	-			TCGA-CZ-5460-01A-01D-1501-10	TCGA-CZ-5460-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:149271714_149271715delGG	uc003qmg.2	+							NM_005715	NP_005706	Q9Y2C2	UST_HUMAN	uronyl-2-sulfotransferase						protein sulfation	Golgi membrane|integral to membrane	sulfotransferase activity			ovary(2)	2		Ovarian(120;0.0907)		OV - Ovarian serous cystadenocarcinoma(155;1.78e-10)|GBM - Glioblastoma multiforme(68;0.138)		gaacacctctggcacactgaac	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	163824879	163824879	+	IGR	DEL	T	-	-			TCGA-CZ-5460-01A-01D-1501-10	TCGA-CZ-5460-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:163824879delT								LOC285796 (79385 upstream) : QKI (10796 downstream)																							ATCATCTAAGTTTTTGCTGTG	0.393													4	2	---	---	---	---	
AHR	196	broad.mit.edu	37	7	17379447	17379448	+	Frame_Shift_Ins	INS	-	C	C			TCGA-CZ-5460-01A-01D-1501-10	TCGA-CZ-5460-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:17379447_17379448insC	uc011jxz.1	+	10	2611_2612	c.1998_1999insC	c.(1996-2001)CAGCAAfs	p.Q666fs	AHR_uc003stt.3_RNA	NM_001621	NP_001612	P35869	AHR_HUMAN	aryl hydrocarbon receptor precursor	666_667					apoptosis|blood vessel development|cell cycle|regulation of B cell proliferation|response to stress|transcription from RNA polymerase II promoter|xenobiotic metabolic process	cytosolic aryl hydrocarbon receptor complex|transcription factor complex	Hsp90 protein binding|ligand-dependent nuclear receptor activity|protein heterodimerization activity|sequence-specific DNA binding transcription factor activity|transcription factor binding|transcription regulatory region DNA binding			urinary_tract(1)|kidney(1)|pancreas(1)	3	Lung NSC(10;0.0392)|all_lung(11;0.0754)					ATTGTCCACAGCAAGACCCACA	0.401													65	30	---	---	---	---	
TNS3	64759	broad.mit.edu	37	7	47463952	47463952	+	Intron	DEL	T	-	-			TCGA-CZ-5460-01A-01D-1501-10	TCGA-CZ-5460-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:47463952delT	uc003tnv.2	-						TNS3_uc003tnw.2_Intron|TNS3_uc010kyo.1_Intron	NM_022748	NP_073585	Q68CZ2	TENS3_HUMAN	tensin 3							focal adhesion	protein binding			ovary(4)	4						TTAGACTTCATTTCCCCCGCA	0.478													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	64528813	64528814	+	Intron	INS	-	T	T			TCGA-CZ-5460-01A-01D-1501-10	TCGA-CZ-5460-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:64528813_64528814insT	uc003ttt.1	+						uc010kzt.1_Intron|uc003ttu.1_5'Flank					Homo sapiens cDNA clone IMAGE:4215179, partial cds.																		CTTTCTGTAACTTTTTTTTTTT	0.317													4	2	---	---	---	---	
ABCB4	5244	broad.mit.edu	37	7	87073977	87073977	+	Intron	DEL	T	-	-			TCGA-CZ-5460-01A-01D-1501-10	TCGA-CZ-5460-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:87073977delT	uc003uiv.1	-						ABCB4_uc003uiw.1_Intron|ABCB4_uc003uix.1_Intron	NM_018849	NP_061337	P21439	MDR3_HUMAN	ATP-binding cassette, subfamily B, member 4						cellular lipid metabolic process	apical plasma membrane|Golgi membrane|integral to plasma membrane|intercellular canaliculus|membrane fraction	ATP binding|xenobiotic-transporting ATPase activity			ovary(4)|skin(1)|pancreas(1)	6	Esophageal squamous(14;0.0058)|all_lung(186;0.201)|Lung NSC(181;0.203)					ttatattatctaaagatacat	0.254													3	3	---	---	---	---	
PRKRIP1	79706	broad.mit.edu	37	7	102051823	102051823	+	Intron	DEL	T	-	-			TCGA-CZ-5460-01A-01D-1501-10	TCGA-CZ-5460-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:102051823delT	uc003uzh.2	+						PRKRIP1_uc003uzf.2_Intron|PRKRIP1_uc003uzg.2_Intron|PRKRIP1_uc011kkq.1_Intron|PRKRIP1_uc011kkr.1_Intron	NM_024653	NP_078929	Q9H875	PKRI1_HUMAN	PRKR interacting protein 1 (IL11 inducible)							nucleolus				ovary(1)	1						TGGCtgcttgttttttttttg	0.075													4	3	---	---	---	---	
SYPL1	6856	broad.mit.edu	37	7	105752910	105752910	+	Intron	DEL	C	-	-			TCGA-CZ-5460-01A-01D-1501-10	TCGA-CZ-5460-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:105752910delC	uc003vdp.2	-						SYPL1_uc003vdo.2_5'Flank	NM_006754	NP_006745	Q16563	SYPL1_HUMAN	synaptophysin-like 1 isoform a						synaptic transmission	cytoplasmic vesicle membrane|integral to plasma membrane|melanosome|synaptic vesicle	transporter activity				0						cgggaggcttctcctcaggcc	0.209													4	2	---	---	---	---	
SLC26A3	1811	broad.mit.edu	37	7	107420612	107420612	+	Intron	DEL	A	-	-			TCGA-CZ-5460-01A-01D-1501-10	TCGA-CZ-5460-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:107420612delA	uc003ver.2	-						SLC26A3_uc003ves.2_Intron	NM_000111	NP_000102	P40879	S26A3_HUMAN	solute carrier family 26, member 3						excretion	integral to membrane|membrane fraction	inorganic anion exchanger activity|secondary active sulfate transmembrane transporter activity|sequence-specific DNA binding transcription factor activity|transcription cofactor activity			ovary(3)|skin(1)	4						GCTCTTTGTTAAAAAAAAAAA	0.333													4	3	---	---	---	---	
LAMB4	22798	broad.mit.edu	37	7	107690122	107690123	+	Intron	INS	-	GAGGT	GAGGT			TCGA-CZ-5460-01A-01D-1501-10	TCGA-CZ-5460-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:107690122_107690123insGAGGT	uc010ljo.1	-						LAMB4_uc003vey.2_Intron|LAMB4_uc010ljp.1_Intron	NM_007356	NP_031382	A4D0S4	LAMB4_HUMAN	laminin, beta 4 precursor						cell adhesion	basement membrane				ovary(4)|breast(2)|large_intestine(1)|skin(1)	8						TTGAATTTGCAATTGATGGGGG	0.213													7	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	143218162	143218163	+	RNA	INS	-	T	T			TCGA-CZ-5460-01A-01D-1501-10	TCGA-CZ-5460-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:143218162_143218163insT	uc003wda.2	+	5		c.2638_2639insT								Homo sapiens mRNA; cDNA DKFZp686O0656 (from clone DKFZp686O0656).																		gtcagagtgactttttttttcc	0.000													4	2	---	---	---	---	
SNX16	64089	broad.mit.edu	37	8	82727368	82727369	+	Intron	INS	-	C	C			TCGA-CZ-5460-01A-01D-1501-10	TCGA-CZ-5460-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:82727368_82727369insC	uc011lft.1	-						SNX16_uc003ycn.2_Intron|SNX16_uc003yco.2_Intron	NM_022133	NP_071416	P57768	SNX16_HUMAN	sorting nexin 16 isoform a						cell communication|early endosome to late endosome transport|endosome to lysosome transport|protein targeting to lysosome	early endosome membrane|extrinsic to endosome membrane|late endosome membrane|lysosome	identical protein binding|phosphatidylinositol binding			ovary(1)|pancreas(1)	2						GAATTTTTACTTTTTCACTGAG	0.282													13	6	---	---	---	---	
TRPS1	7227	broad.mit.edu	37	8	116554170	116554170	+	Intron	DEL	C	-	-			TCGA-CZ-5460-01A-01D-1501-10	TCGA-CZ-5460-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:116554170delC	uc003ynz.2	-						TRPS1_uc011lhy.1_Intron|TRPS1_uc003yny.2_Intron|TRPS1_uc010mcy.2_Intron	NM_014112	NP_054831	Q9UHF7	TRPS1_HUMAN	zinc finger transcription factor TRPS1						negative regulation of transcription from RNA polymerase II promoter|NLS-bearing substrate import into nucleus|regulation of chondrocyte differentiation|skeletal system development|transcription from RNA polymerase II promoter	nucleus	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(2)|skin(2)|pancreas(1)|lung(1)|kidney(1)	7	all_cancers(13;5.44e-23)|all_epithelial(1;2.14e-27)|Lung NSC(37;2.55e-05)|Ovarian(258;0.0219)		Epithelial(1;9.78e-37)|all cancers(1;3.14e-31)|BRCA - Breast invasive adenocarcinoma(1;2.56e-12)			AGAGAAGCCACACAGAGCCCT	0.418									Langer-Giedion_syndrome				4	2	---	---	---	---	
ASAP1	50807	broad.mit.edu	37	8	131072649	131072650	+	Intron	DEL	AA	-	-			TCGA-CZ-5460-01A-01D-1501-10	TCGA-CZ-5460-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:131072649_131072650delAA	uc003yta.1	-						ASAP1_uc003ysz.1_Intron|ASAP1_uc011liw.1_Intron	NM_018482	NP_060952	Q9ULH1	ASAP1_HUMAN	development and differentiation enhancing factor						cilium morphogenesis|filopodium assembly|regulation of ARF GTPase activity|signal transduction	cytoplasm|membrane	ARF GTPase activator activity|cytoskeletal adaptor activity|SH3 domain binding|zinc ion binding			ovary(4)	4						gctggagcctaaagcctgggtt	0.203													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	139956970	139956970	+	IGR	DEL	A	-	-			TCGA-CZ-5460-01A-01D-1501-10	TCGA-CZ-5460-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:139956970delA								COL22A1 (30734 upstream) : KCNK9 (656112 downstream)																							gaagaggtggaaaatggcatt	0.085													4	2	---	---	---	---	
KCNK9	51305	broad.mit.edu	37	8	140630025	140630026	+	Intron	INS	-	AC	AC			TCGA-CZ-5460-01A-01D-1501-10	TCGA-CZ-5460-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:140630025_140630026insAC	uc003yvf.1	-						KCNK9_uc003yve.1_Intron	NM_016601	NP_057685	Q9NPC2	KCNK9_HUMAN	potassium channel, subfamily K, member 9							integral to membrane|membrane fraction	potassium channel activity|voltage-gated ion channel activity			ovary(2)|lung(1)	3	all_cancers(97;3.94e-14)|all_epithelial(106;4.81e-13)|Lung NSC(106;8.18e-05)|all_lung(105;0.00015)|Ovarian(258;0.00235)|Acute lymphoblastic leukemia(118;0.155)	Ovarian(118;0.134)	BRCA - Breast invasive adenocarcinoma(115;0.0855)			gcacacacacaacacacacaca	0.376													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	31541815	31541815	+	IGR	DEL	G	-	-			TCGA-CZ-5460-01A-01D-1501-10	TCGA-CZ-5460-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:31541815delG								None (None upstream) : ACO1 (842786 downstream)																							GTAAAAGCAAGCCCTGATAAA	0.428													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	33572394	33572395	+	IGR	DEL	TT	-	-			TCGA-CZ-5460-01A-01D-1501-10	TCGA-CZ-5460-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:33572394_33572395delTT								SUGT1P1 (61347 upstream) : ANXA2P2 (51828 downstream)																							GAAGAGAATATTTAACCATAAA	0.312													4	2	---	---	---	---	
CLTA	1211	broad.mit.edu	37	9	36278264	36278265	+	Intron	DEL	AA	-	-			TCGA-CZ-5460-01A-01D-1501-10	TCGA-CZ-5460-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:36278264_36278265delAA	uc003zzf.1	+						GNE_uc010mli.2_5'Flank|GNE_uc010mlj.2_5'Flank	NM_001833		P09496	CLCA_HUMAN	clathrin, light polypeptide A isoform a						axon guidance|epidermal growth factor receptor signaling pathway|intracellular protein transport|negative regulation of epidermal growth factor receptor signaling pathway|nerve growth factor receptor signaling pathway|post-Golgi vesicle-mediated transport	clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|cytosol	structural molecule activity			central_nervous_system(1)	1			STAD - Stomach adenocarcinoma(86;0.228)			AAACTCTGTTAAAAAAAAAAAA	0.386													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	68417570	68417571	+	IGR	INS	-	AA	AA	rs111263548		TCGA-CZ-5460-01A-01D-1501-10	TCGA-CZ-5460-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:68417570_68417571insAA								FAM27B (623381 upstream) : MIR1299 (584668 downstream)																							AGGATAGGAATAAAACATCAGT	0.243													7	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	68418028	68418029	+	IGR	DEL	AG	-	-	rs71861265		TCGA-CZ-5460-01A-01D-1501-10	TCGA-CZ-5460-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:68418028_68418029delAG								FAM27B (623839 upstream) : MIR1299 (584210 downstream)																							ATCTAGTAACAGGGTAACATTT	0.272													5	3	---	---	---	---	
AGTPBP1	23287	broad.mit.edu	37	9	88258051	88258052	+	Intron	DEL	TA	-	-			TCGA-CZ-5460-01A-01D-1501-10	TCGA-CZ-5460-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:88258051_88258052delTA	uc011ltd.1	-						AGTPBP1_uc004aod.3_5'UTR|AGTPBP1_uc011ltc.1_Intron|AGTPBP1_uc010mqc.2_Intron|AGTPBP1_uc011lte.1_Intron	NM_015239	NP_056054	Q9UPW5	CBPC1_HUMAN	ATP/GTP binding protein 1						C-terminal protein deglutamylation|cerebellar Purkinje cell differentiation|eye photoreceptor cell differentiation|mitochondrion organization|neuromuscular process|olfactory bulb development|protein side chain deglutamylation|proteolysis	cytosol|mitochondrion|nucleus	metallocarboxypeptidase activity|tubulin binding|zinc ion binding			ovary(4)|large_intestine(2)|skin(1)	7						TATTGTTGGGTAGTTTTGTTTT	0.267													5	3	---	---	---	---	
NOL8	55035	broad.mit.edu	37	9	95062034	95062034	+	Intron	DEL	A	-	-			TCGA-CZ-5460-01A-01D-1501-10	TCGA-CZ-5460-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:95062034delA	uc004arv.2	-						NOL8_uc010mqw.2_Intron|NOL8_uc004arw.2_Intron|NOL8_uc011ltw.1_Intron	NM_017948	NP_060418	Q76FK4	NOL8_HUMAN	nucleolar protein 8						DNA replication|positive regulation of cell growth	nucleolus	nucleotide binding|protein binding|RNA binding			ovary(1)	1						actccgtctcaaaaaaaaaaa	0.100													5	3	---	---	---	---	
ABCA1	19	broad.mit.edu	37	9	107558222	107558222	+	Intron	DEL	C	-	-			TCGA-CZ-5460-01A-01D-1501-10	TCGA-CZ-5460-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:107558222delC	uc004bcl.2	-							NM_005502	NP_005493	O95477	ABCA1_HUMAN	ATP-binding cassette, sub-family A member 1						Cdc42 protein signal transduction|cellular lipid metabolic process|cholesterol efflux|cholesterol homeostasis|cholesterol metabolic process|endosome transport|G-protein coupled receptor protein signaling pathway|high-density lipoprotein particle assembly|interleukin-1 beta secretion|intracellular cholesterol transport|lysosome organization|negative regulation of cholesterol storage|negative regulation of macrophage derived foam cell differentiation|phospholipid efflux|phospholipid homeostasis|platelet dense granule organization|positive regulation of cAMP biosynthetic process|reverse cholesterol transport	integral to plasma membrane|membrane fraction|membrane raft|phagocytic vesicle	anion transmembrane transporter activity|apolipoprotein A-I receptor activity|ATP binding|ATPase activity|cholesterol transporter activity|phospholipid transporter activity|small GTPase binding|syntaxin-13 binding			large_intestine(4)|lung(4)|ovary(4)|upper_aerodigestive_tract(1)|central_nervous_system(1)|breast(1)|skin(1)|pancreas(1)	17				OV - Ovarian serous cystadenocarcinoma(323;0.023)	Adenosine triphosphate(DB00171)|Glibenclamide(DB01016)	caggacaaggcagtcagcagt	0.104													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	46217501	46217501	+	IGR	DEL	G	-	-			TCGA-CZ-5460-01A-01D-1501-10	TCGA-CZ-5460-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:46217501delG								ANUBL1 (49250 upstream) : FAM21C (5166 downstream)																							AAGAAAATAAGAAAAAGGTCA	0.343													6	3	---	---	---	---	
FRMPD2	143162	broad.mit.edu	37	10	49382781	49382781	+	Intron	DEL	A	-	-			TCGA-CZ-5460-01A-01D-1501-10	TCGA-CZ-5460-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:49382781delA	uc001jgi.2	-						FRMPD2_uc001jgh.2_Intron|FRMPD2_uc001jgj.2_Intron|FRMPD2L1_uc001jgf.2_Intron|FRMPD2_uc001jgg.2_Intron|FRMPD2_uc001jgk.2_Intron	NM_001018071	NP_001018081	Q68DX3	FRPD2_HUMAN	FERM and PDZ domain containing 2 isoform 3						tight junction assembly	basolateral plasma membrane|cytoplasm|cytoskeleton|tight junction	1-phosphatidylinositol binding|protein binding			large_intestine(1)	1				Kidney(211;0.201)		AATGGAAGAGAAAAAAAAAAC	0.423													4	2	---	---	---	---	
DRGX	644168	broad.mit.edu	37	10	50600501	50600501	+	5'Flank	DEL	C	-	-			TCGA-CZ-5460-01A-01D-1501-10	TCGA-CZ-5460-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:50600501delC	uc010qgq.1	-							NM_001080520	NP_001073989	A6NNA5	DRGX_HUMAN	dorsal root ganglia homeobox						multicellular organismal development	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity				0						ACCTTAGTTACAGGTATTTCT	0.388													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	77465333	77465333	+	IGR	DEL	T	-	-			TCGA-CZ-5460-01A-01D-1501-10	TCGA-CZ-5460-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:77465333delT								MIR606 (153022 upstream) : C10orf11 (77186 downstream)																							AGTGGGAGAGTTACCTGGAAA	0.507													4	2	---	---	---	---	
DNMBP	23268	broad.mit.edu	37	10	101729922	101729922	+	Intron	DEL	C	-	-			TCGA-CZ-5460-01A-01D-1501-10	TCGA-CZ-5460-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:101729922delC	uc001kqj.2	-							NM_015221	NP_056036	Q6XZF7	DNMBP_HUMAN	dynamin binding protein						intracellular signal transduction|regulation of Rho protein signal transduction	cell junction|cytoskeleton|Golgi stack|synapse	protein binding|Rho guanyl-nucleotide exchange factor activity			ovary(5)|skin(1)	6		Colorectal(252;0.234)		Epithelial(162;2.94e-10)|all cancers(201;3.15e-08)		cttgctaactccttctcatca	0.055													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	116660862	116660862	+	IGR	DEL	C	-	-			TCGA-CZ-5460-01A-01D-1501-10	TCGA-CZ-5460-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:116660862delC								FAM160B1 (1277 upstream) : TRUB1 (37053 downstream)																							GGTGAAGATTCCACATACAAA	0.473													4	2	---	---	---	---	
GFRA1	2674	broad.mit.edu	37	10	117865501	117865501	+	Intron	DEL	T	-	-			TCGA-CZ-5460-01A-01D-1501-10	TCGA-CZ-5460-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:117865501delT	uc001lcj.2	-						GFRA1_uc001lci.2_Intron|GFRA1_uc009xyr.2_Intron	NM_005264	NP_005255	P56159	GFRA1_HUMAN	GDNF family receptor alpha 1 isoform a						axon guidance	anchored to membrane|extrinsic to membrane|plasma membrane	glial cell-derived neurotrophic factor receptor activity			ovary(1)|pancreas(1)	2		Lung NSC(174;0.21)		all cancers(201;0.0337)		attttcccggtaggaccaata	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	126030727	126030727	+	IGR	DEL	C	-	-			TCGA-CZ-5460-01A-01D-1501-10	TCGA-CZ-5460-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:126030727delC								CHST15 (177521 upstream) : OAT (55145 downstream)																							TCCCACGTCACCATTTGTGCT	0.483													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	129351051	129351052	+	IGR	INS	-	A	A	rs141748490	by1000genomes	TCGA-CZ-5460-01A-01D-1501-10	TCGA-CZ-5460-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:129351051_129351052insA								NPS (116 upstream) : FOXI2 (184486 downstream)																							GTAAATTGAGTAAAAAAAGAAA	0.351													3	5	---	---	---	---	
ZDHHC13	54503	broad.mit.edu	37	11	19172490	19172491	+	Intron	INS	-	T	T			TCGA-CZ-5460-01A-01D-1501-10	TCGA-CZ-5460-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:19172490_19172491insT	uc001mpi.2	+						ZDHHC13_uc001mpj.2_Intron	NM_019028	NP_061901	Q8IUH4	ZDH13_HUMAN	zinc finger, DHHC domain containing 13 isoform						positive regulation of I-kappaB kinase/NF-kappaB cascade	Golgi-associated vesicle membrane|integral to membrane	magnesium ion transmembrane transporter activity|palmitoyltransferase activity|signal transducer activity|zinc ion binding				0						TGACTTTTAAGGTAGTTATAGT	0.292													8	5	---	---	---	---	
MTCH2	23788	broad.mit.edu	37	11	47648879	47648879	+	Intron	DEL	T	-	-			TCGA-CZ-5460-01A-01D-1501-10	TCGA-CZ-5460-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:47648879delT	uc010rho.1	-						MTCH2_uc001nge.2_Intron|MTCH2_uc010rhp.1_Intron	NM_014342	NP_055157	Q9Y6C9	MTCH2_HUMAN	mitochondrial carrier 2						transport	integral to membrane|mitochondrial inner membrane					0						AAATGGTGTCttttttttttt	0.119													5	3	---	---	---	---	
TUT1	64852	broad.mit.edu	37	11	62346643	62346643	+	Intron	DEL	T	-	-			TCGA-CZ-5460-01A-01D-1501-10	TCGA-CZ-5460-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:62346643delT	uc001nto.2	-						TUT1_uc001ntp.1_5'Flank	NM_022830	NP_073741	Q9H6E5	STPAP_HUMAN	terminal uridylyl transferase 1, U6						mRNA cleavage|mRNA polyadenylation|snRNA processing	nuclear speck|nucleolus	ATP binding|enzyme binding|mRNA 3'-UTR binding|polynucleotide adenylyltransferase activity|RNA uridylyltransferase activity|zinc ion binding			central_nervous_system(1)|skin(1)	2						acaggaaccctTTTTTTTTTT	0.104													4	2	---	---	---	---	
PPP1R14B	26472	broad.mit.edu	37	11	64012659	64012659	+	Intron	DEL	C	-	-			TCGA-CZ-5460-01A-01D-1501-10	TCGA-CZ-5460-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:64012659delC	uc001nza.2	-							NM_138689	NP_619634	Q96C90	PP14B_HUMAN	protein phosphatase 1 regulatory subunit 14B						regulation of phosphorylation	cytoplasm	protein phosphatase inhibitor activity				0						CAACCCATCGCCCCCCAGCCC	0.632													4	2	---	---	---	---	
RSF1	51773	broad.mit.edu	37	11	77457917	77457917	+	Intron	DEL	A	-	-			TCGA-CZ-5460-01A-01D-1501-10	TCGA-CZ-5460-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:77457917delA	uc001oyn.2	-							NM_016578	NP_057662	Q96T23	RSF1_HUMAN	remodeling and spacing factor 1						CenH3-containing nucleosome assembly at centromere|negative regulation of DNA binding|negative regulation of transcription, DNA-dependent|nucleosome positioning|positive regulation of transcription, DNA-dependent|positive regulation of viral transcription|transcription initiation, DNA-dependent	RSF complex	histone binding|protein binding|zinc ion binding			ovary(2)|central_nervous_system(2)	4	all_cancers(14;1.54e-17)|all_epithelial(13;4.06e-20)|Ovarian(111;0.152)		Epithelial(5;3e-50)|all cancers(3;6.37e-47)|BRCA - Breast invasive adenocarcinoma(5;9.82e-31)			TTTATGCATCAAAAAACAGCA	0.294													4	2	---	---	---	---	
ME3	10873	broad.mit.edu	37	11	86249573	86249574	+	Intron	DEL	CA	-	-			TCGA-CZ-5460-01A-01D-1501-10	TCGA-CZ-5460-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:86249573_86249574delCA	uc001pbz.2	-						ME3_uc001pca.2_Intron|ME3_uc009yvk.2_Intron|ME3_uc010rtr.1_Intron	NM_001014811	NP_001014811	Q16798	MAON_HUMAN	mitochondrial malic enzyme 3 precursor						aerobic respiration|malate metabolic process|oxygen metabolic process|pyruvate metabolic process	mitochondrial matrix	malate dehydrogenase (oxaloacetate-decarboxylating) (NADP+) activity|metal ion binding|NAD binding			ovary(1)	1		Acute lymphoblastic leukemia(157;4.34e-06)|all_hematologic(158;0.00252)			NADH(DB00157)	CAACACAGTTCACAATCTGACA	0.446													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	92069104	92069104	+	IGR	DEL	T	-	-			TCGA-CZ-5460-01A-01D-1501-10	TCGA-CZ-5460-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:92069104delT								None (None upstream) : FAT3 (16158 downstream)																							CTCCTATGGATTTTTTTTTCA	0.413													4	3	---	---	---	---	
ZW10	9183	broad.mit.edu	37	11	113618699	113618700	+	Intron	DEL	TA	-	-			TCGA-CZ-5460-01A-01D-1501-10	TCGA-CZ-5460-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:113618699_113618700delTA	uc001poe.2	-						ZW10_uc009yyv.2_Intron	NM_004724	NP_004715	O43264	ZW10_HUMAN	centromere/kinetochore protein zw10						cell division|ER to Golgi vesicle-mediated transport|establishment of mitotic spindle orientation|meiosis|mitotic cell cycle checkpoint|mitotic metaphase plate congression|mitotic prometaphase|protein complex assembly|protein localization to kinetochore|protein transport|regulation of exit from mitosis	condensed chromosome kinetochore|cytosol|endoplasmic reticulum membrane|kinetochore microtubule|nucleus|spindle pole	centromeric DNA binding|protein binding			central_nervous_system(1)|skin(1)	2		all_cancers(61;3.84e-16)|all_epithelial(67;1e-09)|Melanoma(852;1.46e-05)|all_hematologic(158;0.000237)|Acute lymphoblastic leukemia(157;0.000967)|Breast(348;0.0101)|all_neural(223;0.0281)|Prostate(24;0.0421)|Medulloblastoma(222;0.0425)		BRCA - Breast invasive adenocarcinoma(274;2.94e-06)|Epithelial(105;0.000103)|all cancers(92;0.000786)		AAGGAAACACTAAAAAGAAGCA	0.248													3	3	---	---	---	---	
ZW10	9183	broad.mit.edu	37	11	113618706	113618707	+	Intron	INS	-	C	C			TCGA-CZ-5460-01A-01D-1501-10	TCGA-CZ-5460-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:113618706_113618707insC	uc001poe.2	-						ZW10_uc009yyv.2_Intron	NM_004724	NP_004715	O43264	ZW10_HUMAN	centromere/kinetochore protein zw10						cell division|ER to Golgi vesicle-mediated transport|establishment of mitotic spindle orientation|meiosis|mitotic cell cycle checkpoint|mitotic metaphase plate congression|mitotic prometaphase|protein complex assembly|protein localization to kinetochore|protein transport|regulation of exit from mitosis	condensed chromosome kinetochore|cytosol|endoplasmic reticulum membrane|kinetochore microtubule|nucleus|spindle pole	centromeric DNA binding|protein binding			central_nervous_system(1)|skin(1)	2		all_cancers(61;3.84e-16)|all_epithelial(67;1e-09)|Melanoma(852;1.46e-05)|all_hematologic(158;0.000237)|Acute lymphoblastic leukemia(157;0.000967)|Breast(348;0.0101)|all_neural(223;0.0281)|Prostate(24;0.0421)|Medulloblastoma(222;0.0425)		BRCA - Breast invasive adenocarcinoma(274;2.94e-06)|Epithelial(105;0.000103)|all cancers(92;0.000786)		CACTAAAAAGAAGCAAAAAGTA	0.248													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	119884994	119884995	+	IGR	INS	-	T	T	rs141846231	by1000genomes	TCGA-CZ-5460-01A-01D-1501-10	TCGA-CZ-5460-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:119884994_119884995insT								PVRL1 (285559 upstream) : TRIM29 (97000 downstream)																							CAGTTCTCAGCGCCCTTCCTGC	0.594													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	134729378	134729378	+	IGR	DEL	T	-	-			TCGA-CZ-5460-01A-01D-1501-10	TCGA-CZ-5460-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:134729378delT								B3GAT1 (447566 upstream) : None (None downstream)																							TATTCTGATCTGGACCACCAC	0.562													4	2	---	---	---	---	
CD163L1	283316	broad.mit.edu	37	12	7584833	7584833	+	Intron	DEL	A	-	-			TCGA-CZ-5460-01A-01D-1501-10	TCGA-CZ-5460-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:7584833delA	uc001qsy.2	-						CD163L1_uc010sge.1_Intron	NM_174941	NP_777601	Q9NR16	C163B_HUMAN	scavenger receptor cysteine-rich type 1							extracellular region|integral to membrane|plasma membrane	scavenger receptor activity			ovary(8)|skin(2)|central_nervous_system(1)	11						atttGTTAGGAAGAGCAGTTT	0.194													4	2	---	---	---	---	
OVCH1	341350	broad.mit.edu	37	12	29586943	29586943	+	Intron	DEL	G	-	-			TCGA-CZ-5460-01A-01D-1501-10	TCGA-CZ-5460-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:29586943delG	uc001rix.1	-							NM_183378	NP_899234	Q7RTY7	OVCH1_HUMAN	ovochymase 1 precursor						proteolysis	extracellular region	metal ion binding|serine-type endopeptidase activity			ovary(3)|central_nervous_system(3)|pancreas(3)|large_intestine(1)	10	Lung NSC(12;1.84e-09)|Acute lymphoblastic leukemia(23;0.00885)|all_hematologic(23;0.0155)					TAAATATAATGGCAAATGTTT	0.328													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	34403122	34403123	+	IGR	INS	-	G	G	rs68186223		TCGA-CZ-5460-01A-01D-1501-10	TCGA-CZ-5460-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:34403122_34403123insG								ALG10 (221888 upstream) : None (None downstream)																							aaaaaaaaaaaaaaaaaaGAAA	0.163													5	3	---	---	---	---	
ARID2	196528	broad.mit.edu	37	12	46245726	46245726	+	Frame_Shift_Del	DEL	G	-	-			TCGA-CZ-5460-01A-01D-1501-10	TCGA-CZ-5460-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:46245726delG	uc001ros.1	+	15	3820	c.3820delG	c.(3820-3822)GGAfs	p.G1274fs	ARID2_uc001ror.2_Frame_Shift_Del_p.G1274fs|ARID2_uc009zkg.1_Frame_Shift_Del_p.G730fs|ARID2_uc009zkh.1_Frame_Shift_Del_p.G901fs|ARID2_uc001rou.1_Frame_Shift_Del_p.G608fs	NM_152641	NP_689854	Q68CP9	ARID2_HUMAN	AT rich interactive domain 2 (ARID, RFX-like)	1274					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)		CTGCCGACGAGGAGCCACAAA	0.428													15	16	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	57054386	57054386	+	IGR	DEL	G	-	-			TCGA-CZ-5460-01A-01D-1501-10	TCGA-CZ-5460-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:57054386delG								ATP5B (14534 upstream) : PTGES3 (2741 downstream)																							ACTGTGTTGAGGGAAAGATAT	0.343													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	76118853	76118854	+	IGR	DEL	GA	-	-			TCGA-CZ-5460-01A-01D-1501-10	TCGA-CZ-5460-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:76118853_76118854delGA								KRR1 (213435 upstream) : PHLDA1 (300374 downstream)																							ggagggaggggagagagagaga	0.356													3	3	---	---	---	---	
LIN7A	8825	broad.mit.edu	37	12	81226090	81226090	+	Intron	DEL	C	-	-			TCGA-CZ-5460-01A-01D-1501-10	TCGA-CZ-5460-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:81226090delC	uc001szj.1	-						LIN7A_uc001szk.1_Intron	NM_004664	NP_004655	O14910	LIN7A_HUMAN	lin-7 homolog A						exocytosis|protein complex assembly|protein transport	basolateral plasma membrane|postsynaptic density|postsynaptic membrane|synaptosome|tight junction	L27 domain binding			ovary(1)|skin(1)	2						AGACATGGTACCATGGTTAAT	0.338													4	2	---	---	---	---	
C12orf26	84190	broad.mit.edu	37	12	82792557	82792557	+	Intron	DEL	T	-	-			TCGA-CZ-5460-01A-01D-1501-10	TCGA-CZ-5460-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:82792557delT	uc001szq.2	+							NM_032230	NP_115606	Q8N6Q8	CL026_HUMAN	hypothetical protein LOC84190												0						TAATTTATTCTTTTTTTCTAA	0.259													4	2	---	---	---	---	
ANO4	121601	broad.mit.edu	37	12	101168874	101168874	+	Intron	DEL	C	-	-			TCGA-CZ-5460-01A-01D-1501-10	TCGA-CZ-5460-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:101168874delC	uc010svl.1	+									Q32M45	ANO4_HUMAN	Homo sapiens cDNA FLJ34272 fis, clone FEBRA2003128.							chloride channel complex	chloride channel activity			ovary(4)|skin(2)	6						CTTAAATCTTCTCTCCCCAAC	0.358										HNSCC(74;0.22)			4	2	---	---	---	---	
ALDH1L2	160428	broad.mit.edu	37	12	105423830	105423831	+	Intron	DEL	CC	-	-			TCGA-CZ-5460-01A-01D-1501-10	TCGA-CZ-5460-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:105423830_105423831delCC	uc001tlc.2	-						ALDH1L2_uc009zuo.2_Intron|ALDH1L2_uc009zup.2_Intron	NM_001034173	NP_001029345	Q3SY69	AL1L2_HUMAN	aldehyde dehydrogenase 1 family, member L2						10-formyltetrahydrofolate catabolic process|biosynthetic process	mitochondrion	acyl carrier activity|cofactor binding|formyltetrahydrofolate dehydrogenase activity|hydroxymethyl-, formyl- and related transferase activity|methyltransferase activity|phosphopantetheine binding			skin(1)	1						TTACTTTGTTCCACAGACATCT	0.322													4	2	---	---	---	---	
P2RX7	5027	broad.mit.edu	37	12	121618470	121618471	+	Intron	DEL	AA	-	-			TCGA-CZ-5460-01A-01D-1501-10	TCGA-CZ-5460-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:121618470_121618471delAA	uc001tzm.2	+						P2RX7_uc001tzn.2_Intron|P2RX7_uc001tzo.2_Intron|P2RX7_uc001tzp.2_Intron|P2RX7_uc001tzq.2_Intron	NM_002562	NP_002553	Q99572	P2RX7_HUMAN	purinergic receptor P2X7							integral to membrane	ATP binding|ion channel activity|receptor activity			large_intestine(2)|lung(1)|breast(1)|skin(1)	5	all_neural(191;0.0684)|Medulloblastoma(191;0.0922)					CTCCTTTTTTAATTTTTAAAAT	0.015													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	126996260	126996261	+	IGR	DEL	AA	-	-	rs4765098	byFrequency	TCGA-CZ-5460-01A-01D-1501-10	TCGA-CZ-5460-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:126996260_126996261delAA								LOC100128554 (38930 upstream) : None (None downstream)																							ctcaggtattaaacctagtacc	0.213													4	2	---	---	---	---	
TPTE2	93492	broad.mit.edu	37	13	20000806	20000807	+	Intron	INS	-	G	G			TCGA-CZ-5460-01A-01D-1501-10	TCGA-CZ-5460-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:20000806_20000807insG	uc001umd.2	-						TPTE2_uc009zzk.2_Intron|TPTE2_uc009zzl.2_Intron|TPTE2_uc001ume.2_Intron|TPTE2_uc009zzm.2_Intron|TPTE2_uc010tcm.1_Intron|TPTE2_uc010tcl.1_Intron	NM_199254	NP_954863	Q6XPS3	TPTE2_HUMAN	TPTE and PTEN homologous inositol lipid							endoplasmic reticulum membrane|integral to membrane	ion channel activity|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity|protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity				0		all_cancers(29;1.23e-20)|all_lung(29;1.97e-20)|all_epithelial(30;5.86e-20)|Lung NSC(5;3.36e-17)|Lung SC(185;0.0262)|Ovarian(182;0.162)		all cancers(112;1.73e-05)|Epithelial(112;7.42e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.000785)|Lung(94;0.0176)|LUSC - Lung squamous cell carcinoma(192;0.089)		TAATAATCTTTTCTAGTTGCAA	0.213													9	5	---	---	---	---	
PRHOXNB	646625	broad.mit.edu	37	13	28560847	28560848	+	Intron	DEL	TT	-	-	rs35797377		TCGA-CZ-5460-01A-01D-1501-10	TCGA-CZ-5460-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:28560847_28560848delTT	uc010aan.1	-							NM_001105577	NP_001099047	A6NGE7	URAD_HUMAN	parahox cluster neighbor						allantoin biosynthetic process|purine base metabolic process	peroxisome	carboxy-lyase activity				0	all_cancers(110;0.12)|all_hematologic(3;0.0119)|Acute lymphoblastic leukemia(6;0.04)	Lung SC(185;0.0161)	Colorectal(13;0.000157)|READ - Rectum adenocarcinoma(15;0.105)	GBM - Glioblastoma multiforme(144;0.0407)|all cancers(112;0.0491)|OV - Ovarian serous cystadenocarcinoma(117;0.199)		TATGCCTCTCTTTTTTTTTCCT	0.450													2	5	---	---	---	---	
FLT3	2322	broad.mit.edu	37	13	28627044	28627045	+	Intron	DEL	CA	-	-			TCGA-CZ-5460-01A-01D-1501-10	TCGA-CZ-5460-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:28627044_28627045delCA	uc001urw.2	-						FLT3_uc010aao.2_Intron|FLT3_uc010tdn.1_Intron	NM_004119	NP_004110	P36888	FLT3_HUMAN	fms-related tyrosine kinase 3 precursor						positive regulation of cell proliferation	integral to plasma membrane	ATP binding|vascular endothelial growth factor receptor activity			haematopoietic_and_lymphoid_tissue(8536)|lung(7)|ovary(3)|stomach(1)|central_nervous_system(1)|skin(1)	8549	Acute lymphoblastic leukemia(6;0.04)	Lung SC(185;0.0156)|Ovarian(182;0.0392)	Colorectal(13;0.000157)|READ - Rectum adenocarcinoma(15;0.105)	OV - Ovarian serous cystadenocarcinoma(117;0.00154)|all cancers(112;0.00459)|GBM - Glioblastoma multiforme(144;0.00562)|Epithelial(112;0.0959)|Lung(94;0.212)	Sorafenib(DB00398)|Sunitinib(DB01268)	TTGGGTATTTCACAAATCCACA	0.351			Mis|O		AML|ALL								4	2	---	---	---	---	
DCLK1	9201	broad.mit.edu	37	13	36485681	36485681	+	Intron	DEL	C	-	-			TCGA-CZ-5460-01A-01D-1501-10	TCGA-CZ-5460-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:36485681delC	uc001uvf.2	-							NM_004734	NP_004725	O15075	DCLK1_HUMAN	doublecortin-like kinase 1						cell differentiation|central nervous system development|endosome transport|intracellular signal transduction|response to virus	integral to plasma membrane	ATP binding|protein serine/threonine kinase activity|receptor signaling protein activity			stomach(6)|ovary(2)|skin(1)	9		Breast(139;0.0147)|Lung SC(185;0.0685)|Prostate(109;0.122)	KIRC - Kidney renal clear cell carcinoma(5;0.119)|Kidney(79;0.169)	all cancers(112;1.72e-06)|Epithelial(112;4.24e-05)|BRCA - Breast invasive adenocarcinoma(63;0.00159)|OV - Ovarian serous cystadenocarcinoma(117;0.0158)|GBM - Glioblastoma multiforme(144;0.0638)		CTGGTCTAGACCCTAGGATGT	0.483													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	53051649	53051649	+	IGR	DEL	C	-	-			TCGA-CZ-5460-01A-01D-1501-10	TCGA-CZ-5460-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:53051649delC								CKAP2 (886 upstream) : TPTE2P3 (11479 downstream)																							GATGTTCTTTCTTTCCAATTT	0.239													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	85661485	85661485	+	IGR	DEL	C	-	-			TCGA-CZ-5460-01A-01D-1501-10	TCGA-CZ-5460-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:85661485delC								None (None upstream) : SLITRK6 (705437 downstream)																							CTCTGAGTCTCCAACTATAAA	0.318													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	95988466	95988466	+	IGR	DEL	T	-	-			TCGA-CZ-5460-01A-01D-1501-10	TCGA-CZ-5460-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:95988466delT								ABCC4 (34779 upstream) : CLDN10 (97387 downstream)																							CCACATAGgattttgactcag	0.020													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	103760999	103760999	+	IGR	DEL	G	-	-			TCGA-CZ-5460-01A-01D-1501-10	TCGA-CZ-5460-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:103760999delG								SLC10A2 (41803 upstream) : None (None downstream)																							AATCAGCAGTGATGAGGCAGT	0.542													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	112009003	112009004	+	IGR	DEL	AG	-	-	rs144001274	by1000genomes	TCGA-CZ-5460-01A-01D-1501-10	TCGA-CZ-5460-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:112009003_112009004delAG								C13orf16 (12410 upstream) : SOX1 (712909 downstream)																							TTGACTTCCTAGGTGTCCAGGT	0.460													4	2	---	---	---	---	
SUPT16H	11198	broad.mit.edu	37	14	21833520	21833521	+	Intron	INS	-	C	C			TCGA-CZ-5460-01A-01D-1501-10	TCGA-CZ-5460-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:21833520_21833521insC	uc001wao.2	-							NM_007192	NP_009123	Q9Y5B9	SP16H_HUMAN	chromatin-specific transcription elongation						DNA repair|DNA replication|nucleosome disassembly|positive regulation of transcription elongation, DNA-dependent|positive regulation of viral transcription|transcription elongation from RNA polymerase II promoter|viral reproduction	chromosome|nucleoplasm	GTP binding				0	all_cancers(95;0.00115)		Epithelial(56;1.62e-06)|all cancers(55;1.49e-05)	GBM - Glioblastoma multiforme(265;0.0159)		CTAATTGATTATATCGAGCCTT	0.351													2	5	---	---	---	---	
PSMB5	5693	broad.mit.edu	37	14	23495667	23495667	+	Intron	DEL	T	-	-			TCGA-CZ-5460-01A-01D-1501-10	TCGA-CZ-5460-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:23495667delT	uc001wii.2	-						PSMB5_uc001wij.2_Intron|PSMB5_uc010tni.1_Intron	NM_002797	NP_002788	P28074	PSB5_HUMAN	proteasome beta 5 subunit isoform 1						anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|G1/S transition of mitotic cell cycle|interspecies interaction between organisms|M/G1 transition of mitotic cell cycle|mRNA metabolic process|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|regulation of apoptosis|regulation of cellular amino acid metabolic process|S phase of mitotic cell cycle|viral reproduction	cytoplasm|nucleus	protein binding|threonine-type endopeptidase activity			ovary(1)	1	all_cancers(95;3.3e-05)			GBM - Glioblastoma multiforme(265;0.0121)	Bortezomib(DB00188)	GCAGTAGttctttttttttga	0.204													4	3	---	---	---	---	
MTHFD1	4522	broad.mit.edu	37	14	64891344	64891344	+	Intron	DEL	A	-	-			TCGA-CZ-5460-01A-01D-1501-10	TCGA-CZ-5460-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:64891344delA	uc001xhb.2	+						MTHFD1_uc010aqe.2_Intron|MTHFD1_uc010aqf.2_Intron	NM_005956	NP_005947	P11586	C1TC_HUMAN	methylenetetrahydrofolate dehydrogenase 1						folic acid metabolic process|folic acid-containing compound biosynthetic process|histidine biosynthetic process|methionine biosynthetic process|one-carbon metabolic process|purine nucleotide biosynthetic process	cytosol|mitochondrion	ATP binding|formate-tetrahydrofolate ligase activity|methenyltetrahydrofolate cyclohydrolase activity|methylenetetrahydrofolate dehydrogenase (NADP+) activity|methylenetetrahydrofolate dehydrogenase|protein binding			ovary(2)	2				OV - Ovarian serous cystadenocarcinoma(108;8.7e-12)|all cancers(60;3.29e-11)|BRCA - Breast invasive adenocarcinoma(234;0.0488)	NADH(DB00157)|Tetrahydrofolic acid(DB00116)	TTTTGCAGGTAAAATAATTTT	0.363													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	76719539	76719539	+	IGR	DEL	G	-	-			TCGA-CZ-5460-01A-01D-1501-10	TCGA-CZ-5460-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:76719539delG								C14orf118 (50406 upstream) : ESRRB (118151 downstream)																							ACAATAAAATGGGGATTGGGA	0.383													4	2	---	---	---	---	
STON2	85439	broad.mit.edu	37	14	81799173	81799173	+	Intron	DEL	T	-	-			TCGA-CZ-5460-01A-01D-1501-10	TCGA-CZ-5460-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:81799173delT	uc010tvu.1	-						STON2_uc001xvk.1_Intron	NM_033104	NP_149095	Q8WXE9	STON2_HUMAN	stonin 2						endocytosis|intracellular protein transport|regulation of endocytosis	clathrin adaptor complex|nucleolus	protein binding			skin(3)|pancreas(2)	5				BRCA - Breast invasive adenocarcinoma(234;0.0348)		TTTTAAGAGCTTTTTTTTCAC	0.284													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	90741314	90741315	+	IGR	DEL	CA	-	-			TCGA-CZ-5460-01A-01D-1501-10	TCGA-CZ-5460-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:90741314_90741315delCA								PSMC1 (2350 upstream) : C14orf102 (3083 downstream)																							acaccgtcttcaccaagtggtc	0.000													4	2	---	---	---	---	
SERPINA10	51156	broad.mit.edu	37	14	94756558	94756560	+	In_Frame_Del	DEL	TGA	-	-			TCGA-CZ-5460-01A-01D-1501-10	TCGA-CZ-5460-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:94756558_94756560delTGA	uc001yct.2	-	2	837_839	c.371_373delTCA	c.(370-375)ATCAAG>AAG	p.I124del	SERPINA10_uc001ycu.3_In_Frame_Del_p.I124del	NM_016186	NP_057270	Q9UK55	ZPI_HUMAN	serine (or cysteine) proteinase inhibitor, clade	124					regulation of proteolysis	extracellular region	serine-type endopeptidase inhibitor activity			ovary(2)|skin(1)	3		all_cancers(154;0.105)		Epithelial(152;0.135)|COAD - Colon adenocarcinoma(157;0.207)|all cancers(159;0.221)		AGCCCTCTCTTGATCTGGGTTTC	0.591													13	8	---	---	---	---	
APBA2	321	broad.mit.edu	37	15	29212034	29212036	+	5'Flank	DEL	GGA	-	-			TCGA-CZ-5460-01A-01D-1501-10	TCGA-CZ-5460-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:29212034_29212036delGGA	uc001zck.2	+						APBA2_uc010azj.2_Intron|APBA2_uc010uat.1_Intron|APBA2_uc001zcl.2_5'Flank|APBA2_uc010uas.1_Intron	NM_005503	NP_005494	Q99767	APBA2_HUMAN	amyloid beta A4 precursor protein-binding,						nervous system development|protein transport		protein binding				0		all_lung(180;1.73e-12)|Breast(32;2.89e-05)|Colorectal(260;0.234)		all cancers(64;7.44e-11)|Epithelial(43;5.74e-10)|GBM - Glioblastoma multiforme(186;0.026)|BRCA - Breast invasive adenocarcinoma(123;0.0286)|Lung(196;0.24)		CGAAACATCTGGAGGCCCCGTTT	0.571													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	39037722	39037722	+	IGR	DEL	A	-	-	rs5812051		TCGA-CZ-5460-01A-01D-1501-10	TCGA-CZ-5460-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:39037722delA								C15orf53 (45483 upstream) : C15orf54 (505163 downstream)																							TGGTATAGTTAAAAATCTTGA	0.388													2	4	---	---	---	---	
SECISBP2L	9728	broad.mit.edu	37	15	49301196	49301197	+	Intron	INS	-	A	A			TCGA-CZ-5460-01A-01D-1501-10	TCGA-CZ-5460-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:49301196_49301197insA	uc001zxe.1	-						SECISBP2L_uc001zxd.1_Intron|SECISBP2L_uc010bep.1_Intron	NM_014701	NP_055516	Q93073	SBP2L_HUMAN	SECIS binding protein 2-like											breast(1)|skin(1)	2						ATAAAGAGAATATACTTACTGT	0.307													3	3	---	---	---	---	
PARP6	56965	broad.mit.edu	37	15	72542160	72542160	+	Intron	DEL	A	-	-			TCGA-CZ-5460-01A-01D-1501-10	TCGA-CZ-5460-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:72542160delA	uc002auc.2	-						PARP6_uc002aua.2_Intron|PARP6_uc002aub.2_Intron|PARP6_uc002aud.3_Intron|PARP6_uc002auf.1_Intron	NM_020214	NP_064599	Q2NL67	PARP6_HUMAN	poly (ADP-ribose) polymerase family, member 6								NAD+ ADP-ribosyltransferase activity				0						CCAAACCACCAAAAAAACGCA	0.398													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	92917737	92917737	+	IGR	DEL	G	-	-			TCGA-CZ-5460-01A-01D-1501-10	TCGA-CZ-5460-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:92917737delG								SLCO3A1 (202072 upstream) : ST8SIA2 (19403 downstream)																							tgggtgttttggcctaagaaa	0.179													4	2	---	---	---	---	
ARHGDIG	398	broad.mit.edu	37	16	332799	332799	+	Frame_Shift_Del	DEL	G	-	-			TCGA-CZ-5460-01A-01D-1501-10	TCGA-CZ-5460-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:332799delG	uc002cgm.1	+	6	738	c.663delG	c.(661-663)CAGfs	p.Q221fs	PDIA2_uc002cgn.1_5'UTR|PDIA2_uc010bqt.1_5'UTR|PDIA2_uc002cgo.1_5'Flank	NM_001176	NP_001167	Q99819	GDIR3_HUMAN	Rho GDP dissociation inhibitor (GDI) gamma	221					negative regulation of cell adhesion|regulation of small GTPase mediated signal transduction|Rho protein signal transduction	cytoplasmic membrane-bounded vesicle|cytosol	GTPase activator activity|Rho GDP-dissociation inhibitor activity			central_nervous_system(1)	1		all_cancers(16;6.71e-07)|all_epithelial(16;1.59e-06)|Hepatocellular(16;0.000105)|Lung NSC(18;0.00769)|all_lung(18;0.0186)				GCATCTGCCAGGACTGGAAGG	0.647											OREG0003697	type=REGULATORY REGION|Gene=PDIA2|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay	4	2	---	---	---	---	
SEZ6L2	26470	broad.mit.edu	37	16	29910021	29910021	+	Intron	DEL	C	-	-			TCGA-CZ-5460-01A-01D-1501-10	TCGA-CZ-5460-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:29910021delC	uc002duq.3	-						uc002dtf.2_Intron|BOLA2_uc010bzb.1_Intron|SEZ6L2_uc002dup.3_Intron|SEZ6L2_uc002dur.3_Intron|SEZ6L2_uc002dus.3_Intron|SEZ6L2_uc010vec.1_Intron|SEZ6L2_uc010ved.1_Intron|ASPHD1_uc002dut.2_5'Flank|ASPHD1_uc002duu.3_5'Flank|ASPHD1_uc010bzi.2_5'Flank	NM_201575	NP_963869	Q6UXD5	SE6L2_HUMAN	seizure related 6 homolog (mouse)-like 2 isoform							endoplasmic reticulum membrane|integral to membrane|plasma membrane				ovary(1)|skin(1)	2						AGCCCTCCTTCTTGGATCTAG	0.557													4	2	---	---	---	---	
PRSS53	339105	broad.mit.edu	37	16	31107201	31107202	+	5'Flank	DEL	CA	-	-			TCGA-CZ-5460-01A-01D-1501-10	TCGA-CZ-5460-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:31107201_31107202delCA	uc002ear.2	-						VKORC1_uc002eas.2_5'Flank|VKORC1_uc002eat.2_5'Flank|VKORC1_uc002eau.2_5'Flank	NM_001039503	NP_001034592	Q2L4Q9	PRS53_HUMAN	polyserase 3 precursor						proteolysis	extracellular region	serine-type endopeptidase activity				0						agaggtccttcaccagcctcct	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	87915349	87915349	+	IGR	DEL	T	-	-			TCGA-CZ-5460-01A-01D-1501-10	TCGA-CZ-5460-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:87915349delT								SLC7A5 (12249 upstream) : CA5A (6276 downstream)																							CTCCTGTTTGTTTTTTGTCCC	0.572													4	2	---	---	---	---	
TRPV2	51393	broad.mit.edu	37	17	16336661	16336662	+	Intron	INS	-	TC	TC			TCGA-CZ-5460-01A-01D-1501-10	TCGA-CZ-5460-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:16336661_16336662insTC	uc002gpy.2	+						TRPV2_uc002gpz.2_Intron	NM_016113	NP_057197	Q9Y5S1	TRPV2_HUMAN	transient receptor potential cation channel,						sensory perception	integral to plasma membrane|melanosome	calcium channel activity			ovary(1)	1				UCEC - Uterine corpus endometrioid carcinoma (92;0.0837)		TGTCTGaggcactttgtcctca	0.243													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	20606761	20606761	+	IGR	DEL	A	-	-	rs74578995		TCGA-CZ-5460-01A-01D-1501-10	TCGA-CZ-5460-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:20606761delA								LGALS9B (235913 upstream) : CCDC144NL (159949 downstream)																							acttcatctcaaaaaaaaaaa	0.179													6	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	20620154	20620154	+	IGR	DEL	A	-	-			TCGA-CZ-5460-01A-01D-1501-10	TCGA-CZ-5460-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:20620154delA								LGALS9B (249306 upstream) : CCDC144NL (146556 downstream)																							CCTCATCTGTAAAATTTTATC	0.323													4	2	---	---	---	---	
DDX52	11056	broad.mit.edu	37	17	35988434	35988434	+	Intron	DEL	T	-	-			TCGA-CZ-5460-01A-01D-1501-10	TCGA-CZ-5460-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:35988434delT	uc002hoi.1	-						DDX52_uc002hoh.1_Intron	NM_007010	NP_008941	Q9Y2R4	DDX52_HUMAN	ATP-dependent RNA helicase ROK1 isoform a							nucleolus	ATP binding|ATP-dependent helicase activity|RNA binding			ovary(1)|skin(1)	2		Breast(25;0.00637)|Ovarian(249;0.15)				ctgGTATATATTTATGTATAA	0.149													3	9	---	---	---	---	
MSI2	124540	broad.mit.edu	37	17	55401059	55401059	+	Intron	DEL	G	-	-			TCGA-CZ-5460-01A-01D-1501-10	TCGA-CZ-5460-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:55401059delG	uc002iuz.1	+						MSI2_uc010wnm.1_Intron|MSI2_uc002iva.2_Intron	NM_138962	NP_620412	Q96DH6	MSI2H_HUMAN	musashi 2 isoform a							cytoplasm	nucleotide binding|RNA binding			central_nervous_system(1)|pancreas(1)	2	Breast(9;1.78e-08)			GBM - Glioblastoma multiforme(1;0.0025)		TTGCCAGGATGGGCAGAGAAG	0.587			T	HOXA9	CML								4	2	---	---	---	---	
NAT9	26151	broad.mit.edu	37	17	72768568	72768568	+	Intron	DEL	A	-	-			TCGA-CZ-5460-01A-01D-1501-10	TCGA-CZ-5460-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:72768568delA	uc002jlq.2	-						NAT9_uc002jlr.2_Intron	NM_015654	NP_056469	Q9BTE0	NAT9_HUMAN	N-acetyltransferase 9							protein complex	N-acetyltransferase activity				0						aagaagtgtgaaaggcctcac	0.075													4	2	---	---	---	---	
NDC80	10403	broad.mit.edu	37	18	2595857	2595858	+	Intron	DEL	AA	-	-			TCGA-CZ-5460-01A-01D-1501-10	TCGA-CZ-5460-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:2595857_2595858delAA	uc002kli.2	+							NM_006101	NP_006092	O14777	NDC80_HUMAN	kinetochore associated 2						attachment of spindle microtubules to kinetochore|cell division|establishment of mitotic spindle orientation|mitotic prometaphase|mitotic sister chromatid segregation|mitotic spindle organization|phosphatidylinositol-mediated signaling	condensed nuclear chromosome outer kinetochore|cytosol|Ndc80 complex	protein binding			ovary(1)	1						AAAAGTCTCTAAAACTATGAAA	0.257													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	10070319	10070319	+	IGR	DEL	G	-	-			TCGA-CZ-5460-01A-01D-1501-10	TCGA-CZ-5460-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:10070319delG								VAPA (110302 upstream) : APCDD1 (384306 downstream)																							GAGCTCTGGTGGGGTTGGAAC	0.527													4	2	---	---	---	---	
NEDD4L	23327	broad.mit.edu	37	18	55915164	55915164	+	Intron	DEL	T	-	-			TCGA-CZ-5460-01A-01D-1501-10	TCGA-CZ-5460-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:55915164delT	uc002lgy.2	+						NEDD4L_uc002lgz.2_Intron|NEDD4L_uc002lgx.2_Intron|NEDD4L_uc010xee.1_Intron|NEDD4L_uc002lhc.2_Intron|NEDD4L_uc002lhd.2_Intron|NEDD4L_uc002lhb.2_Intron|NEDD4L_uc002lhe.2_Intron|NEDD4L_uc002lhf.2_Intron|NEDD4L_uc010dpl.1_Intron|NEDD4L_uc002lhg.2_Intron|NEDD4L_uc002lhh.2_Intron	NM_001144967	NP_001138439	Q96PU5	NED4L_HUMAN	neural precursor cell expressed, developmentally						cellular sodium ion homeostasis|excretion|interspecies interaction between organisms|positive regulation of endocytosis|protein ubiquitination involved in ubiquitin-dependent protein catabolic process|regulation of protein catabolic process|response to metal ion|sodium ion transport|water homeostasis	cytoplasm	protein binding|sodium channel regulator activity|ubiquitin-protein ligase activity			lung(4)	4						AAGTGCTGAATTTTTGAAAAC	0.393													4	2	---	---	---	---	
MKNK2	2872	broad.mit.edu	37	19	2052599	2052600	+	5'Flank	DEL	GT	-	-			TCGA-CZ-5460-01A-01D-1501-10	TCGA-CZ-5460-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:2052599_2052600delGT	uc002lus.2	-						MKNK2_uc010xgv.1_5'Flank|MKNK2_uc002lur.2_5'Flank	NM_199054	NP_951009	Q9HBH9	MKNK2_HUMAN	MAP kinase-interacting serine/threonine kinase 2						cell surface receptor linked signaling pathway|intracellular protein kinase cascade|regulation of translation		ATP binding|metal ion binding|protein serine/threonine kinase activity			lung(1)|breast(1)	2		Ovarian(11;2.11e-07)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		aaggatAAGAGTGTGTGTGTGT	0.297													4	2	---	---	---	---	
ZFR2	23217	broad.mit.edu	37	19	3853304	3853305	+	Intron	DEL	CA	-	-			TCGA-CZ-5460-01A-01D-1501-10	TCGA-CZ-5460-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:3853304_3853305delCA	uc002lyw.2	-						ZFR2_uc010xhx.1_Intron|ZFR2_uc002lyx.3_Intron|ZFR2_uc010xhy.1_Intron	NM_015174	NP_055989	Q9UPR6	ZFR2_HUMAN	zinc finger RNA binding protein 2 isoform 1							intracellular	nucleic acid binding|zinc ion binding			central_nervous_system(1)|pancreas(1)	2				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.00514)|STAD - Stomach adenocarcinoma(1328;0.19)		CTTGCCTTCTCACAGTTTAGAG	0.589													4	2	---	---	---	---	
DUS3L	56931	broad.mit.edu	37	19	5788290	5788290	+	Intron	DEL	G	-	-			TCGA-CZ-5460-01A-01D-1501-10	TCGA-CZ-5460-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:5788290delG	uc002mdc.2	-						DUS3L_uc002mdd.2_Intron|DUS3L_uc010duk.2_Intron|DUS3L_uc010xiw.1_Intron	NM_020175	NP_064560	Q96G46	DUS3L_HUMAN	dihydrouridine synthase 3-like isoform 1						tRNA processing		flavin adenine dinucleotide binding|nucleic acid binding|tRNA dihydrouridine synthase activity|zinc ion binding				0						TCCAGTAGGTGGGGACAGACA	0.502													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	12530210	12530211	+	IGR	DEL	AC	-	-	rs148782163		TCGA-CZ-5460-01A-01D-1501-10	TCGA-CZ-5460-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:12530210_12530211delAC								ZNF799 (18176 upstream) : ZNF443 (10310 downstream)																							gcctctactgacacagactgca	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	16163220	16163220	+	IGR	DEL	G	-	-			TCGA-CZ-5460-01A-01D-1501-10	TCGA-CZ-5460-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:16163220delG								FLJ25328 (10305 upstream) : TPM4 (15097 downstream)																							TATGCTGGTTGCCTGACCCAG	0.512													4	2	---	---	---	---	
SIN3B	23309	broad.mit.edu	37	19	16964428	16964428	+	Intron	DEL	G	-	-			TCGA-CZ-5460-01A-01D-1501-10	TCGA-CZ-5460-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:16964428delG	uc002ney.1	+						SIN3B_uc002new.2_Intron|SIN3B_uc002nex.2_Intron|SIN3B_uc002nez.1_Intron	NM_015260	NP_056075	O75182	SIN3B_HUMAN	SIN3 homolog B, transcription regulator						cellular lipid metabolic process|transcription, DNA-dependent	nucleoplasm	protein binding			ovary(2)	2						TGGACTGTGTGAATTGCTGCA	0.537													4	2	---	---	---	---	
ZNF100	163227	broad.mit.edu	37	19	21909967	21909967	+	Frame_Shift_Del	DEL	A	-	-			TCGA-CZ-5460-01A-01D-1501-10	TCGA-CZ-5460-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:21909967delA	uc002nqi.2	-	5	1346	c.1147delT	c.(1147-1149)TACfs	p.Y383fs	ZNF100_uc002nqh.2_Frame_Shift_Del_p.Y319fs	NM_173531	NP_775802	Q8IYN0	ZN100_HUMAN	zinc finger protein 100	383	C2H2-type 8.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0						GAGAATCGGTAAAAAGCTTTG	0.403													17	10	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	29980910	29980910	+	Intron	DEL	A	-	-	rs111606199		TCGA-CZ-5460-01A-01D-1501-10	TCGA-CZ-5460-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:29980910delA	uc002nse.1	-											Homo sapiens cDNA FLJ37474 fis, clone BRAWH2012619.																		ATTTGGGTCCAAAAAAAAAAG	0.274													3	3	---	---	---	---	
UBA2	10054	broad.mit.edu	37	19	34922498	34922499	+	Intron	INS	-	TT	TT	rs113731177		TCGA-CZ-5460-01A-01D-1501-10	TCGA-CZ-5460-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:34922498_34922499insTT	uc002nvk.2	+						UBA2_uc010xrx.1_Intron|UBA2_uc002nvl.2_Intron	NM_005499	NP_005490	Q9UBT2	SAE2_HUMAN	SUMO-1 activating enzyme subunit 2						protein sumoylation	nucleus	ATP binding|enzyme activator activity|ligase activity|metal ion binding|protein heterodimerization activity|SUMO activating enzyme activity			ovary(1)	1	Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.211)			ACTTCATGTTGTATTTTTGCTG	0.287													6	4	---	---	---	---	
ZNF540	163255	broad.mit.edu	37	19	38059865	38059865	+	Intron	DEL	T	-	-			TCGA-CZ-5460-01A-01D-1501-10	TCGA-CZ-5460-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:38059865delT	uc002ogq.2	+						uc002ogm.2_Intron|uc002ogn.2_Intron|ZNF540_uc002ogo.2_Intron|ZNF540_uc002ogp.2_Intron|ZNF571_uc002ogr.1_Intron|ZNF571_uc002ogt.2_Intron|ZNF571_uc010efp.2_Intron	NM_152606	NP_689819	Q8NDQ6	ZN540_HUMAN	zinc finger protein 540						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			large_intestine(1)	1			COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)			ccaaggcatcttttttttttt	0.005													4	3	---	---	---	---	
ZNF540	163255	broad.mit.edu	37	19	38077905	38077905	+	Intron	DEL	C	-	-			TCGA-CZ-5460-01A-01D-1501-10	TCGA-CZ-5460-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:38077905delC	uc002ogq.2	+						uc002ogm.2_RNA|uc002ogn.2_RNA|ZNF540_uc002ogo.2_RNA|ZNF540_uc002ogp.2_RNA|ZNF571_uc002ogr.1_Intron|ZNF571_uc002ogt.2_Intron|ZNF571_uc010efp.2_Intron	NM_152606	NP_689819	Q8NDQ6	ZN540_HUMAN	zinc finger protein 540						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			large_intestine(1)	1			COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)			GCCCAGGGAGCCCCCCACCAT	0.517													4	2	---	---	---	---	
NPAS1	4861	broad.mit.edu	37	19	47539293	47539293	+	Frame_Shift_Del	DEL	G	-	-			TCGA-CZ-5460-01A-01D-1501-10	TCGA-CZ-5460-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:47539293delG	uc002pfw.2	+	6	790	c.594delG	c.(592-594)CTGfs	p.L198fs	NPAS1_uc002pfx.2_Frame_Shift_Del_p.L22fs|NPAS1_uc002pfy.2_Frame_Shift_Del_p.L198fs|NPAS1_uc010xyj.1_Frame_Shift_Del_p.L22fs	NM_002517	NP_002508	Q99742	NPAS1_HUMAN	neuronal PAS domain protein 1	198	PAS 1.				central nervous system development	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|signal transducer activity				0		all_cancers(25;4.31e-08)|all_epithelial(76;2.96e-06)|all_lung(116;7.86e-06)|Lung NSC(112;2.31e-05)|all_neural(266;0.026)|Ovarian(192;0.0392)|Breast(70;0.102)		all cancers(93;6.02e-05)|OV - Ovarian serous cystadenocarcinoma(262;7.35e-05)|Epithelial(262;0.00389)|GBM - Glioblastoma multiforme(486;0.0252)		TGGAGCAACTGGGGCTGCGGA	0.552											OREG0025586	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	4	2	---	---	---	---	
NAPSB	256236	broad.mit.edu	37	19	50845448	50845448	+	Intron	DEL	A	-	-			TCGA-CZ-5460-01A-01D-1501-10	TCGA-CZ-5460-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:50845448delA	uc002prw.2	-						NR1H2_uc002prv.3_Intron	NR_002798				Homo sapiens napsin B pseudogene, mRNA sequence.											central_nervous_system(1)	1						agaaaatcttaaaaaaaaGCT	0.065													4	2	---	---	---	---	
TGM3	7053	broad.mit.edu	37	20	2306109	2306109	+	Intron	DEL	G	-	-			TCGA-CZ-5460-01A-01D-1501-10	TCGA-CZ-5460-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:2306109delG	uc002wfx.3	+							NM_003245	NP_003236	Q08188	TGM3_HUMAN	transglutaminase 3 precursor						cell envelope organization|hair follicle morphogenesis|keratinization|peptide cross-linking|protein tetramerization	cytoplasm|extrinsic to internal side of plasma membrane	acyltransferase activity|calcium ion binding|GDP binding|GTP binding|GTPase activity|magnesium ion binding|protein-glutamine gamma-glutamyltransferase activity			large_intestine(4)|ovary(3)|breast(1)|skin(1)	9					L-Glutamine(DB00130)	GGCAGAGGGAGAAAGCTGTGT	0.453													4	2	---	---	---	---	
SNRPB2	6629	broad.mit.edu	37	20	16717270	16717270	+	Intron	DEL	A	-	-			TCGA-CZ-5460-01A-01D-1501-10	TCGA-CZ-5460-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:16717270delA	uc002wph.1	+						SNRPB2_uc002wpi.1_Intron	NM_003092	NP_003083	P08579	RU2B_HUMAN	small nuclear ribonucleoprotein polypeptide B''							catalytic step 2 spliceosome|nucleoplasm|U2 snRNP	nucleotide binding|protein binding|RNA binding			large_intestine(1)	1						TTCTATCTGTAAAACAGGATT	0.448													4	2	---	---	---	---	
ZNF831	128611	broad.mit.edu	37	20	57766859	57766860	+	Frame_Shift_Del	DEL	GG	-	-			TCGA-CZ-5460-01A-01D-1501-10	TCGA-CZ-5460-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:57766859_57766860delGG	uc002yan.2	+	1	785_786	c.785_786delGG	c.(784-786)AGGfs	p.R262fs		NM_178457	NP_848552	Q5JPB2	ZN831_HUMAN	zinc finger protein 831	262						intracellular	nucleic acid binding|zinc ion binding			skin(13)|ovary(1)	14	all_lung(29;0.0085)					CTGGATGTGAGGACCGAAGCTG	0.663													4	2	---	---	---	---	
BAGE2	85319	broad.mit.edu	37	21	11039696	11039696	+	Intron	DEL	G	-	-			TCGA-CZ-5460-01A-01D-1501-10	TCGA-CZ-5460-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:11039696delG	uc002yit.1	-						TPTE_uc002yis.1_5'Flank	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)		AAATtacacaggaaaagttct	0.194													4	2	---	---	---	---	
BAGE2	85319	broad.mit.edu	37	21	11062428	11062429	+	Intron	DEL	TG	-	-	rs150460070		TCGA-CZ-5460-01A-01D-1501-10	TCGA-CZ-5460-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:11062428_11062429delTG	uc002yit.1	-						BAGE_uc002yiw.1_5'Flank|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)		CATTTATGTATGTGTGTGTGTG	0.173													6	4	---	---	---	---	
BAGE2	85319	broad.mit.edu	37	21	11066363	11066363	+	Intron	DEL	T	-	-	rs151040810		TCGA-CZ-5460-01A-01D-1501-10	TCGA-CZ-5460-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:11066363delT	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)		agaggttaaatttccttgttc	0.060													8	6	---	---	---	---	
SON	6651	broad.mit.edu	37	21	34918411	34918412	+	Intron	DEL	GT	-	-			TCGA-CZ-5460-01A-01D-1501-10	TCGA-CZ-5460-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:34918411_34918412delGT	uc002yse.1	+						SON_uc002ysb.1_Intron|SON_uc002ysc.2_Intron|SON_uc002ysd.2_Intron|SON_uc002ysf.1_Intron	NM_138927	NP_620305	P18583	SON_HUMAN	SON DNA-binding protein isoform F						anti-apoptosis|cytokinesis|mRNA processing|regulation of cell cycle|regulation of RNA splicing|RNA splicing|spindle pole body separation	nuclear speck	DNA binding|double-stranded RNA binding			ovary(4)|skin(2)	6						TAGGAAAAAGGTAAAACATCTG	0.233													4	2	---	---	---	---	
KCNE1	3753	broad.mit.edu	37	21	35822028	35822028	+	Intron	DEL	A	-	-			TCGA-CZ-5460-01A-01D-1501-10	TCGA-CZ-5460-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:35822028delA	uc010gmp.2	-						KCNE1_uc002ytz.2_Intron|KCNE1_uc010gmq.2_Intron|KCNE1_uc010gmr.2_Intron|KCNE1_uc010gms.2_Intron|KCNE1_uc002yua.2_Intron	NM_001127670	NP_001121142	P15382	KCNE1_HUMAN	potassium voltage-gated channel, Isk-related						blood circulation|membrane depolarization|muscle contraction|sensory perception of sound	lysosome	delayed rectifier potassium channel activity|potassium channel regulator activity			ovary(2)	2					Indapamide(DB00808)	CGTATTGGCCAAAACCCACAC	0.303													4	2	---	---	---	---	
ABCG1	9619	broad.mit.edu	37	21	43665732	43665733	+	Intron	DEL	GG	-	-			TCGA-CZ-5460-01A-01D-1501-10	TCGA-CZ-5460-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:43665732_43665733delGG	uc002zaq.2	+						ABCG1_uc002zan.2_Intron|ABCG1_uc002zam.2_Intron|ABCG1_uc002zao.2_Intron|ABCG1_uc002zap.2_Intron|ABCG1_uc002zar.2_Intron|ABCG1_uc011aev.1_Intron	NM_004915	NP_004906	P45844	ABCG1_HUMAN	ATP-binding cassette sub-family G member 1						amyloid precursor protein catabolic process|cholesterol efflux|cholesterol homeostasis|cholesterol metabolic process|detection of hormone stimulus|high-density lipoprotein particle remodeling|intracellular cholesterol transport|lipoprotein metabolic process|low-density lipoprotein particle remodeling|negative regulation of cholesterol storage|negative regulation of macrophage derived foam cell differentiation|phospholipid efflux|phospholipid homeostasis|positive regulation of cholesterol biosynthetic process|regulation of cholesterol esterification|regulation of transcription, DNA-dependent|response to lipid|reverse cholesterol transport	endoplasmic reticulum membrane|external side of plasma membrane|Golgi membrane|recycling endosome	ADP binding|ATP binding|cholesterol transporter activity|glycoprotein transporter activity|phospholipid transporter activity|protein heterodimerization activity|protein homodimerization activity|sterol-transporting ATPase activity|toxin transporter activity			ovary(2)|central_nervous_system(1)	3					Adenosine triphosphate(DB00171)	TGTGGTGTGAGGGAGGCAGGGA	0.569													4	2	---	---	---	---	
TFF2	7032	broad.mit.edu	37	21	43766895	43766895	+	Intron	DEL	A	-	-			TCGA-CZ-5460-01A-01D-1501-10	TCGA-CZ-5460-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:43766895delA	uc002zaw.2	-							NM_005423	NP_005414	Q03403	TFF2_HUMAN	trefoil factor 2 precursor						digestion	extracellular region				pancreas(1)	1						TAGGTCACATAAAAAAAATCA	0.438													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	44467423	44467423	+	IGR	DEL	G	-	-	rs35192629		TCGA-CZ-5460-01A-01D-1501-10	TCGA-CZ-5460-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:44467423delG								PKNOX1 (13735 upstream) : CBS (5878 downstream)																							ctttacataagtggggtcacg	0.000													2	4	---	---	---	---	
XKR3	150165	broad.mit.edu	37	22	17281097	17281098	+	Intron	INS	-	A	A	rs151238544	by1000genomes	TCGA-CZ-5460-01A-01D-1501-10	TCGA-CZ-5460-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:17281097_17281098insA	uc002zlv.2	-						XKR3_uc011agf.1_Intron	NM_175878	NP_787074	Q5GH77	XKR3_HUMAN	X Kell blood group precursor-related family,							integral to membrane|plasma membrane				large_intestine(1)|ovary(1)|skin(1)	3	all_hematologic(4;0.00567)|Acute lymphoblastic leukemia(84;0.0977)	all_epithelial(15;0.0157)|Lung NSC(13;0.147)|all_lung(157;0.175)				TTATTTATGGTAGTTCTTCCCC	0.252													4	2	---	---	---	---	
LOC96610	96610	broad.mit.edu	37	22	22775976	22775976	+	Intron	DEL	A	-	-			TCGA-CZ-5460-01A-01D-1501-10	TCGA-CZ-5460-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:22775976delA	uc011aim.1	+											Parts of antibodies, mostly variable regions.												0						TGTATTTTCTAAGGAGTGAAT	0.448													4	2	---	---	---	---	
GCAT	23464	broad.mit.edu	37	22	38204400	38204401	+	Intron	DEL	TG	-	-			TCGA-CZ-5460-01A-01D-1501-10	TCGA-CZ-5460-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:38204400_38204401delTG	uc003atz.2	+						GCAT_uc003aua.1_Intron	NM_014291	NP_055106	O75600	KBL_HUMAN	glycine C-acetyltransferase precursor						biosynthetic process|cellular amino acid metabolic process		glycine C-acetyltransferase activity|pyridoxal phosphate binding|transferase activity, transferring nitrogenous groups				0	Melanoma(58;0.045)				Glycine(DB00145)|Pyridoxal Phosphate(DB00114)	gcggctcctttgtgaaggtctc	0.153													4	2	---	---	---	---	
FAM83F	113828	broad.mit.edu	37	22	40406444	40406444	+	Intron	DEL	T	-	-			TCGA-CZ-5460-01A-01D-1501-10	TCGA-CZ-5460-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:40406444delT	uc003ayk.1	+							NM_138435	NP_612444	Q8NEG4	FA83F_HUMAN	hypothetical protein LOC113828											breast(1)	1						CAGCAATTGATTTTTTTTTCT	0.483													4	2	---	---	---	---	
ADSL	158	broad.mit.edu	37	22	40760092	40760092	+	Intron	DEL	A	-	-	rs71925942		TCGA-CZ-5460-01A-01D-1501-10	TCGA-CZ-5460-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:40760092delA	uc003ayp.3	+						ADSL_uc003ays.3_Intron|ADSL_uc003ayq.3_Intron|ADSL_uc003ayr.3_Intron|ADSL_uc003ayt.3_Intron	NM_000026	NP_000017	P30566	PUR8_HUMAN	adenylosuccinate lyase isoform a						AMP biosynthetic process|protein tetramerization|purine base metabolic process	cytosol	(S)-2-(5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxamido)succinate AMP-lyase (fumarate-forming) activity|N6-(1,2-dicarboxyethyl)AMP AMP-lyase (fumarate-forming) activity			ovary(1)	1						aaaaaaaaagaaaaaaaaaaT	0.149													6	3	---	---	---	---	
ZC3H7B	23264	broad.mit.edu	37	22	41752644	41752645	+	Intron	DEL	CC	-	-	rs115593507	by1000genomes	TCGA-CZ-5460-01A-01D-1501-10	TCGA-CZ-5460-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:41752644_41752645delCC	uc003azw.2	+						ZC3H7B_uc010gyl.1_Intron	NM_017590	NP_060060	Q9UGR2	Z3H7B_HUMAN	zinc finger CCCH-type containing 7B						interspecies interaction between organisms	nucleus	nucleic acid binding|protein binding|zinc ion binding			central_nervous_system(1)	1						TGGCTGTGCTCCCAGATGGGCT	0.644													4	2	---	---	---	---	
ARFGAP3	26286	broad.mit.edu	37	22	43205043	43205043	+	Intron	DEL	A	-	-			TCGA-CZ-5460-01A-01D-1501-10	TCGA-CZ-5460-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:43205043delA	uc003bdd.2	-						ARFGAP3_uc010gzf.2_Intron	NM_014570	NP_055385	Q9NP61	ARFG3_HUMAN	ADP-ribosylation factor GTPase activating						intracellular protein transport|protein secretion|regulation of ARF GTPase activity|vesicle-mediated transport	cytosol|Golgi membrane	ARF GTPase activator activity|protein transporter activity|zinc ion binding			breast(1)	1						AATTCTAATTAAAAAAAAAAG	0.259													9	5	---	---	---	---	
MOV10L1	54456	broad.mit.edu	37	22	50581271	50581272	+	Intron	INS	-	A	A			TCGA-CZ-5460-01A-01D-1501-10	TCGA-CZ-5460-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:50581271_50581272insA	uc003bjj.2	+						MOV10L1_uc003bjk.3_Intron|MOV10L1_uc011arp.1_Intron|MOV10L1_uc011arq.1_Intron	NM_018995	NP_061868	Q9BXT6	M10L1_HUMAN	MOV10-like 1 isoform 1						germ cell development|multicellular organismal development|spermatogenesis		ATP binding|ATP-dependent RNA helicase activity|magnesium ion binding|RNA binding			ovary(2)|skin(1)	3		all_cancers(38;3.31e-11)|all_epithelial(38;5.69e-10)|all_lung(38;3.73e-05)|Breast(42;0.000525)|Lung NSC(38;0.000954)|Ovarian(80;0.0367)|Lung SC(80;0.114)		LUAD - Lung adenocarcinoma(64;0.0215)|BRCA - Breast invasive adenocarcinoma(115;0.24)		tctcaaaaaagaaaaaaaaaaT	0.218													4	2	---	---	---	---	
REPS2	9185	broad.mit.edu	37	X	17059523	17059523	+	Intron	DEL	T	-	-			TCGA-CZ-5460-01A-01D-1501-10	TCGA-CZ-5460-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:17059523delT	uc004cxv.1	+						REPS2_uc004cxw.1_Intron|REPS2_uc011miw.1_Intron	NM_004726	NP_004717	Q8NFH8	REPS2_HUMAN	RALBP1 associated Eps domain containing 2						epidermal growth factor receptor signaling pathway|protein complex assembly	cytoplasm	calcium ion binding|protein binding			skin(2)|central_nervous_system(1)	3	Hepatocellular(33;0.183)					cttctgtgacttttttttctc	0.164													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	120336957	120336957	+	IGR	DEL	C	-	-			TCGA-CZ-5460-01A-01D-1501-10	TCGA-CZ-5460-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:120336957delC								GLUD2 (153163 upstream) : None (None downstream)																							CAATGGTGGGCCCTGAGGAAG	0.488													4	2	---	---	---	---	
RBMY3AP	64593	broad.mit.edu	37	Y	9454990	9454990	+	5'Flank	DEL	T	-	-			TCGA-CZ-5460-01A-01D-1501-10	TCGA-CZ-5460-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:9454990delT	uc004fsg.1	-						RBMY3AP_uc010nwq.1_5'Flank	NR_001573				Homo sapiens RNA binding motif protein, Y-linked, family 3, member A pseudogene (RBMY3AP), non-coding RNA.												0						CCTAAGCACATTTTACTAACA	0.299													4	2	---	---	---	---	
