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
KLHL17	339451	broad.mit.edu	37	1	900441	900441	+	Missense_Mutation	SNP	G	A	A			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:900441G>A	uc001aca.1	+	12	1906	c.1799G>A	c.(1798-1800)AGG>AAG	p.R600K	KLHL17_uc001acc.1_RNA|PLEKHN1_uc001acd.2_5'Flank|PLEKHN1_uc001acf.2_5'Flank|PLEKHN1_uc001ace.2_5'Flank	NM_198317	NP_938073	Q6TDP4	KLH17_HUMAN	kelch-like 17	600	Kelch 6.|Interaction with F-actin (By similarity).				actin cytoskeleton organization	actin cytoskeleton|cell junction|postsynaptic density|postsynaptic membrane	protein complex scaffold				0	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)		UCEC - Uterine corpus endometrioid carcinoma (11;0.00459)|Epithelial(90;1.52e-38)|OV - Ovarian serous cystadenocarcinoma(86;5.59e-23)|Colorectal(212;0.000155)|COAD - Colon adenocarcinoma(227;0.000193)|BRCA - Breast invasive adenocarcinoma(365;0.000469)|Kidney(185;0.00227)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0339)|Lung(427;0.199)		TACAACCCGAGGACCAACAAG	0.632													11	32	---	---	---	---	PASS
UBR4	23352	broad.mit.edu	37	1	19471346	19471346	+	Silent	SNP	G	A	A			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:19471346G>A	uc001bbi.2	-	54	8005	c.8001C>T	c.(7999-8001)TAC>TAT	p.Y2667Y	UBR4_uc001bbk.1_Silent_p.Y349Y	NM_020765	NP_065816	Q5T4S7	UBR4_HUMAN	retinoblastoma-associated factor 600	2667					interspecies interaction between organisms	cytoplasm|cytoskeleton|integral to membrane|nucleus	calmodulin binding|ubiquitin-protein ligase activity|zinc ion binding			kidney(10)|ovary(7)|breast(4)|pancreas(2)|skin(2)	25		Colorectal(325;3.46e-05)|Renal(390;0.000147)|all_lung(284;0.000328)|Lung NSC(340;0.000406)|Breast(348;0.000814)|Ovarian(437;0.00774)|Myeloproliferative disorder(586;0.0256)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00674)|BRCA - Breast invasive adenocarcinoma(304;5.43e-05)|Kidney(64;0.000337)|KIRC - Kidney renal clear cell carcinoma(64;0.00426)|STAD - Stomach adenocarcinoma(196;0.00715)|READ - Rectum adenocarcinoma(331;0.0816)		CACAGGTACAGTAGCCATGGA	0.428													37	184	---	---	---	---	PASS
WDR65	149465	broad.mit.edu	37	1	43649511	43649511	+	Missense_Mutation	SNP	G	A	A			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:43649511G>A	uc001cip.1	+	4	845	c.724G>A	c.(724-726)GGC>AGC	p.G242S	EBNA1BP2_uc001cio.2_Intron|WDR65_uc010ojz.1_Missense_Mutation_p.G231S|WDR65_uc001ciq.1_Missense_Mutation_p.G242S	NM_152498	NP_689711	Q96MR6	WDR65_HUMAN	WD repeat domain 65	242										skin(1)	1	Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0505)				ACCTACCAATGGCTCAAAGAG	0.483													48	76	---	---	---	---	PASS
TOE1	114034	broad.mit.edu	37	1	45808092	45808092	+	Missense_Mutation	SNP	T	G	G			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:45808092T>G	uc009vxq.2	+	6	1112	c.529T>G	c.(529-531)TTC>GTC	p.F177V	MUTYH_uc001cnf.2_5'Flank|MUTYH_uc009vxo.2_5'Flank|MUTYH_uc001cng.2_5'Flank|MUTYH_uc001cnj.2_5'Flank|MUTYH_uc001cni.2_5'Flank|MUTYH_uc001cnh.2_5'Flank|MUTYH_uc001cno.2_5'Flank|MUTYH_uc001cnk.2_5'Flank|MUTYH_uc010oll.1_5'Flank|MUTYH_uc001cnm.2_5'Flank|MUTYH_uc001cnl.2_5'Flank|MUTYH_uc009vxp.2_5'Flank|MUTYH_uc001cnn.2_5'Flank|TOE1_uc001cnq.3_RNA|TOE1_uc010olm.1_Missense_Mutation_p.F97V|TOE1_uc010oln.1_Missense_Mutation_p.F183V|TOE1_uc001cnr.3_RNA	NM_025077	NP_079353	Q96GM8	TOE1_HUMAN	target of EGR1, member 1 (nuclear)	177						nuclear speck|nucleolus	nucleic acid binding|zinc ion binding			central_nervous_system(1)	1	Acute lymphoblastic leukemia(166;0.155)					ACGGACCCTATTCCTGGAGCT	0.562													17	41	---	---	---	---	PASS
ABCA4	24	broad.mit.edu	37	1	94466632	94466632	+	Missense_Mutation	SNP	C	A	A			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:94466632C>A	uc001dqh.2	-	46	6416	c.6312G>T	c.(6310-6312)CAG>CAT	p.Q2104H		NM_000350	NP_000341	P78363	ABCA4_HUMAN	ATP-binding cassette, sub-family A member 4	2104	ABC transporter 2.|Cytoplasmic.				phototransduction, visible light|visual perception	integral to plasma membrane|membrane fraction	ATP binding|ATPase activity, coupled to transmembrane movement of substances			ovary(4)|skin(4)|central_nervous_system(2)|upper_aerodigestive_tract(1)|breast(1)	12		all_lung(203;0.000757)|Lung NSC(277;0.00335)		all cancers(265;0.00432)|GBM - Glioblastoma multiforme(16;0.00715)|Epithelial(280;0.171)		TGCGGCGTGCCTGGGGGTCCA	0.632													25	42	---	---	---	---	PASS
ABCA4	24	broad.mit.edu	37	1	94568687	94568687	+	Nonsense_Mutation	SNP	G	A	A			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:94568687G>A	uc001dqh.2	-	5	558	c.454C>T	c.(454-456)CGA>TGA	p.R152*	ABCA4_uc010otn.1_Nonsense_Mutation_p.R152*	NM_000350	NP_000341	P78363	ABCA4_HUMAN	ATP-binding cassette, sub-family A member 4	152	Extracellular.		R -> Q.		phototransduction, visible light|visual perception	integral to plasma membrane|membrane fraction	ATP binding|ATPase activity, coupled to transmembrane movement of substances			ovary(4)|skin(4)|central_nervous_system(2)|upper_aerodigestive_tract(1)|breast(1)	12		all_lung(203;0.000757)|Lung NSC(277;0.00335)		all cancers(265;0.00432)|GBM - Glioblastoma multiforme(16;0.00715)|Epithelial(280;0.171)		TCCCTTATTCGTATTCCTCTT	0.393													80	180	---	---	---	---	PASS
ARHGAP29	9411	broad.mit.edu	37	1	94697168	94697168	+	5'UTR	SNP	C	A	A			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:94697168C>A	uc001dqj.3	-	2					ARHGAP29_uc009wdq.1_RNA|ARHGAP29_uc001dql.2_5'UTR	NM_004815	NP_004806	Q52LW3	RHG29_HUMAN	PTPL1-associated RhoGAP 1						Rho protein signal transduction	cytosol	metal ion binding|Rho GTPase activator activity			breast(4)|skin(3)|lung(2)|upper_aerodigestive_tract(1)|ovary(1)	11		all_lung(203;0.000732)|Lung NSC(277;0.00328)		all cancers(265;0.0187)|Epithelial(280;0.159)		GAGCAATCATCCTTTCATGTA	0.388													76	353	---	---	---	---	PASS
ADORA3	140	broad.mit.edu	37	1	112031474	112031474	+	Silent	SNP	G	C	C			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:112031474G>C	uc001ebf.2	-	3	1397	c.630C>G	c.(628-630)GCC>GCG	p.A210A	ADORA3_uc001ebg.3_Silent_p.A129A	NM_020683	NP_065734	P33765	AA3R_HUMAN	adenosine A3 receptor isoform 1	Error:Variant_position_missing_in_P33765_after_alignment					activation of adenylate cyclase activity|inflammatory response|regulation of heart contraction	integral to plasma membrane	adenosine receptor activity, G-protein coupled			ovary(2)|large_intestine(1)|skin(1)	4		all_cancers(81;1.63e-06)|all_epithelial(167;5.01e-06)|all_lung(203;8.02e-05)|Lung NSC(277;0.000156)		all cancers(265;0.0185)|Colorectal(144;0.0186)|Lung(183;0.0238)|COAD - Colon adenocarcinoma(174;0.0644)|Epithelial(280;0.0872)|LUSC - Lung squamous cell carcinoma(189;0.134)	Adenosine(DB00640)|Aminophylline(DB01223)	TGTCCCTCAGGGCCACATGAT	0.552													60	270	---	---	---	---	PASS
NBPF10	100132406	broad.mit.edu	37	1	145323666	145323666	+	Missense_Mutation	SNP	A	G	G			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:145323666A>G	uc001end.3	+	29	3763	c.3728A>G	c.(3727-3729)GAC>GGC	p.D1243G	NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF10_uc001emp.3_Intron|NBPF10_uc010oyi.1_Intron|NBPF10_uc010oyk.1_Intron|NBPF10_uc010oyl.1_Intron|NBPF10_uc001enc.2_Intron|NBPF10_uc010oym.1_Intron|NBPF10_uc010oyn.1_Intron|NBPF10_uc010oyo.1_Intron|NBPF10_uc010oyp.1_5'Flank	NM_001039703	NP_001034792	A6NDV3	A6NDV3_HUMAN	hypothetical protein LOC100132406	1168											0	all_hematologic(923;0.032)			Colorectal(1306;1.36e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.00258)		ATTAAAAAGGACGAAGAAGAG	0.468													5	31	---	---	---	---	PASS
RPRD2	23248	broad.mit.edu	37	1	150445629	150445629	+	Nonsense_Mutation	SNP	C	A	A			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:150445629C>A	uc009wlr.2	+	11	4406	c.4205C>A	c.(4204-4206)TCA>TAA	p.S1402*	RPRD2_uc010pcc.1_3'UTR|RPRD2_uc001eup.3_Nonsense_Mutation_p.S1376*	NM_015203	NP_056018	Q5VT52	RPRD2_HUMAN	Regulation of nuclear pre-mRNA domain containing	1402	Pro-rich.						protein binding			ovary(1)	1						TTGGGTCCCTCACACAGAGAC	0.602													8	38	---	---	---	---	PASS
DENND4B	9909	broad.mit.edu	37	1	153913052	153913052	+	Missense_Mutation	SNP	A	T	T			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:153913052A>T	uc001fdd.1	-	10	1758	c.1357T>A	c.(1357-1359)TAC>AAC	p.Y453N		NM_014856	NP_055671	O75064	DEN4B_HUMAN	DENN/MADD domain containing 4B	453	DENN.									ovary(1)	1	all_lung(78;2.89e-32)|Lung NSC(65;2.27e-30)|Hepatocellular(266;0.0877)|Melanoma(130;0.199)		LUSC - Lung squamous cell carcinoma(543;0.151)			AGAGGAATGTAGGGGCACTGC	0.582													11	25	---	---	---	---	PASS
FLAD1	80308	broad.mit.edu	37	1	154960848	154960848	+	Missense_Mutation	SNP	G	A	A	rs145054820	byFrequency	TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:154960848G>A	uc001fgf.1	+	2	994	c.640G>A	c.(640-642)GGG>AGG	p.G214R	FLAD1_uc001fgc.2_Missense_Mutation_p.G115R|FLAD1_uc001fgd.1_Missense_Mutation_p.G214R|FLAD1_uc001fge.1_Missense_Mutation_p.G117R|FLAD1_uc001fgg.1_Missense_Mutation_p.G117R|FLAD1_uc001fgh.1_5'UTR	NM_025207	NP_079483	Q8NFF5	FAD1_HUMAN	flavin adenine dinucleotide synthetase isoform	214					FAD biosynthetic process|Mo-molybdopterin cofactor biosynthetic process|water-soluble vitamin metabolic process	cytosol	ATP binding|FMN adenylyltransferase activity			ovary(2)|skin(1)	3	all_epithelial(22;2.77e-30)|all_lung(78;4.1e-28)|all_hematologic(923;0.0359)|Hepatocellular(266;0.0877)		BRCA - Breast invasive adenocarcinoma(34;0.00034)			AGCCCTAGGAGGGGAAGGCTG	0.562													9	17	---	---	---	---	PASS
GBA	2629	broad.mit.edu	37	1	155205090	155205090	+	Silent	SNP	A	T	T			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:155205090A>T	uc001fjh.2	-	10	1551	c.1401T>A	c.(1399-1401)CCT>CCA	p.P467P	RAG1AP1_uc010pey.1_Intron|GBA_uc010pfw.1_Silent_p.P354P|GBA_uc010pfx.1_Silent_p.P418P|GBA_uc001fji.2_Silent_p.P467P|GBA_uc001fjj.2_Silent_p.P467P|GBA_uc001fjk.2_Silent_p.P467P|GBA_uc001fjl.2_Silent_p.P467P|GBA_uc010pfy.1_Silent_p.P380P	NM_000157	NP_000148	P04062	GLCM_HUMAN	glucocerebrosidase precursor	467					carbohydrate metabolic process|cell death|cellular response to tumor necrosis factor|ceramide biosynthetic process|glucosylceramide catabolic process|lysosome organization|negative regulation of interleukin-6 production|negative regulation of MAP kinase activity|positive regulation of protein dephosphorylation|sphingosine biosynthetic process|termination of signal transduction	lysosomal lumen|lysosomal membrane	cation binding|glucosylceramidase activity|receptor binding			ovary(1)|skin(1)	2	all_lung(78;2.32e-23)|Hepatocellular(266;0.0877)|all_hematologic(923;0.088)		Epithelial(20;3.72e-10)|all cancers(21;1.19e-09)|BRCA - Breast invasive adenocarcinoma(34;0.000752)|LUSC - Lung squamous cell carcinoma(543;0.193)		Alglucerase(DB00088)|Imiglucerase(DB00053)	GGGAGCCCTCAGGAATGAACT	0.577									Gaucher_disease_type_I				20	39	---	---	---	---	PASS
HSD17B7	51478	broad.mit.edu	37	1	162769603	162769603	+	Missense_Mutation	SNP	G	A	A			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:162769603G>A	uc001gci.2	+	5	613	c.518G>A	c.(517-519)AGT>AAT	p.S173N	HSD17B7_uc009wuv.2_RNA	NM_016371	NP_057455	P56937	DHB7_HUMAN	hydroxysteroid (17-beta) dehydrogenase 7	173	Extracellular (Potential).				cholesterol biosynthetic process	endoplasmic reticulum membrane|integral to membrane|plasma membrane	3-keto sterol reductase activity|estradiol 17-beta-dehydrogenase activity			ovary(1)	1	all_hematologic(112;0.115)				NADH(DB00157)	TCATCTCGCAGTGCAAGGAAA	0.458													4	99	---	---	---	---	PASS
TNR	7143	broad.mit.edu	37	1	175355202	175355202	+	Silent	SNP	G	A	A			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:175355202G>A	uc001gkp.1	-	6	1824	c.1743C>T	c.(1741-1743)AAC>AAT	p.N581N	TNR_uc009wwu.1_Silent_p.N581N	NM_003285	NP_003276	Q92752	TENR_HUMAN	tenascin R precursor	581	Fibronectin type-III 3.				axon guidance|cell adhesion|signal transduction	proteinaceous extracellular matrix				pancreas(5)|ovary(4)|central_nervous_system(1)|skin(1)	11	Renal(580;0.146)					AATCGCTCTCGTTGGTCCCTC	0.632													5	22	---	---	---	---	PASS
CFHR3	10878	broad.mit.edu	37	1	196762628	196762628	+	Silent	SNP	C	T	T			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:196762628C>T	uc001gtl.2	+	6	1065	c.978C>T	c.(976-978)TAC>TAT	p.Y326Y	CFHR3_uc010poy.1_Silent_p.Y265Y|CFHR1_uc001gtm.2_Intron	NM_021023	NP_066303	Q02985	FHR3_HUMAN	complement factor H-related 3 precursor	326	Sushi 5.					extracellular space					0						TAGTGGAATACCCCAGATGCG	0.388													46	251	---	---	---	---	PASS
KDM5B	10765	broad.mit.edu	37	1	202725626	202725626	+	Missense_Mutation	SNP	C	A	A			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:202725626C>A	uc001gyf.2	-	10	1332	c.1216G>T	c.(1216-1218)GTT>TTT	p.V406F	KDM5B_uc009xag.2_Missense_Mutation_p.V442F|KDM5B_uc001gyg.1_Missense_Mutation_p.V248F	NM_006618	NP_006609	Q9UGL1	KDM5B_HUMAN	jumonji, AT rich interactive domain 1B	406					negative regulation of transcription, DNA-dependent	nucleolus	DNA binding|histone demethylase activity (H3-dimethyl-K4 specific)|histone demethylase activity (H3-trimethyl-K4 specific)|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|protein binding|sequence-specific DNA binding transcription factor activity|transcription corepressor activity|zinc ion binding			ovary(2)|breast(2)|urinary_tract(1)	5						TCTTTCTCAACAAGCTCTGTG	0.418													20	97	---	---	---	---	PASS
CDC42BPA	8476	broad.mit.edu	37	1	227288695	227288695	+	Silent	SNP	T	C	C			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:227288695T>C	uc001hqr.2	-	15	3190	c.2247A>G	c.(2245-2247)GAA>GAG	p.E749E	CDC42BPA_uc001hqq.2_Silent_p.E13E|CDC42BPA_uc001hqs.2_Silent_p.E668E|CDC42BPA_uc009xes.2_Silent_p.E749E|CDC42BPA_uc010pvs.1_Silent_p.E749E	NM_003607	NP_003598	Q5VT25	MRCKA_HUMAN	CDC42-binding protein kinase alpha isoform B	749	Potential.				actin cytoskeleton reorganization|intracellular signal transduction	cell leading edge|cell-cell junction|cytoplasm	ATP binding|identical protein binding|magnesium ion binding|protein serine/threonine kinase activity|small GTPase regulator activity			lung(6)|breast(2)|stomach(1)|ovary(1)|pancreas(1)	11		all_cancers(173;0.156)|Prostate(94;0.0792)				ATTCTTACCTTTCTCTTCTGG	0.179													62	105	---	---	---	---	PASS
PXDN	7837	broad.mit.edu	37	2	1642647	1642647	+	Missense_Mutation	SNP	G	C	C			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:1642647G>C	uc002qxa.2	-	21	4241	c.4177C>G	c.(4177-4179)CAG>GAG	p.Q1393E		NM_012293	NP_036425	Q92626	PXDN_HUMAN	peroxidasin precursor	1393					extracellular matrix organization|hydrogen peroxide catabolic process|immune response	endoplasmic reticulum|extracellular space|proteinaceous extracellular matrix	extracellular matrix structural constituent|heme binding|interleukin-1 receptor antagonist activity|peroxidase activity			pancreas(6)|ovary(2)	8	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.0797)	all_cancers(51;0.0845)|Lung NSC(108;0.00641)|all_epithelial(98;0.00716)		all cancers(51;0.0492)|OV - Ovarian serous cystadenocarcinoma(76;0.0973)|Epithelial(75;0.17)|GBM - Glioblastoma multiforme(21;0.228)		ATGGTCTTCTGCATTTCCAGA	0.557													36	236	---	---	---	---	PASS
BRE	9577	broad.mit.edu	37	2	28532988	28532988	+	Intron	SNP	C	T	T			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:28532988C>T	uc002rlr.2	+						BRE_uc002rlp.1_Intron|BRE_uc002rlq.2_Silent_p.A376A|BRE_uc002rls.2_Intron|BRE_uc002rlt.2_Silent_p.A376A|BRE_uc002rlu.2_Intron|BRE_uc002rlv.2_Intron|BRE_uc002rlx.2_Intron|uc002rly.2_Intron	NM_199194	NP_954664	Q9NXR7	BRE_HUMAN	brain and reproductive organ-expressed (TNFRSF1A						apoptosis|chromatin modification|double-strand break repair|G2/M transition DNA damage checkpoint|positive regulation of anti-apoptosis|positive regulation of DNA repair|response to ionizing radiation|signal transduction	BRCA1-A complex|BRISC complex|cytoplasm|nuclear ubiquitin ligase complex	peroxisome targeting sequence binding|polyubiquitin binding|tumor necrosis factor receptor binding			lung(1)|kidney(1)|skin(1)	3	Acute lymphoblastic leukemia(172;0.155)					CCAGCTCTGCCTGACATCCAG	0.413													28	219	---	---	---	---	PASS
NRXN1	9378	broad.mit.edu	37	2	50733648	50733648	+	Missense_Mutation	SNP	G	T	T			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:50733648G>T	uc010fbq.2	-	13	4079	c.2602C>A	c.(2602-2604)CAA>AAA	p.Q868K	NRXN1_uc002rxb.3_Missense_Mutation_p.Q500K|NRXN1_uc002rxe.3_Missense_Mutation_p.Q828K|NRXN1_uc002rxc.1_RNA	NM_001135659	NP_001129131	P58400	NRX1B_HUMAN	neurexin 1 isoform alpha2 precursor	Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment					angiogenesis|neuron cell-cell adhesion|neuronal signal transduction	cell surface|endocytic vesicle|integral to membrane|presynaptic membrane	cell adhesion molecule binding|receptor binding			ovary(2)	2		all_hematologic(82;0.152)|Acute lymphoblastic leukemia(82;0.192)	Lung(47;0.0813)|LUSC - Lung squamous cell carcinoma(58;0.116)			ATGGCCTGTTGGTCATCCACT	0.463													65	154	---	---	---	---	PASS
USP34	9736	broad.mit.edu	37	2	61431456	61431456	+	Missense_Mutation	SNP	T	C	C			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:61431456T>C	uc002sbe.2	-	74	9341	c.9319A>G	c.(9319-9321)AAT>GAT	p.N3107D	USP34_uc002sbd.2_Intron	NM_014709	NP_055524	Q70CQ2	UBP34_HUMAN	ubiquitin specific protease 34	3107					positive regulation of canonical Wnt receptor signaling pathway|protein K48-linked deubiquitination|ubiquitin-dependent protein catabolic process|Wnt receptor signaling pathway		cysteine-type endopeptidase activity|protein binding|ubiquitin thiolesterase activity|ubiquitin-specific protease activity			ovary(8)|breast(5)|skin(3)|lung(2)|prostate(1)	19			Epithelial(17;0.229)			GGCCGAATATTGCTTTTCCCT	0.408													81	149	---	---	---	---	PASS
B3GNT2	10678	broad.mit.edu	37	2	62450343	62450343	+	Missense_Mutation	SNP	C	T	T			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:62450343C>T	uc002sbs.2	+	2	1226	c.988C>T	c.(988-990)CCC>TCC	p.P330S		NM_006577	NP_006568	Q9NY97	B3GN2_HUMAN	UDP-GlcNAc:betaGal	330	Lumenal (Potential).					Golgi membrane|integral to membrane	UDP-galactose:beta-N-acetylglucosamine beta-1,3-galactosyltransferase activity			ovary(1)	1	Lung NSC(7;0.031)|all_lung(7;0.0634)		LUSC - Lung squamous cell carcinoma(7;3.55e-06)|Epithelial(17;0.0963)			CCATCTCTACCCCATTGATGA	0.527													3	29	---	---	---	---	PASS
C2orf65	130951	broad.mit.edu	37	2	74808954	74808954	+	Missense_Mutation	SNP	C	T	T			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:74808954C>T	uc002smy.2	-	5	733	c.616G>A	c.(616-618)GAC>AAC	p.D206N	C2orf65_uc010ysa.1_Missense_Mutation_p.D206N|C2orf65_uc002smz.2_Missense_Mutation_p.D206N	NM_138804	NP_620159	Q8TC57	CB065_HUMAN	hypothetical protein LOC130951	206					chromatin assembly|female gamete generation|RNA processing|spermatogenesis	integral to membrane				ovary(1)|pancreas(1)	2						AGGTCAATGTCAGTTCCCAGA	0.348													48	270	---	---	---	---	PASS
KIAA1310	55683	broad.mit.edu	37	2	97285435	97285435	+	Silent	SNP	G	T	T			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:97285435G>T	uc002swn.3	-	4	597	c.451C>A	c.(451-453)CGG>AGG	p.R151R	KIAA1310_uc002swh.3_Silent_p.R39R|KIAA1310_uc002swi.3_Silent_p.R52R|KIAA1310_uc002swj.3_Intron|KIAA1310_uc002swk.3_Silent_p.R64R|KIAA1310_uc010fhz.2_Intron|KIAA1310_uc002swl.3_Silent_p.R52R|KIAA1310_uc002swm.3_RNA|KIAA1310_uc010yur.1_Intron|KIAA1310_uc002swp.1_Silent_p.R52R|KIAA1310_uc002swq.1_5'UTR|KIAA1310_uc010fhy.1_Silent_p.R52R	NM_001115016	NP_001108488	Q9P2N6	K1310_HUMAN	hypothetical protein LOC55683 isoform a	151											0						CGGGCAAGCCGGTCAGACTGC	0.542													14	46	---	---	---	---	PASS
INPP4A	3631	broad.mit.edu	37	2	99155379	99155379	+	Missense_Mutation	SNP	T	G	G			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:99155379T>G	uc002syy.2	+	9	998	c.605T>G	c.(604-606)TTG>TGG	p.L202W	INPP4A_uc010yvj.1_Missense_Mutation_p.L202W|INPP4A_uc010yvk.1_Missense_Mutation_p.L202W|INPP4A_uc002syx.2_Missense_Mutation_p.L202W|INPP4A_uc010fik.2_Intron	NM_001134224	NP_001127696	Q96PE3	INP4A_HUMAN	inositol polyphosphate-4-phosphatase, type 1	202					signal transduction		phosphatidylinositol-3,4-bisphosphate 4-phosphatase activity|phosphatidylinositol-4,5-bisphosphate 4-phosphatase activity			kidney(1)	1						GATGAGAGCTTGACGGAGGCG	0.443													82	162	---	---	---	---	PASS
FHL2	2274	broad.mit.edu	37	2	105977880	105977880	+	Missense_Mutation	SNP	T	C	C			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:105977880T>C	uc002tcu.2	-	6	1037	c.700A>G	c.(700-702)ACA>GCA	p.T234A	FHL2_uc002tdc.2_Missense_Mutation_p.T120A|FHL2_uc002tdd.2_Missense_Mutation_p.T234A|FHL2_uc002tct.2_Missense_Mutation_p.T120A|FHL2_uc002tcv.2_Missense_Mutation_p.T234A|FHL2_uc002tcw.2_Missense_Mutation_p.T234A|FHL2_uc002tcx.2_Missense_Mutation_p.T234A|FHL2_uc010fje.2_Missense_Mutation_p.T147A|FHL2_uc002tcy.2_Missense_Mutation_p.T234A|FHL2_uc002tcz.2_Missense_Mutation_p.T344A|FHL2_uc002tda.2_RNA|FHL2_uc002tdb.2_Missense_Mutation_p.T350A	NM_201557	NP_963851	Q14192	FHL2_HUMAN	four and a half LIM domains 2	234	LIM zinc-binding 4.				androgen receptor signaling pathway|cellular lipid metabolic process|positive regulation of transcription, DNA-dependent|response to hormone stimulus|transcription, DNA-dependent	actin cytoskeleton|focal adhesion|nucleus	androgen receptor binding|identical protein binding|transcription coactivator activity|zinc ion binding			ovary(1)	1						ATGTATTTTGTGCCACCAAGT	0.458													8	49	---	---	---	---	PASS
GCC2	9648	broad.mit.edu	37	2	109100625	109100625	+	Missense_Mutation	SNP	G	C	C			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:109100625G>C	uc002tec.2	+	13	3625	c.3471G>C	c.(3469-3471)TTG>TTC	p.L1157F	GCC2_uc002ted.2_Missense_Mutation_p.L1056F	NM_181453	NP_852118	Q8IWJ2	GCC2_HUMAN	GRIP and coiled-coil domain-containing 2	1157	Potential.				Golgi ribbon formation|late endosome to Golgi transport|microtubule anchoring|microtubule organizing center organization|protein localization in Golgi apparatus|protein targeting to lysosome|recycling endosome to Golgi transport|regulation of protein exit from endoplasmic reticulum	membrane|trans-Golgi network	identical protein binding			ovary(1)	1						AAACCACATTGATGAATATGG	0.269													44	164	---	---	---	---	PASS
WDR33	55339	broad.mit.edu	37	2	128477700	128477700	+	Silent	SNP	T	A	A			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:128477700T>A	uc002tpg.1	-	16	2082	c.1899A>T	c.(1897-1899)GGA>GGT	p.G633G		NM_018383	NP_060853	Q9C0J8	WDR33_HUMAN	WD repeat domain 33 isoform 1	633	Collagen-like.				postreplication repair|spermatogenesis	collagen|nucleus	protein binding				0	Colorectal(110;0.1)			BRCA - Breast invasive adenocarcinoma(221;0.0695)		GTCCCATTTGTCCCTGGGGTC	0.617													5	48	---	---	---	---	PASS
NFE2L2	4780	broad.mit.edu	37	2	178095480	178095480	+	3'UTR	SNP	A	T	T			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:178095480A>T	uc002ulh.3	-	5					NFE2L2_uc002ulg.3_3'UTR|NFE2L2_uc010zfa.1_3'UTR|NFE2L2_uc002uli.3_3'UTR	NM_006164	NP_006155	Q16236	NF2L2_HUMAN	nuclear factor erythroid 2-like 2 isoform 1						transcription from RNA polymerase II promoter	centrosome|cytosol|nucleus|plasma membrane	protein dimerization activity|protein domain specific binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			central_nervous_system(1)	1			Epithelial(96;0.00442)|OV - Ovarian serous cystadenocarcinoma(117;0.00739)|all cancers(119;0.0195)|LUSC - Lung squamous cell carcinoma(2;0.036)|Lung(16;0.0935)			AGTACAAAAAAACTAGCTCAG	0.318			Mis		NSCLC|HNSCC					HNSCC(56;0.16)			4	14	---	---	---	---	PASS
OBFC2A	64859	broad.mit.edu	37	2	192548411	192548411	+	Intron	SNP	C	G	G			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:192548411C>G	uc002usx.2	+						OBFC2A_uc002usw.2_Intron|OBFC2A_uc002usy.2_Intron|OBFC2A_uc002usz.2_RNA|OBFC2A_uc002uta.2_Intron	NM_001031716	NP_001026886	Q96AH0	SOSB2_HUMAN	oligonucleotide/oligosaccharide-binding fold						double-strand break repair via homologous recombination|G2/M transition checkpoint|response to ionizing radiation	SOSS complex	single-stranded DNA binding				0			OV - Ovarian serous cystadenocarcinoma(117;0.061)|Epithelial(96;0.244)			GGGTTGAGGACTTTATTTCAG	0.294													51	202	---	---	---	---	PASS
FAM126B	285172	broad.mit.edu	37	2	201862090	201862090	+	Intron	SNP	C	T	T			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:201862090C>T	uc002uws.3	-						FAM126B_uc002uwu.2_Intron|FAM126B_uc002uwv.2_Intron|FAM126B_uc002uww.1_3'UTR	NM_173822	NP_776183	Q8IXS8	F126B_HUMAN	hypothetical protein LOC285172							intracellular				ovary(1)	1						gaagttagaacagtgcttggc	0.154													11	48	---	---	---	---	PASS
ABCA12	26154	broad.mit.edu	37	2	215838696	215838696	+	Missense_Mutation	SNP	A	C	C			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:215838696A>C	uc002vew.2	-	36	5759	c.5539T>G	c.(5539-5541)TGC>GGC	p.C1847G	ABCA12_uc002vev.2_Missense_Mutation_p.C1529G|ABCA12_uc010zjn.1_Missense_Mutation_p.C774G	NM_173076	NP_775099	Q86UK0	ABCAC_HUMAN	ATP-binding cassette, sub-family A, member 12	1847					cellular homeostasis|lipid transport	integral to membrane	ATP binding|ATPase activity			ovary(6)|upper_aerodigestive_tract(1)|central_nervous_system(1)|breast(1)|skin(1)|pancreas(1)	11		Renal(323;0.127)		Epithelial(149;1.01e-05)|all cancers(144;0.00112)|LUSC - Lung squamous cell carcinoma(224;0.00829)|Lung(261;0.011)		GAGCAGGAGCAAACACCAAAA	0.388													178	242	---	---	---	---	PASS
DOCK10	55619	broad.mit.edu	37	2	225668898	225668898	+	Missense_Mutation	SNP	G	T	T			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:225668898G>T	uc010fwz.1	-	39	4438	c.4199C>A	c.(4198-4200)TCC>TAC	p.S1400Y	DOCK10_uc002vob.2_Missense_Mutation_p.S1394Y|DOCK10_uc002voa.2_Missense_Mutation_p.S56Y|DOCK10_uc002voc.2_Missense_Mutation_p.S254Y	NM_014689	NP_055504	Q96BY6	DOC10_HUMAN	dedicator of cytokinesis 10	1400							GTP binding			ovary(2)	2		Renal(207;0.0113)|all_lung(227;0.0486)|Lung NSC(271;0.0653)|all_hematologic(139;0.14)		Epithelial(121;2.37e-10)|all cancers(144;2.26e-07)|Lung(261;0.0143)|LUSC - Lung squamous cell carcinoma(224;0.0178)		GTTCTGGGTGGACTGCACAAA	0.353													78	124	---	---	---	---	PASS
DOCK10	55619	broad.mit.edu	37	2	225688296	225688296	+	Silent	SNP	G	A	A			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:225688296G>A	uc010fwz.1	-	28	3344	c.3105C>T	c.(3103-3105)TCC>TCT	p.S1035S	DOCK10_uc002vob.2_Silent_p.S1029S	NM_014689	NP_055504	Q96BY6	DOC10_HUMAN	dedicator of cytokinesis 10	1035							GTP binding			ovary(2)	2		Renal(207;0.0113)|all_lung(227;0.0486)|Lung NSC(271;0.0653)|all_hematologic(139;0.14)		Epithelial(121;2.37e-10)|all cancers(144;2.26e-07)|Lung(261;0.0143)|LUSC - Lung squamous cell carcinoma(224;0.0178)		TCACATGGTCGGATAGGACCA	0.418													4	191	---	---	---	---	PASS
CAND2	23066	broad.mit.edu	37	3	12856884	12856884	+	Missense_Mutation	SNP	G	T	T			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:12856884G>T	uc003bxk.2	+	8	1300	c.1251G>T	c.(1249-1251)ATG>ATT	p.M417I	CAND2_uc003bxj.2_Missense_Mutation_p.M324I	NM_001162499	NP_001155971	O75155	CAND2_HUMAN	TBP-interacting protein isoform 1	417					positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	protein binding			skin(3)|pancreas(1)	4						TGGAGGCCATGGAGGAACCCA	0.607													4	6	---	---	---	---	PASS
TTC21A	199223	broad.mit.edu	37	3	39179047	39179047	+	Missense_Mutation	SNP	G	T	T			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:39179047G>T	uc003cjc.2	+	26	3719	c.3542G>T	c.(3541-3543)CGT>CTT	p.R1181L	TTC21A_uc003cje.2_Missense_Mutation_p.R1182L|TTC21A_uc003cjd.2_RNA|TTC21A_uc011ayx.1_Missense_Mutation_p.R1133L|TTC21A_uc003cjf.2_Missense_Mutation_p.R302L	NM_145755	NP_665698	Q8NDW8	TT21A_HUMAN	tetratricopeptide repeat domain 21A isoform 2	1181							binding			ovary(1)	1				KIRC - Kidney renal clear cell carcinoma(284;0.0588)|Kidney(284;0.0738)		CCCAAGGCGCGTATGCAGTTG	0.612													16	29	---	---	---	---	PASS
CADPS	8618	broad.mit.edu	37	3	62385148	62385148	+	Missense_Mutation	SNP	C	A	A			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:62385148C>A	uc003dll.2	-	30	4355	c.3995G>T	c.(3994-3996)AGT>ATT	p.S1332I	CADPS_uc003dlj.1_Missense_Mutation_p.S287I|CADPS_uc003dlk.1_Missense_Mutation_p.S780I|CADPS_uc003dlm.2_Missense_Mutation_p.S1293I|CADPS_uc003dln.2_Missense_Mutation_p.S1253I	NM_003716	NP_003707	Q9ULU8	CAPS1_HUMAN	Ca2+-dependent secretion activator isoform 1	1332	Mediates targeting and association with DCVs (By similarity).				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)		CCCACCTTCACTCACTGATGC	0.527													51	77	---	---	---	---	PASS
ZPLD1	131368	broad.mit.edu	37	3	102181210	102181210	+	Missense_Mutation	SNP	A	C	C			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:102181210A>C	uc003dvs.1	+	13	1550	c.668A>C	c.(667-669)AAT>ACT	p.N223T	ZPLD1_uc003dvt.1_Missense_Mutation_p.N239T|ZPLD1_uc011bhg.1_Missense_Mutation_p.N223T	NM_175056	NP_778226	Q8TCW7	ZPLD1_HUMAN	zona pellucida-like domain containing 1	223	ZP.|Extracellular (Potential).					integral to membrane				ovary(2)|skin(2)|central_nervous_system(1)	5						CAAGCCACTAATTTGGATGGC	0.358													25	56	---	---	---	---	PASS
COL29A1	256076	broad.mit.edu	37	3	130103994	130103994	+	Silent	SNP	T	C	C			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:130103994T>C	uc010htj.1	+	5	2142	c.1648T>C	c.(1648-1650)TTG>CTG	p.L550L	COL29A1_uc010hti.1_RNA	NM_153264	NP_694996	A8TX70	CO6A5_HUMAN	collagen, type XXIX, alpha 1	550	VWFA 3.|Nonhelical region.				axon guidance|cell adhesion	collagen					0						CCTCATTGTGTTGACTGATGG	0.433													5	145	---	---	---	---	PASS
LXN	56925	broad.mit.edu	37	3	158387254	158387254	+	Missense_Mutation	SNP	A	G	G			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:158387254A>G	uc003fch.2	-	3	553	c.338T>C	c.(337-339)ATG>ACG	p.M113T	GFM1_uc003fcd.2_Intron|GFM1_uc003fce.2_Intron|GFM1_uc003fcf.2_Intron|GFM1_uc003fcg.2_Intron|LXN_uc011bov.1_Missense_Mutation_p.M113T	NM_020169	NP_064554	Q9BS40	LXN_HUMAN	latexin	113						cytoplasm	metalloendopeptidase inhibitor activity|protein binding				0			Lung(72;0.00309)|LUSC - Lung squamous cell carcinoma(72;0.0043)			CGGTTCCTTCATGGACTTAAG	0.348													179	352	---	---	---	---	PASS
BCHE	590	broad.mit.edu	37	3	165503969	165503969	+	Missense_Mutation	SNP	A	T	T			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:165503969A>T	uc003fem.3	-	3	1808	c.1648T>A	c.(1648-1650)TGG>AGG	p.W550R	BCHE_uc003fen.3_RNA	NM_000055	NP_000046	P06276	CHLE_HUMAN	butyrylcholinesterase precursor	550					choline metabolic process|cocaine metabolic process|synaptic transmission, cholinergic	endoplasmic reticulum lumen|extracellular space|membrane	acetylcholinesterase activity|beta-amyloid binding|carboxylesterase activity|cholinesterase activity|enzyme binding			ovary(3)|pancreas(1)	4					Ambenonium(DB01122)|Atropine(DB00572)|Bambuterol(DB01408)|Chlorpromazine(DB00477)|Choline(DB00122)|Cinnarizine(DB00568)|Demecarium bromide(DB00944)|Dibucaine(DB00527)|Donepezil(DB00843)|Echothiophate Iodide(DB01057)|Edrophonium(DB01010)|Ethopropazine(DB00392)|Etomidate(DB00292)|Galantamine(DB00674)|Hexafluronium bromide(DB00941)|Isoflurophate(DB00677)|Mefloquine(DB00358)|Mivacurium(DB01226)|Neostigmine(DB01400)|Pancuronium(DB01337)|Pralidoxime(DB00733)|Procainamide(DB01035)|Pyridostigmine(DB00545)|Rivastigmine(DB00989)|Succinylcholine(DB00202)|Terbutaline(DB00871)|Trimethaphan(DB01116)	AATGATGTCCAGAATCGACAT	0.353													66	470	---	---	---	---	PASS
ZBBX	79740	broad.mit.edu	37	3	167000224	167000224	+	Missense_Mutation	SNP	T	G	G			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:167000224T>G	uc003fep.2	-	19	2262	c.1939A>C	c.(1939-1941)AGC>CGC	p.S647R	ZBBX_uc011bpc.1_Missense_Mutation_p.S686R|ZBBX_uc003feq.2_Missense_Mutation_p.S618R	NM_024687	NP_078963	A8MT70	ZBBX_HUMAN	zinc finger, B-box domain containing	647	Ser-rich.					intracellular	zinc ion binding			ovary(2)	2						CAACTGGAGCTTTCTTTAACA	0.338													110	203	---	---	---	---	PASS
ECT2	1894	broad.mit.edu	37	3	172502507	172502507	+	Missense_Mutation	SNP	C	G	G			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:172502507C>G	uc003fii.2	+	16	1784	c.1646C>G	c.(1645-1647)GCA>GGA	p.A549G	ECT2_uc010hwv.1_Missense_Mutation_p.A580G|ECT2_uc003fih.2_Missense_Mutation_p.A548G|ECT2_uc003fij.1_Missense_Mutation_p.A549G|ECT2_uc003fik.1_Missense_Mutation_p.A549G|ECT2_uc003fil.1_Missense_Mutation_p.A580G	NM_018098	NP_060568	Q9H8V3	ECT2_HUMAN	epithelial cell transforming sequence 2 oncogene	549	DH.				apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|positive regulation of I-kappaB kinase/NF-kappaB cascade|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol	Rho guanyl-nucleotide exchange factor activity|signal transducer activity			breast(2)|ovary(1)|skin(1)	4	Ovarian(172;0.00197)|Breast(254;0.158)		Lung(28;1.33e-14)|LUSC - Lung squamous cell carcinoma(14;1.48e-14)			ATAAACCAAGCAAAACCAGAA	0.363													97	206	---	---	---	---	PASS
CPZ	8532	broad.mit.edu	37	4	8609117	8609117	+	Missense_Mutation	SNP	G	A	A			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:8609117G>A	uc003glm.2	+	7	1318	c.1192G>A	c.(1192-1194)GAG>AAG	p.E398K	CPZ_uc003gll.2_RNA|CPZ_uc003gln.2_Missense_Mutation_p.E261K|CPZ_uc003glo.2_Missense_Mutation_p.E387K|CPZ_uc003glp.2_RNA	NM_001014447	NP_001014447	Q66K79	CBPZ_HUMAN	carboxypeptidase Z isoform 1	398					proteolysis|Wnt receptor signaling pathway	proteinaceous extracellular matrix	metallocarboxypeptidase activity|zinc ion binding			ovary(2)|pancreas(1)	3						GCACCCCCAGGAGGAGAAGAT	0.612											OREG0016100	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	4	30	---	---	---	---	PASS
RHOH	399	broad.mit.edu	37	4	40245316	40245316	+	Missense_Mutation	SNP	A	G	G			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:40245316A>G	uc003guz.2	+	3	1034	c.310A>G	c.(310-312)AGC>GGC	p.S104G		NM_004310	NP_004301	Q15669	RHOH_HUMAN	ras homolog gene family, member H precursor	104					negative regulation of I-kappaB kinase/NF-kappaB cascade|regulation of small GTPase mediated signal transduction|regulation of transcription, DNA-dependent|small GTPase mediated signal transduction|T cell differentiation	cytosol|mitochondrion|plasma membrane	GTP binding|GTPase inhibitor activity|kinase inhibitor activity|Rho GTPase binding			ovary(1)|lung(1)	2						TGAAATTAGGAGCAACTTGCC	0.567													4	71	---	---	---	---	PASS
PRKG2	5593	broad.mit.edu	37	4	82126026	82126026	+	Missense_Mutation	SNP	G	A	A			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:82126026G>A	uc003hmh.2	-	1	190	c.176C>T	c.(175-177)TCG>TTG	p.S59L	PRKG2_uc011cch.1_Missense_Mutation_p.S59L	NM_006259	NP_006250	Q13237	KGP2_HUMAN	protein kinase, cGMP-dependent, type II	59					platelet activation|signal transduction	cytosol	ATP binding|cGMP binding|cGMP-dependent protein kinase activity			breast(3)|central_nervous_system(2)|ovary(1)|large_intestine(1)	7						AGTCTGCTTCGACAGCTGCTC	0.557													18	79	---	---	---	---	PASS
HERC3	8916	broad.mit.edu	37	4	89607937	89607937	+	Missense_Mutation	SNP	T	A	A			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:89607937T>A	uc003hrw.1	+	22	2724	c.2558T>A	c.(2557-2559)TTC>TAC	p.F853Y	HERC3_uc011cdn.1_Missense_Mutation_p.F735Y|HERC3_uc011cdo.1_Missense_Mutation_p.F297Y	NM_014606	NP_055421	Q15034	HERC3_HUMAN	hect domain and RLD 3	853					protein ubiquitination involved in ubiquitin-dependent protein catabolic process	cytoplasmic membrane-bounded vesicle	ubiquitin-protein ligase activity			lung(2)|prostate(1)|skin(1)	4				OV - Ovarian serous cystadenocarcinoma(123;0.000319)		GAGGAGACTTTCTGCCTCAAC	0.418													118	214	---	---	---	---	PASS
H2AFZ	3015	broad.mit.edu	37	4	100871392	100871392	+	5'UTR	SNP	T	C	C			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:100871392T>C	uc003hvo.1	-	1					H2AFZ_uc003hvn.1_5'UTR|LOC256880_uc003hvp.1_5'Flank	NM_002106	NP_002097	P0C0S5	H2AZ_HUMAN	H2A histone family, member Z						nucleosome assembly	nucleosome|nucleus	DNA binding				0				OV - Ovarian serous cystadenocarcinoma(123;2.32e-08)		CACGGTGAGATCCCACCACCT	0.552													21	55	---	---	---	---	PASS
C4orf29	80167	broad.mit.edu	37	4	128905506	128905506	+	Missense_Mutation	SNP	C	A	A			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:128905506C>A	uc003ifr.2	+	3	423	c.105C>A	c.(103-105)TTC>TTA	p.F35L	C4orf29_uc003ifq.1_RNA|C4orf29_uc003ifs.2_5'UTR	NM_001039717	NP_001034806	Q0P651	CD029_HUMAN	hypothetical protein LOC80167 precursor	35						extracellular region				ovary(1)	1						TCTTTGAATTCAGAAAGATGA	0.313													113	257	---	---	---	---	PASS
PCDH18	54510	broad.mit.edu	37	4	138453257	138453257	+	5'UTR	SNP	G	A	A			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:138453257G>A	uc003ihe.3	-	1					PCDH18_uc003ihf.3_5'UTR|PCDH18_uc011cgz.1_Intron|PCDH18_uc003ihg.3_Intron|PCDH18_uc011cha.1_Intron	NM_019035	NP_061908	Q9HCL0	PCD18_HUMAN	protocadherin 18 precursor						brain development|homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			pancreas(3)|skin(2)	5	all_hematologic(180;0.24)					CAGTTTATGAGATTTCCCTCA	0.388													21	46	---	---	---	---	PASS
ACSL1	2180	broad.mit.edu	37	4	185694256	185694256	+	Silent	SNP	T	C	C			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:185694256T>C	uc003iww.2	-	10	1188	c.894A>G	c.(892-894)TCA>TCG	p.S298S	ACSL1_uc011ckm.1_Silent_p.S127S|ACSL1_uc003iwt.1_Silent_p.S298S|ACSL1_uc003iwu.1_Silent_p.S298S|ACSL1_uc011ckn.1_Silent_p.S264S|ACSL1_uc003iwv.1_Silent_p.S298S|ACSL1_uc010ise.1_RNA	NM_001995	NP_001986	P33121	ACSL1_HUMAN	acyl-CoA synthetase long-chain family member 1	298	Cytoplasmic (Potential).				digestion|fatty acid metabolic process|long-chain fatty-acyl-CoA biosynthetic process|regulation of fatty acid oxidation|triglyceride biosynthetic process	endoplasmic reticulum membrane|integral to membrane|microsome|mitochondrial outer membrane|peroxisomal membrane	ATP binding|long-chain fatty acid-CoA ligase activity			ovary(2)	2		all_lung(41;7.57e-14)|Lung NSC(41;1.81e-13)|Colorectal(36;0.00172)|Hepatocellular(41;0.00826)|Renal(120;0.00988)|Prostate(90;0.0235)|all_hematologic(60;0.0315)|all_neural(102;0.107)|Medulloblastoma(177;0.146)		all cancers(43;1.33e-28)|Epithelial(43;5.3e-25)|OV - Ovarian serous cystadenocarcinoma(60;4.88e-11)|Colorectal(24;3.59e-06)|STAD - Stomach adenocarcinoma(60;2.72e-05)|GBM - Glioblastoma multiforme(59;2.83e-05)|BRCA - Breast invasive adenocarcinoma(30;7.66e-05)|COAD - Colon adenocarcinoma(29;0.000538)|LUSC - Lung squamous cell carcinoma(40;0.008)|READ - Rectum adenocarcinoma(43;0.0419)	Adenosine monophosphate(DB00131)|Adenosine triphosphate(DB00171)	TCACAAAAGCTGAACAATCGC	0.433													78	162	---	---	---	---	PASS
ANKRD55	79722	broad.mit.edu	37	5	55407454	55407454	+	Missense_Mutation	SNP	T	C	C			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:55407454T>C	uc003jqu.2	-	10	1273	c.1121A>G	c.(1120-1122)GAC>GGC	p.D374G	ANKRD55_uc003jqt.2_Missense_Mutation_p.D86G	NM_024669	NP_078945	Q3KP44	ANR55_HUMAN	ankyrin repeat domain 55 isoform 1	373										skin(1)	1		Lung NSC(810;8.69e-05)|Prostate(74;0.00634)|Breast(144;0.0334)|Ovarian(174;0.223)				TTCTGAGGTGTCCTCCTCTCT	0.478													132	196	---	---	---	---	PASS
VCAN	1462	broad.mit.edu	37	5	82815673	82815673	+	Silent	SNP	T	G	G			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:82815673T>G	uc003kii.3	+	7	1904	c.1548T>G	c.(1546-1548)ACT>ACG	p.T516T	VCAN_uc003kij.3_Intron|VCAN_uc010jau.2_Silent_p.T516T|VCAN_uc003kik.3_Intron	NM_004385	NP_004376	P13611	CSPG2_HUMAN	versican isoform 1 precursor	516	GAG-alpha (glucosaminoglycan attachment domain).				cell adhesion|cell recognition|glial cell migration	extracellular space|proteinaceous extracellular matrix	calcium ion binding|hyaluronic acid binding|sugar binding			ovary(7)|skin(6)|lung(2)|central_nervous_system(1)	16		Lung NSC(167;0.0216)|all_lung(232;0.0251)|Ovarian(174;0.142)		OV - Ovarian serous cystadenocarcinoma(54;2.47e-41)|Epithelial(54;2.51e-34)|all cancers(79;5.19e-29)		TCCCTGTAACTGAAACACCAT	0.388													66	163	---	---	---	---	PASS
ANKRD32	84250	broad.mit.edu	37	5	93987546	93987546	+	Missense_Mutation	SNP	A	C	C			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:93987546A>C	uc003kkr.3	+	7	958	c.878A>C	c.(877-879)AAT>ACT	p.N293T	ANKRD32_uc011cul.1_RNA	NM_032290	NP_115666	Q9BQI6	ANR32_HUMAN	ankyrin repeat domain 32	293										ovary(2)	2		all_cancers(142;1.51e-09)|all_epithelial(76;4.68e-12)|all_lung(232;5.94e-05)|Ovarian(174;0.000953)|Lung NSC(167;0.00105)|Colorectal(57;0.122)|Lung SC(612;0.152)		all cancers(79;3.88e-18)		ACATATGAAAATCAGGTACAA	0.209													19	98	---	---	---	---	PASS
APC	324	broad.mit.edu	37	5	112176941	112176941	+	Missense_Mutation	SNP	G	T	T			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:112176941G>T	uc010jby.2	+	16	6030	c.5650G>T	c.(5650-5652)GCA>TCA	p.A1884S	APC_uc011cvt.1_Missense_Mutation_p.A1866S|APC_uc003kpz.3_Missense_Mutation_p.A1884S|APC_uc003kpy.3_Missense_Mutation_p.A1884S|APC_uc010jbz.2_Missense_Mutation_p.A1601S|APC_uc010jca.2_Missense_Mutation_p.A1184S	NM_001127511	NP_001120983	P25054	APC_HUMAN	adenomatous polyposis coli	1884	Ser-rich.|Highly charged.				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	p.K1192fs*3(1)|p.?(1)		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)		ATTAAGAAAGGCAAAAGAAAA	0.388		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)			31	267	---	---	---	---	PASS
SEC24A	10802	broad.mit.edu	37	5	134002663	134002663	+	Missense_Mutation	SNP	T	A	A			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:134002663T>A	uc003kzs.2	+	3	1004	c.716T>A	c.(715-717)TTT>TAT	p.F239Y	SEC24A_uc011cxu.1_Missense_Mutation_p.L7I	NM_021982	NP_068817	O95486	SC24A_HUMAN	SEC24 related gene family, member A	239					COPII vesicle coating|intracellular protein transport|post-translational protein modification|protein N-linked glycosylation via asparagine	COPII vesicle coat|cytosol|endoplasmic reticulum membrane|Golgi membrane|perinuclear region of cytoplasm	zinc ion binding				0			KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			CAGCCCTTATTTAATTCAGCT	0.488													43	59	---	---	---	---	PASS
TRPC7	57113	broad.mit.edu	37	5	135561036	135561036	+	Missense_Mutation	SNP	G	C	C			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:135561036G>C	uc003lbn.1	-	9	2269	c.2266C>G	c.(2266-2268)CGC>GGC	p.R756G	TRPC7_uc010jef.1_Missense_Mutation_p.R693G|TRPC7_uc010jeg.1_RNA|TRPC7_uc010jeh.1_Missense_Mutation_p.R687G|TRPC7_uc010jei.1_Missense_Mutation_p.R632G|TRPC7_uc010jej.1_Missense_Mutation_p.R308G	NM_020389	NP_065122	Q9HCX4	TRPC7_HUMAN	transient receptor potential cation channel,	757	Cytoplasmic (Potential).				axon guidance|platelet activation	integral to membrane|plasma membrane	calcium channel activity|protein binding				0			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)			GCCTGGTAGCGAGTCTTCTGG	0.448													140	224	---	---	---	---	PASS
RBM27	54439	broad.mit.edu	37	5	145643071	145643071	+	Missense_Mutation	SNP	G	C	C			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:145643071G>C	uc003lnz.3	+	14	2374	c.2208G>C	c.(2206-2208)CAG>CAC	p.Q736H	RBM27_uc003lny.2_Missense_Mutation_p.Q681H	NM_018989	NP_061862	Q9P2N5	RBM27_HUMAN	RNA binding motif protein 27	736					mRNA processing	cytoplasm|nuclear speck	nucleotide binding|RNA binding|zinc ion binding			central_nervous_system(2)|pancreas(1)	3			KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			GCAAACCACAGACATCAGGTG	0.274													55	250	---	---	---	---	PASS
UBLCP1	134510	broad.mit.edu	37	5	158697539	158697539	+	Missense_Mutation	SNP	A	T	T			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:158697539A>T	uc003lxq.2	+	5	662	c.336A>T	c.(334-336)GAA>GAT	p.E112D		NM_145049	NP_659486	Q8WVY7	UBCP1_HUMAN	ubiquitin-like domain containing CTD phosphatase	112						nucleus	phosphoprotein phosphatase activity			ovary(1)	1	Renal(175;0.00196)	Medulloblastoma(196;0.0523)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			CCATTAGGGAAGAAAACCTAC	0.343													44	222	---	---	---	---	PASS
DRD1	1812	broad.mit.edu	37	5	174869226	174869226	+	Missense_Mutation	SNP	A	T	T			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:174869226A>T	uc003mcz.2	-	2	1822	c.877T>A	c.(877-879)TGC>AGC	p.C293S		NM_000794	NP_000785	P21728	DRD1_HUMAN	dopamine receptor D1	293	Helical; Name=6; (Potential).				activation of adenylate cyclase activity by dopamine receptor signaling pathway|activation of phospholipase C activity by dopamine receptor signaling pathway|adult walking behavior|cerebral cortex GABAergic interneuron migration|elevation of cytosolic calcium ion concentration involved in G-protein signaling coupled to IP3 second messenger|mating behavior|positive regulation of cAMP biosynthetic process|positive regulation of cell migration|positive regulation of potassium ion transport|positive regulation of release of sequestered calcium ion into cytosol|positive regulation of synaptic transmission, glutamatergic|prepulse inhibition|response to drug|synapse assembly|visual learning	endoplasmic reticulum membrane|membrane fraction	protein binding			ovary(2)|skin(1)	3	all_cancers(89;0.00895)|Renal(175;0.000159)|Lung NSC(126;0.00625)|all_lung(126;0.0104)	Medulloblastoma(196;0.0208)|all_neural(177;0.0277)|all_hematologic(541;0.214)	Kidney(164;3.85e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000183)		Acetophenazine(DB01063)|Amantadine(DB00915)|Apomorphine(DB00714)|Carphenazine(DB01038)|Chlorprothixene(DB01239)|Clozapine(DB00363)|Cocaine(DB00907)|Dopamine(DB00988)|Fenoldopam(DB00800)|Flupenthixol(DB00875)|Fluphenazine(DB00623)|Haloperidol(DB00502)|Levodopa(DB01235)|Lisuride(DB00589)|Loxapine(DB00408)|Methylergonovine(DB00353)|Minaprine(DB00805)|Olanzapine(DB00334)|Pegademase bovine(DB00061)|Pergolide(DB01186)|Perphenazine(DB00850)|Prochlorperazine(DB00433)|Promazine(DB00420)|Propiomazine(DB00777)|Quetiapine(DB01224)|Thiethylperazine(DB00372)|Thioridazine(DB00679)|Triflupromazine(DB00508)|Zuclopenthixol(DB01624)	GGCAAAATGCAGTTCAAGATG	0.458													22	98	---	---	---	---	PASS
DPCR1	135656	broad.mit.edu	37	6	30916609	30916609	+	Missense_Mutation	SNP	A	T	T			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:30916609A>T	uc003nsg.2	+	2	368	c.368A>T	c.(367-369)GAA>GTA	p.E123V		NM_080870	NP_543146	Q3MIW9	DPCR1_HUMAN	diffuse panbronchiolitis critical region 1	123	Extracellular (Potential).					integral to membrane					0						ACTTCTGAAGAAAACTCCAGC	0.468													47	81	---	---	---	---	PASS
HLA-B	3106	broad.mit.edu	37	6	31323941	31323941	+	Intron	SNP	T	A	A	rs45482298		TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:31323941T>A	uc003nth.2	-						HLA-C_uc003ntb.2_5'Flank|HLA-C_uc003ntc.1_5'Flank|HLA-B_uc010jsm.1_5'Flank|HLA-B_uc011dnk.1_5'Flank|HLA-B_uc003ntf.2_Intron|HLA-B_uc003ntg.1_Intron|HLA-B_uc003nti.1_5'Flank|HLA-B_uc010jsn.1_RNA|HLA-B_uc010jso.2_Missense_Mutation_p.T180S	NM_005514	NP_005505	P01889	1B07_HUMAN	major histocompatibility complex, class I, B						antigen processing and presentation of peptide antigen via MHC class I|interferon-gamma-mediated signaling pathway|interspecies interaction between organisms|regulation of immune response|type I interferon-mediated signaling pathway	integral to plasma membrane|MHC class I protein complex	MHC class I receptor activity				0						CTGCCCCTGGTACCAGCGCGC	0.642									Melanoma_Familial_Clustering_of|Lichen_Sclerosis_et_Atrophicus_Familial_Clustering_of				11	11	---	---	---	---	PASS
PHF3	23469	broad.mit.edu	37	6	64395089	64395089	+	Missense_Mutation	SNP	A	T	T			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:64395089A>T	uc003pep.1	+	3	1492	c.1466A>T	c.(1465-1467)AAA>ATA	p.K489I	PHF3_uc010kaf.1_Missense_Mutation_p.K489I|PHF3_uc003pem.2_Missense_Mutation_p.K442I|PHF3_uc010kag.1_Missense_Mutation_p.K401I|PHF3_uc010kah.1_Missense_Mutation_p.K303I|PHF3_uc003pen.2_Missense_Mutation_p.K401I|PHF3_uc011dxs.1_Intron|PHF3_uc003peo.2_Missense_Mutation_p.K489I	NM_015153	NP_055968	Q92576	PHF3_HUMAN	PHD finger protein 3	489					multicellular organismal development|transcription, DNA-dependent	nucleus	zinc ion binding			ovary(3)|lung(1)|skin(1)	5	all_cancers(3;0.0241)|all_epithelial(2;0.00306)|Lung NSC(77;0.121)		LUSC - Lung squamous cell carcinoma(74;0.0644)|Lung(124;0.148)			GTAAAATCCAAACATACAAAA	0.353													7	17	---	---	---	---	PASS
ASCC3	10973	broad.mit.edu	37	6	101248212	101248212	+	Missense_Mutation	SNP	A	T	T			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:101248212A>T	uc003pqk.2	-	6	1420	c.1091T>A	c.(1090-1092)CTT>CAT	p.L364H	ASCC3_uc011eai.1_Missense_Mutation_p.L266H|ASCC3_uc003pql.2_Missense_Mutation_p.L364H	NM_006828	NP_006819	Q8N3C0	HELC1_HUMAN	activating signal cointegrator 1 complex subunit	364					regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|microtubule cytoskeleton	ATP binding|ATP-dependent helicase activity|nucleic acid binding			ovary(5)|skin(1)	6		all_cancers(76;1.45e-07)|Acute lymphoblastic leukemia(125;4.99e-11)|all_hematologic(75;5.82e-08)|all_epithelial(87;0.00149)|Hepatocellular(1;0.0893)|Colorectal(196;0.13)		BRCA - Breast invasive adenocarcinoma(108;0.0539)|all cancers(137;0.103)|GBM - Glioblastoma multiforme(226;0.199)		AAAGCACATAAGTCCTTCTGA	0.353													246	494	---	---	---	---	PASS
CDK13	8621	broad.mit.edu	37	7	40134425	40134425	+	Missense_Mutation	SNP	A	G	G			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:40134425A>G	uc003thh.3	+	14	4667	c.4385A>G	c.(4384-4386)TAT>TGT	p.Y1462C	CDK13_uc003thi.3_Missense_Mutation_p.Y1402C|CDK13_uc003thj.2_Missense_Mutation_p.Y513C|CDK13_uc003thk.2_Missense_Mutation_p.Y395C	NM_003718	NP_003709	Q14004	CDK13_HUMAN	cell division cycle 2-like 5 isoform 1	1462					alternative nuclear mRNA splicing, via spliceosome|hemopoiesis|interspecies interaction between organisms|phosphorylation of RNA polymerase II C-terminal domain|positive regulation of cell proliferation|regulation of mitosis	nuclear cyclin-dependent protein kinase holoenzyme complex|nuclear speck	ATP binding|cyclin-dependent protein kinase activity|protein binding|RNA polymerase II carboxy-terminal domain kinase activity			lung(2)|skin(2)|ovary(1)	5						AACTATAACTATGGTGGTAAC	0.512													80	91	---	---	---	---	PASS
ZNF107	51427	broad.mit.edu	37	7	64169511	64169511	+	3'UTR	SNP	G	A	A			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:64169511G>A	uc003ttd.2	+	7					ZNF107_uc003tte.2_3'UTR	NM_016220	NP_057304	Q9UII5	ZN107_HUMAN	zinc finger protein 107						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1		Lung NSC(55;0.00948)|all_lung(88;0.0249)				CTACAATTGTGAAGAATGTGG	0.373													4	21	---	---	---	---	PASS
ZNF117	51351	broad.mit.edu	37	7	64437831	64437831	+	3'UTR	SNP	G	A	A			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:64437831G>A	uc003ttr.2	-	4						NM_015852	NP_056936	Q03924	ZN117_HUMAN	zinc finger protein 117							nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			skin(1)	1		Lung NSC(55;0.0295)|all_lung(88;0.0691)				AGCATCGACTGAAAGTTTTGC	0.353													7	27	---	---	---	---	PASS
KIAA1324L	222223	broad.mit.edu	37	7	86568243	86568243	+	Missense_Mutation	SNP	T	C	C			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:86568243T>C	uc011kha.1	-	7	1066	c.881A>G	c.(880-882)AAG>AGG	p.K294R	KIAA1324L_uc003uif.1_Missense_Mutation_p.K54R|KIAA1324L_uc011kgz.1_Missense_Mutation_p.K180R|KIAA1324L_uc003uie.2_Missense_Mutation_p.K127R	NM_001142749	NP_001136221	A8MWY0	K132L_HUMAN	hypothetical protein LOC222223 isoform 1	294	Extracellular (Potential).					integral to membrane				ovary(6)|skin(1)	7	Esophageal squamous(14;0.0058)					TGTGCCTGGCTTGCAAGGAAA	0.458													7	313	---	---	---	---	PASS
ZNF804B	219578	broad.mit.edu	37	7	88964500	88964500	+	Missense_Mutation	SNP	G	A	A			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:88964500G>A	uc011khi.1	+	4	2742	c.2204G>A	c.(2203-2205)AGC>AAC	p.S735N		NM_181646	NP_857597	A4D1E1	Z804B_HUMAN	zinc finger protein 804B	735						intracellular	zinc ion binding			ovary(5)|skin(3)|pancreas(2)|upper_aerodigestive_tract(1)	11	all_hematologic(106;0.125)|Lung NSC(181;0.15)|all_lung(186;0.151)		STAD - Stomach adenocarcinoma(171;0.0513)			AATGGTAATAGCAGAGGTAAT	0.403										HNSCC(36;0.09)			10	238	---	---	---	---	PASS
ZNF804B	219578	broad.mit.edu	37	7	88966113	88966113	+	Missense_Mutation	SNP	G	A	A			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:88966113G>A	uc011khi.1	+	4	4355	c.3817G>A	c.(3817-3819)GCT>ACT	p.A1273T		NM_181646	NP_857597	A4D1E1	Z804B_HUMAN	zinc finger protein 804B	1273						intracellular	zinc ion binding			ovary(5)|skin(3)|pancreas(2)|upper_aerodigestive_tract(1)	11	all_hematologic(106;0.125)|Lung NSC(181;0.15)|all_lung(186;0.151)		STAD - Stomach adenocarcinoma(171;0.0513)			TTTAGTAGCTGCTACCCCCTT	0.473										HNSCC(36;0.09)			30	348	---	---	---	---	PASS
CNPY4	245812	broad.mit.edu	37	7	99722440	99722440	+	Missense_Mutation	SNP	G	C	C			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:99722440G>C	uc003uto.2	+	6	779	c.676G>C	c.(676-678)GAG>CAG	p.E226Q	MBLAC1_uc003utp.2_5'Flank	NM_152755	NP_689968	Q8N129	CNPY4_HUMAN	canopy 4 homolog precursor	226	Glu-rich.					extracellular region					0	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)					ggaggaagaggaggaagagga	0.373													46	205	---	---	---	---	PASS
NAPEPLD	222236	broad.mit.edu	37	7	102768831	102768831	+	Intron	SNP	C	G	G			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:102768831C>G	uc003vbc.2	-						NAPEPLD_uc003vbd.2_Intron|NAPEPLD_uc011klj.1_Intron|NAPEPLD_uc003vbe.2_Intron|NAPEPLD_uc003vbf.2_3'UTR	NM_198990	NP_945341	Q6IQ20	NAPEP_HUMAN	N-acyl phosphatidylethanolamine phospholipase D						phospholipid catabolic process	membrane	metal ion binding			skin(1)	1						tttatctcctcagacctaatt	0.109													12	80	---	---	---	---	PASS
PSMC2	5701	broad.mit.edu	37	7	103008447	103008447	+	Silent	SNP	C	T	T			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:103008447C>T	uc003vbs.2	+	12	1318	c.1248C>T	c.(1246-1248)GTC>GTT	p.V416V	SLC26A5_uc003vbt.1_Intron|SLC26A5_uc003vbu.1_Intron|SLC26A5_uc003vbv.1_Intron|PSMC2_uc011klo.1_Silent_p.V279V	NM_002803	NP_002794	P35998	PRS7_HUMAN	proteasome 26S ATPase subunit 2	416					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	mitochondrion|nucleus|proteasome complex	ATP binding|ATPase activity|protein binding				0						TAAATAAGGTCATTAAGTCTT	0.418													68	314	---	---	---	---	PASS
ASB15	142685	broad.mit.edu	37	7	123267202	123267202	+	Missense_Mutation	SNP	G	T	T			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:123267202G>T	uc003vku.1	+	9	1028	c.736G>T	c.(736-738)GTG>TTG	p.V246L	ASB15_uc003vkv.1_Missense_Mutation_p.V246L|ASB15_uc003vkw.1_Missense_Mutation_p.V246L	NM_080928	NP_563616	Q8WXK1	ASB15_HUMAN	ankyrin repeat and SOCS box-containing 15	246	ANK 5.				intracellular signal transduction					skin(2)|lung(1)	3						TGGGGCGTCGGTGCTGTTTGA	0.498													51	228	---	---	---	---	PASS
TMEM229A	730130	broad.mit.edu	37	7	123672673	123672673	+	Missense_Mutation	SNP	G	A	A			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:123672673G>A	uc011kob.1	-	1	851	c.385C>T	c.(385-387)CAC>TAC	p.H129Y	uc011koc.1_Intron	NM_001136002	NP_001129474	B2RXF0	T229A_HUMAN	transmembrane protein 229A	129	Helical; (Potential).					host cell nucleus|integral to membrane	sequence-specific DNA binding transcription factor activity				0						AGCCCCACGTGGGCCGAGGGG	0.697													12	71	---	---	---	---	PASS
CCDC136	64753	broad.mit.edu	37	7	128434749	128434749	+	Silent	SNP	G	A	A			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:128434749G>A	uc003vnv.1	+	3	640	c.273G>A	c.(271-273)GGG>GGA	p.G91G	CCDC136_uc003vnu.1_Silent_p.G141G|CCDC136_uc003vnw.1_Silent_p.G91G	NM_022742	NP_073579	Q96JN2	CC136_HUMAN	coiled-coil domain containing 136	91	Glu-rich.					integral to membrane	protein binding			ovary(2)	2						TCCCTGCAGGGCTCCTGGAGG	0.652													5	30	---	---	---	---	PASS
CALD1	800	broad.mit.edu	37	7	134618264	134618264	+	Silent	SNP	A	T	T			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:134618264A>T	uc003vrz.2	+	5	1203	c.744A>T	c.(742-744)TCA>TCT	p.S248S	CALD1_uc003vry.2_Intron|CALD1_uc003vsa.2_Intron|CALD1_uc003vsb.2_Intron|CALD1_uc010lmm.2_Intron|CALD1_uc011kpt.1_Intron|CALD1_uc003vsc.2_Intron|CALD1_uc003vsd.2_Intron|CALD1_uc011kpu.1_Intron|CALD1_uc011kpv.1_Intron|CALD1_uc003vse.2_Silent_p.S112S	NM_033138	NP_149129	Q05682	CALD1_HUMAN	caldesmon 1 isoform 1	248					cellular component movement|muscle contraction	cytosol|focal adhesion|myofibril	actin binding|calmodulin binding|myosin binding|tropomyosin binding				0						AACAAGGTTCAGATGAGATTT	0.428													18	251	---	---	---	---	PASS
UBN2	254048	broad.mit.edu	37	7	138958118	138958118	+	Missense_Mutation	SNP	A	G	G			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:138958118A>G	uc011kqr.1	+	10	1791	c.1791A>G	c.(1789-1791)ATA>ATG	p.I597M	UBN2_uc003vuv.2_Missense_Mutation_p.I320M	NM_173569	NP_775840	Q6ZU65	UBN2_HUMAN	ubinuclein 2	597										ovary(1)|skin(1)	2						AACGTGTCATAGGACCAAGAA	0.318													302	306	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	7	142045734	142045734	+	Intron	SNP	C	A	A			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:142045734C>A	uc011kro.1	+						uc011krp.1_Intron|uc011krr.1_Intron|uc003vxp.3_Missense_Mutation_p.P88T|uc011krt.1_Missense_Mutation_p.P70T					SubName: Full=V_segment translation product; Flags: Fragment;																		ACCTGAATGCCCCAACAGCTC	0.498													6	176	---	---	---	---	PASS
SSPO	23145	broad.mit.edu	37	7	149481051	149481051	+	Missense_Mutation	SNP	G	A	A			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:149481051G>A	uc010lpk.2	+	18	2533	c.2533G>A	c.(2533-2535)GGG>AGG	p.G845R	SSPO_uc010lpl.1_Missense_Mutation_p.G180R	NM_198455	NP_940857	A2VEC9	SSPO_HUMAN	SCO-spondin precursor	845	TIL 2.				cell adhesion	extracellular space	peptidase inhibitor activity				0	Melanoma(164;0.165)|Ovarian(565;0.177)		OV - Ovarian serous cystadenocarcinoma(82;0.00625)			TCAACACTGCGGGAAACCAGA	0.627													4	104	---	---	---	---	PASS
C8orf79	57604	broad.mit.edu	37	8	12879542	12879542	+	Missense_Mutation	SNP	G	C	C			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:12879542G>C	uc010lsq.2	+	5	1846	c.1354G>C	c.(1354-1356)GGT>CGT	p.G452R	C8orf79_uc011kxw.1_Intron|C8orf79_uc003wwj.3_Missense_Mutation_p.G365R|C8orf79_uc010lsr.2_Missense_Mutation_p.G326R	NM_020844	NP_065895	Q9P272	K1456_HUMAN	hypothetical protein LOC57604 isoform 1	452							methyltransferase activity				0						GAAAAAGAGAGGTTGTGATTG	0.423													17	74	---	---	---	---	PASS
ENPP2	5168	broad.mit.edu	37	8	120580427	120580427	+	Missense_Mutation	SNP	G	C	C			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:120580427G>C	uc003yot.1	-	22	2205	c.2119C>G	c.(2119-2121)CCT>GCT	p.P707A	ENPP2_uc011lic.1_Missense_Mutation_p.P245A|ENPP2_uc003yor.1_Missense_Mutation_p.P342A|ENPP2_uc003yos.1_Missense_Mutation_p.P759A|ENPP2_uc010mdd.1_Missense_Mutation_p.P732A	NM_001040092	NP_001035181	Q13822	ENPP2_HUMAN	autotaxin isoform 2 preproprotein	707					cellular component movement|chemotaxis|G-protein coupled receptor protein signaling pathway|immune response|phosphate metabolic process|phosphatidylcholine catabolic process|regulation of cell migration	extracellular space|integral to plasma membrane	alkylglycerophosphoethanolamine phosphodiesterase activity|calcium ion binding|lysophospholipase activity|nucleic acid binding|nucleotide diphosphatase activity|phosphodiesterase I activity|polysaccharide binding|scavenger receptor activity|transcription factor binding|zinc ion binding			ovary(2)|central_nervous_system(2)|upper_aerodigestive_tract(1)|large_intestine(1)|kidney(1)	7	Lung NSC(37;5.03e-06)|Ovarian(258;0.0249)|Hepatocellular(40;0.161)		STAD - Stomach adenocarcinoma(47;0.00185)			TTGAAAGCAGGATACATTGGA	0.318													6	343	---	---	---	---	PASS
ZHX1	11244	broad.mit.edu	37	8	124265779	124265779	+	Missense_Mutation	SNP	A	T	T			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:124265779A>T	uc003yqe.2	-	3	2838	c.2408T>A	c.(2407-2409)CTT>CAT	p.L803H	C8orf76_uc003yqd.2_Intron|ZHX1_uc003yqf.2_Missense_Mutation_p.L803H|ZHX1_uc003yqg.2_Intron|ZHX1_uc010mdi.2_Missense_Mutation_p.L803H	NM_007222	NP_009153	Q9UKY1	ZHX1_HUMAN	zinc fingers and homeoboxes 1	803	Homeobox 5.				negative regulation of transcription, DNA-dependent	nucleus	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)	1	Lung NSC(37;1.25e-09)|Ovarian(258;0.0154)		STAD - Stomach adenocarcinoma(47;0.00527)			TTTGTTAACAAGTTCATCAAG	0.368													134	260	---	---	---	---	PASS
ZFAT	57623	broad.mit.edu	37	8	135622881	135622881	+	Missense_Mutation	SNP	C	G	G			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:135622881C>G	uc003yup.2	-	4	641	c.466G>C	c.(466-468)GAA>CAA	p.E156Q	ZFAT_uc003yun.2_Missense_Mutation_p.E144Q|ZFAT_uc003yuo.2_Missense_Mutation_p.E144Q|ZFAT_uc010meh.2_Missense_Mutation_p.E144Q|ZFAT_uc010mei.2_RNA|ZFAT_uc003yuq.2_Missense_Mutation_p.E144Q|ZFAT_uc010mej.2_Intron|ZFAT_uc003yur.2_Missense_Mutation_p.E144Q	NM_020863	NP_065914	Q9P243	ZFAT_HUMAN	zinc finger protein 406 isoform ZFAT-1	156					regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytosol|nucleus	DNA binding|zinc ion binding			central_nervous_system(1)	1	all_epithelial(106;8.26e-19)|Lung NSC(106;3.47e-07)|all_lung(105;1.39e-06)|Ovarian(258;0.0102)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0432)			TTTTCTAGTTCAAGGTCAGAC	0.438													38	354	---	---	---	---	PASS
EIF2C2	27161	broad.mit.edu	37	8	141559351	141559351	+	Missense_Mutation	SNP	G	C	C			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:141559351G>C	uc003yvn.2	-	12	1490	c.1450C>G	c.(1450-1452)CCC>GCC	p.P484A	EIF2C2_uc010men.2_Missense_Mutation_p.P407A|EIF2C2_uc010meo.2_Missense_Mutation_p.P484A	NM_012154	NP_036286	Q9UKV8	AGO2_HUMAN	argonaute 2 isoform 1	484					mRNA cleavage involved in gene silencing by miRNA|negative regulation of translation involved in gene silencing by miRNA|negative regulation of translational initiation|pre-miRNA processing|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasmic mRNA processing body|cytosol|micro-ribonucleoprotein complex|mRNA cap binding complex|nucleus|polysome|RNA-induced silencing complex	endoribonuclease activity, cleaving siRNA-paired mRNA|metal ion binding|protein binding|RNA 7-methylguanosine cap binding|siRNA binding|translation initiation factor activity				0	all_cancers(97;2.54e-14)|all_epithelial(106;5.99e-13)|Lung NSC(106;1.45e-05)|all_lung(105;2.07e-05)|Ovarian(258;0.0154)|Acute lymphoblastic leukemia(118;0.155)	Breast(495;0.159)	BRCA - Breast invasive adenocarcinoma(115;0.158)			CCCTGGATGGGCATGCCGGCG	0.617													7	36	---	---	---	---	PASS
EIF2C2	27161	broad.mit.edu	37	8	141559352	141559352	+	Missense_Mutation	SNP	C	A	A			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:141559352C>A	uc003yvn.2	-	12	1489	c.1449G>T	c.(1447-1449)ATG>ATT	p.M483I	EIF2C2_uc010men.2_Missense_Mutation_p.M406I|EIF2C2_uc010meo.2_Missense_Mutation_p.M483I	NM_012154	NP_036286	Q9UKV8	AGO2_HUMAN	argonaute 2 isoform 1	483					mRNA cleavage involved in gene silencing by miRNA|negative regulation of translation involved in gene silencing by miRNA|negative regulation of translational initiation|pre-miRNA processing|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasmic mRNA processing body|cytosol|micro-ribonucleoprotein complex|mRNA cap binding complex|nucleus|polysome|RNA-induced silencing complex	endoribonuclease activity, cleaving siRNA-paired mRNA|metal ion binding|protein binding|RNA 7-methylguanosine cap binding|siRNA binding|translation initiation factor activity				0	all_cancers(97;2.54e-14)|all_epithelial(106;5.99e-13)|Lung NSC(106;1.45e-05)|all_lung(105;2.07e-05)|Ovarian(258;0.0154)|Acute lymphoblastic leukemia(118;0.155)	Breast(495;0.159)	BRCA - Breast invasive adenocarcinoma(115;0.158)			CCTGGATGGGCATGCCGGCGT	0.622													7	36	---	---	---	---	PASS
TYRP1	7306	broad.mit.edu	37	9	12708083	12708083	+	Missense_Mutation	SNP	A	G	G			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:12708083A>G	uc003zkv.3	+	7	1526	c.1348A>G	c.(1348-1350)ACA>GCA	p.T450A		NM_000550	NP_000541	P17643	TYRP1_HUMAN	tyrosinase-related protein 1 precursor	450	Lumenal, melanosome (Potential).				melanin biosynthetic process	clathrin-coated endocytic vesicle membrane|endosome membrane|integral to membrane|melanosome membrane	copper ion binding|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, another compound as one donor, and incorporation of one atom of oxygen|protein heterodimerization activity|protein homodimerization activity			lung(1)	1		all_cancers(3;3.1e-05)|all_lung(3;1.7e-06)|Lung NSC(3;2.09e-06)|all_epithelial(3;0.000695)|all_hematologic(3;0.0033)|Acute lymphoblastic leukemia(23;0.0744)		GBM - Glioblastoma multiforme(50;9.85e-06)		AGTCACCAACACAGAAATGTT	0.378									Oculocutaneous_Albinism				24	103	---	---	---	---	PASS
NOL6	65083	broad.mit.edu	37	9	33469655	33469655	+	Missense_Mutation	SNP	T	A	A			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:33469655T>A	uc003zsz.2	-	5	670	c.569A>T	c.(568-570)CAG>CTG	p.Q190L	SUGT1P1_uc010mjq.1_Intron|NOL6_uc003zta.2_Missense_Mutation_p.Q190L|NOL6_uc010mjv.2_Missense_Mutation_p.Q190L|NOL6_uc011lob.1_Missense_Mutation_p.Q130L|NOL6_uc003ztb.1_Missense_Mutation_p.Q190L	NM_022917	NP_075068	Q9H6R4	NOL6_HUMAN	nucleolar protein family 6 alpha isoform	190					rRNA processing	condensed nuclear chromosome|nucleolus	RNA binding			ovary(2)	2			LUSC - Lung squamous cell carcinoma(29;0.00788)	GBM - Glioblastoma multiforme(74;0.152)		GTCCTTGTCCTGTAGGATTTC	0.612													20	35	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	9	69440119	69440119	+	Missense_Mutation	SNP	C	A	A			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:69440119C>A	uc010mnx.1	+	3	372	c.203C>A	c.(202-204)TCT>TAT	p.S68Y		NM_001098806	NP_001092276			coiled-coil domain containing 29																		GAGTTTTTATCTATGAAAAAA	0.313													15	47	---	---	---	---	PASS
C9orf41	138199	broad.mit.edu	37	9	77632363	77632363	+	Missense_Mutation	SNP	T	C	C			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:77632363T>C	uc004ajq.2	-	2	385	c.232A>G	c.(232-234)ACC>GCC	p.T78A	C9orf41_uc011lsi.1_RNA	NM_152420	NP_689633	Q8N4J0	CI041_HUMAN	hypothetical protein LOC138199	78										ovary(1)|skin(1)	2						TGCATACTGGTGCTAAAACAT	0.368													79	88	---	---	---	---	PASS
COL27A1	85301	broad.mit.edu	37	9	117069829	117069829	+	Intron	SNP	C	T	T	rs1265892	by1000genomes	TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:117069829C>T	uc011lxl.1	+						COL27A1_uc004bii.2_Intron|COL27A1_uc011lxn.1_5'UTR	NM_032888	NP_116277	Q8IZC6	CORA1_HUMAN	collagen, type XXVII, alpha 1 precursor						cell adhesion		extracellular matrix structural constituent			ovary(3)|skin(1)	4						TGCTCACCCACCCTGACTTCA	0.562													10	5	---	---	---	---	PASS
DIP2C	22982	broad.mit.edu	37	10	409187	409187	+	Missense_Mutation	SNP	G	T	T			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:409187G>T	uc001ifp.2	-	21	2632	c.2542C>A	c.(2542-2544)CCT>ACT	p.P848T	DIP2C_uc009xhi.1_Missense_Mutation_p.P234T|DIP2C_uc010pzz.1_Missense_Mutation_p.P169T	NM_014974	NP_055789	Q9Y2E4	DIP2C_HUMAN	DIP2 disco-interacting protein 2 homolog C	848						nucleus	catalytic activity|transcription factor binding			breast(4)|ovary(2)|large_intestine(1)	7		all_cancers(4;0.00336)|all_lung(4;0.00732)|Lung NSC(4;0.00785)|all_epithelial(10;0.0159)|Colorectal(49;0.235)	OV - Ovarian serous cystadenocarcinoma(33;0.136)	Epithelial(11;0.0123)|all cancers(11;0.0467)|Lung(33;0.0864)|OV - Ovarian serous cystadenocarcinoma(14;0.106)		GTGGAGTCAGGCCTCTGCTCA	0.637													6	25	---	---	---	---	PASS
KIN	22944	broad.mit.edu	37	10	7829795	7829795	+	Silent	SNP	C	T	T			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:7829795C>T	uc001ijt.2	-	1	150	c.102G>A	c.(100-102)CAG>CAA	p.Q34Q	KIN_uc010qaz.1_RNA|KIN_uc009xip.2_Silent_p.Q34Q|KIN_uc010qba.1_Translation_Start_Site|ATP5C1_uc010qbb.1_5'Flank|ATP5C1_uc009xiq.1_5'Flank|ATP5C1_uc010qbc.1_5'Flank|ATP5C1_uc001iju.2_5'Flank|ATP5C1_uc001ijv.2_5'Flank	NM_012311	NP_036443	O60870	KIN17_HUMAN	HsKin17 protein	34	C2H2-type.				DNA recombination|DNA repair|DNA replication|interspecies interaction between organisms|mRNA processing	cytoplasm|nuclear matrix	double-stranded DNA binding|RNA binding|zinc ion binding			ovary(1)|pancreas(1)|skin(1)	3						CGTCCCGGCACTGCTTCTGGC	0.637													9	32	---	---	---	---	PASS
CCNY	219771	broad.mit.edu	37	10	35819094	35819094	+	Missense_Mutation	SNP	C	G	G			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:35819094C>G	uc001iyw.3	+	7	682	c.502C>G	c.(502-504)CAG>GAG	p.Q168E	CCNY_uc001iyu.3_Missense_Mutation_p.Q114E|CCNY_uc001iyv.3_Missense_Mutation_p.Q114E|CCNY_uc001iyx.3_Missense_Mutation_p.Q114E|CCNY_uc009xmb.2_Missense_Mutation_p.Q143E|CCNY_uc010qet.1_Missense_Mutation_p.Q35E	NM_145012	NP_659449	Q8ND76	CCNY_HUMAN	cyclin Y isoform 1	168	Cyclin N-terminal.				cell division|G2/M transition of mitotic cell cycle|positive regulation of cyclin-dependent protein kinase activity|regulation of canonical Wnt receptor signaling pathway|Wnt receptor signaling pathway	cytoplasmic cyclin-dependent protein kinase holoenzyme complex|nucleus|plasma membrane	cyclin-dependent protein kinase regulator activity|protein kinase binding				0						CAACCCAGAGCAGAAGCAGAT	0.493													32	95	---	---	---	---	PASS
ZMYND17	118490	broad.mit.edu	37	10	75185797	75185797	+	Missense_Mutation	SNP	C	T	T			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:75185797C>T	uc001jud.2	-	5	907	c.841G>A	c.(841-843)GGG>AGG	p.G281R	ZMYND17_uc001juc.2_Missense_Mutation_p.G281R|ZMYND17_uc009xrh.2_Missense_Mutation_p.G304R|ZMYND17_uc009xrg.2_Intron	NM_001024593	NP_001019764	Q4VC12	ZMY17_HUMAN	zinc finger, MYND domain containing 17	281							zinc ion binding			ovary(1)	1	Prostate(51;0.0119)					TCATAGTCCCCTGGGCGAGTA	0.532													20	43	---	---	---	---	PASS
ANO9	338440	broad.mit.edu	37	11	441994	441994	+	5'UTR	SNP	C	T	T			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:441994C>T	uc001lpi.2	-	1					ANO9_uc010qvv.1_5'UTR	NM_001012302	NP_001012302	A1A5B4	ANO9_HUMAN	tumor protein p53 inducible protein 5							chloride channel complex	chloride channel activity			central_nervous_system(2)|ovary(1)|skin(1)	4						GGCGGGTGCTCCTACCTGACT	0.697													8	18	---	---	---	---	PASS
OR51L1	119682	broad.mit.edu	37	11	5020665	5020665	+	Missense_Mutation	SNP	G	T	T			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:5020665G>T	uc010qyu.1	+	1	453	c.453G>T	c.(451-453)TTG>TTT	p.L151F		NM_001004755	NP_001004755	Q8NGJ5	O51L1_HUMAN	olfactory receptor, family 51, subfamily L,	151	Helical; Name=4; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			skin(1)	1		Medulloblastoma(188;0.0061)|all_neural(188;0.0479)|Breast(177;0.086)		Epithelial(150;1.75e-11)|BRCA - Breast invasive adenocarcinoma(625;0.0285)|LUSC - Lung squamous cell carcinoma(625;0.19)		TGGCCTGTTTGCTACGAAGCT	0.507													9	359	---	---	---	---	PASS
MRGPRX3	117195	broad.mit.edu	37	11	18159570	18159570	+	Missense_Mutation	SNP	T	A	A			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:18159570T>A	uc001mnu.2	+	3	1182	c.821T>A	c.(820-822)TTC>TAC	p.F274Y		NM_054031	NP_473372	Q96LB0	MRGX3_HUMAN	MAS-related GPR, member X3	274	Helical; Name=7; (Potential).					integral to membrane|plasma membrane	G-protein coupled receptor activity			ovary(1)|pancreas(1)	2						ATTTACTTCTTCGTGGGCTCC	0.507													28	83	---	---	---	---	PASS
QSER1	79832	broad.mit.edu	37	11	32996944	32996944	+	Intron	SNP	C	T	T			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:32996944C>T	uc001mty.2	+						QSER1_uc001mtz.1_Intron|QSER1_uc001mua.2_Silent_p.L1213L	NM_001076786	NP_001070254	Q2KHR3	QSER1_HUMAN	glutamine and serine rich 1											ovary(3)|central_nervous_system(2)|skin(1)	6	Breast(20;0.158)					TAAGGAGACTCTAGCCATAGT	0.284													7	48	---	---	---	---	PASS
VPS37C	55048	broad.mit.edu	37	11	60899492	60899492	+	Silent	SNP	T	G	G			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:60899492T>G	uc001nqv.1	-	5	928	c.868A>C	c.(868-870)AGG>CGG	p.R290R		NM_017966	NP_060436	A5D8V6	VP37C_HUMAN	vacuolar protein sorting 37C	290	Pro-rich.				cellular membrane organization|endosome transport|protein transport	late endosome membrane					0						CTGGGGGCCCTGCCTCCCCGC	0.647													20	54	---	---	---	---	PASS
LOC645332	645332	broad.mit.edu	37	11	67560384	67560384	+	3'UTR	SNP	C	T	T			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:67560384C>T	uc001omt.3	-	4					LOC645332_uc001omu.3_3'UTR	NR_024249				SubName: Full=cDNA FLJ57700, weakly similar to Protein FAM86A;												0						TTGATACACACGTTTTTATTT	0.468													3	34	---	---	---	---	PASS
GAB2	9846	broad.mit.edu	37	11	77931466	77931466	+	Missense_Mutation	SNP	C	T	T	rs145573768		TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:77931466C>T	uc001ozh.2	-	9	1786	c.1786G>A	c.(1786-1788)GTT>ATT	p.V596I	GAB2_uc001ozg.2_Missense_Mutation_p.V558I	NM_080491	NP_536739	Q9UQC2	GAB2_HUMAN	GRB2-associated binding protein 2 isoform a	596					osteoclast differentiation|phosphatidylinositol-mediated signaling|positive regulation of cell proliferation|positive regulation of mast cell degranulation	cytosol|plasma membrane	phosphatidylinositol-3,4,5-trisphosphate binding|phosphatidylinositol-3,4-bisphosphate binding|transmembrane receptor protein tyrosine kinase adaptor activity			ovary(5)|lung(1)	6	all_cancers(14;3.31e-18)|all_epithelial(13;5.3e-21)|Breast(9;5.6e-16)|Ovarian(111;0.152)		OV - Ovarian serous cystadenocarcinoma(8;1.58e-23)			CCACTGGGAACGGGAGATGCA	0.562													23	55	---	---	---	---	PASS
PAFAH1B2	5049	broad.mit.edu	37	11	117030704	117030704	+	Missense_Mutation	SNP	G	A	A			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:117030704G>A	uc001pqe.1	+	3	238	c.136G>A	c.(136-138)GGA>AGA	p.G46R	PAFAH1B2_uc009yzk.1_Missense_Mutation_p.G46R|PAFAH1B2_uc009yzl.1_Missense_Mutation_p.G46R|PAFAH1B2_uc009yzm.2_RNA|PAFAH1B2_uc009yzn.2_RNA|PAFAH1B2_uc009yzj.1_Intron	NM_002572	NP_002563	P68402	PA1B2_HUMAN	platelet-activating factor acetylhydrolase,	46					lipid catabolic process	cytoplasm	1-alkyl-2-acetylglycerophosphocholine esterase activity			kidney(1)	1	all_hematologic(175;0.0487)	Medulloblastoma(222;0.0523)|Breast(348;0.056)|all_hematologic(192;0.232)		BRCA - Breast invasive adenocarcinoma(274;1.68e-05)|Epithelial(105;0.000162)|all cancers(92;0.00111)		ACTGTTCGTGGGAGACTCCAT	0.393			T	IGH@	MLCLS								5	231	---	---	---	---	PASS
RNF26	79102	broad.mit.edu	37	11	119205888	119205888	+	Missense_Mutation	SNP	C	A	A			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:119205888C>A	uc001pwh.2	+	1	652	c.56C>A	c.(55-57)ACC>AAC	p.T19N		NM_032015	NP_114404	Q9BY78	RNF26_HUMAN	ring finger protein 26	19	Leu-rich.						zinc ion binding			ovary(1)	1		Medulloblastoma(222;0.0425)|Breast(348;0.052)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;3.8e-05)		GACGTGCTGACCTTGGTGTTG	0.577													83	108	---	---	---	---	PASS
ST3GAL4	6484	broad.mit.edu	37	11	126283944	126283944	+	3'UTR	SNP	C	A	A			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:126283944C>A	uc001qds.2	+	11					ST3GAL4_uc001qdt.2_3'UTR|ST3GAL4_uc009zcc.2_3'UTR|ST3GAL4_uc009zcd.2_3'UTR|ST3GAL4_uc001qdu.2_3'UTR|ST3GAL4_uc001qdv.2_3'UTR|ST3GAL4_uc009zce.2_3'UTR|ST3GAL4_uc001qdw.2_3'UTR|ST3GAL4_uc001qdx.1_Intron|ST3GAL4_uc001qdy.2_3'UTR|ST3GAL4_uc001qdz.2_3'UTR	NM_006278	NP_006269	Q11206	SIA4C_HUMAN	ST3 beta-galactoside alpha-2,3-sialyltransferase						post-translational protein modification|protein N-linked glycosylation via asparagine	extracellular region|Golgi cisterna membrane|integral to Golgi membrane	beta-galactoside alpha-2,3-sialyltransferase activity				0	all_hematologic(175;0.145)	Breast(109;0.00867)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.0739)|all_lung(97;0.0798)|all_neural(223;0.138)		BRCA - Breast invasive adenocarcinoma(274;1.13e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0767)		TCCTTCTGACCTGGGCAAGAG	0.592													13	68	---	---	---	---	PASS
IGSF9B	22997	broad.mit.edu	37	11	133789678	133789678	+	Silent	SNP	C	T	T			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:133789678C>T	uc001qgx.3	-	18	4173	c.3942G>A	c.(3940-3942)TTG>TTA	p.L1314L		NM_014987	NP_055802	Q9UPX0	TUTLB_HUMAN	immunoglobulin superfamily, member 9B	1314	Pro-rich.|Cytoplasmic (Potential).					integral to membrane|plasma membrane					0	all_hematologic(175;0.127)	all_cancers(12;1.58e-21)|all_epithelial(12;5.17e-16)|all_lung(97;1.6e-05)|Lung NSC(97;3.86e-05)|Breast(109;0.000126)|Medulloblastoma(222;0.0245)|all_neural(223;0.0505)|Esophageal squamous(93;0.0559)		Epithelial(10;7.19e-10)|BRCA - Breast invasive adenocarcinoma(10;9.69e-09)|all cancers(11;1.23e-08)|OV - Ovarian serous cystadenocarcinoma(99;0.00328)|Lung(977;0.221)		CCGGTCGGAGCAATTCCTCCC	0.682													3	4	---	---	---	---	PASS
SFRS2IP	9169	broad.mit.edu	37	12	46321850	46321850	+	Missense_Mutation	SNP	T	C	C			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:46321850T>C	uc001rox.2	-	11	1921	c.1634A>G	c.(1633-1635)CAT>CGT	p.H545R	SFRS2IP_uc001row.2_Missense_Mutation_p.H230R|SFRS2IP_uc001roy.1_Missense_Mutation_p.H619R	NM_004719	NP_004710	Q99590	SCAFB_HUMAN	splicing factor, arginine/serine-rich 2,	545					spliceosome assembly	nucleus	protein binding|zinc ion binding				0	Lung SC(27;0.192)|Renal(347;0.236)	Lung NSC(34;0.209)	OV - Ovarian serous cystadenocarcinoma(5;0.00691)	GBM - Glioblastoma multiforme(48;0.1)		ATTTGGAAGATGAACTGTACA	0.373													83	63	---	---	---	---	PASS
KRT2	3849	broad.mit.edu	37	12	53043743	53043743	+	Silent	SNP	G	A	A			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:53043743G>A	uc001sat.2	-	3	849	c.816C>T	c.(814-816)ATC>ATT	p.I272I		NM_000423	NP_000414	P35908	K22E_HUMAN	keratin 2	272	Coil 1B.|Rod.				keratinization|keratinocyte activation|keratinocyte migration|keratinocyte proliferation	Golgi apparatus|keratin filament	protein binding|structural constituent of cytoskeleton			ovary(2)	2				BRCA - Breast invasive adenocarcinoma(357;0.19)		TGCGCTTATTGATTTCATCCT	0.438													152	395	---	---	---	---	PASS
SPRYD3	84926	broad.mit.edu	37	12	53471044	53471044	+	Missense_Mutation	SNP	A	C	C			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:53471044A>C	uc001sbt.1	-	2	46	c.25T>G	c.(25-27)TTT>GTT	p.F9V	SPRYD3_uc010snw.1_5'UTR	NM_032840	NP_116229	Q8NCJ5	SPRY3_HUMAN	SPRY domain containing 3	9										central_nervous_system(1)	1						ATGAGAACAAACCTGCCAAGG	0.557													10	116	---	---	---	---	PASS
NXPH4	11247	broad.mit.edu	37	12	57618903	57618903	+	Silent	SNP	G	A	A			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:57618903G>A	uc010srf.1	+	2	475	c.300G>A	c.(298-300)GCG>GCA	p.A100A	NXPH4_uc009zpj.2_5'UTR	NM_007224	NP_009155	O95158	NXPH4_HUMAN	neurexophilin 4 precursor	100	III.				neuropeptide signaling pathway	extracellular region					0						TCAAGGCGGCGCGCGCCAAAA	0.667													2	0	---	---	---	---	PASS
MARS	4141	broad.mit.edu	37	12	57881962	57881962	+	Missense_Mutation	SNP	T	A	A			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:57881962T>A	uc001sog.2	+	1	112	c.89T>A	c.(88-90)ATC>AAC	p.I30N	ARHGAP9_uc001sod.2_Intron|ARHGAP9_uc001soe.1_Intron|MARS_uc001sof.1_RNA|MARS_uc010srp.1_Missense_Mutation_p.I30N|MARS_uc010srq.1_5'UTR	NM_004990	NP_004981	P56192	SYMC_HUMAN	methionyl-tRNA synthetase	30					methionyl-tRNA aminoacylation	cytosol	ATP binding|methionine-tRNA ligase activity|protein binding|tRNA binding			ovary(3)|central_nervous_system(1)|pancreas(1)	5			GBM - Glioblastoma multiforme(3;4.27e-41)		L-Methionine(DB00134)	GAGGTGCTCATCAGCACTGTA	0.647													17	4	---	---	---	---	PASS
PTPRQ	374462	broad.mit.edu	37	12	80940449	80940449	+	Missense_Mutation	SNP	G	A	A			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:80940449G>A	uc001sze.2	+	21	3988	c.3988G>A	c.(3988-3990)GTA>ATA	p.V1330I		NM_001145026	NP_001138498			protein tyrosine phosphatase, receptor type, Q												0						ATTTAGTAATGTAGTAAAATT	0.343													142	124	---	---	---	---	PASS
CLIP1	6249	broad.mit.edu	37	12	122831951	122831951	+	Missense_Mutation	SNP	T	C	C			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:122831951T>C	uc001ucg.1	-	9	1583	c.1477A>G	c.(1477-1479)AAA>GAA	p.K493E	CLIP1_uc001uch.1_Missense_Mutation_p.K482E|CLIP1_uc001uci.1_Intron|CLIP1_uc001ucj.1_Missense_Mutation_p.K183E|CLIP1_uc009zxo.1_Intron	NM_002956	NP_002947	P30622	CLIP1_HUMAN	restin isoform a	493	Potential.				mitotic prometaphase|positive regulation of microtubule polymerization	centrosome|cytosol|endosome|intermediate filament|kinetochore	nucleic acid binding|protein homodimerization activity|zinc ion binding			ovary(2)|breast(1)	3	all_neural(191;0.0837)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;1.81e-05)|Epithelial(86;6.85e-05)|BRCA - Breast invasive adenocarcinoma(302;0.226)		CTCTGGAGTTTGTCAGCTTTG	0.458													181	141	---	---	---	---	PASS
MED4	29079	broad.mit.edu	37	13	48669155	48669155	+	Silent	SNP	C	T	T			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:48669155C>T	uc001vby.1	-	1	86	c.60G>A	c.(58-60)GTG>GTA	p.V20V	MED4_uc010tge.1_Silent_p.V20V|MED4_uc010tgf.1_Intron	NM_014166	NP_054885	Q9NPJ6	MED4_HUMAN	mediator complex subunit 4	20					androgen receptor signaling pathway|positive regulation of transcription, DNA-dependent|regulation of transcription from RNA polymerase II promoter|transcription initiation from RNA polymerase II promoter	mediator complex	ligand-dependent nuclear receptor transcription coactivator activity|receptor activity|RNA polymerase II transcription cofactor activity|thyroid hormone receptor binding|vitamin D receptor binding			ovary(1)	1		all_cancers(8;2.93e-25)|all_epithelial(8;4.38e-13)|all_lung(13;7.37e-06)|all_hematologic(8;8.61e-05)|Breast(56;0.000141)|Lung NSC(96;0.000518)|Prostate(109;0.00132)|Acute lymphoblastic leukemia(8;0.00559)|Myeloproliferative disorder(33;0.039)|Hepatocellular(98;0.0556)|Lung SC(185;0.102)|Glioma(44;0.236)		GBM - Glioblastoma multiforme(144;5.18e-07)		TACCACCCGCCACTCCCAAAC	0.652											OREG0022406	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	5	8	---	---	---	---	PASS
TDRD3	81550	broad.mit.edu	37	13	61102560	61102560	+	Nonsense_Mutation	SNP	C	T	T			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:61102560C>T	uc001via.2	+	11	1710	c.922C>T	c.(922-924)CAA>TAA	p.Q308*	TDRD3_uc010aef.2_Nonsense_Mutation_p.Q133*|TDRD3_uc001vhz.3_Nonsense_Mutation_p.Q308*|TDRD3_uc010aeg.2_Nonsense_Mutation_p.Q401*|TDRD3_uc001vib.3_Nonsense_Mutation_p.Q307*	NM_030794	NP_110421	Q9H7E2	TDRD3_HUMAN	tudor domain containing 3 isoform 2	308					chromatin modification	cytoplasm|nucleus	chromatin binding|methylated histone residue binding|nucleic acid binding|transcription coactivator activity			upper_aerodigestive_tract(1)|skin(1)	2		Prostate(109;0.173)|Breast(118;0.174)		GBM - Glioblastoma multiforme(99;0.000291)		AAATACTGAGCAAAATGGAGT	0.388													8	147	---	---	---	---	PASS
CTAGE5	4253	broad.mit.edu	37	14	39763224	39763224	+	Silent	SNP	G	A	A	rs141828907		TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:39763224G>A	uc001wvg.3	+	7	852	c.516G>A	c.(514-516)AGG>AGA	p.R172R	CTAGE5_uc010tqe.1_Silent_p.R134R|CTAGE5_uc001wuz.3_Silent_p.R160R|CTAGE5_uc001wuy.3_Silent_p.R92R|CTAGE5_uc001wvb.3_Silent_p.R143R|CTAGE5_uc001wvc.3_Silent_p.R117R|CTAGE5_uc001wva.3_Silent_p.R143R|CTAGE5_uc001wve.1_Silent_p.R148R|CTAGE5_uc001wvh.3_Silent_p.R172R|CTAGE5_uc001wvf.3_Silent_p.R97R|CTAGE5_uc001wvi.3_Silent_p.R177R|CTAGE5_uc010amz.2_5'UTR|CTAGE5_uc001wvj.3_Silent_p.R143R	NM_005930	NP_005921	O15320	CTGE5_HUMAN	CTAGE family, member 5 isoform 1	172	Potential.						enzyme activator activity|protein binding				0	Hepatocellular(127;0.213)		LUAD - Lung adenocarcinoma(48;0.000565)|Lung(238;0.000711)	GBM - Glioblastoma multiforme(112;0.0475)		TTTCAAAAAGGATACAGTCTC	0.318													169	270	---	---	---	---	PASS
SGPP1	81537	broad.mit.edu	37	14	64152863	64152863	+	Missense_Mutation	SNP	A	C	C			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:64152863A>C	uc001xgj.2	-	3	1380	c.1286T>G	c.(1285-1287)TTT>TGT	p.F429C		NM_030791	NP_110418	Q9BX95	SGPP1_HUMAN	sphingosine-1-phosphate phosphatase 1	429	Helical; (Potential).					endoplasmic reticulum membrane|integral to membrane	dihydrosphingosine-1-phosphate phosphatase activity|sphingosine-1-phosphate phosphatase activity			central_nervous_system(1)	1				OV - Ovarian serous cystadenocarcinoma(108;0.0056)|all cancers(60;0.0141)|BRCA - Breast invasive adenocarcinoma(234;0.103)		AGGAACAAAAAATGTGATGGA	0.333													55	97	---	---	---	---	PASS
CASC5	57082	broad.mit.edu	37	15	40949238	40949238	+	Splice_Site	SNP	A	T	T			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:40949238A>T	uc010bbs.1	+	24	6724	c.6563_splice	c.e24-2	p.E2188_splice	CASC5_uc010bbt.1_Splice_Site_p.E2162_splice	NM_170589	NP_733468	Q8NG31	CASC5_HUMAN	cancer susceptibility candidate 5 isoform 1						acrosome assembly|attachment of spindle microtubules to kinetochore|cell division|CenH3-containing nucleosome assembly at centromere|mitotic prometaphase|spindle assembly checkpoint	acrosomal vesicle|condensed chromosome kinetochore|cytosol|nucleoplasm	protein binding			breast(3)|central_nervous_system(1)|skin(1)	5		all_cancers(109;2.03e-18)|all_epithelial(112;4.26e-15)|Lung NSC(122;1.12e-10)|all_lung(180;2.59e-09)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.0946)		GBM - Glioblastoma multiforme(113;4.99e-05)|BRCA - Breast invasive adenocarcinoma(123;0.0861)|COAD - Colon adenocarcinoma(120;0.211)		ttccttccccagaggatcaag	0.075													16	25	---	---	---	---	PASS
PYGO1	26108	broad.mit.edu	37	15	55841181	55841181	+	Missense_Mutation	SNP	C	T	T			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:55841181C>T	uc010bfl.1	-	2	118	c.62G>A	c.(61-63)GGA>GAA	p.G21E	PYGO1_uc002adf.1_Missense_Mutation_p.G21E	NM_015617	NP_056432	Q9Y3Y4	PYGO1_HUMAN	pygopus homolog 1	21					Wnt receptor signaling pathway	nucleus	zinc ion binding			ovary(1)|skin(1)	2				all cancers(107;0.0131)|GBM - Glioblastoma multiforme(80;0.18)		CCCATCCAGTCCACTATCACC	0.338													78	185	---	---	---	---	PASS
TLN2	83660	broad.mit.edu	37	15	63092888	63092888	+	Missense_Mutation	SNP	G	A	A			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:63092888G>A	uc002alb.3	+	47	6397	c.6397G>A	c.(6397-6399)GTA>ATA	p.V2133I	TLN2_uc002alc.3_Missense_Mutation_p.V526I	NM_015059	NP_055874	Q9Y4G6	TLN2_HUMAN	talin 2	2133					cell adhesion|cell-cell junction assembly|cytoskeletal anchoring at plasma membrane	actin cytoskeleton|cytoplasm|focal adhesion|ruffle|synapse	actin binding|insulin receptor binding|structural constituent of cytoskeleton			ovary(5)|upper_aerodigestive_tract(2)|lung(2)|breast(2)	11						CCTCAAGACTGTAAAGGCAGT	0.537													15	32	---	---	---	---	PASS
MAN2C1	4123	broad.mit.edu	37	15	75648339	75648339	+	Missense_Mutation	SNP	G	T	T			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:75648339G>T	uc002baf.2	-	26	3048	c.3031C>A	c.(3031-3033)CAC>AAC	p.H1011N	MIR631_hsa-mir-631|MI0003645_5'Flank|MAN2C1_uc002bag.2_Missense_Mutation_p.H988N|MAN2C1_uc002bah.2_Missense_Mutation_p.H1028N|MAN2C1_uc010bkk.2_Missense_Mutation_p.H912N	NM_006715	NP_006706	Q9NTJ4	MA2C1_HUMAN	mannosidase, alpha, class 2C, member 1	1011					mannose metabolic process		alpha-mannosidase activity|carbohydrate binding|protein binding|zinc ion binding				0						AGGGTCAAGTGGCCAGCAGGG	0.627													20	85	---	---	---	---	PASS
C15orf26	161502	broad.mit.edu	37	15	81436057	81436057	+	Missense_Mutation	SNP	C	T	T			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:81436057C>T	uc002bgb.2	+	5	559	c.532C>T	c.(532-534)CTC>TTC	p.L178F	C15orf26_uc010blp.1_Missense_Mutation_p.L153F	NM_173528	NP_775799	Q6P656	CO026_HUMAN	hypothetical protein LOC161502	178											0						GAGGTCTTGGCTCCAGGAAGT	0.507													4	169	---	---	---	---	PASS
RHBDF1	64285	broad.mit.edu	37	16	109255	109255	+	Silent	SNP	C	T	T			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:109255C>T	uc002cfl.3	-	19	2134	c.1986G>A	c.(1984-1986)CTG>CTA	p.L662L		NM_022450	NP_071895	Q96CC6	RHDF1_HUMAN	rhomboid family 1	662	Helical; (Potential).				cell migration|cell proliferation|negative regulation of protein secretion|protein transport|proteolysis|regulation of epidermal growth factor receptor signaling pathway|regulation of proteasomal protein catabolic process	endoplasmic reticulum membrane|Golgi membrane|integral to membrane	growth factor binding|serine-type endopeptidase activity			ovary(1)|pancreas(1)	2		all_cancers(16;2.56e-05)|all_epithelial(16;0.000116)|Hepatocellular(780;0.0068)|Lung NSC(18;0.0795)|all_lung(18;0.159)				GCCCGGCGTGCAGGAAGAGGG	0.627													5	29	---	---	---	---	PASS
CLCN7	1186	broad.mit.edu	37	16	1515299	1515299	+	Missense_Mutation	SNP	C	T	T			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:1515299C>T	uc002clv.2	-	2	292	c.182G>A	c.(181-183)AGC>AAC	p.S61N	CLCN7_uc002clw.2_Intron	NM_001287	NP_001278	P51798	CLCN7_HUMAN	chloride channel 7 isoform a	61	Cytoplasmic (By similarity).					integral to membrane|lysosomal membrane	antiporter activity|ATP binding|voltage-gated chloride channel activity			central_nervous_system(2)|ovary(1)|skin(1)	4		Hepatocellular(780;0.0893)				CAGCTCCACGCTGCTCATATG	0.572													18	63	---	---	---	---	PASS
RAB26	25837	broad.mit.edu	37	16	2200042	2200042	+	Missense_Mutation	SNP	T	A	A			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:2200042T>A	uc002cou.2	+	2	430	c.296T>A	c.(295-297)ATT>AAT	p.I99N	RAB26_uc010bsf.2_Missense_Mutation_p.I33N	NM_014353	NP_055168	Q9ULW5	RAB26_HUMAN	RAB26, member RAS oncogene family	99	Effector region (By similarity).				exocrine system development|protein transport|regulation of exocytosis|small GTPase mediated signal transduction	intrinsic to plasma membrane	GTP binding|protein binding				0						ACCGTAGGCATTGACTTCCGG	0.617													32	87	---	---	---	---	PASS
UBN1	29855	broad.mit.edu	37	16	4925034	4925034	+	Missense_Mutation	SNP	A	G	G			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:4925034A>G	uc002cyb.2	+	15	2962	c.2623A>G	c.(2623-2625)ACC>GCC	p.T875A	UBN1_uc010uxw.1_Missense_Mutation_p.T875A|UBN1_uc002cyc.2_Missense_Mutation_p.T875A	NM_001079514	NP_001072982	Q9NPG3	UBN1_HUMAN	ubinuclein 1	875	Ser-rich.				chromatin modification|interspecies interaction between organisms|regulation of transcription from RNA polymerase II promoter	PML body|tight junction	DNA binding|sequence-specific DNA binding transcription factor activity			skin(2)	2						CTCTCACAAGACCCCAGCCTC	0.572													4	27	---	---	---	---	PASS
ZC3H7A	29066	broad.mit.edu	37	16	11870658	11870658	+	Silent	SNP	T	C	C			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:11870658T>C	uc002dbk.2	-	4	612	c.414A>G	c.(412-414)AGA>AGG	p.R138R	ZC3H7A_uc002dbl.2_Silent_p.R138R|ZC3H7A_uc002dbm.1_Silent_p.R138R	NM_014153	NP_054872	Q8IWR0	Z3H7A_HUMAN	zinc finger CCCH-type containing 7A	138	TPR 3.					nucleus	nucleic acid binding|zinc ion binding			ovary(2)|pancreas(1)|skin(1)	4						CCTTTTTGTATCTTCCTAAAT	0.363													6	149	---	---	---	---	PASS
MKL2	57496	broad.mit.edu	37	16	14342734	14342734	+	Intron	SNP	A	T	T			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:14342734A>T	uc010uza.1	+						MKL2_uc002dcg.2_Intron|MKL2_uc002dcj.2_5'UTR	NM_014048	NP_054767	Q9ULH7	MKL2_HUMAN	megakaryoblastic leukemia 2 protein						cell differentiation|muscle organ development|positive regulation of striated muscle tissue development|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent		identical protein binding|nucleic acid binding|transcription coactivator activity			ovary(3)|kidney(1)|pancreas(1)	5						CTGATTTCTAACTTTGATTCT	0.388													18	36	---	---	---	---	PASS
MYH11	4629	broad.mit.edu	37	16	15826565	15826565	+	Missense_Mutation	SNP	C	G	G			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:15826565C>G	uc002ddy.2	-	27	3614	c.3507G>C	c.(3505-3507)AGG>AGC	p.R1169S	MYH11_uc002ddv.2_Missense_Mutation_p.R1176S|MYH11_uc002ddw.2_Missense_Mutation_p.R1169S|MYH11_uc002ddx.2_Missense_Mutation_p.R1176S|MYH11_uc010bvg.2_Missense_Mutation_p.R1001S	NM_002474	NP_002465	P35749	MYH11_HUMAN	smooth muscle myosin heavy chain 11 isoform	1169	Potential.				axon guidance|cardiac muscle fiber development|elastic fiber assembly|skeletal muscle myosin thick filament assembly|smooth muscle contraction	cytosol|melanosome|muscle myosin complex|myosin filament	actin binding|ATP binding|calmodulin binding|motor activity|structural constituent of muscle			ovary(6)|skin(3)|lung(2)|breast(2)|upper_aerodigestive_tract(1)|pancreas(1)	15						CCCTCTTGGCCCTTGGTGGGA	0.453			T	CBFB	AML								11	82	---	---	---	---	PASS
XYLT1	64131	broad.mit.edu	37	16	17202837	17202837	+	Silent	SNP	A	G	G			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:17202837A>G	uc002dfa.2	-	12	2680	c.2595T>C	c.(2593-2595)AAT>AAC	p.N865N		NM_022166	NP_071449	Q86Y38	XYLT1_HUMAN	xylosyltransferase I	865	Lumenal (Potential).				glycosaminoglycan biosynthetic process	endoplasmic reticulum membrane|extracellular region|Golgi membrane|integral to membrane	acetylglucosaminyltransferase activity|protein xylosyltransferase activity			ovary(4)	4						CCATGTAGGCATTGCGGAGGG	0.567													26	72	---	---	---	---	PASS
TMC5	79838	broad.mit.edu	37	16	19460864	19460864	+	Missense_Mutation	SNP	T	G	G			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:19460864T>G	uc002dgc.3	+	5	1708	c.959T>G	c.(958-960)GTG>GGG	p.V320G	TMC5_uc010vaq.1_Missense_Mutation_p.V320G|TMC5_uc002dgb.3_Missense_Mutation_p.V320G|TMC5_uc010var.1_Missense_Mutation_p.V320G	NM_001105248	NP_001098718	Q6UXY8	TMC5_HUMAN	transmembrane channel-like 5 isoform a	320	Extracellular (Potential).					integral to membrane				skin(1)	1						TTCCCTCCAGTGAACCCTGCT	0.453													62	163	---	---	---	---	PASS
KIAA0174	9798	broad.mit.edu	37	16	71951006	71951006	+	Missense_Mutation	SNP	G	A	A			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:71951006G>A	uc002fbj.1	+	6	648	c.365G>A	c.(364-366)CGA>CAA	p.R122Q	KIAA0174_uc010cgh.1_Missense_Mutation_p.R122Q|KIAA0174_uc002fbk.1_Missense_Mutation_p.R109Q|KIAA0174_uc002fbm.1_Missense_Mutation_p.R109Q|KIAA0174_uc002fbl.1_Missense_Mutation_p.R109Q|KIAA0174_uc002fbn.1_Intron|KIAA0174_uc010cgi.1_Intron|KIAA0174_uc010cgj.1_Missense_Mutation_p.R41Q|KIAA0174_uc010vmk.1_Intron			P53990	IST1_HUMAN	SubName: Full=cDNA FLJ32696 fis, clone TESTI2000358; SubName: Full=cDNA FLJ77725;	109	Interaction with VPS37B.|Interaction with CHMP1A and CHMP1B.				cell cycle|cell division	cytoplasmic membrane-bounded vesicle|ER-Golgi intermediate compartment	protein binding			ovary(1)	1						GCTGCTCCTCGACTCCAGTCA	0.363													55	252	---	---	---	---	PASS
CNTNAP4	85445	broad.mit.edu	37	16	76501348	76501348	+	Missense_Mutation	SNP	T	A	A			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:76501348T>A	uc002feu.1	+	12	1968	c.1583T>A	c.(1582-1584)CTG>CAG	p.L528Q	CNTNAP4_uc002fev.1_Missense_Mutation_p.L392Q|CNTNAP4_uc010chb.1_Missense_Mutation_p.L455Q|CNTNAP4_uc002fex.1_Missense_Mutation_p.L531Q|CNTNAP4_uc002few.2_Missense_Mutation_p.L503Q	NM_033401	NP_207837	Q9C0A0	CNTP4_HUMAN	cell recognition protein CASPR4 isoform 1	528	Extracellular (Potential).|Laminin G-like 2.				cell adhesion|signal transduction	integral to membrane	receptor binding			ovary(1)|pancreas(1)	2						GTGGTAGATCTGATTTCAGTT	0.458													65	328	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	17	16735046	16735046	+	Missense_Mutation	SNP	G	A	A			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:16735046G>A	uc010vwr.1	-	2	666	c.224C>T	c.(223-225)GCC>GTC	p.A75V						SubName: Full=cDNA FLJ53570, highly similar to Keratin, type I cytoskeletal 16;																		TGCCAGCCTGGCATTGTCAAT	0.582													15	26	---	---	---	---	PASS
CDK12	51755	broad.mit.edu	37	17	37646824	37646824	+	Missense_Mutation	SNP	T	G	G			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:37646824T>G	uc010cvv.2	+	3	2532	c.1946T>G	c.(1945-1947)CTT>CGT	p.L649R	CDK12_uc010wef.1_Missense_Mutation_p.L648R|CDK12_uc002hrw.3_Missense_Mutation_p.L649R	NM_016507	NP_057591	Q9NYV4	CDK12_HUMAN	Cdc2-related kinase, arginine/serine-rich	649					mRNA processing|phosphorylation of RNA polymerase II C-terminal domain|protein autophosphorylation|regulation of MAP kinase activity|RNA splicing	nuclear cyclin-dependent protein kinase holoenzyme complex|nuclear speck|nucleolus	ATP binding|cyclin-dependent protein kinase activity|protein binding|RNA polymerase II carboxy-terminal domain kinase activity			ovary(10)|lung(4)|breast(2)|skin(2)|large_intestine(1)	19						AAAGAAACTCTTCCTTCAAAA	0.398										TCGA Ovarian(9;0.13)			16	91	---	---	---	---	PASS
CD300LG	146894	broad.mit.edu	37	17	41931340	41931340	+	Missense_Mutation	SNP	C	G	G			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:41931340C>G	uc002iem.2	+	4	688	c.647C>G	c.(646-648)CCC>CGC	p.P216R	CD300LG_uc002iel.1_Missense_Mutation_p.P131R|CD300LG_uc010czk.2_Missense_Mutation_p.P216R|CD300LG_uc010wil.1_Missense_Mutation_p.P182R|CD300LG_uc010czl.2_Missense_Mutation_p.P131R	NM_145273	NP_660316	Q6UXG3	CLM9_HUMAN	CD300 molecule-like family member g precursor	216	Extracellular (Potential).					apical plasma membrane|basolateral plasma membrane|integral to membrane|multivesicular body membrane	receptor activity				0		Breast(137;0.0199)		BRCA - Breast invasive adenocarcinoma(366;0.115)		AGCTCCCGCCCCCCCATGCAG	0.622													5	18	---	---	---	---	PASS
ARL17A	51326	broad.mit.edu	37	17	44630855	44630855	+	3'UTR	SNP	G	C	C	rs144516284	by1000genomes	TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:44630855G>C	uc002iks.2	-	4					LRRC37A2_uc002ikn.1_Intron|ARL17A_uc002iko.3_Intron|LRRC37A2_uc002ikq.1_Intron	NM_001113738	NP_001107210	Q8IVW1	ARL17_HUMAN	hypothetical protein LOC51326 isoform a						protein transport|vesicle-mediated transport	Golgi apparatus	GTP binding				0						cttctcttttgagacggagtt	0.139													11	241	---	---	---	---	PASS
HLF	3131	broad.mit.edu	37	17	53345220	53345220	+	Missense_Mutation	SNP	C	T	T			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:53345220C>T	uc002iug.1	+	2	749	c.224C>T	c.(223-225)CCC>CTC	p.P75L	HLF_uc010dce.1_5'UTR|HLF_uc002iuh.2_5'UTR|HLF_uc010wni.1_Missense_Mutation_p.P24S	NM_002126	NP_002117	Q16534	HLF_HUMAN	hepatic leukemia factor	75					multicellular organismal development|rhythmic process|transcription from RNA polymerase II promoter	nucleus	double-stranded DNA binding|protein dimerization activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			ovary(2)	2						AAAACCCTTCCCTATGACGGA	0.507			T	TCF3	ALL								18	31	---	---	---	---	PASS
MPO	4353	broad.mit.edu	37	17	56349016	56349016	+	Missense_Mutation	SNP	C	T	T			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:56349016C>T	uc002ivu.1	-	11	2207	c.2030G>A	c.(2029-2031)CGG>CAG	p.R677Q		NM_000250	NP_000241	P05164	PERM_HUMAN	myeloperoxidase	677					anti-apoptosis|hydrogen peroxide catabolic process|low-density lipoprotein particle remodeling	extracellular space|lysosome|nucleus|stored secretory granule	chromatin binding|heme binding|heparin binding|peroxidase activity			ovary(2)|large_intestine(1)|pancreas(1)	4					Cefdinir(DB00535)	CCCTCCTCACCGATCACCATC	0.642													3	12	---	---	---	---	PASS
MARCH10	162333	broad.mit.edu	37	17	60814440	60814440	+	Silent	SNP	C	A	A			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:60814440C>A	uc010ddr.2	-	6	1027	c.789G>T	c.(787-789)GGG>GGT	p.G263G	MARCH10_uc002jag.3_Silent_p.G263G|MARCH10_uc010dds.2_Silent_p.G301G|MARCH10_uc002jah.2_Silent_p.G262G|uc002jaj.1_RNA|uc002jak.2_RNA	NM_001100875	NP_001094345	Q8NA82	MARHA_HUMAN	ring finger protein 190	263							ligase activity|zinc ion binding				0						CCTTTCTTGGCCCTCCTACAG	0.483													19	69	---	---	---	---	PASS
MARCH10	162333	broad.mit.edu	37	17	60814441	60814441	+	Missense_Mutation	SNP	C	G	G			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:60814441C>G	uc010ddr.2	-	6	1026	c.788G>C	c.(787-789)GGG>GCG	p.G263A	MARCH10_uc002jag.3_Missense_Mutation_p.G263A|MARCH10_uc010dds.2_Missense_Mutation_p.G301A|MARCH10_uc002jah.2_Missense_Mutation_p.G262A|uc002jaj.1_RNA|uc002jak.2_RNA	NM_001100875	NP_001094345	Q8NA82	MARHA_HUMAN	ring finger protein 190	263							ligase activity|zinc ion binding				0						CTTTCTTGGCCCTCCTACAGT	0.488													20	72	---	---	---	---	PASS
SDK2	54549	broad.mit.edu	37	17	71420174	71420174	+	Silent	SNP	G	A	A			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:71420174G>A	uc010dfm.2	-	13	1641	c.1641C>T	c.(1639-1641)CGC>CGT	p.R547R	SDK2_uc010dfn.2_Silent_p.R226R	NM_001144952	NP_001138424	Q58EX2	SDK2_HUMAN	sidekick 2	547	Extracellular (Potential).|Ig-like C2-type 6.				cell adhesion	integral to membrane				ovary(2)	2						TTCTGTCCAGGCGGATACGAG	0.587													7	11	---	---	---	---	PASS
RNF213	57674	broad.mit.edu	37	17	78321744	78321744	+	Silent	SNP	A	G	G			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:78321744A>G	uc002jyh.1	+	4	4051	c.3828A>G	c.(3826-3828)GCA>GCG	p.A1276A		NM_020914	NP_065965	Q9HCF4	ALO17_HUMAN	ring finger protein 213	Error:Variant_position_missing_in_Q9HCF4_after_alignment										ovary(8)|lung(6)|breast(3)|large_intestine(2)|central_nervous_system(1)|pancreas(1)	21	all_neural(118;0.0538)		BRCA - Breast invasive adenocarcinoma(99;0.0252)|OV - Ovarian serous cystadenocarcinoma(97;0.057)			ATGTCAAAGCACATCATTTCC	0.532													18	132	---	---	---	---	PASS
KIAA1012	22878	broad.mit.edu	37	18	29410858	29410858	+	Silent	SNP	G	A	A			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:29410858G>A	uc002kxc.3	-	29	4532	c.4168C>T	c.(4168-4170)CTG>TTG	p.L1390L	KIAA1012_uc002kxb.3_Silent_p.L1336L|KIAA1012_uc002kxd.3_RNA	NM_014939	NP_055754	Q9Y2L5	TPPC8_HUMAN	hypothetical protein LOC22878	1390					ER to Golgi vesicle-mediated transport	cis-Golgi network					0						CATGCTTTCAGCTGCAGACTG	0.418													44	157	---	---	---	---	PASS
CDH7	1005	broad.mit.edu	37	18	63530103	63530103	+	Missense_Mutation	SNP	T	A	A			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:63530103T>A	uc002ljz.2	+	11	2139	c.1814T>A	c.(1813-1815)CTC>CAC	p.L605H	CDH7_uc002lka.2_Missense_Mutation_p.L605H|CDH7_uc002lkb.2_Missense_Mutation_p.L605H	NM_033646	NP_387450	Q9ULB5	CADH7_HUMAN	cadherin 7, type 2 preproprotein	605	Extracellular (Potential).				adherens junction organization|cell junction assembly|homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(2)|pancreas(1)|skin(1)	4		Esophageal squamous(42;0.129)				CCTGCTGGCCTCAGTACAGGA	0.542													10	47	---	---	---	---	PASS
ZNF536	9745	broad.mit.edu	37	19	30936491	30936491	+	Silent	SNP	G	A	A			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:30936491G>A	uc002nsu.1	+	2	2160	c.2022G>A	c.(2020-2022)TCG>TCA	p.S674S	ZNF536_uc010edd.1_Silent_p.S674S	NM_014717	NP_055532	O15090	ZN536_HUMAN	zinc finger protein 536	674					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	zinc ion binding			ovary(7)|large_intestine(2)|skin(2)	11	Esophageal squamous(110;0.0834)					GGCGTGGCTCGGGCAGTGACC	0.697													3	10	---	---	---	---	PASS
GAPDHS	26330	broad.mit.edu	37	19	36036175	36036175	+	3'UTR	SNP	C	T	T			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:36036175C>T	uc002oaf.1	+	11					uc010eec.1_5'Flank|uc002oag.2_Intron|TMEM147_uc002oai.1_5'Flank|TMEM147_uc002oaj.1_5'Flank|TMEM147_uc002oak.1_5'Flank	NM_014364	NP_055179	O14556	G3PT_HUMAN	glyceraldehyde-3-phosphate dehydrogenase,						gluconeogenesis|glycolysis|positive regulation of glycolysis|sperm motility	cytosol	glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity|NAD binding|protein binding				0	all_lung(56;1.05e-07)|Lung NSC(56;1.63e-07)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0724)		NADH(DB00157)	CCGGGGCGGGCGCCCCACGCC	0.657													4	8	---	---	---	---	PASS
U2AF1L4	199746	broad.mit.edu	37	19	36236275	36236275	+	5'UTR	SNP	A	G	G			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:36236275A>G	uc002obg.2	-	1					TMEM149_uc002obc.2_5'Flank|TMEM149_uc002obd.3_5'Flank|TMEM149_uc010xsy.1_5'Flank|TMEM149_uc010eej.2_5'UTR|U2AF1L4_uc002obh.1_5'Flank|U2AF1L4_uc002obe.2_Silent_p.A6A|U2AF1L4_uc002obf.2_Silent_p.A6A|PSENEN_uc002obi.1_5'Flank|PSENEN_uc002obj.1_5'Flank|PSENEN_uc002obk.1_5'Flank			Q8WU68	U2AF4_HUMAN	Homo sapiens cDNA FLJ35525 fis, clone SPLEN2001650.						mRNA processing|RNA splicing	nuclear speck|spliceosomal complex	nucleotide binding|RNA binding|zinc ion binding				0	all_lung(56;3.33e-07)|Lung NSC(56;5.02e-07)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0515)			CGAATATCGAAGCTAAATATT	0.587													5	172	---	---	---	---	PASS
CCDC97	90324	broad.mit.edu	37	19	41826334	41826334	+	Silent	SNP	C	T	T			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:41826334C>T	uc002oqg.2	+	4	992	c.870C>T	c.(868-870)CAC>CAT	p.H290H	CYP2F1_uc010xvw.1_Intron	NM_052848	NP_443080	Q96F63	CCD97_HUMAN	coiled-coil domain containing 97	290											0						GCCGCATGCACCAGCGCTTCC	0.637													3	34	---	---	---	---	PASS
PSG8	440533	broad.mit.edu	37	19	43262176	43262176	+	Missense_Mutation	SNP	G	T	T			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:43262176G>T	uc002ouo.2	-	3	785	c.687C>A	c.(685-687)GAC>GAA	p.D229E	PSG3_uc002ouf.2_Intron|PSG1_uc002oug.1_Intron|PSG8_uc010eim.2_RNA|PSG8_uc002oui.2_Missense_Mutation_p.D68E|PSG8_uc002ouh.2_Missense_Mutation_p.D229E|PSG8_uc010ein.2_Missense_Mutation_p.D107E|PSG8_uc002ouj.3_Intron|PSG8_uc002ouk.3_Missense_Mutation_p.D68E|PSG8_uc002oul.3_Missense_Mutation_p.D229E|PSG8_uc002oum.3_Intron|PSG1_uc002oun.2_Intron|PSG8_uc002oup.3_Intron	NM_182707	NP_874366	Q9UQ74	PSG8_HUMAN	pregnancy specific beta-1-glycoprotein 8 isoform	229	Ig-like C2-type 1.					extracellular region					0		Prostate(69;0.00899)				GGGTGAATGGGTCACTGCGGC	0.527													6	34	---	---	---	---	PASS
PVRL2	5819	broad.mit.edu	37	19	45391608	45391608	+	Missense_Mutation	SNP	T	C	C			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:45391608T>C	uc002ozw.1	+	9	1979	c.1589T>C	c.(1588-1590)TTT>TCT	p.F530S	TOMM40_uc002ozx.3_5'Flank|TOMM40_uc002ozy.3_5'Flank|TOMM40_uc002paa.3_5'Flank|TOMM40_uc002ozz.2_5'Flank	NM_001042724	NP_001036189	Q92692	PVRL2_HUMAN	poliovirus receptor related 2 isoform delta	530	Cytoplasmic (Potential).				adherens junction organization|adhesion to symbiont|cell junction assembly|homophilic cell adhesion|positive regulation of immunoglobulin mediated immune response|positive regulation of mast cell activation|positive regulation of natural killer cell mediated cytotoxicity directed against tumor cell target|susceptibility to natural killer cell mediated cytotoxicity|susceptibility to T cell mediated cytotoxicity|viral envelope fusion with host membrane|virion attachment, binding of host cell surface coreceptor	cell surface|integral to membrane|zonula adherens	cell adhesion molecule binding|coreceptor activity|protein homodimerization activity				0	Lung NSC(12;0.00195)|all_lung(12;0.00522)	Ovarian(192;0.0728)|all_neural(266;0.112)		OV - Ovarian serous cystadenocarcinoma(262;0.0143)		GGCAAAGGCTTTGTCATGTCC	0.468													35	65	---	---	---	---	PASS
RELB	5971	broad.mit.edu	37	19	45525450	45525450	+	Missense_Mutation	SNP	A	G	G			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:45525450A>G	uc002paj.1	+	6	770	c.644A>G	c.(643-645)CAC>CGC	p.H215R		NM_006509	NP_006500	Q01201	RELB_HUMAN	reticuloendotheliosis viral oncogene homolog B	215	RHD.					nucleus	protein binding|sequence-specific DNA binding transcription factor activity|transcription corepressor activity			ovary(1)	1		Ovarian(192;0.0728)|all_neural(266;0.112)		OV - Ovarian serous cystadenocarcinoma(262;0.00986)		CTCCGGCCTCACGTCAGCCCC	0.632													4	3	---	---	---	---	PASS
SYMPK	8189	broad.mit.edu	37	19	46319803	46319803	+	Silent	SNP	G	T	T			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:46319803G>T	uc002pdn.2	-	25	3536	c.3291C>A	c.(3289-3291)ATC>ATA	p.I1097I	RSPH6A_uc002pdm.2_5'Flank	NM_004819	NP_004810	Q92797	SYMPK_HUMAN	symplekin	1097					cell adhesion|mRNA processing	cytoplasm|cytoskeleton|nucleoplasm|tight junction	protein binding			ovary(1)	1		all_neural(266;0.0299)|Ovarian(192;0.0308)		OV - Ovarian serous cystadenocarcinoma(262;0.00509)|GBM - Glioblastoma multiforme(486;0.0593)		TGGCCTCCAAGATGGTCATGA	0.652													20	24	---	---	---	---	PASS
ZNF600	162966	broad.mit.edu	37	19	53269213	53269213	+	Missense_Mutation	SNP	C	G	G			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:53269213C>G	uc002qab.3	-	3	2082	c.1796G>C	c.(1795-1797)AGA>ACA	p.R599T		NM_198457	NP_940859	Q6ZNG1	ZN600_HUMAN	zinc finger protein 600	599	C2H2-type 16.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0				OV - Ovarian serous cystadenocarcinoma(262;0.0241)|GBM - Glioblastoma multiforme(134;0.0404)		TCTGGTATGTCTTGCCAGGTA	0.393													20	120	---	---	---	---	PASS
ZNF600	162966	broad.mit.edu	37	19	53269727	53269727	+	Missense_Mutation	SNP	C	A	A			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:53269727C>A	uc002qab.3	-	3	1568	c.1282G>T	c.(1282-1284)GAT>TAT	p.D428Y		NM_198457	NP_940859	Q6ZNG1	ZN600_HUMAN	zinc finger protein 600	428	C2H2-type 10.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0				OV - Ovarian serous cystadenocarcinoma(262;0.0241)|GBM - Glioblastoma multiforme(134;0.0404)		ATTAGAAGATCTGAATTTTGA	0.363													26	125	---	---	---	---	PASS
ZNF600	162966	broad.mit.edu	37	19	53269746	53269746	+	Missense_Mutation	SNP	C	A	A			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:53269746C>A	uc002qab.3	-	3	1549	c.1263G>T	c.(1261-1263)AAG>AAT	p.K421N		NM_198457	NP_940859	Q6ZNG1	ZN600_HUMAN	zinc finger protein 600	421	C2H2-type 10.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0				OV - Ovarian serous cystadenocarcinoma(262;0.0241)|GBM - Glioblastoma multiforme(134;0.0404)		GACCAAAGGTCTTCCCACATT	0.373													25	128	---	---	---	---	PASS
UBOX5	22888	broad.mit.edu	37	20	3103217	3103217	+	Missense_Mutation	SNP	C	T	T			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:3103217C>T	uc002whw.2	-	3	238	c.68G>A	c.(67-69)GGT>GAT	p.G23D	uc002whv.1_Intron|UBOX5_uc002whx.2_Missense_Mutation_p.G23D|UBOX5_uc002why.1_Missense_Mutation_p.G23D	NM_014948	NP_055763	O94941	RNF37_HUMAN	U-box domain containing 5 isoform a	23						nucleus|ubiquitin ligase complex	ubiquitin-protein ligase activity|zinc ion binding			ovary(1)|skin(1)	2						TACTTCGTAACCATCAGCTGA	0.363													29	122	---	---	---	---	PASS
ABHD12	26090	broad.mit.edu	37	20	25282909	25282909	+	Missense_Mutation	SNP	A	C	C			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:25282909A>C	uc002wus.1	-	12	1241	c.1103T>G	c.(1102-1104)CTT>CGT	p.L368R	ABHD12_uc002wuq.2_Missense_Mutation_p.L368R|ABHD12_uc002wur.2_Missense_Mutation_p.L367R|ABHD12_uc002wut.1_Missense_Mutation_p.L367R|ABHD12_uc002wuu.1_Missense_Mutation_p.L148R	NM_001042472	NP_001035937	Q8N2K0	ABD12_HUMAN	abhydrolase domain containing 12 isoform a	368	Extracellular (Potential).					integral to membrane	acylglycerol lipase activity			skin(1)	1						CCTGTAGCCAAGGTCTGAATG	0.542													78	111	---	---	---	---	PASS
PHF20	51230	broad.mit.edu	37	20	34459730	34459730	+	Missense_Mutation	SNP	C	A	A			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:34459730C>A	uc002xek.1	+	9	1372	c.1261C>A	c.(1261-1263)CAA>AAA	p.Q421K	PHF20_uc002xei.1_Missense_Mutation_p.Q421K|PHF20_uc010gfo.1_Missense_Mutation_p.Q421K|PHF20_uc002xej.1_Missense_Mutation_p.Q305K	NM_016436	NP_057520	Q9BVI0	PHF20_HUMAN	PHD finger protein 20	421					regulation of transcription, DNA-dependent|transcription, DNA-dependent	MLL1 complex	DNA binding|zinc ion binding			ovary(1)	1	Breast(12;0.00631)|all_lung(11;0.0145)					TGTGGAATTACAAGAGATTTC	0.388													23	236	---	---	---	---	PASS
LIPI	149998	broad.mit.edu	37	21	15579141	15579141	+	Missense_Mutation	SNP	C	T	T			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:15579141C>T	uc002yjm.2	-	1	114	c.104G>A	c.(103-105)AGA>AAA	p.R35K		NM_198996	NP_945347	Q6XZB0	LIPI_HUMAN	lipase, member I	14					lipid catabolic process	extracellular region|extracellular space|membrane|plasma membrane	heparin binding|phospholipase activity			ovary(2)	2				Epithelial(23;0.000155)|COAD - Colon adenocarcinoma(22;0.0015)|Colorectal(24;0.00693)|Lung(58;0.166)		attacctgatctcaggcacac	0.239													35	247	---	---	---	---	PASS
RWDD2B	10069	broad.mit.edu	37	21	30380357	30380357	+	Silent	SNP	A	G	G			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:30380357A>G	uc002yms.2	-	4	537	c.450T>C	c.(448-450)TGT>TGC	p.C150C	RWDD2B_uc002ymt.2_Silent_p.C121C|RWDD2B_uc002ymu.2_RNA|RWDD2B_uc002ymv.2_Silent_p.C70C	NM_016940	NP_058636	P57060	RWD2B_HUMAN	RWD domain containing 2B	150	RWD.										0						CATTCAGTATACAAACATCTC	0.443													87	72	---	---	---	---	PASS
DSCAM	1826	broad.mit.edu	37	21	41741148	41741148	+	Missense_Mutation	SNP	G	A	A			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:41741148G>A	uc002yyq.1	-	4	985	c.533C>T	c.(532-534)ACG>ATG	p.T178M	DSCAM_uc002yyr.1_RNA	NM_001389	NP_001380	O60469	DSCAM_HUMAN	Down syndrome cell adhesion molecule isoform	178	Ig-like C2-type 2.|Extracellular (Potential).				cell adhesion|dendrite self-avoidance|negative regulation of cell adhesion|positive regulation of axon extension involved in axon guidance|positive regulation of phosphorylation	axon|extracellular region|growth cone|integral to plasma membrane|membrane fraction	protein binding			ovary(6)|skin(4)|upper_aerodigestive_tract(1)	11		all_cancers(19;0.186)|Prostate(19;1.15e-05)|all_epithelial(19;0.0103)				CAAGGCTCCCGTGGATGTGAT	0.438													114	138	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	22	18844766	18844766	+	RNA	SNP	G	A	A			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:18844766G>A	uc002zoe.2	+	4		c.2020G>A			uc002zof.2_5'Flank					Homo sapiens cDNA FLJ76361 complete cds.																		CAGCCTCTGAGGGCAGCAGTG	0.557													9	20	---	---	---	---	PASS
PPIL2	23759	broad.mit.edu	37	22	22024876	22024876	+	Missense_Mutation	SNP	G	A	A			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:22024876G>A	uc010gtj.1	+	3	220	c.104G>A	c.(103-105)CGT>CAT	p.R35H	PPIL2_uc002zvh.3_Missense_Mutation_p.R35H|PPIL2_uc002zvi.3_Missense_Mutation_p.R35H|PPIL2_uc002zvg.3_Missense_Mutation_p.R35H|PPIL2_uc011aij.1_Missense_Mutation_p.R35H	NM_148175	NP_680480	Q13356	PPIL2_HUMAN	peptidylprolyl isomerase-like 2 isoform a	35					blood coagulation|leukocyte migration|protein folding|protein polyubiquitination	Golgi lumen|nucleus|ubiquitin ligase complex	peptidyl-prolyl cis-trans isomerase activity|ubiquitin-ubiquitin ligase activity			ovary(2)	2	Colorectal(54;0.105)					ACAAATTTTCGTCGTTTACCT	0.373													147	234	---	---	---	---	PASS
PPM1F	9647	broad.mit.edu	37	22	22293778	22293778	+	Intron	SNP	T	C	C			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:22293778T>C	uc002zvp.1	-						PPM1F_uc011aik.1_5'Flank|PPM1F_uc002zvq.2_Intron|uc011ail.1_RNA	NM_014634	NP_055449	P49593	PPM1F_HUMAN	protein phosphatase 1F						apoptosis|protein dephosphorylation	protein serine/threonine phosphatase complex	metal ion binding|protein serine/threonine phosphatase activity			ovary(2)|large_intestine(1)|breast(1)|kidney(1)	5	Colorectal(54;0.105)			READ - Rectum adenocarcinoma(21;0.155)		TCCTTGATTCTGCTGCCGTTG	0.617													3	9	---	---	---	---	PASS
LOC96610	96610	broad.mit.edu	37	22	22975975	22975975	+	Intron	SNP	A	G	G			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:22975975A>G	uc011aim.1	+						POM121L1P_uc011ait.1_RNA					Parts of antibodies, mostly variable regions.												0						CTGCATTTCCATGCTCTTTCC	0.582													8	7	---	---	---	---	PASS
ENTHD1	150350	broad.mit.edu	37	22	40283658	40283658	+	Missense_Mutation	SNP	G	A	A			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:40283658G>A	uc003ayg.2	-	2	346	c.95C>T	c.(94-96)CCC>CTC	p.P32L		NM_152512	NP_689725	Q8IYW4	ENTD1_HUMAN	ENTH domain containing 1	32	ENTH.									ovary(2)|skin(1)	3	Melanoma(58;0.0749)					AGAACTAGAGGGACCCCAAGG	0.403													76	96	---	---	---	---	PASS
MXRA5	25878	broad.mit.edu	37	X	3235733	3235733	+	Missense_Mutation	SNP	G	A	A			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:3235733G>A	uc004crg.3	-	6	6146	c.5989C>T	c.(5989-5991)CCC>TCC	p.P1997S		NM_015419	NP_056234	Q9NR99	MXRA5_HUMAN	adlican precursor	1997	Ig-like C2-type 4.					extracellular region				ovary(5)|lung(1)|central_nervous_system(1)|skin(1)	8		all_lung(23;0.00031)|Lung NSC(23;0.000946)				CCCTCCACGGGGGACACAGTT	0.592													26	9	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	M	15048	15048	+	Silent	SNP	G	A	A			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrM:15048G>A	uc004coy.2	+	1	288	c.213G>A	c.(211-213)AGG>AGA	p.R71R	uc004coz.1_5'Flank					Homo sapiens clone 35w unknown mRNA; mitochondrial.																		CATCGGGCGAGGCCTATATTA	0.473													37	22	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	1	2438875	2438875	+	IGR	DEL	G	-	-			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:2438875delG								PLCH2 (1906 upstream) : PANK4 (1100 downstream)																							ATGGGGTTCCGGGGGCTGGGC	0.692													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	2620367	2620368	+	IGR	INS	-	T	T	rs143571734		TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:2620367_2620368insT								MMEL1 (55886 upstream) : ACTRT2 (317678 downstream)																							GAGCAGCACCCACATCCCCAGG	0.639													6	3	---	---	---	---	
CAMTA1	23261	broad.mit.edu	37	1	7613429	7613430	+	Intron	DEL	TG	-	-			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:7613429_7613430delTG	uc001aoi.2	+							NM_015215	NP_056030	Q9Y6Y1	CMTA1_HUMAN	calmodulin-binding transcription activator 1						regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	calmodulin binding			ovary(5)|central_nervous_system(2)|breast(1)|pancreas(1)	9	Ovarian(185;0.0634)	all_epithelial(116;8.38e-23)|all_lung(118;5.87e-07)|Lung NSC(185;3.43e-06)|Renal(390;0.000219)|Breast(487;0.000307)|Colorectal(325;0.000615)|Hepatocellular(190;0.0088)|Myeloproliferative disorder(586;0.0303)|Ovarian(437;0.0388)		UCEC - Uterine corpus endometrioid carcinoma (279;0.101)|Colorectal(212;1.33e-05)|COAD - Colon adenocarcinoma(227;0.000235)|BRCA - Breast invasive adenocarcinoma(304;0.000864)|Kidney(185;0.00244)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0179)|READ - Rectum adenocarcinoma(331;0.133)		TGCAGAAATCTGTGCTTTAGAG	0.208													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	9094253	9094254	+	IGR	INS	-	TA	TA	rs145309097	by1000genomes	TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:9094253_9094254insTA								SLC2A7 (7849 upstream) : SLC2A5 (2753 downstream)																							tgtccaaaaagtatatgacctt	0.144													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	28474471	28474472	+	IGR	DEL	CA	-	-			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:28474471_28474472delCA								LOC653566 (51402 upstream) : PTAFR (1392 downstream)																							AAGTCCAGCCCACAGCTACCAT	0.391													4	2	---	---	---	---	
RIMS3	9783	broad.mit.edu	37	1	41128088	41128089	+	Intron	INS	-	CTCC	CTCC	rs140023407	by1000genomes	TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:41128088_41128089insCTCC	uc001cfu.1	-						RIMS3_uc001cfv.1_Intron	NM_014747	NP_055562	Q9UJD0	RIMS3_HUMAN	regulating synaptic membrane exocytosis 3						neurotransmitter transport	cell junction|synapse					0	Ovarian(52;0.00769)|all_hematologic(146;0.0501)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;1.47e-17)			aggttccagagcccaagtccct	0.025													2	5	---	---	---	---	
MUTYH	4595	broad.mit.edu	37	1	45796197	45796197	+	Frame_Shift_Del	DEL	C	-	-			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:45796197delC	uc001cnm.2	-	15	1716	c.1500delG	c.(1498-1500)GGGfs	p.G500fs	MUTYH_uc009vxn.2_Frame_Shift_Del_p.G325fs|MUTYH_uc001cnf.2_Frame_Shift_Del_p.G475fs|MUTYH_uc009vxo.2_Frame_Shift_Del_p.G475fs|MUTYH_uc001cng.2_Frame_Shift_Del_p.G486fs|MUTYH_uc001cnj.2_Frame_Shift_Del_p.G383fs|MUTYH_uc001cni.2_Frame_Shift_Del_p.G475fs|MUTYH_uc001cnh.2_Frame_Shift_Del_p.G476fs|MUTYH_uc001cno.2_Frame_Shift_Del_p.G383fs|MUTYH_uc001cnk.2_Frame_Shift_Del_p.G360fs|MUTYH_uc010oll.1_Frame_Shift_Del_p.G184fs|MUTYH_uc001cnl.2_Frame_Shift_Del_p.G489fs|MUTYH_uc009vxp.2_Frame_Shift_Del_p.G503fs|MUTYH_uc001cnn.2_Frame_Shift_Del_p.G490fs	NM_012222	NP_036354	Q9UIF7	MUTYH_HUMAN	mutY homolog isoform 1	500					depurination|mismatch repair	nucleoplasm	4 iron, 4 sulfur cluster binding|DNA N-glycosylase activity|endonuclease activity|metal ion binding|MutSalpha complex binding				0	Acute lymphoblastic leukemia(166;0.155)					CCATACAGGTCCCTGGCTGTT	0.507			Mis			colorectal		BER_DNA_glycosylases	MUTYH-associated_polyposis				113	58	---	---	---	---	
FAF1	11124	broad.mit.edu	37	1	51295006	51295006	+	Intron	DEL	G	-	-			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:51295006delG	uc009vyx.1	-						FAF1_uc009vyw.1_Intron|FAF1_uc001cse.1_Intron	NM_007051	NP_008982	Q9UNN5	FAF1_HUMAN	FAS-associated factor 1						apoptosis|cytoplasmic sequestering of NF-kappaB|positive regulation of apoptosis|positive regulation of protein complex assembly|proteasomal ubiquitin-dependent protein catabolic process|regulation of protein catabolic process	CD95 death-inducing signaling complex|cytosol|perinuclear region of cytoplasm	heat shock protein binding|NF-kappaB binding|protein kinase binding|protein kinase regulator activity	p.0?(2)		ovary(1)|pancreas(1)	2				GBM - Glioblastoma multiforme(3;3.18e-11)|all cancers(3;0.00526)		TCTGTTGTGTGGTGGGGTAAA	0.403													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	51466517	51466517	+	IGR	DEL	T	-	-			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:51466517delT								CDKN2C (26210 upstream) : C1orf185 (101389 downstream)														p.0?(1)|p.?(1)									cagctgcacatttgttttgag	0.000													4	2	---	---	---	---	
C1orf185	284546	broad.mit.edu	37	1	51578489	51578489	+	Intron	DEL	T	-	-			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:51578489delT	uc001csh.2	+							NM_001136508	NP_001129980	Q5T7R7	CA185_HUMAN	hypothetical protein LOC284546							integral to membrane					0						Ctttcttttcttttttttttt	0.144													6	3	---	---	---	---	
DAB1	1600	broad.mit.edu	37	1	57724031	57724032	+	Intron	INS	-	T	T			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:57724031_57724032insT	uc001cys.1	-						DAB1_uc001cyt.1_Intron|DAB1_uc001cyq.1_Intron|DAB1_uc001cyr.1_Intron|DAB1_uc009vzw.1_Intron|DAB1_uc009vzx.1_Intron	NM_021080	NP_066566	O75553	DAB1_HUMAN	disabled homolog 1						cell differentiation|nervous system development					skin(2)|ovary(1)	3						GAGTGTGAGCATTTTTTTGCCT	0.267													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	81235088	81235088	+	IGR	DEL	G	-	-			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:81235088delG								None (None upstream) : LPHN2 (536757 downstream)																							TCTTGCTTTTGTGTGCTGCTG	0.448													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	81235090	81235090	+	IGR	DEL	G	-	-			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:81235090delG								None (None upstream) : LPHN2 (536755 downstream)																							TTGCTTTTGTGTGCTGCTGTT	0.443													4	2	---	---	---	---	
TBX15	6913	broad.mit.edu	37	1	119441498	119441498	+	Intron	DEL	T	-	-			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:119441498delT	uc001ehl.1	-						TBX15_uc009whj.1_Intron	NM_152380	NP_689593	Q96SF7	TBX15_HUMAN	T-box 15							nucleus	DNA binding|sequence-specific DNA binding transcription factor activity			large_intestine(1)|pancreas(1)	2	all_neural(166;0.117)	all_cancers(81;0.000692)|all_lung(203;3.05e-06)|Lung NSC(69;2.13e-05)|all_epithelial(167;0.000237)		Lung(183;0.044)|LUSC - Lung squamous cell carcinoma(189;0.141)		GTGGTGATGCTTTGGTTATTT	0.433													17	8	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	120428847	120428847	+	IGR	DEL	T	-	-			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:120428847delT								NBPF7 (41068 upstream) : ADAM30 (7310 downstream)																							GATCATGAGGTTTTCCCTCCT	0.488											OREG0013732	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	152958945	152958948	+	IGR	DEL	TCTC	-	-	rs67468856		TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:152958945_152958948delTCTC								SPRR1A (656 upstream) : SPRR3 (15275 downstream)																							ACATGCActttctctctctctctc	0.240													3	3	---	---	---	---	
IL6R	3570	broad.mit.edu	37	1	154387728	154387728	+	Intron	DEL	G	-	-			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:154387728delG	uc001fez.1	+						IL6R_uc001ffa.1_Intron	NM_000565	NP_000556	P08887	IL6RA_HUMAN	interleukin 6 receptor isoform 1 precursor						acute-phase response|ciliary neurotrophic factor-mediated signaling pathway|defense response to Gram-negative bacterium|defense response to Gram-positive bacterium|endocrine pancreas development|hepatic immune response|negative regulation of collagen biosynthetic process|negative regulation of interleukin-8 production|positive regulation of activation of Janus kinase activity|positive regulation of anti-apoptosis|positive regulation of chemokine production|positive regulation of chemokine production|positive regulation of interleukin-6 production|positive regulation of leukocyte chemotaxis|positive regulation of MAPKKK cascade|positive regulation of osteoblast differentiation|positive regulation of smooth muscle cell proliferation|positive regulation of tyrosine phosphorylation of Stat3 protein|regulation of apoptosis	apical plasma membrane|basolateral plasma membrane|extracellular space|interleukin-6 receptor complex	ciliary neurotrophic factor binding|enzyme binding|protein homodimerization activity			ovary(3)|breast(1)	4	all_lung(78;1.72e-29)|Lung NSC(65;2.96e-27)|Hepatocellular(266;0.0877)		LUSC - Lung squamous cell carcinoma(543;0.185)			ctccttttctggtattgttaa	0.234													4	2	---	---	---	---	
KCNN3	3782	broad.mit.edu	37	1	154698196	154698196	+	Intron	DEL	T	-	-			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:154698196delT	uc001ffp.2	-						KCNN3_uc001ffo.2_Intron	NM_002249	NP_002240	Q9UGI6	KCNN3_HUMAN	small conductance calcium-activated potassium							integral to membrane	calmodulin binding			lung(1)	1	all_lung(78;2.29e-27)|all_hematologic(923;0.088)|Hepatocellular(266;0.108)|all_neural(408;0.245)		BRCA - Breast invasive adenocarcinoma(34;0.00819)			attttctgtatttttagtaga	0.000													4	2	---	---	---	---	
ATF6	22926	broad.mit.edu	37	1	161884157	161884157	+	Intron	DEL	G	-	-			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:161884157delG	uc001gbr.2	+							NM_007348	NP_031374	P18850	ATF6A_HUMAN	activating transcription factor 6						positive regulation of transcription from RNA polymerase II promoter involved in unfolded protein response|protein folding	endoplasmic reticulum membrane|Golgi membrane|integral to membrane|nuclear envelope|nucleoplasm	protein dimerization activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription coactivator activity			ovary(2)|skin(1)	3	all_hematologic(112;0.156)		BRCA - Breast invasive adenocarcinoma(70;0.00953)			ttgcaaatctgtcacatcaca	0.000													4	2	---	---	---	---	
MAEL	84944	broad.mit.edu	37	1	166960900	166960900	+	Intron	DEL	T	-	-			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:166960900delT	uc001gdy.1	+						MAEL_uc001gdz.1_Intron|MAEL_uc009wvf.1_Intron	NM_032858	NP_116247	Q96JY0	MAEL_HUMAN	maelstrom homolog						cell differentiation|DNA methylation involved in gamete generation|gene silencing by RNA|multicellular organismal development|piRNA metabolic process|spermatogenesis	piP-body	DNA binding			skin(1)	1						AGGAGAGTGGTTTTTTTTTTA	0.264													5	3	---	---	---	---	
BAT2L2	23215	broad.mit.edu	37	1	171558958	171558958	+	Intron	DEL	T	-	-			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:171558958delT	uc010pmg.1	+						BAT2L2_uc010pmh.1_Intron|BAT2L2_uc010pmi.1_Intron|BAT2L2_uc010pmj.1_Intron	NM_015172	NP_055987	Q9Y520	PRC2C_HUMAN	HBxAg transactivated protein 2								protein C-terminus binding				0						tttctttttctttttttttGC	0.274													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	177589992	177589992	+	IGR	DEL	T	-	-			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:177589992delT								FAM5B (338435 upstream) : SEC16B (307497 downstream)																							gtcactgacattttttttccc	0.134													4	2	---	---	---	---	
SOX13	9580	broad.mit.edu	37	1	204059314	204059314	+	Intron	DEL	G	-	-			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:204059314delG	uc001ham.2	+						SOX13_uc001hal.2_Intron	NM_005686	NP_005677	Q9UN79	SOX13_HUMAN	SRY-box 13						anatomical structure morphogenesis	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			breast(1)|central_nervous_system(1)	2	all_cancers(21;0.0754)|Breast(84;0.116)|all_epithelial(62;0.189)		KIRC - Kidney renal clear cell carcinoma(13;0.0584)|Kidney(21;0.0934)|BRCA - Breast invasive adenocarcinoma(75;0.109)			AAGCTCTGGTGGGACTCTGGG	0.547													4	2	---	---	---	---	
PLEKHA6	22874	broad.mit.edu	37	1	204193972	204193975	+	Intron	DEL	AGTC	-	-			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:204193972_204193975delAGTC	uc001hau.2	-							NM_014935	NP_055750	Q9Y2H5	PKHA6_HUMAN	phosphoinositol 3-phosphate-binding protein-3											ovary(3)|pancreas(1)	4	all_cancers(21;0.0222)|Breast(84;0.179)		KIRC - Kidney renal clear cell carcinoma(13;0.0584)|BRCA - Breast invasive adenocarcinoma(75;0.0833)|Kidney(21;0.0934)|Epithelial(59;0.229)			cccaacgcttagtcatctagcagt	0.157													4	2	---	---	---	---	
USH2A	7399	broad.mit.edu	37	1	216073925	216073925	+	Intron	DEL	A	-	-			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:216073925delA	uc001hku.1	-							NM_206933	NP_996816	O75445	USH2A_HUMAN	usherin isoform B						maintenance of organ identity|photoreceptor cell maintenance|response to stimulus|sensory perception of sound	basement membrane|cytoplasm|integral to membrane|stereocilium membrane	collagen binding			ovary(20)|upper_aerodigestive_tract(2)|skin(2)|kidney(1)|central_nervous_system(1)	26				OV - Ovarian serous cystadenocarcinoma(81;0.0547)|all cancers(67;0.0875)		TACATAAATGAAAAATAGATA	0.289										HNSCC(13;0.011)			4	2	---	---	---	---	
MOSC1	64757	broad.mit.edu	37	1	220975452	220975452	+	Intron	DEL	C	-	-			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:220975452delC	uc001hms.2	+						MOSC1_uc001hmt.2_Intron	NM_022746	NP_073583	Q5VT66	MOSC1_HUMAN	MOCO sulphurase C-terminal domain containing 1								molybdenum ion binding|oxidoreductase activity|pyridoxal phosphate binding				0				GBM - Glioblastoma multiforme(131;0.0358)		TCCCTTACTTCCAAAAGTTCT	0.512													4	2	---	---	---	---	
LEFTY1	10637	broad.mit.edu	37	1	226111564	226111566	+	Intron	DEL	CCA	-	-			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:226111564_226111566delCCA	uc010pvj.1	-						PYCR2_uc001hpp.2_5'Flank|PYCR2_uc001hpq.2_Intron|PYCR2_uc001hpr.2_Intron|PYCR2_uc001hps.1_5'Flank			O75610	LFTY1_HUMAN	SubName: Full=cDNA FLJ54750, moderately similar to Pyrroline-5-carboxylate reductase 2 (EC 1.5.1.2);						cell growth|multicellular organismal development|transforming growth factor beta receptor signaling pathway	extracellular space	cytokine activity|growth factor activity|transforming growth factor beta receptor binding				0	Breast(184;0.197)					CCTAACAGTGCCAGTCTCCCTCT	0.576													11	6	---	---	---	---	
JMJD4	65094	broad.mit.edu	37	1	227922141	227922141	+	Intron	DEL	A	-	-	rs13373815	by1000genomes	TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:227922141delA	uc001hrb.2	-						SNAP47_uc001hqz.2_Intron|SNAP47_uc001hra.2_Intron|SNAP47_uc001hrd.2_5'Flank|SNAP47_uc001hre.2_5'Flank|SNAP47_uc001hrf.2_5'Flank|JMJD4_uc001hrc.2_Intron	NM_023007	NP_075383	Q9H9V9	JMJD4_HUMAN	jumonji domain containing 4 isoform 1												0		Prostate(94;0.0885)				GATCTCTCTCAAAAAAAAAGG	0.209													4	2	---	---	---	---	
URB2	9816	broad.mit.edu	37	1	229763687	229763687	+	Intron	DEL	T	-	-			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:229763687delT	uc001hts.1	+						URB2_uc009xfd.1_Intron|TAF5L_uc001htq.2_5'Flank|TAF5L_uc001htr.2_5'Flank	NM_014777	NP_055592	Q14146	URB2_HUMAN	URB2 ribosome biogenesis 2 homolog							nucleolus				central_nervous_system(2)|ovary(1)	3						CATTAATACATTTTTTTTTTC	0.164													6	3	---	---	---	---	
GALNT2	2590	broad.mit.edu	37	1	230258362	230258363	+	Intron	DEL	TG	-	-	rs5781568		TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:230258362_230258363delTG	uc010pwa.1	+						GALNT2_uc010pvy.1_Intron|GALNT2_uc010pvz.1_Intron	NM_004481	NP_004472	Q10471	GALT2_HUMAN	polypeptide N-acetylgalactosaminyltransferase 2						immunoglobulin biosynthetic process|protein O-linked glycosylation via serine|protein O-linked glycosylation via threonine	extracellular region|Golgi cisterna membrane|integral to Golgi membrane|perinuclear region of cytoplasm	manganese ion binding|polypeptide N-acetylgalactosaminyltransferase activity|sugar binding			ovary(2)	2	Breast(184;0.193)|Ovarian(103;0.249)	all_cancers(173;0.156)|Prostate(94;0.179)				AGGGTGGCTCtgtgtgtgtgtg	0.292													4	2	---	---	---	---	
RYR2	6262	broad.mit.edu	37	1	237220495	237220495	+	Intron	DEL	T	-	-			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:237220495delT	uc001hyl.1	+							NM_001035	NP_001026	Q92736	RYR2_HUMAN	cardiac muscle ryanodine receptor						cardiac muscle contraction|detection of calcium ion|induction of apoptosis by ionic changes|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum|response to caffeine|response to hypoxia|response to redox state	calcium channel complex|cytosol|plasma membrane|plasma membrane enriched fraction|sarcoplasmic reticulum membrane	calcium ion binding|calmodulin binding|identical protein binding|protein kinase A catalytic subunit binding|protein kinase A regulatory subunit binding|receptor activity|ryanodine-sensitive calcium-release channel activity|suramin binding			ovary(17)|large_intestine(6)|central_nervous_system(6)|pancreas(3)|breast(1)	33	Ovarian(103;0.103)	all_cancers(173;0.000368)|Melanoma(53;0.0179)|all_epithelial(177;0.0225)	OV - Ovarian serous cystadenocarcinoma(106;0.00606)			AGGAAACttcttttttttttg	0.239													9	4	---	---	---	---	
PLD5	200150	broad.mit.edu	37	1	242353003	242353003	+	Intron	DEL	A	-	-			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:242353003delA	uc001hzn.1	-						PLD5_uc001hzl.3_Intron|PLD5_uc001hzm.3_Intron|PLD5_uc001hzo.1_Intron			Q8N7P1	PLD5_HUMAN	RecName: Full=Inactive phospholipase D5;          Short=Inactive PLD 5; AltName: Full=Inactive choline phosphatase 5; AltName: Full=Inactive phosphatidylcholine-hydrolyzing phospholipase D5; AltName: Full=PLDc;							integral to membrane	catalytic activity			ovary(6)	6	Melanoma(84;0.242)		OV - Ovarian serous cystadenocarcinoma(106;0.0329)			aaaattaggtaatatggcaga	0.000													4	2	---	---	---	---	
CEP170	9859	broad.mit.edu	37	1	243414296	243414296	+	Intron	DEL	G	-	-			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:243414296delG	uc001hzs.2	-						CEP170_uc001hzt.2_Intron|CEP170_uc001hzu.2_Intron	NM_014812	NP_055627	Q5SW79	CE170_HUMAN	centrosomal protein 170kDa isoform alpha							centriole|microtubule|spindle				ovary(1)|haematopoietic_and_lymphoid_tissue(1)	2	all_neural(11;0.101)	all_cancers(173;0.003)	all cancers(7;5.81e-06)|GBM - Glioblastoma multiforme(7;0.000443)|OV - Ovarian serous cystadenocarcinoma(106;0.0101)			tgtgagggatggcaaaggaaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	6898262	6898262	+	Intron	DEL	G	-	-			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:6898262delG	uc002qym.1	-											Homo sapiens cDNA FLJ42418 fis, clone BLADE2001987.																		TCTAGAACCTGGAACCTTCAC	0.527													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	8634103	8634103	+	IGR	DEL	A	-	-			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:8634103delA								LOC339788 (517126 upstream) : ID2 (185237 downstream)																							TCCCTTaaagaaaaaaaaaga	0.388													8	4	---	---	---	---	
GRHL1	29841	broad.mit.edu	37	2	10104727	10104728	+	Intron	DEL	CT	-	-			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:10104727_10104728delCT	uc002raa.2	+						GRHL1_uc002rab.2_Intron|GRHL1_uc002rad.2_Intron|GRHL1_uc010yjb.1_Intron	NM_198182	NP_937825	Q9NZI5	GRHL1_HUMAN	grainyhead-like 1						cellular lipid metabolic process|multicellular organismal development|regulation of transcription, DNA-dependent|transcription, DNA-dependent	Golgi apparatus|nucleus	DNA binding			pancreas(1)|skin(1)	2	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)			Epithelial(75;0.172)|OV - Ovarian serous cystadenocarcinoma(76;0.246)		ATGTAGCTGGCTAACCTGAGAA	0.470													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	16002905	16002905	+	IGR	DEL	A	-	-			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:16002905delA								DDX1 (231681 upstream) : MYCNOS (77115 downstream)																							gccagtgctgaaaaaggaaga	0.030													4	2	---	---	---	---	
DTNB	1838	broad.mit.edu	37	2	25862940	25862940	+	Intron	DEL	C	-	-			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:25862940delC	uc002rgh.2	-						DTNB_uc010yko.1_Intron|DTNB_uc010ykp.1_Intron|DTNB_uc002rgo.2_Intron|DTNB_uc002rgi.2_Intron|DTNB_uc002rgj.2_Intron|DTNB_uc002rgk.2_Intron|DTNB_uc002rgl.2_Intron|DTNB_uc002rgq.2_Intron|DTNB_uc002rgm.2_Intron|DTNB_uc002rgn.2_Intron|DTNB_uc002rgr.1_Intron|DTNB_uc010ykq.1_Intron	NM_021907	NP_068707	O60941	DTNB_HUMAN	dystrobrevin, beta isoform 1							cytoplasm	calcium ion binding|zinc ion binding			large_intestine(2)|ovary(2)	4	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					tgagtctagacccacaaaacg	0.129													4	2	---	---	---	---	
ASXL2	55252	broad.mit.edu	37	2	25976750	25976750	+	Intron	DEL	G	-	-			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:25976750delG	uc002rgs.2	-						ASXL2_uc002rgt.1_Intron	NM_018263	NP_060733	Q76L83	ASXL2_HUMAN	additional sex combs like 2						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	metal ion binding|protein binding			pancreas(1)	1	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					CCTTTTCGCTGGGCTTCCCTG	0.418													4	2	---	---	---	---	
OTOF	9381	broad.mit.edu	37	2	26757754	26757754	+	Intron	DEL	A	-	-			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:26757754delA	uc002rhk.2	-							NM_194248	NP_919224	Q9HC10	OTOF_HUMAN	otoferlin isoform a						cellular membrane fusion|sensory perception of sound|synaptic vesicle exocytosis	basolateral plasma membrane|cell junction|cytosol|endoplasmic reticulum membrane|integral to membrane|membrane fraction|synaptic vesicle membrane	calcium ion binding			ovary(3)|breast(2)|central_nervous_system(1)|pancreas(1)	7	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					GGGGGATTTGAAAGGGCTCTT	0.532													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	34362373	34362374	+	IGR	INS	-	A	A	rs66927271		TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:34362373_34362374insA								MYADML (409089 upstream) : None (None downstream)																							tgaaaacattcaaaaaaaaaaa	0.069													3	3	---	---	---	---	
MAP4K3	8491	broad.mit.edu	37	2	39560920	39560921	+	Intron	INS	-	AG	AG			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:39560920_39560921insAG	uc002rro.2	-						MAP4K3_uc002rrp.2_Intron	NM_003618	NP_003609	Q8IVH8	M4K3_HUMAN	mitogen-activated protein kinase kinase kinase						JNK cascade		ATP binding|protein binding|protein serine/threonine kinase activity|small GTPase regulator activity			ovary(3)|lung(3)|stomach(1)|pancreas(1)	8		all_hematologic(82;0.211)				TATAAAATGTTCTGCCTTGCAA	0.282													5	3	---	---	---	---	
THADA	63892	broad.mit.edu	37	2	43478622	43478623	+	Intron	DEL	GC	-	-			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:43478622_43478623delGC	uc002rsw.3	-						THADA_uc010far.2_Intron|THADA_uc002rsx.3_Intron|THADA_uc002rsy.3_Intron	NM_001083953	NP_001077422	Q6YHU6	THADA_HUMAN	thyroid adenoma associated								binding			ovary(2)|skin(1)	3		Acute lymphoblastic leukemia(82;0.00361)|all_hematologic(82;0.00837)				GTTGCTCTCTGCTCTCTAAAAG	0.495													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	46888786	46888786	+	IGR	DEL	T	-	-			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:46888786delT								CRIPT (35906 upstream) : SOCS5 (37313 downstream)																							atttatcagattccaaaaagg	0.234													4	2	---	---	---	---	
STON1-GTF2A1L	286749	broad.mit.edu	37	2	48817293	48817294	+	Intron	DEL	GG	-	-	rs146977147	by1000genomes	TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:48817293_48817294delGG	uc010yol.1	+						STON1_uc002rwo.3_Intron|STON1_uc010fbm.2_Intron|STON1-GTF2A1L_uc002rwp.1_Intron|STON1_uc002rwr.2_Intron|STON1_uc002rwq.2_Intron	NM_006873	NP_006864	B7ZL16	B7ZL16_HUMAN	stonin 1						endocytosis|intracellular protein transport|transcription initiation from RNA polymerase II promoter	clathrin adaptor complex|transcription factor TFIIA complex				ovary(3)|pancreas(1)|skin(1)	5		all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.176)	Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151)			CAATCTTTCTGGGTGTGTGTGT	0.436													4	2	---	---	---	---	
CCDC85A	114800	broad.mit.edu	37	2	56478863	56478863	+	Intron	DEL	T	-	-			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:56478863delT	uc002rzn.2	+							NM_001080433	NP_001073902	Q96PX6	CC85A_HUMAN	coiled-coil domain containing 85A											breast(3)|ovary(2)	5			LUSC - Lung squamous cell carcinoma(58;0.127)|Lung(47;0.132)			CTTTTACTGATTTTTTTTTTG	0.448													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	58607615	58607616	+	IGR	DEL	CC	-	-			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:58607615_58607616delCC								FANCL (139100 upstream) : None (None downstream)																							AGATAAAGCTCCAATGCCACCG	0.416													4	2	---	---	---	---	
USP34	9736	broad.mit.edu	37	2	61433496	61433496	+	Intron	DEL	A	-	-			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:61433496delA	uc002sbe.2	-						USP34_uc002sbd.2_5'Flank	NM_014709	NP_055524	Q70CQ2	UBP34_HUMAN	ubiquitin specific protease 34						positive regulation of canonical Wnt receptor signaling pathway|protein K48-linked deubiquitination|ubiquitin-dependent protein catabolic process|Wnt receptor signaling pathway		cysteine-type endopeptidase activity|protein binding|ubiquitin thiolesterase activity|ubiquitin-specific protease activity			ovary(8)|breast(5)|skin(3)|lung(2)|prostate(1)	19			Epithelial(17;0.229)			GTATATGAAGAAGTTCAGAGT	0.318													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	81674299	81674299	+	IGR	DEL	A	-	-			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:81674299delA								CTNNA2 (798395 upstream) : None (None downstream)																							tctgtacaggaaaaaaaaaaa	0.000													5	3	---	---	---	---	
ELMOD3	84173	broad.mit.edu	37	2	85598004	85598004	+	Intron	DEL	C	-	-			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:85598004delC	uc002spf.3	+						ELMOD3_uc010fgg.2_Intron|ELMOD3_uc002spg.3_Intron|ELMOD3_uc002sph.3_Intron|ELMOD3_uc010ysn.1_Intron|ELMOD3_uc010yso.1_Intron|ELMOD3_uc010ysp.1_Intron	NM_001135021	NP_001128493	Q96FG2	ELMD3_HUMAN	ELMO/CED-12 domain containing 3 isoform b						phagocytosis	cytoskeleton				ovary(2)	2						TTTCACCTTGCAAAAAATCTG	0.512													4	2	---	---	---	---	
RGPD1	400966	broad.mit.edu	37	2	87204958	87204958	+	Intron	DEL	T	-	-			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:87204958delT	uc010fgv.2	+						RMND5A_uc002srs.3_Intron|RGPD1_uc002ssb.2_Intron|RGPD1_uc002ssc.2_Intron	NM_001024457	NP_001019628	Q68DN6	RGPD1_HUMAN	RANBP2-like and GRIP domain containing 1						intracellular transport		binding				0						Gttatttttattttttttttt	0.318													3	6	---	---	---	---	
FLJ40330	645784	broad.mit.edu	37	2	89100946	89100954	+	Intron	DEL	GCTATATCA	-	-	rs66488382		TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:89100946_89100954delGCTATATCA	uc010fhg.2	+						FLJ40330_uc010fhh.2_RNA|FLJ40330_uc010fhi.1_Intron	NR_015424				Homo sapiens mRNA; cDNA DKFZp434J1630 (from clone DKFZp434J1630).												0						AAATATATCTGCTATATCAGCTTAGAAAC	0.268													9	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	96617496	96617496	+	Intron	DEL	A	-	-	rs141504763		TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:96617496delA	uc010yug.1	-											Homo sapiens cDNA FLJ54441 complete cds, highly similar to Homo sapiens ankyrin repeat domain 36 (ANKRD36), mRNA.																		AACTAATAATAAAAAAAGTAA	0.249													4	2	---	---	---	---	
C2orf29	55571	broad.mit.edu	37	2	101886151	101886152	+	3'UTR	DEL	TT	-	-			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:101886151_101886152delTT	uc002taw.3	+	7						NM_017546	NP_060016	Q9UKZ1	CB029_HUMAN	hypothetical protein LOC55571						cell proliferation|nuclear-transcribed mRNA poly(A) tail shortening	cytosol				ovary(2)|pancreas(1)|central_nervous_system(1)|skin(1)	5						GATGAGTTTCTTTTTTTTTTAA	0.351													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	123452355	123452355	+	IGR	DEL	C	-	-			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:123452355delC								TSN (926929 upstream) : None (None downstream)																							tcttcttcctcttcctcttct	0.124													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	124665912	124665913	+	IGR	DEL	GT	-	-			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:124665912_124665913delGT								None (None upstream) : CNTNAP5 (116951 downstream)																							GGAAGGCAGGGTGATCAAGGTA	0.455													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	129393141	129393141	+	IGR	DEL	T	-	-			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:129393141delT								HS6ST1 (316970 upstream) : None (None downstream)																							TTAGTATGTGTTAGCACTTTA	0.483													4	2	---	---	---	---	
SLC4A10	57282	broad.mit.edu	37	2	162719785	162719785	+	Intron	DEL	A	-	-			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:162719785delA	uc002ubx.3	+						SLC4A10_uc010fpa.1_Intron|SLC4A10_uc010zcr.1_Intron|SLC4A10_uc002uby.3_Intron|SLC4A10_uc010zcs.1_Intron	NM_022058	NP_071341	Q6U841	S4A10_HUMAN	solute carrier family 4, sodium bicarbonate						bicarbonate transport|chloride transport|sodium ion transport	integral to membrane|plasma membrane	inorganic anion exchanger activity|symporter activity			ovary(2)|lung(2)|pancreas(1)	5						AAGGTTCAGGAAAAAAATGCA	0.274													4	2	---	---	---	---	
ALS2CR4	65062	broad.mit.edu	37	2	202505346	202505346	+	Intron	DEL	A	-	-			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:202505346delA	uc002uyh.1	-						ALS2CR4_uc002uyg.1_Intron|ALS2CR4_uc010zhp.1_5'Flank	NM_001044385	NP_001037850	Q96Q45	TM237_HUMAN	amyotrophic lateral sclerosis 2 (juvenile)							integral to membrane	protein binding				0						ATTCTGATTTAAAAAAAAAAA	0.299													4	3	---	---	---	---	
DNPEP	23549	broad.mit.edu	37	2	220248126	220248126	+	Intron	DEL	T	-	-			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:220248126delT	uc010zlg.1	-						DNPEP_uc010zlf.1_Intron|DNPEP_uc002vle.2_Intron|DNPEP_uc002vlf.1_Intron|DNPEP_uc002vlh.2_Intron|DNPEP_uc002vli.1_Intron	NM_012100	NP_036232	Q9ULA0	DNPEP_HUMAN	aspartyl aminopeptidase						peptide metabolic process|proteolysis	cytoplasm	aminopeptidase activity|metallopeptidase activity|protein binding|zinc ion binding				0		Renal(207;0.0474)		Epithelial(149;1.09e-06)|all cancers(144;0.000179)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)	L-Glutamic Acid(DB00142)	GGTGGGGACCTTTTTTTTCTT	0.403													4	2	---	---	---	---	
DNER	92737	broad.mit.edu	37	2	230282300	230282300	+	Intron	DEL	G	-	-			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:230282300delG	uc002vpv.2	-							NM_139072	NP_620711	Q8NFT8	DNER_HUMAN	delta-notch-like EGF repeat-containing						central nervous system development|endocytosis|neuron migration|Notch signaling pathway|synapse assembly	dendrite|early endosome|integral to membrane|plasma membrane	calcium ion binding|clathrin binding|transmembrane receptor activity			lung(5)|ovary(2)|skin(1)	8		all_lung(227;0.00413)|Renal(207;0.0113)|Lung NSC(271;0.0211)|all_hematologic(139;0.105)|Acute lymphoblastic leukemia(138;0.175)		Epithelial(121;1.4e-11)|all cancers(144;7.7e-09)|LUSC - Lung squamous cell carcinoma(224;0.034)|Lung(119;0.0375)		tagggttctcggggggattta	0.204													4	2	---	---	---	---	
UGT1A8	54576	broad.mit.edu	37	2	234526756	234526757	+	Frame_Shift_Ins	INS	-	A	A			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:234526756_234526757insA	uc002vup.2	+	1	466_467	c.403_404insA	c.(403-405)GAAfs	p.E135fs	UGT1A8_uc010zmv.1_Frame_Shift_Ins_p.E135fs	NM_019076	NP_061949	Q9HAW9	UD18_HUMAN	UDP glycosyltransferase 1 family, polypeptide A8	135					drug metabolic process|fatty acid metabolic process|flavone metabolic process|xenobiotic metabolic process	endoplasmic reticulum membrane|integral to membrane|microsome	enzyme inhibitor activity|fatty acid binding|glucuronosyltransferase activity|protein heterodimerization activity|protein homodimerization activity|steroid binding			ovary(2)	2		Breast(86;0.000766)|all_lung(227;0.00271)|Renal(207;0.00339)|all_hematologic(139;0.0116)|Acute lymphoblastic leukemia(138;0.0334)|Lung NSC(271;0.0461)|Lung SC(224;0.128)		Epithelial(121;2.56e-17)|BRCA - Breast invasive adenocarcinoma(100;0.000482)|Lung(119;0.00404)|LUSC - Lung squamous cell carcinoma(224;0.008)		AAAATTAGTAGAATACTTAAAG	0.361													303	179	---	---	---	---	
ITPR1	3708	broad.mit.edu	37	3	4562470	4562471	+	Intron	INS	-	G	G			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:4562470_4562471insG	uc003bqa.2	+						ITPR1_uc010hbz.2_Intron|ITPR1_uc010hca.1_Intron|ITPR1_uc011asu.1_Intron|ITPR1_uc010hcb.1_Intron	NM_001099952	NP_001093422	Q14643	ITPR1_HUMAN	inositol 1,4,5-triphosphate receptor, type 1						activation of phospholipase C activity|cell death|energy reserve metabolic process|nerve growth factor receptor signaling pathway|platelet activation|regulation of insulin secretion|response to hypoxia	endoplasmic reticulum membrane|integral to membrane|platelet dense granule membrane|platelet dense tubular network membrane	calcium ion transmembrane transporter activity|inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity|intracellular ligand-gated calcium channel activity|phosphatidylinositol binding|protein binding			lung(7)|breast(5)|ovary(4)|large_intestine(1)|liver(1)|skin(1)|kidney(1)|pancreas(1)	21				Epithelial(13;0.0199)|OV - Ovarian serous cystadenocarcinoma(96;0.0361)|all cancers(10;0.0982)		GACATGGTTATGGGAAAGGAGC	0.421													4	2	---	---	---	---	
ZFYVE20	64145	broad.mit.edu	37	3	15140071	15140071	+	Intron	DEL	G	-	-			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:15140071delG	uc003bzm.1	-						ZFYVE20_uc010hek.1_Intron|ZFYVE20_uc011avn.1_Intron	NM_022340	NP_071735	Q9H1K0	RBNS5_HUMAN	FYVE-finger-containing Rab5 effector protein						blood coagulation|endosome transport|protein transport	early endosome membrane|plasma membrane	protein binding|zinc ion binding			skin(2)	2						TCCCACAGCCGCACTCAACCC	0.478													4	2	---	---	---	---	
RBMS3	27303	broad.mit.edu	37	3	29490018	29490018	+	Intron	DEL	A	-	-			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:29490018delA	uc003cel.2	+						RBMS3_uc003cek.2_Intron|RBMS3_uc010hfq.2_Intron|RBMS3_uc003cem.2_Intron|RBMS3_uc010hfr.2_Intron	NM_001003793	NP_001003793	Q6XE24	RBMS3_HUMAN	RNA binding motif, single stranded interacting							cytoplasm	nucleotide binding|RNA binding			central_nervous_system(1)	1		Ovarian(412;0.0956)				ACTTTACGCTAAATCTGTGGA	0.353													4	2	---	---	---	---	
VIPR1	7433	broad.mit.edu	37	3	42572567	42572568	+	Intron	DEL	TC	-	-			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:42572567_42572568delTC	uc003clf.2	+						VIPR1_uc011azl.1_Intron|VIPR1_uc011azm.1_Intron|VIPR1_uc011azn.1_Intron|VIPR1_uc003clg.2_5'Flank	NM_004624	NP_004615	P32241	VIPR1_HUMAN	vasoactive intestinal peptide receptor 1						digestion|G-protein signaling, coupled to cyclic nucleotide second messenger|immune response|muscle contraction|positive regulation of cell proliferation|synaptic transmission	integral to plasma membrane	vasoactive intestinal polypeptide receptor activity			skin(1)	1				KIRC - Kidney renal clear cell carcinoma(284;0.241)		CAGCCAAGGGTCAAGAAAGTCC	0.540													4	2	---	---	---	---	
CLEC3B	7123	broad.mit.edu	37	3	45067086	45067086	+	5'Flank	DEL	C	-	-			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:45067086delC	uc003cok.3	+							NM_003278	NP_003269	P05452	TETN_HUMAN	C-type lectin domain family 3, member B						skeletal system development	extracellular space	protein binding|sugar binding				0				BRCA - Breast invasive adenocarcinoma(193;0.00863)|KIRC - Kidney renal clear cell carcinoma(197;0.0475)|Kidney(197;0.0595)	Alteplase(DB00009)|Anistreplase(DB00029)|Reteplase(DB00015)|Tenecteplase(DB00031)	CTGCTGGGCTCCCACACCCCA	0.622													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	48275852	48275853	+	IGR	DEL	TT	-	-			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:48275852_48275853delTT								CAMP (8877 upstream) : ZNF589 (6743 downstream)																							ATTCATCTTGTTAACATTTTCA	0.460													4	2	---	---	---	---	
VPRBP	9730	broad.mit.edu	37	3	51470603	51470603	+	Intron	DEL	T	-	-			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:51470603delT	uc003dbe.1	-							NM_014703	NP_055518	Q9Y4B6	VPRBP_HUMAN	HIV-1 Vpr binding protein						interspecies interaction between organisms	cytoplasm|nucleus	protein binding			ovary(1)|skin(1)	2				BRCA - Breast invasive adenocarcinoma(193;0.000272)|Kidney(197;0.000729)|KIRC - Kidney renal clear cell carcinoma(197;0.000875)		TCTTCTTGTATCTTTCCTTCC	0.303													3	3	---	---	---	---	
RAD54L2	23132	broad.mit.edu	37	3	51665274	51665275	+	Intron	DEL	TT	-	-			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:51665274_51665275delTT	uc011bdt.1	+						RAD54L2_uc003dbh.2_Intron|RAD54L2_uc011bdu.1_Intron|RAD54L2_uc003dbj.2_Intron	NM_015106	NP_055921	Q9Y4B4	ARIP4_HUMAN	RAD54-like 2							nucleus	ATP binding|DNA binding|helicase activity			ovary(3)	3				BRCA - Breast invasive adenocarcinoma(193;0.000102)|Kidney(197;0.000758)|KIRC - Kidney renal clear cell carcinoma(197;0.000896)		AGTGCTTTGATTAGGAAGGTCT	0.272													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	75908941	75908942	+	IGR	INS	-	A	A	rs144875585		TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:75908941_75908942insA								ZNF717 (74271 upstream) : None (None downstream)																							ttgaatcacccaaagacaactt	0.000													4	4	---	---	---	---	
NIT2	56954	broad.mit.edu	37	3	100060223	100060223	+	Intron	DEL	T	-	-			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:100060223delT	uc003dtv.2	+						NIT2_uc011bha.1_Intron	NM_020202	NP_064587	Q9NQR4	NIT2_HUMAN	nitrilase family, member 2						nitrogen compound metabolic process		omega-amidase activity			ovary(1)	1						gctatagtaattttttttttg	0.045													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	109696256	109696257	+	IGR	DEL	TT	-	-			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:109696256_109696257delTT								FLJ25363 (482242 upstream) : None (None downstream)																							TCAACAAACATTTAGGATCAGC	0.292													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	134384816	134384817	+	IGR	DEL	AG	-	-			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:134384816_134384817delAG								KY (14338 upstream) : EPHB1 (129443 downstream)																							aaagaaagacagagagaacaac	0.025													4	2	---	---	---	---	
EPHB1	2047	broad.mit.edu	37	3	134603191	134603191	+	Intron	DEL	T	-	-			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:134603191delT	uc003eqt.2	+						EPHB1_uc010htz.1_Intron|EPHB1_uc011bly.1_Intron	NM_004441	NP_004432	P54762	EPHB1_HUMAN	ephrin receptor EphB1 precursor							integral to plasma membrane	ATP binding|ephrin receptor activity|protein binding			lung(11)|ovary(6)|stomach(4)|breast(3)|central_nervous_system(2)|skin(2)|large_intestine(1)|pancreas(1)	30						CATAATTCTATTACTTTATTA	0.378													4	2	---	---	---	---	
CLSTN2	64084	broad.mit.edu	37	3	139788649	139788650	+	Intron	INS	-	G	G			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:139788649_139788650insG	uc003etn.2	+						CLSTN2_uc003etm.2_Intron	NM_022131	NP_071414	Q9H4D0	CSTN2_HUMAN	calsyntenin 2 precursor						homophilic cell adhesion	endoplasmic reticulum membrane|Golgi membrane|integral to membrane|plasma membrane	calcium ion binding			skin(3)|large_intestine(2)|pancreas(1)|central_nervous_system(1)	7						GAGGGTCAGCAGGGGGCACTGG	0.347										HNSCC(16;0.037)			4	2	---	---	---	---	
MED12L	116931	broad.mit.edu	37	3	151011751	151011762	+	Intron	DEL	GCCATTAACCCT	-	-	rs67834444		TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:151011751_151011762delGCCATTAACCCT	uc003eyp.2	+						MED12L_uc011bnz.1_Intron	NM_053002	NP_443728	Q86YW9	MD12L_HUMAN	mediator of RNA polymerase II transcription,						regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	mediator complex				ovary(4)|large_intestine(1)|central_nervous_system(1)|skin(1)	7			LUSC - Lung squamous cell carcinoma(72;0.0394)|Lung(72;0.0517)			CAGACTTCCAGCCATTAACCCTGCCATTCACC	0.443													6	3	---	---	---	---	
PRKCI	5584	broad.mit.edu	37	3	170021195	170021196	+	3'UTR	INS	-	A	A			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:170021195_170021196insA	uc003fgs.2	+	18					PRKCI_uc003fgt.2_3'UTR	NM_002740	NP_002731	P41743	KPCI_HUMAN	protein kinase C, iota						anti-apoptosis|cellular membrane organization|cellular response to insulin stimulus|establishment or maintenance of epithelial cell apical/basal polarity|intracellular signal transduction|nerve growth factor receptor signaling pathway|positive regulation of establishment of protein localization in plasma membrane|positive regulation of glucose import|protein targeting to membrane|secretion|tight junction assembly|vesicle-mediated transport	cytosol|endosome|nucleus|polarisome	ATP binding|phospholipid binding|protein binding|protein kinase C activity|zinc ion binding			lung(2)|ovary(1)|breast(1)|skin(1)	5	all_cancers(22;6.45e-23)|all_epithelial(15;8.52e-28)|all_lung(20;6.31e-17)|Lung NSC(18;2.61e-16)|Ovarian(172;0.000337)|Breast(254;0.169)		Lung(28;2.71e-13)|STAD - Stomach adenocarcinoma(35;0.197)			CTTTTTTGTTTAAAAAAAAAAA	0.292													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	184197637	184197638	+	IGR	INS	-	T	T	rs140295853	by1000genomes	TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:184197637_184197638insT								CHRD (90018 upstream) : EPHB3 (81949 downstream)																							ttccaagactgtacttccagtc	0.168													4	3	---	---	---	---	
MASP1	5648	broad.mit.edu	37	3	186964879	186964880	+	Intron	INS	-	T	T	rs137929458	by1000genomes	TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:186964879_186964880insT	uc003frh.1	-						MASP1_uc003fri.2_Intron|MASP1_uc003frj.2_Intron|MASP1_uc003frk.1_3'UTR|MASP1_uc011bse.1_3'UTR	NM_001879	NP_001870	P48740	MASP1_HUMAN	mannan-binding lectin serine protease 1 isoform						complement activation, lectin pathway|negative regulation of complement activation|proteolysis	extracellular space	calcium ion binding|calcium-dependent protein binding|protein binding|protein homodimerization activity|serine-type endopeptidase activity			ovary(2)|breast(1)|liver(1)	4	all_cancers(143;5.33e-12)|Ovarian(172;0.0339)		OV - Ovarian serous cystadenocarcinoma(80;3.49e-18)	GBM - Glioblastoma multiforme(93;0.0366)		TAAATCCCACATTTTTTTTTCA	0.371													2	4	---	---	---	---	
TP63	8626	broad.mit.edu	37	3	189349597	189349598	+	Intron	INS	-	A	A			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:189349597_189349598insA	uc003fry.2	+						TP63_uc003frx.2_Intron|TP63_uc003frz.2_Intron|TP63_uc010hzc.1_Intron	NM_003722	NP_003713	Q9H3D4	P63_HUMAN	tumor protein p63 isoform 1						anti-apoptosis|cellular response to UV|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator|mitotic cell cycle G1/S transition DNA damage checkpoint|negative regulation of transcription from RNA polymerase II promoter|Notch signaling pathway|positive regulation of Notch signaling pathway|protein homotetramerization|regulation of neuron apoptosis|response to gamma radiation|response to X-ray	chromatin|cytosol|dendrite|Golgi apparatus|transcription factor complex	chromatin binding|damaged DNA binding|double-stranded DNA binding|identical protein binding|metal ion binding|p53 binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			skin(5)|lung(4)|ovary(2)|upper_aerodigestive_tract(1)	12	all_cancers(143;3.35e-10)|Ovarian(172;0.0925)		Lung(62;3.33e-05)	GBM - Glioblastoma multiforme(93;0.0227)		TCTTCCCATTTAAAAAAAATTA	0.317									Hay-Wells_syndrome	HNSCC(45;0.13)			6	3	---	---	---	---	
PAK2	5062	broad.mit.edu	37	3	196486179	196486179	+	Intron	DEL	C	-	-			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:196486179delC	uc003fwy.3	+							NM_002577	NP_002568	Q13177	PAK2_HUMAN	p21-activated kinase 2						axon guidance|cellular component disassembly involved in apoptosis|interspecies interaction between organisms|negative regulation of protein kinase activity|peptidyl-serine phosphorylation|positive regulation of peptidyl-tyrosine phosphorylation|protein autophosphorylation|regulation of apoptosis|regulation of defense response to virus by virus|regulation of growth|T cell costimulation|T cell receptor signaling pathway|viral reproduction	cytosol|nucleus|perinuclear region of cytoplasm|plasma membrane	ATP binding|identical protein binding|protein kinase binding|protein serine/threonine kinase activity|protein tyrosine kinase activator activity			ovary(1)|lung(1)	2	all_cancers(143;1.8e-08)|Ovarian(172;0.0634)|Breast(254;0.135)		Epithelial(36;1.07e-23)|all cancers(36;6.38e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.5e-18)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(46;0.00405)		agagtttcttcttcaccagag	0.164													4	2	---	---	---	---	
HTT	3064	broad.mit.edu	37	4	3129358	3129358	+	Intron	DEL	T	-	-			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:3129358delT	uc011bvq.1	+							NM_002111	NP_002102	P42858	HD_HUMAN	huntingtin						establishment of mitotic spindle orientation|Golgi organization|retrograde vesicle-mediated transport, Golgi to ER|vesicle transport along microtubule	autophagic vacuole|axon|cytoplasmic vesicle membrane|cytosol|dendrite|endoplasmic reticulum|Golgi apparatus|late endosome|membrane fraction|nucleus|protein complex	beta-tubulin binding|dynactin binding|dynein intermediate chain binding|p53 binding|transcription factor binding			skin(2)|ovary(1)|lung(1)	4		all_epithelial(65;0.18)		UCEC - Uterine corpus endometrioid carcinoma (64;0.187)		GCCTGACATCtttttttttat	0.279													4	2	---	---	---	---	
KCNIP4	80333	broad.mit.edu	37	4	20731976	20731978	+	Intron	DEL	GCA	-	-			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:20731976_20731978delGCA	uc003gqe.2	-						KCNIP4_uc003gqf.1_Intron|KCNIP4_uc003gqg.1_Intron|KCNIP4_uc003gqh.1_Intron|KCNIP4_uc003gqi.1_Intron|PACRGL_uc003gpu.2_Intron|PACRGL_uc003gpx.3_Intron|PACRGL_uc003gpw.2_Intron|KCNIP4_uc010iel.2_Intron|KCNIP4_uc003gqd.3_Intron	NM_147182	NP_671711	Q6PIL6	KCIP4_HUMAN	Kv channel interacting protein 4 isoform 3							plasma membrane	calcium ion binding|potassium channel activity|protein binding|voltage-gated ion channel activity				0		Breast(46;0.134)				TATTGACCAGGCATTAAACCACT	0.325													4	2	---	---	---	---	
CORIN	10699	broad.mit.edu	37	4	47679468	47679468	+	Intron	DEL	A	-	-			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:47679468delA	uc003gxm.2	-						CORIN_uc011bzf.1_Intron|CORIN_uc011bzg.1_Intron|CORIN_uc011bzh.1_Intron|CORIN_uc011bzi.1_Intron	NM_006587	NP_006578	Q9Y5Q5	CORIN_HUMAN	corin						peptide hormone processing|regulation of systemic arterial blood pressure by atrial natriuretic peptide	integral to membrane|plasma membrane	scavenger receptor activity|serine-type endopeptidase activity|serine-type exopeptidase activity			ovary(1)|central_nervous_system(1)	2						AGTTACATTTAAAAAACAATT	0.368													4	2	---	---	---	---	
TXK	7294	broad.mit.edu	37	4	48107866	48107867	+	Intron	INS	-	C	C			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:48107866_48107867insC	uc003gxx.3	-						TXK_uc003gxy.1_Intron	NM_003328	NP_003319	P42681	TXK_HUMAN	TXK tyrosine kinase							cytoplasm	ATP binding|non-membrane spanning protein tyrosine kinase activity				0						ccccttttctgcccccaatcat	0.094													4	2	---	---	---	---	
KIT	3815	broad.mit.edu	37	4	55573651	55573652	+	Intron	DEL	CA	-	-			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:55573651_55573652delCA	uc010igr.2	+						KIT_uc010igs.2_Intron	NM_000222	NP_000213	P10721	KIT_HUMAN	v-kit Hardy-Zuckerman 4 feline sarcoma viral						male gonad development|transmembrane receptor protein tyrosine kinase signaling pathway	extracellular space|integral to membrane	ATP binding|protein binding|receptor signaling protein tyrosine kinase activity			soft_tissue(3273)|haematopoietic_and_lymphoid_tissue(1572)|skin(99)|testis(49)|bone(21)|genital_tract(18)|kidney(17)|ovary(16)|salivary_gland(15)|large_intestine(11)|thymus(6)|lung(6)|central_nervous_system(4)|NS(3)|eye(2)|endometrium(2)|breast(1)|stomach(1)|autonomic_ganglia(1)|pancreas(1)	5118	all_cancers(7;0.00453)|all_lung(4;0.000565)|Lung NSC(11;0.00129)|all_epithelial(27;0.0104)|Glioma(25;0.08)|all_neural(26;0.101)		LUSC - Lung squamous cell carcinoma(32;0.000276)|Epithelial(7;0.209)	Colorectal(1;0.0276)|COAD - Colon adenocarcinoma(1;0.171)	Dasatinib(DB01254)|Imatinib(DB00619)|Sorafenib(DB00398)|Sunitinib(DB01268)	CACACGCATGCACACAcacacc	0.327		1	Mis|O		GIST|AML|TGCT|mastocytosis|mucosal melanoma	GIST|epithelioma	Piebald trait		Mast_Cell_disease_Familial_Clustering_of|Piebaldism|Gastrointestinal_Stromal_Tumors_Sporadic_Multiple_Primary|Familial_Gastrointestinal_Stromal_Tumors				4	2	---	---	---	---	
GRSF1	2926	broad.mit.edu	37	4	71692162	71692163	+	Intron	DEL	TT	-	-			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:71692162_71692163delTT	uc010iia.1	-						GRSF1_uc011caz.1_Intron|GRSF1_uc003hfs.2_Intron	NM_002092	NP_002083	Q12849	GRSF1_HUMAN	G-rich RNA sequence binding factor 1 isoform 1						mRNA polyadenylation		mRNA binding|nucleotide binding				0		all_hematologic(202;0.21)	Lung(101;0.235)			CCATTACCAGTTTAAGAACTTA	0.347													4	2	---	---	---	---	
DCK	1633	broad.mit.edu	37	4	71895356	71895357	+	3'UTR	INS	-	CT	CT			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:71895356_71895357insCT	uc003hfx.2	+	7					DCK_uc011cbb.1_3'UTR	NM_000788	NP_000779	P27707	DCK_HUMAN	deoxycytidine kinase						purine base metabolic process|purine-containing compound salvage|pyrimidine base metabolic process|pyrimidine nucleoside salvage|pyrimidine nucleotide metabolic process	cytosol|nucleus	ATP binding|deoxycytidine kinase activity|drug binding|phosphotransferase activity, alcohol group as acceptor|protein homodimerization activity			ovary(1)	1			Lung(101;0.235)		Cladribine(DB00242)|Clofarabine(DB00631)|Decitabine(DB01262)|Fludarabine(DB01073)|Gemcitabine(DB00441)|Pemetrexed(DB00642)|Zalcitabine(DB00943)	tggttccagtatcagcatagtg	0.109													4	4	---	---	---	---	
SLC4A4	8671	broad.mit.edu	37	4	72130451	72130453	+	Intron	DEL	AAC	-	-			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:72130451_72130453delAAC	uc003hfy.2	+						SLC4A4_uc010iic.2_Intron|SLC4A4_uc010iib.2_Intron|SLC4A4_uc003hfz.2_Intron|SLC4A4_uc003hga.2_Intron	NM_001098484	NP_001091954	Q9Y6R1	S4A4_HUMAN	solute carrier family 4, sodium bicarbonate							basolateral plasma membrane|integral to plasma membrane	inorganic anion exchanger activity|protein binding|sodium:bicarbonate symporter activity			ovary(3)|kidney(1)|skin(1)	5			Lung(101;0.0739)|LUSC - Lung squamous cell carcinoma(112;0.225)			GAATGCCACAAACAACAACAACC	0.374													4	2	---	---	---	---	
NAAA	27163	broad.mit.edu	37	4	76852681	76852681	+	Intron	DEL	A	-	-			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:76852681delA	uc003hjb.2	-						NAAA_uc003hja.2_Intron|NAAA_uc003hjc.3_Intron|NAAA_uc003hjd.3_Intron|NAAA_uc011cbq.1_Intron	NM_014435	NP_055250	Q02083	NAAA_HUMAN	N-acylethanolamine acid amidase isoform 1						lipid metabolic process	lysosome	hydrolase activity			skin(1)	1						cttggatgggaaaaaaaaaga	0.144													6	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	81895621	81895622	+	IGR	INS	-	C	C			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:81895621_81895622insC								C4orf22 (10725 upstream) : BMP3 (56497 downstream)																							ACATTTTTTTTCAAGTAGTTTT	0.168													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	109133858	109133858	+	IGR	DEL	T	-	-			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:109133858delT								LEF1 (44280 upstream) : LOC285456 (325488 downstream)																							TCTTTTACTATTTTTTTTTCT	0.284													4	2	---	---	---	---	
FAM160A1	729830	broad.mit.edu	37	4	152507625	152507627	+	Intron	DEL	CAC	-	-			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:152507625_152507627delCAC	uc003imj.2	+							NM_001109977	NP_001103447	Q05DH4	F16A1_HUMAN	hypothetical protein LOC729830												0						CTACTGTCTTCACCTGTTTGCAT	0.325													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	154050753	154050755	+	IGR	DEL	CCA	-	-			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:154050753_154050755delCCA								FHDC1 (149905 upstream) : TRIM2 (23515 downstream)																							atcaccacccccaccaccaccac	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	157350420	157350420	+	IGR	DEL	G	-	-			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:157350420delG								CTSO (475372 upstream) : PDGFC (332344 downstream)																							aagtcattaagaagataacat	0.035													4	2	---	---	---	---	
ODZ3	55714	broad.mit.edu	37	4	183128321	183128321	+	Intron	DEL	A	-	-			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:183128321delA	uc010irv.1	+									Q9P273	TEN3_HUMAN	Homo sapiens ODZ3 (ODZ3) mRNA, partial cds.						signal transduction	integral to membrane					0		all_lung(41;2.69e-14)|Lung NSC(41;1.92e-11)|Melanoma(52;1.74e-05)|Colorectal(36;0.0062)|Breast(14;0.00748)|all_hematologic(60;0.0162)|Renal(120;0.0246)|Hepatocellular(41;0.0268)|Prostate(90;0.0283)|all_neural(102;0.155)|Medulloblastoma(177;0.184)		all cancers(43;1.42e-24)|Epithelial(43;6.86e-23)|OV - Ovarian serous cystadenocarcinoma(60;2.16e-11)|Colorectal(24;9.75e-06)|STAD - Stomach adenocarcinoma(60;2.96e-05)|COAD - Colon adenocarcinoma(29;0.00103)|GBM - Glioblastoma multiforme(59;0.00462)|LUSC - Lung squamous cell carcinoma(40;0.0391)|READ - Rectum adenocarcinoma(43;0.0487)		GGACTTTCTGACCTGAAAGGA	0.428													4	2	---	---	---	---	
PDLIM3	27295	broad.mit.edu	37	4	186427563	186427564	+	Intron	INS	-	A	A			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:186427563_186427564insA	uc003ixw.3	-						PDLIM3_uc003ixx.3_Intron|PDLIM3_uc010isi.2_Intron	NM_014476	NP_055291	Q53GG5	PDLI3_HUMAN	PDZ and LIM domain protein 3 isoform a							sarcomere	zinc ion binding			ovary(2)	2		all_lung(41;1.03e-13)|Lung NSC(41;2.49e-13)|Melanoma(20;1.91e-06)|Hepatocellular(41;0.00826)|Renal(120;0.00988)|Prostate(90;0.00996)|Colorectal(36;0.0161)|all_hematologic(60;0.0592)|all_neural(102;0.243)		OV - Ovarian serous cystadenocarcinoma(60;1.4e-10)|BRCA - Breast invasive adenocarcinoma(30;8.64e-05)|GBM - Glioblastoma multiforme(59;0.000167)|STAD - Stomach adenocarcinoma(60;0.000828)|LUSC - Lung squamous cell carcinoma(40;0.00984)|COAD - Colon adenocarcinoma(29;0.0115)|READ - Rectum adenocarcinoma(43;0.171)		ATTTGGCTCCCAATGAAAACCA	0.470													10	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	6545727	6545728	+	IGR	INS	-	T	T	rs144489657	by1000genomes	TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:6545727_6545728insT								UBE2QL1 (53022 upstream) : LOC255167 (36559 downstream)																							tccaccagtgcgagtggagtgg	0.000													1	5	---	---	---	---	
SEMA5A	9037	broad.mit.edu	37	5	9227108	9227109	+	Intron	INS	-	AT	AT	rs146979886	by1000genomes	TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:9227108_9227109insAT	uc003jek.2	-							NM_003966	NP_003957	Q13591	SEM5A_HUMAN	semaphorin 5A precursor						cell adhesion|cell-cell signaling	integral to membrane|plasma membrane				ovary(1)|central_nervous_system(1)	2						attaattaaaaatatatatata	0.351													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	17485741	17485742	+	IGR	INS	-	C	C			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:17485741_17485742insC								BASP1 (208806 upstream) : None (None downstream)																							AGGGAGATTTGCCCCCCTTCCC	0.282													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	21264446	21264446	+	IGR	DEL	A	-	-			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:21264446delA								None (None upstream) : GUSBP1 (77496 downstream)																							CATCGGACATAAAGAACACAG	0.393													4	2	---	---	---	---	
ZFR	51663	broad.mit.edu	37	5	32387978	32387978	+	Intron	DEL	A	-	-			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:32387978delA	uc003jhr.1	-						ZFR_uc011cny.1_Intron	NM_016107	NP_057191	Q96KR1	ZFR_HUMAN	zinc finger RNA binding protein						multicellular organismal development	chromosome|cytoplasm|nucleus	DNA binding|RNA binding|zinc ion binding				0				STAD - Stomach adenocarcinoma(35;0.19)		CAATGTGGataaaaaaaaaaa	0.294													9	4	---	---	---	---	
C7	730	broad.mit.edu	37	5	40962631	40962631	+	Intron	DEL	T	-	-			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:40962631delT	uc003jmh.2	+						C7_uc011cpn.1_Intron	NM_000587	NP_000578	P10643	CO7_HUMAN	complement component 7 precursor						complement activation, alternative pathway|complement activation, classical pathway|cytolysis	extracellular region|membrane attack complex					0		Ovarian(839;0.0112)				TGCCACTGACTTTTTTTTTTC	0.428													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	49810998	49810998	+	IGR	DEL	T	-	-			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:49810998delT								EMB (73764 upstream) : PARP8 (150735 downstream)																							tgctgcagaataagtgagaga	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	51999925	51999926	+	IGR	INS	-	T	T			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:51999925_51999926insT								None (None upstream) : ITGA1 (83848 downstream)																							GGTTTGGGTTATTTTTTTTTCA	0.376													0	6	---	---	---	---	
CENPK	64105	broad.mit.edu	37	5	64848599	64848599	+	Intron	DEL	A	-	-			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:64848599delA	uc003jts.2	-						CENPK_uc003jtt.2_Intron|CENPK_uc003jtu.2_Intron	NM_022145	NP_071428	Q9BS16	CENPK_HUMAN	SoxLZ/Sox6 leucine zipper binding protein						CenH3-containing nucleosome assembly at centromere|mitotic prometaphase	condensed chromosome kinetochore|cytosol|nucleoplasm					0		Lung NSC(167;7.21e-05)|Prostate(74;0.0174)|Ovarian(174;0.186)		Lung(70;0.00466)		AATGAAGAGGAAAAAAAAAAA	0.318													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	67207529	67207529	+	IGR	DEL	T	-	-			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:67207529delT								CD180 (714912 upstream) : PIK3R1 (304075 downstream)																							CACTTCAGCATTTATCAGCCC	0.403													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	79655916	79655916	+	5'Flank	DEL	A	-	-	rs111607880		TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:79655916delA	uc003kgo.2	-											SubName: Full=Putative uncharacterized protein; Flags: Fragment;																		CCATGGGCAGAAAAAAAAAAA	0.383													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	101478059	101478059	+	IGR	DEL	T	-	-			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:101478059delT								None (None upstream) : SLCO4C1 (91635 downstream)																							cccatcatcctttttagagtc	0.000													4	2	---	---	---	---	
COMMD10	51397	broad.mit.edu	37	5	115481142	115481143	+	Intron	DEL	TG	-	-	rs149068119		TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:115481142_115481143delTG	uc003krt.1	+							NM_016144	NP_057228	Q9Y6G5	COMDA_HUMAN	COMM domain containing 10								protein binding			ovary(1)	1		all_cancers(142;0.0834)|all_epithelial(76;0.00314)|Prostate(80;0.0102)|Ovarian(225;0.232)		OV - Ovarian serous cystadenocarcinoma(64;4.3e-07)|Epithelial(69;8.06e-07)|all cancers(49;4.06e-05)		agggtttgtctgtgtctatgaa	0.000													4	2	---	---	---	---	
TNFAIP8	25816	broad.mit.edu	37	5	118674747	118674748	+	Intron	INS	-	A	A	rs144956027	by1000genomes	TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:118674747_118674748insA	uc011cwf.1	+						TNFAIP8_uc003ksf.1_Intron|TNFAIP8_uc003ksg.2_Intron	NM_001077654	NP_001071122	O95379	TFIP8_HUMAN	tumor necrosis factor, alpha-induced protein 8						anti-apoptosis|apoptosis|negative regulation of anti-apoptosis	cytoplasm	caspase inhibitor activity|protein binding			ovary(1)	1		all_cancers(142;0.0317)|Prostate(80;0.111)|Breast(839;0.231)		Epithelial(69;4.63e-83)|OV - Ovarian serous cystadenocarcinoma(64;1.39e-82)|all cancers(49;4.88e-75)|GBM - Glioblastoma multiforme(465;0.00338)|BRCA - Breast invasive adenocarcinoma(61;0.0148)|COAD - Colon adenocarcinoma(49;0.0829)		tctcttaaaacaaaaaaaaaaG	0.144													3	5	---	---	---	---	
C5orf48	389320	broad.mit.edu	37	5	125971528	125971528	+	Intron	DEL	A	-	-	rs71573967		TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:125971528delA	uc003kub.1	+							NM_207408	NP_997291	Q6ZNM6	CE048_HUMAN	hypothetical protein LOC389320											ovary(1)	1						ctaattttttattttttgtat	0.000													3	4	---	---	---	---	
SLC12A2	6558	broad.mit.edu	37	5	127486660	127486660	+	Intron	DEL	T	-	-			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:127486660delT	uc003kus.2	+						SLC12A2_uc010jdf.2_Intron|SLC12A2_uc010jdg.2_Intron	NM_001046	NP_001037	P55011	S12A2_HUMAN	solute carrier family 12						potassium ion transport|sodium ion transport|transepithelial ammonium transport|transepithelial chloride transport	integral to plasma membrane|membrane fraction	ammonia transmembrane transporter activity|sodium:potassium:chloride symporter activity			ovary(3)	3		all_cancers(142;0.0972)|Prostate(80;0.151)	KIRC - Kidney renal clear cell carcinoma(527;0.0268)|Kidney(363;0.0488)	Epithelial(69;0.0433)|OV - Ovarian serous cystadenocarcinoma(64;0.0978)	Bumetanide(DB00887)|Potassium Chloride(DB00761)	GGTAGGTTGATTTTTTTTTTA	0.289													4	2	---	---	---	---	
GDF9	2661	broad.mit.edu	37	5	132198373	132198374	+	Intron	INS	-	A	A			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:132198373_132198374insA	uc003kxz.1	-						GDF9_uc011cxj.1_Intron	NM_005260	NP_005251	O60383	GDF9_HUMAN	growth differentiation factor 9 precursor						female gamete generation|transforming growth factor beta receptor signaling pathway	extracellular space	cytokine activity|growth factor activity			skin(1)	1		all_cancers(142;0.105)|Breast(839;0.198)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			TCTCAAGCCTCAAAAAAAAAAA	0.361													2	4	---	---	---	---	
ANXA6	309	broad.mit.edu	37	5	150509258	150509259	+	Intron	INS	-	TTTG	TTTG	rs144537590	by1000genomes	TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:150509258_150509259insTTTG	uc003ltl.1	-						ANXA6_uc011dcp.1_Intron|ANXA6_uc003ltm.1_Intron|ANXA6_uc003ltn.1_Intron|ANXA6_uc003lto.1_Intron	NM_001155	NP_001146	P08133	ANXA6_HUMAN	annexin VI isoform 1							melanosome	calcium ion binding|calcium-dependent phospholipid binding|protein binding				0		Medulloblastoma(196;0.0912)|all_hematologic(541;0.208)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			CCTCTTACTGTtttgtttgttt	0.163													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	164685566	164685566	+	IGR	DEL	A	-	-			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:164685566delA								None (None upstream) : None (None downstream)																							TTGGAAGAGCAAATTTTCTTT	0.458													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	171630474	171630474	+	IGR	DEL	T	-	-			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:171630474delT								STK10 (15128 upstream) : UBTD2 (6176 downstream)																							TTATAATGACttttttttttt	0.144													9	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	180546248	180546248	+	IGR	DEL	G	-	-			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:180546248delG								BTNL9 (57726 upstream) : OR2V2 (35695 downstream)																							GAGCAGGTCTGGGATTCCATC	0.378													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	2600526	2600526	+	IGR	DEL	A	-	-			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:2600526delA								GMDS (354680 upstream) : C6orf195 (22446 downstream)																							GTGAGGGAGTAGGTGAAGCTG	0.289													4	2	---	---	---	---	
C6orf105	84830	broad.mit.edu	37	6	11735554	11735555	+	Intron	DEL	GA	-	-			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:11735554_11735555delGA	uc003nab.2	-						C6orf105_uc003naa.2_Intron|C6orf105_uc011dip.1_Intron	NM_032744	NP_116133	Q96IZ2	CF105_HUMAN	hypothetical protein LOC84830 isoform 2							integral to membrane					0	Ovarian(93;0.0848)|Breast(50;0.0871)	all_hematologic(90;0.135)	Epithelial(50;0.146)|BRCA - Breast invasive adenocarcinoma(129;0.193)			AATTCTTCACGAGAGAGAGAGG	0.421													4	2	---	---	---	---	
BTN2A3	54718	broad.mit.edu	37	6	26422627	26422628	+	Intron	INS	-	A	A	rs147936124	by1000genomes	TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:26422627_26422628insA	uc011dkl.1	+						BTN2A3_uc011dkm.1_Intron					RecName: Full=Butyrophilin subfamily 2 member A3; Flags: Precursor;												0						gcaaattttccaaaaaaattaa	0.054													4	3	---	---	---	---	
C6orf136	221545	broad.mit.edu	37	6	30619030	30619030	+	Intron	DEL	C	-	-			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:30619030delC	uc003nqw.3	+						C6orf136_uc003nqx.3_Intron|C6orf136_uc011dmn.1_Intron	NM_001109938	NP_001103408	Q5SQH8	CF136_HUMAN	hypothetical protein LOC221545 isoform 1												0						TCTTTCCCATCCCTTCTTCAC	0.473													24	18	---	---	---	---	
SKIV2L	6499	broad.mit.edu	37	6	31935285	31935286	+	Intron	DEL	CT	-	-	rs10646736		TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:31935285_31935286delCT	uc003nyn.1	+						SKIV2L_uc011dou.1_Intron|SKIV2L_uc011dov.1_Intron	NM_006929	NP_008860	Q15477	SKIV2_HUMAN	superkiller viralicidic activity 2-like homolog							nucleus	ATP binding|ATP-dependent RNA helicase activity|protein binding|RNA binding			ovary(1)|large_intestine(1)|breast(1)|central_nervous_system(1)	4						CCTTTTCACCCTCTCCCTTCCC	0.574													1	5	---	---	---	---	
FTSJD2	23070	broad.mit.edu	37	6	37446420	37446421	+	Intron	DEL	CT	-	-			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:37446420_37446421delCT	uc003ons.2	+							NM_015050	NP_055865	Q8N1G2	MTR1_HUMAN	FtsJ methyltransferase domain containing 2						mRNA capping	cytoplasm|nucleus	mRNA (nucleoside-2'-O-)-methyltransferase activity|nucleic acid binding			ovary(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)|pancreas(1)	5						AGCAGCCAGGCTGGCATTTCTC	0.609													6	3	---	---	---	---	
KLHDC3	116138	broad.mit.edu	37	6	42987302	42987302	+	Intron	DEL	A	-	-	rs112870593		TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:42987302delA	uc003otl.2	+						C6orf153_uc003otp.1_5'Flank|KLHDC3_uc003otm.2_Intron|KLHDC3_uc010jyf.2_Intron|KLHDC3_uc003otn.2_Intron|KLHDC3_uc003oto.2_Intron	NM_057161	NP_476502	Q9BQ90	KLDC3_HUMAN	kelch domain containing 3						reciprocal meiotic recombination	cytoplasm|nuclear chromatin	chromatin binding|protein binding			upper_aerodigestive_tract(1)	1			Colorectal(64;0.00237)|all cancers(41;0.0034)|COAD - Colon adenocarcinoma(64;0.00473)|OV - Ovarian serous cystadenocarcinoma(102;0.0539)|KIRC - Kidney renal clear cell carcinoma(15;0.133)|Kidney(15;0.188)			AAATTATATGAAAAAAAAATA	0.363													8	4	---	---	---	---	
PRIM2	5558	broad.mit.edu	37	6	57225741	57225742	+	Intron	INS	-	T	T	rs139693489	by1000genomes	TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57225741_57225742insT	uc003pdx.2	+						PRIM2_uc003pdw.2_Intron	NM_000947	NP_000938	P49643	PRI2_HUMAN	DNA primase polypeptide 2						DNA replication, synthesis of RNA primer|DNA strand elongation involved in DNA replication|DNA-dependent DNA replication initiation|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|S phase of mitotic cell cycle|telomere maintenance via recombination|telomere maintenance via semi-conservative replication	alpha DNA polymerase:primase complex|nucleoplasm	4 iron, 4 sulfur cluster binding|DNA binding|DNA primase activity|metal ion binding				0				Colorectal(6;0.041)|READ - Rectum adenocarcinoma(7;0.193)		AGTGTTTTCTCTTTTTTTGCAG	0.371													3	4	---	---	---	---	
AKIRIN2	55122	broad.mit.edu	37	6	88387902	88387902	+	Intron	DEL	A	-	-			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:88387902delA	uc003pmk.2	-							NM_018064	NP_060534	Q53H80	AKIR2_HUMAN	akirin 2						innate immune response|transcription, DNA-dependent	transcriptional repressor complex					0						TAATTAAGATAAAAAAGACTA	0.229													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	89843274	89843274	+	IGR	DEL	T	-	-			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:89843274delT								SFRS13B (15474 upstream) : PM20D2 (12495 downstream)																							cctttatgcctgctatatttc	0.000													4	2	---	---	---	---	
REV3L	5980	broad.mit.edu	37	6	111694884	111694885	+	Frame_Shift_Ins	INS	-	T	T			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:111694884_111694885insT	uc003puy.3	-	13	4996_4997	c.4673_4674insA	c.(4672-4674)AATfs	p.N1558fs	REV3L_uc003pux.3_Frame_Shift_Ins_p.N1480fs|REV3L_uc003puz.3_Frame_Shift_Ins_p.N1480fs	NM_002912	NP_002903	O60673	DPOLZ_HUMAN	DNA polymerase zeta	1558					DNA-dependent DNA replication|translesion synthesis	nucleus|zeta DNA polymerase complex	DNA binding|DNA-directed DNA polymerase activity|metal ion binding|nucleotide binding			large_intestine(2)|ovary(2)|skin(2)	6		all_cancers(87;7.57e-06)|Acute lymphoblastic leukemia(125;2.46e-08)|all_hematologic(75;1.08e-06)|all_epithelial(87;0.00138)|Colorectal(196;0.021)		OV - Ovarian serous cystadenocarcinoma(136;0.0314)|Epithelial(106;0.057)|all cancers(137;0.0663)		AAATATTTTTATTTGGTTGATG	0.371								DNA_polymerases_(catalytic_subunits)|Direct_reversal_of_damage					442	201	---	---	---	---	
WISP3	8838	broad.mit.edu	37	6	112375244	112375248	+	5'Flank	DEL	TCACT	-	-			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:112375244_112375248delTCACT	uc003pvm.2	+						WISP3_uc003pvn.2_5'Flank|WISP3_uc003pvo.2_5'Flank	NM_003880	NP_003871	O95389	WISP3_HUMAN	WNT1 inducible signaling pathway protein 3						cell-cell signaling|regulation of cell growth|signal transduction	extracellular region|soluble fraction	growth factor activity|insulin-like growth factor binding				0		all_cancers(87;0.000196)|Acute lymphoblastic leukemia(125;1.18e-05)|all_hematologic(75;0.000114)|all_epithelial(87;0.00542)|Colorectal(196;0.0209)		all cancers(137;0.0283)|OV - Ovarian serous cystadenocarcinoma(136;0.0613)|Epithelial(106;0.0827)|GBM - Glioblastoma multiforme(226;0.0972)|BRCA - Breast invasive adenocarcinoma(108;0.246)		GGTAACACAGTCACTTAGAGAACAG	0.576													4	2	---	---	---	---	
NKAIN2	154215	broad.mit.edu	37	6	125026570	125026572	+	Intron	DEL	TTG	-	-			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:125026570_125026572delTTG	uc003pzo.2	+						NKAIN2_uc003pzp.2_Intron|NKAIN2_uc010keq.2_Intron|NKAIN2_uc010ker.2_Intron	NM_001040214	NP_001035304	Q5VXU1	NKAI2_HUMAN	T-cell lymphoma breakpoint-associated target 1							integral to membrane|plasma membrane					0				GBM - Glioblastoma multiforme(226;0.104)		agctgctttcttgttgttgtctg	0.000													2	4	---	---	---	---	
TPD52L1	7164	broad.mit.edu	37	6	125497832	125497833	+	Intron	DEL	AA	-	-			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:125497832_125497833delAA	uc003pzu.1	+						TPD52L1_uc003pzv.1_Intron|TPD52L1_uc003pzw.1_Intron|TPD52L1_uc003pzx.1_Intron|TPD52L1_uc003pzy.1_Intron	NM_003287	NP_003278	Q16890	TPD53_HUMAN	tumor protein D52-like 1 isoform 1						DNA fragmentation involved in apoptotic nuclear change|G2/M transition of mitotic cell cycle|induction of apoptosis|positive regulation of JNK cascade|positive regulation of MAP kinase activity	perinuclear region of cytoplasm	caspase activator activity|protein heterodimerization activity|protein homodimerization activity				0			LUSC - Lung squamous cell carcinoma(4;0.0263)|Lung(4;0.0828)	GBM - Glioblastoma multiforme(226;0.0265)		AATAGATGTTAAAATTCCGATA	0.252													4	2	---	---	---	---	
AHI1	54806	broad.mit.edu	37	6	135726363	135726364	+	Intron	INS	-	GG	GG			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:135726363_135726364insGG	uc003qgi.2	-						AHI1_uc003qgf.2_Intron|AHI1_uc003qgg.2_Intron|AHI1_uc003qgh.2_Intron|AHI1_uc003qgj.2_Intron|AHI1_uc003qgk.3_Intron|AHI1_uc003qgl.3_Intron	NM_001134831	NP_001128303	Q8N157	AHI1_HUMAN	Abelson helper integration site 1 isoform a							adherens junction|cilium|microtubule basal body				ovary(1)|kidney(1)|central_nervous_system(1)	3	Breast(56;0.239)|Colorectal(23;0.24)			GBM - Glioblastoma multiforme(68;0.00904)|OV - Ovarian serous cystadenocarcinoma(155;0.00991)		GTTATCTGCCTCAAGAAAAACT	0.351													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	138441191	138441192	+	IGR	INS	-	A	A	rs147495892	by1000genomes	TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:138441191_138441192insA								PERP (12531 upstream) : KIAA1244 (42032 downstream)																							CACCTCTGTTTAAAAAAAAAAG	0.272													3	4	---	---	---	---	
C6orf115	58527	broad.mit.edu	37	6	139348732	139348732	+	5'Flank	DEL	G	-	-			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:139348732delG	uc003qil.2	+						C6orf115_uc003qim.2_5'Flank	NM_021243	NP_067066	Q9P1F3	CF115_HUMAN	hypothetical protein LOC58527												0				GBM - Glioblastoma multiforme(68;0.000278)|OV - Ovarian serous cystadenocarcinoma(155;0.000413)		AATGAAGCGTGggaagtggat	0.219													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	148197158	148197158	+	IGR	DEL	C	-	-			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:148197158delC								SAMD5 (306001 upstream) : SASH1 (466571 downstream)																							tgaaaccagtccctgggtgcc	0.144													4	2	---	---	---	---	
ARID1B	57492	broad.mit.edu	37	6	157150706	157150706	+	Intron	DEL	T	-	-			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:157150706delT	uc003qqn.2	+						ARID1B_uc003qqo.2_Intron|ARID1B_uc003qqp.2_Intron	NM_017519	NP_059989	Q8NFD5	ARI1B_HUMAN	AT rich interactive domain 1B (SWI1-like)						chromatin-mediated maintenance of transcription|nervous system development|transcription, DNA-dependent	SWI/SNF complex	DNA binding|protein binding|transcription coactivator activity			ovary(1)|breast(1)	2		Breast(66;0.000162)|Ovarian(120;0.0265)		OV - Ovarian serous cystadenocarcinoma(65;3.19e-17)|BRCA - Breast invasive adenocarcinoma(81;1.01e-05)		ACAGGTATAATTTTTTTTTTC	0.373													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	164180426	164180427	+	Intron	DEL	TT	-	-			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:164180426_164180427delTT	uc003quk.1	+											Homo sapiens cDNA FLJ35795 fis, clone TESTI2005827.																		TTGGAGTGAGTTAAGGAGAGAA	0.495													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	165274196	165274197	+	IGR	DEL	TG	-	-			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:165274196_165274197delTG								None (None upstream) : C6orf118 (418958 downstream)																							ttcatatgcatgtgtgtgtgtg	0.228													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	170347909	170347909	+	IGR	DEL	T	-	-			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:170347909delT								C6orf208 (144940 upstream) : LOC154449 (215513 downstream)																							TCACTCCCAATTTAGAACAAG	0.582													4	2	---	---	---	---	
ADAP1	11033	broad.mit.edu	37	7	945055	945056	+	Intron	INS	-	G	G	rs149600787		TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:945055_945056insG	uc003sjo.3	-						ADAP1_uc003sjm.3_5'Flank|ADAP1_uc011jvs.1_Intron|ADAP1_uc003sjn.3_Intron|ADAP1_uc010ksc.2_Intron	NM_006869	NP_006860	O75689	ADAP1_HUMAN	centaurin, alpha 1						cell surface receptor linked signaling pathway|regulation of ARF GTPase activity	cytoplasm|nucleus|plasma membrane	ARF GTPase activator activity|inositol 1,3,4,5 tetrakisphosphate binding|protein binding|zinc ion binding			upper_aerodigestive_tract(1)	1						aaagggagaaagagaaaggaga	0.114													4	2	---	---	---	---	
ADAP1	11033	broad.mit.edu	37	7	945073	945073	+	Intron	DEL	A	-	-			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:945073delA	uc003sjo.3	-						ADAP1_uc003sjm.3_5'Flank|ADAP1_uc011jvs.1_Intron|ADAP1_uc003sjn.3_Intron|ADAP1_uc010ksc.2_Intron	NM_006869	NP_006860	O75689	ADAP1_HUMAN	centaurin, alpha 1						cell surface receptor linked signaling pathway|regulation of ARF GTPase activity	cytoplasm|nucleus|plasma membrane	ARF GTPase activator activity|inositol 1,3,4,5 tetrakisphosphate binding|protein binding|zinc ion binding			upper_aerodigestive_tract(1)	1						gagaaaggagaaagggagaaa	0.060													1	5	---	---	---	---	
ADAP1	11033	broad.mit.edu	37	7	945081	945081	+	Intron	DEL	A	-	-			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:945081delA	uc003sjo.3	-						ADAP1_uc003sjm.3_5'Flank|ADAP1_uc011jvs.1_Intron|ADAP1_uc003sjn.3_Intron|ADAP1_uc010ksc.2_Intron	NM_006869	NP_006860	O75689	ADAP1_HUMAN	centaurin, alpha 1						cell surface receptor linked signaling pathway|regulation of ARF GTPase activity	cytoplasm|nucleus|plasma membrane	ARF GTPase activator activity|inositol 1,3,4,5 tetrakisphosphate binding|protein binding|zinc ion binding			upper_aerodigestive_tract(1)	1						agaaagggagaaagggagaaa	0.035													4	3	---	---	---	---	
LOC389458	389458	broad.mit.edu	37	7	5041085	5041086	+	Intron	DEL	TC	-	-			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:5041085_5041086delTC	uc003snr.2	+											Synthetic construct DNA, clone: pF1KB3788, Homo sapiens RBAK gene for RB-associated KRAB repressor, complete cds, without stop codon, in Flexi system.												0						cctttctctttctctctctctc	0.094													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	20478925	20478925	+	IGR	DEL	T	-	-			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:20478925delT								ITGB8 (23547 upstream) : ABCB5 (176320 downstream)																							TAGTGGGGTGTTTTTTTTTTT	0.418													4	2	---	---	---	---	
BBS9	27241	broad.mit.edu	37	7	33196281	33196284	+	Intron	DEL	TGAA	-	-	rs75961358	byFrequency	TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:33196281_33196284delTGAA	uc003tdn.1	+						BBS9_uc003tdo.1_Intron|BBS9_uc003tdp.1_Intron|BBS9_uc003tdq.1_Intron|BBS9_uc010kwn.1_Intron|BBS9_uc011kan.1_Intron|BBS9_uc011kao.1_5'Flank	NM_198428	NP_940820	Q3SYG4	PTHB1_HUMAN	parathyroid hormone-responsive B1 isoform 2						fat cell differentiation|response to stimulus|visual perception	BBSome|cilium membrane|microtubule organizing center|nucleus	protein binding			ovary(3)|upper_aerodigestive_tract(1)|skin(1)	5			GBM - Glioblastoma multiforme(11;0.0894)			aaatacttgttgaatgaatgaatG	0.328									Bardet-Biedl_syndrome				4	2	---	---	---	---	
BBS9	27241	broad.mit.edu	37	7	33466183	33466184	+	Intron	INS	-	T	T	rs149020338	by1000genomes	TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:33466183_33466184insT	uc003tdn.1	+						BBS9_uc003tdo.1_Intron|BBS9_uc003tdp.1_Intron|BBS9_uc003tdq.1_Intron|BBS9_uc010kwn.1_Intron|BBS9_uc003tdr.1_Intron|BBS9_uc003tds.1_Intron|BBS9_uc003tdt.2_Intron	NM_198428	NP_940820	Q3SYG4	PTHB1_HUMAN	parathyroid hormone-responsive B1 isoform 2						fat cell differentiation|response to stimulus|visual perception	BBSome|cilium membrane|microtubule organizing center|nucleus	protein binding			ovary(3)|upper_aerodigestive_tract(1)|skin(1)	5			GBM - Glioblastoma multiforme(11;0.0894)			tagatgttctgtaaaaaatggg	0.099									Bardet-Biedl_syndrome				1	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	52537973	52537974	+	IGR	DEL	GA	-	-			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:52537973_52537974delGA								None (None upstream) : POM121L12 (565375 downstream)																							TTCagacggggagagagagaga	0.252													4	2	---	---	---	---	
GUSB	2990	broad.mit.edu	37	7	65429637	65429637	+	Intron	DEL	A	-	-			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:65429637delA	uc003tun.2	-						GUSB_uc011kdt.1_Intron	NM_000181	NP_000172	P08236	BGLR_HUMAN	glucuronidase, beta precursor						glycosaminoglycan catabolic process	lysosome	beta-glucuronidase activity|cation binding				0						AAGGAGGTTTAAAAAAAAAAA	0.388													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	70266324	70266324	+	IGR	DEL	A	-	-			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:70266324delA								AUTS2 (8440 upstream) : WBSCR17 (331465 downstream)																							tcagtcctccaagatgtttcc	0.000													4	2	---	---	---	---	
FKBP6	8468	broad.mit.edu	37	7	72755632	72755635	+	Intron	DEL	AAAC	-	-	rs5884906		TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:72755632_72755635delAAAC	uc003tya.2	+						FKBP6_uc003twz.2_Intron|FKBP6_uc011kew.1_Intron	NM_003602	NP_003593	O75344	FKBP6_HUMAN	FK506 binding protein 6 isoform a						protein folding	membrane	FK506 binding|peptidyl-prolyl cis-trans isomerase activity				0		Lung NSC(55;0.0908)|all_lung(88;0.198)				TACCGCAAATAAACAACCCCTAGA	0.363													6	3	---	---	---	---	
WBSCR16	81554	broad.mit.edu	37	7	74480144	74480144	+	Intron	DEL	A	-	-			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:74480144delA	uc003ubr.2	-						WBSCR16_uc010lca.2_Intron|WBSCR16_uc010lcb.1_Intron	NM_030798	NP_110425	Q96I51	WBS16_HUMAN	Williams-Beuren syndrome chromosome region 16												0						agtccatctcaaaaaaaaaaa	0.194													3	3	---	---	---	---	
SRRM3	222183	broad.mit.edu	37	7	75846558	75846559	+	Intron	DEL	AC	-	-			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:75846558_75846559delAC	uc010ldi.2	+							NM_001110199	NP_001103669			serine/arginine repetitive matrix 3												0						ttatagaaagacacacacacag	0.158													4	2	---	---	---	---	
MAGI2	9863	broad.mit.edu	37	7	77934548	77934548	+	Intron	DEL	T	-	-			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:77934548delT	uc003ugx.2	-						MAGI2_uc003ugy.2_Intron|MAGI2_uc010ldx.1_Intron|MAGI2_uc010ldy.1_Intron|MAGI2_uc011kgr.1_Intron|MAGI2_uc011kgs.1_Intron	NM_012301	NP_036433	Q86UL8	MAGI2_HUMAN	membrane associated guanylate kinase, WW and PDZ							cell junction|synapse|synaptosome	phosphatase binding			ovary(5)|lung(4)|breast(1)|skin(1)	11		all_cancers(73;0.0064)|all_epithelial(88;0.087)|all_neural(109;0.0936)|Medulloblastoma(109;0.166)|Melanoma(862;0.236)				CAGCTCTGTCTTTCAAAAAGC	0.453													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	79389453	79389454	+	IGR	INS	-	A	A			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:79389453_79389454insA								MAGI2 (306563 upstream) : GNAI1 (374686 downstream)																							atatgagaaggaaaaaccagta	0.000													4	2	---	---	---	---	
PCLO	27445	broad.mit.edu	37	7	82595299	82595299	+	Frame_Shift_Del	DEL	C	-	-			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:82595299delC	uc003uhx.2	-	4	4094	c.3805delG	c.(3805-3807)GTAfs	p.V1269fs	PCLO_uc003uhv.2_Frame_Shift_Del_p.V1269fs	NM_033026	NP_149015	Q9Y6V0	PCLO_HUMAN	piccolo isoform 1	1208					cytoskeleton organization|synaptic vesicle exocytosis	cell junction|cytoskeleton|synaptic vesicle	calcium ion binding|calcium-dependent phospholipid binding|profilin binding|transporter activity			ovary(7)	7						GCAATTTGTACTTGAGATTTA	0.438													1063	473	---	---	---	---	
ZNF804B	219578	broad.mit.edu	37	7	88735688	88735688	+	Intron	DEL	T	-	-			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:88735688delT	uc011khi.1	+							NM_181646	NP_857597	A4D1E1	Z804B_HUMAN	zinc finger protein 804B							intracellular	zinc ion binding			ovary(5)|skin(3)|pancreas(2)|upper_aerodigestive_tract(1)	11	all_hematologic(106;0.125)|Lung NSC(181;0.15)|all_lung(186;0.151)		STAD - Stomach adenocarcinoma(171;0.0513)			GGCACCAGTGTTTATACTACA	0.348										HNSCC(36;0.09)			4	2	---	---	---	---	
ZNF789	285989	broad.mit.edu	37	7	99076416	99076416	+	Intron	DEL	T	-	-			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:99076416delT	uc003uqq.1	+						ZNF789_uc003uqp.2_Intron|ZNF789_uc010lfw.1_Intron	NM_213603	NP_998768	Q5FWF6	ZN789_HUMAN	zinc finger protein 789 isoform 1						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0	all_cancers(62;2.54e-08)|all_epithelial(64;2.55e-09)|Lung NSC(181;0.0053)|all_lung(186;0.00895)|Esophageal squamous(72;0.0166)					ggtctgtaccttttatattct	0.134													4	2	---	---	---	---	
GPC2	221914	broad.mit.edu	37	7	99771762	99771763	+	Intron	DEL	CA	-	-			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:99771762_99771763delCA	uc003utv.2	-						GPC2_uc010lgr.2_Intron|GPC2_uc003utw.1_3'UTR	NM_152742	NP_689955	Q8N158	GPC2_HUMAN	glypican 2 precursor							anchored to membrane|endoplasmic reticulum|extracellular space|plasma membrane|proteinaceous extracellular matrix	heparan sulfate proteoglycan binding			breast(1)|pancreas(1)	2	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)					GTGAGATTGTCACAGATCTGAG	0.564													4	2	---	---	---	---	
ZAN	7455	broad.mit.edu	37	7	100369721	100369721	+	Intron	DEL	T	-	-			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:100369721delT	uc003uwj.2	+						ZAN_uc003uwk.2_Intron|ZAN_uc003uwl.2_Intron|ZAN_uc010lhh.2_Intron|ZAN_uc010lhi.2_Intron|ZAN_uc011kkd.1_Intron|ZAN_uc011kke.1_5'Flank	NM_003386	NP_003377	Q9Y493	ZAN_HUMAN	zonadhesin isoform 3						binding of sperm to zona pellucida|cell-cell adhesion	integral to membrane|plasma membrane				ovary(4)|large_intestine(3)|central_nervous_system(2)|pancreas(2)	11	Lung NSC(181;0.041)|all_lung(186;0.0581)		STAD - Stomach adenocarcinoma(171;0.19)			ctctaaattcttttttttttt	0.254													3	3	---	---	---	---	
RELN	5649	broad.mit.edu	37	7	103127001	103127001	+	Intron	DEL	A	-	-			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:103127001delA	uc003vca.2	-						RELN_uc010liz.2_Intron	NM_005045	NP_005036	P78509	RELN_HUMAN	reelin isoform a						axon guidance|cell adhesion|cerebral cortex tangential migration|glial cell differentiation|neuron migration|peptidyl-tyrosine phosphorylation|positive regulation of protein kinase activity|positive regulation of small GTPase mediated signal transduction|response to pain|spinal cord patterning	cytoplasm|dendrite|extracellular space|proteinaceous extracellular matrix	metal ion binding|protein serine/threonine/tyrosine kinase activity|serine-type peptidase activity			ovary(8)|upper_aerodigestive_tract(5)|large_intestine(2)|central_nervous_system(2)|skin(1)|pancreas(1)	19				COAD - Colon adenocarcinoma(1;8.98e-05)|Colorectal(1;0.00184)		acaactttacaaaaaaaaaaa	0.124													4	2	---	---	---	---	
RELN	5649	broad.mit.edu	37	7	103494811	103494811	+	Intron	DEL	T	-	-			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:103494811delT	uc003vca.2	-						RELN_uc010liz.2_Intron	NM_005045	NP_005036	P78509	RELN_HUMAN	reelin isoform a						axon guidance|cell adhesion|cerebral cortex tangential migration|glial cell differentiation|neuron migration|peptidyl-tyrosine phosphorylation|positive regulation of protein kinase activity|positive regulation of small GTPase mediated signal transduction|response to pain|spinal cord patterning	cytoplasm|dendrite|extracellular space|proteinaceous extracellular matrix	metal ion binding|protein serine/threonine/tyrosine kinase activity|serine-type peptidase activity			ovary(8)|upper_aerodigestive_tract(5)|large_intestine(2)|central_nervous_system(2)|skin(1)|pancreas(1)	19				COAD - Colon adenocarcinoma(1;8.98e-05)|Colorectal(1;0.00184)		cattctgaactttttttgttt	0.000													4	2	---	---	---	---	
RINT1	60561	broad.mit.edu	37	7	105204547	105204547	+	Intron	DEL	T	-	-			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:105204547delT	uc003vda.1	+						RINT1_uc010ljj.1_Intron	NM_021930	NP_068749	Q6NUQ1	RINT1_HUMAN	RAD50 interactor 1						cell cycle|G2/M transition DNA damage checkpoint|protein transport|vesicle-mediated transport	endoplasmic reticulum membrane	protein binding			ovary(3)|central_nervous_system(1)	4						CTCTTGGACAttttttttgag	0.174													6	3	---	---	---	---	
C7orf53	286006	broad.mit.edu	37	7	112129720	112129720	+	Intron	DEL	G	-	-			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:112129720delG	uc011kmq.1	+						C7orf53_uc003vgl.2_Intron|C7orf53_uc003vgm.2_Intron	NM_001134468	NP_001127940	Q8N8F7	CG053_HUMAN	hypothetical protein LOC286006							integral to membrane				ovary(1)	1						TTTCTCTACTGGGCTTCTGGC	0.458													18	10	---	---	---	---	
CADPS2	93664	broad.mit.edu	37	7	121959917	121959917	+	3'UTR	DEL	A	-	-			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:121959917delA	uc010lkp.2	-	29					CADPS2_uc011knx.1_3'UTR|CADPS2_uc003vkg.3_3'UTR|CADPS2_uc010lkq.2_3'UTR	NM_017954	NP_060424	Q86UW7	CAPS2_HUMAN	Ca2+-dependent activator protein for secretion 2						exocytosis|protein transport	cell junction|cytoplasmic vesicle membrane|synapse	lipid binding|metal ion binding			ovary(1)|central_nervous_system(1)	2						AATCTTCTTTAAAAAAAAAAG	0.308													6	3	---	---	---	---	
ZC3HC1	51530	broad.mit.edu	37	7	129663647	129663647	+	Intron	DEL	T	-	-			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:129663647delT	uc003vpi.2	-						ZC3HC1_uc003vph.2_Intron|ZC3HC1_uc010lma.2_Intron	NM_016478	NP_057562	Q86WB0	NIPA_HUMAN	zinc finger, C3HC type 1						cell division|mitosis	nucleus	protein kinase binding|zinc ion binding				0	Melanoma(18;0.0435)					atcttttttcttttttttttt	0.159													12	8	---	---	---	---	
COPG2	26958	broad.mit.edu	37	7	130292119	130292120	+	Intron	INS	-	ATAAATAA	ATAAATAA	rs137932108	by1000genomes	TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:130292119_130292120insATAAATAA	uc003vqh.1	-							NM_012133	NP_036265	Q9UBF2	COPG2_HUMAN	coatomer protein complex, subunit gamma 2						intra-Golgi vesicle-mediated transport|intracellular protein transport|retrograde vesicle-mediated transport, Golgi to ER	COPI vesicle coat	protein binding|structural molecule activity				0	Melanoma(18;0.0435)					gaGAGACTGTCataaataaata	0.025													2	4	---	---	---	---	
KIAA1549	57670	broad.mit.edu	37	7	138523008	138523008	+	Intron	DEL	C	-	-			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:138523008delC	uc011kql.1	-						KIAA1549_uc011kqi.1_Intron|KIAA1549_uc003vuk.3_Intron|KIAA1549_uc011kqj.1_Intron|KIAA1549_uc011kqk.1_Intron	NM_020910	NP_065961	Q9HCM3	K1549_HUMAN	hypothetical protein LOC57670 isoform 1							integral to membrane			KIAA1549/BRAF(229)	central_nervous_system(229)|pancreas(1)	230						CCACGTCCATCCACCAACTCA	0.547			O	BRAF	pilocytic astrocytoma								33	21	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	139202972	139202972	+	IGR	DEL	A	-	-			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:139202972delA								KLRG2 (34515 upstream) : CLEC2L (5702 downstream)																							GTAAATAAATAAAAAAAAAAA	0.448													4	2	---	---	---	---	
ARHGEF35	445328	broad.mit.edu	37	7	143893958	143893958	+	5'Flank	DEL	T	-	-			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:143893958delT	uc003wdz.1	-							NM_001003702	NP_001003702	A5YM69	ARG35_HUMAN	Rho guanine nucleotide exchange factor (GEF)												0						CGTTTTGTTCTGTTAGTCTTG	0.378													4	3	---	---	---	---	
KRBA1	84626	broad.mit.edu	37	7	149416983	149416983	+	Intron	DEL	A	-	-			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:149416983delA	uc003wfz.2	+						KRBA1_uc010lpj.2_Intron|KRBA1_uc003wga.2_5'Flank	NM_032534	NP_115923	A5PL33	KRBA1_HUMAN	KRAB A domain containing 1											ovary(1)|central_nervous_system(1)	2	Melanoma(164;0.165)|Ovarian(565;0.177)		OV - Ovarian serous cystadenocarcinoma(82;0.00625)			CGGTTCTTTGAGTTTAAGTGG	0.577													4	2	---	---	---	---	
ZNF775	285971	broad.mit.edu	37	7	150079984	150079985	+	Intron	INS	-	T	T	rs149109479	by1000genomes	TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:150079984_150079985insT	uc003whf.1	+							NM_173680	NP_775951	Q96BV0	ZN775_HUMAN	zinc finger protein 775						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0	Ovarian(565;0.183)|Melanoma(164;0.226)		OV - Ovarian serous cystadenocarcinoma(82;0.0173)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)		ATGGCCATGGGTGTACAAGGAT	0.535													4	3	---	---	---	---	
SMARCD3	6604	broad.mit.edu	37	7	150954078	150954078	+	Intron	DEL	C	-	-			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:150954078delC	uc003wjt.2	-						SMARCD3_uc003wju.2_Intron	NM_001003802	NP_001003802	Q6STE5	SMRD3_HUMAN	SWI/SNF related, matrix associated, actin						cellular lipid metabolic process|chromatin modification|nervous system development|positive regulation of transcription, DNA-dependent|regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	nBAF complex|npBAF complex|nucleoplasm|SWI/SNF complex	nuclear hormone receptor binding|protein binding|transcription coactivator activity|transcription factor binding			ovary(1)|lung(1)	2			OV - Ovarian serous cystadenocarcinoma(82;0.00448)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)		ccctggagttcccccagcagc	0.000													4	2	---	---	---	---	
MLL3	58508	broad.mit.edu	37	7	151949945	151949945	+	Intron	DEL	T	-	-			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:151949945delT	uc003wla.2	-							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)		GGGTACATGCttttttttttt	0.139			N		medulloblastoma								9	4	---	---	---	---	
DPP6	1804	broad.mit.edu	37	7	154140442	154140442	+	Intron	DEL	A	-	-	rs112705816		TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:154140442delA	uc003wlk.2	+						DPP6_uc003wli.2_Intron|DPP6_uc003wlj.2_Intron|DPP6_uc010lqh.1_Intron|DPP6_uc003wlm.2_Intron|DPP6_uc011kvq.1_Intron	NM_130797	NP_570629	P42658	DPP6_HUMAN	dipeptidyl-peptidase 6 isoform 1						cell death|proteolysis	integral to membrane	dipeptidyl-peptidase activity|serine-type peptidase activity			pancreas(3)|breast(1)	4	all_neural(206;0.181)	all_hematologic(28;0.0044)|all_lung(21;0.0176)|Lung NSC(21;0.0204)	OV - Ovarian serous cystadenocarcinoma(82;0.0562)			aaaaaaaatgaaaaaaaaaat	0.075													6	3	---	---	---	---	
CSMD1	64478	broad.mit.edu	37	8	3006324	3006324	+	Intron	DEL	T	-	-	rs146258626	by1000genomes	TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:3006324delT	uc011kwk.1	-						CSMD1_uc011kwj.1_Intron|CSMD1_uc010lrg.2_Intron	NM_033225	NP_150094	Q96PZ7	CSMD1_HUMAN	CUB and Sushi multiple domains 1 precursor							integral to membrane				breast(20)|large_intestine(5)	25		all_cancers(1;5.7e-41)|all_epithelial(1;2.54e-36)|Lung NSC(1;7.54e-11)|all_lung(1;3.2e-10)|Hepatocellular(1;3.78e-05)|Breast(1;0.000196)|Myeloproliferative disorder(4;0.000374)|Esophageal squamous(1;0.0157)|Ovarian(12;0.091)|Renal(68;0.144)|Colorectal(14;0.234)		all cancers(1;5.03e-41)|Epithelial(1;4.78e-31)|Lung(1;1.14e-14)|LUSC - Lung squamous cell carcinoma(1;2.34e-14)|GBM - Glioblastoma multiforme(1;4.49e-10)|Colorectal(4;1.18e-07)|OV - Ovarian serous cystadenocarcinoma(1;3.2e-07)|BRCA - Breast invasive adenocarcinoma(1;6.17e-07)|COAD - Colon adenocarcinoma(4;0.000539)|READ - Rectum adenocarcinoma(4;0.00896)|Kidney(5;0.00957)|KIRC - Kidney renal clear cell carcinoma(5;0.0689)		CTCACATGCCTCTCCTCCCAA	0.398													4	2	---	---	---	---	
FAM66D	100132923	broad.mit.edu	37	8	12039175	12039175	+	Intron	DEL	G	-	-			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:12039175delG	uc011kxp.1	+											Homo sapiens cDNA FLJ37098 fis, clone BRACE2019004.												0						GTGGGACCATGGGGGGTCTGG	0.607													4	2	---	---	---	---	
PSD3	23362	broad.mit.edu	37	8	18398194	18398194	+	Intron	DEL	G	-	-			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:18398194delG	uc003wza.2	-						PSD3_uc003wyx.3_Intron|PSD3_uc003wyy.2_Intron|PSD3_uc003wyz.2_Intron	NM_015310	NP_056125	Q9NYI0	PSD3_HUMAN	ADP-ribosylation factor guanine nucleotide						regulation of ARF protein signal transduction	cell junction|cytoplasm|postsynaptic density|postsynaptic membrane	ARF guanyl-nucleotide exchange factor activity			ovary(3)	3				Colorectal(111;0.0281)|READ - Rectum adenocarcinoma(644;0.183)		tgctctccctgttccctcctt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	24806491	24806491	+	IGR	DEL	G	-	-			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:24806491delG								NEFM (29886 upstream) : NEFL (1980 downstream)																							ACTAAGATATGGACATAAGTC	0.423													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	26522871	26522871	+	IGR	DEL	T	-	-	rs67745572		TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:26522871delT								DPYSL2 (7178 upstream) : ADRA1A (82796 downstream)																							tttgaaaatcttttttttttt	0.000													6	3	---	---	---	---	
NKAIN3	286183	broad.mit.edu	37	8	63611018	63611018	+	Intron	DEL	C	-	-			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:63611018delC	uc010lyq.1	+							NM_173688	NP_775959	Q8N8D7	NKAI3_HUMAN	Na+/K+ transporting ATPase interacting 3							integral to membrane|plasma membrane					0	Breast(64;0.127)	Lung NSC(129;0.187)				cagctgtggtccctgcaacac	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	65034503	65034503	+	IGR	DEL	A	-	-			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:65034503delA								YTHDF3 (909158 upstream) : MIR124-2 (257203 downstream)																							tgtttgtaacaaaaaaaaagg	0.000													7	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	68823279	68823279	+	IGR	DEL	A	-	-	rs72169266		TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:68823279delA								CPA6 (164659 upstream) : PREX2 (41069 downstream)																							TTGCTGATCTAAAAAAAAATA	0.348													4	2	---	---	---	---	
WWP1	11059	broad.mit.edu	37	8	87374058	87374058	+	Intron	DEL	T	-	-			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:87374058delT	uc003ydt.2	+							NM_007013	NP_008944	Q9H0M0	WWP1_HUMAN	WW domain containing E3 ubiquitin protein ligase						central nervous system development|entry of virus into host cell|negative regulation of transcription, DNA-dependent|protein ubiquitination involved in ubiquitin-dependent protein catabolic process|signal transduction	cytoplasm|nucleus|plasma membrane|ubiquitin ligase complex	protein binding|ubiquitin-protein ligase activity			lung(1)|liver(1)	2						tgcacacccctttctgtcaat	0.000													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	88800612	88800612	+	IGR	DEL	T	-	-			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:88800612delT								CNBD1 (405657 upstream) : DCAF4L2 (82361 downstream)																							GCTTGTCATATTTTTTTTTGT	0.358													10	5	---	---	---	---	
ZFPM2	23414	broad.mit.edu	37	8	106596711	106596711	+	Intron	DEL	A	-	-			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:106596711delA	uc003ymd.2	+							NM_012082	NP_036214	Q8WW38	FOG2_HUMAN	zinc finger protein, multitype 2						blood coagulation|negative regulation of fat cell differentiation|outflow tract septum morphogenesis|right ventricular cardiac muscle tissue morphogenesis|ventricular septum morphogenesis	nucleoplasm	DNA binding|RNA polymerase II transcription coactivator activity|transcription corepressor activity|transcription factor binding|zinc ion binding			ovary(4)|large_intestine(1)	5			OV - Ovarian serous cystadenocarcinoma(57;8.28e-08)			CCGTGGCGTCAAAAACACAAA	0.403													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	117120645	117120645	+	IGR	DEL	A	-	-			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:117120645delA								TRPS1 (439417 upstream) : EIF3H (536411 downstream)																							CTAACAAAAGAAAAAAAACAT	0.408													5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	117300811	117300811	+	IGR	DEL	A	-	-			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:117300811delA								TRPS1 (619583 upstream) : EIF3H (356245 downstream)																							TTATCAACATAAAAAGGCAAC	0.398													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	119751105	119751105	+	IGR	DEL	A	-	-			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:119751105delA								SAMD12 (116871 upstream) : TNFRSF11B (184692 downstream)																							TAATTTTTTTAAAATGGCACC	0.378													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	124617335	124617335	+	IGR	DEL	G	-	-			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:124617335delG								FBXO32 (63889 upstream) : KLHL38 (40580 downstream)																							gatccttcctgcttcaaaaca	0.000													4	2	---	---	---	---	
FAM49B	51571	broad.mit.edu	37	8	131025015	131025015	+	Intron	DEL	A	-	-	rs80049825		TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:131025015delA	uc003ysw.2	-						FAM49B_uc003ysx.2_Intron|FAM49B_uc003ysy.1_Intron	NM_016623	NP_057707	Q9NUQ9	FA49B_HUMAN	hypothetical protein LOC51571												0	Ovarian(5;0.000567)|Esophageal squamous(12;0.00693)|Acute lymphoblastic leukemia(118;0.155)		LUAD - Lung adenocarcinoma(14;0.0989)			GGAGGAGAGGAAAAAAAAAAT	0.274													5	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	134909404	134909405	+	IGR	INS	-	G	G	rs138887496	by1000genomes	TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:134909404_134909405insG								ST3GAL1 (325221 upstream) : ZFAT (580628 downstream)																							CCACAGATCCTCTTGTAGCAAT	0.386													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	137556039	137556039	+	IGR	DEL	A	-	-			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:137556039delA								KHDRBS3 (896193 upstream) : None (None downstream)																							catgtaaggtaaaaagcaata	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	142632362	142632362	+	IGR	DEL	G	-	-	rs36067019		TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:142632362delG								FLJ43860 (115032 upstream) : MIR1302-7 (235241 downstream)																							CGGAGGCAGCGGCAGGAGACG	0.542													4	2	---	---	---	---	
SMARCA2	6595	broad.mit.edu	37	9	2192380	2192380	+	Intron	DEL	T	-	-			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:2192380delT	uc003zhc.2	+						SMARCA2_uc003zhd.2_Intron|SMARCA2_uc010mha.2_Intron|SMARCA2_uc011llw.1_Intron|SMARCA2_uc003zhf.2_Intron|SMARCA2_uc011llx.1_Intron|SMARCA2_uc003zhe.2_Intron|SMARCA2_uc003zhg.2_Intron|SMARCA2_uc010mhb.2_Intron	NM_003070	NP_003061	P51531	SMCA2_HUMAN	SWI/SNF-related matrix-associated						chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development	intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex	ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding			ovary(2)|central_nervous_system(1)	3		all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09)		GBM - Glioblastoma multiforme(50;0.0475)		ATGCAGGGTATTTTTTTTTCT	0.348													6	3	---	---	---	---	
FREM1	158326	broad.mit.edu	37	9	14747964	14747965	+	Intron	INS	-	T	T			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:14747964_14747965insT	uc003zlm.2	-						FREM1_uc010mic.2_Intron|FREM1_uc003zlk.2_Intron|FREM1_uc003zll.2_Intron	NM_144966	NP_659403	Q5H8C1	FREM1_HUMAN	FRAS1 related extracellular matrix 1 precursor						cell communication|multicellular organismal development	basement membrane|integral to membrane	metal ion binding|sugar binding			ovary(2)|breast(2)|pancreas(1)	5				GBM - Glioblastoma multiforme(50;3.53e-06)		GTACATCTTTATTTTTTGGTAT	0.317													4	2	---	---	---	---	
PLAA	9373	broad.mit.edu	37	9	26908166	26908166	+	Intron	DEL	T	-	-			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:26908166delT	uc003zqd.2	-						PLAA_uc003zqe.2_Intron	NM_001031689	NP_001026859	Q9Y263	PLAP_HUMAN	phospholipase A2-activating protein						phospholipid metabolic process|signal transduction		phospholipase A2 activator activity				0		all_neural(3;3.53e-10)|Glioma(3;2.71e-09)		Lung(218;1.32e-05)|LUSC - Lung squamous cell carcinoma(38;0.00011)		GAGCtttgtcttttttttttt	0.169													3	6	---	---	---	---	
TLN1	7094	broad.mit.edu	37	9	35714892	35714893	+	Intron	DEL	TC	-	-			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:35714892_35714893delTC	uc003zxt.2	-							NM_006289	NP_006280	Q9Y490	TLN1_HUMAN	talin 1						axon guidance|cell adhesion|cell-cell junction assembly|cellular component movement|cytoskeletal anchoring at plasma membrane|muscle contraction|platelet activation|platelet degranulation	actin cytoskeleton|centrosome|cytosol|extracellular region|focal adhesion|intracellular membrane-bounded organelle|ruffle membrane	actin binding|insulin receptor binding|LIM domain binding|structural constituent of cytoskeleton|vinculin binding			lung(7)|breast(3)|ovary(2)|central_nervous_system(1)	13	all_epithelial(49;0.167)		Lung(28;0.00276)|LUSC - Lung squamous cell carcinoma(32;0.00418)|STAD - Stomach adenocarcinoma(86;0.194)			ACAAGAGTAGTCAGACCAAGCC	0.584													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	38572276	38572276	+	Intron	DEL	A	-	-			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:38572276delA	uc004abb.1	-						uc010mmc.1_Intron|uc010mmd.1_Intron|uc004abf.1_3'UTR|uc004abg.3_Intron					Homo sapiens mRNA for KIAA2015 protein.																		tcatgtactcaacagccacgt	0.119													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	66481328	66481329	+	IGR	INS	-	T	T			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:66481328_66481329insT								FAM74A4 (986942 upstream) : LOC442421 (15141 downstream)																							agattctggtgttttttgtctt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	66545694	66545695	+	Intron	INS	-	A	A			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:66545694_66545695insA	uc010mnh.1	-						uc004aef.2_Intron					Homo sapiens cDNA FLJ20444 fis, clone KAT05128.																		CCTGTAAGAGGAAAAAAAAACA	0.371													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	68406889	68406889	+	IGR	DEL	G	-	-	rs113316891		TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:68406889delG								FAM27B (612700 upstream) : MIR1299 (595350 downstream)																							atccagggcagtcatagtggt	0.000													1	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	69443200	69443201	+	Intron	INS	-	TA	TA			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:69443200_69443201insTA	uc010mnx.1	+							NM_001098806	NP_001092276			coiled-coil domain containing 29																		ATAAGAATTCCTATTTCAAGCC	0.381													6	4	---	---	---	---	
C9orf85	138241	broad.mit.edu	37	9	74526979	74526980	+	Intron	DEL	CA	-	-	rs146995342		TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:74526979_74526980delCA	uc004ain.2	+						C9orf85_uc004aio.2_Intron|C9orf85_uc010mou.2_Intron|C9orf85_uc010mov.2_Intron|FAM108B1_uc004ail.2_5'Flank|FAM108B1_uc004aim.1_5'Flank	NM_182505	NP_872311	Q96MD7	CI085_HUMAN	hypothetical protein LOC138241												0						TAACTAATTGCACAGAGTGAAC	0.441													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	83138576	83138577	+	IGR	INS	-	T	T			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:83138576_83138577insT								TLE4 (796919 upstream) : None (None downstream)																							ccctccatctctgacaaacatc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	85309726	85309727	+	IGR	INS	-	T	T			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:85309726_85309727insT								FLJ46321 (699556 upstream) : RASEF (287590 downstream)																							tttccttgttgtttttttttta	0.000													3	3	---	---	---	---	
AUH	549	broad.mit.edu	37	9	94075022	94075023	+	Intron	INS	-	A	A			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:94075022_94075023insA	uc004arf.3	-						AUH_uc004arg.3_Intron|AUH_uc011ltu.1_Intron	NM_001698	NP_001689	Q13825	AUHM_HUMAN	AU RNA binding protein/enoyl-Coenzyme A						branched chain family amino acid catabolic process|mRNA catabolic process	mitochondrial matrix	enoyl-CoA hydratase activity|methylglutaconyl-CoA hydratase activity|mRNA 3'-UTR binding				0						ttaaaacaaacaaaaaaaaatt	0.074													6	3	---	---	---	---	
NIPSNAP3A	25934	broad.mit.edu	37	9	107521087	107521087	+	Intron	DEL	A	-	-			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:107521087delA	uc004bch.1	+						NIPSNAP3A_uc011lvt.1_Intron|NIPSNAP3A_uc011lvu.1_Intron	NM_015469	NP_056284	Q9UFN0	NPS3A_HUMAN	nipsnap homolog 3A							cytosol					0						ctaaaaatacaaaaaaaaaaa	0.000													8	4	---	---	---	---	
PTGR1	22949	broad.mit.edu	37	9	114325091	114325091	+	Intron	DEL	A	-	-			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:114325091delA	uc011lwr.1	-						ZNF483_uc004bfg.2_Intron	NM_001146109	NP_001139581	Q14914	PTGR1_HUMAN	prostaglandin reductase 1 isoform 2						leukotriene metabolic process	cytoplasm	15-oxoprostaglandin 13-oxidase activity|2-alkenal reductase activity|alcohol dehydrogenase (NAD) activity|zinc ion binding				0						atgtgttctcattgttcagct	0.100													4	2	---	---	---	---	
STOM	2040	broad.mit.edu	37	9	124103031	124103031	+	3'UTR	DEL	A	-	-	rs74746469	by1000genomes	TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:124103031delA	uc004blh.2	-	7					STOM_uc011lyk.1_3'UTR|STOM_uc004bli.2_3'UTR	NM_004099	NP_004090	P27105	STOM_HUMAN	stomatin isoform a						protein homooligomerization	cytoskeleton|integral to plasma membrane|melanosome|membrane raft	protein binding				0				OV - Ovarian serous cystadenocarcinoma(323;0.00107)|GBM - Glioblastoma multiforme(294;0.0137)		tccatctcagaaaaaaaaaaa	0.204													3	5	---	---	---	---	
SCAI	286205	broad.mit.edu	37	9	127786239	127786240	+	Intron	DEL	GT	-	-	rs113566875		TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:127786239_127786240delGT	uc004bpe.2	-						SCAI_uc004bpd.2_Intron|SCAI_uc010mwu.2_Intron	NM_001144877	NP_001138349	Q8N9R8	SCAI_HUMAN	suppressor of cancer cell invasion isoform 2						negative regulation of cell migration|negative regulation of Rho protein signal transduction|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|integral to membrane|nucleus	protein binding|transcription corepressor activity			ovary(2)|breast(2)|central_nervous_system(1)	5						AGAAAAAAGAGTGTGACTCACT	0.436													4	2	---	---	---	---	
GARNL3	84253	broad.mit.edu	37	9	130154945	130154946	+	Intron	INS	-	AA	AA			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:130154945_130154946insAA	uc011mae.1	+						GARNL3_uc011mad.1_Intron|GARNL3_uc010mxi.2_Intron	NM_032293	NP_115669	Q5VVW2	GARL3_HUMAN	GTPase activating Rap/RanGAP domain-like 3						regulation of small GTPase mediated signal transduction	intracellular	GTPase activator activity|small GTPase regulator activity			ovary(1)|central_nervous_system(1)|skin(1)	3						ATGCAGCTATTGAGAGAGTCCT	0.490													4	2	---	---	---	---	
C9orf98	158067	broad.mit.edu	37	9	135649038	135649039	+	Intron	DEL	GT	-	-			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:135649038_135649039delGT	uc004cbu.1	-						C9orf98_uc010mzx.1_Intron|C9orf98_uc004cbv.1_Intron	NM_152572	NP_689785	Q96MA6	KAD8_HUMAN	putative adenylate kinase-like protein C9orf98							cytosol	adenylate kinase activity|ATP binding|cytidylate kinase activity				0				OV - Ovarian serous cystadenocarcinoma(145;4.89e-06)|Epithelial(140;0.00016)		atagttcagagtgacaaatacc	0.005													4	2	---	---	---	---	
MAN1B1	11253	broad.mit.edu	37	9	139996194	139996195	+	Intron	DEL	TG	-	-	rs4880203	by1000genomes	TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:139996194_139996195delTG	uc004cld.2	+						MAN1B1_uc004clc.2_Frame_Shift_Del_p.C343fs|MAN1B1_uc011meo.1_Intron|MAN1B1_uc011mep.1_Intron|MAN1B1_uc010ncc.2_Intron|MAN1B1_uc004clf.1_5'Flank|MAN1B1_uc004clg.1_5'Flank	NM_016219	NP_057303	Q9UKM7	MA1B1_HUMAN	alpha 1,2-mannosidase						oligosaccharide metabolic process|post-translational protein modification|protein folding|protein N-linked glycosylation via asparagine	endoplasmic reticulum membrane|endoplasmic reticulum quality control compartment|integral to membrane	alpha-mannosidase activity|calcium ion binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity			ovary(1)|central_nervous_system(1)	2	all_cancers(76;0.0926)	Myeloproliferative disorder(178;0.0511)	STAD - Stomach adenocarcinoma(284;0.0878)	OV - Ovarian serous cystadenocarcinoma(145;3.08e-05)|Epithelial(140;0.000513)		CAGCAGGTACtgtgtgtgtgtg	0.297													4	3	---	---	---	---	
LOC100216001	100216001	broad.mit.edu	37	10	4641535	4641535	+	Intron	DEL	C	-	-			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:4641535delC	uc001ihe.3	-											Homo sapiens, clone IMAGE:4450067, mRNA.												0						CAAAATTCCTCCACAGCTGCA	0.438													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	4799069	4799070	+	IGR	DEL	TA	-	-	rs139210517		TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:4799069_4799070delTA								LOC100216001 (78807 upstream) : AKR1E2 (69332 downstream)																							tctctgttcctatgtcttcttc	0.074													0	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	4806125	4806125	+	IGR	DEL	T	-	-			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:4806125delT								LOC100216001 (85863 upstream) : AKR1E2 (62277 downstream)																							gagccttcccttttttccact	0.000													4	2	---	---	---	---	
PARG	8505	broad.mit.edu	37	10	51371731	51371731	+	5'Flank	DEL	T	-	-			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:51371731delT	uc001jif.2	-						PARG_uc001jih.2_Intron|uc010qha.1_Intron|uc001jin.2_Intron|uc010qhb.1_Intron|uc010qhc.1_Intron|PARG_uc001jig.2_5'Flank|PARG_uc010qgv.1_5'Flank|PARG_uc009xoi.2_5'Flank|PARG_uc010qgw.1_5'Flank|PARG_uc009xoj.2_5'Flank|PARG_uc010qgx.1_5'Flank|AGAP8_uc001jik.2_5'Flank|PARG_uc010qgz.1_5'Flank	NM_003631	NP_003622	Q86W56	PARG_HUMAN	poly (ADP-ribose) glycohydrolase						carbohydrate metabolic process	nucleus	poly(ADP-ribose) glycohydrolase activity			ovary(2)	2				Epithelial(53;0.213)		TATGTTGTTGTTTTTTTTTTC	0.453													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	69483995	69483995	+	IGR	DEL	G	-	-			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:69483995delG								CTNNA3 (28046 upstream) : DNAJC12 (72433 downstream)																							gtttataccaggagtgggcct	0.025													4	2	---	---	---	---	
LRRC20	55222	broad.mit.edu	37	10	72122493	72122493	+	Intron	DEL	T	-	-	rs77013813		TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:72122493delT	uc001jqx.1	-						LRRC20_uc001jqy.1_Intron|LRRC20_uc001jqz.1_Intron	NM_207119	NP_997002	Q8TCA0	LRC20_HUMAN	leucine rich repeat containing 20 isoform 1												0						aggggggcagttttgccccca	0.269													5	5	---	---	---	---	
PPP3CB	5532	broad.mit.edu	37	10	75199339	75199360	+	Intron	DEL	GCTATACTGTATAGCATAACAT	-	-			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:75199339_75199360delGCTATACTGTATAGCATAACAT	uc001jue.2	-						PPP3CB_uc001juf.2_Intron|PPP3CB_uc001jug.2_Intron|PPP3CB_uc010qkj.1_Intron	NM_021132	NP_066955	P16298	PP2BB_HUMAN	protein phosphatase 3, catalytic subunit, beta											skin(1)	1	Prostate(51;0.0119)					ACTTTATAAAGCTATACTGTATAGCATAACATGCTATACTCT	0.333													4	2	---	---	---	---	
SORBS1	10580	broad.mit.edu	37	10	97141212	97141212	+	Intron	DEL	A	-	-			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:97141212delA	uc001kkp.2	-						SORBS1_uc001kkk.2_Intron|SORBS1_uc001kkl.2_Intron|SORBS1_uc001kkn.2_Intron|SORBS1_uc001kkm.2_Intron|SORBS1_uc001kko.2_Intron|SORBS1_uc001kkq.2_Intron|SORBS1_uc001kkr.2_Intron|SORBS1_uc001kks.2_Intron|SORBS1_uc001kkt.2_Intron|SORBS1_uc001kku.2_Intron|SORBS1_uc001kkv.2_Intron|SORBS1_uc001kkw.2_Intron|SORBS1_uc010qoe.1_Intron|SORBS1_uc010qof.1_Intron	NM_001034954	NP_001030126	Q9BX66	SRBS1_HUMAN	sorbin and SH3 domain containing 1 isoform 3						focal adhesion assembly|glucose transport|insulin receptor signaling pathway|muscle contraction|positive regulation of establishment of protein localization in plasma membrane|positive regulation of glucose import|positive regulation of glycogen biosynthetic process|positive regulation of lipid biosynthetic process|stress fiber assembly	centrosome|cytosol|focal adhesion|membrane raft|nucleus|stress fiber|zonula adherens	actin binding|insulin receptor binding|SH3/SH2 adaptor activity			breast(1)	1		Colorectal(252;0.0429)		Epithelial(162;1.7e-06)|all cancers(201;6.52e-05)		AACCATGCACAAAAAAAGCAA	0.323													4	2	---	---	---	---	
C10orf76	79591	broad.mit.edu	37	10	103755633	103755634	+	Intron	DEL	TG	-	-			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:103755633_103755634delTG	uc009xwy.1	-							NM_024541	NP_078817	Q5T2E6	CJ076_HUMAN	hypothetical protein LOC79591							integral to membrane					0		Colorectal(252;0.123)		Epithelial(162;2.41e-08)|all cancers(201;6.41e-07)		CCTAGAAAGCTGTGAACTCTTG	0.272													4	2	---	---	---	---	
PDCD4	27250	broad.mit.edu	37	10	112654478	112654478	+	Intron	DEL	T	-	-			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:112654478delT	uc001kzh.2	+						PDCD4_uc001kzg.2_Intron|PDCD4_uc010qre.1_Intron	NM_014456	NP_055271	Q53EL6	PDCD4_HUMAN	programmed cell death 4 isoform 1						apoptosis|cell aging|negative regulation of cell cycle|negative regulation of JUN kinase activity|negative regulation of transcription, DNA-dependent	cytosol|nucleus	protein binding|RNA binding			ovary(1)|breast(1)|skin(1)	3		Breast(234;0.0848)|Lung NSC(174;0.238)		Epithelial(162;0.000526)|all cancers(201;0.00794)|BRCA - Breast invasive adenocarcinoma(275;0.125)		CACTGCAGTGTTTTTTTTTTT	0.279													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	113743856	113743859	+	IGR	DEL	TGTG	-	-			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:113743856_113743859delTGTG								ADRA2A (903196 upstream) : GPAM (165763 downstream)																							AGCCACAAACTGTGTGTGTGTGTG	0.422													3	3	---	---	---	---	
GPAM	57678	broad.mit.edu	37	10	113932973	113932973	+	Intron	DEL	T	-	-			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:113932973delT	uc009xxy.1	-						GPAM_uc001kzp.2_Intron|GPAM_uc001kzq.1_Intron	NM_020918	NP_065969	Q9HCL2	GPAT1_HUMAN	mitochondrial glycerol 3-phosphate						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)		TGCACATGCATGCACGTATGT	0.323													3	3	---	---	---	---	
PLEKHA1	59338	broad.mit.edu	37	10	124189046	124189046	+	Intron	DEL	G	-	-			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:124189046delG	uc001lge.1	+						PLEKHA1_uc001lgf.1_Intron|PLEKHA1_uc001lgg.1_Intron	NM_001001974	NP_001001974	Q9HB21	PKHA1_HUMAN	pleckstrin homology domain containing, family A						B cell receptor signaling pathway|cellular response to hydrogen peroxide|establishment of protein localization|negative regulation of protein kinase B signaling cascade|phosphatidylinositol 3-kinase cascade|ruffle organization	cytoplasm|nucleus|ruffle membrane	PDZ domain binding|phosphatidylinositol-3,4-bisphosphate binding			kidney(1)	1		all_neural(114;0.0765)|Lung NSC(174;0.132)|all_lung(145;0.163)|Breast(234;0.238)				gtgtgtgtgtgtTTTATTTGT	0.363													4	2	---	---	---	---	
DOCK1	1793	broad.mit.edu	37	10	129073518	129073518	+	Intron	DEL	A	-	-			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:129073518delA	uc001ljt.2	+						DOCK1_uc010qun.1_Intron	NM_001380	NP_001371	Q14185	DOCK1_HUMAN	dedicator of cytokinesis 1						apoptosis|axon guidance|blood coagulation|integrin-mediated signaling pathway|phagocytosis, engulfment|small GTPase mediated signal transduction	cytosol|membrane	GTP binding|GTPase activator activity|GTPase binding|guanyl-nucleotide exchange factor activity|SH3 domain binding			central_nervous_system(4)|ovary(2)|lung(1)|breast(1)|kidney(1)	9		all_epithelial(44;2.3e-07)|all_lung(145;0.00466)|Lung NSC(174;0.00685)|Colorectal(57;0.0107)|Renal(717;0.0113)|Breast(234;0.0492)|all_neural(114;0.108)|all_hematologic(284;0.14)		BRCA - Breast invasive adenocarcinoma(275;0.0221)|Colorectal(40;0.115)		taataggaagaaaaaaaaaaa	0.000													4	2	---	---	---	---	
SYT9	143425	broad.mit.edu	37	11	7478624	7478625	+	Intron	DEL	CC	-	-			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:7478624_7478625delCC	uc001mfe.2	+						SYT9_uc009yfi.2_Intron|uc001mff.1_Intron|uc001mfg.2_Intron	NM_175733	NP_783860	Q86SS6	SYT9_HUMAN	synaptotagmin IX							cell junction|integral to membrane|synaptic vesicle membrane	metal ion binding|transporter activity			ovary(2)|large_intestine(1)	3				Epithelial(150;1.34e-07)|LUSC - Lung squamous cell carcinoma(625;0.0949)		tgtgtgtcatccccagcacctc	0.000													4	2	---	---	---	---	
TUB	7275	broad.mit.edu	37	11	8121531	8121531	+	Intron	DEL	G	-	-			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:8121531delG	uc001mga.2	+						TUB_uc010rbk.1_Intron|TUB_uc001mfy.2_Intron	NM_177972	NP_813977	P50607	TUB_HUMAN	tubby isoform b						phagocytosis|positive regulation of phagocytosis|response to stimulus	cytoplasm|extracellular region|nucleus|plasma membrane				ovary(1)	1		all_lung(207;6.91e-20)|Lung NSC(207;3.36e-17)		Epithelial(150;1.69e-62)|BRCA - Breast invasive adenocarcinoma(625;8.54e-06)|LUSC - Lung squamous cell carcinoma(625;0.000184)		gagagccactggagagttctg	0.000													4	2	---	---	---	---	
SBF2	81846	broad.mit.edu	37	11	10275316	10275317	+	Intron	INS	-	A	A	rs146748255	by1000genomes	TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:10275316_10275317insA	uc001mib.2	-							NM_030962	NP_112224	Q86WG5	MTMRD_HUMAN	SET binding factor 2						myelination	cytoplasm|membrane	phosphatase activity|protein binding			upper_aerodigestive_tract(1)|ovary(1)|skin(1)	3				all cancers(16;2.88e-11)|Epithelial(150;3.61e-10)|BRCA - Breast invasive adenocarcinoma(625;0.00887)		TCCAAATCTCCAAAAAAAAACA	0.327													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	13810122	13810123	+	IGR	INS	-	C	C	rs148722632	by1000genomes	TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:13810122_13810123insC								FAR1 (56231 upstream) : SPON1 (173791 downstream)																							AGCCCACCTCATCATTTTCAGA	0.347													4	2	---	---	---	---	
COPB1	1315	broad.mit.edu	37	11	14497084	14497084	+	Intron	DEL	A	-	-			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:14497084delA	uc001mli.2	-						COPB1_uc001mlg.2_Intron|COPB1_uc001mlh.2_Intron	NM_016451	NP_057535	P53618	COPB_HUMAN	coatomer protein complex, subunit beta 1						COPI coating of Golgi vesicle|interspecies interaction between organisms|intra-Golgi vesicle-mediated transport|intracellular protein transport|retrograde vesicle-mediated transport, Golgi to ER	COPI vesicle coat|cytosol|ER-Golgi intermediate compartment|plasma membrane	protein binding|structural molecule activity			ovary(1)|central_nervous_system(1)	2						TTTTCTGAGTAAAAATAATTT	0.303													4	2	---	---	---	---	
NAV2	89797	broad.mit.edu	37	11	20097782	20097787	+	Intron	DEL	TCTAAA	-	-	rs141829686		TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:20097782_20097787delTCTAAA	uc010rdm.1	+						NAV2_uc001mpp.2_Intron|NAV2_uc001mpr.3_Intron|NAV2_uc001mpt.2_Intron|NAV2_uc009yhx.2_Intron|NAV2_uc009yhy.1_Intron|NAV2_uc009yhz.2_Intron|NAV2_uc001mpu.2_Intron	NM_145117	NP_660093	Q8IVL1	NAV2_HUMAN	neuron navigator 2 isoform 2							nucleus	ATP binding|helicase activity			skin(4)|ovary(1)|pancreas(1)	6						gacctctaactctaaatcctgttccc	0.058													1	5	---	---	---	---	
NELL1	4745	broad.mit.edu	37	11	21058281	21058282	+	Intron	DEL	CA	-	-			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:21058281_21058282delCA	uc001mqe.2	+						NELL1_uc001mqf.2_Intron|NELL1_uc009yid.2_Intron|NELL1_uc010rdo.1_Intron|NELL1_uc010rdp.1_Intron	NM_006157	NP_006148	Q92832	NELL1_HUMAN	nel-like 1 isoform 1 precursor						cell adhesion|nervous system development	extracellular region	calcium ion binding|structural molecule activity			ovary(2)|large_intestine(1)	3						ctctctgtctcacacacacaca	0.000													4	2	---	---	---	---	
ABTB2	25841	broad.mit.edu	37	11	34259777	34259778	+	Intron	INS	-	C	C			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:34259777_34259778insC	uc001mvl.1	-							NM_145804	NP_665803	Q8N961	ABTB2_HUMAN	ankyrin repeat and BTB (POZ) domain containing								DNA binding			central_nervous_system(1)|skin(1)	2		Acute lymphoblastic leukemia(5;0.0508)|all_hematologic(20;0.0691)				agtattcctttcccctggcatc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	44874299	44874299	+	IGR	DEL	G	-	-			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:44874299delG								CD82 (232986 upstream) : TSPAN18 (7580 downstream)																							AGCCAGACGTGGGGGTTACTA	0.498													4	2	---	---	---	---	
CD6	923	broad.mit.edu	37	11	60780726	60780726	+	Intron	DEL	C	-	-			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:60780726delC	uc001nqq.2	+						CD6_uc009yni.2_Intron|CD6_uc009ynj.2_Intron|CD6_uc001nqp.2_Intron|CD6_uc001nqr.2_Intron|CD6_uc001nqs.2_Intron|CD6_uc001nqt.2_Intron	NM_006725	NP_006716	P30203	CD6_HUMAN	CD6 molecule precursor						cell adhesion	cell surface|integral to plasma membrane	scavenger receptor activity			pancreas(1)	1						atttattgagcgcctaatata	0.299													4	2	---	---	---	---	
CYBASC3	220002	broad.mit.edu	37	11	61118229	61118230	+	Intron	INS	-	G	G			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:61118229_61118230insG	uc001nrf.3	-						CYBASC3_uc010rlh.1_Intron|CYBASC3_uc001nrg.2_Intron|CYBASC3_uc009ynn.2_Intron|CYBASC3_uc001nrh.2_Intron|CYBASC3_uc001nri.2_Intron	NM_001161452	NP_001154924	Q8NBI2	CYAC3_HUMAN	cytochrome b, ascorbate dependent 3 isoform 2						electron transport chain|transport	integral to membrane|late endosome membrane|lysosomal membrane	metal ion binding|oxidoreductase activity				0						CACAGTGATTTGGGGGGGAAAT	0.545													4	2	---	---	---	---	
UCP2	7351	broad.mit.edu	37	11	73688106	73688107	+	Intron	INS	-	T	T			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:73688106_73688107insT	uc001oup.1	-						UCP2_uc001ouq.1_Intron	NM_003355	NP_003346	P55851	UCP2_HUMAN	uncoupling protein 2						proton transport|respiratory electron transport chain	integral to membrane|mitochondrial inner membrane	binding				0	Breast(11;0.000112)					GCTTGCACTCATTTTCTACCTC	0.564													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	125025693	125025694	+	IGR	DEL	TG	-	-			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:125025693_125025694delTG								TMEM218 (44218 upstream) : PKNOX2 (8865 downstream)																							tctgtgtgattgtgtgtgtgac	0.144													4	2	---	---	---	---	
FLI1	2313	broad.mit.edu	37	11	128678624	128678624	+	Intron	DEL	A	-	-			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:128678624delA	uc010sbu.1	+						FLI1_uc010sbt.1_Intron|FLI1_uc010sbv.1_Intron|FLI1_uc009zci.2_Intron	NM_002017	NP_002008	Q01543	FLI1_HUMAN	Friend leukemia virus integration 1						hemostasis|organ morphogenesis	nucleus	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity		EWSR1/FLI1(2266)	bone(2210)|soft_tissue(48)|autonomic_ganglia(4)|central_nervous_system(4)|lung(3)|ovary(2)|pancreas(2)	2273	all_hematologic(175;0.0641)	Lung NSC(97;0.00588)|all_lung(97;0.00764)|Breast(109;0.0115)|Medulloblastoma(222;0.0523)|all_neural(223;0.0862)|all_hematologic(192;0.182)		OV - Ovarian serous cystadenocarcinoma(99;0.01)|LUSC - Lung squamous cell carcinoma(976;0.0324)|Lung(977;0.0327)		tgctACATTTAAAAAAAAAAA	0.179			T	EWSR1	Ewing sarcoma								5	3	---	---	---	---	
KDM5A	5927	broad.mit.edu	37	12	492921	492921	+	Intron	DEL	T	-	-	rs71839973		TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:492921delT	uc001qif.1	-						KDM5A_uc001qie.1_Intron|KDM5A_uc010sdn.1_Intron|KDM5A_uc010sdo.1_Intron	NM_001042603	NP_001036068	P29375	KDM5A_HUMAN	retinoblastoma binding protein 2 isoform 1						chromatin modification|multicellular organismal development|positive regulation of transcription, DNA-dependent|transcription from RNA polymerase II promoter	cytoplasm|nucleolus	DNA binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|sequence-specific DNA binding transcription factor activity|zinc ion binding			skin(2)|ovary(1)	3						TTCATTGTCCttttttttttt	0.109			T 	NUP98	AML								3	3	---	---	---	---	
ANO2	57101	broad.mit.edu	37	12	5802940	5802940	+	Intron	DEL	T	-	-			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:5802940delT	uc001qnm.2	-							NM_020373	NP_065106	Q9NQ90	ANO2_HUMAN	anoctamin 2							chloride channel complex|plasma membrane	intracellular calcium activated chloride channel activity			ovary(4)|large_intestine(2)|central_nervous_system(1)	7						catcaggacctttgcatttgc	0.000													4	2	---	---	---	---	
ART4	420	broad.mit.edu	37	12	14994216	14994216	+	Intron	DEL	A	-	-			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:14994216delA	uc001rcl.1	-						ART4_uc009zid.1_Intron|ART4_uc009zie.1_Intron|ART4_uc001rcm.1_Intron	NM_021071	NP_066549	Q93070	NAR4_HUMAN	ADP-ribosyltransferase 4 precursor						arginine metabolic process|protein ADP-ribosylation	anchored to membrane|plasma membrane	NAD(P)+-protein-arginine ADP-ribosyltransferase activity				0						AGTTACACTGAAAATCATTAC	0.338													4	2	---	---	---	---	
ITPR2	3709	broad.mit.edu	37	12	26877951	26877952	+	Intron	INS	-	CA	CA			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:26877951_26877952insCA	uc001rhg.2	-						ITPR2_uc001rhh.1_Intron|ITPR2_uc001rhi.1_Intron	NM_002223	NP_002214	Q14571	ITPR2_HUMAN	inositol 1,4,5-triphosphate receptor, type 2						activation of phospholipase C activity|energy reserve metabolic process|nerve growth factor receptor signaling pathway|platelet activation|regulation of insulin secretion|response to hypoxia	integral to membrane|plasma membrane enriched fraction|platelet dense tubular network membrane|sarcoplasmic reticulum membrane	calcium ion transmembrane transporter activity|inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity			kidney(6)|ovary(4)|skin(2)|upper_aerodigestive_tract(1)|lung(1)	14	Colorectal(261;0.0847)					TAAATGATTATAATATAGTGTG	0.366													4	2	---	---	---	---	
CCDC91	55297	broad.mit.edu	37	12	28611068	28611068	+	Intron	DEL	G	-	-			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:28611068delG	uc001riq.2	+						CCDC91_uc001rio.2_Intron|CCDC91_uc009zjk.2_Intron|CCDC91_uc001rir.2_Intron|CCDC91_uc009zjl.2_Intron	NM_018318	NP_060788	Q7Z6B0	CCD91_HUMAN	GGA binding partner						protein transport	Golgi apparatus|membrane				central_nervous_system(1)	1	Acute lymphoblastic leukemia(23;0.00718)|all_hematologic(23;0.0113)|Lung SC(9;0.184)					TTTTAGCTTAGCAGGCTATTT	0.284													4	2	---	---	---	---	
NELL2	4753	broad.mit.edu	37	12	45111648	45111648	+	Intron	DEL	G	-	-			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:45111648delG	uc001rog.2	-						NELL2_uc001rof.3_Intron|NELL2_uc001roh.2_Intron|NELL2_uc009zkd.2_Intron|NELL2_uc010skz.1_Intron|NELL2_uc010sla.1_Intron|NELL2_uc001roi.1_Intron|NELL2_uc010slb.1_Intron|NELL2_uc001roj.2_Intron	NM_001145108	NP_001138580	Q99435	NELL2_HUMAN	NEL-like protein 2 isoform b precursor						cell adhesion	extracellular region	calcium ion binding|protein binding|structural molecule activity			skin(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)	4	Lung SC(27;0.192)	Lung NSC(34;0.144)		GBM - Glioblastoma multiforme(48;0.092)		tagctggcaaggagaccagag	0.015													4	2	---	---	---	---	
ARID2	196528	broad.mit.edu	37	12	46299067	46299067	+	3'UTR	DEL	A	-	-			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:46299067delA	uc001ros.1	+	21					ARID2_uc009zkg.1_3'UTR|ARID2_uc009zkh.1_3'UTR|ARID2_uc001rou.1_3'UTR	NM_152641	NP_689854	Q68CP9	ARID2_HUMAN	AT rich interactive domain 2 (ARID, RFX-like)						chromatin modification|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|protein binding|zinc ion binding			ovary(6)|skin(3)|upper_aerodigestive_tract(1)	10	Lung SC(27;0.192)|Renal(347;0.236)	Lung NSC(34;0.106)|all_lung(34;0.22)	OV - Ovarian serous cystadenocarcinoma(5;0.00691)	GBM - Glioblastoma multiforme(48;0.0153)		aagaaaaaggaaaaaaaaaaa	0.333													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	65900516	65900516	+	IGR	DEL	T	-	-			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:65900516delT								MSRB3 (39836 upstream) : RPSAP52 (251287 downstream)																							GGATGTCGAGTTTTATCtgtg	0.234													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	69512573	69512573	+	IGR	DEL	A	-	-			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:69512573delA								CPM (155553 upstream) : CPSF6 (120744 downstream)																							cagacacattaaaaaaaaaac	0.000													5	5	---	---	---	---	
LGR5	8549	broad.mit.edu	37	12	71966814	71966818	+	Intron	DEL	TATAT	-	-			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:71966814_71966818delTATAT	uc001swl.2	+						LGR5_uc001swm.2_Intron|LGR5_uc001swn.1_Intron	NM_003667	NP_003658	O75473	LGR5_HUMAN	leucine-rich repeat-containing G protein-coupled							integral to plasma membrane	protein-hormone receptor activity			lung(4)|skin(3)|ovary(1)|pancreas(1)	9						CTTTTGTGCATATATTTGCTATGAA	0.395													32	20	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	88883447	88883448	+	IGR	INS	-	T	T			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:88883447_88883448insT								TMTC3 (289784 upstream) : KITLG (3121 downstream)																							tgaaagttatcttttttttttt	0.030													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	93548778	93548778	+	IGR	DEL	A	-	-			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:93548778delA								EEA1 (225671 upstream) : NUDT4 (222923 downstream)																							gacataggctactccagtgaa	0.104													4	2	---	---	---	---	
SOCS2	8835	broad.mit.edu	37	12	93968379	93968379	+	Intron	DEL	T	-	-	rs35259505		TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:93968379delT	uc001tcw.1	+						uc001tcv.1_5'Flank|uc001tcu.2_5'Flank|SOCS2_uc001tcx.1_Intron|SOCS2_uc009zsu.2_3'UTR|SOCS2_uc001tcy.1_Intron|SOCS2_uc001tcz.2_3'UTR	NM_003877	NP_003868	O14508	SOCS2_HUMAN	suppressor of cytokine signaling-2						anti-apoptosis|growth hormone receptor signaling pathway|JAK-STAT cascade|negative regulation of signal transduction|regulation of cell growth|response to estradiol stimulus	cytoplasm	growth hormone receptor binding|insulin-like growth factor receptor binding|JAK pathway signal transduction adaptor activity|prolactin receptor binding|SH3/SH2 adaptor activity			lung(1)	1						ACACACCACCTTTTTTTTTTT	0.328													4	3	---	---	---	---	
HSP90B1	7184	broad.mit.edu	37	12	104325827	104325828	+	Intron	INS	-	T	T	rs36044446		TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:104325827_104325828insT	uc001tkb.1	+						HSP90B1_uc010swg.1_Intron|HSP90B1_uc009zui.1_Intron|LOC253724_uc010swf.1_5'Flank|LOC253724_uc009zuh.2_5'Flank	NM_003299	NP_003290	P14625	ENPL_HUMAN	heat shock protein 90kDa beta, member 1						actin rod assembly|anti-apoptosis|cellular response to ATP|ER-associated protein catabolic process|protein folding|protein transport|regulation of phosphoprotein phosphatase activity|response to hypoxia|sequestering of calcium ion	cytosol|endoplasmic reticulum lumen|endoplasmic reticulum membrane|melanosome|microsome|midbody|perinuclear region of cytoplasm	ATP binding|calcium ion binding|low-density lipoprotein particle receptor binding|protein phosphatase binding|RNA binding|unfolded protein binding|virion binding			ovary(2)|skin(1)	3					Rifabutin(DB00615)	GAAAGTTGGGATTTTTTTTTTT	0.347													4	2	---	---	---	---	
GIT2	9815	broad.mit.edu	37	12	110403605	110403605	+	Intron	DEL	A	-	-			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:110403605delA	uc001tps.2	-						GIT2_uc001tpq.2_Intron|GIT2_uc001tpv.2_Intron|GIT2_uc001tpu.2_Intron|GIT2_uc001tpt.2_Intron|GIT2_uc010sxu.1_Intron|GIT2_uc001tpw.2_Intron|GIT2_uc010sxv.1_Intron	NM_057169	NP_476510	Q14161	GIT2_HUMAN	G protein-coupled receptor kinase interacting						regulation of ARF GTPase activity|regulation of G-protein coupled receptor protein signaling pathway	nucleoplasm	ARF GTPase activator activity|protein binding|zinc ion binding			central_nervous_system(1)	1						GTTAAAGAGGAAAAAAAAATC	0.383													3	4	---	---	---	---	
TCTN1	79600	broad.mit.edu	37	12	111084202	111084202	+	Intron	DEL	T	-	-			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:111084202delT	uc009zvs.2	+						TCTN1_uc001trp.3_Intron|TCTN1_uc001trn.3_Intron|TCTN1_uc001trk.3_Intron|HVCN1_uc001trq.1_Intron	NM_001082537	NP_001076006	Q2MV58	TECT1_HUMAN	tectonic family member 1 isoform 2						multicellular organismal development	extracellular region					0						ATTTTAAAGCttttttttttt	0.214													7	4	---	---	---	---	
MAP1LC3B2	643246	broad.mit.edu	37	12	116997874	116997874	+	Intron	DEL	A	-	-			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:116997874delA	uc009zwk.1	+							NM_001085481	NP_001078950	A6NCE7	MP3B2_HUMAN	microtubule-associated protein 1 light chain 3						autophagy	autophagic vacuole membrane|cytoplasmic vesicle|endomembrane system|microtubule					0						CACTGTCAAGAAAAAAAAAAC	0.448													4	2	---	---	---	---	
TAOK3	51347	broad.mit.edu	37	12	118646230	118646230	+	Intron	DEL	A	-	-	rs35706767		TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:118646230delA	uc001twx.2	-						TAOK3_uc001tww.2_Intron|TAOK3_uc001twy.3_Intron	NM_016281	NP_057365	Q9H2K8	TAOK3_HUMAN	TAO kinase 3						MAPKKK cascade|negative regulation of JNK cascade|positive regulation of JNK cascade|protein autophosphorylation	mitochondrion|plasma membrane	ATP binding|protein kinase inhibitor activity|protein serine/threonine kinase activity			lung(5)|central_nervous_system(1)	6	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)					GAGAAATAGGAAAAAAAAAAT	0.209													2	4	---	---	---	---	
NCOR2	9612	broad.mit.edu	37	12	124979559	124979560	+	Intron	DEL	GG	-	-			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:124979559_124979560delGG	uc010tba.1	-						NCOR2_uc010tay.1_Intron|NCOR2_uc010taz.1_Intron|NCOR2_uc010tbb.1_Intron|NCOR2_uc010tbc.1_Intron|NCOR2_uc001ugj.1_Intron|NCOR2_uc001ugk.1_Intron	NM_001077261	NP_001070729	Q9Y618	NCOR2_HUMAN	nuclear receptor co-repressor 2 isoform 2						cellular lipid metabolic process|negative regulation of transcription from RNA polymerase II promoter|regulation of cellular ketone metabolic process by negative regulation of transcription from an RNA polymerase II promoter|transcription, DNA-dependent	nuclear body|nucleus|transcriptional repressor complex	DNA binding|histone deacetylase binding|Notch binding|protein N-terminus binding|transcription corepressor activity			skin(3)|ovary(1)	4	all_neural(191;0.0804)|Medulloblastoma(191;0.163)			Epithelial(86;3.99e-05)|OV - Ovarian serous cystadenocarcinoma(86;9.14e-05)|all cancers(50;0.000402)|BRCA - Breast invasive adenocarcinoma(302;0.0764)		TCTCTGTGGCGGCCTCCCCTCT	0.550													3	5	---	---	---	---	
GOLGA3	2802	broad.mit.edu	37	12	133378244	133378245	+	Intron	DEL	AC	-	-	rs149456851	by1000genomes	TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:133378244_133378245delAC	uc001ukz.1	-						GOLGA3_uc001ula.1_Intron|GOLGA3_uc001ulb.2_Intron	NM_005895	NP_005886	Q08378	GOGA3_HUMAN	Golgi autoantigen, golgin subfamily a, 3						intra-Golgi vesicle-mediated transport	Golgi cisterna membrane|Golgi transport complex	protein binding|transporter activity			ovary(3)|central_nervous_system(2)|pancreas(1)	6	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_epithelial(31;0.0176)|Lung NSC(355;0.204)		OV - Ovarian serous cystadenocarcinoma(86;2.27e-08)|Epithelial(86;3.34e-07)|all cancers(50;9.4e-06)		CAGGTTAAAAACAAAAACATGC	0.525													6	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	42576371	42576372	+	IGR	INS	-	T	T			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:42576371_42576372insT								KIAA0564 (41150 upstream) : DGKH (37800 downstream)																							ctctgtctttctgtttttctgt	0.366													4	2	---	---	---	---	
LOC647288	647288	broad.mit.edu	37	13	75813748	75813749	+	3'UTR	INS	-	T	T			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:75813748_75813749insT	uc010ths.1	-	1						NR_027466				Homo sapiens mRNA; cDNA DKFZp434F0327 (from clone DKFZp434F0327).												0						GTCTTCAAATGTTATTTTCTGT	0.366													250	116	---	---	---	---	
TM9SF2	9375	broad.mit.edu	37	13	100201164	100201165	+	Intron	INS	-	AA	AA			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:100201164_100201165insAA	uc001voj.1	+						TM9SF2_uc010afz.1_Intron	NM_004800	NP_004791	Q99805	TM9S2_HUMAN	transmembrane 9 superfamily member 2 precursor						transport	endosome membrane|integral to plasma membrane				ovary(1)	1	all_neural(89;0.0837)|Medulloblastoma(90;0.18)|Lung SC(71;0.218)					TTGGTTGTGAGGGGAAAAGAAG	0.436													4	2	---	---	---	---	
FGF14	2259	broad.mit.edu	37	13	102542693	102542693	+	Intron	DEL	A	-	-			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:102542693delA	uc001vpe.2	-						FGF14_uc001vpf.2_Intron	NM_004115	NP_004106	Q92915	FGF14_HUMAN	fibroblast growth factor 14 isoform 1A						cell death|cell-cell signaling|JNK cascade|nervous system development|signal transduction	nucleus	growth factor activity|heparin binding			ovary(2)|lung(1)|large_intestine(1)	4	all_neural(89;0.0239)|Medulloblastoma(90;0.163)|Lung SC(71;0.184)					GTCTTACCTGAAAAAAAAAAC	0.418													7	4	---	---	---	---	
FAM155A	728215	broad.mit.edu	37	13	107857974	107857974	+	Intron	DEL	A	-	-			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:107857974delA	uc001vql.2	-							NM_001080396	NP_001073865	B1AL88	F155A_HUMAN	family with sequence similarity 155, member A							integral to membrane	binding			skin(1)	1						AAAGAAAAAGAAAAAAAATGG	0.363											OREG0022505	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	30662647	30662648	+	IGR	DEL	GT	-	-			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:30662647_30662648delGT								PRKD1 (265748 upstream) : G2E3 (365681 downstream)																							atgtcattacgtgaagaatagc	0.000													4	2	---	---	---	---	
SNX6	58533	broad.mit.edu	37	14	35051043	35051044	+	Intron	DEL	TT	-	-	rs33966364		TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:35051043_35051044delTT	uc001wsf.1	-						SNX6_uc001wse.1_Intron|SNX6_uc010tpm.1_Intron|SNX6_uc010amm.1_Intron	NM_152233	NP_689419	Q9UNH7	SNX6_HUMAN	sorting nexin 6 isoform b						cell communication|intracellular protein transport|negative regulation of epidermal growth factor receptor activity|negative regulation of transcription, DNA-dependent|negative regulation of transforming growth factor beta receptor signaling pathway|retrograde transport, endosome to Golgi	cytoplasmic vesicle membrane|early endosome membrane|nucleus	phosphatidylinositol binding|protein homodimerization activity				0	Breast(36;0.0473)|Hepatocellular(127;0.158)		LUAD - Lung adenocarcinoma(48;0.00169)|Lung(238;0.00199)|Epithelial(34;0.187)	GBM - Glioblastoma multiforme(112;0.0245)		TTGAtttttgtttttttttgcg	0.144													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	46280517	46280517	+	IGR	DEL	C	-	-			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:46280517delC								C14orf106 (557912 upstream) : RPL10L (839705 downstream)																							CTTTAAAGTGCAGCTGGTGCT	0.527													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	57242017	57242017	+	IGR	DEL	A	-	-			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:57242017delA								C14orf101 (125787 upstream) : OTX2 (25410 downstream)																							TACACCTATTAAAAAAAAATA	0.239													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	57498028	57498029	+	IGR	DEL	AC	-	-			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:57498028_57498029delAC								OTX2 (220844 upstream) : EXOC5 (171167 downstream)																							cagatccagtaccacaaagcaa	0.015													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	69946009	69946009	+	IGR	DEL	G	-	-			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:69946009delG								SLC39A9 (16904 upstream) : UPF0639 (5462 downstream)																							atatttgggtggggacacagc	0.209													4	2	---	---	---	---	
FBLN5	10516	broad.mit.edu	37	14	92409556	92409556	+	Intron	DEL	A	-	-			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:92409556delA	uc001xzx.3	-						FBLN5_uc010aud.2_Intron|FBLN5_uc010aue.2_Intron	NM_006329	NP_006320	Q9UBX5	FBLN5_HUMAN	fibulin 5 precursor						cell-matrix adhesion|elastic fiber assembly|protein localization at cell surface|regulation of removal of superoxide radicals	extracellular space|proteinaceous extracellular matrix|soluble fraction	calcium ion binding|integrin binding|protein C-terminus binding			ovary(3)|upper_aerodigestive_tract(1)|lung(1)|skin(1)	6		all_cancers(154;0.0722)				tggctgcttcaaaaaaaaAAG	0.010													4	3	---	---	---	---	
ATXN3	4287	broad.mit.edu	37	14	92554953	92554956	+	Intron	DEL	AAAC	-	-			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:92554953_92554956delAAAC	uc001yac.3	-						ATXN3_uc010aug.2_Intron|ATXN3_uc001yad.3_Intron|ATXN3_uc010auh.2_Intron|ATXN3_uc001yae.3_Intron|ATXN3_uc010twl.1_Intron	NM_004993	NP_004984	P54252	ATX3_HUMAN	ataxin 3 reference isoform						cell death|nervous system development|nucleotide-excision repair|regulation of transcription, DNA-dependent|synaptic transmission|transcription, DNA-dependent	cytoplasm|nuclear matrix|nucleoplasm	cysteine-type peptidase activity|protein binding				0		all_cancers(154;0.0768)		COAD - Colon adenocarcinoma(157;0.224)		CACCACGTCAAAACTAAAGATTGT	0.279													16	13	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	99270688	99270689	+	IGR	INS	-	G	G	rs150220230	by1000genomes	TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:99270688_99270689insG								C14orf177 (86591 upstream) : BCL11B (364938 downstream)																							AAGAATTCACATACCTGGTACT	0.421													1	5	---	---	---	---	
MIR1197	100302250	broad.mit.edu	37	14	101491574	101491575	+	5'Flank	INS	-	A	A			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:101491574_101491575insA	hsa-mir-1197|MI0006656	+						uc001yjy.1_5'Flank|MIR323_hsa-mir-323|MI0000807_5'Flank|MIR758_hsa-mir-758|MI0003757_5'Flank|MIR329-1_hsa-mir-329-1|MI0001725_5'Flank|MIR329-2_hsa-mir-329-2|MI0001726_5'Flank																	0						GCATGGTCCACTCATTCTCAGT	0.554													6	3	---	---	---	---	
MIR1197	100302250	broad.mit.edu	37	14	101491577	101491577	+	5'Flank	DEL	A	-	-			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:101491577delA	hsa-mir-1197|MI0006656	+						uc001yjy.1_5'Flank|MIR323_hsa-mir-323|MI0000807_5'Flank|MIR758_hsa-mir-758|MI0003757_5'Flank|MIR329-1_hsa-mir-329-1|MI0001725_5'Flank|MIR329-2_hsa-mir-329-2|MI0001726_5'Flank																	0						TGGTCCACTCATTCTCAGTAT	0.547													5	3	---	---	---	---	
POTEB	339010	broad.mit.edu	37	15	22070888	22070889	+	Intron	INS	-	T	T			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:22070888_22070889insT	uc010tzr.1	-						POTEB_uc010tzq.1_Intron	NM_207355	NP_997238	Q6S5H4	POTEB_HUMAN	protein expressed in prostate, ovary, testis,												0						CCAACTCTGCATAagtcctagc	0.193													2	4	---	---	---	---	
KLF13	51621	broad.mit.edu	37	15	31648878	31648879	+	Intron	DEL	GA	-	-			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:31648878_31648879delGA	uc001zfo.2	+							NM_015995	NP_057079	Q9Y2Y9	KLF13_HUMAN	Kruppel-like factor 13						transcription from RNA polymerase II promoter	nucleus	DNA binding|protein binding|zinc ion binding				0		all_lung(180;3.71e-11)		all cancers(64;1.11e-18)|Epithelial(43;1.73e-14)|GBM - Glioblastoma multiforme(186;0.00016)|Colorectal(1;0.00158)|BRCA - Breast invasive adenocarcinoma(123;0.00255)|COAD - Colon adenocarcinoma(236;0.0446)|READ - Rectum adenocarcinoma(1;0.13)|Lung(196;0.171)		gtctgaggttgattcacgtttc	0.000													4	2	---	---	---	---	
OTUD7A	161725	broad.mit.edu	37	15	31804426	31804426	+	Intron	DEL	T	-	-			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:31804426delT	uc001zfq.2	-						OTUD7A_uc001zfr.2_Intron	NM_130901	NP_570971	Q8TE49	OTU7A_HUMAN	OTU domain containing 7A							cytoplasm|nucleus	cysteine-type peptidase activity|DNA binding|zinc ion binding			pancreas(1)|skin(1)	2		all_lung(180;1.6e-09)		all cancers(64;2.44e-19)|Epithelial(43;6.82e-14)|GBM - Glioblastoma multiforme(186;1.49e-05)|BRCA - Breast invasive adenocarcinoma(123;0.00189)|Lung(196;0.208)		tgaggaattgttttttttttg	0.000													4	2	---	---	---	---	
C15orf41	84529	broad.mit.edu	37	15	36989330	36989330	+	Intron	DEL	A	-	-	rs35110312		TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:36989330delA	uc001zje.3	+						C15orf41_uc001zjd.2_Intron|C15orf41_uc010bbb.1_Intron|C15orf41_uc001zjf.2_Intron|C15orf41_uc010uci.1_Intron	NM_001130010	NP_001123482	Q9Y2V0	CO041_HUMAN	hypothetical protein LOC84529 isoform 1								protein binding			pancreas(1)	1		all_epithelial(112;3.06e-10)|Lung NSC(122;6.48e-08)|all_lung(180;8.31e-07)|Melanoma(134;0.222)		all cancers(64;1.76e-19)|GBM - Glioblastoma multiforme(113;5.03e-07)|BRCA - Breast invasive adenocarcinoma(123;0.11)		tgtctctattaaaaaaaaaaa	0.139													6	3	---	---	---	---	
FRMD5	84978	broad.mit.edu	37	15	44182851	44182852	+	Intron	DEL	CA	-	-			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:44182851_44182852delCA	uc001ztl.2	-						FRMD5_uc001ztj.1_Intron|FRMD5_uc001ztk.1_Intron|FRMD5_uc001ztm.2_Intron|FRMD5_uc001ztn.2_Intron	NM_032892	NP_116281	Q7Z6J6	FRMD5_HUMAN	FERM domain containing 5 isoform 2							cytoplasm|cytoskeleton|extrinsic to membrane|integral to membrane	cytoskeletal protein binding			ovary(1)	1		all_cancers(109;2.29e-15)|all_epithelial(112;9.98e-13)|Lung NSC(122;4.89e-08)|all_lung(180;5.08e-07)|Melanoma(134;0.0275)		all cancers(107;8.63e-20)|GBM - Glioblastoma multiforme(94;3.63e-06)		CTCACATCTTCACCCAGAGAGC	0.520													4	2	---	---	---	---	
EIF3J	8669	broad.mit.edu	37	15	44829409	44829410	+	In_Frame_Ins	INS	-	ACT	ACT			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:44829409_44829410insACT	uc001ztv.2	+	1	144_145	c.17_18insACT	c.(16-18)GCG>GCACTG	p.6_7insL	uc001ztu.2_5'Flank|EIF3J_uc010ueg.1_In_Frame_Ins_p.6_7insL|EIF3J_uc001ztw.2_In_Frame_Ins_p.6_7insL	NM_003758	NP_003749	O75822	EIF3J_HUMAN	eukaryotic translation initiation factor 3,	6_7	Sufficient for interaction with EIF3B.|Poly-Ala.					cytosol|eukaryotic translation initiation factor 3 complex	protein binding|translation initiation factor activity				0		all_cancers(109;2.81e-14)|all_epithelial(112;2.8e-12)|Lung NSC(122;1.66e-07)|all_lung(180;1.47e-06)|Melanoma(134;0.0122)		all cancers(107;3.13e-20)|GBM - Glioblastoma multiforme(94;9.81e-07)|COAD - Colon adenocarcinoma(120;0.0754)|Colorectal(105;0.0758)		gcggcggcggcggcggcggGGG	0.480													5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	46006736	46006736	+	IGR	DEL	T	-	-	rs66930690		TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:46006736delT								SQRDL (23258 upstream) : None (None downstream)																							CGTTCTTTTCTTTTTTTTTTT	0.398											OREG0023112	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	9	6	---	---	---	---	
UBL7	84993	broad.mit.edu	37	15	74744055	74744055	+	Intron	DEL	A	-	-			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:74744055delA	uc002axw.1	-						UBL7_uc002axx.1_Intron|UBL7_uc010bjr.1_Intron|UBL7_uc002axy.1_Intron|UBL7_uc002axz.1_Intron	NM_032907	NP_116296	Q96S82	UBL7_HUMAN	ubiquitin-like 7								protein binding			ovary(1)	1						CAAACAATTTAAAAAAAAAAA	0.393													6	4	---	---	---	---	
CSK	1445	broad.mit.edu	37	15	75074098	75074101	+	5'Flank	DEL	TGAA	-	-			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:75074098_75074101delTGAA	uc010bkb.1	+						CSK_uc010bka.2_5'Flank|CSK_uc002ays.2_5'Flank	NM_001127190	NP_001120662	P41240	CSK_HUMAN	c-src tyrosine kinase						blood coagulation|epidermal growth factor receptor signaling pathway|T cell costimulation|T cell receptor signaling pathway	centrosome|cytosol|Golgi apparatus	ATP binding|non-membrane spanning protein tyrosine kinase activity|protein C-terminus binding			lung(2)|central_nervous_system(1)	3						gaaatgttggtgaatgaatgaatG	0.294													4	2	---	---	---	---	
PTPN9	5780	broad.mit.edu	37	15	75797824	75797824	+	Intron	DEL	A	-	-			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:75797824delA	uc002bal.2	-							NM_002833	NP_002824	P43378	PTN9_HUMAN	protein tyrosine phosphatase, non-receptor type							cytoplasmic part	non-membrane spanning protein tyrosine phosphatase activity|protein binding			lung(1)|skin(1)	2						aaaaaaaaagaaaaaaaaaaa	0.189													4	2	---	---	---	---	
FAM174B	400451	broad.mit.edu	37	15	93162692	93162692	+	Intron	DEL	A	-	-			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:93162692delA	uc010boe.2	-						FAM174B_uc002bsl.3_Intron	NM_207446	NP_997329	Q3ZCQ3	F174B_HUMAN	hypothetical protein LOC400451							integral to membrane					0						GGTTTTACCTAAAAGAAAGGG	0.552													95	53	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	2701922	2701922	+	IGR	DEL	A	-	-			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:2701922delA								FLJ42627 (5794 upstream) : KCTD5 (30573 downstream)																							TTTCTCTACTAAAAAAaaaat	0.055													4	2	---	---	---	---	
SEPT12	124404	broad.mit.edu	37	16	4838250	4838251	+	Intron	DEL	AG	-	-			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:4838250_4838251delAG	uc002cxq.2	-						SEPT12_uc002cxr.2_Intron|SEPT12_uc010bty.2_Intron|uc002cxt.2_5'Flank	NM_144605	NP_653206	Q8IYM1	SEP12_HUMAN	septin 12 isoform 2						cell cycle|cell division	cleavage furrow|midbody|perinuclear region of cytoplasm|septin complex|spindle|stress fiber	GDP binding|GTP binding|phosphatidylinositol binding|protein homodimerization activity			skin(1)	1						CACGGGGGGCAGAGAGAGAGAG	0.634													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	5261400	5261401	+	IGR	INS	-	G	G			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:5261400_5261401insG								FAM86A (113611 upstream) : A2BP1 (807731 downstream)																							CAAGGATGAAACAGAAGTTTCA	0.267													4	2	---	---	---	---	
PAPD5	64282	broad.mit.edu	37	16	50263428	50263428	+	3'UTR	DEL	A	-	-			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:50263428delA	uc010vgo.1	+	13					PAPD5_uc010cbi.2_Intron|PAPD5_uc002efz.2_3'UTR|PAPD5_uc002ega.2_3'UTR	NM_001040284	NP_001035374	Q8NDF8	PAPD5_HUMAN	PAP associated domain containing 5 isoform a						cell division|DNA replication|histone mRNA catabolic process|mitosis	cytoplasm|nucleus	DNA binding|DNA-directed DNA polymerase activity|metal ion binding				0		all_cancers(37;0.0452)		BRCA - Breast invasive adenocarcinoma(181;0.0843)|GBM - Glioblastoma multiforme(240;0.231)		aaaacaaaacaaaaaaaaaag	0.299													4	2	---	---	---	---	
FTO	79068	broad.mit.edu	37	16	54147207	54147207	+	3'UTR	DEL	G	-	-	rs5816925		TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:54147207delG	uc002ehr.2	+	9					FTO_uc010vha.1_3'UTR|FTO_uc010cbz.2_3'UTR|FTO_uc002ehs.2_RNA	NM_001080432	NP_001073901	Q9C0B1	FTO_HUMAN	fat mass and obesity associated						DNA dealkylation involved in DNA repair|oxidative single-stranded DNA demethylation|oxidative single-stranded RNA demethylation|RNA repair	nucleus	DNA-N1-methyladenine dioxygenase activity|ferrous iron binding|oxidative DNA demethylase activity|oxidative RNA demethylase activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen				0						TTAGCCCCCCGTCTCCCCAGC	0.478													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	54941799	54941800	+	IGR	DEL	TG	-	-			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:54941799_54941800delTG								IRX3 (621421 upstream) : IRX5 (23311 downstream)																							ctttggcagatgaatggattat	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	60712872	60712872	+	IGR	DEL	A	-	-			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:60712872delA								None (None upstream) : CDH8 (974363 downstream)																							GACAACGGTGAATCAATGAAA	0.408													4	2	---	---	---	---	
PLA2G15	23659	broad.mit.edu	37	16	68292301	68292301	+	Intron	DEL	C	-	-			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:68292301delC	uc002evr.2	+						PLA2G15_uc010vld.1_Intron|PLA2G15_uc010vle.1_Intron|PLA2G15_uc010vlf.1_Intron|PLA2G15_uc002evs.2_Intron	NM_012320	NP_036452	Q8NCC3	PAG15_HUMAN	lysophospholipase 3 (lysosomal phospholipase A2)						fatty acid catabolic process	extracellular region|lysosome	lysophospholipase activity|phosphatidylcholine-sterol O-acyltransferase activity|phospholipid binding			ovary(1)	1						TAGGTCAGTGCCCACAGGCCT	0.483													4	2	---	---	---	---	
ZNF821	55565	broad.mit.edu	37	16	71898485	71898485	+	Intron	DEL	T	-	-			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:71898485delT	uc010vmj.1	-						ATXN1L_uc010vmi.1_Intron|ZNF821_uc002fbe.2_Intron|ZNF821_uc002fbf.2_Intron|ZNF821_uc002fbg.3_Intron|ZNF821_uc002fbh.3_Intron|ZNF821_uc002fbi.3_Intron	NM_017530	NP_060000	O75541	ZN821_HUMAN	zinc finger protein 821						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1						TTGACTTAGATTTGCAAGCAC	0.473													4	2	---	---	---	---	
CLEC18B	497190	broad.mit.edu	37	16	74444233	74444234	+	Intron	INS	-	G	G	rs143495339	by1000genomes	TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:74444233_74444234insG	uc002fct.2	-						CLEC18B_uc002fcu.2_Intron	NM_001011880	NP_001011880	Q6UXF7	CL18B_HUMAN	C-type lectin domain family 18, member B							extracellular region	sugar binding				0						CTCTCCCCCACGTGACGTGCCT	0.634													4	2	---	---	---	---	
ANKRD11	29123	broad.mit.edu	37	16	89469959	89469959	+	Intron	DEL	A	-	-			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:89469959delA	uc002fmx.1	-						ANKRD11_uc002fmy.1_Intron|ANKRD11_uc002fnc.1_Intron|ANKRD11_uc002fnd.2_Intron|ANKRD11_uc002fne.2_Intron|ANKRD11_uc002fng.1_Intron	NM_013275	NP_037407	Q6UB99	ANR11_HUMAN	ankyrin repeat domain 11							nucleus				ovary(4)|large_intestine(1)|central_nervous_system(1)	6		all_hematologic(23;0.00824)|Colorectal(91;0.0475)		Epithelial(1;5.33e-11)|all cancers(4;2.6e-09)|OV - Ovarian serous cystadenocarcinoma(4;2.29e-07)|BRCA - Breast invasive adenocarcinoma(80;0.0142)		ACAGTAGCTTAAAAAAAAAAA	0.507													4	3	---	---	---	---	
DBNDD1	79007	broad.mit.edu	37	16	90075393	90075393	+	Intron	DEL	G	-	-			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:90075393delG	uc002fqf.1	-						DBNDD1_uc002fqe.1_Intron|DBNDD1_uc002fqg.1_Intron	NM_001042610	NP_001036075	Q9H9R9	DBND1_HUMAN	dysbindin (dystrobrevin binding protein 1)							cytoplasm					0		all_cancers(9;4.44e-13)|Lung NSC(15;1.56e-06)|all_lung(18;2.18e-06)|all_neural(9;0.00118)|all_hematologic(23;0.0194)		BRCA - Breast invasive adenocarcinoma(80;0.0275)		TCAGAGCCCCGGGGGTCTAGG	0.617													4	2	---	---	---	---	
INPP5K	51763	broad.mit.edu	37	17	1412407	1412416	+	Intron	DEL	GTGGGGGTTA	-	-	rs11279273		TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:1412407_1412416delGTGGGGGTTA	uc002fsr.2	-						INPP5K_uc002fss.2_Intron|INPP5K_uc002fsq.2_Intron|INPP5K_uc010cjr.2_Intron|INPP5K_uc010vql.1_Intron|INPP5K_uc010vqm.1_Intron	NM_016532	NP_057616	Q9BT40	INP5K_HUMAN	inositol polyphosphate-5-phosphatase K isoform						actin cytoskeleton organization	cytosol|endoplasmic reticulum|membrane fraction|neuron projection|ruffle	inositol 1,3,4,5-tetrakisphosphate 5-phosphatase activity|inositol bisphosphate phosphatase activity|inositol bisphosphate phosphatase activity|inositol trisphosphate phosphatase activity|inositol-1,4,5-trisphosphate 5-phosphatase activity|inositol-polyphosphate 5-phosphatase activity|lipid phosphatase activity|protein binding				0						AGGCTCACTCGTGGGGGTTAGTGGGGGTTA	0.671													4	2	---	---	---	---	
PIK3R5	23533	broad.mit.edu	37	17	8785829	8785829	+	Intron	DEL	C	-	-			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:8785829delC	uc002glt.2	-						PIK3R5_uc010vuz.1_Intron|PIK3R5_uc002glu.3_Intron	NM_014308	NP_055123	Q8WYR1	PI3R5_HUMAN	phosphoinositide-3-kinase, regulatory subunit 5						platelet activation	cytosol|membrane|nucleus				breast(2)|large_intestine(1)|central_nervous_system(1)|skin(1)	5						ttccctgcttccccccttcag	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	21518737	21518737	+	IGR	DEL	A	-	-			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21518737delA								C17orf51 (41006 upstream) : FAM27L (306633 downstream)																							TATTGGTAGCAAAACAGCCAT	0.259													4	6	---	---	---	---	
ACCN1	40	broad.mit.edu	37	17	32469443	32469444	+	Intron	INS	-	AG	AG			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:32469443_32469444insAG	uc002hhu.2	-							NM_001094	NP_001085	Q16515	ACCN1_HUMAN	amiloride-sensitive cation channel 1, neuronal						central nervous system development|peripheral nervous system development|synaptic transmission	integral to plasma membrane	ligand-gated sodium channel activity|protein binding			ovary(2)|large_intestine(1)|central_nervous_system(1)	4		Breast(31;0.042)|Ovarian(249;0.202)		UCEC - Uterine corpus endometrioid carcinoma (308;0.13)|BRCA - Breast invasive adenocarcinoma(366;0.215)	Amiloride(DB00594)	TGGGGATGACAAGAGAGAGAAC	0.361													4	2	---	---	---	---	
BECN1	8678	broad.mit.edu	37	17	40971839	40971839	+	Intron	DEL	T	-	-			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:40971839delT	uc002ibo.3	-						BECN1_uc010whb.1_Intron|BECN1_uc010whc.1_Intron|BECN1_uc002ibn.2_Intron	NM_003766	NP_003757	Q14457	BECN1_HUMAN	beclin 1						anti-apoptosis|cell cycle|cellular defense response|cytokinesis|response to virus	membrane	protein binding			ovary(1)	1		Breast(137;0.00104)		BRCA - Breast invasive adenocarcinoma(366;0.0745)		TCCCATTTGATTTTTTTTTTG	0.383											OREG0024429	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	4	2	---	---	---	---	
UBTF	7343	broad.mit.edu	37	17	42299008	42299009	+	5'Flank	INS	-	T	T			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:42299008_42299009insT	uc010czs.2	-						UBTF_uc002igc.2_5'Flank|UBTF_uc002igd.2_5'Flank|UBTF_uc010czt.2_5'Flank	NM_014233	NP_055048	P17480	UBF1_HUMAN	upstream binding transcription factor, RNA						positive regulation of transcription from RNA polymerase I promoter|termination of RNA polymerase I transcription|transcription elongation from RNA polymerase I promoter|transcription initiation from RNA polymerase I promoter	nucleolus|nucleoplasm	DNA binding|protein binding				0		Breast(137;0.00765)|Prostate(33;0.0181)		BRCA - Breast invasive adenocarcinoma(366;0.114)		TGTGTGCGCGGTTTTTTTTTTT	0.505													5	4	---	---	---	---	
CBX1	10951	broad.mit.edu	37	17	46153958	46153958	+	Intron	DEL	G	-	-			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:46153958delG	uc002ind.3	-						CBX1_uc002ine.3_Intron	NM_006807	NP_006798	P83916	CBX1_HUMAN	heterochromatin protein 1-beta							nuclear heterochromatin|nucleoplasm|spindle	chromatin binding|enzyme binding				0						ccttgagcctgggaggttgag	0.010													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	54058001	54058001	+	IGR	DEL	T	-	-			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:54058001delT								PCTP (203254 upstream) : ANKFN1 (172835 downstream)																							GCAAGGGTTCTCAGGAGGCTC	0.428													4	2	---	---	---	---	
MTMR4	9110	broad.mit.edu	37	17	56592621	56592621	+	Intron	DEL	A	-	-			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:56592621delA	uc002iwj.2	-						MTMR4_uc010dcx.1_5'Flank	NM_004687	NP_004678	Q9NYA4	MTMR4_HUMAN	myotubularin related protein 4							cytoplasm|membrane	metal ion binding|protein tyrosine phosphatase activity			skin(1)	1	Medulloblastoma(34;0.127)|all_neural(34;0.237)					GAAGCTATACAAAAAAACGAA	0.458													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	68938032	68938032	+	IGR	DEL	A	-	-			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:68938032delA								KCNJ2 (761851 upstream) : None (None downstream)																							TTTCTTTTATAAAAGATCACT	0.353													4	2	---	---	---	---	
SUMO2	6613	broad.mit.edu	37	17	73164227	73164227	+	3'UTR	DEL	A	-	-			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:73164227delA	uc002jne.2	-	4					SUMO2_uc002jnf.2_3'UTR	NM_006937	NP_008868	P61956	SUMO2_HUMAN	SMT3 suppressor of mif two 3 homolog 2 isoform a						positive regulation of proteasomal ubiquitin-dependent protein catabolic process|protein sumoylation	nucleus	ubiquitin protein ligase binding				0	all_lung(278;0.14)|Lung NSC(278;0.168)					CTGTTTAGTTAAAAAAAAAAA	0.353													5	3	---	---	---	---	
FOXK2	3607	broad.mit.edu	37	17	80508847	80508847	+	Intron	DEL	G	-	-			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:80508847delG	uc002kfn.2	+						FOXK2_uc002kfm.1_Intron|FOXK2_uc010diu.2_Intron	NM_004514	NP_004505	Q01167	FOXK2_HUMAN	forkhead box K2						embryo development|pattern specification process|regulation of sequence-specific DNA binding transcription factor activity|regulation of transcription from RNA polymerase II promoter|tissue development	transcription factor complex	DNA bending activity|double-stranded DNA binding|magnesium ion binding|promoter binding|sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|specific RNA polymerase II transcription factor activity|specific transcriptional repressor activity|transcription activator activity|transcription factor binding				0	Breast(20;0.00106)|all_neural(118;0.0952)		OV - Ovarian serous cystadenocarcinoma(97;0.0371)|BRCA - Breast invasive adenocarcinoma(99;0.0415)			GTACTGAGCCGGGTCGTTAGG	0.388													4	2	---	---	---	---	
NDC80	10403	broad.mit.edu	37	18	2594606	2594609	+	Intron	DEL	AGTC	-	-			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:2594606_2594609delAGTC	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						AGCCTGCACAAGTCAGTTCATTTT	0.387													3	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	12067998	12067998	+	IGR	DEL	G	-	-			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:12067998delG								IMPA2 (37122 upstream) : CIDEA (186320 downstream)																							TGCGTCACCTGGGGCCATACT	0.701													4	2	---	---	---	---	
FAM59A	64762	broad.mit.edu	37	18	29848873	29848873	+	Intron	DEL	T	-	-			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:29848873delT	uc002kxl.2	-						FAM59A_uc002kxk.1_Intron	NM_022751	NP_073588	Q9H706	FA59A_HUMAN	family with sequence similarity 59, member A											ovary(1)|skin(1)	2						CTTCACTGGGTTTTTTTTTTA	0.284													3	3	---	---	---	---	
DTNA	1837	broad.mit.edu	37	18	32457924	32457924	+	Intron	DEL	T	-	-			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:32457924delT	uc010dmn.1	+						DTNA_uc002kxw.2_Intron|DTNA_uc010dmj.2_Intron|DTNA_uc002kxz.2_Intron|DTNA_uc002kxy.2_Intron|DTNA_uc010xby.1_Intron|DTNA_uc010xbz.1_Intron|DTNA_uc010xca.1_Intron|DTNA_uc002kye.2_Intron	NM_001390	NP_001381	Q9Y4J8	DTNA_HUMAN	dystrobrevin alpha isoform 1						neuromuscular synaptic transmission|signal transduction|striated muscle contraction	cell junction|cytoplasm|synapse	calcium ion binding|protein binding|zinc ion binding				0						ATTTGAGGGGttttttttttg	0.179													8	4	---	---	---	---	
ZNF236	7776	broad.mit.edu	37	18	74679478	74679480	+	Intron	DEL	GGT	-	-			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:74679478_74679480delGGT	uc002lmi.2	+						ZNF236_uc002lmj.2_Intron	NM_007345	NP_031371	Q9UL36	ZN236_HUMAN	zinc finger protein 236						cellular response to glucose stimulus	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(4)	4		Prostate(75;0.0405)|Esophageal squamous(42;0.129)|Melanoma(33;0.132)		OV - Ovarian serous cystadenocarcinoma(15;4.36e-06)|BRCA - Breast invasive adenocarcinoma(31;0.0686)		tggtgttggaggtggtggtgtga	0.094													9	6	---	---	---	---	
GALR1	2587	broad.mit.edu	37	18	74980423	74980423	+	Intron	DEL	A	-	-			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:74980423delA	uc002lms.3	+							NM_001480	NP_001471	P47211	GALR1_HUMAN	galanin receptor 1						digestion|negative regulation of adenylate cyclase activity	integral to membrane|plasma membrane	galanin receptor activity			lung(1)	1		Prostate(75;0.0865)|Esophageal squamous(42;0.129)|Melanoma(33;0.211)		OV - Ovarian serous cystadenocarcinoma(15;1.03e-06)|BRCA - Breast invasive adenocarcinoma(31;0.104)		AAATTAGCTTAGGATGTATTT	0.214													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	9314803	9314803	+	IGR	DEL	A	-	-	rs57442285	by1000genomes	TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:9314803delA								OR7D2 (15310 upstream) : OR7D4 (9772 downstream)																							agtctaaaataaaaaaaaaga	0.134													4	2	---	---	---	---	
EMR2	30817	broad.mit.edu	37	19	14854057	14854058	+	Intron	INS	-	A	A			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:14854057_14854058insA	uc002mzp.1	-						EMR2_uc010dzs.1_Intron|EMR2_uc010xnw.1_Intron|EMR2_uc002mzo.1_Intron|EMR2_uc002mzq.1_Intron|EMR2_uc002mzr.1_Intron|EMR2_uc002mzs.1_Intron|EMR2_uc002mzt.1_Intron|EMR2_uc002mzu.1_Intron	NM_013447	NP_038475	Q9UHX3	EMR2_HUMAN	egf-like module containing, mucin-like, hormone						cell adhesion|neuropeptide signaling pathway	integral to membrane|plasma membrane	calcium ion binding|G-protein coupled receptor activity			lung(2)|ovary(1)|skin(1)	4						TATGACTGATTAAAAAAAAACA	0.272													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	22684456	22684457	+	IGR	DEL	AT	-	-			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:22684456_22684457delAT								ZNF98 (79308 upstream) : ZNF492 (132669 downstream)																							AAAATGACACATATCTCAAAGT	0.351													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	35125600	35125601	+	Intron	INS	-	T	T			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:35125600_35125601insT	uc002nvo.1	-											Homo sapiens cDNA FLJ36176 fis, clone TESTI2026491.																		CTCCAGTGTGATTTTTTTTTTA	0.426													3	3	---	---	---	---	
SIRT2	22933	broad.mit.edu	37	19	39372335	39372335	+	Intron	DEL	T	-	-			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:39372335delT	uc002ojt.1	-						SIRT2_uc010egh.1_Intron|SIRT2_uc010egi.1_Intron|SIRT2_uc002ojs.1_Intron|SIRT2_uc002oju.1_Intron|SIRT2_uc010egj.1_Intron|SIRT2_uc002ojv.1_Intron	NM_012237	NP_036369	Q8IXJ6	SIRT2_HUMAN	sirtuin 2 isoform 1						cell division|chromatin silencing at rDNA|chromatin silencing at telomere|mitosis|negative regulation of striated muscle tissue development|protein ADP-ribosylation|regulation of exit from mitosis|regulation of phosphorylation|response to redox state	chromatin silencing complex|cytoplasm|microtubule	histone acetyltransferase binding|histone deacetylase binding|NAD+ binding|NAD-dependent histone deacetylase activity|transcription factor binding|tubulin deacetylase activity|ubiquitin binding|zinc ion binding				0	all_cancers(60;6.83e-06)|Ovarian(47;0.0454)		Lung(45;0.00125)|LUSC - Lung squamous cell carcinoma(53;0.00191)			tttttctttcttttttttttt	0.199													4	2	---	---	---	---	
AXL	558	broad.mit.edu	37	19	41730693	41730694	+	Intron	INS	-	TG	TG	rs144332865	by1000genomes	TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:41730693_41730694insTG	uc010ehj.2	+						CYP2F1_uc010xvw.1_Intron|AXL_uc010ehi.1_Intron|AXL_uc010ehk.2_Intron	NM_021913	NP_068713	P30530	UFO_HUMAN	AXL receptor tyrosine kinase isoform 1							integral to plasma membrane	ATP binding|transmembrane receptor protein tyrosine kinase activity			lung(4)|stomach(3)|ovary(3)|upper_aerodigestive_tract(1)|central_nervous_system(1)|breast(1)	13						AGTCACAGACCtgtgtgtgtgt	0.465													4	3	---	---	---	---	
AXL	558	broad.mit.edu	37	19	41730706	41730707	+	Intron	INS	-	GC	GC			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:41730706_41730707insGC	uc010ehj.2	+						CYP2F1_uc010xvw.1_Intron|AXL_uc010ehi.1_Intron|AXL_uc010ehk.2_Intron	NM_021913	NP_068713	P30530	UFO_HUMAN	AXL receptor tyrosine kinase isoform 1							integral to plasma membrane	ATP binding|transmembrane receptor protein tyrosine kinase activity			lung(4)|stomach(3)|ovary(3)|upper_aerodigestive_tract(1)|central_nervous_system(1)|breast(1)	13						tgtgtgtgtgtgtgtgtgtAAC	0.465													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	46795954	46795954	+	IGR	DEL	C	-	-			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:46795954delC								IGFL1 (61456 upstream) : HIF3A (4351 downstream)																							ggtctccactccagcccagcc	0.000													4	2	---	---	---	---	
RPL28	6158	broad.mit.edu	37	19	55898970	55898970	+	Intron	DEL	T	-	-			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:55898970delT	uc002qkv.2	+						RPL28_uc010yfy.1_3'UTR|RPL28_uc010yga.1_Intron|RPL28_uc010ygb.1_Intron|RPL28_uc002qkw.1_3'UTR	NM_000991	NP_000982	P46779	RL28_HUMAN	ribosomal protein L28 isoform 2						endocrine pancreas development|translational elongation|translational termination|viral transcription	cytosolic large ribosomal subunit	protein binding|RNA binding|structural constituent of ribosome				0	Breast(117;0.191)	Renal(1328;0.245)	LUSC - Lung squamous cell carcinoma(43;0.13)|BRCA - Breast invasive adenocarcinoma(297;0.209)	GBM - Glioblastoma multiforme(193;0.0443)		AAGCTGTTCATACCCATTGCC	0.567													4	2	---	---	---	---	
RFPL4A	342931	broad.mit.edu	37	19	56273182	56273182	+	Frame_Shift_Del	DEL	A	-	-			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:56273182delA	uc010yge.1	+	2	60	c.16delA	c.(16-18)AAAfs	p.K6fs		NM_001145014	NP_001138486	A6NLU0	RFPLA_HUMAN	ret finger protein-like 4A	6							zinc ion binding				0						TGAGCACTTCAAACAGATCAT	0.413													5	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	10973663	10973663	+	IGR	DEL	T	-	-			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:10973663delT								JAG1 (318969 upstream) : BTBD3 (897814 downstream)																							TTTTTCTTTCTTTTTTTTTCC	0.388													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	23305506	23305506	+	IGR	DEL	C	-	-			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:23305506delC								CD93 (238529 upstream) : NXT1 (25867 downstream)																							CAATACCCTGCCACTGCACCC	0.438													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	37836143	37836143	+	IGR	DEL	T	-	-			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:37836143delT								DHX35 (167780 upstream) : LOC339568 (6281 downstream)																							TGTCCTTACATTTTTTTTTCT	0.383													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	38844668	38844669	+	IGR	DEL	GT	-	-			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:38844668_38844669delGT								LOC339568 (991277 upstream) : MAFB (469850 downstream)																							AGATATAAAGGTGTGTGTGTGT	0.267													4	2	---	---	---	---	
CHD6	84181	broad.mit.edu	37	20	40054992	40054993	+	Intron	INS	-	T	T			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:40054992_40054993insT	uc002xka.1	-							NM_032221	NP_115597	Q8TD26	CHD6_HUMAN	chromodomain helicase DNA binding protein 6						chromatin remodeling|nervous system development|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	ATP binding|ATP-dependent helicase activity|chromatin binding|DNA binding			ovary(6)|skin(5)|lung(2)|central_nervous_system(1)	14		Myeloproliferative disorder(115;0.00425)				TTTAAAATAAGTTTTTTTTTTC	0.406													3	5	---	---	---	---	
EYA2	2139	broad.mit.edu	37	20	45645538	45645539	+	Intron	DEL	TT	-	-			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:45645538_45645539delTT	uc002xsm.2	+						EYA2_uc010ghp.2_Intron|EYA2_uc002xsn.2_Intron|EYA2_uc002xso.2_Intron|EYA2_uc002xsp.2_Intron|EYA2_uc002xsq.2_Intron	NM_005244	NP_005235	O00167	EYA2_HUMAN	eyes absent 2 isoform a						DNA repair|histone dephosphorylation|mesodermal cell fate specification|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	magnesium ion binding|protein binding|protein tyrosine phosphatase activity			ovary(1)	1		Myeloproliferative disorder(115;0.0241)				tttgcttgtattttaagtgtga	0.203													4	2	---	---	---	---	
LAMA5	3911	broad.mit.edu	37	20	60894926	60894926	+	Intron	DEL	G	-	-			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:60894926delG	uc002ycq.2	-							NM_005560	NP_005551	O15230	LAMA5_HUMAN	laminin alpha 5 precursor						angiogenesis|cell proliferation|cell recognition|cytoskeleton organization|endothelial cell differentiation|focal adhesion assembly|integrin-mediated signaling pathway|regulation of cell adhesion|regulation of cell migration|regulation of embryonic development|substrate adhesion-dependent cell spreading	extracellular space|laminin-1 complex|laminin-10 complex|laminin-11 complex	integrin binding			ovary(1)|pancreas(1)|skin(1)	3	Breast(26;1.57e-08)		BRCA - Breast invasive adenocarcinoma(19;4.36e-06)		Alteplase(DB00009)|Anistreplase(DB00029)|Reteplase(DB00015)|Tenecteplase(DB00031)	CCTGGGGTCTGGGGGAGCGCC	0.572													4	2	---	---	---	---	
SLCO4A1	28231	broad.mit.edu	37	20	61310089	61310089	+	Intron	DEL	G	-	-	rs147133863		TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:61310089delG	uc002ydc.1	+									Q96BD0	SO4A1_HUMAN	Homo sapiens mRNA for organic anion transporter OATP-E, complete cds.						sodium-independent organic anion transport	integral to membrane|plasma membrane	thyroid hormone transmembrane transporter activity			ovary(1)	1	Breast(26;3.65e-08)		BRCA - Breast invasive adenocarcinoma(19;2.33e-06)			agccgtgagaggggggcactg	0.000													3	3	---	---	---	---	
PRPF6	24148	broad.mit.edu	37	20	62658152	62658153	+	Intron	INS	-	A	A	rs147732258	by1000genomes	TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:62658152_62658153insA	uc002yho.2	+						PRPF6_uc002yhp.2_Intron	NM_012469	NP_036601	O94906	PRP6_HUMAN	PRP6 pre-mRNA processing factor 6 homolog						assembly of spliceosomal tri-snRNP|positive regulation of transcription from RNA polymerase II promoter|spliceosome assembly	catalytic step 2 spliceosome|nucleoplasm|U4/U6 snRNP|U4/U6 x U5 tri-snRNP complex|U5 snRNP	androgen receptor binding|ribonucleoprotein binding|transcription coactivator activity			ovary(2)	2	all_cancers(38;6.47e-12)|all_epithelial(29;1.26e-13)|Lung NSC(23;9.37e-10)|all_lung(23;3.23e-09)					gactctatctcaaaaaaaaaca	0.144													4	2	---	---	---	---	
BAGE2	85319	broad.mit.edu	37	21	11057305	11057306	+	Intron	INS	-	G	G	rs150202290		TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:11057305_11057306insG	uc002yit.1	-							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)		TGGAGAAGATAGGAAAAAAAGC	0.347													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	37667354	37667354	+	IGR	DEL	A	-	-	rs71326671		TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:37667354delA								DOPEY2 (783 upstream) : MORC3 (25133 downstream)																							TTTCTTCtttaaaaaaaaaaa	0.289													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	39730748	39730748	+	IGR	DEL	A	-	-			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:39730748delA								KCNJ15 (57004 upstream) : ERG (21204 downstream)																							CTTCTTGCATAACCCTGAGGC	0.562													4	2	---	---	---	---	
DSCAM	1826	broad.mit.edu	37	21	42058101	42058102	+	Intron	DEL	AT	-	-			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:42058101_42058102delAT	uc002yyq.1	-						DSCAM_uc002yyr.1_Intron	NM_001389	NP_001380	O60469	DSCAM_HUMAN	Down syndrome cell adhesion molecule isoform						cell adhesion|dendrite self-avoidance|negative regulation of cell adhesion|positive regulation of axon extension involved in axon guidance|positive regulation of phosphorylation	axon|extracellular region|growth cone|integral to plasma membrane|membrane fraction	protein binding			ovary(6)|skin(4)|upper_aerodigestive_tract(1)	11		all_cancers(19;0.186)|Prostate(19;1.15e-05)|all_epithelial(19;0.0103)				acacacacacatacagagcaca	0.054													4	2	---	---	---	---	
TMPRSS2	7113	broad.mit.edu	37	21	42841237	42841238	+	Intron	DEL	CG	-	-	rs67617179		TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:42841237_42841238delCG	uc002yzj.2	-						TMPRSS2_uc010gor.2_Intron|TMPRSS2_uc010gos.1_Intron	NM_005656	NP_005647	O15393	TMPS2_HUMAN	transmembrane protease, serine 2 isoform 2						proteolysis	cytoplasm|extracellular region|integral to plasma membrane	scavenger receptor activity|serine-type endopeptidase activity		TMPRSS2/ERG(2499)|TMPRSS2/ETV1(24)	prostate(2523)|central_nervous_system(1)	2524		Prostate(19;4.48e-07)|all_epithelial(19;0.031)				catccacgcccgcactctgcta	0.000			T	ERG|ETV1|ETV4|ETV5	prostate 								1	5	---	---	---	---	
UMODL1	89766	broad.mit.edu	37	21	43538619	43538620	+	Intron	DEL	GT	-	-			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:43538619_43538620delGT	uc002zaf.1	+						UMODL1_uc002zad.1_Intron|UMODL1_uc002zae.1_Intron|UMODL1_uc002zag.1_Intron|UMODL1_uc002zal.1_5'Flank	NM_001004416	NP_001004416	Q5DID0	UROL1_HUMAN	uromodulin-like 1 isoform 1 precursor							cytoplasm|extracellular region|integral to membrane|plasma membrane	calcium ion binding|peptidase inhibitor activity			ovary(2)|skin(1)	3						ATAGCGTGTGGTGTGTGACTGT	0.480													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	44359378	44359381	+	IGR	DEL	CTTG	-	-	rs36157889		TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:44359378_44359381delCTTG								NDUFV3 (29606 upstream) : PKNOX1 (35262 downstream)																							ttttttgtttcttgtttttttttt	0.221													8	7	---	---	---	---	
TRPM2	7226	broad.mit.edu	37	21	45824752	45824753	+	Intron	INS	-	TGA	TGA			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:45824752_45824753insTGA	uc002zet.1	+						TRPM2_uc002zeu.1_Intron|TRPM2_uc002zew.1_Intron|TRPM2_uc010gpt.1_Intron|TRPM2_uc002zex.1_Intron|TRPM2_uc002zey.1_Intron	NM_003307	NP_003298	O94759	TRPM2_HUMAN	transient receptor potential cation channel,							integral to plasma membrane	ADP-ribose diphosphatase activity|calcium channel activity|sodium channel activity			ovary(1)|central_nervous_system(1)|pancreas(1)	3						gacagtgactgtgatgatagtg	0.114													9	8	---	---	---	---	
TRPM2	7226	broad.mit.edu	37	21	45853672	45853672	+	Intron	DEL	G	-	-			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:45853672delG	uc002zet.1	+						TRPM2_uc002zeu.1_Intron|TRPM2_uc002zew.1_Intron|TRPM2_uc010gpt.1_Intron|TRPM2_uc002zex.1_Intron|TRPM2_uc002zey.1_Intron|TRPM2_uc011aff.1_Intron	NM_003307	NP_003298	O94759	TRPM2_HUMAN	transient receptor potential cation channel,							integral to plasma membrane	ADP-ribose diphosphatase activity|calcium channel activity|sodium channel activity			ovary(1)|central_nervous_system(1)|pancreas(1)	3						CTGGCCAGGTGGGCCCTACAC	0.682													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	46453574	46453574	+	IGR	DEL	G	-	-			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:46453574delG								NCRNA00162 (28932 upstream) : C21orf122 (37299 downstream)																							CATGCTCCTCGGGTTTGTTCT	0.423													4	2	---	---	---	---	
psiTPTE22	387590	broad.mit.edu	37	22	17088404	17088404	+	Intron	DEL	T	-	-			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:17088404delT	uc010gqq.2	+						psiTPTE22_uc002zls.1_Intron|psiTPTE22_uc002zlq.3_Intron|psiTPTE22_uc002zlr.2_Intron					Homo sapiens cDNA FLJ10437 fis, clone NT2RP1000581.												0						TTGCCTTTACTTTTTTTTTTC	0.289													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	20114718	20114718	+	IGR	DEL	T	-	-	rs143470990		TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:20114718delT								RANBP1 (14 upstream) : ZDHHC8 (4647 downstream)																							ATTCAGGTTGTTTTTTTTTTT	0.313													4	2	---	---	---	---	
ADRBK2	157	broad.mit.edu	37	22	26086505	26086505	+	Intron	DEL	A	-	-			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:26086505delA	uc003abx.3	+						ADRBK2_uc010gux.2_Intron|ADRBK2_uc003abw.2_Intron|ADRBK2_uc003aby.3_Intron	NM_005160	NP_005151	P35626	ARBK2_HUMAN	beta-adrenergic receptor kinase 2								ATP binding|beta-adrenergic receptor kinase activity|signal transducer activity			lung(3)|ovary(2)|stomach(1)|central_nervous_system(1)	7					Adenosine triphosphate(DB00171)	GGACCTCAGCAAAAAATCAGA	0.473													4	2	---	---	---	---	
RFPL2	10739	broad.mit.edu	37	22	32590491	32590495	+	Intron	DEL	ATAAC	-	-			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:32590491_32590495delATAAC	uc003amg.3	-						RFPL2_uc003ame.3_5'Flank|RFPL2_uc003amf.3_Intron|RFPL2_uc003amh.3_Intron	NM_001098527	NP_001091997	O75678	RFPL2_HUMAN	ret finger protein-like 2 isoform 2								zinc ion binding			skin(1)	1						TGATTTAATTATAACAGGGAATTAG	0.420													52	24	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	38421365	38421366	+	IGR	DEL	AC	-	-			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:38421365_38421366delAC								POLR2F (37024 upstream) : PICK1 (31896 downstream)																							atcacaacgtacacacacacac	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	48026099	48026101	+	5'Flank	DEL	CTT	-	-	rs76990952		TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:48026099_48026101delCTT	uc003bik.1	+						uc003bii.2_5'Flank|uc011ard.1_5'Flank|uc011are.1_5'Flank|uc003bij.2_5'Flank					Homo sapiens cDNA FLJ35788 fis, clone TESTI2005683.																		CCTCAACCCCCTTCTTCTTCAGC	0.542													4	2	---	---	---	---	
DGKK	139189	broad.mit.edu	37	X	50130864	50130864	+	Intron	DEL	C	-	-			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:50130864delC	uc010njr.1	-							NM_001013742	NP_001013764	Q5KSL6	DGKK_HUMAN	diacylglycerol kinase kappa						activation of protein kinase C activity by G-protein coupled receptor protein signaling pathway|diacylglycerol metabolic process|intracellular signal transduction|platelet activation|response to oxidative stress	cytoplasm|plasma membrane	ATP binding|diacylglycerol kinase activity|metal ion binding			ovary(1)|kidney(1)	2	Ovarian(276;0.236)					CAGTGTCACACCACTTCCCAA	0.308													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	68616397	68616398	+	IGR	DEL	GT	-	-			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:68616397_68616398delGT								PJA1 (231057 upstream) : FAM155B (108680 downstream)																							CAGCTCCTTGGTGAAGCCCCCA	0.500													4	2	---	---	---	---	
SEPT6	23157	broad.mit.edu	37	X	118759293	118759294	+	Intron	INS	-	T	T			TCGA-CZ-5468-01A-01D-1501-10	TCGA-CZ-5468-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:118759293_118759294insT	uc004erv.2	-						SEPT6_uc010nqk.2_Intron|SEPT6_uc004ers.2_Intron|SEPT6_uc004ert.2_Intron|SEPT6_uc004eru.2_Intron|SEPT6_uc004erw.2_3'UTR	NM_015129	NP_055944	Q14141	SEPT6_HUMAN	septin 6 isoform B						cell cycle|cytokinesis|interspecies interaction between organisms	cleavage furrow|condensed chromosome kinetochore|midbody|septin complex|spindle	GTP binding|protein binding			lung(1)|ovary(1)|prostate(1)|kidney(1)	4						GTTAATCAAGCTTACCAGGACC	0.465													52	77	---	---	---	---	
