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
SLC45A1	50651	broad.mit.edu	37	1	8398053	8398053	+	Splice_Site	SNP	G	T	T			TCGA-CH-5771-01A-21D-1576-08	TCGA-CH-5771-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:8398053G>T	uc001apb.2	+	6	1774	c.1774_splice	c.e6+1	p.A592_splice	SLC45A1_uc001apc.2_Splice_Site_p.A290_splice	NM_001080397	NP_001073866	Q9Y2W3	S45A1_HUMAN	DNB5						carbohydrate transport	integral to membrane	symporter activity			central_nervous_system(2)|pancreas(1)|skin(1)	4	Ovarian(185;0.0661)|all_lung(157;0.127)	all_epithelial(116;1.22e-15)|all_lung(118;0.000147)|Lung NSC(185;0.000251)|Renal(390;0.000469)|Colorectal(325;0.00578)|Breast(348;0.00686)|Hepatocellular(190;0.0228)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.11)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|all cancers(8;3.95e-66)|GBM - Glioblastoma multiforme(8;5.93e-33)|Colorectal(212;2.86e-07)|COAD - Colon adenocarcinoma(227;3.11e-05)|Kidney(185;5.33e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000513)|KIRC - Kidney renal clear cell carcinoma(229;0.000979)|STAD - Stomach adenocarcinoma(132;0.00199)|READ - Rectum adenocarcinoma(331;0.0649)		TTCTACTCAGGTACCCGCTGC	0.582													6	47	---	---	---	---	PASS
PRAMEF8	391002	broad.mit.edu	37	1	12979764	12979764	+	Missense_Mutation	SNP	G	A	A			TCGA-CH-5771-01A-21D-1576-08	TCGA-CH-5771-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:12979764G>A	uc001aup.2	+	4	1039	c.956G>A	c.(955-957)CGT>CAT	p.R319H		NM_001012276	NP_001012276	Q5VWM4	PRAM8_HUMAN	PRAME family member 8	319	LRR 1.										0	Ovarian(185;0.249)	Renal(390;0.000469)|Lung NSC(185;0.00143)|all_lung(284;0.00181)|Colorectal(325;0.00215)|Breast(348;0.00224)|Myeloproliferative disorder(586;0.0393)|Hepatocellular(190;0.0623)|Ovarian(437;0.0731)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00812)|Colorectal(212;4.88e-06)|Kidney(185;4.89e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.000194)|COAD - Colon adenocarcinoma(227;0.000241)|BRCA - Breast invasive adenocarcinoma(304;0.000293)|STAD - Stomach adenocarcinoma(313;0.0072)|READ - Rectum adenocarcinoma(331;0.0649)		CCGAGCATCCGTCAATTAAAG	0.587													8	309	---	---	---	---	PASS
CROCCL1	84809	broad.mit.edu	37	1	16945027	16945027	+	RNA	SNP	T	C	C	rs1050322	by1000genomes	TCGA-CH-5771-01A-21D-1576-08	TCGA-CH-5771-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:16945027T>C	uc010ocf.1	-	4		c.1130A>G			CROCCL1_uc009vov.1_RNA|CROCCL1_uc001aze.2_RNA|CROCCL1_uc001azf.2_RNA					Homo sapiens mRNA for FLJ00313 protein.												0						gcaaaaatgctctctgcagca	0.095													2	1	---	---	---	---	PASS
KPNA6	23633	broad.mit.edu	37	1	32636498	32636498	+	3'UTR	SNP	T	C	C			TCGA-CH-5771-01A-21D-1576-08	TCGA-CH-5771-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:32636498T>C	uc001bug.2	+	14					KPNA6_uc001buh.2_3'UTR|KPNA6_uc010ogx.1_3'UTR|KPNA6_uc010ogy.1_3'UTR|KPNA6_uc009vtz.2_3'UTR	NM_012316	NP_036448	O60684	IMA7_HUMAN	karyopherin alpha 6						NLS-bearing substrate import into nucleus	cytoplasm|nuclear pore	protein binding				0		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0837)|Ovarian(437;0.101)|Breast(348;0.174)				AGCTATAATATCTGCCTCCAG	0.602													16	62	---	---	---	---	PASS
CSMD2	114784	broad.mit.edu	37	1	34112373	34112373	+	Missense_Mutation	SNP	G	A	A			TCGA-CH-5771-01A-21D-1576-08	TCGA-CH-5771-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:34112373G>A	uc001bxn.1	-	29	4558	c.4529C>T	c.(4528-4530)CCT>CTT	p.P1510L	CSMD2_uc001bxm.1_Missense_Mutation_p.P1550L|CSMD2_uc001bxo.1_Missense_Mutation_p.P423L	NM_052896	NP_443128	Q7Z408	CSMD2_HUMAN	CUB and Sushi multiple domains 2	1510	CUB 9.|Extracellular (Potential).					integral to membrane|plasma membrane	protein binding			ovary(6)|skin(5)|pancreas(1)	12		Myeloproliferative disorder(586;0.0294)|all_neural(195;0.249)				TCCTATGAGAGGGCTGAGAGA	0.562													4	35	---	---	---	---	PASS
KIAA0319L	79932	broad.mit.edu	37	1	35915489	35915489	+	Missense_Mutation	SNP	T	C	C			TCGA-CH-5771-01A-21D-1576-08	TCGA-CH-5771-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:35915489T>C	uc001byx.2	-	15	2590	c.2332A>G	c.(2332-2334)ACC>GCC	p.T778A	KIAA0319L_uc001byw.2_Missense_Mutation_p.T220A|KIAA0319L_uc010ohv.1_Missense_Mutation_p.T420A	NM_024874	NP_079150	Q8IZA0	K319L_HUMAN	dyslexia susceptibility 2-like	778	PKD 5.|Extracellular (Potential).					cytoplasmic vesicle part|integral to membrane	protein binding			skin(2)	2		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0887)				TCCACAGTGGTCCGGTCTGTG	0.488													22	154	---	---	---	---	PASS
CSF3R	1441	broad.mit.edu	37	1	36935383	36935383	+	Silent	SNP	G	T	T			TCGA-CH-5771-01A-21D-1576-08	TCGA-CH-5771-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:36935383G>T	uc001caw.1	-	11	1522	c.1344C>A	c.(1342-1344)GGC>GGA	p.G448G	CSF3R_uc001cat.1_Silent_p.G11G|CSF3R_uc009vvc.1_Silent_p.G11G|CSF3R_uc001cau.1_Translation_Start_Site|CSF3R_uc001cav.1_Silent_p.G448G|CSF3R_uc001cax.1_Silent_p.G448G|CSF3R_uc001cay.1_Silent_p.G448G	NM_000760	NP_000751	Q99062	CSF3R_HUMAN	colony stimulating factor 3 receptor isoform a	448	Extracellular (Potential).|Fibronectin type-III 4.				cell adhesion|defense response	extracellular region|integral to plasma membrane	cytokine receptor activity			central_nervous_system(2)|ovary(1)	3		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.164)			Filgrastim(DB00099)|Pegfilgrastim(DB00019)	GGGGCTCCCAGCCTACCCAGA	0.587													5	74	---	---	---	---	PASS
ZFYVE9	9372	broad.mit.edu	37	1	52704167	52704167	+	Missense_Mutation	SNP	G	C	C			TCGA-CH-5771-01A-21D-1576-08	TCGA-CH-5771-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:52704167G>C	uc001cto.2	+	4	1250	c.1078G>C	c.(1078-1080)GAT>CAT	p.D360H	ZFYVE9_uc001ctn.2_Missense_Mutation_p.D360H|ZFYVE9_uc001ctp.2_Missense_Mutation_p.D360H	NM_004799	NP_004790	O95405	ZFYV9_HUMAN	zinc finger, FYVE domain containing 9 isoform 3	360					endocytosis|SMAD protein complex assembly|SMAD protein import into nucleus|transforming growth factor beta receptor signaling pathway	early endosome membrane	metal ion binding|protein binding|receptor activity|serine-type peptidase activity			ovary(2)|lung(2)|central_nervous_system(2)|skin(2)	8						ACGGTGTTCAGATTGCCTTGT	0.428													17	206	---	---	---	---	PASS
GDAP2	54834	broad.mit.edu	37	1	118420506	118420506	+	Intron	SNP	G	T	T			TCGA-CH-5771-01A-21D-1576-08	TCGA-CH-5771-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:118420506G>T	uc001ehf.2	-						GDAP2_uc001ehg.2_3'UTR	NM_017686	NP_060156	Q9NXN4	GDAP2_HUMAN	ganglioside induced differentiation associated											ovary(2)	2		all_cancers(81;0.0156)|all_lung(203;5.81e-05)|Lung NSC(69;0.000446)|all_epithelial(167;0.00295)		Lung(183;0.0583)|LUSC - Lung squamous cell carcinoma(189;0.194)		ATATTACCAAGTTTATTAAGA	0.353													3	28	---	---	---	---	PASS
SEMA4A	64218	broad.mit.edu	37	1	156131152	156131152	+	Missense_Mutation	SNP	G	A	A			TCGA-CH-5771-01A-21D-1576-08	TCGA-CH-5771-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:156131152G>A	uc001fnl.2	+	9	930	c.826G>A	c.(826-828)GAA>AAA	p.E276K	SEMA4A_uc009wrq.2_Missense_Mutation_p.E276K|SEMA4A_uc001fnm.2_Missense_Mutation_p.E276K|SEMA4A_uc001fnn.2_Missense_Mutation_p.E144K|SEMA4A_uc001fno.2_Missense_Mutation_p.E276K	NM_022367	NP_071762	Q9H3S1	SEM4A_HUMAN	semaphorin B precursor	276	Sema.|Extracellular (Potential).				axon guidance	integral to membrane|plasma membrane	receptor activity			ovary(1)|skin(1)	2	Hepatocellular(266;0.158)					CGTGGGCGGCGAAAAGCTGCT	0.512													10	59	---	---	---	---	PASS
MRPS14	63931	broad.mit.edu	37	1	174987689	174987689	+	Silent	SNP	G	T	T			TCGA-CH-5771-01A-21D-1576-08	TCGA-CH-5771-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:174987689G>T	uc001gkk.2	-	2	86	c.69C>A	c.(67-69)GGC>GGA	p.G23G	MRPS14_uc009wwr.2_Silent_p.G8G	NM_022100	NP_071383	O60783	RT14_HUMAN	mitochondrial ribosomal protein S14	23					translation	mitochondrial ribosome	protein binding|structural constituent of ribosome				0						TTCGAACTTGGCCTGAAGCTG	0.458													9	131	---	---	---	---	PASS
TNN	63923	broad.mit.edu	37	1	175046577	175046577	+	Missense_Mutation	SNP	G	A	A			TCGA-CH-5771-01A-21D-1576-08	TCGA-CH-5771-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:175046577G>A	uc001gkl.1	+	2	136	c.23G>A	c.(22-24)CGC>CAC	p.R8H	TNN_uc010pmx.1_Missense_Mutation_p.R8H	NM_022093	NP_071376	Q9UQP3	TENN_HUMAN	tenascin N precursor	8					cell growth|cell migration|signal transduction	extracellular space|proteinaceous extracellular matrix				large_intestine(5)|ovary(3)|central_nervous_system(1)	9		Breast(1374;0.000962)		KIRC - Kidney renal clear cell carcinoma(1967;0.00198)		GAGATGTTCCGCTTCCCTATG	0.572													8	239	---	---	---	---	PASS
PTPN14	5784	broad.mit.edu	37	1	214656022	214656022	+	Intron	SNP	T	C	C	rs74709691	by1000genomes	TCGA-CH-5771-01A-21D-1576-08	TCGA-CH-5771-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:214656022T>C	uc001hkk.1	-						PTPN14_uc010pty.1_Intron|uc010ptz.1_RNA	NM_005401	NP_005392	Q15678	PTN14_HUMAN	protein tyrosine phosphatase, non-receptor type						lymphangiogenesis	cytoplasm|cytoskeleton	protein tyrosine phosphatase activity|receptor tyrosine kinase binding			breast(2)|ovary(1)|kidney(1)|skin(1)	5				OV - Ovarian serous cystadenocarcinoma(81;0.00181)|all cancers(67;0.00194)|Epithelial(68;0.0157)|GBM - Glioblastoma multiforme(131;0.155)		AACTTCTATATAGTACCTTGA	0.328													4	20	---	---	---	---	PASS
POTEE	445582	broad.mit.edu	37	2	132021050	132021050	+	Missense_Mutation	SNP	G	C	C			TCGA-CH-5771-01A-21D-1576-08	TCGA-CH-5771-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:132021050G>C	uc002tsn.2	+	15	2074	c.2022G>C	c.(2020-2022)AAG>AAC	p.K674N	PLEKHB2_uc002tsh.2_Intron|POTEE_uc002tsk.2_Missense_Mutation_p.K274N|POTEE_uc002tsl.2_Missense_Mutation_p.K256N|POTEE_uc010fmy.1_Missense_Mutation_p.K138N	NM_001083538	NP_001077007	Q6S8J3	POTEE_HUMAN	protein expressed in prostate, ovary, testis,	674	Potential.						ATP binding				0						TAAGAGAAAAGAAATATTTGG	0.383													6	43	---	---	---	---	PASS
SCN7A	6332	broad.mit.edu	37	2	167262388	167262388	+	Missense_Mutation	SNP	C	A	A			TCGA-CH-5771-01A-21D-1576-08	TCGA-CH-5771-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:167262388C>A	uc002udu.1	-	25	4878	c.4751G>T	c.(4750-4752)AGA>ATA	p.R1584I		NM_002976	NP_002967	Q01118	SCN7A_HUMAN	sodium channel, voltage-gated, type VII, alpha	1584					muscle contraction	voltage-gated sodium channel complex	voltage-gated sodium channel activity			large_intestine(1)	1						ACCCATAACTCTCTTTGTAAA	0.428													51	357	---	---	---	---	PASS
STK36	27148	broad.mit.edu	37	2	219566800	219566800	+	3'UTR	SNP	G	A	A			TCGA-CH-5771-01A-21D-1576-08	TCGA-CH-5771-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:219566800G>A	uc002viu.2	+	27					STK36_uc002viv.2_3'UTR|STK36_uc002viw.2_3'UTR|STK36_uc002vix.2_3'UTR	NM_015690	NP_056505	Q9NRP7	STK36_HUMAN	serine/threonine kinase 36						cilium assembly|positive regulation of hh target transcription factor activity|positive regulation of smoothened signaling pathway|post-embryonic development	aggresome|cytoplasm|focal adhesion|intermediate filament cytoskeleton|nucleus	ATP binding|protein serine/threonine kinase activity|transcription factor binding			ovary(4)|stomach(2)|lung(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)|breast(1)	11		Renal(207;0.0915)		Epithelial(149;9.65e-07)|all cancers(144;0.000174)|LUSC - Lung squamous cell carcinoma(224;0.00813)|Lung(261;0.00984)		TACACAAGCCGCCAACTCAAC	0.438													3	22	---	---	---	---	PASS
POC1A	25886	broad.mit.edu	37	3	52156492	52156492	+	Missense_Mutation	SNP	A	C	C			TCGA-CH-5771-01A-21D-1576-08	TCGA-CH-5771-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:52156492A>C	uc003dcu.2	-	9	1202	c.884T>G	c.(883-885)GTG>GGG	p.V295G	POC1A_uc003dcv.2_Missense_Mutation_p.V257G|POC1A_uc003dcw.2_Missense_Mutation_p.V295G	NM_015426	NP_056241	Q8NBT0	POC1A_HUMAN	WD repeat domain 51A isoform 1	295	WD 7.					centriole|microtubule basal body					0						CCAAACCATCACCTGCCAAAA	0.517													7	29	---	---	---	---	PASS
COPG	22820	broad.mit.edu	37	3	128996231	128996231	+	Missense_Mutation	SNP	G	C	C			TCGA-CH-5771-01A-21D-1576-08	TCGA-CH-5771-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:128996231G>C	uc003els.2	+	24	2689	c.2589G>C	c.(2587-2589)GAG>GAC	p.E863D	COPG_uc010htb.2_Missense_Mutation_p.E769D|C3orf37_uc003elt.2_5'Flank|C3orf37_uc003elu.2_5'Flank|C3orf37_uc003elv.2_5'Flank|C3orf37_uc003elw.2_5'Flank	NM_016128	NP_057212	Q9Y678	COPG_HUMAN	coatomer protein complex, subunit gamma 1	863	Interaction with ZNF289/ARFGAP2.				COPI coating of Golgi vesicle|intracellular protein transport|retrograde vesicle-mediated transport, Golgi to ER	COPI vesicle coat|cytosol	protein binding|structural molecule activity			ovary(3)|breast(1)	4						GTTTGGAGGAGCTGCCAGTAG	0.547													7	32	---	---	---	---	PASS
CRIPAK	285464	broad.mit.edu	37	4	1388998	1388998	+	Silent	SNP	G	A	A			TCGA-CH-5771-01A-21D-1576-08	TCGA-CH-5771-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:1388998G>A	uc003gdf.2	+	1	3659	c.699G>A	c.(697-699)ACG>ACA	p.T233T		NM_175918	NP_787114	Q8N1N5	CRPAK_HUMAN	cysteine-rich PAK1 inhibitor	233	6.				ER-nucleus signaling pathway|negative regulation of protein kinase activity|regulation of cytoskeleton organization|response to estrogen stimulus	endoplasmic reticulum|nucleus|plasma membrane	protein binding				0			OV - Ovarian serous cystadenocarcinoma(23;0.0106)			CTGCTCACACGTGCCGATGCG	0.667													5	101	---	---	---	---	PASS
PDGFRA	5156	broad.mit.edu	37	4	55138618	55138618	+	Missense_Mutation	SNP	C	T	T			TCGA-CH-5771-01A-21D-1576-08	TCGA-CH-5771-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:55138618C>T	uc003han.3	+	9	1626	c.1295C>T	c.(1294-1296)ACG>ATG	p.T432M	PDGFRA_uc003haa.2_Intron|PDGFRA_uc010igq.1_Missense_Mutation_p.T326M|PDGFRA_uc003ham.2_RNA	NM_006206	NP_006197	P16234	PGFRA_HUMAN	platelet-derived growth factor receptor alpha	432	Ig-like C2-type 5.|Extracellular (Potential).				cardiac myofibril assembly|cell activation|luteinization|metanephric glomerular capillary formation|peptidyl-tyrosine phosphorylation|positive regulation of cell migration|positive regulation of DNA replication|positive regulation of fibroblast proliferation|protein autophosphorylation|retina vasculature development in camera-type eye	cytoplasm|integral to plasma membrane|nucleus	ATP binding|platelet-derived growth factor alpha-receptor activity|platelet-derived growth factor binding|platelet-derived growth factor receptor binding|protein homodimerization activity|vascular endothelial growth factor receptor activity			soft_tissue(572)|small_intestine(40)|stomach(16)|lung(16)|central_nervous_system(13)|haematopoietic_and_lymphoid_tissue(7)|skin(3)|ovary(3)|gastrointestinal_tract_(site_indeterminate)(1)|autonomic_ganglia(1)|prostate(1)|bone(1)	674	all_cancers(7;0.000425)|all_lung(4;0.000343)|Lung NSC(11;0.000467)|all_epithelial(27;0.0131)|all_neural(26;0.0209)|Glioma(25;0.08)		GBM - Glioblastoma multiforme(1;4.18e-71)|all cancers(1;4.76e-45)|LUSC - Lung squamous cell carcinoma(32;0.00256)		Becaplermin(DB00102)|Imatinib(DB00619)|Sunitinib(DB01268)	GGGGGACAGACGGTGAGGTGC	0.473			Mis|O|T	FIP1L1	GIST|idiopathic hypereosinophilic syndrome				Gastrointestinal_Stromal_Tumors_Sporadic_Multiple_Primary|Familial_Intestinal_Neurofibromatosis	TSP Lung(21;0.16)			17	118	---	---	---	---	PASS
ALPK1	80216	broad.mit.edu	37	4	113362622	113362622	+	3'UTR	SNP	C	G	G	rs231253	by1000genomes	TCGA-CH-5771-01A-21D-1576-08	TCGA-CH-5771-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:113362622C>G	uc003iap.3	+	16					ALPK1_uc003ian.3_3'UTR|ALPK1_uc011cfx.1_3'UTR|ALPK1_uc003iao.3_RNA|ALPK1_uc010imo.2_3'UTR	NM_025144	NP_079420	Q96QP1	ALPK1_HUMAN	alpha-kinase 1								ATP binding|protein serine/threonine kinase activity			ovary(5)	5		Ovarian(17;0.0446)|Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;0.00325)		gaaaagcactcttgagaaagg	0.065													5	3	---	---	---	---	PASS
ANK2	287	broad.mit.edu	37	4	114251487	114251487	+	Missense_Mutation	SNP	C	T	T			TCGA-CH-5771-01A-21D-1576-08	TCGA-CH-5771-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:114251487C>T	uc003ibe.3	+	27	3086	c.2986C>T	c.(2986-2988)CGG>TGG	p.R996W	ANK2_uc003ibd.3_Missense_Mutation_p.R987W|ANK2_uc003ibf.3_Missense_Mutation_p.R996W|ANK2_uc011cgc.1_Missense_Mutation_p.R205W|ANK2_uc003ibg.3_Missense_Mutation_p.R24W|ANK2_uc003ibc.2_Missense_Mutation_p.R972W|ANK2_uc011cgb.1_Missense_Mutation_p.R1011W	NM_001148	NP_001139	Q01484	ANK2_HUMAN	ankyrin 2 isoform 1	996	ZU5.|Interaction with SPTBN1.				axon guidance|signal transduction	apical plasma membrane|basolateral plasma membrane|cytoskeleton|cytosol|sarcomere	protein binding|protein binding			central_nervous_system(7)|ovary(3)|large_intestine(2)|breast(1)|skin(1)	14		Ovarian(17;0.0448)|Hepatocellular(203;0.218)		OV - Ovarian serous cystadenocarcinoma(123;4.92e-05)		TATTCCACCTCGGAAATGTAC	0.512													7	59	---	---	---	---	PASS
SV2C	22987	broad.mit.edu	37	5	75427791	75427791	+	Silent	SNP	C	T	T			TCGA-CH-5771-01A-21D-1576-08	TCGA-CH-5771-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:75427791C>T	uc003kei.1	+	2	350	c.216C>T	c.(214-216)GAC>GAT	p.D72D		NM_014979	NP_055794	Q496J9	SV2C_HUMAN	synaptic vesicle glycoprotein 2C	72	Cytoplasmic (Potential).				neurotransmitter transport	cell junction|integral to membrane|synaptic vesicle membrane	transmembrane transporter activity			skin(1)	1		all_lung(232;0.007)|Lung NSC(167;0.0148)|Ovarian(174;0.0798)|Prostate(461;0.184)		OV - Ovarian serous cystadenocarcinoma(47;1.16e-50)|all cancers(79;7.25e-40)		CCAACGATGACGAAGGCTCAA	0.498													7	52	---	---	---	---	PASS
CDKN2AIPNL	91368	broad.mit.edu	37	5	133747428	133747428	+	Missense_Mutation	SNP	G	A	A			TCGA-CH-5771-01A-21D-1576-08	TCGA-CH-5771-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:133747428G>A	uc011cxs.1	-	1	162	c.118C>T	c.(118-120)CGC>TGC	p.R40C	CDKN2AIPNL_uc003kzi.1_Missense_Mutation_p.R40C	NM_080656	NP_542387	Q96HQ2	C2AIL_HUMAN	CDKN2A interacting protein N-terminal like	40											0			KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			AATTCCATGCGGGCCTTCCAT	0.677											OREG0016789	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	3	32	---	---	---	---	PASS
DND1	373863	broad.mit.edu	37	5	140052312	140052312	+	Silent	SNP	T	G	G			TCGA-CH-5771-01A-21D-1576-08	TCGA-CH-5771-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140052312T>G	uc003lgt.2	-	3	366	c.322A>C	c.(322-324)AGG>CGG	p.R108R		NM_194249	NP_919225	Q8IYX4	DND1_HUMAN	dead end homolog 1	108	RRM 1.				multicellular organismal development|negative regulation of gene silencing by miRNA	cytoplasm|nucleus	AU-rich element binding|nucleotide binding				0			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GCGCCGCGCCTCGAGCTGTAG	0.687													3	4	---	---	---	---	PASS
DND1	373863	broad.mit.edu	37	5	140052331	140052331	+	Silent	SNP	G	T	T			TCGA-CH-5771-01A-21D-1576-08	TCGA-CH-5771-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140052331G>T	uc003lgt.2	-	3	347	c.303C>A	c.(301-303)GCC>GCA	p.A101A		NM_194249	NP_919225	Q8IYX4	DND1_HUMAN	dead end homolog 1	101	RRM 1.				multicellular organismal development|negative regulation of gene silencing by miRNA	cytoplasm|nucleus	AU-rich element binding|nucleotide binding				0			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			AGCGGGCATAGGCGAAGCCGC	0.687													3	9	---	---	---	---	PASS
NUDCD2	134492	broad.mit.edu	37	5	162886898	162886898	+	Silent	SNP	C	A	A			TCGA-CH-5771-01A-21D-1576-08	TCGA-CH-5771-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:162886898C>A	uc003lze.2	-	1	246	c.159G>T	c.(157-159)GCG>GCT	p.A53A	HMMR_uc003lzh.2_5'Flank|HMMR_uc003lzf.2_5'Flank|HMMR_uc003lzg.2_5'Flank|HMMR_uc011dem.1_5'Flank	NM_145266	NP_660309	Q8WVJ2	NUDC2_HUMAN	NudC domain containing 2	53	CS.					intracellular					0	Renal(175;0.000281)	Medulloblastoma(196;0.0207)|all_neural(177;0.0966)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	all cancers(165;0.0981)|OV - Ovarian serous cystadenocarcinoma(192;0.183)|Epithelial(171;0.247)		CCACCGACAGCGCCACATGCC	0.642													10	72	---	---	---	---	PASS
TRIM27	5987	broad.mit.edu	37	6	28891458	28891458	+	5'UTR	SNP	T	C	C	rs1061625		TCGA-CH-5771-01A-21D-1576-08	TCGA-CH-5771-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:28891458T>C	uc003nlr.2	-	1					TRIM27_uc003nls.2_5'UTR|TRIM27_uc003nlt.1_5'UTR	NM_006510	NP_006501	P14373	TRI27_HUMAN	ret finger protein						cell proliferation|negative regulation of gene expression, epigenetic|negative regulation of transcription from RNA polymerase II promoter|protein trimerization|spermatogenesis|transcription, DNA-dependent	cytoplasm|integral to plasma membrane|membrane fraction|nuclear membrane|PML body	DNA binding|protein binding|transmembrane receptor protein tyrosine kinase activity|zinc ion binding			ovary(1)	1						CGCCGAGCTCTGCACTGAGCC	0.756			T	RET	papillary thyroid								4	6	---	---	---	---	PASS
POLH	5429	broad.mit.edu	37	6	43565468	43565468	+	Missense_Mutation	SNP	G	C	C			TCGA-CH-5771-01A-21D-1576-08	TCGA-CH-5771-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:43565468G>C	uc003ovq.3	+	5	830	c.526G>C	c.(526-528)GAT>CAT	p.D176H	POLH_uc010jyu.2_Missense_Mutation_p.D52H|POLH_uc011dvl.1_RNA|POLH_uc003ovr.3_Missense_Mutation_p.D77H	NM_006502	NP_006493	Q9Y253	POLH_HUMAN	DNA-directed DNA polymerase eta	176	UmuC.				DNA replication|DNA synthesis involved in DNA repair|regulation of DNA repair|response to UV-C	cytoplasm|nucleoplasm	damaged DNA binding|DNA-directed DNA polymerase activity|metal ion binding			breast(2)	2	all_cancers(18;1.89e-05)|Lung NSC(15;0.00161)|all_lung(25;0.004)		all cancers(41;0.000753)|Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|STAD - Stomach adenocarcinoma(11;0.0826)|OV - Ovarian serous cystadenocarcinoma(102;0.167)			TCAATGGCTCGATTCTCTTCA	0.408								DNA_polymerases_(catalytic_subunits)	Xeroderma_Pigmentosum				6	59	---	---	---	---	PASS
KIAA1324L	222223	broad.mit.edu	37	7	86556150	86556150	+	Missense_Mutation	SNP	T	C	C			TCGA-CH-5771-01A-21D-1576-08	TCGA-CH-5771-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:86556150T>C	uc011kha.1	-	9	1357	c.1172A>G	c.(1171-1173)GAG>GGG	p.E391G	KIAA1324L_uc003uif.1_Missense_Mutation_p.E151G|KIAA1324L_uc011kgz.1_Missense_Mutation_p.E277G|KIAA1324L_uc003uie.2_Missense_Mutation_p.E224G	NM_001142749	NP_001136221	A8MWY0	K132L_HUMAN	hypothetical protein LOC222223 isoform 1	391	Extracellular (Potential).					integral to membrane				ovary(6)|skin(1)	7	Esophageal squamous(14;0.0058)					ATCCTTCTTCTCTCCAGAAGG	0.428													14	265	---	---	---	---	PASS
MET	4233	broad.mit.edu	37	7	116340051	116340051	+	Missense_Mutation	SNP	A	G	G			TCGA-CH-5771-01A-21D-1576-08	TCGA-CH-5771-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:116340051A>G	uc003vij.2	+	2	1100	c.913A>G	c.(913-915)AAA>GAA	p.K305E	MET_uc010lkh.2_Missense_Mutation_p.K305E|MET_uc011knc.1_Missense_Mutation_p.K305E|MET_uc011knd.1_Missense_Mutation_p.K305E|MET_uc011kne.1_Missense_Mutation_p.K305E|MET_uc011knf.1_Missense_Mutation_p.K305E|MET_uc011kng.1_Missense_Mutation_p.K305E|MET_uc011knh.1_Missense_Mutation_p.K305E|MET_uc011kni.1_Missense_Mutation_p.K305E|MET_uc003vii.1_Missense_Mutation_p.K324E|MET_uc010lkg.2_Missense_Mutation_p.K305E|MET_uc011kmz.1_Missense_Mutation_p.K305E|MET_uc011kna.1_Missense_Mutation_p.K305E|MET_uc011knb.1_Missense_Mutation_p.K305E	NM_000245	NP_000236	P08581	MET_HUMAN	met proto-oncogene isoform b precursor	305	Extracellular (Potential).|Sema.				axon guidance|cell proliferation	basal plasma membrane|integral to plasma membrane	ATP binding|hepatocyte growth factor receptor activity|protein binding			upper_aerodigestive_tract(63)|lung(41)|kidney(18)|NS(10)|ovary(5)|thyroid(4)|central_nervous_system(4)|stomach(3)|liver(3)|pleura(2)|large_intestine(2)|breast(2)|testis(1)|skin(1)	159	all_cancers(3;1.25e-07)|all_epithelial(6;4.07e-08)|Lung NSC(10;0.00108)|all_lung(10;0.00125)	Ovarian(593;0.133)	GBM - Glioblastoma multiforme(2;2.31e-07)|all cancers(2;0.000419)|STAD - Stomach adenocarcinoma(10;0.000512)			AGAAAAGAGAAAAAAGAGATC	0.428			Mis		papillary renal|head-neck squamous cell 	papillary renal			Hereditary_Papillary_Renal_Carcinoma_(type_1)				11	202	---	---	---	---	PASS
TRY6	154754	broad.mit.edu	37	7	142482229	142482229	+	Silent	SNP	T	A	A	rs145494190	by1000genomes	TCGA-CH-5771-01A-21D-1576-08	TCGA-CH-5771-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:142482229T>A	uc011ksq.1	+	5	692	c.609T>A	c.(607-609)CCT>CCA	p.P203P	uc003vzp.2_Intron|uc011ksh.1_Intron|uc011ksi.1_Intron|uc003vzw.1_Intron|uc010loj.1_Intron|uc003wad.2_Intron|uc003wag.1_Intron|uc003wan.1_Intron	NR_001296				SubName: Full=Protease, serine, 3; Flags: Fragment;												0						CTGGTGGCCCTGTGGTCTGCA	0.493													4	65	---	---	---	---	PASS
SSPO	23145	broad.mit.edu	37	7	149518961	149518961	+	Silent	SNP	T	C	C	rs1008335	by1000genomes	TCGA-CH-5771-01A-21D-1576-08	TCGA-CH-5771-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:149518961T>C	uc010lpk.2	+	91	12765	c.12765T>C	c.(12763-12765)GCT>GCC	p.A4255A	SSPO_uc010lpm.1_RNA|SSPO_uc003wgg.2_RNA|SSPO_uc003wgh.2_RNA|SSPO_uc003wgi.1_5'Flank	NM_198455	NP_940857	A2VEC9	SSPO_HUMAN	SCO-spondin precursor	4255	TSP type-1 20.				cell adhesion	extracellular space	peptidase inhibitor activity				0	Melanoma(164;0.165)|Ovarian(565;0.177)		OV - Ovarian serous cystadenocarcinoma(82;0.00625)			TGCCTGAGGCTTGGACGCTGT	0.667													3	6	---	---	---	---	PASS
CHRNA6	8973	broad.mit.edu	37	8	42608268	42608268	+	3'UTR	SNP	A	G	G			TCGA-CH-5771-01A-21D-1576-08	TCGA-CH-5771-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:42608268A>G	uc003xpj.2	-	6					CHRNA6_uc011lcw.1_3'UTR	NM_004198	NP_004189	Q15825	ACHA6_HUMAN	cholinergic receptor, nicotinic, alpha 6							cell junction|nicotinic acetylcholine-gated receptor-channel complex|postsynaptic membrane	acetylcholine receptor activity|nicotinic acetylcholine-activated cation-selective channel activity				0	all_lung(13;3.33e-12)|Lung NSC(13;9.17e-11)|Ovarian(28;0.01)|Prostate(17;0.0119)|Lung SC(25;0.184)	all_lung(54;0.00439)|Lung NSC(58;0.0124)|Esophageal squamous(32;0.131)|Hepatocellular(245;0.133)|Renal(179;0.151)	Lung(22;0.0252)|LUSC - Lung squamous cell carcinoma(45;0.0869)			TGTGGCAGGGAATGCAGAACA	0.413													8	35	---	---	---	---	PASS
RP1	6101	broad.mit.edu	37	8	55540711	55540711	+	Nonsense_Mutation	SNP	T	A	A			TCGA-CH-5771-01A-21D-1576-08	TCGA-CH-5771-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:55540711T>A	uc003xsd.1	+	4	4417	c.4269T>A	c.(4267-4269)TGT>TGA	p.C1423*	RP1_uc011ldy.1_Intron	NM_006269	NP_006260	P56715	RP1_HUMAN	retinitis pigmentosa RP1 protein	1423					axoneme assembly|intracellular signal transduction|photoreceptor cell maintenance|photoreceptor cell outer segment organization|phototransduction, visible light|retinal cone cell development|retinal rod cell development	cilium axoneme|cytoplasm|microtubule|microtubule associated complex|photoreceptor connecting cilium|photoreceptor inner segment|photoreceptor outer segment	microtubule binding			skin(7)|ovary(4)|pancreas(1)	12		all_lung(136;0.0831)|Lung NSC(129;0.109)|all_epithelial(80;0.123)	OV - Ovarian serous cystadenocarcinoma(7;4.4e-07)|Epithelial(17;3.37e-05)|all cancers(17;0.000285)			TTGAAAATTGTTCACTAAGGA	0.363													15	110	---	---	---	---	PASS
MSC	9242	broad.mit.edu	37	8	72756371	72756371	+	Missense_Mutation	SNP	G	A	A			TCGA-CH-5771-01A-21D-1576-08	TCGA-CH-5771-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:72756371G>A	uc003xyx.1	-	1	361	c.43C>T	c.(43-45)CGG>TGG	p.R15W	uc011lff.1_Intron|uc003xyy.2_RNA	NM_005098	NP_005089	O60682	MUSC_HUMAN	musculin	15					transcription from RNA polymerase II promoter	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|transcription corepressor activity				0	Breast(64;0.176)		Epithelial(68;0.137)|BRCA - Breast invasive adenocarcinoma(89;0.203)			TGCAGCCCCCGAAGCTCCATC	0.692													4	21	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	9	66459820	66459820	+	5'Flank	SNP	G	C	C			TCGA-CH-5771-01A-21D-1576-08	TCGA-CH-5771-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:66459820G>C	uc010mng.1	-						uc004aeb.2_5'Flank|uc004aec.2_RNA					Homo sapiens cDNA, FLJ98602.																		tttgtccccagtgccttattt	0.000													2	2	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	9	66459884	66459884	+	5'Flank	SNP	T	G	G	rs139166660	by1000genomes	TCGA-CH-5771-01A-21D-1576-08	TCGA-CH-5771-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:66459884T>G	uc010mng.1	-						uc004aeb.2_5'Flank|uc004aec.2_RNA					Homo sapiens cDNA, FLJ98602.																		tagtagatgttcttcagtgtc	0.000													2	3	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	9	66466226	66466226	+	RNA	SNP	A	G	G			TCGA-CH-5771-01A-21D-1576-08	TCGA-CH-5771-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:66466226A>G	uc004aec.2	+	3		c.859A>G								Homo sapiens, clone IMAGE:5213378, mRNA.																		cctagcggagagagagccgga	0.104													2	6	---	---	---	---	PASS
C9orf98	158067	broad.mit.edu	37	9	135702270	135702270	+	Missense_Mutation	SNP	T	G	G			TCGA-CH-5771-01A-21D-1576-08	TCGA-CH-5771-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:135702270T>G	uc004cbu.1	-	8	1284	c.728A>C	c.(727-729)GAC>GCC	p.D243A	C9orf98_uc010mzx.1_RNA|C9orf98_uc004cbv.1_Missense_Mutation_p.D39A	NM_152572	NP_689785	Q96MA6	KAD8_HUMAN	putative adenylate kinase-like protein C9orf98	243						cytosol	adenylate kinase activity|ATP binding|cytidylate kinase activity				0				OV - Ovarian serous cystadenocarcinoma(145;4.89e-06)|Epithelial(140;0.00016)		ACATGGCTGGTCAGCACTGAT	0.557													15	168	---	---	---	---	PASS
PIPSL	266971	broad.mit.edu	37	10	95719865	95719865	+	Missense_Mutation	SNP	T	G	G			TCGA-CH-5771-01A-21D-1576-08	TCGA-CH-5771-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:95719865T>G	uc009xuj.2	-	1	1808	c.1289A>C	c.(1288-1290)TAC>TCC	p.Y430S		NR_002319				RecName: Full=Phosphatidylinositol-4-phosphate 5-kinase type-1 alpha;          Short=PtdIns(4)P-5-kinase alpha;          Short=PIP5KIalpha;          EC=2.7.1.68; AltName: Full=Phosphatidylinositol-4-phosphate 5-kinase type I alpha; AltName: Full=68 kDa type I phosphatidylinositol-4-phosphate 5-kinase alpha;												0						CAATGGCTGGTAAGTAATGCA	0.493													6	42	---	---	---	---	PASS
CTR9	9646	broad.mit.edu	37	11	10800740	10800740	+	3'UTR	SNP	A	G	G			TCGA-CH-5771-01A-21D-1576-08	TCGA-CH-5771-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:10800740A>G	uc001mja.2	+	25						NM_014633	NP_055448	Q6PD62	CTR9_HUMAN	SH2 domain binding protein 1						histone H2B ubiquitination|histone monoubiquitination	Cdc73/Paf1 complex|nuclear speck				ovary(2)	2				all cancers(16;1.64e-07)|Epithelial(150;2.47e-07)|BRCA - Breast invasive adenocarcinoma(625;0.111)		TGTTTAGTCAATTGTGAAATT	0.308													7	13	---	---	---	---	PASS
KLC2	64837	broad.mit.edu	37	11	66032690	66032690	+	Missense_Mutation	SNP	G	T	T			TCGA-CH-5771-01A-21D-1576-08	TCGA-CH-5771-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:66032690G>T	uc010rov.1	+	11	1561	c.1318G>T	c.(1318-1320)GCC>TCC	p.A440S	KLC2_uc010row.1_Missense_Mutation_p.A440S|KLC2_uc009yra.2_Intron|KLC2_uc001ohb.2_Missense_Mutation_p.A440S|KLC2_uc010rox.1_Missense_Mutation_p.A363S|KLC2_uc001ohc.2_Missense_Mutation_p.A440S|KLC2_uc001ohd.2_Missense_Mutation_p.A363S|KLC2_uc001ohe.1_Missense_Mutation_p.A301S	NM_001134775	NP_001128247	Q9H0B6	KLC2_HUMAN	kinesin light chain 2 isoform 1	440					blood coagulation	cytosol|kinesin complex|microtubule	microtubule motor activity|protein binding				0						CTGGTACAAGGCCTGTAAAGT	0.373													7	71	---	---	---	---	PASS
TMPRSS4	56649	broad.mit.edu	37	11	117988097	117988097	+	Silent	SNP	C	T	T			TCGA-CH-5771-01A-21D-1576-08	TCGA-CH-5771-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:117988097C>T	uc010rxo.1	+	12	1521	c.1230C>T	c.(1228-1230)TGC>TGT	p.C410C	TMPRSS4_uc010rxp.1_Silent_p.C405C|TMPRSS4_uc010rxq.1_Silent_p.C263C|TMPRSS4_uc010rxr.1_Silent_p.C385C|TMPRSS4_uc010rxs.1_Silent_p.C370C|TMPRSS4_uc009yzu.2_RNA|TMPRSS4_uc010rxt.1_Silent_p.C385C	NM_019894	NP_063947	Q9NRS4	TMPS4_HUMAN	transmembrane protease, serine 4 isoform 1	410	Extracellular (Potential).|Peptidase S1.				proteolysis	integral to membrane	scavenger receptor activity|serine-type endopeptidase activity			large_intestine(1)|central_nervous_system(1)	2	all_hematologic(175;0.0487)	Medulloblastoma(222;0.0431)|all_hematologic(192;0.164)|Breast(348;0.183)|all_neural(223;0.238)		BRCA - Breast invasive adenocarcinoma(274;4.16e-05)|Epithelial(105;0.00204)		GCTATGGCTGCGGGGGCCCGA	0.562													29	183	---	---	---	---	PASS
RNF26	79102	broad.mit.edu	37	11	119207000	119207000	+	Missense_Mutation	SNP	G	T	T			TCGA-CH-5771-01A-21D-1576-08	TCGA-CH-5771-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:119207000G>T	uc001pwh.2	+	1	1764	c.1168G>T	c.(1168-1170)GTG>TTG	p.V390L		NM_032015	NP_114404	Q9BY78	RNF26_HUMAN	ring finger protein 26	390	RING-type.						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)		GAGCAAGACAGTGTTGCTCCT	0.607													16	95	---	---	---	---	PASS
DCP1B	196513	broad.mit.edu	37	12	2102359	2102359	+	Intron	SNP	A	G	G			TCGA-CH-5771-01A-21D-1576-08	TCGA-CH-5771-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:2102359A>G	uc001qjx.1	-						DCP1B_uc010sdy.1_Intron|DCP1B_uc010sdz.1_Silent_p.C130C	NM_152640	NP_689853	Q8IZD4	DCP1B_HUMAN	decapping enzyme Dcp1b						exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay	cytosol|nucleus	hydrolase activity|protein binding			skin(1)	1			OV - Ovarian serous cystadenocarcinoma(31;0.00193)			ACAATGGCAAACACTGTACAA	0.388													8	190	---	---	---	---	PASS
BIN2	51411	broad.mit.edu	37	12	51696475	51696475	+	Missense_Mutation	SNP	C	T	T			TCGA-CH-5771-01A-21D-1576-08	TCGA-CH-5771-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:51696475C>T	uc001ryg.2	-	4	359	c.307G>A	c.(307-309)GTA>ATA	p.V103I	BIN2_uc009zlz.2_Missense_Mutation_p.V103I|BIN2_uc001ryh.2_5'UTR|BIN2_uc010sng.1_Missense_Mutation_p.V77I	NM_016293	NP_057377	Q9UBW5	BIN2_HUMAN	bridging integrator 2	103	BAR.					cytoplasm	protein binding			ovary(1)	1						CTTACCCATACGATGGCCTTC	0.448													47	320	---	---	---	---	PASS
KCNC2	3747	broad.mit.edu	37	12	75601572	75601572	+	Silent	SNP	C	A	A			TCGA-CH-5771-01A-21D-1576-08	TCGA-CH-5771-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:75601572C>A	uc001sxg.1	-	2	736	c.192G>T	c.(190-192)CCG>CCT	p.P64P	KCNC2_uc009zry.2_Silent_p.P64P|KCNC2_uc001sxe.2_Silent_p.P64P|KCNC2_uc001sxf.2_Silent_p.P64P|KCNC2_uc010stw.1_Silent_p.P64P	NM_139137	NP_631875	Q96PR1	KCNC2_HUMAN	Shaw-related voltage-gated potassium channel	64	Gly/Pro-rich (insert).|Cytoplasmic (Potential).				energy reserve metabolic process|regulation of insulin secretion	voltage-gated potassium channel complex	voltage-gated potassium channel activity			breast(2)|pancreas(2)|skin(1)|lung(1)	6						gcgctctcggcggcggcgaca	0.527													2	0	---	---	---	---	PASS
SBNO1	55206	broad.mit.edu	37	12	123834911	123834911	+	Silent	SNP	A	G	G			TCGA-CH-5771-01A-21D-1576-08	TCGA-CH-5771-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:123834911A>G	uc010tap.1	-	1	78	c.78T>C	c.(76-78)ATT>ATC	p.I26I	SBNO1_uc010tao.1_Silent_p.I26I|SBNO1_uc010taq.1_5'UTR|SBNO1_uc001uet.2_Silent_p.I26I|SBNO1_uc001ueu.2_Silent_p.I26I|SBNO1_uc001uev.2_Silent_p.I26I|SBNO1_uc009zxy.1_Silent_p.I26I	NM_018183	NP_060653	A3KN83	SBNO1_HUMAN	sno, strawberry notch homolog 1	26							ATP binding|DNA binding|hydrolase activity			breast(5)|skin(2)|ovary(1)|kidney(1)	9	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000701)|Epithelial(86;0.00197)		CTCCACCATCAATATCAAAGA	0.438													16	386	---	---	---	---	PASS
INTS6	26512	broad.mit.edu	37	13	51942011	51942011	+	Missense_Mutation	SNP	G	T	T			TCGA-CH-5771-01A-21D-1576-08	TCGA-CH-5771-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:51942011G>T	uc001vfk.2	-	17	3114	c.2500C>A	c.(2500-2502)CTG>ATG	p.L834M	INTS6_uc001vfi.2_Missense_Mutation_p.L518M|INTS6_uc001vfj.2_Missense_Mutation_p.L821M|INTS6_uc001vfl.2_Missense_Mutation_p.L656M	NM_012141	NP_036273	Q9UL03	INT6_HUMAN	integrator complex subunit 6 isoform a	834					snRNA processing	actin cytoskeleton|integrator complex	protein binding|transmembrane receptor activity			ovary(1)|lung(1)	2		Breast(56;0.000286)|Lung NSC(96;0.00145)|Prostate(109;0.00403)|Hepatocellular(98;0.065)|Myeloproliferative disorder(33;0.163)|all_neural(104;0.19)		GBM - Glioblastoma multiforme(99;7.7e-08)		ACATGCTTCAGTAAAGTGAAG	0.269													3	76	---	---	---	---	PASS
PRMT5	10419	broad.mit.edu	37	14	23397824	23397824	+	Silent	SNP	C	A	A			TCGA-CH-5771-01A-21D-1576-08	TCGA-CH-5771-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:23397824C>A	uc001whm.1	-	2	202	c.111G>T	c.(109-111)GGG>GGT	p.G37G	PRMT5_uc001whl.1_Silent_p.G20G|PRMT5_uc010akd.1_RNA|PRMT5_uc010tnf.1_Intron|PRMT5_uc010tng.1_Silent_p.G20G|PRMT5_uc010tnh.1_Silent_p.G37G|PRMT5_uc001whn.1_Silent_p.G20G	NM_006109	NP_006100	O14744	ANM5_HUMAN	protein arginine methyltransferase 5 isoform a	37					cell proliferation|histone H4-R3 methylation|ncRNA metabolic process|regulation of mitosis|spliceosomal snRNP assembly|transcription, DNA-dependent	cytosol|nucleus	histone-arginine N-methyltransferase activity|protein binding|protein-arginine omega-N symmetric methyltransferase activity|ribonucleoprotein binding			ovary(1)	1	all_cancers(95;2.76e-05)			GBM - Glioblastoma multiforme(265;0.0126)		GGAAATCAAACCTACAACCGC	0.512													4	100	---	---	---	---	PASS
TSSK4	283629	broad.mit.edu	37	14	24675030	24675030	+	5'UTR	SNP	C	A	A			TCGA-CH-5771-01A-21D-1576-08	TCGA-CH-5771-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:24675030C>A	uc001wng.2	+	1					TM9SF1_uc010tob.1_Intron|TSSK4_uc001wne.2_Intron|TSSK4_uc001wnf.2_Intron|TSSK4_uc001wnh.2_5'UTR	NM_174944	NP_777604	Q6SA08	TSSK4_HUMAN	testis-specific serine kinase 4						cell differentiation|multicellular organismal development|positive regulation of CREB transcription factor activity|spermatogenesis		ATP binding|magnesium ion binding|protein binding|protein serine/threonine kinase activity				0				GBM - Glioblastoma multiforme(265;0.018)		TGGGGACCTACTTCACTTTGA	0.512													3	21	---	---	---	---	PASS
CLMN	79789	broad.mit.edu	37	14	95670136	95670136	+	Missense_Mutation	SNP	C	T	T	rs78561092	byFrequency	TCGA-CH-5771-01A-21D-1576-08	TCGA-CH-5771-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:95670136C>T	uc001yef.2	-	9	1666	c.1550G>A	c.(1549-1551)CGC>CAC	p.R517H		NM_024734	NP_079010	Q96JQ2	CLMN_HUMAN	calmin	517						integral to membrane	actin binding				0				Epithelial(152;0.193)		TTCATCGTGGCGGGCTGTACT	0.458													11	112	---	---	---	---	PASS
ATG2B	55102	broad.mit.edu	37	14	96800092	96800092	+	Silent	SNP	G	A	A			TCGA-CH-5771-01A-21D-1576-08	TCGA-CH-5771-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:96800092G>A	uc001yfi.2	-	8	1505	c.1140C>T	c.(1138-1140)CTC>CTT	p.L380L		NM_018036	NP_060506	Q96BY7	ATG2B_HUMAN	ATG2 autophagy related 2 homolog B	380										ovary(1)|kidney(1)|skin(1)	3		all_cancers(154;0.0462)|all_epithelial(191;0.123)|Melanoma(154;0.155)		Epithelial(152;0.21)|COAD - Colon adenocarcinoma(157;0.244)		CACCCACAGAGAGGGAATCTT	0.413													4	165	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	15	28929317	28929317	+	RNA	SNP	T	G	G			TCGA-CH-5771-01A-21D-1576-08	TCGA-CH-5771-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:28929317T>G	uc010azc.2	+	14		c.2022T>G								Homo sapiens I.M.A.G.E. clone 321824, mRNA sequence.																		AGAATTATATTGAGATCTACT	0.363													6	30	---	---	---	---	PASS
UBR1	197131	broad.mit.edu	37	15	43276106	43276106	+	Missense_Mutation	SNP	C	T	T			TCGA-CH-5771-01A-21D-1576-08	TCGA-CH-5771-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:43276106C>T	uc001zqq.2	-	37	4205	c.4139G>A	c.(4138-4140)CGT>CAT	p.R1380H		NM_174916	NP_777576	Q8IWV7	UBR1_HUMAN	ubiquitin protein ligase E3 component n-recognin	1380					cellular response to leucine|negative regulation of TOR signaling cascade	cytosol	leucine binding|zinc ion binding			lung(1)	1		all_cancers(109;4.32e-15)|all_epithelial(112;4.05e-13)|Lung NSC(122;1.75e-08)|all_lung(180;2e-07)|Melanoma(134;0.0179)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;4.08e-07)|COAD - Colon adenocarcinoma(120;0.185)|Colorectal(105;0.214)		TGATAGAAGACGAACCAGATG	0.343													5	50	---	---	---	---	PASS
FBN1	2200	broad.mit.edu	37	15	48729540	48729540	+	Missense_Mutation	SNP	C	T	T			TCGA-CH-5771-01A-21D-1576-08	TCGA-CH-5771-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:48729540C>T	uc001zwx.1	-	52	6686	c.6358G>A	c.(6358-6360)GGA>AGA	p.G2120R	FBN1_uc010beo.1_RNA	NM_000138	NP_000129	P35555	FBN1_HUMAN	fibrillin 1 precursor	2120					heart development|negative regulation of BMP signaling pathway by extracellular sequestering of BMP|negative regulation of transforming growth factor beta receptor signaling pathway by extracellular sequestering of TGFbeta|skeletal system development	basement membrane|extracellular space|microfibril	calcium ion binding|extracellular matrix structural constituent|protein binding			ovary(2)|large_intestine(1)	3		all_lung(180;0.00279)		all cancers(107;4.24e-07)|GBM - Glioblastoma multiforme(94;1.41e-05)		TCATCAGGTCCCACGATGATC	0.423													3	59	---	---	---	---	PASS
MRPL28	10573	broad.mit.edu	37	16	418564	418564	+	Silent	SNP	C	T	T			TCGA-CH-5771-01A-21D-1576-08	TCGA-CH-5771-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:418564C>T	uc002cgr.1	-	3	529	c.513G>A	c.(511-513)CGG>CGA	p.R171R	MRPL28_uc010bqu.1_Silent_p.R171R|MRPL28_uc002cgs.1_Silent_p.R171R|MRPL28_uc002cgt.1_Silent_p.R171R	NM_006428	NP_006419	Q13084	RM28_HUMAN	mitochondrial ribosomal protein L28 precursor	171					translation	mitochondrial ribosome	protein binding|structural constituent of ribosome				0		Hepatocellular(16;0.000105)|Lung NSC(18;0.0324)|all_lung(18;0.064)				GGGGGTCCTGCCGGGCAAGCC	0.657													7	64	---	---	---	---	PASS
BCMO1	53630	broad.mit.edu	37	16	81298375	81298375	+	Missense_Mutation	SNP	T	C	C			TCGA-CH-5771-01A-21D-1576-08	TCGA-CH-5771-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:81298375T>C	uc002fgn.1	+	5	820	c.602T>C	c.(601-603)ATC>ACC	p.I201T	BCMO1_uc010vnp.1_Missense_Mutation_p.I132T	NM_017429	NP_059125	Q9HAY6	BCDO1_HUMAN	beta-carotene 15,15'-monooxygenase	201					retinoid metabolic process|steroid metabolic process	cytosol	beta-carotene 15,15'-monooxygenase activity|metal ion binding|monooxygenase activity				0						ATTTTTAAGATCCCTGCCACA	0.438													7	60	---	---	---	---	PASS
SLC13A5	284111	broad.mit.edu	37	17	6597493	6597493	+	Missense_Mutation	SNP	G	A	A			TCGA-CH-5771-01A-21D-1576-08	TCGA-CH-5771-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:6597493G>A	uc002gdj.2	-	8	1167	c.1079C>T	c.(1078-1080)GCC>GTC	p.A360V	SLC13A5_uc010vtf.1_Missense_Mutation_p.A360V|SLC13A5_uc010clq.2_Missense_Mutation_p.A317V|SLC13A5_uc002gdk.2_Missense_Mutation_p.A343V	NM_177550	NP_808218	Q86YT5	S13A5_HUMAN	solute carrier family 13, member 5 isoform a	360	Helical; (Potential).					integral to membrane	citrate transmembrane transporter activity				0						CACAAAGATGGCCACAGTGGC	0.522													6	28	---	---	---	---	PASS
ZBTB4	57659	broad.mit.edu	37	17	7366921	7366921	+	Silent	SNP	T	G	G			TCGA-CH-5771-01A-21D-1576-08	TCGA-CH-5771-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:7366921T>G	uc002ghc.3	-	4	1630	c.1380A>C	c.(1378-1380)CCA>CCC	p.P460P	ZBTB4_uc002ghd.3_Silent_p.P460P	NM_001128833	NP_001122305	Q9P1Z0	ZBTB4_HUMAN	zinc finger and BTB domain containing 4	460	Pro-rich.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			skin(2)|ovary(1)|central_nervous_system(1)	4		Colorectal(1115;3.46e-05)|Myeloproliferative disorder(207;0.0255)		COAD - Colon adenocarcinoma(228;4.1e-06)|READ - Rectum adenocarcinoma(115;0.0642)		CTGGGGCAGGTGGAGGCCCAG	0.667													8	31	---	---	---	---	PASS
CDRT15	146822	broad.mit.edu	37	17	14139888	14139888	+	Intron	SNP	C	T	T	rs11650811	by1000genomes	TCGA-CH-5771-01A-21D-1576-08	TCGA-CH-5771-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:14139888C>T	uc010vvu.1	-						CDRT15_uc010coq.2_Intron	NM_001007530	NP_001007531	Q96T59	CDRTF_HUMAN	CMT1A duplicated region transcript 15												0				UCEC - Uterine corpus endometrioid carcinoma (92;0.0822)		GGCCACCTCACCAAGTGTCTG	0.552													3	5	---	---	---	---	PASS
C17orf62	79415	broad.mit.edu	37	17	80401837	80401837	+	3'UTR	SNP	T	C	C	rs11557531	by1000genomes	TCGA-CH-5771-01A-21D-1576-08	TCGA-CH-5771-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:80401837T>C	uc002kez.2	-	6					C17orf62_uc002kex.2_Silent_p.P54P|C17orf62_uc002key.2_Silent_p.P54P|C17orf62_uc002kfa.2_3'UTR|C17orf62_uc010dir.2_3'UTR|C17orf62_uc002kfb.3_3'UTR|C17orf62_uc002kfc.3_3'UTR|C17orf62_uc002kfd.3_Silent_p.P54P|C17orf62_uc002kfe.3_Silent_p.P54P	NM_001100407	NP_001093877	Q9BQA9	CQ062_HUMAN	hypothetical protein LOC79415 isoform a							integral to membrane	protein binding				0	Breast(20;0.00106)|all_neural(118;0.0804)		OV - Ovarian serous cystadenocarcinoma(97;0.0143)|BRCA - Breast invasive adenocarcinoma(99;0.0369)			GAATGTGCCATGGGTCCTGTG	0.687													14	274	---	---	---	---	PASS
WDR62	284403	broad.mit.edu	37	19	36595436	36595436	+	Missense_Mutation	SNP	A	C	C	rs1008328	byFrequency	TCGA-CH-5771-01A-21D-1576-08	TCGA-CH-5771-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:36595436A>C	uc002odc.2	+	31	4246	c.4155A>C	c.(4153-4155)TTA>TTC	p.L1385F	WDR62_uc002odd.2_Missense_Mutation_p.L1390F	NM_173636	NP_775907	O43379	WDR62_HUMAN	WD repeat domain 62 isoform 2	1385					cerebral cortex development	nucleus					0	Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.06)			TTGGTCTGTTACAGGGCAGCC	0.602													3	101	---	---	---	---	PASS
MARK4	57787	broad.mit.edu	37	19	45762287	45762287	+	Missense_Mutation	SNP	C	T	T			TCGA-CH-5771-01A-21D-1576-08	TCGA-CH-5771-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:45762287C>T	uc002pbb.1	+	2	97	c.92C>T	c.(91-93)CCG>CTG	p.P31L	MARK4_uc002paz.1_Intron|MARK4_uc002pba.1_Missense_Mutation_p.P31L			Q96L34	MARK4_HUMAN	RecName: Full=MAP/microtubule affinity-regulating kinase 4;          EC=2.7.11.1; AltName: Full=MAP/microtubule affinity-regulating kinase-like 1;	31					microtubule bundle formation|nervous system development|positive regulation of programmed cell death	centrosome|neuron projection	ATP binding|gamma-tubulin binding|microtubule binding|protein serine/threonine kinase activity|tau-protein kinase activity|ubiquitin binding			central_nervous_system(2)|large_intestine(1)	3		all_neural(266;0.224)|Ovarian(192;0.231)		OV - Ovarian serous cystadenocarcinoma(262;0.0102)		GACAAAGGCCCGTCCTGGTCC	0.672													6	26	---	---	---	---	PASS
C19orf75	284369	broad.mit.edu	37	19	51768703	51768703	+	Missense_Mutation	SNP	C	T	T			TCGA-CH-5771-01A-21D-1576-08	TCGA-CH-5771-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:51768703C>T	uc002pwb.1	+	3	485	c.104C>T	c.(103-105)CCC>CTC	p.P35L	C19orf75_uc010eov.1_Intron|C19orf75_uc010ycw.1_Intron	NM_173635	NP_775906	Q8N7X8	CS075_HUMAN	hypothetical protein LOC284369	35						integral to membrane				ovary(1)|pancreas(1)	2						ATTCCCACACCCTCTGTGCAG	0.587													29	152	---	---	---	---	PASS
SNPH	9751	broad.mit.edu	37	20	1276943	1276943	+	Intron	SNP	C	A	A			TCGA-CH-5771-01A-21D-1576-08	TCGA-CH-5771-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:1276943C>A	uc002wes.2	+						SNPH_uc002wet.2_Silent_p.G20G	NM_014723	NP_055538	O15079	SNPH_HUMAN	syntaphilin						synaptic vesicle docking involved in exocytosis	cell junction|integral to membrane|synapse|synaptosome	syntaxin-1 binding			ovary(2)	2						TTTCTGCGGGCCCCCCAACCC	0.687													4	7	---	---	---	---	PASS
NPEPL1	79716	broad.mit.edu	37	20	57290253	57290253	+	Silent	SNP	C	T	T			TCGA-CH-5771-01A-21D-1576-08	TCGA-CH-5771-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:57290253C>T	uc010zzs.1	+	12	1538	c.1443C>T	c.(1441-1443)GCC>GCT	p.A481A	NPEPL1_uc010zzr.1_Silent_p.A433A|NPEPL1_uc002xzn.2_RNA|NPEPL1_uc010gjo.1_Silent_p.A453A|NPEPL1_uc002xzp.2_3'UTR	NM_024663	NP_078939	Q8NDH3	PEPL1_HUMAN	aminopeptidase-like 1	481					proteolysis	cytoplasm	aminopeptidase activity|manganese ion binding|metalloexopeptidase activity				0	all_lung(29;0.0175)		BRCA - Breast invasive adenocarcinoma(13;2.88e-09)|Colorectal(105;0.109)			TCGGTGTGGCCCTCCTGCTGG	0.672													5	9	---	---	---	---	PASS
C21orf99	149992	broad.mit.edu	37	21	14439357	14439357	+	RNA	SNP	C	G	G			TCGA-CH-5771-01A-21D-1576-08	TCGA-CH-5771-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:14439357C>G	uc002yja.3	+	10		c.2875C>G				NR_026916				Homo sapiens C21orf99 protein (C21orf99) mRNA, complete cds.												0						TGAATCAGCTCAATCAATCGC	0.274													4	10	---	---	---	---	PASS
PLAC4	191585	broad.mit.edu	37	21	42551425	42551425	+	Missense_Mutation	SNP	C	G	G	rs5019195	by1000genomes	TCGA-CH-5771-01A-21D-1576-08	TCGA-CH-5771-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:42551425C>G	uc002yyz.2	-	1	5742	c.131G>C	c.(130-132)CGT>CCT	p.R44P	BACE2_uc002yyw.2_Intron|BACE2_uc002yyx.2_Intron|BACE2_uc002yyy.2_Intron	NM_182832	NP_878252	Q8WY50	PLAC4_HUMAN	placenta-specific 4	44											0		Prostate(19;2.29e-06)				TGAGGAGTGACGGTGTCTGGG	0.493													6	12	---	---	---	---	PASS
PCNT	5116	broad.mit.edu	37	21	47766650	47766650	+	Intron	SNP	G	A	A	rs2839217	by1000genomes	TCGA-CH-5771-01A-21D-1576-08	TCGA-CH-5771-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:47766650G>A	uc002zji.3	+						PCNT_uc002zjj.2_Intron|PCNT_uc010gqk.1_RNA	NM_006031	NP_006022	O95613	PCNT_HUMAN	pericentrin						cilium assembly|G2/M transition of mitotic cell cycle	cytosol|microtubule	calmodulin binding			ovary(4)|breast(2)|pancreas(2)	8	Breast(49;0.112)					CCTTTTCTCCGCCGCAGGCCG	0.577													5	4	---	---	---	---	PASS
POM121L9P	29774	broad.mit.edu	37	22	24659809	24659809	+	RNA	SNP	G	A	A			TCGA-CH-5771-01A-21D-1576-08	TCGA-CH-5771-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:24659809G>A	uc002zzs.3	+	7		c.3541G>A			uc011ajp.1_5'Flank	NR_003714				Homo sapiens mRNA; cDNA DKFZp434P211 (from clone DKFZp434P211).												0						CCCTATCTGCGCACCCGGAGG	0.612													3	8	---	---	---	---	PASS
CYP2D6	1565	broad.mit.edu	37	22	42523636	42523636	+	Missense_Mutation	SNP	C	A	A	rs3915951		TCGA-CH-5771-01A-21D-1576-08	TCGA-CH-5771-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:42523636C>A	uc003bce.2	-	7	1076	c.986G>T	c.(985-987)CGC>CTC	p.R329L	uc003bcd.1_Intron|CYP2D6_uc010gyu.2_Missense_Mutation_p.R23L|CYP2D6_uc003bcf.2_Missense_Mutation_p.R278L	NM_000106	NP_000097	Q6NWU0	Q6NWU0_HUMAN	cytochrome P450, family 2, subfamily D,	329							electron carrier activity|heme binding|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen			breast(1)|skin(1)	2						TTGGACACGGCCTGGACAGAC	0.602													4	63	---	---	---	---	PASS
DMD	1756	broad.mit.edu	37	X	31676189	31676189	+	Missense_Mutation	SNP	G	A	A			TCGA-CH-5771-01A-21D-1576-08	TCGA-CH-5771-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:31676189G>A	uc004dda.1	-	54	8189	c.7945C>T	c.(7945-7947)CGG>TGG	p.R2649W	DMD_uc004dcr.1_Missense_Mutation_p.R189W|DMD_uc004dcs.1_Missense_Mutation_p.R189W|DMD_uc004dct.1_Missense_Mutation_p.R189W|DMD_uc004dcu.1_Missense_Mutation_p.R189W|DMD_uc004dcv.1_Missense_Mutation_p.R189W|DMD_uc004dcw.2_Missense_Mutation_p.R1305W|DMD_uc004dcx.2_Missense_Mutation_p.R1308W|DMD_uc004dcz.2_Missense_Mutation_p.R2526W|DMD_uc004dcy.1_Missense_Mutation_p.R2645W|DMD_uc004ddb.1_Missense_Mutation_p.R2641W	NM_004006	NP_003997	P11532	DMD_HUMAN	dystrophin Dp427m isoform	2649	Spectrin 18.				muscle filament sliding|peptide biosynthetic process	cell surface|costamere|cytoskeleton|cytosol|dystrophin-associated glycoprotein complex|sarcolemma	actin binding|dystroglycan binding|nitric-oxide synthase binding|protein binding|structural constituent of cytoskeleton|structural constituent of muscle|zinc ion binding			ovary(3)|pancreas(2)|large_intestine(1)	6		all_cancers(2;1.22e-16)|Acute lymphoblastic leukemia(2;4.65e-06)|all_hematologic(2;0.00108)|all_epithelial(3;0.00626)|all_neural(2;0.0189)|all_lung(315;0.182)|Glioma(3;0.203)				GAATAATCCCGGAGAAGTTTC	0.393													38	113	---	---	---	---	PASS
CDR1	1038	broad.mit.edu	37	X	139866376	139866376	+	Missense_Mutation	SNP	C	A	A			TCGA-CH-5771-01A-21D-1576-08	TCGA-CH-5771-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:139866376C>A	uc004fbg.1	-	1	348	c.156G>T	c.(154-156)TTG>TTT	p.L52F	uc004fbf.1_RNA	NM_004065	NP_004056	P51861	CDR1_HUMAN	cerebellar degeneration-related protein 1,	52	23 X 6 AA approximate repeats.|9.										0	Acute lymphoblastic leukemia(192;7.65e-05)	Lung SC(4;0.051)				CCACGTCTTCCAACAAAGCCA	0.438													37	101	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	1	4204652	4204653	+	IGR	DEL	CA	-	-			TCGA-CH-5771-01A-21D-1576-08	TCGA-CH-5771-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:4204652_4204653delCA								LOC100133612 (370775 upstream) : LOC284661 (267458 downstream)																							ccaccactaccacaccaccacc	0.035													4	2	---	---	---	---	
CAMTA1	23261	broad.mit.edu	37	1	7164187	7164188	+	Intron	DEL	AT	-	-	rs138903042		TCGA-CH-5771-01A-21D-1576-08	TCGA-CH-5771-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:7164187_7164188delAT	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)		cacaacacacataactacacac	0.000													1	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	8337158	8337174	+	IGR	DEL	ACACACACCACACATAC	-	-	rs70990546		TCGA-CH-5771-01A-21D-1576-08	TCGA-CH-5771-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:8337158_8337174delACACACACCACACATAC								ERRFI1 (250765 upstream) : SLC45A1 (47216 downstream)																							acacacacatacacacaccacacatacacacacacca	0.005													3	7	---	---	---	---	
SPATA21	374955	broad.mit.edu	37	1	16729987	16729987	+	Intron	DEL	C	-	-	rs57948110		TCGA-CH-5771-01A-21D-1576-08	TCGA-CH-5771-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:16729987delC	uc001ayn.2	-						SPATA21_uc001ayl.1_Intron|SPATA21_uc010occ.1_Intron	NM_198546	NP_940948	Q7Z572	SPT21_HUMAN	spermatogenesis associated 21								calcium ion binding			ovary(2)|breast(1)	3		Colorectal(325;0.000147)|Renal(390;0.00145)|Lung NSC(340;0.00215)|Breast(348;0.00224)|all_lung(284;0.00351)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0646)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0182)|COAD - Colon adenocarcinoma(227;1.15e-05)|BRCA - Breast invasive adenocarcinoma(304;4.2e-05)|Kidney(64;0.000183)|KIRC - Kidney renal clear cell carcinoma(64;0.00269)|STAD - Stomach adenocarcinoma(313;0.0122)|READ - Rectum adenocarcinoma(331;0.0651)		tcttttttttctttttttttt	0.010													9	4	---	---	---	---	
NBPF6	653149	broad.mit.edu	37	1	108995631	108995632	+	Intron	DEL	TA	-	-	rs4265454	by1000genomes	TCGA-CH-5771-01A-21D-1576-08	TCGA-CH-5771-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:108995631_108995632delTA	uc009weq.2	+						NBPF6_uc009wep.2_Intron	NM_001143988	NP_001137460	Q5VWK0	NBPF6_HUMAN	neuroblastoma breakpoint family, member 6							cytoplasm					0						tgtgtgtgtgtATATATATATA	0.287													6	3	---	---	---	---	
NBPF10	100132406	broad.mit.edu	37	1	146419788	146419789	+	Intron	DEL	TG	-	-			TCGA-CH-5771-01A-21D-1576-08	TCGA-CH-5771-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:146419788_146419789delTG	uc001emp.3	+						uc010ozk.1_Intron|uc010ozl.1_Intron	NM_017940	NP_060410	A6NDV3	A6NDV3_HUMAN	hypothetical protein LOC55672												0	all_hematologic(923;0.032)			Colorectal(1306;1.36e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.00258)		GAGCTCACACtgtgtgtgtgtg	0.351													4	2	---	---	---	---	
NUP210L	91181	broad.mit.edu	37	1	153995008	153995008	+	Intron	DEL	T	-	-	rs78839111		TCGA-CH-5771-01A-21D-1576-08	TCGA-CH-5771-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:153995008delT	uc001fdw.2	-						NUP210L_uc009woq.2_Intron|NUP210L_uc010peh.1_Intron	NM_207308	NP_997191	Q5VU65	P210L_HUMAN	nucleoporin 210kDa-like isoform 1							integral to membrane				skin(5)|ovary(4)|large_intestine(1)|central_nervous_system(1)	11	all_lung(78;9.35e-31)|Lung NSC(65;1.33e-28)|Hepatocellular(266;0.0877)|Melanoma(130;0.128)		LUSC - Lung squamous cell carcinoma(543;0.151)|Colorectal(543;0.198)			CCAGGAAGGCTTTTTTTTTTT	0.363													5	4	---	---	---	---	
DARS2	55157	broad.mit.edu	37	1	173819744	173819744	+	Intron	DEL	T	-	-	rs66665709		TCGA-CH-5771-01A-21D-1576-08	TCGA-CH-5771-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:173819744delT	uc001gjh.1	+							NM_018122	NP_060592	Q6PI48	SYDM_HUMAN	aspartyl-tRNA synthetase 2, mitochondrial						tRNA aminoacylation for protein translation	mitochondrial matrix|nucleus	aspartate-tRNA ligase activity|ATP binding|nucleic acid binding			central_nervous_system(2)	2					L-Aspartic Acid(DB00128)	TGCATAAATCttttttttttt	0.184													6	3	---	---	---	---	
ACBD6	84320	broad.mit.edu	37	1	180471041	180471041	+	Intron	DEL	A	-	-	rs5779061		TCGA-CH-5771-01A-21D-1576-08	TCGA-CH-5771-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:180471041delA	uc001gog.2	-							NM_032360	NP_115736	Q9BR61	ACBD6_HUMAN	acyl-coenzyme A binding domain containing 6							cytoplasm|nucleus	fatty-acyl-CoA binding			ovary(1)	1						GCAGATGGTCAAAAAAAAAAA	0.383													5	3	---	---	---	---	
CACNA1E	777	broad.mit.edu	37	1	181485480	181485483	+	Intron	DEL	CACA	-	-	rs143897241		TCGA-CH-5771-01A-21D-1576-08	TCGA-CH-5771-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:181485480_181485483delCACA	uc001gow.2	+						CACNA1E_uc009wxr.2_Intron|CACNA1E_uc009wxs.2_Intron	NM_000721	NP_000712	Q15878	CAC1E_HUMAN	calcium channel, voltage-dependent, R type,						energy reserve metabolic process|membrane depolarization|synaptic transmission	voltage-gated calcium channel complex	voltage-gated calcium channel activity			ovary(3)|central_nervous_system(2)|pancreas(1)	6						TGCCAAAGACcacacacacacaca	0.294													4	2	---	---	---	---	
CAMK1G	57172	broad.mit.edu	37	1	209782678	209782678	+	Intron	DEL	G	-	-	rs68076482		TCGA-CH-5771-01A-21D-1576-08	TCGA-CH-5771-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:209782678delG	uc001hhd.2	+						CAMK1G_uc001hhf.3_Intron|CAMK1G_uc001hhe.2_Intron	NM_020439	NP_065172	Q96NX5	KCC1G_HUMAN	calcium/calmodulin-dependent protein kinase IG							Golgi membrane|plasma membrane	ATP binding|calmodulin binding|calmodulin-dependent protein kinase activity			breast(1)	1				OV - Ovarian serous cystadenocarcinoma(81;0.0475)		AAAAGGAGATGGGGGGGCAGT	0.463													4	2	---	---	---	---	
EPRS	2058	broad.mit.edu	37	1	220198771	220198771	+	Intron	DEL	A	-	-	rs147361881		TCGA-CH-5771-01A-21D-1576-08	TCGA-CH-5771-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:220198771delA	uc001hly.1	-						EPRS_uc010puf.1_Intron|EPRS_uc001hlz.1_Intron|EPRS_uc009xdt.1_Intron	NM_004446	NP_004437	P07814	SYEP_HUMAN	glutamyl-prolyl tRNA synthetase						glutamyl-tRNA aminoacylation|prolyl-tRNA aminoacylation|protein complex assembly	cytosol|soluble fraction	ATP binding|glutamate-tRNA ligase activity|proline-tRNA ligase activity|protein binding|RNA binding			ovary(1)|skin(1)	2				GBM - Glioblastoma multiforme(131;0.0735)	L-Glutamic Acid(DB00142)|L-Proline(DB00172)	CCCTGACAGGAAAAAAAAAAA	0.308													5	3	---	---	---	---	
DISC1	27185	broad.mit.edu	37	1	231868755	231868757	+	Intron	DEL	TGT	-	-	rs61835413		TCGA-CH-5771-01A-21D-1576-08	TCGA-CH-5771-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:231868755_231868757delTGT	uc001huz.2	+						TSNAX-DISC1_uc010pwf.1_Intron|TSNAX-DISC1_uc010pwg.1_Intron|TSNAX-DISC1_uc010pwh.1_Intron|TSNAX-DISC1_uc010pwi.1_Intron|TSNAX-DISC1_uc010pwj.1_Intron|TSNAX-DISC1_uc010pwk.1_Intron|TSNAX-DISC1_uc010pwl.1_Intron|DISC1_uc010pwo.1_Intron|DISC1_uc010pwp.1_Intron|DISC1_uc010pwq.1_Intron|DISC1_uc010pwr.1_Intron|DISC1_uc010pws.1_Intron|DISC1_uc010pwt.1_Intron|DISC1_uc010pwu.1_Intron|DISC1_uc010pwv.1_Intron|DISC1_uc010pww.1_Intron|DISC1_uc010pwx.1_Intron|DISC1_uc010pwy.1_Intron|DISC1_uc010pwz.1_Intron|DISC1_uc010pxa.1_Intron|DISC1_uc001huy.2_Intron|DISC1_uc010pxb.1_Intron|DISC1_uc010pxc.1_Intron|DISC1_uc010pxd.1_Intron|DISC1_uc010pxe.1_Intron|DISC1_uc009xfr.2_Intron|DISC1_uc010pxf.1_Intron|DISC1_uc010pxg.1_Intron|DISC1_uc010pxh.1_Intron|DISC1_uc010pxi.1_Intron|DISC1_uc010pxj.1_Intron|DISC1_uc010pxk.1_Intron|DISC1_uc010pxl.1_Intron|DISC1_uc010pxm.1_Intron|DISC1_uc010pxn.1_Intron|DISC1_uc001hva.2_Intron	NM_018662	NP_061132	Q9NRI5	DISC1_HUMAN	disrupted in schizophrenia 1 isoform L						microtubule cytoskeleton organization|neuron migration|positive regulation of neuroblast proliferation|positive regulation of Wnt receptor signaling pathway|Wnt receptor signaling pathway	centrosome|microtubule	protein binding			skin(1)	1		all_cancers(173;0.0208)|Prostate(94;0.0975)				gttgtagcagtgttgttggtaat	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	234637998	234637999	+	IGR	INS	-	AT	AT	rs519250	by1000genomes	TCGA-CH-5771-01A-21D-1576-08	TCGA-CH-5771-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:234637998_234637999insAT								TARBP1 (23149 upstream) : IRF2BP2 (102018 downstream)																							cacacacacacGCTAGGATAGA	0.322													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	1600084	1600087	+	IGR	DEL	CAGA	-	-			TCGA-CH-5771-01A-21D-1576-08	TCGA-CH-5771-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:1600084_1600087delCAGA								TPO (53586 upstream) : PXDN (35573 downstream)																							gcacacagatcagacacacacaag	0.069													4	2	---	---	---	---	
SLC3A1	6519	broad.mit.edu	37	2	44508298	44508299	+	Intron	INS	-	T	T	rs67090188		TCGA-CH-5771-01A-21D-1576-08	TCGA-CH-5771-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:44508298_44508299insT	uc002ruc.3	+						SLC3A1_uc002rty.2_Intron|SLC3A1_uc002rtz.2_Intron|SLC3A1_uc002rua.2_Intron|SLC3A1_uc002rub.2_Intron	NM_000341	NP_000332	Q07837	SLC31_HUMAN	solute carrier family 3, member 1						carbohydrate metabolic process|cellular amino acid metabolic process|ion transport	integral to plasma membrane|membrane fraction	basic amino acid transmembrane transporter activity|catalytic activity|cation binding|L-cystine transmembrane transporter activity				0		all_hematologic(82;0.166)|Acute lymphoblastic leukemia(82;0.17)			L-Cystine(DB00138)	cctttccCTGCttttttttttt	0.015													3	4	---	---	---	---	
KDM3A	55818	broad.mit.edu	37	2	86717003	86717004	+	Intron	DEL	TG	-	-			TCGA-CH-5771-01A-21D-1576-08	TCGA-CH-5771-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:86717003_86717004delTG	uc002sri.3	+						KDM3A_uc010ytj.1_Intron|KDM3A_uc010ytk.1_Intron	NM_018433	NP_060903	Q9Y4C1	KDM3A_HUMAN	jumonji domain containing 1A						androgen receptor signaling pathway|cell differentiation|formaldehyde biosynthetic process|histone H3-K9 demethylation|hormone-mediated signaling pathway|positive regulation of transcription, DNA-dependent|spermatogenesis|transcription, DNA-dependent	cytoplasm|nucleus	androgen receptor binding|iron ion binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen			breast(2)|ovary(1)|central_nervous_system(1)|skin(1)	5						CTTTTATGTCTGTGTTTTGTGT	0.366													4	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	132890386	132890391	+	IGR	DEL	GTTGTT	-	-			TCGA-CH-5771-01A-21D-1576-08	TCGA-CH-5771-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:132890386_132890391delGTTGTT								C2orf27B (331152 upstream) : NCRNA00164 (14773 downstream)																							ATGAAATAAAGTTGTTGTTAGAAATA	0.214													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	137308240	137308241	+	IGR	DEL	GT	-	-	rs143292529		TCGA-CH-5771-01A-21D-1576-08	TCGA-CH-5771-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:137308240_137308241delGT								CXCR4 (432515 upstream) : THSD7B (214874 downstream)																							acttgtacgcgtgtgtgtgtgt	0.000													3	3	---	---	---	---	
RQCD1	9125	broad.mit.edu	37	2	219452151	219452151	+	Intron	DEL	T	-	-	rs139839364		TCGA-CH-5771-01A-21D-1576-08	TCGA-CH-5771-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:219452151delT	uc010zkh.1	+						RQCD1_uc002vih.1_Intron|RQCD1_uc010zki.1_Intron	NM_005444	NP_005435	Q92600	RCD1_HUMAN	RCD1 required for cell differentiation1 homolog						nuclear-transcribed mRNA poly(A) tail shortening|regulation of transcription, DNA-dependent|sex differentiation|transcription, DNA-dependent	cytoplasmic mRNA processing body|cytosol|nucleus	protein binding			ovary(1)|skin(1)	2		Renal(207;0.0915)		Epithelial(149;1.13e-06)|all cancers(144;0.000192)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		GCCCTCTTCCTTTTTTTTTTT	0.194													6	3	---	---	---	---	
CCDC66	285331	broad.mit.edu	37	3	56598292	56598292	+	Intron	DEL	A	-	-	rs11285260		TCGA-CH-5771-01A-21D-1576-08	TCGA-CH-5771-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:56598292delA	uc003dhz.2	+						CCDC66_uc003dhy.2_Intron|CCDC66_uc003dhu.2_Intron|CCDC66_uc003dhx.2_Intron|CCDC66_uc003dhv.2_Intron|CCDC66_uc003dhw.2_Intron	NM_001141947	NP_001135419	A2RUB6	CCD66_HUMAN	coiled-coil domain containing 66 isoform 1											breast(1)	1				KIRC - Kidney renal clear cell carcinoma(284;0.0478)|Kidney(284;0.0597)|OV - Ovarian serous cystadenocarcinoma(275;0.233)		TTGTTCTTTTAGAGGACTTTC	0.264													7	7	---	---	---	---	
ATP13A3	79572	broad.mit.edu	37	3	194168812	194168812	+	Intron	DEL	T	-	-			TCGA-CH-5771-01A-21D-1576-08	TCGA-CH-5771-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:194168812delT	uc003fty.3	-						ATP13A3_uc003ftz.1_Intron	NM_024524	NP_078800	Q9H7F0	AT133_HUMAN	ATPase type 13A3						ATP biosynthetic process|cation transport	integral to membrane	ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|metal ion binding			ovary(1)	1	all_cancers(143;6.01e-09)|Ovarian(172;0.0634)	Melanoma(1037;0.211)	OV - Ovarian serous cystadenocarcinoma(49;3.83e-18)|LUSC - Lung squamous cell carcinoma(58;3.55e-06)|Lung(62;4.19e-06)	GBM - Glioblastoma multiforme(46;5.98e-05)		AGAATCTCTCttttttttttt	0.144													56	7	---	---	---	---	
DOK7	285489	broad.mit.edu	37	4	3494670	3494671	+	Frame_Shift_Ins	INS	-	A	A			TCGA-CH-5771-01A-21D-1576-08	TCGA-CH-5771-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:3494670_3494671insA	uc003ghd.2	+	7	1027_1028	c.957_958insA	c.(955-960)CCCAAGfs	p.P319fs	DOK7_uc003ghe.2_Frame_Shift_Ins_p.P181fs|DOK7_uc003ghf.2_Frame_Shift_Ins_p.P61fs|DOK7_uc003ghg.1_Frame_Shift_Ins_p.P9fs	NM_173660	NP_775931	Q18PE1	DOK7_HUMAN	downstream of tyrosine kinase 7 isoform 1	319_320	Ser-rich.				positive regulation of protein tyrosine kinase activity	cell junction|synapse	insulin receptor binding|protein kinase binding			skin(1)	1				UCEC - Uterine corpus endometrioid carcinoma (64;0.163)		GGCCACCCCCCAAGCCGCTGCG	0.688													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	8688704	8688705	+	IGR	DEL	GT	-	-	rs147173147		TCGA-CH-5771-01A-21D-1576-08	TCGA-CH-5771-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:8688704_8688705delGT								CPZ (67218 upstream) : HMX1 (180068 downstream)																							ggtgtgtgtagtgtgtgtgtgg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	10836735	10836742	+	IGR	DEL	CGCACACA	-	-	rs71181064		TCGA-CH-5771-01A-21D-1576-08	TCGA-CH-5771-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:10836735_10836742delCGCACACA								CLNK (150349 upstream) : MIR572 (533709 downstream)																							cacacacgcgcgcacacacacacacaca	0.322													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	37751959	37751964	+	IGR	DEL	ACACAT	-	-	rs35022540		TCGA-CH-5771-01A-21D-1576-08	TCGA-CH-5771-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:37751959_37751964delACACAT								RELL1 (63960 upstream) : PGM2 (76318 downstream)																							acatacacacacacatacacacacac	0.141													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	37751961	37751964	+	IGR	DEL	ACAT	-	-	rs35022540		TCGA-CH-5771-01A-21D-1576-08	TCGA-CH-5771-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:37751961_37751964delACAT								RELL1 (63962 upstream) : PGM2 (76318 downstream)																							atacacacacacatacacacacac	0.142													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	45611310	45611313	+	IGR	DEL	ACAG	-	-	rs149887931		TCGA-CH-5771-01A-21D-1576-08	TCGA-CH-5771-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:45611310_45611313delACAG								GNPDA2 (882698 upstream) : GABRG1 (426476 downstream)																							agaggcaaaaacagacagagtttc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	49657203	49657204	+	IGR	DEL	TG	-	-			TCGA-CH-5771-01A-21D-1576-08	TCGA-CH-5771-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:49657203_49657204delTG								CWH43 (593110 upstream) : None (None downstream)																							tggaatttaatgaaatggaatg	0.000													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	68264381	68264381	+	IGR	DEL	T	-	-	rs138861461		TCGA-CH-5771-01A-21D-1576-08	TCGA-CH-5771-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:68264381delT								None (None upstream) : CENPC1 (73608 downstream)																							acttgcagactttacaaagag	0.000													6	3	---	---	---	---	
CDKL2	8999	broad.mit.edu	37	4	76521214	76521217	+	Intron	DEL	AAGA	-	-	rs5017983		TCGA-CH-5771-01A-21D-1576-08	TCGA-CH-5771-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:76521214_76521217delAAGA	uc003hiq.2	-						CDKL2_uc011cbp.1_Intron	NM_003948	NP_003939	Q92772	CDKL2_HUMAN	cyclin-dependent kinase-like 2						sex differentiation|signal transduction	cytoplasm|nucleus	ATP binding|cyclin-dependent protein kinase activity			ovary(2)|stomach(2)|breast(2)|skin(1)	7			Lung(101;0.0973)|LUSC - Lung squamous cell carcinoma(112;0.122)			ggaaggaaggaagaaaggaaggaa	0.127													3	3	---	---	---	---	
TMEM150C	441027	broad.mit.edu	37	4	83406549	83406550	+	3'UTR	INS	-	TG	TG	rs144382768	by1000genomes	TCGA-CH-5771-01A-21D-1576-08	TCGA-CH-5771-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:83406549_83406550insTG	uc003hmy.1	-	8					TMEM150C_uc011ccj.1_3'UTR	NM_001080506	NP_001073975	B9EJG8	T150C_HUMAN	transmembrane protein 150C							integral to membrane				ovary(1)	1						GTGGCCATGAAtgtgtgtgtgt	0.416													5	4	---	---	---	---	
GPRIN3	285513	broad.mit.edu	37	4	90175279	90175280	+	Intron	INS	-	GTGTGTGTGTGT	GTGTGTGTGTGT	rs150483417	by1000genomes	TCGA-CH-5771-01A-21D-1576-08	TCGA-CH-5771-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:90175279_90175280insGTGTGTGTGTGT	uc003hsm.1	-							NM_198281	NP_938022	Q6ZVF9	GRIN3_HUMAN	G protein-regulated inducer of neurite outgrowth											ovary(3)	3		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;5.67e-05)		GTTGCATCTGGgtgtgtgtgtg	0.248													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	119797853	119797854	+	IGR	DEL	TT	-	-			TCGA-CH-5771-01A-21D-1576-08	TCGA-CH-5771-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:119797853_119797854delTT								SEC24D (38026 upstream) : SYNPO2 (12142 downstream)																							tctttctttctttctttctttc	0.079													6	3	---	---	---	---	
SORBS2	8470	broad.mit.edu	37	4	186748908	186748913	+	Intron	DEL	CATCAC	-	-	rs139462423		TCGA-CH-5771-01A-21D-1576-08	TCGA-CH-5771-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:186748908_186748913delCATCAC	uc003iyl.2	-						SORBS2_uc003iym.2_Intron|SORBS2_uc011cky.1_Intron	NM_021069	NP_066547	O94875	SRBS2_HUMAN	sorbin and SH3 domain containing 2 isoform 2							actin cytoskeleton|nucleus|perinuclear region of cytoplasm|Z disc	cytoskeletal adaptor activity|structural constituent of cytoskeleton|structural constituent of muscle|zinc ion binding			ovary(1)	1		all_cancers(14;4.27e-52)|all_epithelial(14;6.58e-39)|all_lung(41;1.42e-13)|Lung NSC(41;3.73e-13)|Melanoma(20;1.91e-06)|Colorectal(36;0.00692)|Hepatocellular(41;0.00826)|Renal(120;0.00994)|Prostate(90;0.0101)|all_hematologic(60;0.0174)|all_neural(102;0.244)		OV - Ovarian serous cystadenocarcinoma(60;1.54e-09)|BRCA - Breast invasive adenocarcinoma(30;0.000232)|GBM - Glioblastoma multiforme(59;0.000385)|STAD - Stomach adenocarcinoma(60;0.00109)|LUSC - Lung squamous cell carcinoma(40;0.0205)		tcatcaccatcatcaccatcatcatc	0.000													4	2	---	---	---	---	
LPCAT1	79888	broad.mit.edu	37	5	1465452	1465455	+	Intron	DEL	TAAC	-	-	rs146512410		TCGA-CH-5771-01A-21D-1576-08	TCGA-CH-5771-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:1465452_1465455delTAAC	uc003jcm.2	-						LPCAT1_uc003jcl.2_Intron	NM_024830	NP_079106	Q8NF37	PCAT1_HUMAN	lysophosphatidylcholine acyltransferase 1						phospholipid biosynthetic process	endoplasmic reticulum membrane|Golgi membrane|integral to membrane	1-acylglycerophosphocholine O-acyltransferase activity|1-alkylglycerophosphocholine O-acetyltransferase activity|calcium ion binding			ovary(2)	2			OV - Ovarian serous cystadenocarcinoma(19;0.0274)|all cancers(22;0.0534)	GBM - Glioblastoma multiforme(108;0.156)		aggcacacagtaactaaacacaca	0.000													3	3	---	---	---	---	
ADAMTS16	170690	broad.mit.edu	37	5	5305440	5305441	+	Intron	INS	-	C	C			TCGA-CH-5771-01A-21D-1576-08	TCGA-CH-5771-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:5305440_5305441insC	uc003jdl.2	+							NM_139056	NP_620687	Q8TE57	ATS16_HUMAN	ADAM metallopeptidase with thrombospondin type 1						proteolysis	proteinaceous extracellular matrix	metalloendopeptidase activity|zinc ion binding			ovary(3)|lung(2)|large_intestine(1)|breast(1)|pancreas(1)	8						cacacacacatccacaccacac	0.000													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	90475785	90475786	+	IGR	INS	-	A	A	rs140241795	by1000genomes	TCGA-CH-5771-01A-21D-1576-08	TCGA-CH-5771-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:90475785_90475786insA								GPR98 (15753 upstream) : ARRDC3 (188755 downstream)																							aggaaggaaggaggaaggaagg	0.030													6	3	---	---	---	---	
FBN2	2201	broad.mit.edu	37	5	127713243	127713244	+	Intron	INS	-	A	A	rs111488675		TCGA-CH-5771-01A-21D-1576-08	TCGA-CH-5771-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:127713243_127713244insA	uc003kuu.2	-						FBN2_uc003kuv.2_Intron	NM_001999	NP_001990	P35556	FBN2_HUMAN	fibrillin 2 precursor						bone trabecula formation|negative regulation of transforming growth factor beta receptor signaling pathway by extracellular sequestering of TGFbeta|positive regulation of bone mineralization|positive regulation of osteoblast differentiation	microfibril	calcium ion binding|extracellular matrix structural constituent			ovary(8)|large_intestine(4)|pancreas(1)|kidney(1)|skin(1)	15		all_cancers(142;0.0216)|Prostate(80;0.0551)	KIRC - Kidney renal clear cell carcinoma(527;0.0268)|Kidney(363;0.0488)	OV - Ovarian serous cystadenocarcinoma(64;0.0821)|Epithelial(69;0.146)		CCTCCACCACCAAAAAAAAAAA	0.312													6	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	93379861	93379862	+	IGR	INS	-	AC	AC	rs146274693	by1000genomes	TCGA-CH-5771-01A-21D-1576-08	TCGA-CH-5771-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:93379861_93379862insAC								None (None upstream) : EPHA7 (569880 downstream)																							CTGGAAGTAATacacacacaca	0.238													3	3	---	---	---	---	
THBS2	7058	broad.mit.edu	37	6	169642909	169642909	+	Intron	DEL	C	-	-			TCGA-CH-5771-01A-21D-1576-08	TCGA-CH-5771-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:169642909delC	uc003qwt.2	-							NM_003247	NP_003238	P35442	TSP2_HUMAN	thrombospondin 2 precursor						cell adhesion	extracellular region	calcium ion binding|heparin binding|protein binding|structural molecule activity			ovary(5)	5		Breast(66;1.78e-05)|Ovarian(120;0.0728)|Esophageal squamous(34;0.247)		OV - Ovarian serous cystadenocarcinoma(33;1.85e-21)|BRCA - Breast invasive adenocarcinoma(81;1.43e-06)|GBM - Glioblastoma multiforme(31;0.000379)		caccttcccaccactcccacc	0.000													4	3	---	---	---	---	
DFNA5	1687	broad.mit.edu	37	7	24758439	24758440	+	Intron	DEL	TA	-	-	rs137893101		TCGA-CH-5771-01A-21D-1576-08	TCGA-CH-5771-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:24758439_24758440delTA	uc010kus.1	-						DFNA5_uc003swz.2_Intron|DFNA5_uc003sxa.1_Intron|DFNA5_uc010kut.1_Intron|DFNA5_uc003sxb.2_Intron	NM_001127453	NP_001120925	O60443	DFNA5_HUMAN	deafness, autosomal dominant 5 protein isoform						sensory perception of sound					ovary(1)	1						agcagctccctatatatcctca	0.005													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	35378487	35378488	+	IGR	INS	-	GT	GT	rs147015443	by1000genomes	TCGA-CH-5771-01A-21D-1576-08	TCGA-CH-5771-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:35378487_35378488insGT								TBX20 (85245 upstream) : HERPUD2 (293784 downstream)																							ATTTTCAAGGAgtgtgtgtgtg	0.371													3	3	---	---	---	---	
ZNF138	7697	broad.mit.edu	37	7	64276251	64276254	+	Intron	DEL	AGTG	-	-	rs142497687		TCGA-CH-5771-01A-21D-1576-08	TCGA-CH-5771-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:64276251_64276254delAGTG	uc011kdp.1	+						ZNF138_uc003ttg.2_Intron|ZNF138_uc011kdq.1_Intron|ZNF138_uc003tth.2_Intron|ZNF138_uc010kzs.2_Intron	NM_001160183	NP_001153655	B4DFX2	B4DFX2_HUMAN	zinc finger protein 138 isoform 2						regulation of transcription, DNA-dependent	intracellular	nucleic acid binding				0		Lung NSC(55;0.0795)|all_lung(88;0.18)				tcaagttcacagtgagagccaacg	0.167													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	67875331	67875331	+	IGR	DEL	A	-	-			TCGA-CH-5771-01A-21D-1576-08	TCGA-CH-5771-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:67875331delA								None (None upstream) : None (None downstream)																							TAAGTTATCCAAAAAAAAAAA	0.204													6	3	---	---	---	---	
TRIM50	135892	broad.mit.edu	37	7	72729266	72729267	+	Intron	INS	-	A	A			TCGA-CH-5771-01A-21D-1576-08	TCGA-CH-5771-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:72729266_72729267insA	uc010lbd.1	-						FKBP6_uc003twz.2_Intron|TRIM50_uc003txy.1_Intron|TRIM50_uc003txz.1_Intron	NM_178125	NP_835226	Q86XT4	TRI50_HUMAN	tripartite motif protein 50A							cytoplasm|intracellular membrane-bounded organelle	ligase activity|zinc ion binding			skin(1)	1						AATTTTCCTTCAAAAAAAAAAA	0.287													6	3	---	---	---	---	
CCDC146	57639	broad.mit.edu	37	7	76763145	76763146	+	Intron	INS	-	AC	AC	rs142218364	by1000genomes	TCGA-CH-5771-01A-21D-1576-08	TCGA-CH-5771-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:76763145_76763146insAC	uc003uga.2	+						CCDC146_uc003ufz.1_Intron	NM_020879	NP_065930	Q8IYE0	CC146_HUMAN	coiled-coil domain containing 146											ovary(1)|central_nervous_system(1)	2		all_cancers(73;0.128)|all_lung(88;0.0986)|all_epithelial(88;0.163)|Myeloproliferative disorder(862;0.205)				tatgcttaggtacacacacaca	0.005													3	3	---	---	---	---	
CACNA2D1	781	broad.mit.edu	37	7	81603967	81603967	+	Intron	DEL	A	-	-			TCGA-CH-5771-01A-21D-1576-08	TCGA-CH-5771-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:81603967delA	uc003uhr.1	-							NM_000722	NP_000713	P54289	CA2D1_HUMAN	calcium channel, voltage-dependent, alpha							voltage-gated calcium channel complex	metal ion binding			ovary(5)|pancreas(1)	6					Felodipine(DB01023)|Gabapentin(DB00996)|Ibutilide(DB00308)|Isradipine(DB00270)|Magnesium Sulfate(DB00653)|Nifedipine(DB01115)	tattagccacaagactttgca	0.095													6	3	---	---	---	---	
ZNF800	168850	broad.mit.edu	37	7	127013340	127013340	+	Intron	DEL	T	-	-			TCGA-CH-5771-01A-21D-1576-08	TCGA-CH-5771-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:127013340delT	uc003vlx.1	-						ZNF800_uc003vlw.1_Intron|ZNF800_uc003vly.1_Intron|ZNF800_uc010lla.2_3'UTR	NM_176814	NP_789784	Q2TB10	ZN800_HUMAN	zinc finger protein 800						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1						GGTCAAATGATTTTTTTTTTA	0.368													125	9	---	---	---	---	
JHDM1D	80853	broad.mit.edu	37	7	139878082	139878089	+	5'Flank	DEL	TCCCTCCC	-	-	rs142303955		TCGA-CH-5771-01A-21D-1576-08	TCGA-CH-5771-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:139878082_139878089delTCCCTCCC	uc003vvm.2	-						LOC100134229_uc011kqy.1_RNA	NM_030647	NP_085150	Q6ZMT4	KDM7_HUMAN	jumonji C domain containing histone demethylase						midbrain development|transcription, DNA-dependent	nucleolus	histone demethylase activity (H3-K27 specific)|histone demethylase activity (H3-K36 specific)|histone demethylase activity (H3-K9 specific)|histone demethylase activity (H4-K20 specific)|iron ion binding|methylated histone residue binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|zinc ion binding			ovary(1)	1	Melanoma(164;0.0142)					cttccttccttccctccctccCTTTCCT	0.106													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	150606830	150606831	+	IGR	INS	-	G	G	rs146968730		TCGA-CH-5771-01A-21D-1576-08	TCGA-CH-5771-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:150606830_150606831insG								ABP1 (48451 upstream) : KCNH2 (35219 downstream)																							gtggtgtgtgtgtgtgtgtgtg	0.000													4	6	---	---	---	---	
PIWIL2	55124	broad.mit.edu	37	8	22165710	22165711	+	Intron	INS	-	T	T			TCGA-CH-5771-01A-21D-1576-08	TCGA-CH-5771-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:22165710_22165711insT	uc003xbn.2	+						PIWIL2_uc011kzf.1_Intron|PIWIL2_uc010ltv.2_Intron	NM_018068	NP_060538	Q8TC59	PIWL2_HUMAN	piwi-like 2						DNA methylation involved in gamete generation|gene silencing by RNA|germ-line stem cell maintenance|multicellular organismal development|oogenesis|piRNA metabolic process|positive regulation of translation|RNA 5'-end processing|spermatogenesis	chromatoid body|pi-body	piRNA binding			skin(1)	1				Colorectal(74;0.018)|COAD - Colon adenocarcinoma(73;0.0707)		ATTTTTCTAAGTTTTTTTTTTT	0.322													7	6	---	---	---	---	
SYBU	55638	broad.mit.edu	37	8	110631459	110631460	+	Intron	INS	-	T	T	rs142578497		TCGA-CH-5771-01A-21D-1576-08	TCGA-CH-5771-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:110631459_110631460insT	uc003ynj.3	-						SYBU_uc003yni.3_Intron|SYBU_uc003ynk.3_Intron|SYBU_uc010mco.2_Intron|SYBU_uc003ynl.3_Intron|SYBU_uc010mcp.2_Intron|SYBU_uc010mcq.2_Intron|SYBU_uc003yno.3_Intron|SYBU_uc010mcr.2_Intron|SYBU_uc003ynm.3_Intron|SYBU_uc003ynn.3_Intron|SYBU_uc010mcs.2_Intron|SYBU_uc010mct.2_Intron|SYBU_uc010mcu.2_Intron|SYBU_uc003ynp.3_Intron|SYBU_uc010mcv.2_Intron	NM_001099754	NP_001093224	Q9NX95	SYBU_HUMAN	Golgi-localized syntaphilin-related protein							cytoplasmic membrane-bounded vesicle|cytoskeleton|Golgi membrane|integral to membrane				ovary(1)	1						AATGCAAAACCttttttttttt	0.228													6	4	---	---	---	---	
TMEM71	137835	broad.mit.edu	37	8	133769300	133769301	+	Intron	DEL	TT	-	-	rs113664875		TCGA-CH-5771-01A-21D-1576-08	TCGA-CH-5771-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:133769300_133769301delTT	uc003ytp.2	-						TMEM71_uc003ytn.2_Intron|TMEM71_uc003yto.2_Intron	NM_144649	NP_653250	Q6P5X7	TMM71_HUMAN	transmembrane protein 71 isoform 1							integral to membrane				ovary(2)	2	all_neural(3;2.72e-06)|Medulloblastoma(3;7.08e-05)|Ovarian(258;0.00438)|Esophageal squamous(12;0.00507)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;4.46e-05)			gcagcgctgatttttttttttt	0.000													3	4	---	---	---	---	
COL22A1	169044	broad.mit.edu	37	8	139818308	139818309	+	Intron	INS	-	GT	GT			TCGA-CH-5771-01A-21D-1576-08	TCGA-CH-5771-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:139818308_139818309insGT	uc003yvd.2	-							NM_152888	NP_690848	Q8NFW1	COMA1_HUMAN	collagen, type XXII, alpha 1						cell adhesion	collagen|cytoplasm	structural molecule activity			ovary(11)|pancreas(1)|skin(1)	13	all_epithelial(106;1.55e-12)|Lung NSC(106;1.67e-05)|all_lung(105;3.39e-05)|Ovarian(258;0.00672)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0517)			ggtgtgtggtggtgtgtgtgat	0.000										HNSCC(7;0.00092)			4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	143094521	143094522	+	IGR	INS	-	ATT	ATT			TCGA-CH-5771-01A-21D-1576-08	TCGA-CH-5771-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:143094521_143094522insATT								MIR1302-7 (226847 upstream) : NCRNA00051 (185195 downstream)																							atcattacatcatcaccatcac	0.000													2	5	---	---	---	---	
C9orf44	158314	broad.mit.edu	37	9	94904432	94904432	+	Intron	DEL	G	-	-	rs34310564		TCGA-CH-5771-01A-21D-1576-08	TCGA-CH-5771-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:94904432delG	uc004arp.1	+							NR_027341				Homo sapiens cDNA FLJ13600 fis, clone PLACE1009947.												0						GGCCTTCTTTGGGGGGGGGGT	0.612													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	134206019	134206020	+	IGR	INS	-	G	G	rs142843997		TCGA-CH-5771-01A-21D-1576-08	TCGA-CH-5771-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:134206019_134206020insG								LRRC27 (11009 upstream) : PWWP2B (4682 downstream)																							atgatggtgatgtgataatggt	0.000													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	15442249	15442250	+	IGR	DEL	AC	-	-			TCGA-CH-5771-01A-21D-1576-08	TCGA-CH-5771-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:15442249_15442250delAC								RERG (67945 upstream) : PTPRO (33237 downstream)																							tcacacacatacacacacacac	0.000													4	2	---	---	---	---	
TMCC3	57458	broad.mit.edu	37	12	94971940	94971941	+	Intron	INS	-	AAAAAAAA	AAAAAAAA	rs10659097		TCGA-CH-5771-01A-21D-1576-08	TCGA-CH-5771-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:94971940_94971941insAAAAAAAA	uc001tdj.2	-						TMCC3_uc001tdi.2_Intron	NM_020698	NP_065749	Q9ULS5	TMCC3_HUMAN	transmembrane and coiled-coil domain family 3							integral to membrane				ovary(1)|skin(1)	2						aaaaaaaaaaaaaaagaaaaag	0.114													4	3	---	---	---	---	
CIT	11113	broad.mit.edu	37	12	120204681	120204681	+	Intron	DEL	A	-	-	rs36109532		TCGA-CH-5771-01A-21D-1576-08	TCGA-CH-5771-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:120204681delA	uc001txi.1	-						CIT_uc001txh.1_Intron|CIT_uc001txj.1_Intron	NM_007174	NP_009105	O14578	CTRO_HUMAN	citron						intracellular signal transduction		ATP binding|metal ion binding|protein serine/threonine kinase activity|SH3 domain binding|small GTPase regulator activity			ovary(6)|urinary_tract(1)|lung(1)|breast(1)|skin(1)	10	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)	Myeloproliferative disorder(1001;0.0255)		BRCA - Breast invasive adenocarcinoma(302;0.211)		GACCACATTTAAAAAAAAAAA	0.274													4	2	---	---	---	---	
RSRC2	65117	broad.mit.edu	37	12	123003304	123003305	+	Intron	INS	-	T	T			TCGA-CH-5771-01A-21D-1576-08	TCGA-CH-5771-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:123003304_123003305insT	uc001ucr.2	-						RSRC2_uc001uco.2_Intron|RSRC2_uc001ucp.2_Intron|RSRC2_uc001ucq.2_Intron|RSRC2_uc001ucs.2_Intron|RSRC2_uc001uct.2_Intron|RSRC2_uc001ucu.2_Intron	NM_023012	NP_075388	Q7L4I2	RSRC2_HUMAN	arginine/serine-rich coiled-coil 2 isoform a											ovary(1)	1	all_neural(191;0.0837)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;5.14e-05)|Epithelial(86;0.000183)|BRCA - Breast invasive adenocarcinoma(302;0.201)		CCTAATTATGATTTTTTTGGGT	0.351													190	33	---	---	---	---	
KNTC1	9735	broad.mit.edu	37	12	123031380	123031380	+	Intron	DEL	T	-	-			TCGA-CH-5771-01A-21D-1576-08	TCGA-CH-5771-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:123031380delT	uc001ucv.2	+						KNTC1_uc010taf.1_Intron	NM_014708	NP_055523	P50748	KNTC1_HUMAN	Rough Deal homolog, centromere/kinetochore						cell division|mitotic cell cycle checkpoint|mitotic prometaphase|protein complex assembly|regulation of exit from mitosis	condensed chromosome kinetochore|cytosol|kinetochore microtubule|nucleus|spindle pole	protein binding			ovary(5)|kidney(3)|lung(1)|central_nervous_system(1)	10	all_neural(191;0.0837)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;7.21e-05)|Epithelial(86;0.000178)|BRCA - Breast invasive adenocarcinoma(302;0.217)		TGAAATGTAAttttttttttt	0.179													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	73610506	73610507	+	IGR	DEL	AC	-	-			TCGA-CH-5771-01A-21D-1576-08	TCGA-CH-5771-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:73610506_73610507delAC								PIBF1 (19917 upstream) : KLF5 (18607 downstream)																							ctgtctcaaaaCACACACACAC	0.252													98	8	---	---	---	---	
ABCC4	10257	broad.mit.edu	37	13	95673939	95673939	+	Intron	DEL	A	-	-	rs9524765	by1000genomes	TCGA-CH-5771-01A-21D-1576-08	TCGA-CH-5771-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:95673939delA	uc001vmd.3	-						ABCC4_uc010afj.2_Intron|ABCC4_uc010afk.2_Intron	NM_005845	NP_005836	O15439	MRP4_HUMAN	ATP-binding cassette, sub-family C, member 4						platelet activation|platelet degranulation	integral to membrane|membrane fraction|plasma membrane|platelet dense granule membrane	15-hydroxyprostaglandin dehydrogenase (NAD+) activity|ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|chloride channel activity			central_nervous_system(3)|skin(1)	4	all_neural(89;0.0878)|Medulloblastoma(90;0.163)				Cefazolin(DB01327)	AAGTATACCTAGAAAAAAAAA	0.358													97	7	---	---	---	---	
HS6ST3	266722	broad.mit.edu	37	13	97320445	97320446	+	Intron	DEL	CA	-	-			TCGA-CH-5771-01A-21D-1576-08	TCGA-CH-5771-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:97320445_97320446delCA	uc001vmw.2	+							NM_153456	NP_703157	Q8IZP7	H6ST3_HUMAN	heparan sulfate 6-O-sulfotransferase 3							integral to membrane	sulfotransferase activity			ovary(1)|skin(1)	2	all_neural(89;0.0878)|Medulloblastoma(90;0.163)					cacacacacgcacacacacaca	0.020													4	2	---	---	---	---	
ATP11A	23250	broad.mit.edu	37	13	113528139	113528157	+	Intron	DEL	CCTGGGATACAGTCGGGGG	-	-	rs67506160		TCGA-CH-5771-01A-21D-1576-08	TCGA-CH-5771-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:113528139_113528157delCCTGGGATACAGTCGGGGG	uc001vsi.3	+						ATP11A_uc001vsj.3_Intron|ATP11A_uc010ago.2_Intron	NM_015205	NP_056020	P98196	AT11A_HUMAN	ATPase, class VI, type 11A isoform a						ATP biosynthetic process	integral to membrane	ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|magnesium ion binding|phospholipid-translocating ATPase activity			large_intestine(2)|ovary(2)	4	all_lung(23;0.000374)|Lung NSC(43;0.0107)|Lung SC(71;0.0753)|all_neural(89;0.0804)|Hepatocellular(20;0.0877)|Medulloblastoma(90;0.163)	all_lung(25;0.134)|all_epithelial(44;0.141)				gtcgtggggtcctgggatacagtcgggggcaagacaccg	0.114													8	8	---	---	---	---	
DHRS4	10901	broad.mit.edu	37	14	24473479	24473479	+	Intron	DEL	A	-	-			TCGA-CH-5771-01A-21D-1576-08	TCGA-CH-5771-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:24473479delA	uc001wlc.3	+						DHRS4L2_uc001wld.3_Intron|DHRS4L2_uc001wle.3_Intron|DHRS4L2_uc001wlg.3_Intron|DHRS4L2_uc001wlh.3_Intron|DHRS4L2_uc010tnt.1_Intron|DHRS4L2_uc001wli.3_Intron|DHRS4L2_uc010alb.2_Intron	NM_021004	NP_066284	Q9BTZ2	DHRS4_HUMAN	peroxisomal short-chain alcohol dehydrogenase							mitochondrion|nuclear membrane|peroxisome	binding|carbonyl reductase (NADPH) activity			ovary(1)	1				GBM - Glioblastoma multiforme(265;0.00962)	Vitamin A(DB00162)	ctccgtctctaaaaaaaaaaa	0.134													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	95117489	95117490	+	IGR	DEL	GC	-	-	rs117537795	by1000genomes	TCGA-CH-5771-01A-21D-1576-08	TCGA-CH-5771-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:95117489_95117490delGC								SERPINA13 (4159 upstream) : GSC (117071 downstream)																							acacacagaggcacacacacac	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	99799224	99799225	+	IGR	DEL	AT	-	-			TCGA-CH-5771-01A-21D-1576-08	TCGA-CH-5771-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:99799224_99799225delAT								BCL11B (61402 upstream) : SETD3 (64859 downstream)																							gcacacacacatgcccgcacat	0.000													4	3	---	---	---	---	
ATP10A	57194	broad.mit.edu	37	15	26024992	26024993	+	Intron	INS	-	AC	AC	rs139149034	by1000genomes	TCGA-CH-5771-01A-21D-1576-08	TCGA-CH-5771-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:26024992_26024993insAC	uc010ayu.2	-							NM_024490	NP_077816	O60312	AT10A_HUMAN	ATPase, class V, type 10A						ATP biosynthetic process|regulation of cell shape	integral to membrane|plasma membrane	ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|magnesium ion binding|phospholipid-translocating ATPase activity			pancreas(2)|ovary(1)|breast(1)|liver(1)	5		all_cancers(20;5.16e-25)|all_lung(180;1.51e-14)|Acute lymphoblastic leukemia(1;2.53e-05)|all_hematologic(1;0.000267)|Breast(32;0.00125)		all cancers(64;9.48e-07)|Epithelial(43;1.69e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0252)|Lung(196;0.244)		AGAAGGTTAAAacacacacaca	0.213													3	3	---	---	---	---	
PKM2	5315	broad.mit.edu	37	15	72502473	72502473	+	Intron	DEL	A	-	-			TCGA-CH-5771-01A-21D-1576-08	TCGA-CH-5771-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:72502473delA	uc002atx.1	-						PKM2_uc002att.1_5'Flank|PKM2_uc002atu.1_5'Flank|PKM2_uc010bit.1_Intron|PKM2_uc010uki.1_Intron|PKM2_uc002atv.1_Intron|PKM2_uc002atw.1_Intron|PKM2_uc002aty.1_Intron|PKM2_uc010ukj.1_Intron|PKM2_uc010ukk.1_Intron|PKM2_uc010biu.1_Intron|PKM2_uc002atz.1_Intron	NM_182471	NP_872271	P14618	KPYM_HUMAN	pyruvate kinase, muscle isoform M1						glycolysis|programmed cell death	cytosol|nucleus|plasma membrane	ATP binding|magnesium ion binding|potassium ion binding|protein binding|pyruvate kinase activity			breast(1)	1					Pyruvic acid(DB00119)	TTTTTAGGGTAAAAAAAAAAG	0.333													25	7	---	---	---	---	
ACAN	176	broad.mit.edu	37	15	89384726	89384727	+	Intron	INS	-	A	A	rs140276078	by1000genomes	TCGA-CH-5771-01A-21D-1576-08	TCGA-CH-5771-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:89384726_89384727insA	uc010upo.1	+						ACAN_uc002bmx.2_Intron|ACAN_uc010upp.1_Intron|ACAN_uc002bna.2_Intron	NM_013227	NP_037359	E7EX88	E7EX88_HUMAN	aggrecan isoform 2 precursor						cell adhesion		hyaluronic acid binding|sugar binding			ovary(2)|central_nervous_system(1)	3	Lung NSC(78;0.0392)|all_lung(78;0.077)		BRCA - Breast invasive adenocarcinoma(143;0.146)			gccttttatagaaaaaaatatg	0.139													4	2	---	---	---	---	
LMF1	64788	broad.mit.edu	37	16	909247	909247	+	Intron	DEL	C	-	-	rs67965864		TCGA-CH-5771-01A-21D-1576-08	TCGA-CH-5771-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:909247delC	uc002ckj.2	-						LMF1_uc010brg.2_Intron|LMF1_uc010brh.2_Intron|LMF1_uc010bri.2_Intron|LMF1_uc002ckk.2_Intron	NM_022773	NP_073610	Q96S06	LMF1_HUMAN	lipase maturation factor 1							endoplasmic reticulum membrane|integral to membrane					0		Hepatocellular(780;0.00308)				GACGGGTGTGCAGTGGTGTCA	0.652													4	2	---	---	---	---	
RBL2	5934	broad.mit.edu	37	16	53495453	53495454	+	Intron	INS	-	T	T			TCGA-CH-5771-01A-21D-1576-08	TCGA-CH-5771-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:53495453_53495454insT	uc002ehi.3	+						RBL2_uc010vgv.1_Intron|RBL2_uc002ehj.2_Intron|RBL2_uc010vgw.1_Intron	NM_005611	NP_005602	Q08999	RBL2_HUMAN	retinoblastoma-like 2 (p130)						cell cycle|chromatin modification|regulation of cell cycle|regulation of lipid kinase activity|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleolus	DNA binding|protein binding			ovary(2)|lung(2)|upper_aerodigestive_tract(1)	5						CACAAGAAAAGTTTTTTTTTTT	0.218													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	72564152	72564155	+	Intron	DEL	TGTG	-	-	rs71784649		TCGA-CH-5771-01A-21D-1576-08	TCGA-CH-5771-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:72564152_72564155delTGTG	uc002fci.1	+											Homo sapiens cDNA FLJ38299 fis, clone FCBBF3017255.																		CACTATTTTAtgtgtgtgtgtgtg	0.294													3	3	---	---	---	---	
C16orf46	123775	broad.mit.edu	37	16	81095915	81095915	+	Intron	DEL	A	-	-			TCGA-CH-5771-01A-21D-1576-08	TCGA-CH-5771-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:81095915delA	uc002fgc.3	-						C16orf46_uc010chf.2_Intron|C16orf46_uc010vno.1_Intron	NM_152337	NP_689550	Q6P387	CP046_HUMAN	chromosome 16 open reading frame 46 isoform 2												0						TCATTCACTTAAAAAAAAAAT	0.274													4	2	---	---	---	---	
TSR1	55720	broad.mit.edu	37	17	2228914	2228915	+	Intron	INS	-	T	T			TCGA-CH-5771-01A-21D-1576-08	TCGA-CH-5771-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:2228914_2228915insT	uc002fuj.2	-							NM_018128	NP_060598	Q2NL82	TSR1_HUMAN	TSR1, 20S rRNA accumulation						ribosome assembly	nucleolus	protein binding			ovary(1)	1						ttttttttttctttttttttga	0.183													4	2	---	---	---	---	
GOSR1	9527	broad.mit.edu	37	17	28811554	28811558	+	Intron	DEL	TTTTG	-	-	rs5819900		TCGA-CH-5771-01A-21D-1576-08	TCGA-CH-5771-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:28811554_28811558delTTTTG	uc002hfe.2	+						GOSR1_uc002hfd.2_Intron|GOSR1_uc002hff.2_Intron|GOSR1_uc002hfc.1_Intron	NM_004871	NP_004862	O95249	GOSR1_HUMAN	golgi SNAP receptor complex member 1 isoform 1						intra-Golgi vesicle-mediated transport|protein transport|retrograde transport, endosome to Golgi	Golgi membrane|integral to membrane|SNARE complex	SNAP receptor activity				0						CTTGTTTGTTttttgttttgttttg	0.288													9	5	---	---	---	---	
NEUROD2	4761	broad.mit.edu	37	17	37762300	37762308	+	In_Frame_Del	DEL	GGTCTGGCC	-	-			TCGA-CH-5771-01A-21D-1576-08	TCGA-CH-5771-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:37762300_37762308delGGTCTGGCC	uc002hry.2	-	2	745_753	c.545_553delGGCCAGACC	c.(544-555)CGGCCAGACCTA>CTA	p.RPD182del		NM_006160	NP_006151	Q15784	NDF2_HUMAN	neurogenic differentiation 2	182_184					cellular response to calcium ion|cellular response to electrical stimulus|cerebellar cortex development|negative regulation of synapse maturation|positive regulation of calcium-mediated signaling|positive regulation of neuron differentiation|positive regulation of sequence-specific DNA binding transcription factor activity|positive regulation of synapse maturation|positive regulation of synaptic plasticity|protein ubiquitination|regulation of transcription from RNA polymerase II promoter	nucleus	E-box binding|protein heterodimerization activity|sequence-specific DNA binding transcription factor activity|transcription corepressor activity				0	Lung NSC(9;1.15e-09)|all_lung(9;6.24e-09)|Colorectal(19;0.000442)|Esophageal squamous(10;0.052)		UCEC - Uterine corpus endometrioid carcinoma (11;0.000126)|Lung(15;0.00549)|LUAD - Lung adenocarcinoma(14;0.0664)			TAGGACACTAGGTCTGGCCGCTTGCCGGA	0.603													81	8	---	---	---	---	
KRT20	54474	broad.mit.edu	37	17	39037480	39037481	+	Intron	DEL	TG	-	-	rs149120741		TCGA-CH-5771-01A-21D-1576-08	TCGA-CH-5771-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:39037480_39037481delTG	uc002hvl.2	-							NM_019010	NP_061883	P35900	K1C20_HUMAN	keratin 20						apoptosis|intermediate filament organization	Golgi apparatus|intermediate filament	protein binding|structural constituent of cytoskeleton			large_intestine(1)|kidney(1)|skin(1)	3		Breast(137;0.000301)|Ovarian(249;0.15)				ACATACACACtgtgtgtgtgtg	0.168													3	5	---	---	---	---	
JUP	3728	broad.mit.edu	37	17	39789866	39789867	+	Intron	DEL	GT	-	-	rs151010375		TCGA-CH-5771-01A-21D-1576-08	TCGA-CH-5771-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:39789866_39789867delGT	uc010wfs.1	-						uc010cxq.1_Intron|uc002hxi.1_Intron	NM_021991	NP_068831	P14923	PLAK_HUMAN	junction plakoglobin						adherens junction organization|atrioventricular valve morphogenesis|cell migration|cell morphogenesis|cellular response to indole-3-methanol|cytoskeletal anchoring at plasma membrane|detection of mechanical stimulus|ectoderm development|endothelial cell-cell adhesion|gastrulation|morphogenesis of embryonic epithelium|negative regulation of heart induction by canonical Wnt receptor signaling pathway|negative regulation of Wnt receptor signaling pathway involved in heart development|nervous system development|oocyte development|positive regulation of protein import into nucleus|positive regulation of sequence-specific DNA binding transcription factor activity|skin development	actin cytoskeleton|Axin-APC-beta-catenin-GSK3B complex|basolateral plasma membrane|catenin complex|desmosome|fascia adherens|gamma-catenin-TCF7L2 complex|internal side of plasma membrane|nucleus|protein-DNA complex|Z disc|zonula adherens	alpha-catenin binding|cadherin binding|protein homodimerization activity|protein kinase binding|protein phosphatase binding|RPTP-like protein binding|specific RNA polymerase II transcription factor activity|transcription coactivator activity			ovary(2)|lung(2)|breast(1)	5		Breast(137;0.000162)	BRCA - Breast invasive adenocarcinoma(4;0.233)	BRCA - Breast invasive adenocarcinoma(366;0.15)		gctgtgtgtggtgtgtgtgtgg	0.000													4	3	---	---	---	---	
ANKFN1	162282	broad.mit.edu	37	17	54468730	54468739	+	Intron	DEL	TGTGTGTGTG	-	-	rs8072043		TCGA-CH-5771-01A-21D-1576-08	TCGA-CH-5771-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:54468730_54468739delTGTGTGTGTG	uc002iun.1	+							NM_153228	NP_694960	Q8N957	ANKF1_HUMAN	ankyrin-repeat and fibronectin type III domain											large_intestine(1)|ovary(1)	2						catatatatatgtgtgtgtgtgtgtgtgtg	0.114													4	2	---	---	---	---	
USP32	84669	broad.mit.edu	37	17	58332410	58332410	+	Intron	DEL	T	-	-	rs35284371		TCGA-CH-5771-01A-21D-1576-08	TCGA-CH-5771-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:58332410delT	uc002iyo.1	-						USP32_uc002iyn.1_Intron|USP32_uc010wov.1_Intron	NM_032582	NP_115971	Q8NFA0	UBP32_HUMAN	ubiquitin specific protease 32						protein deubiquitination|ubiquitin-dependent protein catabolic process	Golgi apparatus|membrane	calcium ion binding|cysteine-type peptidase activity|ubiquitin thiolesterase activity			lung(2)|breast(2)|large_intestine(1)	5	all_neural(34;0.0878)|Medulloblastoma(34;0.0922)		Epithelial(12;2.02e-11)|all cancers(12;5.23e-10)|Colorectal(3;0.198)			AATGTAGTTCttttttttttt	0.353													13	6	---	---	---	---	
ABCA8	10351	broad.mit.edu	37	17	66871571	66871571	+	Intron	DEL	A	-	-	rs4148027		TCGA-CH-5771-01A-21D-1576-08	TCGA-CH-5771-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:66871571delA	uc002jhp.2	-						ABCA8_uc002jhq.2_Intron|ABCA8_uc010wqq.1_Intron	NM_007168	NP_009099	O94911	ABCA8_HUMAN	ATP-binding cassette, sub-family A member 8							integral to membrane|plasma membrane	ATP binding|ATPase activity, coupled to transmembrane movement of substances			ovary(2)|skin(1)	3	Breast(10;4.56e-13)					GAGAAAGGAGAAAAAAAAAAC	0.413													98	7	---	---	---	---	
EVPL	2125	broad.mit.edu	37	17	74017493	74017501	+	Intron	DEL	CCGCCCCTG	-	-			TCGA-CH-5771-01A-21D-1576-08	TCGA-CH-5771-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:74017493_74017501delCCGCCCCTG	uc002jqi.2	-						EVPL_uc010wss.1_Intron|EVPL_uc010wst.1_Intron	NM_001988	NP_001979	Q92817	EVPL_HUMAN	envoplakin						keratinization|peptide cross-linking	cornified envelope|cytoplasm|desmosome	protein binding, bridging|structural molecule activity			pancreas(2)|central_nervous_system(1)|skin(1)	4						TGCTGTGCTCccgcccctgccgcccctgc	0.383													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	75714850	75714851	+	IGR	INS	-	GCAT	GCAT	rs150198570	by1000genomes	TCGA-CH-5771-01A-21D-1576-08	TCGA-CH-5771-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:75714850_75714851insGCAT								SEPT9 (218174 upstream) : FLJ45079 (160258 downstream)																							tgtgtgtgcacgcatgtgtgtc	0.050													4	2	---	---	---	---	
FSCN2	25794	broad.mit.edu	37	17	79499473	79499475	+	Intron	DEL	TGG	-	-			TCGA-CH-5771-01A-21D-1576-08	TCGA-CH-5771-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:79499473_79499475delTGG	uc010wup.1	+						FSCN2_uc010wuo.1_Intron	NM_012418	NP_036550	O14926	FSCN2_HUMAN	fascin 2 isoform 1						actin filament bundle assembly|anatomical structure morphogenesis|visual perception	actin cytoskeleton|cytoplasm|stereocilium	actin filament binding|protein binding, bridging				0	all_neural(118;0.0878)|Melanoma(429;0.242)		BRCA - Breast invasive adenocarcinoma(99;0.0282)|OV - Ovarian serous cystadenocarcinoma(97;0.0371)			gtgatgatgatggtgatggtggt	0.000													5	3	---	---	---	---	
LOC647946	647946	broad.mit.edu	37	18	37248431	37248454	+	Intron	DEL	AGGGAGGAAGGAAGGAAGGAAGGA	-	-	rs11270312	by1000genomes	TCGA-CH-5771-01A-21D-1576-08	TCGA-CH-5771-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:37248431_37248454delAGGGAGGAAGGAAGGAAGGAAGGA	uc010xcj.1	-						LOC647946_uc002lal.1_Intron	NR_024391				Homo sapiens cDNA FLJ33284 fis, clone ASTRO2009458.												0						ggagggagggagggaggaaggaaggaaggaaggaaggaaggaag	0.098													6	4	---	---	---	---	
PRSSL1	400668	broad.mit.edu	37	19	691212	691213	+	Intron	INS	-	A	A	rs147436553		TCGA-CH-5771-01A-21D-1576-08	TCGA-CH-5771-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:691212_691213insA	uc002lpl.1	-						PRSSL1_uc010xfs.1_Intron	NM_214710	NP_999875	Q6UWY2	PRS57_HUMAN	protease, serine-like 1 precursor						proteolysis	extracellular region	serine-type endopeptidase activity				0		all_epithelial(18;2.19e-21)|Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;3.55e-06)|all_lung(49;5.41e-06)|Breast(49;4.08e-05)|Hepatocellular(1079;0.137)|Renal(1328;0.228)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		ATTAAGCCTGGAAAAAAAAAAT	0.238													8	4	---	---	---	---	
MUC16	94025	broad.mit.edu	37	19	8969553	8969554	+	Intron	INS	-	TT	TT	rs36058947		TCGA-CH-5771-01A-21D-1576-08	TCGA-CH-5771-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:8969553_8969554insTT	uc002mkp.2	-						MUC16_uc010dwi.2_Intron|MUC16_uc010dwj.2_Intron|MUC16_uc010xki.1_Intron	NM_024690	NP_078966	Q8WXI7	MUC16_HUMAN	mucin 16						cell adhesion	extracellular space|extrinsic to membrane|integral to membrane|plasma membrane	protein binding			lung(30)|ovary(15)|breast(8)|large_intestine(1)|skin(1)|prostate(1)|pancreas(1)	57						tttttcttttcttttttttttt	0.178													3	7	---	---	---	---	
FBXL12	54850	broad.mit.edu	37	19	9931205	9931206	+	5'Flank	DEL	TG	-	-			TCGA-CH-5771-01A-21D-1576-08	TCGA-CH-5771-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:9931205_9931206delTG	uc002mme.2	-						FBXL12_uc002mmd.2_5'Flank|FBXL12_uc002mmf.2_5'Flank|FBXL12_uc002mmg.2_5'Flank|FBXL12_uc002mmh.2_Intron	NM_017703	NP_060173	Q9NXK8	FXL12_HUMAN	F-box and leucine-rich repeat protein 12								protein binding			lung(1)|kidney(1)	2						AAAAAAAAAAtgtgtgtgtgtg	0.302													19	7	---	---	---	---	
MED25	81857	broad.mit.edu	37	19	50331486	50331486	+	Intron	DEL	A	-	-			TCGA-CH-5771-01A-21D-1576-08	TCGA-CH-5771-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:50331486delA	uc002ppw.1	+						MED25_uc010ybe.1_Intron	NM_030973	NP_112235	Q71SY5	MED25_HUMAN	mediator complex subunit 25						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleoplasm				ovary(1)	1		all_lung(116;3.24e-07)|Lung NSC(112;1.6e-06)|all_neural(266;0.0459)|Ovarian(192;0.0728)		OV - Ovarian serous cystadenocarcinoma(262;0.00822)|GBM - Glioblastoma multiforme(134;0.0122)		actccatctcaaaaaaaaaaa	0.259													9	4	---	---	---	---	
ZNF615	284370	broad.mit.edu	37	19	52504869	52504870	+	Intron	INS	-	A	A	rs10561184		TCGA-CH-5771-01A-21D-1576-08	TCGA-CH-5771-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:52504869_52504870insA	uc002pye.1	-						ZNF615_uc002pyf.1_Intron|ZNF615_uc002pyg.1_Intron|ZNF615_uc002pyh.1_Intron|ZNF615_uc010epi.1_Intron|ZNF615_uc010ydg.1_Intron	NM_198480	NP_940882	Q8N8J6	ZN615_HUMAN	zinc finger protein 615						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(4)|skin(1)	5		all_neural(266;0.117)		GBM - Glioblastoma multiforme(134;0.00142)|OV - Ovarian serous cystadenocarcinoma(262;0.019)		gactccatctcaaaaaaaaaaa	0.163													4	2	---	---	---	---	
U2AF2	11338	broad.mit.edu	37	19	56181884	56181884	+	Intron	DEL	G	-	-	rs66506071		TCGA-CH-5771-01A-21D-1576-08	TCGA-CH-5771-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:56181884delG	uc002qlu.2	+						U2AF2_uc002qlt.2_Intron	NM_007279	NP_009210	P26368	U2AF2_HUMAN	U2 (RNU2) small nuclear RNA auxiliary factor 2						mRNA 3'-end processing|mRNA export from nucleus|termination of RNA polymerase II transcription	nucleoplasm|spliceosomal complex	enzyme binding|nucleotide binding|RNA binding			ovary(1)	1		Colorectal(82;0.00244)|Ovarian(87;0.133)	BRCA - Breast invasive adenocarcinoma(297;0.18)	GBM - Glioblastoma multiforme(193;0.107)		CTGCTGTCCCGTGCACCCTGC	0.532													3	5	---	---	---	---	
JAG1	182	broad.mit.edu	37	20	10653815	10653815	+	Intron	DEL	A	-	-	rs33929314		TCGA-CH-5771-01A-21D-1576-08	TCGA-CH-5771-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:10653815delA	uc002wnw.2	-							NM_000214	NP_000205	P78504	JAG1_HUMAN	jagged 1 precursor						angiogenesis|cell communication|cell fate determination|endothelial cell differentiation|hemopoiesis|keratinocyte differentiation|myoblast differentiation|Notch receptor processing|Notch signaling pathway|regulation of cell migration|regulation of cell proliferation	extracellular region|integral to plasma membrane	calcium ion binding|growth factor activity|Notch binding|structural molecule activity			lung(3)|ovary(2)|central_nervous_system(2)|breast(1)|pancreas(1)	9						ATTCCGGGGCAAAAAAAAAAA	0.587									Alagille_Syndrome				4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	10713040	10713040	+	IGR	DEL	A	-	-			TCGA-CH-5771-01A-21D-1576-08	TCGA-CH-5771-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:10713040delA								None (None upstream) : TPTE (193703 downstream)																							cataggcctcaaagccctcac	0.000													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	10725174	10725174	+	IGR	DEL	G	-	-			TCGA-CH-5771-01A-21D-1576-08	TCGA-CH-5771-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:10725174delG								None (None upstream) : TPTE (181569 downstream)																							aggcttcaaagcactccaaat	0.000													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	14363881	14363882	+	IGR	DEL	AG	-	-			TCGA-CH-5771-01A-21D-1576-08	TCGA-CH-5771-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:14363881_14363882delAG								None (None upstream) : C21orf99 (46605 downstream)																							ttctacaaaaagagagtttcaa	0.000													4	2	---	---	---	---	
CCT8L2	150160	broad.mit.edu	37	22	17075871	17075872	+	5'Flank	INS	-	A	A	rs77265374		TCGA-CH-5771-01A-21D-1576-08	TCGA-CH-5771-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:17075871_17075872insA	uc002zlp.1	-							NM_014406	NP_055221	Q96SF2	TCPQM_HUMAN	T-complex protein 1						cellular protein metabolic process	cytoplasm	anion channel activity|ATP binding|calcium-activated potassium channel activity			ovary(1)	1	all_hematologic(4;0.00567)|Acute lymphoblastic leukemia(84;0.0977)	all_epithelial(15;0.0157)|Lung NSC(13;0.147)|all_lung(157;0.175)				ACACAGTAATGAAAAAAAAAAA	0.327													5	3	---	---	---	---	
TCN2	6948	broad.mit.edu	37	22	31019234	31019235	+	Intron	INS	-	C	C	rs141234711	by1000genomes	TCGA-CH-5771-01A-21D-1576-08	TCGA-CH-5771-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:31019234_31019235insC	uc003aip.1	+						TCN2_uc003aiq.1_Intron|TCN2_uc003air.1_Intron	NM_000355	NP_000346	P20062	TCO2_HUMAN	transcobalamin II precursor						cobalamin metabolic process|cobalamin transport|cobalt ion transport	extracellular space	cobalamin binding			central_nervous_system(1)	1					Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)	TGAAGCCTTAGAATTTTTATGC	0.366													4	2	---	---	---	---	
ARFGAP3	26286	broad.mit.edu	37	22	43213780	43213780	+	Frame_Shift_Del	DEL	T	-	-			TCGA-CH-5771-01A-21D-1576-08	TCGA-CH-5771-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:43213780delT	uc003bdd.2	-	10	1116	c.896delA	c.(895-897)AATfs	p.N299fs	ARFGAP3_uc010gzf.2_Frame_Shift_Del_p.N255fs|ARFGAP3_uc011apu.1_Frame_Shift_Del_p.N227fs	NM_014570	NP_055385	Q9NP61	ARFG3_HUMAN	ADP-ribosylation factor GTPase activating	299					intracellular protein transport|protein secretion|regulation of ARF GTPase activity|vesicle-mediated transport	cytosol|Golgi membrane	ARF GTPase activator activity|protein transporter activity|zinc ion binding			breast(1)	1						TGAGTCAACATTTTTTTTGCC	0.224													389	7	---	---	---	---	
FAM19A5	25817	broad.mit.edu	37	22	48979728	48979738	+	Intron	DEL	ACACCACACAC	-	-			TCGA-CH-5771-01A-21D-1576-08	TCGA-CH-5771-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:48979728_48979738delACACCACACAC	uc003bim.3	+						FAM19A5_uc003bio.3_Intron	NM_001082967	NP_001076436	Q7Z5A7	F19A5_HUMAN	family with sequence similarity 19 (chemokine							extracellular region|integral to membrane				large_intestine(1)	1		all_cancers(38;2.95e-11)|all_epithelial(38;3.07e-10)|all_lung(38;2.89e-05)|Breast(42;0.000396)|Lung NSC(38;0.000471)|Ovarian(80;0.00934)|Lung SC(80;0.195)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0227)|BRCA - Breast invasive adenocarcinoma(115;0.119)		TAAACCTCATacaccacacacacaccacaca	0.014													4	2	---	---	---	---	
IL9R	3581	broad.mit.edu	37	X	155238586	155238587	+	Intron	INS	-	TG	TG			TCGA-CH-5771-01A-21D-1576-08	TCGA-CH-5771-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:155238586_155238587insTG	uc004fnv.1	+						IL9R_uc004fnu.1_Intron	NM_002186	NP_002177	Q01113	IL9R_HUMAN	interleukin 9 receptor precursor						cell proliferation	extracellular space|integral to plasma membrane	interleukin-9 receptor activity				0	all_cancers(53;1.86e-17)|all_epithelial(53;2.71e-11)|all_lung(58;1.84e-07)|Lung NSC(58;5.62e-07)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)|Renal(33;0.214)					gtgtgtgtgtctgtgtgtgtgt	0.099													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	Y	13487812	13487812	+	IGR	DEL	C	-	-			TCGA-CH-5771-01A-21D-1576-08	TCGA-CH-5771-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:13487812delC								None (None upstream) : None (None downstream)																							GGCTGGCTGTCCCAGGGCTCA	0.398													4	2	---	---	---	---	
