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
TPRG1L	127262	broad.mit.edu	37	1	3545158	3545158	+	Missense_Mutation	SNP	A	G	G			TCGA-CJ-4639-01A-02D-1386-10	TCGA-CJ-4639-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:3545158A>G	uc001akm.2	+	5	891	c.810A>G	c.(808-810)ATA>ATG	p.I270M	TPRG1L_uc009vlj.2_Missense_Mutation_p.I211M	NM_182752	NP_877429	Q5T0D9	TPRGL_HUMAN	tumor protein p63 regulated 1-like	270						cell junction|synaptic vesicle					0	all_cancers(77;0.0119)|all_epithelial(69;0.00481)|Ovarian(185;0.0634)|Lung NSC(156;0.162)|all_lung(157;0.172)	all_epithelial(116;7.37e-22)|all_lung(118;8.23e-09)|Lung NSC(185;3.55e-06)|Breast(487;0.000659)|Renal(390;0.00121)|Hepatocellular(190;0.00308)|Myeloproliferative disorder(586;0.0255)|Lung SC(97;0.0262)|Ovarian(437;0.0308)|Medulloblastoma(700;0.211)		Epithelial(90;3.41e-38)|OV - Ovarian serous cystadenocarcinoma(86;3.83e-22)|GBM - Glioblastoma multiforme(42;4.77e-14)|Colorectal(212;1.12e-05)|COAD - Colon adenocarcinoma(227;5.61e-05)|Kidney(185;0.000351)|BRCA - Breast invasive adenocarcinoma(365;0.000688)|KIRC - Kidney renal clear cell carcinoma(229;0.00553)|STAD - Stomach adenocarcinoma(132;0.00645)|Lung(427;0.201)		GGGGCAAAATAGGCTTTTAGC	0.617													18	40	---	---	---	---	PASS
PTCHD2	57540	broad.mit.edu	37	1	11594487	11594487	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-4639-01A-02D-1386-10	TCGA-CJ-4639-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:11594487G>A	uc001ash.3	+	18	3563	c.3425G>A	c.(3424-3426)CGC>CAC	p.R1142H		NM_020780	NP_065831	Q9P2K9	PTHD2_HUMAN	patched domain containing 2	1142	Extracellular (Potential).				cholesterol homeostasis|regulation of lipid transport|smoothened signaling pathway	endoplasmic reticulum|integral to membrane|nuclear membrane	hedgehog receptor activity			skin(3)|ovary(2)|pancreas(1)|breast(1)	7	Ovarian(185;0.249)	Lung NSC(185;4.16e-05)|all_lung(284;4.76e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Hepatocellular(190;0.00913)|Ovarian(437;0.00965)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;3.13e-07)|COAD - Colon adenocarcinoma(227;4.83e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000325)|Kidney(185;0.000877)|KIRC - Kidney renal clear cell carcinoma(229;0.00273)|STAD - Stomach adenocarcinoma(313;0.00766)|READ - Rectum adenocarcinoma(331;0.0549)		GACTACCTGCGCTGGGAGAGC	0.617													37	83	---	---	---	---	PASS
PTCHD2	57540	broad.mit.edu	37	1	11594488	11594488	+	Silent	SNP	C	T	T			TCGA-CJ-4639-01A-02D-1386-10	TCGA-CJ-4639-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:11594488C>T	uc001ash.3	+	18	3564	c.3426C>T	c.(3424-3426)CGC>CGT	p.R1142R		NM_020780	NP_065831	Q9P2K9	PTHD2_HUMAN	patched domain containing 2	1142	Extracellular (Potential).				cholesterol homeostasis|regulation of lipid transport|smoothened signaling pathway	endoplasmic reticulum|integral to membrane|nuclear membrane	hedgehog receptor activity			skin(3)|ovary(2)|pancreas(1)|breast(1)	7	Ovarian(185;0.249)	Lung NSC(185;4.16e-05)|all_lung(284;4.76e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Hepatocellular(190;0.00913)|Ovarian(437;0.00965)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;3.13e-07)|COAD - Colon adenocarcinoma(227;4.83e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000325)|Kidney(185;0.000877)|KIRC - Kidney renal clear cell carcinoma(229;0.00273)|STAD - Stomach adenocarcinoma(313;0.00766)|READ - Rectum adenocarcinoma(331;0.0549)		ACTACCTGCGCTGGGAGAGCT	0.617													38	83	---	---	---	---	PASS
PRAMEF4	400735	broad.mit.edu	37	1	12942186	12942186	+	Missense_Mutation	SNP	T	C	C			TCGA-CJ-4639-01A-02D-1386-10	TCGA-CJ-4639-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:12942186T>C	uc001aun.2	-	3	435	c.364A>G	c.(364-366)ATG>GTG	p.M122V		NM_001009611	NP_001009611	O60810	PRAM4_HUMAN	PRAME family member 4	122										ovary(1)	1	Ovarian(185;0.249)	Lung NSC(185;3.67e-05)|all_lung(284;4.03e-05)|Renal(390;0.000147)|Breast(348;0.000278)|Colorectal(325;0.00058)|Ovarian(437;0.00965)|Hepatocellular(190;0.0245)|Myeloproliferative disorder(586;0.0255)		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)		CCATGGGCCATAGCTTCAGAC	0.488													3	38	---	---	---	---	PASS
CROCCL1	84809	broad.mit.edu	37	1	16972068	16972068	+	5'Flank	SNP	A	G	G	rs1360575	by1000genomes	TCGA-CJ-4639-01A-02D-1386-10	TCGA-CJ-4639-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:16972068A>G	uc001azg.1	-						CROCCL1_uc001azi.1_5'Flank|uc001azj.1_5'Flank|MST1P2_uc009vow.2_5'Flank|MST1P2_uc010ocg.1_5'Flank|MST1P2_uc010och.1_5'Flank|MST1P2_uc010oci.1_5'Flank|MST1P2_uc001azk.2_5'Flank|MST1P2_uc001azl.3_5'Flank|MST1P2_uc009vox.2_5'Flank|MST1P2_uc001azm.3_5'Flank					Homo sapiens mRNA for FLJ00313 protein.												0						GACAGGTTTCACAACTTCCCG	0.627													7	24	---	---	---	---	PASS
MST1P9	11223	broad.mit.edu	37	1	17084968	17084968	+	Missense_Mutation	SNP	G	C	C	rs2761533		TCGA-CJ-4639-01A-02D-1386-10	TCGA-CJ-4639-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:17084968G>C	uc010ock.1	-	11	1507	c.1507C>G	c.(1507-1509)CGG>GGG	p.R503G	CROCC_uc009voy.1_Intron|MST1P9_uc001azp.3_Missense_Mutation_p.R77G	NR_002729				SubName: Full=Hepatocyte growth factor-like protein homolog;												0						CACCGATTCCGCAAGCTGACT	0.617													11	109	---	---	---	---	PASS
UBR4	23352	broad.mit.edu	37	1	19445444	19445444	+	Missense_Mutation	SNP	T	G	G			TCGA-CJ-4639-01A-02D-1386-10	TCGA-CJ-4639-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:19445444T>G	uc001bbi.2	-	71	10467	c.10463A>C	c.(10462-10464)GAG>GCG	p.E3488A	UBR4_uc001bbj.1_5'Flank	NM_020765	NP_065816	Q5T4S7	UBR4_HUMAN	retinoblastoma-associated factor 600	3488					interspecies interaction between organisms	cytoplasm|cytoskeleton|integral to membrane|nucleus	calmodulin binding|ubiquitin-protein ligase activity|zinc ion binding			kidney(10)|ovary(7)|breast(4)|pancreas(2)|skin(2)	25		Colorectal(325;3.46e-05)|Renal(390;0.000147)|all_lung(284;0.000328)|Lung NSC(340;0.000406)|Breast(348;0.000814)|Ovarian(437;0.00774)|Myeloproliferative disorder(586;0.0256)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00674)|BRCA - Breast invasive adenocarcinoma(304;5.43e-05)|Kidney(64;0.000337)|KIRC - Kidney renal clear cell carcinoma(64;0.00426)|STAD - Stomach adenocarcinoma(196;0.00715)|READ - Rectum adenocarcinoma(331;0.0816)		CTGTGAATACTCCTTCAACTG	0.388													60	204	---	---	---	---	PASS
VWA5B1	127731	broad.mit.edu	37	1	20644082	20644082	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-4639-01A-02D-1386-10	TCGA-CJ-4639-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:20644082C>T	uc009vps.2	+	5	819	c.623C>T	c.(622-624)GCG>GTG	p.A208V	VWA5B1_uc001bdd.2_5'UTR|VWA5B1_uc010odc.1_Missense_Mutation_p.A103V	NM_001039500	NP_001034589	Q5TIE3	VW5B1_HUMAN	von Willebrand factor A domain containing 5B1	208						extracellular region					0						TTGTGCCTGGCGACTCTCCTG	0.597													13	152	---	---	---	---	PASS
AK2	204	broad.mit.edu	37	1	33476292	33476292	+	3'UTR	SNP	A	G	G	rs74066439		TCGA-CJ-4639-01A-02D-1386-10	TCGA-CJ-4639-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:33476292A>G	uc001bwo.1	-	7					uc001bwn.2_Intron|AK2_uc010ohq.1_3'UTR|AK2_uc009vud.1_3'UTR	NM_013411	NP_037543	P54819	KAD2_HUMAN	adenylate kinase 2 isoform b						nucleobase, nucleoside and nucleotide interconversion	mitochondrial intermembrane space	adenylate kinase activity|ATP binding				0		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0837)				TGTTGTTCCAAGTATTCCTCT	0.473													17	43	---	---	---	---	PASS
SERBP1	26135	broad.mit.edu	37	1	67889915	67889915	+	Silent	SNP	T	C	C			TCGA-CJ-4639-01A-02D-1386-10	TCGA-CJ-4639-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:67889915T>C	uc001ddv.2	-	5	926	c.786A>G	c.(784-786)GAA>GAG	p.E262E	SERBP1_uc001ddx.2_Silent_p.E256E|SERBP1_uc001ddy.2_Silent_p.E241E|SERBP1_uc001ddw.2_Silent_p.E247E	NM_001018067	NP_001018077	Q8NC51	PAIRB_HUMAN	SERPINE1 mRNA binding protein 1 isoform 1	262					regulation of mRNA stability	nucleus|perinuclear region of cytoplasm	mRNA 3'-UTR binding|protein binding			skin(1)	1						GATGATGTTCTTCACCTTCAG	0.368													5	211	---	---	---	---	PASS
DDAH1	23576	broad.mit.edu	37	1	85824476	85824476	+	Missense_Mutation	SNP	T	C	C			TCGA-CJ-4639-01A-02D-1386-10	TCGA-CJ-4639-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:85824476T>C	uc001dlb.2	-	2	519	c.358A>G	c.(358-360)AAA>GAA	p.K120E	DDAH1_uc001dlc.2_Missense_Mutation_p.K17E|uc001dla.1_Intron|DDAH1_uc010osb.1_Missense_Mutation_p.K20E|DDAH1_uc009wco.2_Missense_Mutation_p.K17E	NM_012137	NP_036269	O94760	DDAH1_HUMAN	dimethylarginine dimethylaminohydrolase 1	120					arginine catabolic process|citrulline metabolic process|nitric oxide mediated signal transduction		dimethylargininase activity|metal ion binding				0				all cancers(265;0.0318)|Epithelial(280;0.0657)	L-Citrulline(DB00155)	TTTTCATCTTTCATCTCTACT	0.289													7	287	---	---	---	---	PASS
TCHHL1	126637	broad.mit.edu	37	1	152059708	152059708	+	Silent	SNP	T	C	C			TCGA-CJ-4639-01A-02D-1386-10	TCGA-CJ-4639-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:152059708T>C	uc001ezo.1	-	3	515	c.450A>G	c.(448-450)GGA>GGG	p.G150G		NM_001008536	NP_001008536	Q5QJ38	TCHL1_HUMAN	trichohyalin-like 1	150							calcium ion binding			ovary(1)|skin(1)	2	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.246)			TTCCAACTGCTCCACTTTCTT	0.468													5	213	---	---	---	---	PASS
OLFML2B	25903	broad.mit.edu	37	1	161967670	161967670	+	Silent	SNP	G	T	T			TCGA-CJ-4639-01A-02D-1386-10	TCGA-CJ-4639-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:161967670G>T	uc001gbu.2	-	6	1843	c.1419C>A	c.(1417-1419)ACC>ACA	p.T473T	OLFML2B_uc010pkq.1_Silent_p.T474T	NM_015441	NP_056256	Q68BL8	OLM2B_HUMAN	olfactomedin-like 2B precursor	473										skin(1)	1	all_hematologic(112;0.156)		BRCA - Breast invasive adenocarcinoma(70;0.0172)			GGCTGGCAGGGGTTGTTCCCC	0.562													7	143	---	---	---	---	PASS
POU2F1	5451	broad.mit.edu	37	1	167365546	167365546	+	Silent	SNP	G	A	A			TCGA-CJ-4639-01A-02D-1386-10	TCGA-CJ-4639-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:167365546G>A	uc001gec.2	+	11	1104	c.942G>A	c.(940-942)GGG>GGA	p.G314G	POU2F1_uc010plg.1_RNA|POU2F1_uc001ged.2_Silent_p.G312G|POU2F1_uc001gee.2_Silent_p.G314G|POU2F1_uc010plh.1_Silent_p.G251G|POU2F1_uc001gef.2_Silent_p.G326G|POU2F1_uc001geg.2_Silent_p.G212G|POU2F1_uc009wvg.1_5'Flank	NM_002697	NP_002688	P14859	PO2F1_HUMAN	POU class 2 homeobox 1	314	POU-specific.				negative regulation of transcription, DNA-dependent|transcription from RNA polymerase III promoter	nucleoplasm	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			central_nervous_system(2)|skin(2)|breast(1)	5						TCGCTATGGGGAAACTATATG	0.448													67	190	---	---	---	---	PASS
TPR	7175	broad.mit.edu	37	1	186282774	186282774	+	3'UTR	SNP	T	C	C			TCGA-CJ-4639-01A-02D-1386-10	TCGA-CJ-4639-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:186282774T>C	uc001grv.2	-	51					PRG4_uc001gru.3_Intron|PRG4_uc001grt.3_Intron|PRG4_uc009wyl.2_Intron|PRG4_uc009wym.2_Intron|PRG4_uc010poo.1_Intron	NM_003292	NP_003283	P12270	TPR_HUMAN	nuclear pore complex-associated protein TPR						carbohydrate metabolic process|glucose transport|mitotic cell cycle spindle assembly checkpoint|mRNA transport|protein import into nucleus|regulation of glucose transport|seryl-tRNA aminoacylation|transmembrane transport|viral reproduction	condensed chromosome kinetochore|cytoplasm|nuclear membrane|nuclear pore|nucleoplasm	ATP binding|protein binding|serine-tRNA ligase activity			ovary(2)|lung(2)|urinary_tract(1)|central_nervous_system(1)|skin(1)	7		Breast(1374;0.000659)|Lung SC(1967;0.0262)|Prostate(1639;0.157)		Colorectal(1306;1.12e-05)|KIRC - Kidney renal clear cell carcinoma(1967;0.00553)		TGGGCATTGTTTTCTTTTTAA	0.274			T	NTRK1	papillary thyroid								3	23	---	---	---	---	PASS
RGS2	5997	broad.mit.edu	37	1	192780679	192780679	+	Missense_Mutation	SNP	G	T	T			TCGA-CJ-4639-01A-02D-1386-10	TCGA-CJ-4639-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:192780679G>T	uc001gsl.2	+	5	622	c.589G>T	c.(589-591)GAC>TAC	p.D197Y		NM_002923	NP_002914	P41220	RGS2_HUMAN	regulator of G-protein signaling 2	197	RGS.				cell cycle|negative regulation of cardiac muscle hypertrophy|negative regulation of G-protein coupled receptor protein signaling pathway|negative regulation of MAP kinase activity|negative regulation of phospholipase activity|positive regulation of cardiac muscle contraction|regulation of adrenergic receptor signaling pathway|regulation of translation|relaxation of cardiac muscle	cytosol|internal side of plasma membrane|mitochondrion|nucleolus	calmodulin binding|GTPase activator activity|signal transducer activity				0						ATTCTACCAGGACTTGTGTAA	0.438													45	102	---	---	---	---	PASS
NUCKS1	64710	broad.mit.edu	37	1	205696856	205696856	+	Missense_Mutation	SNP	G	C	C			TCGA-CJ-4639-01A-02D-1386-10	TCGA-CJ-4639-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:205696856G>C	uc001hdb.2	-	3	405	c.145C>G	c.(145-147)CGA>GGA	p.R49G		NM_022731	NP_073568	Q9H1E3	NUCKS_HUMAN	nuclear casein kinase and cyclin-dependent	49						nucleus					0	Breast(84;0.07)		BRCA - Breast invasive adenocarcinoma(75;0.0194)			TTTCCAGATCGCCTCTTATTT	0.408													60	208	---	---	---	---	PASS
CTSE	1510	broad.mit.edu	37	1	206331351	206331351	+	3'UTR	SNP	C	T	T			TCGA-CJ-4639-01A-02D-1386-10	TCGA-CJ-4639-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:206331351C>T	uc001hdu.2	+	9					CTSE_uc001hdv.2_3'UTR|CTSE_uc010prs.1_3'UTR	NM_001910	NP_001901	P14091	CATE_HUMAN	cathepsin E isoform a preproprotein						antigen processing and presentation of exogenous peptide antigen via MHC class II|digestion|proteolysis	endosome	aspartic-type endopeptidase activity			ovary(1)	1			BRCA - Breast invasive adenocarcinoma(75;0.0754)			cacacacacacatatacacac	0.264													4	28	---	---	---	---	PASS
USH2A	7399	broad.mit.edu	37	1	216019306	216019306	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-4639-01A-02D-1386-10	TCGA-CJ-4639-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:216019306G>A	uc001hku.1	-	45	9302	c.8915C>T	c.(8914-8916)TCT>TTT	p.S2972F		NM_206933	NP_996816	O75445	USH2A_HUMAN	usherin isoform B	2972	Fibronectin type-III 16.|Extracellular (Potential).				maintenance of organ identity|photoreceptor cell maintenance|response to stimulus|sensory perception of sound	basement membrane|cytoplasm|integral to membrane|stereocilium membrane	collagen binding			ovary(20)|upper_aerodigestive_tract(2)|skin(2)|kidney(1)|central_nervous_system(1)	26				OV - Ovarian serous cystadenocarcinoma(81;0.0547)|all cancers(67;0.0875)		GATTTTTAGAGAGTCGTTTGA	0.403										HNSCC(13;0.011)			48	136	---	---	---	---	PASS
RYR2	6262	broad.mit.edu	37	1	237819173	237819173	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-4639-01A-02D-1386-10	TCGA-CJ-4639-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:237819173C>T	uc001hyl.1	+	53	8138	c.8018C>T	c.(8017-8019)GCG>GTG	p.A2673V		NM_001035	NP_001026	Q92736	RYR2_HUMAN	cardiac muscle ryanodine receptor	2673	Modulator (Potential).|Cytoplasmic (By similarity).|4 X approximate repeats.				cardiac muscle contraction|detection of calcium ion|induction of apoptosis by ionic changes|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum|response to caffeine|response to hypoxia|response to redox state	calcium channel complex|cytosol|plasma membrane|plasma membrane enriched fraction|sarcoplasmic reticulum membrane	calcium ion binding|calmodulin binding|identical protein binding|protein kinase A catalytic subunit binding|protein kinase A regulatory subunit binding|receptor activity|ryanodine-sensitive calcium-release channel activity|suramin binding			ovary(17)|large_intestine(6)|central_nervous_system(6)|pancreas(3)|breast(1)	33	Ovarian(103;0.103)	all_cancers(173;0.000368)|Melanoma(53;0.0179)|all_epithelial(177;0.0225)	OV - Ovarian serous cystadenocarcinoma(106;0.00606)			AGTGCAGTTGCGGGAGCTTTG	0.398													5	105	---	---	---	---	PASS
C2orf86	51057	broad.mit.edu	37	2	63401948	63401948	+	Missense_Mutation	SNP	G	C	C			TCGA-CJ-4639-01A-02D-1386-10	TCGA-CJ-4639-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:63401948G>C	uc002sch.2	-	15	2381	c.1935C>G	c.(1933-1935)GAC>GAG	p.D645E	C2orf86_uc002sce.2_RNA|C2orf86_uc002scf.2_Missense_Mutation_p.D486E|C2orf86_uc010ypu.1_RNA|C2orf86_uc002scg.2_Missense_Mutation_p.D453E	NM_015910	NP_056994	O95876	FRITZ_HUMAN	hypothetical protein LOC51057 isoform 2	645					cilium morphogenesis|regulation of embryonic cell shape|regulation of protein localization|septin cytoskeleton organization	cilium axoneme|cytoplasm|cytoskeleton|plasma membrane					0						TATCCCCTCTGTCCAAGGGTC	0.413													63	148	---	---	---	---	PASS
ANKRD20B	729171	broad.mit.edu	37	2	95511171	95511171	+	RNA	SNP	T	C	C			TCGA-CJ-4639-01A-02D-1386-10	TCGA-CJ-4639-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:95511171T>C	uc010fhp.2	-	6		c.653A>G				NR_003366				Homo sapiens ankyrin repeat domain 20B (ANKRD20B), non-coding RNA.												0						CCAAAATTTGTTGTTGAATTC	0.269													5	211	---	---	---	---	PASS
LRP1B	53353	broad.mit.edu	37	2	141128833	141128833	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-4639-01A-02D-1386-10	TCGA-CJ-4639-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:141128833C>T	uc002tvj.1	-	70	11762	c.10790G>A	c.(10789-10791)CGT>CAT	p.R3597H		NM_018557	NP_061027	Q9NZR2	LRP1B_HUMAN	low density lipoprotein-related protein 1B	3597	Extracellular (Potential).|LDL-receptor class A 28.				protein transport|receptor-mediated endocytosis	integral to membrane	calcium ion binding			lung(17)|skin(12)|ovary(12)|pancreas(3)|upper_aerodigestive_tract(2)|central_nervous_system(2)|liver(1)|kidney(1)	50		all_cancers(3;1.1e-60)|all_epithelial(3;1.94e-59)|all_lung(3;1.09e-24)|Lung NSC(3;5.65e-24)|Esophageal squamous(3;5.41e-13)|Renal(3;0.000147)|Breast(3;0.000527)|Hepatocellular(3;0.011)|all_neural(3;0.014)|Colorectal(150;0.101)		UCEC - Uterine corpus endometrioid carcinoma (2;0.00139)|Epithelial(1;1.25e-24)|all cancers(1;8.86e-24)|OV - Ovarian serous cystadenocarcinoma(1;2.45e-12)|LUSC - Lung squamous cell carcinoma(1;2.97e-10)|Lung(1;6.05e-09)|BRCA - Breast invasive adenocarcinoma(221;0.0103)		TATATATTCACGTGATGAGCA	0.284										TSP Lung(27;0.18)			4	35	---	---	---	---	PASS
SSFA2	6744	broad.mit.edu	37	2	182778643	182778643	+	Missense_Mutation	SNP	T	C	C			TCGA-CJ-4639-01A-02D-1386-10	TCGA-CJ-4639-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:182778643T>C	uc002uoi.2	+	10	1880	c.1558T>C	c.(1558-1560)TCC>CCC	p.S520P	SSFA2_uc002uoh.2_Missense_Mutation_p.S520P|SSFA2_uc002uoj.2_Missense_Mutation_p.S520P|SSFA2_uc002uok.2_RNA|SSFA2_uc010zfo.1_Missense_Mutation_p.S367P|SSFA2_uc002uol.2_Missense_Mutation_p.S367P|SSFA2_uc002uom.2_5'Flank	NM_001130445	NP_001123917	P28290	SSFA2_HUMAN	sperm specific antigen 2 isoform 1	520						cytoplasm|plasma membrane	actin binding			breast(1)|central_nervous_system(1)	2			OV - Ovarian serous cystadenocarcinoma(117;0.0856)			AGACTGCCTATCCCTTAATCA	0.323													5	237	---	---	---	---	PASS
DNAH7	56171	broad.mit.edu	37	2	196750888	196750888	+	Nonsense_Mutation	SNP	G	A	A			TCGA-CJ-4639-01A-02D-1386-10	TCGA-CJ-4639-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:196750888G>A	uc002utj.3	-	34	5616	c.5515C>T	c.(5515-5517)CGA>TGA	p.R1839*		NM_018897	NP_061720	Q8WXX0	DYH7_HUMAN	dynein, axonemal, heavy chain 7	1839					ciliary or flagellar motility|microtubule-based movement	axonemal dynein complex|cilium axoneme|cytoplasm|microtubule	ATP binding|microtubule motor activity			skin(10)|ovary(2)	12						TAAGTTTCTCGATCATTTCTC	0.403													58	183	---	---	---	---	PASS
C2orf60	129450	broad.mit.edu	37	2	200797818	200797818	+	Missense_Mutation	SNP	T	C	C			TCGA-CJ-4639-01A-02D-1386-10	TCGA-CJ-4639-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:200797818T>C	uc002uvi.3	-	8	1186	c.920A>G	c.(919-921)GAC>GGC	p.D307G	C2orf60_uc002uvj.3_Missense_Mutation_p.D144G|C2orf60_uc002uvk.3_RNA|C2orf60_uc010fss.2_Missense_Mutation_p.D144G	NM_001039693	NP_001034782	A2RUC4	TYW5_HUMAN	hypothetical protein LOC129450	307					wybutosine biosynthetic process		iron ion binding|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|protein homodimerization activity|tRNA binding				0						GTAGGCTTTGTCTTGAATGTG	0.378													6	220	---	---	---	---	PASS
ATG3	64422	broad.mit.edu	37	3	112267482	112267482	+	Missense_Mutation	SNP	A	G	G			TCGA-CJ-4639-01A-02D-1386-10	TCGA-CJ-4639-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:112267482A>G	uc003dzd.2	-	5	351	c.241T>C	c.(241-243)TGC>CGC	p.C81R	ATG3_uc003dzc.2_Missense_Mutation_p.C81R|ATG3_uc010hqe.2_Missense_Mutation_p.C81R	NM_022488	NP_071933	Q9NT62	ATG3_HUMAN	Apg3p	81					autophagic vacuole assembly|mitochondrial fragmentation involved in apoptosis|protein targeting to membrane|protein ubiquitination	cytoplasmic ubiquitin ligase complex|cytosol	Atg12 ligase activity|Atg8 ligase activity|enzyme binding			ovary(3)	3						CGCTTATAGCACGGCACTATA	0.373													5	195	---	---	---	---	PASS
MCM2	4171	broad.mit.edu	37	3	127337930	127337930	+	Nonsense_Mutation	SNP	G	T	T			TCGA-CJ-4639-01A-02D-1386-10	TCGA-CJ-4639-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:127337930G>T	uc003ejp.2	+	13	2131	c.2074G>T	c.(2074-2076)GAG>TAG	p.E692*	MCM2_uc011bkm.1_Nonsense_Mutation_p.E562*|MCM2_uc010hsl.2_RNA|MCM2_uc011bkn.1_Nonsense_Mutation_p.E645*	NM_004526	NP_004517	P49736	MCM2_HUMAN	minichromosome maintenance complex component 2	692					cell cycle checkpoint|DNA strand elongation involved in DNA replication|DNA-dependent DNA replication initiation|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|S phase of mitotic cell cycle	chromatin|MCM complex	ATP binding|helicase activity|metal ion binding			ovary(3)|skin(1)	4						CAGCAACAAGGAGGAGGAGGG	0.617													8	29	---	---	---	---	PASS
TRIM42	287015	broad.mit.edu	37	3	140401925	140401925	+	Silent	SNP	C	T	T			TCGA-CJ-4639-01A-02D-1386-10	TCGA-CJ-4639-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:140401925C>T	uc003eto.1	+	2	1154	c.963C>T	c.(961-963)CAC>CAT	p.H321H		NM_152616	NP_689829	Q8IWZ5	TRI42_HUMAN	tripartite motif-containing 42	321	B box-type 2.					intracellular	zinc ion binding			lung(2)|skin(2)|upper_aerodigestive_tract(1)|breast(1)|central_nervous_system(1)	7						ACAATGGCCACGACACCATTA	0.552													61	153	---	---	---	---	PASS
GK5	256356	broad.mit.edu	37	3	141904801	141904801	+	Missense_Mutation	SNP	T	C	C			TCGA-CJ-4639-01A-02D-1386-10	TCGA-CJ-4639-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:141904801T>C	uc003euq.1	-	9	917	c.786A>G	c.(784-786)ATA>ATG	p.I262M	GK5_uc003eup.1_5'Flank|GK5_uc010hus.1_RNA	NM_001039547	NP_001034636	Q6ZS86	GLPK5_HUMAN	glycerol kinase 5 (putative)	262					glycerol metabolic process		ATP binding|glycerol kinase activity				0						GCACACCAAATATCTCTTCAT	0.303													5	203	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	3	159819495	159819495	+	Intron	SNP	A	G	G			TCGA-CJ-4639-01A-02D-1386-10	TCGA-CJ-4639-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:159819495A>G	uc003fcw.1	-						uc003fcz.1_RNA					Homo sapiens cDNA FLJ39842 fis, clone SPLEN2014293.																		CGCCTTCAAGAGTCCCAGCAA	0.473													48	154	---	---	---	---	PASS
OTOL1	131149	broad.mit.edu	37	3	161221335	161221335	+	Missense_Mutation	SNP	G	C	C			TCGA-CJ-4639-01A-02D-1386-10	TCGA-CJ-4639-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:161221335G>C	uc011bpb.1	+	4	1039	c.1039G>C	c.(1039-1041)GCT>CCT	p.A347P		NM_001080440	NP_001073909	A6NHN0	OTOL1_HUMAN	otolin-1 precursor	347	C1q.					collagen					0						GGCTTTCAGCGCTGGTTTGTC	0.517													11	43	---	---	---	---	PASS
MUC4	4585	broad.mit.edu	37	3	195509498	195509498	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-4639-01A-02D-1386-10	TCGA-CJ-4639-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:195509498C>T	uc011bto.1	-	3	9029	c.8569G>A	c.(8569-8571)GCA>ACA	p.A2857T	MUC4_uc003fvo.2_Intron|MUC4_uc003fvp.2_Intron|MUC4_uc010hzu.1_Intron	NM_018406	NP_060876	Q99102	MUC4_HUMAN	mucin 4 isoform a	Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment					cell-matrix adhesion	integral to plasma membrane|proteinaceous extracellular matrix	ErbB-2 class receptor binding|extracellular matrix constituent, lubricant activity				0	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		CCTGTGGATGCTGAGGAAGTG	0.572													6	48	---	---	---	---	PASS
PTPN13	5783	broad.mit.edu	37	4	87662970	87662970	+	Splice_Site	SNP	G	T	T			TCGA-CJ-4639-01A-02D-1386-10	TCGA-CJ-4639-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:87662970G>T	uc003hpz.2	+	16	2967	c.2487_splice	c.e16+1	p.S829_splice	PTPN13_uc003hpy.2_Splice_Site_p.S829_splice|PTPN13_uc003hqa.2_Splice_Site_p.S829_splice|PTPN13_uc003hqb.2_Splice_Site_p.S829_splice	NM_080683	NP_542414	Q12923	PTN13_HUMAN	protein tyrosine phosphatase, non-receptor type							cytoplasm|cytoskeleton|plasma membrane	protein binding|protein binding|protein tyrosine phosphatase activity			ovary(4)|breast(1)|kidney(1)	6		Hepatocellular(203;0.114)|all_hematologic(202;0.21)|Acute lymphoblastic leukemia(40;0.242)		OV - Ovarian serous cystadenocarcinoma(123;0.00082)		ATCTTTTTCTGTATGTCCATT	0.373													37	108	---	---	---	---	PASS
HHIP	64399	broad.mit.edu	37	4	145655993	145655993	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-4639-01A-02D-1386-10	TCGA-CJ-4639-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:145655993G>A	uc003ijs.1	+	12	2516	c.1861G>A	c.(1861-1863)GGA>AGA	p.G621R		NM_022475	NP_071920	Q96QV1	HHIP_HUMAN	hedgehog-interacting protein precursor	621	EGF-like 1.					cytoplasm|extracellular region	catalytic activity|protein binding|zinc ion binding			ovary(2)|skin(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)	6	all_hematologic(180;0.151)			GBM - Glioblastoma multiforme(119;0.0185)		CACCCCCACGGGAAAGTGCTG	0.537													28	69	---	---	---	---	PASS
TRIO	7204	broad.mit.edu	37	5	14387923	14387923	+	Missense_Mutation	SNP	A	G	G			TCGA-CJ-4639-01A-02D-1386-10	TCGA-CJ-4639-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:14387923A>G	uc003jff.2	+	23	3854	c.3848A>G	c.(3847-3849)AAT>AGT	p.N1283S	TRIO_uc003jfg.2_RNA|TRIO_uc011cna.1_Missense_Mutation_p.N1234S|TRIO_uc003jfh.1_Missense_Mutation_p.N932S	NM_007118	NP_009049	O75962	TRIO_HUMAN	triple functional domain (PTPRF interacting)	1283					apoptosis|axon guidance|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction|transmembrane receptor protein tyrosine phosphatase signaling pathway	cytosol	ATP binding|protein serine/threonine kinase activity|Rho guanyl-nucleotide exchange factor activity			skin(4)|central_nervous_system(3)|ovary(3)|large_intestine(2)|stomach(2)|breast(2)|upper_aerodigestive_tract(1)|kidney(1)	18	Lung NSC(4;0.000742)					CATGAACTTAATGAAGAGAAG	0.453													6	138	---	---	---	---	PASS
SNX18	112574	broad.mit.edu	37	5	53815390	53815390	+	Silent	SNP	C	T	T			TCGA-CJ-4639-01A-02D-1386-10	TCGA-CJ-4639-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:53815390C>T	uc003jpj.3	+	1	1798	c.1608C>T	c.(1606-1608)ATC>ATT	p.I536I	SNX18_uc011cqg.1_Silent_p.I536I|SNX18_uc003jpi.3_Silent_p.I536I	NM_052870	NP_443102	Q96RF0	SNX18_HUMAN	sorting nexin 18 isoform b	536	BAR.				cell communication|endocytosis|positive regulation of GTPase activity|protein transport	endomembrane system|endosome membrane|extrinsic to internal side of plasma membrane	phosphatidylinositol binding|protein binding				0		Lung NSC(810;3.46e-05)|Breast(144;0.102)				CGGACATCATCCACGTTCAGA	0.552													39	119	---	---	---	---	PASS
ERBB2IP	55914	broad.mit.edu	37	5	65338939	65338939	+	Silent	SNP	T	C	C			TCGA-CJ-4639-01A-02D-1386-10	TCGA-CJ-4639-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:65338939T>C	uc003juk.1	+	16	1649	c.1341T>C	c.(1339-1341)CCT>CCC	p.P447P	ERBB2IP_uc003juh.1_Silent_p.P447P|ERBB2IP_uc003jui.1_Silent_p.P447P|ERBB2IP_uc003juj.1_Silent_p.P447P|ERBB2IP_uc011cqx.1_Silent_p.P447P|ERBB2IP_uc011cqy.1_Silent_p.P447P|ERBB2IP_uc011cqz.1_Intron|ERBB2IP_uc010iwx.1_Silent_p.P447P|ERBB2IP_uc003jul.1_Silent_p.P447P	NM_018695	NP_061165	Q96RT1	LAP2_HUMAN	ERBB2 interacting protein isoform 2	447					basal protein localization|cell adhesion|cell cycle|cell growth|epidermal growth factor receptor signaling pathway|establishment or maintenance of epithelial cell apical/basal polarity|integrin-mediated signaling pathway|intermediate filament cytoskeleton organization	basement membrane|cytoplasm|hemidesmosome|nucleus	ErbB-2 class receptor binding|integrin binding|structural constituent of cytoskeleton			ovary(3)|lung(2)|central_nervous_system(2)	7		Lung NSC(167;9.45e-06)|Prostate(74;0.0139)|Ovarian(174;0.0547)|Breast(144;0.093)|Colorectal(97;0.234)		UCEC - Uterine corpus endometrioid carcinoma (4;0.0767)|Lung(70;0.00191)		GTTTTAACCCTTCATTGTGGG	0.368													5	223	---	---	---	---	PASS
CENPH	64946	broad.mit.edu	37	5	68505612	68505612	+	Missense_Mutation	SNP	G	T	T			TCGA-CJ-4639-01A-02D-1386-10	TCGA-CJ-4639-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:68505612G>T	uc003jvp.2	+	9	817	c.730G>T	c.(730-732)GTT>TTT	p.V244F	CENPH_uc010ixc.2_Missense_Mutation_p.V225F	NM_022909	NP_075060	Q9H3R5	CENPH_HUMAN	centromere protein H	244					cell division|CenH3-containing nucleosome assembly at centromere|chromosome segregation|kinetochore organization|mitotic prometaphase	condensed chromosome kinetochore|cytosol|nucleoplasm	kinetochore binding|protein binding			large_intestine(1)	1		Lung NSC(167;5.51e-05)|Prostate(74;0.00634)|Ovarian(174;0.0448)|Breast(144;0.198)		OV - Ovarian serous cystadenocarcinoma(47;1.41e-56)|Epithelial(20;1.29e-52)|all cancers(19;3.15e-48)|Lung(70;0.0178)		TGAGAAGAATGTTGACATGAT	0.353													84	191	---	---	---	---	PASS
SPOCK1	6695	broad.mit.edu	37	5	136448175	136448175	+	Silent	SNP	C	A	A			TCGA-CJ-4639-01A-02D-1386-10	TCGA-CJ-4639-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:136448175C>A	uc003lbo.2	-	4	614	c.423G>T	c.(421-423)GTG>GTT	p.V141V	SPOCK1_uc003lbp.2_Silent_p.V141V	NM_004598	NP_004589	Q08629	TICN1_HUMAN	sparc/osteonectin, cwcv and kazal-like domains	141	Kazal-like.				cell adhesion|cell proliferation|cellular component movement|nervous system development|signal transduction	proteinaceous extracellular matrix	calcium ion binding			ovary(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)			CTGACTGTGCCACGGGACAGG	0.473													22	169	---	---	---	---	PASS
SLC17A2	10246	broad.mit.edu	37	6	25913557	25913557	+	Silent	SNP	A	C	C			TCGA-CJ-4639-01A-02D-1386-10	TCGA-CJ-4639-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:25913557A>C	uc011dkb.1	-	11	1508	c.1425T>G	c.(1423-1425)CTT>CTG	p.L475L	SLC17A2_uc011dkc.1_3'UTR|SLC17A2_uc003nfl.2_Nonsense_Mutation_p.L426*			O00624	NPT3_HUMAN	SubName: Full=Solute carrier family 17 (Sodium phosphate), member 2, isoform CRA_b; SubName: Full=Putative uncharacterized protein SLC17A2;	Error:Variant_position_missing_in_O00624_after_alignment					phosphate metabolic process	integral to plasma membrane|membrane fraction	sodium:phosphate symporter activity			ovary(1)	1						AGAGGCGGGTAAGGGTCCTCT	0.418													47	139	---	---	---	---	PASS
BTN2A2	10385	broad.mit.edu	37	6	26392525	26392525	+	Intron	SNP	A	G	G			TCGA-CJ-4639-01A-02D-1386-10	TCGA-CJ-4639-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:26392525A>G	uc003nhq.2	+						BTN2A2_uc011dkg.1_3'UTR|BTN2A2_uc003nhr.2_Intron|BTN2A2_uc011dkh.1_Intron|BTN2A2_uc003nhs.2_Intron|BTN2A2_uc003nht.2_Intron|BTN2A2_uc011dki.1_3'UTR	NM_006995	NP_008926	Q8WVV5	BT2A2_HUMAN	butyrophilin, subfamily 2, member A2 isoform a						negative regulation of activated T cell proliferation|negative regulation of cellular metabolic process|negative regulation of cytokine secretion	integral to membrane					0						GCTTTCTGAGACTTCTCTGGG	0.557													3	15	---	---	---	---	PASS
PHIP	55023	broad.mit.edu	37	6	79700608	79700608	+	Missense_Mutation	SNP	T	C	C			TCGA-CJ-4639-01A-02D-1386-10	TCGA-CJ-4639-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:79700608T>C	uc003pir.2	-	20	2522	c.2296A>G	c.(2296-2298)AAT>GAT	p.N766D	PHIP_uc011dyp.1_Missense_Mutation_p.N765D	NM_017934	NP_060404	Q8WWQ0	PHIP_HUMAN	pleckstrin homology domain interacting protein	766					insulin receptor signaling pathway|negative regulation of apoptosis|positive regulation of cell proliferation|positive regulation of insulin-like growth factor receptor signaling pathway|positive regulation of mitosis	nucleus	insulin receptor binding			large_intestine(2)|central_nervous_system(2)|upper_aerodigestive_tract(1)|ovary(1)	6		all_cancers(76;0.00125)|Acute lymphoblastic leukemia(125;1.1e-05)|all_hematologic(105;0.00117)|all_epithelial(107;0.219)		BRCA - Breast invasive adenocarcinoma(397;0.231)		GGTATTTTATTCTCTTTTGGA	0.313													5	163	---	---	---	---	PASS
SFRS18	25957	broad.mit.edu	37	6	99849341	99849341	+	Missense_Mutation	SNP	T	C	C			TCGA-CJ-4639-01A-02D-1386-10	TCGA-CJ-4639-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:99849341T>C	uc003ppo.3	-	12	1721	c.1493A>G	c.(1492-1494)GAG>GGG	p.E498G	SFRS18_uc003ppl.2_Missense_Mutation_p.E44G|SFRS18_uc003ppp.3_Missense_Mutation_p.E498G|SFRS18_uc011eag.1_Missense_Mutation_p.E498G	NM_032870	NP_116259	Q8TF01	PNISR_HUMAN	splicing factor, arginine/serine-rich 130	498						nuclear speck					0		all_cancers(76;1.24e-06)|Acute lymphoblastic leukemia(125;4.99e-11)|all_hematologic(75;5.82e-08)|all_epithelial(107;0.00716)|Colorectal(196;0.0691)|Lung NSC(302;0.186)		BRCA - Breast invasive adenocarcinoma(108;0.0631)		TTCTTTATGCTCTTTTTTTGG	0.284													6	233	---	---	---	---	PASS
PMS2CL	441194	broad.mit.edu	37	7	6785797	6785797	+	RNA	SNP	C	T	T	rs141880038	by1000genomes	TCGA-CJ-4639-01A-02D-1386-10	TCGA-CJ-4639-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:6785797C>T	uc003squ.2	+	11		c.1943C>T			PMS2CL_uc003sqv.1_RNA					Homo sapiens PMS2CL mRNA for PMS2-C terminal -like, complete cds.												0						AGAATGGCTTCGATTTTGTTA	0.229													5	97	---	---	---	---	PASS
STAG3L4	64940	broad.mit.edu	37	7	66774119	66774119	+	Silent	SNP	C	T	T			TCGA-CJ-4639-01A-02D-1386-10	TCGA-CJ-4639-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:66774119C>T	uc003tvt.3	+	3	552	c.285C>T	c.(283-285)ACC>ACT	p.T95T	STAG3L4_uc010laj.2_RNA	NM_022906	NP_075057	Q8TBR4	STG34_HUMAN	stromal antigen 3-like 4	95											0		Lung NSC(55;0.0839)|all_lung(88;0.181)				ACACTAGCACCCTGGCTGGTG	0.488													4	161	---	---	---	---	PASS
SAMD9	54809	broad.mit.edu	37	7	92735318	92735318	+	Silent	SNP	T	C	C			TCGA-CJ-4639-01A-02D-1386-10	TCGA-CJ-4639-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:92735318T>C	uc003umf.2	-	3	349	c.93A>G	c.(91-93)AAA>AAG	p.K31K	SAMD9_uc003umg.2_Silent_p.K31K	NM_017654	NP_060124	Q5K651	SAMD9_HUMAN	sterile alpha motif domain containing 9	31	SAM.					cytoplasm				ovary(3)|skin(2)|breast(1)|central_nervous_system(1)	7	all_cancers(62;5.71e-11)|all_epithelial(64;3.25e-10)|Breast(17;0.000675)|Lung NSC(181;0.0969)|all_lung(186;0.125)		STAD - Stomach adenocarcinoma(171;0.000302)			TTTCCCTGTGTTTTTGGTCAA	0.378													4	85	---	---	---	---	PASS
MUC17	140453	broad.mit.edu	37	7	100696341	100696341	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-4639-01A-02D-1386-10	TCGA-CJ-4639-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:100696341G>A	uc003uxp.1	+	10	13231	c.13178G>A	c.(13177-13179)GGC>GAC	p.G4393D	MUC17_uc010lho.1_RNA	NM_001040105	NP_001035194	Q685J3	MUC17_HUMAN	mucin 17 precursor	4393	Extracellular (Potential).					extracellular region|integral to membrane|plasma membrane	extracellular matrix constituent, lubricant activity			ovary(14)|skin(8)|breast(3)|lung(2)	27	Lung NSC(181;0.136)|all_lung(186;0.182)					CTGGTGTACGGCCTCGTGGGG	0.597													14	133	---	---	---	---	PASS
SLC26A4	5172	broad.mit.edu	37	7	107350574	107350574	+	Missense_Mutation	SNP	T	C	C			TCGA-CJ-4639-01A-02D-1386-10	TCGA-CJ-4639-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:107350574T>C	uc003vep.2	+	19	2389	c.2165T>C	c.(2164-2166)GTC>GCC	p.V722A	SLC26A4_uc011kmb.1_Missense_Mutation_p.V309A|SLC26A4_uc011kmc.1_Missense_Mutation_p.V283A|SLC26A4_uc011kmd.1_Missense_Mutation_p.V291A	NM_000441	NP_000432	O43511	S26A4_HUMAN	pendrin	722	STAS.|Cytoplasmic (Potential).				regulation of pH|regulation of protein localization|sensory perception of sound	apical plasma membrane|integral to membrane	chloride transmembrane transporter activity|inorganic anion exchanger activity|iodide transmembrane transporter activity|secondary active sulfate transmembrane transporter activity			ovary(3)|central_nervous_system(2)|skin(2)	7						TTTTTGACGGTCCATGATGCT	0.368									Pendred_syndrome				6	281	---	---	---	---	PASS
IFRD1	3475	broad.mit.edu	37	7	112098995	112098995	+	Silent	SNP	A	G	G			TCGA-CJ-4639-01A-02D-1386-10	TCGA-CJ-4639-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:112098995A>G	uc003vgh.2	+	6	932	c.489A>G	c.(487-489)GAA>GAG	p.E163E	IFRD1_uc011kmn.1_Silent_p.E113E|IFRD1_uc003vgj.2_Silent_p.E163E|IFRD1_uc011kmo.1_Intron|IFRD1_uc011kmp.1_Silent_p.E113E	NM_001007245	NP_001007246	O00458	IFRD1_HUMAN	interferon-related developmental regulator 1	163					multicellular organismal development|myoblast cell fate determination		binding			kidney(1)|central_nervous_system(1)	2						TTGAAAGTGAAGAGATTTTGA	0.408													6	281	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	7	142498874	142498874	+	RNA	SNP	G	T	T			TCGA-CJ-4639-01A-02D-1386-10	TCGA-CJ-4639-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:142498874G>T	uc011ksh.1	+	3		c.253G>T			uc011ksi.1_RNA|uc003vzw.1_RNA|uc010loj.1_RNA|uc003wad.2_RNA|uc003wag.1_3'UTR|uc003wbe.3_RNA|uc003wbf.3_RNA|uc003wbg.3_RNA|uc003wbh.3_Nonsense_Mutation_p.E97*|uc003wbi.3_RNA|uc003wbj.3_RNA|uc003wbm.3_RNA|uc003wbn.3_RNA|uc010los.2_RNA					Homo sapiens mRNA for T-cell receptor beta chain, partial cds, clone:TCRVB.3.																		GAATGGGAAGGAGGTGCACAG	0.632													20	125	---	---	---	---	PASS
NUB1	51667	broad.mit.edu	37	7	151064852	151064852	+	Intron	SNP	C	T	T			TCGA-CJ-4639-01A-02D-1386-10	TCGA-CJ-4639-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:151064852C>T	uc003wjx.2	+						NUB1_uc003wjw.2_Intron|NUB1_uc010lqc.2_Intron|uc003wjz.1_RNA	NM_016118	NP_057202	Q9Y5A7	NUB1_HUMAN	NEDD8 ultimate buster-1						positive regulation of proteasomal ubiquitin-dependent protein catabolic process|protein ubiquitination|response to interferon-gamma|response to tumor necrosis factor|ubiquitin-dependent protein catabolic process	nucleus	protein binding				0			OV - Ovarian serous cystadenocarcinoma(82;0.00569)	UCEC - Uterine corpus endometrioid carcinoma (81;0.172)		TATCATGTTGCCCCTCTGGAG	0.393											OREG0018452	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	3	43	---	---	---	---	PASS
MFHAS1	9258	broad.mit.edu	37	8	8748320	8748320	+	Missense_Mutation	SNP	T	C	C			TCGA-CJ-4639-01A-02D-1386-10	TCGA-CJ-4639-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:8748320T>C	uc003wsj.1	-	1	2812	c.2249A>G	c.(2248-2250)CAT>CGT	p.H750R		NM_004225	NP_004216	Q9Y4C4	MFHA1_HUMAN	malignant fibrous histiocytoma amplified	750											0		Hepatocellular(245;0.217)		COAD - Colon adenocarcinoma(149;0.124)		GAGCAGCTTATGCAGCAGCAA	0.632													16	53	---	---	---	---	PASS
FAM86B2	653333	broad.mit.edu	37	8	12285132	12285132	+	Intron	SNP	C	G	G			TCGA-CJ-4639-01A-02D-1386-10	TCGA-CJ-4639-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:12285132C>G	uc003wvt.3	-						FAM66D_uc011kxp.1_Intron|uc003wvm.1_Intron|uc011kxs.1_5'Flank|uc003wvp.1_5'Flank|FAM86B2_uc003wvq.3_Intron|FAM86B2_uc003wvr.3_Intron|FAM86B2_uc003wvs.3_Intron|FAM86B2_uc010lsn.2_Intron|FAM86B2_uc003wvu.3_Intron|FAM86B2_uc010lso.2_Intron|FAM86B2_uc011kxt.1_Missense_Mutation_p.C81S|FAM86B2_uc011kxu.1_RNA|FAM86B2_uc010lsl.2_Intron	NM_001137610	NP_001131082	P0C5J1	F86B2_HUMAN	hypothetical protein LOC653333												0						ACAGCTCGGGCACCATGTAGG	0.622													3	7	---	---	---	---	PASS
RBM12B	389677	broad.mit.edu	37	8	94746348	94746348	+	Missense_Mutation	SNP	C	A	A			TCGA-CJ-4639-01A-02D-1386-10	TCGA-CJ-4639-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:94746348C>A	uc003yfz.2	-	3	2484	c.2291G>T	c.(2290-2292)AGG>ATG	p.R764M		NM_203390	NP_976324	Q8IXT5	RB12B_HUMAN	RNA binding motif protein 12B	764							nucleotide binding|RNA binding				0	Breast(36;4.14e-07)		BRCA - Breast invasive adenocarcinoma(8;0.0168)			GGGTGGCCGCCTGAAGTGCTC	0.682													4	14	---	---	---	---	PASS
CSMD3	114788	broad.mit.edu	37	8	113988089	113988089	+	Missense_Mutation	SNP	T	C	C			TCGA-CJ-4639-01A-02D-1386-10	TCGA-CJ-4639-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:113988089T>C	uc003ynu.2	-	7	1478	c.1319A>G	c.(1318-1320)GAG>GGG	p.E440G	CSMD3_uc003ynt.2_Missense_Mutation_p.E400G|CSMD3_uc011lhx.1_Intron	NM_198123	NP_937756	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3 isoform 1	440	Extracellular (Potential).					integral to membrane|plasma membrane				ovary(21)|lung(11)|skin(11)|kidney(8)|large_intestine(6)|upper_aerodigestive_tract(2)|central_nervous_system(2)|urinary_tract(1)|breast(1)	63						AACTGCAAGCTCTTTAGTTCT	0.408										HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)			6	391	---	---	---	---	PASS
GRINA	2907	broad.mit.edu	37	8	145065887	145065887	+	Missense_Mutation	SNP	A	G	G			TCGA-CJ-4639-01A-02D-1386-10	TCGA-CJ-4639-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:145065887A>G	uc003zan.1	+	3	573	c.407A>G	c.(406-408)GAG>GGG	p.E136G	GRINA_uc003zao.1_Missense_Mutation_p.E136G|GRINA_uc003zap.1_Missense_Mutation_p.E136G	NM_001009184	NP_001009184	Q7Z429	GRINA_HUMAN	glutamate receptor, ionotropic, N-methyl	136	Pro-rich.					integral to membrane				central_nervous_system(1)	1	all_cancers(97;8.2e-11)|all_epithelial(106;1.1e-09)|Lung NSC(106;5.89e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;1.31e-40)|Epithelial(56;1.16e-39)|all cancers(56;6.43e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.105)			TACCAGGAGGAGGGTCCCCCA	0.627													4	66	---	---	---	---	PASS
ZNF484	83744	broad.mit.edu	37	9	95608762	95608762	+	Silent	SNP	A	G	G			TCGA-CJ-4639-01A-02D-1386-10	TCGA-CJ-4639-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:95608762A>G	uc004asu.1	-	5	2456	c.2307T>C	c.(2305-2307)ATT>ATC	p.I769I	ANKRD19_uc004asr.3_Intron|ZNF484_uc011lub.1_Silent_p.I771I|ZNF484_uc010mrb.1_Silent_p.I733I|ZNF484_uc004asv.1_Silent_p.I733I	NM_031486	NP_113674	Q5JVG2	ZN484_HUMAN	zinc finger protein 484 isoform a	769	C2H2-type 18.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0						CTCCTGTGTGAATTCGATGAT	0.383													5	209	---	---	---	---	PASS
GOLGA1	2800	broad.mit.edu	37	9	127693673	127693673	+	Missense_Mutation	SNP	T	C	C			TCGA-CJ-4639-01A-02D-1386-10	TCGA-CJ-4639-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:127693673T>C	uc004bpc.2	-	4	490	c.148A>G	c.(148-150)AGC>GGC	p.S50G	GOLGA1_uc010mwt.1_Missense_Mutation_p.S50G	NM_002077	NP_002068	Q92805	GOGA1_HUMAN	golgin 97	50	Potential.					Golgi cisterna membrane				ovary(1)	1						CTGGAGCTGCTTCCATCGGAA	0.423													5	160	---	---	---	---	PASS
TUBBP5	643224	broad.mit.edu	37	9	141070687	141070687	+	Silent	SNP	C	T	T			TCGA-CJ-4639-01A-02D-1386-10	TCGA-CJ-4639-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:141070687C>T	uc004com.2	+	4	351	c.90C>T	c.(88-90)GCC>GCT	p.A30A	TUBBP5_uc010ncq.2_Nonsense_Mutation_p.Q208*					RecName: Full=Putative tubulin beta-4q chain;												0						ACAACTGGGCCAAGGGACGCT	0.577													3	9	---	---	---	---	PASS
PFKFB3	5209	broad.mit.edu	37	10	6257233	6257233	+	Silent	SNP	C	T	T			TCGA-CJ-4639-01A-02D-1386-10	TCGA-CJ-4639-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:6257233C>T	uc001ije.2	+	3	636	c.252C>T	c.(250-252)TCC>TCT	p.S84S	PFKFB3_uc001ijd.2_Silent_p.S64S|PFKFB3_uc009xii.2_RNA|PFKFB3_uc010qaw.1_Silent_p.S98S|PFKFB3_uc001ijf.2_Silent_p.S84S	NM_004566	NP_004557	Q16875	F263_HUMAN	6-phosphofructo-2-kinase/fructose-2,	84	6-phosphofructo-2-kinase.				fructose 2,6-bisphosphate metabolic process|glycolysis	cytosol	6-phosphofructo-2-kinase activity|ATP binding|fructose-2,6-bisphosphate 2-phosphatase activity|identical protein binding			ovary(2)|central_nervous_system(1)	3						AGTACAGCTCCTACAACTTCT	0.423													22	34	---	---	---	---	PASS
BEND7	222389	broad.mit.edu	37	10	13483882	13483882	+	Intron	SNP	G	A	A			TCGA-CJ-4639-01A-02D-1386-10	TCGA-CJ-4639-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:13483882G>A	uc001imm.2	-						BEND7_uc001iml.2_Intron|BEND7_uc001imn.2_3'UTR|BEND7_uc001imo.3_Intron	NM_152751	NP_689964	Q8N7W2	BEND7_HUMAN	BEN domain containing 7 isoform 1								protein binding			ovary(1)|breast(1)	2						AGAAGAAAAAGAAGCCACACA	0.403													5	24	---	---	---	---	PASS
ALDH18A1	5832	broad.mit.edu	37	10	97366442	97366442	+	3'UTR	SNP	G	C	C			TCGA-CJ-4639-01A-02D-1386-10	TCGA-CJ-4639-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:97366442G>C	uc001kkz.2	-	18					ALDH18A1_uc001kky.2_3'UTR|ALDH18A1_uc010qog.1_3'UTR|ALDH18A1_uc010qoh.1_3'UTR	NM_002860	NP_002851	P54886	P5CS_HUMAN	pyrroline-5-carboxylate synthetase isoform 1						proline biosynthetic process	mitochondrial inner membrane	ATP binding|glutamate 5-kinase activity|glutamate-5-semialdehyde dehydrogenase activity			pancreas(1)|central_nervous_system(1)|skin(1)	3		Colorectal(252;0.0402)		Epithelial(162;9.1e-07)|all cancers(201;2.55e-05)	L-Glutamic Acid(DB00142)	TGGGAGACAAGAGCGGGCTCT	0.493													7	15	---	---	---	---	PASS
CCNJ	54619	broad.mit.edu	37	10	97817942	97817942	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-4639-01A-02D-1386-10	TCGA-CJ-4639-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:97817942C>T	uc001klm.2	+	6	1422	c.1063C>T	c.(1063-1065)CGG>TGG	p.R355W	uc001klg.1_Intron|uc001klj.1_Intron|uc009xvb.1_Intron|CCNJ_uc010qoq.1_Missense_Mutation_p.R366W|CCNJ_uc001kln.2_Missense_Mutation_p.R354W	NM_019084	NP_061957	Q5T5M9	CCNJ_HUMAN	cyclin J isoform 2	355						nucleus				ovary(1)	1				Epithelial(162;6.1e-08)|all cancers(201;2.32e-06)		TTCTTACAACCGGAGTTATCA	0.438													4	183	---	---	---	---	PASS
SEMA4G	57715	broad.mit.edu	37	10	102740600	102740600	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-4639-01A-02D-1386-10	TCGA-CJ-4639-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:102740600C>T	uc010qpt.1	+	13	1932	c.1489C>T	c.(1489-1491)CCT>TCT	p.P497S	SEMA4G_uc001krv.2_RNA|SEMA4G_uc001krw.1_Missense_Mutation_p.P497S|SEMA4G_uc001krx.2_Missense_Mutation_p.P497S|MRPL43_uc001kry.1_Intron|MRPL43_uc010qpu.1_Intron	NM_017893	NP_060363	Q9NTN9	SEM4G_HUMAN	semaphorin 4G	497	Extracellular (Potential).|Sema.				cell differentiation|nervous system development	integral to membrane	receptor activity			breast(1)	1		Colorectal(252;0.234)		Epithelial(162;3.71e-09)|all cancers(201;2.1e-07)		TGTGGGGGCTCCTAGCGGAGT	0.617													11	34	---	---	---	---	PASS
MKI67	4288	broad.mit.edu	37	10	129907513	129907513	+	Missense_Mutation	SNP	T	C	C			TCGA-CJ-4639-01A-02D-1386-10	TCGA-CJ-4639-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:129907513T>C	uc001lke.2	-	13	2786	c.2591A>G	c.(2590-2592)GAG>GGG	p.E864G	MKI67_uc001lkf.2_Missense_Mutation_p.E504G|MKI67_uc009yav.1_Missense_Mutation_p.E439G|MKI67_uc009yaw.1_Missense_Mutation_p.E14G	NM_002417	NP_002408	P46013	KI67_HUMAN	antigen identified by monoclonal antibody Ki-67	864					cell proliferation	nucleolus	ATP binding|protein C-terminus binding			ovary(4)|central_nervous_system(2)|skin(1)	7		all_epithelial(44;2.12e-05)|all_lung(145;0.00679)|Lung NSC(174;0.00998)|all_neural(114;0.0936)|Colorectal(57;0.14)|Breast(234;0.166)|Melanoma(40;0.203)				TTTTGAAGGCTCTGTCTCAGT	0.413													6	402	---	---	---	---	PASS
ARFIP2	23647	broad.mit.edu	37	11	6499971	6499971	+	Silent	SNP	A	T	T			TCGA-CJ-4639-01A-02D-1386-10	TCGA-CJ-4639-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:6499971A>T	uc001mdk.2	-	5	671	c.534T>A	c.(532-534)CTT>CTA	p.L178L	ARFIP2_uc001mdl.2_Silent_p.L178L|ARFIP2_uc010ral.1_Silent_p.L140L|ARFIP2_uc010ram.1_Silent_p.L84L|ARFIP2_uc010ran.1_Silent_p.L211L|ARFIP2_uc001mdm.2_Intron|FXC1_uc001mdn.3_5'Flank|FXC1_uc001mdo.3_5'Flank	NM_012402	NP_036534	P53365	ARFP2_HUMAN	ADP-ribosylation factor interacting protein 2	178	AH.				actin cytoskeleton organization|cellular component movement|lamellipodium assembly|ruffle organization|small GTPase mediated signal transduction	cell cortex|plasma membrane|ruffle	GTP binding|GTP-dependent protein binding|Rac GTPase binding				0		Medulloblastoma(188;0.00263)|all_neural(188;0.026)|Breast(177;0.029)		Epithelial(150;3.41e-08)|BRCA - Breast invasive adenocarcinoma(625;0.189)		GAGGCACCTGAAGCTCTGGGG	0.637													14	23	---	---	---	---	PASS
USP47	55031	broad.mit.edu	37	11	11964488	11964488	+	Missense_Mutation	SNP	A	G	G			TCGA-CJ-4639-01A-02D-1386-10	TCGA-CJ-4639-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:11964488A>G	uc001mjq.1	+	21	3743	c.2980A>G	c.(2980-2982)AGA>GGA	p.R994G	USP47_uc001mjr.2_Missense_Mutation_p.R906G|USP47_uc001mjs.2_Missense_Mutation_p.R974G|USP47_uc001mjt.1_Missense_Mutation_p.R280G	NM_017944	NP_060414	Q96K76	UBP47_HUMAN	ubiquitin specific protease 47	994					base-excision repair|cellular response to UV|monoubiquitinated protein deubiquitination|negative regulation of apoptosis|negative regulation of caspase activity|negative regulation of G2/M transition of mitotic cell cycle|negative regulation of transcription, DNA-dependent|positive regulation of cell growth|response to drug|ubiquitin-dependent protein catabolic process	cytoplasm|SCF ubiquitin ligase complex	ubiquitin thiolesterase activity|ubiquitin-specific protease activity|WD40-repeat domain binding			ovary(1)|skin(1)	2				Epithelial(150;0.000339)		CACAAGTAGTAGAAGAACGAA	0.418													4	192	---	---	---	---	PASS
KIAA1731	85459	broad.mit.edu	37	11	93432025	93432025	+	Missense_Mutation	SNP	T	A	A			TCGA-CJ-4639-01A-02D-1386-10	TCGA-CJ-4639-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:93432025T>A	uc009ywb.1	+	15	4098	c.3947T>A	c.(3946-3948)TTT>TAT	p.F1316Y	KIAA1731_uc001pdu.1_Intron	NM_033395	NP_203753	Q9C0D2	K1731_HUMAN	hypothetical protein LOC85459	1316						centrosome					0		Acute lymphoblastic leukemia(157;2.31e-05)|all_hematologic(158;0.00824)				GAACCTCTTTTTACAGAGAGT	0.413													27	86	---	---	---	---	PASS
KIAA1731	85459	broad.mit.edu	37	11	93461850	93461850	+	Missense_Mutation	SNP	A	G	G			TCGA-CJ-4639-01A-02D-1386-10	TCGA-CJ-4639-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:93461850A>G	uc009ywb.1	+	25	7316	c.7165A>G	c.(7165-7167)ACA>GCA	p.T2389A	KIAA1731_uc001pdu.1_Missense_Mutation_p.T569A|KIAA1731_uc001pdw.1_Missense_Mutation_p.T401A|KIAA1731_uc001pdx.1_Missense_Mutation_p.T255A	NM_033395	NP_203753	Q9C0D2	K1731_HUMAN	hypothetical protein LOC85459	2389						centrosome					0		Acute lymphoblastic leukemia(157;2.31e-05)|all_hematologic(158;0.00824)				TTCACAGGAAACAGAAACTGG	0.328													5	184	---	---	---	---	PASS
ATM	472	broad.mit.edu	37	11	108106450	108106450	+	Nonsense_Mutation	SNP	A	T	T			TCGA-CJ-4639-01A-02D-1386-10	TCGA-CJ-4639-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:108106450A>T	uc001pkb.1	+	5	770	c.385A>T	c.(385-387)AAA>TAA	p.K129*	ATM_uc009yxr.1_Nonsense_Mutation_p.K129*	NM_000051	NP_000042	Q13315	ATM_HUMAN	ataxia telangiectasia mutated isoform 1	129					cell cycle arrest|cellular response to gamma radiation|DNA damage induced protein phosphorylation|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|double-strand break repair via homologous recombination|G2/M transition DNA damage checkpoint|histone mRNA catabolic process|mitotic cell cycle spindle assembly checkpoint|negative regulation of B cell proliferation|peptidyl-serine phosphorylation|positive regulation of DNA damage response, signal transduction by p53 class mediator|pre-B cell allelic exclusion|protein autophosphorylation|reciprocal meiotic recombination|replicative senescence	cytoplasmic membrane-bounded vesicle|nucleoplasm	1-phosphatidylinositol-3-kinase activity|ATP binding|DNA binding|DNA-dependent protein kinase activity|identical protein binding|protein complex binding|protein dimerization activity|protein N-terminus binding			haematopoietic_and_lymphoid_tissue(174)|lung(25)|breast(15)|large_intestine(9)|ovary(5)|kidney(5)|central_nervous_system(4)|upper_aerodigestive_tract(1)|stomach(1)|NS(1)	240		all_cancers(61;9.64e-12)|all_epithelial(67;9.97e-08)|Melanoma(852;2.55e-06)|Acute lymphoblastic leukemia(157;3.95e-05)|all_hematologic(158;0.00014)|Breast(348;0.0258)|all_neural(303;0.072)		Epithelial(105;9.05e-06)|BRCA - Breast invasive adenocarcinoma(274;1.06e-05)|all cancers(92;0.000208)|Colorectal(284;0.116)|OV - Ovarian serous cystadenocarcinoma(223;0.147)		GGATACAGTGAAAGATTCATC	0.308			D|Mis|N|F|S		T-PLL	leukemia|lymphoma|medulloblastoma|glioma		Genes_defective_in_diseases_associated_with_sensitivity_to_DNA_damaging_agents	Ataxia_Telangiectasia	TSP Lung(14;0.12)			34	274	---	---	---	---	PASS
ATM	472	broad.mit.edu	37	11	108216609	108216609	+	Missense_Mutation	SNP	C	G	G	rs141534716		TCGA-CJ-4639-01A-02D-1386-10	TCGA-CJ-4639-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:108216609C>G	uc001pkb.1	+	58	8943	c.8558C>G	c.(8557-8559)ACG>AGG	p.T2853R	ATM_uc009yxr.1_Missense_Mutation_p.T2853R|C11orf65_uc010rvx.1_Intron|C11orf65_uc009yxu.1_Intron|ATM_uc001pke.1_Missense_Mutation_p.T1505R	NM_000051	NP_000042	Q13315	ATM_HUMAN	ataxia telangiectasia mutated isoform 1	2853	PI3K/PI4K.				cell cycle arrest|cellular response to gamma radiation|DNA damage induced protein phosphorylation|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|double-strand break repair via homologous recombination|G2/M transition DNA damage checkpoint|histone mRNA catabolic process|mitotic cell cycle spindle assembly checkpoint|negative regulation of B cell proliferation|peptidyl-serine phosphorylation|positive regulation of DNA damage response, signal transduction by p53 class mediator|pre-B cell allelic exclusion|protein autophosphorylation|reciprocal meiotic recombination|replicative senescence	cytoplasmic membrane-bounded vesicle|nucleoplasm	1-phosphatidylinositol-3-kinase activity|ATP binding|DNA binding|DNA-dependent protein kinase activity|identical protein binding|protein complex binding|protein dimerization activity|protein N-terminus binding			haematopoietic_and_lymphoid_tissue(174)|lung(25)|breast(15)|large_intestine(9)|ovary(5)|kidney(5)|central_nervous_system(4)|upper_aerodigestive_tract(1)|stomach(1)|NS(1)	240		all_cancers(61;9.64e-12)|all_epithelial(67;9.97e-08)|Melanoma(852;2.55e-06)|Acute lymphoblastic leukemia(157;3.95e-05)|all_hematologic(158;0.00014)|Breast(348;0.0258)|all_neural(303;0.072)		Epithelial(105;9.05e-06)|BRCA - Breast invasive adenocarcinoma(274;1.06e-05)|all cancers(92;0.000208)|Colorectal(284;0.116)|OV - Ovarian serous cystadenocarcinoma(223;0.147)		TTGGCTTATACGCGCAGTGTA	0.368			D|Mis|N|F|S		T-PLL	leukemia|lymphoma|medulloblastoma|glioma		Genes_defective_in_diseases_associated_with_sensitivity_to_DNA_damaging_agents	Ataxia_Telangiectasia	TSP Lung(14;0.12)			39	233	---	---	---	---	PASS
TMPRSS13	84000	broad.mit.edu	37	11	117774795	117774795	+	Missense_Mutation	SNP	C	G	G			TCGA-CJ-4639-01A-02D-1386-10	TCGA-CJ-4639-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:117774795C>G	uc001prs.1	-	11	1496	c.1403G>C	c.(1402-1404)CGG>CCG	p.R468P	TMPRSS13_uc009yzr.1_Missense_Mutation_p.R147P|TMPRSS13_uc001prt.1_Missense_Mutation_p.R147P	NM_001077263	NP_001070731	Q9BYE2	TMPSD_HUMAN	transmembrane protease, serine 13	463	Extracellular (Potential).|Peptidase S1.				proteolysis	integral to membrane	scavenger receptor activity|serine-type endopeptidase activity			pancreas(1)	1	all_hematologic(175;0.0487)	Medulloblastoma(222;0.0425)|all_hematologic(192;0.196)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;1.78e-05)|Epithelial(105;0.00106)		CTGCACCTCCCGGAGGAAGGG	0.527													30	89	---	---	---	---	PASS
PRDM10	56980	broad.mit.edu	37	11	129830865	129830865	+	5'UTR	SNP	C	G	G			TCGA-CJ-4639-01A-02D-1386-10	TCGA-CJ-4639-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:129830865C>G	uc001qfm.2	-	2					PRDM10_uc001qfn.2_5'UTR|PRDM10_uc009zct.1_5'UTR	NM_020228	NP_064613	Q9NQV6	PRD10_HUMAN	PR domain containing 10 isoform 1						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			pancreas(1)	1	all_hematologic(175;0.0537)	Breast(109;0.000496)|Lung NSC(97;0.000693)|all_lung(97;0.00151)|Medulloblastoma(222;0.0425)|all_neural(223;0.0837)		OV - Ovarian serous cystadenocarcinoma(99;0.0174)|Lung(977;0.176)|LUSC - Lung squamous cell carcinoma(976;0.185)		TCCATCTTCTCCCAACTGGAC	0.527													40	96	---	---	---	---	PASS
SLC38A4	55089	broad.mit.edu	37	12	47186806	47186806	+	Missense_Mutation	SNP	T	C	C			TCGA-CJ-4639-01A-02D-1386-10	TCGA-CJ-4639-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:47186806T>C	uc001rpi.2	-	3	448	c.49A>G	c.(49-51)AGC>GGC	p.S17G	SLC38A4_uc001rpj.2_Missense_Mutation_p.S17G|SLC38A4_uc009zkl.2_Missense_Mutation_p.S17G	NM_018018	NP_060488	Q969I6	S38A4_HUMAN	solute carrier family 38, member 4	17	Cytoplasmic (Potential).				cellular nitrogen compound metabolic process|sodium ion transport	integral to membrane|plasma membrane	amino acid transmembrane transporter activity|symporter activity			ovary(2)|central_nervous_system(1)|skin(1)	4	Lung SC(27;0.192)|Renal(347;0.236)					CCACTGCTGCTCTCATCATCT	0.443													6	382	---	---	---	---	PASS
VDR	7421	broad.mit.edu	37	12	48272814	48272814	+	Missense_Mutation	SNP	C	G	G			TCGA-CJ-4639-01A-02D-1386-10	TCGA-CJ-4639-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:48272814C>G	uc001rqm.2	-	4	365	c.83G>C	c.(82-84)GGA>GCA	p.G28A	VDR_uc001rql.2_Missense_Mutation_p.G78A|VDR_uc001rqn.2_Missense_Mutation_p.G28A|VDR_uc010slq.1_5'UTR	NM_001017535	NP_001017535	P11473	VDR_HUMAN	vitamin D (1,25-dihydroxyvitamin D3) receptor	28	Nuclear receptor.|NR C4-type.				decidualization|negative regulation of cell proliferation|negative regulation of transcription from RNA polymerase II promoter|positive regulation of vitamin D 24-hydroxylase activity|regulation of calcidiol 1-monooxygenase activity|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor	nucleoplasm	retinoid X receptor binding|sequence-specific DNA binding transcription factor activity|steroid hormone receptor activity|vitamin D3 receptor activity|zinc ion binding			ovary(1)|central_nervous_system(1)|skin(1)	3		Acute lymphoblastic leukemia(13;0.109)|all_hematologic(14;0.214)		GBM - Glioblastoma multiforme(48;0.17)	Calcidiol(DB00146)|Calcipotriol(DB02300)|Calcitriol(DB00136)|Dihydrotachysterol(DB01070)|Ergocalciferol(DB00153)|Paricalcitol(DB00910)	GGCTCGGTCTCCACACACCCC	0.592													19	52	---	---	---	---	PASS
FIGNL2	401720	broad.mit.edu	37	12	52216199	52216199	+	5'UTR	SNP	T	G	G			TCGA-CJ-4639-01A-02D-1386-10	TCGA-CJ-4639-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:52216199T>G	uc001rzc.2	-	1						NM_001013690	NP_001013712	A6NMB9	FIGL2_HUMAN	fidgetin-like 2								ATP binding|nucleoside-triphosphatase activity				0				BRCA - Breast invasive adenocarcinoma(357;0.135)		CCAGTGCATCTTCAACAGAGC	0.642													16	46	---	---	---	---	PASS
HNRNPA1	3178	broad.mit.edu	37	12	54674577	54674577	+	5'UTR	SNP	C	G	G			TCGA-CJ-4639-01A-02D-1386-10	TCGA-CJ-4639-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:54674577C>G	uc001sfl.2	+	1					CBX5_uc001sfk.3_5'Flank|CBX5_uc001sfi.3_5'Flank|HNRNPA1_uc001sfm.2_5'UTR|HNRNPA1_uc009zng.2_5'UTR|HNRNPA1_uc009znh.2_5'UTR|HNRNPA1_uc009zni.2_5'UTR|HNRNPA1_uc001sfn.2_5'UTR|HNRNPA1_uc001sfo.3_RNA|HNRNPA1_uc001sfp.1_5'UTR|HNRNPA1_uc009znj.1_5'Flank	NM_031157	NP_112420	P09651	ROA1_HUMAN	heterogeneous nuclear ribonucleoprotein A1						interspecies interaction between organisms|mRNA transport|nuclear import	catalytic step 2 spliceosome|cytoplasm|heterogeneous nuclear ribonucleoprotein complex|nucleolus|nucleoplasm	nucleotide binding|protein binding|single-stranded DNA binding			skin(2)|ovary(1)	3						TAAAGTCTCTCTTCACCCTGC	0.527													5	333	---	---	---	---	PASS
BAZ2A	11176	broad.mit.edu	37	12	57000469	57000469	+	Missense_Mutation	SNP	T	C	C			TCGA-CJ-4639-01A-02D-1386-10	TCGA-CJ-4639-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:57000469T>C	uc001slq.1	-	11	2341	c.2147A>G	c.(2146-2148)AAG>AGG	p.K716R	BAZ2A_uc001slp.1_Missense_Mutation_p.K714R|BAZ2A_uc009zov.1_5'Flank|BAZ2A_uc009zow.1_Missense_Mutation_p.K684R	NM_013449	NP_038477	Q9UIF9	BAZ2A_HUMAN	bromodomain adjacent to zinc finger domain, 2A	716	Lys-rich.|Potential.				chromatin silencing at rDNA|DNA methylation|transcription, DNA-dependent	chromatin silencing complex|nucleolus|rDNA heterochromatin	DNA binding|histone acetyl-lysine binding|ligand-dependent nuclear receptor binding|RNA binding|zinc ion binding				0						CTGCCTCATCTTCTTCTTGCT	0.428													6	483	---	---	---	---	PASS
GLTP	51228	broad.mit.edu	37	12	110318107	110318107	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-4639-01A-02D-1386-10	TCGA-CJ-4639-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:110318107C>T	uc001tpm.2	-	1	187	c.73G>A	c.(73-75)GAG>AAG	p.E25K	GLTP_uc010sxt.1_RNA	NM_016433	NP_057517	Q9NZD2	GLTP_HUMAN	glycolipid transfer protein	25						cytoplasm	glycolipid binding|glycolipid transporter activity				0		Lung NSC(355;2.38e-06)|Breast(359;0.00354)|Myeloproliferative disorder(1001;0.0122)		BRCA - Breast invasive adenocarcinoma(302;0.0025)		GACACCGCCTCGAGGAAGGGC	0.687													3	50	---	---	---	---	PASS
MMP17	4326	broad.mit.edu	37	12	132329961	132329961	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-4639-01A-02D-1386-10	TCGA-CJ-4639-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:132329961C>T	uc001ujc.1	+	8	1270	c.1171C>T	c.(1171-1173)CGC>TGC	p.R391C	MMP17_uc001ujd.1_Missense_Mutation_p.R307C	NM_016155	NP_057239	Q9ULZ9	MMP17_HUMAN	matrix metalloproteinase 17 preproprotein	391	Hemopexin-like 2.				proteolysis	anchored to membrane|integral to plasma membrane|proteinaceous extracellular matrix	calcium ion binding|enzyme activator activity|metalloendopeptidase activity|zinc ion binding				0	all_neural(191;0.0982)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;1.82e-07)|Epithelial(86;1.51e-06)|all cancers(50;2.35e-05)		CGTGTACGAGCGCACCAGCGA	0.692													6	10	---	---	---	---	PASS
EP400NL	347918	broad.mit.edu	37	12	132611059	132611059	+	RNA	SNP	G	C	C			TCGA-CJ-4639-01A-02D-1386-10	TCGA-CJ-4639-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:132611059G>C	uc001ujx.1	+	7		c.1965G>C								Homo sapiens cDNA FLJ33915 fis, clone CTONG2016658.												0						TTGGCAAAGAGTACAAGGAGG	0.448													21	91	---	---	---	---	PASS
EBPL	84650	broad.mit.edu	37	13	50235138	50235138	+	Missense_Mutation	SNP	T	G	G			TCGA-CJ-4639-01A-02D-1386-10	TCGA-CJ-4639-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:50235138T>G	uc001vdg.2	-	4	650	c.587A>C	c.(586-588)CAG>CCG	p.Q196P	EBPL_uc001vdh.2_RNA|EBPL_uc001vdi.2_3'UTR	NM_032565	NP_115954	Q9BY08	EBPL_HUMAN	emopamil binding related protein, delta8-delta7	196					sterol metabolic process	endoplasmic reticulum membrane|integral to membrane	cholestenol delta-isomerase activity				0		Lung NSC(96;0.000468)|Breast(56;0.0011)|Prostate(109;0.00243)|Hepatocellular(98;0.0556)|Glioma(44;0.236)		GBM - Glioblastoma multiforme(99;2.06e-09)		GGTTTCTTTCTGATGCATTTT	0.383													6	172	---	---	---	---	PASS
EBPL	84650	broad.mit.edu	37	13	50235160	50235160	+	Missense_Mutation	SNP	G	C	C			TCGA-CJ-4639-01A-02D-1386-10	TCGA-CJ-4639-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:50235160G>C	uc001vdg.2	-	4	628	c.565C>G	c.(565-567)CTA>GTA	p.L189V	EBPL_uc001vdh.2_RNA|EBPL_uc001vdi.2_3'UTR	NM_032565	NP_115954	Q9BY08	EBPL_HUMAN	emopamil binding related protein, delta8-delta7	189					sterol metabolic process	endoplasmic reticulum membrane|integral to membrane	cholestenol delta-isomerase activity				0		Lung NSC(96;0.000468)|Breast(56;0.0011)|Prostate(109;0.00243)|Hepatocellular(98;0.0556)|Glioma(44;0.236)		GBM - Glioblastoma multiforme(99;2.06e-09)		TTGAGTTCTAGCCATGACTGC	0.418													7	173	---	---	---	---	PASS
PRMT5	10419	broad.mit.edu	37	14	23395374	23395374	+	Missense_Mutation	SNP	T	C	C			TCGA-CJ-4639-01A-02D-1386-10	TCGA-CJ-4639-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:23395374T>C	uc001whm.1	-	7	836	c.745A>G	c.(745-747)ATG>GTG	p.M249V	PRMT5_uc001whl.1_Missense_Mutation_p.M232V|PRMT5_uc010akd.1_RNA|PRMT5_uc010tnf.1_Missense_Mutation_p.M143V|PRMT5_uc010tng.1_Missense_Mutation_p.M188V|PRMT5_uc010tnh.1_Missense_Mutation_p.M205V|PRMT5_uc001whn.1_Intron	NM_006109	NP_006100	O14744	ANM5_HUMAN	protein arginine methyltransferase 5 isoform a	249					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)		CTCTGGTGCATCTTAGAAAGA	0.478													6	214	---	---	---	---	PASS
ZFP106	64397	broad.mit.edu	37	15	42744055	42744055	+	Missense_Mutation	SNP	T	A	A			TCGA-CJ-4639-01A-02D-1386-10	TCGA-CJ-4639-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:42744055T>A	uc001zpw.2	-	2	681	c.346A>T	c.(346-348)AGT>TGT	p.S116C	ZFP106_uc001zpv.2_Intron|ZFP106_uc001zpx.2_Intron|ZFP106_uc010udh.1_5'UTR|ZFP106_uc001zpy.1_Missense_Mutation_p.S139C	NM_022473	NP_071918	Q9H2Y7	ZF106_HUMAN	zinc finger protein 106 homolog	116						nucleolus	zinc ion binding			central_nervous_system(2)|ovary(1)	3		all_cancers(109;1.63e-12)|all_epithelial(112;3.97e-11)|Lung NSC(122;2.04e-07)|all_lung(180;8.31e-07)|Melanoma(134;0.091)		GBM - Glioblastoma multiforme(94;8.6e-07)		TGACTGTAACTCTCTCTGTCT	0.448													75	221	---	---	---	---	PASS
CATSPER2	117155	broad.mit.edu	37	15	43924495	43924495	+	Missense_Mutation	SNP	T	C	C			TCGA-CJ-4639-01A-02D-1386-10	TCGA-CJ-4639-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:43924495T>C	uc001zsh.2	-	12	1678	c.1463A>G	c.(1462-1464)GAC>GGC	p.D488G	STRC_uc010udz.1_RNA|CATSPER2_uc010bdm.2_RNA|CATSPER2_uc001zsi.2_Missense_Mutation_p.D486G|CATSPER2_uc001zsj.2_Missense_Mutation_p.D486G	NM_172095	NP_742093	Q96P56	CTSR2_HUMAN	sperm-associated cation channel 2 isoform 2	488	Cytoplasmic (Potential).				cell differentiation|multicellular organismal development|spermatogenesis	cilium|flagellar membrane|integral to membrane	calcium channel activity|protein binding|voltage-gated ion channel activity			ovary(1)	1		all_cancers(109;3.26e-15)|all_epithelial(112;1.48e-12)|Lung NSC(122;2.76e-08)|all_lung(180;3.1e-07)|Melanoma(134;0.027)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;3.56e-07)		CCAAACACGGTCATCCTGATC	0.468													6	164	---	---	---	---	PASS
DAPK2	23604	broad.mit.edu	37	15	64231441	64231441	+	Silent	SNP	C	T	T			TCGA-CJ-4639-01A-02D-1386-10	TCGA-CJ-4639-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:64231441C>T	uc002amr.2	-	5	604	c.573G>A	c.(571-573)CCG>CCA	p.P191P	DAPK2_uc010uim.1_RNA|DAPK2_uc010bgu.1_Silent_p.P181P	NM_014326	NP_055141	Q9UIK4	DAPK2_HUMAN	death-associated kinase 2	191	Protein kinase.				apoptosis|induction of apoptosis|intracellular protein kinase cascade	cytoplasm	ATP binding|calmodulin binding|calmodulin-dependent protein kinase activity|identical protein binding			stomach(1)|central_nervous_system(1)	2				LUAD - Lung adenocarcinoma(2;0.215)		CAACAAATTCCGGCGTCCCAA	0.438													4	137	---	---	---	---	PASS
BNC1	646	broad.mit.edu	37	15	83932464	83932464	+	Silent	SNP	C	T	T			TCGA-CJ-4639-01A-02D-1386-10	TCGA-CJ-4639-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:83932464C>T	uc002bjt.1	-	4	1627	c.1539G>A	c.(1537-1539)CTG>CTA	p.L513L	BNC1_uc010uos.1_Silent_p.L501L	NM_001717	NP_001708	Q01954	BNC1_HUMAN	basonuclin 1	513					epidermis development|positive regulation of cell proliferation	cytoplasm|nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(3)	3						AAGAGGACAACAGCGGGAGGG	0.512													4	117	---	---	---	---	PASS
ADCY9	115	broad.mit.edu	37	16	4033433	4033433	+	Missense_Mutation	SNP	C	A	A			TCGA-CJ-4639-01A-02D-1386-10	TCGA-CJ-4639-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:4033433C>A	uc002cvx.2	-	7	2858	c.2319G>T	c.(2317-2319)AAG>AAT	p.K773N		NM_001116	NP_001107	O60503	ADCY9_HUMAN	adenylate cyclase 9	773	Cytoplasmic (Potential).				activation of adenylate cyclase activity by G-protein signaling pathway|activation of phospholipase C activity|activation of protein kinase A activity|cellular response to glucagon stimulus|energy reserve metabolic process|inhibition of adenylate cyclase activity by G-protein signaling pathway|nerve growth factor receptor signaling pathway|synaptic transmission|transmembrane transport|water transport	integral to plasma membrane	adenylate cyclase activity|ATP binding|metal ion binding			ovary(4)|large_intestine(1)|central_nervous_system(1)	6						CGGGGGAGTTCTTTATGACCT	0.577													46	111	---	---	---	---	PASS
RRN3P3	100131998	broad.mit.edu	37	16	22444123	22444123	+	RNA	SNP	G	A	A			TCGA-CJ-4639-01A-02D-1386-10	TCGA-CJ-4639-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:22444123G>A	uc002dkp.2	-	4		c.1060C>T			RRN3P3_uc010vbu.1_RNA	NR_027460				Homo sapiens cDNA FLJ31180 fis, clone KIDNE2000266.												0						ATCACTATCCGCTCAAAATTC	0.333													3	41	---	---	---	---	PASS
RBL2	5934	broad.mit.edu	37	16	53487478	53487478	+	Missense_Mutation	SNP	A	C	C			TCGA-CJ-4639-01A-02D-1386-10	TCGA-CJ-4639-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:53487478A>C	uc002ehi.3	+	6	999	c.881A>C	c.(880-882)AAG>ACG	p.K294T	RBL2_uc010vgv.1_Missense_Mutation_p.K220T|RBL2_uc002ehj.2_5'UTR|RBL2_uc010vgw.1_Missense_Mutation_p.K78T	NM_005611	NP_005602	Q08999	RBL2_HUMAN	retinoblastoma-like 2 (p130)	294					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						AAGGGGATAAAGGAACATTTC	0.353													35	128	---	---	---	---	PASS
GOT2	2806	broad.mit.edu	37	16	58749998	58749998	+	Silent	SNP	A	C	C			TCGA-CJ-4639-01A-02D-1386-10	TCGA-CJ-4639-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:58749998A>C	uc002eof.1	-	8	1053	c.939T>G	c.(937-939)CGT>CGG	p.R313R	GOT2_uc010vim.1_Silent_p.R270R	NM_002080	NP_002071	P00505	AATM_HUMAN	aspartate aminotransferase 2 precursor	313					aspartate catabolic process|fatty acid transport|gluconeogenesis|response to ethanol	mitochondrial matrix|plasma membrane	L-aspartate:2-oxoglutarate aminotransferase activity|protein binding|pyridoxal phosphate binding			central_nervous_system(1)|skin(1)	2					L-Aspartic Acid(DB00128)|L-Glutamic Acid(DB00142)|Pyridoxal Phosphate(DB00114)	AATACATGGGACGGATCAAGA	0.488													61	235	---	---	---	---	PASS
MFSD6L	162387	broad.mit.edu	37	17	8702333	8702333	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-4639-01A-02D-1386-10	TCGA-CJ-4639-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:8702333G>A	uc002glp.1	-	1	254	c.106C>T	c.(106-108)CTT>TTT	p.L36F		NM_152599	NP_689812	Q8IWD5	MFS6L_HUMAN	major facilitator superfamily domain containing	36						integral to membrane				central_nervous_system(1)	1						CTCAGGTAAAGGGTCAGGAAC	0.667													6	30	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	17	20319816	20319816	+	RNA	SNP	T	C	C			TCGA-CJ-4639-01A-02D-1386-10	TCGA-CJ-4639-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:20319816T>C	uc010vzg.1	+	2		c.187T>C			uc002gwx.2_RNA					Homo sapiens cDNA FLJ59693 complete cds, moderately similar to Ankyrin repeat domain-containing protein 26.																		CAAAGGAAAATGACAGGCCCT	0.507													5	38	---	---	---	---	PASS
ATAD5	79915	broad.mit.edu	37	17	29196281	29196281	+	Missense_Mutation	SNP	T	C	C			TCGA-CJ-4639-01A-02D-1386-10	TCGA-CJ-4639-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:29196281T>C	uc002hfs.1	+	13	3675	c.3329T>C	c.(3328-3330)ATA>ACA	p.I1110T	ATAD5_uc002hft.1_Missense_Mutation_p.I1007T	NM_024857	NP_079133	Q96QE3	ATAD5_HUMAN	ATPase family, AAA domain containing 5	1110					response to DNA damage stimulus	nucleus	ATP binding|nucleoside-triphosphatase activity			ovary(3)	3		all_hematologic(16;0.0202)|Acute lymphoblastic leukemia(14;0.0238)|Myeloproliferative disorder(56;0.0393)				TCGGGTGGCATAGACTTTAAA	0.393													61	182	---	---	---	---	PASS
KIAA1267	284058	broad.mit.edu	37	17	44248335	44248335	+	Missense_Mutation	SNP	C	G	G			TCGA-CJ-4639-01A-02D-1386-10	TCGA-CJ-4639-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:44248335C>G	uc002ikb.2	-	1	1260	c.1175G>C	c.(1174-1176)AGG>ACG	p.R392T	KIAA1267_uc002ikc.2_Missense_Mutation_p.R392T|KIAA1267_uc002ikd.2_Missense_Mutation_p.R392T|KIAA1267_uc010dav.2_Missense_Mutation_p.R392T	NM_015443	NP_056258	Q7Z3B3	K1267_HUMAN	hypothetical protein LOC284058	392						MLL1 complex	protein binding			skin(2)	2		Melanoma(429;0.211)				TTCACTGCACCTCAAGTTGGC	0.453													16	105	---	---	---	---	PASS
AKAP1	8165	broad.mit.edu	37	17	55184285	55184285	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-4639-01A-02D-1386-10	TCGA-CJ-4639-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:55184285G>A	uc002iux.2	+	2	1691	c.1460G>A	c.(1459-1461)TGT>TAT	p.C487Y	AKAP1_uc010wnl.1_Missense_Mutation_p.C487Y|AKAP1_uc002iuy.2_RNA|AKAP1_uc010dcm.2_Missense_Mutation_p.C487Y	NM_003488	NP_003479	Q92667	AKAP1_HUMAN	A-kinase anchor protein 1 precursor	487					blood coagulation	cytosol|integral to membrane|mitochondrial outer membrane	protein binding|RNA binding			ovary(1)	1	Breast(9;5.46e-08)					GATGCCACCTGTGTCACCTGC	0.577													20	33	---	---	---	---	PASS
POLG2	11232	broad.mit.edu	37	17	62492539	62492539	+	Missense_Mutation	SNP	T	A	A			TCGA-CJ-4639-01A-02D-1386-10	TCGA-CJ-4639-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:62492539T>A	uc002jei.2	-	1	631	c.548A>T	c.(547-549)GAG>GTG	p.E183V	POLG2_uc010deg.1_Missense_Mutation_p.E183V	NM_007215	NP_009146	Q9UHN1	DPOG2_HUMAN	DNA polymerase subunit gamma-2, mitochondrial	183					DNA repair|DNA-dependent DNA replication|glycyl-tRNA aminoacylation	mitochondrial chromosome	ATP binding|DNA-directed DNA polymerase activity|glycine-tRNA ligase activity|identical protein binding|single-stranded DNA binding			central_nervous_system(1)	1	Breast(5;2.15e-14)		BRCA - Breast invasive adenocarcinoma(8;4.97e-11)			AAGAAGGTTCTCCCGTAGTTT	0.468													43	115	---	---	---	---	PASS
ZACN	353174	broad.mit.edu	37	17	74076506	74076506	+	Splice_Site	SNP	G	A	A			TCGA-CJ-4639-01A-02D-1386-10	TCGA-CJ-4639-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:74076506G>A	uc002jqn.2	+	5	627	c.544_splice	c.e5+1	p.A182_splice	ZACN_uc002jqo.2_RNA|ZACN_uc010dgu.2_Intron	NM_180990	NP_851321	Q401N2	ZACN_HUMAN	zinc activated ligand-gated ion channel						response to zinc ion	integral to membrane|membrane fraction|plasma membrane|postsynaptic membrane	extracellular ligand-gated ion channel activity|receptor activity				0						AGCAACACGGGTGCTGACAGG	0.662													12	34	---	---	---	---	PASS
POTEC	388468	broad.mit.edu	37	18	14542791	14542791	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-4639-01A-02D-1386-10	TCGA-CJ-4639-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:14542791C>T	uc010dln.2	-	1	809	c.355G>A	c.(355-357)GCT>ACT	p.A119T	POTEC_uc010xaj.1_RNA	NM_001137671	NP_001131143	B2RU33	POTEC_HUMAN	ANKRD26-like family B, member 2	119										skin(3)	3						TCTCCCCAAGCGCCCACGTTG	0.597													5	118	---	---	---	---	PASS
NFATC1	4772	broad.mit.edu	37	18	77170523	77170523	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-4639-01A-02D-1386-10	TCGA-CJ-4639-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:77170523C>T	uc010xfg.1	+	2	701	c.248C>T	c.(247-249)GCG>GTG	p.A83V	NFATC1_uc002lnc.1_Missense_Mutation_p.A83V|NFATC1_uc010xff.1_Missense_Mutation_p.A83V|NFATC1_uc002lnd.2_Missense_Mutation_p.A83V|NFATC1_uc002lne.2_Intron|NFATC1_uc010xfh.1_Missense_Mutation_p.A83V|NFATC1_uc010xfi.1_Missense_Mutation_p.A70V|NFATC1_uc010xfj.1_Intron|NFATC1_uc002lnf.2_Missense_Mutation_p.A70V|NFATC1_uc002lng.2_Missense_Mutation_p.A70V|NFATC1_uc010xfk.1_Missense_Mutation_p.A70V	NM_006162	NP_006153	O95644	NFAC1_HUMAN	nuclear factor of activated T-cells, cytosolic	83					intracellular signal transduction|positive regulation of transcription, DNA-dependent|transcription from RNA polymerase II promoter	cytoplasm|nucleus	FK506 binding|protein binding|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding			large_intestine(1)|ovary(1)	2		Esophageal squamous(42;0.0157)|Melanoma(33;0.144)		OV - Ovarian serous cystadenocarcinoma(15;3.73e-07)|BRCA - Breast invasive adenocarcinoma(31;0.0257)		ATCCCGCCGGCGGATCACCCC	0.721													8	25	---	---	---	---	PASS
ZNF846	162993	broad.mit.edu	37	19	9870574	9870574	+	Missense_Mutation	SNP	C	G	G			TCGA-CJ-4639-01A-02D-1386-10	TCGA-CJ-4639-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:9870574C>G	uc002mmb.1	-	5	805	c.274G>C	c.(274-276)GAT>CAT	p.D92H	ZNF846_uc010xky.1_Intron|ZNF846_uc010xkz.1_Intron|ZNF846_uc010dww.2_Intron|ZNF846_uc002mmc.1_Intron	NM_001077624	NP_001071092	Q147U1	ZN846_HUMAN	zinc finger protein 846	92					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1						GCAGAAATATCTTGCAGCAGT	0.368													10	370	---	---	---	---	PASS
ZNF788	388507	broad.mit.edu	37	19	12222173	12222173	+	5'UTR	SNP	A	G	G			TCGA-CJ-4639-01A-02D-1386-10	TCGA-CJ-4639-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:12222173A>G	uc002mtd.2	+	3						NR_027049				RecName: Full=Zinc finger protein 788;												0						ATCATGTGAAAGGAATGTGTG	0.433													4	88	---	---	---	---	PASS
APLP1	333	broad.mit.edu	37	19	36362632	36362632	+	Missense_Mutation	SNP	C	A	A	rs142658251		TCGA-CJ-4639-01A-02D-1386-10	TCGA-CJ-4639-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:36362632C>A	uc002oce.2	+	5	794	c.656C>A	c.(655-657)TCT>TAT	p.S219Y	APLP1_uc010xsz.1_Missense_Mutation_p.S180Y|APLP1_uc002ocf.2_Missense_Mutation_p.S219Y|APLP1_uc002ocg.2_Missense_Mutation_p.S122Y|APLP1_uc010xta.1_Missense_Mutation_p.S213Y	NM_005166	NP_005157	P51693	APLP1_HUMAN	amyloid precursor-like protein 1 isoform 2	219	Extracellular (Potential).				apoptosis|cell adhesion|cellular response to norepinephrine stimulus|endocytosis|negative regulation of cAMP biosynthetic process|nervous system development|organ morphogenesis	basement membrane|integral to membrane|perinuclear region of cytoplasm|plasma membrane	alpha-2A adrenergic receptor binding|alpha-2B adrenergic receptor binding|alpha-2C adrenergic receptor binding|heparin binding|identical protein binding|metal ion binding			ovary(2)	2	all_lung(56;7.14e-07)|Lung NSC(56;1.12e-06)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0515)			CCCGACCCATCTGGGACAGCA	0.632													41	123	---	---	---	---	PASS
GSK3A	2931	broad.mit.edu	37	19	42736808	42736808	+	Missense_Mutation	SNP	C	A	A			TCGA-CJ-4639-01A-02D-1386-10	TCGA-CJ-4639-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:42736808C>A	uc002otb.1	-	9	1244	c.1125G>T	c.(1123-1125)GAG>GAT	p.E375D	GSK3A_uc002ota.1_Missense_Mutation_p.E293D|GSK3A_uc002otc.2_RNA	NM_019884	NP_063937	P49840	GSK3A_HUMAN	glycogen synthase kinase 3 alpha	375	Protein kinase.				insulin receptor signaling pathway|negative regulation of glucose import|negative regulation of insulin receptor signaling pathway|negative regulation of transferase activity|nerve growth factor receptor signaling pathway|phosphatidylinositol-mediated signaling|positive regulation of protein catabolic process	beta-catenin destruction complex|cytosol	ATP binding|protein kinase A catalytic subunit binding|protein serine/threonine kinase activity|tau-protein kinase activity			ovary(2)|lung(2)	4		Prostate(69;0.00682)				GCGCGATGGCCTCTGGCGGCG	0.582													23	80	---	---	---	---	PASS
KLC3	147700	broad.mit.edu	37	19	45854226	45854226	+	Missense_Mutation	SNP	T	G	G			TCGA-CJ-4639-01A-02D-1386-10	TCGA-CJ-4639-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:45854226T>G	uc002pbf.1	+	12	1509	c.1394T>G	c.(1393-1395)ATG>AGG	p.M465R	KLC3_uc010ejy.1_Missense_Mutation_p.M464R|KLC3_uc002pbg.1_Missense_Mutation_p.M479R	NM_177417	NP_803136	Q6P597	KLC3_HUMAN	kinesin light chain 3	465						cytoplasm|kinesin complex|microtubule	microtubule motor activity			ovary(1)	1		Ovarian(192;0.0728)|all_neural(266;0.112)		OV - Ovarian serous cystadenocarcinoma(262;0.0226)		AAGAGAGCCATGTCACTCAAC	0.557													24	79	---	---	---	---	PASS
ZNF579	163033	broad.mit.edu	37	19	56089233	56089233	+	3'UTR	SNP	G	T	T			TCGA-CJ-4639-01A-02D-1386-10	TCGA-CJ-4639-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:56089233G>T	uc002qlh.2	-	2						NM_152600	NP_689813	Q8NAF0	ZN579_HUMAN	zinc finger protein 579						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0			BRCA - Breast invasive adenocarcinoma(297;0.18)	GBM - Glioblastoma multiforme(193;0.106)		TGGGTAGACAGAGGAGGTGGC	0.687													5	3	---	---	---	---	PASS
NLRP4	147945	broad.mit.edu	37	19	56369989	56369989	+	Missense_Mutation	SNP	C	A	A			TCGA-CJ-4639-01A-02D-1386-10	TCGA-CJ-4639-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:56369989C>A	uc002qmd.3	+	3	1652	c.1230C>A	c.(1228-1230)GAC>GAA	p.D410E	NLRP4_uc002qmf.2_Missense_Mutation_p.D335E|NLRP4_uc010etf.2_Missense_Mutation_p.D241E	NM_134444	NP_604393	Q96MN2	NALP4_HUMAN	NLR family, pyrin domain containing 4	410	NACHT.						ATP binding	p.D410N(1)		ovary(5)|skin(4)|lung(3)|upper_aerodigestive_tract(1)|kidney(1)|pancreas(1)	15		Colorectal(82;0.0002)|Ovarian(87;0.221)		GBM - Glioblastoma multiforme(193;0.0606)		TGTGGACAGACACATTTGAGT	0.577													13	74	---	---	---	---	PASS
ZNF211	10520	broad.mit.edu	37	19	58153552	58153552	+	3'UTR	SNP	G	A	A			TCGA-CJ-4639-01A-02D-1386-10	TCGA-CJ-4639-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:58153552G>A	uc002qpq.2	+	3					ZNF211_uc010yhb.1_3'UTR|ZNF211_uc002qpp.2_3'UTR|ZNF211_uc002qpr.2_3'UTR|ZNF211_uc002qps.2_3'UTR|ZNF211_uc002qpt.2_3'UTR|ZNF211_uc010yhc.1_3'UTR|ZNF211_uc010yhd.1_3'UTR|ZNF211_uc010yhe.1_3'UTR	NM_198855	NP_942152	Q13398	ZN211_HUMAN	zinc finger protein 211 isoform 2							nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(2)	2		Colorectal(82;5.46e-05)|all_neural(62;0.0218)|Breast(46;0.0389)|Ovarian(87;0.0443)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.026)		AGCCTTAGCTGTACTGAGAAT	0.413													12	47	---	---	---	---	PASS
ADA	100	broad.mit.edu	37	20	43264906	43264906	+	Silent	SNP	G	A	A			TCGA-CJ-4639-01A-02D-1386-10	TCGA-CJ-4639-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:43264906G>A	uc002xmj.2	-	2	185	c.57C>T	c.(55-57)GAC>GAT	p.D19D	ADA_uc010ggt.2_RNA	NM_000022	NP_000013	P00813	ADA_HUMAN	adenosine deaminase	19		Substrate.			adenosine catabolic process|cell adhesion|hypoxanthine salvage|inosine biosynthetic process|negative regulation of adenosine receptor signaling pathway|purine nucleotide salvage|purine ribonucleoside monophosphate biosynthetic process|regulation of cell-cell adhesion mediated by integrin|response to hypoxia|T cell activation	cell junction|cytoplasmic membrane-bounded vesicle lumen|cytosol|external side of plasma membrane|lysosome	adenosine deaminase activity|protein binding|zinc ion binding			pancreas(2)|ovary(1)	3		all_lung(126;1.24e-07)|Lung NSC(126;1.94e-07)|Myeloproliferative disorder(115;0.0122)	COAD - Colon adenocarcinoma(18;0.00189)		Adenosine(DB00640)|Cladribine(DB00242)|Dipyridamole(DB00975)|Erythromycin(DB00199)|Fludarabine(DB01073)|Idoxuridine(DB00249)|Nelarabine(DB01280)|Pentostatin(DB00552)|Theophylline(DB00277)|Vidarabine(DB00194)	TGATGGATCCGTCTAGGTGGA	0.463									Adenosine_Deaminase_Deficiency				5	142	---	---	---	---	PASS
CDC45	8318	broad.mit.edu	37	22	19471488	19471488	+	Missense_Mutation	SNP	A	G	G			TCGA-CJ-4639-01A-02D-1386-10	TCGA-CJ-4639-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:19471488A>G	uc002zpr.2	+	5	522	c.446A>G	c.(445-447)GAT>GGT	p.D149G	CDC45_uc011agz.1_Missense_Mutation_p.D144G|CDC45_uc011aha.1_Missense_Mutation_p.D149G|CDC45_uc002zps.2_Missense_Mutation_p.D149G|CDC45_uc002zpt.2_Missense_Mutation_p.D103G	NM_003504	NP_003495	O75419	CDC45_HUMAN	CDC45-like	149					DNA replication checkpoint|DNA strand elongation involved in DNA replication|DNA-dependent DNA replication initiation|M/G1 transition of mitotic cell cycle|regulation of transcription involved in G1/S phase of mitotic cell cycle|S phase of mitotic cell cycle	centrosome|nucleoplasm	protein binding			lung(1)	1						AATGACAGTGATGGGTCAGAG	0.483													5	162	---	---	---	---	PASS
SNAP29	9342	broad.mit.edu	37	22	21242130	21242130	+	3'UTR	SNP	G	C	C			TCGA-CJ-4639-01A-02D-1386-10	TCGA-CJ-4639-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:21242130G>C	uc011ahw.1	+	5						NM_004782	NP_004773	O95721	SNP29_HUMAN	synaptosomal-associated protein 29						cellular membrane fusion|exocytosis|protein transport|vesicle targeting	cell junction|cytoplasm|nucleus|synapse|synaptosome	SNAP receptor activity				0	all_cancers(11;2.77e-25)|all_epithelial(7;8.92e-24)|Lung NSC(8;1.49e-15)|all_lung(8;2.54e-14)|Melanoma(16;0.000465)|Ovarian(15;0.00167)|Colorectal(54;0.0332)|all_neural(72;0.142)	Lung SC(17;0.0262)	LUSC - Lung squamous cell carcinoma(15;0.000592)|Lung(15;0.0117)			TCTGAAGACAGACGGATTTCC	0.338													5	133	---	---	---	---	PASS
LOC96610	96610	broad.mit.edu	37	22	23135421	23135421	+	RNA	SNP	A	G	G			TCGA-CJ-4639-01A-02D-1386-10	TCGA-CJ-4639-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:23135421A>G	uc011aim.1	+	251		c.12063A>G								Parts of antibodies, mostly variable regions.												0						GGCCTCCCTGACCATCTCTGG	0.547													5	140	---	---	---	---	PASS
APOBEC3D	140564	broad.mit.edu	37	22	39427817	39427817	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-4639-01A-02D-1386-10	TCGA-CJ-4639-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:39427817C>T	uc011aoe.1	+	6	935	c.881C>T	c.(880-882)CCA>CTA	p.P294L	APOBEC3D_uc011aof.1_Missense_Mutation_p.P110L|APOBEC3D_uc003awu.3_Missense_Mutation_p.P110L|APOBEC3D_uc003awt.3_Missense_Mutation_p.P294L|APOBEC3D_uc010gxu.2_Missense_Mutation_p.P90L	NM_152426	NP_689639	Q96AK3	ABC3D_HUMAN	apolipoprotein B mRNA editing enzyme, catalytic	294					negative regulation of transposition		hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amidines|zinc ion binding				0	Melanoma(58;0.04)					AGCCCTTGCCCAGAGTGTGCA	0.542													4	90	---	---	---	---	PASS
TNRC6B	23112	broad.mit.edu	37	22	40677210	40677210	+	Missense_Mutation	SNP	T	C	C			TCGA-CJ-4639-01A-02D-1386-10	TCGA-CJ-4639-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:40677210T>C	uc011aor.1	+	11	3710	c.3499T>C	c.(3499-3501)TCT>CCT	p.S1167P	TNRC6B_uc003aym.2_Intron|TNRC6B_uc003ayn.3_Intron|TNRC6B_uc003ayo.2_Intron	NM_001162501	NP_001155973	Q9UPQ9	TNR6B_HUMAN	trinucleotide repeat containing 6B isoform 1	1167	Gln-rich.				gene silencing by RNA|regulation of translation	cytoplasmic mRNA processing body	nucleotide binding|RNA binding				0						CTACAAGCTGTCTCCCTCTGG	0.542													7	241	---	---	---	---	PASS
TBL1X	6907	broad.mit.edu	37	X	9677737	9677737	+	Missense_Mutation	SNP	C	A	A			TCGA-CJ-4639-01A-02D-1386-10	TCGA-CJ-4639-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:9677737C>A	uc010ndq.2	+	15	1744	c.1376C>A	c.(1375-1377)ACC>AAC	p.T459N	TBL1X_uc004csq.3_Missense_Mutation_p.T408N|TBL1X_uc010ndr.2_Missense_Mutation_p.T408N|TBL1X_uc004csr.2_Missense_Mutation_p.T459N|TBL1X_uc004css.2_Missense_Mutation_p.T410N	NM_001139466	NP_001132938	O60907	TBL1X_HUMAN	transducin beta-like 1X isoform a	459	WD 6.				canonical Wnt receptor signaling pathway|cellular lipid metabolic process|negative regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase II promoter|proteasomal ubiquitin-dependent protein catabolic process|sensory perception of sound|transcription, DNA-dependent	spindle microtubule|transcriptional repressor complex	beta-catenin binding|histone binding|protein C-terminus binding|protein domain specific binding|transcription corepressor activity|transcription factor binding|transcription regulatory region DNA binding			ovary(1)	1		Hepatocellular(5;0.000888)				GAGATCTACACCATCAAGTGG	0.522											OREG0019658	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	15	66	---	---	---	---	PASS
MAGEB4	4115	broad.mit.edu	37	X	30260561	30260561	+	Silent	SNP	A	G	G			TCGA-CJ-4639-01A-02D-1386-10	TCGA-CJ-4639-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:30260561A>G	uc004dcb.2	+	1	393	c.309A>G	c.(307-309)AGA>AGG	p.R103R	MAGEB1_uc004dcc.2_5'Flank|MAGEB1_uc004dcd.2_5'Flank	NM_002367	NP_002358	O15481	MAGB4_HUMAN	melanoma antigen family B, 4	103										ovary(1)	1						CCACTGAGAGATCACTCAAAG	0.463													4	95	---	---	---	---	PASS
XK	7504	broad.mit.edu	37	X	37586901	37586901	+	Missense_Mutation	SNP	C	A	A			TCGA-CJ-4639-01A-02D-1386-10	TCGA-CJ-4639-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:37586901C>A	uc004ddq.2	+	3	603	c.521C>A	c.(520-522)ACC>AAC	p.T174N		NM_021083	NP_066569	P51811	XK_HUMAN	membrane transport protein XK	174	Helical; (Potential).				amino acid transport	integral to membrane	protein binding|transporter activity				0		all_lung(315;0.175)				CTCCTCATGACCATATCCCTG	0.393													8	96	---	---	---	---	PASS
ACTRT1	139741	broad.mit.edu	37	X	127185839	127185839	+	Missense_Mutation	SNP	C	A	A			TCGA-CJ-4639-01A-02D-1386-10	TCGA-CJ-4639-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:127185839C>A	uc004eum.2	-	1	544	c.347G>T	c.(346-348)AGG>ATG	p.R116M		NM_138289	NP_612146	Q8TDG2	ACTT1_HUMAN	actin-related protein T1	116						cytoplasm|cytoskeleton				ovary(2)|central_nervous_system(2)|skin(1)	5						TCGAATTTCCCTAGGATTCAA	0.488													88	227	---	---	---	---	PASS
AIFM1	9131	broad.mit.edu	37	X	129290574	129290574	+	Missense_Mutation	SNP	T	G	G			TCGA-CJ-4639-01A-02D-1386-10	TCGA-CJ-4639-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:129290574T>G	uc004evg.2	-	2	288	c.110A>C	c.(109-111)AAC>ACC	p.N37T	AIFM1_uc011mus.1_Missense_Mutation_p.N37T|AIFM1_uc004evh.2_Intron|AIFM1_uc004evi.2_Intron|AIFM1_uc004evk.2_Intron	NM_004208	NP_004199	O95831	AIFM1_HUMAN	programmed cell death 8 isoform 1	37					activation of caspase activity|apoptosis in response to endoplasmic reticulum stress|cell redox homeostasis|DNA damage response, signal transduction resulting in induction of apoptosis|DNA fragmentation involved in apoptotic nuclear change	cytosol|mitochondrial inner membrane|mitochondrial intermembrane space|nucleus|perinuclear region of cytoplasm	DNA binding|electron carrier activity|flavin adenine dinucleotide binding|oxidoreductase activity|protein binding			ovary(4)|central_nervous_system(1)	5						CTGGAACAAGTTGCCTAAGAA	0.358													21	117	---	---	---	---	PASS
IDS	3423	broad.mit.edu	37	X	148568486	148568486	+	Missense_Mutation	SNP	A	G	G			TCGA-CJ-4639-01A-02D-1386-10	TCGA-CJ-4639-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:148568486A>G	uc011mxe.1	-	8	1348	c.1150T>C	c.(1150-1152)TTT>CTT	p.F384L	IDS_uc011mxd.1_Intron|IDS_uc011mxf.1_Missense_Mutation_p.F294L|IDS_uc011mxg.1_Missense_Mutation_p.F173L|IDS_uc010nsu.1_5'UTR|IDS_uc004fcw.3_Missense_Mutation_p.F173L	NM_000202	NP_000193	P22304	IDS_HUMAN	iduronate-2-sulfatase isoform a precursor	384						lysosome	iduronate-2-sulfatase activity|metal ion binding				0	Acute lymphoblastic leukemia(192;6.56e-05)|Colorectal(9;0.0662)					GCGGAATCAAAAGGGTCGAGG	0.433													4	97	---	---	---	---	PASS
FUNDC2	65991	broad.mit.edu	37	X	154279946	154279946	+	Missense_Mutation	SNP	T	C	C			TCGA-CJ-4639-01A-02D-1386-10	TCGA-CJ-4639-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:154279946T>C	uc004fmw.2	+	4	512	c.362T>C	c.(361-363)CTT>CCT	p.L121P		NM_023934	NP_076423	Q9BWH2	FUND2_HUMAN	FUN14 domain containing 2	121						mitochondrion					0	all_cancers(53;3.51e-17)|all_epithelial(53;5.13e-11)|all_lung(58;3.84e-07)|Lung NSC(58;1.2e-06)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)|Renal(33;0.214)					ATACTGTAGCTTGCAAACCAT	0.398													5	234	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	M	6473	6473	+	5'UTR	SNP	C	T	T			TCGA-CJ-4639-01A-02D-1386-10	TCGA-CJ-4639-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrM:6473C>T	uc011mfh.1	+	1					uc004cou.3_5'Flank|uc011mfi.1_5'Flank					Homo sapiens cDNA: FLJ22894 fis, clone KAT04907.																		TCCGTCCTAATCACAGCAGTC	0.483													4	41	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	1	37123252	37123252	+	IGR	DEL	T	-	-			TCGA-CJ-4639-01A-02D-1386-10	TCGA-CJ-4639-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:37123252delT								CSF3R (174743 upstream) : GRIK3 (137876 downstream)																							ATGGGTGAGGttttttttttt	0.269													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	39410851	39410852	+	IGR	DEL	GG	-	-			TCGA-CJ-4639-01A-02D-1386-10	TCGA-CJ-4639-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:39410851_39410852delGG								RHBDL2 (3395 upstream) : AKIRIN1 (46064 downstream)																							gagaatggatgggggggttggg	0.005													4	2	---	---	---	---	
SLC5A9	200010	broad.mit.edu	37	1	48691623	48691623	+	Intron	DEL	C	-	-			TCGA-CJ-4639-01A-02D-1386-10	TCGA-CJ-4639-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:48691623delC	uc001cro.2	+						SLC5A9_uc010oms.1_Intron|SLC5A9_uc001crn.2_Intron|SLC5A9_uc010omt.1_Intron|SLC5A9_uc001crp.2_Intron|SLC5A9_uc010omu.1_Intron	NM_001011547	NP_001011547	Q2M3M2	SC5A9_HUMAN	solute carrier family 5 (sodium/glucose							integral to membrane|plasma membrane	low-affinity glucose:sodium symporter activity			ovary(3)	3						TCACCACCTTCCCCACTCTCT	0.403													4	2	---	---	---	---	
COL11A1	1301	broad.mit.edu	37	1	103364485	103364485	+	Intron	DEL	T	-	-			TCGA-CJ-4639-01A-02D-1386-10	TCGA-CJ-4639-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:103364485delT	uc001dul.2	-						COL11A1_uc001duk.2_Intron|COL11A1_uc001dum.2_Intron|COL11A1_uc001dun.2_Intron|COL11A1_uc009weh.2_Intron	NM_001854	NP_001845	P12107	COBA1_HUMAN	alpha 1 type XI collagen isoform A						collagen fibril organization|detection of mechanical stimulus involved in sensory perception of sound|visual perception	collagen type XI	extracellular matrix binding|extracellular matrix structural constituent|protein binding, bridging			ovary(6)|breast(3)|upper_aerodigestive_tract(1)|central_nervous_system(1)|pancreas(1)	12		all_epithelial(167;2.52e-07)|all_lung(203;3.11e-05)|Lung NSC(277;6.61e-05)|Breast(1374;0.181)		Lung(183;0.186)|all cancers(265;0.242)|Epithelial(280;0.248)		gtatatattatttttttttta	0.264													4	2	---	---	---	---	
SEC22B	9554	broad.mit.edu	37	1	145116193	145116193	+	3'UTR	DEL	G	-	-	rs66989703		TCGA-CJ-4639-01A-02D-1386-10	TCGA-CJ-4639-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:145116193delG	uc001eml.1	+	7					NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron	NM_004892	NP_004883	O75396	SC22B_HUMAN	SEC22 vesicle trafficking protein homolog B						ER to Golgi vesicle-mediated transport|protein transport	endoplasmic reticulum membrane|ER-Golgi intermediate compartment membrane|Golgi membrane|integral to membrane|melanosome	protein binding				0						AGCACTGGCTGGGGCATTCTC	0.428													2	5	---	---	---	---	
PRUNE	58497	broad.mit.edu	37	1	150996972	150996972	+	Intron	DEL	A	-	-			TCGA-CJ-4639-01A-02D-1386-10	TCGA-CJ-4639-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:150996972delA	uc001ewh.1	+						PRUNE_uc001ewi.1_Intron|PRUNE_uc010pco.1_Intron|PRUNE_uc001ewj.1_Intron|PRUNE_uc001ewk.1_5'Flank	NM_021222	NP_067045	Q86TP1	PRUNE_HUMAN	prune							cytoplasm|focal adhesion|nucleus	inorganic diphosphatase activity|manganese ion binding|protein binding			ovary(1)	1	all_lung(15;1.09e-34)|Lung NSC(24;1.1e-30)|Lung SC(34;0.00202)|Ovarian(49;0.0167)|all_hematologic(923;0.0597)|Hepatocellular(266;0.0997)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.0486)|LUSC - Lung squamous cell carcinoma(543;0.211)			actccgtctcaaaaaaaaaaa	0.209													7	7	---	---	---	---	
POGZ	23126	broad.mit.edu	37	1	151384339	151384339	+	Intron	DEL	A	-	-			TCGA-CJ-4639-01A-02D-1386-10	TCGA-CJ-4639-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:151384339delA	uc001eyd.1	-						POGZ_uc001eye.1_Intron|POGZ_uc010pdb.1_Intron|POGZ_uc001eyf.1_Intron|POGZ_uc010pdc.1_Intron|POGZ_uc009wmv.1_Intron|POGZ_uc010pdd.1_Intron	NM_015100	NP_055915	Q7Z3K3	POGZ_HUMAN	pogo transposable element with ZNF domain						cell division|kinetochore assembly|mitotic sister chromatid cohesion|regulation of transcription, DNA-dependent	cytoplasm|nuclear chromatin	DNA binding|protein binding|zinc ion binding			ovary(3)	3	Lung SC(34;0.00471)|Ovarian(49;0.00672)|Hepatocellular(266;0.0997)|all_hematologic(923;0.127)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.112)|LUSC - Lung squamous cell carcinoma(543;0.181)			tttttaaattaaaaaaaaaaa	0.299													7	4	---	---	---	---	
ARHGEF2	9181	broad.mit.edu	37	1	155924926	155924927	+	Intron	INS	-	T	T			TCGA-CJ-4639-01A-02D-1386-10	TCGA-CJ-4639-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:155924926_155924927insT	uc001fmt.2	-						ARHGEF2_uc001fmr.2_Intron|ARHGEF2_uc001fms.2_Intron|ARHGEF2_uc001fmu.2_Intron	NM_001162383	NP_001155855	Q92974	ARHG2_HUMAN	Rho/Rac guanine nucleotide exchange factor 2						actin filament organization|apoptosis|cell division|cell morphogenesis|induction of apoptosis by extracellular signals|intracellular protein transport|mitosis|negative regulation of microtubule depolymerization|nerve growth factor receptor signaling pathway|positive regulation of NF-kappaB transcription factor activity|regulation of cell proliferation|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol|Golgi apparatus|microtubule|ruffle membrane|spindle|tight junction	microtubule binding|Rac GTPase binding|Rac guanyl-nucleotide exchange factor activity|zinc ion binding			ovary(1)	1	Hepatocellular(266;0.133)|all_hematologic(923;0.145)|all_neural(408;0.195)					CCttttctttcttttttttttg	0.218													6	3	---	---	---	---	
HMCN1	83872	broad.mit.edu	37	1	185992421	185992421	+	Intron	DEL	T	-	-			TCGA-CJ-4639-01A-02D-1386-10	TCGA-CJ-4639-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:185992421delT	uc001grq.1	+							NM_031935	NP_114141	Q96RW7	HMCN1_HUMAN	hemicentin 1 precursor						response to stimulus|visual perception	basement membrane	calcium ion binding			ovary(22)|skin(1)	23						AAACCTAGGGTTTTTTTTTTT	0.269													9	4	---	---	---	---	
CDK18	5129	broad.mit.edu	37	1	205494568	205494569	+	Intron	INS	-	T	T	rs76098475		TCGA-CJ-4639-01A-02D-1386-10	TCGA-CJ-4639-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:205494568_205494569insT	uc001hcr.2	+						CDK18_uc010pri.1_Intron|CDK18_uc001hcp.2_Intron|CDK18_uc001hcq.2_Intron|CDK18_uc010prj.1_Intron|CDK18_uc001hcs.2_Intron|CDK18_uc009xbm.1_Intron	NM_212503	NP_997668	Q07002	CDK18_HUMAN	PCTAIRE protein kinase 3 isoform a								ATP binding|cyclin-dependent protein kinase activity|protein binding|signal transducer activity			stomach(2)	2						AGAATCCAGTCTTTTTTTTTTC	0.332													4	2	---	---	---	---	
WDR64	128025	broad.mit.edu	37	1	241838266	241838272	+	Intron	DEL	TTCTTTT	-	-	rs113533869	by1000genomes	TCGA-CJ-4639-01A-02D-1386-10	TCGA-CJ-4639-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:241838266_241838272delTTCTTTT	uc001hze.1	+									B1ANS9	WDR64_HUMAN	RecName: Full=WD repeat-containing protein 64;											skin(1)	1	Ovarian(103;0.103)	all_cancers(173;0.0121)	OV - Ovarian serous cystadenocarcinoma(106;0.0116)			ctctcctcccttctttttctttccttc	0.000													2	4	---	---	---	---	
STRN	6801	broad.mit.edu	37	2	37120837	37120837	+	Intron	DEL	T	-	-			TCGA-CJ-4639-01A-02D-1386-10	TCGA-CJ-4639-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:37120837delT	uc002rpn.2	-						STRN_uc010ezx.2_Intron	NM_003162	NP_003153	O43815	STRN_HUMAN	striatin, calmodulin binding protein						dendrite development|locomotory behavior|negative regulation of cell proliferation|tight junction assembly|Wnt receptor signaling pathway	cytoplasm|dendritic spine|neuronal cell body|postsynaptic density|postsynaptic membrane|tight junction	armadillo repeat domain binding|calmodulin binding|estrogen receptor binding|protein complex binding|protein phosphatase 2A binding			skin(1)	1		Ovarian(717;0.0129)|all_hematologic(82;0.21)				ATTGTTGTTGTTTTTTTTTCT	0.299													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	45273116	45273117	+	IGR	DEL	TC	-	-			TCGA-CJ-4639-01A-02D-1386-10	TCGA-CJ-4639-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:45273116_45273117delTC								SIX2 (36573 upstream) : SRBD1 (342703 downstream)																							cagcgagtgatctctctctctc	0.000													4	2	---	---	---	---	
PUS10	150962	broad.mit.edu	37	2	61189741	61189741	+	Intron	DEL	A	-	-	rs58980134	byFrequency	TCGA-CJ-4639-01A-02D-1386-10	TCGA-CJ-4639-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:61189741delA	uc010fci.2	-						PUS10_uc002sao.2_Intron|PUS10_uc010ypk.1_Intron	NM_144709	NP_653310	Q3MIT2	PUS10_HUMAN	pseudouridylate synthase 10						pseudouridine synthesis|tRNA processing		pseudouridine synthase activity|RNA binding			ovary(2)|large_intestine(1)|kidney(1)	4			LUSC - Lung squamous cell carcinoma(5;1.56e-06)|Lung(5;2.48e-05)|Epithelial(17;0.113)			AGTATTTTTTAAAAAAAAAAG	0.035													4	2	---	---	---	---	
RAB1A	5861	broad.mit.edu	37	2	65316354	65316354	+	Intron	DEL	T	-	-			TCGA-CJ-4639-01A-02D-1386-10	TCGA-CJ-4639-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:65316354delT	uc002sdm.2	-						RAB1A_uc002sdn.2_Intron|RAB1A_uc010yqe.1_Intron|RAB1A_uc002sdo.2_Intron	NM_004161	NP_004152	P62820	RAB1A_HUMAN	RAB1A, member RAS oncogene family isoform 1						protein transport|small GTPase mediated signal transduction|vesicle-mediated transport	endoplasmic reticulum|Golgi apparatus	GTP binding|GTPase activity				0						AGTGAAGAGAttttttttttt	0.194													4	2	---	---	---	---	
BUB1	699	broad.mit.edu	37	2	111413141	111413141	+	Intron	DEL	A	-	-			TCGA-CJ-4639-01A-02D-1386-10	TCGA-CJ-4639-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:111413141delA	uc002tgc.2	-						BUB1_uc010yxh.1_Intron|BUB1_uc010fkb.2_Intron	NM_004336	NP_004327	O43683	BUB1_HUMAN	budding uninhibited by benzimidazoles 1						apoptosis|cell division|chromosome segregation|interspecies interaction between organisms|mitotic cell cycle spindle assembly checkpoint|mitotic prometaphase|regulation of sister chromatid cohesion	condensed chromosome kinetochore|cytosol	ATP binding|protein binding|protein serine/threonine kinase activity			lung(2)|breast(2)|stomach(1)|ovary(1)|kidney(1)	7		Ovarian(717;0.0822)		BRCA - Breast invasive adenocarcinoma(221;0.0556)		ATGCCAAAGGAAAAAAAAACC	0.274													4	2	---	---	---	---	
LOC150776	150776	broad.mit.edu	37	2	132273797	132273798	+	5'Flank	INS	-	A	A			TCGA-CJ-4639-01A-02D-1386-10	TCGA-CJ-4639-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:132273797_132273798insA	uc002tsz.3	+						LOC150776_uc010zaz.1_Intron|LOC150776_uc010fna.2_Intron|LOC150776_uc002tsy.3_Intron					Homo sapiens cDNA FLJ41352 fis, clone BRAWH2014645.												0						CACGGTGGAGCCAACCCTCACT	0.450													14	11	---	---	---	---	
LOC150776	150776	broad.mit.edu	37	2	132273798	132273799	+	5'Flank	INS	-	T	T			TCGA-CJ-4639-01A-02D-1386-10	TCGA-CJ-4639-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:132273798_132273799insT	uc002tsz.3	+						LOC150776_uc010zaz.1_Intron|LOC150776_uc010fna.2_Intron|LOC150776_uc002tsy.3_Intron					Homo sapiens cDNA FLJ41352 fis, clone BRAWH2014645.												0						ACGGTGGAGCCAACCCTCACTA	0.455													14	11	---	---	---	---	
LOC150776	150776	broad.mit.edu	37	2	132273802	132273803	+	5'Flank	INS	-	ATTAG	ATTAG			TCGA-CJ-4639-01A-02D-1386-10	TCGA-CJ-4639-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:132273802_132273803insATTAG	uc002tsz.3	+						LOC150776_uc010zaz.1_Intron|LOC150776_uc010fna.2_Intron|LOC150776_uc002tsy.3_Intron					Homo sapiens cDNA FLJ41352 fis, clone BRAWH2014645.												0						TGGAGCCAACCCTCACTAATGG	0.465													22	11	---	---	---	---	
MAP1D	254042	broad.mit.edu	37	2	172935959	172935959	+	Intron	DEL	A	-	-			TCGA-CJ-4639-01A-02D-1386-10	TCGA-CJ-4639-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:172935959delA	uc002uhk.2	+						MAP1D_uc010zdw.1_Intron	NM_199227	NP_954697	Q6UB28	AMP1D_HUMAN	methionine aminopeptidase 1D precursor						N-terminal protein amino acid modification|peptidyl-methionine modification|proteolysis	mitochondrion	aminopeptidase activity|metal ion binding|metalloexopeptidase activity				0			OV - Ovarian serous cystadenocarcinoma(117;0.216)			CCCTGAGTTGAAAAAAAAAAA	0.328													3	4	---	---	---	---	
RUFY4	285180	broad.mit.edu	37	2	218947665	218947665	+	Intron	DEL	A	-	-			TCGA-CJ-4639-01A-02D-1386-10	TCGA-CJ-4639-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:218947665delA	uc002vgw.2	+						RUFY4_uc002vgy.1_Intron|RUFY4_uc010fvl.1_Intron	NM_198483	NP_940885	Q6ZNE9	RUFY4_HUMAN	RUN and FYVE domain containing 4								metal ion binding			pancreas(1)	1		Renal(207;0.0915)		Epithelial(149;4.11e-06)|all cancers(144;0.000519)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00948)		gttgtgttgtaggcatgtgtg	0.333													4	2	---	---	---	---	
FANCD2	2177	broad.mit.edu	37	3	10108735	10108735	+	Intron	DEL	T	-	-			TCGA-CJ-4639-01A-02D-1386-10	TCGA-CJ-4639-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:10108735delT	uc003buw.2	+						FANCD2_uc003bux.1_Intron|FANCD2_uc003buy.1_Intron|FANCD2_uc010hcw.1_Intron	NM_033084	NP_149075	Q9BXW9	FACD2_HUMAN	Fanconi anemia complementation group D2 isoform						DNA repair|response to gamma radiation	nucleoplasm	protein binding|protein binding			central_nervous_system(2)|ovary(1)|skin(1)	4				OV - Ovarian serous cystadenocarcinoma(96;0.148)		GGGCCAGAGATTTTTTTTCTG	0.219			D|Mis|N|F			AML|leukemia		Involved_in_tolerance_or_repair_of_DNA_crosslinks	Fanconi_Anemia				4	2	---	---	---	---	
SLC4A7	9497	broad.mit.edu	37	3	27478676	27478679	+	Intron	DEL	TACT	-	-			TCGA-CJ-4639-01A-02D-1386-10	TCGA-CJ-4639-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:27478676_27478679delTACT	uc003cdv.2	-						SLC4A7_uc011awu.1_Intron|SLC4A7_uc011awv.1_Intron|SLC4A7_uc003cdu.3_Intron|SLC4A7_uc011aww.1_Intron|SLC4A7_uc011awx.1_Intron|SLC4A7_uc011awy.1_Intron|SLC4A7_uc011awz.1_Intron|SLC4A7_uc011axa.1_Intron|SLC4A7_uc011axb.1_Intron|SLC4A7_uc010hfm.2_Intron|SLC4A7_uc003cdw.2_Intron	NM_003615	NP_003606	Q9Y6M7	S4A7_HUMAN	solute carrier family 4, sodium bicarbonate							apical plasma membrane|basolateral plasma membrane|integral to membrane|stereocilium	inorganic anion exchanger activity|protein binding|sodium:bicarbonate symporter activity			ovary(3)|central_nervous_system(1)|skin(1)	5						accccatctctactaaaaatacaa	0.000													4	2	---	---	---	---	
PARP3	10039	broad.mit.edu	37	3	51977862	51977862	+	Intron	DEL	C	-	-			TCGA-CJ-4639-01A-02D-1386-10	TCGA-CJ-4639-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:51977862delC	uc003dby.2	+						RRP9_uc003dbw.1_5'Flank|PARP3_uc003dbz.2_Intron	NM_005485	NP_005476	Q9Y6F1	PARP3_HUMAN	poly (ADP-ribose) polymerase family, member 3						DNA repair|protein ADP-ribosylation	centriole|nucleus	NAD+ ADP-ribosyltransferase activity|protein binding			ovary(1)	1				BRCA - Breast invasive adenocarcinoma(193;8.01e-05)|Kidney(197;0.000541)|KIRC - Kidney renal clear cell carcinoma(197;0.000716)		CTCTCAGATTCCCCCATCCAG	0.622													4	2	---	---	---	---	
C3orf63	23272	broad.mit.edu	37	3	56673790	56673791	+	Intron	DEL	CT	-	-	rs77904576		TCGA-CJ-4639-01A-02D-1386-10	TCGA-CJ-4639-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:56673790_56673791delCT	uc003did.3	-						C3orf63_uc003dic.3_Intron|C3orf63_uc003die.3_Intron	NM_015224	NP_056039	Q9UK61	CC063_HUMAN	retinoblastoma-associated protein 140 isoform b											ovary(3)|kidney(1)|central_nervous_system(1)	5				KIRC - Kidney renal clear cell carcinoma(284;0.0126)|Kidney(284;0.0147)		TCTTAAATCCCTGTTTTTAAGG	0.416													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	115529092	115529093	+	IGR	INS	-	TCTC	TCTC	rs56145932		TCGA-CJ-4639-01A-02D-1386-10	TCGA-CJ-4639-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:115529092_115529093insTCTC								LSAMP (5074 upstream) : LOC285194 (899542 downstream)																							ctctctctctgtctctctctct	0.262													6	3	---	---	---	---	
PIK3R4	30849	broad.mit.edu	37	3	130404893	130404893	+	Intron	DEL	A	-	-			TCGA-CJ-4639-01A-02D-1386-10	TCGA-CJ-4639-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:130404893delA	uc003enj.2	-							NM_014602	NP_055417	Q99570	PI3R4_HUMAN	phosphoinositide-3-kinase, regulatory subunit 4						fibroblast growth factor receptor signaling pathway|innate immune response|insulin receptor signaling pathway	cytosol	ATP binding|protein binding|protein serine/threonine kinase activity			ovary(3)|lung(2)|breast(2)|skin(2)|stomach(1)|central_nervous_system(1)|kidney(1)	12						TTTTTTAATGAAAAAAAAATA	0.294													6	3	---	---	---	---	
RNF212	285498	broad.mit.edu	37	4	1103538	1103538	+	Intron	DEL	C	-	-	rs33984933		TCGA-CJ-4639-01A-02D-1386-10	TCGA-CJ-4639-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:1103538delC	uc003gcj.2	-						RNF212_uc003gci.2_Intron|RNF212_uc010ibp.2_Intron|RNF212_uc010ibq.2_Intron|RNF212_uc003gck.2_Intron	NM_001131034	NP_001124506	Q495C1	RN212_HUMAN	ring finger protein 212 isoform a								zinc ion binding				0			OV - Ovarian serous cystadenocarcinoma(23;0.0179)	UCEC - Uterine corpus endometrioid carcinoma (64;0.151)		CACCACAGAACAACCCACTTC	0.537													5	3	---	---	---	---	
STK32B	55351	broad.mit.edu	37	4	5431698	5431699	+	Intron	INS	-	G	G	rs146930619	by1000genomes	TCGA-CJ-4639-01A-02D-1386-10	TCGA-CJ-4639-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:5431698_5431699insG	uc003gih.1	+						STK32B_uc010ida.1_Intron	NM_018401	NP_060871	Q9NY57	ST32B_HUMAN	serine/threonine kinase 32B								ATP binding|metal ion binding|protein serine/threonine kinase activity			breast(2)|large_intestine(1)|central_nervous_system(1)|skin(1)	5						gttcctctgtaggtaacatgct	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	12306626	12306627	+	IGR	DEL	AA	-	-			TCGA-CJ-4639-01A-02D-1386-10	TCGA-CJ-4639-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:12306626_12306627delAA								HS3ST1 (876089 upstream) : None (None downstream)																							AGTTTGTGTTAAGGTATTGAGA	0.287													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	49246087	49246087	+	IGR	DEL	C	-	-			TCGA-CJ-4639-01A-02D-1386-10	TCGA-CJ-4639-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:49246087delC								CWH43 (181994 upstream) : None (None downstream)																							CAAAAACAAACAAAAAAAAAT	0.249													5	4	---	---	---	---	
TMEM144	55314	broad.mit.edu	37	4	159138498	159138499	+	Frame_Shift_Ins	INS	-	A	A			TCGA-CJ-4639-01A-02D-1386-10	TCGA-CJ-4639-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:159138498_159138499insA	uc003ipx.2	+	5	778_779	c.258_259insA	c.(256-261)ATCAAAfs	p.I86fs	TMEM144_uc010iqi.2_RNA	NM_018342	NP_060812	Q7Z5S9	TM144_HUMAN	transmembrane protein 144	86_87						integral to membrane					0	all_hematologic(180;0.24)	Renal(120;0.0854)		COAD - Colon adenocarcinoma(41;0.0539)		TCCCAATTATCAAAACCATTGG	0.317													280	132	---	---	---	---	
MTRR	4552	broad.mit.edu	37	5	7871264	7871266	+	Intron	DEL	CTT	-	-	rs139287124		TCGA-CJ-4639-01A-02D-1386-10	TCGA-CJ-4639-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:7871264_7871266delCTT	uc003jed.2	+						FASTKD3_uc011cmp.1_5'Flank|FASTKD3_uc003jeb.2_5'Flank|FASTKD3_uc003jec.2_5'Flank|MTRR_uc010itn.1_Intron|MTRR_uc003jee.3_Intron|MTRR_uc003jef.3_Intron|MTRR_uc003jeg.3_Intron|MTRR_uc010ito.2_Intron	NM_024010	NP_076915	Q9UBK8	MTRR_HUMAN	methionine synthase reductase isoform 2						methionine biosynthetic process	cytosol	[methionine synthase] reductase activity|flavin adenine dinucleotide binding|FMN binding|iron ion binding|NADP binding			ovary(1)	1					Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)|L-Methionine(DB00134)	GTAACAACtccttaactgtaaat	0.227													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	10489309	10489320	+	IGR	DEL	AGAGAGAGAGAC	-	-	rs71582424		TCGA-CJ-4639-01A-02D-1386-10	TCGA-CJ-4639-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:10489309_10489320delAGAGAGAGAGAC								ROPN1L (24172 upstream) : DAP (190023 downstream)																							AGAAaaagaaagagagagagacagagagagag	0.269													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	17339381	17339381	+	IGR	DEL	A	-	-			TCGA-CJ-4639-01A-02D-1386-10	TCGA-CJ-4639-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:17339381delA								BASP1 (62446 upstream) : None (None downstream)																							TGCACTGTGTAACAGGGGAGG	0.418													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	23305428	23305428	+	IGR	DEL	C	-	-	rs144280787		TCGA-CJ-4639-01A-02D-1386-10	TCGA-CJ-4639-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:23305428delC								CDH12 (451697 upstream) : PRDM9 (202296 downstream)																							TGTGCAGCCGCCCCCCCCGGT	0.398													4	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	31038047	31038048	+	IGR	INS	-	A	A			TCGA-CJ-4639-01A-02D-1386-10	TCGA-CJ-4639-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:31038047_31038048insA								None (None upstream) : CDH6 (155748 downstream)																							atgcctgcatcaaaaaatctga	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	63256093	63256093	+	IGR	DEL	T	-	-			TCGA-CJ-4639-01A-02D-1386-10	TCGA-CJ-4639-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:63256093delT								None (None upstream) : HTR1A (186 downstream)																							CTGGGTCTCCTTTGCACAAAG	0.552													4	2	---	---	---	---	
BDP1	55814	broad.mit.edu	37	5	70761707	70761707	+	Intron	DEL	A	-	-	rs71612562		TCGA-CJ-4639-01A-02D-1386-10	TCGA-CJ-4639-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:70761707delA	uc003kbp.1	+						BDP1_uc003kbn.1_Intron|BDP1_uc003kbo.2_Intron	NM_018429	NP_060899	A6H8Y1	BDP1_HUMAN	transcription factor-like nuclear regulator						regulation of transcription, DNA-dependent|transcription from RNA polymerase III promoter	nucleoplasm	DNA binding			skin(2)	2		Lung NSC(167;0.000422)|Prostate(74;0.00815)|Ovarian(174;0.0176)|Breast(144;0.198)		OV - Ovarian serous cystadenocarcinoma(47;5.28e-56)|Epithelial(20;2.31e-50)		aactccatctaaaaaaaaaaa	0.134													4	2	---	---	---	---	
CAST	831	broad.mit.edu	37	5	96058638	96058639	+	Intron	INS	-	TTGTT	TTGTT			TCGA-CJ-4639-01A-02D-1386-10	TCGA-CJ-4639-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:96058638_96058639insTTGTT	uc003klz.1	+						CAST_uc003klt.2_Intron|CAST_uc003klu.2_Intron|CAST_uc003klv.2_Intron|CAST_uc003klw.2_Intron|CAST_uc003klx.2_Intron|CAST_uc003kly.2_Intron|CAST_uc011cuo.1_Intron|CAST_uc011cup.1_Intron|CAST_uc011cuq.1_Intron|CAST_uc011cur.1_Intron|CAST_uc011cus.1_Intron|CAST_uc003kma.1_Intron|CAST_uc011cut.1_Intron|CAST_uc003kmb.2_Intron|CAST_uc003kmc.2_Intron|CAST_uc003kmd.2_Intron|CAST_uc003kme.2_Intron|CAST_uc003kmf.2_Intron	NM_001042443	NP_001035908	P20810	ICAL_HUMAN	calpastatin isoform i								calcium-dependent cysteine-type endopeptidase inhibitor activity|protein binding			central_nervous_system(3)|ovary(1)|kidney(1)	5		all_cancers(142;5.27e-07)|all_epithelial(76;8.21e-10)|all_lung(232;0.000396)|Lung NSC(167;0.000539)|Ovarian(225;0.024)|Colorectal(57;0.0341)|Breast(839;0.244)		all cancers(79;6.85e-15)		GTCACCTAGAGttgttttgttt	0.178													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	117580783	117580784	+	IGR	INS	-	G	G	rs139054002	by1000genomes	TCGA-CJ-4639-01A-02D-1386-10	TCGA-CJ-4639-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:117580783_117580784insG								None (None upstream) : DTWD2 (591787 downstream)																							ATGAACAAAAAGCAAAAAGCAA	0.317													5	6	---	---	---	---	
ZNF608	57507	broad.mit.edu	37	5	123973399	123973400	+	3'UTR	DEL	TA	-	-			TCGA-CJ-4639-01A-02D-1386-10	TCGA-CJ-4639-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:123973399_123973400delTA	uc003ktq.1	-	9					ZNF608_uc003ktr.1_RNA|ZNF608_uc003ktp.1_3'UTR	NM_020747	NP_065798	Q9ULD9	ZN608_HUMAN	zinc finger protein 608							intracellular	zinc ion binding			skin(3)|ovary(2)|lung(1)	6		all_cancers(142;0.186)|Prostate(80;0.081)	KIRC - Kidney renal clear cell carcinoma(527;0.159)|Kidney(363;0.221)	OV - Ovarian serous cystadenocarcinoma(64;0.00126)|Epithelial(69;0.00238)|all cancers(49;0.00783)		tatgtatacgtatatatatata	0.243													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	125171394	125171394	+	IGR	DEL	A	-	-	rs34330689		TCGA-CJ-4639-01A-02D-1386-10	TCGA-CJ-4639-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:125171394delA								None (None upstream) : GRAMD3 (524394 downstream)																							GAGTCAGCTCAGCACCTCAAT	0.478											OREG0016749	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	5	5	---	---	---	---	
PHAX	51808	broad.mit.edu	37	5	125943848	125943848	+	Intron	DEL	G	-	-			TCGA-CJ-4639-01A-02D-1386-10	TCGA-CJ-4639-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:125943848delG	uc003kua.1	+							NM_032177	NP_115553	Q9H814	PHAX_HUMAN	RNA U, small nuclear RNA export adaptor						ncRNA metabolic process|protein transport|snRNA export from nucleus|spliceosomal snRNP assembly	Cajal body|cytosol	RNA binding				0						CCAATTATGAGAGTTTAGATG	0.348													4	2	---	---	---	---	
CD83	9308	broad.mit.edu	37	6	14134204	14134204	+	Intron	DEL	A	-	-			TCGA-CJ-4639-01A-02D-1386-10	TCGA-CJ-4639-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:14134204delA	uc003nbi.2	+						CD83_uc003nbh.2_Intron	NM_004233	NP_004224	Q01151	CD83_HUMAN	CD83 antigen isoform a						defense response|humoral immune response|signal transduction	integral to plasma membrane					0	Breast(50;0.00245)|Ovarian(93;0.137)	all_hematologic(90;0.117)				AGCATTGTGGAAAAAAAAAAC	0.458													6	3	---	---	---	---	
KIF13A	63971	broad.mit.edu	37	6	17785982	17785982	+	Intron	DEL	A	-	-			TCGA-CJ-4639-01A-02D-1386-10	TCGA-CJ-4639-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:17785982delA	uc003ncg.3	-						KIF13A_uc003ncf.2_Intron|KIF13A_uc003nch.3_Intron|KIF13A_uc003nci.3_Intron	NM_022113	NP_071396	Q9H1H9	KI13A_HUMAN	kinesin family member 13A isoform a						cargo loading into vesicle|cell cycle|cytokinesis|endosome to lysosome transport|Golgi to plasma membrane protein transport|melanosome organization|plus-end-directed vesicle transport along microtubule	centrosome|endosome membrane|microtubule|midbody|trans-Golgi network membrane	ATP binding|microtubule motor activity|protein binding			large_intestine(2)|ovary(2)	4	Breast(50;0.0107)|Ovarian(93;0.016)	all_hematologic(90;0.125)	all cancers(50;0.0865)|Epithelial(50;0.0974)			catctctaccaaaaaaaaaaa	0.109													14	10	---	---	---	---	
LRRC16A	55604	broad.mit.edu	37	6	25342690	25342690	+	Intron	DEL	G	-	-			TCGA-CJ-4639-01A-02D-1386-10	TCGA-CJ-4639-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:25342690delG	uc011djw.1	+						LRRC16A_uc010jpx.2_Intron|LRRC16A_uc010jpy.2_Intron	NM_017640	NP_060110	Q5VZK9	LR16A_HUMAN	leucine rich repeat containing 16A						actin filament organization|blood coagulation|cell migration|lamellipodium assembly|ruffle organization|urate metabolic process	cytosol|lamellipodium|nucleus				ovary(1)|breast(1)|central_nervous_system(1)|pancreas(1)	4						cattgattttgggataggcct	0.214													4	2	---	---	---	---	
HLA-G	3135	broad.mit.edu	37	6	29975193	29975194	+	Intron	DEL	AT	-	-			TCGA-CJ-4639-01A-02D-1386-10	TCGA-CJ-4639-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:29975193_29975194delAT	uc011dmb.1	+						NCRNA00171_uc011dme.1_Intron|HLA-J_uc003nou.3_Intron|HLA-J_uc003rtl.3_Intron|HLA-J_uc003nov.3_Intron	NM_002127	NP_002118	P17693	HLAG_HUMAN	major histocompatibility complex, class I, G						antigen processing and presentation of peptide antigen via MHC class I|cellular defense response|interferon-gamma-mediated signaling pathway|regulation of immune response|type I interferon-mediated signaling pathway	integral to membrane|MHC class I protein complex	MHC class I receptor activity			ovary(3)|central_nervous_system(1)	4						CAAGGATTACATCGCCCTGAAC	0.619													4	2	---	---	---	---	
CAPN11	11131	broad.mit.edu	37	6	44145212	44145213	+	Intron	INS	-	CTTT	CTTT			TCGA-CJ-4639-01A-02D-1386-10	TCGA-CJ-4639-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:44145212_44145213insCTTT	uc003owt.1	+						CAPN11_uc011dvn.1_Intron	NM_007058	NP_008989	Q9UMQ6	CAN11_HUMAN	calpain 11						proteolysis	acrosomal vesicle	calcium ion binding|calcium-dependent cysteine-type endopeptidase activity			ovary(1)|breast(1)	2	all_cancers(18;3.19e-06)|Lung NSC(15;0.00108)|all_lung(25;0.00278)|Hepatocellular(11;0.00908)|Ovarian(13;0.0273)		Colorectal(64;0.00337)|COAD - Colon adenocarcinoma(64;0.00536)			TGACCTCACTCCtttctttctt	0.332													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	48380505	48380506	+	IGR	INS	-	A	A	rs144666150	by1000genomes	TCGA-CJ-4639-01A-02D-1386-10	TCGA-CJ-4639-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:48380505_48380506insA								C6orf138 (301562 upstream) : None (None downstream)																							TAATTCAACAGAAAAAATTGGT	0.421													5	6	---	---	---	---	
MUT	4594	broad.mit.edu	37	6	49408202	49408202	+	Intron	DEL	T	-	-			TCGA-CJ-4639-01A-02D-1386-10	TCGA-CJ-4639-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:49408202delT	uc003ozg.3	-							NM_000255	NP_000246	P22033	MUTA_HUMAN	methylmalonyl Coenzyme A mutase precursor						fatty acid beta-oxidation	mitochondrial matrix	cobalamin binding|metal ion binding|methylmalonyl-CoA mutase activity				0	Lung NSC(77;0.0376)				Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)	TTTTGGGTTGttttttttttc	0.129													4	2	---	---	---	---	
REV3L	5980	broad.mit.edu	37	6	111670212	111670212	+	Intron	DEL	A	-	-	rs74728098		TCGA-CJ-4639-01A-02D-1386-10	TCGA-CJ-4639-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:111670212delA	uc003puy.3	-						REV3L_uc003pux.3_Intron|REV3L_uc003puz.3_Intron|REV3L_uc003pva.1_Intron	NM_002912	NP_002903	O60673	DPOLZ_HUMAN	DNA polymerase zeta						DNA-dependent DNA replication|translesion synthesis	nucleus|zeta DNA polymerase complex	DNA binding|DNA-directed DNA polymerase activity|metal ion binding|nucleotide binding			large_intestine(2)|ovary(2)|skin(2)	6		all_cancers(87;7.57e-06)|Acute lymphoblastic leukemia(125;2.46e-08)|all_hematologic(75;1.08e-06)|all_epithelial(87;0.00138)|Colorectal(196;0.021)		OV - Ovarian serous cystadenocarcinoma(136;0.0314)|Epithelial(106;0.057)|all cancers(137;0.0663)		TAGACACAAGAAAAAAAAAAA	0.199								DNA_polymerases_(catalytic_subunits)|Direct_reversal_of_damage					5	3	---	---	---	---	
NXPH1	30010	broad.mit.edu	37	7	8475126	8475126	+	Intron	DEL	T	-	-			TCGA-CJ-4639-01A-02D-1386-10	TCGA-CJ-4639-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:8475126delT	uc003srv.2	+						NXPH1_uc011jxh.1_Intron	NM_152745	NP_689958	P58417	NXPH1_HUMAN	neurexophilin 1 precursor							extracellular region				ovary(1)|central_nervous_system(1)	2		Ovarian(82;0.0628)		UCEC - Uterine corpus endometrioid carcinoma (126;0.101)		CCTCCCTCCCTTTTTTTTTTG	0.572													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	61661760	61661761	+	IGR	INS	-	A	A			TCGA-CJ-4639-01A-02D-1386-10	TCGA-CJ-4639-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:61661760_61661761insA								None (None upstream) : None (None downstream)																							AATTATATCACACATGATAGTT	0.317													4	6	---	---	---	---	
MAGI2	9863	broad.mit.edu	37	7	78869395	78869395	+	Intron	DEL	A	-	-			TCGA-CJ-4639-01A-02D-1386-10	TCGA-CJ-4639-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:78869395delA	uc003ugx.2	-						MAGI2_uc003ugy.2_Intron	NM_012301	NP_036433	Q86UL8	MAGI2_HUMAN	membrane associated guanylate kinase, WW and PDZ							cell junction|synapse|synaptosome	phosphatase binding			ovary(5)|lung(4)|breast(1)|skin(1)	11		all_cancers(73;0.0064)|all_epithelial(88;0.087)|all_neural(109;0.0936)|Medulloblastoma(109;0.166)|Melanoma(862;0.236)				aaggagaaataaaccccatgt	0.035													4	2	---	---	---	---	
DPY19L2P2	349152	broad.mit.edu	37	7	102895483	102895484	+	Intron	DEL	TG	-	-			TCGA-CJ-4639-01A-02D-1386-10	TCGA-CJ-4639-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:102895483_102895484delTG	uc003vbh.3	-						DPY19L2P2_uc003vbg.3_Intron|DPY19L2P2_uc010lit.2_Intron	NR_003561				RecName: Full=Protein dpy-19 homolog 2-like 2; AltName: Full=Dpy-19-like protein 2 pseudogene 2;												0						TATAAGAgtttgtgtgtgtgtg	0.228													6	4	---	---	---	---	
TTC26	79989	broad.mit.edu	37	7	138857969	138857969	+	Intron	DEL	A	-	-			TCGA-CJ-4639-01A-02D-1386-10	TCGA-CJ-4639-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:138857969delA	uc003vus.2	+						TTC26_uc011kqn.1_Intron|TTC26_uc011kqo.1_Intron|TTC26_uc011kqp.1_Intron|TTC26_uc003vut.2_Intron|TTC26_uc011kqq.1_Intron	NM_024926	NP_079202	A0AVF1	TTC26_HUMAN	tetratricopeptide repeat domain 26 isoform 1								binding			ovary(1)	1						GTACAAAGTCACCtttttttt	0.214													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	957634	957635	+	Intron	INS	-	GG	GG	rs149432488	by1000genomes	TCGA-CJ-4639-01A-02D-1386-10	TCGA-CJ-4639-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:957634_957635insGG	uc003wpj.1	+						uc003wpk.2_Intron					Homo sapiens cDNA clone IMAGE:4824304.																		GTTTTTTTTTTTGGGGGGGGGA	0.495													4	2	---	---	---	---	
DEFB134	613211	broad.mit.edu	37	8	11853468	11853468	+	Intron	DEL	A	-	-	rs77552285		TCGA-CJ-4639-01A-02D-1386-10	TCGA-CJ-4639-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:11853468delA	uc011kxn.1	-							NM_001033019	NP_001028191	Q4QY38	DB134_HUMAN	beta-defensin 134 precursor						defense response to bacterium	extracellular region					0			STAD - Stomach adenocarcinoma(15;0.033)	COAD - Colon adenocarcinoma(149;0.159)		CAGTTCAGCCAAAAAAAAAAa	0.060													5	3	---	---	---	---	
KIAA0146	23514	broad.mit.edu	37	8	48586205	48586205	+	Intron	DEL	T	-	-			TCGA-CJ-4639-01A-02D-1386-10	TCGA-CJ-4639-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:48586205delT	uc003xqd.2	+						KIAA0146_uc011ldb.1_Intron|KIAA0146_uc010lxs.2_Intron|KIAA0146_uc011ldc.1_Intron|KIAA0146_uc011ldd.1_Intron|KIAA0146_uc003xqe.2_Intron|KIAA0146_uc003xqf.2_Intron|KIAA0146_uc011lde.1_Intron|KIAA0146_uc010lxt.2_Intron|KIAA0146_uc011ldf.1_Intron|KIAA0146_uc011ldg.1_5'UTR|KIAA0146_uc010lxv.1_Intron	NM_001080394	NP_001073863	Q14159	K0146_HUMAN	hypothetical protein LOC23514												0		Lung NSC(58;0.175)				AGTGGATTTCTTTTTTTTTTC	0.343													3	3	---	---	---	---	
PGCP	10404	broad.mit.edu	37	8	98145078	98145078	+	Intron	DEL	T	-	-			TCGA-CJ-4639-01A-02D-1386-10	TCGA-CJ-4639-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:98145078delT	uc003yhw.2	+							NM_016134	NP_057218	Q9Y646	PGCP_HUMAN	plasma glutamate carboxypeptidase precursor						peptide metabolic process|proteolysis	cytoplasm|extracellular space	metal ion binding|metallocarboxypeptidase activity			upper_aerodigestive_tract(1)	1	Breast(36;1.86e-05)					AAGAGGGAACTTTATTGACGT	0.413													4	2	---	---	---	---	
C8orf76	84933	broad.mit.edu	37	8	124244006	124244006	+	Intron	DEL	A	-	-	rs77482613		TCGA-CJ-4639-01A-02D-1386-10	TCGA-CJ-4639-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:124244006delA	uc003yqc.1	-						C8orf76_uc003yqd.2_Intron	NM_032847	NP_116236	Q96K31	CH076_HUMAN	hypothetical protein LOC84933								binding			ovary(2)	2	Lung NSC(37;1.25e-09)|Ovarian(258;0.0154)		STAD - Stomach adenocarcinoma(47;0.00527)			TCCTAAGGAGAAAAAAAAAAG	0.313													8	4	---	---	---	---	
PSIP1	11168	broad.mit.edu	37	9	15473903	15473903	+	Intron	DEL	A	-	-			TCGA-CJ-4639-01A-02D-1386-10	TCGA-CJ-4639-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:15473903delA	uc003zlv.3	-						PSIP1_uc003zlw.3_Intron|PSIP1_uc003zlz.3_Intron|PSIP1_uc003zma.3_Intron|PSIP1_uc003zly.2_Intron	NM_033222	NP_150091	O75475	PSIP1_HUMAN	PC4 and SFRS1 interacting protein 1 isoform 2						initiation of viral infection|interspecies interaction between organisms|nuclear mRNA 5'-splice site recognition|provirus integration|regulation of transcription, DNA-dependent|response to heat|response to oxidative stress|transcription, DNA-dependent	cytosol|nuclear heterochromatin|nuclear periphery|nucleoplasm|nucleoplasm|transcriptionally active chromatin	activating transcription factor binding|chromatin binding|DNA secondary structure binding|RNA polymerase II transcription coactivator activity			breast(1)	1				GBM - Glioblastoma multiforme(50;2.38e-06)		catctcaaacaaaaaaaaaac	0.045													4	2	---	---	---	---	
MLLT3	4300	broad.mit.edu	37	9	20448401	20448401	+	Intron	DEL	A	-	-			TCGA-CJ-4639-01A-02D-1386-10	TCGA-CJ-4639-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:20448401delA	uc003zoe.2	-						MLLT3_uc011lne.1_Intron|MLLT3_uc011lnf.1_Intron|MLLT3_uc003zof.2_Intron|MLLT3_uc011lng.1_Intron	NM_004529	NP_004520	P42568	AF9_HUMAN	myeloid/lymphoid or mixed-lineage leukemia						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	protein binding			lung(2)|ovary(1)	3				GBM - Glioblastoma multiforme(3;4.35e-105)|Lung(42;3.48e-06)|LUSC - Lung squamous cell carcinoma(42;7.92e-05)		TAGTACTGGGAAAAAAAAAAG	0.299			T	MLL	ALL								10	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	68424949	68424949	+	IGR	DEL	T	-	-	rs66909768		TCGA-CJ-4639-01A-02D-1386-10	TCGA-CJ-4639-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:68424949delT								FAM27B (630760 upstream) : MIR1299 (577290 downstream)																							ATTTAGAGCATTTTAACTATa	0.244													4	2	---	---	---	---	
TMEM38B	55151	broad.mit.edu	37	9	108468184	108468184	+	Intron	DEL	T	-	-	rs75898442		TCGA-CJ-4639-01A-02D-1386-10	TCGA-CJ-4639-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:108468184delT	uc004bcu.1	+						TMEM38B_uc010mtn.1_Intron	NM_018112	NP_060582	Q9NVV0	TM38B_HUMAN	transmembrane protein 38B							integral to membrane|nuclear membrane|sarcoplasmic reticulum membrane	potassium channel activity			ovary(1)|skin(1)	2						TGCTAAGGGGttttttttttt	0.149													11	5	---	---	---	---	
C9orf5	23731	broad.mit.edu	37	9	111813111	111813112	+	Intron	INS	-	A	A			TCGA-CJ-4639-01A-02D-1386-10	TCGA-CJ-4639-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:111813111_111813112insA	uc004bdt.3	-						C9orf5_uc004bds.3_Intron|C9orf5_uc004bdr.3_Intron	NM_032012	NP_114401	Q9H330	CI005_HUMAN	hypothetical protein LOC23731							integral to membrane				central_nervous_system(1)	1		Myeloproliferative disorder(63;0.204)		OV - Ovarian serous cystadenocarcinoma(323;3.08e-05)|STAD - Stomach adenocarcinoma(157;0.0823)		AAATGAAAATTAAAAAAAAAAA	0.272													5	4	---	---	---	---	
ASTN2	23245	broad.mit.edu	37	9	119759925	119759925	+	Intron	DEL	A	-	-			TCGA-CJ-4639-01A-02D-1386-10	TCGA-CJ-4639-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:119759925delA	uc004bjs.1	-						ASTN2_uc004bjr.1_Intron|ASTN2_uc004bjt.1_Intron	NM_198187	NP_937830	O75129	ASTN2_HUMAN	astrotactin 2 isoform c							integral to membrane				skin(4)|ovary(3)|breast(1)|kidney(1)	9						TAgcttggccaaatcccagca	0.174													4	2	---	---	---	---	
DNM1	1759	broad.mit.edu	37	9	131006221	131006222	+	Intron	DEL	TG	-	-			TCGA-CJ-4639-01A-02D-1386-10	TCGA-CJ-4639-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:131006221_131006222delTG	uc011mau.1	+						DNM1_uc011mat.1_Intron|DNM1_uc004bub.1_Intron|DNM1_uc004buc.1_Intron|DNM1_uc004bud.3_Intron	NM_004408	NP_004399	Q05193	DYN1_HUMAN	dynamin 1 isoform 1						receptor-mediated endocytosis	microtubule	GTP binding|GTPase activity			ovary(2)	2						GGGgtgtgtttgtgtgtgtgtg	0.411													8	5	---	---	---	---	
PANK1	53354	broad.mit.edu	37	10	91403704	91403704	+	Intron	DEL	A	-	-			TCGA-CJ-4639-01A-02D-1386-10	TCGA-CJ-4639-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:91403704delA	uc001kgp.1	-						PANK1_uc001kgn.1_5'Flank|PANK1_uc001kgo.1_5'Flank|PANK1_uc009xtu.1_5'Flank	NM_148977	NP_683878	Q8TE04	PANK1_HUMAN	pantothenate kinase 1 isoform alpha						coenzyme A biosynthetic process|pantothenate metabolic process	cytosol|nucleus	ATP binding|pantothenate kinase activity				0					Bezafibrate(DB01393)	CCCTTCGTTGAAAAAAAAAAT	0.443													5	3	---	---	---	---	
PKD2L1	9033	broad.mit.edu	37	10	102048435	102048435	+	Intron	DEL	T	-	-			TCGA-CJ-4639-01A-02D-1386-10	TCGA-CJ-4639-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:102048435delT	uc001kqx.1	-						BLOC1S2_uc001kqv.1_5'Flank|BLOC1S2_uc001kqw.1_5'Flank|PKD2L1_uc009xwm.1_Intron	NM_016112	NP_057196	Q9P0L9	PK2L1_HUMAN	polycystic kidney disease 2-like 1						signal transduction	integral to membrane	calcium activated cation channel activity|calcium ion binding|cytoskeletal protein binding			ovary(4)	4		Colorectal(252;0.117)		Epithelial(162;6.15e-10)|all cancers(201;5.14e-08)		GTTTGTTAACTTTTTTTTTTT	0.423													4	3	---	---	---	---	
PDCD4	27250	broad.mit.edu	37	10	112654487	112654488	+	Intron	INS	-	C	C			TCGA-CJ-4639-01A-02D-1386-10	TCGA-CJ-4639-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:112654487_112654488insC	uc001kzh.2	+						PDCD4_uc001kzg.2_Intron|PDCD4_uc010qre.1_Intron	NM_014456	NP_055271	Q53EL6	PDCD4_HUMAN	programmed cell death 4 isoform 1						apoptosis|cell aging|negative regulation of cell cycle|negative regulation of JUN kinase activity|negative regulation of transcription, DNA-dependent	cytosol|nucleus	protein binding|RNA binding			ovary(1)|breast(1)|skin(1)	3		Breast(234;0.0848)|Lung NSC(174;0.238)		Epithelial(162;0.000526)|all cancers(201;0.00794)|BRCA - Breast invasive adenocarcinoma(275;0.125)		GTTTTTTTTTTTTTTTTTACCT	0.277													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	116661155	116661155	+	IGR	DEL	A	-	-			TCGA-CJ-4639-01A-02D-1386-10	TCGA-CJ-4639-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:116661155delA								FAM160B1 (1570 upstream) : TRUB1 (36760 downstream)																							AGGACAGTCCAAAAAAAATAT	0.313													4	2	---	---	---	---	
SIRT3	23410	broad.mit.edu	37	11	219242	219243	+	Intron	DEL	CT	-	-			TCGA-CJ-4639-01A-02D-1386-10	TCGA-CJ-4639-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:219242_219243delCT	uc001lok.3	-						SIRT3_uc001loj.3_Intron|SIRT3_uc010qvm.1_Intron|SIRT3_uc010qvn.1_Intron|SIRT3_uc010qvo.1_Intron|SIRT3_uc010qvp.1_Intron|SIRT3_uc010qvq.1_Intron	NM_012239	NP_036371	Q9NTG7	SIRT3_HUMAN	sirtuin 3 isoform a						chromatin silencing|protein ADP-ribosylation|protein deacetylation	mitochondrial matrix	hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides|NAD+ ADP-ribosyltransferase activity|NAD+ binding|protein binding|zinc ion binding			urinary_tract(1)	1		all_cancers(49;1.58e-09)|all_epithelial(84;2.71e-06)|Breast(177;0.000162)|Ovarian(85;0.000626)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.0538)|all_lung(207;0.0713)		all cancers(45;3.66e-27)|Epithelial(43;2.02e-26)|OV - Ovarian serous cystadenocarcinoma(40;2.9e-21)|BRCA - Breast invasive adenocarcinoma(625;3.88e-05)|Lung(200;0.111)|LUSC - Lung squamous cell carcinoma(625;0.129)		TCCCCTCCGCCTCTCTCTCTCT	0.554													5	4	---	---	---	---	
OSBPL5	114879	broad.mit.edu	37	11	3113601	3113603	+	Intron	DEL	GGT	-	-			TCGA-CJ-4639-01A-02D-1386-10	TCGA-CJ-4639-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:3113601_3113603delGGT	uc001lxk.2	-						OSBPL5_uc010qxq.1_Intron|OSBPL5_uc009ydw.2_Intron|OSBPL5_uc001lxl.2_Intron|OSBPL5_uc001lxj.2_Intron	NM_020896	NP_065947	Q9H0X9	OSBL5_HUMAN	oxysterol-binding protein-like protein 5 isoform						cholesterol metabolic process|cholesterol transport|Golgi to plasma membrane transport	cytosol	oxysterol binding|protein binding			large_intestine(2)|central_nervous_system(1)	3		all_epithelial(84;0.000236)|Medulloblastoma(188;0.00106)|Breast(177;0.00328)|Ovarian(85;0.00556)|all_neural(188;0.00681)		BRCA - Breast invasive adenocarcinoma(625;0.00607)|LUSC - Lung squamous cell carcinoma(625;0.207)		aggagcgaggggTGGTGGTGGCC	0.379											OREG0020694	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	4	2	---	---	---	---	
COPB1	1315	broad.mit.edu	37	11	14481519	14481519	+	Intron	DEL	A	-	-			TCGA-CJ-4639-01A-02D-1386-10	TCGA-CJ-4639-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:14481519delA	uc001mli.2	-						COPB1_uc001mlg.2_Intron|COPB1_uc001mlh.2_Intron	NM_016451	NP_057535	P53618	COPB_HUMAN	coatomer protein complex, subunit beta 1						COPI coating of Golgi vesicle|interspecies interaction between organisms|intra-Golgi vesicle-mediated transport|intracellular protein transport|retrograde vesicle-mediated transport, Golgi to ER	COPI vesicle coat|cytosol|ER-Golgi intermediate compartment|plasma membrane	protein binding|structural molecule activity			ovary(1)|central_nervous_system(1)	2						AAAAGAAAATAAAAAAAAAAT	0.269													6	3	---	---	---	---	
TRIM44	54765	broad.mit.edu	37	11	35698298	35698299	+	Intron	INS	-	GT	GT			TCGA-CJ-4639-01A-02D-1386-10	TCGA-CJ-4639-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:35698298_35698299insGT	uc001mwi.2	+							NM_017583	NP_060053	Q96DX7	TRI44_HUMAN	DIPB protein							intracellular	protein binding|zinc ion binding			skin(1)	1	all_lung(20;0.0317)|Lung NSC(22;0.0661)|all_epithelial(35;0.115)	all_hematologic(20;0.107)				GTGAATTTTGAGTGTGTGTGAA	0.386													4	2	---	---	---	---	
CD82	3732	broad.mit.edu	37	11	44615938	44615939	+	Intron	INS	-	CCAGCC	CCAGCC	rs142553689	by1000genomes	TCGA-CJ-4639-01A-02D-1386-10	TCGA-CJ-4639-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:44615938_44615939insCCAGCC	uc001myc.2	+						CD82_uc001myd.2_Intron	NM_002231	NP_002222	P27701	CD82_HUMAN	CD82 antigen isoform 1							integral to plasma membrane	protein binding			ovary(1)	1						TTTTGCTCCCAccagccccagc	0.485													3	3	---	---	---	---	
HEPHL1	341208	broad.mit.edu	37	11	93839460	93839460	+	Intron	DEL	T	-	-	rs144455207		TCGA-CJ-4639-01A-02D-1386-10	TCGA-CJ-4639-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:93839460delT	uc001pep.2	+						uc001pen.1_Intron	NM_001098672	NP_001092142	Q6MZM0	HPHL1_HUMAN	hephaestin-like 1 precursor						copper ion transport	integral to membrane	copper ion binding|oxidoreductase activity			ovary(3)	3		Acute lymphoblastic leukemia(157;2.34e-05)|all_hematologic(158;0.00824)				Atttcttttcttttttttttt	0.179													6	3	---	---	---	---	
IGSF9B	22997	broad.mit.edu	37	11	133788723	133788724	+	Intron	INS	-	G	G	rs150958113		TCGA-CJ-4639-01A-02D-1386-10	TCGA-CJ-4639-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:133788723_133788724insG	uc001qgx.3	-							NM_014987	NP_055802	Q9UPX0	TUTLB_HUMAN	immunoglobulin superfamily, member 9B							integral to membrane|plasma membrane					0	all_hematologic(175;0.127)	all_cancers(12;1.58e-21)|all_epithelial(12;5.17e-16)|all_lung(97;1.6e-05)|Lung NSC(97;3.86e-05)|Breast(109;0.000126)|Medulloblastoma(222;0.0245)|all_neural(223;0.0505)|Esophageal squamous(93;0.0559)		Epithelial(10;7.19e-10)|BRCA - Breast invasive adenocarcinoma(10;9.69e-09)|all cancers(11;1.23e-08)|OV - Ovarian serous cystadenocarcinoma(99;0.00328)|Lung(977;0.221)		GAGAAGAGGGCGGGGGACGGGG	0.490													6	3	---	---	---	---	
A2ML1	144568	broad.mit.edu	37	12	8998288	8998288	+	Intron	DEL	A	-	-			TCGA-CJ-4639-01A-02D-1386-10	TCGA-CJ-4639-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:8998288delA	uc001quz.3	+						A2ML1_uc001qva.1_Intron|A2ML1_uc010sgm.1_Intron	NM_144670	NP_653271	A8K2U0	A2ML1_HUMAN	alpha-2-macroglobulin-like 1 precursor							extracellular space	endopeptidase inhibitor activity			ovary(2)|skin(1)	3						ctaaaaatacaaaaaaaaatt	0.000													4	2	---	---	---	---	
FAR2	55711	broad.mit.edu	37	12	29464599	29464600	+	Intron	INS	-	CTCA	CTCA	rs149591152	by1000genomes	TCGA-CJ-4639-01A-02D-1386-10	TCGA-CJ-4639-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:29464599_29464600insCTCA	uc001ris.3	+						FAR2_uc001rit.2_Intron|FAR2_uc009zjm.2_Intron|uc001riu.1_Intron	NM_018099	NP_060569	Q96K12	FACR2_HUMAN	fatty acyl CoA reductase 2						ether lipid biosynthetic process	endoplasmic reticulum membrane|integral to membrane|peroxisomal matrix|peroxisomal membrane	binding|oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor				0						AACATCTCTTTcacacacacac	0.277													3	3	---	---	---	---	
DNM1L	10059	broad.mit.edu	37	12	32889843	32889843	+	Intron	DEL	A	-	-			TCGA-CJ-4639-01A-02D-1386-10	TCGA-CJ-4639-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:32889843delA	uc001rld.2	+						DNM1L_uc001rle.2_Intron|DNM1L_uc001rlf.2_Intron|DNM1L_uc010skh.1_Intron|DNM1L_uc001rlg.2_Intron|DNM1L_uc001rlh.2_Intron|DNM1L_uc010ski.1_Intron	NM_012062	NP_036192	O00429	DNM1L_HUMAN	dynamin 1-like isoform 1						cellular component disassembly involved in apoptosis|mitochondrial fragmentation involved in apoptosis|mitochondrial membrane organization|positive regulation of mitochondrial fission	cis-Golgi network|cytosol|endomembrane system|endoplasmic reticulum|mitochondrial outer membrane	GTP binding|GTPase activity|ubiquitin protein ligase binding			ovary(1)|pancreas(1)	2	Lung NSC(5;2.15e-06)|Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.0429)|Esophageal squamous(101;0.239)					GTGTGGGCAGAAAAAAAAAAG	0.398													7	5	---	---	---	---	
USP30	84749	broad.mit.edu	37	12	109519423	109519424	+	Intron	INS	-	GC	GC			TCGA-CJ-4639-01A-02D-1386-10	TCGA-CJ-4639-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:109519423_109519424insGC	uc010sxi.1	+						USP30_uc001tnu.3_Intron|USP30_uc001tnw.3_5'Flank	NM_032663	NP_116052	Q70CQ3	UBP30_HUMAN	ubiquitin specific peptidase 30						ubiquitin-dependent protein catabolic process	integral to membrane|mitochondrial outer membrane	cysteine-type peptidase activity|ubiquitin thiolesterase activity			lung(1)	1						cacgcacgcatgcgcgcacaca	0.252													7	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	110073801	110073803	+	IGR	DEL	ATT	-	-			TCGA-CJ-4639-01A-02D-1386-10	TCGA-CJ-4639-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:110073801_110073803delATT								MVK (38731 upstream) : C12orf34 (78387 downstream)																							aagcaccatcattatcaccacta	0.034													3	8	---	---	---	---	
TMTC4	84899	broad.mit.edu	37	13	101286909	101286909	+	Intron	DEL	A	-	-			TCGA-CJ-4639-01A-02D-1386-10	TCGA-CJ-4639-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:101286909delA	uc001vou.2	-						TMTC4_uc001vot.2_Intron|TMTC4_uc010tja.1_Intron|TMTC4_uc001vov.1_Intron|TMTC4_uc001vow.1_Intron	NM_001079669	NP_001073137	Q5T4D3	TMTC4_HUMAN	transmembrane and tetratricopeptide repeat							integral to membrane	binding			ovary(2)|breast(1)	3	all_neural(89;0.0837)|Medulloblastoma(90;0.18)|Lung SC(71;0.184)					CAAAATCATTAAAAAAAACCA	0.328													6	3	---	---	---	---	
MYO16	23026	broad.mit.edu	37	13	109736705	109736706	+	Intron	INS	-	GACA	GACA			TCGA-CJ-4639-01A-02D-1386-10	TCGA-CJ-4639-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:109736705_109736706insGACA	uc001vqt.1	+						MYO16_uc010agk.1_Intron|MYO16_uc010tjh.1_Intron	NM_015011	NP_055826	Q9Y6X6	MYO16_HUMAN	myosin heavy chain Myr 8						cerebellum development|negative regulation of cell proliferation|negative regulation of S phase of mitotic cell cycle	myosin complex|nucleoplasm|perinuclear region of cytoplasm|plasma membrane	actin filament binding|ATP binding|motor activity			ovary(6)|large_intestine(1)|kidney(1)|breast(1)|central_nervous_system(1)	10	all_lung(23;0.000332)|all_neural(89;0.00294)|Medulloblastoma(90;0.00596)|Lung NSC(43;0.00751)|Lung SC(71;0.104)		BRCA - Breast invasive adenocarcinoma(86;0.19)|all cancers(43;0.201)			AGCAGGTTGATGACTTGATGAT	0.406													3	4	---	---	---	---	
PSMB5	5693	broad.mit.edu	37	14	23502434	23502434	+	Intron	DEL	A	-	-			TCGA-CJ-4639-01A-02D-1386-10	TCGA-CJ-4639-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:23502434delA	uc001wii.2	-						PSMB5_uc001wij.2_Intron|PSMB5_uc010tni.1_Intron	NM_002797	NP_002788	P28074	PSB5_HUMAN	proteasome beta 5 subunit isoform 1						anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|G1/S transition of mitotic cell cycle|interspecies interaction between organisms|M/G1 transition of mitotic cell cycle|mRNA metabolic process|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|regulation of apoptosis|regulation of cellular amino acid metabolic process|S phase of mitotic cell cycle|viral reproduction	cytoplasm|nucleus	protein binding|threonine-type endopeptidase activity			ovary(1)	1	all_cancers(95;3.3e-05)			GBM - Glioblastoma multiforme(265;0.0121)	Bortezomib(DB00188)	aaaaaacaggaaaaaaaaaaa	0.194													4	3	---	---	---	---	
MNAT1	4331	broad.mit.edu	37	14	61247546	61247546	+	Intron	DEL	T	-	-			TCGA-CJ-4639-01A-02D-1386-10	TCGA-CJ-4639-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:61247546delT	uc001xfd.2	+						MNAT1_uc010apq.1_Intron|MNAT1_uc001xfe.2_Intron	NM_002431	NP_002422	P51948	MAT1_HUMAN	menage a trois 1 (CAK assembly factor)						cell proliferation|G1 phase of mitotic cell cycle|G1/S transition of mitotic cell cycle|G2/M transition of mitotic cell cycle|mRNA capping|nucleotide-excision repair, DNA damage removal|positive regulation of transcription from RNA polymerase II promoter|positive regulation of viral transcription|protein complex assembly|protein phosphorylation|regulation of cyclin-dependent protein kinase activity|S phase of mitotic cell cycle|termination of RNA polymerase I transcription|transcription elongation from RNA polymerase I promoter|transcription elongation from RNA polymerase II promoter|transcription initiation from RNA polymerase I promoter|transcription initiation from RNA polymerase II promoter|transcription-coupled nucleotide-excision repair|viral reproduction	cytoplasm|holo TFIIH complex	protein N-terminus binding|zinc ion binding			ovary(1)|lung(1)	2				OV - Ovarian serous cystadenocarcinoma(108;0.0174)		AACCAGGAGGTTTTTTTTTTG	0.323								Direct_reversal_of_damage|NER					4	3	---	---	---	---	
SPATA7	55812	broad.mit.edu	37	14	88862742	88862742	+	Intron	DEL	A	-	-			TCGA-CJ-4639-01A-02D-1386-10	TCGA-CJ-4639-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:88862742delA	uc001xwq.2	+						SPATA7_uc001xwr.2_Intron	NM_018418	NP_060888	Q9P0W8	SPAT7_HUMAN	spermatogenesis-associated protein 7 isoform a						response to stimulus|visual perception					ovary(1)	1						ccacataaacaataatttcct	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	31192611	31192611	+	IGR	DEL	T	-	-			TCGA-CJ-4639-01A-02D-1386-10	TCGA-CJ-4639-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:31192611delT								ARHGAP11B (214802 upstream) : MTMR15 (3444 downstream)																							CCTATCtttcttttttttttg	0.154													5	3	---	---	---	---	
UBR1	197131	broad.mit.edu	37	15	43237806	43237806	+	Intron	DEL	T	-	-	rs11352938		TCGA-CJ-4639-01A-02D-1386-10	TCGA-CJ-4639-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:43237806delT	uc001zqq.2	-							NM_174916	NP_777576	Q8IWV7	UBR1_HUMAN	ubiquitin protein ligase E3 component n-recognin						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)		AAAAGGGATATTTTCCCTTCA	0.393													6	5	---	---	---	---	
UBR1	197131	broad.mit.edu	37	15	43237814	43237823	+	Intron	DEL	TCACCATTGA	-	-	rs67230215		TCGA-CJ-4639-01A-02D-1386-10	TCGA-CJ-4639-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:43237814_43237823delTCACCATTGA	uc001zqq.2	-							NM_174916	NP_777576	Q8IWV7	UBR1_HUMAN	ubiquitin protein ligase E3 component n-recognin						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)		TATTTTCCCTTCACCATTGATCACTAAGAA	0.410													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	45212151	45212151	+	IGR	DEL	G	-	-	rs7179454		TCGA-CJ-4639-01A-02D-1386-10	TCGA-CJ-4639-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:45212151delG								TRIM69 (152126 upstream) : C15orf43 (36752 downstream)																							aaaaaaaaaagaaagaaaGAT	0.129													5	3	---	---	---	---	
VPS13C	54832	broad.mit.edu	37	15	62160677	62160677	+	Intron	DEL	T	-	-	rs71125954		TCGA-CJ-4639-01A-02D-1386-10	TCGA-CJ-4639-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:62160677delT	uc002agz.2	-						VPS13C_uc002aha.2_Intron|VPS13C_uc002ahb.1_Intron|VPS13C_uc002ahc.1_Intron	NM_020821	NP_065872	Q709C8	VP13C_HUMAN	vacuolar protein sorting 13C protein isoform 2A						protein localization					ovary(2)	2						AGAAAAAAAATCATCTGTAAT	0.289													4	3	---	---	---	---	
VPS13C	54832	broad.mit.edu	37	15	62265442	62265442	+	Intron	DEL	A	-	-			TCGA-CJ-4639-01A-02D-1386-10	TCGA-CJ-4639-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:62265442delA	uc002agz.2	-						VPS13C_uc002aha.2_Intron|VPS13C_uc002ahb.1_Intron|VPS13C_uc002ahc.1_Intron	NM_020821	NP_065872	Q709C8	VP13C_HUMAN	vacuolar protein sorting 13C protein isoform 2A						protein localization					ovary(2)	2						TGTCAACTACAAAAAAaaacc	0.159													8	4	---	---	---	---	
PTPN9	5780	broad.mit.edu	37	15	75815801	75815801	+	Intron	DEL	A	-	-			TCGA-CJ-4639-01A-02D-1386-10	TCGA-CJ-4639-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:75815801delA	uc002bal.2	-							NM_002833	NP_002824	P43378	PTN9_HUMAN	protein tyrosine phosphatase, non-receptor type							cytoplasmic part	non-membrane spanning protein tyrosine phosphatase activity|protein binding			lung(1)|skin(1)	2						CTGTGGTAAGAAAAAAAAAAC	0.428													6	3	---	---	---	---	
NPW	283869	broad.mit.edu	37	16	2070327	2070328	+	Intron	INS	-	A	A	rs148115495	by1000genomes	TCGA-CJ-4639-01A-02D-1386-10	TCGA-CJ-4639-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:2070327_2070328insA	uc002coh.3	+							NM_001099456	NP_001092926	Q8N729	NPW_HUMAN	neuropeptide W preproprotein						feeding behavior|neuropeptide signaling pathway	extracellular region					0						CGTGAGAGGGGAGAGGCCTGGA	0.738													3	3	---	---	---	---	
CASKIN1	57524	broad.mit.edu	37	16	2234529	2234530	+	Intron	DEL	CA	-	-			TCGA-CJ-4639-01A-02D-1386-10	TCGA-CJ-4639-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:2234529_2234530delCA	uc010bsg.1	-							NM_020764	NP_065815	Q8WXD9	CSKI1_HUMAN	CASK interacting protein 1						signal transduction	cytoplasm				skin(2)	2						GTCCCACCATcacacacacaca	0.302													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	28513069	28513070	+	Intron	DEL	CT	-	-	rs497094		TCGA-CJ-4639-01A-02D-1386-10	TCGA-CJ-4639-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:28513069_28513070delCT	uc010vct.1	-						IL27_uc002dqc.2_Intron					RecName: Full=Nuclear pore complex-interacting protein-like 2; Flags: Precursor;																		cactcacacactctcacagtca	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	46409653	46409656	+	IGR	DEL	TTCA	-	-	rs112162925		TCGA-CJ-4639-01A-02D-1386-10	TCGA-CJ-4639-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:46409653_46409656delTTCA								None (None upstream) : ANKRD26P1 (93593 downstream)																							tccattcgatttcattcaatgatt	0.000													3	3	---	---	---	---	
ABCC11	85320	broad.mit.edu	37	16	48265572	48265572	+	Intron	DEL	A	-	-			TCGA-CJ-4639-01A-02D-1386-10	TCGA-CJ-4639-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:48265572delA	uc002eff.1	-						ABCC11_uc002efg.1_Intron|ABCC11_uc002efh.1_Intron|ABCC11_uc010vgl.1_Intron	NM_033151	NP_149163	Q96J66	ABCCB_HUMAN	ATP-binding cassette, sub-family C, member 11							integral to membrane	ATP binding|ATPase activity, coupled to transmembrane movement of substances			ovary(3)|skin(2)|central_nervous_system(1)	6		all_cancers(37;0.127)|all_lung(18;0.132)|Breast(268;0.166)				accctgagtcaaaaaaaaaaa	0.129									Cerumen_Type				11	5	---	---	---	---	
RLTPR	146206	broad.mit.edu	37	16	67688027	67688028	+	Intron	DEL	CC	-	-			TCGA-CJ-4639-01A-02D-1386-10	TCGA-CJ-4639-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:67688027_67688028delCC	uc002etn.2	+						RLTPR_uc010vjr.1_Intron	NM_001013838	NP_001013860	Q6F5E8	LR16C_HUMAN	RGD motif, leucine rich repeats, tropomodulin											breast(1)	1		Acute lymphoblastic leukemia(13;3.23e-05)|all_hematologic(13;0.00251)|Ovarian(137;0.192)		OV - Ovarian serous cystadenocarcinoma(108;0.0146)|Epithelial(162;0.0481)|all cancers(182;0.232)		TCAACCCTGACCCCTGACCCCA	0.545													25	11	---	---	---	---	
PDPR	55066	broad.mit.edu	37	16	70176729	70176730	+	Intron	INS	-	G	G			TCGA-CJ-4639-01A-02D-1386-10	TCGA-CJ-4639-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:70176729_70176730insG	uc002eyf.1	+						CLEC18C_uc002exy.2_Intron|PDPR_uc010vlr.1_Intron|PDPR_uc002eyg.1_Intron|PDPR_uc002eyh.2_5'Flank|PDPR_uc010vls.1_5'Flank	NM_017990	NP_060460	Q8NCN5	PDPR_HUMAN	pyruvate dehydrogenase phosphatase regulatory						glycine catabolic process|pyruvate metabolic process|regulation of acetyl-CoA biosynthetic process from pyruvate	mitochondrial matrix	aminomethyltransferase activity|oxidoreductase activity			breast(1)	1				BRCA - Breast invasive adenocarcinoma(221;0.124)		tgggaggccaagggggcgtgga	0.064													11	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	1169562	1169563	+	IGR	INS	-	C	C	rs72530000		TCGA-CJ-4639-01A-02D-1386-10	TCGA-CJ-4639-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:1169562_1169563insC								ABR (78946 upstream) : TUSC5 (13394 downstream)																							ATGACTGCTTATCTCTACGCTG	0.386													13	9	---	---	---	---	
TBC1D3C	414060	broad.mit.edu	37	17	34587956	34587957	+	Intron	DEL	AA	-	-			TCGA-CJ-4639-01A-02D-1386-10	TCGA-CJ-4639-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:34587956_34587957delAA	uc002hlk.1	-						TBC1D3C_uc002hll.1_Intron|TBC1D3G_uc010wcv.1_Intron|TBC1D3G_uc002hlm.2_Intron|uc002hlo.1_5'Flank	NM_001001418	NP_001001418	Q6IPX1	TBC3C_HUMAN	TBC1 domain family member 3C							intracellular	Rab GTPase activator activity				0		Breast(25;0.102)|Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0182)		CCCAGGACTGAAAGAGTGGATG	0.545													12	13	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	49547765	49547765	+	IGR	DEL	T	-	-			TCGA-CJ-4639-01A-02D-1386-10	TCGA-CJ-4639-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:49547765delT								UTP18 (172475 upstream) : CA10 (159910 downstream)																							AGTTCAGGCGTTTTTTTTTTT	0.393													6	5	---	---	---	---	
KIAA0195	9772	broad.mit.edu	37	17	73495648	73495649	+	3'UTR	INS	-	G	G	rs140042808	by1000genomes	TCGA-CJ-4639-01A-02D-1386-10	TCGA-CJ-4639-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:73495648_73495649insG	uc002jnz.3	+	32					KIAA0195_uc010wsa.1_3'UTR|KIAA0195_uc010wsb.1_3'UTR|KIAA0195_uc002job.3_3'UTR	NM_014738	NP_055553	Q12767	K0195_HUMAN	hypothetical protein LOC9772						ATP biosynthetic process|cation transport	integral to membrane	ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism			ovary(1)	1	all_cancers(13;3.15e-09)|all_epithelial(9;5.94e-10)|Breast(9;1.85e-09)|all_lung(278;0.246)		all cancers(21;5.01e-07)|Epithelial(20;5e-06)|Lung(188;0.0809)|LUSC - Lung squamous cell carcinoma(166;0.154)			GGGCCTCACCAGGGACACTCTT	0.644													5	4	---	---	---	---	
MYOM1	8736	broad.mit.edu	37	18	3072053	3072053	+	Intron	DEL	T	-	-			TCGA-CJ-4639-01A-02D-1386-10	TCGA-CJ-4639-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:3072053delT	uc002klp.2	-						MYOM1_uc002klq.2_Intron	NM_003803	NP_003794	P52179	MYOM1_HUMAN	myomesin 1 isoform a							striated muscle myosin thick filament	structural constituent of muscle			ovary(3)|central_nervous_system(1)|pancreas(1)	5						GGATTCAGGAttttttttttt	0.179													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	28103049	28103050	+	IGR	INS	-	GTA	GTA	rs3052755		TCGA-CJ-4639-01A-02D-1386-10	TCGA-CJ-4639-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:28103049_28103050insGTA								MIR302F (224123 upstream) : DSC3 (467003 downstream)																							TTTCCCCCAAGGTTAGCAGTTT	0.431													6	3	---	---	---	---	
SPPL2B	56928	broad.mit.edu	37	19	2341103	2341103	+	Intron	DEL	G	-	-			TCGA-CJ-4639-01A-02D-1386-10	TCGA-CJ-4639-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:2341103delG	uc002lvs.2	+						SPPL2B_uc010dsw.1_Frame_Shift_Del_p.R321fs|SPPL2B_uc010dsy.1_Frame_Shift_Del_p.R321fs|SPPL2B_uc010dsz.1_Frame_Shift_Del_p.R349fs|SPPL2B_uc002lvr.2_Intron|SPPL2B_uc010dta.1_Frame_Shift_Del_p.R201fs|SPPL2B_uc002lvu.2_Frame_Shift_Del_p.R143fs	NM_152988	NP_694533	Q8TCT7	PSL1_HUMAN	signal peptide peptidase-like 2B isoform 2							Golgi membrane|integral to membrane	aspartic-type endopeptidase activity				0		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		CCTCCCTGGAGGCCGCCCCAG	0.711													8	5	---	---	---	---	
GCDH	2639	broad.mit.edu	37	19	13004060	13004060	+	Intron	DEL	A	-	-			TCGA-CJ-4639-01A-02D-1386-10	TCGA-CJ-4639-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:13004060delA	uc002mvq.2	+						GCDH_uc010xms.1_Intron|GCDH_uc002mvp.2_Intron|GCDH_uc010xmt.1_Intron|GCDH_uc010xmu.1_Intron	NM_000159	NP_000150	Q92947	GCDH_HUMAN	glutaryl-Coenzyme A dehydrogenase isoform a						lysine catabolic process	mitochondrial matrix	flavin adenine dinucleotide binding|glutaryl-CoA dehydrogenase activity|protein binding				0						ttctcaagtgatcctcttgcc	0.020													7	4	---	---	---	---	
ZNF708	7562	broad.mit.edu	37	19	21493258	21493258	+	Intron	DEL	T	-	-	rs669560		TCGA-CJ-4639-01A-02D-1386-10	TCGA-CJ-4639-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:21493258delT	uc002npq.1	-						ZNF708_uc002npr.1_Intron|ZNF708_uc010ecs.1_Intron	NM_021269	NP_067092	P17019	ZN708_HUMAN	zinc finger protein 708						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			central_nervous_system(4)|skin(2)	6						aaaaaaaaaataataataaat	0.119													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	28447093	28447093	+	IGR	DEL	T	-	-			TCGA-CJ-4639-01A-02D-1386-10	TCGA-CJ-4639-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:28447093delT								LOC148189 (162245 upstream) : None (None downstream)																							AATTATCACATTTTTTTTTCT	0.318													6	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	29289946	29289947	+	IGR	INS	-	A	A	rs144973564	by1000genomes	TCGA-CJ-4639-01A-02D-1386-10	TCGA-CJ-4639-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:29289946_29289947insA								None (None upstream) : LOC148145 (166093 downstream)																							agtttaaaaagaaaaaaaaact	0.000													3	5	---	---	---	---	
SPHK2	56848	broad.mit.edu	37	19	49131657	49131657	+	Intron	DEL	C	-	-			TCGA-CJ-4639-01A-02D-1386-10	TCGA-CJ-4639-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:49131657delC	uc002pjr.2	+						SPHK2_uc010xzt.1_Intron|SPHK2_uc002pjs.2_Intron|SPHK2_uc002pjt.2_Intron|SPHK2_uc002pju.2_Intron|SPHK2_uc002pjv.2_Intron|SPHK2_uc002pjw.2_Intron|SPHK2_uc010xzu.1_3'UTR	NM_020126	NP_064511	Q9NRA0	SPHK2_HUMAN	sphingosine kinase 2						activation of protein kinase C activity by G-protein coupled receptor protein signaling pathway|anti-apoptosis|cell proliferation|sphinganine-1-phosphate biosynthetic process	cytosol|lysosomal membrane|membrane fraction	ATP binding|D-erythro-sphingosine kinase activity|diacylglycerol kinase activity|Ras GTPase binding|sphinganine kinase activity			lung(1)	1		all_lung(116;0.000125)|Lung NSC(112;0.000202)|all_epithelial(76;0.000283)|all_neural(266;0.0506)|Ovarian(192;0.113)		OV - Ovarian serous cystadenocarcinoma(262;0.000102)|all cancers(93;0.000117)|GBM - Glioblastoma multiforme(486;0.00627)|Epithelial(262;0.0158)		GGGATGCTCACCCCCAGCTCC	0.343													4	2	---	---	---	---	
FAM182A	284800	broad.mit.edu	37	20	26054752	26054754	+	Intron	DEL	ATC	-	-	rs112967123		TCGA-CJ-4639-01A-02D-1386-10	TCGA-CJ-4639-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:26054752_26054754delATC	uc010gdq.2	+							NR_026713				Homo sapiens cDNA FLJ38374 fis, clone FEBRA2002552.												0						caccatcattatcatcattacta	0.025													5	4	---	---	---	---	
RBM39	9584	broad.mit.edu	37	20	34315105	34315105	+	Intron	DEL	A	-	-	rs113921117		TCGA-CJ-4639-01A-02D-1386-10	TCGA-CJ-4639-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:34315105delA	uc002xeb.2	-						RBM39_uc002xdz.2_Intron|RBM39_uc002xea.2_Intron|RBM39_uc010gfn.2_Intron|RBM39_uc010zvm.1_Intron|RBM39_uc002xeg.2_Intron|RBM39_uc002xec.2_Intron|RBM39_uc002xed.2_Intron|RBM39_uc002xee.2_Intron|RBM39_uc002xef.2_Intron|RBM39_uc010zvn.1_Intron	NM_184234	NP_909122	Q14498	RBM39_HUMAN	RNA binding motif protein 39 isoform a						mRNA processing|regulation of transcription, DNA-dependent|RNA splicing|transcription, DNA-dependent	centrosome|nuclear speck	nucleotide binding|protein binding|RNA binding			ovary(1)|central_nervous_system(1)	2	all_epithelial(2;0.00295)|Lung NSC(9;0.00453)|Breast(12;0.00544)|all_lung(11;0.00676)					ttgtctctacaaaaaaaaaat	0.050													5	5	---	---	---	---	
ACTR5	79913	broad.mit.edu	37	20	37384237	37384237	+	Intron	DEL	G	-	-	rs111326757		TCGA-CJ-4639-01A-02D-1386-10	TCGA-CJ-4639-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:37384237delG	uc002xjd.2	+							NM_024855	NP_079131	Q9H9F9	ARP5_HUMAN	ARP5 actin-related protein 5 homolog						DNA recombination|double-strand break repair|regulation of transcription, DNA-dependent|transcription, DNA-dependent|UV-damage excision repair	cytoplasm|Ino80 complex	ATP binding|protein binding				0		Myeloproliferative disorder(115;0.00878)				CACATCCCCCGCCCCACCAAA	0.249													4	2	---	---	---	---	
MMP9	4318	broad.mit.edu	37	20	44638964	44638965	+	Intron	INS	-	C	C	rs112211583		TCGA-CJ-4639-01A-02D-1386-10	TCGA-CJ-4639-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:44638964_44638965insC	uc002xqz.2	+							NM_004994	NP_004985	P14780	MMP9_HUMAN	matrix metalloproteinase 9 preproprotein						collagen catabolic process|macrophage differentiation|positive regulation of keratinocyte migration|proteolysis	extracellular space|proteinaceous extracellular matrix	collagen binding|metalloendopeptidase activity|zinc ion binding			ovary(1)|pancreas(1)	2		Myeloproliferative disorder(115;0.0122)			Glucosamine(DB01296)|Marimastat(DB00786)|Minocycline(DB01017)|Simvastatin(DB00641)	agtagacaaAAAAAAAAAAAAA	0.208													11	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	59367336	59367337	+	IGR	INS	-	GGCC	GGCC	rs141122391	by1000genomes	TCGA-CJ-4639-01A-02D-1386-10	TCGA-CJ-4639-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:59367336_59367337insGGCC								MIR646 (483711 upstream) : CDH4 (460222 downstream)																							aagccagggatggccggggaag	0.000													4	2	---	---	---	---	
LAMA5	3911	broad.mit.edu	37	20	60892951	60892952	+	Intron	INS	-	GGAGGGG	GGAGGGG			TCGA-CJ-4639-01A-02D-1386-10	TCGA-CJ-4639-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:60892951_60892952insGGAGGGG	uc002ycq.2	-							NM_005560	NP_005551	O15230	LAMA5_HUMAN	laminin alpha 5 precursor						angiogenesis|cell proliferation|cell recognition|cytoskeleton organization|endothelial cell differentiation|focal adhesion assembly|integrin-mediated signaling pathway|regulation of cell adhesion|regulation of cell migration|regulation of embryonic development|substrate adhesion-dependent cell spreading	extracellular space|laminin-1 complex|laminin-10 complex|laminin-11 complex	integrin binding			ovary(1)|pancreas(1)|skin(1)	3	Breast(26;1.57e-08)		BRCA - Breast invasive adenocarcinoma(19;4.36e-06)		Alteplase(DB00009)|Anistreplase(DB00029)|Reteplase(DB00015)|Tenecteplase(DB00031)	atggggggtgaggaggggggag	0.094													6	3	---	---	---	---	
BAGE2	85319	broad.mit.edu	37	21	11071749	11071750	+	Intron	INS	-	ACTT	ACTT	rs148241564		TCGA-CJ-4639-01A-02D-1386-10	TCGA-CJ-4639-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:11071749_11071750insACTT	uc002yit.1	-						BAGE_uc002yix.2_Intron	NM_182482	NP_872288			B melanoma antigen family, member 2 precursor												0			Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723)	UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247)		gctcagtgataacttaaccacc	0.000													4	2	---	---	---	---	
ASCC2	84164	broad.mit.edu	37	22	30185352	30185365	+	Intron	DEL	TGACCAGCCCCGAG	-	-	rs142877772	by1000genomes	TCGA-CJ-4639-01A-02D-1386-10	TCGA-CJ-4639-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:30185352_30185365delTGACCAGCCCCGAG	uc003agr.2	-						ASCC2_uc003ags.2_Intron|ASCC2_uc003agt.2_Intron|ASCC2_uc011akr.1_Intron	NM_032204	NP_115580	Q9H1I8	ASCC2_HUMAN	activating signal cointegrator 1 complex subunit						regulation of transcription, DNA-dependent|transcription, DNA-dependent						0			OV - Ovarian serous cystadenocarcinoma(5;0.000103)|Epithelial(10;0.0169)|all cancers(5;0.0259)			CCTGGGGCTCTGACCAGCCCCGAGCCTGGTGTTT	0.607													3	3	---	---	---	---	
SEC14L3	266629	broad.mit.edu	37	22	30858399	30858399	+	Intron	DEL	T	-	-			TCGA-CJ-4639-01A-02D-1386-10	TCGA-CJ-4639-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:30858399delT	uc003ahy.2	-						SEC14L3_uc003ahz.2_Intron|SEC14L3_uc003aia.2_Intron|SEC14L3_uc003aib.2_Intron	NM_174975	NP_777635	Q9UDX4	S14L3_HUMAN	SEC14-like 3							integral to membrane|intracellular	lipid binding|transporter activity			ovary(3)|pancreas(1)|skin(1)	5					Vitamin E(DB00163)	GAATCAGCACtttttttttct	0.244													9	4	---	---	---	---	
ARFGAP3	26286	broad.mit.edu	37	22	43227348	43227348	+	Intron	DEL	T	-	-	rs71754335		TCGA-CJ-4639-01A-02D-1386-10	TCGA-CJ-4639-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:43227348delT	uc003bdd.2	-						ARFGAP3_uc010gzf.2_Intron|ARFGAP3_uc011apu.1_Intron	NM_014570	NP_055385	Q9NP61	ARFG3_HUMAN	ADP-ribosylation factor GTPase activating						intracellular protein transport|protein secretion|regulation of ARF GTPase activity|vesicle-mediated transport	cytosol|Golgi membrane	ARF GTPase activator activity|protein transporter activity|zinc ion binding			breast(1)	1						TAGGTTTCAGttttttttttt	0.045													4	2	---	---	---	---	
TMSL3	7117	broad.mit.edu	37	X	12994867	12994868	+	Intron	INS	-	T	T	rs138495959		TCGA-CJ-4639-01A-02D-1386-10	TCGA-CJ-4639-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:12994867_12994868insT	uc004cvf.2	+							NM_021109	NP_066932			thymosin, beta 4												0		all_cancers(2;6.48e-24)|all_epithelial(2;3.86e-25)|Colorectal(2;8.52e-12)|all_lung(2;3.73e-07)|Lung NSC(2;7.99e-07)|Renal(2;0.0243)|Hepatocellular(203;0.0411)		Epithelial(2;5.28e-11)|OV - Ovarian serous cystadenocarcinoma(123;8.9e-10)|all cancers(2;3.21e-09)|STAD - Stomach adenocarcinoma(1;0.0201)		CTCCCTCCATCTTTTTTTTTTT	0.396													5	3	---	---	---	---	
SMS	6611	broad.mit.edu	37	X	21997306	21997307	+	Intron	INS	-	T	T			TCGA-CJ-4639-01A-02D-1386-10	TCGA-CJ-4639-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:21997306_21997307insT	uc004dag.2	+						SMS_uc010nfs.2_Intron|SMS_uc010nft.2_Intron	NM_004595	NP_004586	P52788	SPSY_HUMAN	spermine synthase						methionine metabolic process|spermine biosynthetic process	cytosol	spermidine synthase activity|spermine synthase activity			ovary(1)	1					Spermine(DB00127)	AAAATTAATtcttttttttttt	0.158													2	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	47547849	47547850	+	IGR	INS	-	A	A			TCGA-CJ-4639-01A-02D-1386-10	TCGA-CJ-4639-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:47547849_47547850insA								LOC100133957 (28073 upstream) : ZNF81 (148451 downstream)																							cctgtctctacaaaaaaaaaaa	0.000													11	7	---	---	---	---	
WDR13	64743	broad.mit.edu	37	X	48457035	48457035	+	Intron	DEL	C	-	-			TCGA-CJ-4639-01A-02D-1386-10	TCGA-CJ-4639-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:48457035delC	uc004dkh.1	+						WDR13_uc010nif.1_Intron|WDR13_uc004dki.1_Intron|WDR13_uc004dkj.1_Intron|WDR13_uc004dkk.1_Intron|WDR13_uc004dkl.3_5'UTR|WDR13_uc011mme.1_5'Flank	NM_017883	NP_060353	Q9H1Z4	WDR13_HUMAN	WD repeat domain 13 protein							cytoplasm|nucleus				ovary(2)	2						TCCTGCCGTACCCCCCCCCCC	0.602													5	4	---	---	---	---	
DLG3	1741	broad.mit.edu	37	X	69718131	69718132	+	Intron	INS	-	T	T			TCGA-CJ-4639-01A-02D-1386-10	TCGA-CJ-4639-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:69718131_69718132insT	uc004dyi.1	+						DLG3_uc004dyj.1_Intron|DLG3_uc011mpn.1_Intron	NM_021120	NP_066943	Q92796	DLG3_HUMAN	synapse-associated protein 102 isoform a						axon guidance|negative regulation of cell proliferation|synaptic transmission	plasma membrane	guanylate kinase activity			large_intestine(1)|pancreas(1)	2	Renal(35;0.156)					GGCTTCATGGCTTCTGGGCCTT	0.510													5	3	---	---	---	---	
CENPI	2491	broad.mit.edu	37	X	100356526	100356526	+	Intron	DEL	T	-	-			TCGA-CJ-4639-01A-02D-1386-10	TCGA-CJ-4639-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:100356526delT	uc004egx.2	+						CENPI_uc011mrg.1_Intron|CENPI_uc004egy.2_Intron	NM_006733	NP_006724	Q92674	CENPI_HUMAN	centromere protein I						CenH3-containing nucleosome assembly at centromere|mitotic prometaphase	cytosol|kinetochore|nucleoplasm	protein binding			skin(1)	1						cctttTTTTCTTTTTTTTTTT	0.095													4	2	---	---	---	---	
ODZ1	10178	broad.mit.edu	37	X	124004504	124004504	+	Intron	DEL	T	-	-			TCGA-CJ-4639-01A-02D-1386-10	TCGA-CJ-4639-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:124004504delT	uc004euj.2	-						ODZ1_uc011muj.1_Intron|ODZ1_uc010nqy.2_Intron	NM_014253	NP_055068	Q9UKZ4	TEN1_HUMAN	odz, odd Oz/ten-m homolog 1 isoform 3						immune response|negative regulation of cell proliferation|nervous system development|signal transduction	extracellular region	heparin binding			ovary(11)|breast(4)|large_intestine(2)|skin(2)|pancreas(2)|upper_aerodigestive_tract(1)|lung(1)	23						gcctcaagtattttttttttt	0.000													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	134358968	134358969	+	IGR	DEL	AC	-	-			TCGA-CJ-4639-01A-02D-1386-10	TCGA-CJ-4639-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:134358968_134358969delAC								CXorf48 (53217 upstream) : ZNF75D (23920 downstream)																							CAGAGAATAAacacacacacac	0.337													7	4	---	---	---	---	
