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
VPS13D	55187	broad.mit.edu	37	1	12302569	12302569	+	Splice_Site	SNP	G	T	T			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:12302569G>T	uc001atv.2	+	3	239	c.98_splice	c.e3-1	p.G33_splice	VPS13D_uc001atw.2_Splice_Site_p.G33_splice	NM_015378	NP_056193	Q5THJ4	VP13D_HUMAN	vacuolar protein sorting 13D isoform 1						protein localization					ovary(4)|pancreas(1)	5	Ovarian(185;0.249)	Lung NSC(185;4.08e-05)|all_lung(284;4.55e-05)|Renal(390;0.000147)|Colorectal(325;0.00058)|Breast(348;0.00093)|Ovarian(437;0.00965)|Hepatocellular(190;0.0202)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0327)|Colorectal(212;4.63e-06)|BRCA - Breast invasive adenocarcinoma(304;0.000289)|COAD - Colon adenocarcinoma(227;0.000801)|Kidney(185;0.00216)|KIRC - Kidney renal clear cell carcinoma(229;0.00544)|STAD - Stomach adenocarcinoma(313;0.012)|READ - Rectum adenocarcinoma(331;0.0476)|Lung(427;0.209)		TTTATTTTTAGGTGCTGTTGA	0.343													8	759	---	---	---	---	PASS
NBPF1	55672	broad.mit.edu	37	1	16918543	16918543	+	5'UTR	SNP	A	G	G			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:16918543A>G	uc009vos.1	-	7					NBPF1_uc010oce.1_Intron	NM_017940	NP_060410	Q3BBV0	NBPF1_HUMAN	hypothetical protein LOC55672							cytoplasm					0				UCEC - Uterine corpus endometrioid carcinoma (279;0.00459)|BRCA - Breast invasive adenocarcinoma(304;7.52e-06)|COAD - Colon adenocarcinoma(227;1.05e-05)|Kidney(64;0.00016)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.179)		GAAGAGGTGGAGCCAGGGACT	0.458													8	148	---	---	---	---	PASS
RBBP4	5928	broad.mit.edu	37	1	33138418	33138418	+	Missense_Mutation	SNP	G	T	T			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:33138418G>T	uc001bvr.2	+	11	1287	c.1128G>T	c.(1126-1128)AAG>AAT	p.K376N	RBBP4_uc001bvs.2_Missense_Mutation_p.K375N|RBBP4_uc010ohj.1_Missense_Mutation_p.K124N|RBBP4_uc010ohk.1_Missense_Mutation_p.K341N	NM_005610	NP_005601	Q09028	RBBP4_HUMAN	retinoblastoma binding protein 4 isoform a	376	WD 6.				cell cycle|CenH3-containing nucleosome assembly at centromere|DNA replication|negative regulation of cell proliferation|regulation of transcription, DNA-dependent|transcription, DNA-dependent	CAF-1 complex|ESC/E(Z) complex|NuRD complex|NURF complex|Sin3 complex	histone binding|histone deacetylase binding			ovary(1)	1		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0837)				ATACTGCCAAGATATCTGATT	0.378													6	391	---	---	---	---	PASS
ZMYM4	9202	broad.mit.edu	37	1	35790967	35790967	+	Nonsense_Mutation	SNP	C	T	T			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:35790967C>T	uc001byt.2	+	2	126	c.46C>T	c.(46-48)CAA>TAA	p.Q16*	ZMYM4_uc009vuu.2_5'UTR|ZMYM4_uc001byu.2_5'UTR	NM_005095	NP_005086	Q5VZL5	ZMYM4_HUMAN	zinc finger protein 262	16					multicellular organismal development		DNA binding|zinc ion binding			large_intestine(2)|ovary(1)|kidney(1)|skin(1)	5		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0887)				CCAGTTTGAACAAAAAAGTGG	0.318													59	717	---	---	---	---	PASS
GNL2	29889	broad.mit.edu	37	1	38048399	38048399	+	Missense_Mutation	SNP	G	T	T			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:38048399G>T	uc001cbk.2	-	7	938	c.775C>A	c.(775-777)CTT>ATT	p.L259I	GNL2_uc010oif.1_Missense_Mutation_p.L100I	NM_013285	NP_037417	Q13823	NOG2_HUMAN	guanine nucleotide binding protein-like 2	259					ribosome biogenesis	nucleolus	GTP binding|GTPase activity|protein binding			ovary(1)|central_nervous_system(1)	2		Myeloproliferative disorder(586;0.0393)				GTTGGAACAAGGTCACATTTG	0.393													6	404	---	---	---	---	PASS
DAB1	1600	broad.mit.edu	37	1	57481090	57481090	+	Missense_Mutation	SNP	C	T	T			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:57481090C>T	uc001cys.1	-	14	1584	c.910G>A	c.(910-912)GGC>AGC	p.G304S	DAB1_uc001cyt.1_Missense_Mutation_p.G302S|DAB1_uc001cyq.1_Missense_Mutation_p.G302S|DAB1_uc001cyr.1_Missense_Mutation_p.G218S|DAB1_uc009vzw.1_Missense_Mutation_p.G286S|DAB1_uc009vzx.1_Missense_Mutation_p.G304S	NM_021080	NP_066566	O75553	DAB1_HUMAN	disabled homolog 1	337					cell differentiation|nervous system development					skin(2)|ovary(1)	3						AGGACAGCGCCCATTGCAACG	0.552													4	8	---	---	---	---	PASS
JUN	3725	broad.mit.edu	37	1	59248705	59248705	+	Missense_Mutation	SNP	G	T	T			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:59248705G>T	uc001cze.2	-	1	1081	c.38C>A	c.(37-39)GCC>GAC	p.A13D	uc001czf.2_5'Flank|uc010oop.1_5'Flank	NM_002228	NP_002219	P05412	JUN_HUMAN	jun oncogene	13					innate immune response|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|negative regulation by host of viral transcription|negative regulation of DNA binding|negative regulation of transcription, DNA-dependent|positive regulation by host of viral transcription|positive regulation of transcription from RNA polymerase II promoter|regulation of sequence-specific DNA binding transcription factor activity|SMAD protein import into nucleus|SMAD protein signal transduction|stress-activated MAPK cascade|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway|transforming growth factor beta receptor signaling pathway		R-SMAD binding|Rho GTPase activator activity|sequence-specific enhancer binding RNA polymerase II transcription factor activity|transcription coactivator activity|transcription factor binding|transcription regulatory region DNA binding				0	all_cancers(7;8.55e-07)				Arsenic trioxide(DB01169)|Irbesartan(DB01029)|Vinblastine(DB00570)	GGCGTTGAGGGCATCGTCATA	0.557			A		sarcoma								5	13	---	---	---	---	PASS
INADL	10207	broad.mit.edu	37	1	62330053	62330053	+	Silent	SNP	G	A	A			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:62330053G>A	uc001dab.2	+	20	2697	c.2583G>A	c.(2581-2583)TTG>TTA	p.L861L	INADL_uc009waf.1_Silent_p.L861L|INADL_uc001daa.2_Silent_p.L861L|INADL_uc001dad.3_Silent_p.L558L|INADL_uc001dac.2_RNA	NM_176877	NP_795352	Q8NI35	INADL_HUMAN	InaD-like	861					intracellular signal transduction|tight junction assembly	apical plasma membrane|perinuclear region of cytoplasm|tight junction	protein binding			ovary(3)|skin(1)	4						CTCCTAGATTGCAGGAAATGG	0.408													5	223	---	---	---	---	PASS
SGIP1	84251	broad.mit.edu	37	1	67199498	67199498	+	Missense_Mutation	SNP	C	A	A			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:67199498C>A	uc001dcr.2	+	21	2183	c.1966C>A	c.(1966-1968)CTA>ATA	p.L656I	SGIP1_uc010opd.1_Missense_Mutation_p.L256I|SGIP1_uc001dcs.2_Missense_Mutation_p.L256I|SGIP1_uc001dct.2_Missense_Mutation_p.L258I|SGIP1_uc009wat.2_Missense_Mutation_p.L450I|SGIP1_uc001dcu.2_Missense_Mutation_p.L161I	NM_032291	NP_115667	Q9BQI5	SGIP1_HUMAN	SH3-domain GRB2-like (endophilin) interacting	656					positive regulation of energy homeostasis|positive regulation of feeding behavior|positive regulation of receptor-mediated endocytosis|response to dietary excess	AP-2 adaptor complex	microtubule binding|phospholipid binding|SH3 domain binding			ovary(3)	3						GATGACTCACCTAAAGAAAGT	0.368													6	457	---	---	---	---	PASS
RPF1	80135	broad.mit.edu	37	1	84955374	84955374	+	Missense_Mutation	SNP	C	A	A			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:84955374C>A	uc001djv.3	+	4	470	c.425C>A	c.(424-426)CCC>CAC	p.P142H		NM_025065	NP_079341	Q9H9Y2	RPF1_HUMAN	RNA processing factor 1	142	Brix.				rRNA processing|translation	nucleolus	aminoacyl-tRNA ligase activity|ATP binding|rRNA binding				0						CAGACTTCTCCCAAGATTCTC	0.318													6	461	---	---	---	---	PASS
EXTL2	2135	broad.mit.edu	37	1	101339639	101339639	+	Nonsense_Mutation	SNP	C	T	T			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:101339639C>T	uc001dtk.1	-	5	1189	c.852G>A	c.(850-852)TGG>TGA	p.W284*	EXTL2_uc001dtl.1_Nonsense_Mutation_p.W284*|EXTL2_uc010ouk.1_Nonsense_Mutation_p.W271*|EXTL2_uc001dtm.1_Nonsense_Mutation_p.W283*	NM_001439	NP_001430	Q9UBQ6	EXTL2_HUMAN	exostoses-like 2	284	Lumenal (Potential).				N-acetylglucosamine metabolic process|UDP-N-acetylgalactosamine metabolic process	extracellular region|integral to membrane|intrinsic to endoplasmic reticulum membrane	alpha-1,4-N-acetylgalactosaminyltransferase activity|glucuronyl-galactosyl-proteoglycan 4-alpha-N-acetylglucosaminyltransferase activity|metal ion binding			skin(1)	1		all_epithelial(167;2.48e-06)|all_lung(203;0.000414)|Lung NSC(277;0.000946)		Epithelial(280;0.0425)|all cancers(265;0.0628)|COAD - Colon adenocarcinoma(174;0.148)|Colorectal(144;0.167)|Lung(183;0.195)		CAGCTCGATGCCACATTCCAG	0.398													5	234	---	---	---	---	PASS
NBPF9	400818	broad.mit.edu	37	1	144620095	144620095	+	Splice_Site	SNP	G	T	T			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:144620095G>T	uc009wig.1	+	8	854	c.778_splice	c.e8+1	p.V260_splice	NBPF9_uc010oxn.1_Intron|NBPF9_uc010oxo.1_Splice_Site_p.V260_splice|NBPF9_uc010oxr.1_Intron|NBPF9_uc010oxt.1_Intron|NBPF9_uc001ekg.1_Intron|NBPF9_uc001ekk.1_Intron|NBPF10_uc009wir.2_Intron|NBPF9_uc010oyd.1_Intron|NBPF9_uc010oye.1_Splice_Site_p.V191_splice|NBPF9_uc001eli.3_Splice_Site|NBPF9_uc010oyf.1_Splice_Site_p.V191_splice|NBPF9_uc010oyg.1_Splice_Site_p.V225_splice|NBPF9_uc009wii.1_Splice_Site	NM_001037675	NP_001032764	Q3BBV1	NBPFK_HUMAN	hypothetical protein LOC400818							cytoplasm					0						ATTCTCCCAGGTAGCCTCTAT	0.393													7	83	---	---	---	---	PASS
MTMR11	10903	broad.mit.edu	37	1	149908474	149908474	+	Intron	SNP	C	T	T			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:149908474C>T	uc001etl.3	-						MTMR11_uc001etm.1_5'Flank|MTMR11_uc010pbm.1_5'Flank|MTMR11_uc010pbn.1_5'Flank|MTMR11_uc010pbo.1_Intron	NM_001145862	NP_001139334	A4FU01	MTMRB_HUMAN	myotubularin related protein 11 isoform a								phosphatase activity			central_nervous_system(1)	1	Breast(34;0.0009)|Ovarian(49;0.0377)|all_hematologic(923;0.0597)|Hepatocellular(266;0.161)|Colorectal(459;0.171)		LUSC - Lung squamous cell carcinoma(543;0.221)|STAD - Stomach adenocarcinoma(528;0.247)			cttctccttacccccatctct	0.244													54	101	---	---	---	---	PASS
DCST2	127579	broad.mit.edu	37	1	155006218	155006218	+	5'UTR	SNP	C	A	A			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:155006218C>A	uc001fgm.2	-	1					DCST2_uc009wpb.2_RNA|DCST1_uc010per.1_5'Flank|DCST1_uc001fgn.1_5'Flank|DCST1_uc010pes.1_5'Flank	NM_144622	NP_653223	Q5T1A1	DCST2_HUMAN	DC-STAMP domain containing 2							integral to membrane				ovary(2)|central_nervous_system(1)	3	all_epithelial(22;2.77e-30)|all_lung(78;4.1e-28)|all_hematologic(923;0.0359)|Hepatocellular(266;0.0877)		BRCA - Breast invasive adenocarcinoma(34;0.00034)			CAGGAGATGCCCGCTGACTTC	0.537													5	17	---	---	---	---	PASS
ASH1L	55870	broad.mit.edu	37	1	155452156	155452156	+	Nonsense_Mutation	SNP	C	A	A			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:155452156C>A	uc009wqq.2	-	3	985	c.505G>T	c.(505-507)GGA>TGA	p.G169*	ASH1L_uc001fkt.2_Nonsense_Mutation_p.G169*|ASH1L_uc009wqr.1_Nonsense_Mutation_p.G169*	NM_018489	NP_060959	Q9NR48	ASH1L_HUMAN	absent, small, or homeotic 1-like	169					cell-cell signaling|DNA packaging|regulation of transcription, DNA-dependent|transcription from RNA polymerase II promoter	chromosome|Golgi apparatus|nucleus|tight junction	DNA binding|histone-lysine N-methyltransferase activity|zinc ion binding			skin(5)|ovary(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)|kidney(1)|pancreas(1)	11	Hepatocellular(266;0.0997)|all_neural(408;0.129)|all_hematologic(923;0.145)		Epithelial(20;1.74e-08)|all cancers(21;3.29e-08)|BRCA - Breast invasive adenocarcinoma(34;0.021)			TTGTTTTCTCCCTGTGAATGA	0.423													6	292	---	---	---	---	PASS
NES	10763	broad.mit.edu	37	1	156641308	156641308	+	Missense_Mutation	SNP	G	A	A			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:156641308G>A	uc001fpq.2	-	4	2805	c.2672C>T	c.(2671-2673)TCA>TTA	p.S891L		NM_006617	NP_006608	P48681	NEST_HUMAN	nestin	891	Tail.			QGAMNPLEKEIQEPLESVEVNQETFRLLEEENQESLRSLGA WNLENLRSPEE -> KSGGNESSRKGNSRTTGVCGSEPRDI QTPGRGESGIIEISGSMEPGEFEISRG (in Ref. 1; CAA46780).	brain development|embryonic camera-type eye development|G2/M transition of mitotic cell cycle|negative regulation of apoptosis|positive regulation of intermediate filament depolymerization|positive regulation of neural precursor cell proliferation|stem cell proliferation	cytoplasm|intermediate filament	intermediate filament binding|structural molecule activity			ovary(6)	6	all_hematologic(923;0.088)|Hepatocellular(266;0.158)					AGATCTCAATGATTCCTGATT	0.463													11	161	---	---	---	---	PASS
KCNT2	343450	broad.mit.edu	37	1	196254849	196254849	+	Nonsense_Mutation	SNP	G	A	A			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:196254849G>A	uc001gtd.1	-	23	2695	c.2635C>T	c.(2635-2637)CGA>TGA	p.R879*	KCNT2_uc009wyt.1_RNA|KCNT2_uc001gte.1_Nonsense_Mutation_p.R805*|KCNT2_uc001gtf.1_Nonsense_Mutation_p.R855*|KCNT2_uc001gtg.1_RNA|KCNT2_uc009wyu.2_Nonsense_Mutation_p.R855*|KCNT2_uc001gth.1_Nonsense_Mutation_p.R376*	NM_198503	NP_940905	Q6UVM3	KCNT2_HUMAN	potassium channel, subfamily T, member 2	879	Cytoplasmic (Potential).					voltage-gated potassium channel complex	ATP binding|calcium-activated potassium channel activity|voltage-gated potassium channel activity			ovary(5)|breast(1)|skin(1)	7						AAAGGCAGTCGAAACATAAAG	0.383													61	137	---	---	---	---	PASS
ASPM	259266	broad.mit.edu	37	1	197074130	197074130	+	Silent	SNP	A	G	G			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:197074130A>G	uc001gtu.2	-	18	4508	c.4251T>C	c.(4249-4251)TAT>TAC	p.Y1417Y	ASPM_uc001gtv.2_Intron|ASPM_uc001gtw.3_Intron	NM_018136	NP_060606	Q8IZT6	ASPM_HUMAN	asp (abnormal spindle)-like, microcephaly	1417	IQ 2.				mitosis	cytoplasm|nucleus	calmodulin binding			ovary(4)|central_nervous_system(2)	6						TTAGCATTTCATATCTTTGTT	0.313													9	667	---	---	---	---	PASS
ASPM	259266	broad.mit.edu	37	1	197111830	197111830	+	Missense_Mutation	SNP	T	C	C			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:197111830T>C	uc001gtu.2	-	3	1809	c.1552A>G	c.(1552-1554)AAA>GAA	p.K518E	ASPM_uc001gtv.2_Missense_Mutation_p.K518E|ASPM_uc001gtw.3_Intron	NM_018136	NP_060606	Q8IZT6	ASPM_HUMAN	asp (abnormal spindle)-like, microcephaly	518					mitosis	cytoplasm|nucleus	calmodulin binding			ovary(4)|central_nervous_system(2)	6						AGACATCTTTTTGCTTTTGGT	0.338													7	521	---	---	---	---	PASS
KIF14	9928	broad.mit.edu	37	1	200555334	200555334	+	Missense_Mutation	SNP	G	C	C			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:200555334G>C	uc010ppk.1	-	19	3575	c.3136C>G	c.(3136-3138)CGC>GGC	p.R1046G	KIF14_uc010ppj.1_Missense_Mutation_p.R555G	NM_014875	NP_055690	Q15058	KIF14_HUMAN	kinesin family member 14	1046	Potential.|Required for CIT-binding.				microtubule-based movement	cytoplasm|microtubule|nucleus|spindle	ATP binding|microtubule motor activity|protein binding			breast(3)|ovary(2)|skin(2)	7						CTTGCATGGCGGATGCTATGG	0.328													150	435	---	---	---	---	PASS
CEP170	9859	broad.mit.edu	37	1	243303430	243303430	+	Intron	SNP	C	A	A			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:243303430C>A	uc001hzs.2	-						CEP170_uc001hzt.2_Intron|CEP170_uc001hzu.2_Intron|CEP170_uc001hzr.2_Translation_Start_Site|CEP170_uc001hzv.1_Intron	NM_014812	NP_055627	Q5SW79	CE170_HUMAN	centrosomal protein 170kDa isoform alpha							centriole|microtubule|spindle				ovary(1)|haematopoietic_and_lymphoid_tissue(1)	2	all_neural(11;0.101)	all_cancers(173;0.003)	all cancers(7;5.81e-06)|GBM - Glioblastoma multiforme(7;0.000443)|OV - Ovarian serous cystadenocarcinoma(106;0.0101)			GAAAGCAAACCTTTATGAGAA	0.353													46	126	---	---	---	---	PASS
RNF144A	9781	broad.mit.edu	37	2	7164573	7164573	+	Missense_Mutation	SNP	G	C	C			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:7164573G>C	uc002qys.2	+	7	1025	c.583G>C	c.(583-585)GAC>CAC	p.D195H	RNF144A_uc002qyt.2_Missense_Mutation_p.D44H	NM_014746	NP_055561	P50876	R144A_HUMAN	ring finger protein 144	195	RING-type 2; degenerate.					Golgi apparatus|integral to membrane	ligase activity|zinc ion binding			ovary(1)|kidney(1)	2	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)	all_cancers(51;0.226)		OV - Ovarian serous cystadenocarcinoma(76;0.195)		CATCGAGCGAGACGAAGGCTG	0.557													7	29	---	---	---	---	PASS
IFT172	26160	broad.mit.edu	37	2	27693862	27693862	+	Missense_Mutation	SNP	T	C	C			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:27693862T>C	uc002rku.2	-	16	1676	c.1625A>G	c.(1624-1626)AAC>AGC	p.N542S	IFT172_uc002rkw.2_Missense_Mutation_p.N542S	NM_015662	NP_056477	Q9UG01	IF172_HUMAN	selective LIM binding factor homolog	542	WD 9.				cilium assembly	cilium	binding			large_intestine(1)|ovary(1)	2	Acute lymphoblastic leukemia(172;0.155)					ACTGTTTCGGTTCTGAGCTAC	0.473													5	160	---	---	---	---	PASS
MOBKL1B	55233	broad.mit.edu	37	2	74392329	74392329	+	Intron	SNP	G	T	T			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:74392329G>T	uc002skh.3	-						MOBKL1B_uc002ski.2_Nonsense_Mutation_p.S142*	NM_018221	NP_060691	Q9H8S9	MOL1B_HUMAN	Mob4B protein						hippo signaling cascade		metal ion binding|protein binding				0						AGAATACTTCGACAATGTTAA	0.219													5	211	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	2	96643871	96643871	+	RNA	SNP	T	C	C			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:96643871T>C	uc010yug.1	-	6		c.883A>G								Homo sapiens cDNA FLJ54441 complete cds, highly similar to Homo sapiens ankyrin repeat domain 36 (ANKRD36), mRNA.																		AAATCTTACCTGGATTGCTAT	0.234													6	164	---	---	---	---	PASS
PMS1	5378	broad.mit.edu	37	2	190728600	190728600	+	Missense_Mutation	SNP	C	T	T			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:190728600C>T	uc002urh.3	+	10	2517	c.1988C>T	c.(1987-1989)GCC>GTC	p.A663V	PMS1_uc010zga.1_3'UTR|PMS1_uc010zgb.1_Missense_Mutation_p.A602V|PMS1_uc002urk.3_Missense_Mutation_p.A624V|PMS1_uc002uri.3_Intron|PMS1_uc010zgc.1_Missense_Mutation_p.A487V|PMS1_uc010zgd.1_Missense_Mutation_p.A487V|PMS1_uc002urj.2_RNA|PMS1_uc010fry.1_Missense_Mutation_p.A624V|PMS1_uc010frz.2_Intron|PMS1_uc002url.2_Intron|PMS1_uc002urm.2_RNA|PMS1_uc002urn.1_Missense_Mutation_p.A331V	NM_000534	NP_000525	P54277	PMS1_HUMAN	postmeiotic segregation 1 isoform a	663					mismatch repair|reciprocal meiotic recombination	MutLalpha complex	ATP binding|ATPase activity|mismatched DNA binding			ovary(2)|kidney(1)|central_nervous_system(1)	4			OV - Ovarian serous cystadenocarcinoma(117;0.0013)|Epithelial(96;0.0263)|all cancers(119;0.0751)			TGGAATTTGGCCCAGAAGCAC	0.363			Mis|N			colorectal|endometrial|ovarian		Direct_reversal_of_damage|MMR					6	376	---	---	---	---	PASS
FN1	2335	broad.mit.edu	37	2	216295472	216295472	+	Silent	SNP	T	A	A			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:216295472T>A	uc002vfa.2	-	5	917	c.651A>T	c.(649-651)GGA>GGT	p.G217G	FN1_uc002vfb.2_Silent_p.G217G|FN1_uc002vfc.2_Silent_p.G217G|FN1_uc002vfd.2_Silent_p.G217G|FN1_uc002vfe.2_Silent_p.G217G|FN1_uc002vff.2_Silent_p.G217G|FN1_uc002vfg.2_Silent_p.G217G|FN1_uc002vfh.2_Silent_p.G217G|FN1_uc002vfi.2_Silent_p.G217G|FN1_uc002vfj.2_Silent_p.G217G|FN1_uc002vfl.2_Silent_p.G217G	NM_212482	NP_997647	P02751	FINC_HUMAN	fibronectin 1 isoform 1 preproprotein	217	Fibrin- and heparin-binding 1.|Fibronectin type-I 4.				acute-phase response|angiogenesis|leukocyte migration|peptide cross-linking|platelet activation|platelet degranulation|regulation of cell shape|substrate adhesion-dependent cell spreading	ER-Golgi intermediate compartment|fibrinogen complex|platelet alpha granule lumen|proteinaceous extracellular matrix	collagen binding|extracellular matrix structural constituent|heparin binding			central_nervous_system(7)|large_intestine(2)|breast(2)|ovary(1)|pancreas(1)	13		Renal(323;0.127)		Epithelial(149;9.59e-07)|all cancers(144;0.000174)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00948)	Alteplase(DB00009)|Anistreplase(DB00029)|Reteplase(DB00015)|Tenecteplase(DB00031)	CGCTGCCTTCTCCCAGGCAAG	0.453													7	102	---	---	---	---	PASS
TM4SF20	79853	broad.mit.edu	37	2	228230921	228230921	+	Missense_Mutation	SNP	C	A	A			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:228230921C>A	uc002vpb.2	-	3	327	c.289G>T	c.(289-291)GGT>TGT	p.G97C		NM_024795	NP_079071	Q53R12	T4S20_HUMAN	transmembrane 4 L six family member 20	97	Helical; (Potential).					integral to membrane|plasma membrane					0		Renal(207;0.025)|all_lung(227;0.123)|Esophageal squamous(248;0.23)|all_hematologic(139;0.248)		Epithelial(121;3.8e-11)|all cancers(144;2.57e-08)|Lung(261;0.00942)|LUSC - Lung squamous cell carcinoma(224;0.0115)		TACAGAGCACCAATGACTGTG	0.368													6	313	---	---	---	---	PASS
KIF1A	547	broad.mit.edu	37	2	241686667	241686667	+	Nonsense_Mutation	SNP	G	A	A			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:241686667G>A	uc002vzy.2	-	27	2892	c.2746C>T	c.(2746-2748)CAG>TAG	p.Q916*	KIF1A_uc010fzk.2_Nonsense_Mutation_p.Q1017*|KIF1A_uc002vzz.1_Nonsense_Mutation_p.Q1017*	NM_004321	NP_004312	Q12756	KIF1A_HUMAN	axonal transport of synaptic vesicles	916					anterograde axon cargo transport	cytoplasm|microtubule|nucleus	ATP binding|microtubule motor activity			lung(1)	1		all_epithelial(40;1.35e-15)|Breast(86;2.14e-05)|Renal(207;0.00183)|Ovarian(221;0.0228)|all_lung(227;0.0295)|all_neural(83;0.0459)|Lung NSC(271;0.0942)|all_hematologic(139;0.158)|Melanoma(123;0.16)|Hepatocellular(293;0.244)		Epithelial(32;6.12e-30)|all cancers(36;3.46e-27)|OV - Ovarian serous cystadenocarcinoma(60;1.38e-14)|Kidney(56;5e-09)|KIRC - Kidney renal clear cell carcinoma(57;5e-08)|BRCA - Breast invasive adenocarcinoma(100;5.87e-06)|Lung(119;0.00209)|LUSC - Lung squamous cell carcinoma(224;0.00902)|Colorectal(34;0.0282)|COAD - Colon adenocarcinoma(134;0.176)		TCAAAATGCTGGTCATCAAAG	0.552													19	58	---	---	---	---	PASS
CHL1	10752	broad.mit.edu	37	3	367660	367660	+	Missense_Mutation	SNP	T	A	A			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:367660T>A	uc003bou.2	+	4	381	c.110T>A	c.(109-111)ATC>AAC	p.I37N	CHL1_uc003bot.2_Missense_Mutation_p.I37N|CHL1_uc003bow.1_Missense_Mutation_p.I37N|CHL1_uc011asi.1_Missense_Mutation_p.I37N	NM_006614	NP_006605	O00533	CHL1_HUMAN	cell adhesion molecule with homology to L1CAM	37	Ig-like C2-type 1.|Extracellular (Potential).				axon guidance|cell adhesion|signal transduction	integral to membrane|plasma membrane|proteinaceous extracellular matrix				skin(5)|central_nervous_system(4)|large_intestine(2)|ovary(1)	12		all_cancers(2;1.14e-06)|all_epithelial(2;0.00367)|all_lung(1;0.061)|Lung NSC(2;0.201)		Epithelial(13;5.36e-06)|all cancers(10;1.4e-05)|OV - Ovarian serous cystadenocarcinoma(96;0.00323)|COAD - Colon adenocarcinoma(1;0.00925)|Colorectal(20;0.0198)		GTTCCAACAATCATAAAACAG	0.333													66	115	---	---	---	---	PASS
VHL	7428	broad.mit.edu	37	3	10188200	10188200	+	Missense_Mutation	SNP	C	A	A	rs5030811		TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:10188200C>A	uc003bvc.2	+	2	556	c.343C>A	c.(343-345)CAC>AAC	p.H115N	VHL_uc003bvd.2_Intron	NM_000551	NP_000542	P40337	VHL_HUMAN	von Hippel-Lindau tumor suppressor isoform 1	115	Involved in binding to CCT complex.		H -> Q (in VHLD; type II).		anti-apoptosis|cell morphogenesis|negative regulation of cell proliferation|negative regulation of transcription from RNA polymerase II promoter|positive regulation of cell differentiation|positive regulation of transcription, DNA-dependent|protein stabilization|protein ubiquitination|proteolysis	cytosol|endoplasmic reticulum|membrane|mitochondrion|nucleus	protein binding|transcription factor binding	p.H115N(5)|p.?(3)|p.H115Y(3)|p.H115fs*44(3)|p.H115D(1)|p.H115fs*41(1)|p.H115fs*42(1)|p.H115P(1)		kidney(1273)|soft_tissue(24)|adrenal_gland(15)|large_intestine(13)|pancreas(5)|endometrium(4)|thyroid(3)|upper_aerodigestive_tract(3)|central_nervous_system(2)|lung(2)|pleura(1)|paratesticular_tissues(1)	1346				Kidney(1;0.000404)|KIRC - Kidney renal clear cell carcinoma(1;0.000569)		CCCGATAGGTCACCTTTGGCT	0.333		1	D|Mis|N|F|S		renal|hemangioma|pheochromocytoma	renal|hemangioma|pheochromocytoma			von_Hippel-Lindau_disease|Chuvash_Polycythemia_|Pheochromocytoma_(Adrenal)_Familial				47	81	---	---	---	---	PASS
SETD2	29072	broad.mit.edu	37	3	47163209	47163209	+	Nonsense_Mutation	SNP	T	A	A			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:47163209T>A	uc003cqs.2	-	3	2970	c.2917A>T	c.(2917-2919)AGA>TGA	p.R973*	SETD2_uc003cqv.2_Nonsense_Mutation_p.R962*	NM_014159	NP_054878	Q9BYW2	SETD2_HUMAN	SET domain containing 2	973					regulation of transcription, DNA-dependent|transcription, DNA-dependent	chromosome|nucleus	DNA binding|histone-lysine N-methyltransferase activity|oxidoreductase activity|transition metal ion binding			kidney(24)|ovary(5)|skin(1)|central_nervous_system(1)|breast(1)	32		Acute lymphoblastic leukemia(5;0.0169)		BRCA - Breast invasive adenocarcinoma(193;0.000302)|KIRC - Kidney renal clear cell carcinoma(197;0.00732)|Kidney(197;0.00844)		CTTCCTCTTCTTTCAGGCAAT	0.408			N|F|S|Mis		clear cell renal carcinoma								37	75	---	---	---	---	PASS
NFKBIZ	64332	broad.mit.edu	37	3	101573504	101573504	+	Missense_Mutation	SNP	G	T	T			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:101573504G>T	uc003dvp.2	+	6	1535	c.1420G>T	c.(1420-1422)GAT>TAT	p.D474Y	NFKBIZ_uc003dvo.2_Missense_Mutation_p.D374Y|NFKBIZ_uc010hpo.2_Missense_Mutation_p.D374Y|NFKBIZ_uc003dvq.2_Missense_Mutation_p.D352Y	NM_031419	NP_113607	Q9BYH8	IKBZ_HUMAN	nuclear factor of kappa light polypeptide gene	474	Interaction with NFKB1/p50 (By similarity).				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus				ovary(2)	2						TCACATGCTGGATATTAAAGA	0.463													48	142	---	---	---	---	PASS
ALCAM	214	broad.mit.edu	37	3	105266275	105266275	+	Missense_Mutation	SNP	G	A	A			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:105266275G>A	uc003dvx.2	+	11	1822	c.1282G>A	c.(1282-1284)GGA>AGA	p.G428R	ALCAM_uc003dvw.1_Missense_Mutation_p.G428R|ALCAM_uc003dvy.2_Missense_Mutation_p.G428R|ALCAM_uc010hpp.2_Missense_Mutation_p.G150R|ALCAM_uc003dvz.2_Missense_Mutation_p.G62R	NM_001627	NP_001618	Q13740	CD166_HUMAN	activated leukocyte cell adhesion molecule	428	Extracellular (Potential).|Ig-like C2-type 3.				cell adhesion|signal transduction	integral to membrane	receptor binding			ovary(2)|breast(1)	3						TGATCCCAGTGGACTATCTAA	0.353													30	88	---	---	---	---	PASS
NAA50	80218	broad.mit.edu	37	3	113440571	113440571	+	3'UTR	SNP	G	T	T			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:113440571G>T	uc003ean.1	-	5					NAA50_uc010hqm.1_3'UTR|NAA50_uc011bij.1_3'UTR	NM_025146	NP_079422	Q9GZZ1	NAA50_HUMAN	N-acetyltransferase 13						N-terminal protein amino acid acetylation	cytoplasm	N-acetyltransferase activity|protein binding				0						TTTATTTGGCGACAAGCAAGT	0.408													5	247	---	---	---	---	PASS
PARP9	83666	broad.mit.edu	37	3	122259473	122259473	+	Silent	SNP	G	T	T			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:122259473G>T	uc010hri.2	-	8	1861	c.1716C>A	c.(1714-1716)TCC>TCA	p.S572S	PARP9_uc003eff.3_Silent_p.S537S|PARP9_uc011bjs.1_Silent_p.S537S|PARP9_uc003efg.2_Silent_p.S117S|PARP9_uc003efi.2_Silent_p.S537S|PARP9_uc003efh.2_Silent_p.S572S|PARP9_uc003efj.2_Silent_p.S537S	NM_001146102	NP_001139574	Q8IXQ6	PARP9_HUMAN	poly (ADP-ribose) polymerase family, member 9	572					cell migration	cytosol|nucleus	NAD+ ADP-ribosyltransferase activity|protein binding			ovary(1)|pancreas(1)|prostate(1)|skin(1)	4				GBM - Glioblastoma multiforme(114;0.0519)		TTTCTGTGATGGAGACACTTG	0.423													6	409	---	---	---	---	PASS
PIK3R4	30849	broad.mit.edu	37	3	130399522	130399522	+	Nonsense_Mutation	SNP	C	A	A			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:130399522C>A	uc003enj.2	-	19	4422	c.3841G>T	c.(3841-3843)GGA>TGA	p.G1281*		NM_014602	NP_055417	Q99570	PI3R4_HUMAN	phosphoinositide-3-kinase, regulatory subunit 4	1281					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						CTAGTACTTCCTGCAACAACA	0.408													6	270	---	---	---	---	PASS
ATP2C1	27032	broad.mit.edu	37	3	130678132	130678132	+	Missense_Mutation	SNP	G	T	T			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:130678132G>T	uc003enl.2	+	12	1068	c.846G>T	c.(844-846)TTG>TTT	p.L282F	ATP2C1_uc011blg.1_Missense_Mutation_p.L316F|ATP2C1_uc011blh.1_Missense_Mutation_p.L277F|ATP2C1_uc011bli.1_Missense_Mutation_p.L316F|ATP2C1_uc003enk.2_Missense_Mutation_p.L266F|ATP2C1_uc003enm.2_Missense_Mutation_p.L282F|ATP2C1_uc003enn.2_Missense_Mutation_p.L266F|ATP2C1_uc003eno.2_Missense_Mutation_p.L282F|ATP2C1_uc003enp.2_Missense_Mutation_p.L282F|ATP2C1_uc003enq.2_Missense_Mutation_p.L282F|ATP2C1_uc003enr.2_Missense_Mutation_p.L282F|ATP2C1_uc003ens.2_Missense_Mutation_p.L282F|ATP2C1_uc003ent.2_Missense_Mutation_p.L282F	NM_014382	NP_055197	P98194	AT2C1_HUMAN	calcium-transporting ATPase 2C1 isoform 1a	282	Helical; Name=3; (By similarity).				actin cytoskeleton reorganization|ATP biosynthetic process|calcium-dependent cell-cell adhesion|cellular calcium ion homeostasis|cellular manganese ion homeostasis|epidermis development|Golgi calcium ion homeostasis|Golgi calcium ion transport|positive regulation of I-kappaB kinase/NF-kappaB cascade	Golgi apparatus|Golgi membrane|integral to membrane|trans-Golgi network	ATP binding|ATP binding|calcium ion binding|calcium-transporting ATPase activity|manganese ion binding|manganese-transporting ATPase activity|metal ion binding|signal transducer activity			skin(1)	1					Arsenic trioxide(DB01169)|Desflurane(DB01189)|Enflurane(DB00228)|Halothane(DB01159)|Isoflurane(DB00753)|Methoxyflurane(DB01028)|Miconazole(DB01110)|Sevoflurane(DB01236)	TCATCATGTTGGTTGGCTGGT	0.338									Hailey-Hailey_disease				7	795	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	3	133921621	133921621	+	IGR	SNP	T	C	C			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:133921621T>C								RYK (-47965 upstream) : RYK (-45643 downstream)																							GCAAAACAGCTAATATTATTG	0.348													5	310	---	---	---	---	PASS
STAG1	10274	broad.mit.edu	37	3	136323188	136323188	+	Nonsense_Mutation	SNP	A	T	T			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:136323188A>T	uc003era.1	-	4	552	c.260T>A	c.(259-261)TTA>TAA	p.L87*	STAG1_uc003erb.1_Nonsense_Mutation_p.L87*|STAG1_uc003erc.1_5'UTR|STAG1_uc010hua.1_5'UTR|STAG1_uc003erd.2_5'UTR|STAG1_uc003ere.2_Nonsense_Mutation_p.L87*	NM_005862	NP_005853	Q8WVM7	STAG1_HUMAN	stromal antigen 1	87					cell division|chromosome segregation|mitotic metaphase/anaphase transition|mitotic prometaphase	cell junction|chromatin|chromosome, centromeric region|nucleoplasm	protein binding			ovary(2)	2						CACCTCAAATAATGTGACAGG	0.433													6	195	---	---	---	---	PASS
ATR	545	broad.mit.edu	37	3	142169377	142169377	+	Intron	SNP	A	C	C			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:142169377A>C	uc003eux.3	-						XRN1_uc003eus.2_5'Flank|XRN1_uc003eut.2_5'Flank|XRN1_uc003euu.2_5'Flank|XRN1_uc003euw.2_5'Flank|XRN1_uc011bnh.1_5'Flank|ATR_uc003euy.1_3'UTR	NM_001184	NP_001175	Q13535	ATR_HUMAN	ataxia telangiectasia and Rad3 related protein						cell cycle|cellular response to gamma radiation|cellular response to UV|DNA damage checkpoint|DNA repair|DNA replication|multicellular organismal development|negative regulation of DNA replication|peptidyl-serine phosphorylation|positive regulation of DNA damage response, signal transduction by p53 class mediator|protein autophosphorylation|replicative senescence	PML body	ATP binding|DNA binding|MutLalpha complex binding|MutSalpha complex binding|protein serine/threonine kinase activity			lung(5)|skin(5)|breast(4)|ovary(3)|stomach(1)|central_nervous_system(1)|liver(1)	20						CCAGAAAATCAGATCAAGGGA	0.388								Other_conserved_DNA_damage_response_genes					9	205	---	---	---	---	PASS
SERPINI2	5276	broad.mit.edu	37	3	167167189	167167189	+	Silent	SNP	A	G	G			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:167167189A>G	uc003fer.1	-	6	1024	c.966T>C	c.(964-966)GAT>GAC	p.D322D	SERPINI2_uc003fes.1_Silent_p.D332D|SERPINI2_uc003fet.1_Silent_p.D322D	NM_006217	NP_006208	O75830	SPI2_HUMAN	serpin peptidase inhibitor, clade I (pancpin),	322					cellular component movement|regulation of proteolysis	extracellular region	serine-type endopeptidase inhibitor activity			skin(2)|urinary_tract(1)	3						CTTCAGATGAATCTGGTTAAA	0.289													10	192	---	---	---	---	PASS
PRKCI	5584	broad.mit.edu	37	3	169998965	169998965	+	Missense_Mutation	SNP	G	T	T			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:169998965G>T	uc003fgs.2	+	10	1132	c.894G>T	c.(892-894)TGG>TGT	p.W298C		NM_002740	NP_002731	P41743	KPCI_HUMAN	protein kinase C, iota	298	Protein kinase.				anti-apoptosis|cellular membrane organization|cellular response to insulin stimulus|establishment or maintenance of epithelial cell apical/basal polarity|intracellular signal transduction|nerve growth factor receptor signaling pathway|positive regulation of establishment of protein localization in plasma membrane|positive regulation of glucose import|protein targeting to membrane|secretion|tight junction assembly|vesicle-mediated transport	cytosol|endosome|nucleus|polarisome	ATP binding|phospholipid binding|protein binding|protein kinase C activity|zinc ion binding			lung(2)|ovary(1)|breast(1)|skin(1)	5	all_cancers(22;6.45e-23)|all_epithelial(15;8.52e-28)|all_lung(20;6.31e-17)|Lung NSC(18;2.61e-16)|Ovarian(172;0.000337)|Breast(254;0.169)		Lung(28;2.71e-13)|STAD - Stomach adenocarcinoma(35;0.197)			ATATTGATTGGGTACAGACAG	0.368													6	443	---	---	---	---	PASS
USP13	8975	broad.mit.edu	37	3	179474854	179474854	+	Missense_Mutation	SNP	C	A	A			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:179474854C>A	uc003fkh.2	+	16	2017	c.1936C>A	c.(1936-1938)CAA>AAA	p.Q646K	USP13_uc003fkf.2_3'UTR	NM_003940	NP_003931	Q92995	UBP13_HUMAN	ubiquitin thiolesterase 13	646					ubiquitin-dependent protein catabolic process		cysteine-type endopeptidase activity|omega peptidase activity|protein binding|ubiquitin thiolesterase activity|ubiquitin-specific protease activity|zinc ion binding			ovary(1)	1	all_cancers(143;7.79e-15)|Ovarian(172;0.0338)|Breast(254;0.148)		OV - Ovarian serous cystadenocarcinoma(80;1e-25)|GBM - Glioblastoma multiforme(14;0.0169)			CCTGATGAACCAATTGATAGA	0.363													7	716	---	---	---	---	PASS
KIAA0232	9778	broad.mit.edu	37	4	6864413	6864413	+	Silent	SNP	G	A	A			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:6864413G>A	uc003gjr.3	+	7	2767	c.2304G>A	c.(2302-2304)CAG>CAA	p.Q768Q	KIAA0232_uc003gjq.3_Silent_p.Q768Q	NM_014743	NP_055558	Q92628	K0232_HUMAN	hypothetical protein LOC9778	768							ATP binding			ovary(2)	2						AAACTTGCCAGCAAAACAGTA	0.328													15	188	---	---	---	---	PASS
FRYL	285527	broad.mit.edu	37	4	48592777	48592777	+	Missense_Mutation	SNP	G	T	T			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:48592777G>T	uc003gyh.1	-	17	2011	c.1406C>A	c.(1405-1407)CCC>CAC	p.P469H	FRYL_uc003gyk.2_Missense_Mutation_p.P469H	NM_015030	NP_055845	O94915	FRYL_HUMAN	furry-like	469					regulation of transcription, DNA-dependent|transcription, DNA-dependent		protein binding			skin(1)	1						TGTTGGCATGGGTGGTTCACC	0.378													7	423	---	---	---	---	PASS
BBS12	166379	broad.mit.edu	37	4	123663519	123663519	+	Missense_Mutation	SNP	T	C	C			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:123663519T>C	uc003ieu.2	+	2	665	c.472T>C	c.(472-474)TGT>CGT	p.C158R		NM_152618	NP_689831	Q6ZW61	BBS12_HUMAN	Bardet-Biedl syndrome 12	158					cellular protein metabolic process	cilium	ATP binding			ovary(2)	2						TGTAAGTTTGTGTCCTTTTCT	0.378									Bardet-Biedl_syndrome				6	230	---	---	---	---	PASS
GK3P	2713	broad.mit.edu	37	4	166200096	166200096	+	Silent	SNP	C	A	A			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:166200096C>A	uc003ird.3	-	1	1080	c.702G>T	c.(700-702)CGG>CGT	p.R234R	KLHL2_uc003irb.2_Intron|KLHL2_uc011cjm.1_Intron|KLHL2_uc003irc.2_Intron|KLHL2_uc010ira.2_Intron	NM_000167	NP_000158			glycerol kinase isoform b												0						CAGAAGAACTCCGAACATGTG	0.438													8	309	---	---	---	---	PASS
PRKAA1	5562	broad.mit.edu	37	5	40764744	40764744	+	Splice_Site	SNP	T	C	C			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:40764744T>C	uc003jmc.2	-	8	1315	c.1309_splice	c.e8-1	p.V437_splice	PRKAA1_uc003jmb.2_Splice_Site_p.V452_splice	NM_006251	NP_006242	Q13131	AAPK1_HUMAN	protein kinase, AMP-activated, alpha 1 catalytic						activation of MAPK activity|cell cycle arrest|cholesterol biosynthetic process|fatty acid biosynthetic process|insulin receptor signaling pathway|negative regulation of glucosylceramide biosynthetic process|positive regulation of anti-apoptosis|positive regulation of cholesterol biosynthetic process|regulation of fatty acid oxidation|response to hypoxia	cytosol	ATP binding|cAMP-dependent protein kinase activity|metal ion binding|protein binding			breast(1)	1					Adenosine monophosphate(DB00131)|Adenosine triphosphate(DB00171)|Phenformin(DB00914)	GTTTACAACCTAGCACATGGT	0.323													5	322	---	---	---	---	PASS
BDP1	55814	broad.mit.edu	37	5	70806519	70806519	+	Missense_Mutation	SNP	G	T	T			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:70806519G>T	uc003kbp.1	+	17	3863	c.3600G>T	c.(3598-3600)TTG>TTT	p.L1200F	BDP1_uc003kbn.1_Missense_Mutation_p.L1200F|BDP1_uc003kbo.2_Missense_Mutation_p.L1200F	NM_018429	NP_060899	A6H8Y1	BDP1_HUMAN	transcription factor-like nuclear regulator	1200	7.|9 X 55 AA repeats of G-R-R-X-I-S-P-X-E-N- G-X-E-E-V-K-P-X-X-E-M-E-T-D-L-K-X-T-G-R- E-X-X-X-R-E-K-T-X-E-X-X-D-A-X-E-E-I-D-X- D-L-E-E-T.				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)		AGACAGATTTGGAAGAAACTG	0.423													5	143	---	---	---	---	PASS
FEM1C	56929	broad.mit.edu	37	5	114860153	114860153	+	Missense_Mutation	SNP	T	C	C			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:114860153T>C	uc003krb.1	-	3	2268	c.1706A>G	c.(1705-1707)GAT>GGT	p.D569G		NM_020177	NP_064562	Q96JP0	FEM1C_HUMAN	feminization 1 homolog a	569						cytoplasm				breast(2)|ovary(1)	3		all_cancers(142;0.000575)|all_epithelial(76;9.98e-06)|Prostate(80;0.00955)|Ovarian(225;0.0443)|all_lung(232;0.132)|Breast(839;0.195)		OV - Ovarian serous cystadenocarcinoma(64;2.5e-07)|Epithelial(69;2.66e-07)|all cancers(49;1.39e-05)		TTCCTTCTCATCCAGCAAGTC	0.363													65	229	---	---	---	---	PASS
SEPT8	23176	broad.mit.edu	37	5	132086877	132086877	+	3'UTR	SNP	C	A	A			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:132086877C>A	uc003kxr.2	-	10					CCNI2_uc003kxq.1_Intron|CCNI2_uc011cxg.1_Intron|CCNI2_uc011cxh.1_Intron	NM_001098811	NP_001092281	Q92599	SEPT8_HUMAN	septin 8 isoform a						cell cycle	septin complex	GTP binding|protein binding			ovary(2)	2		all_cancers(142;0.0751)|Breast(839;0.198)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			ACAGTTCCACCAGACTCCCAC	0.408													3	14	---	---	---	---	PASS
ANKHD1-EIF4EBP3	404734	broad.mit.edu	37	5	139905891	139905891	+	Silent	SNP	C	T	T			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:139905891C>T	uc003lfs.1	+	26	4927	c.4803C>T	c.(4801-4803)TGC>TGT	p.C1601C	ANKHD1_uc003lfr.2_Silent_p.C1601C|ANKHD1_uc003lfu.1_Silent_p.C1081C|ANKHD1-EIF4EBP3_uc011czh.1_Silent_p.C340C|ANKHD1_uc003lfw.2_Silent_p.C239C|ANKHD1_uc010jfl.2_Silent_p.C36C|ANKHD1-EIF4EBP3_uc003lfx.1_5'Flank	NM_020690	NP_065741	Q8IWZ2	Q8IWZ2_HUMAN	ANKHD1-EIF4EBP3 protein	1601						cytoplasm|nucleus	RNA binding			ovary(6)	6			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GCACAGACTGCAACAGTGAGA	0.423													75	260	---	---	---	---	PASS
PCDH12	51294	broad.mit.edu	37	5	141337114	141337114	+	Missense_Mutation	SNP	C	A	A			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:141337114C>A	uc003llx.2	-	1	1514	c.303G>T	c.(301-303)TGG>TGT	p.W101C		NM_016580	NP_057664	Q9NPG4	PCD12_HUMAN	protocadherin 12 precursor	101	Cadherin 1.|Extracellular (Potential).				neuron recognition	integral to plasma membrane	calcium ion binding			ovary(3)	3		all_hematologic(541;0.0999)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GGCAGGGATCCCACTGTCGGC	0.587													3	10	---	---	---	---	PASS
SLU7	10569	broad.mit.edu	37	5	159841423	159841423	+	Missense_Mutation	SNP	G	T	T			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:159841423G>T	uc003lyg.2	-	3	382	c.227C>A	c.(226-228)CCT>CAT	p.P76H	SLU7_uc003lyh.1_Missense_Mutation_p.P76H|SLU7_uc003lyi.1_Missense_Mutation_p.P76H	NM_006425	NP_006416	O95391	SLU7_HUMAN	step II splicing factor SLU7	76					alternative nuclear mRNA splicing, via spliceosome|nuclear mRNA 3'-splice site recognition	catalytic step 2 spliceosome|cytoplasm|nuclear speck|small nuclear ribonucleoprotein complex	pre-mRNA 3'-splice site binding|second spliceosomal transesterification activity|zinc ion binding			ovary(1)	1	Renal(175;0.00196)	Medulloblastoma(196;0.0354)|all_neural(177;0.116)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			TCTTTTTGAAGGATCAATATA	0.343													7	689	---	---	---	---	PASS
SLIT3	6586	broad.mit.edu	37	5	168671711	168671711	+	Silent	SNP	T	C	C			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:168671711T>C	uc003mab.2	-	3	759	c.339A>G	c.(337-339)CGA>CGG	p.R113R	SLIT3_uc010jjg.2_Silent_p.R113R|SLIT3_uc010jji.2_Silent_p.R113R	NM_003062	NP_003053	O75094	SLIT3_HUMAN	slit homolog 3 precursor	113	LRR 3.				apoptosis involved in luteolysis|axon extension involved in axon guidance|cellular response to hormone stimulus|negative chemotaxis|negative regulation of cell growth|negative regulation of chemokine-mediated signaling pathway|response to cortisol stimulus|Roundabout signaling pathway	extracellular space|mitochondrion	calcium ion binding|Roundabout binding			ovary(3)|skin(1)	4	Renal(175;0.000159)|Lung NSC(126;0.0174)|all_lung(126;0.0392)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			GTACTTACAGTCGCTCTAGCT	0.393													6	151	---	---	---	---	PASS
LCP2	3937	broad.mit.edu	37	5	169694070	169694070	+	Missense_Mutation	SNP	G	A	A			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:169694070G>A	uc003man.1	-	9	838	c.631C>T	c.(631-633)CCA>TCA	p.P211S	LCP2_uc011des.1_Missense_Mutation_p.P6S|LCP2_uc011det.1_Missense_Mutation_p.P40S|LCP2_uc010jjo.1_Missense_Mutation_p.P18S	NM_005565	NP_005556	Q13094	LCP2_HUMAN	lymphocyte cytosolic protein 2	211					immune response|platelet activation|T cell receptor signaling pathway|transmembrane receptor protein tyrosine kinase signaling pathway	cytosol	protein binding			ovary(1)	1	Renal(175;0.000159)|Lung NSC(126;0.0221)|all_lung(126;0.0337)	Medulloblastoma(196;0.0109)|all_neural(177;0.0146)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	OV - Ovarian serous cystadenocarcinoma(192;0.247)		GTCTGGGGTGGGGGCAGTGGC	0.378													43	168	---	---	---	---	PASS
ELOVL2	54898	broad.mit.edu	37	6	10983953	10983953	+	3'UTR	SNP	C	G	G			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:10983953C>G	uc003mzp.3	-	8						NM_017770	NP_060240	Q9NXB9	ELOV2_HUMAN	elongation of very long chain fatty acids-like						fatty acid elongation, polyunsaturated fatty acid|long-chain fatty-acyl-CoA biosynthetic process|triglyceride biosynthetic process|very long-chain fatty acid biosynthetic process	endoplasmic reticulum membrane|integral to membrane	fatty acid elongase activity|protein binding				0	Breast(50;0.0418)|Ovarian(93;0.0919)	all_hematologic(90;0.117)	Epithelial(50;0.176)			TCAATTCAGTCTTTGCTTTAA	0.308													5	258	---	---	---	---	PASS
HIVEP1	3096	broad.mit.edu	37	6	12125187	12125187	+	Nonsense_Mutation	SNP	C	A	A			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:12125187C>A	uc003nac.2	+	4	5338	c.5159C>A	c.(5158-5160)TCA>TAA	p.S1720*	HIVEP1_uc011diq.1_RNA	NM_002114	NP_002105	P15822	ZEP1_HUMAN	human immunodeficiency virus type I enhancer	1720					transcription, DNA-dependent	cytoplasm|nucleus	DNA binding|protein binding|zinc ion binding			ovary(3)|large_intestine(1)|central_nervous_system(1)|skin(1)	6	Breast(50;0.0639)|Ovarian(93;0.0816)	all_hematologic(90;0.117)				TCTTCTCTATCAGAATCCTTG	0.388													33	79	---	---	---	---	PASS
FTSJD2	23070	broad.mit.edu	37	6	37447813	37447813	+	Missense_Mutation	SNP	C	G	G			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:37447813C>G	uc003ons.2	+	24	2653	c.2400C>G	c.(2398-2400)TTC>TTG	p.F800L		NM_015050	NP_055865	Q8N1G2	MTR1_HUMAN	FtsJ methyltransferase domain containing 2	800	Interaction with POLR2A.				mRNA capping	cytoplasm|nucleus	mRNA (nucleoside-2'-O-)-methyltransferase activity|nucleic acid binding			ovary(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)|pancreas(1)	5						GCCGGCTCTTCTGGGAGTGGG	0.577													3	17	---	---	---	---	PASS
ICK	22858	broad.mit.edu	37	6	52878676	52878676	+	Silent	SNP	G	T	T			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:52878676G>T	uc003pbh.2	-	10	1426	c.936C>A	c.(934-936)GGC>GGA	p.G312G	ICK_uc003pbi.2_Silent_p.G312G	NM_016513	NP_057597	Q9UPZ9	ICK_HUMAN	intestinal cell kinase	312					intracellular protein kinase cascade|multicellular organismal development	cytosol|nucleus	ATP binding|cyclin-dependent protein kinase activity|magnesium ion binding			ovary(1)|large_intestine(1)|lung(1)|kidney(1)|central_nervous_system(1)	5	Lung NSC(77;0.103)					AAGGAGGTGGGCCTGCCTTTT	0.527													11	192	---	---	---	---	PASS
REV3L	5980	broad.mit.edu	37	6	111698993	111698993	+	Missense_Mutation	SNP	G	A	A			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:111698993G>A	uc003puy.3	-	12	1831	c.1508C>T	c.(1507-1509)TCA>TTA	p.S503L	REV3L_uc003pux.3_Missense_Mutation_p.S425L|REV3L_uc003puz.3_Missense_Mutation_p.S425L	NM_002912	NP_002903	O60673	DPOLZ_HUMAN	DNA polymerase zeta	503					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)		TTCTTCTCCTGAAGATGAGTC	0.383								DNA_polymerases_(catalytic_subunits)|Direct_reversal_of_damage					9	368	---	---	---	---	PASS
LAMA2	3908	broad.mit.edu	37	6	129833510	129833510	+	Missense_Mutation	SNP	G	T	T			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:129833510G>T	uc003qbn.2	+	62	8965	c.8860G>T	c.(8860-8862)GGT>TGT	p.G2954C	LAMA2_uc003qbo.2_Missense_Mutation_p.G2950C|uc003qbq.2_Intron	NM_000426	NP_000417	P24043	LAMA2_HUMAN	laminin alpha 2 subunit isoform a precursor	2954	Laminin G-like 5.				cell adhesion|muscle organ development|regulation of cell adhesion|regulation of cell migration|regulation of embryonic development	laminin-1 complex	receptor binding|structural molecule activity			ovary(8)|breast(1)|skin(1)	10				OV - Ovarian serous cystadenocarcinoma(136;0.178)|all cancers(137;0.245)		TTTTACAGTTGGTGGATTCAA	0.343													8	428	---	---	---	---	PASS
SYNE1	23345	broad.mit.edu	37	6	152787175	152787175	+	Missense_Mutation	SNP	C	A	A			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:152787175C>A	uc010kiw.2	-	17	2273	c.1671G>T	c.(1669-1671)GAG>GAT	p.E557D	SYNE1_uc003qot.3_Missense_Mutation_p.E564D|SYNE1_uc003qou.3_Missense_Mutation_p.E557D|SYNE1_uc010kjb.1_Missense_Mutation_p.E540D|SYNE1_uc003qpa.1_Missense_Mutation_p.E557D|SYNE1_uc003qox.1_Missense_Mutation_p.E73D|SYNE1_uc003qoz.2_Translation_Start_Site|SYNE1_uc003qoy.2_Missense_Mutation_p.E124D	NM_182961	NP_892006	Q8NF91	SYNE1_HUMAN	spectrin repeat containing, nuclear envelope 1	557	Cytoplasmic (Potential).				cell death|cytoskeletal anchoring at nuclear membrane|Golgi organization|muscle cell differentiation|nuclear matrix anchoring at nuclear membrane	cytoskeleton|Golgi apparatus|integral to membrane|nuclear outer membrane|postsynaptic membrane|sarcomere|SUN-KASH complex	actin binding|lamin binding			central_nervous_system(15)|upper_aerodigestive_tract(9)|ovary(8)|skin(6)|large_intestine(5)|pancreas(2)	45		Ovarian(120;0.0955)	BRCA - Breast invasive adenocarcinoma(37;0.243)	OV - Ovarian serous cystadenocarcinoma(155;2.24e-10)		GGTATGTCACCTCATATTGTT	0.368										HNSCC(10;0.0054)			6	405	---	---	---	---	PASS
AVL9	23080	broad.mit.edu	37	7	32663045	32663045	+	Intron	SNP	G	T	T			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:32663045G>T	uc011kai.1	+						uc003tcw.2_RNA	NM_015060	NP_055875	Q8NBF6	AVL9_HUMAN	AVL9 homolog (S. cerevisiase)							integral to membrane					0						CAAAGTGCAAGAGAAATCTGG	0.279													7	19	---	---	---	---	PASS
FZD9	8326	broad.mit.edu	37	7	72849270	72849270	+	Silent	SNP	G	A	A			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:72849270G>A	uc003tyb.2	+	1	1162	c.933G>A	c.(931-933)ACG>ACA	p.T311T		NM_003508	NP_003499	O00144	FZD9_HUMAN	frizzled 9 precursor	311	Extracellular (Potential).				B cell differentiation|brain development|canonical Wnt receptor signaling pathway|embryo development|gonad development|neuroblast proliferation|vasculature development	cell surface|filopodium membrane|integral to membrane|perinuclear region of cytoplasm	G-protein coupled receptor activity|PDZ domain binding|protein heterodimerization activity|protein homodimerization activity|Wnt receptor activity|Wnt-protein binding			central_nervous_system(1)	1		Lung NSC(55;0.0659)|all_lung(88;0.152)				TGGAGAACACGGGCTGCACGC	0.667													6	31	---	---	---	---	PASS
ABCB1	5243	broad.mit.edu	37	7	87183249	87183249	+	Splice_Site	SNP	C	A	A			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:87183249C>A	uc003uiz.1	-	10	1246	c.828_splice	c.e10-1	p.R276_splice	ABCB1_uc011khc.1_Splice_Site_p.R212_splice	NM_000927	NP_000918	P08183	MDR1_HUMAN	ATP-binding cassette, subfamily B, member 1						G2/M transition of mitotic cell cycle|stem cell proliferation	apical plasma membrane|cell surface|Golgi membrane|integral to membrane|intercellular canaliculus|membrane fraction	ATP binding|protein binding|xenobiotic-transporting ATPase activity			ovary(4)|upper_aerodigestive_tract(1)|large_intestine(1)|central_nervous_system(1)	7	Esophageal squamous(14;0.00164)				Adenosine triphosphate(DB00171)|Alfentanil(DB00802)|Arsenic trioxide(DB01169)|Atazanavir(DB01072)|Carvedilol(DB01136)|Colchicine(DB01394)|Cyclosporine(DB00091)|Daunorubicin(DB00694)|Dipyridamole(DB00975)|Estramustine(DB01196)|Flupenthixol(DB00875)|Imatinib(DB00619)|Itraconazole(DB01167)|Nicardipine(DB00622)|Propafenone(DB01182)|Quinacrine(DB01103)|Quinidine(DB00908)|Ranolazine(DB00243)|Rifampin(DB01045)|Roxithromycin(DB00778)|Saquinavir(DB01232)|Tamoxifen(DB00675)|Vinblastine(DB00570)	TTTGTTGTACCTGAGAAAAAG	0.259													9	592	---	---	---	---	PASS
ANKIB1	54467	broad.mit.edu	37	7	91980391	91980391	+	Missense_Mutation	SNP	C	A	A			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:91980391C>A	uc003ulw.2	+	8	1589	c.1213C>A	c.(1213-1215)CTA>ATA	p.L405I		NM_019004	NP_061877	Q9P2G1	AKIB1_HUMAN	ankyrin repeat and IBR domain containing 1	405	IBR-type; degenerate.						protein binding|zinc ion binding			lung(1)	1	all_cancers(62;2.06e-09)|all_epithelial(64;9.24e-09)|Breast(17;0.0034)|all_lung(186;0.0509)|Lung NSC(181;0.0692)		STAD - Stomach adenocarcinoma(171;6.16e-05)|all cancers(6;0.00183)|Lung(22;0.123)|LUSC - Lung squamous cell carcinoma(200;0.225)			CAAACGATACCTACAGTTTGA	0.313													6	345	---	---	---	---	PASS
TRRAP	8295	broad.mit.edu	37	7	98507681	98507681	+	Silent	SNP	T	C	C			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:98507681T>C	uc003upp.2	+	15	1562	c.1353T>C	c.(1351-1353)GTT>GTC	p.V451V	TRRAP_uc011kis.1_Silent_p.V451V|TRRAP_uc003upr.2_Silent_p.V143V	NM_003496	NP_003487	Q9Y4A5	TRRAP_HUMAN	transformation/transcription domain-associated	451					histone deubiquitination|histone H2A acetylation|histone H4 acetylation|regulation of transcription, DNA-dependent|transcription, DNA-dependent	NuA4 histone acetyltransferase complex|PCAF complex|STAGA complex|transcription factor TFTC complex	phosphotransferase activity, alcohol group as acceptor|protein binding|transcription cofactor activity			ovary(9)|large_intestine(8)|central_nervous_system(6)|skin(6)|stomach(5)|upper_aerodigestive_tract(1)|lung(1)|liver(1)	37	all_cancers(62;6.96e-09)|all_epithelial(64;4.86e-09)|Lung NSC(181;0.01)|all_lung(186;0.016)|Esophageal squamous(72;0.0274)		STAD - Stomach adenocarcinoma(171;0.215)			CCCGTTAGGTTTTCGTTCTCA	0.443													8	64	---	---	---	---	PASS
ZNF655	79027	broad.mit.edu	37	7	99169358	99169358	+	Intron	SNP	C	A	A			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:99169358C>A	uc003urh.2	+						ZNF655_uc010lga.2_Missense_Mutation_p.L62I|ZNF655_uc010lgc.2_Missense_Mutation_p.L62I|ZNF655_uc003urj.2_Intron|ZNF655_uc003urk.2_5'UTR|ZNF655_uc010lgd.2_5'UTR	NM_138494	NP_612503	Q8N720	ZN655_HUMAN	zinc finger protein 655 isoform a						G1 phase|regulation of mitotic cell cycle|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleolus	DNA binding|protein binding|zinc ion binding			ovary(1)	1	all_epithelial(64;3.19e-09)|Lung NSC(181;0.0066)|all_lung(186;0.011)|Esophageal squamous(72;0.0166)					GGAACAGGATCTACAGGTCTT	0.443													69	158	---	---	---	---	PASS
OR6V1	346517	broad.mit.edu	37	7	142749937	142749937	+	Missense_Mutation	SNP	G	A	A			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:142749937G>A	uc011ksv.1	+	1	500	c.500G>A	c.(499-501)TGC>TAC	p.C167Y		NM_001001667	NP_001001667	Q8N148	OR6V1_HUMAN	olfactory receptor, family 6, subfamily V,	167	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)	1	Melanoma(164;0.059)					CTTGATTACTGCCATGGCGAC	0.547													13	30	---	---	---	---	PASS
MSR1	4481	broad.mit.edu	37	8	16035394	16035394	+	Splice_Site	SNP	C	T	T	rs150131889	byFrequency	TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:16035394C>T	uc003wwz.2	-	2	301	c.103_splice	c.e2+1	p.N35_splice	MSR1_uc010lsu.2_Splice_Site_p.N53_splice|MSR1_uc003wxa.2_Splice_Site_p.N35_splice|MSR1_uc003wxb.2_Splice_Site_p.N35_splice|MSR1_uc011kxz.1_Splice_Site	NM_138715	NP_619729	P21757	MSRE_HUMAN	macrophage scavenger receptor 1 isoform type 1						cholesterol transport|plasma lipoprotein particle clearance|positive regulation of cholesterol storage|positive regulation of macrophage derived foam cell differentiation|receptor-mediated endocytosis	collagen|integral to plasma membrane|low-density lipoprotein particle	low-density lipoprotein particle binding|protein binding|scavenger receptor activity			ovary(1)	1				Colorectal(111;0.00475)|COAD - Colon adenocarcinoma(73;0.0164)		CCTCTACTTACTCGGAGGAAG	0.428													18	83	---	---	---	---	PASS
MTUS1	57509	broad.mit.edu	37	8	17510721	17510721	+	Missense_Mutation	SNP	T	C	C			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:17510721T>C	uc003wxv.2	-	12	3832	c.3358A>G	c.(3358-3360)AGA>GGA	p.R1120G	MTUS1_uc003wxt.2_Missense_Mutation_p.R367G|MTUS1_uc011kyg.1_Missense_Mutation_p.R265G|MTUS1_uc010lsy.2_RNA|MTUS1_uc003wxw.2_Missense_Mutation_p.R1066G|MTUS1_uc003wxs.2_Missense_Mutation_p.R286G	NM_001001924	NP_001001924	Q9ULD2	MTUS1_HUMAN	mitochondrial tumor suppressor 1 isoform 1	1120	Potential.					Golgi apparatus|microtubule|microtubule organizing center|mitochondrion|nucleus|plasma membrane|spindle				ovary(1)|skin(1)	2				Colorectal(111;0.0778)		CTTGCTCTTCTTTTTTGTTCT	0.313													9	778	---	---	---	---	PASS
POLB	5423	broad.mit.edu	37	8	42227395	42227395	+	Missense_Mutation	SNP	G	T	T			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:42227395G>T	uc003xoz.1	+	13	915	c.802G>T	c.(802-804)GGT>TGT	p.G268C	POLB_uc003xpa.1_Missense_Mutation_p.G239C|POLB_uc011lcs.1_Missense_Mutation_p.G114C	NM_002690	NP_002681	P06746	DPOLB_HUMAN	DNA-directed DNA polymerase beta	268					DNA-dependent DNA replication	cytoplasm|nucleoplasm|spindle microtubule	DNA-(apurinic or apyrimidinic site) lyase activity|DNA-directed DNA polymerase activity|enzyme binding|metal ion binding|microtubule binding			ovary(1)|breast(1)	2	all_cancers(6;1.42e-24)|all_epithelial(6;1.02e-25)|all_lung(13;2.58e-12)|Lung NSC(13;4.24e-11)|Ovarian(28;0.00769)|Prostate(17;0.0119)|Colorectal(14;0.1)|Lung SC(25;0.211)	all_lung(54;0.00671)|Lung NSC(58;0.0184)|Esophageal squamous(32;0.131)|Hepatocellular(245;0.133)|Renal(179;0.151)	BRCA - Breast invasive adenocarcinoma(8;3.18e-11)|Lung(22;0.00467)|OV - Ovarian serous cystadenocarcinoma(14;0.00523)|LUSC - Lung squamous cell carcinoma(45;0.024)		Cytarabine(DB00987)	GTATTACTGTGGTGTTCTCTA	0.358								DNA_polymerases_(catalytic_subunits)					7	653	---	---	---	---	PASS
TTPA	7274	broad.mit.edu	37	8	63973792	63973792	+	3'UTR	SNP	A	C	C			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:63973792A>C	uc003xux.1	-	5						NM_000370	NP_000361	P49638	TTPA_HUMAN	tocopherol (alpha) transfer protein						lipid metabolic process		transporter activity|vitamin E binding				0	Breast(64;0.0716)	all_cancers(86;0.145)|Lung NSC(129;0.0324)|all_lung(136;0.0593)|all_epithelial(80;0.123)			Vitamin E(DB00163)	TTAGGAAGCCATTCACATGAC	0.338													47	174	---	---	---	---	PASS
CNGB3	54714	broad.mit.edu	37	8	87638223	87638223	+	Silent	SNP	G	T	T			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:87638223G>T	uc003ydx.2	-	13	1612	c.1566C>A	c.(1564-1566)GTC>GTA	p.V522V	CNGB3_uc010maj.2_Silent_p.V384V	NM_019098	NP_061971	Q9NQW8	CNGB3_HUMAN	cyclic nucleotide gated channel beta 3	522	Helical; Name=H6; (Potential).				signal transduction|visual perception	integral to membrane	cGMP binding			ovary(2)|pancreas(1)	3						TGAACAAGTCGACTTTGCTGA	0.363													5	418	---	---	---	---	PASS
RBM12B	389677	broad.mit.edu	37	8	94748137	94748137	+	Missense_Mutation	SNP	C	G	G			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:94748137C>G	uc003yfz.2	-	3	695	c.502G>C	c.(502-504)GAA>CAA	p.E168Q		NM_203390	NP_976324	Q8IXT5	RB12B_HUMAN	RNA binding motif protein 12B	168	RRM 1.						nucleotide binding|RNA binding				0	Breast(36;4.14e-07)		BRCA - Breast invasive adenocarcinoma(8;0.0168)			ACATCATCTTCATTTACTAGG	0.388													15	252	---	---	---	---	PASS
RGS22	26166	broad.mit.edu	37	8	101117709	101117709	+	Intron	SNP	C	T	T			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:101117709C>T	uc003yjb.1	-						RGS22_uc003yja.1_5'UTR|RGS22_uc003yjc.1_Intron|RGS22_uc010mbo.1_Intron	NM_015668	NP_056483	Q8NE09	RGS22_HUMAN	regulator of G-protein signaling 22						negative regulation of signal transduction	cytoplasm|plasma membrane	GTPase activator activity|signal transducer activity			ovary(3)|skin(2)|breast(1)|central_nervous_system(1)	7			Epithelial(11;6.71e-08)|all cancers(13;4.19e-06)|OV - Ovarian serous cystadenocarcinoma(57;0.000469)|STAD - Stomach adenocarcinoma(118;0.169)			GAGACAGCACCTAGCCCTACG	0.403													4	243	---	---	---	---	PASS
FBXO43	286151	broad.mit.edu	37	8	101157415	101157415	+	5'UTR	SNP	A	G	G			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:101157415A>G	uc003yjd.2	-	1					FBXO43_uc003yje.2_5'UTR|FBXO43_uc010mbp.1_5'UTR	NM_001029860	NP_001025031	Q4G163	FBX43_HUMAN	F-box protein 43 isoform b						meiosis		zinc ion binding			kidney(1)|skin(1)	2	all_cancers(14;0.000139)|all_epithelial(15;2.84e-07)|Lung NSC(17;0.000274)|all_lung(17;0.000798)		Epithelial(11;1.17e-09)|all cancers(13;1.34e-07)|OV - Ovarian serous cystadenocarcinoma(57;3.82e-05)|STAD - Stomach adenocarcinoma(118;0.0957)			CAATTAATTGAAAGGTGCAGC	0.388													6	277	---	---	---	---	PASS
WDYHV1	55093	broad.mit.edu	37	8	124449463	124449463	+	Missense_Mutation	SNP	A	G	G			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:124449463A>G	uc003yqn.1	+	5	522	c.397A>G	c.(397-399)ATC>GTC	p.I133V	WDYHV1_uc011lij.1_Missense_Mutation_p.I73V|WDYHV1_uc003yqo.1_RNA	NM_018024	NP_060494	Q96HA8	NTAQ1_HUMAN	WDYHV motif containing 1	133					protein modification process	cytosol|nucleus	protein binding|protein N-terminal glutamine amidohydrolase activity			ovary(1)|skin(1)	2						ATTTAGAGTGATCCGTGCAGA	0.403													6	300	---	---	---	---	PASS
COL22A1	169044	broad.mit.edu	37	8	139768035	139768035	+	Missense_Mutation	SNP	C	T	T			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:139768035C>T	uc003yvd.2	-	19	2387	c.1940G>A	c.(1939-1941)GGC>GAC	p.G647D	COL22A1_uc011ljo.1_5'UTR	NM_152888	NP_690848	Q8NFW1	COMA1_HUMAN	collagen, type XXII, alpha 1	647	Pro-rich.|Gly-rich.				cell adhesion	collagen|cytoplasm	structural molecule activity			ovary(11)|pancreas(1)|skin(1)	13	all_epithelial(106;1.55e-12)|Lung NSC(106;1.67e-05)|all_lung(105;3.39e-05)|Ovarian(258;0.00672)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0517)			CACCACTGAGCCTGGTACACC	0.542										HNSCC(7;0.00092)			6	110	---	---	---	---	PASS
KIAA1797	54914	broad.mit.edu	37	9	20717853	20717853	+	Missense_Mutation	SNP	C	A	A			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:20717853C>A	uc003zog.1	+	5	481	c.118C>A	c.(118-120)CAA>AAA	p.Q40K		NM_017794	NP_060264	Q5VW36	K1797_HUMAN	hypothetical protein LOC54914	40						integral to membrane	binding			ovary(8)|breast(1)|kidney(1)	10				GBM - Glioblastoma multiforme(3;2.1e-125)|Lung(42;2.76e-14)|LUSC - Lung squamous cell carcinoma(42;1.99e-11)		AAAGATTCACCAATCTACAAA	0.284													8	601	---	---	---	---	PASS
TLN1	7094	broad.mit.edu	37	9	35699139	35699139	+	Missense_Mutation	SNP	C	A	A			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:35699139C>A	uc003zxt.2	-	52	7243	c.6889G>T	c.(6889-6891)GAC>TAC	p.D2297Y		NM_006289	NP_006280	Q9Y490	TLN1_HUMAN	talin 1	2297	I/LWEQ.				axon guidance|cell adhesion|cell-cell junction assembly|cellular component movement|cytoskeletal anchoring at plasma membrane|muscle contraction|platelet activation|platelet degranulation	actin cytoskeleton|centrosome|cytosol|extracellular region|focal adhesion|intracellular membrane-bounded organelle|ruffle membrane	actin binding|insulin receptor binding|LIM domain binding|structural constituent of cytoskeleton|vinculin binding			lung(7)|breast(3)|ovary(2)|central_nervous_system(1)	13	all_epithelial(49;0.167)		Lung(28;0.00276)|LUSC - Lung squamous cell carcinoma(32;0.00418)|STAD - Stomach adenocarcinoma(86;0.194)			TCCTCTGGgtctacccattct	0.358													4	62	---	---	---	---	PASS
RGP1	9827	broad.mit.edu	37	9	35751400	35751400	+	Missense_Mutation	SNP	C	T	T			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:35751400C>T	uc011lpf.1	+	6	766	c.625C>T	c.(625-627)CGC>TGC	p.R209C	GBA2_uc011lpb.1_5'Flank|GBA2_uc003zxw.2_5'Flank|GBA2_uc011lpc.1_5'Flank|GBA2_uc011lpd.1_5'Flank|RGP1_uc011lpe.1_Missense_Mutation_p.R249C	NM_001080496	NP_001073965	Q92546	RGP1_HUMAN	RGP1 retrograde golgi transport homolog	209										ovary(1)	1	all_epithelial(49;0.167)		Lung(28;0.00416)|LUSC - Lung squamous cell carcinoma(32;0.00418)|STAD - Stomach adenocarcinoma(86;0.194)			CACATCCTGCCGCAGCCTCCG	0.527													7	10	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	9	68414259	68414259	+	RNA	SNP	C	T	T			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:68414259C>T	uc004aex.2	+	1		c.814C>T								Homo sapiens mRNA; cDNA DKFZp564N0763 (from clone DKFZp564N0763).																		ccacagtggcctcaaagaact	0.254													3	4	---	---	---	---	PASS
LOC286238	286238	broad.mit.edu	37	9	91262512	91262512	+	Missense_Mutation	SNP	G	C	C			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:91262512G>C	uc010mql.1	-	2	264	c.131C>G	c.(130-132)CCT>CGT	p.P44R		NM_001100111	NP_001093581			hypothetical protein LOC286238												0						CAGTGAGTAAGGGGTTGGATT	0.393													66	188	---	---	---	---	PASS
SLC2A8	29988	broad.mit.edu	37	9	130169437	130169437	+	Missense_Mutation	SNP	G	A	A			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:130169437G>A	uc004bqu.2	+	10	1388	c.1343G>A	c.(1342-1344)TGC>TAC	p.C448Y	SLC2A8_uc010mxj.2_Silent_p.L399L|SLC2A8_uc004bqv.2_Missense_Mutation_p.C120Y	NM_014580	NP_055395	Q9NY64	GTR8_HUMAN	solute carrier family 2 (facilitated glucose	448	Helical; Name=12; (Potential).					cytoplasmic vesicle membrane|integral to plasma membrane	D-glucose transmembrane transporter activity			ovary(1)|haematopoietic_and_lymphoid_tissue(1)	2						TCCGCTTTCTGCATCTTCAGT	0.542													25	67	---	---	---	---	PASS
MLLT10	8028	broad.mit.edu	37	10	21971160	21971160	+	Nonsense_Mutation	SNP	C	G	G			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:21971160C>G	uc001iqs.2	+	13	2021	c.1673C>G	c.(1672-1674)TCA>TGA	p.S558*	MLLT10_uc001iqt.2_Nonsense_Mutation_p.S558*|MLLT10_uc001iqv.2_RNA|MLLT10_uc001iqy.2_Nonsense_Mutation_p.S558*|MLLT10_uc001ira.2_Nonsense_Mutation_p.S15*|MLLT10_uc001irb.2_Intron	NM_004641	NP_004632	P55197	AF10_HUMAN	myeloid/lymphoid or mixed-lineage leukemia	558	DNA-binding.				positive regulation of transcription from RNA polymerase II promoter	cytoplasm|nucleus	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			lung(1)|skin(1)	2						AAAGCGTTCTCAGAGTTGCTG	0.328			T	MLL|PICALM|CDK6	AL								18	634	---	---	---	---	PASS
ABI1	10006	broad.mit.edu	37	10	27066064	27066064	+	Missense_Mutation	SNP	T	C	C			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:27066064T>C	uc001isx.2	-	3	559	c.392A>G	c.(391-393)GAG>GGG	p.E131G	ABI1_uc001ite.2_Missense_Mutation_p.E131G|ABI1_uc010qdh.1_Missense_Mutation_p.E131G|ABI1_uc010qdi.1_Intron|ABI1_uc001isy.2_Missense_Mutation_p.E131G|ABI1_uc001ita.2_Missense_Mutation_p.E131G|ABI1_uc001isz.2_Missense_Mutation_p.E131G|ABI1_uc001itb.2_Missense_Mutation_p.E148G|ABI1_uc001itc.2_Missense_Mutation_p.E131G|ABI1_uc010qdj.1_Missense_Mutation_p.E131G|ABI1_uc001itd.2_Missense_Mutation_p.E131G|ABI1_uc010qdk.1_Missense_Mutation_p.E131G|ABI1_uc010qdg.1_Missense_Mutation_p.E2G	NM_005470	NP_005461	Q8IZP0	ABI1_HUMAN	abl-interactor 1 isoform a	131					actin polymerization or depolymerization|cellular component movement|negative regulation of cell proliferation|peptidyl-tyrosine phosphorylation|transmembrane receptor protein tyrosine kinase signaling pathway	cell junction|cytoskeleton|cytosol|endoplasmic reticulum|filopodium|growth cone|lamellipodium|nucleus|soluble fraction|synapse|synaptosome	cytoskeletal protein binding			central_nervous_system(1)	1						TACAGGGCGCTCCATATTCGC	0.378													8	411	---	---	---	---	PASS
ITGB1	3688	broad.mit.edu	37	10	33199315	33199315	+	Missense_Mutation	SNP	T	C	C			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:33199315T>C	uc001iws.3	-	14	2136	c.2000A>G	c.(1999-2001)TAT>TGT	p.Y667C	ITGB1_uc001iwp.3_Missense_Mutation_p.Y667C|ITGB1_uc001iwq.3_Missense_Mutation_p.Y667C|ITGB1_uc001iwr.3_Missense_Mutation_p.Y667C|ITGB1_uc001iwt.3_Missense_Mutation_p.Y667C|ITGB1_uc001iwu.1_Missense_Mutation_p.Y667C	NM_133376	NP_596867	P05556	ITB1_HUMAN	integrin beta 1 isoform 1A precursor	667	Extracellular (Potential).				axon guidance|blood coagulation|cell-cell adhesion mediated by integrin|cell-matrix adhesion|cellular defense response|homophilic cell adhesion|integrin-mediated signaling pathway|interspecies interaction between organisms|leukocyte cell-cell adhesion|leukocyte migration|positive regulation of apoptosis|regulation of immune response	cell surface|cleavage furrow|focal adhesion|melanosome|neuromuscular junction|ruffle|sarcolemma	identical protein binding|protein heterodimerization activity|receptor activity			upper_aerodigestive_tract(1)|ovary(1)	2		Ovarian(717;1.34e-05)|Breast(68;0.0634)				AATGTTAAAATAGGAACATTC	0.408													34	64	---	---	---	---	PASS
UBE2D1	7321	broad.mit.edu	37	10	60127764	60127764	+	Nonsense_Mutation	SNP	C	A	A			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:60127764C>A	uc001jke.1	+	6	609	c.386C>A	c.(385-387)TCA>TAA	p.S129*		NM_003338	NP_003329	P51668	UB2D1_HUMAN	ubiquitin-conjugating enzyme E2D 1	129					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|BMP signaling pathway|mitotic cell cycle spindle assembly checkpoint|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|protein K48-linked ubiquitination|transforming growth factor beta receptor signaling pathway	cytosol|nucleoplasm	ATP binding|protein binding|ubiquitin-protein ligase activity			skin(2)	2						ATCTATAAATCAGACAAAGAA	0.294													7	509	---	---	---	---	PASS
PIK3C2A	5286	broad.mit.edu	37	11	17141463	17141463	+	Missense_Mutation	SNP	G	T	T			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:17141463G>T	uc001mmq.3	-	15	2782	c.2716C>A	c.(2716-2718)CCA>ACA	p.P906T	PIK3C2A_uc009ygu.1_Intron|PIK3C2A_uc010rcw.1_Missense_Mutation_p.P526T|PIK3C2A_uc001mmr.3_Intron	NM_002645	NP_002636	O00443	P3C2A_HUMAN	phosphoinositide-3-kinase, class 2 alpha	906					cell communication|phosphatidylinositol biosynthetic process|phosphatidylinositol-mediated signaling	clathrin-coated vesicle|Golgi apparatus|nucleus|phosphatidylinositol 3-kinase complex|plasma membrane	1-phosphatidylinositol-3-kinase activity|ATP binding|phosphatidylinositol binding|phosphatidylinositol-4-phosphate 3-kinase activity			lung(4)|central_nervous_system(4)|stomach(1)|ovary(1)	10					Phosphatidylserine(DB00144)	AGACAATTTGGGTGTTTGAAG	0.353													7	486	---	---	---	---	PASS
NAV2	89797	broad.mit.edu	37	11	20078166	20078166	+	Missense_Mutation	SNP	A	G	G			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:20078166A>G	uc010rdm.1	+	21	5352	c.4991A>G	c.(4990-4992)TAT>TGT	p.Y1664C	NAV2_uc001mpp.2_Intron|NAV2_uc001mpr.3_Intron|NAV2_uc001mpt.2_Intron|NAV2_uc009yhx.2_Intron|NAV2_uc009yhy.1_Intron|NAV2_uc009yhz.2_Intron|NAV2_uc001mpu.2_Intron	NM_145117	NP_660093	Q8IVL1	NAV2_HUMAN	neuron navigator 2 isoform 2	1664	Ser-rich.					nucleus	ATP binding|helicase activity			skin(4)|ovary(1)|pancreas(1)	6						CACGCAAGGTATGAGTTAGGT	0.448													13	404	---	---	---	---	PASS
ELP4	26610	broad.mit.edu	37	11	31669288	31669288	+	Splice_Site	SNP	G	T	T			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:31669288G>T	uc001mtb.2	+	8	963	c.928_splice	c.e8-1	p.N310_splice	ELP4_uc001mta.1_Splice_Site|ELP4_uc001mtc.2_Splice_Site_p.N310_splice|ELP4_uc010rdz.1_Splice_Site_p.N311_splice	NM_019040	NP_061913	Q96EB1	ELP4_HUMAN	elongation protein 4 homolog						histone acetylation|regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	cytoplasm|DNA-directed RNA polymerase II, holoenzyme|Elongator holoenzyme complex|transcription elongation factor complex	phosphorylase kinase regulator activity|protein binding			upper_aerodigestive_tract(1)|ovary(1)|prostate(1)	3	Lung SC(675;0.225)					ATGTTTTGCAGAATAAAGCCA	0.338													8	540	---	---	---	---	PASS
SLC22A25	387601	broad.mit.edu	37	11	62932102	62932102	+	Missense_Mutation	SNP	C	A	A			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:62932102C>A	uc001nwr.1	-	8	1290	c.1290G>T	c.(1288-1290)ATG>ATT	p.M430I	SLC22A10_uc010rmo.1_Intron|SLC22A25_uc009yoq.1_RNA|SLC22A25_uc001nws.1_RNA	NM_199352	NP_955384	Q6T423	S22AP_HUMAN	putative UST1-like organic anion transporter	430	Extracellular (Potential).				transmembrane transport	integral to membrane				ovary(3)|skin(1)	4						GCAGGGTCTGCATTTCTGGAG	0.483													5	126	---	---	---	---	PASS
KBTBD3	143879	broad.mit.edu	37	11	105923665	105923665	+	Missense_Mutation	SNP	G	T	T			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:105923665G>T	uc001pja.2	-	4	2391	c.1751C>A	c.(1750-1752)CCA>CAA	p.P584Q	KBTBD3_uc001pjb.2_Missense_Mutation_p.P584Q|KBTBD3_uc009yxm.2_Missense_Mutation_p.P505Q	NM_198439	NP_940841	Q8NAB2	KBTB3_HUMAN	BTB and kelch domain containing 3	580	Kelch 5.									ovary(1)|central_nervous_system(1)	2		Melanoma(852;0.000878)|Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.0017)|Breast(348;0.0321)		BRCA - Breast invasive adenocarcinoma(274;5.43e-05)|Epithelial(105;0.00418)|all cancers(92;0.0299)		TCTAGGCATTGGTGAAACTTC	0.373													6	261	---	---	---	---	PASS
DIXDC1	85458	broad.mit.edu	37	11	111859689	111859689	+	Intron	SNP	C	A	A			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:111859689C>A	uc001pml.2	+						DIXDC1_uc001pmm.2_Intron|DIXDC1_uc001pmn.2_Intron|DIXDC1_uc010rwq.1_Silent_p.T6T	NM_001037954	NP_001033043	Q155Q3	DIXC1_HUMAN	DIX domain containing 1 isoform a						multicellular organismal development|positive regulation of canonical Wnt receptor signaling pathway|Wnt receptor signaling pathway	cytosol|focal adhesion	actin binding|gamma-tubulin binding|signal transducer activity			ovary(1)	1		all_cancers(61;7.58e-15)|all_epithelial(67;5.42e-09)|Melanoma(852;1.91e-06)|all_hematologic(158;0.000405)|Acute lymphoblastic leukemia(157;0.000967)|Breast(348;0.0112)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)		Epithelial(105;2.99e-07)|BRCA - Breast invasive adenocarcinoma(274;6.72e-07)|all cancers(92;6.25e-06)|OV - Ovarian serous cystadenocarcinoma(223;0.0548)		CTGAAGCAACCCAGATGTCAC	0.403													5	296	---	---	---	---	PASS
MLL	4297	broad.mit.edu	37	11	118373819	118373819	+	Silent	SNP	C	A	A			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:118373819C>A	uc001pta.2	+	27	7226	c.7203C>A	c.(7201-7203)ACC>ACA	p.T2401T	MLL_uc001ptb.2_Silent_p.T2404T	NM_005933	NP_005924	Q03164	MLL1_HUMAN	myeloid/lymphoid or mixed-lineage leukemia	2401					apoptosis|embryonic hemopoiesis|histone H4-K16 acetylation|positive regulation of transcription, DNA-dependent|protein complex assembly|transcription from RNA polymerase II promoter	MLL1 complex	AT DNA binding|histone acetyl-lysine binding|histone methyltransferase activity (H3-K4 specific)|protein homodimerization activity|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding|unmethylated CpG binding|zinc ion binding			lung(7)|ovary(5)|kidney(5)|central_nervous_system(3)|pancreas(2)|urinary_tract(1)|breast(1)|skin(1)	25	all_hematologic(175;0.046)	all_hematologic(192;1.13e-50)|all_neural(223;3.18e-06)|Breast(348;1.07e-05)|Medulloblastoma(222;0.0425)|Hepatocellular(160;0.244)		OV - Ovarian serous cystadenocarcinoma(223;2.77e-44)|BRCA - Breast invasive adenocarcinoma(274;1.2e-11)|Lung(307;3.48e-06)|LUSC - Lung squamous cell carcinoma(976;7.92e-05)|Colorectal(284;0.144)		AAGTCAAAACCTTGAAGCTAT	0.423			T|O	MLL|MLLT1|MLLT2|MLLT3|MLLT4|MLLT7|MLLT10|MLLT6|ELL|EPS15|AF1Q|CREBBP|SH3GL1|FNBP1|PNUTL1|MSF|GPHN|GMPS|SSH3BP1|ARHGEF12|GAS7|FOXO3A|LAF4|LCX|SEPT6|LPP|CBFA2T1|GRAF|EP300|PICALM|HEAB	AML|ALL								6	190	---	---	---	---	PASS
TMEM225	338661	broad.mit.edu	37	11	123756009	123756009	+	Missense_Mutation	SNP	T	C	C			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:123756009T>C	uc001pzi.2	-	1	332	c.124A>G	c.(124-126)AGA>GGA	p.R42G		NM_001013743	NP_001013765	Q6GV28	TM225_HUMAN	transmembrane protein 225	42						integral to membrane				upper_aerodigestive_tract(1)|pancreas(1)|skin(1)	3						ATCTTGGCTCTTTCATCTTCT	0.453													5	145	---	---	---	---	PASS
STT3A	3703	broad.mit.edu	37	11	125481352	125481352	+	Missense_Mutation	SNP	T	C	C			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:125481352T>C	uc001qcd.2	+	11	1257	c.1147T>C	c.(1147-1149)TCT>CCT	p.S383P	STT3A_uc001qce.2_Missense_Mutation_p.S383P|STT3A_uc010sbg.1_Missense_Mutation_p.S291P|STT3A_uc009zbn.2_Missense_Mutation_p.S105P	NM_152713	NP_689926	P46977	STT3A_HUMAN	integral membrane protein 1	383	Lumenal (Potential).				post-translational protein modification|protein N-linked glycosylation via asparagine	integral to membrane|oligosaccharyltransferase complex	dolichyl-diphosphooligosaccharide-protein glycotransferase activity				0	all_hematologic(175;0.228)	Breast(109;0.0115)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.0919)|all_lung(97;0.0994)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;1.13e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0996)		TAGCAACCTGTCTGATGCCCG	0.428													10	717	---	---	---	---	PASS
HSN2	378465	broad.mit.edu	37	12	977348	977348	+	Missense_Mutation	SNP	A	G	G			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:977348A>G	uc001qiq.2	+	1	479	c.353A>G	c.(352-354)CAT>CGT	p.H118R	WNK1_uc001qio.3_Intron|WNK1_uc001qip.3_Intron|WNK1_uc001qir.3_Intron	NM_213655	NP_998820			hereditary sensory neuropathy, type II												0	all_cancers(10;0.0107)|all_epithelial(11;0.0151)|Ovarian(42;0.0512)|all_lung(10;0.0521)|Lung NSC(10;0.0987)		OV - Ovarian serous cystadenocarcinoma(31;0.000967)|BRCA - Breast invasive adenocarcinoma(9;0.0178)			ATACAGGTCCATCCTATGTTT	0.458													35	70	---	---	---	---	PASS
MYO1A	4640	broad.mit.edu	37	12	57437136	57437136	+	Missense_Mutation	SNP	C	T	T			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:57437136C>T	uc001smw.3	-	11	1142	c.899G>A	c.(898-900)CGG>CAG	p.R300Q	MYO1A_uc010sqz.1_Missense_Mutation_p.R138Q|MYO1A_uc009zpd.2_Missense_Mutation_p.R300Q	NM_005379	NP_005370	Q9UBC5	MYO1A_HUMAN	myosin IA	300	Myosin head-like.				sensory perception of sound|vesicle localization	brush border|cortical actin cytoskeleton|filamentous actin|lateral plasma membrane|microvillus|myosin complex	actin binding|ATP binding|calmodulin binding|motor activity			skin(4)|ovary(2)|urinary_tract(1)	7						CCCAATCTCCCGAACACCTGG	0.502													15	247	---	---	---	---	PASS
FAM19A2	338811	broad.mit.edu	37	12	62103959	62103959	+	3'UTR	SNP	A	T	T			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:62103959A>T	uc001sqw.2	-	5					FAM19A2_uc001sqv.2_RNA|FAM19A2_uc001sqx.2_3'UTR|FAM19A2_uc001sqy.2_RNA	NM_178539	NP_848634	Q8N3H0	F19A2_HUMAN	family with sequence similarity 19 (chemokine							cytoplasm				ovary(1)	1			GBM - Glioblastoma multiforme(1;0.00484)	GBM - Glioblastoma multiforme(3;0.02)		ACAATTTACAAGTTGAACACA	0.368													14	34	---	---	---	---	PASS
EXOSC8	11340	broad.mit.edu	37	13	37577107	37577107	+	Missense_Mutation	SNP	A	G	G			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:37577107A>G	uc001uwa.2	+	4	420	c.155A>G	c.(154-156)AAG>AGG	p.K52R	EXOSC8_uc001uvz.2_RNA|EXOSC8_uc001uwb.2_Missense_Mutation_p.K52R|EXOSC8_uc001uwc.2_RNA	NM_181503	NP_852480	Q96B26	EXOS8_HUMAN	exosome component 8	52					exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay|rRNA processing	cytosol|exosome (RNase complex)|nucleolus	AU-rich element binding|identical protein binding			pancreas(1)	1		Lung NSC(96;6.57e-05)|Breast(139;0.0615)|Lung SC(185;0.0743)|Prostate(109;0.184)		all cancers(112;3.67e-07)|Epithelial(112;1.31e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00699)|BRCA - Breast invasive adenocarcinoma(63;0.0117)|GBM - Glioblastoma multiforme(144;0.0411)		GCTTTAGTGAAGTTGGGAAAT	0.313													9	759	---	---	---	---	PASS
EXOSC8	11340	broad.mit.edu	37	13	37578662	37578662	+	Missense_Mutation	SNP	G	C	C			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:37578662G>C	uc001uwa.2	+	5	467	c.202G>C	c.(202-204)GCA>CCA	p.A68P	EXOSC8_uc001uvz.2_RNA|EXOSC8_uc001uwb.2_Missense_Mutation_p.A68P|EXOSC8_uc001uwc.2_RNA	NM_181503	NP_852480	Q96B26	EXOS8_HUMAN	exosome component 8	68					exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay|rRNA processing	cytosol|exosome (RNase complex)|nucleolus	AU-rich element binding|identical protein binding			pancreas(1)	1		Lung NSC(96;6.57e-05)|Breast(139;0.0615)|Lung SC(185;0.0743)|Prostate(109;0.184)		all cancers(112;3.67e-07)|Epithelial(112;1.31e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00699)|BRCA - Breast invasive adenocarcinoma(63;0.0117)|GBM - Glioblastoma multiforme(144;0.0411)		GGAATTTGCAGCACCATCAAC	0.294													8	315	---	---	---	---	PASS
RPGRIP1	57096	broad.mit.edu	37	14	21771545	21771545	+	Missense_Mutation	SNP	C	A	A			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:21771545C>A	uc001wag.2	+	5	643	c.643C>A	c.(643-645)CCC>ACC	p.P215T		NM_020366	NP_065099	Q96KN7	RPGR1_HUMAN	retinitis pigmentosa GTPase regulator	215					response to stimulus|visual perception	cilium				ovary(4)|breast(2)|pancreas(1)	7	all_cancers(95;0.0017)	all_cancers(140;0.0973)	Epithelial(56;6.24e-07)|all cancers(55;6.56e-06)	GBM - Glioblastoma multiforme(265;0.00888)		TATGGCTAAACCCATTGGTCT	0.413													6	70	---	---	---	---	PASS
SDCCAG1	9147	broad.mit.edu	37	14	50298943	50298943	+	Missense_Mutation	SNP	G	T	T			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:50298943G>T	uc001wxc.2	-	9	856	c.788C>A	c.(787-789)CCA>CAA	p.P263Q	SDCCAG1_uc010anj.1_Missense_Mutation_p.P263Q|SDCCAG1_uc010tqi.1_Missense_Mutation_p.P263Q|SDCCAG1_uc001wxe.2_Missense_Mutation_p.P221Q|SDCCAG1_uc001wxd.1_5'Flank|SDCCAG1_uc010anq.1_Missense_Mutation_p.P34Q	NM_004713	NP_004704	O60524	NEMF_HUMAN	serologically defined colon cancer antigen 1	263						cytoplasm|nucleus					0	all_epithelial(31;0.000822)|Breast(41;0.0117)	all_lung(585;1.02e-05)		OV - Ovarian serous cystadenocarcinoma(311;5.99e-34)		GTCTTCAACTGGTTTATCTGC	0.308													5	284	---	---	---	---	PASS
PYGL	5836	broad.mit.edu	37	14	51390764	51390764	+	Missense_Mutation	SNP	G	A	A			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:51390764G>A	uc001wyu.2	-	5	710	c.583C>T	c.(583-585)CCA>TCA	p.P195S	PYGL_uc010tqq.1_Missense_Mutation_p.P161S|PYGL_uc001wyv.2_5'UTR|PYGL_uc010anz.1_5'UTR|PYGL_uc001wyw.3_Missense_Mutation_p.P195S	NM_002863	NP_002854	P06737	PYGL_HUMAN	liver glycogen phosphorylase isoform 1	195					glucose homeostasis|glucose metabolic process|glycogen catabolic process	cytosol|soluble fraction	AMP binding|ATP binding|bile acid binding|drug binding|glucose binding|glycogen phosphorylase activity|protein homodimerization activity|purine base binding|pyridoxal phosphate binding			skin(1)	1	all_epithelial(31;0.00825)|Breast(41;0.148)				Adenosine monophosphate(DB00131)|Pyridoxal Phosphate(DB00114)|Riboflavin(DB00140)	ATGAATTCTGGGCGGGACTTC	0.443													8	182	---	---	---	---	PASS
CALM1	801	broad.mit.edu	37	14	90870251	90870251	+	Missense_Mutation	SNP	G	T	T			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:90870251G>T	uc001xyl.1	+	4	426	c.224G>T	c.(223-225)AGA>ATA	p.R75I	CALM1_uc010atq.1_Missense_Mutation_p.R76I|CALM1_uc010atr.1_Intron|CALM1_uc001xym.1_Missense_Mutation_p.R39I	NM_006888	NP_008819	P62158	CALM_HUMAN	calmodulin 1 isoform 1	75	EF-hand 2.				activation of phospholipase C activity|G-protein coupled receptor protein signaling pathway|glucose metabolic process|glycogen catabolic process|muscle contraction|negative regulation of ryanodine-sensitive calcium-release channel activity|nerve growth factor receptor signaling pathway|nitric oxide metabolic process|platelet activation|platelet degranulation|positive regulation of ryanodine-sensitive calcium-release channel activity|regulation of cytokinesis|regulation of nitric-oxide synthase activity|regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum|response to calcium ion|synaptic transmission	centrosome|cytosol|extracellular region|nucleoplasm|plasma membrane|spindle microtubule|spindle pole	calcium ion binding|N-terminal myristoylation domain binding|phospholipase binding|protein domain specific binding|thioesterase binding|titin binding			central_nervous_system(1)	1		all_cancers(154;0.13)		COAD - Colon adenocarcinoma(157;0.208)	Aprindine(DB01429)|Bepridil(DB01244)|Dibucaine(DB00527)|Felodipine(DB01023)|Flunarizine(DB04841)|Fluphenazine(DB00623)|Isoflurane(DB00753)|Loperamide(DB00836)|Miconazole(DB01110)|Perphenazine(DB00850)|Phenoxybenzamine(DB00925)|Pimozide(DB01100)|Promethazine(DB01069)	ATGATGGCTAGAAAAATGAAA	0.388													10	359	---	---	---	---	PASS
OR4N3P	390539	broad.mit.edu	37	15	22414024	22414024	+	Missense_Mutation	SNP	C	T	T			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:22414024C>T	uc001yuf.2	+	1	323	c.323C>T	c.(322-324)GCT>GTT	p.A108V		NM_001080841	NP_001074310			RecName: Full=Olfactory receptor 4N2; AltName: Full=Olfactory receptor OR14-8; AltName: Full=Olfactory receptor OR14-13;												0						ATCAAGCTGGCTTGCACCGAC	0.507													29	176	---	---	---	---	PASS
PLEKHO2	80301	broad.mit.edu	37	15	65157277	65157277	+	Silent	SNP	G	A	A			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:65157277G>A	uc002anv.2	+	6	797	c.663G>A	c.(661-663)AGG>AGA	p.R221R	PLEKHO2_uc010bgz.2_Intron|PLEKHO2_uc002anw.2_Silent_p.R171R	NM_025201	NP_079477	Q8TD55	PKHO2_HUMAN	pleckstrin homology domain containing, family O	221	Pro-rich.									ovary(1)|lung(1)	2						CTGGTGACAGGGTGGAGACCC	0.627													7	11	---	---	---	---	PASS
DENND4A	10260	broad.mit.edu	37	15	66015282	66015282	+	Missense_Mutation	SNP	C	A	A			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:66015282C>A	uc002aph.2	-	12	1870	c.1492G>T	c.(1492-1494)GGT>TGT	p.G498C	DENND4A_uc002api.2_Missense_Mutation_p.G498C|DENND4A_uc002apj.3_Missense_Mutation_p.G498C|DENND4A_uc010ujj.1_Missense_Mutation_p.G498C	NM_005848	NP_005839	Q7Z401	MYCPP_HUMAN	DENN/MADD domain containing 4A isoform 2	498					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|protein binding			ovary(2)|haematopoietic_and_lymphoid_tissue(1)|skin(1)	4						TTCTTGTCACCAATTCTAAGA	0.313													7	586	---	---	---	---	PASS
ARIH1	25820	broad.mit.edu	37	15	72847625	72847625	+	Missense_Mutation	SNP	T	G	G			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:72847625T>G	uc002aut.3	+	4	916	c.602T>G	c.(601-603)CTT>CGT	p.L201R		NM_005744	NP_005735	Q9Y4X5	ARI1_HUMAN	ariadne ubiquitin-conjugating enzyme E2 binding	201	Interaction with UBE2L3.|RING-type 1; atypical.				ubiquitin-dependent protein catabolic process	cytoplasm|ubiquitin ligase complex	ubiquitin protein ligase binding|ubiquitin-protein ligase activity|zinc ion binding				0						TTCACTGGCCTTGAATGTGGA	0.353													102	652	---	---	---	---	PASS
NOMO1	23420	broad.mit.edu	37	16	14951429	14951429	+	Silent	SNP	T	C	C			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:14951429T>C	uc002dcv.2	+	11	1203	c.1137T>C	c.(1135-1137)GCT>GCC	p.A379A		NM_014287	NP_055102	Q15155	NOMO1_HUMAN	nodal modulator 1 precursor	379	Extracellular (Potential).					integral to membrane	carbohydrate binding|carboxypeptidase activity|protein binding			ovary(1)	1						CCATCCATGCTCAGAAAGAGC	0.433													7	373	---	---	---	---	PASS
KIAA0430	9665	broad.mit.edu	37	16	15690453	15690453	+	3'UTR	SNP	T	G	G			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:15690453T>G	uc002ddr.2	-	27					KIAA0430_uc002ddq.2_3'UTR|KIAA0430_uc010uzv.1_3'UTR|KIAA0430_uc010uzw.1_3'UTR	NM_014647	NP_055462	Q9Y4F3	LKAP_HUMAN	limkain b1							peroxisome	nucleotide binding|RNA binding				0						CTTCGGGGGGTTTTCATGACA	0.343													13	131	---	---	---	---	PASS
METTL9	51108	broad.mit.edu	37	16	21629221	21629221	+	Missense_Mutation	SNP	C	A	A			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:21629221C>A	uc002dje.2	+	3	591	c.392C>A	c.(391-393)CCA>CAA	p.P131Q	uc002diq.3_Intron|METTL9_uc002djf.2_Missense_Mutation_p.P131Q	NM_016025	NP_057109	Q9H1A3	METL9_HUMAN	methyltransferase like 9 isoform 1	131										ovary(1)	1				GBM - Glioblastoma multiforme(48;0.0759)		GTGTTTTCACCAGATCAGTTT	0.398													7	621	---	---	---	---	PASS
CBLN1	869	broad.mit.edu	37	16	49314850	49314850	+	Missense_Mutation	SNP	T	C	C			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:49314850T>C	uc002efq.2	-	2	707	c.368A>G	c.(367-369)AAC>AGC	p.N123S		NM_004352	NP_004343	P23435	CBLN1_HUMAN	cerebellin 1 precursor	123	C1q.|Necessary for interaction with CBLN3, and homotrimerization (By similarity).				nervous system development|synaptic transmission	cell junction|extracellular region|synapse					0		all_cancers(37;0.0766)|all_lung(18;0.24)				GGTTTGTCTGTTGTAGACTTT	0.567													11	157	---	---	---	---	PASS
C17orf107	100130311	broad.mit.edu	37	17	4805700	4805700	+	3'UTR	SNP	G	T	T			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:4805700G>T	uc002fzl.3	+	3					CHRNE_uc002fzk.1_Intron	NM_001145536	NP_001139008	Q6ZR85	CQ107_HUMAN	hypothetical protein LOC100130311												0						GGGGAAAAGGGGTGCCCTGGA	0.577													9	77	---	---	---	---	PASS
AP2B1	163	broad.mit.edu	37	17	33921061	33921061	+	Silent	SNP	C	A	A			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:33921061C>A	uc002hjr.2	+	2	201	c.12C>A	c.(10-12)TCC>TCA	p.S4S	AP2B1_uc002hjq.2_Silent_p.S4S|AP2B1_uc010wci.1_Silent_p.S4S|AP2B1_uc002hjs.2_5'UTR|AP2B1_uc002hjt.2_Silent_p.S4S|AP2B1_uc010ctv.2_Silent_p.S4S	NM_001282	NP_001273	P63010	AP2B1_HUMAN	adaptor-related protein complex 2, beta 1	4					axon guidance|epidermal growth factor receptor signaling pathway|intracellular protein transport|negative regulation of epidermal growth factor receptor signaling pathway|nerve growth factor receptor signaling pathway|regulation of defense response to virus by virus|synaptic transmission|vesicle-mediated transport|viral reproduction	clathrin adaptor complex|coated pit|cytosol|endocytic vesicle membrane|plasma membrane	clathrin binding|protein transporter activity			ovary(1)	1		Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0227)		TGACTGACTCCAAGTATTTCA	0.333													5	306	---	---	---	---	PASS
ACACA	31	broad.mit.edu	37	17	35545266	35545266	+	Missense_Mutation	SNP	T	C	C			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:35545266T>C	uc002hnm.2	-	39	4807	c.4616A>G	c.(4615-4617)TAC>TGC	p.Y1539C	ACACA_uc002hnk.2_Missense_Mutation_p.Y1461C|ACACA_uc002hnl.2_Missense_Mutation_p.Y1481C|ACACA_uc002hnn.2_Missense_Mutation_p.Y1539C|ACACA_uc002hno.2_Missense_Mutation_p.Y1576C|ACACA_uc010cuy.2_Missense_Mutation_p.Y233C	NM_198836	NP_942133	Q13085	ACACA_HUMAN	acetyl-Coenzyme A carboxylase alpha isoform 2	1539					acetyl-CoA metabolic process|energy reserve metabolic process|fatty acid biosynthetic process|long-chain fatty-acyl-CoA biosynthetic process|positive regulation of cellular metabolic process|protein homotetramerization|triglyceride biosynthetic process	cytosol	acetyl-CoA carboxylase activity|ATP binding|biotin carboxylase activity|metal ion binding|protein binding			large_intestine(1)|ovary(1)	2		Breast(25;0.00157)|Ovarian(249;0.15)			Biotin(DB00121)	GATATCCAAGTAATAGCCAGA	0.473													5	345	---	---	---	---	PASS
LRRC37A4	55073	broad.mit.edu	37	17	43580698	43580698	+	Intron	SNP	G	A	A			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:43580698G>A	uc002ije.2	-						uc010wjo.1_RNA					Homo sapiens cDNA FLJ34414 fis, clone HEART2003168, highly similar to Homo sapiens c114 SLIT-like testicular protein (LOC474170), mRNA.												0						atgtagtcacgtggaatttgg	0.020													3	12	---	---	---	---	PASS
TCF4	6925	broad.mit.edu	37	18	53128311	53128311	+	Silent	SNP	G	A	A			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:53128311G>A	uc002lfz.2	-	5	855	c.243C>T	c.(241-243)ACC>ACT	p.T81T	TCF4_uc002lfy.2_Silent_p.T39T|TCF4_uc010xdx.1_Silent_p.T57T|TCF4_uc010dph.1_Silent_p.T81T|TCF4_uc010xdy.1_Silent_p.T57T|TCF4_uc002lga.2_Silent_p.T183T|TCF4_uc010dpi.2_Silent_p.T81T|TCF4_uc002lgc.3_Silent_p.T2T	NM_003199	NP_003190	P15884	ITF2_HUMAN	transcription factor 4 isoform b	81	Essential for MYOD1 inhibition (By similarity).				positive regulation of neuron differentiation|protein-DNA complex assembly|transcription initiation from RNA polymerase II promoter	transcription factor complex	E-box binding|protein C-terminus binding|protein heterodimerization activity|RNA polymerase II core promoter proximal region sequence-specific DNA binding|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription|sequence-specific DNA binding RNA polymerase recruiting transcription factor activity|TFIIB-class binding transcription factor activity|TFIIB-class transcription factor binding			ovary(1)|lung(1)	2				Colorectal(16;0.00108)|READ - Rectum adenocarcinoma(59;0.0649)|COAD - Colon adenocarcinoma(17;0.0718)		GGTCCCTGCTGGTCATGTGGT	0.348													5	367	---	---	---	---	PASS
TXNL1	9352	broad.mit.edu	37	18	54270139	54270139	+	3'UTR	SNP	A	G	G			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:54270139A>G	uc002lgg.2	-	8					TXNL1_uc010xdz.1_RNA|TXNL1_uc002lgh.2_RNA|TXNL1_uc002lgi.2_3'UTR	NM_004786	NP_004777	O43396	TXNL1_HUMAN	thioredoxin-like 1						cell redox homeostasis|electron transport chain|glycerol ether metabolic process|transport	cytoplasm	electron carrier activity|protein disulfide oxidoreductase activity				0				READ - Rectum adenocarcinoma(59;0.193)|Colorectal(16;0.211)		TCTGAACAAAAGCAATGATTT	0.353													7	337	---	---	---	---	PASS
CDH19	28513	broad.mit.edu	37	18	64202297	64202297	+	Missense_Mutation	SNP	G	A	A			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:64202297G>A	uc002lkc.1	-	8	1400	c.1262C>T	c.(1261-1263)ACA>ATA	p.T421I	CDH19_uc010dql.1_RNA|CDH19_uc010xey.1_Missense_Mutation_p.T421I|CDH19_uc002lkd.2_Missense_Mutation_p.T421I	NM_021153	NP_066976	Q9H159	CAD19_HUMAN	cadherin 19, type 2 preproprotein	421	Cadherin 4.|Extracellular (Potential).				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(1)|skin(1)	2		Esophageal squamous(42;0.0132)				TGTAGTGATTGTACCATTATC	0.328													33	415	---	---	---	---	PASS
ZNF676	163223	broad.mit.edu	37	19	22364212	22364212	+	Missense_Mutation	SNP	G	T	T			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:22364212G>T	uc002nqs.1	-	3	625	c.307C>A	c.(307-309)CAG>AAG	p.Q103K		NM_001001411	NP_001001411	Q8N7Q3	ZN676_HUMAN	zinc finger protein 676	103					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0		Lung NSC(12;0.0207)|all_lung(12;0.0214)|all_epithelial(12;0.114)				GTTAAACTCTGGTTAAGTTTA	0.318													6	580	---	---	---	---	PASS
ZNF677	342926	broad.mit.edu	37	19	53740807	53740807	+	Silent	SNP	G	T	T			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:53740807G>T	uc002qbf.1	-	5	1358	c.1173C>A	c.(1171-1173)ACC>ACA	p.T391T	ZNF677_uc002qbg.1_Silent_p.T391T	NM_182609	NP_872415	Q86XU0	ZN677_HUMAN	zinc finger protein 677	391	C2H2-type 5.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1				GBM - Glioblastoma multiforme(134;0.00352)		TCTTATGTTGGGTAAGGCTTG	0.408													5	169	---	---	---	---	PASS
ZNF765	91661	broad.mit.edu	37	19	53901283	53901283	+	Missense_Mutation	SNP	G	T	T			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:53901283G>T	uc010ydx.1	+	4	342	c.15G>T	c.(13-15)CAG>CAT	p.Q5H	ZNF765_uc002qbm.2_Missense_Mutation_p.Q5H|ZNF765_uc002qbn.2_RNA	NM_001040185	NP_001035275	Q7L2R6	ZN765_HUMAN	zinc finger protein 765	5					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0				GBM - Glioblastoma multiforme(134;0.00379)		CTCTTCCTCAGGTGAGATGAT	0.438													6	485	---	---	---	---	PASS
LILRA1	11024	broad.mit.edu	37	19	55105673	55105673	+	5'UTR	SNP	C	T	T	rs28545324	by1000genomes	TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:55105673C>T	uc002qgh.1	+	2					LILRA2_uc010yfg.1_Intron|LILRA1_uc010yfh.1_5'UTR	NM_006863	NP_006854	O75019	LIRA1_HUMAN	leukocyte immunoglobulin-like receptor,						cell surface receptor linked signaling pathway|defense response|regulation of immune response	integral to membrane|plasma membrane	antigen binding|transmembrane receptor activity			skin(2)|ovary(1)	3				GBM - Glioblastoma multiforme(193;0.0348)		ACCGAGGGCTCATCCATCCGC	0.587													20	43	---	---	---	---	PASS
GZF1	64412	broad.mit.edu	37	20	23350858	23350858	+	Missense_Mutation	SNP	T	G	G			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:23350858T>G	uc010gdb.2	+	7	2090	c.1916T>G	c.(1915-1917)CTG>CGG	p.L639R	GZF1_uc002wsy.2_Missense_Mutation_p.L639R|GZF1_uc010zsq.1_Missense_Mutation_p.L163R|GZF1_uc010zsr.1_Missense_Mutation_p.L148R|GZF1_uc002wsz.2_Missense_Mutation_p.L639R	NM_022482	NP_071927	Q9H116	GZF1_HUMAN	GDNF-inducible zinc finger protein 1	639					transcription, DNA-dependent	nucleolus|nucleoplasm	sequence-specific DNA binding|zinc ion binding			kidney(1)	1	Lung NSC(19;0.0605)|Colorectal(13;0.0993)|all_lung(19;0.135)					GATAAATTGCTGTCTTTTGCA	0.488													26	44	---	---	---	---	PASS
KIF3B	9371	broad.mit.edu	37	20	30904366	30904366	+	Missense_Mutation	SNP	A	G	G			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:30904366A>G	uc002wxq.2	+	4	1710	c.1543A>G	c.(1543-1545)AGT>GGT	p.S515G	KIF3B_uc010ztw.1_Missense_Mutation_p.S453G	NM_004798	NP_004789	O15066	KIF3B_HUMAN	kinesin family member 3B	515	Potential.				anterograde axon cargo transport|blood coagulation|determination of left/right symmetry|mitotic centrosome separation|plus-end-directed vesicle transport along microtubule|spindle assembly involved in mitosis	centrosome|cytosol|kinesin II complex|plus-end kinesin complex|spindle microtubule	ATP binding|plus-end-directed microtubule motor activity|Rho GTPase binding			central_nervous_system(3)|ovary(2)	5			UCEC - Uterine corpus endometrioid carcinoma (5;0.0241)			ACAGATGGAAAGTCGAGATGA	0.438													5	160	---	---	---	---	PASS
DDTL	100037417	broad.mit.edu	37	22	24313673	24313673	+	3'UTR	SNP	C	T	T			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:24313673C>T	uc002zyy.3	+	3					DDT_uc011ajf.1_Intron|DDT_uc002zyz.3_3'UTR|DDT_uc002zza.3_3'UTR	NM_001084393	NP_001077862	A6NHG4	DDTL_HUMAN	D-dopachrome tautomerase-like							cytoplasm	lyase activity				0						CAGGCCCTCACTCTGCCAAGA	0.468													37	74	---	---	---	---	PASS
ZNRF3	84133	broad.mit.edu	37	22	29440812	29440812	+	Missense_Mutation	SNP	C	G	G			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:29440812C>G	uc003aeg.2	+	5	543	c.378C>G	c.(376-378)TTC>TTG	p.F126L	ZNRF3_uc003aeh.1_Missense_Mutation_p.F126L	NM_032173	NP_115549	Q9ULT6	ZNRF3_HUMAN	zinc and ring finger 3	226	Helical; (Potential).					integral to membrane	zinc ion binding			ovary(1)	1						TGGCTTTCTTCGTCGTGGTCT	0.537													5	232	---	---	---	---	PASS
C22orf30	253143	broad.mit.edu	37	22	32112888	32112888	+	Missense_Mutation	SNP	G	T	T			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:32112888G>T	uc003alp.3	-	4	1130	c.937C>A	c.(937-939)CAA>AAA	p.Q313K	C22orf30_uc003alo.1_Missense_Mutation_p.Q112K|C22orf30_uc010gwj.1_Missense_Mutation_p.Q112K	NM_173566	NP_775837	Q5THK1	PR14L_HUMAN	hypothetical protein LOC253143	313											0						TGAAGCTGTTGGTGATTGTCA	0.428													6	574	---	---	---	---	PASS
CACNA1I	8911	broad.mit.edu	37	22	40062013	40062013	+	Splice_Site	SNP	T	A	A			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:40062013T>A	uc003ayc.2	+	23	4104	c.4104_splice	c.e23+2	p.Q1368_splice	CACNA1I_uc003ayd.2_Splice_Site_p.Q1333_splice|CACNA1I_uc003aye.2_Splice_Site_p.Q1283_splice|CACNA1I_uc003ayf.2_Splice_Site_p.Q1248_splice	NM_021096	NP_066919	Q9P0X4	CAC1I_HUMAN	calcium channel, voltage-dependent, T type,						axon guidance|signal transduction	voltage-gated calcium channel complex	low voltage-gated calcium channel activity|protein binding			breast(1)|central_nervous_system(1)	2	Melanoma(58;0.0749)				Flunarizine(DB04841)|Paramethadione(DB00617)|Verapamil(DB00661)	CTGGGCCAGGTGAGCACCACC	0.463													9	41	---	---	---	---	PASS
XRCC6	2547	broad.mit.edu	37	22	42024232	42024232	+	Missense_Mutation	SNP	C	A	A			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:42024232C>A	uc003bao.1	+	3	263	c.193C>A	c.(193-195)CAG>AAG	p.Q65K	XRCC6_uc003bap.1_Missense_Mutation_p.Q65K|XRCC6_uc011apc.1_Intron|XRCC6_uc003baq.1_Missense_Mutation_p.Q65K|XRCC6_uc003bar.1_Missense_Mutation_p.Q65K|XRCC6_uc003bas.1_Intron	NM_001469	NP_001460	P12956	XRCC6_HUMAN	ATP-dependent DNA helicase II, 70 kDa subunit	65					DNA ligation|double-strand break repair via nonhomologous end joining|initiation of viral infection|negative regulation of transcription, DNA-dependent|positive regulation of transcription from RNA polymerase II promoter|provirus integration|telomere maintenance|transcription, DNA-dependent	DNA-dependent protein kinase-DNA ligase 4 complex|Ku70:Ku80 complex|membrane fraction|nuclear telomere cap complex|transcription factor complex	5'-deoxyribose-5-phosphate lyase activity|ATP binding|ATP-dependent DNA helicase activity|double-stranded DNA binding|protein C-terminus binding|transcription regulatory region DNA binding			skin(2)|ovary(1)|lung(1)|kidney(1)	5						CATGAGCATCCAGGTAAGACT	0.244								Direct_reversal_of_damage|NHEJ					6	424	---	---	---	---	PASS
OFD1	8481	broad.mit.edu	37	X	13778278	13778278	+	Missense_Mutation	SNP	G	T	T			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:13778278G>T	uc004cvp.3	+	16	2058	c.1699G>T	c.(1699-1701)GAT>TAT	p.D567Y	OFD1_uc004cvr.3_Missense_Mutation_p.D134Y|OFD1_uc011mil.1_Missense_Mutation_p.D134Y|OFD1_uc004cvq.3_Missense_Mutation_p.D427Y|OFD1_uc010nen.2_Missense_Mutation_p.D566Y|OFD1_uc004cvs.3_RNA|OFD1_uc004cvu.3_Missense_Mutation_p.D526Y|OFD1_uc004cvv.3_Missense_Mutation_p.D526Y	NM_003611	NP_003602	O75665	OFD1_HUMAN	oral-facial-digital syndrome 1	567					cilium movement involved in determination of left/right asymmetry|G2/M transition of mitotic cell cycle	centriole|cilium|cytosol|microtubule basal body|nuclear membrane	alpha-tubulin binding|gamma-tubulin binding				0						GTCTGTGATCGATCGTTCTGT	0.408													7	303	---	---	---	---	PASS
SAT1	6303	broad.mit.edu	37	X	23801393	23801393	+	5'UTR	SNP	G	A	A			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:23801393G>A	uc004dau.2	+	1					SAT1_uc010nfv.2_5'UTR|SAT1_uc004dav.2_RNA	NM_002970	NP_002961	P21673	SAT1_HUMAN	diamine N-acetyltransferase 1						angiogenesis|polyamine biosynthetic process	cytosol	diamine N-acetyltransferase activity|protein binding				0					Spermine(DB00127)	CCCGGGAGACGAATGAGGAAC	0.562											OREG0019712	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	4	43	---	---	---	---	PASS
NDP	4693	broad.mit.edu	37	X	43809267	43809267	+	Silent	SNP	C	A	A			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:43809267C>A	uc004dga.3	-	3	759	c.180G>T	c.(178-180)GTG>GTT	p.V60V		NM_000266	NP_000257	Q00604	NDP_HUMAN	norrin precursor	60	CTCK.		V -> E (in ND; reduction of protein amount in the extracellular matrix).		canonical Wnt receptor signaling pathway|cell proliferation|cell-cell signaling|nervous system development|positive regulation of transcription, DNA-dependent|sensory perception of sound|vacuole organization|visual perception	extracellular matrix|extracellular space	cell surface binding|frizzled binding|growth factor activity|protein homodimerization activity				0						TGGCCAGGAGCACCATCTGGG	0.567											OREG0019744	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	4	12	---	---	---	---	PASS
CCDC120	90060	broad.mit.edu	37	X	48923285	48923285	+	Missense_Mutation	SNP	C	T	T			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:48923285C>T	uc010nik.2	+	9	1372	c.865C>T	c.(865-867)CGC>TGC	p.R289C	CCDC120_uc011mmq.1_Missense_Mutation_p.R277C|CCDC120_uc004dmf.2_Missense_Mutation_p.R289C|CCDC120_uc010nil.2_Missense_Mutation_p.R289C|CCDC120_uc011mmr.1_Missense_Mutation_p.R289C|CCDC120_uc011mms.1_Missense_Mutation_p.R277C	NM_033626	NP_296375	Q96HB5	CC120_HUMAN	coiled-coil domain containing 120 isoform 3	289							protein binding			pancreas(1)	1						TAGCCCCACACGCTCGCTGCC	0.647													11	18	---	---	---	---	PASS
TAF1	6872	broad.mit.edu	37	X	70607246	70607246	+	Missense_Mutation	SNP	C	T	T			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:70607246C>T	uc004dzu.3	+	15	2410	c.2359C>T	c.(2359-2361)CCC>TCC	p.P787S	BCYRN1_uc011mpt.1_Intron|TAF1_uc004dzt.3_Missense_Mutation_p.P808S|TAF1_uc004dzv.3_5'Flank	NM_138923	NP_620278	P21675	TAF1_HUMAN	TBP-associated factor 1 isoform 2	787					G1 phase of mitotic cell cycle|interspecies interaction between organisms|peptidyl-serine phosphorylation|peptidyl-threonine phosphorylation|positive regulation of proteasomal ubiquitin-dependent protein catabolic process|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription initiation from RNA polymerase II promoter|protein autophosphorylation|regulation of transcription involved in G2/M-phase of mitotic cell cycle|RNA polymerase II transcriptional preinitiation complex assembly|transcription elongation from RNA polymerase II promoter|viral reproduction	MLL1 complex|transcription factor TFIID complex	ATP binding|histone acetyl-lysine binding|histone acetyltransferase activity|p53 binding|protein binding|protein serine/threonine kinase activity|sequence-specific DNA binding|TBP-class protein binding|transcription coactivator activity			ovary(7)|breast(4)|large_intestine(2)|central_nervous_system(2)|lung(1)|skin(1)	17	Renal(35;0.156)	all_lung(315;0.000321)				CCAGCAGTGTCCCTTGTTTGA	0.443													182	366	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	X	114953432	114953432	+	RNA	SNP	G	T	T			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:114953432G>T	uc004eqf.2	-	1		c.233C>A								full-length cDNA clone CS0DJ015YA07 of T cells (Jurkat cell line) Cot 10-normalized of Homo sapiens (human).																		AGTTTACTAAGTGGTGTATGC	0.448													7	50	---	---	---	---	PASS
MAGEC1	9947	broad.mit.edu	37	X	140993373	140993373	+	Silent	SNP	G	A	A			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:140993373G>A	uc004fbt.2	+	4	469	c.183G>A	c.(181-183)GAG>GAA	p.E61E	MAGEC1_uc010nsl.1_Intron	NM_005462	NP_005453	O60732	MAGC1_HUMAN	melanoma antigen family C, 1	61							protein binding			ovary(1)|kidney(1)|central_nervous_system(1)|skin(1)	4	Acute lymphoblastic leukemia(192;6.56e-05)					CTGAGGGGGAGGACTCCTCGG	0.602										HNSCC(15;0.026)			12	27	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	M	2267	2267	+	5'Flank	SNP	T	C	C			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrM:2267T>C	uc004coq.3	-						uc004cos.3_RNA					Homo sapiens cDNA: FLJ22857 fis, clone KAT01615.																		CTCACACCCAATTGGACCAAT	0.403													14	43	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	M	13676	13676	+	RNA	SNP	A	G	G			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrM:13676A>G	uc004cox.3	+	1		c.1340A>G			uc004coy.2_5'Flank|uc004coz.1_5'Flank					Homo sapiens NADH dehydrogenase subunit 5 (MTND5) mRNA, RNA 5, complete cds; mitochondrial gene for mitochondrial product.																		TAACGAAAATAACCCCACCCT	0.493													8	20	---	---	---	---	PASS
MEGF6	1953	broad.mit.edu	37	1	3519151	3519152	+	Frame_Shift_Del	DEL	CA	-	-			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:3519151_3519152delCA	uc001akl.2	-	2	371_372	c.144_145delTG	c.(142-147)TGTGCTfs	p.C48fs		NM_001409	NP_001400	O75095	MEGF6_HUMAN	EGF-like-domain, multiple 3 precursor	48_49	EMI.					extracellular region	calcium ion binding			large_intestine(1)	1	all_cancers(77;0.00681)|all_epithelial(69;0.00301)|Ovarian(185;0.0634)|Lung NSC(156;0.0969)|all_lung(157;0.105)	all_epithelial(116;7.41e-22)|all_lung(118;8.3e-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;3.78e-37)|OV - Ovarian serous cystadenocarcinoma(86;6.86e-22)|GBM - Glioblastoma multiforme(42;1.96e-12)|Colorectal(212;6.15e-05)|COAD - Colon adenocarcinoma(227;0.000241)|Kidney(185;0.000448)|BRCA - Breast invasive adenocarcinoma(365;0.000779)|KIRC - Kidney renal clear cell carcinoma(229;0.00645)|STAD - Stomach adenocarcinoma(132;0.00669)|Lung(427;0.213)		TCCTGCTCAGCACACACGTGGG	0.708													4	2	---	---	---	---	
UBE4B	10277	broad.mit.edu	37	1	10132438	10132438	+	Intron	DEL	T	-	-			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:10132438delT	uc001aqs.3	+						UBE4B_uc001aqr.3_Intron|UBE4B_uc010oai.1_Intron|UBE4B_uc010oaj.1_Intron	NM_001105562	NP_001099032	O95155	UBE4B_HUMAN	ubiquitination factor E4B isoform 1						apoptosis|protein ubiquitination involved in ubiquitin-dependent protein catabolic process|response to UV	cytoplasm|ubiquitin ligase complex	enzyme binding			ovary(2)|skin(2)	4		all_lung(284;1.13e-05)|Lung NSC(185;1.74e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Hepatocellular(190;0.00913)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0268)|Colorectal(212;1.42e-07)|COAD - Colon adenocarcinoma(227;2.77e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000435)|Kidney(185;0.000482)|KIRC - Kidney renal clear cell carcinoma(229;0.00164)|STAD - Stomach adenocarcinoma(132;0.0117)|READ - Rectum adenocarcinoma(331;0.046)		GTGTTATCGCTTTTTTTTTTA	0.308													4	2	---	---	---	---	
NBPF1	55672	broad.mit.edu	37	1	16932109	16932109	+	Intron	DEL	A	-	-			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:16932109delA	uc009vos.1	-						NBPF1_uc001aza.3_Intron|NBPF1_uc001azb.1_RNA|NBPF1_uc001azc.1_RNA	NM_017940	NP_060410	Q3BBV0	NBPF1_HUMAN	hypothetical protein LOC55672							cytoplasm					0				UCEC - Uterine corpus endometrioid carcinoma (279;0.00459)|BRCA - Breast invasive adenocarcinoma(304;7.52e-06)|COAD - Colon adenocarcinoma(227;1.05e-05)|Kidney(64;0.00016)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.179)		aaagtGTGAGAAAAAAAGATA	0.209													4	2	---	---	---	---	
UBXN11	91544	broad.mit.edu	37	1	26608878	26608883	+	In_Frame_Del	DEL	CCGGGA	-	-	rs1134581		TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:26608878_26608883delCCGGGA	uc001blw.2	-	16	1743_1748	c.1470_1475delTCCCGG	c.(1468-1476)GGTCCCGGC>GGC	p.490_492GPG>G	UBXN11_uc001blz.1_In_Frame_Del_p.457_459GPG>G|UBXN11_uc001blv.2_In_Frame_Del_p.452_454GPG>G|UBXN11_uc001bly.2_In_Frame_Del_p.370_372GPG>G|UBXN11_uc001blx.2_In_Frame_Del_p.248_250GPG>G|UBXN11_uc001bma.2_In_Frame_Del_p.457_459GPG>G|UBXN11_uc001bmb.1_In_Frame_Del_p.490_492GPG>G	NM_183008	NP_892120	Q5T124	UBX11_HUMAN	socius isoform 2	490_492	Pro-rich.|3 X 8 AA tandem repeats of P-G-P-G-P-G-P- S.|1.		Missing.|Missing.			cytoplasm|cytoskeleton				ovary(1)	1						gggactggggccgggaccgggaccgg	0.282													4	2	---	---	---	---	
AHDC1	27245	broad.mit.edu	37	1	27891215	27891215	+	Intron	DEL	C	-	-			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:27891215delC	uc009vsy.2	-						AHDC1_uc009vsz.1_Intron|AHDC1_uc001boh.1_Intron	NM_001029882	NP_001025053	Q5TGY3	AHDC1_HUMAN	AT hook, DNA binding motif, containing 1								DNA binding			central_nervous_system(1)	1		all_lung(284;1.06e-05)|Lung NSC(340;1.86e-05)|Colorectal(325;3.46e-05)|Renal(390;0.0007)|Breast(348;0.0021)|Ovarian(437;0.00503)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0434)|OV - Ovarian serous cystadenocarcinoma(117;8.48e-25)|Colorectal(126;9.17e-09)|COAD - Colon adenocarcinoma(152;1.84e-06)|KIRC - Kidney renal clear cell carcinoma(1967;0.00192)|BRCA - Breast invasive adenocarcinoma(304;0.00259)|STAD - Stomach adenocarcinoma(196;0.00311)|READ - Rectum adenocarcinoma(331;0.0291)		TGCCTCCCTGCCGCCCGATGA	0.478													4	2	---	---	---	---	
SNRNP40	9410	broad.mit.edu	37	1	31769359	31769360	+	Intron	INS	-	C	C			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:31769359_31769360insC	uc001bso.2	-						SNRNP40_uc010oge.1_Intron|ZCCHC17_uc001bsp.1_5'Flank|ZCCHC17_uc001bsq.1_5'Flank|ZCCHC17_uc010ogf.1_5'Flank|ZCCHC17_uc009vtu.1_5'Flank|ZCCHC17_uc001bsr.1_5'Flank|ZCCHC17_uc009vtv.1_5'Flank	NM_004814	NP_004805	Q96DI7	SNR40_HUMAN	WD repeat domain 57 (U5 snRNP specific)							catalytic step 2 spliceosome|cytoplasm|nucleoplasm|small nucleolar ribonucleoprotein complex|U5 snRNP	protein binding				0						CTCTCGTTCTGCCCCCGCAATG	0.564													4	2	---	---	---	---	
TESK2	10420	broad.mit.edu	37	1	45810346	45810346	+	3'UTR	DEL	C	-	-			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:45810346delC	uc001cns.1	-	11					TESK2_uc009vxr.1_3'UTR|TESK2_uc010olo.1_3'UTR|TESK2_uc009vxs.1_3'UTR	NM_007170	NP_009101	Q96S53	TESK2_HUMAN	testis-specific protein kinase 2						actin cytoskeleton organization|focal adhesion assembly|spermatogenesis	nucleus	ATP binding|metal ion binding|protein serine/threonine kinase activity|protein tyrosine kinase activity			ovary(2)|breast(2)|pancreas(1)	5	Acute lymphoblastic leukemia(166;0.155)					ACTGCTGCCTCCCGTCATACA	0.587													4	2	---	---	---	---	
INADL	10207	broad.mit.edu	37	1	62317047	62317047	+	Intron	DEL	G	-	-			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:62317047delG	uc001dab.2	+						INADL_uc009waf.1_Intron|INADL_uc001daa.2_Intron|INADL_uc001dad.3_Intron|INADL_uc001dac.2_Intron	NM_176877	NP_795352	Q8NI35	INADL_HUMAN	InaD-like						intracellular signal transduction|tight junction assembly	apical plasma membrane|perinuclear region of cytoplasm|tight junction	protein binding			ovary(3)|skin(1)	4						agctgactctggggcaaactc	0.045													4	2	---	---	---	---	
ROR1	4919	broad.mit.edu	37	1	64614698	64614698	+	Intron	DEL	A	-	-	rs63695161		TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:64614698delA	uc001dbj.2	+						uc001dbl.2_Intron	NM_005012	NP_005003	Q01973	ROR1_HUMAN	receptor tyrosine kinase-like orphan receptor 1						transmembrane receptor protein tyrosine kinase signaling pathway	cytoplasm|integral to plasma membrane	ATP binding|transmembrane receptor protein tyrosine kinase activity|Wnt-protein binding			ovary(6)|large_intestine(3)|breast(3)|stomach(2)|lung(2)|central_nervous_system(1)|skin(1)|kidney(1)	19						aatcagatggaaaaaaaaata	0.119													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	69008683	69008684	+	IGR	INS	-	A	A	rs142593864	by1000genomes	TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:69008683_69008684insA								DEPDC1 (45884 upstream) : None (None downstream)																							CCTGCATTTACAAAATTAATTG	0.307													7	4	---	---	---	---	
SLC44A5	204962	broad.mit.edu	37	1	75706840	75706840	+	Intron	DEL	A	-	-			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:75706840delA	uc001dgu.2	-						SLC44A5_uc001dgt.2_Intron|SLC44A5_uc001dgs.2_Intron|SLC44A5_uc001dgr.2_Intron|SLC44A5_uc010oqz.1_Intron|SLC44A5_uc010ora.1_Intron|SLC44A5_uc010orb.1_Intron	NM_152697	NP_689910	Q8NCS7	CTL5_HUMAN	solute carrier family 44, member 5 isoform A							integral to membrane|plasma membrane	choline transmembrane transporter activity			ovary(2)|skin(2)	4						ATTTTAATGTAAAGCTTTTTT	0.179													4	2	---	---	---	---	
WDR63	126820	broad.mit.edu	37	1	85570522	85570524	+	Intron	DEL	TTC	-	-	rs66689432		TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:85570522_85570524delTTC	uc001dkt.2	+						WDR63_uc009wcl.2_Intron	NM_145172	NP_660155	Q8IWG1	WDR63_HUMAN	WD repeat domain 63											upper_aerodigestive_tract(2)|ovary(2)|skin(1)	5				all cancers(265;0.00391)|Epithelial(280;0.00922)|Colorectal(170;0.166)		TTATCCATAGTTCTTCTTCACAT	0.251													9	7	---	---	---	---	
DNTTIP2	30836	broad.mit.edu	37	1	94336499	94336499	+	Intron	DEL	A	-	-	rs71897107		TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:94336499delA	uc001dqf.2	-						DNTTIP2_uc010otm.1_Intron	NM_014597	NP_055412	Q5QJE6	TDIF2_HUMAN	deoxynucleotidyltransferase, terminal,						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus					0		all_lung(203;0.0111)|Lung NSC(277;0.0347)		all cancers(265;0.00679)|GBM - Glioblastoma multiforme(16;0.0278)|Epithelial(280;0.128)		TATTTAAAGCAAAAAAAAAAA	0.284													15	11	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	117784462	117784462	+	IGR	DEL	G	-	-			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:117784462delG								VTCN1 (30913 upstream) : MAN1A2 (125623 downstream)																							cacatcttctgggatgctgct	0.144													4	2	---	---	---	---	
MAN1A2	10905	broad.mit.edu	37	1	117945223	117945223	+	Intron	DEL	T	-	-			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:117945223delT	uc001ehd.1	+						MAN1A2_uc009whg.1_Intron	NM_006699	NP_006690	O60476	MA1A2_HUMAN	mannosidase, alpha, class 1A, member 2						N-glycan processing|post-translational protein modification|protein N-linked glycosylation via asparagine	Golgi membrane|integral to membrane|membrane fraction	calcium ion binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity				0	Lung SC(450;0.225)	all_cancers(81;7.9e-06)|all_epithelial(167;7.39e-07)|all_lung(203;2.84e-06)|Lung NSC(69;1.99e-05)		Lung(183;0.0688)|Kidney(133;0.114)|LUSC - Lung squamous cell carcinoma(189;0.223)|KIRC - Kidney renal clear cell carcinoma(1967;0.237)|Colorectal(144;0.243)		CTCTTTCTTGttttttttttt	0.269													5	3	---	---	---	---	
NBPF9	400818	broad.mit.edu	37	1	145092864	145092864	+	Intron	DEL	A	-	-	rs11401146		TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:145092864delA	uc010oye.1	+						NBPF10_uc009wir.2_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron			Q3BBV1	NBPFK_HUMAN	RecName: Full=Neuroblastoma breakpoint family member 8;							cytoplasm					0						aatctgtaagaaaatgttcca	0.199													3	4	---	---	---	---	
ATP1A2	477	broad.mit.edu	37	1	160094739	160094739	+	Intron	DEL	A	-	-			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:160094739delA	uc001fvc.2	+						ATP1A2_uc001fvb.2_Intron|ATP1A2_uc010piz.1_Intron|ATP1A2_uc001fvd.2_5'Flank	NM_000702	NP_000693	P50993	AT1A2_HUMAN	Na+/K+ -ATPase alpha 2 subunit proprotein						ATP biosynthetic process		ATP binding|metal ion binding|sodium:potassium-exchanging ATPase activity			central_nervous_system(3)|ovary(2)|skin(2)	7	all_cancers(52;1.11e-16)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.111)|LUSC - Lung squamous cell carcinoma(543;0.246)			agaagtcaggaggagtcagaa	0.174													4	2	---	---	---	---	
RGS5	8490	broad.mit.edu	37	1	163122757	163122758	+	Intron	INS	-	AG	AG	rs142129808	by1000genomes	TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:163122757_163122758insAG	uc001gcn.2	-						RGS5_uc009wvb.2_Intron	NM_003617	NP_003608	O15539	RGS5_HUMAN	regulator of G-protein signalling 5						negative regulation of signal transduction|regulation of G-protein coupled receptor protein signaling pathway	cytoplasm|plasma membrane	GTPase activator activity|signal transducer activity				0			LUSC - Lung squamous cell carcinoma(543;0.187)			TAGAACTAGACAGAGATTTACC	0.386													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	165039724	165039725	+	IGR	DEL	AC	-	-			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:165039724_165039725delAC								PBX1 (185424 upstream) : LMX1A (131380 downstream)																							TTAACATCAAacacacacacac	0.312													4	2	---	---	---	---	
RFWD2	64326	broad.mit.edu	37	1	176015105	176015105	+	Intron	DEL	A	-	-			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:176015105delA	uc001gku.1	-						RFWD2_uc001gkv.1_Intron|RFWD2_uc001gkw.1_Intron|RFWD2_uc009wwv.2_Intron|RFWD2_uc001gkt.1_Intron	NM_022457	NP_071902	Q8NHY2	RFWD2_HUMAN	ring finger and WD repeat domain 2 isoform a						DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest	centrosome|cytosol|focal adhesion|nuclear speck	protein binding|ubiquitin-protein ligase activity|zinc ion binding				0						TGGCAACCAGAAAAAAAAAAA	0.299													4	5	---	---	---	---	
C1orf125	126859	broad.mit.edu	37	1	179335930	179335932	+	Intron	DEL	CTC	-	-	rs150638150		TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:179335930_179335932delCTC	uc001gmo.2	+						C1orf125_uc009wxg.2_Intron|C1orf125_uc001gmn.1_Intron|C1orf125_uc010pnl.1_Intron|C1orf125_uc001gmp.2_Intron	NM_144696	NP_653297	Q5T1B0	AXDN1_HUMAN	hypothetical protein LOC126859 isoform 1												0						TGTTTCACTACTCCATCTAAATA	0.271													6	9	---	---	---	---	
MYOG	4656	broad.mit.edu	37	1	203053907	203053908	+	Intron	DEL	TC	-	-			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:203053907_203053908delTC	uc001gzd.2	-							NM_002479	NP_002470	P15173	MYOG_HUMAN	myogenin						muscle cell fate commitment|positive regulation of muscle cell differentiation|positive regulation of transcription from RNA polymerase II promoter	transcription factor complex	E-box binding|protein heterodimerization activity|sequence-specific DNA binding transcription factor activity			skin(2)	2						TTCTTTGATGTCTCTCTCTGCC	0.634													4	2	---	---	---	---	
ESRRG	2104	broad.mit.edu	37	1	217008496	217008498	+	Intron	DEL	ATC	-	-	rs145716421		TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:217008496_217008498delATC	uc001hky.1	-						ESRRG_uc009xdp.1_Intron|ESRRG_uc001hkz.1_Intron|ESRRG_uc010puc.1_Intron|ESRRG_uc001hla.1_Intron|ESRRG_uc001hlb.1_Intron|ESRRG_uc010pud.1_Intron|ESRRG_uc001hlc.1_Intron|ESRRG_uc001hld.1_Intron	NM_206595	NP_996318	P62508	ERR3_HUMAN	estrogen-related receptor gamma isoform 2						positive regulation of transcription, DNA-dependent|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor	nucleoplasm	AF-2 domain binding|retinoic acid receptor activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|steroid hormone receptor activity|zinc ion binding			ovary(1)|kidney(1)	2				OV - Ovarian serous cystadenocarcinoma(81;0.0358)|all cancers(67;0.0693)|GBM - Glioblastoma multiforme(131;0.0713)	Diethylstilbestrol(DB00255)	CCAACTGATAATCAGAGTTGAAT	0.256													6	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	16279402	16279402	+	IGR	DEL	C	-	-			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:16279402delC								MYCN (192274 upstream) : FAM49A (454499 downstream)																							TGCACATCTTCCCCCTTGTCT	0.458													4	2	---	---	---	---	
ALK	238	broad.mit.edu	37	2	29902598	29902599	+	Intron	INS	-	A	A	rs139619353	by1000genomes	TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:29902598_29902599insA	uc002rmy.2	-							NM_004304	NP_004295	Q9UM73	ALK_HUMAN	anaplastic lymphoma kinase precursor						protein autophosphorylation|transmembrane receptor protein tyrosine kinase signaling pathway	integral to plasma membrane	ATP binding|protein binding|transmembrane receptor protein tyrosine kinase activity		NPM1/ALK(632)|EML4/ALK(246)|CLTC/ALK(44)|TPM3/ALK(33)|ATIC/ALK(24)|RANBP2/ALK(16)|TPM4/ALK(12)|TFG/ALK(7)|MSN/ALK(6)|CARS/ALK(5)|VCL/ALK(4)|KIF5B/ALK(4)|PPFIBP1/ALK(3)|SEC31A/ALK(3)|SQSTM1/ALK(2)	haematopoietic_and_lymphoid_tissue(726)|lung(262)|autonomic_ganglia(148)|soft_tissue(61)|breast(4)|kidney(4)|large_intestine(3)|skin(3)|ovary(3)|thyroid(2)|central_nervous_system(1)|pancreas(1)	1218	Acute lymphoblastic leukemia(172;0.155)				Adenosine triphosphate(DB00171)	agaagaataagaaaaaggttgt	0.000			T|Mis|A	NPM1|TPM3|TFG|TPM4|ATIC|CLTC|MSN|ALO17|CARS|EML4	ALCL|NSCLC|Neuroblastoma	neuroblastoma			Neuroblastoma_Familial_Clustering_of|Congenital_Central_Hypoventilation_Syndrome				4	2	---	---	---	---	
TTC27	55622	broad.mit.edu	37	2	32892037	32892037	+	Intron	DEL	T	-	-	rs66516618		TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:32892037delT	uc002rom.2	+						TTC27_uc010ymx.1_Intron	NM_017735	NP_060205	Q6P3X3	TTC27_HUMAN	tetratricopeptide repeat domain 27								protein binding			central_nervous_system(1)	1						AAAACTGGTGTTTTTTTTTTC	0.308													8	5	---	---	---	---	
DHX57	90957	broad.mit.edu	37	2	39085574	39085575	+	Intron	DEL	TG	-	-	rs144247886		TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:39085574_39085575delTG	uc002rrf.2	-						DHX57_uc002rre.2_Intron|DHX57_uc002rrg.2_Intron	NM_198963	NP_945314	Q6P158	DHX57_HUMAN	DEAH (Asp-Glu-Ala-Asp/His) box polypeptide 57								ATP binding|ATP-dependent helicase activity|nucleic acid binding|protein binding|zinc ion binding			ovary(1)|lung(1)|skin(1)	3		all_hematologic(82;0.248)				CACATGACTCTGAGACTATTTG	0.327													6	6	---	---	---	---	
PUS10	150962	broad.mit.edu	37	2	61192799	61192800	+	Intron	INS	-	T	T			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:61192799_61192800insT	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)			AAATAGTTTTGTTTTTTTTTTT	0.297													6	3	---	---	---	---	
ANKRD36	375248	broad.mit.edu	37	2	97890533	97890534	+	Intron	INS	-	T	T			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:97890533_97890534insT	uc010yva.1	+						ANKRD36_uc002sxr.1_Intron	NM_001164315	NP_001157787	A6QL64	AN36A_HUMAN	ankyrin repeat domain 36												0						TAAATATATAATTTTTTTAGCA	0.248													4	3	---	---	---	---	
VWA3B	200403	broad.mit.edu	37	2	98919885	98919886	+	Intron	DEL	GT	-	-			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:98919885_98919886delGT	uc002syo.2	+						VWA3B_uc002syn.1_Intron|VWA3B_uc010yvi.1_Intron|VWA3B_uc002syp.1_Intron|VWA3B_uc002syq.1_Intron|VWA3B_uc002syr.1_Intron|VWA3B_uc002sys.2_Intron	NM_144992	NP_659429	Q502W6	VWA3B_HUMAN	von Willebrand factor A domain containing 3B											ovary(3)|large_intestine(2)|skin(1)	6						TTATGTGAAGgtgtgtgtgtgt	0.381													5	3	---	---	---	---	
TGFBRAP1	9392	broad.mit.edu	37	2	105892365	105892365	+	Intron	DEL	A	-	-			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:105892365delA	uc002tcq.2	-						TGFBRAP1_uc010fjc.2_Intron|TGFBRAP1_uc002tcr.3_Intron	NM_004257	NP_004248	Q8WUH2	TGFA1_HUMAN	transforming growth factor, beta receptor						regulation of transcription, DNA-dependent|transforming growth factor beta receptor signaling pathway	cytoplasm|membrane	SMAD binding|small GTPase regulator activity|transforming growth factor beta receptor binding			central_nervous_system(1)|skin(1)	2						TCCAAGAAATAAAAAAAAAAA	0.234													4	2	---	---	---	---	
PLGLA	285189	broad.mit.edu	37	2	107003270	107003270	+	Intron	DEL	A	-	-			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:107003270delA	uc002tdp.2	+							NR_003506				Homo sapiens plasminogen-like A (PLGLA), non-coding RNA.												0						ATATAATGTTAAAAAAAAAAA	0.403													2	4	---	---	---	---	
GCC2	9648	broad.mit.edu	37	2	109084943	109084943	+	Intron	DEL	T	-	-			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:109084943delT	uc002tec.2	+						GCC2_uc002ted.2_Intron	NM_181453	NP_852118	Q8IWJ2	GCC2_HUMAN	GRIP and coiled-coil domain-containing 2						Golgi ribbon formation|late endosome to Golgi transport|microtubule anchoring|microtubule organizing center organization|protein localization in Golgi apparatus|protein targeting to lysosome|recycling endosome to Golgi transport|regulation of protein exit from endoplasmic reticulum	membrane|trans-Golgi network	identical protein binding			ovary(1)	1						ggcttattgatttttttttcc	0.109													4	2	---	---	---	---	
RANBP2	5903	broad.mit.edu	37	2	109375192	109375193	+	Intron	INS	-	G	G			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:109375192_109375193insG	uc002tem.3	+							NM_006267	NP_006258	P49792	RBP2_HUMAN	RAN binding protein 2						carbohydrate metabolic process|glucose transport|mitotic prometaphase|mRNA transport|protein folding|protein import into nucleus|regulation of glucose transport|transmembrane transport|viral reproduction	cytosol|nuclear pore	peptidyl-prolyl cis-trans isomerase activity|Ran GTPase binding|zinc ion binding		RANBP2/ALK(16)	soft_tissue(16)|lung(1)|pancreas(1)	18						GCAGAAAAAACGAGCCGTATGT	0.322													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	122566295	122566295	+	IGR	DEL	T	-	-	rs35866378		TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:122566295delT								TSN (40869 upstream) : None (None downstream)																							TTTGGGTCCATTTTTTTTTCT	0.383													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	133102450	133102451	+	IGR	INS	-	TT	TT	rs141217632	by1000genomes	TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:133102450_133102451insTT								NCRNA00164 (86908 upstream) : GPR39 (71696 downstream)																							gtcaggagttcaagaccagcct	0.000													3	3	---	---	---	---	
THSD7B	80731	broad.mit.edu	37	2	137872510	137872510	+	Intron	DEL	T	-	-			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:137872510delT	uc002tva.1	+						THSD7B_uc010zbj.1_Intron|THSD7B_uc002tvb.2_Intron	NM_001080427	NP_001073896			thrombospondin, type I, domain containing 7B											ovary(4)|central_nervous_system(2)|pancreas(1)	7				BRCA - Breast invasive adenocarcinoma(221;0.19)		CTGCTGGATGTTTTTTTTTTC	0.393													6	3	---	---	---	---	
FMNL2	114793	broad.mit.edu	37	2	153378772	153378774	+	Intron	DEL	TAT	-	-			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:153378772_153378774delTAT	uc002tye.2	+							NM_052905	NP_443137	Q96PY5	FMNL2_HUMAN	formin-like 2						actin cytoskeleton organization	cytoplasm	actin binding|Rho GTPase binding			central_nervous_system(2)|ovary(1)	3						aaattgggaatatttgattagtg	0.020													6	3	---	---	---	---	
CCDC148	130940	broad.mit.edu	37	2	159061241	159061241	+	Intron	DEL	T	-	-	rs34562513		TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:159061241delT	uc002tzq.2	-						CCDC148_uc002tzr.2_Intron|CCDC148_uc010foh.2_Intron	NM_138803	NP_620158	Q8NFR7	CC148_HUMAN	coiled-coil domain containing 148											ovary(2)	2						tacttgactcTGTCCAAATTC	0.119													3	3	---	---	---	---	
TTN	7273	broad.mit.edu	37	2	179561115	179561115	+	Intron	DEL	T	-	-			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179561115delT	uc010zfg.1	-						TTN_uc010zfh.1_Intron|TTN_uc010zfi.1_Intron|TTN_uc010zfj.1_Intron|TTN_uc002umz.1_Intron|TTN_uc010fre.1_Intron	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A								ATP binding|nucleic acid binding|protein serine/threonine kinase activity|protein tyrosine kinase activity			ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1)	153			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			TGATAATTTGTTTTTTTTTTT	0.159													11	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	186674103	186674103	+	Intron	DEL	T	-	-			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:186674103delT	uc002upm.2	+						uc010zfu.1_Intron					Homo sapiens cDNA FLJ44048 fis, clone TESTI4030669.																		CTTTTGAAAGTTTTTTTTTAA	0.323													4	2	---	---	---	---	
ALS2CR4	65062	broad.mit.edu	37	2	202505346	202505346	+	Intron	DEL	A	-	-			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:202505346delA	uc002uyh.1	-						ALS2CR4_uc002uyg.1_Intron|ALS2CR4_uc010zhp.1_5'Flank	NM_001044385	NP_001037850	Q96Q45	TM237_HUMAN	amyotrophic lateral sclerosis 2 (juvenile)							integral to membrane	protein binding				0						ATTCTGATTTAAAAAAAAAAA	0.299													13	6	---	---	---	---	
PARD3B	117583	broad.mit.edu	37	2	206266126	206266126	+	Intron	DEL	T	-	-			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:206266126delT	uc002var.1	+						PARD3B_uc002vao.1_Intron|PARD3B_uc002vap.1_Intron|PARD3B_uc002vaq.1_Intron	NM_152526	NP_689739	Q8TEW8	PAR3L_HUMAN	par-3 partitioning defective 3 homolog B isoform						cell cycle|cell division	endomembrane system|tight junction				skin(2)|ovary(1)|breast(1)	4		all_cancers(1;2.88e-06)|all_epithelial(1;3.23e-06)		Epithelial(149;0.0739)		TCTCCATGTCTTTTTTTTTCC	0.328													4	4	---	---	---	---	
ACADL	33	broad.mit.edu	37	2	211053947	211053948	+	Intron	INS	-	A	A	rs141418871	by1000genomes	TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:211053947_211053948insA	uc002vdz.3	-							NM_001608	NP_001599	P28330	ACADL_HUMAN	long-chain acyl-CoA dehydrogenase precursor						carnitine catabolic process|carnitine metabolic process, CoA-linked|fatty acid beta-oxidation using acyl-CoA dehydrogenase|negative regulation of fatty acid biosynthetic process|negative regulation of fatty acid oxidation|regulation of cholesterol metabolic process|temperature homeostasis	mitochondrial matrix	long-chain-acyl-CoA dehydrogenase activity|palmitoyl-CoA oxidase activity				0		Renal(323;0.202)		Epithelial(149;0.00631)|Lung(261;0.0438)|LUSC - Lung squamous cell carcinoma(261;0.0466)|all cancers(144;0.0621)		GGAATAATAGTAAAAAAAACTA	0.213													4	6	---	---	---	---	
SPAG16	79582	broad.mit.edu	37	2	214162318	214162320	+	Intron	DEL	CTT	-	-	rs111937407		TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:214162318_214162320delCTT	uc002veq.2	+						SPAG16_uc010fuz.1_Intron|SPAG16_uc002ver.2_Intron|SPAG16_uc010zjk.1_Intron|SPAG16_uc002veo.2_Intron|SPAG16_uc002vep.1_Intron|SPAG16_uc002ves.1_Intron	NM_024532	NP_078808	Q8N0X2	SPG16_HUMAN	sperm associated antigen 16 isoform 1						cilium assembly	cilium axoneme|flagellar axoneme				ovary(1)|skin(1)	2		Renal(323;0.00461)		UCEC - Uterine corpus endometrioid carcinoma (47;0.0525)|Epithelial(149;7.07e-07)|all cancers(144;7.96e-05)|Lung(261;0.00255)|LUSC - Lung squamous cell carcinoma(224;0.00599)		CAAGTGACACCTTCTCTCTGAAC	0.350													6	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	229464385	229464386	+	IGR	DEL	AA	-	-			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:229464385_229464386delAA								SPHKAP (418024 upstream) : PID1 (424304 downstream)																							tttgcattttaaaaagttaaac	0.054													4	2	---	---	---	---	
MSL3L2	151507	broad.mit.edu	37	2	234776114	234776115	+	Intron	INS	-	G	G			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:234776114_234776115insG	uc010znf.1	-							NR_024322				SubName: Full=cDNA FLJ52683, highly similar to Male-specific lethal 3-like 1; SubName: Full=cDNA, FLJ79271, highly similar to Male-specific lethal 3-like 1; SubName: Full=HCG1642047;												0						TACGAAtttctttctttctttc	0.243													10	5	---	---	---	---	
TRPM8	79054	broad.mit.edu	37	2	234912812	234912812	+	Intron	DEL	C	-	-			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:234912812delC	uc002vvh.2	+						TRPM8_uc010fyj.2_Intron|TRPM8_uc010fyk.2_Intron	NM_024080	NP_076985	Q7Z2W7	TRPM8_HUMAN	transient receptor potential cation channel,							integral to membrane				skin(4)	4		Breast(86;0.00205)|Renal(207;0.00694)|all_lung(227;0.0129)|Lung NSC(271;0.0408)|all_hematologic(139;0.0753)|Acute lymphoblastic leukemia(138;0.224)		Epithelial(121;1.19e-17)|BRCA - Breast invasive adenocarcinoma(100;0.000139)|Lung(119;0.00758)|LUSC - Lung squamous cell carcinoma(224;0.0108)	Menthol(DB00825)	CTCATAATAACCAGAGAAATG	0.418													4	2	---	---	---	---	
COL6A3	1293	broad.mit.edu	37	2	238305661	238305664	+	Intron	DEL	GATA	-	-			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:238305661_238305664delGATA	uc002vwl.2	-						COL6A3_uc002vwo.2_Intron|COL6A3_uc010znj.1_Intron|COL6A3_uc002vwq.2_Intron|COL6A3_uc002vwr.2_Intron|COL6A3_uc010znk.1_Intron	NM_004369	NP_004360	P12111	CO6A3_HUMAN	alpha 3 type VI collagen isoform 1 precursor						axon guidance|cell adhesion|muscle organ development	collagen type VI|extracellular space	serine-type endopeptidase inhibitor activity			ovary(8)|central_nervous_system(6)|skin(2)|upper_aerodigestive_tract(1)|pancreas(1)	18		Breast(86;0.000301)|Renal(207;0.000966)|all_hematologic(139;0.067)|Ovarian(221;0.0694)|all_lung(227;0.0943)|Melanoma(123;0.203)		Epithelial(121;1.23e-21)|OV - Ovarian serous cystadenocarcinoma(60;1.34e-10)|Kidney(56;5.71e-09)|KIRC - Kidney renal clear cell carcinoma(57;1.51e-07)|BRCA - Breast invasive adenocarcinoma(100;0.00025)|Lung(119;0.0142)|LUSC - Lung squamous cell carcinoma(224;0.034)		ttagatagatgatagatagataga	0.196													4	3	---	---	---	---	
MLPH	79083	broad.mit.edu	37	2	238463513	238463513	+	3'UTR	DEL	G	-	-			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:238463513delG	uc002vwt.2	+	16					MLPH_uc002vws.2_3'UTR|MLPH_uc002vwu.2_3'UTR|MLPH_uc002vwv.2_3'UTR|MLPH_uc002vww.2_3'UTR|MLPH_uc002vwx.2_3'UTR|MLPH_uc010fyu.2_3'UTR	NM_024101	NP_077006	Q9BV36	MELPH_HUMAN	melanophilin isoform 1								metal ion binding			ovary(1)	1		Breast(86;0.000381)|Renal(207;0.000966)|Ovarian(221;0.0695)|all_hematologic(139;0.095)|all_lung(227;0.17)|Melanoma(123;0.203)		Epithelial(121;1.17e-21)|OV - Ovarian serous cystadenocarcinoma(60;1.02e-10)|Kidney(56;4.23e-09)|KIRC - Kidney renal clear cell carcinoma(57;1.15e-07)|BRCA - Breast invasive adenocarcinoma(100;0.000439)|Lung(119;0.0132)|LUSC - Lung squamous cell carcinoma(224;0.0316)		GGAGACCTGTGAGCACACATT	0.418													4	2	---	---	---	---	
MLPH	79083	broad.mit.edu	37	2	238463515	238463515	+	3'UTR	DEL	G	-	-			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:238463515delG	uc002vwt.2	+	16					MLPH_uc002vws.2_3'UTR|MLPH_uc002vwu.2_3'UTR|MLPH_uc002vwv.2_3'UTR|MLPH_uc002vww.2_3'UTR|MLPH_uc002vwx.2_3'UTR|MLPH_uc010fyu.2_3'UTR	NM_024101	NP_077006	Q9BV36	MELPH_HUMAN	melanophilin isoform 1								metal ion binding			ovary(1)	1		Breast(86;0.000381)|Renal(207;0.000966)|Ovarian(221;0.0695)|all_hematologic(139;0.095)|all_lung(227;0.17)|Melanoma(123;0.203)		Epithelial(121;1.17e-21)|OV - Ovarian serous cystadenocarcinoma(60;1.02e-10)|Kidney(56;4.23e-09)|KIRC - Kidney renal clear cell carcinoma(57;1.15e-07)|BRCA - Breast invasive adenocarcinoma(100;0.000439)|Lung(119;0.0132)|LUSC - Lung squamous cell carcinoma(224;0.0316)		AGACCTGTGAGCACACATTAG	0.413													4	2	---	---	---	---	
JAGN1	84522	broad.mit.edu	37	3	9934142	9934143	+	Intron	INS	-	GCCACCAT	GCCACCAT	rs145566429	by1000genomes	TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:9934142_9934143insGCCACCAT	uc003btt.3	+						CIDEC_uc003bto.2_Intron	NM_032492	NP_115881	Q8N5M9	JAGN1_HUMAN	jagunal homolog 1							endoplasmic reticulum membrane|integral to membrane				ovary(1)	1	Medulloblastoma(99;0.227)					tagagttgtgagccCAGCCTCT	0.035													3	4	---	---	---	---	
ZCWPW2	152098	broad.mit.edu	37	3	28469684	28469684	+	Intron	DEL	A	-	-			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:28469684delA	uc003ceh.2	+						ZCWPW2_uc003cei.2_Intron	NM_001040432	NP_001035522	Q504Y3	ZCPW2_HUMAN	zinc finger, CW type with PWWP domain 2								zinc ion binding			ovary(2)	2						TGAACCTGATAATAACCAGAG	0.398													4	2	---	---	---	---	
HIGD1A	25994	broad.mit.edu	37	3	42842324	42842324	+	Intron	DEL	A	-	-			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:42842324delA	uc003cma.3	-						HIGD1A_uc010hid.2_Intron|HIGD1A_uc003cmb.3_Intron	NM_001099669	NP_001093139	Q9Y241	HIG1A_HUMAN	HIG1 domain family, member 1A isoform b						response to stress	integral to membrane|protein complex	protein binding				0				KIRC - Kidney renal clear cell carcinoma(284;0.217)		CCGGTCCTTTAAAAAAAAAAA	0.398													4	2	---	---	---	---	
DNAH1	25981	broad.mit.edu	37	3	52419124	52419124	+	Intron	DEL	C	-	-			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:52419124delC	uc011bef.1	+						DNAH1_uc003ddv.2_Intron	NM_015512	NP_056327	Q9P2D7	DYH1_HUMAN	dynein, axonemal, heavy chain 1						ciliary or flagellar motility|microtubule-based movement|response to mechanical stimulus	axonemal dynein complex|cilium axoneme|cytoplasm|microtubule	ATP binding|ATPase activity|microtubule motor activity			large_intestine(3)	3				BRCA - Breast invasive adenocarcinoma(193;2.02e-05)|OV - Ovarian serous cystadenocarcinoma(275;0.000207)|Kidney(197;0.0022)|KIRC - Kidney renal clear cell carcinoma(197;0.00245)		TGGGTGGCTTCCCCCCTCATC	0.597											OREG0015612	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	4	2	---	---	---	---	
PBRM1	55193	broad.mit.edu	37	3	52610659	52610659	+	Frame_Shift_Del	DEL	T	-	-			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:52610659delT	uc003des.2	-	22	3601	c.3589delA	c.(3589-3591)ATTfs	p.I1197fs	PBRM1_uc003dex.2_RNA|PBRM1_uc003deq.2_Frame_Shift_Del_p.I1197fs|PBRM1_uc003der.2_Frame_Shift_Del_p.I1165fs|PBRM1_uc003det.2_Frame_Shift_Del_p.I1212fs|PBRM1_uc003deu.2_Frame_Shift_Del_p.I1212fs|PBRM1_uc003dev.2_RNA|PBRM1_uc003dew.2_Frame_Shift_Del_p.I1197fs|PBRM1_uc010hmk.1_Frame_Shift_Del_p.I1172fs|PBRM1_uc003dey.2_Frame_Shift_Del_p.I1172fs|PBRM1_uc003dez.1_Frame_Shift_Del_p.I1196fs	NM_181042	NP_060635	Q86U86	PB1_HUMAN	polybromo 1 isoform 4	1197	BAH 2.				chromatin remodeling|mitosis|negative regulation of cell proliferation|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nuclear chromosome	chromatin binding|DNA binding|protein binding			kidney(136)|breast(4)	140				BRCA - Breast invasive adenocarcinoma(193;1.8e-05)|Kidney(197;0.00105)|KIRC - Kidney renal clear cell carcinoma(197;0.00122)|OV - Ovarian serous cystadenocarcinoma(275;0.0613)		TCTGGGTGAATGAAGATGGGG	0.363			Mis|N|F|S|D|O		clear cell renal carcinoma|breast								316	185	---	---	---	---	
CACNA2D3	55799	broad.mit.edu	37	3	54880124	54880124	+	Intron	DEL	A	-	-			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:54880124delA	uc003dhf.2	+						CACNA2D3_uc011beu.1_Intron|CACNA2D3_uc003dhg.1_Intron|CACNA2D3_uc003dhh.1_Intron|CACNA2D3_uc010hmv.1_Intron	NM_018398	NP_060868	Q8IZS8	CA2D3_HUMAN	calcium channel, voltage-dependent, alpha							integral to membrane	calcium channel activity|metal ion binding|voltage-gated ion channel activity			large_intestine(3)|ovary(1)|breast(1)|central_nervous_system(1)|skin(1)	7				KIRC - Kidney renal clear cell carcinoma(284;0.00287)|Kidney(284;0.00327)		CTTTCTTGTTAAAAAAAAAAG	0.353													4	2	---	---	---	---	
DNAH12	201625	broad.mit.edu	37	3	57493917	57493917	+	Intron	DEL	A	-	-			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:57493917delA	uc003dit.2	-						DNAH12_uc003diu.2_Intron	NM_178504	NP_848599	Q6ZR08	DYH12_HUMAN	dynein heavy chain domain 2 isoform 1						microtubule-based movement	cilium axoneme|cytoplasm|dynein complex|microtubule	ATP binding|ATPase activity|microtubule motor activity			pancreas(1)|skin(1)	2						ccatcacgggaaaaaaaaaac	0.104													6	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	74588740	74588740	+	IGR	DEL	A	-	-			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:74588740delA								CNTN3 (18397 upstream) : FAM86D (881965 downstream)																							TTCTGGGATGAAAAAAAAAAT	0.418													6	3	---	---	---	---	
PROS1	5627	broad.mit.edu	37	3	93598122	93598122	+	Frame_Shift_Del	DEL	A	-	-			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:93598122delA	uc003drb.3	-	13	1870	c.1529delT	c.(1528-1530)GTGfs	p.V510fs	PROS1_uc010hoo.2_Frame_Shift_Del_p.V379fs|PROS1_uc003dqz.3_Frame_Shift_Del_p.V379fs	NM_000313	NP_000304	P07225	PROS_HUMAN	protein S, alpha preproprotein	510	Laminin G-like 2.				leukocyte migration|peptidyl-glutamic acid carboxylation|platelet activation|platelet degranulation|post-translational protein modification|proteolysis	endoplasmic reticulum membrane|extracellular region|Golgi lumen|Golgi membrane|platelet alpha granule lumen	calcium ion binding|endopeptidase inhibitor activity			large_intestine(1)	1					Antihemophilic Factor(DB00025)|Drotrecogin alfa(DB00055)|Menadione(DB00170)	ATTCAAGGTCACATTTACATG	0.433													108	58	---	---	---	---	
LOC285205	285205	broad.mit.edu	37	3	107609946	107609947	+	Intron	DEL	AA	-	-	rs147319621		TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:107609946_107609947delAA	uc003dws.3	+							NR_015394				Homo sapiens cDNA clone IMAGE:5721886.												0						actcagtctcaaaaaaaaaaaa	0.000													5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	134052820	134052820	+	IGR	DEL	C	-	-			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:134052820delC								RYK (83234 upstream) : AMOTL2 (17874 downstream)																							CACTCTGAGGCCAAGGACAAC	0.542													4	2	---	---	---	---	
MECOM	2122	broad.mit.edu	37	3	169171708	169171709	+	Intron	INS	-	A	A	rs146943907	by1000genomes	TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:169171708_169171709insA	uc011bpj.1	-						MECOM_uc011bpk.1_Intron|MECOM_uc010hwn.2_Intron|MECOM_uc011bpl.1_Intron	NM_004991	NP_004982	Q03112	EVI1_HUMAN	MDS1 and EVI1 complex locus isoform c						apoptosis|cell differentiation|hemopoietic stem cell proliferation|negative regulation of JNK cascade|negative regulation of programmed cell death|negative regulation of transcription, DNA-dependent|regulation of cell cycle	nuclear speck	DNA binding|protein binding|protein homodimerization activity|sequence-specific DNA binding transcription factor activity|zinc ion binding			lung(5)|skin(5)|upper_aerodigestive_tract(1)|central_nervous_system(1)|ovary(1)|pancreas(1)	14						CAATGGATAATAAAAAAAAAAC	0.426													6	3	---	---	---	---	
ATP11B	23200	broad.mit.edu	37	3	182634505	182634505	+	Intron	DEL	A	-	-			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:182634505delA	uc003flb.2	+						ATP11B_uc010hxg.2_Intron	NM_014616	NP_055431	Q9Y2G3	AT11B_HUMAN	ATPase, class VI, type 11B						aminophospholipid transport|ATP biosynthetic process	integral to membrane|nuclear inner membrane|plasma membrane	ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|magnesium ion binding|phospholipid-translocating ATPase activity			ovary(2)|pancreas(1)	3	all_cancers(143;9.04e-15)|Ovarian(172;0.0355)		all cancers(12;1.2e-42)|Epithelial(37;2.77e-36)|LUSC - Lung squamous cell carcinoma(7;7.58e-24)|Lung(8;4.66e-22)|OV - Ovarian serous cystadenocarcinoma(80;2.35e-20)			GTGTGCTTTGAAAAAAAATTT	0.259													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	197186754	197186754	+	IGR	DEL	G	-	-			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:197186754delG								DLG1 (160611 upstream) : BDH1 (49901 downstream)																							GTGGTCAGGAGGGGATGCAGT	0.373													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	3610214	3610215	+	IGR	INS	-	C	C	rs145974626	by1000genomes	TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:3610214_3610215insC								LRPAP1 (75990 upstream) : ADRA2C (157860 downstream)																							actctcagcatctagcacgatg	0.282													8	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	17372060	17372060	+	IGR	DEL	C	-	-			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:17372060delC								LDB2 (471636 upstream) : QDPR (115960 downstream)																							ATATTTTTTTCACCTATAAAG	0.323													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	63573845	63573845	+	IGR	DEL	A	-	-			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:63573845delA								LPHN3 (635678 upstream) : None (None downstream)																							aagtactagtaaaaaaatgca	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	68265657	68265657	+	IGR	DEL	G	-	-	rs75980594		TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:68265657delG								None (None upstream) : CENPC1 (72332 downstream)																							ataagttactgagaattcttc	0.000													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	111141695	111141695	+	IGR	DEL	C	-	-			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:111141695delC								ELOVL6 (21875 upstream) : ENPEP (255534 downstream)																							cttctcttctctcctcttctc	0.000													4	2	---	---	---	---	
GYPA	2993	broad.mit.edu	37	4	145062082	145062082	+	5'Flank	DEL	G	-	-	rs78866988		TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:145062082delG	uc003ijo.3	-						GYPA_uc003ijn.2_5'Flank|GYPA_uc011cia.1_5'Flank|GYPA_uc011cib.1_5'Flank|GYPA_uc003ijp.3_5'Flank|GYPA_uc010ioq.2_5'Flank|GYPA_uc010ior.2_5'Flank|GYPA_uc010ios.1_5'Flank	NM_002099	NP_002090	P02724	GLPA_HUMAN	glycophorin A precursor						interspecies interaction between organisms	membrane fraction	receptor activity			central_nervous_system(2)	2	all_hematologic(180;0.15)					GGCATGGTAAGGTGGTAGACA	0.483													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	177812924	177812924	+	IGR	DEL	G	-	-	rs4494980	by1000genomes	TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:177812924delG								VEGFC (99029 upstream) : NEIL3 (418067 downstream)																							GACAAAGATtgtgtgtgtgtg	0.274													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	177812926	177812926	+	IGR	DEL	G	-	-			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:177812926delG								VEGFC (99031 upstream) : NEIL3 (418065 downstream)																							CAAAGATtgtgtgtgtgtgtg	0.279													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	190545676	190545676	+	IGR	DEL	G	-	-			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:190545676delG								None (None upstream) : FRG1 (316298 downstream)																							agttgtacctggttgatctcc	0.000													4	2	---	---	---	---	
FRG1	2483	broad.mit.edu	37	4	190875086	190875086	+	Intron	DEL	G	-	-			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:190875086delG	uc003izs.2	+							NM_004477	NP_004468	Q14331	FRG1_HUMAN	FSHD region gene 1						rRNA processing	Cajal body|catalytic step 2 spliceosome|nuclear speck|nucleolus					0		all_cancers(14;1.44e-58)|all_epithelial(14;6.32e-41)|all_lung(41;8.13e-17)|Lung NSC(41;2.13e-16)|Breast(6;2.54e-06)|Melanoma(20;0.000263)|Hepatocellular(41;0.00213)|Renal(120;0.0183)|all_hematologic(60;0.0358)|Prostate(90;0.0421)|all_neural(102;0.147)		all cancers(3;1.73e-30)|Epithelial(3;5.85e-30)|OV - Ovarian serous cystadenocarcinoma(60;5.56e-15)|BRCA - Breast invasive adenocarcinoma(30;9.14e-06)|Lung(3;3.54e-05)|STAD - Stomach adenocarcinoma(60;8.83e-05)|LUSC - Lung squamous cell carcinoma(40;0.000198)|GBM - Glioblastoma multiforme(59;0.00892)|READ - Rectum adenocarcinoma(43;0.161)		TGACAAATGAGGAAAATATTT	0.294													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	40137299	40137300	+	IGR	INS	-	C	C			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:40137299_40137300insC								DAB2 (711964 upstream) : PTGER4 (542732 downstream)																							TTCCTCTATTTCCCCCTACCAC	0.371													4	2	---	---	---	---	
GHR	2690	broad.mit.edu	37	5	42699752	42699752	+	Intron	DEL	A	-	-			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:42699752delA	uc003jmt.2	+						GHR_uc011cpq.1_Intron	NM_000163	NP_000154	P10912	GHR_HUMAN	growth hormone receptor precursor						2-oxoglutarate metabolic process|activation of JAK2 kinase activity|activation of MAPK activity|allantoin metabolic process|citrate metabolic process|creatine metabolic process|creatinine metabolic process|endocytosis|fatty acid metabolic process|growth hormone receptor signaling pathway|insulin-like growth factor receptor signaling pathway|isoleucine metabolic process|JAK-STAT cascade|multicellular organismal metabolic process|oxaloacetate metabolic process|positive regulation of multicellular organism growth|positive regulation of tyrosine phosphorylation of Stat3 protein|positive regulation of tyrosine phosphorylation of Stat5 protein|receptor internalization|response to cycloheximide|response to estradiol stimulus|succinate metabolic process|taurine metabolic process|valine metabolic process	cell surface|extracellular space|growth hormone receptor complex|integral to plasma membrane	growth factor binding|peptide hormone binding|proline-rich region binding|protein homodimerization activity|protein kinase binding			lung(4)|kidney(1)|skin(1)	6		Myeloproliferative disorder(839;0.00878)			Pegvisomant(DB00082)|Somatropin recombinant(DB00052)	TCCTTGAGTTAAAAAAAAAAG	0.274													6	3	---	---	---	---	
FAM13B	51306	broad.mit.edu	37	5	137290194	137290195	+	Intron	INS	-	AC	AC	rs151026681	by1000genomes	TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:137290194_137290195insAC	uc003lbz.2	-						FAM13B_uc003lcb.2_Intron|FAM13B_uc003lca.2_Intron	NM_016603	NP_057687	Q9NYF5	FA13B_HUMAN	hypothetical protein LOC51306 isoform 1						regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol	GTPase activator activity				0						catacacacatacacacacaca	0.228													9	5	---	---	---	---	
GRIA1	2890	broad.mit.edu	37	5	153056891	153056891	+	Intron	DEL	A	-	-			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:153056891delA	uc003lva.3	+						GRIA1_uc003luy.3_Intron|GRIA1_uc003luz.3_Intron|GRIA1_uc011dcv.1_Intron|GRIA1_uc011dcw.1_Intron|GRIA1_uc011dcx.1_Intron|GRIA1_uc011dcy.1_Intron|GRIA1_uc011dcz.1_Intron|GRIA1_uc010jia.1_Intron	NM_001114183	NP_001107655	P42261	GRIA1_HUMAN	glutamate receptor, ionotropic, AMPA 1 isoform						synaptic transmission	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|dendritic spine|endocytic vesicle membrane|endoplasmic reticulum membrane|neuronal cell body|postsynaptic density|postsynaptic membrane	alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity|kainate selective glutamate receptor activity|PDZ domain binding			ovary(4)|skin(2)	6		Medulloblastoma(196;0.0391)|all_neural(177;0.16)|all_hematologic(541;0.21)	Kidney(363;0.000173)|KIRC - Kidney renal clear cell carcinoma(527;0.000785)		Desflurane(DB01189)|Enflurane(DB00228)|Halothane(DB01159)|Isoflurane(DB00753)|L-Glutamic Acid(DB00142)|Methoxyflurane(DB01028)|Sevoflurane(DB01236)	AAGCTCATATAAAAAAAAAAT	0.348													6	3	---	---	---	---	
TXNDC5	81567	broad.mit.edu	37	6	8060612	8060612	+	Intron	DEL	T	-	-			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:8060612delT	uc003mxw.2	-						MUTED_uc003mxy.2_Intron|MUTED_uc010joc.2_Intron|MUTED_uc010job.2_Intron	NM_001145549	NP_001139021	Q8NBS9	TXND5_HUMAN	thioredoxin domain containing 5 isoform 3						anti-apoptosis|cell redox homeostasis|cellular membrane organization|glycerol ether metabolic process|post-Golgi vesicle-mediated transport	endoplasmic reticulum lumen|lysosomal lumen	electron carrier activity|isomerase activity|protein disulfide oxidoreductase activity				0	Ovarian(93;0.0398)					tcatctaggatttttaagtag	0.000													4	2	---	---	---	---	
PHACTR1	221692	broad.mit.edu	37	6	13064103	13064103	+	Intron	DEL	G	-	-			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:13064103delG	uc010jpc.2	+						PHACTR1_uc011dir.1_Intron|PHACTR1_uc003nag.1_Intron|PHACTR1_uc003nah.1_Intron	NM_030948	NP_112210	Q9C0D0	PHAR1_HUMAN	phosphatase and actin regulator 1							cell junction|cytoplasm|synapse	actin binding|protein phosphatase inhibitor activity				0	Breast(50;0.0427)|Ovarian(93;0.12)	all_hematologic(90;0.122)|Lung SC(78;0.195)	Epithelial(50;0.146)|BRCA - Breast invasive adenocarcinoma(129;0.239)			acaagaatctgctcatgaagg	0.030													4	2	---	---	---	---	
DEK	7913	broad.mit.edu	37	6	18257956	18257956	+	Intron	DEL	A	-	-			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:18257956delA	uc003ncr.1	-						DEK_uc011djf.1_Intron|DEK_uc011djg.1_Intron	NM_003472	NP_003463	P35659	DEK_HUMAN	DEK oncogene isoform 1						chromatin modification|regulation of transcription from RNA polymerase II promoter|signal transduction|transcription from RNA polymerase II promoter|viral genome replication	nucleus	DNA binding|histone binding			kidney(1)	1	Ovarian(93;0.00769)|Breast(50;0.0495)	all_hematologic(90;0.053)	OV - Ovarian serous cystadenocarcinoma(7;0.00291)|all cancers(50;0.031)|Epithelial(50;0.0332)			taaaagaaagaaaaaaaaaag	0.000			T	NUP214	AML								9	4	---	---	---	---	
BTN2A1	11120	broad.mit.edu	37	6	26465762	26465762	+	Intron	DEL	A	-	-			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:26465762delA	uc003nib.1	+						BTN2A1_uc003nic.1_Intron|BTN2A1_uc003nid.1_Intron|BTN2A1_uc011dko.1_Intron|BTN2A1_uc010jqk.1_Intron	NM_007049	NP_008980	Q7KYR7	BT2A1_HUMAN	butyrophilin, subfamily 2, member A1 isoform 1						lipid metabolic process	integral to plasma membrane				ovary(1)|skin(1)	2						ctgtttaattaaaaaaaaaaa	0.199													4	2	---	---	---	---	
STK38	11329	broad.mit.edu	37	6	36491824	36491824	+	Intron	DEL	A	-	-	rs34668978		TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:36491824delA	uc003omg.2	-						STK38_uc003omh.2_Intron|STK38_uc003omi.2_Intron	NM_007271	NP_009202	Q15208	STK38_HUMAN	serine/threonine kinase 38						intracellular protein kinase cascade|negative regulation of MAP kinase activity	cytoplasm|MLL5-L complex	ATP binding|magnesium ion binding|mitogen-activated protein kinase kinase kinase binding|protein serine/threonine kinase activity			ovary(3)|upper_aerodigestive_tract(1)|lung(1)|skin(1)	6						TGATTATGGGAAAAAAGCAGC	0.219													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	99482929	99482929	+	IGR	DEL	T	-	-			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:99482929delT								FBXL4 (87080 upstream) : C6orf168 (237865 downstream)																							gtcagctttatttttttccTT	0.154													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	112893131	112893131	+	IGR	DEL	T	-	-			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:112893131delT								RFPL4B (220633 upstream) : None (None downstream)																							tactagcccatttttttttta	0.005													4	2	---	---	---	---	
MAP3K4	4216	broad.mit.edu	37	6	161529438	161529438	+	Intron	DEL	G	-	-			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:161529438delG	uc003qtn.2	+						MAP3K4_uc010kkc.1_Intron|MAP3K4_uc003qto.2_Intron|MAP3K4_uc011efz.1_Intron|MAP3K4_uc011ega.1_Intron|MAP3K4_uc003qtp.2_Intron|MAP3K4_uc003qtq.2_Intron	NM_005922	NP_005913	Q9Y6R4	M3K4_HUMAN	mitogen-activated protein kinase kinase kinase 4						activation of MAPKK activity|JNK cascade|positive regulation of JUN kinase activity	perinuclear region of cytoplasm	ATP binding|MAP kinase kinase kinase activity|metal ion binding|protein binding			ovary(3)|lung(3)|skin(2)|stomach(1)	9		Breast(66;0.000776)|Ovarian(120;0.0367)|Prostate(117;0.0771)		OV - Ovarian serous cystadenocarcinoma(65;1.85e-18)|BRCA - Breast invasive adenocarcinoma(81;3.04e-05)		TGCTGTCTGTGGAGACATCCG	0.567													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	169068681	169068681	+	IGR	DEL	T	-	-	rs113513902		TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:169068681delT								SMOC2 (10 upstream) : THBS2 (547195 downstream)																							TATATTAGTCTTTTTTTTTTC	0.229													2	4	---	---	---	---	
NXPH1	30010	broad.mit.edu	37	7	8672115	8672115	+	Intron	DEL	G	-	-			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:8672115delG	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)		AGTGGTGAGTGGGAAATCAGT	0.413													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	25044106	25044106	+	IGR	DEL	A	-	-			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:25044106delA								OSBPL3 (24346 upstream) : CYCS (114171 downstream)																							CATGTCAGTGAGGCCTTGGCC	0.328													4	2	---	---	---	---	
KPNA7	402569	broad.mit.edu	37	7	98800494	98800495	+	Intron	INS	-	AAG	AAG	rs72158609		TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:98800494_98800495insAAG	uc010lft.2	-							NM_001145715	NP_001139187	A9QM74	IMA8_HUMAN	karyopherin 7						protein import into nucleus	cytoplasm|nuclear pore	binding|protein transporter activity			kidney(1)|skin(1)	2						aagtataataaaaaTCCTCTCC	0.223													4	3	---	---	---	---	
DNAJC2	27000	broad.mit.edu	37	7	102963381	102963381	+	Intron	DEL	T	-	-	rs75138416		TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:102963381delT	uc003vbo.2	-						PMPCB_uc011kll.1_Intron|DNAJC2_uc003vbn.2_Intron|DNAJC2_uc010lix.2_Intron|DNAJC2_uc003vbp.2_Intron	NM_014377	NP_055192	Q99543	DNJC2_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 2						'de novo' cotranslational protein folding|chromatin modification|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytosol|nuclear membrane	chromatin binding|DNA binding|histone binding|Hsp70 protein binding|ubiquitin binding			kidney(1)	1						TAAACAATGAttttttttttt	0.129													12	6	---	---	---	---	
KLHDC10	23008	broad.mit.edu	37	7	129739335	129739335	+	Intron	DEL	G	-	-			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:129739335delG	uc003vpj.1	+						KLHDC10_uc003vpk.1_Intron|KLHDC10_uc010lmb.1_Intron	NM_014997	NP_055812	Q6PID8	KLD10_HUMAN	kelch domain containing 10												0						ggctgaaggagggtgacagag	0.000													4	2	---	---	---	---	
ZC3HAV1L	92092	broad.mit.edu	37	7	138711009	138711009	+	3'UTR	DEL	A	-	-	rs72045931		TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:138711009delA	uc003vum.1	-	5						NM_080660	NP_542391	Q96H79	ZCCHL_HUMAN	zinc finger CCCH-type, antiviral 1-like												0						ATATTAAGTGAAAAAAAAAAA	0.318													9	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	150253655	150253656	+	IGR	DEL	TG	-	-	rs144419483		TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:150253655_150253656delTG								GIMAP7 (35495 upstream) : GIMAP4 (10802 downstream)																							agaaggaatttgtgtgtgtgtg	0.000													4	3	---	---	---	---	
NOS3	4846	broad.mit.edu	37	7	150707426	150707426	+	Intron	DEL	G	-	-			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:150707426delG	uc003wif.2	+						NOS3_uc011kuy.1_Intron	NM_000603	NP_000594	P29474	NOS3_HUMAN	nitric oxide synthase 3 isoform 1						anti-apoptosis|arginine catabolic process|blood vessel remodeling|endothelial cell migration|mitochondrion organization|negative regulation of muscle hyperplasia|negative regulation of platelet activation|nitric oxide biosynthetic process|platelet activation|positive regulation of angiogenesis|positive regulation of guanylate cyclase activity|positive regulation of vasodilation|regulation of blood vessel size|regulation of nitric-oxide synthase activity|regulation of systemic arterial blood pressure by endothelin|response to fluid shear stress|response to heat|smooth muscle hyperplasia	caveola|cytoskeleton|cytosol|Golgi membrane	actin monomer binding|arginine binding|cadmium ion binding|calmodulin binding|flavin adenine dinucleotide binding|FMN binding|heme binding|NADP binding|nitric-oxide synthase activity|tetrahydrobiopterin binding			central_nervous_system(5)|large_intestine(2)|skin(1)	8	all_neural(206;0.219)		OV - Ovarian serous cystadenocarcinoma(82;0.0121)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)	L-Arginine(DB00125)|L-Citrulline(DB00155)|Rosuvastatin(DB01098)|Tetrahydrobiopterin(DB00360)	GGGATGAGCTGGGGGGACCCC	0.632													4	2	---	---	---	---	
MCPH1	79648	broad.mit.edu	37	8	6414040	6414040	+	Intron	DEL	A	-	-	rs140643562	by1000genomes	TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:6414040delA	uc003wqi.2	+						ANGPT2_uc003wqj.3_Intron|ANGPT2_uc003wqk.3_Intron|ANGPT2_uc010lri.2_Intron|ANGPT2_uc003wql.3_Intron	NM_024596	NP_078872	Q8NEM0	MCPH1_HUMAN	microcephalin							microtubule organizing center				central_nervous_system(1)|skin(1)	2		Hepatocellular(245;0.0663)		Colorectal(4;0.0505)		TCATTCATTTACCCCTTCTGT	0.473													5	4	---	---	---	---	
RAB11FIP1	80223	broad.mit.edu	37	8	37727720	37727720	+	Intron	DEL	A	-	-			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:37727720delA	uc003xkm.1	-						RAB11FIP1_uc010lvz.1_Intron|RAB11FIP1_uc003xkn.1_Intron|RAB11FIP1_uc003xkl.1_Intron|RAB11FIP1_uc003xko.1_3'UTR|RAB11FIP1_uc003xkp.1_3'UTR	NM_001002814	NP_001002814	Q6WKZ4	RFIP1_HUMAN	RAB11 family interacting protein 1 isoform 3						protein transport	centrosome|phagocytic vesicle membrane|recycling endosome	protein binding			ovary(1)|central_nervous_system(1)|skin(1)	3		Lung NSC(58;0.118)|all_lung(54;0.195)	LUSC - Lung squamous cell carcinoma(8;3.62e-11)			TGCTTGAGACAAAAAAAAAAA	0.224													7	4	---	---	---	---	
ADAM9	8754	broad.mit.edu	37	8	38865693	38865693	+	Intron	DEL	T	-	-			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:38865693delT	uc003xmr.2	+						ADAM9_uc011lcf.1_Intron|ADAM9_uc011lcg.1_Intron|ADAM9_uc010lwr.2_Intron|ADAM9_uc003xmo.1_Intron|ADAM9_uc003xmp.2_Intron	NM_003816	NP_003807	Q13443	ADAM9_HUMAN	ADAM metallopeptidase domain 9 isoform 1						activation of MAPKK activity|cell-cell adhesion mediated by integrin|cell-matrix adhesion|keratinocyte differentiation|monocyte activation|PMA-inducible membrane protein ectodomain proteolysis|PMA-inducible membrane protein ectodomain proteolysis|positive regulation of cell adhesion mediated by integrin|positive regulation of keratinocyte migration|positive regulation of macrophage fusion|positive regulation of membrane protein ectodomain proteolysis|positive regulation of protein secretion|response to calcium ion|response to glucocorticoid stimulus|response to hydrogen peroxide|response to manganese ion|response to tumor necrosis factor|transforming growth factor beta receptor signaling pathway	extracellular space|extracellular space|integral to membrane|intrinsic to external side of plasma membrane	collagen binding|integrin binding|laminin binding|metalloendopeptidase activity|protein kinase C binding|SH3 domain binding|zinc ion binding			ovary(1)|central_nervous_system(1)	2		all_lung(54;0.00292)|Lung NSC(58;0.0115)|Hepatocellular(245;0.0153)	LUSC - Lung squamous cell carcinoma(45;2.74e-07)			CTTAATATCCttttttttttt	0.189													9	5	---	---	---	---	
ATP6V1H	51606	broad.mit.edu	37	8	54723453	54723454	+	Intron	DEL	AA	-	-			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:54723453_54723454delAA	uc003xrl.2	-						ATP6V1H_uc003xrk.2_Intron|ATP6V1H_uc003xrm.2_Intron|ATP6V1H_uc003xrn.2_Intron|ATP6V1H_uc011ldv.1_Intron|ATP6V1H_uc010lyd.2_Intron	NM_213620	NP_998785	Q9UI12	VATH_HUMAN	ATPase, H+ transporting, lysosomal 50/57kDa, V1						ATP hydrolysis coupled proton transport|cellular iron ion homeostasis|endocytosis|insulin receptor signaling pathway|interspecies interaction between organisms|regulation of defense response to virus by virus|transferrin transport|vacuolar acidification|viral reproduction	cytosol|plasma membrane|vacuolar proton-transporting V-type ATPase, V1 domain	enzyme regulator activity|protein binding|proton-transporting ATPase activity, rotational mechanism				0		all_epithelial(80;0.0487)|Lung NSC(129;0.109)|all_lung(136;0.181)	OV - Ovarian serous cystadenocarcinoma(7;2.79e-06)|Epithelial(17;0.000629)|all cancers(17;0.00359)			TGTGCTTCTGAATTCTGATTTT	0.332													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	64829092	64829093	+	IGR	INS	-	T	T			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:64829092_64829093insT								YTHDF3 (703747 upstream) : MIR124-2 (462613 downstream)																							gactTTATAAATTTTTTTTAAT	0.020													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	94855789	94855790	+	IGR	INS	-	T	T	rs142098786	by1000genomes	TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:94855789_94855790insT								TMEM67 (25443 upstream) : PDP1 (73293 downstream)																							AATGGGAAGCCTAAAGCAGGAG	0.554													4	3	---	---	---	---	
RRM2B	50484	broad.mit.edu	37	8	103249583	103249583	+	Intron	DEL	T	-	-			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:103249583delT	uc003ykn.2	-						RRM2B_uc003yko.2_Intron|RRM2B_uc010mbv.1_Intron|RRM2B_uc010mbw.1_Intron|RRM2B_uc010mbx.1_Intron|RRM2B_uc010mby.1_Intron	NM_015713	NP_056528	Q7LG56	RIR2B_HUMAN	ribonucleotide reductase M2 B (TP53 inducible)						deoxyribonucleoside diphosphate metabolic process|DNA repair|nucleobase, nucleoside and nucleotide interconversion	nucleoplasm	ribonucleoside-diphosphate reductase activity|transition metal ion binding			ovary(2)	2	all_cancers(14;8e-07)|all_epithelial(15;2.18e-08)|Lung NSC(17;2.55e-05)|all_lung(17;8.85e-05)		OV - Ovarian serous cystadenocarcinoma(57;0.000728)			CAGTGGGGGGTTTTTTGTTTT	0.050								Direct_reversal_of_damage|Modulation_of_nucleotide_pools					4	2	---	---	---	---	
MTSS1	9788	broad.mit.edu	37	8	125728528	125728529	+	Intron	INS	-	G	G	rs139997981	by1000genomes	TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:125728528_125728529insG	uc003yrk.2	-						MTSS1_uc003yrj.2_Intron|MTSS1_uc003yrl.2_Intron	NM_014751	NP_055566	O43312	MTSS1_HUMAN	metastasis suppressor 1						actin cytoskeleton organization|cell adhesion|cellular component movement|filopodium assembly|transmembrane receptor protein tyrosine kinase signaling pathway	actin cytoskeleton|endocytic vesicle|ruffle	actin monomer binding|cytoskeletal adaptor activity|receptor binding|SH3 domain binding			ovary(1)	1	Ovarian(258;0.00438)|all_neural(195;0.00459)|Hepatocellular(40;0.108)		STAD - Stomach adenocarcinoma(47;0.00288)			TGAAACAAAGAGGGAGGAAGCG	0.470													2	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	128259898	128259899	+	IGR	INS	-	A	A	rs139139898	by1000genomes	TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:128259898_128259899insA								FAM84B (689432 upstream) : LOC727677 (42163 downstream)																							agaagcagaagaaaaaaaaagt	0.000													5	3	---	---	---	---	
ADCY8	114	broad.mit.edu	37	8	132046017	132046018	+	Intron	DEL	CA	-	-			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:132046017_132046018delCA	uc003ytd.3	-						ADCY8_uc010mds.2_Intron	NM_001115	NP_001106	P40145	ADCY8_HUMAN	adenylate cyclase 8						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 membrane|membrane fraction|plasma membrane	ATP binding|calcium- and calmodulin-responsive adenylate cyclase activity|metal ion binding			skin(4)|large_intestine(1)|central_nervous_system(1)	6	Esophageal squamous(12;0.00693)|Ovarian(258;0.00707)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.000538)			tacacaaaagcacacacacaca	0.257										HNSCC(32;0.087)			4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	66477358	66477358	+	IGR	DEL	T	-	-			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:66477358delT								FAM74A4 (982972 upstream) : LOC442421 (19112 downstream)																							agaagaaaaatttaaaaattt	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	70182346	70182346	+	RNA	DEL	G	-	-			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:70182346delG	uc004afw.2	-	3		c.1766delC								Homo sapiens COBW domain containing 5, mRNA (cDNA clone IMAGE:5287337), complete cds.																		TCTGTGTATTGTTTTTTTTTT	0.239													12	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	90796556	90796557	+	IGR	INS	-	A	A	rs34909606		TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:90796556_90796557insA								CDK20 (206889 upstream) : SPIN1 (206283 downstream)																							TCCTCAAGGTGAAAAAAAAAAa	0.317													7	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	113978418	113978419	+	IGR	DEL	AT	-	-			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:113978418_113978419delAT								LPAR1 (176892 upstream) : OR2K2 (111345 downstream)																							taggttgtcaatttgtgctctt	0.000													8	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	117367002	117367002	+	IGR	DEL	A	-	-			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:117367002delA								ATP6V1G1 (5851 upstream) : C9orf91 (6704 downstream)																							AAACTTGTAGAAAAAAAAAAG	0.358													4	2	---	---	---	---	
EXOSC2	23404	broad.mit.edu	37	9	133570570	133570571	+	Intron	INS	-	G	G			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:133570570_133570571insG	uc004bzu.2	+						EXOSC2_uc011mbz.1_Intron|EXOSC2_uc011mca.1_Intron	NM_014285	NP_055100	Q13868	EXOS2_HUMAN	exosome component 2						exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay|positive regulation of cell growth|rRNA processing	cytosol|exosome (RNase complex)|nucleolus	3'-5'-exoribonuclease activity|7S RNA binding|protein binding			ovary(1)	1		Acute lymphoblastic leukemia(5;0.0508)|all_hematologic(13;0.0588)		OV - Ovarian serous cystadenocarcinoma(145;0.000324)		ataatgcaatagggaaaaaagt	0.030													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	318412	318415	+	IGR	DEL	ACTC	-	-	rs71857079		TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:318412_318415delACTC								ZMYND11 (17836 upstream) : DIP2C (1717 downstream)																							TCAGGCACAAACTCACTGTGCCCA	0.544													3	3	---	---	---	---	
ST8SIA6	338596	broad.mit.edu	37	10	17373739	17373740	+	Intron	INS	-	T	T	rs139279166	by1000genomes	TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:17373739_17373740insT	uc001ipd.2	-						ST8SIA6_uc010qce.1_Intron	NM_001004470	NP_001004470	P61647	SIA8F_HUMAN	ST8 alpha-N-acetyl-neuraminide						post-translational protein modification|protein N-linked glycosylation via asparagine	integral to Golgi membrane	alpha-N-acetylneuraminate alpha-2,8-sialyltransferase activity			ovary(1)	1						GACTGACTCTCTTTTTTTTCAT	0.228													8	4	---	---	---	---	
MPP7	143098	broad.mit.edu	37	10	28358549	28358549	+	Intron	DEL	A	-	-	rs2763319		TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:28358549delA	uc001iua.1	-						MPP7_uc009xkz.1_Intron|MPP7_uc001iub.1_Intron|MPP7_uc009xla.2_Intron|MPP7_uc010qdv.1_Intron	NM_173496	NP_775767	Q5T2T1	MPP7_HUMAN	palmitoylated membrane protein 7						establishment of cell polarity|positive regulation of protein complex assembly|protein localization to adherens junction|tight junction assembly	MPP7-DLG1-LIN7 complex|tight junction	protein complex scaffold|protein domain specific binding|protein heterodimerization activity|signaling adaptor activity			ovary(1)	1						caaaacaaacaaaaaaaaaac	0.010													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	42656032	42656032	+	IGR	DEL	A	-	-			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:42656032delA								None (None upstream) : LOC441666 (171283 downstream)																							ttctctttttaaaaaaagtta	0.030													4	2	---	---	---	---	
CSTF2T	23283	broad.mit.edu	37	10	53457289	53457289	+	3'UTR	DEL	A	-	-	rs143102624		TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:53457289delA	uc001jjp.2	-	1					PRKG1_uc001jjm.2_Intron|PRKG1_uc001jjn.2_Intron|PRKG1_uc001jjo.2_Intron	NM_015235	NP_056050	Q9H0L4	CSTFT_HUMAN	cleavage stimulation factor, 3' pre-RNA, subunit						mRNA processing	nucleus	nucleotide binding|RNA binding			ovary(1)	1				COAD - Colon adenocarcinoma(2;0.00736)|Colorectal(2;0.00898)|all cancers(4;0.0188)|GBM - Glioblastoma multiforme(4;0.0778)|Epithelial(53;0.122)		ACCCTCAATTaaaaaaaaaag	0.313													4	2	---	---	---	---	
TSPAN14	81619	broad.mit.edu	37	10	82248751	82248751	+	Intron	DEL	T	-	-			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:82248751delT	uc001kcj.3	+						TSPAN14_uc009xss.2_Intron|TSPAN14_uc001kci.3_Intron	NM_030927	NP_112189	Q8NG11	TSN14_HUMAN	tetraspanin 14 isoform 1							integral to membrane				ovary(1)|central_nervous_system(1)	2			Colorectal(32;0.229)			TCTTTCTTCCTTTCAAAAATC	0.239													4	2	---	---	---	---	
LIPN	643418	broad.mit.edu	37	10	90521476	90521483	+	Intron	DEL	CTATCTAT	-	-	rs10580566		TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:90521476_90521483delCTATCTAT	uc010qmw.1	+							NM_001102469	NP_001095939	Q5VXI9	LIPN_HUMAN	lipase-like, ab-hydrolase domain containing 4						lipid catabolic process	extracellular region	hydrolase activity				0		Colorectal(252;0.0161)		Colorectal(12;4.83e-05)|COAD - Colon adenocarcinoma(12;6.5e-05)		TGCTATTGTGctatctatctatctatct	0.207													7	6	---	---	---	---	
ATRNL1	26033	broad.mit.edu	37	10	117001184	117001184	+	Intron	DEL	T	-	-			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:117001184delT	uc001lcg.2	+							NM_207303	NP_997186	Q5VV63	ATRN1_HUMAN	attractin-like 1 precursor							integral to membrane	sugar binding			ovary(5)|lung(1)|central_nervous_system(1)	7		all_lung(145;0.0686)|Breast(234;0.0969)|Lung NSC(174;0.17)|Colorectal(252;0.234)		Epithelial(162;0.00031)|all cancers(201;0.000753)|LUSC - Lung squamous cell carcinoma(1;0.0515)|Lung(30;0.0827)		CCTCAAAATATTTTTTTTTGA	0.239													3	3	---	---	---	---	
KNDC1	85442	broad.mit.edu	37	10	134986596	134986597	+	Intron	DEL	CA	-	-			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:134986596_134986597delCA	uc001llz.1	+						KNDC1_uc001lma.1_Intron	NM_152643	NP_689856	Q76NI1	VKIND_HUMAN	kinase non-catalytic C-lobe domain (KIND)						regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction					upper_aerodigestive_tract(1)|ovary(1)	2		all_cancers(35;4.16e-10)|all_epithelial(44;2.07e-08)|Lung NSC(174;0.000845)|all_lung(145;0.00145)|all_neural(114;0.0299)|Melanoma(40;0.123)|Colorectal(31;0.173)|Glioma(114;0.203)		OV - Ovarian serous cystadenocarcinoma(35;8.77e-06)|Epithelial(32;1.13e-05)|all cancers(32;1.51e-05)		ctctggccttcagctgcaggtg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	3362946	3362946	+	IGR	DEL	T	-	-	rs111594087		TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:3362946delT								MRGPRE (109330 upstream) : ZNF195 (17065 downstream)																							ACTTCCCTGATTTTTTTTTTT	0.303													7	7	---	---	---	---	
QSER1	79832	broad.mit.edu	37	11	32998372	32998372	+	3'UTR	DEL	T	-	-			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:32998372delT	uc001mty.2	+	13					QSER1_uc001mtz.1_Intron	NM_001076786	NP_001070254	Q2KHR3	QSER1_HUMAN	glutamine and serine rich 1											ovary(3)|central_nervous_system(2)|skin(1)	6	Breast(20;0.158)					AAAGTAACGATTTTTTTTTTC	0.333													10	5	---	---	---	---	
CSTF3	1479	broad.mit.edu	37	11	33112401	33112402	+	Intron	INS	-	T	T	rs148434560	by1000genomes	TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:33112401_33112402insT	uc001muh.2	-						TCP11L1_uc001muf.1_Intron	NM_001326	NP_001317	Q12996	CSTF3_HUMAN	cleavage stimulation factor subunit 3 isoform 1						mRNA cleavage|mRNA polyadenylation|nuclear mRNA splicing, via spliceosome|termination of RNA polymerase II transcription	nucleoplasm	protein binding|RNA binding				0						tattataaagatttttagacta	0.158													4	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	34019464	34019464	+	IGR	DEL	A	-	-	rs36065659		TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:34019464delA								LMO2 (105628 upstream) : CAPRIN1 (53766 downstream)																							GAGGGGAATGAAGTGGAGTCA	0.552													1	5	---	---	---	---	
RNF214	257160	broad.mit.edu	37	11	117110765	117110765	+	Intron	DEL	A	-	-			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:117110765delA	uc001pqt.2	+						RNF214_uc001pqu.2_Intron|RNF214_uc010rxf.1_Intron	NM_207343	NP_997226	Q8ND24	RN214_HUMAN	ring finger protein 214								zinc ion binding				0	all_hematologic(175;0.0487)	Breast(348;0.00908)|Medulloblastoma(222;0.0425)|all_hematologic(192;0.196)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;1.88e-05)|Epithelial(105;0.000397)|all cancers(92;0.00258)		agttacgtttaaaaaaaaaaa	0.000													11	6	---	---	---	---	
UBE4A	9354	broad.mit.edu	37	11	118247607	118247607	+	Intron	DEL	A	-	-	rs1784239		TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:118247607delA	uc001psw.2	+						UBE4A_uc001psv.2_Intron	NM_004788	NP_004779	Q14139	UBE4A_HUMAN	ubiquitination factor E4A						ubiquitin-dependent protein catabolic process	ubiquitin ligase complex	protein binding			ovary(2)|upper_aerodigestive_tract(1)|breast(1)|kidney(1)	5	all_hematologic(175;0.046)	Medulloblastoma(222;0.0425)|Breast(348;0.181)|all_hematologic(192;0.196)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;3.28e-05)		catctctaccaaaaaaaaaaa	0.000													8	5	---	---	---	---	
ZBTB44	29068	broad.mit.edu	37	11	130108689	130108689	+	Intron	DEL	T	-	-			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:130108689delT	uc001qga.2	-						ZBTB44_uc001qgb.3_Intron|ZBTB44_uc001qfx.2_Intron|ZBTB44_uc001qfz.2_Intron	NM_014155	NP_054874	Q8NCP5	ZBT44_HUMAN	zinc finger and BTB domain containing 44						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1	all_hematologic(175;0.0429)	Lung NSC(97;0.000601)|Breast(109;0.000962)|all_lung(97;0.00125)|Medulloblastoma(222;0.0425)|all_neural(223;0.0837)		OV - Ovarian serous cystadenocarcinoma(99;0.0192)|Lung(977;0.235)		ATGCCTTTTGTTTTTTTTTTT	0.134													10	5	---	---	---	---	
ERC1	23085	broad.mit.edu	37	12	1261696	1261696	+	Intron	DEL	G	-	-			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:1261696delG	uc001qjb.2	+						ERC1_uc001qiz.2_Intron|ERC1_uc001qjc.2_Intron|ERC1_uc001qja.2_Intron|ERC1_uc001qjd.2_Intron|ERC1_uc001qjf.2_Intron|ERC1_uc010sdv.1_Intron|ERC1_uc009zdp.2_Intron	NM_178040	NP_829884	Q8IUD2	RB6I2_HUMAN	RAB6-interacting protein 2 isoform epsilon						I-kappaB phosphorylation|multicellular organismal development|positive regulation of anti-apoptosis|positive regulation of NF-kappaB transcription factor activity|protein transport	Golgi membrane|IkappaB kinase complex|presynaptic membrane	leucine zipper domain binding			ovary(2)|lung(2)|breast(1)	5	all_epithelial(11;0.0698)|Ovarian(42;0.107)		OV - Ovarian serous cystadenocarcinoma(31;0.00239)|BRCA - Breast invasive adenocarcinoma(9;0.0567)			TGTTCTTGTTGGGCAATGTGT	0.498													4	2	---	---	---	---	
ITPR2	3709	broad.mit.edu	37	12	26811406	26811406	+	Intron	DEL	A	-	-			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:26811406delA	uc001rhg.2	-							NM_002223	NP_002214	Q14571	ITPR2_HUMAN	inositol 1,4,5-triphosphate receptor, type 2						activation of phospholipase C activity|energy reserve metabolic process|nerve growth factor receptor signaling pathway|platelet activation|regulation of insulin secretion|response to hypoxia	integral to membrane|plasma membrane enriched fraction|platelet dense tubular network membrane|sarcoplasmic reticulum membrane	calcium ion transmembrane transporter activity|inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity			kidney(6)|ovary(4)|skin(2)|upper_aerodigestive_tract(1)|lung(1)	14	Colorectal(261;0.0847)					AAGGCAGATCAAAGCTAATGC	0.408													4	3	---	---	---	---	
SOAT2	8435	broad.mit.edu	37	12	53502221	53502222	+	Intron	INS	-	T	T	rs145718124	by1000genomes	TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:53502221_53502222insT	uc001sbv.2	+						SOAT2_uc009zms.2_Intron	NM_003578	NP_003569	O75908	SOAT2_HUMAN	acyl-CoA:cholesterol acyltransferase 2						cholesterol efflux|cholesterol esterification|cholesterol homeostasis|cholesterol metabolic process|macrophage derived foam cell differentiation|very-low-density lipoprotein particle assembly	brush border|endoplasmic reticulum membrane|integral to membrane|microsome	cholesterol binding|cholesterol O-acyltransferase activity|fatty-acyl-CoA binding			ovary(1)	1						tcttattgtactatgcaaataa	0.000													4	2	---	---	---	---	
SOAT2	8435	broad.mit.edu	37	12	53502235	53502235	+	Intron	DEL	A	-	-	rs34562978		TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:53502235delA	uc001sbv.2	+						SOAT2_uc009zms.2_Intron	NM_003578	NP_003569	O75908	SOAT2_HUMAN	acyl-CoA:cholesterol acyltransferase 2						cholesterol efflux|cholesterol esterification|cholesterol homeostasis|cholesterol metabolic process|macrophage derived foam cell differentiation|very-low-density lipoprotein particle assembly	brush border|endoplasmic reticulum membrane|integral to membrane|microsome	cholesterol binding|cholesterol O-acyltransferase activity|fatty-acyl-CoA binding			ovary(1)	1						gcaaataactaatattgcaaa	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	54088250	54088251	+	IGR	INS	-	GT	GT	rs148772367	by1000genomes	TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:54088250_54088251insGT								ATP5G2 (17738 upstream) : CALCOCO1 (16652 downstream)																							GTTTGGGGTCAGTGTGTGTGTG	0.450													4	2	---	---	---	---	
KIF5A	3798	broad.mit.edu	37	12	57965358	57965358	+	Intron	DEL	T	-	-			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:57965358delT	uc001sor.1	+						KIF5A_uc010srr.1_Intron	NM_004984	NP_004975	Q12840	KIF5A_HUMAN	kinesin family member 5A						blood coagulation|cell death|microtubule-based movement|synaptic transmission	cytosol|kinesin complex|membrane fraction|microtubule|perinuclear region of cytoplasm	ATP binding|microtubule motor activity			ovary(2)|skin(1)	3						ttttcttttcttttttttttt	0.204													8	4	---	---	---	---	
TMTC2	160335	broad.mit.edu	37	12	83219634	83219637	+	Intron	DEL	CACA	-	-			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:83219634_83219637delCACA	uc001szt.2	+						TMTC2_uc001szr.1_Intron|TMTC2_uc001szs.1_Intron|TMTC2_uc010suk.1_Intron	NM_152588	NP_689801	Q8N394	TMTC2_HUMAN	transmembrane and tetratricopeptide repeat							endoplasmic reticulum|integral to membrane	binding			ovary(2)	2						ATAGGGAAAGcacacacacacaca	0.319													4	2	---	---	---	---	
STAB2	55576	broad.mit.edu	37	12	104068025	104068026	+	Intron	INS	-	G	G			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:104068025_104068026insG	uc001tjw.2	+							NM_017564	NP_060034	Q8WWQ8	STAB2_HUMAN	stabilin 2 precursor						angiogenesis|cell adhesion|defense response to bacterium|receptor-mediated endocytosis	cytoplasm|external side of plasma membrane|integral to plasma membrane	Gram-negative bacterial cell surface binding|hyaluronic acid binding|low-density lipoprotein receptor activity|protein disulfide oxidoreductase activity|scavenger receptor activity			ovary(9)|skin(5)	14						ttgtgaaaagaacctcagtctg	0.183													4	2	---	---	---	---	
GALNT9	50614	broad.mit.edu	37	12	132682466	132682466	+	Frame_Shift_Del	DEL	C	-	-			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:132682466delC	uc001ukc.3	-	10	1652	c.1536delG	c.(1534-1536)GGGfs	p.G512fs	GALNT9_uc009zyr.2_Frame_Shift_Del_p.G286fs|GALNT9_uc001ukb.2_Frame_Shift_Del_p.G369fs|GALNT9_uc001uka.2_Frame_Shift_Del_p.G146fs	NM_001122636	NP_001116108	Q9HCQ5	GALT9_HUMAN	UDP-N-acetyl-alpha-D-galactosamine:polypeptide	512	Ricin B-type lectin.|Lumenal (Potential).				protein O-linked glycosylation	Golgi membrane|integral to membrane	polypeptide N-acetylgalactosaminyltransferase activity|sugar binding				0	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_epithelial(31;0.241)		OV - Ovarian serous cystadenocarcinoma(86;7.49e-08)|Epithelial(86;3.55e-07)|all cancers(50;2.09e-05)		AGCCCAGAGGCCCCAGCTGCA	0.657													4	2	---	---	---	---	
PGAM5	192111	broad.mit.edu	37	12	133297240	133297241	+	Intron	INS	-	TC	TC			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:133297240_133297241insTC	uc009zyv.2	+						PGAM5_uc010tbr.1_Intron	NM_138575	NP_612642	Q96HS1	PGAM5_HUMAN	phosphoglycerate mutase family member 5							integral to membrane|mitochondrial outer membrane	phosphoprotein phosphatase activity				0	all_neural(191;0.0982)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;1.89e-08)|Epithelial(86;1.14e-07)|all cancers(50;3.57e-06)		AACGTGctctttctctctctct	0.371													4	2	---	---	---	---	
GOLGA3	2802	broad.mit.edu	37	12	133349938	133349938	+	Intron	DEL	C	-	-			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:133349938delC	uc001ukz.1	-							NM_005895	NP_005886	Q08378	GOGA3_HUMAN	Golgi autoantigen, golgin subfamily a, 3						intra-Golgi vesicle-mediated transport	Golgi cisterna membrane|Golgi transport complex	protein binding|transporter activity			ovary(3)|central_nervous_system(2)|pancreas(1)	6	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_epithelial(31;0.0176)|Lung NSC(355;0.204)		OV - Ovarian serous cystadenocarcinoma(86;2.27e-08)|Epithelial(86;3.34e-07)|all cancers(50;9.4e-06)		GCAGAACGCGCCACCTGTGGA	0.617													4	2	---	---	---	---	
TPTE2P3	220115	broad.mit.edu	37	13	53158749	53158750	+	Intron	INS	-	T	T			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:53158749_53158750insT	uc001vgw.2	+							NR_002793				Homo sapiens TPTE and PTEN homologous inositol lipid phosphatase pseudogene, mRNA (cDNA clone IMAGE:5298506), with apparent retained intron.												0						cttttaaaatattttttttttC	0.223													6	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	59783742	59783743	+	IGR	INS	-	GG	GG	rs144037370	by1000genomes	TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:59783742_59783743insGG								None (None upstream) : DIAPH3 (455982 downstream)																							ATATACTGGGCGGGGGGGAAAA	0.351													6	7	---	---	---	---	
NALCN	259232	broad.mit.edu	37	13	102028868	102028872	+	Intron	DEL	AAAAT	-	-			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:102028868_102028872delAAAAT	uc001vox.1	-						NALCN_uc001voy.2_Intron|NALCN_uc001voz.2_Intron|NALCN_uc001vpa.2_Intron	NM_052867	NP_443099	Q8IZF0	NALCN_HUMAN	voltage gated channel like 1							integral to membrane	sodium channel activity|voltage-gated ion channel activity			ovary(8)|breast(4)|skin(2)|pancreas(1)|central_nervous_system(1)	16	all_neural(89;0.0438)|Medulloblastoma(90;0.163)|Lung SC(71;0.184)					ctccatctcaaaaataaaataaaat	0.141													4	4	---	---	---	---	
TPP2	7174	broad.mit.edu	37	13	103260728	103260728	+	Intron	DEL	T	-	-			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:103260728delT	uc001vpi.3	+							NM_003291	NP_003282	P29144	TPP2_HUMAN	tripeptidyl peptidase II						proteolysis	cytoplasm|nucleus	aminopeptidase activity|serine-type endopeptidase activity|tripeptidyl-peptidase activity			upper_aerodigestive_tract(1)|ovary(1)	2	all_neural(89;0.0438)|Medulloblastoma(90;0.163)|Lung SC(71;0.184)					tttccaagaattttttttgca	0.000													2	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	105579428	105579429	+	IGR	INS	-	A	A	rs12429940		TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:105579428_105579429insA								None (None upstream) : DAOA (538787 downstream)																							TTACAATATTTAAAAAAAAAAT	0.356													4	2	---	---	---	---	
MGAT2	4247	broad.mit.edu	37	14	50087975	50087976	+	5'UTR	INS	-	T	T			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:50087975_50087976insT	uc001wwr.2	+	1					SDCCAG1_uc010anj.1_Intron|RPL36AL_uc001wwq.1_5'Flank	NM_002408	NP_002399	Q10469	MGAT2_HUMAN	mannosyl (alpha-1,6-)-glycoprotein						oligosaccharide biosynthetic process|post-translational protein modification|protein N-linked glycosylation via asparagine	Golgi membrane|Golgi stack|integral to membrane|membrane fraction	alpha-1,6-mannosylglycoprotein 2-beta-N-acetylglucosaminyltransferase activity				0	all_epithelial(31;0.0021)|Breast(41;0.0124)					TGCGCTCCCGGCCCTGGAGACC	0.584													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	62038925	62038925	+	Intron	DEL	T	-	-			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:62038925delT	uc001xfp.2	+											Homo sapiens cDNA: FLJ22447 fis, clone HRC09479.																		AGACTCTCACTTTTCCCCCAT	0.448													4	2	---	---	---	---	
SNW1	22938	broad.mit.edu	37	14	78185057	78185057	+	Intron	DEL	T	-	-			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:78185057delT	uc001xuf.2	-						SNW1_uc010tvm.1_Intron|SNW1_uc010asu.2_Intron|SNW1_uc010tvn.1_Intron	NM_012245	NP_036377	Q13573	SNW1_HUMAN	SKI-interacting protein						negative regulation of transcription, DNA-dependent|nuclear mRNA splicing, via spliceosome|regulation of transcription from RNA polymerase II promoter	catalytic step 2 spliceosome|nucleoplasm	Notch binding			ovary(1)	1			Kidney(204;0.164)	BRCA - Breast invasive adenocarcinoma(234;0.0291)		CTTTGGAttcttttttttttt	0.154													4	4	---	---	---	---	
NRXN3	9369	broad.mit.edu	37	14	80328463	80328464	+	3'UTR	DEL	AC	-	-			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:80328463_80328464delAC	uc001xun.2	+	17					NRXN3_uc001xum.1_RNA|NRXN3_uc001xup.2_RNA|NRXN3_uc001xuq.2_3'UTR|NRXN3_uc010asw.2_3'UTR|NRXN3_uc001xur.3_3'UTR	NM_004796	NP_004787	Q9Y4C0	NRX3A_HUMAN	neurexin 3 isoform 1 precursor						axon guidance|cell adhesion	integral to plasma membrane	metal ion binding|receptor activity			ovary(3)|upper_aerodigestive_tract(2)|pancreas(2)|central_nervous_system(1)|breast(1)|skin(1)	10		Renal(4;0.00876)		BRCA - Breast invasive adenocarcinoma(234;0.00544)|Kidney(3;0.029)|KIRC - Kidney renal clear cell carcinoma(182;0.223)		TTTTTAAAGGACACACACACAC	0.510													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	20616539	20616539	+	Intron	DEL	A	-	-			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:20616539delA	uc001ytg.2	-						uc010tyx.1_Intron|uc001yth.3_Intron					RecName: Full=Putative HERC2-like protein 3;																		aacaaaaaacaaaaacaaaac	0.328													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	21103409	21103409	+	IGR	DEL	C	-	-			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:21103409delC								POTEB (31432 upstream) : NF1P1 (18612 downstream)																							agtgtagaaacaaaaaaaaaa	0.000													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	21166427	21166427	+	Intron	DEL	T	-	-	rs142665520		TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:21166427delT	uc001ytw.1	+											Homo sapiens hypothetical protein LOC348120, mRNA (cDNA clone IMAGE:4838061).																		TTTGTGCTCATTTTTGTGATC	0.443													1	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	22490587	22490588	+	IGR	INS	-	A	A	rs147677085		TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:22490587_22490588insA								OR4N3P (76202 upstream) : MIR1268 (22641 downstream)																							TATTCACTGGTAAAAAAAAGAA	0.515													4	2	---	---	---	---	
HERC2P2	400322	broad.mit.edu	37	15	23331163	23331163	+	Intron	DEL	A	-	-			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:23331163delA	uc001yvr.2	-						HERC2P2_uc010ayf.1_Intron					RecName: Full=Putative HERC2-like protein 3;												0						AATAAATACTAAAAAAAAAAA	0.368													4	2	---	---	---	---	
WHAMML2	440253	broad.mit.edu	37	15	29009478	29009478	+	Intron	DEL	A	-	-			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:29009478delA	uc001zci.1	+											Homo sapiens cDNA FLJ33935 fis, clone CTONG2017910.												0						TTTGTGCTTTAAAAAAAAAAG	0.279													6	4	---	---	---	---	
CLN6	54982	broad.mit.edu	37	15	68515469	68515469	+	Intron	DEL	A	-	-			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:68515469delA	uc002arf.2	-						CLN6_uc010ujy.1_Intron|CLN6_uc010ujz.1_Intron	NM_017882	NP_060352	Q9NWW5	CLN6_HUMAN	CLN6 protein						cell death|cholesterol metabolic process|ganglioside metabolic process|glycosaminoglycan metabolic process|lysosomal lumen acidification|positive regulation of proteolysis|protein catabolic process	endoplasmic reticulum lumen|endoplasmic reticulum membrane|integral to membrane	protein homodimerization activity				0						ataaatactgaaaaaaaaaaa	0.229													7	4	---	---	---	---	
GLCE	26035	broad.mit.edu	37	15	69454251	69454252	+	Intron	INS	-	TG	TG	rs142220141	by1000genomes	TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:69454251_69454252insTG	uc002ary.1	+						GLCE_uc002arw.2_Intron|GLCE_uc002arx.2_Intron	NM_015554	NP_056369	O94923	GLCE_HUMAN	D-glucuronyl C5-epimerase						heparan sulfate proteoglycan biosynthetic process|heparin biosynthetic process	Golgi membrane|integral to membrane	UDP-glucuronate 5'-epimerase activity			ovary(2)	2						GTGGGGAAGACTGATTTTGGCT	0.525											OREG0023231	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	4	2	---	---	---	---	
MIR631	693216	broad.mit.edu	37	15	75648066	75648066	+	5'Flank	DEL	C	-	-			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:75648066delC	hsa-mir-631|MI0003645	-																							0						GGGAAGCCATCCCACCCCAGA	0.592													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	79774578	79774579	+	IGR	INS	-	C	C	rs139489469	by1000genomes	TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:79774578_79774579insC								KIAA1024 (9936 upstream) : MTHFS (362741 downstream)																							attgtcctgaacaagtctccag	0.000													2	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	93896174	93896174	+	Intron	DEL	A	-	-			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:93896174delA	uc002bsu.1	+											Homo sapiens cDNA FLJ37033 fis, clone BRACE2011389.																		tgcaaaggggaaaaaaaaaca	0.189													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	98035404	98035404	+	IGR	DEL	C	-	-			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:98035404delC								SPATA8 (706560 upstream) : LOC91948 (250442 downstream)																							ACAGGGAAGACCCCAAGGCCA	0.478													4	2	---	---	---	---	
A2BP1	54715	broad.mit.edu	37	16	6589125	6589126	+	Intron	INS	-	AA	AA	rs151241064		TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:6589125_6589126insAA	uc002cys.2	+						A2BP1_uc010buf.1_Intron|A2BP1_uc002cyr.1_Intron|A2BP1_uc002cyt.2_Intron|A2BP1_uc010uxz.1_Intron|A2BP1_uc010uya.1_Intron|A2BP1_uc002cyv.1_Intron	NM_018723	NP_061193	Q9NWB1	RFOX1_HUMAN	ataxin 2-binding protein 1 isoform 4						mRNA processing|RNA splicing|RNA transport	nucleus|trans-Golgi network	nucleotide binding|protein C-terminus binding|RNA binding				0		all_cancers(2;4.54e-52)|Colorectal(2;6.95e-44)|all_epithelial(2;1.15e-37)|Lung NSC(2;0.000289)|all_lung(2;0.00148)|Myeloproliferative disorder(2;0.0122)|Medulloblastoma(2;0.0354)|all_neural(2;0.0381)|all_hematologic(2;0.0749)|Renal(2;0.0758)|Melanoma(2;0.211)		Colorectal(1;3.55e-51)|COAD - Colon adenocarcinoma(2;1.92e-46)|all cancers(1;5.36e-16)|Epithelial(1;3.98e-15)|READ - Rectum adenocarcinoma(2;3.71e-05)|GBM - Glioblastoma multiforme(1;0.0499)		GATATTTGGTGAAAAAAAAAAA	0.376													7	6	---	---	---	---	
C16orf63	123811	broad.mit.edu	37	16	15973387	15973388	+	Intron	INS	-	AAAC	AAAC	rs148309464	by1000genomes	TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:15973387_15973388insAAAC	uc002dec.1	-						C16orf63_uc002ded.1_Intron	NM_144600	NP_653201	Q96NB1	FOPNL_HUMAN	hypothetical protein LOC123811						cilium assembly|microtubule anchoring	centriolar satellite|microtubule basal body|motile cilium	identical protein binding				0						TATAAATTAAAAAACAAACAAA	0.203													5	3	---	---	---	---	
SRCAP	10847	broad.mit.edu	37	16	30725222	30725222	+	Intron	DEL	T	-	-	rs66608116		TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:30725222delT	uc002dze.1	+						SRCAP_uc002dzf.2_Intron|SRCAP_uc002dzg.1_Intron|SRCAP_uc010bzz.1_Intron	NM_006662	NP_006653	Q6ZRS2	SRCAP_HUMAN	Snf2-related CBP activator protein						interspecies interaction between organisms|regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	Golgi apparatus|nucleus|protein complex	ATP binding|DNA binding|helicase activity|histone acetyltransferase activity|transcription coactivator activity			ovary(3)|skin(1)	4			Colorectal(24;0.198)			ATCAAttctgttttttttttt	0.219													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	32266881	32266881	+	RNA	DEL	T	-	-			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:32266881delT	uc002ecy.2	+	4		c.1520delT			uc010cav.1_RNA					Homo sapiens mRNA for TP53TG3b, complete cds.																		ttctttaaacttttttttttc	0.144													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	32817417	32817418	+	IGR	INS	-	TC	TC	rs138071874		TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:32817417_32817418insTC								TP53TG3B (128539 upstream) : SLC6A10P (71379 downstream)																							tcatcatttcatcatttcatct	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	34004011	34004011	+	IGR	DEL	C	-	-	rs142533648		TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:34004011delC								MIR1826 (38419 upstream) : UBE2MP1 (399791 downstream)																							caaaagagagcttgtactctg	0.000													4	2	---	---	---	---	
COTL1	23406	broad.mit.edu	37	16	84641520	84641520	+	Intron	DEL	G	-	-			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:84641520delG	uc002fid.2	-						COTL1_uc002fie.2_Intron|COTL1_uc010chk.2_Intron	NM_021149	NP_066972	Q14019	COTL1_HUMAN	coactosin-like 1							cytoplasm|cytoskeleton	actin binding|enzyme binding			skin(1)	1						ttatcgggcaggaagcagaag	0.020													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	86557634	86557636	+	IGR	DEL	AGA	-	-	rs66586415		TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:86557634_86557636delAGA								FOXF1 (9565 upstream) : MTHFSD (6147 downstream)																							aatgaagagcagaaggtttccca	0.172													0	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	88367727	88367728	+	IGR	DEL	TG	-	-			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:88367727_88367728delTG								BANP (256804 upstream) : ZNF469 (126151 downstream)																							tgtctgtgtctgtgtgtgtgCC	0.203													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	14285947	14285947	+	IGR	DEL	T	-	-			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:14285947delT								HS3ST3B1 (36455 upstream) : PMP22 (847150 downstream)																							CATATGATGGTTATACGATCT	0.378													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	21337822	21337822	+	IGR	DEL	T	-	-	rs67990702		TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21337822delT								KCNJ12 (14643 upstream) : C17orf51 (93750 downstream)																							AAGGACAGTGTTTTTTCCTCT	0.478													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	25299747	25299747	+	IGR	DEL	T	-	-	rs111243274		TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:25299747delT								None (None upstream) : WSB1 (321359 downstream)																							agaatttgaatttttttgtga	0.144													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	43690625	43690625	+	IGR	DEL	T	-	-			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:43690625delT								LOC644172 (10877 upstream) : CRHR1 (7087 downstream)																							TGACTCATGGttttttttttt	0.239													4	2	---	---	---	---	
ITGB3	3690	broad.mit.edu	37	17	45367839	45367841	+	Intron	DEL	AGA	-	-	rs78819126		TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:45367839_45367841delAGA	uc002ilj.2	+						ITGB3_uc002ili.1_Intron|ITGB3_uc010wkr.1_Intron	NM_000212	NP_000203	P05106	ITB3_HUMAN	integrin beta chain, beta 3 precursor						activation of protein kinase activity|angiogenesis involved in wound healing|axon guidance|cell-matrix adhesion|integrin-mediated signaling pathway|interspecies interaction between organisms|leukocyte migration|negative regulation of lipid storage|negative regulation of lipid transport|negative regulation of lipoprotein metabolic process|negative regulation of low-density lipoprotein particle receptor biosynthetic process|negative regulation of macrophage derived foam cell differentiation|platelet activation|platelet degranulation|positive regulation of endothelial cell migration|positive regulation of endothelial cell proliferation|positive regulation of peptidyl-tyrosine phosphorylation|positive regulation of vascular endothelial growth factor receptor signaling pathway|regulation of bone resorption|smooth muscle cell migration|tube development	alphav-beta3 integrin-vitronectin complex|integrin complex|platelet alpha granule membrane	cell adhesion molecule binding|identical protein binding|platelet-derived growth factor receptor binding|receptor activity|vascular endothelial growth factor receptor 2 binding			central_nervous_system(5)|large_intestine(1)	6					Abciximab(DB00054)|Tirofiban(DB00775)	aggaaggaagagagaaagaagga	0.453													6	5	---	---	---	---	
CALCOCO2	10241	broad.mit.edu	37	17	46929188	46929188	+	Intron	DEL	A	-	-			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:46929188delA	uc002iof.2	+						CALCOCO2_uc010wlp.1_Intron|CALCOCO2_uc010wlq.1_Intron|CALCOCO2_uc010wlr.1_Intron|CALCOCO2_uc010wls.1_Intron	NM_005831	NP_005822	Q13137	CACO2_HUMAN	calcium binding and coiled-coil domain 2						response to interferon-gamma|viral reproduction	cytoskeleton|Golgi apparatus|nucleus|perinuclear region of cytoplasm|soluble fraction	protein homodimerization activity			ovary(1)	1						CCCTGCTTTTAAAAAAAAAAA	0.229													10	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	61057860	61057860	+	IGR	DEL	A	-	-			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:61057860delA								MIR633 (36187 upstream) : TANC2 (29038 downstream)																							ccaaaatctgaaaaaaatttg	0.000													6	3	---	---	---	---	
AXIN2	8313	broad.mit.edu	37	17	63525463	63525463	+	3'UTR	DEL	A	-	-			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:63525463delA	uc002jfi.2	-	11					AXIN2_uc002jfh.2_3'UTR	NM_004655	NP_004646	Q9Y2T1	AXIN2_HUMAN	axin 2						cellular protein localization|cellular response to organic cyclic compound|dorsal/ventral axis specification|intramembranous ossification|maintenance of DNA repeat elements|mRNA stabilization|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of catenin import into nucleus|negative regulation of cell proliferation|negative regulation of osteoblast differentiation|odontogenesis|positive regulation of cell death|positive regulation of epithelial to mesenchymal transition|positive regulation of protein phosphorylation|regulation of centromeric sister chromatid cohesion|regulation of mismatch repair|Wnt receptor signaling pathway involved in somitogenesis	Axin-APC-beta-catenin-GSK3B complex|cell cortex|centrosome|cytoplasmic membrane-bounded vesicle|cytoplasmic microtubule|nucleus|plasma membrane|postsynaptic density	armadillo repeat domain binding|beta-catenin binding|GTPase activator activity|protein kinase binding|signal transducer activity|ubiquitin protein ligase binding			central_nervous_system(1)|skin(1)	2						GCAGCATAGGAAAAAAAAAAA	0.418									Oligodontia_Ectodermal_Dysplasia_and_Colorectal_Polyp_syndrome				4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	14645043	14645043	+	IGR	DEL	T	-	-			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:14645043delT								POTEC (101444 upstream) : ANKRD30B (103196 downstream)																							tgttgagcccttttttatttc	0.114													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	42221560	42221560	+	IGR	DEL	A	-	-			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:42221560delA								None (None upstream) : SETBP1 (38578 downstream)																							ACTTCTATTGAATTAAGTCAT	0.358													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	63302906	63302906	+	IGR	DEL	T	-	-			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:63302906delT								None (None upstream) : CDH7 (114582 downstream)																							aatgtctaagttttttttttt	0.040													6	4	---	---	---	---	
CDH19	28513	broad.mit.edu	37	18	64236185	64236185	+	Intron	DEL	A	-	-			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:64236185delA	uc002lkc.1	-						CDH19_uc010dql.1_Intron|CDH19_uc010xey.1_Intron|CDH19_uc002lkd.2_Intron	NM_021153	NP_066976	Q9H159	CAD19_HUMAN	cadherin 19, type 2 preproprotein						homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(1)|skin(1)	2		Esophageal squamous(42;0.0132)				AAACAGAAACAAAAATAATTG	0.254													4	2	---	---	---	---	
DMRTC2	63946	broad.mit.edu	37	19	42352414	42352414	+	Intron	DEL	A	-	-	rs79959130		TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:42352414delA	uc002ors.2	+						DMRTC2_uc002orr.1_Intron|DMRTC2_uc010xwe.1_Intron	NM_001040283	NP_001035373	Q8IXT2	DMRTD_HUMAN	DMRT-like family C2						cell differentiation|sex differentiation	nucleus	DNA binding|metal ion binding|sequence-specific DNA binding transcription factor activity				0						actccatctcaaaaaaaaaaa	0.244													4	3	---	---	---	---	
XRCC1	7515	broad.mit.edu	37	19	44064552	44064552	+	Intron	DEL	A	-	-			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:44064552delA	uc002owt.2	-						XRCC1_uc010xwp.1_Intron	NM_006297	NP_006288	P18887	XRCC1_HUMAN	X-ray repair cross complementing protein 1						base-excision repair|single strand break repair	nucleoplasm	damaged DNA binding|protein binding			ovary(2)|lung(2)|large_intestine(1)|prostate(1)|breast(1)	7		Prostate(69;0.0153)				actccgtctcaaaaaaaaaaa	0.000								Other_BER_factors					4	3	---	---	---	---	
ZNF180	7733	broad.mit.edu	37	19	45001484	45001484	+	Intron	DEL	C	-	-			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:45001484delC	uc002ozf.3	-						ZNF180_uc002ozh.3_Intron|ZNF180_uc002ozi.3_Intron|ZNF180_uc002ozg.3_Intron|ZNF180_uc010ejm.2_Intron	NM_013256	NP_037388	Q9UJW8	ZN180_HUMAN	zinc finger protein 180						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(2)	2		Prostate(69;0.0435)				AACCGCTGGGCCCCCCACCCC	0.592													4	2	---	---	---	---	
EHD2	30846	broad.mit.edu	37	19	48239457	48239457	+	Intron	DEL	A	-	-			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:48239457delA	uc002phj.3	+						EHD2_uc010xyu.1_Intron|EHD2_uc010xyv.1_Intron	NM_014601	NP_055416	Q9NZN4	EHD2_HUMAN	EH-domain containing 2						blood coagulation|endocytic recycling	nucleus|plasma membrane|recycling endosome membrane	ATP binding|calcium ion binding|GTP binding|GTPase activity|nucleic acid binding			ovary(1)|skin(1)	2		all_cancers(25;6.74e-07)|all_lung(116;2.02e-05)|Lung NSC(112;3.77e-05)|all_epithelial(76;4.89e-05)|all_neural(266;0.0332)|Ovarian(192;0.086)		OV - Ovarian serous cystadenocarcinoma(262;0.000336)|all cancers(93;0.000415)|Epithelial(262;0.0132)|GBM - Glioblastoma multiforme(486;0.0537)		cgtctcaaagaaaaaaaaaga	0.005													4	2	---	---	---	---	
KLK11	11012	broad.mit.edu	37	19	51530249	51530250	+	Intron	INS	-	AGCCC	AGCCC	rs149645631	by1000genomes	TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:51530249_51530250insAGCCC	uc002pvd.1	-						KLK11_uc002pvb.1_5'Flank|KLK11_uc002pve.1_Intron|KLK11_uc002pvf.1_Intron|KLK11_uc002pvc.3_5'Flank|KLK11_uc010eom.2_5'Flank	NM_144947	NP_659196	Q9UBX7	KLK11_HUMAN	kallikrein 11 isoform 2 precursor						proteolysis	extracellular region	serine-type endopeptidase activity				0		all_neural(266;0.026)		OV - Ovarian serous cystadenocarcinoma(262;0.00327)|GBM - Glioblastoma multiforme(134;0.00878)		ctccatctccactcttctctct	0.084													4	2	---	---	---	---	
HSPA12B	116835	broad.mit.edu	37	20	3719691	3719691	+	Intron	DEL	G	-	-			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:3719691delG	uc002wjd.2	+						HSPA12B_uc010zqi.1_Intron|HSPA12B_uc002wje.2_Intron|HSPA12B_uc010zqj.1_Intron	NM_052970	NP_443202	Q96MM6	HS12B_HUMAN	heat shock 70kD protein 12B								ATP binding				0						TGTGCACACAGGAGTGTATGC	0.537													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	16884635	16884635	+	IGR	DEL	A	-	-	rs79920701	byFrequency	TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:16884635delA								OTOR (151827 upstream) : PCSK2 (322117 downstream)																							AAAATGCATTAAAAAAACTTC	0.373													4	2	---	---	---	---	
RRBP1	6238	broad.mit.edu	37	20	17622594	17622594	+	Intron	DEL	G	-	-			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:17622594delG	uc002wpv.1	-						RRBP1_uc002wpu.2_Intron|RRBP1_uc002wpw.1_Intron|RRBP1_uc010gcl.1_Intron	NM_001042576	NP_001036041	Q9P2E9	RRBP1_HUMAN	ribosome binding protein 1						protein transport|translation|transmembrane transport	integral to endoplasmic reticulum membrane|ribosome	receptor activity			ovary(1)	1						CGTTAACAGAGGGGACAAATG	0.562													41	19	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	29593345	29593346	+	IGR	DEL	AG	-	-	rs113305967		TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:29593345_29593346delAG								None (None upstream) : FRG1B (18533 downstream)																							aaattgactaagacaATTGGTG	0.158													4	2	---	---	---	---	
EDEM2	55741	broad.mit.edu	37	20	33799348	33799349	+	Intron	INS	-	T	T			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:33799348_33799349insT	uc010zuv.1	-							NM_018217	NP_060687	Q9BV94	EDEM2_HUMAN	ER degradation enhancer, mannosidase alpha-like						post-translational protein modification|protein folding|protein N-linked glycosylation via asparagine|response to unfolded protein	endoplasmic reticulum lumen|endoplasmic reticulum membrane|extracellular region	calcium ion binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity|misfolded protein binding				0			BRCA - Breast invasive adenocarcinoma(18;0.00936)			tatatggctgattttttaacac	0.297													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	37256021	37256022	+	IGR	INS	-	TC	TC	rs72084961		TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:37256021_37256022insTC								ADIG (38917 upstream) : SLC32A1 (97083 downstream)																							gtgtgttggtgtgtgtgttggg	0.104													4	3	---	---	---	---	
B4GALT5	9334	broad.mit.edu	37	20	48253232	48253233	+	Intron	INS	-	C	C			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:48253232_48253233insC	uc002xuu.3	-							NM_004776	NP_004767	O43286	B4GT5_HUMAN	UDP-Gal:betaGlcNAc beta 1,4-						post-translational protein modification|protein N-linked glycosylation via asparagine	Golgi cisterna membrane|integral to membrane	galactosyltransferase activity|metal ion binding			ovary(1)	1			BRCA - Breast invasive adenocarcinoma(9;2.51e-06)			gctcacgccagcccctgctagc	0.134													4	2	---	---	---	---	
BAGE2	85319	broad.mit.edu	37	21	11029407	11029407	+	Intron	DEL	A	-	-			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:11029407delA	uc002yit.1	-						TPTE_uc002yis.1_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)		AATTAACCATAAAAAGAGGTA	0.269													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	11149030	11149032	+	IGR	DEL	GAA	-	-	rs143833307		TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:11149030_11149032delGAA								BAGE (50093 upstream) : None (None downstream)																							catctaaagggaagaagacaaat	0.000													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	11150043	11150043	+	IGR	DEL	T	-	-			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:11150043delT								BAGE (51106 upstream) : None (None downstream)																							agacctcgaattaaaaaacta	0.000													8	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	14602544	14602545	+	IGR	INS	-	TT	TT			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:14602544_14602545insTT								C21orf99 (111975 upstream) : POTED (379953 downstream)																							tttgctgagagttttaatcata	0.000													4	2	---	---	---	---	
URB1	9875	broad.mit.edu	37	21	33705412	33705412	+	Intron	DEL	T	-	-			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:33705412delT	uc002ypn.2	-							NM_014825	NP_055640	O60287	NPA1P_HUMAN	URB1 ribosome biogenesis 1 homolog							nucleolus	protein binding				0						aaaattacaattttttttttt	0.284													1	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	35715212	35715213	+	IGR	INS	-	G	G	rs147167532	by1000genomes	TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:35715212_35715213insG								C21orf82 (152992 upstream) : KCNE2 (21110 downstream)																							TGGCAGTGGCTGTCCCAGCCCT	0.584													4	2	---	---	---	---	
ABCG1	9619	broad.mit.edu	37	21	43710525	43710525	+	Intron	DEL	A	-	-			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:43710525delA	uc002zaq.2	+						ABCG1_uc002zan.2_Intron|ABCG1_uc002zam.2_Intron|ABCG1_uc002zao.2_Intron|ABCG1_uc002zap.2_Intron|ABCG1_uc002zar.2_Intron|ABCG1_uc011aev.1_Intron|ABCG1_uc010gpb.1_Intron	NM_004915	NP_004906	P45844	ABCG1_HUMAN	ATP-binding cassette sub-family G member 1						amyloid precursor protein catabolic process|cholesterol efflux|cholesterol homeostasis|cholesterol metabolic process|detection of hormone stimulus|high-density lipoprotein particle remodeling|intracellular cholesterol transport|lipoprotein metabolic process|low-density lipoprotein particle remodeling|negative regulation of cholesterol storage|negative regulation of macrophage derived foam cell differentiation|phospholipid efflux|phospholipid homeostasis|positive regulation of cholesterol biosynthetic process|regulation of cholesterol esterification|regulation of transcription, DNA-dependent|response to lipid|reverse cholesterol transport	endoplasmic reticulum membrane|external side of plasma membrane|Golgi membrane|recycling endosome	ADP binding|ATP binding|cholesterol transporter activity|glycoprotein transporter activity|phospholipid transporter activity|protein heterodimerization activity|protein homodimerization activity|sterol-transporting ATPase activity|toxin transporter activity			ovary(2)|central_nervous_system(1)	3					Adenosine triphosphate(DB00171)	TACTTAAGCCAAAGGAATGAA	0.343													4	2	---	---	---	---	
CCT8L2	150160	broad.mit.edu	37	22	17075872	17075872	+	5'Flank	DEL	A	-	-	rs148690764		TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:17075872delA	uc002zlp.1	-							NM_014406	NP_055221	Q96SF2	TCPQM_HUMAN	T-complex protein 1						cellular protein metabolic process	cytoplasm	anion channel activity|ATP binding|calcium-activated potassium channel activity			ovary(1)	1	all_hematologic(4;0.00567)|Acute lymphoblastic leukemia(84;0.0977)	all_epithelial(15;0.0157)|Lung NSC(13;0.147)|all_lung(157;0.175)				CACAGTAATGAAAAAAAAAAA	0.323													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	25864389	25864392	+	IGR	DEL	ACAC	-	-			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:25864389_25864392delACAC								ARX (830324 upstream) : MAGEB18 (292071 downstream)																							aaacagaccaacacacacacacac	0.000													5	5	---	---	---	---	
RPGR	6103	broad.mit.edu	37	X	38136289	38136289	+	Intron	DEL	A	-	-			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:38136289delA	uc004deb.2	-						RPGR_uc004dea.2_Intron|RPGR_uc004dec.2_Intron	NM_000328	NP_000319	Q92834	RPGR_HUMAN	retinitis pigmentosa GTPase regulator isoform A						intracellular protein transport|response to stimulus|visual perception	Golgi apparatus|photoreceptor outer segment	guanyl-nucleotide exchange factor activity|protein binding			ovary(1)	1						GTTACAATGGAAAAAAAAAAT	0.328													5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	40480324	40480324	+	IGR	DEL	T	-	-			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:40480324delT								ATP6AP2 (14437 upstream) : CXorf38 (7961 downstream)																							ATGTCCAAAGttttttttttc	0.234													7	4	---	---	---	---	
ZNF185	7739	broad.mit.edu	37	X	152114208	152114208	+	Intron	DEL	G	-	-			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:152114208delG	uc010ntv.1	+						ZNF185_uc011myg.1_Intron|ZNF185_uc011myh.1_Intron|ZNF185_uc011myi.1_Intron|ZNF185_uc011myj.1_Intron|ZNF185_uc011myk.1_Intron|ZNF185_uc004fgw.3_Intron|ZNF185_uc004fgu.2_Intron|ZNF185_uc004fgv.2_Intron|ZNF185_uc004fgx.2_Intron	NM_007150	NP_009081	O15231	ZN185_HUMAN	zinc finger protein 185							cytoplasm|cytoskeleton|focal adhesion	zinc ion binding			ovary(3)	3	Acute lymphoblastic leukemia(192;6.56e-05)					TCAAGGAGCTGGGAGGGGACT	0.562													4	2	---	---	---	---	
