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
MST1P2	11209	broad.mit.edu	37	1	16975947	16975947	+	RNA	SNP	C	T	T			TCGA-EJ-5497-01A-02D-1576-08	TCGA-EJ-5497-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:16975947C>T	uc010och.1	+	11		c.1969C>T			MST1P2_uc001azl.3_RNA|MST1P2_uc009vox.2_RNA|MST1P2_uc001azm.3_RNA	NR_027504				Homo sapiens cDNA FLJ43241 fis, clone HEART1000010, weakly  similar to Hepatocyte growth factor-like protein precursor.												0						AGAGCCAGGCCTACAGCGGGT	0.577													3	92	---	---	---	---	PASS
SRRM1	10250	broad.mit.edu	37	1	24998071	24998071	+	Silent	SNP	G	A	A			TCGA-EJ-5497-01A-02D-1576-08	TCGA-EJ-5497-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:24998071G>A	uc001bjm.2	+	16	2819	c.2595G>A	c.(2593-2595)GCG>GCA	p.A865A	SRRM1_uc010oel.1_Silent_p.A877A|SRRM1_uc009vri.1_Silent_p.A794A	NM_005839	NP_005830	Q8IYB3	SRRM1_HUMAN	serine/arginine repetitive matrix 1	865	Ala-rich.				mRNA 3'-end processing|mRNA export from nucleus|termination of RNA polymerase II transcription	catalytic step 2 spliceosome|cytosol|nuclear matrix|nuclear speck	DNA binding|protein binding|RNA binding			ovary(2)|haematopoietic_and_lymphoid_tissue(1)	3		Colorectal(325;3.46e-05)|Renal(390;0.0007)|Lung NSC(340;0.000946)|all_lung(284;0.00125)|Ovarian(437;0.00764)|Breast(348;0.0148)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.19)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0422)|OV - Ovarian serous cystadenocarcinoma(117;1.01e-24)|Colorectal(126;5.95e-08)|COAD - Colon adenocarcinoma(152;3.24e-06)|GBM - Glioblastoma multiforme(114;0.000148)|BRCA - Breast invasive adenocarcinoma(304;0.00177)|KIRC - Kidney renal clear cell carcinoma(1967;0.00348)|STAD - Stomach adenocarcinoma(196;0.00483)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.138)		CAGTGGCAGCGCCAGAGCCGA	0.299													7	60	---	---	---	---	PASS
YBX1	4904	broad.mit.edu	37	1	43162410	43162410	+	Missense_Mutation	SNP	G	C	C			TCGA-EJ-5497-01A-02D-1576-08	TCGA-EJ-5497-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:43162410G>C	uc001chs.2	+	5	623	c.452G>C	c.(451-453)CGT>CCT	p.R151P		NM_004559	NP_004550	P67809	YBOX1_HUMAN	nuclease sensitive element binding protein 1	151					CRD-mediated mRNA stabilization|negative regulation of transcription, DNA-dependent|nuclear mRNA splicing, via spliceosome|positive regulation of cell division|transcription from RNA polymerase II promoter	CRD-mediated mRNA stability complex|extracellular region|histone pre-mRNA 3'end processing complex|nucleoplasm|stress granule|U12-type spliceosomal complex	double-stranded DNA binding|protein binding|RNA binding|sequence-specific DNA binding transcription factor activity|single-stranded DNA binding			ovary(4)|upper_aerodigestive_tract(1)	5	Ovarian(52;0.00744)|all_hematologic(146;0.0977)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0333)				TATCCACGTCGTAGGGGTCCT	0.517													3	105	---	---	---	---	PASS
LRRC8B	23507	broad.mit.edu	37	1	90058622	90058622	+	3'UTR	SNP	T	A	A			TCGA-EJ-5497-01A-02D-1576-08	TCGA-EJ-5497-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:90058622T>A	uc001dni.2	+	8					LRRC8B_uc001dnh.2_3'UTR|LRRC8B_uc001dnj.2_3'UTR	NM_001134476	NP_001127948	Q6P9F7	LRC8B_HUMAN	leucine rich repeat containing 8 family, member							integral to membrane				ovary(2)	2		all_lung(203;0.17)		all cancers(265;0.00515)|Epithelial(280;0.0241)		AAGAGACCCGTGTTTCAAAAT	0.244													6	159	---	---	---	---	PASS
PDE4DIP	9659	broad.mit.edu	37	1	144863199	144863199	+	Intron	SNP	G	A	A	rs142749426	by1000genomes	TCGA-EJ-5497-01A-02D-1576-08	TCGA-EJ-5497-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:144863199G>A	uc001elw.3	-						NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Intron|PDE4DIP_uc001elv.3_Intron|PDE4DIP_uc001ema.2_3'UTR	NM_014644	NP_055459	Q5VU43	MYOME_HUMAN	phosphodiesterase 4D interacting protein isoform						cellular protein complex assembly	centrosome|Golgi apparatus|myofibril|nucleus	enzyme binding			ovary(4)|haematopoietic_and_lymphoid_tissue(1)	5				Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126)		CTCGGGTGGGGGTTTCTGCAA	0.532			T	PDGFRB	MPD								7	68	---	---	---	---	PASS
LCE1F	353137	broad.mit.edu	37	1	152748962	152748962	+	Missense_Mutation	SNP	C	G	G	rs116630978	by1000genomes	TCGA-EJ-5497-01A-02D-1576-08	TCGA-EJ-5497-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:152748962C>G	uc010pdv.1	+	1	115	c.115C>G	c.(115-117)CCT>GCT	p.P39A		NM_178354	NP_848131	Q5T754	LCE1F_HUMAN	late cornified envelope 1F	39	Pro-rich.				keratinization						0	Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.206)			taagtgccctccTGTCTCTTC	0.413													14	84	---	---	---	---	PASS
LCE1F	353137	broad.mit.edu	37	1	152748963	152748963	+	Missense_Mutation	SNP	C	T	T			TCGA-EJ-5497-01A-02D-1576-08	TCGA-EJ-5497-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:152748963C>T	uc010pdv.1	+	1	116	c.116C>T	c.(115-117)CCT>CTT	p.P39L		NM_178354	NP_848131	Q5T754	LCE1F_HUMAN	late cornified envelope 1F	39	Pro-rich.				keratinization						0	Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.206)			aagtgccctccTGTCTCTTCC	0.408													13	84	---	---	---	---	PASS
FCRL6	343413	broad.mit.edu	37	1	159779044	159779044	+	Intron	SNP	G	A	A			TCGA-EJ-5497-01A-02D-1576-08	TCGA-EJ-5497-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:159779044G>A	uc001fud.3	+						FCRL6_uc010pix.1_3'UTR|FCRL6_uc001fuc.2_Intron|FCRL6_uc009wsz.1_Intron|FCRL6_uc009wta.2_Intron	NM_001004310	NP_001004310	Q6DN72	FCRL6_HUMAN	Fc receptor-like 6 precursor							integral to membrane				ovary(2)|skin(1)	3	all_hematologic(112;0.0597)					GGGTAAGTGCGCGAGAGAGTG	0.657													4	90	---	---	---	---	PASS
ASPM	259266	broad.mit.edu	37	1	197073334	197073334	+	Missense_Mutation	SNP	T	C	C			TCGA-EJ-5497-01A-02D-1576-08	TCGA-EJ-5497-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:197073334T>C	uc001gtu.2	-	18	5304	c.5047A>G	c.(5047-5049)ATA>GTA	p.I1683V	ASPM_uc001gtv.2_Intron|ASPM_uc001gtw.3_Intron	NM_018136	NP_060606	Q8IZT6	ASPM_HUMAN	asp (abnormal spindle)-like, microcephaly	1683	IQ 5.				mitosis	cytoplasm|nucleus	calmodulin binding			ovary(4)|central_nervous_system(2)	6						TGCAATTTTATTGTAGCATTT	0.303													4	125	---	---	---	---	PASS
FMN2	56776	broad.mit.edu	37	1	240371469	240371469	+	Silent	SNP	C	T	T			TCGA-EJ-5497-01A-02D-1576-08	TCGA-EJ-5497-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:240371469C>T	uc010pyd.1	+	5	3582	c.3357C>T	c.(3355-3357)CCC>CCT	p.P1119P	FMN2_uc010pye.1_Silent_p.P1123P	NM_020066	NP_064450	Q9NZ56	FMN2_HUMAN	formin 2	1119	Pro-rich.|FH1.				actin cytoskeleton organization|establishment of meiotic spindle localization|intracellular signal transduction|meiotic chromosome movement towards spindle pole|meiotic metaphase I|multicellular organismal development|oogenesis|polar body extrusion after meiotic divisions		actin binding			ovary(4)|pancreas(3)|skin(3)|large_intestine(1)|central_nervous_system(1)	12	Ovarian(103;0.127)	all_cancers(173;0.013)	OV - Ovarian serous cystadenocarcinoma(106;0.0106)			CGGGCATACCCCCTCCTCCCC	0.716													2	5	---	---	---	---	PASS
ZNF695	57116	broad.mit.edu	37	1	247151557	247151557	+	Missense_Mutation	SNP	A	G	G	rs2642992	by1000genomes	TCGA-EJ-5497-01A-02D-1576-08	TCGA-EJ-5497-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:247151557A>G	uc009xgu.2	-	4	405	c.260T>C	c.(259-261)GTT>GCT	p.V87A	ZNF695_uc001ica.2_RNA|ZNF695_uc001icb.1_RNA|ZNF695_uc009xgt.1_RNA|ZNF695_uc001ibx.2_Missense_Mutation_p.V87A|ZNF695_uc001iby.2_Intron|ZNF695_uc001icc.2_Missense_Mutation_p.V75A	NM_020394	NP_065127	Q8IW36	ZN695_HUMAN	zinc finger protein SBZF3	87	KRAB.				regulation of transcription, DNA-dependent	nucleus	nucleic acid binding|zinc ion binding				0	all_cancers(71;4.01e-05)|all_epithelial(71;6.72e-06)|Ovarian(71;0.0173)|Breast(184;0.0318)|all_lung(81;0.0458)|Lung NSC(105;0.0518)	all_cancers(173;0.0266)	OV - Ovarian serous cystadenocarcinoma(106;0.00271)			AGAAGACAAAACTGGAAAAAA	0.328													4	96	---	---	---	---	PASS
CCDC142	84865	broad.mit.edu	37	2	74708964	74708964	+	Missense_Mutation	SNP	A	T	T			TCGA-EJ-5497-01A-02D-1576-08	TCGA-EJ-5497-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:74708964A>T	uc002slr.2	-	1	1394	c.1001T>A	c.(1000-1002)CTG>CAG	p.L334Q	TTC31_uc002sls.2_5'Flank|TTC31_uc010yrv.1_5'Flank|TTC31_uc002slt.2_5'Flank|TTC31_uc002slu.2_5'Flank|CCDC142_uc002slo.2_RNA|CCDC142_uc002slq.2_Missense_Mutation_p.L334Q|CCDC142_uc002slp.2_Missense_Mutation_p.L334Q	NM_032779	NP_116168	Q17RM4	CC142_HUMAN	coiled-coil domain containing 142	334										central_nervous_system(1)	1						TGCCTGACTCAGCTGTTGCGC	0.612													8	111	---	---	---	---	PASS
AFF3	3899	broad.mit.edu	37	2	100199303	100199303	+	Missense_Mutation	SNP	G	C	C			TCGA-EJ-5497-01A-02D-1576-08	TCGA-EJ-5497-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:100199303G>C	uc002tag.2	-	16	2986	c.2750C>G	c.(2749-2751)CCT>CGT	p.P917R	AFF3_uc002taf.2_Missense_Mutation_p.P942R|AFF3_uc010fiq.1_Missense_Mutation_p.P917R|AFF3_uc010yvr.1_Missense_Mutation_p.P1070R|AFF3_uc002tah.1_Missense_Mutation_p.P942R	NM_002285	NP_002276	P51826	AFF3_HUMAN	AF4/FMR2 family, member 3 isoform 1	917					multicellular organismal development|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding			ovary(2)|pancreas(1)|lung(1)|kidney(1)|skin(1)	6						GTCGGCCTTAGGCTTTTTGCT	0.478													8	158	---	---	---	---	PASS
CPS1	1373	broad.mit.edu	37	2	211454904	211454904	+	Silent	SNP	G	A	A			TCGA-EJ-5497-01A-02D-1576-08	TCGA-EJ-5497-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:211454904G>A	uc002vee.3	+	8	918	c.786G>A	c.(784-786)GCG>GCA	p.A262A	CPS1_uc010fur.2_Silent_p.A268A	NM_001875	NP_001866	P31327	CPSM_HUMAN	carbamoyl-phosphate synthetase 1 isoform b	262	Glutamine amidotransferase type-1.				carbamoyl phosphate biosynthetic process|citrulline biosynthetic process|glutamine metabolic process|glycogen catabolic process|nitric oxide metabolic process|positive regulation of vasodilation|response to lipopolysaccharide|triglyceride catabolic process|urea cycle	mitochondrial nucleoid	ATP binding|carbamoyl-phosphate synthase (ammonia) activity			ovary(8)|central_nervous_system(3)|breast(1)|skin(1)	13				Epithelial(149;0.00697)|Lung(261;0.0521)|LUSC - Lung squamous cell carcinoma(261;0.0544)|all cancers(144;0.0843)		TTTTGATCGCGGGAGGACCGG	0.483													24	534	---	---	---	---	PASS
SLC9A10	285335	broad.mit.edu	37	3	112005630	112005630	+	Silent	SNP	T	C	C			TCGA-EJ-5497-01A-02D-1576-08	TCGA-EJ-5497-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:112005630T>C	uc003dyu.2	-	2	231	c.9A>G	c.(7-9)GGA>GGG	p.G3G	SLC9A10_uc011bhu.1_5'UTR|SLC9A10_uc010hqc.2_Silent_p.G3G	NM_183061	NP_898884	Q4G0N8	S9A10_HUMAN	sperm-specific sodium proton exchanger	3					cell differentiation|multicellular organismal development|sodium ion transport|spermatogenesis	cilium|flagellar membrane|integral to membrane	solute:hydrogen antiporter activity			ovary(3)|breast(2)	5						CCTTAAATATTCCAGCCATGT	0.353													8	38	---	---	---	---	PASS
SH3BP2	6452	broad.mit.edu	37	4	2831383	2831383	+	Silent	SNP	T	G	G	rs231399	byFrequency	TCGA-EJ-5497-01A-02D-1576-08	TCGA-EJ-5497-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:2831383T>G	uc003gfi.3	+	8	870	c.750T>G	c.(748-750)GCT>GCG	p.A250A	SH3BP2_uc011bvp.1_Silent_p.A278A|SH3BP2_uc003gfj.3_Silent_p.A307A|SH3BP2_uc003gfk.3_Silent_p.A250A|SH3BP2_uc003gfl.3_Silent_p.A183A|SH3BP2_uc003gfm.3_Silent_p.A225A	NM_001122681	NP_001116153	P78314	3BP2_HUMAN	SH3-domain binding protein 2 isoform a	250					signal transduction		SH3 domain binding|SH3/SH2 adaptor activity			central_nervous_system(1)	1				UCEC - Uterine corpus endometrioid carcinoma (64;0.164)		TTGGCCTGGCTGCTGAGGACT	0.677									Cherubism				3	66	---	---	---	---	PASS
RAPGEF2	9693	broad.mit.edu	37	4	160260299	160260299	+	Missense_Mutation	SNP	C	T	T			TCGA-EJ-5497-01A-02D-1576-08	TCGA-EJ-5497-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:160260299C>T	uc003iqg.3	+	13	2154	c.1844C>T	c.(1843-1845)GCT>GTT	p.A615V		NM_014247	NP_055062	Q9Y4G8	RPGF2_HUMAN	Rap guanine nucleotide exchange factor 2	615	Ras-associating.				cAMP-mediated signaling|MAPKKK cascade|small GTPase mediated signal transduction	integral to plasma membrane|intracellular	calcium ion binding|diacylglycerol binding|Rap GTPase activator activity|Rap guanyl-nucleotide exchange factor activity|signal transducer activity			lung(2)|upper_aerodigestive_tract(1)|skin(1)	4	all_hematologic(180;0.24)			COAD - Colon adenocarcinoma(41;0.0817)		GTTTTTAAGGCTGATCAGCAA	0.423													6	355	---	---	---	---	PASS
FRG1	2483	broad.mit.edu	37	4	190878569	190878569	+	Missense_Mutation	SNP	T	C	C			TCGA-EJ-5497-01A-02D-1576-08	TCGA-EJ-5497-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:190878569T>C	uc003izs.2	+	6	640	c.449T>C	c.(448-450)TTG>TCG	p.L150S		NM_004477	NP_004468	Q14331	FRG1_HUMAN	FSHD region gene 1	150					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)		ATGGCTTTGTTGGCCTCAAAT	0.358													3	55	---	---	---	---	PASS
PSD2	84249	broad.mit.edu	37	5	139201586	139201586	+	Silent	SNP	G	A	A			TCGA-EJ-5497-01A-02D-1576-08	TCGA-EJ-5497-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:139201586G>A	uc003leu.1	+	6	1411	c.1206G>A	c.(1204-1206)TCG>TCA	p.S402S		NM_032289	NP_115665	Q9BQI7	PSD2_HUMAN	pleckstrin and Sec7 domain containing 2	402	SEC7.				regulation of ARF protein signal transduction	cytoplasm|integral to membrane	ARF guanyl-nucleotide exchange factor activity			ovary(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			ACAGCACTTCGGAAGGTATGG	0.637													9	82	---	---	---	---	PASS
PCDHA2	56146	broad.mit.edu	37	5	140176553	140176553	+	Silent	SNP	G	A	A			TCGA-EJ-5497-01A-02D-1576-08	TCGA-EJ-5497-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140176553G>A	uc003lhd.2	+	1	2110	c.2004G>A	c.(2002-2004)TCG>TCA	p.S668S	PCDHA1_uc003lha.2_Intron|PCDHA1_uc003lhb.2_Intron|PCDHA2_uc003lhc.1_Silent_p.S668S|PCDHA2_uc011czy.1_Silent_p.S668S	NM_018905	NP_061728	Q9Y5H9	PCDA2_HUMAN	protocadherin alpha 2 isoform 1 precursor	668	Cadherin 6.|Extracellular (Potential).				homophilic cell adhesion|nervous system development	integral to plasma membrane	calcium ion binding|protein binding			ovary(4)	4			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TGTTAGTGTCGTTGGTGGAAA	0.652													11	126	---	---	---	---	PASS
SNRNP48	154007	broad.mit.edu	37	6	7601562	7601562	+	Intron	SNP	A	T	T			TCGA-EJ-5497-01A-02D-1576-08	TCGA-EJ-5497-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:7601562A>T	uc003mxr.2	+						SNRNP48_uc003mxs.2_RNA	NM_152551	NP_689764	Q6IEG0	SNR48_HUMAN	U11/U12 snRNP 48K						mRNA processing	cytoplasm|U12-type spliceosomal complex	metal ion binding				0						TTTTATTTTTACTTTAGGAAT	0.289													4	117	---	---	---	---	PASS
TMEM14B	81853	broad.mit.edu	37	6	10756854	10756854	+	3'UTR	SNP	C	T	T			TCGA-EJ-5497-01A-02D-1576-08	TCGA-EJ-5497-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:10756854C>T	uc003mzk.3	+	6					SYCP2L_uc011dim.1_Intron|TMEM14B_uc010jor.2_3'UTR|TMEM14B_uc010jos.1_Intron	NM_030969	NP_112231	Q9NUH8	TM14B_HUMAN	transmembrane protein 14B isoform a							integral to membrane					0	Ovarian(93;0.107)|Breast(50;0.137)	all_hematologic(90;0.135)				TTGCATCTGACATTTTACCTA	0.373													4	20	---	---	---	---	PASS
BAT2	7916	broad.mit.edu	37	6	31595605	31595605	+	Silent	SNP	C	A	A			TCGA-EJ-5497-01A-02D-1576-08	TCGA-EJ-5497-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:31595605C>A	uc003nvb.3	+	12	1603	c.1354C>A	c.(1354-1356)CGA>AGA	p.R452R	BAT2_uc011dnv.1_RNA|BAT2_uc003nvc.3_Silent_p.R452R	NM_080686	NP_542417	P48634	PRC2A_HUMAN	HLA-B associated transcript-2	452	4 X 57 AA type A repeats.|2 X type B repeats.					cytoplasm|nucleus	protein binding				0						ATGGCGGCAGCGACGAAAGCA	0.642													3	64	---	---	---	---	PASS
PBX2	5089	broad.mit.edu	37	6	32157563	32157563	+	Missense_Mutation	SNP	C	A	A			TCGA-EJ-5497-01A-02D-1576-08	TCGA-EJ-5497-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:32157563C>A	uc003oav.1	-	1	401	c.130G>T	c.(130-132)GTC>TTC	p.V44F	PBX2_uc003oaw.2_Missense_Mutation_p.V44F	NM_002586	NP_002577	P40425	PBX2_HUMAN	pre-B-cell leukemia homeobox 2	44							transcription factor binding			ovary(1)	1						CCTCCCGGGACCCCCCCGCTA	0.607													3	38	---	---	---	---	PASS
RSPH4A	345895	broad.mit.edu	37	6	116948990	116948990	+	Missense_Mutation	SNP	C	T	T			TCGA-EJ-5497-01A-02D-1576-08	TCGA-EJ-5497-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:116948990C>T	uc003pxe.2	+	3	1265	c.1120C>T	c.(1120-1122)CGT>TGT	p.R374C	RSPH4A_uc010kee.2_Missense_Mutation_p.R374C	NM_001010892	NP_001010892	Q5TD94	RSH4A_HUMAN	radial spoke head 4 homolog A isoform 1	374	Glu-rich.				cilium axoneme assembly|cilium movement	cytoplasm|cytoskeleton|radial spoke					0						AGTGGAATTTCGTgaggggga	0.239									Kartagener_syndrome				18	100	---	---	---	---	PASS
SYNE1	23345	broad.mit.edu	37	6	152639275	152639275	+	Missense_Mutation	SNP	T	C	C			TCGA-EJ-5497-01A-02D-1576-08	TCGA-EJ-5497-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:152639275T>C	uc010kiw.2	-	86	17115	c.16513A>G	c.(16513-16515)ACT>GCT	p.T5505A	SYNE1_uc010kiv.2_Missense_Mutation_p.T29A|SYNE1_uc003qos.3_Missense_Mutation_p.T29A|SYNE1_uc003qot.3_Missense_Mutation_p.T5434A|SYNE1_uc003qou.3_Missense_Mutation_p.T5505A|SYNE1_uc010kiz.2_Missense_Mutation_p.T1260A	NM_182961	NP_892006	Q8NF91	SYNE1_HUMAN	spectrin repeat containing, nuclear envelope 1	5505	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)		TGAAGTTCAGTCAGTTTTCCT	0.448										HNSCC(10;0.0054)			9	188	---	---	---	---	PASS
SLC22A2	6582	broad.mit.edu	37	6	160671507	160671507	+	Intron	SNP	C	T	T			TCGA-EJ-5497-01A-02D-1576-08	TCGA-EJ-5497-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:160671507C>T	uc003qtf.2	-						SLC22A2_uc003qte.1_Intron|SLC22A2_uc003qth.1_3'UTR	NM_003058	NP_003049	O15244	S22A2_HUMAN	solute carrier family 22 member 2						body fluid secretion|neurotransmitter biosynthetic process|neurotransmitter secretion	integral to plasma membrane|membrane fraction	neurotransmitter transporter activity|organic cation transmembrane transporter activity			breast(1)|skin(1)	2		Breast(66;0.000776)|Ovarian(120;0.0303)		OV - Ovarian serous cystadenocarcinoma(65;2.28e-17)|BRCA - Breast invasive adenocarcinoma(81;6.29e-06)		TTCTTGCATGCCGCCCCCCAC	0.423													4	100	---	---	---	---	PASS
CARD11	84433	broad.mit.edu	37	7	2946346	2946346	+	Missense_Mutation	SNP	G	T	T			TCGA-EJ-5497-01A-02D-1576-08	TCGA-EJ-5497-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:2946346G>T	uc003smv.2	-	25	3795	c.3391C>A	c.(3391-3393)CTG>ATG	p.L1131M		NM_032415	NP_115791	Q9BXL7	CAR11_HUMAN	caspase recruitment domain family, member 11	1131	Guanylate kinase-like.				positive regulation of cytokine production|positive regulation of NF-kappaB transcription factor activity|regulation of apoptosis|T cell costimulation|T cell receptor signaling pathway	cytosol|membrane raft|plasma membrane	CARD domain binding|guanylate kinase activity			haematopoietic_and_lymphoid_tissue(43)|ovary(2)|kidney(2)|skin(2)|central_nervous_system(1)	50		Ovarian(82;0.0115)		OV - Ovarian serous cystadenocarcinoma(56;8.44e-14)		ACGCGGAGCAGCTCCTCTACG	0.657			Mis		DLBCL								7	102	---	---	---	---	PASS
POM121	9883	broad.mit.edu	37	7	72413243	72413243	+	Missense_Mutation	SNP	A	C	C			TCGA-EJ-5497-01A-02D-1576-08	TCGA-EJ-5497-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:72413243A>C	uc003twk.2	+	11	2711	c.2711A>C	c.(2710-2712)CAC>CCC	p.H904P	POM121_uc003twj.2_Missense_Mutation_p.H639P|POM121_uc010lam.1_Missense_Mutation_p.H639P	NM_172020	NP_742017	Q96HA1	P121A_HUMAN	nuclear pore membrane protein 121	904	Thr-rich.|Pore side (Potential).			H -> P (in Ref. 3; BAB14097).	carbohydrate metabolic process|glucose transport|mRNA transport|protein transport|regulation of glucose transport|transmembrane transport|viral reproduction	endoplasmic reticulum membrane|nuclear membrane|nuclear pore					0		Lung NSC(55;0.163)				CAGTCCCTGCACACTGCCGTG	0.647													4	127	---	---	---	---	PASS
KRBA1	84626	broad.mit.edu	37	7	149431015	149431015	+	Missense_Mutation	SNP	C	G	G			TCGA-EJ-5497-01A-02D-1576-08	TCGA-EJ-5497-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:149431015C>G	uc003wfz.2	+	18	3371	c.2972C>G	c.(2971-2973)GCA>GGA	p.A991G	KRBA1_uc010lpj.2_RNA|KRBA1_uc003wga.2_RNA|KRBA1_uc003wgb.2_Missense_Mutation_p.A598G	NM_032534	NP_115923	A5PL33	KRBA1_HUMAN	KRAB A domain containing 1	991	Pro-rich.									ovary(1)|central_nervous_system(1)	2	Melanoma(164;0.165)|Ovarian(565;0.177)		OV - Ovarian serous cystadenocarcinoma(82;0.00625)			TCAGGAGTGGCACCAGACGGG	0.667													2	10	---	---	---	---	PASS
RIPK2	8767	broad.mit.edu	37	8	90801576	90801576	+	Missense_Mutation	SNP	A	G	G			TCGA-EJ-5497-01A-02D-1576-08	TCGA-EJ-5497-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:90801576A>G	uc003yee.2	+	10	1465	c.1151A>G	c.(1150-1152)AAG>AGG	p.K384R	RIPK2_uc003yef.2_Missense_Mutation_p.K247R	NM_003821	NP_003812	O43353	RIPK2_HUMAN	receptor-interacting serine-threonine kinase 2	384					activation of MAPK activity|anti-apoptosis|apoptosis|inflammatory response|innate immune response|JNK cascade|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|nerve growth factor receptor signaling pathway|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of NF-kappaB transcription factor activity|positive regulation of protein ubiquitination|stress-activated MAPK cascade|T cell receptor signaling pathway|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	cytosol	ATP binding|CARD domain binding|LIM domain binding|protein homodimerization activity|protein serine/threonine kinase activity|signal transducer activity			ovary(2)	2			BRCA - Breast invasive adenocarcinoma(11;0.0474)			TATTTTATGAAGCTGCATCAC	0.398													6	259	---	---	---	---	PASS
HSF1	3297	broad.mit.edu	37	8	145534873	145534873	+	Silent	SNP	C	T	T			TCGA-EJ-5497-01A-02D-1576-08	TCGA-EJ-5497-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:145534873C>T	uc003zbt.3	+	5	672	c.502C>T	c.(502-504)CTG>TTG	p.L168L	HSF1_uc003zbu.3_RNA	NM_005526	NP_005517	Q00613	HSF1_HUMAN	heat shock transcription factor 1	168	Hydrophobic repeat HR-A/B.					cytoplasm	protein binding|sequence-specific DNA binding transcription factor activity				0	all_cancers(97;6.64e-12)|all_epithelial(106;2.89e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;3.94e-40)|Epithelial(56;1.12e-39)|all cancers(56;9.11e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0547)|Colorectal(110;0.055)			GAATGAGGCTCTGTGGCGGGA	0.667													3	3	---	---	---	---	PASS
FAM75A3	727830	broad.mit.edu	37	9	40702847	40702847	+	Silent	SNP	C	A	A			TCGA-EJ-5497-01A-02D-1576-08	TCGA-EJ-5497-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:40702847C>A	uc010mmj.2	+	4	533	c.504C>A	c.(502-504)ACC>ACA	p.T168T		NM_001083124	NP_001076593	Q5VYP0	F75A3_HUMAN	hypothetical protein LOC727830	168	Pro-rich.					integral to membrane				ovary(2)|skin(1)	3				GBM - Glioblastoma multiforme(29;0.02)|Lung(182;0.0681)		TGGCCTCCACCCCATCACCAG	0.597													17	374	---	---	---	---	PASS
SVEP1	79987	broad.mit.edu	37	9	113208250	113208250	+	Missense_Mutation	SNP	T	G	G	rs7863519	by1000genomes	TCGA-EJ-5497-01A-02D-1576-08	TCGA-EJ-5497-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:113208250T>G	uc010mtz.2	-	26	4667	c.4330A>C	c.(4330-4332)ATG>CTG	p.M1444L	SVEP1_uc010mua.1_Missense_Mutation_p.M1444L	NM_153366	NP_699197	Q4LDE5	SVEP1_HUMAN	polydom	1444	Pentaxin.				cell adhesion	cytoplasm|extracellular region|membrane	calcium ion binding			ovary(7)	7						GATGGGAGCATGCCATCTAGC	0.438													3	115	---	---	---	---	PASS
LPAR1	1902	broad.mit.edu	37	9	113703743	113703743	+	Missense_Mutation	SNP	C	T	T			TCGA-EJ-5497-01A-02D-1576-08	TCGA-EJ-5497-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:113703743C>T	uc004bfa.2	-	4	1006	c.751G>A	c.(751-753)GAT>AAT	p.D251N	LPAR1_uc011lwm.1_Missense_Mutation_p.D252N|LPAR1_uc004bfb.2_Missense_Mutation_p.D251N|LPAR1_uc004bfc.2_Missense_Mutation_p.D251N|LPAR1_uc011lwn.1_Missense_Mutation_p.D233N|LPAR1_uc011lwo.1_Missense_Mutation_p.D252N|LPAR1_uc010mub.2_Missense_Mutation_p.D251N	NM_057159	NP_476500	Q92633	LPAR1_HUMAN	lysophosphatidic acid receptor 1	251	Cytoplasmic (Potential).				positive regulation of I-kappaB kinase/NF-kappaB cascade	cell surface|integral to plasma membrane				ovary(2)	2						ATCATGGTATCCCGATTCCGC	0.443													24	98	---	---	---	---	PASS
HNRNPA3P1	10151	broad.mit.edu	37	10	44284972	44284972	+	3'UTR	SNP	A	C	C			TCGA-EJ-5497-01A-02D-1576-08	TCGA-EJ-5497-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:44284972A>C	uc010qfe.1	-	1						NR_002726				SubName: Full=cDNA FLJ52659, highly similar to Heterogeneous nuclear ribonucleoprotein A3; SubName: Full=cDNA, FLJ79333, highly similar to Heterogeneous nuclear ribonucleoprotein A3; SubName: Full=Heterogeneous nuclear ribonucleoprotein A3, isoform CRA_a;												0						ccaccaccatacccgcctcta	0.199													4	59	---	---	---	---	PASS
UNC5B	219699	broad.mit.edu	37	10	73050857	73050857	+	Missense_Mutation	SNP	G	A	A			TCGA-EJ-5497-01A-02D-1576-08	TCGA-EJ-5497-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:73050857G>A	uc001jro.2	+	9	1730	c.1285G>A	c.(1285-1287)GCA>ACA	p.A429T	UNC5B_uc001jrp.2_Missense_Mutation_p.A418T	NM_170744	NP_734465	Q8IZJ1	UNC5B_HUMAN	unc-5 homolog B precursor	429	Cytoplasmic (Potential).				apoptosis|axon guidance|regulation of apoptosis	integral to membrane				ovary(2)|lung(1)	3						CTTTAAGACGGCAAGGCCCAG	0.597													7	330	---	---	---	---	PASS
MBL1P	8512	broad.mit.edu	37	10	81666473	81666473	+	RNA	SNP	A	G	G			TCGA-EJ-5497-01A-02D-1576-08	TCGA-EJ-5497-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:81666473A>G	uc001kbf.2	+	2		c.298A>G								Homo sapiens mannose-binding protein-A pseudogene (MBL1P1) mRNA sequence.												0						GAAGATGCCCAGAAGAGAAAT	0.438													5	94	---	---	---	---	PASS
OR9G4	283189	broad.mit.edu	37	11	56511197	56511197	+	Missense_Mutation	SNP	C	T	T			TCGA-EJ-5497-01A-02D-1576-08	TCGA-EJ-5497-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:56511197C>T	uc010rjo.1	-	1	91	c.91G>A	c.(91-93)GGT>AGT	p.G31S		NM_001005284	NP_001005284	Q8NGQ1	OR9G4_HUMAN	olfactory receptor, family 9, subfamily G,	31	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(2)|skin(1)	3						GCTGAGAAACCCAACAAGATG	0.428													4	107	---	---	---	---	PASS
NCAPD3	23310	broad.mit.edu	37	11	134054637	134054637	+	Silent	SNP	C	T	T			TCGA-EJ-5497-01A-02D-1576-08	TCGA-EJ-5497-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:134054637C>T	uc001qhd.1	-	19	2952	c.2346G>A	c.(2344-2346)AAG>AAA	p.K782K	NCAPD3_uc010scm.1_RNA|NCAPD3_uc009zda.1_RNA	NM_015261	NP_056076	P42695	CNDD3_HUMAN	non-SMC condensin II complex, subunit D3	782					cell division|mitotic chromosome condensation	nuclear centromeric heterochromatin|nuclear condensin complex	methylated histone residue binding			ovary(2)|upper_aerodigestive_tract(1)|lung(1)|kidney(1)	5	all_hematologic(175;0.127)	all_cancers(12;1.68e-21)|all_epithelial(12;5.86e-16)|all_lung(97;1.19e-05)|Lung NSC(97;2.76e-05)|Breast(109;0.000182)|Medulloblastoma(222;0.0245)|all_neural(223;0.0505)|Esophageal squamous(93;0.0559)		Epithelial(10;8.74e-10)|BRCA - Breast invasive adenocarcinoma(10;1e-08)|all cancers(11;1.46e-08)|OV - Ovarian serous cystadenocarcinoma(99;0.00345)|Lung(977;0.227)		TCAGCTTACACTTGACAGCAT	0.368													19	96	---	---	---	---	PASS
RPL13AP20	387841	broad.mit.edu	37	12	13028952	13028952	+	Missense_Mutation	SNP	T	C	C			TCGA-EJ-5497-01A-02D-1576-08	TCGA-EJ-5497-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:13028952T>C	uc010sho.1	+	1	542	c.520T>C	c.(520-522)TTC>CTC	p.F174L		NR_003932				SubName: Full=Ribosomal protein L13a variant; Flags: Fragment;												0						GAAGAAACAGTTCATGAGGCT	0.512													2	12	---	---	---	---	PASS
ANKRD52	283373	broad.mit.edu	37	12	56639366	56639366	+	Missense_Mutation	SNP	A	C	C			TCGA-EJ-5497-01A-02D-1576-08	TCGA-EJ-5497-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:56639366A>C	uc001skm.3	-	21	2289	c.2199T>G	c.(2197-2199)TGT>TGG	p.C733W		NM_173595	NP_775866	Q8NB46	ANR52_HUMAN	ankyrin repeat domain 52	733	ANK 21.						protein binding			ovary(2)	2						GGCAGTCCTCACAGCCAGTCA	0.592													8	35	---	---	---	---	PASS
LOC284232	284232	broad.mit.edu	37	13	19415778	19415778	+	RNA	SNP	C	A	A	rs2801692		TCGA-EJ-5497-01A-02D-1576-08	TCGA-EJ-5497-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:19415778C>A	uc010tcj.1	-	1		c.30332G>T				NR_027995				Homo sapiens ankyrin repeat domain 20 family, member A2 pseudogene (LOC284232), non-coding RNA.												0						TCAGCAGCAGCAGAAGATGTA	0.308													4	80	---	---	---	---	PASS
LMO7	4008	broad.mit.edu	37	13	76374992	76374992	+	5'UTR	SNP	A	G	G			TCGA-EJ-5497-01A-02D-1576-08	TCGA-EJ-5497-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:76374992A>G	uc001vjv.2	+	4					LMO7_uc010thv.1_Missense_Mutation_p.D264G|LMO7_uc001vjt.1_Missense_Mutation_p.D212G|LMO7_uc010thw.1_Missense_Mutation_p.D173G|LMO7_uc001vju.1_RNA	NM_015842	NP_056667	Q8WWI1	LMO7_HUMAN	LIM domain only 7 isoform 2							cytoplasm|nucleus|ubiquitin ligase complex	ubiquitin-protein ligase activity|zinc ion binding			large_intestine(2)|ovary(1)|prostate(1)|skin(1)	5		Breast(118;0.0992)		GBM - Glioblastoma multiforme(99;0.0109)		TGCTCCTCTGATATCACGTTG	0.458													14	328	---	---	---	---	PASS
GPHN	10243	broad.mit.edu	37	14	67525623	67525623	+	Intron	SNP	C	A	A			TCGA-EJ-5497-01A-02D-1576-08	TCGA-EJ-5497-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:67525623C>A	uc001xiy.2	+						GPHN_uc001xiw.2_3'UTR|GPHN_uc001xix.2_Intron|GPHN_uc010tss.1_Intron|GPHN_uc010tst.1_Intron|GPHN_uc010tsu.1_Intron	NM_001024218	NP_001019389	Q9NQX3	GEPH_HUMAN	gephyrin isoform 2						Mo-molybdopterin cofactor biosynthetic process|water-soluble vitamin metabolic process	cell junction|cytoplasm|cytoskeleton|postsynaptic membrane	ATP binding|metal ion binding|nucleotidyltransferase activity			ovary(2)	2		all_cancers(7;0.0476)|all_hematologic(31;0.0116)		Epithelial(1;1.73e-08)|all cancers(60;3.15e-07)|OV - Ovarian serous cystadenocarcinoma(108;0.000275)|BRCA - Breast invasive adenocarcinoma(234;0.00323)|Colorectal(3;0.0938)|KIRC - Kidney renal clear cell carcinoma(182;0.184)		TTACAGTTATCATCATTCTTT	0.284			T	MLL	AL								3	59	---	---	---	---	PASS
SIPA1L1	26037	broad.mit.edu	37	14	72054698	72054698	+	Missense_Mutation	SNP	C	T	T			TCGA-EJ-5497-01A-02D-1576-08	TCGA-EJ-5497-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:72054698C>T	uc001xms.2	+	2	457	c.109C>T	c.(109-111)CGG>TGG	p.R37W	SIPA1L1_uc001xmt.2_Missense_Mutation_p.R37W|SIPA1L1_uc001xmu.2_Missense_Mutation_p.R37W|SIPA1L1_uc001xmv.2_Missense_Mutation_p.R37W	NM_015556	NP_056371	O43166	SI1L1_HUMAN	signal-induced proliferation-associated 1 like	37					actin cytoskeleton reorganization|activation of Rap GTPase activity|regulation of dendritic spine morphogenesis	cell junction|cytoplasm|dendritic spine|postsynaptic density|postsynaptic membrane|synaptosome	GTPase activator activity			ovary(3)|breast(1)	4				all cancers(60;0.00169)|BRCA - Breast invasive adenocarcinoma(234;0.00912)|OV - Ovarian serous cystadenocarcinoma(108;0.0109)		TTTCTACATGCGGCGCTTCCG	0.547													7	190	---	---	---	---	PASS
ADAM6	8755	broad.mit.edu	37	14	106866661	106866661	+	RNA	SNP	T	G	G			TCGA-EJ-5497-01A-02D-1576-08	TCGA-EJ-5497-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:106866661T>G	uc010tyt.1	-	281		c.11570A>C								Parts of antibodies, mostly variable regions.												0						CCCTAGGCTGTACCAAGCCTC	0.582													4	169	---	---	---	---	PASS
VPS13C	54832	broad.mit.edu	37	15	62146723	62146723	+	Missense_Mutation	SNP	G	A	A			TCGA-EJ-5497-01A-02D-1576-08	TCGA-EJ-5497-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:62146723G>A	uc002agz.2	-	85	11269	c.11195C>T	c.(11194-11196)ACG>ATG	p.T3732M	VPS13C_uc002aha.2_Missense_Mutation_p.T3689M	NM_020821	NP_065872	Q709C8	VP13C_HUMAN	vacuolar protein sorting 13C protein isoform 2A	3732					protein localization					ovary(2)	2						CTGCTGTCTCGTTGACTGTGC	0.408													10	453	---	---	---	---	PASS
ADAMTS7	11173	broad.mit.edu	37	15	79067063	79067063	+	Silent	SNP	A	G	G	rs117662146	byFrequency	TCGA-EJ-5497-01A-02D-1576-08	TCGA-EJ-5497-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:79067063A>G	uc002bej.3	-	12	1990	c.1779T>C	c.(1777-1779)CCT>CCC	p.P593P	ADAMTS7_uc010und.1_Intron|ADAMTS7_uc002bek.1_Silent_p.P593P	NM_014272	NP_055087	Q9UKP4	ATS7_HUMAN	ADAM metallopeptidase with thrombospondin type 1	593	TSP type-1 1.				proteolysis	proteinaceous extracellular matrix	metalloendopeptidase activity|zinc ion binding				0						GGCGGCCAGCAGGGCAGGCCT	0.642													9	57	---	---	---	---	PASS
ADAMTS7	11173	broad.mit.edu	37	15	79067065	79067065	+	Missense_Mutation	SNP	G	A	A			TCGA-EJ-5497-01A-02D-1576-08	TCGA-EJ-5497-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:79067065G>A	uc002bej.3	-	12	1988	c.1777C>T	c.(1777-1779)CCT>TCT	p.P593S	ADAMTS7_uc010und.1_Intron|ADAMTS7_uc002bek.1_Missense_Mutation_p.P593S	NM_014272	NP_055087	Q9UKP4	ATS7_HUMAN	ADAM metallopeptidase with thrombospondin type 1	593	TSP type-1 1.				proteolysis	proteinaceous extracellular matrix	metalloendopeptidase activity|zinc ion binding				0						CGGCCAGCAGGGCAGGCCTGC	0.642													8	62	---	---	---	---	PASS
LASS3	204219	broad.mit.edu	37	15	101013167	101013167	+	Missense_Mutation	SNP	C	A	A			TCGA-EJ-5497-01A-02D-1576-08	TCGA-EJ-5497-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:101013167C>A	uc002bvz.2	-	10	1202	c.700G>T	c.(700-702)GTG>TTG	p.V234L	LASS3_uc002bwa.2_Missense_Mutation_p.V245L|LASS3_uc002bwb.2_Missense_Mutation_p.V234L	NM_178842	NP_849164	Q8IU89	CERS3_HUMAN	LAG1 longevity assurance homolog 3	234	TLC.					endoplasmic reticulum membrane|integral to membrane|nuclear membrane	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|sphingosine N-acyltransferase activity			ovary(2)|pancreas(1)|skin(1)	4	Lung NSC(78;0.0018)|all_lung(78;0.00278)|Melanoma(26;0.00852)		OV - Ovarian serous cystadenocarcinoma(32;0.000867)|LUSC - Lung squamous cell carcinoma(107;0.132)|Lung(145;0.161)			ACAATCATCACGAGGGTCCCA	0.438													18	149	---	---	---	---	PASS
C17orf97	400566	broad.mit.edu	37	17	263705	263705	+	Silent	SNP	C	T	T	rs149163238	byFrequency	TCGA-EJ-5497-01A-02D-1576-08	TCGA-EJ-5497-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:263705C>T	uc002frh.2	+	3	1117	c.1101C>T	c.(1099-1101)CCC>CCT	p.P367P	C17orf97_uc010vpz.1_RNA	NM_001013672	NP_001013694	Q6ZQX7	CQ097_HUMAN	hypothetical protein LOC400566	387	20 X 10 AA approximative tandem repeat of A-L-K-G-F-H-P-D-P-E.|19.									ovary(1)	1						GCTTCCACCCCGACCCCGAGG	0.672													3	58	---	---	---	---	PASS
ZBTB4	57659	broad.mit.edu	37	17	7366921	7366921	+	Silent	SNP	T	G	G			TCGA-EJ-5497-01A-02D-1576-08	TCGA-EJ-5497-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:7366921T>G	uc002ghc.3	-	4	1630	c.1380A>C	c.(1378-1380)CCA>CCC	p.P460P	ZBTB4_uc002ghd.3_Silent_p.P460P	NM_001128833	NP_001122305	Q9P1Z0	ZBTB4_HUMAN	zinc finger and BTB domain containing 4	460	Pro-rich.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			skin(2)|ovary(1)|central_nervous_system(1)	4		Colorectal(1115;3.46e-05)|Myeloproliferative disorder(207;0.0255)		COAD - Colon adenocarcinoma(228;4.1e-06)|READ - Rectum adenocarcinoma(115;0.0642)		CTGGGGCAGGTGGAGGCCCAG	0.667													7	26	---	---	---	---	PASS
ALDOC	230	broad.mit.edu	37	17	26901519	26901519	+	Missense_Mutation	SNP	G	T	T			TCGA-EJ-5497-01A-02D-1576-08	TCGA-EJ-5497-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:26901519G>T	uc002hbp.2	-	6	762	c.617C>A	c.(616-618)ACA>AAA	p.T206K	PIGS_uc002hbo.2_5'Flank|PIGS_uc010wap.1_5'Flank|ALDOC_uc010cro.2_Intron	NM_005165	NP_005156	P09972	ALDOC_HUMAN	fructose-bisphosphate aldolase C	206					fructose 1,6-bisphosphate metabolic process|gluconeogenesis|glycolysis	cytosol	cytoskeletal protein binding|fructose-bisphosphate aldolase activity			ovary(1)	1	Lung NSC(42;0.00431)					CACCTTCTCTGTAACATACTG	0.517													12	314	---	---	---	---	PASS
BAHCC1	57597	broad.mit.edu	37	17	79409621	79409621	+	Missense_Mutation	SNP	G	A	A			TCGA-EJ-5497-01A-02D-1576-08	TCGA-EJ-5497-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:79409621G>A	uc002kaf.2	+	3	1246	c.1246G>A	c.(1246-1248)GTG>ATG	p.V416M	BAHCC1_uc002kae.2_5'Flank	NM_001080519	NP_001073988	Q9P281	BAHC1_HUMAN	BAH domain and coiled-coil containing 1	416							DNA binding			ovary(1)	1	all_neural(118;0.0804)|Melanoma(429;0.242)		BRCA - Breast invasive adenocarcinoma(99;0.0224)|OV - Ovarian serous cystadenocarcinoma(97;0.116)			GGCCTGTGCCGTGGCAGGGGA	0.701													6	11	---	---	---	---	PASS
ST8SIA3	51046	broad.mit.edu	37	18	55027527	55027527	+	3'UTR	SNP	G	A	A			TCGA-EJ-5497-01A-02D-1576-08	TCGA-EJ-5497-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:55027527G>A	uc002lgn.2	+	4						NM_015879	NP_056963	O43173	SIA8C_HUMAN	ST8 alpha-N-acetyl-neuraminide						glycosphingolipid biosynthetic process|N-glycan processing|post-translational protein modification|protein N-linked glycosylation via asparagine	integral to Golgi membrane	alpha-N-acetylneuraminate alpha-2,8-sialyltransferase activity			breast(1)|skin(1)	2				READ - Rectum adenocarcinoma(59;0.19)|Colorectal(16;0.205)		AACGGAAAGCGCCAAATGGCT	0.458													6	40	---	---	---	---	PASS
FAM108A1	81926	broad.mit.edu	37	19	1881418	1881418	+	Missense_Mutation	SNP	C	T	T			TCGA-EJ-5497-01A-02D-1576-08	TCGA-EJ-5497-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:1881418C>T	uc002lug.2	-	2	554	c.148G>A	c.(148-150)GCC>ACC	p.A50T	FAM108A1_uc002lud.2_Missense_Mutation_p.A50T|FAM108A1_uc002lue.2_Missense_Mutation_p.A50T|FAM108A1_uc002luf.2_Missense_Mutation_p.A50T	NM_001130111	NP_001123583	Q96GS6	F18A1_HUMAN	hypothetical protein LOC81926 isoform 2	50						extracellular region	hydrolase activity				0		Ovarian(11;0.000137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		AAGGGGGCGGCCCCGGCCCCA	0.751													4	35	---	---	---	---	PASS
ZNF333	84449	broad.mit.edu	37	19	14829747	14829747	+	Silent	SNP	C	T	T			TCGA-EJ-5497-01A-02D-1576-08	TCGA-EJ-5497-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:14829747C>T	uc002mzn.2	+	12	1742	c.1608C>T	c.(1606-1608)TGC>TGT	p.C536C	ZNF333_uc002mzk.3_Silent_p.C427C	NM_032433	NP_115809	Q96JL9	ZN333_HUMAN	zinc finger protein 333	536	C2H2-type 7.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)|central_nervous_system(1)|pancreas(1)	3						TGTATGAGTGCGCGACTTGCG	0.527													13	76	---	---	---	---	PASS
ZNF181	339318	broad.mit.edu	37	19	35232875	35232875	+	Nonsense_Mutation	SNP	C	G	G			TCGA-EJ-5497-01A-02D-1576-08	TCGA-EJ-5497-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:35232875C>G	uc002nvu.3	+	4	2052	c.1589C>G	c.(1588-1590)TCA>TGA	p.S530*	ZNF181_uc010xsa.1_Nonsense_Mutation_p.S529*|ZNF181_uc010xsb.1_Nonsense_Mutation_p.S529*|ZNF181_uc010xsc.1_Nonsense_Mutation_p.S465*	NM_001029997	NP_001025168	Q2M3W8	ZN181_HUMAN	zinc finger protein 181 isoform 1	530	C2H2-type 11.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1	all_lung(56;1.13e-07)|Lung NSC(56;1.81e-07)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.138)			AGCAAAGGCTCAAATCTTACT	0.388													5	201	---	---	---	---	PASS
PRODH2	58510	broad.mit.edu	37	19	36297714	36297714	+	Missense_Mutation	SNP	C	T	T			TCGA-EJ-5497-01A-02D-1576-08	TCGA-EJ-5497-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:36297714C>T	uc002obx.1	-	7	943	c.925G>A	c.(925-927)GTG>ATG	p.V309M		NM_021232	NP_067055	Q9UF12	PROD2_HUMAN	kidney and liver proline oxidase 1	309					glutamate biosynthetic process|proline catabolic process		proline dehydrogenase activity			ovary(2)	2	all_lung(56;2.87e-07)|Lung NSC(56;4.32e-07)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0515)			AGGAGCCGCACGTGCTGGGCC	0.682													4	17	---	---	---	---	PASS
CYP2A7	1549	broad.mit.edu	37	19	41533022	41533022	+	Intron	SNP	G	C	C			TCGA-EJ-5497-01A-02D-1576-08	TCGA-EJ-5497-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:41533022G>C	uc002opo.2	-						uc002ops.1_RNA	NM_000764	NP_000755	P20853	CP2A7_HUMAN	cytochrome P450, family 2, subfamily A,							endoplasmic reticulum membrane|microsome	aromatase activity|electron carrier activity|heme binding|oxygen binding			ovary(1)|haematopoietic_and_lymphoid_tissue(1)|skin(1)	3			LUSC - Lung squamous cell carcinoma(20;0.000219)|Lung(22;0.000959)			CCTTTGAAGAGCCAGTCGAAG	0.662													3	68	---	---	---	---	PASS
DKKL1	27120	broad.mit.edu	37	19	49878289	49878289	+	3'UTR	SNP	T	G	G			TCGA-EJ-5497-01A-02D-1576-08	TCGA-EJ-5497-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:49878289T>G	uc002pnk.2	+	5						NM_014419	NP_055234	Q9UK85	DKKL1_HUMAN	dickkopf-like 1 precursor						anatomical structure morphogenesis	extracellular space	protein binding|signal transducer activity				0		all_lung(116;1.66e-06)|Lung NSC(112;5.89e-06)|all_neural(266;0.0189)|Ovarian(192;0.0392)		OV - Ovarian serous cystadenocarcinoma(262;0.00156)|GBM - Glioblastoma multiforme(486;0.0456)		GCTGTAGGGGTGGGGACCGGG	0.572													6	36	---	---	---	---	PASS
PAK7	57144	broad.mit.edu	37	20	9520008	9520008	+	3'UTR	SNP	T	G	G			TCGA-EJ-5497-01A-02D-1576-08	TCGA-EJ-5497-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:9520008T>G	uc002wnl.2	-	11					PAK7_uc002wnk.2_3'UTR|PAK7_uc002wnj.2_3'UTR|PAK7_uc010gby.1_3'UTR	NM_020341	NP_065074	Q9P286	PAK7_HUMAN	p21-activated kinase 7								ATP binding|protein binding|protein serine/threonine kinase activity			lung(11)|skin(5)|central_nervous_system(3)|ovary(2)|large_intestine(1)|stomach(1)	23			COAD - Colon adenocarcinoma(9;0.194)			AATTGGCTGGTCTAGAATGCA	0.498													12	48	---	---	---	---	PASS
ASXL1	171023	broad.mit.edu	37	20	31021261	31021261	+	Silent	SNP	C	T	T			TCGA-EJ-5497-01A-02D-1576-08	TCGA-EJ-5497-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:31021261C>T	uc002wxs.2	+	11	1686	c.1260C>T	c.(1258-1260)GCC>GCT	p.A420A	ASXL1_uc010geb.2_Silent_p.A311A	NM_015338	NP_056153	Q8IXJ9	ASXL1_HUMAN	additional sex combs like 1 isoform 1	420					chromatin modification|regulation of transcription, DNA-dependent|transcription, DNA-dependent	PR-DUB complex	metal ion binding|protein binding			haematopoietic_and_lymphoid_tissue(239)|large_intestine(6)|central_nervous_system(2)|ovary(1)	248						GAACCAGAGCCAGAAGGAATC	0.527			F|N|Mis		MDS|CMML								5	169	---	---	---	---	PASS
PHF20	51230	broad.mit.edu	37	20	34458923	34458923	+	Silent	SNP	A	G	G			TCGA-EJ-5497-01A-02D-1576-08	TCGA-EJ-5497-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:34458923A>G	uc002xek.1	+	8	1080	c.969A>G	c.(967-969)TTA>TTG	p.L323L	PHF20_uc002xei.1_Silent_p.L323L|PHF20_uc010gfo.1_Silent_p.L323L|PHF20_uc002xej.1_Silent_p.L207L	NM_016436	NP_057520	Q9BVI0	PHF20_HUMAN	PHD finger protein 20	323					regulation of transcription, DNA-dependent|transcription, DNA-dependent	MLL1 complex	DNA binding|zinc ion binding			ovary(1)	1	Breast(12;0.00631)|all_lung(11;0.0145)					ACAAAGACTTATCGAGGAGAC	0.423													7	149	---	---	---	---	PASS
EYA2	2139	broad.mit.edu	37	20	45797830	45797830	+	Missense_Mutation	SNP	A	C	C	rs143610627		TCGA-EJ-5497-01A-02D-1576-08	TCGA-EJ-5497-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:45797830A>C	uc002xsm.2	+	11	1396	c.1022A>C	c.(1021-1023)AAT>ACT	p.N341T	EYA2_uc010ghp.2_Missense_Mutation_p.N341T|EYA2_uc002xsn.2_Missense_Mutation_p.N346T|EYA2_uc002xso.2_Missense_Mutation_p.N341T|EYA2_uc002xsp.2_Missense_Mutation_p.N341T|EYA2_uc002xsq.2_Missense_Mutation_p.N311T	NM_005244	NP_005235	O00167	EYA2_HUMAN	eyes absent 2 isoform a	341					DNA repair|histone dephosphorylation|mesodermal cell fate specification|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	magnesium ion binding|protein binding|protein tyrosine phosphatase activity			ovary(1)	1		Myeloproliferative disorder(115;0.0241)				TCAGATGACAATGGCCAAGAT	0.378													43	196	---	---	---	---	PASS
SMARCB1	6598	broad.mit.edu	37	22	24143165	24143165	+	Missense_Mutation	SNP	C	A	A			TCGA-EJ-5497-01A-02D-1576-08	TCGA-EJ-5497-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:24143165C>A	uc002zyb.2	+	4	604	c.397C>A	c.(397-399)CCC>ACC	p.P133T	SMARCB1_uc002zyg.2_Missense_Mutation_p.P133T|SMARCB1_uc011ajb.1_Missense_Mutation_p.P124T|SMARCB1_uc002zya.2_Missense_Mutation_p.P133T|SMARCB1_uc002zyc.2_Missense_Mutation_p.P124T|SMARCB1_uc002zyd.2_Missense_Mutation_p.P124T|SMARCB1_uc002zye.1_Intron|SMARCB1_uc002zyf.1_Intron|SMARCB1_uc010gue.1_Intron	NM_003073	NP_003064	Q12824	SNF5_HUMAN	SWI/SNF related, matrix associated, actin	133	DNA-binding (Potential).				cell cycle|chromatin remodeling|DNA integration|interspecies interaction between organisms|nervous system development|positive regulation of sequence-specific DNA binding transcription factor activity|positive regulation of transcription from RNA polymerase II promoter|retroviral genome replication|transcription, DNA-dependent	nBAF complex|npBAF complex|nucleolus|nucleoplasm|SWI/SNF complex	p53 binding	p.?(5)|p.S129fs*36(1)		soft_tissue(193)|central_nervous_system(172)|haematopoietic_and_lymphoid_tissue(23)|meninges(5)|skin(5)|bone(4)|ovary(2)|endometrium(1)|lung(1)|pancreas(1)	407		Medulloblastoma(6;2.2e-09)|all_neural(6;2.73e-05)				CCAGTGGGTACCCACCCTGCC	0.557			D|N|F|S		malignant rhabdoid 	malignant rhabdoid			Rhabdoid_Predisposition_syndrome|Schwannomatosis				6	79	---	---	---	---	PASS
SAGE1	55511	broad.mit.edu	37	X	134994389	134994389	+	Intron	SNP	A	G	G			TCGA-EJ-5497-01A-02D-1576-08	TCGA-EJ-5497-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:134994389A>G	uc004ezh.2	+						SAGE1_uc010nry.1_3'UTR|SAGE1_uc011mvv.1_Intron	NM_018666	NP_061136	Q9NXZ1	SAGE1_HUMAN	sarcoma antigen 1											ovary(2)|skin(1)	3	Acute lymphoblastic leukemia(192;0.000127)					GTAGCCCATGAAAAATGTATA	0.289													3	13	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	M	13326	13326	+	RNA	SNP	T	C	C			TCGA-EJ-5497-01A-02D-1576-08	TCGA-EJ-5497-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrM:13326T>C	uc004cox.3	+	1		c.990T>C			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.																		CTGCACATCTGTACCCACGCC	0.423													2	8	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	M	13680	13680	+	RNA	SNP	C	T	T			TCGA-EJ-5497-01A-02D-1576-08	TCGA-EJ-5497-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrM:13680C>T	uc004cox.3	+	1		c.1344C>T			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.																		GAAAATAACCCCACCCTACTA	0.488													5	6	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	M	14872	14872	+	Missense_Mutation	SNP	C	T	T			TCGA-EJ-5497-01A-02D-1576-08	TCGA-EJ-5497-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrM:14872C>T	uc004coy.2	+	1	112	c.37C>T	c.(37-39)CCT>TCT	p.P13S	uc004coz.1_5'Flank					Homo sapiens clone 35w unknown mRNA; mitochondrial.																		GCCTGCCTGATCCTCCAAATC	0.488													3	13	---	---	---	---	PASS
MEGF6	1953	broad.mit.edu	37	1	3408980	3408981	+	Intron	DEL	CT	-	-	rs3838972		TCGA-EJ-5497-01A-02D-1576-08	TCGA-EJ-5497-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:3408980_3408981delCT	uc001akl.2	-						MEGF6_uc001akk.2_Intron	NM_001409	NP_001400	O75095	MEGF6_HUMAN	EGF-like-domain, multiple 3 precursor							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)		TGGCCCACCCCTGTCCCCTGGT	0.589													5	3	---	---	---	---	
C1orf109	54955	broad.mit.edu	37	1	38155687	38155688	+	Intron	INS	-	T	T			TCGA-EJ-5497-01A-02D-1576-08	TCGA-EJ-5497-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:38155687_38155688insT	uc001cbp.2	-						C1orf109_uc010oig.1_Intron|C1orf109_uc001cbo.2_Intron|C1orf109_uc001cbq.1_Intron|CDCA8_uc001cbr.2_5'Flank|CDCA8_uc001cbs.2_5'Flank|CDCA8_uc010oih.1_5'Flank	NM_017850	NP_060320	Q9NX04	CA109_HUMAN	hypothetical protein LOC54955												0		Myeloproliferative disorder(586;0.0393)				CAGAAGCAGGGttttttttttg	0.297													3	3	---	---	---	---	
CACHD1	57685	broad.mit.edu	37	1	65100054	65100057	+	Intron	DEL	TATG	-	-	rs151171151	by1000genomes	TCGA-EJ-5497-01A-02D-1576-08	TCGA-EJ-5497-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:65100054_65100057delTATG	uc001dbo.1	+						CACHD1_uc001dbp.1_Intron|CACHD1_uc001dbq.1_Intron	NM_020925	NP_065976	Q5VU97	CAHD1_HUMAN	cache domain containing 1						calcium ion transport	integral to membrane				ovary(2)	2						tttatttatttatgtatgtattta	0.142													1	6	---	---	---	---	
LRRC7	57554	broad.mit.edu	37	1	70501626	70501626	+	Intron	DEL	A	-	-	rs145583703		TCGA-EJ-5497-01A-02D-1576-08	TCGA-EJ-5497-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:70501626delA	uc001dep.2	+						LRRC7_uc009wbg.2_Intron|LRRC7_uc001deq.2_5'Flank	NM_020794	NP_065845	Q96NW7	LRRC7_HUMAN	leucine rich repeat containing 7							centrosome|focal adhesion|nucleolus	protein binding			ovary(9)|breast(2)|central_nervous_system(2)|liver(1)	14						CTTACATTAGAAAAAAAAAAT	0.189													3	4	---	---	---	---	
NBPF9	400818	broad.mit.edu	37	1	144190334	144190335	+	Intron	DEL	TC	-	-			TCGA-EJ-5497-01A-02D-1576-08	TCGA-EJ-5497-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:144190334_144190335delTC	uc010oxr.1	+						NBPF9_uc010oxn.1_Intron|NBPF9_uc010oxo.1_Intron|NBPF9_uc010oxt.1_Intron|NBPF9_uc001ekg.1_Intron|NBPF9_uc001ekk.1_5'Flank|uc001ejx.1_Intron|uc010oxv.1_Intron|uc010oxw.1_Intron|uc010oxx.1_Intron|uc010oxy.1_Intron|uc010oxz.1_Intron|uc010oya.1_5'Flank	NM_001037675	NP_001032764	Q3BBV1	NBPFK_HUMAN	hypothetical protein LOC400818							cytoplasm					0						CTGAGCTCGTTCTCTCTCTCTC	0.376													5	3	---	---	---	---	
HEATR1	55127	broad.mit.edu	37	1	236740444	236740445	+	Intron	INS	-	AAAT	AAAT	rs144706824	by1000genomes	TCGA-EJ-5497-01A-02D-1576-08	TCGA-EJ-5497-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:236740444_236740445insAAAT	uc001hyd.1	-						HEATR1_uc009xgh.1_Intron	NM_018072	NP_060542	Q9H583	HEAT1_HUMAN	protein BAP28						rRNA processing	nucleolus|ribonucleoprotein complex	protein binding			ovary(2)|skin(1)	3	Ovarian(103;0.0634)|Breast(184;0.133)	all_cancers(173;0.0255)|Prostate(94;0.175)	OV - Ovarian serous cystadenocarcinoma(106;0.00117)			TGAAAAtacacaagagcatact	0.168													4	3	---	---	---	---	
SNTG2	54221	broad.mit.edu	37	2	1133188	1133189	+	Intron	INS	-	CACA	CACA	rs143629447	by1000genomes	TCGA-EJ-5497-01A-02D-1576-08	TCGA-EJ-5497-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:1133188_1133189insCACA	uc002qwq.2	+						SNTG2_uc002qwp.2_Intron|SNTG2_uc010ewi.2_Intron	NM_018968	NP_061841	Q9NY99	SNTG2_HUMAN	syntrophin, gamma 2						central nervous system development	cytoplasm|cytoskeleton|sarcolemma|syntrophin complex	actin binding|PDZ domain binding			ovary(1)|large_intestine(1)|breast(1)	3	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.0797)	all_cancers(51;0.00469)		all cancers(51;0.0178)|OV - Ovarian serous cystadenocarcinoma(76;0.07)|Epithelial(75;0.0864)|GBM - Glioblastoma multiforme(21;0.173)		gtggacacatgcacacacacac	0.223													7	6	---	---	---	---	
PUM2	23369	broad.mit.edu	37	2	20453929	20453929	+	Intron	DEL	T	-	-	rs149877577		TCGA-EJ-5497-01A-02D-1576-08	TCGA-EJ-5497-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:20453929delT	uc002rds.1	-						PUM2_uc002rdq.1_Intron|PUM2_uc002rdt.1_Intron|PUM2_uc002rdr.2_Intron|PUM2_uc010yjy.1_Intron|PUM2_uc002rdu.1_Intron|PUM2_uc010yjz.1_Intron	NM_015317	NP_056132	Q8TB72	PUM2_HUMAN	pumilio homolog 2						regulation of translation	perinuclear region of cytoplasm|stress granule	protein binding|RNA binding			ovary(1)	1	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					tattttgttcttttttttttt	0.134													5	3	---	---	---	---	
CIB4	130106	broad.mit.edu	37	2	26839988	26839989	+	Intron	INS	-	TG	TG	rs146713738	by1000genomes	TCGA-EJ-5497-01A-02D-1576-08	TCGA-EJ-5497-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:26839988_26839989insTG	uc002rhm.2	-							NM_001029881	NP_001025052	A0PJX0	CIB4_HUMAN	calcium and integrin binding family member 4								calcium ion binding			ovary(1)	1	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					agAGCATGGAAtgtgtgtgtgt	0.317													2	4	---	---	---	---	
HEATR5B	54497	broad.mit.edu	37	2	37260027	37260028	+	Intron	INS	-	T	T			TCGA-EJ-5497-01A-02D-1576-08	TCGA-EJ-5497-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:37260027_37260028insT	uc002rpp.1	-							NM_019024	NP_061897	Q9P2D3	HTR5B_HUMAN	HEAT repeat containing 5B								binding			ovary(5)|skin(2)|breast(1)	8		all_hematologic(82;0.21)				Gttttgttttgttttttttttt	0.094													6	4	---	---	---	---	
RGPD5	84220	broad.mit.edu	37	2	113127925	113127925	+	Intron	DEL	T	-	-			TCGA-EJ-5497-01A-02D-1576-08	TCGA-EJ-5497-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:113127925delT	uc002ths.1	-						RGPD8_uc010fkk.1_Intron	NM_005054	NP_005045	Q99666	RGPD5_HUMAN	RANBP2-like and GRIP domain containing 5 isoform						intracellular transport	cytoplasm	binding				0						CCTTTTTTGGTGGGGGGGGGG	0.189													9	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	119453657	119453658	+	IGR	DEL	AG	-	-			TCGA-EJ-5497-01A-02D-1576-08	TCGA-EJ-5497-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:119453657_119453658delAG								INSIG2 (586061 upstream) : EN1 (146090 downstream)																							aaagaaagaaagaaagaaagaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	156126552	156126552	+	IGR	DEL	A	-	-	rs77418096		TCGA-EJ-5497-01A-02D-1576-08	TCGA-EJ-5497-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:156126552delA								KCNJ3 (413538 upstream) : None (None downstream)																							ccataatggcaaaaaaaaaaa	0.000													4	2	---	---	---	---	
GLS	2744	broad.mit.edu	37	2	191759678	191759678	+	Intron	DEL	T	-	-	rs3217036		TCGA-EJ-5497-01A-02D-1576-08	TCGA-EJ-5497-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:191759678delT	uc002usf.2	+						GLS_uc002usd.2_Intron|GLS_uc002use.2_Intron	NM_014905	NP_055720	O94925	GLSK_HUMAN	glutaminase precursor						cellular amino acid biosynthetic process|glutamate secretion|glutamine catabolic process|neurotransmitter secretion	mitochondrial matrix	glutaminase activity			ovary(1)|skin(1)	2			OV - Ovarian serous cystadenocarcinoma(117;0.00625)|Epithelial(96;0.0744)|all cancers(119;0.181)		L-Glutamic Acid(DB00142)|L-Glutamine(DB00130)	GTGTTAATGATTTTTTTTCTA	0.353													4	5	---	---	---	---	
OBFC2A	64859	broad.mit.edu	37	2	192548842	192548842	+	Intron	DEL	A	-	-			TCGA-EJ-5497-01A-02D-1576-08	TCGA-EJ-5497-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:192548842delA	uc002usx.2	+						OBFC2A_uc002usw.2_Intron|OBFC2A_uc002usy.2_Intron|OBFC2A_uc002usz.2_Intron|OBFC2A_uc002uta.2_Intron	NM_001031716	NP_001026886	Q96AH0	SOSB2_HUMAN	oligonucleotide/oligosaccharide-binding fold						double-strand break repair via homologous recombination|G2/M transition checkpoint|response to ionizing radiation	SOSS complex	single-stranded DNA binding				0			OV - Ovarian serous cystadenocarcinoma(117;0.061)|Epithelial(96;0.244)			tttgttaattaaaaaaaaaaa	0.234													11	7	---	---	---	---	
FASTKD2	22868	broad.mit.edu	37	2	207636634	207636634	+	Frame_Shift_Del	DEL	A	-	-			TCGA-EJ-5497-01A-02D-1576-08	TCGA-EJ-5497-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:207636634delA	uc002vbu.2	+	5	1417	c.1007delA	c.(1006-1008)GAAfs	p.E336fs	FASTKD2_uc002vbv.2_Frame_Shift_Del_p.E336fs|FASTKD2_uc002vbx.2_Frame_Shift_Del_p.E336fs|FASTKD2_uc002vbw.1_Frame_Shift_Del_p.E336fs	NM_001136193	NP_001129665	Q9NYY8	FAKD2_HUMAN	FAST kinase domains 2	336					apoptosis|cellular respiration	mitochondrion	ATP binding|protein kinase activity			ovary(2)|skin(1)	3				LUSC - Lung squamous cell carcinoma(261;0.0718)|Epithelial(149;0.119)|Lung(261;0.138)		GCCTTGAGGGAATTAGACAGA	0.279													164	38	---	---	---	---	
SETD2	29072	broad.mit.edu	37	3	47129455	47129458	+	Intron	DEL	AAAC	-	-	rs66851205		TCGA-EJ-5497-01A-02D-1576-08	TCGA-EJ-5497-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:47129455_47129458delAAAC	uc003cqs.2	-						SETD2_uc003cqv.2_Intron	NM_014159	NP_054878	Q9BYW2	SETD2_HUMAN	SET domain containing 2						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)		gaccccatctaaacaaacaaacaa	0.078			N|F|S|Mis		clear cell renal carcinoma								4	4	---	---	---	---	
RAB7A	7879	broad.mit.edu	37	3	128517689	128517689	+	Intron	DEL	G	-	-	rs35124528		TCGA-EJ-5497-01A-02D-1576-08	TCGA-EJ-5497-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:128517689delG	uc003eks.1	+						RAB7A_uc010hsv.1_Intron|RAB7A_uc003ekt.2_Intron	NM_004637	NP_004628	P51149	RAB7A_HUMAN	RAB7, member RAS oncogene family						endocytosis|endosome to lysosome transport|epidermal growth factor catabolic process|protein transport|small GTPase mediated signal transduction	Golgi apparatus|late endosome|lysosome|melanosome|phagocytic vesicle	GDP binding|GTP binding|GTPase activity|protein binding				0				GBM - Glioblastoma multiforme(114;0.231)		aaaaaaaaaagaATCCCAGGA	0.209													8	4	---	---	---	---	
FRG1	2483	broad.mit.edu	37	4	190873437	190873439	+	In_Frame_Del	DEL	AAG	-	-			TCGA-EJ-5497-01A-02D-1576-08	TCGA-EJ-5497-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:190873437_190873439delAAG	uc003izs.2	+	3	445_447	c.254_256delAAG	c.(253-258)AAAGAA>AAA	p.E86del		NM_004477	NP_004468	Q14331	FRG1_HUMAN	FSHD region gene 1	86					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)		GCTCCACACAAAGAAGGTTTGTG	0.414													236	7	---	---	---	---	
ADAMTS12	81792	broad.mit.edu	37	5	33561043	33561043	+	Intron	DEL	C	-	-			TCGA-EJ-5497-01A-02D-1576-08	TCGA-EJ-5497-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:33561043delC	uc003jia.1	-						ADAMTS12_uc010iuq.1_Intron	NM_030955	NP_112217	P58397	ATS12_HUMAN	ADAM metallopeptidase with thrombospondin type 1						proteolysis	proteinaceous extracellular matrix	metalloendopeptidase activity|zinc ion binding			ovary(4)|skin(2)|upper_aerodigestive_tract(1)|lung(1)|kidney(1)	9						aaaaaaAAAACGACTTTAGCA	0.229										HNSCC(64;0.19)			160	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	31209091	31209092	+	IGR	INS	-	TTCCTTCCTTCC	TTCCTTCCTTCC	rs11274492		TCGA-EJ-5497-01A-02D-1576-08	TCGA-EJ-5497-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:31209091_31209092insTTCCTTCCTTCC								HCG27 (37347 upstream) : HLA-C (27438 downstream)																							GGAGACTCCTTttccttccttc	0.059													4	2	---	---	---	---	
FAM135A	57579	broad.mit.edu	37	6	71236468	71236469	+	Intron	DEL	AT	-	-	rs111717563		TCGA-EJ-5497-01A-02D-1576-08	TCGA-EJ-5497-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:71236468_71236469delAT	uc003pfj.2	+						FAM135A_uc003pfi.2_Intron|FAM135A_uc003pfh.2_Intron|FAM135A_uc003pfl.2_Intron|FAM135A_uc003pfn.2_Intron|FAM135A_uc003pfo.1_Intron|FAM135A_uc010kan.1_5'Flank	NM_001162529	NP_001156001	Q9P2D6	F135A_HUMAN	hypothetical protein LOC57579 isoform c											central_nervous_system(1)	1						acacacacacatacacacacac	0.218													19	8	---	---	---	---	
FAM133B	257415	broad.mit.edu	37	7	92208488	92208488	+	Intron	DEL	G	-	-	rs113560614		TCGA-EJ-5497-01A-02D-1576-08	TCGA-EJ-5497-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:92208488delG	uc003umc.2	-						FAM133B_uc003umb.2_Intron|FAM133B_uc003umd.2_Intron	NM_152789	NP_690002	Q5BKY9	F133B_HUMAN	hypothetical protein LOC257415 isoform 1											ovary(1)	1	all_cancers(62;7.39e-11)|all_epithelial(64;7.03e-10)|Breast(17;0.00201)|all_lung(186;0.0384)|Lung NSC(181;0.053)|all_hematologic(106;0.237)		STAD - Stomach adenocarcinoma(4;6.16e-07)|GBM - Glioblastoma multiforme(5;9.78e-06)|all cancers(6;1.67e-05)|Epithelial(20;0.113)|LUSC - Lung squamous cell carcinoma(200;0.225)|Lung(22;0.23)			CAAGGGCGGCGGGGGggggcc	0.199													3	3	---	---	---	---	
POT1	25913	broad.mit.edu	37	7	124537448	124537448	+	Intron	DEL	A	-	-	rs11349684		TCGA-EJ-5497-01A-02D-1576-08	TCGA-EJ-5497-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:124537448delA	uc003vlm.2	-						POT1_uc011koe.1_Intron|POT1_uc003vlk.2_Intron|POT1_uc003vll.2_Intron|POT1_uc003vlo.2_Intron|POT1_uc003vln.2_Intron	NM_015450	NP_056265	Q9NUX5	POTE1_HUMAN	protection of telomeres 1 isoform 1						DNA duplex unwinding|negative regulation of telomere maintenance via telomerase|positive regulation of DNA strand elongation|positive regulation of helicase activity|positive regulation of telomerase activity|positive regulation of telomere maintenance via telomerase|telomere capping|telomere formation via telomerase|telomere maintenance via telomerase	nuclear telomere cap complex|nucleoplasm	DEAD/H-box RNA helicase binding|single-stranded telomeric DNA binding|telomerase inhibitor activity			central_nervous_system(1)	1						ACAGAAACTTAAAAAAAAAAG	0.274													3	4	---	---	---	---	
KIAA1549	57670	broad.mit.edu	37	7	138588610	138588611	+	Intron	INS	-	GT	GT	rs150868084	by1000genomes	TCGA-EJ-5497-01A-02D-1576-08	TCGA-EJ-5497-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:138588610_138588611insGT	uc011kql.1	-						KIAA1549_uc003vuk.3_Intron|KIAA1549_uc011kqj.1_Intron	NM_020910	NP_065961	Q9HCM3	K1549_HUMAN	hypothetical protein LOC57670 isoform 1							integral to membrane			KIAA1549/BRAF(229)	central_nervous_system(229)|pancreas(1)	230						CGCGCGCGCGCGCGCGCACATA	0.287			O	BRAF	pilocytic astrocytoma								3	3	---	---	---	---	
NDUFB2	4708	broad.mit.edu	37	7	140404902	140404902	+	Intron	DEL	T	-	-	rs72099907		TCGA-EJ-5497-01A-02D-1576-08	TCGA-EJ-5497-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:140404902delT	uc003vwa.2	+						NDUFB2_uc010lnl.2_Intron	NM_004546	NP_004537	O95178	NDUB2_HUMAN	NADH dehydrogenase (ubiquinone) 1 beta						mitochondrial electron transport, NADH to ubiquinone|transport	mitochondrial respiratory chain complex I	NADH dehydrogenase (ubiquinone) activity			ovary(1)|central_nervous_system(1)	2	Melanoma(164;0.00956)				NADH(DB00157)	CTGTATCTGCttttttttttt	0.164													7	4	---	---	---	---	
CSMD3	114788	broad.mit.edu	37	8	113275870	113275870	+	Frame_Shift_Del	DEL	A	-	-			TCGA-EJ-5497-01A-02D-1576-08	TCGA-EJ-5497-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:113275870delA	uc003ynu.2	-	61	10019	c.9860delT	c.(9859-9861)TTAfs	p.L3287fs	CSMD3_uc003yns.2_Frame_Shift_Del_p.L2489fs|CSMD3_uc003ynt.2_Frame_Shift_Del_p.L3247fs|CSMD3_uc011lhx.1_Frame_Shift_Del_p.L3118fs	NM_198123	NP_937756	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3 isoform 1	3287	Sushi 25.|Extracellular (Potential).					integral to membrane|plasma membrane				ovary(21)|lung(11)|skin(11)|kidney(8)|large_intestine(6)|upper_aerodigestive_tract(2)|central_nervous_system(2)|urinary_tract(1)|breast(1)	63						ATACTTACGTAAGCACTGCGG	0.388										HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)			58	20	---	---	---	---	
PAPSS2	9060	broad.mit.edu	37	10	89505865	89505866	+	3'UTR	INS	-	A	A	rs141653988	by1000genomes	TCGA-EJ-5497-01A-02D-1576-08	TCGA-EJ-5497-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:89505865_89505866insA	uc001kex.2	+	12					PAPSS2_uc001kew.2_3'UTR	NM_004670	NP_004661	O95340	PAPS2_HUMAN	3'-phosphoadenosine 5'-phosphosulfate synthase 2						3'-phosphoadenosine 5'-phosphosulfate biosynthetic process|skeletal system development|sulfate assimilation|xenobiotic metabolic process	cytosol	adenylylsulfate kinase activity|ATP binding|protein binding|sulfate adenylyltransferase (ATP) activity			central_nervous_system(1)|skin(1)	2		Melanoma(5;0.019)|Colorectal(252;0.123)		UCEC - Uterine corpus endometrioid carcinoma (6;0.00164)|Colorectal(12;0.000323)|COAD - Colon adenocarcinoma(12;0.00124)		TGTCTATAATTAAAAAAAAata	0.198													4	3	---	---	---	---	
BET1L	51272	broad.mit.edu	37	11	207255	207255	+	Intron	DEL	G	-	-			TCGA-EJ-5497-01A-02D-1576-08	TCGA-EJ-5497-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:207255delG	uc001loe.2	-						BET1L_uc001lod.2_Intron|RIC8A_uc001lof.2_5'Flank|RIC8A_uc001log.2_5'Flank|RIC8A_uc001loh.2_5'Flank	NM_001098787	NP_001092257	Q9NYM9	BET1L_HUMAN	blocked early in transport 1 homolog (S.						protein transport|retrograde transport, endosome to Golgi	endosome|SNARE complex	SNAP receptor activity				0		all_cancers(49;1.58e-09)|all_epithelial(84;2.71e-06)|Breast(177;0.000162)|Ovarian(85;0.000626)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.0538)|all_lung(207;0.0713)		all cancers(45;4.2e-27)|Epithelial(43;2.8e-26)|OV - Ovarian serous cystadenocarcinoma(40;5.7e-21)|BRCA - Breast invasive adenocarcinoma(625;3.56e-05)|Lung(200;0.105)|LUSC - Lung squamous cell carcinoma(625;0.122)		CAGCGGCGTCGGTTTCGGCCC	0.746													4	2	---	---	---	---	
EED	8726	broad.mit.edu	37	11	85975481	85975482	+	Intron	INS	-	TATT	TATT	rs138959322	by1000genomes	TCGA-EJ-5497-01A-02D-1576-08	TCGA-EJ-5497-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:85975481_85975482insTATT	uc001pbp.2	+						EED_uc010rtm.1_Intron|EED_uc001pbq.2_Intron|EED_uc001pbr.2_Intron|EED_uc001pbs.2_Intron|EED_uc010rtn.1_Intron	NM_003797	NP_003788	O75530	EED_HUMAN	embryonic ectoderm development isoform a						negative regulation of transcription, DNA-dependent|transcription, DNA-dependent	ESC/E(Z) complex	histone methyltransferase activity|identical protein binding			skin(1)|pancreas(1)	2		Acute lymphoblastic leukemia(157;7.24e-07)|all_hematologic(158;0.00092)				AGTAAAGACtatatttatttat	0.312													4	3	---	---	---	---	
MED17	9440	broad.mit.edu	37	11	93529637	93529637	+	Frame_Shift_Del	DEL	T	-	-			TCGA-EJ-5497-01A-02D-1576-08	TCGA-EJ-5497-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:93529637delT	uc001pem.3	+	7	1349	c.1074delT	c.(1072-1074)GCTfs	p.A358fs		NM_004268	NP_004259	Q9NVC6	MED17_HUMAN	mediator complex subunit 17	358					androgen receptor signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription initiation from RNA polymerase II promoter	mediator complex|transcription factor complex	ligand-dependent nuclear receptor transcription coactivator activity|receptor activity|RNA polymerase II transcription cofactor activity|thyroid hormone receptor binding|vitamin D receptor binding			ovary(1)	1		Acute lymphoblastic leukemia(157;2.31e-05)|all_hematologic(158;0.00824)				AAAAATTTGCTACTGAGAAGC	0.358													214	45	---	---	---	---	
CUL5	8065	broad.mit.edu	37	11	107965657	107965658	+	Frame_Shift_Ins	INS	-	A	A			TCGA-EJ-5497-01A-02D-1576-08	TCGA-EJ-5497-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:107965657_107965658insA	uc001pjv.2	+	15	2353_2354	c.1686_1687insA	c.(1684-1689)TACAAAfs	p.Y562fs	CUL5_uc001pju.2_RNA	NM_003478	NP_003469	Q93034	CUL5_HUMAN	Vasopressin-activated calcium-mobilizing	562_563					cell cycle arrest|cell proliferation|G1/S transition of mitotic cell cycle|induction of apoptosis by intracellular signals|interspecies interaction between organisms|negative regulation of cell proliferation|ubiquitin-dependent protein catabolic process|viral reproduction	cullin-RING ubiquitin ligase complex|cytosol	calcium channel activity|receptor activity|ubiquitin protein ligase binding			ovary(1)	1		all_cancers(61;7.09e-10)|all_epithelial(67;2.97e-06)|Acute lymphoblastic leukemia(157;3.95e-05)|Melanoma(852;4.48e-05)|all_hematologic(158;0.00014)|Breast(348;0.0258)|all_neural(303;0.072)		BRCA - Breast invasive adenocarcinoma(274;3.58e-05)|Epithelial(105;4.68e-05)|all cancers(92;0.00122)|OV - Ovarian serous cystadenocarcinoma(223;0.217)		AAGAATTCTACAAAAAAAATCA	0.351													133	9	---	---	---	---	
IFFO1	25900	broad.mit.edu	37	12	6656906	6656907	+	Intron	DEL	AG	-	-			TCGA-EJ-5497-01A-02D-1576-08	TCGA-EJ-5497-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:6656906_6656907delAG	uc001qpd.1	-						IFFO1_uc001qoy.2_Intron|IFFO1_uc001qpa.1_Intron|IFFO1_uc001qpb.1_Intron|IFFO1_uc001qpe.1_Intron|IFFO1_uc010sfe.1_Intron|IFFO1_uc001qpf.1_Intron|IFFO1_uc001qoz.1_Intron|IFFO1_uc001qpc.1_Intron|IFFO1_uc001qpg.2_Intron	NM_080730	NP_542768	Q0D2I5	IFFO1_HUMAN	intermediate filament family orphan isoform 2							intermediate filament					0						ggggaggggaagagagagagag	0.010													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	77402068	77402071	+	IGR	DEL	GGAA	-	-			TCGA-EJ-5497-01A-02D-1576-08	TCGA-EJ-5497-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:77402068_77402071delGGAA								LMO7 (968064 upstream) : KCTD12 (52233 downstream)																							gggggaggggggaaggaaggaagg	0.152													1	5	---	---	---	---	
ABCC4	10257	broad.mit.edu	37	13	95673939	95673939	+	Intron	DEL	A	-	-	rs9524765	by1000genomes	TCGA-EJ-5497-01A-02D-1576-08	TCGA-EJ-5497-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:95673939delA	uc001vmd.3	-						ABCC4_uc010afj.2_Intron|ABCC4_uc010afk.2_Intron	NM_005845	NP_005836	O15439	MRP4_HUMAN	ATP-binding cassette, sub-family C, member 4						platelet activation|platelet degranulation	integral to membrane|membrane fraction|plasma membrane|platelet dense granule membrane	15-hydroxyprostaglandin dehydrogenase (NAD+) activity|ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|chloride channel activity			central_nervous_system(3)|skin(1)	4	all_neural(89;0.0878)|Medulloblastoma(90;0.163)				Cefazolin(DB01327)	AAGTATACCTAGAAAAAAAAA	0.358													94	8	---	---	---	---	
FARP1	10160	broad.mit.edu	37	13	99056280	99056281	+	Intron	INS	-	ACCACT	ACCACT	rs149305965	by1000genomes	TCGA-EJ-5497-01A-02D-1576-08	TCGA-EJ-5497-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:99056280_99056281insACCACT	uc001vnj.2	+						FARP1_uc001vnh.2_Intron|uc001vnl.2_RNA	NM_005766	NP_005757	Q9Y4F1	FARP1_HUMAN	FERM, RhoGEF, and pleckstrin domain protein 1						regulation of Rho protein signal transduction	cytoplasm|cytoskeleton|extrinsic to membrane	cytoskeletal protein binding|Rho guanyl-nucleotide exchange factor activity			breast(2)	2	all_neural(89;0.0982)|Medulloblastoma(90;0.163)|Lung SC(71;0.184)		BRCA - Breast invasive adenocarcinoma(86;0.233)			ccatcaccaccaccactgctac	0.277													4	2	---	---	---	---	
A2LD1	87769	broad.mit.edu	37	13	101192070	101192070	+	Intron	DEL	T	-	-			TCGA-EJ-5497-01A-02D-1576-08	TCGA-EJ-5497-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:101192070delT	uc001vor.2	-							NM_033110	NP_149101	Q9BVM4	A2LD1_HUMAN	AIG2-like domain 1						cellular modified amino acid catabolic process		acyltransferase activity|gamma-glutamylcyclotransferase activity				0						ggtcctgggcttttttttttt	0.154													13	6	---	---	---	---	
RALGAPA1	253959	broad.mit.edu	37	14	36221015	36221016	+	Intron	INS	-	A	A	rs33938683		TCGA-EJ-5497-01A-02D-1576-08	TCGA-EJ-5497-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:36221015_36221016insA	uc001wti.2	-						RALGAPA1_uc001wtj.2_Intron|RALGAPA1_uc010tpv.1_Intron|RALGAPA1_uc010tpw.1_Intron|RALGAPA1_uc001wtk.1_Intron	NM_014990	NP_055805	Q6GYQ0	RGPA1_HUMAN	Ral GTPase activating protein, alpha subunit 1						activation of Ral GTPase activity	cytosol|mitochondrion|nucleus	protein heterodimerization activity|Ral GTPase activator activity			ovary(3)|breast(1)	4						acaacaacaacaacaaaaaaaa	0.104													5	3	---	---	---	---	
GOLGA6L10	647042	broad.mit.edu	37	15	82664400	82664400	+	Intron	DEL	T	-	-			TCGA-EJ-5497-01A-02D-1576-08	TCGA-EJ-5497-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:82664400delT	uc010unt.1	-						uc002bgz.2_Intron|uc010unu.1_Intron			A6NI86	GG6LA_HUMAN	Homo sapiens cDNA FLJ40113 fis, clone TESTI2008621.												0						AACAAAAATCTTTTTTTTTTT	0.308													5	5	---	---	---	---	
GOLGA6L5	374650	broad.mit.edu	37	15	85056104	85056104	+	Intron	DEL	A	-	-			TCGA-EJ-5497-01A-02D-1576-08	TCGA-EJ-5497-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:85056104delA	uc002bkm.2	-							NR_003246				Homo sapiens cDNA FLJ33459 fis, clone BRAMY2000585.												0						CTGGATTCTCAAAAAAAAAAA	0.527													13	6	---	---	---	---	
RPL26	6154	broad.mit.edu	37	17	8285250	8285251	+	Intron	DEL	AA	-	-	rs71739070		TCGA-EJ-5497-01A-02D-1576-08	TCGA-EJ-5497-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:8285250_8285251delAA	uc002glh.1	-							NM_000987	NP_000978	P61254	RL26_HUMAN	ribosomal protein L26						endocrine pancreas development|ribosomal large subunit biogenesis|rRNA processing|translational elongation|translational termination|viral transcription	cytosolic large ribosomal subunit	protein binding|RNA binding|structural constituent of ribosome				0						acttcatctcaaaaaaaaaaaa	0.149													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	16735760	16735761	+	5'UTR	INS	-	A	A			TCGA-EJ-5497-01A-02D-1576-08	TCGA-EJ-5497-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:16735760_16735761insA	uc010vwr.1	-	1										SubName: Full=cDNA FLJ53570, highly similar to Keratin, type I cytoskeletal 16;																		agccaccacccaagccagcacc	0.391													69	7	---	---	---	---	
C17orf42	79736	broad.mit.edu	37	17	29231699	29231700	+	Intron	INS	-	T	T			TCGA-EJ-5497-01A-02D-1576-08	TCGA-EJ-5497-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:29231699_29231700insT	uc002hfu.2	-						C17orf42_uc002hfv.2_Intron|C17orf42_uc002hfw.2_Intron|C17orf42_uc010wbs.1_Intron	NM_024683	NP_078959	Q96QE5	TEFM_HUMAN	hypothetical protein LOC79736						oxidative phosphorylation|regulation of transcription, DNA-dependent|transcription from mitochondrial promoter	mitochondrial nucleoid|ribonucleoprotein complex	DNA polymerase processivity factor activity|nucleic acid binding|protein binding			ovary(1)	1		all_cancers(10;4.64e-07)|all_hematologic(16;0.014)|Acute lymphoblastic leukemia(14;0.0236)|Myeloproliferative disorder(56;0.0255)				GGAGAATCATCttttttttttt	0.168													4	2	---	---	---	---	
MED24	9862	broad.mit.edu	37	17	38183505	38183506	+	Intron	INS	-	G	G	rs144546030	by1000genomes	TCGA-EJ-5497-01A-02D-1576-08	TCGA-EJ-5497-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:38183505_38183506insG	uc002htt.2	-						MED24_uc010wes.1_Intron|MED24_uc010wet.1_Intron|MED24_uc002hts.2_Intron|MED24_uc002htu.2_Intron|MED24_uc010cwn.2_Intron|MED24_uc010weu.1_Intron|MED24_uc010wev.1_Intron|MED24_uc010wew.1_Intron|MED24_uc010wex.1_Intron|SNORD124_uc010wey.1_5'Flank	NM_014815	NP_055630	O75448	MED24_HUMAN	mediator complex subunit 24 isoform 1						androgen receptor signaling pathway|positive regulation of transcription, DNA-dependent|transcription initiation from RNA polymerase II promoter	mediator complex	ligand-dependent nuclear receptor transcription coactivator activity|receptor activity|RNA polymerase II transcription cofactor activity|thyroid hormone receptor binding|vitamin D receptor binding			ovary(1)	1	Colorectal(19;0.000442)					CCAGCCCGGGTGGGCACCTGGT	0.619											OREG0024386	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	6	3	---	---	---	---	
MSI2	124540	broad.mit.edu	37	17	55693643	55693644	+	Intron	DEL	TG	-	-			TCGA-EJ-5497-01A-02D-1576-08	TCGA-EJ-5497-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:55693643_55693644delTG	uc002iuz.1	+						MSI2_uc010wnm.1_Intron|MSI2_uc002iva.2_Intron	NM_138962	NP_620412	Q96DH6	MSI2H_HUMAN	musashi 2 isoform a							cytoplasm	nucleotide binding|RNA binding			central_nervous_system(1)|pancreas(1)	2	Breast(9;1.78e-08)			GBM - Glioblastoma multiforme(1;0.0025)		tgtgcatgcatgtgtgtgtgtg	0.134			T	HOXA9	CML								6	3	---	---	---	---	
CCDC46	201134	broad.mit.edu	37	17	64024255	64024256	+	Intron	INS	-	T	T	rs56239919		TCGA-EJ-5497-01A-02D-1576-08	TCGA-EJ-5497-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:64024255_64024256insT	uc002jfl.2	-						CCDC46_uc010deo.2_Intron|CCDC46_uc002jfm.2_Intron|CCDC46_uc010dep.2_Intron	NM_145036	NP_659473	Q8N8E3	CE112_HUMAN	coiled-coil domain containing 46 isoform a							centrosome					0			BRCA - Breast invasive adenocarcinoma(6;1.53e-06)			CTACATCTCAAAGCATCAATCT	0.198													4	2	---	---	---	---	
NEDD4L	23327	broad.mit.edu	37	18	55992284	55992286	+	In_Frame_Del	DEL	TCC	-	-			TCGA-EJ-5497-01A-02D-1576-08	TCGA-EJ-5497-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:55992284_55992286delTCC	uc002lgy.2	+	9	844_846	c.570_572delTCC	c.(568-573)CTTCCT>CTT	p.P194del	NEDD4L_uc002lgz.2_In_Frame_Del_p.P194del|NEDD4L_uc002lgx.2_In_Frame_Del_p.P194del|NEDD4L_uc010xee.1_In_Frame_Del_p.P73del|NEDD4L_uc002lhc.2_In_Frame_Del_p.P186del|NEDD4L_uc002lhd.2_In_Frame_Del_p.P73del|NEDD4L_uc002lhb.2_In_Frame_Del_p.P73del|NEDD4L_uc002lhe.2_In_Frame_Del_p.P186del|NEDD4L_uc002lhf.2_In_Frame_Del_p.P73del|NEDD4L_uc002lhg.2_In_Frame_Del_p.P73del|NEDD4L_uc002lhh.2_In_Frame_Del_p.P73del|NEDD4L_uc010dpm.1_In_Frame_Del_p.P45del	NM_001144967	NP_001138439	Q96PU5	NED4L_HUMAN	neural precursor cell expressed, developmentally	194	WW 1.				cellular sodium ion homeostasis|excretion|interspecies interaction between organisms|positive regulation of endocytosis|protein ubiquitination involved in ubiquitin-dependent protein catabolic process|regulation of protein catabolic process|response to metal ion|sodium ion transport|water homeostasis	cytoplasm	protein binding|sodium channel regulator activity|ubiquitin-protein ligase activity			lung(4)	4						AAGAGGAACTTCCTCCTCCTCCT	0.498													327	8	---	---	---	---	
ADAMTS10	81794	broad.mit.edu	37	19	8657127	8657128	+	Intron	DEL	AG	-	-	rs35800262		TCGA-EJ-5497-01A-02D-1576-08	TCGA-EJ-5497-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:8657127_8657128delAG	uc002mkj.1	-						ADAMTS10_uc002mki.1_5'Flank|ADAMTS10_uc002mkk.1_Intron	NM_030957	NP_112219	Q9H324	ATS10_HUMAN	ADAM metallopeptidase with thrombospondin type 1						proteolysis	proteinaceous extracellular matrix	metalloendopeptidase activity|zinc ion binding			pancreas(2)|skin(2)	4						ACATGCGAACAGAGTCAGGTTA	0.619													7	6	---	---	---	---	
TULP2	7288	broad.mit.edu	37	19	49384468	49384468	+	Intron	DEL	C	-	-	rs68173909		TCGA-EJ-5497-01A-02D-1576-08	TCGA-EJ-5497-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:49384468delC	uc002pkz.2	-							NM_003323	NP_003314	O00295	TULP2_HUMAN	tubby like protein 2						visual perception	cytoplasm|extracellular region				ovary(1)|kidney(1)|skin(1)	3		all_epithelial(76;5.29e-07)|all_lung(116;1.7e-06)|Lung NSC(112;3.55e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)		OV - Ovarian serous cystadenocarcinoma(262;0.000259)|all cancers(93;0.000435)|Epithelial(262;0.0221)|GBM - Glioblastoma multiforme(486;0.0234)		ttttttttttctttttttttt	0.199													6	4	---	---	---	---	
NINL	22981	broad.mit.edu	37	20	25436392	25436392	+	Frame_Shift_Del	DEL	C	-	-			TCGA-EJ-5497-01A-02D-1576-08	TCGA-EJ-5497-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:25436392delC	uc002wux.1	-	23	3948	c.3874delG	c.(3874-3876)GAAfs	p.E1292fs	NINL_uc010gdn.1_Frame_Shift_Del_p.E943fs|NINL_uc002wuw.1_Frame_Shift_Del_p.E83fs	NM_025176	NP_079452	Q9Y2I6	NINL_HUMAN	ninein-like	1292	Potential.				G2/M transition of mitotic cell cycle	cytosol|microtubule|microtubule organizing center	calcium ion binding			ovary(2)|pancreas(1)|central_nervous_system(1)|skin(1)	5						ACCCGCTCTTCTGTGGCTTTC	0.378													428	11	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	26113543	26113543	+	IGR	DEL	A	-	-			TCGA-EJ-5497-01A-02D-1576-08	TCGA-EJ-5497-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:26113543delA								C20orf191 (18866 upstream) : MIR663 (75279 downstream)																							TCTTTGCCTTAACAACATTAT	0.363													4	2	---	---	---	---	
KCNQ2	3785	broad.mit.edu	37	20	62074712	62074714	+	Intron	DEL	CAT	-	-			TCGA-EJ-5497-01A-02D-1576-08	TCGA-EJ-5497-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:62074712_62074714delCAT	uc002yey.1	-						KCNQ2_uc002yez.1_Intron|KCNQ2_uc002yfa.1_Intron|KCNQ2_uc002yfb.1_Intron|KCNQ2_uc011aax.1_Intron|KCNQ2_uc002yfc.1_Intron	NM_172107	NP_742105	O43526	KCNQ2_HUMAN	potassium voltage-gated channel KQT-like protein						axon guidance|synaptic transmission	voltage-gated potassium channel complex	voltage-gated potassium channel activity			upper_aerodigestive_tract(1)|ovary(1)	2	all_cancers(38;1.24e-11)		BRCA - Breast invasive adenocarcinoma(10;1.04e-05)		Amitriptyline(DB00321)	ccaccaccaccatcaccatcatc	0.000													4	2	---	---	---	---	
NUP50	10762	broad.mit.edu	37	22	45577017	45577019	+	Intron	DEL	CCC	-	-	rs66468525		TCGA-EJ-5497-01A-02D-1576-08	TCGA-EJ-5497-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:45577017_45577019delCCC	uc003bfr.2	+						NUP50_uc003bfs.2_Intron|NUP50_uc011aqn.1_Intron|NUP50_uc003bft.2_Intron|NUP50_uc011aqo.1_Intron	NM_007172	NP_009103	Q9UKX7	NUP50_HUMAN	nucleoporin 50kDa isoform b						carbohydrate metabolic process|glucose transport|intracellular transport|mRNA transport|protein transport|regulation of glucose transport|transmembrane transport|viral reproduction	nuclear membrane|nuclear pore|nucleoplasm	protein binding				0		Ovarian(80;0.00965)|all_neural(38;0.0244)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0178)		CTTCTGGCATCCCCCCCCCCCCC	0.404													4	3	---	---	---	---	
TBC1D22A	25771	broad.mit.edu	37	22	47307815	47307815	+	Intron	DEL	A	-	-			TCGA-EJ-5497-01A-02D-1576-08	TCGA-EJ-5497-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:47307815delA	uc003bib.2	+						TBC1D22A_uc010haf.2_Intron|TBC1D22A_uc003bic.2_Intron|TBC1D22A_uc003bie.2_Intron|TBC1D22A_uc003bid.2_Intron|TBC1D22A_uc010hag.2_Intron|TBC1D22A_uc003bif.2_Intron	NM_014346	NP_055161	Q8WUA7	TB22A_HUMAN	TBC1 domain family, member 22A							intracellular	protein homodimerization activity|Rab GTPase activator activity			ovary(1)	1		all_cancers(38;4.44e-05)|all_epithelial(38;0.000507)|Breast(42;0.0488)|all_lung(38;0.0682)|Ovarian(80;0.0731)|all_neural(38;0.0966)|Glioma(61;0.222)|Lung SC(80;0.236)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0347)|BRCA - Breast invasive adenocarcinoma(115;0.231)		accctgtctcaaaaaaaaaaa	0.095													5	3	---	---	---	---	
GAGE2A	729447	broad.mit.edu	37	X	49208295	49208296	+	Intron	INS	-	TAT	TAT			TCGA-EJ-5497-01A-02D-1576-08	TCGA-EJ-5497-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:49208295_49208296insTAT	uc004dnr.3	+						GAGE12J_uc004dnl.3_Intron|GAGE13_uc004dnn.3_Intron|GAGE8_uc011mne.1_Intron|GAGE8_uc011mnf.1_Intron|GAGE8_uc011mng.1_Intron|GAGE8_uc004dnq.3_Intron|GAGE2A_uc004dnv.3_In_Frame_Ins_p.9_10insY|GAGE10_uc010nis.2_Intron|GAGE12J_uc004dnk.3_Intron|GAGE2D_uc004dnp.3_Intron|GAGE2C_uc004dno.3_Intron|GAGE8_uc011mnh.1_Intron|GAGE2C_uc004dnu.3_In_Frame_Ins_p.9_10insY|GAGE2D_uc010njc.2_In_Frame_Ins_p.9_10insY|GAGE2D_uc004dnt.3_In_Frame_Ins_p.9_10insY|GAGE8_uc011mni.1_In_Frame_Ins_p.9_10insY	NM_001127212	NP_001120684	Q6NT46	GAG2A_HUMAN	G antigen 2A												0	Ovarian(276;0.236)					GAAGATCGACCTATCGGCCTAG	0.465													30	8	---	---	---	---	
