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
ESPN	83715	broad.mit.edu	37	1	6488385	6488385	+	Missense_Mutation	SNP	A	C	C			TCGA-EJ-5519-01A-01D-1576-08	TCGA-EJ-5519-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:6488385A>C	uc001amy.2	+	2	562	c.394A>C	c.(394-396)ACC>CCC	p.T132P		NM_031475	NP_113663	B1AK53	ESPN_HUMAN	espin	132	ANK 4.				sensory perception of sound	brush border|cytoplasm|filamentous actin|stereocilium	actin filament binding|SH3 domain binding				0	Ovarian(185;0.0386)|all_lung(157;0.154)	all_cancers(23;3.6e-37)|all_epithelial(116;2.56e-22)|all_lung(118;7.57e-07)|Lung NSC(185;4.26e-06)|all_hematologic(16;6.92e-06)|Colorectal(325;4.47e-05)|Acute lymphoblastic leukemia(12;4.92e-05)|Breast(487;7.61e-05)|Renal(390;0.0007)|Hepatocellular(190;0.00308)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0392)		Epithelial(90;1.82e-35)|GBM - Glioblastoma multiforme(13;3e-28)|Kidney(185;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(229;5.63e-08)|Colorectal(212;7e-08)|COAD - Colon adenocarcinoma(227;1.41e-05)|BRCA - Breast invasive adenocarcinoma(365;0.000109)|STAD - Stomach adenocarcinoma(132;0.00167)|Lung(427;0.0108)|LUSC - Lung squamous cell carcinoma(448;0.0253)|READ - Rectum adenocarcinoma(331;0.0419)		TGGGGACCCCACCGCGGCCAC	0.622													5	51	---	---	---	---	PASS
CROCCL1	84809	broad.mit.edu	37	1	16959698	16959698	+	Intron	SNP	G	A	A	rs9730434	by1000genomes	TCGA-EJ-5519-01A-01D-1576-08	TCGA-EJ-5519-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:16959698G>A	uc001azf.2	-						CROCCL1_uc009vov.1_5'Flank|CROCCL1_uc001aze.2_5'Flank|CROCCL1_uc001azg.1_RNA|CROCCL1_uc001azi.1_RNA|uc001azj.1_RNA					Homo sapiens mRNA for FLJ00313 protein.												0						GGTCCTTCTCGTGGAGCACCT	0.657													6	16	---	---	---	---	PASS
C1orf38	9473	broad.mit.edu	37	1	28208523	28208523	+	Missense_Mutation	SNP	G	T	T			TCGA-EJ-5519-01A-01D-1576-08	TCGA-EJ-5519-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:28208523G>T	uc001bpc.3	+	4	716	c.688G>T	c.(688-690)GAC>TAC	p.D230Y	C1orf38_uc001boz.2_Intron|C1orf38_uc001bpa.2_Intron|C1orf38_uc010ofn.1_Intron|C1orf38_uc010ofo.1_Missense_Mutation_p.D230Y	NM_001105556	NP_001099026	Q5TEJ8	THMS2_HUMAN	basement membrane-induced gene isoform 3	230	CABIT 1.				cell adhesion|inflammatory response					ovary(1)	1		Colorectal(325;3.46e-05)|all_lung(284;0.000129)|Lung NSC(340;0.000259)|Renal(390;0.00121)|Breast(348;0.00345)|Ovarian(437;0.00503)|all_neural(195;0.0208)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0416)|OV - Ovarian serous cystadenocarcinoma(117;2.52e-24)|Colorectal(126;2.96e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|BRCA - Breast invasive adenocarcinoma(304;0.00244)|KIRC - Kidney renal clear cell carcinoma(1967;0.0027)|STAD - Stomach adenocarcinoma(196;0.00303)|READ - Rectum adenocarcinoma(331;0.0649)		CCTGGAGGTCGACGTGGAGGA	0.642													25	66	---	---	---	---	PASS
YBX1	4904	broad.mit.edu	37	1	43161928	43161928	+	Missense_Mutation	SNP	C	T	T			TCGA-EJ-5519-01A-01D-1576-08	TCGA-EJ-5519-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:43161928C>T	uc001chs.2	+	4	494	c.323C>T	c.(322-324)ACT>ATT	p.T108I		NM_004559	NP_004550	P67809	YBOX1_HUMAN	nuclease sensitive element binding protein 1	108	CSD.				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)				GATGGAGAGACTGTGGAGTTT	0.393													4	160	---	---	---	---	PASS
YBX1	4904	broad.mit.edu	37	1	43162410	43162410	+	Missense_Mutation	SNP	G	C	C			TCGA-EJ-5519-01A-01D-1576-08	TCGA-EJ-5519-10A-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													4	83	---	---	---	---	PASS
INADL	10207	broad.mit.edu	37	1	62456031	62456031	+	Missense_Mutation	SNP	T	G	G			TCGA-EJ-5519-01A-01D-1576-08	TCGA-EJ-5519-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:62456031T>G	uc001dab.2	+	28	3976	c.3862T>G	c.(3862-3864)TTA>GTA	p.L1288V	INADL_uc009waf.1_Missense_Mutation_p.L1288V|INADL_uc001daa.2_Missense_Mutation_p.L1288V|INADL_uc001dad.3_Missense_Mutation_p.L985V|INADL_uc001dac.2_RNA|INADL_uc010oot.1_Missense_Mutation_p.L72V|INADL_uc009wag.2_Missense_Mutation_p.L72V|INADL_uc010oou.1_5'UTR	NM_176877	NP_795352	Q8NI35	INADL_HUMAN	InaD-like	1288	PDZ 7.				intracellular signal transduction|tight junction assembly	apical plasma membrane|perinuclear region of cytoplasm|tight junction	protein binding			ovary(3)|skin(1)	4						AGATGAACTCTTAGAGGTGAG	0.443													8	54	---	---	---	---	PASS
MCOLN3	55283	broad.mit.edu	37	1	85510885	85510885	+	Silent	SNP	G	A	A			TCGA-EJ-5519-01A-01D-1576-08	TCGA-EJ-5519-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:85510885G>A	uc001dkp.2	-	2	252	c.159C>T	c.(157-159)TTC>TTT	p.F53F	MCOLN3_uc001dkq.2_Silent_p.F53F|MCOLN3_uc001dkr.2_Silent_p.F53F|MCOLN3_uc001dks.3_5'UTR	NM_018298	NP_060768	Q8TDD5	MCLN3_HUMAN	mucolipin 3	53						integral to membrane	ion channel activity			skin(1)	1				all cancers(265;0.00957)|Epithelial(280;0.0254)		CTCGAGCCCAGAACTTCTCAC	0.393													7	140	---	---	---	---	PASS
KCND3	3752	broad.mit.edu	37	1	112318709	112318709	+	Missense_Mutation	SNP	G	C	C			TCGA-EJ-5519-01A-01D-1576-08	TCGA-EJ-5519-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:112318709G>C	uc001ebu.1	-	8	2438	c.1958C>G	c.(1957-1959)TCC>TGC	p.S653C	KCND3_uc001ebv.1_Missense_Mutation_p.S634C	NM_004980	NP_004971	Q9UK17	KCND3_HUMAN	potassium voltage-gated channel, Shal-related	653	Cytoplasmic (Potential).					sarcolemma|voltage-gated potassium channel complex	A-type (transient outward) potassium channel activity|metal ion binding			ovary(2)|large_intestine(1)	3		all_cancers(81;8.52e-06)|all_epithelial(167;5.65e-06)|all_lung(203;2.72e-05)|Lung NSC(69;4.56e-05)		all cancers(265;0.056)|Lung(183;0.0576)|Colorectal(144;0.1)|Epithelial(280;0.104)|COAD - Colon adenocarcinoma(174;0.222)|LUSC - Lung squamous cell carcinoma(189;0.231)		TTACAAGGCGGAGACCTTGAC	0.612													29	82	---	---	---	---	PASS
NBPF10	100132406	broad.mit.edu	37	1	145209116	145209116	+	5'UTR	SNP	T	C	C	rs114878133	by1000genomes	TCGA-EJ-5519-01A-01D-1576-08	TCGA-EJ-5519-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:145209116T>C	uc001emp.3	+	1					NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|NOTCH2NL_uc001emn.3_5'UTR|NOTCH2NL_uc001emm.3_5'UTR|NOTCH2NL_uc001emo.2_5'UTR|NOTCH2NL_uc010oyh.1_RNA	NM_017940	NP_060410	A6NDV3	A6NDV3_HUMAN	hypothetical protein LOC55672												0	all_hematologic(923;0.032)			Colorectal(1306;1.36e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.00258)		ACGAGGCTGCTTCGCTGCACA	0.736													3	8	---	---	---	---	PASS
TXNIP	10628	broad.mit.edu	37	1	145441244	145441244	+	3'UTR	SNP	T	G	G			TCGA-EJ-5519-01A-01D-1576-08	TCGA-EJ-5519-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:145441244T>G	uc001enn.3	+	8					NBPF10_uc001emp.3_Intron|TXNIP_uc001enm.1_RNA|TXNIP_uc010oys.1_3'UTR	NM_006472	NP_006463	Q9H3M7	TXNIP_HUMAN	thioredoxin interacting protein						cell cycle|keratinocyte differentiation|transcription, DNA-dependent		ubiquitin protein ligase binding			ovary(2)	2	all_hematologic(18;0.0187)|Acute lymphoblastic leukemia(18;0.0786)					GAAGCAGCTTTACCTACTTGT	0.438													20	81	---	---	---	---	PASS
PIAS3	10401	broad.mit.edu	37	1	145580242	145580242	+	Missense_Mutation	SNP	A	G	G			TCGA-EJ-5519-01A-01D-1576-08	TCGA-EJ-5519-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:145580242A>G	uc001eoc.1	+	6	815	c.724A>G	c.(724-726)ATC>GTC	p.I242V	NBPF10_uc001emp.3_Intron|PIAS3_uc010oyy.1_Missense_Mutation_p.I233V|PIAS3_uc001eod.1_5'Flank	NM_006099	NP_006090	Q9Y6X2	PIAS3_HUMAN	protein inhibitor of activated STAT, 3	242	PINIT.				positive regulation of protein sumoylation|protein sumoylation|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nuclear speck	enzyme binding|nucleic acid binding|protein C-terminus binding|zinc ion binding			ovary(1)	1	all_hematologic(18;0.0187)|Acute lymphoblastic leukemia(18;0.0786)					CAGCCGCCCCATCAACATCAC	0.587													14	205	---	---	---	---	PASS
FLG	2312	broad.mit.edu	37	1	152275293	152275293	+	Silent	SNP	A	G	G			TCGA-EJ-5519-01A-01D-1576-08	TCGA-EJ-5519-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:152275293A>G	uc001ezu.1	-	3	12105	c.12069T>C	c.(12067-12069)GAT>GAC	p.D4023D		NM_002016	NP_002007	P20930	FILA_HUMAN	filaggrin	4023					keratinocyte differentiation	cytoplasmic membrane-bounded vesicle|intermediate filament	calcium ion binding|structural molecule activity			ovary(9)|skin(4)|upper_aerodigestive_tract(3)	16	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			ACCTTGGATGATCTTTACCAA	0.383									Ichthyosis				68	192	---	---	---	---	PASS
KIRREL	55243	broad.mit.edu	37	1	158057827	158057827	+	Missense_Mutation	SNP	G	A	A			TCGA-EJ-5519-01A-01D-1576-08	TCGA-EJ-5519-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:158057827G>A	uc001frn.3	+	7	1203	c.799G>A	c.(799-801)GCC>ACC	p.A267T	KIRREL_uc010pib.1_Missense_Mutation_p.A167T|KIRREL_uc009wsq.2_Missense_Mutation_p.A103T|KIRREL_uc001fro.3_Missense_Mutation_p.A65T	NM_018240	NP_060710	Q96J84	KIRR1_HUMAN	kin of IRRE like precursor	267	Extracellular (Potential).|Ig-like C2-type 3.					integral to membrane				ovary(1)	1	all_hematologic(112;0.0378)					GATTGAAGACGCCCACGAGAG	0.522											OREG0013906	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	14	276	---	---	---	---	PASS
OR6Y1	391112	broad.mit.edu	37	1	158517511	158517511	+	Missense_Mutation	SNP	C	A	A			TCGA-EJ-5519-01A-01D-1576-08	TCGA-EJ-5519-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:158517511C>A	uc010pil.1	-	1	385	c.385G>T	c.(385-387)GTA>TTA	p.V129L		NM_001005189	NP_001005189	Q8NGX8	OR6Y1_HUMAN	olfactory receptor, family 6, subfamily Y,	129	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)	1	all_hematologic(112;0.0378)					CAAATGGCTACATAGCGGTCA	0.473													6	86	---	---	---	---	PASS
IFI16	3428	broad.mit.edu	37	1	159021757	159021757	+	Missense_Mutation	SNP	G	A	A			TCGA-EJ-5519-01A-01D-1576-08	TCGA-EJ-5519-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:159021757G>A	uc001ftg.2	+	9	2076	c.1786G>A	c.(1786-1788)GAT>AAT	p.D596N	IFI16_uc010pis.1_Missense_Mutation_p.D596N|IFI16_uc001fth.2_Missense_Mutation_p.D139N|IFI16_uc010pit.1_Missense_Mutation_p.D195N	NM_005531	NP_005522	Q16666	IF16_HUMAN	interferon, gamma-inducible protein 16	652	HIN-200 2.				cell proliferation|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|monocyte differentiation|negative regulation of transcription, DNA-dependent|response to virus|transcription, DNA-dependent	cytoplasm|nuclear speck|nucleolus	double-stranded DNA binding|protein binding			ovary(1)	1	all_hematologic(112;0.0429)					ACTTGTGGCTGATGTGAATGC	0.428													7	180	---	---	---	---	PASS
IGSF8	93185	broad.mit.edu	37	1	160062140	160062140	+	Missense_Mutation	SNP	G	A	A			TCGA-EJ-5519-01A-01D-1576-08	TCGA-EJ-5519-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:160062140G>A	uc001fva.2	-	5	1703	c.1658C>T	c.(1657-1659)GCC>GTC	p.A553V	IGSF8_uc001fuz.2_Missense_Mutation_p.A553V|IGSF8_uc009wtf.2_Missense_Mutation_p.A553V	NM_052868	NP_443100	Q969P0	IGSF8_HUMAN	immunoglobulin superfamily, member 8	553	Ig-like C2-type 4.|Extracellular (Potential).				cell proliferation|cellular component movement|nervous system development|single fertilization|skeletal muscle tissue development	integral to membrane	protein binding				0	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)			GCTGTAGTCGGCATGCTGCAC	0.647													4	173	---	---	---	---	PASS
LY9	4063	broad.mit.edu	37	1	160783454	160783454	+	Missense_Mutation	SNP	G	C	C			TCGA-EJ-5519-01A-01D-1576-08	TCGA-EJ-5519-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:160783454G>C	uc001fwu.2	+	3	533	c.483G>C	c.(481-483)ATG>ATC	p.M161I	LY9_uc010pjs.1_Missense_Mutation_p.M161I|LY9_uc001fwv.2_Missense_Mutation_p.M161I|LY9_uc001fww.2_Missense_Mutation_p.M161I|LY9_uc001fwx.2_Missense_Mutation_p.M161I|LY9_uc001fwy.1_Missense_Mutation_p.M63I|LY9_uc001fwz.2_5'Flank	NM_002348	NP_002339	Q9HBG7	LY9_HUMAN	lymphocyte antigen 9 isoform a	161	Extracellular (Potential).|Ig-like C2-type 1.				cell adhesion|immunoglobulin mediated immune response	integral to membrane				ovary(1)	1	all_cancers(52;2.72e-17)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.00737)			AAGTCACCATGAAGTCTGTGA	0.532													10	114	---	---	---	---	PASS
POU2F1	5451	broad.mit.edu	37	1	167334739	167334739	+	Missense_Mutation	SNP	C	A	A			TCGA-EJ-5519-01A-01D-1576-08	TCGA-EJ-5519-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:167334739C>A	uc001gec.2	+	4	256	c.94C>A	c.(94-96)CCT>ACT	p.P32T	POU2F1_uc010plg.1_RNA|POU2F1_uc001ged.2_Missense_Mutation_p.P30T|POU2F1_uc001gee.2_Missense_Mutation_p.P32T|POU2F1_uc010plh.1_Missense_Mutation_p.P32T|POU2F1_uc001gef.2_Missense_Mutation_p.P44T	NM_002697	NP_002688	P14859	PO2F1_HUMAN	POU class 2 homeobox 1	32					negative regulation of transcription, DNA-dependent|transcription from RNA polymerase III promoter	nucleoplasm	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			central_nervous_system(2)|skin(2)|breast(1)	5						TCAGAAGCAGCCTGTGCCTGT	0.428													9	153	---	---	---	---	PASS
CEP350	9857	broad.mit.edu	37	1	179989287	179989287	+	Missense_Mutation	SNP	C	G	G			TCGA-EJ-5519-01A-01D-1576-08	TCGA-EJ-5519-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:179989287C>G	uc001gnt.2	+	12	2761	c.2378C>G	c.(2377-2379)ACT>AGT	p.T793S	CEP350_uc009wxl.2_Missense_Mutation_p.T792S|CEP350_uc001gnu.2_Missense_Mutation_p.T627S	NM_014810	NP_055625	Q5VT06	CE350_HUMAN	centrosome-associated protein 350	793						centrosome|nucleus|spindle				ovary(4)	4						AGGCCATTAACTTTTACACCT	0.378													63	131	---	---	---	---	PASS
HMCN1	83872	broad.mit.edu	37	1	186055463	186055463	+	Silent	SNP	T	G	G			TCGA-EJ-5519-01A-01D-1576-08	TCGA-EJ-5519-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:186055463T>G	uc001grq.1	+	58	9199	c.8970T>G	c.(8968-8970)GGT>GGG	p.G2990G		NM_031935	NP_114141	Q96RW7	HMCN1_HUMAN	hemicentin 1 precursor	2990	Ig-like C2-type 28.				response to stimulus|visual perception	basement membrane	calcium ion binding			ovary(22)|skin(1)	23						AGGTCTCTGGTTTTCCACCTC	0.408													27	114	---	---	---	---	PASS
LGTN	1939	broad.mit.edu	37	1	206778810	206778810	+	Missense_Mutation	SNP	G	A	A			TCGA-EJ-5519-01A-01D-1576-08	TCGA-EJ-5519-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:206778810G>A	uc001heh.2	-	5	682	c.473C>T	c.(472-474)ACG>ATG	p.T158M	LGTN_uc009xbw.2_Missense_Mutation_p.T158M|LGTN_uc010prw.1_3'UTR	NM_006893	NP_008824	P41214	EIF2D_HUMAN	ligatin	158	PUA.				intracellular protein transport	cytoplasm	protein binding|receptor activity|translation initiation factor activity				0	Breast(84;0.183)		BRCA - Breast invasive adenocarcinoma(75;0.166)			CAGGCCTGACGTGAGCATCTC	0.537													4	44	---	---	---	---	PASS
CR1L	1379	broad.mit.edu	37	1	207818635	207818635	+	Missense_Mutation	SNP	G	C	C			TCGA-EJ-5519-01A-01D-1576-08	TCGA-EJ-5519-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:207818635G>C	uc001hga.3	+	1	178	c.57G>C	c.(55-57)TTG>TTC	p.L19F	CR1L_uc001hfz.2_RNA	NM_175710	NP_783641	Q2VPA4	CR1L_HUMAN	complement component (3b/4b) receptor 1-like	19						cytoplasm|extracellular region|membrane					0						TTCCTGGGTTGCTTCTGGCGG	0.667													3	80	---	---	---	---	PASS
RASGRP3	25780	broad.mit.edu	37	2	33745725	33745725	+	Silent	SNP	C	T	T			TCGA-EJ-5519-01A-01D-1576-08	TCGA-EJ-5519-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:33745725C>T	uc002rox.2	+	7	969	c.342C>T	c.(340-342)CAC>CAT	p.H114H	RASGRP3_uc010ync.1_Silent_p.H114H|RASGRP3_uc002roy.2_Silent_p.H114H	NM_170672	NP_733772	Q8IV61	GRP3_HUMAN	RAS guanyl releasing protein 3 (calcium and	114	N-terminal Ras-GEF.				MAPKKK cascade|small GTPase mediated signal transduction	integral to plasma membrane|intracellular	calcium ion binding|diacylglycerol binding|guanyl-nucleotide exchange factor activity|protein binding|Rap GTPase activator activity|signal transducer activity			lung(3)|ovary(1)|pancreas(1)	5	all_hematologic(175;0.115)					ATGAAAAACACGTCAGCCTCA	0.448													92	159	---	---	---	---	PASS
ATL2	64225	broad.mit.edu	37	2	38525644	38525644	+	Missense_Mutation	SNP	G	A	A			TCGA-EJ-5519-01A-01D-1576-08	TCGA-EJ-5519-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:38525644G>A	uc002rqq.2	-	12	1304	c.1274C>T	c.(1273-1275)GCG>GTG	p.A425V	ATL2_uc010ynm.1_Missense_Mutation_p.A407V|ATL2_uc010ynn.1_Missense_Mutation_p.A407V|ATL2_uc010yno.1_Missense_Mutation_p.A254V|ATL2_uc002rqs.2_Missense_Mutation_p.A425V|ATL2_uc002rqr.2_Missense_Mutation_p.A254V	NM_001135673	NP_001129145	Q8NHH9	ATLA2_HUMAN	atlastin GTPase 2 isoform 2	425	Cytoplasmic.				endoplasmic reticulum organization|Golgi organization|protein homooligomerization	endoplasmic reticulum membrane|integral to membrane	GTP binding|GTPase activity|identical protein binding			ovary(1)|kidney(1)|skin(1)	3						TTGTTTTATCGCCACTTCCTT	0.428													5	270	---	---	---	---	PASS
ABCG5	64240	broad.mit.edu	37	2	44040309	44040309	+	Silent	SNP	A	T	T			TCGA-EJ-5519-01A-01D-1576-08	TCGA-EJ-5519-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:44040309A>T	uc002rtn.2	-	13	2042	c.1902T>A	c.(1900-1902)CTT>CTA	p.L634L	ABCG5_uc002rtm.2_Silent_p.L239L|ABCG5_uc002rto.2_Silent_p.L463L|ABCG5_uc002rtp.2_Silent_p.L239L	NM_022436	NP_071881	Q9H222	ABCG5_HUMAN	ATP-binding cassette sub-family G member 5	634	Helical; Name=6; (Potential).|ABC transmembrane type-2.				cholesterol efflux|cholesterol homeostasis|excretion|lipid metabolic process|negative regulation of intestinal cholesterol absorption|negative regulation of intestinal phytosterol absorption	apical plasma membrane|integral to membrane	ATP binding|ATPase activity|protein heterodimerization activity			ovary(1)|skin(1)	2		all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.175)				CTAGGATGACAAGAGCTGGAA	0.403													26	60	---	---	---	---	PASS
GPR75	10936	broad.mit.edu	37	2	54081085	54081085	+	Missense_Mutation	SNP	G	A	A			TCGA-EJ-5519-01A-01D-1576-08	TCGA-EJ-5519-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:54081085G>A	uc002rxo.3	-	2	1080	c.809C>T	c.(808-810)GCT>GTT	p.A270V	ASB3_uc002rxi.3_Intron	NM_006794	NP_006785	O95800	GPR75_HUMAN	G protein-coupled receptor 75	270	Cytoplasmic (Potential).					integral to plasma membrane	G-protein coupled receptor activity			ovary(1)|skin(1)	2			Lung(47;0.125)|LUSC - Lung squamous cell carcinoma(58;0.181)			CCTATACAGAGCCGGCATGGC	0.557													3	80	---	---	---	---	PASS
RETSAT	54884	broad.mit.edu	37	2	85571797	85571797	+	Missense_Mutation	SNP	G	C	C			TCGA-EJ-5519-01A-01D-1576-08	TCGA-EJ-5519-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:85571797G>C	uc002spd.2	-	7	1367	c.1176C>G	c.(1174-1176)ATC>ATG	p.I392M	RETSAT_uc010fge.2_RNA|RETSAT_uc010ysm.1_Missense_Mutation_p.I331M|RETSAT_uc010fgf.2_Missense_Mutation_p.I183M	NM_017750	NP_060220	Q6NUM9	RETST_HUMAN	all-trans-13,14-dihydroretinol saturase	392					retinol metabolic process	endoplasmic reticulum membrane|nuclear outer membrane	all-trans-retinol 13,14-reductase activity|electron carrier activity			ovary(2)	2					Vitamin A(DB00162)	CTCGCAGGCAGATGAAAACAG	0.592													3	77	---	---	---	---	PASS
GCC2	9648	broad.mit.edu	37	2	109116021	109116021	+	Missense_Mutation	SNP	G	A	A			TCGA-EJ-5519-01A-01D-1576-08	TCGA-EJ-5519-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:109116021G>A	uc002tec.2	+	22	4949	c.4795G>A	c.(4795-4797)GAA>AAA	p.E1599K	GCC2_uc002ted.2_Missense_Mutation_p.E1498K	NM_181453	NP_852118	Q8IWJ2	GCC2_HUMAN	GRIP and coiled-coil domain-containing 2	1599	Mediates interaction with RAB6A.|Potential.|Mediates interaction with RAB9A.				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						TCTCAAAAGTGAAATAAGAAG	0.388													6	138	---	---	---	---	PASS
SEPT10	151011	broad.mit.edu	37	2	110301775	110301775	+	3'UTR	SNP	C	A	A			TCGA-EJ-5519-01A-01D-1576-08	TCGA-EJ-5519-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:110301775C>A	uc002tew.2	-	11					SEPT10_uc010ywu.1_3'UTR|SEPT10_uc002tex.2_3'UTR|SEPT10_uc002tey.2_Missense_Mutation_p.G520V|SEPT10_uc010ywv.1_3'UTR|SEPT10_uc002tev.1_3'UTR|SEPT10_uc010fjo.2_RNA	NM_144710	NP_653311	Q9P0V9	SEP10_HUMAN	septin 10 isoform 1						cell cycle|cell division	septin complex	GTP binding				0						TGGCTGTTCACCAAATATAGA	0.299													19	22	---	---	---	---	PASS
TTC30B	150737	broad.mit.edu	37	2	178416809	178416809	+	Missense_Mutation	SNP	C	T	T			TCGA-EJ-5519-01A-01D-1576-08	TCGA-EJ-5519-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:178416809C>T	uc002uln.2	-	1	716	c.683G>A	c.(682-684)GGC>GAC	p.G228D	TTC30B_uc010zfc.1_5'UTR	NM_152517	NP_689730	Q8N4P2	TT30B_HUMAN	tetratricopeptide repeat domain 30B	228					cell projection organization	cilium	binding				0			OV - Ovarian serous cystadenocarcinoma(117;0.00151)|Epithelial(96;0.00931)|all cancers(119;0.0362)			AGTGGTCATGCCCACACCTAG	0.522													4	118	---	---	---	---	PASS
VWC2L	402117	broad.mit.edu	37	2	215278952	215278952	+	Missense_Mutation	SNP	T	G	G			TCGA-EJ-5519-01A-01D-1576-08	TCGA-EJ-5519-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:215278952T>G	uc002vet.2	+	2	165	c.35T>G	c.(34-36)CTG>CGG	p.L12R	VWC2L_uc010zjl.1_Missense_Mutation_p.L12R	NM_001080500	NP_001073969	B2RUY7	VWC2L_HUMAN	von Willebrand factor C domain-containing	12						extracellular region					0						TGCATACTTCTGTTGGTCATC	0.433													9	107	---	---	---	---	PASS
BARD1	580	broad.mit.edu	37	2	215645851	215645851	+	Silent	SNP	G	A	A			TCGA-EJ-5519-01A-01D-1576-08	TCGA-EJ-5519-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:215645851G>A	uc002veu.2	-	4	882	c.747C>T	c.(745-747)ATC>ATT	p.I249I	BARD1_uc010zjm.1_Silent_p.I105I	NM_000465	NP_000456	Q99728	BARD1_HUMAN	BRCA1 associated RING domain 1	249					cell cycle arrest|DNA repair|negative regulation of apoptosis|negative regulation of mRNA 3'-end processing|negative regulation of protein export from nucleus|positive regulation of apoptosis|positive regulation of protein catabolic process|protein K6-linked ubiquitination|regulation of phosphorylation|tissue homeostasis	BRCA1-A complex|BRCA1-BARD1 complex|cytoplasm	kinase binding|protein heterodimerization activity|protein homodimerization activity|RNA binding|ubiquitin-protein ligase activity|zinc ion binding			lung(2)	2		Renal(323;0.0243)		Epithelial(149;3.2e-06)|all cancers(144;0.000461)|LUSC - Lung squamous cell carcinoma(224;0.00829)|Lung(261;0.011)		GAGGACTGGAGATAACAGATG	0.383									Neuroblastoma_Familial_Clustering_of|Congenital_Central_Hypoventilation_Syndrome				54	115	---	---	---	---	PASS
STK36	27148	broad.mit.edu	37	2	219538385	219538385	+	Missense_Mutation	SNP	C	T	T			TCGA-EJ-5519-01A-01D-1576-08	TCGA-EJ-5519-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:219538385C>T	uc002viu.2	+	3	388	c.122C>T	c.(121-123)TCA>TTA	p.S41L	STK36_uc002viv.2_Missense_Mutation_p.S41L|RNF25_uc002vit.2_5'Flank|RNF25_uc010fvw.2_5'Flank	NM_015690	NP_056505	Q9NRP7	STK36_HUMAN	serine/threonine kinase 36	41	Protein kinase.				cilium assembly|positive regulation of hh target transcription factor activity|positive regulation of smoothened signaling pathway|post-embryonic development	aggresome|cytoplasm|focal adhesion|intermediate filament cytoskeleton|nucleus	ATP binding|protein serine/threonine kinase activity|transcription factor binding			ovary(4)|stomach(2)|lung(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)|breast(1)	11		Renal(207;0.0915)		Epithelial(149;9.65e-07)|all cancers(144;0.000174)|LUSC - Lung squamous cell carcinoma(224;0.00813)|Lung(261;0.00984)		TTGGGGCGCTCAGAGAAGGAG	0.448													20	39	---	---	---	---	PASS
DNAJB2	3300	broad.mit.edu	37	2	220145308	220145308	+	Missense_Mutation	SNP	G	A	A			TCGA-EJ-5519-01A-01D-1576-08	TCGA-EJ-5519-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:220145308G>A	uc002vkx.1	+	3	311	c.74G>A	c.(73-75)CGC>CAC	p.R25H	DNAJB2_uc010zla.1_Missense_Mutation_p.R25H|DNAJB2_uc002vkw.1_Missense_Mutation_p.R25H|DNAJB2_uc002vky.2_5'Flank|DNAJB2_uc010zlb.1_5'Flank	NM_006736	NP_006727	P25686	DNJB2_HUMAN	DnaJ (Hsp40) homolog, subfamily B, member 2	25	J.				ER-associated protein catabolic process|negative regulation of cell growth|negative regulation of cell proliferation|negative regulation of inclusion body assembly|negative regulation of protein deubiquitination|positive regulation of proteasomal ubiquitin-dependent protein catabolic process|positive regulation of protein ubiquitination|protein folding|response to unfolded protein	inclusion body	heat shock protein binding|Hsp70 protein binding|polyubiquitin binding|proteasome binding|protein binding|unfolded protein binding				0		Renal(207;0.0474)		Epithelial(149;1.97e-06)|all cancers(144;0.00028)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		AGGTATCGGCGCAAGGCTCTC	0.517													3	57	---	---	---	---	PASS
KIAA1486	57624	broad.mit.edu	37	2	226447105	226447105	+	Silent	SNP	G	A	A			TCGA-EJ-5519-01A-01D-1576-08	TCGA-EJ-5519-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:226447105G>A	uc002voe.2	+	4	1147	c.972G>A	c.(970-972)CCG>CCA	p.P324P	KIAA1486_uc010fxa.1_Intron|KIAA1486_uc002vof.1_Silent_p.P94P	NM_020864	NP_065915	Q9P242	K1486_HUMAN	hypothetical protein LOC57624	324	Pro-rich.									ovary(2)|central_nervous_system(1)	3		Renal(207;0.0112)|all_lung(227;0.0477)|Lung NSC(271;0.0644)|all_hematologic(139;0.101)|Esophageal squamous(248;0.129)		Epithelial(121;6.73e-10)|all cancers(144;4.32e-07)|Lung(261;0.0161)|LUSC - Lung squamous cell carcinoma(224;0.0223)		ACATCCCTCCGCCCTTCCCCA	0.647													8	40	---	---	---	---	PASS
PRR21	643905	broad.mit.edu	37	2	240982080	240982080	+	Missense_Mutation	SNP	C	G	G	rs143810849	byFrequency	TCGA-EJ-5519-01A-01D-1576-08	TCGA-EJ-5519-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:240982080C>G	uc010zod.1	-	1	320	c.320G>C	c.(319-321)CGT>CCT	p.R107P		NM_001080835	NP_001074304	Q8WXC7	PRR21_HUMAN	proline rich 21	107	Pro-rich.									ovary(1)|skin(1)	2						GAGGCATGGACGAAGGGCCGT	0.617													7	61	---	---	---	---	PASS
LRRC3B	116135	broad.mit.edu	37	3	26751543	26751543	+	Missense_Mutation	SNP	G	C	C			TCGA-EJ-5519-01A-01D-1576-08	TCGA-EJ-5519-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:26751543G>C	uc003cdp.2	+	2	969	c.380G>C	c.(379-381)AGT>ACT	p.S127T	LRRC3B_uc003cdq.2_Missense_Mutation_p.S127T	NM_052953	NP_443185	Q96PB8	LRC3B_HUMAN	leucine rich repeat containing 3B precursor	127	LRR 3.					integral to membrane				pancreas(2)|ovary(1)|skin(1)	4						CGGATTCAAAGTGTGCACAAA	0.478													25	43	---	---	---	---	PASS
XIRP1	165904	broad.mit.edu	37	3	39226607	39226607	+	Missense_Mutation	SNP	G	T	T			TCGA-EJ-5519-01A-01D-1576-08	TCGA-EJ-5519-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:39226607G>T	uc003cjk.1	-	2	4551	c.4330C>A	c.(4330-4332)CCC>ACC	p.P1444T	XIRP1_uc003cji.2_3'UTR|XIRP1_uc003cjj.2_Missense_Mutation_p.P127T	NM_194293	NP_919269	Q702N8	XIRP1_HUMAN	xin actin-binding repeat containing 1	1444							actin binding			ovary(4)|breast(2)|central_nervous_system(1)|pancreas(1)	8				KIRC - Kidney renal clear cell carcinoma(284;0.0517)|Kidney(284;0.065)		TCTCCTGAGGGGCCGGGGCCC	0.612													34	112	---	---	---	---	PASS
C3orf23	285343	broad.mit.edu	37	3	44399287	44399287	+	Silent	SNP	G	C	C			TCGA-EJ-5519-01A-01D-1576-08	TCGA-EJ-5519-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:44399287G>C	uc010him.2	+	3	329	c.84G>C	c.(82-84)TCG>TCC	p.S28S	C3orf23_uc003cnd.3_Silent_p.S28S|C3orf23_uc003cne.3_5'UTR|C3orf23_uc003cnb.3_Silent_p.S28S|C3orf23_uc003cnc.3_Silent_p.S28S	NM_173826	NP_776187	Q8N3R3	CC023_HUMAN	hypothetical protein LOC285343 isoform 1	28						mitochondrion				upper_aerodigestive_tract(1)|ovary(1)|skin(1)	3				KIRC - Kidney renal clear cell carcinoma(197;0.0468)|Kidney(197;0.0585)		GAGCTTTATCGGGAGCTGAAG	0.398													40	78	---	---	---	---	PASS
CCR9	10803	broad.mit.edu	37	3	45942586	45942586	+	Silent	SNP	C	T	T			TCGA-EJ-5519-01A-01D-1576-08	TCGA-EJ-5519-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:45942586C>T	uc003coz.1	+	3	463	c.306C>T	c.(304-306)CCC>CCT	p.P102P	LZTFL1_uc003coy.1_Intron|LZTFL1_uc011bak.1_Intron|CCR9_uc010hiv.1_Silent_p.P90P|CCR9_uc003cpa.1_Silent_p.P90P	NM_031200	NP_112477	P51686	CCR9_HUMAN	chemokine (C-C motif) receptor 9 isoform A	102	Helical; Name=2; (Potential).				cellular defense response|chemotaxis|elevation of cytosolic calcium ion concentration|immune response	integral to plasma membrane				ovary(2)|breast(1)	3				BRCA - Breast invasive adenocarcinoma(193;0.00118)|KIRC - Kidney renal clear cell carcinoma(197;0.0182)|Kidney(197;0.0214)		TCACTCTTCCCTTCTGGGCCA	0.473													8	396	---	---	---	---	PASS
EIF4G1	1981	broad.mit.edu	37	3	184040943	184040943	+	Missense_Mutation	SNP	C	G	G			TCGA-EJ-5519-01A-01D-1576-08	TCGA-EJ-5519-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:184040943C>G	uc003fnp.2	+	14	2200	c.2002C>G	c.(2002-2004)CCA>GCA	p.P668A	EIF4G1_uc003fno.1_Missense_Mutation_p.P609A|EIF4G1_uc010hxw.1_Missense_Mutation_p.P504A|EIF4G1_uc003fnt.2_Missense_Mutation_p.P379A|EIF4G1_uc003fnq.2_Missense_Mutation_p.P581A|EIF4G1_uc003fnr.2_Missense_Mutation_p.P504A|EIF4G1_uc010hxx.2_Missense_Mutation_p.P675A|EIF4G1_uc003fns.2_Missense_Mutation_p.P628A|EIF4G1_uc010hxy.2_Missense_Mutation_p.P675A|EIF4G1_uc003fnv.3_Missense_Mutation_p.P668A|EIF4G1_uc003fnu.3_Missense_Mutation_p.P668A|EIF4G1_uc003fnw.2_Missense_Mutation_p.P675A|EIF4G1_uc003fnx.2_Missense_Mutation_p.P472A|EIF4G1_uc003fny.3_Missense_Mutation_p.P472A|SNORD66_uc003fnz.2_5'Flank	NM_198241	NP_937884	Q04637	IF4G1_HUMAN	eukaryotic translation initiation factor 4	668	MIF4G.				insulin receptor signaling pathway|interspecies interaction between organisms|nuclear-transcribed mRNA poly(A) tail shortening|regulation of translational initiation	cytosol|eukaryotic translation initiation factor 4F complex	protein binding|translation initiation factor activity			lung(2)|ovary(2)|upper_aerodigestive_tract(1)|large_intestine(1)|central_nervous_system(1)	7	all_cancers(143;1.06e-10)|Ovarian(172;0.0339)		Epithelial(37;1.53e-33)|OV - Ovarian serous cystadenocarcinoma(80;2.72e-22)			AGACTTCACTCCATCCTTTGC	0.607													5	190	---	---	---	---	PASS
DNAJB11	51726	broad.mit.edu	37	3	186302301	186302301	+	Missense_Mutation	SNP	A	G	G			TCGA-EJ-5519-01A-01D-1576-08	TCGA-EJ-5519-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:186302301A>G	uc003fqi.2	+	9	1155	c.935A>G	c.(934-936)AAC>AGC	p.N312S		NM_016306	NP_057390	Q9UBS4	DJB11_HUMAN	DnaJ (Hsp40) homolog, subfamily B, member 11	312					protein folding	endoplasmic reticulum lumen	heat shock protein binding			ovary(1)|lung(1)	2	all_cancers(143;2.84e-12)|Ovarian(172;0.0339)		OV - Ovarian serous cystadenocarcinoma(80;1.44e-20)	GBM - Glioblastoma multiforme(93;0.0476)		TTTGACAACAACAATATCAAG	0.408													25	39	---	---	---	---	PASS
PPEF2	5470	broad.mit.edu	37	4	76813115	76813115	+	Silent	SNP	G	A	A			TCGA-EJ-5519-01A-01D-1576-08	TCGA-EJ-5519-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:76813115G>A	uc003hix.2	-	3	429	c.72C>T	c.(70-72)GCC>GCT	p.A24A	PPEF2_uc003hiy.2_RNA|PPEF2_uc003hiz.1_Silent_p.A24A	NM_006239	NP_006230	O14830	PPE2_HUMAN	serine/threonine protein phosphatase with	24	IQ.				detection of stimulus involved in sensory perception|negative regulation of MAPKKK cascade|negative regulation of peptidyl-threonine phosphorylation|protein dephosphorylation|visual perception	cytoplasm|photoreceptor inner segment|photoreceptor outer segment	calcium ion binding|Hsp70 protein binding|Hsp90 protein binding|iron ion binding|manganese ion binding|mitogen-activated protein kinase kinase kinase binding|protein serine/threonine phosphatase activity			ovary(2)|lung(1)|central_nervous_system(1)	4			Lung(101;0.0809)|LUSC - Lung squamous cell carcinoma(112;0.0934)			TCTGGATCAGGGCTGCTGCCT	0.607													19	69	---	---	---	---	PASS
GHR	2690	broad.mit.edu	37	5	42718930	42718930	+	Missense_Mutation	SNP	C	A	A			TCGA-EJ-5519-01A-01D-1576-08	TCGA-EJ-5519-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:42718930C>A	uc003jmt.2	+	10	1364	c.1321C>A	c.(1321-1323)CCT>ACT	p.P441T	GHR_uc011cpq.1_Missense_Mutation_p.P254T	NM_000163	NP_000154	P10912	GHR_HUMAN	growth hormone receptor precursor	441	Cytoplasmic (Potential).				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)	TGATGCTTGCCCTGCTACTCA	0.463													4	83	---	---	---	---	PASS
AP3S1	1176	broad.mit.edu	37	5	115238635	115238635	+	Silent	SNP	T	C	C	rs147903679	byFrequency	TCGA-EJ-5519-01A-01D-1576-08	TCGA-EJ-5519-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:115238635T>C	uc003krl.2	+	5	515	c.399T>C	c.(397-399)AAT>AAC	p.N133N	AP3S1_uc003krk.2_Silent_p.N111N|AP3S1_uc003krm.2_Intron	NM_001284	NP_001275	Q92572	AP3S1_HUMAN	adaptor-related protein complex 3, sigma 1	133					insulin receptor signaling pathway|intracellular protein transport|vesicle-mediated transport	AP-type membrane coat adaptor complex|cytoplasmic vesicle membrane|Golgi apparatus|transport vesicle	protein binding|protein transporter activity				0		all_cancers(142;0.00377)|all_epithelial(76;0.000129)|Prostate(80;0.0132)|Ovarian(225;0.0776)|Lung NSC(810;0.245)		OV - Ovarian serous cystadenocarcinoma(64;1.08e-07)|Epithelial(69;1.11e-06)|all cancers(49;5.2e-05)		TGGAGACAAATATGAATGAGA	0.328													3	107	---	---	---	---	PASS
CHSY3	337876	broad.mit.edu	37	5	129520761	129520761	+	Silent	SNP	A	G	G			TCGA-EJ-5519-01A-01D-1576-08	TCGA-EJ-5519-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:129520761A>G	uc003kvd.2	+	3	1926	c.1926A>G	c.(1924-1926)GAA>GAG	p.E642E		NM_175856	NP_787052	Q70JA7	CHSS3_HUMAN	chondroitin sulfate synthase 3	642	Lumenal (Potential).					Golgi cisterna membrane|integral to membrane	glucuronosyl-N-acetylgalactosaminyl-proteoglycan 4-beta-N-acetylgalactosaminyltransferase activity|metal ion binding|N-acetylgalactosaminyl-proteoglycan 3-beta-glucuronosyltransferase activity			ovary(2)|pancreas(1)	3		all_cancers(142;0.0227)|Breast(839;0.198)|Prostate(80;0.215)|Lung NSC(810;0.239)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)	OV - Ovarian serous cystadenocarcinoma(64;0.136)		AGAACTTTGAAAACATGTGTC	0.403													3	161	---	---	---	---	PASS
PCDHA12	56137	broad.mit.edu	37	5	140255276	140255276	+	Missense_Mutation	SNP	C	A	A			TCGA-EJ-5519-01A-01D-1576-08	TCGA-EJ-5519-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140255276C>A	uc003lic.2	+	1	346	c.219C>A	c.(217-219)GAC>GAA	p.D73E	PCDHA1_uc003lha.2_Intron|PCDHA1_uc003lhb.2_Intron|PCDHA2_uc003lhd.2_Intron|PCDHA3_uc003lhf.2_Intron|PCDHA4_uc003lhi.2_Intron|PCDHA4_uc003lhh.1_Intron|PCDHA5_uc003lhk.1_Intron|PCDHA5_uc003lhl.2_Intron|PCDHA6_uc003lhn.2_Intron|PCDHA6_uc003lho.2_Intron|PCDHA7_uc003lhq.2_Intron|PCDHA8_uc003lhs.2_Intron|PCDHA9_uc003lhu.2_Intron|PCDHA10_uc003lhw.2_Intron|PCDHA10_uc003lhx.2_Intron|PCDHA11_uc003lia.2_Intron|PCDHA12_uc011daf.1_Missense_Mutation_p.D73E	NM_018903	NP_061726	Q9UN75	PCDAC_HUMAN	protocadherin alpha 12 isoform 1 precursor	73	Cadherin 1.|Extracellular (Potential).				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding|protein binding				0			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GACACGGGGACCTTCTGGAGG	0.622													59	134	---	---	---	---	PASS
LARP1	23367	broad.mit.edu	37	5	154182914	154182914	+	Missense_Mutation	SNP	C	A	A			TCGA-EJ-5519-01A-01D-1576-08	TCGA-EJ-5519-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:154182914C>A	uc003lvp.2	+	12	2603	c.2174C>A	c.(2173-2175)CCT>CAT	p.P725H	LARP1_uc003lvo.2_Missense_Mutation_p.P648H|LARP1_uc010jie.1_Missense_Mutation_p.P520H	NM_033551	NP_291029	Q6PKG0	LARP1_HUMAN	la related protein isoform 2	725							protein binding|RNA binding			ovary(2)|pancreas(1)|skin(1)	4	Renal(175;0.00488)	Medulloblastoma(196;0.0354)|all_neural(177;0.147)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)			ACACTGACCCCTGAGCCCCCT	0.532													3	59	---	---	---	---	PASS
PBX2	5089	broad.mit.edu	37	6	32156280	32156280	+	Silent	SNP	G	T	T			TCGA-EJ-5519-01A-01D-1576-08	TCGA-EJ-5519-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:32156280G>T	uc003oav.1	-	3	568	c.297C>A	c.(295-297)GGC>GGA	p.G99G	PBX2_uc003oaw.2_Silent_p.G99G	NM_002586	NP_002577	P40425	PBX2_HUMAN	pre-B-cell leukemia homeobox 2	99							transcription factor binding			ovary(1)	1						GAATGCTGAGGCCTAGCATGC	0.612													5	59	---	---	---	---	PASS
GRM4	2914	broad.mit.edu	37	6	34100899	34100899	+	Silent	SNP	C	T	T			TCGA-EJ-5519-01A-01D-1576-08	TCGA-EJ-5519-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:34100899C>T	uc003oir.3	-	1	545	c.375G>A	c.(373-375)GCG>GCA	p.A125A	GRM4_uc011dsn.1_Silent_p.A125A|GRM4_uc010jvh.2_Silent_p.A125A|GRM4_uc010jvi.2_5'UTR|GRM4_uc010jvk.1_Silent_p.A44A	NM_000841	NP_000832	Q14833	GRM4_HUMAN	glutamate receptor, metabotropic 4 precursor	125	Extracellular (Potential).				activation of MAPK activity|inhibition of adenylate cyclase activity by metabotropic glutamate receptor signaling pathway|neuroprotection|neurotransmitter secretion|positive regulation of MAPKKK cascade	cytoplasmic vesicle|integral to plasma membrane	G-protein coupled receptor activity|glutamate receptor activity			lung(3)|upper_aerodigestive_tract(1)|ovary(1)|skin(1)	6					L-Glutamic Acid(DB00142)	TCTCGATGAGCGCCTGCACAA	0.632													16	19	---	---	---	---	PASS
CRISP2	7180	broad.mit.edu	37	6	49666128	49666128	+	Missense_Mutation	SNP	C	G	G			TCGA-EJ-5519-01A-01D-1576-08	TCGA-EJ-5519-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:49666128C>G	uc003ozq.2	-	7	620	c.364G>C	c.(364-366)GTC>CTC	p.V122L	CRISP2_uc003ozl.2_Missense_Mutation_p.V122L|CRISP2_uc003ozn.2_Missense_Mutation_p.V122L|CRISP2_uc003ozr.2_Missense_Mutation_p.V122L|CRISP2_uc003ozo.2_Missense_Mutation_p.V122L|CRISP2_uc003ozm.2_Missense_Mutation_p.V122L|CRISP2_uc003ozp.2_Missense_Mutation_p.V122L	NM_001142408	NP_001135880	P16562	CRIS2_HUMAN	cysteine-rich secretory protein 2 precursor	122						extracellular space				skin(1)	1	Lung NSC(77;0.0161)		KIRC - Kidney renal clear cell carcinoma(2;0.106)|Kidney(12;0.156)			ACACCATAGACAAAATCTAGG	0.413													4	182	---	---	---	---	PASS
ZNF292	23036	broad.mit.edu	37	6	87969737	87969737	+	Silent	SNP	C	T	T	rs3734187	by1000genomes	TCGA-EJ-5519-01A-01D-1576-08	TCGA-EJ-5519-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:87969737C>T	uc003plm.3	+	8	6431	c.6390C>T	c.(6388-6390)AAC>AAT	p.N2130N		NM_015021	NP_055836	O60281	ZN292_HUMAN	zinc finger protein 292	2130	C2H2-type 11.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(4)	4		all_cancers(76;3.82e-09)|Prostate(29;1.34e-10)|Acute lymphoblastic leukemia(125;2.17e-10)|all_hematologic(105;1.08e-06)|all_epithelial(107;5.31e-05)		BRCA - Breast invasive adenocarcinoma(108;0.0199)		TACAGCAAAACTTGATTCTCC	0.433													3	93	---	---	---	---	PASS
FOXO3	2309	broad.mit.edu	37	6	108985269	108985269	+	Silent	SNP	C	T	T	rs34079373	by1000genomes	TCGA-EJ-5519-01A-01D-1576-08	TCGA-EJ-5519-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:108985269C>T	uc003psk.2	+	3	1549	c.1233C>T	c.(1231-1233)AGC>AGT	p.S411S	FOXO3_uc003psn.2_Intron|FOXO3_uc003psm.2_Silent_p.S411S|FOXO3_uc011ean.1_Silent_p.S191S|FOXO3_uc010kdj.1_Silent_p.S191S	NM_201559	NP_963853	O43524	FOXO3_HUMAN	forkhead box O3A	411					antral ovarian follicle growth|apoptosis|embryo development|glucose homeostasis|induction of apoptosis|initiation of primordial ovarian follicle growth|insulin receptor signaling pathway|negative regulation of transcription from RNA polymerase II promoter|nerve growth factor receptor signaling pathway|oocyte maturation|ovulation from ovarian follicle|pattern specification process|phosphatidylinositol-mediated signaling|positive regulation of erythrocyte differentiation|positive regulation of transcription from RNA polymerase II promoter|regulation of cell proliferation|regulation of sequence-specific DNA binding transcription factor activity|tissue development	cytosol|transcription factor complex	DNA bending activity|double-stranded DNA binding|promoter binding|protein kinase binding|sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|specific RNA polymerase II transcription factor activity|specific transcriptional repressor activity|transcription factor binding			central_nervous_system(4)|lung(2)	6		all_cancers(87;1.78e-07)|Acute lymphoblastic leukemia(125;2.66e-08)|all_hematologic(75;1.13e-06)|all_epithelial(87;3.88e-05)|Colorectal(196;0.0294)|all_lung(197;0.0487)|Lung SC(18;0.152)		Epithelial(106;0.000759)|all cancers(137;0.00121)|BRCA - Breast invasive adenocarcinoma(108;0.00163)|OV - Ovarian serous cystadenocarcinoma(136;0.00718)		TGCAGCGGAGCTCTAGCTTCC	0.592													4	86	---	---	---	---	PASS
SLC22A16	85413	broad.mit.edu	37	6	110752470	110752470	+	Silent	SNP	C	T	T			TCGA-EJ-5519-01A-01D-1576-08	TCGA-EJ-5519-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:110752470C>T	uc003puf.2	-	7	1492	c.1425G>A	c.(1423-1425)TCG>TCA	p.S475S	SLC22A16_uc003pue.2_Silent_p.S456S	NM_033125	NP_149116	Q86VW1	S22AG_HUMAN	solute carrier family 22, member 16	475					acid secretion|cell differentiation|multicellular organismal development|single fertilization|sperm motility|spermatogenesis	integral to membrane	carnitine transporter activity			ovary(1)	1		all_cancers(87;0.00221)|Acute lymphoblastic leukemia(125;2.27e-07)|all_hematologic(75;1.38e-05)|all_epithelial(87;0.0485)|Colorectal(196;0.101)		OV - Ovarian serous cystadenocarcinoma(136;0.0513)|Epithelial(106;0.0921)|all cancers(137;0.115)		CCACAGCCAGCGATCTGGAAA	0.587													16	23	---	---	---	---	PASS
MOXD1	26002	broad.mit.edu	37	6	132695782	132695782	+	Missense_Mutation	SNP	G	T	T			TCGA-EJ-5519-01A-01D-1576-08	TCGA-EJ-5519-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:132695782G>T	uc003qdf.2	-	2	498	c.399C>A	c.(397-399)GAC>GAA	p.D133E	MOXD1_uc003qde.2_Missense_Mutation_p.D65E	NM_015529	NP_056344	Q6UVY6	MOXD1_HUMAN	monooxygenase, DBH-like 1 isoform 2	133	Lumenal (Potential).|DOMON.				catecholamine metabolic process	endoplasmic reticulum membrane|integral to membrane	copper ion binding|dopamine beta-monooxygenase activity			ovary(1)	1	Breast(56;0.0495)			OV - Ovarian serous cystadenocarcinoma(155;0.0132)|GBM - Glioblastoma multiforme(226;0.0191)		TTATACTCTTGTCATTTATGT	0.343													61	156	---	---	---	---	PASS
NUP43	348995	broad.mit.edu	37	6	150048281	150048281	+	Missense_Mutation	SNP	G	A	A			TCGA-EJ-5519-01A-01D-1576-08	TCGA-EJ-5519-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:150048281G>A	uc003qmz.2	-	8	1024	c.967C>T	c.(967-969)CAC>TAC	p.H323Y	NUP43_uc003qmx.3_RNA|NUP43_uc011eee.1_RNA|NUP43_uc011eef.1_Missense_Mutation_p.H227Y	NM_198887	NP_942590	Q8NFH3	NUP43_HUMAN	nucleoporin 43kDa	323					carbohydrate metabolic process|cell division|chromosome segregation|glucose transport|mitotic prometaphase|mRNA transport|protein transport|regulation of glucose transport|transmembrane transport|viral reproduction	condensed chromosome kinetochore|cytosol|Nup107-160 complex	protein binding			upper_aerodigestive_tract(1)	1		Ovarian(120;0.0164)		OV - Ovarian serous cystadenocarcinoma(155;4.71e-13)|GBM - Glioblastoma multiforme(68;0.101)		ACAGACTGGTGAACATTAGCT	0.393													8	70	---	---	---	---	PASS
SYNE1	23345	broad.mit.edu	37	6	152647137	152647137	+	Missense_Mutation	SNP	T	A	A			TCGA-EJ-5519-01A-01D-1576-08	TCGA-EJ-5519-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:152647137T>A	uc010kiw.2	-	80	15996	c.15394A>T	c.(15394-15396)ACT>TCT	p.T5132S	SYNE1_uc003qot.3_Missense_Mutation_p.T5061S|SYNE1_uc003qou.3_Missense_Mutation_p.T5132S|SYNE1_uc010kiz.2_Missense_Mutation_p.T887S	NM_182961	NP_892006	Q8NF91	SYNE1_HUMAN	spectrin repeat containing, nuclear envelope 1	5132	Spectrin 16.|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)		CTAGACGAAGTCTTCAACAAA	0.348										HNSCC(10;0.0054)			46	79	---	---	---	---	PASS
ABCA13	154664	broad.mit.edu	37	7	48318294	48318294	+	Silent	SNP	T	C	C			TCGA-EJ-5519-01A-01D-1576-08	TCGA-EJ-5519-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:48318294T>C	uc003toq.2	+	18	7528	c.7503T>C	c.(7501-7503)ACT>ACC	p.T2501T	ABCA13_uc010kys.1_5'Flank	NM_152701	NP_689914	Q86UQ4	ABCAD_HUMAN	ATP binding cassette, sub-family A (ABC1),	2501					transport	integral to membrane	ATP binding|ATPase activity			ovary(5)|central_nervous_system(4)|skin(1)	10						TGTCTGGGACTCTGGTCATGC	0.428													29	378	---	---	---	---	PASS
NSUN5P2	260294	broad.mit.edu	37	7	72430608	72430608	+	Missense_Mutation	SNP	G	T	T			TCGA-EJ-5519-01A-01D-1576-08	TCGA-EJ-5519-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:72430608G>T	uc010lao.2	-	4	743	c.670C>A	c.(670-672)CAA>AAA	p.Q224K	uc003tws.1_Missense_Mutation_p.Q224K	NM_198853	NP_942150			tripartite motif-containing 74												0						CACTCGGCTTGGGCCAGCCGC	0.672													5	80	---	---	---	---	PASS
BET1	10282	broad.mit.edu	37	7	93633528	93633528	+	Missense_Mutation	SNP	T	A	A			TCGA-EJ-5519-01A-01D-1576-08	TCGA-EJ-5519-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:93633528T>A	uc003unf.1	-	1	163	c.1A>T	c.(1-3)ATG>TTG	p.M1L	BET1_uc003une.3_RNA	NM_005868	NP_005859	O15155	BET1_HUMAN	blocked early in transport 1	1	Cytoplasmic (Potential).				ER to Golgi vesicle-mediated transport|protein transport	endoplasmic reticulum membrane|Golgi membrane|integral to membrane	protein binding				0	all_cancers(62;2.22e-10)|all_epithelial(64;1.38e-09)|Lung NSC(181;0.218)	Breast(660;0.000162)|Ovarian(593;0.000626)	STAD - Stomach adenocarcinoma(171;0.000967)			GCACGCCTCATCCTGCCAGAG	0.632													37	76	---	---	---	---	PASS
PEG10	23089	broad.mit.edu	37	7	94293408	94293408	+	Silent	SNP	T	C	C			TCGA-EJ-5519-01A-01D-1576-08	TCGA-EJ-5519-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:94293408T>C	uc011kie.1	+	2	985	c.768T>C	c.(766-768)TCT>TCC	p.S256S		NM_001040152	NP_001035242	Q86TG7	PEG10_HUMAN	paternally expressed 10 isoform RF1	180	Necessary for interaction with ALK1.				apoptosis|cell differentiation|negative regulation of transforming growth factor beta receptor signaling pathway	cytoplasm|nucleus	DNA binding|protein binding|zinc ion binding			central_nervous_system(1)	1	all_cancers(62;8.26e-10)|all_epithelial(64;5.59e-09)|Lung NSC(181;0.188)|all_lung(186;0.215)		STAD - Stomach adenocarcinoma(171;0.0031)			GCATGGGGTCTGTCATCGACT	0.547													25	271	---	---	---	---	PASS
SPDYE6	729597	broad.mit.edu	37	7	101987483	101987483	+	3'UTR	SNP	C	T	T			TCGA-EJ-5519-01A-01D-1576-08	TCGA-EJ-5519-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:101987483C>T	uc011kkp.1	-	8					SPDYE6_uc003uzb.2_3'UTR	NM_001146210	NP_001139682	P0CI01	SPDE6_HUMAN	speedy homolog E6												0						CCCCACCCCCCTCCCCCCACC	0.522													2	4	---	---	---	---	PASS
RINT1	60561	broad.mit.edu	37	7	105190573	105190573	+	Missense_Mutation	SNP	G	C	C			TCGA-EJ-5519-01A-01D-1576-08	TCGA-EJ-5519-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:105190573G>C	uc003vda.1	+	8	1299	c.1068G>C	c.(1066-1068)CAG>CAC	p.Q356H	RINT1_uc010ljj.1_Intron	NM_021930	NP_068749	Q6NUQ1	RINT1_HUMAN	RAD50 interactor 1	356	RINT1/TIP20.				cell cycle|G2/M transition DNA damage checkpoint|protein transport|vesicle-mediated transport	endoplasmic reticulum membrane	protein binding			ovary(3)|central_nervous_system(1)	4						AGAAGATTCAGCCAATATTAG	0.378													8	117	---	---	---	---	PASS
MLL3	58508	broad.mit.edu	37	7	151932988	151932988	+	Nonsense_Mutation	SNP	T	A	A			TCGA-EJ-5519-01A-01D-1576-08	TCGA-EJ-5519-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:151932988T>A	uc003wla.2	-	16	2902	c.2683A>T	c.(2683-2685)AGA>TGA	p.R895*	MLL3_uc003wkz.2_5'UTR	NM_170606	NP_733751	Q8NEZ4	MLL3_HUMAN	myeloid/lymphoid or mixed-lineage leukemia 3	895					intracellular signal transduction|regulation of transcription, DNA-dependent|transcription, DNA-dependent		DNA binding|protein binding|zinc ion binding			large_intestine(27)|pancreas(13)|ovary(9)|central_nervous_system(8)|breast(3)|upper_aerodigestive_tract(1)|urinary_tract(1)|skin(1)	63	all_neural(206;0.187)	all_hematologic(28;0.0592)|Prostate(32;0.0906)	OV - Ovarian serous cystadenocarcinoma(82;0.00715)	UCEC - Uterine corpus endometrioid carcinoma (81;0.0597)|BRCA - Breast invasive adenocarcinoma(188;0.0462)		CCTCGAGGTCTCCGCTTTCCT	0.502			N		medulloblastoma								4	104	---	---	---	---	PASS
DPP6	1804	broad.mit.edu	37	7	154667617	154667617	+	Missense_Mutation	SNP	G	A	A			TCGA-EJ-5519-01A-01D-1576-08	TCGA-EJ-5519-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:154667617G>A	uc003wlk.2	+	20	2014	c.1885G>A	c.(1885-1887)GAT>AAT	p.D629N	DPP6_uc003wli.2_Missense_Mutation_p.D565N|DPP6_uc003wlm.2_Missense_Mutation_p.D567N|DPP6_uc011kvq.1_Missense_Mutation_p.D522N	NM_130797	NP_570629	P42658	DPP6_HUMAN	dipeptidyl-peptidase 6 isoform 1	629	Extracellular (Potential).				cell death|proteolysis	integral to membrane	dipeptidyl-peptidase activity|serine-type peptidase activity			pancreas(3)|breast(1)	4	all_neural(206;0.181)	all_hematologic(28;0.0044)|all_lung(21;0.0176)|Lung NSC(21;0.0204)	OV - Ovarian serous cystadenocarcinoma(82;0.0562)			TCTTTCCAGGGATGGCACCCC	0.632													5	13	---	---	---	---	PASS
MTMR7	9108	broad.mit.edu	37	8	17169089	17169089	+	Silent	SNP	C	T	T			TCGA-EJ-5519-01A-01D-1576-08	TCGA-EJ-5519-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:17169089C>T	uc003wxm.2	-	9	1271	c.1032G>A	c.(1030-1032)AGG>AGA	p.R344R	MTMR7_uc003wxn.2_Silent_p.R123R|MTMR7_uc011kya.1_5'UTR|MTMR7_uc011kyb.1_5'UTR	NM_004686	NP_004677	Q9Y216	MTMR7_HUMAN	myotubularin related protein 7	344	Myotubularin phosphatase.|Substrate binding (By similarity).						protein tyrosine phosphatase activity			skin(1)	1				Colorectal(111;0.112)		CCTGAGCGGTCCTGTCCCAGC	0.567													37	203	---	---	---	---	PASS
EBF2	64641	broad.mit.edu	37	8	25745379	25745379	+	Silent	SNP	C	A	A			TCGA-EJ-5519-01A-01D-1576-08	TCGA-EJ-5519-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:25745379C>A	uc003xes.1	-	9	878	c.861G>T	c.(859-861)GGG>GGT	p.G287G	PPP2R2A_uc003xek.2_Intron|EBF2_uc010lug.1_RNA	NM_022659	NP_073150	Q9HAK2	COE2_HUMAN	early B-cell factor 2	287	IPT/TIG.				multicellular organismal development|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|metal ion binding			ovary(3)|skin(1)	4		all_cancers(63;0.0989)|Ovarian(32;2.74e-05)|all_epithelial(46;0.0608)|Prostate(55;0.0845)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0277)|Epithelial(17;3.29e-10)|Colorectal(74;0.00383)|COAD - Colon adenocarcinoma(73;0.00738)		CAAGCATAGTCCCAAACACCA	0.488													35	67	---	---	---	---	PASS
PRKDC	5591	broad.mit.edu	37	8	48769758	48769758	+	Missense_Mutation	SNP	C	A	A			TCGA-EJ-5519-01A-01D-1576-08	TCGA-EJ-5519-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:48769758C>A	uc003xqi.2	-	50	6625	c.6568G>T	c.(6568-6570)GTG>TTG	p.V2190L	PRKDC_uc003xqj.2_Missense_Mutation_p.V2190L|PRKDC_uc011ldh.1_Intron	NM_006904	NP_008835	P78527	PRKDC_HUMAN	protein kinase, DNA-activated, catalytic	2190					cellular response to insulin stimulus|double-strand break repair via nonhomologous end joining|peptidyl-serine phosphorylation|positive regulation of transcription from RNA polymerase II promoter	DNA-dependent protein kinase-DNA ligase 4 complex|transcription factor complex	ATP binding|DNA binding|DNA-dependent protein kinase activity|transcription factor binding			lung(12)|central_nervous_system(9)|ovary(6)|skin(4)|large_intestine(3)	34		all_cancers(86;0.0336)|all_epithelial(80;0.00111)|Lung NSC(129;0.00363)|all_lung(136;0.00391)				ATAGTGGCCACTATCTCAACC	0.458								NHEJ					5	24	---	---	---	---	PASS
ST18	9705	broad.mit.edu	37	8	53071575	53071575	+	Silent	SNP	G	A	A			TCGA-EJ-5519-01A-01D-1576-08	TCGA-EJ-5519-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:53071575G>A	uc003xqz.2	-	10	1845	c.1689C>T	c.(1687-1689)TAC>TAT	p.Y563Y	ST18_uc011ldq.1_Silent_p.Y210Y|ST18_uc011ldr.1_Silent_p.Y528Y|ST18_uc011lds.1_Silent_p.Y468Y|ST18_uc003xra.2_Silent_p.Y563Y|ST18_uc003xrb.2_Silent_p.Y563Y	NM_014682	NP_055497	O60284	ST18_HUMAN	suppression of tumorigenicity 18	563						nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(4)|skin(1)	5		Lung NSC(129;0.131)|all_epithelial(80;0.217)|all_lung(136;0.229)				TACATTGACCGTAGCTATAAG	0.542													4	162	---	---	---	---	PASS
FABP9	646480	broad.mit.edu	37	8	82371574	82371574	+	Splice_Site	SNP	T	C	C			TCGA-EJ-5519-01A-01D-1576-08	TCGA-EJ-5519-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:82371574T>C	uc011lfo.1	-	2	74	c.74_splice	c.e2-1	p.G25_splice		NM_001080526	NP_001073995	Q0Z7S8	FABP9_HUMAN	fatty acid binding protein 9, testis								lipid binding|transporter activity				0			Epithelial(68;0.186)			AATTCACTCCTACAAGACAGA	0.373													3	174	---	---	---	---	PASS
CDH17	1015	broad.mit.edu	37	8	95158181	95158181	+	Silent	SNP	G	A	A	rs147500239	byFrequency	TCGA-EJ-5519-01A-01D-1576-08	TCGA-EJ-5519-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:95158181G>A	uc003ygh.2	-	15	2267	c.2142C>T	c.(2140-2142)AAC>AAT	p.N714N	CDH17_uc011lgo.1_Silent_p.N500N|CDH17_uc011lgp.1_Silent_p.N714N	NM_004063	NP_004054	Q12864	CAD17_HUMAN	cadherin 17 precursor	714	Cadherin 7.|Extracellular (Potential).					integral to membrane	calcium ion binding			ovary(5)|skin(1)	6	Breast(36;4.65e-06)		BRCA - Breast invasive adenocarcinoma(8;0.00691)			CTTCCCAGTCGTTTTGTAAGC	0.408													37	108	---	---	---	---	PASS
ESRP1	54845	broad.mit.edu	37	8	95676990	95676990	+	Nonsense_Mutation	SNP	C	G	G			TCGA-EJ-5519-01A-01D-1576-08	TCGA-EJ-5519-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:95676990C>G	uc003ygq.3	+	7	893	c.710C>G	c.(709-711)TCA>TGA	p.S237*	ESRP1_uc003ygr.3_Nonsense_Mutation_p.S237*|ESRP1_uc003ygs.3_Nonsense_Mutation_p.S237*|ESRP1_uc003ygt.3_Nonsense_Mutation_p.S237*|ESRP1_uc003ygu.3_Nonsense_Mutation_p.S237*|ESRP1_uc003ygv.2_Nonsense_Mutation_p.S77*|ESRP1_uc003ygw.2_Nonsense_Mutation_p.S77*	NM_017697	NP_060167	Q6NXG1	ESRP1_HUMAN	RNA binding motif protein 35A isoform 1	237	RRM 1.				mRNA processing|regulation of RNA splicing|RNA splicing	nucleus|plasma membrane	mRNA binding|nucleotide binding		ESRP1/RAF1(4)	prostate(4)	4						TGGCAGTCTTCAGATCAAGAT	0.373													32	96	---	---	---	---	PASS
TM7SF4	81501	broad.mit.edu	37	8	105361522	105361522	+	Missense_Mutation	SNP	A	G	G			TCGA-EJ-5519-01A-01D-1576-08	TCGA-EJ-5519-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:105361522A>G	uc003ylx.1	+	2	791	c.742A>G	c.(742-744)ACC>GCC	p.T248A		NM_030788	NP_110415	Q9H295	TM7S4_HUMAN	dendritic cell-specific transmembrane protein	248					osteoclast differentiation	cell surface|integral to membrane|plasma membrane				pancreas(2)|large_intestine(1)|ovary(1)	4			OV - Ovarian serous cystadenocarcinoma(57;1.61e-06)|STAD - Stomach adenocarcinoma(118;0.229)			CATCTACATCACCAGACAATT	0.488													11	172	---	---	---	---	PASS
NUDCD1	84955	broad.mit.edu	37	8	110293385	110293385	+	Missense_Mutation	SNP	C	G	G			TCGA-EJ-5519-01A-01D-1576-08	TCGA-EJ-5519-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:110293385C>G	uc003ynb.3	-	6	951	c.840G>C	c.(838-840)TGG>TGC	p.W280C	NUDCD1_uc003yna.2_Missense_Mutation_p.W251C|NUDCD1_uc010mcl.2_Missense_Mutation_p.W193C|NUDCD1_uc010mcm.1_Missense_Mutation_p.W193C	NM_032869	NP_116258	Q96RS6	NUDC1_HUMAN	NudC domain containing 1 isoform 1	280	CS.									ovary(1)|breast(1)	2	all_neural(195;0.219)		OV - Ovarian serous cystadenocarcinoma(57;1.56e-12)			CAGTCTGTTGCCAGTAATACA	0.348													10	140	---	---	---	---	PASS
ASAP1	50807	broad.mit.edu	37	8	131249205	131249205	+	Silent	SNP	C	G	G			TCGA-EJ-5519-01A-01D-1576-08	TCGA-EJ-5519-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:131249205C>G	uc003yta.1	-	3	250	c.222G>C	c.(220-222)GTG>GTC	p.V74V	ASAP1_uc011liw.1_Silent_p.V67V	NM_018482	NP_060952	Q9ULH1	ASAP1_HUMAN	development and differentiation enhancing factor	74					cilium morphogenesis|filopodium assembly|regulation of ARF GTPase activity|signal transduction	cytoplasm|membrane	ARF GTPase activator activity|cytoskeletal adaptor activity|SH3 domain binding|zinc ion binding			ovary(4)	4						CAGACTTCTTCACTTTCTGAA	0.294													20	67	---	---	---	---	PASS
LRRC14	9684	broad.mit.edu	37	8	145746456	145746456	+	Missense_Mutation	SNP	T	G	G			TCGA-EJ-5519-01A-01D-1576-08	TCGA-EJ-5519-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:145746456T>G	uc003zdk.1	+	4	1222	c.1076T>G	c.(1075-1077)CTG>CGG	p.L359R	LRRC14_uc003zdl.1_Missense_Mutation_p.L359R|LRRC14_uc003zdo.2_5'Flank	NM_014665	NP_055480	Q15048	LRC14_HUMAN	leucine rich repeat containing 14	359	LRR 3.										0	all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-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;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055)			TTCCAGGGTCTGTTGCAGGCA	0.597													21	46	---	---	---	---	PASS
TLN1	7094	broad.mit.edu	37	9	35711265	35711265	+	Missense_Mutation	SNP	C	A	A			TCGA-EJ-5519-01A-01D-1576-08	TCGA-EJ-5519-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:35711265C>A	uc003zxt.2	-	30	4360	c.4006G>T	c.(4006-4008)GCT>TCT	p.A1336S		NM_006289	NP_006280	Q9Y490	TLN1_HUMAN	talin 1	1336	Interaction with SYNM.				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)			GCAGCTGCAGCCAGCTGACTC	0.557													4	65	---	---	---	---	PASS
FAM75C1	441452	broad.mit.edu	37	9	90535282	90535282	+	Missense_Mutation	SNP	A	G	G			TCGA-EJ-5519-01A-01D-1576-08	TCGA-EJ-5519-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:90535282A>G	uc010mqi.2	+	4	489	c.460A>G	c.(460-462)ATG>GTG	p.M154V	FAM75C1_uc004apq.3_Missense_Mutation_p.M137V	NM_001145124	NP_001138596			family with sequence similarity 75, member C1												0						TCATGAGCCTATGGAAGATGC	0.582													4	226	---	---	---	---	PASS
OR1J1	347168	broad.mit.edu	37	9	125239347	125239347	+	Missense_Mutation	SNP	G	T	T			TCGA-EJ-5519-01A-01D-1576-08	TCGA-EJ-5519-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:125239347G>T	uc011lyu.1	-	1	859	c.859C>A	c.(859-861)CCA>ACA	p.P287T	OR1J2_uc004bmj.1_Intron	NM_001004451	NP_001004451	Q8NGS3	OR1J1_HUMAN	olfactory receptor, family 1, subfamily J,	287	Helical; Name=7; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			skin(2)	2						TAAATGAATGGGTTCAACATG	0.313													63	151	---	---	---	---	PASS
PFKP	5214	broad.mit.edu	37	10	3176719	3176719	+	Missense_Mutation	SNP	C	G	G			TCGA-EJ-5519-01A-01D-1576-08	TCGA-EJ-5519-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:3176719C>G	uc001igp.2	+	20	2103	c.2067C>G	c.(2065-2067)ATC>ATG	p.I689M	PFKP_uc001igq.2_Missense_Mutation_p.I681M|PFKP_uc009xhr.2_Missense_Mutation_p.I651M|PFKP_uc009xht.2_Missense_Mutation_p.I427M|PFKP_uc009xhu.2_Missense_Mutation_p.I195M	NM_002627	NP_002618	Q01813	K6PP_HUMAN	phosphofructokinase, platelet	689					glycolysis	6-phosphofructokinase complex	6-phosphofructokinase activity|ATP binding|metal ion binding|protein binding			upper_aerodigestive_tract(1)|ovary(1)|lung(1)	3				GBM - Glioblastoma multiforme(1;0.000975)|all cancers(11;0.00351)|Epithelial(11;0.142)		GAACCAAAATCTCTGCCAGAG	0.512													82	212	---	---	---	---	PASS
OR52D1	390066	broad.mit.edu	37	11	5510672	5510672	+	Missense_Mutation	SNP	T	G	G			TCGA-EJ-5519-01A-01D-1576-08	TCGA-EJ-5519-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:5510672T>G	uc010qzg.1	+	1	736	c.736T>G	c.(736-738)TCC>GCC	p.S246A	HBG2_uc001mak.1_Intron|HBE1_uc001mam.1_Intron|OR51B5_uc001maq.1_Intron	NM_001005163	NP_001005163	Q9H346	O52D1_HUMAN	olfactory receptor, family 52, subfamily D,	246	Helical; Name=6; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			central_nervous_system(1)	1		Medulloblastoma(188;0.0075)|all_neural(188;0.0572)|Breast(177;0.0675)		Epithelial(150;3.46e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		TACCTGTGGCTCCCACATTGG	0.498													7	184	---	---	---	---	PASS
UBQLNL	143630	broad.mit.edu	37	11	5537038	5537038	+	Missense_Mutation	SNP	A	T	T			TCGA-EJ-5519-01A-01D-1576-08	TCGA-EJ-5519-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:5537038A>T	uc001maz.3	-	1	919	c.634T>A	c.(634-636)TCC>ACC	p.S212T	HBG2_uc001mak.1_Intron	NM_145053	NP_659490	Q8IYU4	UBQLN_HUMAN	ubiquilin-like	212										large_intestine(2)|skin(1)	3		Medulloblastoma(188;0.00225)|Breast(177;0.0155)|all_neural(188;0.0212)		Epithelial(150;1.92e-09)|BRCA - Breast invasive adenocarcinoma(625;0.136)		AGAAGGCGGGAAACTTCTGGG	0.468													9	287	---	---	---	---	PASS
MRGPRX1	259249	broad.mit.edu	37	11	18955603	18955603	+	Missense_Mutation	SNP	G	T	T			TCGA-EJ-5519-01A-01D-1576-08	TCGA-EJ-5519-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:18955603G>T	uc001mpg.2	-	1	947	c.729C>A	c.(727-729)CAC>CAA	p.H243Q		NM_147199	NP_671732	Q96LB2	MRGX1_HUMAN	MAS-related GPR, member X1	243	Extracellular (Potential).				acute-phase response	integral to membrane|plasma membrane	G-protein coupled receptor activity			pancreas(2)|central_nervous_system(1)	3						CCCTGTCCACGTGGATCCATA	0.478													12	126	---	---	---	---	PASS
KIAA0652	9776	broad.mit.edu	37	11	46670720	46670720	+	Missense_Mutation	SNP	G	A	A			TCGA-EJ-5519-01A-01D-1576-08	TCGA-EJ-5519-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:46670720G>A	uc009yld.2	+	6	988	c.304G>A	c.(304-306)GAA>AAA	p.E102K	KIAA0652_uc001nda.2_Missense_Mutation_p.E102K|KIAA0652_uc001ndb.2_Missense_Mutation_p.E102K|KIAA0652_uc001ncz.2_Missense_Mutation_p.E102K|KIAA0652_uc001ndc.2_Missense_Mutation_p.E102K|KIAA0652_uc010rgv.1_Missense_Mutation_p.E23K	NM_001142673	NP_001136145	O75143	ATG13_HUMAN	autophagy-related protein 13 isoform 1	102					autophagic vacuole assembly	cytosol|pre-autophagosomal structure|ULK1-ATG13-FIP200 complex	protein binding				0				GBM - Glioblastoma multiforme(35;0.226)		ATGGTGTCTTGAAATGAATGA	0.348													37	88	---	---	---	---	PASS
PDE2A	5138	broad.mit.edu	37	11	72295684	72295684	+	Missense_Mutation	SNP	G	T	T			TCGA-EJ-5519-01A-01D-1576-08	TCGA-EJ-5519-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:72295684G>T	uc010rrc.1	-	18	1691	c.1448C>A	c.(1447-1449)GCC>GAC	p.A483D	PDE2A_uc001oso.2_Missense_Mutation_p.A462D|PDE2A_uc010rra.1_Missense_Mutation_p.A476D|PDE2A_uc001osn.2_Missense_Mutation_p.A227D|PDE2A_uc010rrb.1_Missense_Mutation_p.A474D|PDE2A_uc010rrd.1_Missense_Mutation_p.A368D	NM_002599	NP_002590	O00408	PDE2A_HUMAN	phosphodiesterase 2A isoform 1	483	GAF 2.				platelet activation|signal transduction	cytosol	3',5'-cyclic-AMP phosphodiesterase activity|3',5'-cyclic-GMP phosphodiesterase activity|cGMP binding|cGMP-stimulated cyclic-nucleotide phosphodiesterase activity|metal ion binding			ovary(2)|breast(1)|skin(1)	4			BRCA - Breast invasive adenocarcinoma(5;3.55e-05)		Sildenafil(DB00203)|Sulindac(DB00605)	AAGCGGATGGGCATATGCGTC	0.627													6	26	---	---	---	---	PASS
ODZ4	26011	broad.mit.edu	37	11	78516453	78516453	+	Missense_Mutation	SNP	T	A	A			TCGA-EJ-5519-01A-01D-1576-08	TCGA-EJ-5519-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:78516453T>A	uc001ozl.3	-	15	2526	c.2063A>T	c.(2062-2064)AAC>ATC	p.N688I		NM_001098816	NP_001092286	Q6N022	TEN4_HUMAN	odz, odd Oz/ten-m homolog 4	688	EGF-like 4.|Extracellular (Potential).				signal transduction	integral to membrane				ovary(2)|pancreas(2)	4						GGTCTCGCAGTTGGTGCCTCC	0.617													4	9	---	---	---	---	PASS
USP2	9099	broad.mit.edu	37	11	119228895	119228895	+	Silent	SNP	G	A	A			TCGA-EJ-5519-01A-01D-1576-08	TCGA-EJ-5519-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:119228895G>A	uc001pwm.3	-	8	1600	c.1305C>T	c.(1303-1305)TTC>TTT	p.F435F	USP2_uc001pwl.3_Silent_p.F226F|USP2_uc001pwn.3_Silent_p.F192F	NM_004205	NP_004196	O75604	UBP2_HUMAN	ubiquitin specific peptidase 2 isoform a	435	Necessary for interaction with MDM4.				cell cycle|muscle organ development|negative regulation of transcription from RNA polymerase II promoter|positive regulation of mitotic cell cycle|protein deubiquitination|protein stabilization|ubiquitin-dependent protein catabolic process	nucleus|perinuclear region of cytoplasm	cyclin binding|cysteine-type endopeptidase activity|metal ion binding|ubiquitin protein ligase binding|ubiquitin thiolesterase activity			ovary(2)|urinary_tract(1)|skin(1)	4		all_hematologic(192;4.65e-05)|Breast(348;0.0101)|all_neural(223;0.0218)|Medulloblastoma(222;0.0425)|Renal(330;0.157)		BRCA - Breast invasive adenocarcinoma(274;3.93e-06)|OV - Ovarian serous cystadenocarcinoma(223;0.000513)|Colorectal(284;0.0116)|Lung(307;0.0853)|LUSC - Lung squamous cell carcinoma(976;0.0889)		AGAAGGGGTCGAAGACCGTAG	0.517													33	70	---	---	---	---	PASS
SRPR	6734	broad.mit.edu	37	11	126136799	126136799	+	Missense_Mutation	SNP	G	T	T			TCGA-EJ-5519-01A-01D-1576-08	TCGA-EJ-5519-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:126136799G>T	uc001qdh.2	-	5	596	c.545C>A	c.(544-546)GCT>GAT	p.A182D	SRPR_uc010sbm.1_Missense_Mutation_p.A154D|FOXRED1_uc001qdi.2_5'Flank|FOXRED1_uc010sbn.1_5'Flank|FOXRED1_uc010sbo.1_5'Flank|FOXRED1_uc010sbp.1_5'Flank|FOXRED1_uc010sbq.1_5'Flank|FOXRED1_uc001qdj.2_5'Flank|FOXRED1_uc010sbr.1_5'Flank	NM_003139	NP_003130	P08240	SRPR_HUMAN	signal recognition particle receptor	182					SRP-dependent cotranslational protein targeting to membrane	integral to membrane|signal recognition particle receptor complex	GTP binding|GTPase activity|receptor activity|signal recognition particle binding				0	all_hematologic(175;0.145)			BRCA - Breast invasive adenocarcinoma(274;1.1e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0736)		TTTGCTGGTAGCCAAAGGACC	0.478													9	128	---	---	---	---	PASS
C12orf35	55196	broad.mit.edu	37	12	32135815	32135815	+	Silent	SNP	C	T	T			TCGA-EJ-5519-01A-01D-1576-08	TCGA-EJ-5519-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:32135815C>T	uc001rks.2	+	4	2340	c.1926C>T	c.(1924-1926)GGC>GGT	p.G642G		NM_018169	NP_060639	Q9HCM1	CL035_HUMAN	hypothetical protein LOC55196	642										ovary(1)|skin(1)	2	all_cancers(9;3.36e-11)|all_epithelial(9;2.56e-11)|all_lung(12;5.67e-10)|Acute lymphoblastic leukemia(23;0.0122)|Lung SC(12;0.0336)|all_hematologic(23;0.0429)|Esophageal squamous(101;0.204)		OV - Ovarian serous cystadenocarcinoma(6;0.0114)			ATGTAAGTGGCAGGGTTTTGG	0.413													30	47	---	---	---	---	PASS
SLC38A2	54407	broad.mit.edu	37	12	46757763	46757763	+	Silent	SNP	C	G	G			TCGA-EJ-5519-01A-01D-1576-08	TCGA-EJ-5519-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:46757763C>G	uc001rpg.2	-	11	1337	c.897G>C	c.(895-897)CTG>CTC	p.L299L	SLC38A2_uc010sli.1_Silent_p.L137L|SLC38A2_uc001rph.2_Silent_p.L199L	NM_018976	NP_061849	Q96QD8	S38A2_HUMAN	solute carrier family 38, member 2	299	Helical; (Potential).				cellular nitrogen compound metabolic process|glutamate secretion|neurotransmitter secretion|sodium ion transport	integral to membrane|plasma membrane	amino acid transmembrane transporter activity|symporter activity			urinary_tract(1)|skin(1)	2	Lung SC(27;0.192)|Renal(347;0.236)		OV - Ovarian serous cystadenocarcinoma(5;0.0048)|Epithelial(2;0.0374)	GBM - Glioblastoma multiforme(48;0.226)		ATGAAAAGATCAGAATTGGCA	0.328													14	30	---	---	---	---	PASS
NUP107	57122	broad.mit.edu	37	12	69094533	69094533	+	Silent	SNP	C	A	A			TCGA-EJ-5519-01A-01D-1576-08	TCGA-EJ-5519-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:69094533C>A	uc001suf.2	+	7	695	c.580C>A	c.(580-582)CGA>AGA	p.R194R	NUP107_uc001sug.2_Silent_p.R41R|NUP107_uc010stj.1_Silent_p.R165R	NM_020401	NP_065134	P57740	NU107_HUMAN	nucleoporin 107kDa	194					carbohydrate metabolic process|glucose transport|mitotic prometaphase|mRNA export from nucleus|protein transport|regulation of glucose transport|transmembrane transport|viral reproduction	condensed chromosome kinetochore|cytosol|Nup107-160 complex	nucleocytoplasmic transporter activity|protein binding			skin(1)	1	Breast(13;6.25e-06)		Lung(24;0.000131)|LUAD - Lung adenocarcinoma(15;0.00107)|STAD - Stomach adenocarcinoma(21;0.00694)			AATAGTGAGTCGAGCAACACC	0.363													32	67	---	---	---	---	PASS
C12orf63	374467	broad.mit.edu	37	12	97098576	97098576	+	Splice_Site	SNP	T	C	C			TCGA-EJ-5519-01A-01D-1576-08	TCGA-EJ-5519-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:97098576T>C	uc001tet.1	+	14	1881	c.1803_splice	c.e14+2	p.Q601_splice		NM_198520	NP_940922	Q6ZTY8	CL063_HUMAN	hypothetical protein LOC374467											skin(6)|ovary(1)	7						AATATACAGGTAAGGATAATA	0.284													26	27	---	---	---	---	PASS
KCTD10	83892	broad.mit.edu	37	12	109898479	109898479	+	Missense_Mutation	SNP	C	G	G			TCGA-EJ-5519-01A-01D-1576-08	TCGA-EJ-5519-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:109898479C>G	uc001toi.1	-	3	437	c.349G>C	c.(349-351)GTC>CTC	p.V117L	KCTD10_uc001toh.1_5'Flank|KCTD10_uc009zvi.1_Missense_Mutation_p.V114L|KCTD10_uc001toj.1_Missense_Mutation_p.V125L|KCTD10_uc001tok.1_Intron	NM_031954	NP_114160	Q9H3F6	BACD3_HUMAN	potassium channel tetramerisation domain	117					proteasomal ubiquitin-dependent protein catabolic process|protein ubiquitination	Cul3-RING ubiquitin ligase complex|cytoplasm|nucleus|voltage-gated potassium channel complex	voltage-gated potassium channel activity				0						AGGCCTTGGACTAGGTAGTAC	0.522													28	140	---	---	---	---	PASS
ACAD10	80724	broad.mit.edu	37	12	112153696	112153696	+	Missense_Mutation	SNP	G	A	A			TCGA-EJ-5519-01A-01D-1576-08	TCGA-EJ-5519-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:112153696G>A	uc001tsq.2	+	7	1122	c.922G>A	c.(922-924)GAT>AAT	p.D308N	ACAD10_uc001tso.3_Intron|ACAD10_uc001tsp.2_Missense_Mutation_p.D308N|ACAD10_uc009zvx.2_Missense_Mutation_p.D339N|ACAD10_uc001tsr.2_Missense_Mutation_p.D46N|ACAD10_uc001tss.1_RNA	NM_025247	NP_079523	Q6JQN1	ACD10_HUMAN	acyl-Coenzyme A dehydrogenase family, member 10	308							acyl-CoA dehydrogenase activity|flavin adenine dinucleotide binding|hydrolase activity|transferase activity, transferring phosphorus-containing groups			ovary(2)	2						GGCTAATCGTGATCTAGTTCT	0.488													29	387	---	---	---	---	PASS
SETD8	387893	broad.mit.edu	37	12	123875311	123875311	+	Silent	SNP	C	T	T	rs74356260		TCGA-EJ-5519-01A-01D-1576-08	TCGA-EJ-5519-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:123875311C>T	uc001uew.2	+	3	309	c.267C>T	c.(265-267)GCC>GCT	p.A89A	SETD8_uc001uex.2_Silent_p.A24A	NM_020382	NP_065115	Q9NQR1	SETD8_HUMAN	SET domain-containing 8	130					cell division|mitosis|negative regulation of transcription from RNA polymerase II promoter|peptidyl-lysine monomethylation|regulation of DNA damage response, signal transduction by p53 class mediator|transcription, DNA-dependent	chromosome|nucleus	histone-lysine N-methyltransferase activity|p53 binding|transcription corepressor activity				0	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.00101)|Epithelial(86;0.00425)		AACCATTAGCCGGAATCTACA	0.498													4	121	---	---	---	---	PASS
EP400NL	347918	broad.mit.edu	37	12	132589578	132589578	+	Missense_Mutation	SNP	A	G	G			TCGA-EJ-5519-01A-01D-1576-08	TCGA-EJ-5519-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:132589578A>G	uc001ujv.2	+	1	1037	c.1013A>G	c.(1012-1014)AAG>AGG	p.K338R	EP400NL_uc001ujr.2_Missense_Mutation_p.K206R|EP400NL_uc001ujs.3_Missense_Mutation_p.K269R|EP400NL_uc009zyq.2_Missense_Mutation_p.K206R|EP400NL_uc001ujt.2_Missense_Mutation_p.K206R|EP400NL_uc001ujw.1_Missense_Mutation_p.K37R					RecName: Full=EP400 N-terminal-like protein;												0						AAGGTTCCCAAGAAGTTAGAG	0.607													8	41	---	---	---	---	PASS
SACS	26278	broad.mit.edu	37	13	23909862	23909862	+	Missense_Mutation	SNP	G	C	C			TCGA-EJ-5519-01A-01D-1576-08	TCGA-EJ-5519-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:23909862G>C	uc001uon.2	-	10	8742	c.8153C>G	c.(8152-8154)GCA>GGA	p.A2718G	SACS_uc001uoo.2_Missense_Mutation_p.A2571G|SACS_uc001uop.1_Intron|SACS_uc001uoq.1_Intron	NM_014363	NP_055178	Q9NZJ4	SACS_HUMAN	sacsin	2718					cell death|negative regulation of inclusion body assembly|protein folding	axon|cell body fiber|dendrite|mitochondrion|nucleus	ATP binding|chaperone binding|Hsp70 protein binding|proteasome binding			ovary(7)|skin(2)|upper_aerodigestive_tract(1)|large_intestine(1)|pancreas(1)	12		all_cancers(29;1.51e-22)|all_epithelial(30;7.82e-19)|all_lung(29;4.71e-18)|Lung SC(185;0.0225)|Breast(139;0.128)		all cancers(112;0.00197)|Epithelial(112;0.00854)|OV - Ovarian serous cystadenocarcinoma(117;0.0298)|Lung(94;0.189)		TCTGTCTGATGCTGGAACAGA	0.378													55	128	---	---	---	---	PASS
RCBTB1	55213	broad.mit.edu	37	13	50123715	50123715	+	Silent	SNP	G	A	A			TCGA-EJ-5519-01A-01D-1576-08	TCGA-EJ-5519-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:50123715G>A	uc001vde.1	-	9	1185	c.924C>T	c.(922-924)TAC>TAT	p.Y308Y		NM_018191	NP_060661	Q8NDN9	RCBT1_HUMAN	regulator of chromosome condensation (RCC1) and	308	RCC1 6.				cell cycle|chromatin modification|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus				ovary(1)	1		Lung NSC(96;2.1e-05)|Breast(56;0.00015)|Prostate(109;0.00314)|Hepatocellular(98;0.0207)|Myeloproliferative disorder(33;0.163)|Lung SC(185;0.187)|all_neural(104;0.19)	KIRC - Kidney renal clear cell carcinoma(9;0.206)	GBM - Glioblastoma multiforme(99;4.7e-09)		GGCCCCACATGTACACGTGCC	0.577													20	47	---	---	---	---	PASS
MYCBP2	23077	broad.mit.edu	37	13	77664342	77664342	+	Missense_Mutation	SNP	C	A	A			TCGA-EJ-5519-01A-01D-1576-08	TCGA-EJ-5519-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:77664342C>A	uc001vkf.2	-	61	10401	c.10310G>T	c.(10309-10311)AGA>ATA	p.R3437I	MYCBP2_uc010aev.2_Missense_Mutation_p.R2841I|MYCBP2_uc001vke.2_Missense_Mutation_p.R57I	NM_015057	NP_055872	O75592	MYCB2_HUMAN	MYC binding protein 2	3437					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	ligase activity|protein binding|zinc ion binding			ovary(4)|breast(4)|skin(3)|lung(2)|pancreas(1)	14		Breast(118;0.212)|Acute lymphoblastic leukemia(28;0.22)		GBM - Glioblastoma multiforme(99;0.109)		TGAGTATGATCTTTGGAAGAC	0.388													63	118	---	---	---	---	PASS
THTPA	79178	broad.mit.edu	37	14	24027979	24027979	+	Missense_Mutation	SNP	G	A	A			TCGA-EJ-5519-01A-01D-1576-08	TCGA-EJ-5519-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:24027979G>A	uc001wkh.3	+	3	993	c.623G>A	c.(622-624)CGC>CAC	p.R208H	THTPA_uc001wkb.3_RNA|THTPA_uc001wkg.3_Missense_Mutation_p.R208H|THTPA_uc010akr.2_RNA|THTPA_uc001wki.3_3'UTR|uc001wko.1_5'Flank	NM_001126339	NP_001119811	Q9BU02	THTPA_HUMAN	thiamine triphosphatase	208					dephosphorylation|generation of precursor metabolites and energy|thiamine metabolic process	cytosol|nucleolus|soluble fraction	thiamin-triphosphatase activity				0	all_cancers(95;0.000251)			GBM - Glioblastoma multiforme(265;0.00643)	Thiamine(DB00152)	GACTATCAGCGCCTGCTAGAA	0.547											OREG0022604	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	21	80	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	14	28733803	28733803	+	Missense_Mutation	SNP	A	T	T			TCGA-EJ-5519-01A-01D-1576-08	TCGA-EJ-5519-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:28733803A>T	uc001wqd.2	+	1	184	c.44A>T	c.(43-45)CAG>CTG	p.Q15L						SubName: Full=cDNA FLJ60537, highly similar to BCL2/adenovirus E1B 19 kDa protein-interacting protein 3;																		GAGAGCCTGCAGGGCTCCTGG	0.582													3	37	---	---	---	---	PASS
EXOC5	10640	broad.mit.edu	37	14	57675185	57675185	+	3'UTR	SNP	C	G	G	rs10150771	by1000genomes	TCGA-EJ-5519-01A-01D-1576-08	TCGA-EJ-5519-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:57675185C>G	uc001xct.2	-	18					EXOC5_uc001xcs.2_3'UTR|EXOC5_uc010trg.1_3'UTR|EXOC5_uc010trh.1_3'UTR	NM_006544	NP_006535	O00471	EXOC5_HUMAN	SEC10 protein						exocytosis|post-Golgi vesicle-mediated transport|protein transport|vesicle docking	cytoplasm				ovary(2)|breast(1)	3						AGTATGGCTGCTGTTTTGTTC	0.368													3	3	---	---	---	---	PASS
ADAM20	8748	broad.mit.edu	37	14	70989752	70989752	+	Missense_Mutation	SNP	G	C	C			TCGA-EJ-5519-01A-01D-1576-08	TCGA-EJ-5519-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:70989752G>C	uc001xme.2	-	2	2118	c.1873C>G	c.(1873-1875)CTG>GTG	p.L625V		NM_003814	NP_003805	O43506	ADA20_HUMAN	ADAM metallopeptidase domain 20 preproprotein	575	Cys-rich.|Extracellular (Potential).				proteolysis|single fertilization	integral to membrane	metalloendopeptidase activity|zinc ion binding			skin(1)	1			KIRC - Kidney renal clear cell carcinoma(12;0.133)|Kidney(31;0.188)	all cancers(60;0.00294)|BRCA - Breast invasive adenocarcinoma(234;0.00668)|OV - Ovarian serous cystadenocarcinoma(108;0.0344)		TGCTCTATCAGATTGGGAATT	0.448													3	131	---	---	---	---	PASS
SORD	6652	broad.mit.edu	37	15	45365905	45365905	+	3'UTR	SNP	G	C	C	rs149179762	by1000genomes	TCGA-EJ-5519-01A-01D-1576-08	TCGA-EJ-5519-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:45365905G>C	uc001zul.3	+	9					SORD_uc001zum.3_3'UTR|SORD_uc010bdz.2_3'UTR	NM_003104	NP_003095	Q00796	DHSO_HUMAN	sorbitol dehydrogenase						fructose biosynthetic process|glucose metabolic process|L-xylitol catabolic process|sorbitol catabolic process|sperm motility	cilium|extracellular space|flagellum|membrane fraction|mitochondrial membrane|soluble fraction	L-iditol 2-dehydrogenase activity|NAD binding|sugar binding|zinc ion binding				0		all_cancers(109;3.43e-12)|all_epithelial(112;2.33e-10)|Lung NSC(122;6.01e-07)|all_lung(180;4.38e-06)|Melanoma(134;0.0122)		all cancers(107;1.6e-18)|GBM - Glioblastoma multiforme(94;4.95e-07)|COAD - Colon adenocarcinoma(120;0.0704)|Colorectal(133;0.0706)	NADH(DB00157)	ATACAATCTGGGATAGTTTGG	0.433													4	7	---	---	---	---	PASS
DUOX2	50506	broad.mit.edu	37	15	45404868	45404868	+	Missense_Mutation	SNP	T	C	C			TCGA-EJ-5519-01A-01D-1576-08	TCGA-EJ-5519-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:45404868T>C	uc010bea.2	-	4	412	c.209A>G	c.(208-210)TAT>TGT	p.Y70C	DUOX2_uc001zun.2_Missense_Mutation_p.Y70C|DUOXA2_uc001zuo.2_5'Flank|DUOXA2_uc010beb.2_5'Flank	NM_014080	NP_054799	Q9NRD8	DUOX2_HUMAN	dual oxidase 2 precursor	70	Extracellular (Potential).|Peroxidase-like; mediates peroxidase activity (By similarity).				cuticle development|cytokine-mediated signaling pathway|hormone biosynthetic process|hydrogen peroxide catabolic process|response to cAMP|response to virus	apical plasma membrane|integral to membrane	calcium ion binding|electron carrier activity|flavin adenine dinucleotide binding|heme binding|NAD(P)H oxidase activity|peroxidase activity			ovary(2)|skin(2)|pancreas(1)	5		all_cancers(109;3.79e-11)|all_epithelial(112;2.92e-09)|Lung NSC(122;3.55e-06)|all_lung(180;2.56e-05)|Melanoma(134;0.027)		all cancers(107;1.05e-18)|GBM - Glioblastoma multiforme(94;4.23e-07)|COAD - Colon adenocarcinoma(120;0.0668)|Colorectal(133;0.068)		CAGAGCCTGATACACACCGTC	0.687													15	29	---	---	---	---	PASS
DUOX2	50506	broad.mit.edu	37	15	45404890	45404890	+	Missense_Mutation	SNP	C	G	G			TCGA-EJ-5519-01A-01D-1576-08	TCGA-EJ-5519-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:45404890C>G	uc010bea.2	-	4	390	c.187G>C	c.(187-189)GCC>CCC	p.A63P	DUOX2_uc001zun.2_Missense_Mutation_p.A63P|DUOXA2_uc001zuo.2_5'Flank|DUOXA2_uc010beb.2_5'Flank	NM_014080	NP_054799	Q9NRD8	DUOX2_HUMAN	dual oxidase 2 precursor	63	Extracellular (Potential).|Peroxidase-like; mediates peroxidase activity (By similarity).				cuticle development|cytokine-mediated signaling pathway|hormone biosynthetic process|hydrogen peroxide catabolic process|response to cAMP|response to virus	apical plasma membrane|integral to membrane	calcium ion binding|electron carrier activity|flavin adenine dinucleotide binding|heme binding|NAD(P)H oxidase activity|peroxidase activity			ovary(2)|skin(2)|pancreas(1)	5		all_cancers(109;3.79e-11)|all_epithelial(112;2.92e-09)|Lung NSC(122;3.55e-06)|all_lung(180;2.56e-05)|Melanoma(134;0.027)		all cancers(107;1.05e-18)|GBM - Glioblastoma multiforme(94;4.23e-07)|COAD - Colon adenocarcinoma(120;0.0668)|Colorectal(133;0.068)		GCGTAATTGGCTGGTACGCGG	0.682													18	28	---	---	---	---	PASS
GNB5	10681	broad.mit.edu	37	15	52433404	52433404	+	Missense_Mutation	SNP	T	C	C			TCGA-EJ-5519-01A-01D-1576-08	TCGA-EJ-5519-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:52433404T>C	uc002abt.1	-	7	625	c.560A>G	c.(559-561)AAA>AGA	p.K187R	GNB5_uc002abr.1_Missense_Mutation_p.K145R|GNB5_uc002abs.1_Intron	NM_016194	NP_057278	O14775	GBB5_HUMAN	guanine nucleotide-binding protein, beta-5	187						heterotrimeric G-protein complex	GTPase activity|signal transducer activity			lung(1)	1				all cancers(107;0.0163)		AGACTTCTTTTTGGCAGCCAT	0.453													49	80	---	---	---	---	PASS
KIAA1370	56204	broad.mit.edu	37	15	52877000	52877000	+	Missense_Mutation	SNP	T	G	G			TCGA-EJ-5519-01A-01D-1576-08	TCGA-EJ-5519-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:52877000T>G	uc002acg.3	-	12	3172	c.3019A>C	c.(3019-3021)AAT>CAT	p.N1007H	KIAA1370_uc002ach.3_RNA|KIAA1370_uc010bfg.1_Missense_Mutation_p.N919H|KIAA1370_uc002acf.3_Missense_Mutation_p.N37H|KIAA1370_uc010ugf.1_Missense_Mutation_p.N1014H	NM_019600	NP_062546	Q32MH5	K1370_HUMAN	hypothetical protein LOC56204	1007											0				all cancers(107;0.0803)		TTCTCTTTATTAACACTTCTC	0.348													14	53	---	---	---	---	PASS
ANKDD1A	348094	broad.mit.edu	37	15	65235776	65235776	+	Missense_Mutation	SNP	A	G	G	rs34988193	byFrequency	TCGA-EJ-5519-01A-01D-1576-08	TCGA-EJ-5519-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:65235776A>G	uc002aoa.2	+	11	1092	c.1063A>G	c.(1063-1065)AAG>GAG	p.K355E	ANKDD1A_uc002aoc.2_RNA|ANKDD1A_uc010bha.2_Missense_Mutation_p.K264E	NM_182703	NP_874362	Q495B1	AKD1A_HUMAN	ankyrin repeat and death domain containing 1A	355					signal transduction					ovary(1)	1						CCTGAGAGATAAGGTACCTct	0.299													5	301	---	---	---	---	PASS
DPP8	54878	broad.mit.edu	37	15	65739123	65739123	+	3'UTR	SNP	T	C	C			TCGA-EJ-5519-01A-01D-1576-08	TCGA-EJ-5519-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:65739123T>C	uc002aov.2	-	20					DPP8_uc002aow.2_3'UTR|DPP8_uc010uiv.1_RNA|DPP8_uc002aox.2_3'UTR|DPP8_uc002aoy.2_3'UTR|DPP8_uc002aoz.2_3'UTR|DPP8_uc010bhj.2_3'UTR|DPP8_uc002apa.2_3'UTR|DPP8_uc010bhi.2_3'UTR	NM_130434	NP_569118	Q6V1X1	DPP8_HUMAN	dipeptidyl peptidase 8 isoform 1						immune response|proteolysis	cytoplasm|membrane|nucleus	aminopeptidase activity|dipeptidyl-peptidase activity|serine-type peptidase activity			ovary(1)	1						ACATGGCAGGTATCAAAATGT	0.383													27	55	---	---	---	---	PASS
RSPRY1	89970	broad.mit.edu	37	16	57243065	57243065	+	Missense_Mutation	SNP	C	T	T			TCGA-EJ-5519-01A-01D-1576-08	TCGA-EJ-5519-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:57243065C>T	uc002elb.2	+	4	760	c.482C>T	c.(481-483)ACA>ATA	p.T161I	RSPRY1_uc002elc.2_Missense_Mutation_p.T161I|RSPRY1_uc002eld.2_Missense_Mutation_p.T161I	NM_133368	NP_588609	Q96DX4	RSPRY_HUMAN	ring finger and SPRY domain containing 1	161						extracellular region	zinc ion binding			ovary(1)	1						GCTGTTATAACATTGTTACTA	0.348													24	388	---	---	---	---	PASS
PDP2	57546	broad.mit.edu	37	16	66919043	66919043	+	Missense_Mutation	SNP	G	A	A			TCGA-EJ-5519-01A-01D-1576-08	TCGA-EJ-5519-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:66919043G>A	uc002eqk.1	+	2	1018	c.856G>A	c.(856-858)GAC>AAC	p.D286N		NM_020786	NP_065837	Q9P2J9	PDP2_HUMAN	pyruvate dehydrogenase phosphatase isoenzyme 2	286					pyruvate metabolic process|regulation of acetyl-CoA biosynthetic process from pyruvate	mitochondrial matrix|protein serine/threonine phosphatase complex	[pyruvate dehydrogenase (lipoamide)] phosphatase activity|metal ion binding			ovary(1)	1		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.088)|Epithelial(162;0.204)		AAATGCTGGTGACTGCCGAGC	0.557													14	70	---	---	---	---	PASS
TMCO7	79613	broad.mit.edu	37	16	69056743	69056743	+	Nonsense_Mutation	SNP	C	G	G			TCGA-EJ-5519-01A-01D-1576-08	TCGA-EJ-5519-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:69056743C>G	uc002ewi.3	+	16	2867	c.2855C>G	c.(2854-2856)TCA>TGA	p.S952*		NM_024562	NP_078838	Q9C0B7	TMCO7_HUMAN	transmembrane and coiled-coil domains 7	952	HEAT 2.					integral to membrane	binding				0		Ovarian(137;0.0568)		OV - Ovarian serous cystadenocarcinoma(108;0.0446)|Epithelial(162;0.198)		GACATGGTCTCAAAGTACCGA	0.438													3	11	---	---	---	---	PASS
RABEP1	9135	broad.mit.edu	37	17	5264856	5264856	+	Silent	SNP	A	G	G			TCGA-EJ-5519-01A-01D-1576-08	TCGA-EJ-5519-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:5264856A>G	uc002gbm.3	+	9	1673	c.1449A>G	c.(1447-1449)CAA>CAG	p.Q483Q	RABEP1_uc010clc.1_Silent_p.Q476Q|RABEP1_uc010cld.1_Silent_p.Q440Q|RABEP1_uc010vsw.1_Silent_p.Q440Q|RABEP1_uc002gbl.3_Silent_p.Q483Q|NUP88_uc002gbn.2_RNA	NM_004703	NP_004694	Q15276	RABE1_HUMAN	rabaptin, RAB GTPase binding effector protein 1	483					apoptosis|cellular membrane fusion|endocytosis|protein transport	centrosome|early endosome|endocytic vesicle|recycling endosome	growth factor activity|GTPase activator activity|protein homodimerization activity			large_intestine(1)|ovary(1)	2						CACCAGAACAAGAAGAGACAG	0.478													40	34	---	---	---	---	PASS
KCNAB3	9196	broad.mit.edu	37	17	7827736	7827736	+	Silent	SNP	G	T	T	rs145774275		TCGA-EJ-5519-01A-01D-1576-08	TCGA-EJ-5519-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:7827736G>T	uc002gjm.1	-	9	708	c.708C>A	c.(706-708)ATC>ATA	p.I236I	KCNAB3_uc010vul.1_RNA	NM_004732	NP_004723	O43448	KCAB3_HUMAN	potassium voltage-gated channel, shaker-related	236						cytoplasm|integral to membrane	oxidoreductase activity|potassium channel regulator activity|voltage-gated potassium channel activity			ovary(1)	1		Prostate(122;0.157)				CACTCACCATGATTTCTGCAG	0.572													3	57	---	---	---	---	PASS
PEMT	10400	broad.mit.edu	37	17	17412831	17412831	+	Silent	SNP	C	T	T			TCGA-EJ-5519-01A-01D-1576-08	TCGA-EJ-5519-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:17412831C>T	uc002grj.2	-	5	451	c.384G>A	c.(382-384)GCG>GCA	p.A128A	PEMT_uc002grk.2_Silent_p.A128A|PEMT_uc002grl.2_Silent_p.A165A|PEMT_uc010vwx.1_Silent_p.A165A	NM_148173	NP_680478	Q9UBM1	PEMT_HUMAN	phosphatidylethanolamine N-methyltransferase	128					cell proliferation|phosphatidylcholine biosynthetic process	endoplasmic reticulum membrane|integral to membrane|mitochondrial membrane	phosphatidylethanolamine N-methyltransferase activity				0				Colorectal(2;0.0157)|READ - Rectum adenocarcinoma(2;0.0891)		CGGTCACTCTCGCCTCCTTGA	0.592													11	72	---	---	---	---	PASS
MFAP4	4239	broad.mit.edu	37	17	19288435	19288435	+	Missense_Mutation	SNP	G	A	A			TCGA-EJ-5519-01A-01D-1576-08	TCGA-EJ-5519-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:19288435G>A	uc002gvt.2	-	5	522	c.497C>T	c.(496-498)GCA>GTA	p.A166V	MFAP4_uc002gvr.2_RNA|MFAP4_uc002gvs.2_Missense_Mutation_p.A190V	NM_002404	NP_002395	P55083	MFAP4_HUMAN	microfibrillar-associated protein 4 precursor	166	Fibrinogen C-terminal.				cell adhesion|signal transduction	microfibril	receptor binding				0	all_cancers(12;2.87e-05)|all_epithelial(12;0.00114)|Hepatocellular(7;0.00345)|Breast(13;0.206)					CTCAAAGCCTGCCACAAAGAG	0.602													34	37	---	---	---	---	PASS
UBTF	7343	broad.mit.edu	37	17	42284563	42284563	+	3'UTR	SNP	G	C	C			TCGA-EJ-5519-01A-01D-1576-08	TCGA-EJ-5519-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:42284563G>C	uc002igb.2	-	20					UBTF_uc002igc.2_3'UTR|UBTF_uc010czs.2_3'UTR|UBTF_uc002igd.2_3'UTR|UBTF_uc010czt.2_3'UTR	NM_014233	NP_055048	P17480	UBF1_HUMAN	upstream binding transcription factor, RNA						positive regulation of transcription from RNA polymerase I promoter|termination of RNA polymerase I transcription|transcription elongation from RNA polymerase I promoter|transcription initiation from RNA polymerase I promoter	nucleolus|nucleoplasm	DNA binding|protein binding				0		Breast(137;0.00765)|Prostate(33;0.0181)		BRCA - Breast invasive adenocarcinoma(366;0.114)		CAGTTGGGGAGGGGAGCTCCT	0.567													15	25	---	---	---	---	PASS
SEPT4	5414	broad.mit.edu	37	17	56598642	56598642	+	Nonsense_Mutation	SNP	G	A	A			TCGA-EJ-5519-01A-01D-1576-08	TCGA-EJ-5519-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:56598642G>A	uc002iwm.1	-	9	1215	c.1087C>T	c.(1087-1089)CGA>TGA	p.R363*	SEPT4_uc002iwk.1_Nonsense_Mutation_p.R216*|SEPT4_uc010wnw.1_Nonsense_Mutation_p.R216*|SEPT4_uc002iwl.1_Nonsense_Mutation_p.R216*|SEPT4_uc002iwn.1_Nonsense_Mutation_p.R264*|SEPT4_uc002iwo.1_Nonsense_Mutation_p.R344*|SEPT4_uc002iwp.1_3'UTR|SEPT4_uc010wnx.1_Nonsense_Mutation_p.R378*|SEPT4_uc010wny.1_Nonsense_Mutation_p.R355*|SEPT4_uc010dcy.1_3'UTR	NM_004574	NP_004565	O43236	SEPT4_HUMAN	septin 4 isoform 1	363		GTP (By similarity).			apoptosis|cell cycle|cytokinesis|regulation of apoptosis	cytoskeleton|mitochondrion|nucleus	GTP binding|GTPase activity|protein binding|structural molecule activity				0	Medulloblastoma(34;0.127)|all_neural(34;0.237)					GGGTAGAGTCGACCCCGAACT	0.582											OREG0024614	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	13	95	---	---	---	---	PASS
SEPT4	5414	broad.mit.edu	37	17	56604559	56604559	+	Intron	SNP	C	A	A			TCGA-EJ-5519-01A-01D-1576-08	TCGA-EJ-5519-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:56604559C>A	uc002iwm.1	-						SEPT4_uc002iwk.1_5'Flank|SEPT4_uc010wnw.1_Intron|SEPT4_uc002iwl.1_5'UTR|SEPT4_uc002iwn.1_Intron|SEPT4_uc002iwo.1_Intron|SEPT4_uc002iwp.1_Intron|SEPT4_uc010wnx.1_Intron|SEPT4_uc010wny.1_Intron|SEPT4_uc010dcy.1_Intron	NM_004574	NP_004565	O43236	SEPT4_HUMAN	septin 4 isoform 1						apoptosis|cell cycle|cytokinesis|regulation of apoptosis	cytoskeleton|mitochondrion|nucleus	GTP binding|GTPase activity|protein binding|structural molecule activity				0	Medulloblastoma(34;0.127)|all_neural(34;0.237)					GGAAGGGTCCCAGGGTCCAGG	0.542													7	18	---	---	---	---	PASS
TUBD1	51174	broad.mit.edu	37	17	57955539	57955539	+	Missense_Mutation	SNP	C	T	T			TCGA-EJ-5519-01A-01D-1576-08	TCGA-EJ-5519-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:57955539C>T	uc002ixw.1	-	5	972	c.694G>A	c.(694-696)GCA>ACA	p.A232T	TUBD1_uc010ddf.1_Missense_Mutation_p.A232T|TUBD1_uc010ddg.1_Missense_Mutation_p.A197T|TUBD1_uc010ddh.1_Missense_Mutation_p.A113T|TUBD1_uc010wok.1_Missense_Mutation_p.A232T|TUBD1_uc002ixx.1_Missense_Mutation_p.A232T|TUBD1_uc010wol.1_Missense_Mutation_p.A16T|TUBD1_uc010ddi.1_Intron	NM_016261	NP_057345	Q9UJT1	TBD_HUMAN	delta-tubulin	232					cell differentiation|microtubule-based movement|multicellular organismal development|protein polymerization|spermatogenesis	centriole|microtubule|nucleus	GTP binding|GTPase activity|structural molecule activity			ovary(1)	1	all_cancers(5;3.18e-13)|Breast(5;2.91e-25)|all_neural(34;0.0878)|Medulloblastoma(34;0.0922)		Epithelial(12;9.34e-13)|all cancers(12;1.91e-11)			AGCTGATGTGCGAGGACTTGA	0.418													47	120	---	---	---	---	PASS
PSMG2	56984	broad.mit.edu	37	18	12706677	12706677	+	Silent	SNP	G	T	T			TCGA-EJ-5519-01A-01D-1576-08	TCGA-EJ-5519-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:12706677G>T	uc002krk.2	+	2	229	c.186G>T	c.(184-186)GCG>GCT	p.A62A	PSMG2_uc002krg.2_Silent_p.A31A|PSMG2_uc002krj.1_Silent_p.A62A	NM_020232	NP_064617	Q969U7	PSMG2_HUMAN	proteasome (prosome, macropain) assembly	62					proteasome assembly	nucleus	protein binding				0						ATCCATATGCGACCACAGAAG	0.348													48	50	---	---	---	---	PASS
ZNF556	80032	broad.mit.edu	37	19	2878237	2878237	+	Silent	SNP	C	T	T			TCGA-EJ-5519-01A-01D-1576-08	TCGA-EJ-5519-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:2878237C>T	uc002lwp.1	+	4	1368	c.1281C>T	c.(1279-1281)TGC>TGT	p.C427C	ZNF556_uc002lwq.2_Silent_p.C426C	NM_024967	NP_079243	Q9HAH1	ZN556_HUMAN	zinc finger protein 556	427	C2H2-type 9.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			skin(3)	3				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)		CCAGTAAATGCGAAAAATGTG	0.448													5	192	---	---	---	---	PASS
CHAF1A	10036	broad.mit.edu	37	19	4432096	4432096	+	Missense_Mutation	SNP	G	A	A			TCGA-EJ-5519-01A-01D-1576-08	TCGA-EJ-5519-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:4432096G>A	uc002mal.2	+	12	2195	c.2095G>A	c.(2095-2097)GAT>AAT	p.D699N		NM_005483	NP_005474	Q13111	CAF1A_HUMAN	chromatin assembly factor 1, subunit A (p150)	699	Binds to p60.				cell cycle|DNA repair|DNA replication|DNA replication-dependent nucleosome assembly|protein complex assembly|regulation of transcription, DNA-dependent|transcription, DNA-dependent	CAF-1 complex|WINAC complex	chromatin binding|chromo shadow domain binding|unfolded protein binding			ovary(1)|skin(1)	2		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0148)|STAD - Stomach adenocarcinoma(1328;0.18)		CTGCGCAGGCGATGACCTGAA	0.637								Chromatin_Structure					14	65	---	---	---	---	PASS
EMR2	30817	broad.mit.edu	37	19	14865794	14865794	+	Missense_Mutation	SNP	G	A	A	rs146763976		TCGA-EJ-5519-01A-01D-1576-08	TCGA-EJ-5519-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:14865794G>A	uc002mzp.1	-	14	2018	c.1562C>T	c.(1561-1563)GCC>GTC	p.A521V	EMR2_uc010dzs.1_Intron|EMR2_uc010xnw.1_Intron|EMR2_uc002mzo.1_Missense_Mutation_p.A510V|EMR2_uc002mzq.1_Missense_Mutation_p.A461V|EMR2_uc002mzr.1_Missense_Mutation_p.A472V|EMR2_uc002mzs.1_Missense_Mutation_p.A379V|EMR2_uc002mzt.1_Missense_Mutation_p.A417V|EMR2_uc002mzu.1_Missense_Mutation_p.A428V|EMR2_uc010xnx.1_RNA|EMR2_uc010xny.1_Intron	NM_013447	NP_038475	Q9UHX3	EMR2_HUMAN	egf-like module containing, mucin-like, hormone	521	Extracellular (Potential).|GPS.				cell adhesion|neuropeptide signaling pathway	integral to membrane|plasma membrane	calcium ion binding|G-protein coupled receptor activity			lung(2)|ovary(1)|skin(1)	4						CATGAGGACGGCAAAGCTGCT	0.478													5	103	---	---	---	---	PASS
OR7C1	26664	broad.mit.edu	37	19	14910838	14910838	+	Silent	SNP	G	C	C			TCGA-EJ-5519-01A-01D-1576-08	TCGA-EJ-5519-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:14910838G>C	uc010xnz.1	-	1	111	c.111C>G	c.(109-111)GTC>GTG	p.V37V		NM_198944	NP_945182	O76099	OR7C1_HUMAN	olfactory receptor, family 7, subfamily C,	37	Helical; Name=1; (Potential).				sensory perception of smell|spermatogenesis	integral to membrane|plasma membrane	olfactory receptor activity			ovary(2)	2						CGGTGAAAGTGACTAGGTACA	0.493													6	144	---	---	---	---	PASS
OR7A5	26659	broad.mit.edu	37	19	14938095	14938095	+	Nonstop_Mutation	SNP	C	A	A			TCGA-EJ-5519-01A-01D-1576-08	TCGA-EJ-5519-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:14938095C>A	uc002mzw.2	-	1	1182	c.959G>T	c.(958-960)TGA>TTA	p.*320L	OR7A5_uc010xoa.1_3'UTR	NM_017506	NP_059976	Q15622	OR7A5_HUMAN	olfactory receptor, family 7, subfamily A,	320					sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			central_nervous_system(2)	2						GCCCTGCAATCATGGGCACTT	0.383													63	132	---	---	---	---	PASS
B3GNT3	10331	broad.mit.edu	37	19	17922668	17922668	+	Missense_Mutation	SNP	G	C	C			TCGA-EJ-5519-01A-01D-1576-08	TCGA-EJ-5519-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:17922668G>C	uc002nhk.1	+	3	941	c.856G>C	c.(856-858)GCT>CCT	p.A286P	B3GNT3_uc002nhl.1_Missense_Mutation_p.A286P|B3GNT3_uc010ebd.1_Missense_Mutation_p.A286P|B3GNT3_uc010ebe.1_Missense_Mutation_p.A286P	NM_014256	NP_055071	Q9Y2A9	B3GN3_HUMAN	UDP-GlcNAc:betaGal	286	Lumenal (Potential).				protein glycosylation	Golgi membrane|integral to plasma membrane	galactosyltransferase activity			upper_aerodigestive_tract(1)	1						CCTGCGCCGTGCTGCCCATGT	0.602													32	114	---	---	---	---	PASS
KRTDAP	388533	broad.mit.edu	37	19	35981320	35981320	+	Missense_Mutation	SNP	C	T	T			TCGA-EJ-5519-01A-01D-1576-08	TCGA-EJ-5519-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:35981320C>T	uc002nzh.2	-	1	37	c.25G>A	c.(25-27)GTG>ATG	p.V9M		NM_207392	NP_997275	P60985	KTDAP_HUMAN	keratinocyte differentiation-associated protein	9					cell differentiation	extracellular region					0	all_lung(56;1.89e-08)|Lung NSC(56;2.9e-08)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0724)			AGGAGCACCACGGCAGGAAGG	0.572													6	150	---	---	---	---	PASS
SIPA1L3	23094	broad.mit.edu	37	19	38600988	38600988	+	Missense_Mutation	SNP	G	A	A			TCGA-EJ-5519-01A-01D-1576-08	TCGA-EJ-5519-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:38600988G>A	uc002ohk.2	+	8	2764	c.2255G>A	c.(2254-2256)CGA>CAA	p.R752Q		NM_015073	NP_055888	O60292	SI1L3_HUMAN	signal-induced proliferation-associated 1 like	752	Rap-GAP.				regulation of small GTPase mediated signal transduction	intracellular	GTPase activator activity			ovary(1)|central_nervous_system(1)	2			Lung(45;0.000246)|LUSC - Lung squamous cell carcinoma(53;0.000292)			ATCATTGTCCGAGTCCACAAC	0.597													26	31	---	---	---	---	PASS
CYP2A7	1549	broad.mit.edu	37	19	41533104	41533104	+	Intron	SNP	G	A	A			TCGA-EJ-5519-01A-01D-1576-08	TCGA-EJ-5519-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:41533104G>A	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)			CATCATGTCCGCACAGCACCA	0.632													6	78	---	---	---	---	PASS
NANOS2	339345	broad.mit.edu	37	19	46417454	46417454	+	3'UTR	SNP	T	C	C			TCGA-EJ-5519-01A-01D-1576-08	TCGA-EJ-5519-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:46417454T>C	uc002pdu.2	-	1						NM_001029861	NP_001025032	P60321	NANO2_HUMAN	nanos homolog 2						germ-line stem cell maintenance|mRNA catabolic process|multicellular organismal development|negative regulation of meiosis|regulation of translation|spermatogenesis	cytoplasmic mRNA processing body|perinuclear region of cytoplasm	RNA binding|zinc ion binding				0		Ovarian(192;0.0308)|all_neural(266;0.0476)		OV - Ovarian serous cystadenocarcinoma(262;0.00442)|GBM - Glioblastoma multiforme(486;0.0668)|Epithelial(262;0.231)		AAGGGCTGGGTGACTGGAAGA	0.632													3	5	---	---	---	---	PASS
KIF16B	55614	broad.mit.edu	37	20	16360552	16360552	+	Nonsense_Mutation	SNP	C	A	A			TCGA-EJ-5519-01A-01D-1576-08	TCGA-EJ-5519-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:16360552C>A	uc002wpg.1	-	19	2253	c.2095G>T	c.(2095-2097)GAA>TAA	p.E699*	KIF16B_uc002wpe.1_Nonsense_Mutation_p.E81*|KIF16B_uc002wpf.1_Nonsense_Mutation_p.E81*|KIF16B_uc010gch.1_Nonsense_Mutation_p.E699*|KIF16B_uc010gci.1_Nonsense_Mutation_p.E699*|KIF16B_uc010gcj.1_Nonsense_Mutation_p.E710*	NM_024704	NP_078980	Q96L93	KI16B_HUMAN	kinesin-like motor protein C20orf23	699	Glu-rich.|Potential.				cell communication|early endosome to late endosome transport|endoderm development|epidermal growth factor receptor signaling pathway|fibroblast growth factor receptor signaling pathway|formation of primary germ layer|Golgi to endosome transport|microtubule-based movement|receptor catabolic process|regulation of receptor recycling	early endosome membrane|microtubule	ATP binding|phosphatidylinositol-3,4,5-trisphosphate binding|phosphatidylinositol-3,4-bisphosphate binding|phosphatidylinositol-3,5-bisphosphate binding|phosphatidylinositol-3-phosphate binding|plus-end-directed microtubule motor activity			skin(2)|large_intestine(1)|central_nervous_system(1)|lung(1)|breast(1)|ovary(1)|kidney(1)	8						AAGGTCTCTTCTTCTTGTCTC	0.448													76	184	---	---	---	---	PASS
NAA20	51126	broad.mit.edu	37	20	20013297	20013297	+	Missense_Mutation	SNP	G	A	A			TCGA-EJ-5519-01A-01D-1576-08	TCGA-EJ-5519-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:20013297G>A	uc002wrp.2	+	5	555	c.451G>A	c.(451-453)GAT>AAT	p.D151N	NAA20_uc002wrq.2_Intron|NAA20_uc002wrr.2_Missense_Mutation_p.D139N	NM_016100	NP_057184	P61599	NAA20_HUMAN	N-acetyltransferase 5 isoform a	151	N-acetyltransferase.					cytoplasm|nucleus	peptide alpha-N-acetyltransferase activity				0						GGACGCTTATGGTAAGCTCCC	0.408													10	77	---	---	---	---	PASS
STK4	6789	broad.mit.edu	37	20	43703680	43703680	+	Missense_Mutation	SNP	G	A	A			TCGA-EJ-5519-01A-01D-1576-08	TCGA-EJ-5519-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:43703680G>A	uc002xnb.2	+	11	1417	c.1327G>A	c.(1327-1329)GAC>AAC	p.D443N	STK4_uc010ggx.2_3'UTR|STK4_uc010ggy.2_Missense_Mutation_p.D388N	NM_006282	NP_006273	Q13043	STK4_HUMAN	serine/threonine kinase 4	443	SARAH.				apoptosis|cell morphogenesis|hippo signaling cascade|intracellular protein kinase cascade|negative regulation of canonical Wnt receptor signaling pathway|peptidyl-serine phosphorylation|positive regulation of apoptosis|protein autophosphorylation	cytoplasm|nucleus	ATP binding|magnesium ion binding|protein homodimerization activity|protein serine/threonine kinase activator activity|protein serine/threonine kinase activity|transcription factor binding			ovary(1)|skin(1)	2		Myeloproliferative disorder(115;0.0122)				GACAGTGGAGGACCTTCAGAA	0.542													5	68	---	---	---	---	PASS
ADNP	23394	broad.mit.edu	37	20	49509965	49509965	+	Missense_Mutation	SNP	G	C	C			TCGA-EJ-5519-01A-01D-1576-08	TCGA-EJ-5519-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:49509965G>C	uc002xvt.1	-	5	1631	c.1286C>G	c.(1285-1287)GCT>GGT	p.A429G	ADNP_uc002xvu.1_Missense_Mutation_p.A429G	NM_015339	NP_056154	Q9H2P0	ADNP_HUMAN	activity-dependent neuroprotector	429						nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(2)	2						GGCAGCTGCAGCAGGTTTGGA	0.473													64	154	---	---	---	---	PASS
ZNF512B	57473	broad.mit.edu	37	20	62598086	62598086	+	Missense_Mutation	SNP	C	T	T			TCGA-EJ-5519-01A-01D-1576-08	TCGA-EJ-5519-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:62598086C>T	uc002yhl.1	-	5	496	c.442G>A	c.(442-444)GCA>ACA	p.A148T		NM_020713	NP_065764	Q96KM6	Z512B_HUMAN	zinc finger protein 512B	148	C2H2-type 2.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0	all_cancers(38;2.14e-11)|all_epithelial(29;3.41e-13)|Lung NSC(23;3.41e-09)|all_lung(23;1.06e-08)					GAGGTGAATGCGGCCTCGCAG	0.647													3	60	---	---	---	---	PASS
KRTAP10-1	386677	broad.mit.edu	37	21	45959620	45959620	+	Silent	SNP	C	T	T			TCGA-EJ-5519-01A-01D-1576-08	TCGA-EJ-5519-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:45959620C>T	uc002zfh.1	-	1	459	c.414G>A	c.(412-414)CAG>CAA	p.Q138Q	C21orf29_uc002zfe.1_Intron|C21orf29_uc010gpv.1_Intron	NM_198691	NP_941964	P60331	KR101_HUMAN	keratin associated protein 10-1	138	24 X 5 AA repeats of C-C-X(3).					keratin filament				skin(1)	1						AGCAGGACTGCTGGCTGGAGG	0.483													33	26	---	---	---	---	PASS
KRTAP10-10	353333	broad.mit.edu	37	21	46057711	46057711	+	Missense_Mutation	SNP	G	C	C	rs4818948	byFrequency	TCGA-EJ-5519-01A-01D-1576-08	TCGA-EJ-5519-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:46057711G>C	uc002zfq.2	+	1	439	c.377G>C	c.(376-378)TGC>TCC	p.C126S	C21orf29_uc002zfe.1_Intron|C21orf29_uc010gpv.1_Intron	NM_181688	NP_859016	P60014	KR10A_HUMAN	keratin associated protein 10-10	126	15 X 5 AA repeats of C-C-X(3).|8.					keratin filament					0						TCCCCTTCATGCTGCCAGCAG	0.358													4	202	---	---	---	---	PASS
LOC96610	96610	broad.mit.edu	37	22	22662971	22662971	+	Intron	SNP	A	G	G			TCGA-EJ-5519-01A-01D-1576-08	TCGA-EJ-5519-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:22662971A>G	uc011aim.1	+						LOC96610_uc011aiq.1_Intron|LOC96610_uc011aip.1_RNA|LOC96610_uc010gto.2_RNA					Parts of antibodies, mostly variable regions.												0						TGTAAGTAAAATTCACTTTGG	0.323													3	50	---	---	---	---	PASS
LOC96610	96610	broad.mit.edu	37	22	22662995	22662995	+	Intron	SNP	C	T	T	rs79792109	by1000genomes	TCGA-EJ-5519-01A-01D-1576-08	TCGA-EJ-5519-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:22662995C>T	uc011aim.1	+						LOC96610_uc011aiq.1_Intron|LOC96610_uc011aip.1_RNA|LOC96610_uc010gto.2_RNA					Parts of antibodies, mostly variable regions.												0						TTTATTGTGTCACATAGAATT	0.348													3	70	---	---	---	---	PASS
LOC96610	96610	broad.mit.edu	37	22	22664743	22664743	+	RNA	SNP	G	A	A			TCGA-EJ-5519-01A-01D-1576-08	TCGA-EJ-5519-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:22664743G>A	uc011aim.1	+	31		c.2258G>A			LOC96610_uc011aiq.1_RNA					Parts of antibodies, mostly variable regions.												0						CAGACTAAAGGCAAACAAGGA	0.498													5	39	---	---	---	---	PASS
SF3A1	10291	broad.mit.edu	37	22	30736751	30736751	+	Silent	SNP	T	C	C			TCGA-EJ-5519-01A-01D-1576-08	TCGA-EJ-5519-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:30736751T>C	uc003ahl.2	-	8	1254	c.1122A>G	c.(1120-1122)ACA>ACG	p.T374T		NM_005877	NP_005868	Q15459	SF3A1_HUMAN	splicing factor 3a, subunit 1, 120kDa isoform 1	374					nuclear mRNA 3'-splice site recognition	catalytic step 2 spliceosome|nucleoplasm|U2-type spliceosomal complex	protein binding|RNA binding			ovary(3)|large_intestine(1)|pancreas(1)	5						GAGGCATGGGTGTCTCTGGGG	0.582													59	112	---	---	---	---	PASS
ISX	91464	broad.mit.edu	37	22	35481682	35481682	+	Missense_Mutation	SNP	C	G	G			TCGA-EJ-5519-01A-01D-1576-08	TCGA-EJ-5519-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:35481682C>G	uc003anj.2	+	4	1685	c.734C>G	c.(733-735)ACA>AGA	p.T245R	ISX_uc011amg.1_Missense_Mutation_p.T233R	NM_001008494	NP_001008494	Q2M1V0	ISX_HUMAN	intestine-specific homeobox	245						nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			ovary(3)|skin(2)	5						GCTACTTCAACATAGAGATTG	0.532													3	121	---	---	---	---	PASS
MICALL1	85377	broad.mit.edu	37	22	38336890	38336890	+	3'UTR	SNP	G	A	A			TCGA-EJ-5519-01A-01D-1576-08	TCGA-EJ-5519-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:38336890G>A	uc003aui.2	+	16						NM_033386	NP_203744	Q8N3F8	MILK1_HUMAN	molecule interacting with Rab13							cytoplasm|cytoskeleton	protein binding|zinc ion binding			breast(1)	1	Melanoma(58;0.045)					CTCCTGGGCTGTGCTCTGTTT	0.597													3	36	---	---	---	---	PASS
GUCY2F	2986	broad.mit.edu	37	X	108718895	108718895	+	Missense_Mutation	SNP	G	C	C			TCGA-EJ-5519-01A-01D-1576-08	TCGA-EJ-5519-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:108718895G>C	uc004eod.3	-	2	547	c.271C>G	c.(271-273)CTG>GTG	p.L91V	GUCY2F_uc011msq.1_RNA	NM_001522	NP_001513	P51841	GUC2F_HUMAN	guanylate cyclase 2F precursor	91	Extracellular (Potential).				intracellular signal transduction|receptor guanylyl cyclase signaling pathway|visual perception	integral to plasma membrane|nuclear outer membrane	ATP binding|GTP binding|guanylate cyclase activity|protein kinase activity|receptor activity			lung(4)|breast(3)|central_nervous_system(1)	8						GAATAACTCAGGTCAAAAGAT	0.502											OREG0019905	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	96	44	---	---	---	---	PASS
ZZZ3	26009	broad.mit.edu	37	1	78098722	78098723	+	Frame_Shift_Del	DEL	TC	-	-			TCGA-EJ-5519-01A-01D-1576-08	TCGA-EJ-5519-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:78098722_78098723delTC	uc001dhq.2	-	5	793_794	c.317_318delGA	c.(316-318)AGAfs	p.R106fs	ZZZ3_uc001dhr.2_Intron|ZZZ3_uc009wbz.1_Frame_Shift_Del_p.R106fs|ZZZ3_uc001dhp.2_Frame_Shift_Del_p.R106fs	NM_015534	NP_056349	Q8IYH5	ZZZ3_HUMAN	zinc finger, ZZ-type containing 3	106					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(4)|large_intestine(1)	5						CTGTTTGCCTTCTCTCACAATT	0.391													268	117	---	---	---	---	
TTF2	8458	broad.mit.edu	37	1	117628870	117628871	+	Intron	DEL	TG	-	-	rs3831091		TCGA-EJ-5519-01A-01D-1576-08	TCGA-EJ-5519-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:117628870_117628871delTG	uc001egy.2	+							NM_003594	NP_003585	Q9UNY4	TTF2_HUMAN	transcription termination factor, RNA polymerase						mRNA processing|regulation of transcription, DNA-dependent|RNA splicing|termination of RNA polymerase II transcription	cytoplasm|spliceosomal complex|transcription elongation factor complex	ATP binding|ATP-dependent helicase activity|DNA binding|DNA-dependent ATPase activity|protein binding|zinc ion binding			ovary(1)	1	Lung SC(450;0.225)	all_cancers(81;4.23e-06)|all_epithelial(167;3.65e-07)|all_lung(203;2.81e-06)|Lung NSC(69;1.98e-05)		Lung(183;0.0553)|Colorectal(144;0.179)|LUSC - Lung squamous cell carcinoma(189;0.19)		ACCTCCAAAAtgtgtgtgtgtg	0.337													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	121484665	121484668	+	IGR	DEL	TGTT	-	-	rs71221555		TCGA-EJ-5519-01A-01D-1576-08	TCGA-EJ-5519-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:121484665_121484668delTGTT								LOC647121 (170979 upstream) : None (None downstream)																							ggaaacactctgtttgtaaagtct	0.000													1910	7	---	---	---	---	
PYHIN1	149628	broad.mit.edu	37	1	158946181	158946181	+	Intron	DEL	T	-	-			TCGA-EJ-5519-01A-01D-1576-08	TCGA-EJ-5519-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:158946181delT	uc001ftb.2	+						PYHIN1_uc001ftc.2_Intron|PYHIN1_uc001ftd.2_Intron|PYHIN1_uc001fte.2_Intron	NM_152501	NP_689714	Q6K0P9	IFIX_HUMAN	pyrin and HIN domain family, member 1 alpha 1						cell cycle	nuclear speck				ovary(3)|pancreas(1)	4	all_hematologic(112;0.0378)					GAAGTTTCCCTTTAGCCCTTG	0.493													4	2	---	---	---	---	
SPAST	6683	broad.mit.edu	37	2	32312763	32312764	+	Intron	INS	-	TT	TT	rs72286744		TCGA-EJ-5519-01A-01D-1576-08	TCGA-EJ-5519-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:32312763_32312764insTT	uc002roc.2	+						SPAST_uc002rod.2_Intron	NM_014946	NP_055761	Q9UBP0	SPAST_HUMAN	spastin isoform 1						cell cycle|cell death|cell differentiation|cytokinesis, completion of separation|ER to Golgi vesicle-mediated transport|microtubule bundle formation|microtubule severing|nervous system development|protein hexamerization|protein homooligomerization	endoplasmic reticulum|endosome|integral to membrane|microtubule|microtubule organizing center|nucleus|perinuclear region of cytoplasm|spindle	alpha-tubulin binding|ATP binding|beta-tubulin binding|microtubule binding|microtubule-severing ATPase activity			breast(1)	1	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.208)					cttttcttttcttttttttttt	0.079													6	4	---	---	---	---	
CCDC88A	55704	broad.mit.edu	37	2	55546316	55546319	+	Intron	DEL	ACAG	-	-	rs3214665		TCGA-EJ-5519-01A-01D-1576-08	TCGA-EJ-5519-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:55546316_55546319delACAG	uc002ryv.2	-						CCDC88A_uc010yoz.1_Intron|CCDC88A_uc010ypa.1_Intron|CCDC88A_uc002ryu.2_Intron|CCDC88A_uc002rys.2_Intron|CCDC88A_uc002ryw.2_Intron|CCDC88A_uc010fby.1_Intron	NM_001135597	NP_001129069	Q3V6T2	GRDN_HUMAN	coiled-coil domain containing 88A isoform 1						activation of protein kinase B activity|cell migration|cellular membrane organization|DNA replication|lamellipodium assembly|microtubule cytoskeleton organization|regulation of actin cytoskeleton organization|regulation of cell proliferation|regulation of DNA replication|regulation of neuron projection development|TOR signaling cascade	cytoplasmic membrane-bounded vesicle|cytosol|endoplasmic reticulum|Golgi apparatus|lamellipodium|plasma membrane	actin binding|microtubule binding|phosphatidylinositol binding|protein homodimerization activity|protein kinase B binding			ovary(2)|skin(2)	4						CAAATTGTAAACAGACATTTATCA	0.275													3	3	---	---	---	---	
CCT7	10574	broad.mit.edu	37	2	73474707	73474707	+	Intron	DEL	A	-	-			TCGA-EJ-5519-01A-01D-1576-08	TCGA-EJ-5519-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:73474707delA	uc002siz.2	+						CCT7_uc002sja.2_Intron|CCT7_uc010yrf.1_Intron|CCT7_uc010feu.2_Intron|CCT7_uc010yrg.1_Intron|CCT7_uc010yrh.1_Intron|CCT7_uc010yri.1_Intron	NM_006429	NP_006420	Q99832	TCPH_HUMAN	chaperonin containing TCP1, subunit 7 isoform a						'de novo' posttranslational protein folding		ATP binding|unfolded protein binding				0						TGTGTTATTTAAAAAAAAAAA	0.373													3	3	---	---	---	---	
GORASP2	26003	broad.mit.edu	37	2	171812923	171812924	+	Intron	INS	-	T	T			TCGA-EJ-5519-01A-01D-1576-08	TCGA-EJ-5519-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:171812923_171812924insT	uc002ugk.2	+						GORASP2_uc002ugj.2_Intron|GORASP2_uc010zdl.1_Intron|GORASP2_uc010zdm.1_Intron|GORASP2_uc002ugl.2_Intron|GORASP2_uc002ugm.2_Intron	NM_015530	NP_056345	Q9H8Y8	GORS2_HUMAN	golgi reassembly stacking protein 2							Golgi membrane				breast(1)|central_nervous_system(1)	2						TAATCTTTGTGTTTTTTTTTCT	0.381													152	7	---	---	---	---	
WDR48	57599	broad.mit.edu	37	3	39121184	39121185	+	Intron	INS	-	T	T			TCGA-EJ-5519-01A-01D-1576-08	TCGA-EJ-5519-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:39121184_39121185insT	uc003cit.2	+						WDR48_uc011ayt.1_Intron|WDR48_uc011ayu.1_Intron|WDR48_uc011ayv.1_Intron|WDR48_uc003ciu.2_Intron	NM_020839	NP_065890	Q8TAF3	WDR48_HUMAN	WD repeat domain 48						interspecies interaction between organisms|protein deubiquitination	lysosome|nucleus	protein binding			ovary(1)|breast(1)	2				KIRC - Kidney renal clear cell carcinoma(284;0.0588)|Kidney(284;0.0738)		TACCAATTGTGTTTTTTTTTCC	0.312													50	32	---	---	---	---	
RBM6	10180	broad.mit.edu	37	3	50114316	50114316	+	Intron	DEL	A	-	-			TCGA-EJ-5519-01A-01D-1576-08	TCGA-EJ-5519-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:50114316delA	uc003cyc.2	+						RBM6_uc003cyd.2_Intron|RBM6_uc003cye.2_Intron|RBM6_uc011bdi.1_Intron|RBM6_uc010hld.1_Intron|RBM6_uc010hle.1_Intron|RBM6_uc010hlf.1_Intron	NM_005777	NP_005768	P78332	RBM6_HUMAN	RNA binding motif protein 6						RNA processing	nucleus	DNA binding|nucleotide binding|RNA binding|zinc ion binding			ovary(2)	2				BRCA - Breast invasive adenocarcinoma(193;6.81e-05)|KIRC - Kidney renal clear cell carcinoma(197;0.0084)|Kidney(197;0.00977)		gactccatctaaaaaaaaaaa	0.184													7	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	165320296	165320297	+	IGR	DEL	TA	-	-			TCGA-EJ-5519-01A-01D-1576-08	TCGA-EJ-5519-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:165320296_165320297delTA								SLITRK3 (405827 upstream) : BCHE (170397 downstream)																							TGTTGTAACTTACCCTTCTGCC	0.391													127	44	---	---	---	---	
FXR1	8087	broad.mit.edu	37	3	180675619	180675620	+	Frame_Shift_Ins	INS	-	A	A			TCGA-EJ-5519-01A-01D-1576-08	TCGA-EJ-5519-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:180675619_180675620insA	uc003fkq.2	+	10	915_916	c.893_894insA	c.(892-894)GGAfs	p.G298fs	FXR1_uc003fkp.2_Frame_Shift_Ins_p.G213fs|FXR1_uc003fkr.2_Frame_Shift_Ins_p.G298fs|FXR1_uc011bqj.1_Frame_Shift_Ins_p.G212fs|FXR1_uc003fks.2_Frame_Shift_Ins_p.G212fs|FXR1_uc011bqk.1_Frame_Shift_Ins_p.G249fs|FXR1_uc011bql.1_Frame_Shift_Ins_p.G285fs	NM_005087	NP_005078	P51114	FXR1_HUMAN	fragile X mental retardation-related protein 1	298	KH 2.				apoptosis|cell differentiation|muscle organ development	nucleolus|polysome				breast(1)	1	all_cancers(143;6.07e-14)|Ovarian(172;0.0212)		Epithelial(37;3.05e-35)|OV - Ovarian serous cystadenocarcinoma(80;2.4e-22)			AAAGTAATTGGAAAAAATGGCA	0.342													89	41	---	---	---	---	
LRPAP1	4043	broad.mit.edu	37	4	3520097	3520098	+	Intron	INS	-	CAGGCGAGA	CAGGCGAGA	rs142854314	by1000genomes	TCGA-EJ-5519-01A-01D-1576-08	TCGA-EJ-5519-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:3520097_3520098insCAGGCGAGA	uc003ghi.2	-							NM_002337	NP_002328	P30533	AMRP_HUMAN	low density lipoprotein receptor-related protein						negative regulation of protein binding|negative regulation of very-low-density lipoprotein particle clearance|protein folding|vesicle-mediated transport	cell surface|integral to membrane|plasma membrane	asialoglycoprotein receptor activity|heparin binding|low-density lipoprotein particle receptor binding|receptor antagonist activity|unfolded protein binding|very-low-density lipoprotein particle receptor binding			ovary(1)|skin(1)	2				UCEC - Uterine corpus endometrioid carcinoma (64;0.165)		AGCTTCCTTTCCAGGCGAGACA	0.663													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	49644696	49644697	+	IGR	INS	-	AACGA	AACGA			TCGA-EJ-5519-01A-01D-1576-08	TCGA-EJ-5519-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:49644696_49644697insAACGA								CWH43 (580603 upstream) : None (None downstream)																							gaatggaatggaatggaatgga	0.000													16	13	---	---	---	---	
AMACR	23600	broad.mit.edu	37	5	34004589	34004593	+	Intron	DEL	TCTTG	-	-			TCGA-EJ-5519-01A-01D-1576-08	TCGA-EJ-5519-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:34004589_34004593delTCTTG	uc003jig.2	-						AMACR_uc003jih.2_Intron|AMACR_uc003jii.2_Intron|AMACR_uc003jij.2_Intron|AMACR_uc003jil.1_Intron|AMACR_uc003jik.1_Intron	NM_014324	NP_055139	Q9UHK6	AMACR_HUMAN	alpha-methylacyl-CoA racemase isoform 1						bile acid biosynthetic process|fatty acid beta-oxidation using acyl-CoA oxidase	mitochondrion|peroxisomal matrix	alpha-methylacyl-CoA racemase activity				0						GTCATTTATCTCTTGTCTTCTTCTT	0.307													155	14	---	---	---	---	
APC	324	broad.mit.edu	37	5	112113962	112113962	+	Intron	DEL	A	-	-			TCGA-EJ-5519-01A-01D-1576-08	TCGA-EJ-5519-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:112113962delA	uc010jby.2	+						APC_uc011cvt.1_Intron|APC_uc003kpz.3_Intron|APC_uc003kpy.3_Intron|APC_uc010jbz.2_Intron	NM_001127511	NP_001120983	P25054	APC_HUMAN	adenomatous polyposis coli						canonical Wnt receptor signaling pathway|cell adhesion|cell cycle arrest|cell migration|cellular component disassembly involved in apoptosis|cytokinesis after mitosis|mitotic cell cycle spindle assembly checkpoint|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of cyclin-dependent protein kinase activity|negative regulation of microtubule depolymerization|positive regulation of apoptosis|positive regulation of cell migration|positive regulation of pseudopodium assembly|protein complex assembly|regulation of attachment of spindle microtubules to kinetochore|response to DNA damage stimulus|tight junction assembly	adherens junction|APC-Axin-1-beta-catenin complex|Axin-APC-beta-catenin-GSK3B complex|beta-catenin destruction complex|centrosome|cytosol|kinetochore|lamellipodium|lateral plasma membrane|nucleus|ruffle membrane|tight junction	beta-catenin binding|gamma-catenin binding|microtubule plus-end binding|protein kinase binding|protein kinase regulator activity			large_intestine(2123)|stomach(123)|soft_tissue(55)|small_intestine(34)|breast(26)|pancreas(25)|urinary_tract(20)|lung(19)|thyroid(18)|liver(13)|central_nervous_system(10)|ovary(9)|skin(7)|upper_aerodigestive_tract(6)|adrenal_gland(6)|bone(6)|NS(5)|prostate(4)|endometrium(3)|kidney(1)|oesophagus(1)|biliary_tract(1)	2515		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		AGTGTTCTGTAAAAAAAAAAT	0.368		12	D|Mis|N|F|S		colorectal|pancreatic|desmoid|hepatoblastoma|glioma|other CNS	colorectal|pancreatic|desmoid|hepatoblastoma|glioma|other CNS			Hereditary_Desmoid_Disease|Familial_Adenomatous_Polyposis|Turcot_syndrome	TSP Lung(16;0.13)			4	2	---	---	---	---	
KIAA0240	23506	broad.mit.edu	37	6	42790381	42790382	+	Intron	INS	-	A	A			TCGA-EJ-5519-01A-01D-1576-08	TCGA-EJ-5519-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:42790381_42790382insA	uc003osn.1	+						KIAA0240_uc003osm.1_Intron|KIAA0240_uc011duw.1_Intron|KIAA0240_uc003oso.1_Intron|KIAA0240_uc003osp.1_Intron	NM_015349	NP_056164	Q6AI39	K0240_HUMAN	hypothetical protein LOC23506											ovary(1)	1	Colorectal(47;0.196)		Colorectal(64;0.00237)|COAD - Colon adenocarcinoma(64;0.00473)|all cancers(41;0.00524)|KIRC - Kidney renal clear cell carcinoma(15;0.02)|Kidney(15;0.0388)|OV - Ovarian serous cystadenocarcinoma(102;0.104)			AAAACAAGATTAAAAAAAAAAA	0.233													4	2	---	---	---	---	
SERINC1	57515	broad.mit.edu	37	6	122768119	122768119	+	Frame_Shift_Del	DEL	A	-	-			TCGA-EJ-5519-01A-01D-1576-08	TCGA-EJ-5519-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:122768119delA	uc003pyy.1	-	9	1096	c.1026delT	c.(1024-1026)AATfs	p.N342fs	SERINC1_uc003pyx.1_RNA	NM_020755	NP_065806	Q9NRX5	SERC1_HUMAN	serine incorporator 1	342	Cytoplasmic (Potential).				phosphatidylserine metabolic process|phospholipid biosynthetic process|positive regulation of transferase activity|sphingolipid metabolic process	endoplasmic reticulum membrane|integral to membrane|plasma membrane	L-serine transmembrane transporter activity|protein binding			ovary(1)	1				GBM - Glioblastoma multiforme(226;0.126)		GAGTCAGTTTATTAACCTGAC	0.363													116	58	---	---	---	---	
L3MBTL3	84456	broad.mit.edu	37	6	130425882	130425882	+	Intron	DEL	A	-	-			TCGA-EJ-5519-01A-01D-1576-08	TCGA-EJ-5519-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:130425882delA	uc003qbt.2	+						L3MBTL3_uc003qbu.2_Intron	NM_032438	NP_115814	Q96JM7	LMBL3_HUMAN	l(3)mbt-like 3 isoform a						chromatin modification|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus				ovary(5)|skin(1)	6				GBM - Glioblastoma multiforme(226;0.0266)|OV - Ovarian serous cystadenocarcinoma(155;0.154)		ACTTGAACTTAAAAAAAAAAA	0.294													4	2	---	---	---	---	
INTS1	26173	broad.mit.edu	37	7	1514107	1514108	+	Intron	INS	-	AC	AC	rs143283428	by1000genomes	TCGA-EJ-5519-01A-01D-1576-08	TCGA-EJ-5519-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:1514107_1514108insAC	uc003skn.2	-						INTS1_uc003skm.1_Intron	NM_001080453	NP_001073922	Q8N201	INT1_HUMAN	integrator complex subunit 1						snRNA processing	integral to membrane|integrator complex|nuclear membrane					0		Ovarian(82;0.0253)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0181)|OV - Ovarian serous cystadenocarcinoma(56;6.99e-15)		GCTGCCCCCCAACCACCCTCCT	0.728													6	3	---	---	---	---	
WIPI2	26100	broad.mit.edu	37	7	5270696	5270696	+	3'UTR	DEL	A	-	-			TCGA-EJ-5519-01A-01D-1576-08	TCGA-EJ-5519-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:5270696delA	uc003snv.2	+	13					WIPI2_uc003snw.2_3'UTR|WIPI2_uc003snx.2_3'UTR|WIPI2_uc003sny.2_3'UTR|WIPI2_uc010ksv.2_3'UTR|WIPI2_uc003soa.2_3'UTR|WIPI2_uc003sob.2_3'UTR	NM_015610	NP_056425	Q9Y4P8	WIPI2_HUMAN	WD repeat domain, phosphoinositide interacting 2						autophagic vacuole assembly	cytosol|PAS complex|pre-autophagosomal structure membrane	phosphatidylinositol-3,5-bisphosphate binding|phosphatidylinositol-3-phosphate binding			ovary(2)	2		Ovarian(82;0.0175)		UCEC - Uterine corpus endometrioid carcinoma (126;0.0925)|OV - Ovarian serous cystadenocarcinoma(56;2.59e-14)		AGACTTTATTAAAAAAAAAAA	0.418													5	3	---	---	---	---	
C7orf28B	221960	broad.mit.edu	37	7	6840334	6840334	+	Intron	DEL	T	-	-			TCGA-EJ-5519-01A-01D-1576-08	TCGA-EJ-5519-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:6840334delT	uc003sqx.1	-						C7orf28B_uc011jxd.1_Intron	NM_198097	NP_932765	P86791	CCZ1_HUMAN	hypothetical protein LOC221960							lysosomal membrane					0		Ovarian(82;0.232)		UCEC - Uterine corpus endometrioid carcinoma (126;0.175)		TATAAAGTCATTTTTTTTTTT	0.204													5	3	---	---	---	---	
KBTBD2	25948	broad.mit.edu	37	7	32914830	32914831	+	Intron	INS	-	A	A			TCGA-EJ-5519-01A-01D-1576-08	TCGA-EJ-5519-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:32914830_32914831insA	uc003tdb.2	-						AVL9_uc011kai.1_Intron	NM_015483	NP_056298	Q8IY47	KBTB2_HUMAN	kelch repeat and BTB (POZ) domain containing 2												0			GBM - Glioblastoma multiforme(11;0.0499)			ATGTAGAGCTGAAAAGAACAAT	0.272													86	36	---	---	---	---	
BMPER	168667	broad.mit.edu	37	7	34193010	34193011	+	3'UTR	INS	-	TA	TA	rs140714031	by1000genomes	TCGA-EJ-5519-01A-01D-1576-08	TCGA-EJ-5519-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:34193010_34193011insTA	uc011kap.1	+	15						NM_133468	NP_597725	Q8N8U9	BMPER_HUMAN	BMP-binding endothelial regulator precursor						blood vessel endothelial cell proliferation involved in sprouting angiogenesis|endothelial cell activation|negative regulation of BMP signaling pathway|positive regulation of ERK1 and ERK2 cascade|regulation of endothelial cell migration|regulation of pathway-restricted SMAD protein phosphorylation	extracellular space				ovary(2)|central_nervous_system(1)	3						Gtatatatgtgtatatatatat	0.307													7	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	45923555	45923558	+	IGR	DEL	TCTT	-	-	rs71935217		TCGA-EJ-5519-01A-01D-1576-08	TCGA-EJ-5519-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:45923555_45923558delTCTT								SEPT7P2 (114938 upstream) : IGFBP1 (4401 downstream)																							CCAGAACCGAtctttctttctttt	0.235													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	61969237	61969238	+	IGR	DEL	CA	-	-	rs4585624		TCGA-EJ-5519-01A-01D-1576-08	TCGA-EJ-5519-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:61969237_61969238delCA								None (None upstream) : LOC643955 (782434 downstream)																							gccttcaactcacagagtttaa	0.000													1013	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	66318329	66318330	+	IGR	INS	-	GT	GT	rs111249198		TCGA-EJ-5519-01A-01D-1576-08	TCGA-EJ-5519-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:66318329_66318330insGT								LOC729156 (8516 upstream) : C7orf42 (67873 downstream)																							tgggattacaggtgagcgatca	0.139													4	2	---	---	---	---	
GTF2IRD1	9569	broad.mit.edu	37	7	73974113	73974114	+	Intron	INS	-	T	T	rs112974956		TCGA-EJ-5519-01A-01D-1576-08	TCGA-EJ-5519-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:73974113_73974114insT	uc003uaq.2	+						GTF2IRD1_uc010lbq.2_Intron|GTF2IRD1_uc003uap.2_Intron|GTF2IRD1_uc003uar.1_Intron	NM_016328	NP_057412	Q9UHL9	GT2D1_HUMAN	GTF2I repeat domain containing 1 isoform 1							nucleus	DNA binding|protein binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity			ovary(4)	4						CCCTGCCtttcttttttttttt	0.312													4	2	---	---	---	---	
LINGO2	158038	broad.mit.edu	37	9	27949103	27949103	+	Frame_Shift_Del	DEL	C	-	-			TCGA-EJ-5519-01A-01D-1576-08	TCGA-EJ-5519-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:27949103delC	uc003zqu.1	-	2	1761	c.1567delG	c.(1567-1569)GACfs	p.D523fs	LINGO2_uc010mjf.1_Frame_Shift_Del_p.D523fs|LINGO2_uc003zqv.1_Frame_Shift_Del_p.D523fs	NM_152570	NP_689783	Q7L985	LIGO2_HUMAN	leucine rich repeat and Ig domain containing 2	523	Extracellular (Potential).					integral to membrane				upper_aerodigestive_tract(1)|ovary(1)|central_nervous_system(1)	3	Melanoma(11;0.242)	all_neural(11;2.78e-09)		UCEC - Uterine corpus endometrioid carcinoma (5;0.0818)|GBM - Glioblastoma multiforme(2;1.31e-34)|all cancers(2;2.37e-25)|Lung(2;7.48e-08)|LUSC - Lung squamous cell carcinoma(38;5.09e-07)|KIRC - Kidney renal clear cell carcinoma(2;0.0465)|Kidney(2;0.0604)		GAAATGGTGTCATTGGAGTCG	0.458													325	7	---	---	---	---	
ANKRD20A4	728747	broad.mit.edu	37	9	69423761	69423762	+	Frame_Shift_Ins	INS	-	A	A			TCGA-EJ-5519-01A-01D-1576-08	TCGA-EJ-5519-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:69423761_69423762insA	uc004afn.2	+	15	2169_2170	c.2057_2058insA	c.(2056-2058)AGAfs	p.R686fs	uc010mnx.1_5'Flank	NM_001098805	NP_001092275	Q4UJ75	A20A4_HUMAN	ankyrin repeat domain 20 family, member A4	686	Potential.										0						GATAGTCTCAGAAAAAAGTCAT	0.337													174	7	---	---	---	---	
ROR2	4920	broad.mit.edu	37	9	94374511	94374511	+	Intron	DEL	G	-	-			TCGA-EJ-5519-01A-01D-1576-08	TCGA-EJ-5519-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:94374511delG	uc004ari.1	-							NM_004560	NP_004551	Q01974	ROR2_HUMAN	receptor tyrosine kinase-like orphan receptor 2						negative regulation of cell proliferation|positive regulation of cell migration|transmembrane receptor protein tyrosine kinase signaling pathway	integral to plasma membrane	ATP binding|transmembrane receptor protein tyrosine kinase activity|Wnt-protein binding			lung(8)|central_nervous_system(5)|ovary(3)|large_intestine(2)|stomach(1)|breast(1)	20						CTGTATCTGTGGCAGTGGTAG	0.502													4	2	---	---	---	---	
PTGR1	22949	broad.mit.edu	37	9	114338448	114338448	+	Intron	DEL	A	-	-	rs35670507		TCGA-EJ-5519-01A-01D-1576-08	TCGA-EJ-5519-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:114338448delA	uc004bfh.2	-						ZNF483_uc004bfg.2_Intron|PTGR1_uc011lwr.1_Intron|PTGR1_uc004bfi.3_Intron|PTGR1_uc004bfj.3_Intron|PTGR1_uc010mue.2_Intron	NM_012212	NP_036344	Q14914	PTGR1_HUMAN	prostaglandin reductase 1 isoform 1						leukotriene metabolic process	cytoplasm	15-oxoprostaglandin 13-oxidase activity|2-alkenal reductase activity|alcohol dehydrogenase (NAD) activity|zinc ion binding				0						actgagtctcaaaaaaaaaaa	0.020													4	2	---	---	---	---	
LARP4B	23185	broad.mit.edu	37	10	910364	910364	+	Intron	DEL	A	-	-			TCGA-EJ-5519-01A-01D-1576-08	TCGA-EJ-5519-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:910364delA	uc001ifs.1	-							NM_015155	NP_055970	Q92615	LAR4B_HUMAN	La ribonucleoprotein domain family, member 4B								nucleotide binding|RNA binding			ovary(2)|central_nervous_system(1)	3						GTTCaaaattaaaaaaaaaaa	0.388													2	4	---	---	---	---	
DCLRE1C	64421	broad.mit.edu	37	10	14951253	14951253	+	Frame_Shift_Del	DEL	A	-	-			TCGA-EJ-5519-01A-01D-1576-08	TCGA-EJ-5519-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:14951253delA	uc001inn.2	-	14	1318	c.1233delT	c.(1231-1233)TTTfs	p.F411fs	DCLRE1C_uc010qbx.1_Intron|DCLRE1C_uc001ink.2_Frame_Shift_Del_p.F64fs|DCLRE1C_uc001inl.2_Frame_Shift_Del_p.F291fs|DCLRE1C_uc009xji.2_Frame_Shift_Del_p.F296fs|DCLRE1C_uc001inm.2_Frame_Shift_Del_p.F291fs|DCLRE1C_uc001ino.2_Frame_Shift_Del_p.F296fs|DCLRE1C_uc009xjh.2_RNA|DCLRE1C_uc001inp.2_Frame_Shift_Del_p.F291fs|DCLRE1C_uc001inq.2_Frame_Shift_Del_p.F291fs|DCLRE1C_uc001inr.2_Frame_Shift_Del_p.F296fs	NM_001033855	NP_001029027	Q96SD1	DCR1C_HUMAN	artemis protein isoform a	411					DNA recombination	nucleus	5'-3' exonuclease activity|single-stranded DNA specific endodeoxyribonuclease activity			ovary(1)	1						CCTCAGGGTGAAAAGTTTCCG	0.448								Involved_in_tolerance_or_repair_of_DNA_crosslinks|NHEJ					112	17	---	---	---	---	
MRC1	4360	broad.mit.edu	37	10	17875520	17875520	+	Intron	DEL	A	-	-			TCGA-EJ-5519-01A-01D-1576-08	TCGA-EJ-5519-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:17875520delA	uc001ipk.2	+							NM_002438	NP_002429	P22897	MRC1_HUMAN	mannose receptor C type 1 precursor						receptor-mediated endocytosis	endosome membrane|integral to plasma membrane	mannose binding|receptor activity				0						actctgtctcaaaaaaaaaaa	0.085													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	42383711	42383712	+	IGR	INS	-	C	C			TCGA-EJ-5519-01A-01D-1576-08	TCGA-EJ-5519-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:42383711_42383712insC								None (None upstream) : LOC441666 (443603 downstream)																							tcaaatggaatcaaaataacca	0.000													49	11	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	42390479	42390479	+	IGR	DEL	G	-	-	rs72505278		TCGA-EJ-5519-01A-01D-1576-08	TCGA-EJ-5519-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:42390479delG								None (None upstream) : LOC441666 (436836 downstream)																							AAcatcgaatggaatcgaatg	0.040													68	15	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	42400455	42400456	+	IGR	INS	-	G	G	rs71264011		TCGA-EJ-5519-01A-01D-1576-08	TCGA-EJ-5519-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:42400455_42400456insG								None (None upstream) : LOC441666 (426859 downstream)																							cttctttgtgttgtgtgtattc	0.000													486	10	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	42530677	42530678	+	IGR	INS	-	T	T			TCGA-EJ-5519-01A-01D-1576-08	TCGA-EJ-5519-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:42530677_42530678insT								None (None upstream) : LOC441666 (296637 downstream)																							tctaaagaacgttcaactctgt	0.000													8	11	---	---	---	---	
COL13A1	1305	broad.mit.edu	37	10	71692180	71692180	+	Intron	DEL	C	-	-			TCGA-EJ-5519-01A-01D-1576-08	TCGA-EJ-5519-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:71692180delC	uc001jpr.1	+						COL13A1_uc001jqj.1_Intron|COL13A1_uc001jps.1_Intron|COL13A1_uc001jpt.1_Intron|COL13A1_uc001jpu.1_Intron|COL13A1_uc001jpv.1_Intron|COL13A1_uc001jpx.1_Intron|COL13A1_uc001jpw.1_Intron|COL13A1_uc001jpy.1_Intron|COL13A1_uc001jpz.1_Intron|COL13A1_uc001jqa.1_Intron|COL13A1_uc001jqc.1_Intron|COL13A1_uc001jqb.1_Intron|COL13A1_uc001jql.2_Intron|COL13A1_uc001jqd.1_Intron|COL13A1_uc001jqe.1_Intron|COL13A1_uc001jqf.1_Intron|COL13A1_uc001jqg.1_Intron|COL13A1_uc001jqh.1_Intron|COL13A1_uc001jqi.1_Intron|COL13A1_uc010qjf.1_Intron	NM_005203	NP_005194	Q5TAT6	CODA1_HUMAN	alpha 1 type XIII collagen isoform 1						cell differentiation|cell-cell adhesion|cell-matrix adhesion|endochondral ossification|morphogenesis of a branching structure	collagen type XIII|integral to membrane	extracellular matrix structural constituent|heparin binding|protein binding			ovary(1)	1					Atorvastatin(DB01076)|Simvastatin(DB00641)	GCTGACACCTCCACATCCTCC	0.557													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	106059243	106059243	+	5'Flank	DEL	T	-	-			TCGA-EJ-5519-01A-01D-1576-08	TCGA-EJ-5519-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:106059243delT	uc001kyd.1	+											Homo sapiens cDNA FLJ37540 fis, clone BRCAN2026117.																		ttttttttccttttttttttt	0.179													4	2	---	---	---	---	
STK32C	282974	broad.mit.edu	37	10	134041668	134041668	+	Intron	DEL	G	-	-			TCGA-EJ-5519-01A-01D-1576-08	TCGA-EJ-5519-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:134041668delG	uc001lle.1	-						STK32C_uc001lld.1_Intron|STK32C_uc010quu.1_Intron|STK32C_uc009ybc.1_5'UTR|STK32C_uc009ybd.1_Intron|STK32C_uc001llb.2_5'UTR|STK32C_uc001llc.1_Intron	NM_173575	NP_775846	Q86UX6	ST32C_HUMAN	serine/threonine kinase 32C								ATP binding|metal ion binding|protein serine/threonine kinase activity			large_intestine(2)|lung(2)|breast(1)	5		all_cancers(35;2.72e-11)|all_epithelial(44;2.33e-08)|Lung NSC(174;0.000855)|all_lung(145;0.00146)|all_neural(114;0.0299)|Breast(234;0.106)|Colorectal(31;0.112)|Melanoma(40;0.124)|Glioma(114;0.203)		Epithelial(32;3.99e-05)|all cancers(32;5.58e-05)|OV - Ovarian serous cystadenocarcinoma(35;9.96e-05)|BRCA - Breast invasive adenocarcinoma(275;0.222)		GGACGCCTGAGGACGCCTGGG	0.627													66	21	---	---	---	---	
DNAJC24	120526	broad.mit.edu	37	11	31436290	31436291	+	Intron	INS	-	T	T			TCGA-EJ-5519-01A-01D-1576-08	TCGA-EJ-5519-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:31436290_31436291insT	uc001msx.2	+						DNAJC24_uc001msw.1_Intron|DNAJC24_uc009yjm.2_Intron	NM_181706	NP_859057	Q6P3W2	DJC24_HUMAN	zinc finger, CSL domain containing 3						protein folding		heat shock protein binding|metal ion binding|unfolded protein binding			breast(2)	2						CAGATTTACAATTTTTTTAAAT	0.416													60	20	---	---	---	---	
FAM111A	63901	broad.mit.edu	37	11	58920573	58920574	+	Frame_Shift_Ins	INS	-	A	A			TCGA-EJ-5519-01A-01D-1576-08	TCGA-EJ-5519-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:58920573_58920574insA	uc010rkp.1	+	5	1659_1660	c.1432_1433insA	c.(1432-1434)GAAfs	p.E478fs	FAM111A_uc010rkq.1_Frame_Shift_Ins_p.E478fs|FAM111A_uc010rkr.1_Frame_Shift_Ins_p.E478fs|FAM111A_uc001nno.2_Frame_Shift_Ins_p.E478fs|FAM111A_uc001nnp.2_Frame_Shift_Ins_p.E478fs|FAM111A_uc001nnq.2_Frame_Shift_Ins_p.E478fs	NM_001142521	NP_001135993	Q96PZ2	F111A_HUMAN	hypothetical protein LOC63901	478					proteolysis		serine-type endopeptidase activity			ovary(3)	3		all_epithelial(135;0.139)				TCCATATGGAGAAAAAAAGCAG	0.406													165	72	---	---	---	---	
MS4A2	2206	broad.mit.edu	37	11	59856234	59856234	+	5'UTR	DEL	A	-	-			TCGA-EJ-5519-01A-01D-1576-08	TCGA-EJ-5519-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:59856234delA	uc001nop.2	+	1					MS4A2_uc009ymu.2_5'UTR	NM_000139	NP_000130	Q01362	FCERB_HUMAN	membrane-spanning 4-domains, subfamily A, member						cell proliferation|humoral immune response	integral to plasma membrane	calcium channel activity			ovary(1)	1		all_epithelial(135;0.245)			Omalizumab(DB00043)	TCGGTTAATGAAAAAATGGAC	0.398													46	8	---	---	---	---	
GANAB	23193	broad.mit.edu	37	11	62402415	62402416	+	Frame_Shift_Ins	INS	-	GGAC	GGAC			TCGA-EJ-5519-01A-01D-1576-08	TCGA-EJ-5519-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:62402415_62402416insGGAC	uc001nub.2	-	5	470_471	c.437_438insGTCC	c.(436-438)CCCfs	p.P146fs	GANAB_uc001nua.2_Frame_Shift_Ins_p.P146fs|GANAB_uc001nuc.2_Frame_Shift_Ins_p.P49fs|GANAB_uc010rma.1_Frame_Shift_Ins_p.P32fs|GANAB_uc010rmb.1_Frame_Shift_Ins_p.P32fs	NM_198334	NP_938148	Q14697	GANAB_HUMAN	neutral alpha-glucosidase AB isoform 2	146					post-translational protein modification|protein folding|protein N-linked glycosylation via asparagine	endoplasmic reticulum lumen|Golgi apparatus|melanosome	carbohydrate binding|glucan 1,3-alpha-glucosidase activity|protein binding			ovary(3)|central_nervous_system(1)|skin(1)	5						TGATCTTGTAGGGTCCCTCAGC	0.480													138	46	---	---	---	---	
MOGAT2	80168	broad.mit.edu	37	11	75441959	75441960	+	Intron	INS	-	A	A	rs72483665		TCGA-EJ-5519-01A-01D-1576-08	TCGA-EJ-5519-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:75441959_75441960insA	uc010rru.1	+						MOGAT2_uc010rrv.1_Intron	NM_025098	NP_079374	Q3SYC2	MOGT2_HUMAN	monoacylglycerol O-acyltransferase 2						glycerol metabolic process	endoplasmic reticulum membrane|integral to membrane	2-acylglycerol O-acyltransferase activity			ovary(2)	2	Ovarian(111;0.103)					gactctacctcaaaaaaaaaaa	0.114													3	3	---	---	---	---	
C11orf1	64776	broad.mit.edu	37	11	111754316	111754317	+	Intron	INS	-	A	A	rs75371222		TCGA-EJ-5519-01A-01D-1576-08	TCGA-EJ-5519-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:111754316_111754317insA	uc001pmd.2	+						C11orf1_uc001pme.2_Intron	NM_022761	NP_073598	Q9H5F2	CK001_HUMAN	hypothetical protein LOC64776							nucleus					0		all_cancers(61;1.26e-15)|all_epithelial(67;9.52e-10)|Melanoma(852;1.91e-06)|all_hematologic(158;0.000405)|Acute lymphoblastic leukemia(157;0.000967)|Breast(348;0.0112)|Medulloblastoma(222;0.0228)|all_neural(223;0.0281)		all cancers(92;6.28e-09)|Epithelial(105;4.11e-08)|OV - Ovarian serous cystadenocarcinoma(223;1.52e-07)|BRCA - Breast invasive adenocarcinoma(274;1.1e-06)		gactctatctcaaaaaaaaaaa	0.124													4	2	---	---	---	---	
MANSC1	54682	broad.mit.edu	37	12	12482820	12482821	+	3'UTR	INS	-	A	A	rs118108016	by1000genomes	TCGA-EJ-5519-01A-01D-1576-08	TCGA-EJ-5519-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:12482820_12482821insA	uc001rai.1	-	4					MANSC1_uc010shm.1_3'UTR|MANSC1_uc001raj.1_3'UTR|MANSC1_uc009zht.1_3'UTR	NM_018050	NP_060520	Q9H8J5	MANS1_HUMAN	MANSC domain containing 1 precursor							integral to membrane					0		Prostate(47;0.0865)		BRCA - Breast invasive adenocarcinoma(232;0.185)		actctgtctccaaaaaaaaaaa	0.188													4	2	---	---	---	---	
BAZ2A	11176	broad.mit.edu	37	12	56999550	56999550	+	Intron	DEL	T	-	-			TCGA-EJ-5519-01A-01D-1576-08	TCGA-EJ-5519-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:56999550delT	uc001slq.1	-						BAZ2A_uc001slp.1_Intron|BAZ2A_uc009zov.1_5'Flank|BAZ2A_uc009zow.1_Intron	NM_013449	NP_038477	Q9UIF9	BAZ2A_HUMAN	bromodomain adjacent to zinc finger domain, 2A						chromatin silencing at rDNA|DNA methylation|transcription, DNA-dependent	chromatin silencing complex|nucleolus|rDNA heterochromatin	DNA binding|histone acetyl-lysine binding|ligand-dependent nuclear receptor binding|RNA binding|zinc ion binding				0						GCAGAAGTCCTTTTTTTTTTT	0.308													8	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	31652513	31652520	+	IGR	DEL	AAGAAAGA	-	-	rs7986217		TCGA-EJ-5519-01A-01D-1576-08	TCGA-EJ-5519-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:31652513_31652520delAAGAAAGA								C13orf26 (103362 upstream) : HSPH1 (58245 downstream)																							ggaaggaaggaagaaagaaagaaagaaa	0.192													4	2	---	---	---	---	
WDHD1	11169	broad.mit.edu	37	14	55422594	55422595	+	Intron	INS	-	TTCAGA	TTCAGA	rs140324706	by1000genomes	TCGA-EJ-5519-01A-01D-1576-08	TCGA-EJ-5519-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:55422594_55422595insTTCAGA	uc001xbm.1	-						WDHD1_uc010aom.1_Intron|WDHD1_uc001xbn.1_Intron	NM_007086	NP_009017	O75717	WDHD1_HUMAN	WD repeat and HMG-box DNA binding protein 1							cytoplasm|nucleoplasm	DNA binding			skin(1)	1						AAAAACTACACTTCAGATTCCA	0.168													3	4	---	---	---	---	
SYT16	83851	broad.mit.edu	37	14	62542323	62542323	+	Intron	DEL	A	-	-			TCGA-EJ-5519-01A-01D-1576-08	TCGA-EJ-5519-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:62542323delA	uc001xfu.1	+						SYT16_uc010tsd.1_Intron	NM_031914	NP_114120	Q17RD7	SYT16_HUMAN	synaptotagmin XIV-like											central_nervous_system(1)	1				OV - Ovarian serous cystadenocarcinoma(108;0.0438)|BRCA - Breast invasive adenocarcinoma(234;0.118)		GATGAACGGTaaaaaaaaaaa	0.284													6	3	---	---	---	---	
SCG3	29106	broad.mit.edu	37	15	51980761	51980763	+	Intron	DEL	AGG	-	-	rs138925498		TCGA-EJ-5519-01A-01D-1576-08	TCGA-EJ-5519-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:51980761_51980763delAGG	uc002abh.2	+						SCG3_uc010ufz.1_Intron	NM_013243	NP_037375	Q8WXD2	SCG3_HUMAN	secretogranin III isoform 1 precursor						platelet activation|platelet degranulation	extracellular region|stored secretory granule				ovary(1)	1				all cancers(107;0.00488)		ttttttttctaggagtttatcat	0.054													4	3	---	---	---	---	
SLTM	79811	broad.mit.edu	37	15	59182525	59182526	+	Frame_Shift_Del	DEL	TC	-	-			TCGA-EJ-5519-01A-01D-1576-08	TCGA-EJ-5519-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:59182525_59182526delTC	uc002afp.2	-	15	2121_2122	c.2033_2034delGA	c.(2032-2034)AGAfs	p.R678fs	SLTM_uc002afn.2_Frame_Shift_Del_p.R220fs|SLTM_uc002afo.2_Frame_Shift_Del_p.R660fs|SLTM_uc002afq.2_Frame_Shift_Del_p.R247fs|SLTM_uc010bgd.2_Frame_Shift_Del_p.R247fs	NM_024755	NP_079031	Q9NWH9	SLTM_HUMAN	modulator of estrogen induced transcription	678	Arg/Glu-rich.|Potential.				apoptosis|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	nucleotide binding|RNA binding			ovary(1)	1						CGCGTTCCATTCTCTCTCTCTC	0.431													392	7	---	---	---	---	
OSTBETA	123264	broad.mit.edu	37	15	65344105	65344106	+	Intron	INS	-	AAAC	AAAC	rs140336932	by1000genomes	TCGA-EJ-5519-01A-01D-1576-08	TCGA-EJ-5519-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:65344105_65344106insAAAC	uc002aog.2	+						OSTBETA_uc002aoh.2_Intron	NM_178859	NP_849190	Q86UW2	OSTB_HUMAN	organic solute transporter beta							integral to membrane|plasma membrane					0						CAAGCTGTTaaaaacaaacaaa	0.465													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	46405916	46405916	+	IGR	DEL	T	-	-	rs77422485		TCGA-EJ-5519-01A-01D-1576-08	TCGA-EJ-5519-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:46405916delT								None (None upstream) : ANKRD26P1 (97333 downstream)																							ctttcaatcattCCCTTTGAT	0.050													202	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	46407681	46407706	+	IGR	DEL	TGATGATCCCATTCGAGTCCATTCAG	-	-	rs28796684		TCGA-EJ-5519-01A-01D-1576-08	TCGA-EJ-5519-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:46407681_46407706delTGATGATCCCATTCGAGTCCATTCAG								None (None upstream) : ANKRD26P1 (95543 downstream)																							ttccatttgatgatgatcccattcgagtccattcagtgattccatt	0.000													210	9	---	---	---	---	
ABCC11	85320	broad.mit.edu	37	16	48265572	48265572	+	Intron	DEL	A	-	-			TCGA-EJ-5519-01A-01D-1576-08	TCGA-EJ-5519-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:48265572delA	uc002eff.1	-						ABCC11_uc002efg.1_Intron|ABCC11_uc002efh.1_Intron|ABCC11_uc010vgl.1_Intron	NM_033151	NP_149163	Q96J66	ABCCB_HUMAN	ATP-binding cassette, sub-family C, member 11							integral to membrane	ATP binding|ATPase activity, coupled to transmembrane movement of substances			ovary(3)|skin(2)|central_nervous_system(1)	6		all_cancers(37;0.127)|all_lung(18;0.132)|Breast(268;0.166)				accctgagtcaaaaaaaaaaa	0.129									Cerumen_Type				6	4	---	---	---	---	
CALB2	794	broad.mit.edu	37	16	71416027	71416028	+	Intron	INS	-	AAGGAAGGAAGGAAAG	AAGGAAGGAAGGAAAG	rs67540929		TCGA-EJ-5519-01A-01D-1576-08	TCGA-EJ-5519-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:71416027_71416028insAAGGAAGGAAGGAAAG	uc002faa.3	+						CALB2_uc010vme.1_Intron|CALB2_uc002fac.3_Intron	NM_001740	NP_001731	P22676	CALB2_HUMAN	calbindin 2 isoform 1								calcium ion binding				0		Ovarian(137;0.125)				aaaggaagaaaaaggaaggaag	0.054													4	2	---	---	---	---	
MYH13	8735	broad.mit.edu	37	17	10209538	10209539	+	Intron	DEL	TG	-	-	rs66516471		TCGA-EJ-5519-01A-01D-1576-08	TCGA-EJ-5519-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:10209538_10209539delTG	uc002gmk.1	-							NM_003802	NP_003793	Q9UKX3	MYH13_HUMAN	myosin, heavy polypeptide 13, skeletal muscle						muscle contraction	muscle myosin complex|myofibril|myosin filament	actin binding|ATP binding|calmodulin binding|microfilament motor activity			ovary(4)|skin(2)	6						CCAAAATAGAtgtgtgtgtgtg	0.287													4	2	---	---	---	---	
MAPT	4137	broad.mit.edu	37	17	44069147	44069148	+	Intron	INS	-	T	T	rs114790373	by1000genomes	TCGA-EJ-5519-01A-01D-1576-08	TCGA-EJ-5519-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:44069147_44069148insT	uc002ijr.3	+						MAPT_uc010dau.2_Intron|MAPT_uc002ijs.3_Intron|MAPT_uc002ijx.3_Intron|MAPT_uc002ijt.3_Intron|MAPT_uc002iju.3_Intron|MAPT_uc002ijv.3_Intron	NM_016835	NP_058519	P10636	TAU_HUMAN	microtubule-associated protein tau isoform 1						cellular component disassembly involved in apoptosis|microtubule cytoskeleton organization|negative regulation of microtubule depolymerization|positive regulation of axon extension|positive regulation of microtubule polymerization|regulation of autophagy	axon|cytosol|growth cone|microtubule|microtubule associated complex|nuclear periphery|plasma membrane|tubulin complex	apolipoprotein E binding|enzyme binding|identical protein binding|lipoprotein particle binding|microtubule binding|protein binding|SH3 domain binding|structural constituent of cytoskeleton			pancreas(1)	1		Melanoma(429;0.216)				gaatccctaccttttttttttt	0.000													4	2	---	---	---	---	
SLC35B1	10237	broad.mit.edu	37	17	47783738	47783739	+	Intron	INS	-	A	A	rs144238441		TCGA-EJ-5519-01A-01D-1576-08	TCGA-EJ-5519-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:47783738_47783739insA	uc002iph.1	-						SLC35B1_uc002ipi.1_Intron|SLC35B1_uc002ipj.1_Intron|SLC35B1_uc010wly.1_Intron	NM_005827	NP_005818	P78383	S35B1_HUMAN	solute carrier family 35, member B1							endoplasmic reticulum membrane|integral to membrane|microsome	UDP-galactose transmembrane transporter activity				0						gaaaagaaaagaaaaaaaaaaa	0.386													6	3	---	---	---	---	
ROCK1	6093	broad.mit.edu	37	18	18690838	18690839	+	In_Frame_Ins	INS	-	AAA	AAA			TCGA-EJ-5519-01A-01D-1576-08	TCGA-EJ-5519-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:18690838_18690839insAAA	uc002kte.2	-	1	974_975	c.33_34insTTT	c.(31-36)insTTT	p.11_12insF		NM_005406	NP_005397	Q13464	ROCK1_HUMAN	Rho-associated, coiled-coil containing protein	11_12					actin cytoskeleton organization|axon guidance|cellular component disassembly involved in apoptosis|cytokinesis|leukocyte tethering or rolling|membrane to membrane docking|Rho protein signal transduction	centriole|cytosol|Golgi membrane	ATP binding|identical protein binding|metal ion binding|protein serine/threonine kinase activity			lung(2)|breast(2)|central_nervous_system(1)	5	Melanoma(1;0.165)					TCCATTTTTTCAAATCGAGTCT	0.485													140	43	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	27732215	27732216	+	IGR	INS	-	C	C	rs74197760		TCGA-EJ-5519-01A-01D-1576-08	TCGA-EJ-5519-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:27732215_27732216insC								None (None upstream) : LOC148189 (549186 downstream)																							agaaaaggaaatatcttcgtat	0.000													1138	19	---	---	---	---	
PPP1R12C	54776	broad.mit.edu	37	19	55605551	55605551	+	Intron	DEL	T	-	-			TCGA-EJ-5519-01A-01D-1576-08	TCGA-EJ-5519-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:55605551delT	uc002qix.2	-						PPP1R12C_uc010yfs.1_Intron|PPP1R12C_uc002qiy.2_Intron	NM_017607	NP_060077	Q9BZL4	PP12C_HUMAN	protein phosphatase 1, regulatory subunit 12C							cytoplasm				ovary(1)|central_nervous_system(1)	2			BRCA - Breast invasive adenocarcinoma(297;0.209)	GBM - Glioblastoma multiforme(193;0.0449)		agtccagacctccagcccctc	0.000													4	2	---	---	---	---	
ZCCHC3	85364	broad.mit.edu	37	20	278688	278690	+	In_Frame_Del	DEL	CGG	-	-	rs5839847		TCGA-EJ-5519-01A-01D-1576-08	TCGA-EJ-5519-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:278688_278690delCGG	uc002wdf.2	+	1	485_487	c.461_463delCGG	c.(460-465)CCGGCG>CCG	p.A158del	ZCCHC3_uc002wdg.2_Intron	NM_033089	NP_149080	Q9NUD5	ZCHC3_HUMAN	zinc finger, CCHC domain containing 3	158	Poly-Ala.						nucleic acid binding|zinc ion binding				0		all_cancers(10;0.000209)|Lung NSC(37;0.0417)|all_lung(30;0.0713)|all_epithelial(17;0.0748)|Breast(17;0.231)	OV - Ovarian serous cystadenocarcinoma(29;0.149)			CAGGATGAgccggcggcggcggc	0.635													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	16915280	16915281	+	IGR	INS	-	T	T	rs148711386		TCGA-EJ-5519-01A-01D-1576-08	TCGA-EJ-5519-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:16915280_16915281insT								OR11H1 (465476 upstream) : CCT8L2 (156367 downstream)																							CTCCCTCACCAttttttttttt	0.129													3	3	---	---	---	---	
WWC3	55841	broad.mit.edu	37	X	10109659	10109659	+	3'UTR	DEL	A	-	-			TCGA-EJ-5519-01A-01D-1576-08	TCGA-EJ-5519-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:10109659delA	uc004csx.3	+	23					WWC3_uc010nds.2_3'UTR|WWC3_uc010ndt.2_RNA	NM_015691	NP_056506	Q9ULE0	WWC3_HUMAN	WWC family member 3											ovary(4)	4						CACATTTTGTAAAAAAAAAAA	0.279													4	4	---	---	---	---	
NUDT11	55190	broad.mit.edu	37	X	51239296	51239309	+	Translation_Start_Site	DEL	TCCTCGAGGCAGCC	-	-			TCGA-EJ-5519-01A-01D-1576-08	TCGA-EJ-5519-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:51239296_51239309delTCCTCGAGGCAGCC	uc010njt.2	-	1						NM_018159	NP_060629	Q96G61	NUD11_HUMAN	nudix-type motif 11							cytoplasm	diphosphoinositol-polyphosphate diphosphatase activity|metal ion binding				0	Ovarian(276;0.236)					TTGCACTTCATCCTCGAGGCAGCCTCCTCGAGGC	0.584										HNSCC(48;0.14)			4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	Y	58827381	58827381	+	IGR	DEL	A	-	-			TCGA-EJ-5519-01A-01D-1576-08	TCGA-EJ-5519-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:58827381delA								None (None upstream) : None (None downstream)																							tttccattccatttgatttga	0.000													306	8	---	---	---	---	
