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
CROCCL1	84809	broad.mit.edu	37	1	16958033	16958033	+	Intron	SNP	G	A	A	rs41307765	by1000genomes	TCGA-EJ-5496-01A-01D-1576-08	TCGA-EJ-5496-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:16958033G>A	uc001azf.2	-						CROCCL1_uc009vov.1_5'Flank|CROCCL1_uc001aze.2_5'Flank|CROCCL1_uc001azg.1_RNA|CROCCL1_uc001azi.1_RNA					Homo sapiens mRNA for FLJ00313 protein.												0						ACCTGTGCCAGGTCCCTTAGG	0.657													3	7	---	---	---	---	PASS
CROCCL1	84809	broad.mit.edu	37	1	16958047	16958047	+	Intron	SNP	C	T	T	rs9658896	by1000genomes	TCGA-EJ-5496-01A-01D-1576-08	TCGA-EJ-5496-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:16958047C>T	uc001azf.2	-						CROCCL1_uc009vov.1_5'Flank|CROCCL1_uc001aze.2_5'Flank|CROCCL1_uc001azg.1_RNA|CROCCL1_uc001azi.1_RNA					Homo sapiens mRNA for FLJ00313 protein.												0						CCTTAGGCTCCGCTGTAGCCC	0.667													3	9	---	---	---	---	PASS
HSPG2	3339	broad.mit.edu	37	1	22173919	22173919	+	Missense_Mutation	SNP	C	T	T			TCGA-EJ-5496-01A-01D-1576-08	TCGA-EJ-5496-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:22173919C>T	uc001bfj.2	-	62	8132	c.8092G>A	c.(8092-8094)GCC>ACC	p.A2698T	HSPG2_uc009vqd.2_Missense_Mutation_p.A2699T	NM_005529	NP_005520	P98160	PGBM_HUMAN	heparan sulfate proteoglycan 2 precursor	2698	Ig-like C2-type 12.				angiogenesis|cell adhesion|lipid metabolic process|lipoprotein metabolic process	basement membrane|extracellular space|plasma membrane	protein C-terminus binding			ovary(5)|large_intestine(2)|central_nervous_system(1)|skin(1)	9		Colorectal(325;3.46e-05)|all_lung(284;7.93e-05)|Lung NSC(340;8.71e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0498)|OV - Ovarian serous cystadenocarcinoma(117;1.14e-26)|Colorectal(126;4.18e-07)|COAD - Colon adenocarcinoma(152;1.82e-05)|GBM - Glioblastoma multiforme(114;3.13e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000756)|STAD - Stomach adenocarcinoma(196;0.00656)|KIRC - Kidney renal clear cell carcinoma(1967;0.00942)|READ - Rectum adenocarcinoma(331;0.0721)|Lung(427;0.223)	Becaplermin(DB00102)|Palifermin(DB00039)	TTGTTGTTGGCCCGGCACACA	0.642													4	118	---	---	---	---	PASS
ARID1A	8289	broad.mit.edu	37	1	27106761	27106761	+	Silent	SNP	A	G	G			TCGA-EJ-5496-01A-01D-1576-08	TCGA-EJ-5496-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:27106761A>G	uc001bmv.1	+	20	6745	c.6372A>G	c.(6370-6372)AAA>AAG	p.K2124K	ARID1A_uc001bmu.1_Silent_p.K1907K|ARID1A_uc001bmx.1_Silent_p.K970K|ARID1A_uc009vsm.1_Silent_p.K452K|ARID1A_uc009vsn.1_Silent_p.K366K	NM_006015	NP_006006	O14497	ARI1A_HUMAN	AT rich interactive domain 1A isoform a	2124					androgen receptor signaling pathway|chromatin-mediated maintenance of transcription|estrogen receptor signaling pathway|glucocorticoid receptor signaling pathway|nervous system development|nucleosome mobilization|transcription, DNA-dependent	nBAF complex|npBAF complex|SWI/SNF complex	DNA binding|protein binding			ovary(124)|pancreas(5)|central_nervous_system(3)|endometrium(3)|kidney(3)|skin(2)|upper_aerodigestive_tract(1)|lung(1)	142		all_cancers(24;6.36e-27)|all_epithelial(13;5.93e-24)|Colorectal(325;3.46e-05)|all_lung(284;4.76e-05)|Lung NSC(340;5.83e-05)|Breast(348;9.7e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|all cancers(4;2.61e-56)|Epithelial(14;7.53e-55)|OV - Ovarian serous cystadenocarcinoma(117;4.5e-30)|Colorectal(126;2.07e-09)|COAD - Colon adenocarcinoma(152;4.29e-07)|BRCA - Breast invasive adenocarcinoma(304;4.13e-05)|STAD - Stomach adenocarcinoma(196;0.000279)|KIRC - Kidney renal clear cell carcinoma(1967;0.000794)|GBM - Glioblastoma multiforme(114;0.0132)|READ - Rectum adenocarcinoma(331;0.0469)|Lung(427;0.167)|LUSC - Lung squamous cell carcinoma(448;0.242)		CCCTCAGCAAACTCAGCATCC	0.582			Mis|N|F|S|D		clear cell ovarian carcinoma|RCC								37	141	---	---	---	---	PASS
EPB41	2035	broad.mit.edu	37	1	29314300	29314300	+	Silent	SNP	A	G	G			TCGA-EJ-5496-01A-01D-1576-08	TCGA-EJ-5496-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:29314300A>G	uc001brm.1	+	1	358	c.351A>G	c.(349-351)GAA>GAG	p.E117E	EPB41_uc001brg.1_5'UTR|EPB41_uc001brh.1_5'UTR|EPB41_uc001bri.1_Silent_p.E117E|EPB41_uc001brj.1_5'UTR|EPB41_uc009vtk.1_Silent_p.E117E|EPB41_uc001brk.2_Silent_p.E117E|EPB41_uc001brl.1_Silent_p.E117E|EPB41_uc009vtl.1_5'UTR|EPB41_uc009vtm.1_5'UTR	NM_203342	NP_976217	P11171	41_HUMAN	erythrocyte membrane protein band 4.1	117					blood circulation|cortical actin cytoskeleton organization|positive regulation of protein binding	extrinsic to membrane|Golgi apparatus|nucleus|plasma membrane|protein complex|spectrin|spectrin-associated cytoskeleton	1-phosphatidylinositol binding|actin binding|spectrin binding|structural constituent of cytoskeleton			ovary(1)	1		Colorectal(325;3.46e-05)|Prostate(1639;0.000244)|Lung NSC(340;0.00328)|all_lung(284;0.00412)|Breast(348;0.00765)|all_neural(195;0.0199)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)|Medulloblastoma(700;0.123)		Colorectal(126;3.12e-07)|COAD - Colon adenocarcinoma(152;1.21e-05)|STAD - Stomach adenocarcinoma(196;0.00395)|KIRC - Kidney renal clear cell carcinoma(1967;0.0249)|BRCA - Breast invasive adenocarcinoma(304;0.0289)|READ - Rectum adenocarcinoma(331;0.0757)		AAGAGATAGAATTTGGAACCA	0.423													8	286	---	---	---	---	PASS
DMBX1	127343	broad.mit.edu	37	1	46977762	46977762	+	Missense_Mutation	SNP	C	T	T			TCGA-EJ-5496-01A-01D-1576-08	TCGA-EJ-5496-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:46977762C>T	uc001cpx.2	+	4	760	c.745C>T	c.(745-747)CTC>TTC	p.L249F	DMBX1_uc001cpw.2_Missense_Mutation_p.L244F	NM_147192	NP_671725	Q8NFW5	DMBX1_HUMAN	diencephalon/mesencephalon homeobox 1 isoform b	249					brain development|developmental growth|negative regulation of transcription, DNA-dependent	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			ovary(1)	1	Acute lymphoblastic leukemia(166;0.155)					AGGGGGTGGCCTCCTGGGCCC	0.627													59	289	---	---	---	---	PASS
CYP4A11	1579	broad.mit.edu	37	1	47395778	47395778	+	3'UTR	SNP	T	G	G			TCGA-EJ-5496-01A-01D-1576-08	TCGA-EJ-5496-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:47395778T>G	uc001cqp.3	-	12						NM_000778	NP_000769	Q02928	CP4AB_HUMAN	cytochrome P450, family 4, subfamily A,						long-chain fatty acid metabolic process|xenobiotic metabolic process	endoplasmic reticulum membrane|microsome	alkane 1-monooxygenase activity|electron carrier activity|heme binding|oxygen binding			ovary(2)|skin(2)	4					NADH(DB00157)	ggacggcaggTGGAGGCCCTC	0.259													9	45	---	---	---	---	PASS
WARS2	10352	broad.mit.edu	37	1	119576827	119576827	+	Silent	SNP	G	A	A			TCGA-EJ-5496-01A-01D-1576-08	TCGA-EJ-5496-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:119576827G>A	uc001ehn.2	-	5	553	c.525C>T	c.(523-525)CAC>CAT	p.H175H	WARS2_uc010oxf.1_Silent_p.H81H|WARS2_uc001ehm.2_Silent_p.H175H|WARS2_uc010oxg.1_Silent_p.H118H|WARS2_uc010oxh.1_Missense_Mutation_p.R147C|WARS2_uc010oxi.1_Missense_Mutation_p.R53C	NM_015836	NP_056651	Q9UGM6	SYWM_HUMAN	mitochondrial tryptophanyl tRNA synthetase 2	175					tryptophanyl-tRNA aminoacylation	mitochondrial matrix	ATP binding|tryptophan-tRNA ligase activity				0	all_neural(166;0.187)	all_lung(203;2.48e-06)|Lung NSC(69;1.74e-05)|all_epithelial(167;0.000564)		Lung(183;0.0629)	L-Tryptophan(DB00150)	CAACAGGAACGTGTGTGGACC	0.433													8	140	---	---	---	---	PASS
LOC200030	200030	broad.mit.edu	37	1	148251805	148251805	+	Intron	SNP	T	A	A			TCGA-EJ-5496-01A-01D-1576-08	TCGA-EJ-5496-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:148251805T>A	uc001eqe.2	-						LOC200030_uc001eqf.2_Intron|LOC200030_uc001eqg.2_Intron|NBPF14_uc010pab.1_Intron|NBPF14_uc010pac.1_Intron|NBPF14_uc001eqx.2_Intron|NBPF14_uc010pae.1_Intron|NBPF14_uc010paf.1_Intron|NBPF14_uc009wkf.1_Intron|uc010pah.1_3'UTR|uc010pai.1_3'UTR|uc001eqz.2_3'UTR|uc001erb.2_3'UTR|uc001erd.3_3'UTR|uc001erc.3_RNA|uc010paj.1_3'UTR			Q86T75	NBPFB_HUMAN	SubName: Full=cDNA FLJ78770;							cytoplasm					0						AACTGTACTTTCATTCAAATC	0.483													6	247	---	---	---	---	PASS
FCGR3B	2215	broad.mit.edu	37	1	161596188	161596188	+	Missense_Mutation	SNP	C	A	A			TCGA-EJ-5496-01A-01D-1576-08	TCGA-EJ-5496-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:161596188C>A	uc009wul.2	-	4	598	c.324G>T	c.(322-324)TGG>TGT	p.W108C		NM_000570	NP_000561	O75015	FCG3B_HUMAN	low affinity immunoglobulin gamma Fc region	108					immune response	anchored to membrane|extracellular region|plasma membrane	IgG binding|receptor activity				0	all_cancers(52;4.89e-16)|all_hematologic(112;0.0207)		BRCA - Breast invasive adenocarcinoma(70;0.00376)		Abciximab(DB00054)|Adalimumab(DB00051)|Alefacept(DB00092)|Alemtuzumab(DB00087)|Basiliximab(DB00074)|Bevacizumab(DB00112)|Cetuximab(DB00002)|Daclizumab(DB00111)|Efalizumab(DB00095)|Etanercept(DB00005)|Gemtuzumab ozogamicin(DB00056)|Ibritumomab(DB00078)|Immune globulin(DB00028)|Muromonab(DB00075)|Natalizumab(DB00108)|Palivizumab(DB00110)|Rituximab(DB00073)|Tositumomab(DB00081)|Trastuzumab(DB00072)	GGAGCAACAGCCAGCCTGAAA	0.567													3	50	---	---	---	---	PASS
KCNT2	343450	broad.mit.edu	37	1	196459055	196459055	+	Missense_Mutation	SNP	C	T	T			TCGA-EJ-5496-01A-01D-1576-08	TCGA-EJ-5496-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:196459055C>T	uc001gtd.1	-	3	248	c.188G>A	c.(187-189)CGC>CAC	p.R63H	KCNT2_uc001gte.1_Missense_Mutation_p.R63H|KCNT2_uc001gtf.1_Missense_Mutation_p.R63H|KCNT2_uc001gtg.1_RNA|KCNT2_uc009wyu.2_Missense_Mutation_p.R63H|KCNT2_uc009wyv.1_Missense_Mutation_p.R63H	NM_198503	NP_940905	Q6UVM3	KCNT2_HUMAN	potassium channel, subfamily T, member 2	63	Cytoplasmic (Potential).					voltage-gated potassium channel complex	ATP binding|calcium-activated potassium channel activity|voltage-gated potassium channel activity			ovary(5)|breast(1)|skin(1)	7						ATTGAACAGGCGTATCCTTAG	0.289													51	173	---	---	---	---	PASS
FMN2	56776	broad.mit.edu	37	1	240371217	240371217	+	Silent	SNP	A	T	T			TCGA-EJ-5496-01A-01D-1576-08	TCGA-EJ-5496-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:240371217A>T	uc010pyd.1	+	5	3330	c.3105A>T	c.(3103-3105)CCA>CCT	p.P1035P	FMN2_uc010pye.1_Silent_p.P1039P	NM_020066	NP_064450	Q9NZ56	FMN2_HUMAN	formin 2	1035	Pro-rich.|FH1.				actin cytoskeleton organization|establishment of meiotic spindle localization|intracellular signal transduction|meiotic chromosome movement towards spindle pole|meiotic metaphase I|multicellular organismal development|oogenesis|polar body extrusion after meiotic divisions		actin binding			ovary(4)|pancreas(3)|skin(3)|large_intestine(1)|central_nervous_system(1)	12	Ovarian(103;0.127)	all_cancers(173;0.013)	OV - Ovarian serous cystadenocarcinoma(106;0.0106)			CTCCGCCCCCACTTCCCGGAG	0.726													4	6	---	---	---	---	PASS
OR2M1P	388762	broad.mit.edu	37	1	248286076	248286076	+	Silent	SNP	C	T	T			TCGA-EJ-5496-01A-01D-1576-08	TCGA-EJ-5496-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:248286076C>T	uc001idy.1	+	1	639	c.639C>T	c.(637-639)CTC>CTT	p.L213L		NR_002141				RecName: Full=Olfactory receptor 2M5;												0						ACACCATCCTCACTCCCATGC	0.498													7	212	---	---	---	---	PASS
NBAS	51594	broad.mit.edu	37	2	15608534	15608534	+	Missense_Mutation	SNP	C	T	T			TCGA-EJ-5496-01A-01D-1576-08	TCGA-EJ-5496-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:15608534C>T	uc002rcc.1	-	17	1875	c.1849G>A	c.(1849-1851)GCA>ACA	p.A617T	NBAS_uc002rcd.1_RNA	NM_015909	NP_056993	A2RRP1	NBAS_HUMAN	neuroblastoma-amplified protein	617										ovary(2)|liver(1)|skin(1)	4						TTCCCTATTGCTAAAAGAGCC	0.413													52	254	---	---	---	---	PASS
LRP1B	53353	broad.mit.edu	37	2	141751591	141751591	+	Nonsense_Mutation	SNP	C	A	A			TCGA-EJ-5496-01A-01D-1576-08	TCGA-EJ-5496-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:141751591C>A	uc002tvj.1	-	16	3589	c.2617G>T	c.(2617-2619)GGA>TGA	p.G873*	LRP1B_uc010fnl.1_Intron	NM_018557	NP_061027	Q9NZR2	LRP1B_HUMAN	low density lipoprotein-related protein 1B	873	Extracellular (Potential).|LDL-receptor class A 3.				protein transport|receptor-mediated endocytosis	integral to membrane	calcium ion binding	p.G873G(1)		lung(17)|skin(12)|ovary(12)|pancreas(3)|upper_aerodigestive_tract(2)|central_nervous_system(2)|liver(1)|kidney(1)	50		all_cancers(3;1.1e-60)|all_epithelial(3;1.94e-59)|all_lung(3;1.09e-24)|Lung NSC(3;5.65e-24)|Esophageal squamous(3;5.41e-13)|Renal(3;0.000147)|Breast(3;0.000527)|Hepatocellular(3;0.011)|all_neural(3;0.014)|Colorectal(150;0.101)		UCEC - Uterine corpus endometrioid carcinoma (2;0.00139)|Epithelial(1;1.25e-24)|all cancers(1;8.86e-24)|OV - Ovarian serous cystadenocarcinoma(1;2.45e-12)|LUSC - Lung squamous cell carcinoma(1;2.97e-10)|Lung(1;6.05e-09)|BRCA - Breast invasive adenocarcinoma(221;0.0103)		TCATCGCTTCCGTCTAGGCAG	0.433										TSP Lung(27;0.18)			4	153	---	---	---	---	PASS
ORC4L	5000	broad.mit.edu	37	2	148695835	148695835	+	Intron	SNP	G	A	A			TCGA-EJ-5496-01A-01D-1576-08	TCGA-EJ-5496-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:148695835G>A	uc002twi.2	-						ORC4L_uc002twj.2_Intron|ORC4L_uc010zbo.1_Intron|ORC4L_uc010zbp.1_Intron|ORC4L_uc010fnr.2_Intron|ORC4L_uc010zbq.1_Intron|ORC4L_uc002twk.2_Intron|ORC4L_uc010zbr.1_3'UTR|ORC4L_uc002twl.1_5'Flank	NM_181741	NP_859525	O43929	ORC4_HUMAN	origin recognition complex subunit 4						cell cycle checkpoint|DNA-dependent DNA replication initiation|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|S phase of mitotic cell cycle	nuclear origin of replication recognition complex|nucleoplasm	ATP binding|DNA replication origin binding|nucleoside-triphosphatase activity|protein binding				0				BRCA - Breast invasive adenocarcinoma(221;0.0963)|COAD - Colon adenocarcinoma(177;0.203)		GTGGGGAAGAGTCAGAAAAAA	0.328													6	185	---	---	---	---	PASS
CCDC150	284992	broad.mit.edu	37	2	197583282	197583282	+	Missense_Mutation	SNP	G	A	A			TCGA-EJ-5496-01A-01D-1576-08	TCGA-EJ-5496-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:197583282G>A	uc002utp.1	+	18	2057	c.1922G>A	c.(1921-1923)CGT>CAT	p.R641H	CCDC150_uc010zgs.1_Missense_Mutation_p.R288H|CCDC150_uc010zgt.1_Missense_Mutation_p.R58H|CCDC150_uc002utq.1_5'Flank|CCDC150_uc002utr.1_5'Flank	NM_001080539	NP_001074008	Q8NCX0	CC150_HUMAN	coiled-coil domain containing 150	641	Potential.										0						GTGAAGTGTCGTAATGCGGCC	0.428													17	54	---	---	---	---	PASS
OSBPL10	114884	broad.mit.edu	37	3	31710253	31710253	+	Nonsense_Mutation	SNP	C	T	T			TCGA-EJ-5496-01A-01D-1576-08	TCGA-EJ-5496-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:31710253C>T	uc003cev.2	-	11	2358	c.1977G>A	c.(1975-1977)TGG>TGA	p.W659*	OSBPL10_uc003ceu.1_Nonsense_Mutation_p.W416*|OSBPL10_uc011axf.1_Nonsense_Mutation_p.W595*	NM_017784	NP_060254	Q9BXB5	OSB10_HUMAN	oxysterol-binding protein-like protein 10	659					lipid transport		lipid binding			skin(1)	1				STAD - Stomach adenocarcinoma(1;0.00406)		AAGTACCATTCCATTCCCCAT	0.433													72	242	---	---	---	---	PASS
B3GALNT1	8706	broad.mit.edu	37	3	160803633	160803633	+	Missense_Mutation	SNP	G	A	A	rs143966469		TCGA-EJ-5496-01A-01D-1576-08	TCGA-EJ-5496-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:160803633G>A	uc003fdv.2	-	5	1329	c.910C>T	c.(910-912)CGT>TGT	p.R304C	B3GALNT1_uc003fdw.2_Missense_Mutation_p.R304C|B3GALNT1_uc003fdx.2_Missense_Mutation_p.R304C|B3GALNT1_uc003fdy.2_Missense_Mutation_p.R304C|B3GALNT1_uc003fdz.2_Missense_Mutation_p.R304C|B3GALNT1_uc003fea.2_Missense_Mutation_p.R304C|B3GALNT1_uc011bpa.1_Missense_Mutation_p.R64C	NM_033169	NP_149359	O75752	B3GL1_HUMAN	UDP-Gal:betaGlcNAc beta	304	Lumenal (Potential).				protein glycosylation	Golgi membrane|integral to membrane	galactosylgalactosylglucosylceramide beta-D-acetylgalactosaminyltransferase activity|UDP-galactose:beta-N-acetylglucosamine beta-1,3-galactosyltransferase activity			skin(1)	1			LUSC - Lung squamous cell carcinoma(72;4.41e-05)|Lung(72;4.61e-05)			GCAATCACACGTCTCAGTTGA	0.378													20	72	---	---	---	---	PASS
ACOX3	8310	broad.mit.edu	37	4	8416610	8416610	+	Missense_Mutation	SNP	T	C	C			TCGA-EJ-5496-01A-01D-1576-08	TCGA-EJ-5496-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:8416610T>C	uc010idk.2	-	4	569	c.424A>G	c.(424-426)ACA>GCA	p.T142A	ACOX3_uc003glc.3_Missense_Mutation_p.T142A|ACOX3_uc003gld.3_Missense_Mutation_p.T142A|ACOX3_uc003gle.1_Missense_Mutation_p.T47A	NM_003501	NP_003492	O15254	ACOX3_HUMAN	acyl-Coenzyme A oxidase 3 isoform a	142					bile acid metabolic process|fatty acid beta-oxidation using acyl-CoA oxidase	peroxisomal matrix	acyl-CoA dehydrogenase activity|flavin adenine dinucleotide binding|pristanoyl-CoA oxidase activity			central_nervous_system(1)	1						TGAATATATGTGAGATGTCTT	0.403													4	109	---	---	---	---	PASS
STIM2	57620	broad.mit.edu	37	4	27024674	27024674	+	3'UTR	SNP	A	C	C			TCGA-EJ-5496-01A-01D-1576-08	TCGA-EJ-5496-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:27024674A>C	uc003gsh.3	+	13					STIM2_uc003gsg.3_3'UTR|STIM2_uc010iex.2_3'UTR|STIM2_uc010iey.2_3'UTR	NM_020860	NP_065911	Q9P246	STIM2_HUMAN	stromal interaction molecule 2						activation of store-operated calcium channel activity|calcium ion transport|cellular calcium ion homeostasis|negative regulation of calcium ion transport via store-operated calcium channel activity	endoplasmic reticulum membrane|integral to membrane|plasma membrane	calcium channel regulator activity|calcium ion binding|protein binding			central_nervous_system(1)|skin(1)	2		Breast(46;0.0503)				ATTATCCCCCACCCTCCACTC	0.423													12	67	---	---	---	---	PASS
LIMCH1	22998	broad.mit.edu	37	4	41648713	41648713	+	Missense_Mutation	SNP	C	T	T	rs143733086	by1000genomes	TCGA-EJ-5496-01A-01D-1576-08	TCGA-EJ-5496-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:41648713C>T	uc003gvu.3	+	12	1522	c.1468C>T	c.(1468-1470)CGG>TGG	p.R490W	LIMCH1_uc003gvv.3_Missense_Mutation_p.R490W|LIMCH1_uc003gvw.3_Missense_Mutation_p.R490W|LIMCH1_uc003gvx.3_Missense_Mutation_p.R478W|LIMCH1_uc003gwe.3_Missense_Mutation_p.R490W|LIMCH1_uc003gvy.3_Missense_Mutation_p.R319W|LIMCH1_uc003gwa.3_Missense_Mutation_p.R331W|LIMCH1_uc003gvz.3_Missense_Mutation_p.R875W|LIMCH1_uc011byu.1_Missense_Mutation_p.R324W|LIMCH1_uc003gwc.3_Missense_Mutation_p.R336W|LIMCH1_uc003gwd.3_Missense_Mutation_p.R324W|LIMCH1_uc011byv.1_Missense_Mutation_p.R241W	NM_014988	NP_055803	Q9UPQ0	LIMC1_HUMAN	LIM and calponin homology domains 1 isoform a	490					actomyosin structure organization		actin binding|zinc ion binding			ovary(2)|pancreas(1)|skin(1)	4						GAAATACCTGCGGCAACAGTC	0.498													10	408	---	---	---	---	PASS
LPHN3	23284	broad.mit.edu	37	4	62813888	62813888	+	Missense_Mutation	SNP	G	T	T			TCGA-EJ-5496-01A-01D-1576-08	TCGA-EJ-5496-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:62813888G>T	uc010ihh.2	+	14	2668	c.2495G>T	c.(2494-2496)TGG>TTG	p.W832L	LPHN3_uc003hcq.3_Missense_Mutation_p.W832L|LPHN3_uc003hct.2_Missense_Mutation_p.W225L	NM_015236	NP_056051	Q9HAR2	LPHN3_HUMAN	latrophilin 3 precursor	819	GPS.|Extracellular (Potential).				neuropeptide signaling pathway	integral to membrane|plasma membrane	G-protein coupled receptor activity|sugar binding			lung(15)|ovary(1)|central_nervous_system(1)|pancreas(1)	18						ACAGGTTATTGGTCAACACAA	0.403													14	57	---	---	---	---	PASS
SULT1E1	6783	broad.mit.edu	37	4	70721017	70721017	+	Splice_Site	SNP	A	T	T			TCGA-EJ-5496-01A-01D-1576-08	TCGA-EJ-5496-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:70721017A>T	uc003heo.2	-	3	384	c.271_splice	c.e3+1	p.G91_splice	SULT1E1_uc010ihv.1_Splice_Site_p.G91_splice	NM_005420	NP_005411	P49888	ST1E1_HUMAN	estrogen sulfotransferase						3'-phosphoadenosine 5'-phosphosulfate metabolic process|sulfation|xenobiotic metabolic process	cytosol|nuclear membrane	estrone sulfotransferase activity|flavonol 3-sulfotransferase activity|steroid binding|steroid sulfotransferase activity			ovary(1)	1						CTTGAACGTTACCATTCATGA	0.318													10	74	---	---	---	---	PASS
KIAA1109	84162	broad.mit.edu	37	4	123192755	123192755	+	Silent	SNP	G	A	A			TCGA-EJ-5496-01A-01D-1576-08	TCGA-EJ-5496-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:123192755G>A	uc003ieh.2	+	45	8121	c.8076G>A	c.(8074-8076)GTG>GTA	p.V2692V	KIAA1109_uc003iel.1_Silent_p.V627V|KIAA1109_uc003iek.2_Silent_p.V1311V	NM_015312	NP_056127	Q2LD37	K1109_HUMAN	fragile site-associated protein	2692					regulation of cell growth|regulation of epithelial cell differentiation	integral to membrane|nucleus				ovary(8)|skin(2)|pancreas(1)|central_nervous_system(1)	12						CAATTACAGTGTCAGAACAAA	0.373													5	89	---	---	---	---	PASS
MFAP3L	9848	broad.mit.edu	37	4	170913387	170913387	+	Silent	SNP	C	T	T	rs141578578		TCGA-EJ-5496-01A-01D-1576-08	TCGA-EJ-5496-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:170913387C>T	uc003isp.3	-	3	550	c.372G>A	c.(370-372)ACG>ACA	p.T124T	MFAP3L_uc003isn.3_Silent_p.T21T	NM_021647	NP_067679	O75121	MFA3L_HUMAN	microfibrillar-associated protein 3-like isoform	124	Extracellular (Potential).|Ig-like C2-type.					integral to membrane|plasma membrane				ovary(1)	1		Prostate(90;0.00601)|Renal(120;0.0183)|all_neural(102;0.122)|Melanoma(52;0.17)		GBM - Glioblastoma multiforme(119;0.0201)|LUSC - Lung squamous cell carcinoma(193;0.116)		AAGCCACACACGTGTATTTAC	0.512													7	268	---	---	---	---	PASS
ASB5	140458	broad.mit.edu	37	4	177190130	177190130	+	Missense_Mutation	SNP	C	G	G			TCGA-EJ-5496-01A-01D-1576-08	TCGA-EJ-5496-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:177190130C>G	uc003iuq.1	-	1	146	c.130G>C	c.(130-132)GTG>CTG	p.V44L		NM_080874	NP_543150	Q8WWX0	ASB5_HUMAN	ankyrin repeat and SOCS box-containing protein	44					intracellular signal transduction					skin(2)	2		Breast(14;0.00015)|Melanoma(52;0.00886)|Prostate(90;0.00996)|Renal(120;0.0183)|all_hematologic(60;0.107)|all_neural(102;0.164)		all cancers(43;2.13e-20)|Epithelial(43;9.94e-18)|OV - Ovarian serous cystadenocarcinoma(60;2e-09)|GBM - Glioblastoma multiforme(59;0.000254)|STAD - Stomach adenocarcinoma(60;0.000653)|LUSC - Lung squamous cell carcinoma(193;0.0393)		TTGCCTTTCACTATGTAGAAA	0.393													7	128	---	---	---	---	PASS
FAM92A3	403315	broad.mit.edu	37	4	183960200	183960200	+	RNA	SNP	G	T	T			TCGA-EJ-5496-01A-01D-1576-08	TCGA-EJ-5496-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:183960200G>T	uc003ivi.3	+	1		c.1383G>T				NR_003612				Homo sapiens family with sequence similarity 92, member A3, mRNA (cDNA clone IMAGE:4822144).												0						AACAGGACAGGTATCCACTAC	0.388													5	38	---	---	---	---	PASS
RWDD4A	201965	broad.mit.edu	37	4	184567682	184567682	+	Missense_Mutation	SNP	C	G	G			TCGA-EJ-5496-01A-01D-1576-08	TCGA-EJ-5496-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:184567682C>G	uc003ivt.1	-	6	716	c.490G>C	c.(490-492)GGA>CGA	p.G164R	RWDD4A_uc003ivu.1_RNA|RWDD4A_uc003ivv.1_Missense_Mutation_p.G101R|RWDD4A_uc011ckl.1_RNA	NM_152682	NP_689895	Q6NW29	RWDD4_HUMAN	RWD domain containing 4A	164											0		all_lung(41;4.4e-14)|Lung NSC(41;1.03e-13)|Colorectal(36;0.00139)|all_hematologic(60;0.00756)|Hepatocellular(41;0.00826)|Renal(120;0.00988)|Prostate(90;0.0235)|all_neural(102;0.202)		all cancers(43;7.35e-27)|Epithelial(43;1.49e-22)|OV - Ovarian serous cystadenocarcinoma(60;5.76e-10)|GBM - Glioblastoma multiforme(59;5.54e-06)|Colorectal(24;7.92e-06)|STAD - Stomach adenocarcinoma(60;2.35e-05)|COAD - Colon adenocarcinoma(29;6.26e-05)|LUSC - Lung squamous cell carcinoma(40;0.00935)|READ - Rectum adenocarcinoma(43;0.166)		GGAAGTTCTCCTTTGTGATCT	0.289													8	254	---	---	---	---	PASS
TPPP	11076	broad.mit.edu	37	5	678087	678087	+	Missense_Mutation	SNP	C	T	T			TCGA-EJ-5496-01A-01D-1576-08	TCGA-EJ-5496-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:678087C>T	uc003jbg.3	-	1	807	c.89G>A	c.(88-90)AGG>AAG	p.R30K	TPPP_uc003jbh.3_Missense_Mutation_p.R30K	NM_007030	NP_008961	O94811	TPPP_HUMAN	tubulin polymerization promoting protein	30	Mediates interaction with LIMK1.				microtubule bundle formation|microtubule polymerization|positive regulation of protein polymerization	nucleus|perinuclear region of cytoplasm|soluble fraction	calcium ion binding|microtubule binding				0		Ovarian(839;0.0563)	Epithelial(17;0.000445)|all cancers(22;0.00176)|OV - Ovarian serous cystadenocarcinoma(19;0.00227)|Lung(60;0.0863)	GBM - Glioblastoma multiforme(108;0.0191)		CAGCGACAGCCTCTTGGCTGC	0.677													3	16	---	---	---	---	PASS
IRX1	79192	broad.mit.edu	37	5	3599606	3599606	+	Missense_Mutation	SNP	C	T	T			TCGA-EJ-5496-01A-01D-1576-08	TCGA-EJ-5496-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:3599606C>T	uc003jde.2	+	2	596	c.544C>T	c.(544-546)CGC>TGC	p.R182C		NM_024337	NP_077313	P78414	IRX1_HUMAN	iroquois homeobox protein 1	182	Homeobox; TALE-type.					nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			ovary(1)|pancreas(1)	2						CGCCAACGCGCGCCGGCGCCT	0.632													22	124	---	---	---	---	PASS
SNX18	112574	broad.mit.edu	37	5	53813830	53813830	+	Silent	SNP	A	C	C	rs76854460	byFrequency	TCGA-EJ-5496-01A-01D-1576-08	TCGA-EJ-5496-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:53813830A>C	uc003jpj.3	+	1	238	c.48A>C	c.(46-48)CCA>CCC	p.P16P	SNX18_uc011cqg.1_Silent_p.P16P|SNX18_uc003jpi.3_Silent_p.P16P	NM_052870	NP_443102	Q96RF0	SNX18_HUMAN	sorting nexin 18 isoform b	16	SH3.				cell communication|endocytosis|positive regulation of GTPase activity|protein transport	endomembrane system|endosome membrane|extrinsic to internal side of plasma membrane	phosphatidylinositol binding|protein binding				0		Lung NSC(810;3.46e-05)|Breast(144;0.102)				CGGAGAACCCAGGAGAGATCT	0.731													6	5	---	---	---	---	PASS
FAM169A	26049	broad.mit.edu	37	5	74091853	74091853	+	Splice_Site	SNP	A	G	G			TCGA-EJ-5496-01A-01D-1576-08	TCGA-EJ-5496-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:74091853A>G	uc003kdm.2	-	11	1303	c.1260_splice	c.e11+1	p.K420_splice	FAM169A_uc010izm.2_Splice_Site_p.K360_splice|FAM169A_uc003kdl.2_Splice_Site_p.K238_splice	NM_015566	NP_056381	Q9Y6X4	F169A_HUMAN	hypothetical protein LOC26049												0						GTGATCTCATACCTTTTCACC	0.368													5	371	---	---	---	---	PASS
TRIM36	55521	broad.mit.edu	37	5	114466559	114466559	+	Missense_Mutation	SNP	C	T	T			TCGA-EJ-5496-01A-01D-1576-08	TCGA-EJ-5496-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:114466559C>T	uc003kqs.2	-	9	2071	c.1562G>A	c.(1561-1563)TGT>TAT	p.C521Y	TRIM36_uc011cwc.1_Missense_Mutation_p.C509Y|TRIM36_uc003kqt.2_Missense_Mutation_p.C366Y	NM_018700	NP_061170	Q9NQ86	TRI36_HUMAN	tripartite motif-containing 36 isoform 1	521	B30.2/SPRY.					acrosomal vesicle|cytoskeleton	ligase activity|zinc ion binding			ovary(4)|lung(2)|breast(2)	8		all_cancers(142;0.00133)|all_epithelial(76;2.41e-05)|Prostate(80;0.00955)|Ovarian(225;0.0443)|Breast(839;0.195)		OV - Ovarian serous cystadenocarcinoma(64;3.62e-08)|Epithelial(69;7.69e-08)|all cancers(49;9.33e-06)		ATTATAGCCACATTTTTCATC	0.368													25	119	---	---	---	---	PASS
C5orf48	389320	broad.mit.edu	37	5	125967461	125967461	+	Missense_Mutation	SNP	C	G	G			TCGA-EJ-5496-01A-01D-1576-08	TCGA-EJ-5496-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:125967461C>G	uc003kub.1	+	1	48	c.35C>G	c.(34-36)CCT>CGT	p.P12R		NM_207408	NP_997291	Q6ZNM6	CE048_HUMAN	hypothetical protein LOC389320	12										ovary(1)	1						CCTACTTTGCCTAAACTCACT	0.378													5	170	---	---	---	---	PASS
RAPGEF6	51735	broad.mit.edu	37	5	130766663	130766663	+	Missense_Mutation	SNP	G	A	A			TCGA-EJ-5496-01A-01D-1576-08	TCGA-EJ-5496-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:130766663G>A	uc003kvn.1	-	26	4560	c.4354C>T	c.(4354-4356)CGG>TGG	p.R1452W	RAPGEF6_uc003kvp.1_Nonsense_Mutation_p.Q1502*|RAPGEF6_uc003kvo.1_Nonsense_Mutation_p.Q1465*|RAPGEF6_uc010jdi.1_Nonsense_Mutation_p.Q1460*|RAPGEF6_uc010jdj.1_Nonsense_Mutation_p.Q1460*|RAPGEF6_uc003kvm.1_Nonsense_Mutation_p.Q375*	NM_016340	NP_057424	Q8TEU7	RPGF6_HUMAN	PDZ domain-containing guanine nucleotide	1452					Ras protein signal transduction|regulation of GTPase activity|regulation of small GTPase mediated signal transduction	cytoplasm|plasma membrane	GTP-dependent protein binding|guanyl-nucleotide exchange factor activity|Ras GTPase binding			ovary(1)|lung(1)|central_nervous_system(1)	3			KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)	Lung(113;0.0721)		AATACTCTCTGTTTAACTGTC	0.463													73	268	---	---	---	---	PASS
PDE6A	5145	broad.mit.edu	37	5	149247706	149247706	+	Silent	SNP	G	A	A			TCGA-EJ-5496-01A-01D-1576-08	TCGA-EJ-5496-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:149247706G>A	uc003lrg.3	-	18	2271	c.2151C>T	c.(2149-2151)ACC>ACT	p.T717T		NM_000440	NP_000431	P16499	PDE6A_HUMAN	phosphodiesterase 6A	717					cytosolic calcium ion homeostasis|GMP metabolic process|platelet activation|signal transduction|visual perception	cytosol|plasma membrane	3',5'-cyclic-GMP phosphodiesterase activity|metal ion binding			ovary(1)|pancreas(1)	2			KIRC - Kidney renal clear cell carcinoma(527;0.000962)|Kidney(363;0.00147)			GATCACAGGCGGTCATCATCA	0.547													6	218	---	---	---	---	PASS
UNC5A	90249	broad.mit.edu	37	5	176306757	176306757	+	Missense_Mutation	SNP	C	A	A			TCGA-EJ-5496-01A-01D-1576-08	TCGA-EJ-5496-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:176306757C>A	uc003mey.2	+	15	2591	c.2399C>A	c.(2398-2400)ACA>AAA	p.T800K		NM_133369	NP_588610	Q6ZN44	UNC5A_HUMAN	netrin receptor Unc5h1 precursor	800	Death.|Cytoplasmic (Potential).				apoptosis|axon guidance|regulation of apoptosis	integral to membrane|plasma membrane				skin(1)	1	all_cancers(89;0.000119)|Renal(175;0.000269)|Lung NSC(126;0.00696)|all_lung(126;0.0115)	Medulloblastoma(196;0.00498)|all_neural(177;0.0138)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			CCCAGCCCCACAGCCATGATC	0.692													4	65	---	---	---	---	PASS
NSD1	64324	broad.mit.edu	37	5	176636871	176636871	+	Missense_Mutation	SNP	G	A	A			TCGA-EJ-5496-01A-01D-1576-08	TCGA-EJ-5496-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:176636871G>A	uc003mfr.3	+	5	1609	c.1471G>A	c.(1471-1473)GAA>AAA	p.E491K	NSD1_uc003mft.3_Missense_Mutation_p.E222K|NSD1_uc003mfs.1_Missense_Mutation_p.E388K|NSD1_uc011dfx.1_Missense_Mutation_p.E139K	NM_022455	NP_071900	Q96L73	NSD1_HUMAN	nuclear receptor binding SET domain protein 1	491					negative regulation of transcription from RNA polymerase II promoter|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	chromosome|nucleus	androgen receptor binding|chromatin binding|estrogen receptor binding|histone methyltransferase activity (H3-K36 specific)|histone methyltransferase activity (H4-K20 specific)|ligand-dependent nuclear receptor binding|retinoid X receptor binding|thyroid hormone receptor binding|transcription corepressor activity|zinc ion binding			ovary(2)|kidney(1)	3	all_cancers(89;1.57e-05)|Renal(175;0.000269)|Lung NSC(126;0.00111)|all_lung(126;0.002)	all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)|Epithelial(233;0.198)	Kidney(146;0.235)		AGATGAGAAGGAAAAGCCTTG	0.408			T	NUP98	AML		Sotos Syndrome		Beckwith-Wiedemann_syndrome|Sotos_syndrome|Weaver_syndrome	HNSCC(47;0.14)			29	115	---	---	---	---	PASS
HIST1H1A	3024	broad.mit.edu	37	6	26017716	26017716	+	Missense_Mutation	SNP	C	T	T			TCGA-EJ-5496-01A-01D-1576-08	TCGA-EJ-5496-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:26017716C>T	uc003nfo.2	-	1	325	c.245G>A	c.(244-246)CGC>CAC	p.R82H		NM_005325	NP_005316	Q02539	H11_HUMAN	histone cluster 1, H1a	82	H15.				nucleosome assembly|spermatogenesis	nucleosome|nucleus	DNA binding			ovary(2)	2						CAGCTTAATGCGGCTGTTGTT	0.572													6	83	---	---	---	---	PASS
HLA-C	3107	broad.mit.edu	37	6	31238898	31238898	+	Missense_Mutation	SNP	A	C	C			TCGA-EJ-5496-01A-01D-1576-08	TCGA-EJ-5496-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:31238898A>C	uc003nsy.2	-	3	578	c.571T>G	c.(571-573)TGG>GGG	p.W191G	HLA-C_uc011dnj.1_Missense_Mutation_p.W163G|HLA-C_uc003nsx.2_Missense_Mutation_p.W70G|HLA-C_uc003nsz.2_Missense_Mutation_p.W191G|HLA-C_uc010jsl.2_Missense_Mutation_p.W191G|HLA-C_uc003nta.2_Missense_Mutation_p.W191G|HLA-C_uc003ntb.2_Intron|HLA-C_uc003ntc.1_Intron|HLA-B_uc010jsm.1_Intron|HLA-B_uc011dnk.1_Intron|HLA-C_uc011dnl.1_Missense_Mutation_p.W70G|HLA-B_uc003ntf.2_Missense_Mutation_p.W191G	NM_002117	NP_002108	Q9TNN7	1C05_HUMAN	major histocompatibility complex, class I, C	191	Extracellular (Potential).|Alpha-2.				antigen processing and presentation of peptide antigen via MHC class I|interferon-gamma-mediated signaling pathway|interspecies interaction between organisms|regulation of immune response|type I interferon-mediated signaling pathway	integral to membrane|MHC class I protein complex					0						CTGCGGAGCCACTCCACGCAC	0.677													3	54	---	---	---	---	PASS
MAN1A1	4121	broad.mit.edu	37	6	119510998	119510998	+	Silent	SNP	G	A	A			TCGA-EJ-5496-01A-01D-1576-08	TCGA-EJ-5496-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:119510998G>A	uc003pym.1	-	10	1819	c.1377C>T	c.(1375-1377)ATC>ATT	p.I459I		NM_005907	NP_005898	P33908	MA1A1_HUMAN	mannosidase, alpha, class 1A, member 1	459	Lumenal (Potential).				post-translational protein modification|protein N-linked glycosylation via asparagine	endoplasmic reticulum|ER-Golgi intermediate compartment|Golgi membrane|integral to membrane|membrane fraction	calcium ion binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity			ovary(2)|central_nervous_system(1)|skin(1)	4		all_epithelial(87;0.173)		OV - Ovarian serous cystadenocarcinoma(136;0.0612)|GBM - Glioblastoma multiforme(226;0.0702)|all cancers(137;0.115)		TCCACTCTGCGATATAAGTTA	0.498													29	86	---	---	---	---	PASS
MYCT1	80177	broad.mit.edu	37	6	153043291	153043291	+	Missense_Mutation	SNP	G	A	A			TCGA-EJ-5496-01A-01D-1576-08	TCGA-EJ-5496-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:153043291G>A	uc003qpd.3	+	2	619	c.611G>A	c.(610-612)CGT>CAT	p.R204H	MYCT1_uc010kjc.1_Missense_Mutation_p.R156H|MYCT1_uc003qpc.3_Missense_Mutation_p.R204H	NM_025107	NP_079383	Q8N699	MYCT1_HUMAN	myc target 1	204						nucleus				ovary(1)	1		Ovarian(120;0.0654)		OV - Ovarian serous cystadenocarcinoma(155;1.33e-10)|BRCA - Breast invasive adenocarcinoma(81;0.143)		AGTCTGAGCCGTCCTGACTAC	0.532													25	139	---	---	---	---	PASS
ZNRF2	223082	broad.mit.edu	37	7	30402036	30402036	+	Missense_Mutation	SNP	C	A	A			TCGA-EJ-5496-01A-01D-1576-08	TCGA-EJ-5496-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:30402036C>A	uc003tat.2	+	4	1766	c.715C>A	c.(715-717)CAC>AAC	p.H239N		NM_147128	NP_667339	Q8NHG8	ZNRF2_HUMAN	zinc finger/RING finger 2	239	RING-type; atypical.					cell junction|endosome membrane|lysosomal membrane|presynaptic membrane	ligase activity|zinc ion binding				0						TTGCCCTGAGCACCCTTCAGA	0.294													19	106	---	---	---	---	PASS
MIR550-2	693134	broad.mit.edu	37	7	32772646	32772646	+	RNA	SNP	C	A	A			TCGA-EJ-5496-01A-01D-1576-08	TCGA-EJ-5496-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:32772646C>A	hsa-mir-550-2|MI0003601	+			c.54C>A			AVL9_uc011kai.1_Intron|LOC441208_uc003tcy.3_Intron																	0						CTGTTGTTGTCAGATAGTGTC	0.493													7	84	---	---	---	---	PASS
SPDYE7P	441251	broad.mit.edu	37	7	72339511	72339511	+	RNA	SNP	A	C	C			TCGA-EJ-5496-01A-01D-1576-08	TCGA-EJ-5496-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:72339511A>C	uc010lal.1	-	1		c.145T>G				NR_003666				Homo sapiens speedy homolog E7 (Xenopus laevis), pseudogene (SPDYE7P), non-coding RNA.												0						CCACCACTCCATCTTCCTTTT	0.582													4	69	---	---	---	---	PASS
EMID2	136227	broad.mit.edu	37	7	101200916	101200916	+	3'UTR	SNP	A	G	G	rs17393131	by1000genomes	TCGA-EJ-5496-01A-01D-1576-08	TCGA-EJ-5496-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:101200916A>G	uc010lhy.1	+	14					EMID2_uc003uyo.1_3'UTR	NM_133457	NP_597714	Q96A83	EMID2_HUMAN	EMI domain containing 2							collagen				ovary(1)	1	Lung NSC(181;0.215)					GGCTCCAGGCATGGATGATTG	0.622													6	6	---	---	---	---	PASS
SPDYE6	729597	broad.mit.edu	37	7	101988884	101988884	+	Missense_Mutation	SNP	C	T	T			TCGA-EJ-5496-01A-01D-1576-08	TCGA-EJ-5496-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:101988884C>T	uc011kkp.1	-	6	1410	c.989G>A	c.(988-990)CGC>CAC	p.R330H	SPDYE6_uc003uzb.2_Missense_Mutation_p.R186H	NM_001146210	NP_001139682	P0CI01	SPDE6_HUMAN	speedy homolog E6	330	Arg-rich.										0						CAAGGGTATGCGAGAGCGGTT	0.577													34	494	---	---	---	---	PASS
POT1	25913	broad.mit.edu	37	7	124537227	124537227	+	Missense_Mutation	SNP	T	C	C			TCGA-EJ-5496-01A-01D-1576-08	TCGA-EJ-5496-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:124537227T>C	uc003vlm.2	-	5	602	c.1A>G	c.(1-3)ATG>GTG	p.M1V	POT1_uc011koe.1_RNA|POT1_uc003vlk.2_RNA|POT1_uc003vll.2_RNA|POT1_uc003vlo.2_5'UTR|POT1_uc003vln.2_RNA	NM_015450	NP_056265	Q9NUX5	POTE1_HUMAN	protection of telomeres 1 isoform 1	1					DNA duplex unwinding|negative regulation of telomere maintenance via telomerase|positive regulation of DNA strand elongation|positive regulation of helicase activity|positive regulation of telomerase activity|positive regulation of telomere maintenance via telomerase|telomere capping|telomere formation via telomerase|telomere maintenance via telomerase	nuclear telomere cap complex|nucleoplasm	DEAD/H-box RNA helicase binding|single-stranded telomeric DNA binding|telomerase inhibitor activity			central_nervous_system(1)	1						ACCAAAGACATTGATTCTGTA	0.303													22	95	---	---	---	---	PASS
CSMD1	64478	broad.mit.edu	37	8	2830734	2830734	+	Missense_Mutation	SNP	C	T	T			TCGA-EJ-5496-01A-01D-1576-08	TCGA-EJ-5496-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:2830734C>T	uc011kwk.1	-	57	9221	c.8831G>A	c.(8830-8832)CGC>CAC	p.R2944H	CSMD1_uc011kwj.1_Missense_Mutation_p.R2273H|CSMD1_uc010lrg.2_Missense_Mutation_p.R954H	NM_033225	NP_150094	Q96PZ7	CSMD1_HUMAN	CUB and Sushi multiple domains 1 precursor	2944	Extracellular (Potential).|Sushi 22.					integral to membrane				breast(20)|large_intestine(5)	25		all_cancers(1;5.7e-41)|all_epithelial(1;2.54e-36)|Lung NSC(1;7.54e-11)|all_lung(1;3.2e-10)|Hepatocellular(1;3.78e-05)|Breast(1;0.000196)|Myeloproliferative disorder(4;0.000374)|Esophageal squamous(1;0.0157)|Ovarian(12;0.091)|Renal(68;0.144)|Colorectal(14;0.234)		all cancers(1;5.03e-41)|Epithelial(1;4.78e-31)|Lung(1;1.14e-14)|LUSC - Lung squamous cell carcinoma(1;2.34e-14)|GBM - Glioblastoma multiforme(1;4.49e-10)|Colorectal(4;1.18e-07)|OV - Ovarian serous cystadenocarcinoma(1;3.2e-07)|BRCA - Breast invasive adenocarcinoma(1;6.17e-07)|COAD - Colon adenocarcinoma(4;0.000539)|READ - Rectum adenocarcinoma(4;0.00896)|Kidney(5;0.00957)|KIRC - Kidney renal clear cell carcinoma(5;0.0689)		ACAGGAGAAGCGGAGAAGACT	0.537													55	186	---	---	---	---	PASS
SLC18A1	6570	broad.mit.edu	37	8	20036652	20036652	+	Missense_Mutation	SNP	G	T	T			TCGA-EJ-5496-01A-01D-1576-08	TCGA-EJ-5496-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:20036652G>T	uc011kyq.1	-	4	939	c.468C>A	c.(466-468)TTC>TTA	p.F156L	SLC18A1_uc003wzm.2_Missense_Mutation_p.F156L|SLC18A1_uc011kyr.1_Missense_Mutation_p.F156L|SLC18A1_uc003wzn.2_Missense_Mutation_p.F156L|SLC18A1_uc010ltf.2_RNA|SLC18A1_uc003wzo.2_Missense_Mutation_p.F156L	NM_001135691	NP_001129163	P54219	VMAT1_HUMAN	solute carrier family 18 (vesicular monoamine),	156	Helical; (Potential).				neurotransmitter transport	clathrin sculpted monoamine transport vesicle membrane|integral to membrane|membrane fraction	drug transmembrane transporter activity|monoamine transmembrane transporter activity			ovary(2)	2				Colorectal(74;0.0747)		GAGGGCCCACGAATGGGTTGA	0.532													3	107	---	---	---	---	PASS
RP1	6101	broad.mit.edu	37	8	55538481	55538481	+	Missense_Mutation	SNP	C	T	T			TCGA-EJ-5496-01A-01D-1576-08	TCGA-EJ-5496-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:55538481C>T	uc003xsd.1	+	4	2187	c.2039C>T	c.(2038-2040)GCA>GTA	p.A680V	RP1_uc011ldy.1_Intron	NM_006269	NP_006260	P56715	RP1_HUMAN	retinitis pigmentosa RP1 protein	680					axoneme assembly|intracellular signal transduction|photoreceptor cell maintenance|photoreceptor cell outer segment organization|phototransduction, visible light|retinal cone cell development|retinal rod cell development	cilium axoneme|cytoplasm|microtubule|microtubule associated complex|photoreceptor connecting cilium|photoreceptor inner segment|photoreceptor outer segment	microtubule binding			skin(7)|ovary(4)|pancreas(1)	12		all_lung(136;0.0831)|Lung NSC(129;0.109)|all_epithelial(80;0.123)	OV - Ovarian serous cystadenocarcinoma(7;4.4e-07)|Epithelial(17;3.37e-05)|all cancers(17;0.000285)			CGACAGCAAGCAATAAATTCC	0.323													5	69	---	---	---	---	PASS
PAX5	5079	broad.mit.edu	37	9	36923352	36923352	+	Missense_Mutation	SNP	C	A	A			TCGA-EJ-5496-01A-01D-1576-08	TCGA-EJ-5496-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:36923352C>A	uc003zzo.1	-	7	1358	c.910G>T	c.(910-912)GGC>TGC	p.G304C	PAX5_uc011lpt.1_Missense_Mutation_p.G100C|PAX5_uc011lpu.1_Intron|PAX5_uc011lpv.1_Intron|PAX5_uc011lpw.1_Missense_Mutation_p.G304C|PAX5_uc011lpx.1_Missense_Mutation_p.G238W|PAX5_uc011lpy.1_Missense_Mutation_p.G196C|PAX5_uc010mls.1_Intron|PAX5_uc011lpz.1_Missense_Mutation_p.G261C|PAX5_uc011lqa.1_Missense_Mutation_p.G196C|PAX5_uc010mlq.1_Intron|PAX5_uc011lqb.1_Intron|PAX5_uc010mlo.1_Missense_Mutation_p.G304W|PAX5_uc010mlp.1_Missense_Mutation_p.G304C|PAX5_uc011lqc.1_Missense_Mutation_p.G261C|PAX5_uc010mlr.1_Intron	NM_016734	NP_057953	Q02548	PAX5_HUMAN	paired box 5	304		Breakpoint for translocation to form PAX5-ZNF521.			cell differentiation|humoral immune response|nervous system development|organ morphogenesis|spermatogenesis|transcription from RNA polymerase II promoter	nucleus	DNA binding	p.?(23)	PAX5/JAK2(18)	haematopoietic_and_lymphoid_tissue(142)|lung(3)|central_nervous_system(2)	147		all_cancers(2;3.46e-10)|Acute lymphoblastic leukemia(2;7.09e-56)|all_hematologic(2;6.65e-44)		GBM - Glioblastoma multiforme(29;0.0108)		GTGCCCTCACCTGTCACAATG	0.607			T|Mis|D|F|S	IGH@|ETV6|PML|FOXP1|ZNF521|ELN	NHL|ALL|B-ALL								40	131	---	---	---	---	PASS
ZFAND5	7763	broad.mit.edu	37	9	74970894	74970894	+	Missense_Mutation	SNP	A	C	C			TCGA-EJ-5496-01A-01D-1576-08	TCGA-EJ-5496-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:74970894A>C	uc004aiv.2	-	6	895	c.617T>G	c.(616-618)GTG>GGG	p.V206G	ZFAND5_uc010mox.1_Missense_Mutation_p.V103G|ZFAND5_uc010moy.1_Missense_Mutation_p.V206G|ZFAND5_uc004aix.2_Missense_Mutation_p.V206G|ZFAND5_uc004aiw.2_Missense_Mutation_p.V206G|ZFAND5_uc004aiy.2_Missense_Mutation_p.V206G	NM_006007	NP_005998	O76080	ZFAN5_HUMAN	zinc finger, AN1-type domain 5	206							DNA binding|zinc ion binding				0						TTTTTCAGCCACAACAACTGG	0.343													19	104	---	---	---	---	PASS
TRIM14	9830	broad.mit.edu	37	9	100849671	100849671	+	Intron	SNP	A	C	C			TCGA-EJ-5496-01A-01D-1576-08	TCGA-EJ-5496-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:100849671A>C	uc004ayd.2	-						TRIM14_uc004ayf.1_Intron|TRIM14_uc011luz.1_3'UTR|TRIM14_uc011lva.1_3'UTR|TRIM14_uc004ayg.1_Intron|TRIM14_uc004ayh.1_3'UTR|TRIM14_uc004ayi.1_Intron|TRIM14_uc004ayj.1_3'UTR	NM_033220	NP_150089	Q14142	TRI14_HUMAN	tripartite motif protein TRIM14 isoform alpha							cytoplasm|intracellular	zinc ion binding			central_nervous_system(1)	1		Acute lymphoblastic leukemia(62;0.0559)				CAGTAAGGGGACCAGCCACGC	0.622													18	44	---	---	---	---	PASS
HKDC1	80201	broad.mit.edu	37	10	71007216	71007216	+	Missense_Mutation	SNP	G	A	A			TCGA-EJ-5496-01A-01D-1576-08	TCGA-EJ-5496-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:71007216G>A	uc001jpf.3	+	9	1265	c.1132G>A	c.(1132-1134)GTC>ATC	p.V378I	HKDC1_uc010qje.1_Missense_Mutation_p.V241I	NM_025130	NP_079406	Q2TB90	HKDC1_HUMAN	hexokinase domain containing 1	378					glycolysis	mitochondrion|nucleus	ATP binding|hexokinase activity			ovary(4)|skin(1)	5						CTGTACCATCGTCTCCTTCCG	0.582													13	90	---	---	---	---	PASS
CDH23	64072	broad.mit.edu	37	10	73472477	73472477	+	Silent	SNP	C	A	A			TCGA-EJ-5496-01A-01D-1576-08	TCGA-EJ-5496-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:73472477C>A	uc001jrx.3	+	27	3653	c.3276C>A	c.(3274-3276)GTC>GTA	p.V1092V	CDH23_uc001jrz.2_Silent_p.V708V|C10orf105_uc001jsa.1_3'UTR|C10orf105_uc001jsb.1_3'UTR|CDH23_uc001jsc.1_5'UTR	NM_022124	NP_071407	Q9H251	CAD23_HUMAN	cadherin-like 23 isoform 1 precursor	1092	Cadherin 10.|Extracellular (Potential).				calcium ion transport|calcium-dependent cell-cell adhesion|cytosolic calcium ion homeostasis|equilibrioception|homophilic cell adhesion|photoreceptor cell maintenance|response to stimulus|sensory perception of sound	cytosol|integral to membrane|plasma membrane|stereocilium	calcium ion binding|protein binding			central_nervous_system(5)|large_intestine(4)|ovary(2)	11						TCGTCACTGTCCTGGATGTGA	0.582													3	39	---	---	---	---	PASS
PI4K2A	55361	broad.mit.edu	37	10	99410790	99410790	+	Silent	SNP	T	C	C	rs7915721	byFrequency	TCGA-EJ-5496-01A-01D-1576-08	TCGA-EJ-5496-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:99410790T>C	uc001kog.1	+	2	585	c.528T>C	c.(526-528)CCT>CCC	p.P176P	PI4K2A_uc010qoy.1_Silent_p.P146P|PI4K2A_uc009xvw.1_5'UTR	NM_018425	NP_060895	Q9BTU6	P4K2A_HUMAN	phosphatidylinositol 4-kinase type 2 alpha	176	PI3K/PI4K.				phosphatidylinositol biosynthetic process	cytoplasm|integral to plasma membrane|membrane raft	1-phosphatidylinositol 4-kinase activity|ATP binding|magnesium ion binding			lung(1)|skin(1)	2		Colorectal(252;0.162)		Epithelial(162;1.24e-10)|all cancers(201;1.2e-08)		TGTGCTGTCCTTGCTGCTTTG	0.517													3	101	---	---	---	---	PASS
TM7SF2	7108	broad.mit.edu	37	11	64880871	64880871	+	Missense_Mutation	SNP	C	T	T			TCGA-EJ-5496-01A-01D-1576-08	TCGA-EJ-5496-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:64880871C>T	uc001oct.2	+	4	631	c.484C>T	c.(484-486)CCT>TCT	p.P162S	TM7SF2_uc010rny.1_Missense_Mutation_p.P46S|TM7SF2_uc001ocu.2_Missense_Mutation_p.P162S|TM7SF2_uc001ocv.2_Missense_Mutation_p.P183S	NM_003273	NP_003264	O76062	ERG24_HUMAN	transmembrane 7 superfamily member 2	162					cholesterol biosynthetic process	endoplasmic reticulum membrane|integral to plasma membrane	delta14-sterol reductase activity			ovary(1)	1						GGCCCTGGCACCTGGGGGGAA	0.587											OREG0021072	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	55	170	---	---	---	---	PASS
LRP6	4040	broad.mit.edu	37	12	12302059	12302059	+	Missense_Mutation	SNP	G	A	A			TCGA-EJ-5496-01A-01D-1576-08	TCGA-EJ-5496-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:12302059G>A	uc001rah.3	-	14	3165	c.3023C>T	c.(3022-3024)CCG>CTG	p.P1008L	BCL2L14_uc001raf.1_Intron|LRP6_uc010shl.1_Missense_Mutation_p.P1008L	NM_002336	NP_002327	O75581	LRP6_HUMAN	low density lipoprotein receptor-related protein	1008	LDL-receptor class B 16.|Extracellular (Potential).|Beta-propeller 4.				cellular response to cholesterol|negative regulation of protein phosphorylation|negative regulation of protein serine/threonine kinase activity|negative regulation of smooth muscle cell apoptosis|neural crest formation|positive regulation of canonical Wnt receptor signaling pathway|positive regulation of cell cycle|positive regulation of sequence-specific DNA binding transcription factor activity|positive regulation of transcription from RNA polymerase II promoter|positive regulation of Wnt receptor signaling pathway involved in dorsal/ventral axis specification|Wnt receptor signaling pathway involved in dorsal/ventral axis specification	cell surface|cytoplasmic vesicle|endoplasmic reticulum|integral to membrane|plasma membrane	coreceptor activity|frizzled binding|kinase inhibitor activity|low-density lipoprotein receptor activity|protein homodimerization activity|toxin transporter activity|Wnt-protein binding			lung(4)|skin(4)|ovary(2)|kidney(1)|central_nervous_system(1)	12		Prostate(47;0.0865)				GTTCTGACTCGGAACTGAGCT	0.433													11	390	---	---	---	---	PASS
ATF7IP	55729	broad.mit.edu	37	12	14649241	14649241	+	Missense_Mutation	SNP	G	C	C			TCGA-EJ-5496-01A-01D-1576-08	TCGA-EJ-5496-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:14649241G>C	uc001rbw.2	+	14	3515	c.3357G>C	c.(3355-3357)CAG>CAC	p.Q1119H	ATF7IP_uc001rbx.2_Missense_Mutation_p.Q1118H|ATF7IP_uc001rby.3_Missense_Mutation_p.Q1119H|ATF7IP_uc001rca.2_Missense_Mutation_p.Q1119H	NM_018179	NP_060649	Q6VMQ6	MCAF1_HUMAN	activating transcription factor 7 interacting	1119					DNA methylation|interspecies interaction between organisms|positive regulation of transcription, DNA-dependent|regulation of RNA polymerase II transcriptional preinitiation complex assembly|transcription, DNA-dependent		protein binding			lung(3)|ovary(1)|skin(1)	5						CAGGACCTCAGCTCACAGTGC	0.383													19	59	---	---	---	---	PASS
BLOC1S1	2647	broad.mit.edu	37	12	56113258	56113258	+	3'UTR	SNP	T	C	C			TCGA-EJ-5496-01A-01D-1576-08	TCGA-EJ-5496-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:56113258T>C	uc009zny.1	+	3					BLOC1S1_uc001shi.2_Intron|BLOC1S1_uc001shj.3_Intron|RDH5_uc010spt.1_5'Flank|RDH5_uc010spu.1_5'Flank|RDH5_uc001shk.2_5'Flank|RDH5_uc001shl.2_5'Flank			P78537	BL1S1_HUMAN	RecName: Full=Biogenesis of lysosome-related organelles complex 1 subunit 1;          Short=BLOC-1 subunit 1; AltName: Full=GCN5-like protein 1; AltName: Full=Protein RT14;						cellular membrane organization|melanosome organization|platelet dense granule organization|post-Golgi vesicle-mediated transport	BLOC-1 complex|lysosomal membrane	protein binding				0						ATTCCTGGGCTCCCACCTCCT	0.527													13	70	---	---	---	---	PASS
ERBB3	2065	broad.mit.edu	37	12	56481946	56481946	+	Missense_Mutation	SNP	C	A	A			TCGA-EJ-5496-01A-01D-1576-08	TCGA-EJ-5496-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:56481946C>A	uc001sjh.2	+	7	1067	c.874C>A	c.(874-876)CAT>AAT	p.H292N	ERBB3_uc009zoj.2_RNA|ERBB3_uc010sqb.1_Intron|ERBB3_uc010sqc.1_Missense_Mutation_p.H233N|ERBB3_uc001sji.2_5'Flank	NM_001982	NP_001973	P21860	ERBB3_HUMAN	erbB-3 isoform 1 precursor	292	Extracellular (Potential).				cranial nerve development|heart development|negative regulation of cell adhesion|negative regulation of neuron apoptosis|negative regulation of secretion|negative regulation of signal transduction|neuron apoptosis|phosphatidylinositol 3-kinase cascade|positive regulation of phosphatidylinositol 3-kinase cascade|regulation of cell proliferation|Schwann cell differentiation|transmembrane receptor protein tyrosine kinase signaling pathway|wound healing	basolateral plasma membrane|extracellular space|integral to plasma membrane|receptor complex	ATP binding|growth factor binding|protein heterodimerization activity|protein homodimerization activity|protein tyrosine kinase activator activity|receptor signaling protein tyrosine kinase activity|transmembrane receptor protein tyrosine kinase activity			lung(3)|central_nervous_system(2)|stomach(1)|ovary(1)|skin(1)	8			OV - Ovarian serous cystadenocarcinoma(18;0.112)			CAGCTGTCCCCGTAAGTGTCT	0.443													3	81	---	---	---	---	PASS
MGAT4C	25834	broad.mit.edu	37	12	86373542	86373542	+	Missense_Mutation	SNP	G	A	A	rs145801611	byFrequency	TCGA-EJ-5496-01A-01D-1576-08	TCGA-EJ-5496-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:86373542G>A	uc001tai.3	-	8	2212	c.962C>T	c.(961-963)ACG>ATG	p.T321M	MGAT4C_uc001tal.3_Missense_Mutation_p.T321M|MGAT4C_uc001taj.3_Missense_Mutation_p.T321M|MGAT4C_uc001tak.3_Missense_Mutation_p.T321M|MGAT4C_uc010sum.1_Missense_Mutation_p.T345M|MGAT4C_uc001tah.3_Missense_Mutation_p.T321M	NM_013244	NP_037376	Q9UBM8	MGT4C_HUMAN	alpha-1,3-mannosyl-glycoprotein	321	Lumenal (Potential).				post-translational protein modification|protein N-linked glycosylation via asparagine	Golgi membrane|integral to membrane	alpha-1,3-mannosylglycoprotein 4-beta-N-acetylglucosaminyltransferase activity|metal ion binding			ovary(3)	3						CTTATTCTCCGTCCCTTTGTA	0.403													8	162	---	---	---	---	PASS
APAF1	317	broad.mit.edu	37	12	99043447	99043447	+	Missense_Mutation	SNP	C	T	T			TCGA-EJ-5496-01A-01D-1576-08	TCGA-EJ-5496-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:99043447C>T	uc001tfz.2	+	4	1088	c.511C>T	c.(511-513)CAT>TAT	p.H171Y	APAF1_uc001tfy.2_Missense_Mutation_p.H160Y|APAF1_uc001tga.2_Missense_Mutation_p.H160Y|APAF1_uc001tgb.2_Missense_Mutation_p.H171Y|APAF1_uc001tgc.2_Missense_Mutation_p.H171Y	NM_181861	NP_863651	O14727	APAF_HUMAN	apoptotic peptidase activating factor 1 isoform	171	NB-ARC.				activation of caspase activity by cytochrome c|defense response|induction of apoptosis by intracellular signals|nervous system development	cytosol|Golgi apparatus|nucleus	ATP binding|caspase activator activity|protein binding			ovary(2)|lung(1)	3					Adenosine triphosphate(DB00171)	TGTTAGAGATCATTCCCTTTT	0.303													5	58	---	---	---	---	PASS
TUBA3C	7278	broad.mit.edu	37	13	19748209	19748209	+	Missense_Mutation	SNP	C	T	T			TCGA-EJ-5496-01A-01D-1576-08	TCGA-EJ-5496-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:19748209C>T	uc009zzj.2	-	5	1196	c.1147G>A	c.(1147-1149)GCC>ACC	p.A383T		NM_006001	NP_005992	Q13748	TBA3C_HUMAN	tubulin, alpha 3c	383					'de novo' posttranslational protein folding|microtubule-based movement|protein polymerization	cytoplasm|microtubule	GTP binding|GTPase activity|protein binding|structural molecule activity			ovary(3)|skin(2)	5		all_cancers(29;1.31e-20)|all_epithelial(30;1.59e-20)|all_lung(29;6.91e-20)|Lung NSC(5;9.25e-17)|Hepatocellular(1;0.0207)|Lung SC(185;0.0262)|Ovarian(182;0.162)		all cancers(112;6.78e-06)|Epithelial(112;3.79e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00172)|Lung(94;0.0186)|LUSC - Lung squamous cell carcinoma(192;0.108)		TCCGCGATGGCCGTGGTGTTG	0.637													42	85	---	---	---	---	PASS
FAM155A	728215	broad.mit.edu	37	13	107863055	107863055	+	Missense_Mutation	SNP	A	G	G			TCGA-EJ-5496-01A-01D-1576-08	TCGA-EJ-5496-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:107863055A>G	uc001vql.2	-	2	1480	c.964T>C	c.(964-966)TTT>CTT	p.F322L		NM_001080396	NP_001073865	B1AL88	F155A_HUMAN	family with sequence similarity 155, member A	322						integral to membrane	binding			skin(1)	1						CTGCAGTTAAACTGTGTGACT	0.408											OREG0022506	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	22	102	---	---	---	---	PASS
SIPA1L1	26037	broad.mit.edu	37	14	72152099	72152099	+	Missense_Mutation	SNP	G	A	A	rs141106111	byFrequency	TCGA-EJ-5496-01A-01D-1576-08	TCGA-EJ-5496-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:72152099G>A	uc001xms.2	+	10	3473	c.3125G>A	c.(3124-3126)CGC>CAC	p.R1042H	SIPA1L1_uc001xmt.2_Missense_Mutation_p.R1042H|SIPA1L1_uc001xmu.2_Missense_Mutation_p.R1042H|SIPA1L1_uc001xmv.2_Missense_Mutation_p.R1042H|SIPA1L1_uc010ttm.1_Missense_Mutation_p.R517H	NM_015556	NP_056371	O43166	SI1L1_HUMAN	signal-induced proliferation-associated 1 like	1042	PDZ.				actin cytoskeleton reorganization|activation of Rap GTPase activity|regulation of dendritic spine morphogenesis	cell junction|cytoplasm|dendritic spine|postsynaptic density|postsynaptic membrane|synaptosome	GTPase activator activity			ovary(3)|breast(1)	4				all cancers(60;0.00169)|BRCA - Breast invasive adenocarcinoma(234;0.00912)|OV - Ovarian serous cystadenocarcinoma(108;0.0109)		GAAACCTACCGCATGCCAGTG	0.448													9	364	---	---	---	---	PASS
NIPA2	81614	broad.mit.edu	37	15	23006760	23006760	+	Missense_Mutation	SNP	T	A	A			TCGA-EJ-5496-01A-01D-1576-08	TCGA-EJ-5496-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:23006760T>A	uc001yux.2	-	8	1157	c.544A>T	c.(544-546)ATA>TTA	p.I182L	NIPA2_uc001yuy.2_Missense_Mutation_p.I182L|NIPA2_uc001yuz.2_Missense_Mutation_p.I182L|NIPA2_uc001yva.2_Missense_Mutation_p.I163L|NIPA2_uc001yvb.2_Missense_Mutation_p.I182L|NIPA2_uc010ayb.2_Missense_Mutation_p.I163L	NM_030922	NP_112184	Q8N8Q9	NIPA2_HUMAN	non imprinted in Prader-Willi/Angelman syndrome	182	Helical; (Potential).					early endosome|integral to membrane|plasma membrane				haematopoietic_and_lymphoid_tissue(1)	1		all_cancers(20;2.26e-25)|all_epithelial(15;2.1e-22)|Lung NSC(15;3.36e-17)|all_lung(15;1.04e-16)|Breast(32;0.000776)|Colorectal(260;0.0488)		all cancers(64;1.48e-06)|Epithelial(43;1.44e-05)|BRCA - Breast invasive adenocarcinoma(123;0.000353)		CAGATTGTTATGTACACAAGA	0.502													3	74	---	---	---	---	PASS
ACTC1	70	broad.mit.edu	37	15	35086889	35086889	+	Missense_Mutation	SNP	G	A	A			TCGA-EJ-5496-01A-01D-1576-08	TCGA-EJ-5496-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:35086889G>A	uc001ziu.1	-	2	364	c.121C>T	c.(121-123)CGG>TGG	p.R41W	uc001zit.1_Intron	NM_005159	NP_005150	P68032	ACTC_HUMAN	cardiac muscle alpha actin 1 proprotein	41					apoptosis|cardiac muscle tissue morphogenesis|cardiac myofibril assembly|muscle filament sliding|skeletal muscle thin filament assembly	actomyosin, actin part|cytosol|I band	ATP binding|ATPase activity|myosin binding			upper_aerodigestive_tract(1)|ovary(1)	2		all_lung(180;2.3e-08)		all cancers(64;5.83e-19)|GBM - Glioblastoma multiforme(113;1.98e-07)|BRCA - Breast invasive adenocarcinoma(123;0.0244)		ACCTGGTGCCGCGGGCGGCCC	0.672													9	47	---	---	---	---	PASS
CIB2	10518	broad.mit.edu	37	15	78403582	78403582	+	Silent	SNP	G	A	A			TCGA-EJ-5496-01A-01D-1576-08	TCGA-EJ-5496-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:78403582G>A	uc002bdb.1	-	3	444	c.123C>T	c.(121-123)CTC>CTT	p.L41L	CIB2_uc002bdc.1_5'UTR|CIB2_uc010ums.1_Silent_p.L41L	NM_006383	NP_006374	O75838	CIB2_HUMAN	DNA-dependent protein kinase catalytic	41							calcium ion binding				0						CCATTGGGACGAGGTTGGGGG	0.607													7	128	---	---	---	---	PASS
IREB2	3658	broad.mit.edu	37	15	78777134	78777134	+	Missense_Mutation	SNP	A	G	G			TCGA-EJ-5496-01A-01D-1576-08	TCGA-EJ-5496-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:78777134A>G	uc002bdr.2	+	12	1607	c.1445A>G	c.(1444-1446)GAA>GGA	p.E482G	IREB2_uc010unb.1_Missense_Mutation_p.E232G	NM_004136	NP_004127	P48200	IREB2_HUMAN	iron-responsive element binding protein 2	482							4 iron, 4 sulfur cluster binding|metal ion binding|protein binding				0				UCEC - Uterine corpus endometrioid carcinoma (272;0.232)		ATTGCAGCTGAAAAACAAAAG	0.333													3	139	---	---	---	---	PASS
FANCI	55215	broad.mit.edu	37	15	89811688	89811688	+	Missense_Mutation	SNP	A	G	G			TCGA-EJ-5496-01A-01D-1576-08	TCGA-EJ-5496-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:89811688A>G	uc010bnp.1	+	10	904	c.814A>G	c.(814-816)ATT>GTT	p.I272V	FANCI_uc002bnm.1_Missense_Mutation_p.I272V|FANCI_uc002bnn.1_RNA|FANCI_uc002bnp.1_Missense_Mutation_p.I93V	NM_001113378	NP_001106849	Q9NVI1	FANCI_HUMAN	Fanconi anemia, complementation group I isoform	272					cell cycle|DNA repair	nucleoplasm	protein binding			ovary(2)	2	Lung NSC(78;0.0472)|all_lung(78;0.089)					AGGCACCATTATTCTACACAT	0.383								Direct_reversal_of_damage|Involved_in_tolerance_or_repair_of_DNA_crosslinks	Fanconi_Anemia				9	358	---	---	---	---	PASS
PHKB	5257	broad.mit.edu	37	16	47733353	47733353	+	3'UTR	SNP	G	C	C			TCGA-EJ-5496-01A-01D-1576-08	TCGA-EJ-5496-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:47733353G>C	uc002eev.3	+	31					PHKB_uc002eeu.3_3'UTR|PHKB_uc002eew.3_3'UTR	NM_000293	NP_000284	Q93100	KPBB_HUMAN	phosphorylase kinase, beta isoform a						glucose metabolic process|glycogen catabolic process	cytosol|plasma membrane	calmodulin binding|glucan 1,4-alpha-glucosidase activity			ovary(1)|large_intestine(1)|breast(1)	3		all_cancers(37;0.00447)|all_lung(18;0.00616)|Lung NSC(13;0.0418)|Breast(268;0.203)				CTTAATCAAGGCAGCCATTAA	0.468													8	43	---	---	---	---	PASS
GOT2	2806	broad.mit.edu	37	16	58743428	58743428	+	Missense_Mutation	SNP	G	A	A			TCGA-EJ-5496-01A-01D-1576-08	TCGA-EJ-5496-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:58743428G>A	uc002eof.1	-	9	1177	c.1063C>T	c.(1063-1065)CGG>TGG	p.R355W	GOT2_uc010vim.1_Missense_Mutation_p.R312W	NM_002080	NP_002071	P00505	AATM_HUMAN	aspartate aminotransferase 2 precursor	355					aspartate catabolic process|fatty acid transport|gluconeogenesis|response to ethanol	mitochondrial matrix|plasma membrane	L-aspartate:2-oxoglutarate aminotransferase activity|protein binding|pyridoxal phosphate binding			central_nervous_system(1)|skin(1)	2					L-Aspartic Acid(DB00128)|L-Glutamic Acid(DB00142)|Pyridoxal Phosphate(DB00114)	AGTTGAGTCCGCATGCCAATG	0.507													5	344	---	---	---	---	PASS
PLCG2	5336	broad.mit.edu	37	16	81944188	81944188	+	Silent	SNP	C	T	T			TCGA-EJ-5496-01A-01D-1576-08	TCGA-EJ-5496-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:81944188C>T	uc002fgt.2	+	18	1949	c.1797C>T	c.(1795-1797)TAC>TAT	p.Y599Y	PLCG2_uc010chg.1_Silent_p.Y599Y	NM_002661	NP_002652	P16885	PLCG2_HUMAN	phospholipase C, gamma 2	599	SH2 1.				intracellular signal transduction|phospholipid catabolic process|platelet activation	plasma membrane	phosphatidylinositol phospholipase C activity|protein binding|signal transducer activity			large_intestine(4)|lung(2)|ovary(1)|skin(1)	8						CCCTGAAATACTACTTGACTG	0.647													6	230	---	---	---	---	PASS
AMAC1L3	643664	broad.mit.edu	37	17	7386366	7386366	+	3'UTR	SNP	G	A	A			TCGA-EJ-5496-01A-01D-1576-08	TCGA-EJ-5496-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:7386366G>A	uc010cmj.1	+	2					ZBTB4_uc002ghd.3_Intron|POLR2A_uc002ghe.2_5'Flank|POLR2A_uc002ghf.3_5'Flank	NM_001102614	NP_001096084	P0C7Q6	AMCL3_HUMAN	acyl-malonyl condensing enzyme 1-like 3							integral to membrane					0		Prostate(122;0.173)				GGGATAAATAGAGGCAAAGAC	0.537													3	34	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	17	21731144	21731144	+	Missense_Mutation	SNP	T	G	G	rs149119138	by1000genomes	TCGA-EJ-5496-01A-01D-1576-08	TCGA-EJ-5496-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21731144T>G	uc002gyy.3	+	2	571	c.446T>G	c.(445-447)CTG>CGG	p.L149R						SubName: Full=cDNA FLJ51326, highly similar to Homo sapiens ubiquitin B (UBB), mRNA;																		GTCCTGCGTCTGAGAGGTGGT	0.542													5	106	---	---	---	---	PASS
NF1	4763	broad.mit.edu	37	17	29528486	29528486	+	Missense_Mutation	SNP	C	T	T			TCGA-EJ-5496-01A-01D-1576-08	TCGA-EJ-5496-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:29528486C>T	uc002hgg.2	+	11	1576	c.1243C>T	c.(1243-1245)CAT>TAT	p.H415Y	NF1_uc002hge.1_Missense_Mutation_p.H415Y|NF1_uc002hgf.1_Missense_Mutation_p.H415Y|NF1_uc002hgh.2_Missense_Mutation_p.H415Y|NF1_uc010csn.1_Missense_Mutation_p.H275Y	NM_001042492	NP_001035957	P21359	NF1_HUMAN	neurofibromin isoform 1	415					actin cytoskeleton organization|adrenal gland development|artery morphogenesis|camera-type eye morphogenesis|cerebral cortex development|collagen fibril organization|forebrain astrocyte development|forebrain morphogenesis|heart development|liver development|MAPKKK cascade|metanephros development|myelination in peripheral nervous system|negative regulation of cell migration|negative regulation of endothelial cell proliferation|negative regulation of MAP kinase activity|negative regulation of MAPKKK cascade|negative regulation of neuroblast proliferation|negative regulation of oligodendrocyte differentiation|negative regulation of transcription factor import into nucleus|osteoblast differentiation|phosphatidylinositol 3-kinase cascade|pigmentation|positive regulation of adenylate cyclase activity|positive regulation of neuron apoptosis|Ras protein signal transduction|regulation of blood vessel endothelial cell migration|regulation of bone resorption|response to hypoxia|smooth muscle tissue development|spinal cord development|sympathetic nervous system development|visual learning|wound healing	axon|cytoplasm|dendrite|intrinsic to internal side of plasma membrane|nucleus	protein binding|Ras GTPase activator activity	p.?(2)		soft_tissue(159)|central_nervous_system(56)|lung(28)|large_intestine(27)|haematopoietic_and_lymphoid_tissue(18)|ovary(18)|autonomic_ganglia(12)|breast(3)|skin(3)|stomach(2)|thyroid(1)|prostate(1)|kidney(1)|pancreas(1)	330		all_cancers(10;1.29e-12)|all_epithelial(10;0.00347)|all_hematologic(16;0.00556)|Acute lymphoblastic leukemia(14;0.00593)|Breast(31;0.014)|Myeloproliferative disorder(56;0.0255)|all_lung(9;0.0321)|Lung NSC(157;0.0659)		UCEC - Uterine corpus endometrioid carcinoma (4;4.38e-05)|all cancers(4;1.64e-26)|Epithelial(4;9.15e-23)|OV - Ovarian serous cystadenocarcinoma(4;3.58e-21)|GBM - Glioblastoma multiforme(4;0.00146)		AAATTCACTCCATCGAATCAT	0.303			D|Mis|N|F|S|O		neurofibroma|glioma	neurofibroma|glioma			Neurofibromatosis_type_1	TCGA GBM(6;<1E-08)|TSP Lung(7;0.0071)|TCGA Ovarian(3;0.0088)			5	286	---	---	---	---	PASS
UBTF	7343	broad.mit.edu	37	17	42293127	42293127	+	Silent	SNP	G	A	A			TCGA-EJ-5496-01A-01D-1576-08	TCGA-EJ-5496-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:42293127G>A	uc002igb.2	-	4	436	c.369C>T	c.(367-369)TTC>TTT	p.F123F	UBTF_uc002igc.2_Silent_p.F123F|UBTF_uc010czs.2_Silent_p.F123F|UBTF_uc002igd.2_Silent_p.F123F|UBTF_uc010czt.2_Silent_p.F123F|UBTF_uc002ige.2_Silent_p.F123F	NM_014233	NP_055048	P17480	UBF1_HUMAN	upstream binding transcription factor, RNA	123	HMG box 1.				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)		GCTTCTCCATGAAGAAGCGGA	0.493													51	138	---	---	---	---	PASS
KIAA1267	284058	broad.mit.edu	37	17	44248783	44248783	+	Missense_Mutation	SNP	G	C	C	rs142096969	byFrequency	TCGA-EJ-5496-01A-01D-1576-08	TCGA-EJ-5496-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:44248783G>C	uc002ikb.2	-	1	812	c.727C>G	c.(727-729)CAA>GAA	p.Q243E	KIAA1267_uc002ikc.2_Missense_Mutation_p.Q243E|KIAA1267_uc002ikd.2_Missense_Mutation_p.Q243E|KIAA1267_uc010dav.2_Missense_Mutation_p.Q243E	NM_015443	NP_056258	Q7Z3B3	K1267_HUMAN	hypothetical protein LOC284058	243						MLL1 complex	protein binding			skin(2)	2		Melanoma(429;0.211)				CTGCTTCCTTGAAGTGCCGGC	0.438													4	149	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	17	45128792	45128792	+	5'Flank	SNP	G	T	T	rs143713325	by1000genomes	TCGA-EJ-5496-01A-01D-1576-08	TCGA-EJ-5496-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:45128792G>T	uc010wkl.1	-						uc010wkm.1_RNA					Homo sapiens cDNA FLJ38031 fis, clone CTONG2013348.																		AATTCAGGTTGTCAGAATGCA	0.373													6	74	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	17	45128812	45128812	+	5'Flank	SNP	C	T	T			TCGA-EJ-5496-01A-01D-1576-08	TCGA-EJ-5496-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:45128812C>T	uc010wkl.1	-						uc010wkm.1_RNA					Homo sapiens cDNA FLJ38031 fis, clone CTONG2013348.																		AGTCCTGTTTCTGTGTGGATT	0.373													5	52	---	---	---	---	PASS
TBC1D3P2	440452	broad.mit.edu	37	17	60342186	60342186	+	RNA	SNP	T	C	C	rs79096325		TCGA-EJ-5496-01A-01D-1576-08	TCGA-EJ-5496-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:60342186T>C	uc010woz.1	-	14		c.1943A>G				NR_027486				Homo sapiens cDNA FLJ60189 complete cds, highly similar to TBC1 domain family member 3.												0						GCTGGGGGTGTTGGGAGGGGC	0.493													3	17	---	---	---	---	PASS
SLC16A6	9120	broad.mit.edu	37	17	66267452	66267452	+	Silent	SNP	T	C	C			TCGA-EJ-5496-01A-01D-1576-08	TCGA-EJ-5496-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:66267452T>C	uc002jgz.1	-	5	1037	c.849A>G	c.(847-849)CTA>CTG	p.L283L	ARSG_uc002jhc.2_Intron|SLC16A6_uc002jha.1_Silent_p.L283L	NM_004694	NP_004685	O15403	MOT7_HUMAN	solute carrier family 16, member 6	283	Cytoplasmic (Potential).					integral to plasma membrane|membrane fraction	monocarboxylic acid transmembrane transporter activity|symporter activity				0	all_cancers(12;1.24e-09)		BRCA - Breast invasive adenocarcinoma(8;3.17e-08)|LUSC - Lung squamous cell carcinoma(166;0.24)		Pyruvic acid(DB00119)	AGAAGTCTAATAGCGGGGCTT	0.463													3	123	---	---	---	---	PASS
WDR7	23335	broad.mit.edu	37	18	54603078	54603078	+	Missense_Mutation	SNP	C	T	T			TCGA-EJ-5496-01A-01D-1576-08	TCGA-EJ-5496-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:54603078C>T	uc002lgk.1	+	23	3984	c.3773C>T	c.(3772-3774)GCC>GTC	p.A1258V	WDR7_uc002lgl.1_Missense_Mutation_p.A1225V	NM_015285	NP_056100	Q9Y4E6	WDR7_HUMAN	rabconnectin-3 beta isoform 1	1258										ovary(2)|skin(1)	3				Lung(128;0.0238)|Colorectal(16;0.0296)		GCGAGGCATGCCCTCTCGCTC	0.537													4	175	---	---	---	---	PASS
MUC16	94025	broad.mit.edu	37	19	8996458	8996458	+	Missense_Mutation	SNP	G	C	C			TCGA-EJ-5496-01A-01D-1576-08	TCGA-EJ-5496-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:8996458G>C	uc002mkp.2	-	61	41318	c.41114C>G	c.(41113-41115)GCC>GGC	p.A13705G	MUC16_uc010dwi.2_RNA|MUC16_uc010dwj.2_Missense_Mutation_p.A522G|MUC16_uc010xki.1_RNA	NM_024690	NP_078966	Q8WXI7	MUC16_HUMAN	mucin 16	Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment					cell adhesion	extracellular space|extrinsic to membrane|integral to membrane|plasma membrane	protein binding			lung(30)|ovary(15)|breast(8)|large_intestine(1)|skin(1)|prostate(1)|pancreas(1)	57						GGTGCAGATGGCATCCACTCC	0.552													12	79	---	---	---	---	PASS
MUC16	94025	broad.mit.edu	37	19	9047100	9047100	+	Missense_Mutation	SNP	G	A	A			TCGA-EJ-5496-01A-01D-1576-08	TCGA-EJ-5496-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:9047100G>A	uc002mkp.2	-	5	34735	c.34531C>T	c.(34531-34533)CAT>TAT	p.H11511Y		NM_024690	NP_078966	Q8WXI7	MUC16_HUMAN	mucin 16	11513	Thr-rich.|Extracellular (Potential).				cell adhesion	extracellular space|extrinsic to membrane|integral to membrane|plasma membrane	protein binding			lung(30)|ovary(15)|breast(8)|large_intestine(1)|skin(1)|prostate(1)|pancreas(1)	57						GACTTACTATGGGAAAACTTG	0.498													53	140	---	---	---	---	PASS
ZNF98	148198	broad.mit.edu	37	19	22574557	22574557	+	Nonsense_Mutation	SNP	C	A	A			TCGA-EJ-5496-01A-01D-1576-08	TCGA-EJ-5496-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:22574557C>A	uc002nqt.2	-	4	1602	c.1480G>T	c.(1480-1482)GAA>TAA	p.E494*		NM_001098626	NP_001092096	A6NK75	ZNF98_HUMAN	zinc finger protein 98	494	C2H2-type 12.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)|skin(1)	2		all_cancers(12;0.0536)|all_lung(12;0.00187)|Lung NSC(12;0.0019)|all_epithelial(12;0.00542)|Hepatocellular(1079;0.244)				TTGCCACATTCTTCACATTTG	0.403													4	183	---	---	---	---	PASS
FCGBP	8857	broad.mit.edu	37	19	40367797	40367797	+	Missense_Mutation	SNP	C	G	G			TCGA-EJ-5496-01A-01D-1576-08	TCGA-EJ-5496-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:40367797C>G	uc002omp.3	-	29	13171	c.13163G>C	c.(13162-13164)GGC>GCC	p.G4388A		NM_003890	NP_003881	Q9Y6R7	FCGBP_HUMAN	Fc fragment of IgG binding protein precursor	4388	TIL 10.					extracellular region	protein binding			ovary(4)|skin(4)|central_nervous_system(1)	9	all_cancers(60;6.03e-06)|all_lung(34;5.58e-08)|Lung NSC(34;6.62e-08)|Ovarian(47;0.06)		Epithelial(26;6.25e-23)|all cancers(26;1.13e-20)			GCACTGGCAGCCCTCCACACA	0.657													9	44	---	---	---	---	PASS
CEACAM3	1084	broad.mit.edu	37	19	42312921	42312921	+	Silent	SNP	G	A	A	rs61747599	byFrequency	TCGA-EJ-5496-01A-01D-1576-08	TCGA-EJ-5496-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:42312921G>A	uc002orn.1	+	3	571	c.495G>A	c.(493-495)GCG>GCA	p.A165A	CEACAM3_uc010eia.1_Silent_p.A165A|CEACAM3_uc002oro.1_RNA	NM_001815	NP_001806	P40198	CEAM3_HUMAN	carcinoembryonic antigen-related cell adhesion	165	Helical; (Potential).					integral to membrane				skin(1)	1						TCGGAGTGGCGCTGGTGGCCG	0.607													72	282	---	---	---	---	PASS
LRRC4B	94030	broad.mit.edu	37	19	51022077	51022077	+	Missense_Mutation	SNP	G	A	A			TCGA-EJ-5496-01A-01D-1576-08	TCGA-EJ-5496-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:51022077G>A	uc002pss.2	-	3	1030	c.893C>T	c.(892-894)ACG>ATG	p.T298M		NM_001080457	NP_001073926	Q9NT99	LRC4B_HUMAN	leucine rich repeat containing 4B precursor	298	LRR 9.|Extracellular (Potential).					cell junction|integral to membrane|presynaptic membrane				central_nervous_system(1)|skin(1)	2		all_neural(266;0.131)		OV - Ovarian serous cystadenocarcinoma(262;0.00284)|GBM - Glioblastoma multiforme(134;0.0188)		GTGCAGGGGCGTGAAGAGGTC	0.637													27	113	---	---	---	---	PASS
ZNF347	84671	broad.mit.edu	37	19	53644134	53644134	+	Silent	SNP	A	T	T			TCGA-EJ-5496-01A-01D-1576-08	TCGA-EJ-5496-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:53644134A>T	uc002qbb.1	-	5	2016	c.1947T>A	c.(1945-1947)GGT>GGA	p.G649G	ZNF347_uc010eql.1_Silent_p.G650G|ZNF347_uc002qbc.1_Silent_p.G650G	NM_032584	NP_115973	Q96SE7	ZN347_HUMAN	zinc finger protein 347	649					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0				GBM - Glioblastoma multiforme(134;0.0179)		AAGGTTTTTCACCAGTATGGA	0.408													5	321	---	---	---	---	PASS
ASXL1	171023	broad.mit.edu	37	20	31023728	31023728	+	Silent	SNP	G	A	A			TCGA-EJ-5496-01A-01D-1576-08	TCGA-EJ-5496-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:31023728G>A	uc002wxs.2	+	12	3639	c.3213G>A	c.(3211-3213)GCG>GCA	p.A1071A	ASXL1_uc010geb.2_Silent_p.A962A	NM_015338	NP_056153	Q8IXJ9	ASXL1_HUMAN	additional sex combs like 1 isoform 1	1071					chromatin modification|regulation of transcription, DNA-dependent|transcription, DNA-dependent	PR-DUB complex	metal ion binding|protein binding			haematopoietic_and_lymphoid_tissue(239)|large_intestine(6)|central_nervous_system(2)|ovary(1)	248						GAGTATGTGCGGTCCGCCAAA	0.567			F|N|Mis		MDS|CMML								52	137	---	---	---	---	PASS
SALL4	57167	broad.mit.edu	37	20	50401031	50401031	+	Missense_Mutation	SNP	C	T	T			TCGA-EJ-5496-01A-01D-1576-08	TCGA-EJ-5496-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:50401031C>T	uc002xwh.3	-	4	3036	c.2935G>A	c.(2935-2937)GGT>AGT	p.G979S	SALL4_uc010gii.2_Missense_Mutation_p.G542S|SALL4_uc002xwi.3_Missense_Mutation_p.G202S	NM_020436	NP_065169	Q9UJQ4	SALL4_HUMAN	sal-like 4	979					transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(2)	2						ACGGCCAGACCGCCATTGAGC	0.547													25	160	---	---	---	---	PASS
UMODL1	89766	broad.mit.edu	37	21	43496381	43496381	+	Intron	SNP	G	T	T	rs220286	by1000genomes	TCGA-EJ-5496-01A-01D-1576-08	TCGA-EJ-5496-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:43496381G>T	uc002zaf.1	+						UMODL1_uc002zad.1_Intron|UMODL1_uc002zae.1_Intron|UMODL1_uc002zag.1_Intron|uc002zah.1_RNA	NM_001004416	NP_001004416	Q5DID0	UROL1_HUMAN	uromodulin-like 1 isoform 1 precursor							cytoplasm|extracellular region|integral to membrane|plasma membrane	calcium ion binding|peptidase inhibitor activity			ovary(2)|skin(1)	3						GCTGGGCTGGGGCGGGGCCAC	0.592													4	156	---	---	---	---	PASS
KRTAP10-1	386677	broad.mit.edu	37	21	45959773	45959773	+	Silent	SNP	C	T	T			TCGA-EJ-5496-01A-01D-1576-08	TCGA-EJ-5496-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:45959773C>T	uc002zfh.1	-	1	306	c.261G>A	c.(259-261)CCG>CCA	p.P87P	C21orf29_uc002zfe.1_Intron|C21orf29_uc010gpv.1_Intron	NM_198691	NP_941964	P60331	KR101_HUMAN	keratin associated protein 10-1	87	24 X 5 AA repeats of C-C-X(3).					keratin filament				skin(1)	1						tgcagcaagccggctggcagc	0.333													4	89	---	---	---	---	PASS
CACNA1I	8911	broad.mit.edu	37	22	40030575	40030575	+	Missense_Mutation	SNP	C	T	T			TCGA-EJ-5496-01A-01D-1576-08	TCGA-EJ-5496-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:40030575C>T	uc003ayc.2	+	5	586	c.586C>T	c.(586-588)CGG>TGG	p.R196W	CACNA1I_uc003ayd.2_Missense_Mutation_p.R196W|CACNA1I_uc003aye.2_Missense_Mutation_p.R111W|CACNA1I_uc003ayf.2_Missense_Mutation_p.R111W	NM_021096	NP_066919	Q9P0X4	CAC1I_HUMAN	calcium channel, voltage-dependent, T type,	196	I.|Cytoplasmic (Potential).				axon guidance|signal transduction	voltage-gated calcium channel complex	low voltage-gated calcium channel activity|protein binding			breast(1)|central_nervous_system(1)	2	Melanoma(58;0.0749)				Flunarizine(DB04841)|Paramethadione(DB00617)|Verapamil(DB00661)	CCCAGGTATGCGGATCCTGGT	0.552													5	334	---	---	---	---	PASS
CYP2D7P1	1564	broad.mit.edu	37	22	42538870	42538870	+	Missense_Mutation	SNP	A	C	C	rs2982057	by1000genomes	TCGA-EJ-5496-01A-01D-1576-08	TCGA-EJ-5496-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:42538870A>C	uc003bci.2	-	3	475	c.94T>G	c.(94-96)TCG>GCG	p.S32A	CYP2D7P1_uc003bcg.2_5'Flank|CYP2D7P1_uc003bch.2_5'Flank|CYP2D7P1_uc010gyv.2_Intron|CYP2D7P1_uc010gyw.2_RNA|CYP2D7P1_uc010gyx.1_Missense_Mutation_p.S32A	NR_002570				SubName: Full=Cytochrome P450 2D6;          EC=1.14.14.1;												0						CCATAGCGCGACAGGAACACC	0.687													4	22	---	---	---	---	PASS
SPATA21	374955	broad.mit.edu	37	1	16735403	16735404	+	Intron	INS	-	C	C	rs144270101	by1000genomes	TCGA-EJ-5496-01A-01D-1576-08	TCGA-EJ-5496-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:16735403_16735404insC	uc001ayn.2	-						SPATA21_uc001ayl.1_Intron|SPATA21_uc010occ.1_Intron	NM_198546	NP_940948	Q7Z572	SPT21_HUMAN	spermatogenesis associated 21								calcium ion binding			ovary(2)|breast(1)	3		Colorectal(325;0.000147)|Renal(390;0.00145)|Lung NSC(340;0.00215)|Breast(348;0.00224)|all_lung(284;0.00351)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0646)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0182)|COAD - Colon adenocarcinoma(227;1.15e-05)|BRCA - Breast invasive adenocarcinoma(304;4.2e-05)|Kidney(64;0.000183)|KIRC - Kidney renal clear cell carcinoma(64;0.00269)|STAD - Stomach adenocarcinoma(313;0.0122)|READ - Rectum adenocarcinoma(331;0.0651)		atgagttctggcccccccaacc	0.139													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	18427834	18427857	+	IGR	DEL	TTCCTTCCTTCCTTTCTTCCTTTC	-	-	rs66701517		TCGA-EJ-5496-01A-01D-1576-08	TCGA-EJ-5496-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:18427834_18427857delTTCCTTCCTTCCTTTCTTCCTTTC								ACTL8 (274278 upstream) : IGSF21 (6383 downstream)																							ccttccctctttccttccttcctttcttcctttcttccttcctt	0.179													4	2	---	---	---	---	
RPA2	6118	broad.mit.edu	37	1	28223824	28223825	+	Intron	INS	-	T	T	rs150650563	by1000genomes	TCGA-EJ-5496-01A-01D-1576-08	TCGA-EJ-5496-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:28223824_28223825insT	uc001bpe.1	-						RPA2_uc001bpd.1_Intron|RPA2_uc010ofp.1_Intron	NM_002946	NP_002937	P15927	RFA2_HUMAN	replication protein A2, 32kDa						cell cycle checkpoint|DNA recombinase assembly|DNA strand elongation involved in DNA replication|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|nucleotide-excision repair, DNA damage removal|nucleotide-excision repair, DNA gap filling|regulation of double-strand break repair via homologous recombination|S phase of mitotic cell cycle|telomere maintenance via recombination|telomere maintenance via semi-conservative replication|transcription-coupled nucleotide-excision repair	DNA replication factor A complex|PML body	protein phosphatase binding|single-stranded DNA binding			skin(1)	1		Colorectal(325;0.000147)|Renal(390;0.00357)|Lung NSC(340;0.00588)|all_lung(284;0.00645)|Breast(348;0.0174)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0545)|all_neural(195;0.0557)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0429)|OV - Ovarian serous cystadenocarcinoma(117;3.62e-24)|Colorectal(126;3.23e-08)|COAD - Colon adenocarcinoma(152;1.75e-06)|KIRC - Kidney renal clear cell carcinoma(1967;0.00294)|STAD - Stomach adenocarcinoma(196;0.00308)|BRCA - Breast invasive adenocarcinoma(304;0.00613)|READ - Rectum adenocarcinoma(331;0.0649)		gctaagggacattaataatttt	0.188								Direct_reversal_of_damage|NER					2	6	---	---	---	---	
EPHX4	253152	broad.mit.edu	37	1	92510850	92510850	+	Intron	DEL	T	-	-			TCGA-EJ-5496-01A-01D-1576-08	TCGA-EJ-5496-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:92510850delT	uc001don.2	+							NM_173567	NP_775838	Q8IUS5	EPHX4_HUMAN	abhydrolase domain containing 7							integral to membrane	hydrolase activity			central_nervous_system(1)	1						cTATTTCAGATTTTTTTTTTT	0.179													5	3	---	---	---	---	
LOC200030	200030	broad.mit.edu	37	1	148011136	148011137	+	Intron	INS	-	T	T	rs148901736	by1000genomes	TCGA-EJ-5496-01A-01D-1576-08	TCGA-EJ-5496-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:148011136_148011137insT	uc001eqf.2	-						LOC200030_uc001eqe.2_Intron|LOC200030_uc001eqg.2_Intron|FLJ39739_uc001eqo.1_Intron|NBPF14_uc010pab.1_Intron|NBPF14_uc010pac.1_Intron|NBPF14_uc001eqx.2_Intron|NBPF14_uc001eqq.2_Intron|NBPF14_uc010pad.1_Intron|NBPF14_uc001eqs.1_Intron	NM_017940	NP_060410	Q86T75	NBPFB_HUMAN	hypothetical protein LOC55672							cytoplasm					0						CATGGCTAACGTAAGGAAGAGT	0.416													9	6	---	---	---	---	
CDC42SE1	56882	broad.mit.edu	37	1	151027766	151027768	+	Intron	DEL	AAC	-	-	rs142658599		TCGA-EJ-5496-01A-01D-1576-08	TCGA-EJ-5496-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:151027766_151027768delAAC	uc001ewo.2	-						CDC42SE1_uc001ewp.2_Intron	NM_001038707	NP_001033796	Q9NRR8	C42S1_HUMAN	CDC42 small effector 1						phagocytosis|regulation of cell shape|signal transduction	cytoplasm|cytoskeleton|plasma membrane	GTPase inhibitor activity				0	Lung SC(34;0.00471)|Ovarian(49;0.0167)|all_hematologic(923;0.0597)|Hepatocellular(266;0.0997)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.0486)|LUSC - Lung squamous cell carcinoma(543;0.211)			GCAAAGCTGGAACAACAAAAGCA	0.473													3	4	---	---	---	---	
USH2A	7399	broad.mit.edu	37	1	215916729	215916730	+	Intron	DEL	TG	-	-	rs6540907		TCGA-EJ-5496-01A-01D-1576-08	TCGA-EJ-5496-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:215916729_215916730delTG	uc001hku.1	-							NM_206933	NP_996816	O75445	USH2A_HUMAN	usherin isoform B						maintenance of organ identity|photoreceptor cell maintenance|response to stimulus|sensory perception of sound	basement membrane|cytoplasm|integral to membrane|stereocilium membrane	collagen binding			ovary(20)|upper_aerodigestive_tract(2)|skin(2)|kidney(1)|central_nervous_system(1)	26				OV - Ovarian serous cystadenocarcinoma(81;0.0547)|all cancers(67;0.0875)		tatatatatatgtgtgtgtgtg	0.178										HNSCC(13;0.011)			5	3	---	---	---	---	
TTC13	79573	broad.mit.edu	37	1	231052139	231052139	+	Intron	DEL	T	-	-			TCGA-EJ-5496-01A-01D-1576-08	TCGA-EJ-5496-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:231052139delT	uc001huf.3	-						TTC13_uc009xfi.2_Intron|TTC13_uc009xfj.2_Intron|TTC13_uc001hug.3_Intron|TTC13_uc009xfk.1_Intron	NM_024525	NP_078801	Q8NBP0	TTC13_HUMAN	tetratricopeptide repeat domain 13 isoform a								binding			ovary(1)|skin(1)	2	Breast(184;0.0871)|Ovarian(103;0.183)	Prostate(94;0.167)		COAD - Colon adenocarcinoma(196;0.243)		ACCTTACATGTTTTTAAAAAG	0.458													63	11	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	112645772	112645773	+	IGR	DEL	AG	-	-			TCGA-EJ-5496-01A-01D-1576-08	TCGA-EJ-5496-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:112645772_112645773delAG								ANAPC1 (4031 upstream) : MERTK (10418 downstream)																							ttttttttttagtttttttttt	0.183													4	3	---	---	---	---	
CCDC148	130940	broad.mit.edu	37	2	159195423	159195423	+	Intron	DEL	A	-	-			TCGA-EJ-5496-01A-01D-1576-08	TCGA-EJ-5496-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:159195423delA	uc002tzq.2	-						CCDC148_uc002tzr.2_Intron|CCDC148_uc010foh.2_Intron|CCDC148_uc010foi.1_Intron|CCDC148_uc010foj.1_Intron|CCDC148_uc010fok.1_Intron|CCDC148_uc002tzs.1_Intron	NM_138803	NP_620158	Q8NFR7	CC148_HUMAN	coiled-coil domain containing 148											ovary(2)	2						CTAGAATCTGAAAAAAAGTAT	0.313													147	27	---	---	---	---	
SUMF1	285362	broad.mit.edu	37	3	4452827	4452827	+	Intron	DEL	T	-	-	rs72240947		TCGA-EJ-5496-01A-01D-1576-08	TCGA-EJ-5496-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:4452827delT	uc003bpz.1	-						SUMF1_uc003bps.1_Intron|SUMF1_uc011ass.1_Intron|SUMF1_uc010hby.1_Intron|SUMF1_uc011ast.1_Intron	NM_182760	NP_877437	Q8NBK3	SUMF1_HUMAN	sulfatase modifying factor 1 isoform 1							endoplasmic reticulum lumen	metal ion binding|oxidoreductase activity			upper_aerodigestive_tract(1)	1		Melanoma(143;0.068)|Colorectal(144;0.233)		Epithelial(13;0.0147)|OV - Ovarian serous cystadenocarcinoma(96;0.0444)|all cancers(10;0.0549)		GAAAGGGGCATTTTTTTTTTG	0.328													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	42019054	42019055	+	IGR	INS	-	T	T			TCGA-EJ-5496-01A-01D-1576-08	TCGA-EJ-5496-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:42019054_42019055insT								ULK4 (15394 upstream) : TRAK1 (113691 downstream)																							AAGTGTTAATATTTTTCTTTCA	0.282													36	13	---	---	---	---	
CDC25A	993	broad.mit.edu	37	3	48228060	48228060	+	Intron	DEL	A	-	-			TCGA-EJ-5496-01A-01D-1576-08	TCGA-EJ-5496-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:48228060delA	uc003csh.1	-						CDC25A_uc003csi.1_Intron	NM_001789	NP_001780	P30304	MPIP1_HUMAN	cell division cycle 25A isoform a						cell cycle checkpoint|cell division|cell proliferation|cellular response to UV|DNA replication|G1/S transition of mitotic cell cycle|G2/M transition of mitotic cell cycle|mitosis|regulation of cyclin-dependent protein kinase activity|S phase of mitotic cell cycle	cytosol|nucleoplasm	protein binding|protein tyrosine phosphatase activity			lung(3)|kidney(1)|skin(1)	5				BRCA - Breast invasive adenocarcinoma(193;0.000685)|KIRC - Kidney renal clear cell carcinoma(197;0.00596)|Kidney(197;0.00684)		actctgtctcaaaaaaaaaaa	0.179													4	2	---	---	---	---	
FLJ39653	202020	broad.mit.edu	37	4	16257859	16257860	+	Intron	INS	-	T	T	rs146274448		TCGA-EJ-5496-01A-01D-1576-08	TCGA-EJ-5496-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:16257859_16257860insT	uc011bxf.1	+						FLJ39653_uc011bxg.1_Intron	NR_027696				RecName: Full=Uncharacterized protein FLJ39653;												0						GAGGGTTTGTCTTTTTTTTTTT	0.381													5	3	---	---	---	---	
CBR4	84869	broad.mit.edu	37	4	169911112	169911113	+	3'UTR	INS	-	A	A			TCGA-EJ-5496-01A-01D-1576-08	TCGA-EJ-5496-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:169911112_169911113insA	uc003iry.2	-	5					CBR4_uc011cjy.1_Intron	NM_032783	NP_116172	Q8N4T8	CBR4_HUMAN	carbonic reductase 4						fatty acid biosynthetic process|protein homotetramerization	mitochondrial matrix	NADPH binding|NADPH dehydrogenase (quinone) activity|protein binding|quinone binding				0		Prostate(90;0.00263)|Renal(120;0.0183)|Melanoma(52;0.123)		GBM - Glioblastoma multiforme(119;0.0321)		TAACTTAGACCAAAAAAAAAAA	0.188													6	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	6571881	6571884	+	IGR	DEL	GAAG	-	-			TCGA-EJ-5496-01A-01D-1576-08	TCGA-EJ-5496-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:6571881_6571884delGAAG								UBE2QL1 (79176 upstream) : LOC255167 (10403 downstream)																							agggaggagagaaggaaggaagga	0.000													3	4	---	---	---	---	
IPO11	51194	broad.mit.edu	37	5	61763288	61763290	+	Intron	DEL	ATA	-	-	rs143944846		TCGA-EJ-5496-01A-01D-1576-08	TCGA-EJ-5496-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:61763288_61763290delATA	uc003jtc.2	+						IPO11_uc011cqr.1_Intron|IPO11_uc003jtb.1_Intron	NM_016338	NP_057422	Q9UI26	IPO11_HUMAN	Ran binding protein 11 isoform 2							cytoplasm|nucleus	protein binding			lung(2)|skin(2)	4		Lung NSC(810;8.99e-06)|Prostate(74;0.0235)|Ovarian(174;0.0511)|Breast(144;0.077)		Lung(70;0.0613)		GAAAGCACATATAATAAGTTGAA	0.330													5	7	---	---	---	---	
GPR98	84059	broad.mit.edu	37	5	90051084	90051085	+	Intron	INS	-	TCT	TCT	rs147653625	by1000genomes	TCGA-EJ-5496-01A-01D-1576-08	TCGA-EJ-5496-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:90051084_90051085insTCT	uc003kju.2	+						GPR98_uc003kjt.2_Intron|GPR98_uc003kjv.2_Intron	NM_032119	NP_115495	Q8WXG9	GPR98_HUMAN	G protein-coupled receptor 98 precursor						cell communication|cell-cell adhesion|maintenance of organ identity|neuropeptide signaling pathway|photoreceptor cell maintenance	cell surface|cytoplasm|integral to membrane|plasma membrane	calcium ion binding|G-protein coupled receptor activity			ovary(11)|central_nervous_system(3)|pancreas(2)	16		all_cancers(142;1.05e-09)|all_epithelial(76;1.81e-12)|all_lung(232;5.41e-06)|Lung NSC(167;1.72e-05)|Ovarian(174;0.00948)|Colorectal(57;0.133)|Breast(839;0.192)		OV - Ovarian serous cystadenocarcinoma(54;7.01e-30)|Epithelial(54;6.79e-25)|all cancers(79;1.88e-20)		GTAAGTAAAAATCTTTTTTTTA	0.282													7	4	---	---	---	---	
FGF18	8817	broad.mit.edu	37	5	170876405	170876410	+	Intron	DEL	GAGAGA	-	-	rs56932885	by1000genomes	TCGA-EJ-5496-01A-01D-1576-08	TCGA-EJ-5496-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:170876405_170876410delGAGAGA	uc003mbk.2	+							NM_003862	NP_003853	O76093	FGF18_HUMAN	fibroblast growth factor 18 precursor						cell-cell signaling|fibroblast growth factor receptor signaling pathway|insulin receptor signaling pathway|positive regulation of cell proliferation	extracellular space|nucleolus	growth factor activity|type 1 fibroblast growth factor receptor binding|type 2 fibroblast growth factor receptor binding				0	Renal(175;0.000159)|Lung NSC(126;0.011)|all_lung(126;0.0175)	Medulloblastoma(196;0.0208)|all_neural(177;0.0416)	Kidney(164;7.24e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000516)			gtgtgtgtgtgagagagagagagaga	0.325													4	2	---	---	---	---	
HLA-G	3135	broad.mit.edu	37	6	29841217	29841217	+	Intron	DEL	T	-	-	rs111432584		TCGA-EJ-5496-01A-01D-1576-08	TCGA-EJ-5496-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:29841217delT	uc011dmb.1	+							NM_002127	NP_002118	P17693	HLAG_HUMAN	major histocompatibility complex, class I, G						antigen processing and presentation of peptide antigen via MHC class I|cellular defense response|interferon-gamma-mediated signaling pathway|regulation of immune response|type I interferon-mediated signaling pathway	integral to membrane|MHC class I protein complex	MHC class I receptor activity			ovary(3)|central_nervous_system(1)	4						gaagttttgattagtatgtgc	0.000													4	3	---	---	---	---	
RBM16	22828	broad.mit.edu	37	6	155131500	155131502	+	Intron	DEL	AGA	-	-	rs66974158		TCGA-EJ-5496-01A-01D-1576-08	TCGA-EJ-5496-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:155131500_155131502delAGA	uc003qqa.2	+						RBM16_uc011efj.1_Intron|RBM16_uc011efk.1_Intron|RBM16_uc003qpz.2_Intron|RBM16_uc010kji.2_Intron	NM_014892	NP_055707	Q9UPN6	SCAF8_HUMAN	RNA-binding motif protein 16						mRNA processing|RNA splicing	nuclear matrix|spliceosomal complex	nucleotide binding|RNA binding|RNA polymerase core enzyme binding				0		Ovarian(120;0.196)		OV - Ovarian serous cystadenocarcinoma(155;2.33e-15)|BRCA - Breast invasive adenocarcinoma(81;0.00524)		GATAGAGAAGAGAAGAAGAAGGA	0.320													3	3	---	---	---	---	
BMPER	168667	broad.mit.edu	37	7	33977125	33977126	+	Intron	INS	-	GTGT	GTGT			TCGA-EJ-5496-01A-01D-1576-08	TCGA-EJ-5496-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:33977125_33977126insGTGT	uc011kap.1	+							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						GGAGAAGTAGGgtgtgtgtgtg	0.391													9	4	---	---	---	---	
GLI3	2737	broad.mit.edu	37	7	42017541	42017541	+	Intron	DEL	T	-	-	rs68006817		TCGA-EJ-5496-01A-01D-1576-08	TCGA-EJ-5496-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:42017541delT	uc011kbh.1	-						GLI3_uc011kbg.1_Intron	NM_000168	NP_000159	P10071	GLI3_HUMAN	GLI-Kruppel family member GLI3						negative regulation of alpha-beta T cell differentiation|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of smoothened signaling pathway|negative regulation of transcription from RNA polymerase II promoter|negative thymic T cell selection|positive regulation of alpha-beta T cell differentiation|positive regulation of transcription from RNA polymerase II promoter|thymocyte apoptosis	cilium|cytosol|nucleolus	beta-catenin binding|histone acetyltransferase binding|histone deacetylase binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			lung(11)|ovary(3)|large_intestine(2)|central_nervous_system(1)|kidney(1)|pancreas(1)	19						AGTCCTGAAGTTTTTTTTTTT	0.373									Greig_Cephalopolysyndactyly|Pallister-Hall_syndrome		OREG0018015	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	2	5	---	---	---	---	
GCK	2645	broad.mit.edu	37	7	44184604	44184605	+	3'UTR	INS	-	G	G	rs139354711	by1000genomes	TCGA-EJ-5496-01A-01D-1576-08	TCGA-EJ-5496-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:44184604_44184605insG	uc003tkl.2	-	10					GCK_uc003tkh.1_3'UTR|GCK_uc003tki.1_3'UTR|GCK_uc003tkj.1_3'UTR|GCK_uc003tkk.1_3'UTR	NM_000162	NP_000153	P35557	HXK4_HUMAN	glucokinase isoform 1						cellular response to insulin stimulus|cellular response to leptin stimulus|detection of glucose|endocrine pancreas development|glucose homeostasis|glucose transport|glycolysis|negative regulation of gluconeogenesis|positive regulation of glycogen biosynthetic process|positive regulation of insulin secretion|regulation of glucose transport|regulation of glycolysis|transmembrane transport	cytosol|nucleoplasm	ATP binding|glucokinase activity|glucose binding|protein binding			skin(3)|lung(1)	4						GCGGTATGGCAGGCGGCCTGGG	0.683													8	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	55659699	55659699	+	IGR	DEL	C	-	-	rs140374894		TCGA-EJ-5496-01A-01D-1576-08	TCGA-EJ-5496-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:55659699delC								VOPP1 (19499 upstream) : LOC442308 (53613 downstream)																							CTCAGCTGCACCCCCCCTCTT	0.587													9	4	---	---	---	---	
RFC2	5982	broad.mit.edu	37	7	73271842	73271843	+	Intron	INS	-	T	T			TCGA-EJ-5496-01A-01D-1576-08	TCGA-EJ-5496-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:73271842_73271843insT	uc011kfa.1	-							NM_181471		P35250	RFC2_HUMAN	replication factor C 2 isoform 1						cell cycle checkpoint|DNA strand elongation involved in DNA replication|nucleotide-excision repair, DNA gap filling|S phase of mitotic cell cycle|telomere maintenance via recombination|telomere maintenance via semi-conservative replication|transcription-coupled nucleotide-excision repair	DNA replication factor C complex|nucleoplasm	ATP binding|DNA clamp loader activity|protein binding			liver(1)|central_nervous_system(1)	2						tccttccCttcttttttttttt	0.069													3	4	---	---	---	---	
PDK4	5166	broad.mit.edu	37	7	95219250	95219251	+	Intron	INS	-	T	T			TCGA-EJ-5496-01A-01D-1576-08	TCGA-EJ-5496-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:95219250_95219251insT	uc003uoa.2	-						PDK4_uc003unz.2_Intron	NM_002612	NP_002603	Q16654	PDK4_HUMAN	pyruvate dehydrogenase kinase 4 precursor						glucose metabolic process|peptidyl-histidine phosphorylation|pyruvate metabolic process|regulation of acetyl-CoA biosynthetic process from pyruvate	mitochondrial matrix	ATP binding|pyruvate dehydrogenase (acetyl-transferring) kinase activity|two-component sensor activity				0	all_cancers(62;1.06e-10)|all_epithelial(64;1.04e-09)|Lung NSC(181;0.128)|all_lung(186;0.151)		STAD - Stomach adenocarcinoma(171;0.0151)			TTTGTTAATTGTTTTttttttg	0.163													4	3	---	---	---	---	
SLC39A14	23516	broad.mit.edu	37	8	22261976	22261976	+	Intron	DEL	T	-	-	rs66462303		TCGA-EJ-5496-01A-01D-1576-08	TCGA-EJ-5496-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:22261976delT	uc003xbq.3	+						SLC39A14_uc011kzg.1_Intron|SLC39A14_uc003xbp.3_Intron|SLC39A14_uc011kzh.1_Intron	NM_001128431	NP_001121903	Q15043	S39AE_HUMAN	solute carrier family 39 (zinc transporter),							endoplasmic reticulum|Golgi apparatus|integral to membrane|lamellipodium|plasma membrane	zinc ion transmembrane transporter activity				0				Colorectal(74;0.019)|COAD - Colon adenocarcinoma(73;0.0731)		TTGCTGTTTGTTTTTTTTTTT	0.179													5	3	---	---	---	---	
NSMCE2	286053	broad.mit.edu	37	8	126378766	126378766	+	Intron	DEL	A	-	-	rs79862437		TCGA-EJ-5496-01A-01D-1576-08	TCGA-EJ-5496-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:126378766delA	uc003yrw.2	+							NM_173685	NP_775956	Q96MF7	NSE2_HUMAN	non-SMC element 2, MMS21 homolog						DNA recombination|DNA repair	nucleus	ligase activity|zinc ion binding			breast(1)	1	Ovarian(258;0.0028)|all_neural(195;0.00294)|Hepatocellular(40;0.108)		STAD - Stomach adenocarcinoma(47;0.000918)			tccgtctcagaaaaaaaaaag	0.000													4	2	---	---	---	---	
FAM135B	51059	broad.mit.edu	37	8	139207744	139207748	+	Intron	DEL	TGGAC	-	-	rs71956584		TCGA-EJ-5496-01A-01D-1576-08	TCGA-EJ-5496-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:139207744_139207748delTGGAC	uc003yuy.2	-						FAM135B_uc003yux.2_Intron|FAM135B_uc003yuz.2_Intron	NM_015912	NP_056996	Q49AJ0	F135B_HUMAN	hypothetical protein LOC51059											ovary(7)|skin(2)	9	all_epithelial(106;8.29e-14)|Lung NSC(106;6.88e-06)|all_lung(105;1.44e-05)|Ovarian(258;0.00672)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0805)			ATTGGAGCCATGGACTGGACTGAGC	0.444										HNSCC(54;0.14)			9	4	---	---	---	---	
TRUB2	26995	broad.mit.edu	37	9	131075834	131075834	+	Intron	DEL	G	-	-			TCGA-EJ-5496-01A-01D-1576-08	TCGA-EJ-5496-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:131075834delG	uc004buq.1	-							NM_015679	NP_056494	O95900	TRUB2_HUMAN	TruB pseudouridine (psi) synthase homolog 2						pseudouridine synthesis|tRNA processing		pseudouridine synthase activity|RNA binding			ovary(1)	1						aaaaaaaaaagaaaagaaaaG	0.209													7	4	---	---	---	---	
ASS1	445	broad.mit.edu	37	9	133333546	133333546	+	Intron	DEL	A	-	-	rs5900899		TCGA-EJ-5496-01A-01D-1576-08	TCGA-EJ-5496-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:133333546delA	uc004bzm.2	+						ASS1_uc004bzn.2_Intron|ASS1_uc010mza.2_Intron|ASS1_uc004bzo.2_Intron|ASS1_uc010mzb.2_Intron|ASS1_uc004bzp.2_Intron|ASS1_uc010mzc.2_Intron	NM_000050	NP_000041	P00966	ASSY_HUMAN	argininosuccinate synthetase 1						arginine biosynthetic process|urea cycle	cytosol	argininosuccinate synthase activity|ATP binding|protein binding			ovary(1)	1				OV - Ovarian serous cystadenocarcinoma(145;0.000514)	Adenosine triphosphate(DB00171)|L-Arginine(DB00125)|L-Aspartic Acid(DB00128)|L-Citrulline(DB00155)	acttcgactcaaaaaaaaaaa	0.184													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	54148810	54148810	+	IGR	DEL	T	-	-	rs78612093		TCGA-EJ-5496-01A-01D-1576-08	TCGA-EJ-5496-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:54148810delT								DKK1 (71394 upstream) : MBL2 (376331 downstream)																							CCTTCTTGTCTTTTTTTTTTT	0.303													4	2	---	---	---	---	
PI4K2A	55361	broad.mit.edu	37	10	99402622	99402623	+	Intron	INS	-	TC	TC	rs10688390		TCGA-EJ-5496-01A-01D-1576-08	TCGA-EJ-5496-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:99402622_99402623insTC	uc001kog.1	+						PI4K2A_uc010qoy.1_Intron	NM_018425	NP_060895	Q9BTU6	P4K2A_HUMAN	phosphatidylinositol 4-kinase type 2 alpha						phosphatidylinositol biosynthetic process	cytoplasm|integral to plasma membrane|membrane raft	1-phosphatidylinositol 4-kinase activity|ATP binding|magnesium ion binding			lung(1)|skin(1)	2		Colorectal(252;0.162)		Epithelial(162;1.24e-10)|all cancers(201;1.2e-08)		ctttctttctttttctttcttt	0.084													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	49104713	49104713	+	IGR	DEL	C	-	-	rs149147831		TCGA-EJ-5496-01A-01D-1576-08	TCGA-EJ-5496-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:49104713delC								OR4A47 (593441 upstream) : FOLH1 (63475 downstream)																							tttcttCCTTCCCCCCGCAAA	0.428													8	7	---	---	---	---	
CSDA	8531	broad.mit.edu	37	12	10854208	10854208	+	Intron	DEL	A	-	-	rs3214857		TCGA-EJ-5496-01A-01D-1576-08	TCGA-EJ-5496-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:10854208delA	uc001qyt.2	-						CSDA_uc001qyu.2_Intron	NM_003651	NP_003642	P16989	DBPA_HUMAN	cold shock domain protein A isoform a						negative regulation of transcription from RNA polymerase II promoter|response to cold	cytoplasm|nucleus	double-stranded DNA binding|sequence-specific DNA binding transcription factor activity|transcription corepressor activity			ovary(2)|lung(1)|large_intestine(1)	4	Glioma(1;0.155)					AACAGCTTACAAAACGGCAAC	0.294													3	3	---	---	---	---	
STAT2	6773	broad.mit.edu	37	12	56745447	56745451	+	Intron	DEL	GATTT	-	-			TCGA-EJ-5496-01A-01D-1576-08	TCGA-EJ-5496-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:56745447_56745451delGATTT	uc001slc.2	-						STAT2_uc001slb.2_5'Flank|STAT2_uc001sld.2_Intron|STAT2_uc010sqn.1_Intron	NM_005419	NP_005410	P52630	STAT2_HUMAN	signal transducer and activator of transcription						interspecies interaction between organisms|JAK-STAT cascade|regulation of transcription from RNA polymerase II promoter|regulation of type I interferon-mediated signaling pathway|response to virus|type I interferon-mediated signaling pathway	cytosol|nucleoplasm|plasma membrane	calcium ion binding|DNA binding|protein binding|sequence-specific DNA binding transcription factor activity|signal transducer activity			ovary(1)|lung(1)|kidney(1)	3						ACTGCtaatagatttaacataacag	0.122													5	4	---	---	---	---	
TXNRD1	7296	broad.mit.edu	37	12	104661425	104661426	+	Intron	INS	-	TCTTTCTT	TCTTTCTT	rs12424869	by1000genomes	TCGA-EJ-5496-01A-01D-1576-08	TCGA-EJ-5496-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:104661425_104661426insTCTTTCTT	uc010swk.1	+							NM_001093771	NP_001087240	Q16881	TRXR1_HUMAN	thioredoxin reductase 1 isoform 3						cell redox homeostasis|cellular lipid metabolic process|electron transport chain|nucleobase, nucleoside and nucleotide interconversion|signal transduction|transport	cytosol|nucleolus	electron carrier activity|flavin adenine dinucleotide binding|NADP binding|protein disulfide oxidoreductase activity|thioredoxin-disulfide reductase activity				0						ATGTGATGGTAtctttctttct	0.218													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	77402068	77402071	+	IGR	DEL	GGAA	-	-			TCGA-EJ-5496-01A-01D-1576-08	TCGA-EJ-5496-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:77402068_77402071delGGAA								LMO7 (968064 upstream) : KCTD12 (52233 downstream)																							gggggaggggggaaggaaggaagg	0.152													4	2	---	---	---	---	
LRFN5	145581	broad.mit.edu	37	14	42277638	42277639	+	Intron	INS	-	GAGG	GAGG	rs142271830	by1000genomes	TCGA-EJ-5496-01A-01D-1576-08	TCGA-EJ-5496-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:42277638_42277639insGAGG	uc001wvm.2	+						LRFN5_uc010ana.2_Intron	NM_152447	NP_689660	Q96NI6	LRFN5_HUMAN	leucine rich repeat and fibronectin type III							integral to membrane				ovary(5)|pancreas(2)|central_nervous_system(1)	8			LUAD - Lung adenocarcinoma(50;0.0223)|Lung(238;0.0728)	GBM - Glioblastoma multiforme(112;0.00847)		aaggaagaatcgagggagggag	0.099										HNSCC(30;0.082)			4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	56014150	56014151	+	IGR	INS	-	A	A			TCGA-EJ-5496-01A-01D-1576-08	TCGA-EJ-5496-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:56014150_56014151insA								TBPL2 (106887 upstream) : C14orf33 (10539 downstream)																							aacactgtctcaaaaaaaaaaa	0.178													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	28751704	28751705	+	IGR	INS	-	T	T			TCGA-EJ-5496-01A-01D-1576-08	TCGA-EJ-5496-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:28751704_28751705insT								GOLGA8G (114533 upstream) : WHAMML2 (231024 downstream)																							AGTCTCTGAGGTTTTTTTTTTC	0.292													36	13	---	---	---	---	
PPCDC	60490	broad.mit.edu	37	15	75315289	75315289	+	5'Flank	DEL	A	-	-			TCGA-EJ-5496-01A-01D-1576-08	TCGA-EJ-5496-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:75315289delA	uc002azo.2	+							NM_021823	NP_068595	Q96CD2	COAC_HUMAN	phosphopantothenoylcysteine decarboxylase						coenzyme A biosynthetic process|pantothenate metabolic process	cytosol	phosphopantothenoylcysteine decarboxylase activity				0						accctgtctcaaaaaaaaaaa	0.169													9	4	---	---	---	---	
NPW	283869	broad.mit.edu	37	16	2070327	2070328	+	Intron	INS	-	A	A	rs148115495	by1000genomes	TCGA-EJ-5496-01A-01D-1576-08	TCGA-EJ-5496-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:2070327_2070328insA	uc002coh.3	+							NM_001099456	NP_001092926	Q8N729	NPW_HUMAN	neuropeptide W preproprotein						feeding behavior|neuropeptide signaling pathway	extracellular region					0						CGTGAGAGGGGAGAGGCCTGGA	0.738													3	3	---	---	---	---	
PARN	5073	broad.mit.edu	37	16	14700252	14700252	+	Intron	DEL	G	-	-	rs62037478		TCGA-EJ-5496-01A-01D-1576-08	TCGA-EJ-5496-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:14700252delG	uc010uzd.1	-						PARN_uc010uzc.1_Intron|PARN_uc010uze.1_Intron|PARN_uc010uzf.1_Intron|PARN_uc010uzg.1_Intron	NM_002582	NP_002573	O95453	PARN_HUMAN	poly(A)-specific ribonuclease (deadenylation						female gamete generation|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay|nuclear-transcribed mRNA poly(A) tail shortening|RNA modification	cytosol|nucleolus	metal ion binding|mRNA 3'-UTR binding|nucleotide binding|poly(A)-specific ribonuclease activity|protein binding			ovary(2)	2						aagaccctgagggaaaaaaaa	0.139													5	3	---	---	---	---	
HSDL1	83693	broad.mit.edu	37	16	84165089	84165092	+	Intron	DEL	TCTA	-	-	rs36192181	by1000genomes	TCGA-EJ-5496-01A-01D-1576-08	TCGA-EJ-5496-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:84165089_84165092delTCTA	uc002fhk.2	-						HSDL1_uc010vnv.1_Intron	NM_031463	NP_113651	Q3SXM5	HSDL1_HUMAN	hydroxysteroid dehydrogenase like 1 isoform a							mitochondrion	oxidoreductase activity|protein binding				0						ACAGTTTCAGtctatctatctatc	0.206													5	5	---	---	---	---	
CHRNB1	1140	broad.mit.edu	37	17	7359369	7359380	+	Intron	DEL	TTTTTTTTTTTT	-	-	rs67180661		TCGA-EJ-5496-01A-01D-1576-08	TCGA-EJ-5496-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:7359369_7359380delTTTTTTTTTTTT	uc002ghb.2	+						CHRNB1_uc010vty.1_Intron	NM_000747	NP_000738	P11230	ACHB_HUMAN	nicotinic acetylcholine receptor beta 1 subunit						behavioral response to nicotine|muscle contraction|muscle fiber development|neuromuscular synaptic transmission|postsynaptic membrane organization|regulation of membrane potential|synaptic transmission, cholinergic	cell junction|nicotinic acetylcholine-gated receptor-channel complex|postsynaptic membrane	acetylcholine binding|receptor activity			ovary(2)	2		Prostate(122;0.157)				tttttttggctttttttttttttttttttttt	0.241													10	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	15737072	15737073	+	IGR	INS	-	TTTA	TTTA	rs71838018		TCGA-EJ-5496-01A-01D-1576-08	TCGA-EJ-5496-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:15737072_15737073insTTTA								MEIS3P1 (44055 upstream) : ADORA2B (111158 downstream)																							CTCTATCCTGCTTTATCTTGGA	0.460													5	3	---	---	---	---	
CCDC144A	9720	broad.mit.edu	37	17	16649585	16649585	+	Intron	DEL	C	-	-			TCGA-EJ-5496-01A-01D-1576-08	TCGA-EJ-5496-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:16649585delC	uc002gqk.1	+						CCDC144A_uc002gql.1_Intron|LOC162632_uc010cpj.1_Intron	NM_014695	NP_055510	A2RUR9	C144A_HUMAN	coiled-coil domain containing 144A												0						ctctctctctctttttttttt	0.109													6	3	---	---	---	---	
GAA	2548	broad.mit.edu	37	17	78084941	78084941	+	Intron	DEL	C	-	-	rs12945868	by1000genomes	TCGA-EJ-5496-01A-01D-1576-08	TCGA-EJ-5496-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:78084941delC	uc002jxo.2	+						GAA_uc002jxp.2_Intron|GAA_uc002jxq.2_Intron	NM_001079803	NP_001073271	P10253	LYAG_HUMAN	acid alpha-glucosidase preproprotein						cardiac muscle contraction|diaphragm contraction|glycogen catabolic process|lysosome organization|tongue morphogenesis|vacuolar sequestering|ventricular cardiac muscle tissue morphogenesis	lysosomal membrane	carbohydrate binding|maltose alpha-glucosidase activity			ovary(1)	1	all_neural(118;0.117)		OV - Ovarian serous cystadenocarcinoma(97;0.0292)|BRCA - Breast invasive adenocarcinoma(99;0.139)		Acarbose(DB00284)	GGGAAAGGGGCGGGGGGGGGA	0.632													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	35660163	35660166	+	IGR	DEL	CTTC	-	-			TCGA-EJ-5496-01A-01D-1576-08	TCGA-EJ-5496-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:35660163_35660166delCTTC								CELF4 (514163 upstream) : None (None downstream)																							ttcttcttttcttccttccttcct	0.265													6	3	---	---	---	---	
KIAA1632	57724	broad.mit.edu	37	18	43432246	43432247	+	3'UTR	DEL	AC	-	-			TCGA-EJ-5496-01A-01D-1576-08	TCGA-EJ-5496-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:43432246_43432247delAC	uc002lbm.2	-	44						NM_020964	NP_066015	Q9HCE0	EPG5_HUMAN	hypothetical protein LOC57724						autophagy						0						AGCTAAGAAAacacacacacac	0.356													6	3	---	---	---	---	
NCLN	56926	broad.mit.edu	37	19	3192359	3192364	+	Intron	DEL	GGGCTG	-	-	rs11278022		TCGA-EJ-5496-01A-01D-1576-08	TCGA-EJ-5496-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:3192359_3192364delGGGCTG	uc002lxi.2	+						NCLN_uc002lxh.1_Intron	NM_020170	NP_064555	Q969V3	NCLN_HUMAN	nicalin precursor						proteolysis|regulation of signal transduction	endoplasmic reticulum membrane|integral to membrane|nucleus	peptidase activity|protein binding				0		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.83e-113)|Epithelial(107;1.65e-111)|all cancers(105;1.53e-103)|BRCA - Breast invasive adenocarcinoma(158;0.00139)|STAD - Stomach adenocarcinoma(1328;0.18)		TCCAGGTTGTgggctggggctggggc	0.612													6	5	---	---	---	---	
ZNF333	84449	broad.mit.edu	37	19	14810277	14810278	+	Intron	INS	-	T	T			TCGA-EJ-5496-01A-01D-1576-08	TCGA-EJ-5496-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:14810277_14810278insT	uc002mzn.2	+						ZNF333_uc010dzq.2_Intron|ZNF333_uc002mzk.3_Intron|ZNF333_uc002mzl.3_Intron|ZNF333_uc002mzm.2_Intron|ZNF333_uc010dzr.1_Intron	NM_032433	NP_115809	Q96JL9	ZN333_HUMAN	zinc finger protein 333						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)|central_nervous_system(1)|pancreas(1)	3						TTGCTCAAGACttttttttttt	0.257													6	3	---	---	---	---	
C19orf44	84167	broad.mit.edu	37	19	16625197	16625198	+	Intron	INS	-	A	A	rs76201706		TCGA-EJ-5496-01A-01D-1576-08	TCGA-EJ-5496-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:16625197_16625198insA	uc002neh.1	+						MED26_uc002nee.2_Intron|C19orf44_uc002neg.2_Intron|C19orf44_uc010eai.1_Intron	NM_032207	NP_115583	Q9H6X5	CS044_HUMAN	hypothetical protein LOC84167												0						cctgtctccagaaaaaaaaaaa	0.282													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	27738491	27738491	+	IGR	DEL	T	-	-			TCGA-EJ-5496-01A-01D-1576-08	TCGA-EJ-5496-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:27738491delT								None (None upstream) : LOC148189 (542911 downstream)																							tggaaacgggtttttttcatg	0.000													111	8	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	42107414	42107415	+	IGR	DEL	CA	-	-	rs72172011		TCGA-EJ-5496-01A-01D-1576-08	TCGA-EJ-5496-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:42107414_42107415delCA								CEACAM21 (14218 upstream) : CEACAM4 (17929 downstream)																							Gacacgcacgcacgcgcgcgcg	0.183													2	4	---	---	---	---	
PHLDB3	653583	broad.mit.edu	37	19	43999307	43999308	+	Intron	INS	-	A	A	rs148094242	by1000genomes	TCGA-EJ-5496-01A-01D-1576-08	TCGA-EJ-5496-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:43999307_43999308insA	uc002own.3	-						PHLDB3_uc010eit.2_Intron	NM_198850	NP_942147	Q6NSJ2	PHLB3_HUMAN	pleckstrin homology-like domain, family B,												0		Prostate(69;0.0153)				gagggaggaggggctagggcct	0.045													9	4	---	---	---	---	
C20orf70	140683	broad.mit.edu	37	20	31767238	31767238	+	Intron	DEL	A	-	-	rs77930653		TCGA-EJ-5496-01A-01D-1576-08	TCGA-EJ-5496-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:31767238delA	uc002wyo.1	+							NM_080574	NP_542141	Q96DR5	SPLC2_HUMAN	chromosome 20 open reading frame 70 precursor							extracellular region	lipid binding			ovary(1)|central_nervous_system(1)	2						tctgtctcagaaaaaaaaaaa	0.134													4	2	---	---	---	---	
CRYZL1	9946	broad.mit.edu	37	21	34969919	34969920	+	Intron	INS	-	CTTTA	CTTTA	rs150222858		TCGA-EJ-5496-01A-01D-1576-08	TCGA-EJ-5496-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:34969919_34969920insCTTTA	uc011adw.1	-						DONSON_uc002ysn.1_Intron|CRYZL1_uc002ysr.1_Intron|CRYZL1_uc002yss.1_Intron|CRYZL1_uc002yst.1_Intron|DONSON_uc002ysm.2_5'Flank|uc002ysp.2_5'Flank|CRYZL1_uc002ysq.2_5'Flank	NM_145858	NP_665857	O95825	QORL1_HUMAN	crystallin, zeta-like 1						quinone cofactor metabolic process	cytosol	NADP binding|NADPH:quinone reductase activity|zinc ion binding				0						gCCGGCACTCTCtttttgtttt	0.040													3	3	---	---	---	---	
SNRPD3	6634	broad.mit.edu	37	22	24967718	24967719	+	Intron	INS	-	G	G			TCGA-EJ-5496-01A-01D-1576-08	TCGA-EJ-5496-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:24967718_24967719insG	uc003aam.1	+						SNRPD3_uc011aju.1_Intron	NM_004175	NP_004166	P62318	SMD3_HUMAN	small nuclear ribonucleoprotein polypeptide D3						histone mRNA metabolic process|ncRNA metabolic process|spliceosomal snRNP assembly|termination of RNA polymerase II transcription	catalytic step 2 spliceosome|cytosol|nucleoplasm|U12-type spliceosomal complex|U7 snRNP	enzyme binding|histone pre-mRNA DCP binding			ovary(1)	1						tctcaaaaaataaaaaaaaaaa	0.257													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	448557	448568	+	IGR	DEL	GGAAGGAAGGAA	-	-			TCGA-EJ-5496-01A-01D-1576-08	TCGA-EJ-5496-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:448557_448568delGGAAGGAAGGAA								PPP2R3B (100930 upstream) : SHOX (136511 downstream)																							GAGACaggatggaaggaaggaaggaaggaagg	0.024													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	48305869	48305869	+	IGR	DEL	T	-	-			TCGA-EJ-5496-01A-01D-1576-08	TCGA-EJ-5496-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:48305869delT								SSX4 (53084 upstream) : SLC38A5 (11059 downstream)																							ATAATACCCATTTTTTTTCTG	0.353													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	Y	13483364	13483364	+	IGR	DEL	T	-	-			TCGA-EJ-5496-01A-01D-1576-08	TCGA-EJ-5496-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:13483364delT								None (None upstream) : None (None downstream)																							tctgtcacaattcccctttag	0.000													10	5	---	---	---	---	
