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
RHCE	6006	broad.mit.edu	37	1	25688867	25688867	+	3'UTR	SNP	A	C	C			TCGA-CJ-4903-01A-01D-1429-08	TCGA-CJ-4903-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:25688867A>C	uc001bkf.2	-	10					RHCE_uc001bkg.2_3'UTR|RHCE_uc001bkh.2_3'UTR|RHCE_uc001bki.2_3'UTR|RHCE_uc001bkj.2_3'UTR	NM_020485	NP_065231	P18577	RHCE_HUMAN	Rhesus blood group, CcEe antigens isoform 1							integral to plasma membrane					0		Colorectal(325;3.46e-05)|Lung NSC(340;0.000245)|all_lung(284;0.000335)|Renal(390;0.0007)|Ovarian(437;0.00473)|Breast(348;0.0101)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0936)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0426)|OV - Ovarian serous cystadenocarcinoma(117;2.12e-27)|Colorectal(126;3.16e-08)|COAD - Colon adenocarcinoma(152;1.72e-06)|STAD - Stomach adenocarcinoma(196;0.00035)|KIRC - Kidney renal clear cell carcinoma(1967;0.000769)|BRCA - Breast invasive adenocarcinoma(304;0.00101)|GBM - Glioblastoma multiforme(114;0.00458)|READ - Rectum adenocarcinoma(331;0.0649)		TTAGTCTTTAATTTTTTAATA	0.299													11	10	---	---	---	---	PASS
AK2	204	broad.mit.edu	37	1	33476353	33476353	+	3'UTR	SNP	C	T	T	rs66599471		TCGA-CJ-4903-01A-01D-1429-08	TCGA-CJ-4903-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:33476353C>T	uc001bwo.1	-	7					uc001bwn.2_Intron|AK2_uc010ohq.1_3'UTR|AK2_uc009vud.1_3'UTR	NM_013411	NP_037543	P54819	KAD2_HUMAN	adenylate kinase 2 isoform b						nucleobase, nucleoside and nucleotide interconversion	mitochondrial intermembrane space	adenylate kinase activity|ATP binding				0		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0837)				CACCCTTCCCCTCTGCCCAGC	0.552													6	29	---	---	---	---	PASS
HIVEP3	59269	broad.mit.edu	37	1	42049239	42049239	+	Silent	SNP	G	A	A			TCGA-CJ-4903-01A-01D-1429-08	TCGA-CJ-4903-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:42049239G>A	uc001cgz.3	-	4	2443	c.1230C>T	c.(1228-1230)AAC>AAT	p.N410N	HIVEP3_uc001cha.3_Silent_p.N410N|HIVEP3_uc001cgy.2_RNA	NM_024503	NP_078779	Q5T1R4	ZEP3_HUMAN	human immunodeficiency virus type I enhancer	410	Ser-rich.|No DNA binding activity or transactivation activity, but complete prevention of TRAF-dependent NF-Kappa-B activation; associates with TRAF2 and JUN (By similarity).				positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	zinc ion binding			ovary(4)|large_intestine(1)|central_nervous_system(1)	6	Ovarian(52;0.00769)|all_hematologic(146;0.109)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0367)				AGGACTTGGCGTTGGTGTTTG	0.602													52	42	---	---	---	---	PASS
F11R	50848	broad.mit.edu	37	1	160969694	160969694	+	Missense_Mutation	SNP	C	A	A			TCGA-CJ-4903-01A-01D-1429-08	TCGA-CJ-4903-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:160969694C>A	uc009wtt.2	-	6	936	c.666G>T	c.(664-666)ATG>ATT	p.M222I	F11R_uc010pjv.1_Missense_Mutation_p.M173I|F11R_uc001fxe.3_Missense_Mutation_p.M222I|F11R_uc009wtu.2_Missense_Mutation_p.M222I|F11R_uc010pjw.1_Missense_Mutation_p.M226I|F11R_uc001fxf.3_Missense_Mutation_p.M222I	NM_016946	NP_058642	Q9Y624	JAM1_HUMAN	F11 receptor precursor	222	Ig-like V-type 2.|Extracellular (Potential).				blood coagulation|inflammatory response|interspecies interaction between organisms|leukocyte migration|tight junction assembly	integral to membrane|tight junction				ovary(2)	2	all_cancers(52;6.73e-18)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.00207)			CATTTGAAGTCATGGGTGTCC	0.522													29	103	---	---	---	---	PASS
DEGS1	8560	broad.mit.edu	37	1	224377682	224377682	+	Nonsense_Mutation	SNP	G	A	A			TCGA-CJ-4903-01A-01D-1429-08	TCGA-CJ-4903-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:224377682G>A	uc001hoj.2	+	2	597	c.486G>A	c.(484-486)TGG>TGA	p.W162*	DEGS1_uc001hoi.2_Nonsense_Mutation_p.W141*	NM_144780	NP_659004	O15121	DEGS1_HUMAN	degenerative spermatocyte homolog 1, lipid	162	Helical; (Potential).				sphingolipid metabolic process|unsaturated fatty acid biosynthetic process	endoplasmic reticulum membrane|integral to plasma membrane|membrane fraction	electron carrier activity|protein binding|sphingolipid delta-4 desaturase activity				0	Breast(184;0.193)			GBM - Glioblastoma multiforme(131;0.00643)		AGTTTATATGGGTTATTCTTC	0.443													6	332	---	---	---	---	PASS
URB2	9816	broad.mit.edu	37	1	229773890	229773890	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-4903-01A-01D-1429-08	TCGA-CJ-4903-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:229773890C>T	uc001hts.1	+	4	3666	c.3530C>T	c.(3529-3531)GCA>GTA	p.A1177V	URB2_uc009xfd.1_Missense_Mutation_p.A1177V	NM_014777	NP_055592	Q14146	URB2_HUMAN	URB2 ribosome biogenesis 2 homolog	1177						nucleolus				central_nervous_system(2)|ovary(1)	3						TCTTTTCAGGCAGCCTTGCAG	0.493													40	127	---	---	---	---	PASS
PCNXL2	80003	broad.mit.edu	37	1	233150461	233150461	+	Nonsense_Mutation	SNP	G	T	T			TCGA-CJ-4903-01A-01D-1429-08	TCGA-CJ-4903-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:233150461G>T	uc001hvl.2	-	28	5137	c.4902C>A	c.(4900-4902)TGC>TGA	p.C1634*	PCNXL2_uc001hvk.1_Nonsense_Mutation_p.C286*|PCNXL2_uc001hvm.1_RNA	NM_014801	NP_055616	A6NKB5	PCX2_HUMAN	pecanex-like 2	1634						integral to membrane				central_nervous_system(1)|pancreas(1)	2		all_cancers(173;0.0347)|Prostate(94;0.137)				TCCCCAGGGTGCACAGGGCGA	0.537													22	106	---	---	---	---	PASS
RAPGEF4	11069	broad.mit.edu	37	2	173894949	173894949	+	Silent	SNP	C	T	T			TCGA-CJ-4903-01A-01D-1429-08	TCGA-CJ-4903-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:173894949C>T	uc002uhv.3	+	26	2803	c.2616C>T	c.(2614-2616)AAC>AAT	p.N872N	RAPGEF4_uc002uhw.3_Silent_p.N728N	NM_007023	NP_008954	Q8WZA2	RPGF4_HUMAN	Rap guanine nucleotide exchange factor (GEF) 4	872	Ras-GEF.				blood coagulation|energy reserve metabolic process|G-protein coupled receptor protein signaling pathway|regulation of insulin secretion|regulation of protein phosphorylation|regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cAMP-dependent protein kinase complex|membrane fraction|plasma membrane	cAMP binding|cAMP-dependent protein kinase regulator activity|Ras GTPase binding|Ras guanyl-nucleotide exchange factor activity			large_intestine(2)|skin(2)|kidney(1)|central_nervous_system(1)	6			OV - Ovarian serous cystadenocarcinoma(117;0.194)			GACTAAGTAACGTTGCTGTGA	0.443													49	106	---	---	---	---	PASS
RBM45	129831	broad.mit.edu	37	2	178990777	178990777	+	Silent	SNP	C	G	G			TCGA-CJ-4903-01A-01D-1429-08	TCGA-CJ-4903-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:178990777C>G	uc002ulv.2	+	9	1391	c.1299C>G	c.(1297-1299)GCC>GCG	p.A433A		NM_152945	NP_694453	Q8IUH3	RBM45_HUMAN	RNA binding motif protein 45	435	RRM 3.				cell differentiation|nervous system development	cytoplasm|nucleus	nucleotide binding|RNA binding				0			OV - Ovarian serous cystadenocarcinoma(117;0.00854)|Epithelial(96;0.00957)|all cancers(119;0.037)			CCAAGTATGCCGATAGAATAA	0.388													60	133	---	---	---	---	PASS
RAPH1	65059	broad.mit.edu	37	2	204305222	204305222	+	Silent	SNP	T	A	A			TCGA-CJ-4903-01A-01D-1429-08	TCGA-CJ-4903-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:204305222T>A	uc002vad.2	-	14	2916	c.2691A>T	c.(2689-2691)GCA>GCT	p.A897A		NM_213589	NP_998754	Q70E73	RAPH1_HUMAN	Ras association and pleckstrin homology domains	897					cell-matrix adhesion|signal transduction	cytoplasm|cytoskeleton|filopodium|lamellipodium|nucleus|plasma membrane				ovary(3)|breast(3)|central_nervous_system(2)|lung(1)|skin(1)	10						TTGCTTTTACTGCAGGAGGGG	0.552													69	152	---	---	---	---	PASS
VHL	7428	broad.mit.edu	37	3	10188309	10188309	+	Missense_Mutation	SNP	T	C	C			TCGA-CJ-4903-01A-01D-1429-08	TCGA-CJ-4903-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:10188309T>C	uc003bvc.2	+	2	665	c.452T>C	c.(451-453)ATC>ACC	p.I151T	VHL_uc003bvd.2_Intron	NM_000551	NP_000542	P40337	VHL_HUMAN	von Hippel-Lindau tumor suppressor isoform 1	151	Involved in binding to CCT complex.				anti-apoptosis|cell morphogenesis|negative regulation of cell proliferation|negative regulation of transcription from RNA polymerase II promoter|positive regulation of cell differentiation|positive regulation of transcription, DNA-dependent|protein stabilization|protein ubiquitination|proteolysis	cytosol|endoplasmic reticulum|membrane|mitochondrion|nucleus	protein binding|transcription factor binding	p.I151S(6)|p.I151T(3)|p.I151M(2)|p.I151N(2)|p.I151F(1)|p.?(1)|p.N150fs*7(1)|p.I151_T152del(1)|p.I151fs*8(1)|p.G144fs*19(1)		kidney(1273)|soft_tissue(24)|adrenal_gland(15)|large_intestine(13)|pancreas(5)|endometrium(4)|thyroid(3)|upper_aerodigestive_tract(3)|central_nervous_system(2)|lung(2)|pleura(1)|paratesticular_tissues(1)	1346				Kidney(1;0.000404)|KIRC - Kidney renal clear cell carcinoma(1;0.000569)		TTTGCCAATATCACACTGCCA	0.398		1	D|Mis|N|F|S		renal|hemangioma|pheochromocytoma	renal|hemangioma|pheochromocytoma			von_Hippel-Lindau_disease|Chuvash_Polycythemia_|Pheochromocytoma_(Adrenal)_Familial				125	126	---	---	---	---	PASS
WDR48	57599	broad.mit.edu	37	3	39108073	39108073	+	Silent	SNP	A	T	T			TCGA-CJ-4903-01A-01D-1429-08	TCGA-CJ-4903-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:39108073A>T	uc003cit.2	+	4	313	c.303A>T	c.(301-303)GTA>GTT	p.V101V	WDR48_uc011ayt.1_Silent_p.V92V|WDR48_uc011ayu.1_Silent_p.V19V|WDR48_uc011ayv.1_Intron|WDR48_uc003ciu.2_RNA	NM_020839	NP_065890	Q8TAF3	WDR48_HUMAN	WD repeat domain 48	101	WD 2.				interspecies interaction between organisms|protein deubiquitination	lysosome|nucleus	protein binding			ovary(1)|breast(1)	2				KIRC - Kidney renal clear cell carcinoma(284;0.0588)|Kidney(284;0.0738)		CAGTAAAAGTATGGAATGCAC	0.333													25	91	---	---	---	---	PASS
IMPDH2	3615	broad.mit.edu	37	3	49062375	49062375	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-4903-01A-01D-1429-08	TCGA-CJ-4903-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:49062375G>A	uc003cvt.2	-	11	1341	c.1249C>T	c.(1249-1251)CTC>TTC	p.L417F		NM_000884	NP_000875	P12268	IMDH2_HUMAN	inosine monophosphate dehydrogenase 2	417					GMP biosynthetic process|purine base metabolic process	cytosol|nucleus	IMP dehydrogenase activity|metal ion binding|nucleotide binding|protein binding			lung(1)	1				BRCA - Breast invasive adenocarcinoma(193;8.01e-05)|Kidney(197;0.00216)|KIRC - Kidney renal clear cell carcinoma(197;0.00244)	Mycophenolate mofetil(DB00688)|Mycophenolic acid(DB01024)|NADH(DB00157)	ATGGCATCGAGAGAACCCATA	0.532													5	92	---	---	---	---	PASS
PBRM1	55193	broad.mit.edu	37	3	52643360	52643360	+	Nonsense_Mutation	SNP	C	A	A			TCGA-CJ-4903-01A-01D-1429-08	TCGA-CJ-4903-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:52643360C>A	uc003des.2	-	16	2548	c.2536G>T	c.(2536-2538)GAA>TAA	p.E846*	PBRM1_uc003dex.2_RNA|PBRM1_uc003deq.2_Nonsense_Mutation_p.E846*|PBRM1_uc003der.2_Nonsense_Mutation_p.E814*|PBRM1_uc003det.2_Nonsense_Mutation_p.E861*|PBRM1_uc003deu.2_Nonsense_Mutation_p.E861*|PBRM1_uc003dev.2_RNA|PBRM1_uc003dew.2_Nonsense_Mutation_p.E846*|PBRM1_uc010hmk.1_Nonsense_Mutation_p.E846*|PBRM1_uc003dey.2_Nonsense_Mutation_p.E846*|PBRM1_uc003dez.1_Nonsense_Mutation_p.E846*|PBRM1_uc003dfb.1_Nonsense_Mutation_p.E759*|PBRM1_uc003dfa.1_Nonsense_Mutation_p.E192*|PBRM1_uc003dfc.2_Nonsense_Mutation_p.E213*	NM_181042	NP_060635	Q86U86	PB1_HUMAN	polybromo 1 isoform 4	846	Bromo 6.				chromatin remodeling|mitosis|negative regulation of cell proliferation|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nuclear chromosome	chromatin binding|DNA binding|protein binding			kidney(136)|breast(4)	140				BRCA - Breast invasive adenocarcinoma(193;1.8e-05)|Kidney(197;0.00105)|KIRC - Kidney renal clear cell carcinoma(197;0.00122)|OV - Ovarian serous cystadenocarcinoma(275;0.0613)		TCCAATACTTCAAACATATGC	0.328			Mis|N|F|S|D|O		clear cell renal carcinoma|breast								41	62	---	---	---	---	PASS
LAMP3	27074	broad.mit.edu	37	3	182871518	182871518	+	Silent	SNP	A	G	G			TCGA-CJ-4903-01A-01D-1429-08	TCGA-CJ-4903-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:182871518A>G	uc003flh.3	-	2	935	c.711T>C	c.(709-711)TGT>TGC	p.C237C		NM_014398	NP_055213	Q9UQV4	LAMP3_HUMAN	lysosomal-associated membrane protein 3	237	Lumenal (Potential).				cell proliferation	integral to membrane|lysosomal membrane				ovary(2)|central_nervous_system(1)	3	all_cancers(143;9.14e-14)|Ovarian(172;0.0355)		all cancers(12;2.91e-44)|Epithelial(37;5.52e-38)|LUSC - Lung squamous cell carcinoma(7;7.12e-25)|Lung(8;6.39e-23)|OV - Ovarian serous cystadenocarcinoma(80;4.16e-21)			CTGCTTTTATACAGAGTCTGC	0.498													60	112	---	---	---	---	PASS
D4S234E	27065	broad.mit.edu	37	4	4411393	4411393	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-4903-01A-01D-1429-08	TCGA-CJ-4903-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:4411393G>A	uc011bvz.1	+	7	1621	c.340G>A	c.(340-342)GAT>AAT	p.D114N	D4S234E_uc011bwa.1_Missense_Mutation_p.D75N|D4S234E_uc003ghz.2_Missense_Mutation_p.D114N|D4S234E_uc003gia.2_Missense_Mutation_p.D114N|D4S234E_uc003gib.2_Missense_Mutation_p.D114N	NM_014392	NP_055207	P42857	NSG1_HUMAN	brain neuron cytoplasmic protein 1	114	Lumenal (Potential).				dopamine receptor signaling pathway	Golgi membrane|integral to membrane|nucleus	dopamine receptor binding			ovary(1)	1				UCEC - Uterine corpus endometrioid carcinoma (64;0.166)		CGCCTGCCCCGATGGGTTCGT	0.597													11	69	---	---	---	---	PASS
SMARCA5	8467	broad.mit.edu	37	4	144465930	144465930	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-4903-01A-01D-1429-08	TCGA-CJ-4903-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:144465930G>A	uc003ijg.2	+	17	2675	c.2213G>A	c.(2212-2214)AGA>AAA	p.R738K		NM_003601	NP_003592	O60264	SMCA5_HUMAN	SWI/SNF-related matrix-associated	738					CenH3-containing nucleosome assembly at centromere|nucleosome positioning|regulation of transcription from RNA polymerase II promoter|transcription initiation, DNA-dependent	condensed chromosome|nucleolus|nucleoplasm|NURF complex|RSF complex	ATP binding|ATPase activity|DNA binding|helicase activity|nucleosome binding|protein binding			skin(1)	1	all_hematologic(180;0.158)					AAACGAGAAAGAAAAGCCAAC	0.393													27	101	---	---	---	---	PASS
TLR2	7097	broad.mit.edu	37	4	154625344	154625344	+	Missense_Mutation	SNP	C	A	A			TCGA-CJ-4903-01A-01D-1429-08	TCGA-CJ-4903-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:154625344C>A	uc003inq.2	+	3	1504	c.1285C>A	c.(1285-1287)CCT>ACT	p.P429T	TLR2_uc003inr.2_Missense_Mutation_p.P429T|TLR2_uc003ins.2_Missense_Mutation_p.P429T	NM_003264	NP_003255	O60603	TLR2_HUMAN	toll-like receptor 2 precursor	429	LRR 10.|Extracellular (Potential).				cellular response to diacyl bacterial lipopeptide|cellular response to lipoteichoic acid|cellular response to triacyl bacterial lipopeptide|detection of diacyl bacterial lipopeptide|detection of triacyl bacterial lipopeptide|I-kappaB phosphorylation|induction of apoptosis|inflammatory response|innate immune response|MyD88-dependent toll-like receptor signaling pathway|positive regulation of chemokine production|positive regulation of interferon-beta production|positive regulation of interleukin-12 production|positive regulation of interleukin-18 production|positive regulation of interleukin-6 production|positive regulation of interleukin-8 production|positive regulation of NF-kappaB import into nucleus|positive regulation of NF-kappaB transcription factor activity|positive regulation of nitric-oxide synthase biosynthetic process|positive regulation of toll-like receptor signaling pathway|positive regulation of transcription from RNA polymerase II promoter|positive regulation of tumor necrosis factor production|positive regulation of Wnt receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway	cytoplasm|integral to plasma membrane|Toll-like receptor 1-Toll-like receptor 2 protein complex	Gram-positive bacterial cell surface binding|lipopolysaccharide receptor activity|peptidoglycan binding|protein heterodimerization activity|transmembrane receptor activity|triacyl lipopeptide binding			ovary(1)|lung(1)|breast(1)	3	all_hematologic(180;0.093)	Renal(120;0.117)				TCATTCTATGCCTGAAACTTG	0.373													27	86	---	---	---	---	PASS
SLC6A19	340024	broad.mit.edu	37	5	1217053	1217053	+	Missense_Mutation	SNP	T	C	C			TCGA-CJ-4903-01A-01D-1429-08	TCGA-CJ-4903-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:1217053T>C	uc003jbw.3	+	8	1222	c.1166T>C	c.(1165-1167)CTC>CCC	p.L389P		NM_001003841	NP_001003841	Q695T7	S6A19_HUMAN	solute carrier family 6, member 19	389	Extracellular (Potential).				cellular nitrogen compound metabolic process	integral to plasma membrane	amino acid transmembrane transporter activity|neurotransmitter:sodium symporter activity				0	all_cancers(3;3.55e-15)|Lung NSC(6;2.89e-14)|all_lung(6;2.2e-13)|all_epithelial(6;3.75e-10)		Epithelial(17;0.000356)|all cancers(22;0.00137)|OV - Ovarian serous cystadenocarcinoma(19;0.00239)|Lung(60;0.185)			AACGCCTTCCTCTCAGAGGTA	0.662													88	151	---	---	---	---	PASS
CDH18	1016	broad.mit.edu	37	5	19612594	19612594	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-4903-01A-01D-1429-08	TCGA-CJ-4903-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:19612594C>T	uc003jgc.2	-	5	1137	c.760G>A	c.(760-762)GTC>ATC	p.V254I	CDH18_uc003jgd.2_Missense_Mutation_p.V254I|CDH18_uc011cnm.1_Missense_Mutation_p.V254I	NM_004934	NP_004925	Q13634	CAD18_HUMAN	cadherin 18, type 2 preproprotein	254	Extracellular (Potential).|Cadherin 2.				adherens junction organization|cell junction assembly|homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(5)|large_intestine(1)|skin(1)	7	Lung NSC(1;0.00734)|all_lung(1;0.0197)					GTGATGTTGACTGTTGTAGAT	0.408													61	83	---	---	---	---	PASS
MAP1B	4131	broad.mit.edu	37	5	71495395	71495395	+	Silent	SNP	G	A	A			TCGA-CJ-4903-01A-01D-1429-08	TCGA-CJ-4903-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:71495395G>A	uc003kbw.3	+	5	6454	c.6213G>A	c.(6211-6213)AAG>AAA	p.K2071K	MAP1B_uc010iyw.1_Silent_p.K2088K|MAP1B_uc010iyx.1_Silent_p.K1945K|MAP1B_uc010iyy.1_Silent_p.K1945K	NM_005909	NP_005900	P46821	MAP1B_HUMAN	microtubule-associated protein 1B	2071						microtubule|microtubule associated complex	structural molecule activity			large_intestine(2)|ovary(1)|central_nervous_system(1)|pancreas(1)	5		Lung NSC(167;0.00202)|Ovarian(174;0.0175)|Prostate(461;0.142)|Breast(144;0.198)		OV - Ovarian serous cystadenocarcinoma(47;7.99e-54)		CAGAAAAGAAGTCCCCCTCAG	0.478													92	178	---	---	---	---	PASS
PCSK1	5122	broad.mit.edu	37	5	95728885	95728885	+	Missense_Mutation	SNP	G	C	C			TCGA-CJ-4903-01A-01D-1429-08	TCGA-CJ-4903-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:95728885G>C	uc003kls.1	-	14	2288	c.2082C>G	c.(2080-2082)AAC>AAG	p.N694K	PCSK1_uc010jbi.1_Missense_Mutation_p.N384K	NM_000439	NP_000430	P29120	NEC1_HUMAN	proprotein convertase subtilisin/kexin type 1	694					cell-cell signaling|cellular nitrogen compound metabolic process|energy reserve metabolic process|hormone biosynthetic process|peptide biosynthetic process|peptide hormone processing|regulation of insulin secretion	extracellular space|stored secretory granule|transport vesicle	serine-type endopeptidase activity			ovary(2)	2		all_cancers(142;2.67e-06)|all_epithelial(76;6.92e-09)|all_lung(232;0.00307)|Lung NSC(167;0.00452)|Ovarian(225;0.0112)|Colorectal(57;0.0341)|Breast(839;0.244)		all cancers(79;3.44e-16)	Insulin Glargine recombinant(DB00047)|Insulin Lyspro recombinant(DB00046)|Insulin recombinant(DB00030)|Insulin, porcine(DB00071)	CATAAGGGATGTTGAGCTTTG	0.458													43	287	---	---	---	---	PASS
TCOF1	6949	broad.mit.edu	37	5	149755732	149755732	+	Missense_Mutation	SNP	G	C	C			TCGA-CJ-4903-01A-01D-1429-08	TCGA-CJ-4903-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:149755732G>C	uc003lry.2	+	13	2089	c.1981G>C	c.(1981-1983)GTG>CTG	p.V661L	TCOF1_uc003lrw.2_Missense_Mutation_p.V661L|TCOF1_uc011dch.1_Missense_Mutation_p.V661L|TCOF1_uc003lrz.2_Missense_Mutation_p.V661L|TCOF1_uc003lrx.2_Missense_Mutation_p.V584L|TCOF1_uc003lsa.2_Missense_Mutation_p.V584L|TCOF1_uc011dci.1_Missense_Mutation_p.V150L	NM_001135243	NP_001128715	Q13428	TCOF_HUMAN	Treacher Collins-Franceschetti syndrome 1	661					skeletal system development	nucleolus	protein binding|transporter activity			ovary(2)|large_intestine(1)	3		all_hematologic(541;0.224)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			CCCTGTGCGAGTGGGCACCCA	0.597													7	428	---	---	---	---	PASS
DST	667	broad.mit.edu	37	6	56472759	56472759	+	Intron	SNP	C	T	T			TCGA-CJ-4903-01A-01D-1429-08	TCGA-CJ-4903-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:56472759C>T	uc003pdf.2	-						DST_uc003pcz.3_Intron|DST_uc011dxj.1_Intron|DST_uc011dxk.1_Intron|DST_uc003pcy.3_Intron|DST_uc003pdb.2_Missense_Mutation_p.D1686N	NM_001144769	NP_001138241	Q03001	DYST_HUMAN	dystonin isoform 2						cell adhesion|cell cycle arrest|cell motility|hemidesmosome assembly|integrin-mediated signaling pathway|intermediate filament cytoskeleton organization|maintenance of cell polarity|microtubule cytoskeleton organization|response to wounding	actin cytoskeleton|axon|axon part|basement membrane|cell cortex|cell leading edge|cytoplasmic membrane-bounded vesicle|endoplasmic reticulum membrane|hemidesmosome|hemidesmosome|integral to membrane|intermediate filament|intermediate filament cytoskeleton|microtubule cytoskeleton|microtubule plus end|nuclear envelope|sarcomere|Z disc	actin binding|calcium ion binding|integrin binding|microtubule plus-end binding|protein binding|protein C-terminus binding|protein homodimerization activity			ovary(7)|central_nervous_system(6)|upper_aerodigestive_tract(1)	14	Lung NSC(77;0.103)		LUSC - Lung squamous cell carcinoma(124;0.0485)|Lung(124;0.0956)			AAGTCTCCATCGTACAGCAAA	0.393													20	88	---	---	---	---	PASS
MCART3P	442229	broad.mit.edu	37	6	66498794	66498794	+	RNA	SNP	C	T	T			TCGA-CJ-4903-01A-01D-1429-08	TCGA-CJ-4903-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:66498794C>T	uc011dxw.1	+	1		c.1023C>T				NR_026540				Homo sapiens mitochondrial carrier triple repeat 3 pseudogene, mRNA (cDNA clone IMAGE:4821649).												0						GCCTTCAAGGCACTGAAATGT	0.438													79	92	---	---	---	---	PASS
KLHL32	114792	broad.mit.edu	37	6	97562309	97562309	+	Missense_Mutation	SNP	G	T	T			TCGA-CJ-4903-01A-01D-1429-08	TCGA-CJ-4903-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:97562309G>T	uc010kcm.1	+	7	1750	c.1278G>T	c.(1276-1278)TGG>TGT	p.W426C	KLHL32_uc003poy.2_Missense_Mutation_p.W426C|KLHL32_uc011ead.1_Missense_Mutation_p.W390C|KLHL32_uc003poz.2_Intron|KLHL32_uc011eae.1_Missense_Mutation_p.W357C|KLHL32_uc003ppa.2_Intron	NM_052904	NP_443136	Q96NJ5	KLH32_HUMAN	kelch-like 32	426	Kelch 3.									ovary(3)|skin(1)	4		all_cancers(76;1.19e-06)|Acute lymphoblastic leukemia(125;5.83e-10)|all_hematologic(75;3.67e-07)|all_epithelial(107;0.00778)|Colorectal(196;0.122)		BRCA - Breast invasive adenocarcinoma(108;0.0558)		AGAACAAATGGACTTTTGTTC	0.468													28	131	---	---	---	---	PASS
SAMD9	54809	broad.mit.edu	37	7	92733297	92733297	+	Missense_Mutation	SNP	A	G	G			TCGA-CJ-4903-01A-01D-1429-08	TCGA-CJ-4903-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:92733297A>G	uc003umf.2	-	3	2370	c.2114T>C	c.(2113-2115)TTT>TCT	p.F705S	SAMD9_uc003umg.2_Missense_Mutation_p.F705S	NM_017654	NP_060124	Q5K651	SAMD9_HUMAN	sterile alpha motif domain containing 9	705						cytoplasm				ovary(3)|skin(2)|breast(1)|central_nervous_system(1)	7	all_cancers(62;5.71e-11)|all_epithelial(64;3.25e-10)|Breast(17;0.000675)|Lung NSC(181;0.0969)|all_lung(186;0.125)		STAD - Stomach adenocarcinoma(171;0.000302)			CCTTTTGACAAAAGGTGAAGA	0.353													130	291	---	---	---	---	PASS
SLC26A4	5172	broad.mit.edu	37	7	107315556	107315556	+	Splice_Site	SNP	T	C	C			TCGA-CJ-4903-01A-01D-1429-08	TCGA-CJ-4903-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:107315556T>C	uc003vep.2	+	6	989	c.765_splice	c.e6+2	p.Y255_splice		NM_000441	NP_000432	O43511	S26A4_HUMAN	pendrin						regulation of pH|regulation of protein localization|sensory perception of sound	apical plasma membrane|integral to membrane	chloride transmembrane transporter activity|inorganic anion exchanger activity|iodide transmembrane transporter activity|secondary active sulfate transmembrane transporter activity			ovary(3)|central_nervous_system(2)|skin(2)	7						ATTATCTATGTAAGTGTTGCT	0.358									Pendred_syndrome				5	240	---	---	---	---	PASS
ANKRD7	56311	broad.mit.edu	37	7	117876122	117876122	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-4903-01A-01D-1429-08	TCGA-CJ-4903-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:117876122G>A	uc003vji.2	+	4	669	c.496G>A	c.(496-498)GTT>ATT	p.V166I		NM_019644	NP_062618	Q92527	ANKR7_HUMAN	ankyrin repeat domain 7	166	ANK 4.				male gonad development						0						ATTAGTTGCCGTTATTAACAA	0.259													8	223	---	---	---	---	PASS
PLXNA4	91584	broad.mit.edu	37	7	132192713	132192713	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-4903-01A-01D-1429-08	TCGA-CJ-4903-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:132192713C>T	uc003vra.3	-	2	969	c.740G>A	c.(739-741)GGT>GAT	p.G247D	PLXNA4_uc003vrc.2_Missense_Mutation_p.G247D|PLXNA4_uc003vrb.2_Missense_Mutation_p.G247D	NM_020911	NP_065962	Q9HCM2	PLXA4_HUMAN	plexin A4 isoform 1	247	Extracellular (Potential).|Sema.					integral to membrane|intracellular|plasma membrane				ovary(1)	1						ACTGCTAAAACCATAGACATA	0.483													44	73	---	---	---	---	PASS
KIAA1549	57670	broad.mit.edu	37	7	138583876	138583876	+	Silent	SNP	C	A	A			TCGA-CJ-4903-01A-01D-1429-08	TCGA-CJ-4903-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:138583876C>A	uc011kql.1	-	9	3721	c.3672G>T	c.(3670-3672)GTG>GTT	p.V1224V	KIAA1549_uc011kqi.1_Silent_p.V8V|KIAA1549_uc003vuk.3_Silent_p.V1174V|KIAA1549_uc011kqj.1_Silent_p.V1224V|KIAA1549_uc011kqk.1_Silent_p.V8V	NM_020910	NP_065961	Q9HCM3	K1549_HUMAN	hypothetical protein LOC57670 isoform 1	1224						integral to membrane			KIAA1549/BRAF(229)	central_nervous_system(229)|pancreas(1)	230						ACACATTTACCACCTGAAAGA	0.468			O	BRAF	pilocytic astrocytoma								7	362	---	---	---	---	PASS
KEL	3792	broad.mit.edu	37	7	142649604	142649604	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-4903-01A-01D-1429-08	TCGA-CJ-4903-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:142649604G>A	uc003wcb.2	-	10	1405	c.1195C>T	c.(1195-1197)CCA>TCA	p.P399S		NM_000420	NP_000411	P23276	KELL_HUMAN	Kell blood group, metallo-endopeptidase	399	Extracellular (Potential).				proteolysis|vasoconstriction	integral to membrane|plasma membrane	metal ion binding|metalloendopeptidase activity|protein binding			ovary(3)|central_nervous_system(1)	4	Melanoma(164;0.059)					ACCATGGGTGGTTGCTCTGTC	0.542													49	105	---	---	---	---	PASS
KCNH2	3757	broad.mit.edu	37	7	150675001	150675001	+	Missense_Mutation	SNP	T	A	A			TCGA-CJ-4903-01A-01D-1429-08	TCGA-CJ-4903-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:150675001T>A	uc003wic.2	-	1	14	c.1A>T	c.(1-3)ATG>TTG	p.M1L	KCNH2_uc003wie.2_Missense_Mutation_p.M1L	NM_000238	NP_000229	Q12809	KCNH2_HUMAN	voltage-gated potassium channel, subfamily H,	1	Cytoplasmic (Potential).				blood circulation|muscle contraction|regulation of heart contraction|regulation of transcription, DNA-dependent	voltage-gated potassium channel complex	delayed rectifier potassium channel activity|two-component sensor activity			skin(3)|ovary(1)	4	all_neural(206;0.219)		OV - Ovarian serous cystadenocarcinoma(82;0.0121)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)	Amiodarone(DB01118)|Amsacrine(DB00276)|Astemizole(DB00637)|Carvedilol(DB01136)|Cisapride(DB00604)|Dofetilide(DB00204)|Halofantrine(DB01218)|Ibutilide(DB00308)|Pimozide(DB01100)|Propafenone(DB01182)|Quinidine(DB00908)|Sertindole(DB06144)|Sotalol(DB00489)|Terfenadine(DB00342)|Verapamil(DB00661)	CGCACCGGCATCCTGAGCCCA	0.458													10	24	---	---	---	---	PASS
FAM66D	100132923	broad.mit.edu	37	8	12216568	12216568	+	Intron	SNP	G	A	A			TCGA-CJ-4903-01A-01D-1429-08	TCGA-CJ-4903-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:12216568G>A	uc011kxp.1	+						uc003wvm.1_Intron|uc010lsh.1_3'UTR|FAM66A_uc010lsi.2_5'Flank					Homo sapiens cDNA FLJ37098 fis, clone BRACE2019004.												0						ACCTTAGACGGCACAAGATGA	0.383													4	74	---	---	---	---	PASS
PCMTD1	115294	broad.mit.edu	37	8	52732871	52732871	+	3'UTR	SNP	T	C	C	rs77261625	by1000genomes	TCGA-CJ-4903-01A-01D-1429-08	TCGA-CJ-4903-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:52732871T>C	uc003xqx.3	-	6					PCMTD1_uc011ldm.1_3'UTR|PCMTD1_uc003xqw.3_3'UTR|PCMTD1_uc011ldn.1_3'UTR|PCMTD1_uc010lya.2_3'UTR	NM_052937	NP_443169	Q96MG8	PCMD1_HUMAN	protein-L-isoaspartate (D-aspartate)							cytoplasm	protein-L-isoaspartate (D-aspartate) O-methyltransferase activity				0		Lung NSC(129;0.0795)|all_lung(136;0.144)				TTTTCAAGACTAAAGGAATTA	0.313													3	30	---	---	---	---	PASS
CYC1	1537	broad.mit.edu	37	8	145151520	145151520	+	Silent	SNP	C	T	T			TCGA-CJ-4903-01A-01D-1429-08	TCGA-CJ-4903-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:145151520C>T	uc003zaz.3	+	5	688	c.645C>T	c.(643-645)CTC>CTT	p.L215L	CYC1_uc003zay.2_Silent_p.L156L	NM_001916	NP_001907	P08574	CY1_HUMAN	cytochrome c-1	215					respiratory electron transport chain|transport	cell junction|integral to membrane|mitochondrial inner membrane|respiratory chain	electron transporter, transferring electrons from CoQH2-cytochrome c reductase complex and cytochrome c oxidase complex activity|heme binding				0	all_cancers(97;2.87e-11)|all_epithelial(106;2.16e-09)|Lung NSC(106;5.89e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;3.38e-41)|Epithelial(56;8.71e-40)|all cancers(56;3e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.105)			TCTCCCTGCTCACGGGCTACT	0.602											OREG0019052	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	25	85	---	---	---	---	PASS
FLJ43859	389761	broad.mit.edu	37	9	84547870	84547870	+	3'UTR	SNP	T	C	C	rs138226188	by1000genomes	TCGA-CJ-4903-01A-01D-1429-08	TCGA-CJ-4903-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:84547870T>C	uc004amh.2	+	4					uc004ami.1_Intron|uc004amj.1_5'Flank	NM_001145197	NP_001138669	Q6ZUB0	YI020_HUMAN	hypothetical protein LOC389761							integral to membrane					0						CGTGAACCCATAGAAATCTTC	0.428													6	22	---	---	---	---	PASS
ABCA1	19	broad.mit.edu	37	9	107550109	107550109	+	Intron	SNP	T	C	C			TCGA-CJ-4903-01A-01D-1429-08	TCGA-CJ-4903-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:107550109T>C	uc004bcl.2	-						NIPSNAP3B_uc004bcj.1_RNA	NM_005502	NP_005493	O95477	ABCA1_HUMAN	ATP-binding cassette, sub-family A member 1						Cdc42 protein signal transduction|cellular lipid metabolic process|cholesterol efflux|cholesterol homeostasis|cholesterol metabolic process|endosome transport|G-protein coupled receptor protein signaling pathway|high-density lipoprotein particle assembly|interleukin-1 beta secretion|intracellular cholesterol transport|lysosome organization|negative regulation of cholesterol storage|negative regulation of macrophage derived foam cell differentiation|phospholipid efflux|phospholipid homeostasis|platelet dense granule organization|positive regulation of cAMP biosynthetic process|reverse cholesterol transport	integral to plasma membrane|membrane fraction|membrane raft|phagocytic vesicle	anion transmembrane transporter activity|apolipoprotein A-I receptor activity|ATP binding|ATPase activity|cholesterol transporter activity|phospholipid transporter activity|small GTPase binding|syntaxin-13 binding			large_intestine(4)|lung(4)|ovary(4)|upper_aerodigestive_tract(1)|central_nervous_system(1)|breast(1)|skin(1)|pancreas(1)	17				OV - Ovarian serous cystadenocarcinoma(323;0.023)	Adenosine triphosphate(DB00171)|Glibenclamide(DB01016)	GACAAGCCAATCATACAACAG	0.498													12	34	---	---	---	---	PASS
PPP2R4	5524	broad.mit.edu	37	9	131909727	131909727	+	Missense_Mutation	SNP	C	A	A			TCGA-CJ-4903-01A-01D-1429-08	TCGA-CJ-4903-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:131909727C>A	uc004bxm.1	+	11	1328	c.1061C>A	c.(1060-1062)CCT>CAT	p.P354H	PPP2R4_uc004bxl.1_Missense_Mutation_p.P319H|PPP2R4_uc010myr.1_Missense_Mutation_p.P100H|PPP2R4_uc004bxn.1_Missense_Mutation_p.P319H|PPP2R4_uc004bxo.1_Missense_Mutation_p.P277H|PPP2R4_uc011mbp.1_Missense_Mutation_p.P290H|PPP2R4_uc010mys.1_Missense_Mutation_p.P284H|PPP2R4_uc004bxp.2_RNA|PPP2R4_uc004bxq.2_RNA	NM_178001	NP_821068	Q15257	PTPA_HUMAN	protein phosphatase 2A, regulatory subunit B'	354					ATP catabolic process|negative regulation of phosphoprotein phosphatase activity|negative regulation of protein dephosphorylation|positive regulation of apoptosis|positive regulation of phosphoprotein phosphatase activity|positive regulation of protein dephosphorylation	calcium channel complex|cytoplasm|nucleus|protein phosphatase type 2A complex|soluble fraction	ATP binding|peptidyl-prolyl cis-trans isomerase activity|protein heterodimerization activity|protein homodimerization activity|protein phosphatase 2A binding|protein phosphatase type 2A regulator activity|protein tyrosine phosphatase activator activity|receptor binding			ovary(1)|lung(1)|pancreas(1)	3		Medulloblastoma(224;0.235)		UCEC - Uterine corpus endometrioid carcinoma (4;0.0178)		CCCATCCATCCTGTCACGTCG	0.642													26	40	---	---	---	---	PASS
ABI1	10006	broad.mit.edu	37	10	27054165	27054165	+	Missense_Mutation	SNP	G	T	T			TCGA-CJ-4903-01A-01D-1429-08	TCGA-CJ-4903-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:27054165G>T	uc001isx.2	-	7	969	c.802C>A	c.(802-804)CCA>ACA	p.P268T	ABI1_uc001ite.2_Missense_Mutation_p.P263T|ABI1_uc010qdh.1_Missense_Mutation_p.P263T|ABI1_uc010qdi.1_Missense_Mutation_p.P204T|ABI1_uc001isy.2_Missense_Mutation_p.P268T|ABI1_uc001ita.2_Missense_Mutation_p.P268T|ABI1_uc001isz.2_Missense_Mutation_p.P263T|ABI1_uc001itb.2_Missense_Mutation_p.P285T|ABI1_uc001itc.2_Missense_Mutation_p.P268T|ABI1_uc010qdj.1_Missense_Mutation_p.P268T|ABI1_uc001itd.2_Missense_Mutation_p.P268T|ABI1_uc010qdk.1_Missense_Mutation_p.P268T|ABI1_uc010qdg.1_Missense_Mutation_p.P134T	NM_005470	NP_005461	Q8IZP0	ABI1_HUMAN	abl-interactor 1 isoform a	268	Pro-rich.				actin polymerization or depolymerization|cellular component movement|negative regulation of cell proliferation|peptidyl-tyrosine phosphorylation|transmembrane receptor protein tyrosine kinase signaling pathway	cell junction|cytoskeleton|cytosol|endoplasmic reticulum|filopodium|growth cone|lamellipodium|nucleus|soluble fraction|synapse|synaptosome	cytoskeletal protein binding			central_nervous_system(1)	1						ATAGTGGGTGGCGAAGGTGTA	0.363													3	31	---	---	---	---	PASS
NRG3	10718	broad.mit.edu	37	10	84744979	84744979	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-4903-01A-01D-1429-08	TCGA-CJ-4903-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:84744979G>A	uc001kco.2	+	9	1736	c.1709G>A	c.(1708-1710)AGG>AAG	p.R570K	NRG3_uc010qlz.1_Missense_Mutation_p.R569K|NRG3_uc001kcp.2_Missense_Mutation_p.R373K|NRG3_uc001kcq.2_Missense_Mutation_p.R220K|NRG3_uc001kcr.2_Missense_Mutation_p.R244K	NM_001010848	NP_001010848	P56975	NRG3_HUMAN	neuregulin 3 isoform 1	594	Cytoplasmic (Potential).				regulation of cell growth	extracellular region|integral to plasma membrane	growth factor activity|receptor tyrosine kinase binding|transmembrane receptor protein tyrosine kinase activator activity			lung(5)|breast(1)	6				GBM - Glioblastoma multiforme(1;2.5e-18)|all cancers(1;2.85e-09)		TCATCCACAAGGGCCAGTTCT	0.443													82	255	---	---	---	---	PASS
MKI67	4288	broad.mit.edu	37	10	129906582	129906582	+	Missense_Mutation	SNP	C	A	A			TCGA-CJ-4903-01A-01D-1429-08	TCGA-CJ-4903-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:129906582C>A	uc001lke.2	-	13	3717	c.3522G>T	c.(3520-3522)ATG>ATT	p.M1174I	MKI67_uc001lkf.2_Missense_Mutation_p.M814I|MKI67_uc009yav.1_Missense_Mutation_p.M749I|MKI67_uc009yaw.1_Missense_Mutation_p.M324I	NM_002417	NP_002408	P46013	KI67_HUMAN	antigen identified by monoclonal antibody Ki-67	1174	16 X 122 AA approximate repeats.|2.				cell proliferation	nucleolus	ATP binding|protein C-terminus binding			ovary(4)|central_nervous_system(2)|skin(1)	7		all_epithelial(44;2.12e-05)|all_lung(145;0.00679)|Lung NSC(174;0.00998)|all_neural(114;0.0936)|Colorectal(57;0.14)|Breast(234;0.166)|Melanoma(40;0.203)				TGGGCGTAAGCATGGCTTTCC	0.473													205	328	---	---	---	---	PASS
LRRC56	115399	broad.mit.edu	37	11	554294	554294	+	3'UTR	SNP	G	A	A			TCGA-CJ-4903-01A-01D-1429-08	TCGA-CJ-4903-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:554294G>A	uc010qvz.1	+	14						NM_198075	NP_932341	Q8IYG6	LRC56_HUMAN	leucine rich repeat containing 56											skin(1)	1		all_cancers(49;2.16e-06)|all_epithelial(84;0.000256)|Breast(177;0.00122)|Ovarian(85;0.0228)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762)		all cancers(45;7.63e-28)|Epithelial(43;7.29e-27)|OV - Ovarian serous cystadenocarcinoma(40;7.15e-21)|BRCA - Breast invasive adenocarcinoma(625;3.56e-05)|Lung(200;0.0375)|LUSC - Lung squamous cell carcinoma(625;0.0703)		CCCACTGCCAGGCTTCCCTGT	0.627													5	22	---	---	---	---	PASS
FAM160A2	84067	broad.mit.edu	37	11	6233079	6233079	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-4903-01A-01D-1429-08	TCGA-CJ-4903-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:6233079G>A	uc001mcl.3	-	12	2935	c.2576C>T	c.(2575-2577)TCC>TTC	p.S859F	FAM160A2_uc001mck.3_Missense_Mutation_p.S873F	NM_001098794	NP_001092264	Q8N612	F16A2_HUMAN	hypothetical protein LOC84067 isoform 2	859					early endosome to late endosome transport|endosome organization|endosome to lysosome transport|lysosome organization|protein transport	FHF complex	protein binding			skin(2)	2						CTCCCCCAAGGATGGCCTCCG	0.617													32	255	---	---	---	---	PASS
NAV2	89797	broad.mit.edu	37	11	19735259	19735259	+	Silent	SNP	C	A	A			TCGA-CJ-4903-01A-01D-1429-08	TCGA-CJ-4903-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:19735259C>A	uc010rdm.1	+	1	379	c.18C>A	c.(16-18)GTC>GTA	p.V6V	NAV2_uc001mpp.2_Intron|NAV2_uc001mpr.3_Silent_p.V6V|LOC100126784_uc010rdl.1_3'UTR	NM_145117	NP_660093	Q8IVL1	NAV2_HUMAN	neuron navigator 2 isoform 2	6						nucleus	ATP binding|helicase activity			skin(4)|ovary(1)|pancreas(1)	6						CCATCCTGGTCGCCTCCAAAA	0.602													11	28	---	---	---	---	PASS
DCDC1	341019	broad.mit.edu	37	11	31312230	31312230	+	Silent	SNP	C	T	T			TCGA-CJ-4903-01A-01D-1429-08	TCGA-CJ-4903-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:31312230C>T	uc001msv.2	-	7	1126	c.924G>A	c.(922-924)GGG>GGA	p.G308G	DCDC1_uc001msu.1_Intron	NM_181807	NP_861523	P59894	DCDC1_HUMAN	doublecortin domain containing 1	308					intracellular signal transduction					skin(1)	1	Lung SC(675;0.225)					TAATCTCATGCCCATCCTGCC	0.353													5	151	---	---	---	---	PASS
AMBRA1	55626	broad.mit.edu	37	11	46563577	46563577	+	Missense_Mutation	SNP	A	G	G			TCGA-CJ-4903-01A-01D-1429-08	TCGA-CJ-4903-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:46563577A>G	uc010rgu.1	-	7	2350	c.1990T>C	c.(1990-1992)TCC>CCC	p.S664P	AMBRA1_uc010rgt.1_Missense_Mutation_p.S230P|AMBRA1_uc009ylc.1_Missense_Mutation_p.S664P|AMBRA1_uc001ncu.1_Missense_Mutation_p.S574P|AMBRA1_uc001ncv.2_Missense_Mutation_p.S574P|AMBRA1_uc001ncw.2_Missense_Mutation_p.S574P|AMBRA1_uc001ncx.2_Missense_Mutation_p.S664P	NM_017749	NP_060219	Q9C0C7	AMRA1_HUMAN	activating molecule in beclin-1-regulated	664					autophagy|cell differentiation|nervous system development	autophagic vacuole|cytoplasmic vesicle				large_intestine(1)|ovary(1)|central_nervous_system(1)	3				GBM - Glioblastoma multiforme(35;0.0435)|Lung(87;0.182)		GATCTGCTGGACTGGGTGTAA	0.552													13	126	---	---	---	---	PASS
KCTD21	283219	broad.mit.edu	37	11	77884782	77884782	+	3'UTR	SNP	C	T	T	rs230661	by1000genomes	TCGA-CJ-4903-01A-01D-1429-08	TCGA-CJ-4903-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:77884782C>T	uc001ozb.2	-	2						NM_001029859	NP_001025030	Q4G0X4	KCD21_HUMAN	potassium channel tetramerisation domain							voltage-gated potassium channel complex	voltage-gated potassium channel activity			pancreas(1)	1	all_cancers(14;3.77e-18)|all_epithelial(13;6.16e-21)|Breast(9;5.6e-16)|Ovarian(111;0.152)		OV - Ovarian serous cystadenocarcinoma(8;1.46e-24)			CATGAGCTTCCTGGGACTCCC	0.478													5	204	---	---	---	---	PASS
PRKAG1	5571	broad.mit.edu	37	12	49398646	49398646	+	Intron	SNP	C	T	T			TCGA-CJ-4903-01A-01D-1429-08	TCGA-CJ-4903-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:49398646C>T	uc001rsy.2	-						uc001rsw.2_Intron|PRKAG1_uc010smd.1_Intron|PRKAG1_uc001rsx.2_Intron|PRKAG1_uc001rsz.2_Intron|PRKAG1_uc009zlb.2_Intron|PRKAG1_uc010sme.1_3'UTR	NM_002733	NP_002724	P54619	AAKG1_HUMAN	AMP-activated protein kinase, noncatalytic						cell cycle arrest|fatty acid biosynthetic process|insulin receptor signaling pathway|positive regulation of protein kinase activity|regulation of fatty acid oxidation|regulation of glycolysis|spermatogenesis	cytosol	cAMP-dependent protein kinase activity|cAMP-dependent protein kinase regulator activity|protein kinase binding			kidney(1)	1						gtgtgtgtgtCTTTTCTCTCT	0.244													8	82	---	---	---	---	PASS
DHX37	57647	broad.mit.edu	37	12	125465134	125465134	+	Missense_Mutation	SNP	T	C	C			TCGA-CJ-4903-01A-01D-1429-08	TCGA-CJ-4903-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:125465134T>C	uc001ugy.2	-	4	739	c.640A>G	c.(640-642)ATG>GTG	p.M214V		NM_032656	NP_116045	Q8IY37	DHX37_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 37	214							ATP binding|ATP-dependent helicase activity|nucleic acid binding|protein binding			skin(1)	1	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;8.05e-05)|Epithelial(86;0.000486)|all cancers(50;0.00653)		GGAACAGTCATCCCAGCCGGC	0.692													8	50	---	---	---	---	PASS
C1QTNF9	338872	broad.mit.edu	37	13	24893010	24893010	+	Missense_Mutation	SNP	G	T	T			TCGA-CJ-4903-01A-01D-1429-08	TCGA-CJ-4903-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:24893010G>T	uc001upj.2	+	3	282	c.221G>T	c.(220-222)GGA>GTA	p.G74V	C1QTNF9_uc001upe.2_RNA	NM_178540	NP_848635	P0C862	C1T9A_HUMAN	C1q and tumor necrosis factor related protein 9	74	Collagen-like 1.					collagen	hormone activity				0		all_cancers(29;3.55e-20)|all_epithelial(30;4.25e-17)|all_lung(29;1.04e-16)|Lung SC(185;0.0225)|Breast(139;0.052)		all cancers(112;0.00565)|Epithelial(112;0.027)|OV - Ovarian serous cystadenocarcinoma(117;0.115)|Lung(94;0.159)		GGAGAGAAGGGAGAACGAGGT	0.453													44	135	---	---	---	---	PASS
CTSG	1511	broad.mit.edu	37	14	25043508	25043508	+	Silent	SNP	G	A	A			TCGA-CJ-4903-01A-01D-1429-08	TCGA-CJ-4903-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:25043508G>A	uc001wpq.2	-	4	574	c.537C>T	c.(535-537)TAC>TAT	p.Y179Y		NM_001911	NP_001902	P08311	CATG_HUMAN	cathepsin G preproprotein	179	Peptidase S1.				immune response|proteolysis	cell surface|extracellular space|plasma membrane|stored secretory granule	heparin binding|serine-type endopeptidase activity			ovary(2)	2				GBM - Glioblastoma multiforme(265;0.0269)		TTCGGGGGTCGTAGGAACCGA	0.627													21	51	---	---	---	---	PASS
AKAP6	9472	broad.mit.edu	37	14	33293956	33293956	+	Nonsense_Mutation	SNP	C	T	T			TCGA-CJ-4903-01A-01D-1429-08	TCGA-CJ-4903-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:33293956C>T	uc001wrq.2	+	13	7107	c.6937C>T	c.(6937-6939)CGA>TGA	p.R2313*		NM_004274	NP_004265	Q13023	AKAP6_HUMAN	A-kinase anchor protein 6	2313					protein targeting	calcium channel complex|nuclear membrane|sarcoplasmic reticulum	protein kinase A binding|receptor binding			breast(6)|ovary(5)|lung(4)|skin(3)|large_intestine(2)|pancreas(1)	21	Breast(36;0.0388)|Prostate(35;0.15)		LUAD - Lung adenocarcinoma(48;0.00107)|Lung(238;0.00677)|STAD - Stomach adenocarcinoma(7;0.116)	GBM - Glioblastoma multiforme(265;0.019)		TCATGAAAAACGACATAGAAA	0.418													31	133	---	---	---	---	PASS
NRXN3	9369	broad.mit.edu	37	14	79434650	79434650	+	Missense_Mutation	SNP	G	C	C			TCGA-CJ-4903-01A-01D-1429-08	TCGA-CJ-4903-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:79434650G>C	uc001xun.2	+	11	2475	c.1984G>C	c.(1984-1986)GCT>CCT	p.A662P	NRXN3_uc001xum.1_RNA|NRXN3_uc010asv.1_Missense_Mutation_p.A787P	NM_004796	NP_004787	Q9Y4C0	NRX3A_HUMAN	neurexin 3 isoform 1 precursor	1035	Extracellular (Potential).|Laminin G-like 5.				axon guidance|cell adhesion	integral to plasma membrane	metal ion binding|receptor activity			ovary(3)|upper_aerodigestive_tract(2)|pancreas(2)|central_nervous_system(1)|breast(1)|skin(1)	10		Renal(4;0.00876)		BRCA - Breast invasive adenocarcinoma(234;0.00544)|Kidney(3;0.029)|KIRC - Kidney renal clear cell carcinoma(182;0.223)		CATCAATGATGCTCTTCATCG	0.512													21	75	---	---	---	---	PASS
CYP46A1	10858	broad.mit.edu	37	14	100191787	100191787	+	Missense_Mutation	SNP	C	A	A			TCGA-CJ-4903-01A-01D-1429-08	TCGA-CJ-4903-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:100191787C>A	uc001ygo.2	+	13	1236	c.1236C>A	c.(1234-1236)AAC>AAA	p.N412K	CYP46A1_uc001ygp.2_Missense_Mutation_p.N249K	NM_006668	NP_006659	Q9Y6A2	CP46A_HUMAN	cytochrome P450, family 46	412					bile acid biosynthetic process|cholesterol catabolic process|nervous system development|xenobiotic metabolic process	endoplasmic reticulum membrane|integral to membrane|microsome	cholesterol 24-hydroxylase activity|electron carrier activity|heme binding|steroid hydroxylase activity				0		Melanoma(154;0.0866)|all_epithelial(191;0.179)				TGACTTTCAACCCCGATCGCT	0.607													21	50	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	15	28948349	28948349	+	5'Flank	SNP	T	C	C			TCGA-CJ-4903-01A-01D-1429-08	TCGA-CJ-4903-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:28948349T>C	uc001zcd.2	+											DQ593033																		CCACTGGCTCTCAGAAGGGGT	0.567													4	7	---	---	---	---	PASS
EDC3	80153	broad.mit.edu	37	15	74925269	74925269	+	Missense_Mutation	SNP	A	T	T			TCGA-CJ-4903-01A-01D-1429-08	TCGA-CJ-4903-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:74925269A>T	uc002ayn.2	-	10	1699	c.1211T>A	c.(1210-1212)GTG>GAG	p.V404E	EDC3_uc002ayo.2_Missense_Mutation_p.V404E|EDC3_uc002aym.2_Missense_Mutation_p.V404E	NM_001142443	NP_001135915	Q96F86	EDC3_HUMAN	enhancer of mRNA decapping 3	404	YjeF N-terminal.				exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay	cytoplasmic mRNA processing body|cytosol	protein binding|RNA binding			ovary(1)	1						GACCAGGTCCACAGGGCTAGT	0.602											OREG0023286	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	9	40	---	---	---	---	PASS
LOC645752	645752	broad.mit.edu	37	15	78211548	78211548	+	Silent	SNP	T	C	C			TCGA-CJ-4903-01A-01D-1429-08	TCGA-CJ-4903-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:78211548T>C	uc010bky.2	-	11	983	c.219A>G	c.(217-219)CAA>CAG	p.Q73Q		NR_027024				SubName: Full=GOLGA6 protein; Flags: Fragment;												0						CCACCTGGGATTGGAGCTTTC	0.562													4	230	---	---	---	---	PASS
BNC1	646	broad.mit.edu	37	15	83933213	83933213	+	Missense_Mutation	SNP	A	G	G			TCGA-CJ-4903-01A-01D-1429-08	TCGA-CJ-4903-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:83933213A>G	uc002bjt.1	-	4	878	c.790T>C	c.(790-792)TAT>CAT	p.Y264H	BNC1_uc010uos.1_Missense_Mutation_p.Y252H	NM_001717	NP_001708	Q01954	BNC1_HUMAN	basonuclin 1	264					epidermis development|positive regulation of cell proliferation	cytoplasm|nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(3)	3						TCCAACATATATTGTTCGGGC	0.498													51	72	---	---	---	---	PASS
MRPS34	65993	broad.mit.edu	37	16	1822141	1822141	+	3'UTR	SNP	T	G	G			TCGA-CJ-4903-01A-01D-1429-08	TCGA-CJ-4903-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:1822141T>G	uc002cmo.2	-	3					NME3_uc002cmm.2_5'Flank|NME3_uc010brv.2_5'Flank|MRPS34_uc002cmn.2_3'UTR|MRPS34_uc002cmp.1_3'UTR|EME2_uc002cmq.1_5'Flank|EME2_uc010brw.1_5'Flank	NM_023936	NP_076425	P82930	RT34_HUMAN	mitochondrial ribosomal protein S34							mitochondrion|ribosome	protein binding			skin(2)	2						CAGACTCGGGTGTAACGCAAA	0.607													9	113	---	---	---	---	PASS
OR1G1	8390	broad.mit.edu	37	17	3030489	3030489	+	Silent	SNP	G	A	A			TCGA-CJ-4903-01A-01D-1429-08	TCGA-CJ-4903-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:3030489G>A	uc002fvc.1	-	1	357	c.357C>T	c.(355-357)GCC>GCT	p.A119A		NM_003555	NP_003546	P47890	OR1G1_HUMAN	olfactory receptor, family 1, subfamily G,	119	Helical; Name=3; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0						AGCAGTCATAGGCCATGACCG	0.488													13	88	---	---	---	---	PASS
P2RX1	5023	broad.mit.edu	37	17	3819428	3819428	+	Missense_Mutation	SNP	A	G	G			TCGA-CJ-4903-01A-01D-1429-08	TCGA-CJ-4903-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:3819428A>G	uc002fww.2	-	1	533	c.92T>C	c.(91-93)GTT>GCT	p.V31A	P2RX1_uc010ckm.1_5'UTR	NM_002558	NP_002549	P51575	P2RX1_HUMAN	purinergic receptor P2X1	31	Helical; Name=1; (Potential).				platelet activation	integral to plasma membrane	calcium channel activity|extracellular ATP-gated cation channel activity|purinergic nucleotide receptor activity			ovary(1)|skin(1)	2				LUAD - Lung adenocarcinoma(2;1.9e-05)|Lung(3;0.0173)		TCGGAAGATAACGCCCACCTT	0.657													31	109	---	---	---	---	PASS
MFSD6L	162387	broad.mit.edu	37	17	8702126	8702126	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-4903-01A-01D-1429-08	TCGA-CJ-4903-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:8702126C>T	uc002glp.1	-	1	461	c.313G>A	c.(313-315)GTG>ATG	p.V105M		NM_152599	NP_689812	Q8IWD5	MFS6L_HUMAN	major facilitator superfamily domain containing	105						integral to membrane				central_nervous_system(1)	1						GGGAAGTGCACCCGATTTTTG	0.617													14	121	---	---	---	---	PASS
PLEKHH3	79990	broad.mit.edu	37	17	40820279	40820279	+	Missense_Mutation	SNP	G	T	T			TCGA-CJ-4903-01A-01D-1429-08	TCGA-CJ-4903-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:40820279G>T	uc002iau.2	-	13	2715	c.2248C>A	c.(2248-2250)CCC>ACC	p.P750T	PLEKHH3_uc010cyl.1_RNA|PLEKHH3_uc002iat.1_RNA|PLEKHH3_uc002iav.2_RNA|PLEKHH3_uc010cym.1_Missense_Mutation_p.P111T|PLEKHH3_uc002iaw.2_3'UTR	NM_024927	NP_079203	Q7Z736	PKHH3_HUMAN	pleckstrin homology domain containing, family H	750	FERM.				signal transduction	cytoskeleton				large_intestine(1)|ovary(1)	2		Breast(137;0.00116)		BRCA - Breast invasive adenocarcinoma(366;0.14)		TCGGGGGAGGGGTTGGCCAAG	0.627													5	31	---	---	---	---	PASS
VPS25	84313	broad.mit.edu	37	17	40925522	40925522	+	Missense_Mutation	SNP	A	G	G			TCGA-CJ-4903-01A-01D-1429-08	TCGA-CJ-4903-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:40925522A>G	uc002ibi.2	+	1	69	c.29A>G	c.(28-30)CAG>CGG	p.Q10R		NM_032353	NP_115729	Q9BRG1	VPS25_HUMAN	vacuolar protein sorting 25	10					cellular membrane organization|endosome transport|protein transport|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytosol|endosome membrane|nucleoplasm					0		Breast(137;0.00104)		BRCA - Breast invasive adenocarcinoma(366;0.0745)		TGGCCGTGGCAGTATCGCTTC	0.632													25	170	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	17	45128792	45128792	+	5'Flank	SNP	G	T	T	rs143713325	by1000genomes	TCGA-CJ-4903-01A-01D-1429-08	TCGA-CJ-4903-11A-01D-1429-08									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													3	75	---	---	---	---	PASS
OR4D1	26689	broad.mit.edu	37	17	56233390	56233390	+	Missense_Mutation	SNP	G	T	T			TCGA-CJ-4903-01A-01D-1429-08	TCGA-CJ-4903-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:56233390G>T	uc010wno.1	+	1	876	c.876G>T	c.(874-876)CAG>CAT	p.Q292H	MSX2P1_uc002ivn.2_5'Flank	NM_012374	NP_036506	Q15615	OR4D1_HUMAN	olfactory receptor, family 4, subfamily D,	292	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)	1						TGAGAAACCAGGACATGAAAG	0.463													20	88	---	---	---	---	PASS
POLG2	11232	broad.mit.edu	37	17	62481972	62481972	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-4903-01A-01D-1429-08	TCGA-CJ-4903-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:62481972C>T	uc002jei.2	-	5	1066	c.983G>A	c.(982-984)CGA>CAA	p.R328Q	POLG2_uc010deg.1_Missense_Mutation_p.R328Q	NM_007215	NP_009146	Q9UHN1	DPOG2_HUMAN	DNA polymerase subunit gamma-2, mitochondrial	328					DNA repair|DNA-dependent DNA replication|glycyl-tRNA aminoacylation	mitochondrial chromosome	ATP binding|DNA-directed DNA polymerase activity|glycine-tRNA ligase activity|identical protein binding|single-stranded DNA binding			central_nervous_system(1)	1	Breast(5;2.15e-14)		BRCA - Breast invasive adenocarcinoma(8;4.97e-11)			CACATTTTTTCGTCCATCTCG	0.338													35	53	---	---	---	---	PASS
MKNK2	2872	broad.mit.edu	37	19	2043146	2043146	+	Missense_Mutation	SNP	A	T	T			TCGA-CJ-4903-01A-01D-1429-08	TCGA-CJ-4903-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:2043146A>T	uc002lus.2	-	7	715	c.470T>A	c.(469-471)CTG>CAG	p.L157Q	MKNK2_uc002luq.1_5'Flank|MKNK2_uc010xgu.1_Intron|MKNK2_uc010xgv.1_Missense_Mutation_p.L26Q|MKNK2_uc002lur.2_Missense_Mutation_p.L157Q|MKNK2_uc002lut.1_5'Flank	NM_199054	NP_951009	Q9HBH9	MKNK2_HUMAN	MAP kinase-interacting serine/threonine kinase 2	157	Protein kinase.				cell surface receptor linked signaling pathway|intracellular protein kinase cascade|regulation of translation		ATP binding|metal ion binding|protein serine/threonine kinase activity			lung(1)|breast(1)	2		Ovarian(11;2.11e-07)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		CTCAAACACCAGGTAGAAGCG	0.632													68	145	---	---	---	---	PASS
CD209	30835	broad.mit.edu	37	19	7810603	7810603	+	Silent	SNP	A	C	C			TCGA-CJ-4903-01A-01D-1429-08	TCGA-CJ-4903-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:7810603A>C	uc002mht.2	-	4	616	c.549T>G	c.(547-549)CTT>CTG	p.L183L	CD209_uc010xju.1_Intron|CD209_uc010dvp.2_Silent_p.L159L|CD209_uc002mhr.2_Silent_p.L159L|CD209_uc002mhs.2_Silent_p.L159L|CD209_uc002mhu.2_Intron|CD209_uc010dvq.2_Silent_p.L183L|CD209_uc002mhq.2_Silent_p.L183L|CD209_uc002mhv.2_Silent_p.L159L|CD209_uc002mhx.2_Silent_p.L139L|CD209_uc002mhw.2_Intron|CD209_uc010dvr.2_Intron	NM_021155	NP_066978	Q9NNX6	CD209_HUMAN	CD209 molecule isoform 1	183	4.|Extracellular (Probable).|7 X approximate tandem repeats.				cell-cell recognition|endocytosis|heterophilic cell-cell adhesion|innate immune response|intracellular signal transduction|intracellular virion transport|leukocyte cell-cell adhesion|peptide antigen transport|viral genome replication|virion attachment to host cell surface receptor	cytoplasm|extracellular region|integral to membrane|plasma membrane	mannose binding|metal ion binding|peptide antigen binding|receptor activity|virion binding			skin(1)	1						ATTTCTCTGGAAGCTCACCCA	0.547													6	194	---	---	---	---	PASS
ZNF566	84924	broad.mit.edu	37	19	36940632	36940632	+	Missense_Mutation	SNP	C	G	G			TCGA-CJ-4903-01A-01D-1429-08	TCGA-CJ-4903-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:36940632C>G	uc002oea.3	-	5	586	c.504G>C	c.(502-504)AAG>AAC	p.K168N	ZNF566_uc010xte.1_Missense_Mutation_p.K168N|ZNF566_uc010xtf.1_Missense_Mutation_p.K169N|ZNF566_uc002oeb.3_Missense_Mutation_p.K168N|ZNF566_uc002oec.3_Missense_Mutation_p.K64N|ZNF566_uc010xtg.1_Missense_Mutation_p.K64N	NM_032838	NP_116227	Q969W8	ZN566_HUMAN	zinc finger protein 566 isoform 1	168					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0	Esophageal squamous(110;0.162)					CACAGAATTTCTTTTTACTGT	0.368													7	225	---	---	---	---	PASS
CCDC114	93233	broad.mit.edu	37	19	48806933	48806933	+	Missense_Mutation	SNP	T	C	C			TCGA-CJ-4903-01A-01D-1429-08	TCGA-CJ-4903-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:48806933T>C	uc002pir.2	-	8	1534	c.851A>G	c.(850-852)GAC>GGC	p.D284G	CCDC114_uc002piq.2_Missense_Mutation_p.D93G|CCDC114_uc002pio.2_Missense_Mutation_p.D321G|CCDC114_uc002pis.1_5'Flank|CCDC114_uc002pit.1_Missense_Mutation_p.D321G|CCDC114_uc002piu.1_Missense_Mutation_p.D321G	NM_144577	NP_653178	Q96M63	CC114_HUMAN	coiled-coil domain containing 114 isoform 2	284										ovary(1)	1		all_epithelial(76;9.64e-05)|all_lung(116;0.000147)|Lung NSC(112;0.000251)|Prostate(7;0.0187)|all_neural(266;0.0228)|Ovarian(192;0.113)		OV - Ovarian serous cystadenocarcinoma(262;0.000134)|all cancers(93;0.000162)|Epithelial(262;0.0134)|GBM - Glioblastoma multiforme(486;0.0143)		CACCAACAGGTCAGGGTCACT	0.647													4	113	---	---	---	---	PASS
RALGAPB	57148	broad.mit.edu	37	20	37153582	37153582	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-4903-01A-01D-1429-08	TCGA-CJ-4903-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:37153582C>T	uc002xiw.2	+	11	2038	c.1781C>T	c.(1780-1782)CCT>CTT	p.P594L	RALGAPB_uc010zvz.1_3'UTR|RALGAPB_uc002xix.2_Missense_Mutation_p.P594L|RALGAPB_uc002xiy.1_Missense_Mutation_p.P594L|RALGAPB_uc002xiz.2_Missense_Mutation_p.P372L|RALGAPB_uc002xja.1_Missense_Mutation_p.P321L	NM_020336	NP_065069	Q86X10	RLGPB_HUMAN	Ral GTPase activating protein, beta subunit	594					activation of Ral GTPase activity	intracellular	protein heterodimerization activity|Ral GTPase activator activity			pancreas(1)|skin(1)	2						ACCATTTTGCCTGACAGGTAA	0.428													9	544	---	---	---	---	PASS
ARFGEF2	10564	broad.mit.edu	37	20	47591319	47591319	+	Missense_Mutation	SNP	A	C	C			TCGA-CJ-4903-01A-01D-1429-08	TCGA-CJ-4903-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:47591319A>C	uc002xtx.3	+	13	1834	c.1682A>C	c.(1681-1683)AAG>ACG	p.K561T		NM_006420	NP_006411	Q9Y6D5	BIG2_HUMAN	ADP-ribosylation factor guanine	561					exocytosis|intracellular signal transduction|regulation of ARF protein signal transduction	cytosol|Golgi membrane	ARF guanyl-nucleotide exchange factor activity			breast(3)|upper_aerodigestive_tract(1)	4			BRCA - Breast invasive adenocarcinoma(12;0.00148)|Colorectal(8;0.198)			AGCCTGAGGAAGAAAGGCCTG	0.517													23	52	---	---	---	---	PASS
LOC91316	91316	broad.mit.edu	37	22	23980968	23980968	+	RNA	SNP	T	A	A	rs13056126	by1000genomes	TCGA-CJ-4903-01A-01D-1429-08	TCGA-CJ-4903-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:23980968T>A	uc002zxh.3	-	5		c.3522A>T			LOC91316_uc002zxi.3_RNA|LOC91316_uc002zxk.3_RNA|LOC91316_uc010gua.2_RNA|LOC91316_uc002zxl.3_RNA|LOC91316_uc011aiz.1_RNA					Homo sapiens cDNA FLJ32313 fis, clone PROST2003232, weakly similar to BETA-GLUCURONIDASE PRECURSOR (EC 3.2.1.31).												0						GGGCGTGGTCTTCTCCACGCT	0.562													4	87	---	---	---	---	PASS
TRAPPC2	6399	broad.mit.edu	37	X	13738010	13738010	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-4903-01A-01D-1429-08	TCGA-CJ-4903-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:13738010C>T	uc010nek.1	-	3	333	c.73G>A	c.(73-75)GCT>ACT	p.A25T	TRAPPC2_uc010nel.1_Missense_Mutation_p.A25T|TRAPPC2_uc010nem.1_Missense_Mutation_p.A59T	NM_001011658	NP_001011658	Q6IBE5	Q6IBE5_HUMAN	trafficking protein particle complex 2 isoform	25					ER to Golgi vesicle-mediated transport	intracellular					0						GCCTTCCCAGCTGGCAAAAAC	0.338													14	3	---	---	---	---	PASS
ATRX	546	broad.mit.edu	37	X	76855280	76855280	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-4903-01A-01D-1429-08	TCGA-CJ-4903-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:76855280C>T	uc004ecp.3	-	24	5939	c.5707G>A	c.(5707-5709)GAT>AAT	p.D1903N	ATRX_uc004ecq.3_Missense_Mutation_p.D1865N|ATRX_uc004eco.3_Missense_Mutation_p.D1688N	NM_000489	NP_000480	P46100	ATRX_HUMAN	transcriptional regulator ATRX isoform 1	1903					DNA methylation|DNA recombination|DNA repair|regulation of transcription, DNA-dependent	nuclear heterochromatin	ATP binding|chromo shadow domain binding|DNA binding|DNA helicase activity|zinc ion binding			haematopoietic_and_lymphoid_tissue(14)|pancreas(12)|lung(1)|breast(1)|skin(1)|kidney(1)	30					Phosphatidylserine(DB00144)	CTGTCTTCATCAAAATAACCC	0.294			Mis|F|N		Pancreatic neuroendocrine tumors		ATR-X (alpha thalassemia/mental retardation) syndrome						25	60	---	---	---	---	PASS
MARCKSL1	65108	broad.mit.edu	37	1	32799988	32799988	+	3'UTR	DEL	C	-	-			TCGA-CJ-4903-01A-01D-1429-08	TCGA-CJ-4903-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:32799988delC	uc001bvd.2	-	2						NM_023009	NP_075385	P49006	MRP_HUMAN	MARCKS-like 1							plasma membrane	calmodulin binding			ovary(1)	1		Myeloproliferative disorder(586;0.0393)|all_neural(195;0.186)				CTGTAAGGGACCATCTTCAAC	0.552													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	36872302	36872305	+	IGR	DEL	TTCC	-	-	rs28542712		TCGA-CJ-4903-01A-01D-1429-08	TCGA-CJ-4903-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:36872302_36872305delTTCC								LSM10 (8809 upstream) : OSCP1 (11203 downstream)																							ctttctttctttccttccttcctt	0.034													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	51480690	51480693	+	IGR	DEL	AGGA	-	-	rs113970426		TCGA-CJ-4903-01A-01D-1429-08	TCGA-CJ-4903-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:51480690_51480693delAGGA								CDKN2C (40383 upstream) : C1orf185 (87213 downstream)														p.0?(1)|p.?(1)									agagggagggaggaaggaaggaag	0.034													3	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	101117837	101117837	+	IGR	DEL	T	-	-			TCGA-CJ-4903-01A-01D-1429-08	TCGA-CJ-4903-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:101117837delT								GPR88 (110255 upstream) : VCAM1 (67460 downstream)																							TCATCTTTTGTTTTATTATGA	0.199													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	142823570	142823571	+	Intron	INS	-	G	G	rs149994101		TCGA-CJ-4903-01A-01D-1429-08	TCGA-CJ-4903-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:142823570_142823571insG	uc001eiw.1	+						uc001ejb.2_Intron|uc001ejd.1_Intron|uc001ejc.2_Intron					Homo sapiens PNAS-130 mRNA, complete cds.																		AGCCTATAGCAGtttttttttt	0.203													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	148855788	148855788	+	IGR	DEL	G	-	-	rs56347163		TCGA-CJ-4903-01A-01D-1429-08	TCGA-CJ-4903-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:148855788delG								NBPF16 (97477 upstream) : LOC645166 (72498 downstream)																							ccgcggcggcggggggggcgg	0.388													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	148855840	148855842	+	IGR	DEL	GGT	-	-	rs60282471		TCGA-CJ-4903-01A-01D-1429-08	TCGA-CJ-4903-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:148855840_148855842delGGT								NBPF16 (97529 upstream) : LOC645166 (72444 downstream)																							aagccgcggcggtggcggcggag	0.335													9	4	---	---	---	---	
RYR2	6262	broad.mit.edu	37	1	237886196	237886197	+	Intron	DEL	CT	-	-	rs146977948		TCGA-CJ-4903-01A-01D-1429-08	TCGA-CJ-4903-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:237886196_237886197delCT	uc001hyl.1	+						RYR2_uc010pxz.1_Intron	NM_001035	NP_001026	Q92736	RYR2_HUMAN	cardiac muscle ryanodine receptor						cardiac muscle contraction|detection of calcium ion|induction of apoptosis by ionic changes|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum|response to caffeine|response to hypoxia|response to redox state	calcium channel complex|cytosol|plasma membrane|plasma membrane enriched fraction|sarcoplasmic reticulum membrane	calcium ion binding|calmodulin binding|identical protein binding|protein kinase A catalytic subunit binding|protein kinase A regulatory subunit binding|receptor activity|ryanodine-sensitive calcium-release channel activity|suramin binding			ovary(17)|large_intestine(6)|central_nervous_system(6)|pancreas(3)|breast(1)	33	Ovarian(103;0.103)	all_cancers(173;0.000368)|Melanoma(53;0.0179)|all_epithelial(177;0.0225)	OV - Ovarian serous cystadenocarcinoma(106;0.00606)			ctggaatctactctcagcaaat	0.015													4	3	---	---	---	---	
SLC4A5	57835	broad.mit.edu	37	2	74491617	74491618	+	Intron	DEL	GT	-	-	rs71940211		TCGA-CJ-4903-01A-01D-1429-08	TCGA-CJ-4903-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:74491617_74491618delGT	uc002sko.1	-						SLC4A5_uc002skl.2_Intron|SLC4A5_uc002skn.2_Intron|SLC4A5_uc010ffc.1_Intron|SLC4A5_uc002skp.1_Intron|SLC4A5_uc002sks.1_Intron	NM_021196	NP_067019	Q9BY07	S4A5_HUMAN	sodium bicarbonate transporter 4 isoform a							apical plasma membrane|integral to membrane	inorganic anion exchanger activity|sodium:bicarbonate symporter activity			ovary(5)|skin(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)	9						tcaagggcacgtgtgtgtgtgt	0.119													4	2	---	---	---	---	
ACMSD	130013	broad.mit.edu	37	2	135625400	135625401	+	Intron	DEL	TA	-	-			TCGA-CJ-4903-01A-01D-1429-08	TCGA-CJ-4903-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:135625400_135625401delTA	uc002ttz.2	+						ACMSD_uc002tua.2_Intron|uc010zbe.1_Intron	NM_138326	NP_612199	Q8TDX5	ACMSD_HUMAN	aminocarboxymuconate semialdehyde decarboxylase						quinolinate metabolic process|tryptophan catabolic process	cytosol	aminocarboxymuconate-semialdehyde decarboxylase activity|metal ion binding			skin(1)	1				BRCA - Breast invasive adenocarcinoma(221;0.115)		ggattaatgctatatatatata	0.079													4	2	---	---	---	---	
NEB	4703	broad.mit.edu	37	2	152447845	152447846	+	Intron	INS	-	C	C	rs146388415	by1000genomes	TCGA-CJ-4903-01A-01D-1429-08	TCGA-CJ-4903-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:152447845_152447846insC	uc010fnx.2	-							NM_004543	NP_004534	P20929	NEBU_HUMAN	nebulin isoform 3						muscle filament sliding|muscle organ development|regulation of actin filament length|somatic muscle development	actin cytoskeleton|cytosol|Z disc	actin binding|structural constituent of muscle			ovary(8)|large_intestine(5)|breast(3)|central_nervous_system(2)|skin(1)|pancreas(1)	20				BRCA - Breast invasive adenocarcinoma(221;0.219)		TTCCGGTTGGGAAGGAGGAGCT	0.411													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	169770063	169770064	+	IGR	DEL	TG	-	-	rs3830576		TCGA-CJ-4903-01A-01D-1429-08	TCGA-CJ-4903-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:169770063_169770064delTG								G6PC2 (3554 upstream) : ABCB11 (9385 downstream)																							GTTTTGGAGAtgtgtgtgtgtg	0.312													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	172861165	172861168	+	IGR	DEL	CTTC	-	-			TCGA-CJ-4903-01A-01D-1429-08	TCGA-CJ-4903-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:172861165_172861168delCTTC								HAT1 (12566 upstream) : MAP1D (3636 downstream)																							tccttccttgcttccttccttcct	0.054													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	191236966	191236967	+	IGR	DEL	AC	-	-	rs72320033		TCGA-CJ-4903-01A-01D-1429-08	TCGA-CJ-4903-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:191236966_191236967delAC								INPP1 (576 upstream) : MFSD6 (36114 downstream)																							AGACAGGGATacacacacacac	0.188													4	2	---	---	---	---	
PASK	23178	broad.mit.edu	37	2	242075147	242075148	+	Intron	INS	-	C	C	rs140491962	by1000genomes	TCGA-CJ-4903-01A-01D-1429-08	TCGA-CJ-4903-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:242075147_242075148insC	uc002wao.1	-						PASK_uc010zol.1_Intron|PASK_uc010zom.1_Intron|PASK_uc010fzl.1_Intron|PASK_uc010zon.1_Intron|PASK_uc002wap.2_5'Flank|PASK_uc002waq.2_Intron	NM_015148	NP_055963	Q96RG2	PASK_HUMAN	PAS domain containing serine/threonine kinase						regulation of transcription, DNA-dependent	Golgi apparatus	ATP binding|identical protein binding|protein serine/threonine kinase activity|signal transducer activity			ovary(4)|lung(1)|skin(1)	6		all_cancers(19;4.46e-39)|all_epithelial(40;1.34e-17)|Breast(86;1.53e-05)|Renal(207;0.00179)|all_lung(227;0.00481)|Lung NSC(271;0.017)|Ovarian(221;0.0228)|Esophageal squamous(248;0.129)|all_hematologic(139;0.158)|Melanoma(123;0.16)|all_neural(83;0.243)|Hepatocellular(293;0.244)		Epithelial(32;1.34e-31)|all cancers(36;1e-28)|OV - Ovarian serous cystadenocarcinoma(60;3.53e-14)|Kidney(56;4.31e-09)|KIRC - Kidney renal clear cell carcinoma(57;4.35e-08)|BRCA - Breast invasive adenocarcinoma(100;5.64e-06)|Lung(119;0.000596)|LUSC - Lung squamous cell carcinoma(224;0.00481)|Colorectal(34;0.014)|COAD - Colon adenocarcinoma(134;0.0968)		GAAAACAGTCACCCCCTACTCC	0.550													5	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	109093887	109093894	+	IGR	DEL	CCTTCCTG	-	-	rs60684052		TCGA-CJ-4903-01A-01D-1429-08	TCGA-CJ-4903-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:109093887_109093894delCCTTCCTG								DPPA4 (37468 upstream) : FLJ25363 (34943 downstream)																							ttccttccttccttcctgccttccttct	0.038													4	2	---	---	---	---	
ARHGAP31	57514	broad.mit.edu	37	3	119121259	119121262	+	Intron	DEL	GAGG	-	-			TCGA-CJ-4903-01A-01D-1429-08	TCGA-CJ-4903-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:119121259_119121262delGAGG	uc003ecj.3	+							NM_020754	NP_065805	Q2M1Z3	RHG31_HUMAN	Cdc42 GTPase-activating protein						regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol|focal adhesion|lamellipodium	GTPase activator activity			ovary(2)	2						GTAGAGGAGAGAGGGTAtctttcc	0.275													18	19	---	---	---	---	
NOP14	8602	broad.mit.edu	37	4	2953837	2953837	+	Intron	DEL	A	-	-	rs34128991		TCGA-CJ-4903-01A-01D-1429-08	TCGA-CJ-4903-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:2953837delA	uc003ggj.1	-						C4orf10_uc003ggi.1_Intron|NOP14_uc010icp.2_Intron|NOP14_uc003ggk.3_Intron|NOP14_uc003ggl.2_Intron|NOP14_uc010icq.1_Intron	NM_003703	NP_003694	P78316	NOP14_HUMAN	probable nucleolar complex protein 14						endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)|endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)|endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA)	mitochondrion|Noc4p-Nop14p complex|small-subunit processome	snoRNA binding			pancreas(1)	1						tgtctcaaagaaaaaaaaaaa	0.129													4	5	---	---	---	---	
LAP3	51056	broad.mit.edu	37	4	17583329	17583330	+	Intron	INS	-	A	A			TCGA-CJ-4903-01A-01D-1429-08	TCGA-CJ-4903-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:17583329_17583330insA	uc003gph.1	+						LAP3_uc010ieg.2_Intron	NM_015907	NP_056991	P28838	AMPL_HUMAN	leucine aminopeptidase 3						proteolysis	nucleus	aminopeptidase activity|magnesium ion binding|manganese ion binding|metalloexopeptidase activity|zinc ion binding				0						TGTGCCTTCCCAAGTGAACCGA	0.396													59	28	---	---	---	---	
SRP72	6731	broad.mit.edu	37	4	57336139	57336139	+	Intron	DEL	T	-	-	rs34334701		TCGA-CJ-4903-01A-01D-1429-08	TCGA-CJ-4903-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:57336139delT	uc003hbv.2	+						SRP72_uc010ihe.2_Intron	NM_006947	NP_008878	O76094	SRP72_HUMAN	signal recognition particle 72kDa						response to drug|SRP-dependent cotranslational protein targeting to membrane	cytosol|nucleolus|plasma membrane|signal recognition particle, endoplasmic reticulum targeting	7S RNA binding|signal recognition particle binding			ovary(1)	1	Glioma(25;0.08)|all_neural(26;0.101)					CCTTAGAGAGTTTTTTTTTTT	0.373													5	3	---	---	---	---	
SHROOM3	57619	broad.mit.edu	37	4	77589728	77589731	+	Intron	DEL	AAAC	-	-	rs35876473		TCGA-CJ-4903-01A-01D-1429-08	TCGA-CJ-4903-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:77589728_77589731delAAAC	uc011cbx.1	+							NM_020859	NP_065910	Q8TF72	SHRM3_HUMAN	shroom family member 3 protein						apical protein localization|cell morphogenesis|cellular pigment accumulation|pattern specification process|regulation of cell shape	adherens junction|apical junction complex|apical plasma membrane|cytoplasm|microtubule	actin binding			skin(2)|ovary(1)	3			Lung(101;0.0903)			ctccgcctcaaaacaaacaaacaa	0.123													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	79569453	79569454	+	Intron	INS	-	T	T			TCGA-CJ-4903-01A-01D-1429-08	TCGA-CJ-4903-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:79569453_79569454insT	uc003hlf.2	+						uc003hlg.2_Intron|uc003hlh.2_Intron|uc003hli.2_Intron					Homo sapiens cDNA FLJ32651 fis, clone SYNOV2001581.																		ttccttccttcctccctccctc	0.005													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	119428156	119428156	+	IGR	DEL	T	-	-			TCGA-CJ-4903-01A-01D-1429-08	TCGA-CJ-4903-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:119428156delT								PRSS12 (154234 upstream) : CEP170L (9339 downstream)																							GCATAAAttcttttttttttt	0.179													9	5	---	---	---	---	
TMEM154	201799	broad.mit.edu	37	4	153564510	153564513	+	Intron	DEL	ACAA	-	-	rs71919721		TCGA-CJ-4903-01A-01D-1429-08	TCGA-CJ-4903-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:153564510_153564513delACAA	uc003imw.1	-							NM_152680	NP_689893	Q6P9G4	TM154_HUMAN	transmembrane protein 154 precursor							integral to membrane					0	all_hematologic(180;0.093)	Acute lymphoblastic leukemia(8;0.138)				AGGCTACCACACAAACAAACATAC	0.485													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	16629720	16629727	+	IGR	DEL	TGTGTGTT	-	-	rs10604847		TCGA-CJ-4903-01A-01D-1429-08	TCGA-CJ-4903-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:16629720_16629727delTGTGTGTT								FAM134B (12602 upstream) : MYO10 (32290 downstream)																							tgtgtgtgtgtgtgtgtttttacgcgta	0.000													4	3	---	---	---	---	
PDZD2	23037	broad.mit.edu	37	5	32000586	32000597	+	Intron	DEL	TTTGTTTTTGTT	-	-	rs71863988		TCGA-CJ-4903-01A-01D-1429-08	TCGA-CJ-4903-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:32000586_32000597delTTTGTTTTTGTT	uc003jhl.2	+						PDZD2_uc003jhm.2_Intron|PDZD2_uc011cnx.1_Intron	NM_178140	NP_835260	O15018	PDZD2_HUMAN	PDZ domain containing 2						cell adhesion	cell-cell junction|endoplasmic reticulum|extracellular region|nucleus				central_nervous_system(4)|ovary(2)|skin(2)|large_intestine(1)	9						CCTTAAGAAGtttgtttttgtttttgtttttg	0.222													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	58184874	58184875	+	IGR	DEL	AA	-	-			TCGA-CJ-4903-01A-01D-1429-08	TCGA-CJ-4903-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:58184874_58184875delAA								RAB3C (37469 upstream) : PDE4D (79991 downstream)																							agaaagaaagaaagaaagaaag	0.025													5	6	---	---	---	---	
RASGRF2	5924	broad.mit.edu	37	5	80404654	80404659	+	Intron	DEL	TGTGTG	-	-	rs143382125		TCGA-CJ-4903-01A-01D-1429-08	TCGA-CJ-4903-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:80404654_80404659delTGTGTG	uc003kha.1	+						RASGRF2_uc011ctn.1_Intron	NM_006909	NP_008840	O14827	RGRF2_HUMAN	Ras protein-specific guanine						apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction|synaptic transmission	cytosol|endoplasmic reticulum membrane|plasma membrane	protein binding|Rho guanyl-nucleotide exchange factor activity			breast(5)|ovary(3)|large_intestine(2)|central_nervous_system(1)|skin(1)	12		Lung NSC(167;0.00498)|all_lung(232;0.00531)|Ovarian(174;0.0357)		OV - Ovarian serous cystadenocarcinoma(54;4.22e-42)|Epithelial(54;4.04e-35)|all cancers(79;2.52e-29)		TTACCTACTCtgtgtgtgtgtgtgtg	0.272													4	2	---	---	---	---	
ERAP1	51752	broad.mit.edu	37	5	96111927	96111928	+	3'UTR	INS	-	AGCCCATTCATGAAAA	AGCCCATTCATGAAAA	rs142866043	by1000genomes	TCGA-CJ-4903-01A-01D-1429-08	TCGA-CJ-4903-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:96111927_96111928insAGCCCATTCATGAAAA	uc003kmm.2	-	19					CAST_uc003kmk.2_Intron|ERAP1_uc003kml.2_Intron|ERAP1_uc010jbm.1_Intron|ERAP1_uc003kmn.2_3'UTR	NM_001040458	NP_001035548	Q9NZ08	ERAP1_HUMAN	type 1 tumor necrosis factor receptor shedding						angiogenesis|antigen processing and presentation of endogenous peptide antigen via MHC class I|fat cell differentiation|membrane protein ectodomain proteolysis|regulation of blood pressure|regulation of innate immune response|response to bacterium	cytosol|endoplasmic reticulum lumen|endoplasmic reticulum membrane|extracellular region|integral to membrane	aminopeptidase activity|interleukin-1, Type II receptor binding|interleukin-6 receptor binding|metalloexopeptidase activity|zinc ion binding			ovary(1)|pancreas(1)	2		all_cancers(142;1.75e-06)|all_epithelial(76;3.08e-09)|all_lung(232;0.000435)|Lung NSC(167;0.000601)|Ovarian(225;0.024)|Colorectal(57;0.0432)|Breast(839;0.244)		all cancers(79;7.26e-15)|COAD - Colon adenocarcinoma(37;0.071)		ATGGTAGCGATAGCCCATTCAT	0.416													8	4	---	---	---	---	
HSPA4	3308	broad.mit.edu	37	5	132388088	132388088	+	Intron	DEL	G	-	-			TCGA-CJ-4903-01A-01D-1429-08	TCGA-CJ-4903-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:132388088delG	uc003kyj.2	+							NM_002154	NP_002145	P34932	HSP74_HUMAN	heat shock 70kDa protein 4						cellular chaperone-mediated protein complex assembly|protein import into mitochondrial outer membrane|response to unfolded protein	cytoplasm|nucleus	ATP binding			lung(1)|breast(1)	2			KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			ACTGGGGTTAGGAGATAATGC	0.667													4	2	---	---	---	---	
MYOT	9499	broad.mit.edu	37	5	137205977	137205978	+	Intron	INS	-	ACAC	ACAC			TCGA-CJ-4903-01A-01D-1429-08	TCGA-CJ-4903-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:137205977_137205978insACAC	uc011cye.1	+						MYOT_uc003lbv.2_Intron|MYOT_uc011cyg.1_Intron|MYOT_uc011cyh.1_Intron	NM_001135940	NP_001129412	Q9UBF9	MYOTI_HUMAN	myotilin isoform b						muscle contraction	actin cytoskeleton|sarcolemma|sarcomere	actin binding|structural constituent of muscle			large_intestine(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0109)			GATTAAGCAAGacacacacaca	0.144													4	3	---	---	---	---	
LARS	51520	broad.mit.edu	37	5	145518292	145518292	+	Intron	DEL	A	-	-			TCGA-CJ-4903-01A-01D-1429-08	TCGA-CJ-4903-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:145518292delA	uc003lnx.1	-						LARS_uc011dbq.1_Intron|LARS_uc011dbr.1_Intron|LARS_uc011dbs.1_Intron	NM_020117	NP_064502	Q9P2J5	SYLC_HUMAN	leucyl-tRNA synthetase						leucyl-tRNA aminoacylation	cytosol	ATP binding|leucine-tRNA ligase activity|protein binding				0			KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)		L-Leucine(DB00149)	actctgtctcaaaaaaaaaaa	0.114													4	2	---	---	---	---	
GALNT10	55568	broad.mit.edu	37	5	153581135	153581137	+	Intron	DEL	TTG	-	-			TCGA-CJ-4903-01A-01D-1429-08	TCGA-CJ-4903-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:153581135_153581137delTTG	uc003lvh.2	+						GALNT10_uc003lvg.1_Intron|GALNT10_uc010jic.2_Intron	NM_198321	NP_938080	Q86SR1	GLT10_HUMAN	GalNAc transferase 10 isoform a							Golgi membrane|integral to membrane	metal ion binding|polypeptide N-acetylgalactosaminyltransferase activity|sugar binding			skin(2)	2	Renal(175;0.00488)	Medulloblastoma(196;0.0354)|all_neural(177;0.147)|all_hematologic(541;0.21)	Kidney(363;8.21e-05)|KIRC - Kidney renal clear cell carcinoma(527;0.000577)			TAATAAAGTTttgttgttgttgt	0.291													4	2	---	---	---	---	
HLA-DRB5	3127	broad.mit.edu	37	6	32557290	32557291	+	Intron	INS	-	T	T	rs145132878	by1000genomes	TCGA-CJ-4903-01A-01D-1429-08	TCGA-CJ-4903-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:32557290_32557291insT	uc003obk.3	-						HLA-DRB1_uc003obp.3_Intron	NM_002125	NP_002116	Q30154	DRB5_HUMAN	major histocompatibility complex, class II, DR						antigen processing and presentation of peptide or polysaccharide antigen via MHC class II|immune response	endoplasmic reticulum membrane|Golgi apparatus|integral to membrane|late endosome membrane|lysosomal membrane|MHC class II protein complex					0						TTTGGGATCCAATGATAAAGAT	0.416													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	44658013	44658016	+	IGR	DEL	AAGG	-	-			TCGA-CJ-4903-01A-01D-1429-08	TCGA-CJ-4903-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:44658013_44658016delAAGG								CDC5L (243234 upstream) : SUPT3H (119038 downstream)																							gcaagaaggcaaggaaggaaggaa	0.005													4	2	---	---	---	---	
CDK19	23097	broad.mit.edu	37	6	110948558	110948559	+	Intron	DEL	TA	-	-			TCGA-CJ-4903-01A-01D-1429-08	TCGA-CJ-4903-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:110948558_110948559delTA	uc003puh.1	-						CDK19_uc003pui.1_Intron|CDK19_uc011eax.1_Intron	NM_015076	NP_055891	Q9BWU1	CDK19_HUMAN	cell division cycle 2-like 6 (CDK8-like)								ATP binding|cyclin-dependent protein kinase activity|protein binding			ovary(2)|central_nervous_system(1)|skin(1)	4						tgtgtatgtgtatatatatata	0.153													4	2	---	---	---	---	
ROS1	6098	broad.mit.edu	37	6	117631544	117631544	+	Intron	DEL	T	-	-			TCGA-CJ-4903-01A-01D-1429-08	TCGA-CJ-4903-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:117631544delT	uc003pxp.1	-						ROS1_uc011ebi.1_Intron	NM_002944	NP_002935	P08922	ROS_HUMAN	proto-oncogene c-ros-1 protein precursor						transmembrane receptor protein tyrosine kinase signaling pathway	membrane fraction|sodium:potassium-exchanging ATPase complex	ATP binding|transmembrane receptor protein tyrosine kinase activity			lung(8)|ovary(6)|central_nervous_system(3)|skin(3)|stomach(2)|breast(2)|large_intestine(1)	25		all_cancers(87;0.00846)|all_epithelial(87;0.0242)		GBM - Glioblastoma multiforme(226;0.0387)|OV - Ovarian serous cystadenocarcinoma(136;0.0954)|all cancers(137;0.137)		AGAGAAACTAttttttttttt	0.139			T	GOPC|ROS1	glioblastoma|NSCLC								13	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	46174653	46174654	+	IGR	DEL	AC	-	-	rs112792176		TCGA-CJ-4903-01A-01D-1429-08	TCGA-CJ-4903-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:46174653_46174654delAC								IGFBP3 (213782 upstream) : None (None downstream)																							acacacacatacacacacacac	0.178													7	5	---	---	---	---	
DLX5	1749	broad.mit.edu	37	7	96652650	96652653	+	Intron	DEL	GTGT	-	-	rs150476513		TCGA-CJ-4903-01A-01D-1429-08	TCGA-CJ-4903-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:96652650_96652653delGTGT	uc003uon.2	-						DLX5_uc011kim.1_Intron	NM_005221	NP_005212	P56178	DLX5_HUMAN	distal-less homeobox 5						cell proliferation|endochondral ossification|osteoblast differentiation|positive regulation of transcription, DNA-dependent	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding			ovary(1)	1	all_cancers(62;9.56e-09)|all_epithelial(64;7.38e-09)|Esophageal squamous(72;0.0125)|all_lung(186;0.0855)|Lung NSC(181;0.0858)					CCTCTCCAGGgtgtgtgtgtgtgt	0.451													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	98108146	98108152	+	IGR	DEL	CTGTCAC	-	-	rs112906827		TCGA-CJ-4903-01A-01D-1429-08	TCGA-CJ-4903-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:98108146_98108152delCTGTCAC								BAIAP2L1 (77719 upstream) : NPTX2 (138445 downstream)																							gagtcttgctctgtcacccaggctgga	0.116													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	98409190	98409190	+	IGR	DEL	T	-	-	rs112577704		TCGA-CJ-4903-01A-01D-1429-08	TCGA-CJ-4903-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:98409190delT								NPTX2 (150009 upstream) : TMEM130 (34922 downstream)																							gtggtgatggttggtggtggt	0.085													4	3	---	---	---	---	
LOC100124692	100124692	broad.mit.edu	37	7	141894493	141894496	+	Intron	DEL	TGTA	-	-	rs67006045		TCGA-CJ-4903-01A-01D-1429-08	TCGA-CJ-4903-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:141894493_141894496delTGTA	uc003vxa.2	+							NR_003717				Homo sapiens cDNA FLJ16351 fis, clone TESTI2039060, moderately similar to Maltase-glucoamylase, intestinal.												0						AGAACAtgtgtgtatgtgtgtgtg	0.211													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	48144963	48144963	+	IGR	DEL	A	-	-			TCGA-CJ-4903-01A-01D-1429-08	TCGA-CJ-4903-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:48144963delA								BEYLA (377556 upstream) : KIAA0146 (28579 downstream)																							agcaagactcaaaaaaaaaaa	0.000													4	2	---	---	---	---	
TMEM74	157753	broad.mit.edu	37	8	109778429	109778430	+	Intron	INS	-	TTCC	TTCC	rs150712271	by1000genomes	TCGA-CJ-4903-01A-01D-1429-08	TCGA-CJ-4903-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:109778429_109778430insTTCC	uc003ymx.2	-									Q96NL1	TMM74_HUMAN	Homo sapiens cDNA FLJ30668 fis, clone FCBBF1000675.						autophagy	autophagic vacuole membrane|cytoplasmic vesicle|integral to membrane|lysosomal membrane				ovary(1)|lung(1)|kidney(1)|skin(1)	4			OV - Ovarian serous cystadenocarcinoma(57;3.08e-10)			TTAtttctcctttccttccttc	0.243													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	24133869	24133870	+	IGR	INS	-	TG	TG	rs147247136	by1000genomes	TCGA-CJ-4903-01A-01D-1429-08	TCGA-CJ-4903-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:24133869_24133870insTG								ELAVL2 (307806 upstream) : None (None downstream)																							TGGTGCACgtatgtgtgtgtgt	0.317													2	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	33617692	33617703	+	5'Flank	DEL	GGATGTAACACG	-	-	rs113178723		TCGA-CJ-4903-01A-01D-1429-08	TCGA-CJ-4903-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:33617692_33617703delGGATGTAACACG	uc003ztf.1	+											Homo sapiens patient CS-1 clone 1 T cell receptor beta chain CDR3 (TCRB) mRNA, partial cds.																		GCAGAGAGATGGATGTAACACGGGTCATGAGC	0.349											OREG0019139	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	4	2	---	---	---	---	
ANKRD20A3	441425	broad.mit.edu	37	9	67934791	67934794	+	Frame_Shift_Del	DEL	AAAG	-	-			TCGA-CJ-4903-01A-01D-1429-08	TCGA-CJ-4903-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:67934791_67934794delAAAG	uc004aeu.2	+	4	673_676	c.561_564delAAAG	c.(559-564)AAAAGGfs	p.K187fs	ANKRD20A3_uc010mnn.2_Frame_Shift_Del_p.K187fs	NM_001012419	NP_001012419	Q5VUR7	A20A3_HUMAN	ankyrin repeat domain 20 family, member A3	187_188	ANK 4.										0						TTTTATTGAAAAAGAAAGCAAGTT	0.309													4	4	---	---	---	---	
HIATL1	84641	broad.mit.edu	37	9	97208894	97208894	+	Intron	DEL	T	-	-			TCGA-CJ-4903-01A-01D-1429-08	TCGA-CJ-4903-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:97208894delT	uc004aur.2	+						HIATL1_uc011luh.1_Intron	NM_032558	NP_115947	Q5SR56	HIAL1_HUMAN	hippocampus abundant transcript-like 1						transmembrane transport	integral to membrane|plasma membrane	protein binding|transporter activity			ovary(2)	2		Acute lymphoblastic leukemia(62;0.136)				ATTTTTTTGCTTTTTTTTTTA	0.313													4	2	---	---	---	---	
MEGF9	1955	broad.mit.edu	37	9	123374143	123374144	+	Intron	INS	-	AGAG	AGAG	rs141696481	by1000genomes	TCGA-CJ-4903-01A-01D-1429-08	TCGA-CJ-4903-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:123374143_123374144insAGAG	uc004bkj.1	-						MEGF9_uc011lyb.1_Intron	NM_001080497	NP_001073966	Q9H1U4	MEGF9_HUMAN	multiple EGF-like-domains 9							integral to membrane	calcium ion binding				0						ggaaggaagaaagagagagaga	0.040													6	3	---	---	---	---	
STRBP	55342	broad.mit.edu	37	9	125887689	125887690	+	3'UTR	INS	-	T	T	rs34536381		TCGA-CJ-4903-01A-01D-1429-08	TCGA-CJ-4903-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:125887689_125887690insT	uc004bns.2	-	19					STRBP_uc004bnt.2_3'UTR|STRBP_uc004bnu.2_3'UTR|STRBP_uc004bnv.2_3'UTR|STRBP_uc004bnr.2_3'UTR	NM_018387	NP_060857	Q96SI9	STRBP_HUMAN	spermatid perinuclear RNA binding protein						multicellular organismal development	cytoplasm|nucleus	DNA binding			breast(1)|skin(1)	2						GAACTGGTTTCTTTTTTTTTTT	0.292													3	3	---	---	---	---	
TRUB2	26995	broad.mit.edu	37	9	131075834	131075834	+	Intron	DEL	G	-	-			TCGA-CJ-4903-01A-01D-1429-08	TCGA-CJ-4903-11A-01D-1429-08									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													4	3	---	---	---	---	
CCBL1	883	broad.mit.edu	37	9	131598582	131598582	+	Intron	DEL	T	-	-	rs71497420		TCGA-CJ-4903-01A-01D-1429-08	TCGA-CJ-4903-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:131598582delT	uc004bwh.2	-						CCBL1_uc004bwf.2_Intron|CCBL1_uc004bwg.2_Intron|CCBL1_uc010myn.2_Intron|CCBL1_uc004bwj.2_Intron|CCBL1_uc011mbl.1_Intron|CCBL1_uc004bwi.2_Intron|CCBL1_uc010myo.2_Intron	NM_004059	NP_004050	Q16773	KAT1_HUMAN	kynurenine aminotransferase I isoform a						kynurenine metabolic process|L-phenylalanine catabolic process|tryptophan catabolic process	cytosol|nucleus	1-aminocyclopropane-1-carboxylate synthase activity|cysteine-S-conjugate beta-lyase activity|glutamine-phenylpyruvate transaminase activity|kynurenine-oxoglutarate transaminase activity|L-glutamine:pyruvate aminotransferase activity|L-phenylalanine:pyruvate aminotransferase activity|protein homodimerization activity|pyridoxal phosphate binding			ovary(1)	1					L-Glutamine(DB00130)|Pyridoxal Phosphate(DB00114)	tctttctttgttttttttttt	0.090													2	4	---	---	---	---	
ITIH5	80760	broad.mit.edu	37	10	7628110	7628110	+	Intron	DEL	G	-	-	rs78819948		TCGA-CJ-4903-01A-01D-1429-08	TCGA-CJ-4903-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:7628110delG	uc001ijq.2	-						ITIH5_uc001ijp.2_Intron|ITIH5_uc001ijr.1_Intron	NM_030569	NP_085046	Q86UX2	ITIH5_HUMAN	inter-alpha trypsin inhibitor heavy chain						hyaluronan metabolic process	extracellular region	serine-type endopeptidase inhibitor activity			ovary(2)|central_nervous_system(2)	4						AACCGCCCCCGCCCCCCAGGA	0.478													8	9	---	---	---	---	
YME1L1	10730	broad.mit.edu	37	10	27434230	27434231	+	Intron	INS	-	A	A	rs117799729		TCGA-CJ-4903-01A-01D-1429-08	TCGA-CJ-4903-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:27434230_27434231insA	uc001iti.2	-						YME1L1_uc001itj.2_Intron|YME1L1_uc010qdl.1_Intron|YME1L1_uc009xkv.2_Intron	NM_139312	NP_647473	Q96TA2	YMEL1_HUMAN	YME1-like 1 isoform 1						protein catabolic process|proteolysis	membrane|mitochondrion	ATP binding|metal ion binding|metalloendopeptidase activity|nucleoside-triphosphatase activity			ovary(1)	1						AAAAAAAAAACAAAAAAAAAAC	0.158													7	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	31435693	31435694	+	IGR	DEL	CG	-	-	rs146437327		TCGA-CJ-4903-01A-01D-1429-08	TCGA-CJ-4903-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:31435693_31435694delCG								ZNF438 (114827 upstream) : LOC220930 (169764 downstream)																							CGTacacacacgcacacacaca	0.431													1	5	---	---	---	---	
HERC4	26091	broad.mit.edu	37	10	69705574	69705578	+	Intron	DEL	AACAT	-	-	rs35496892		TCGA-CJ-4903-01A-01D-1429-08	TCGA-CJ-4903-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:69705574_69705578delAACAT	uc001jng.3	-						HERC4_uc009xpq.2_Intron|HERC4_uc001jnf.3_Intron|HERC4_uc001jnh.3_Intron|HERC4_uc009xpr.2_Intron|HERC4_uc001jni.3_Intron	NM_022079	NP_071362	Q5GLZ8	HERC4_HUMAN	hect domain and RLD 4 isoform a						cell differentiation|protein ubiquitination involved in ubiquitin-dependent protein catabolic process|spermatogenesis	cytosol	ubiquitin-protein ligase activity			ovary(1)|breast(1)|skin(1)	3						caaatcaaaaaacatacgacagata	0.000													7	4	---	---	---	---	
TRIM5	85363	broad.mit.edu	37	11	5856033	5856034	+	Intron	DEL	AC	-	-			TCGA-CJ-4903-01A-01D-1429-08	TCGA-CJ-4903-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:5856033_5856034delAC	uc001mbq.1	-							NM_033093	NP_149084	Q9C035	TRIM5_HUMAN	tripartite motif protein TRIM5 isoform delta						interspecies interaction between organisms|protein trimerization|response to virus	cytoplasm|cytoplasmic mRNA processing body	ligase activity|protein binding|protein homodimerization activity|zinc ion binding			ovary(1)	1		Medulloblastoma(188;0.00225)|Breast(177;0.0204)|all_neural(188;0.0212)|Lung NSC(207;0.138)|all_lung(207;0.221)		Epithelial(150;7.21e-09)|BRCA - Breast invasive adenocarcinoma(625;0.139)		tcaaacacaaacacacacacac	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	31086042	31086042	+	Frame_Shift_Del	DEL	C	-	-			TCGA-CJ-4903-01A-01D-1429-08	TCGA-CJ-4903-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:31086042delC	uc009yjk.1	-	8	978	c.909delG	c.(907-909)GAGfs	p.E303fs	uc009yjl.1_Frame_Shift_Del_p.E231fs|DCDC1_uc001msu.1_Frame_Shift_Del_p.E474fs					RecName: Full=Doublecortin domain-containing protein 5;																		TAGGATGTTTCTCTTCCAGTT	0.458													275	167	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	43030066	43030067	+	IGR	INS	-	GGAAGGAAGGAAGGAAGGAA	GGAAGGAAGGAAGGAAGGAA	rs72187229		TCGA-CJ-4903-01A-01D-1429-08	TCGA-CJ-4903-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:43030066_43030067insGGAAGGAAGGAAGGAAGGAA								None (None upstream) : API5 (303438 downstream)																							aaggaagaaagggaaggaagga	0.059													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	56249399	56249402	+	IGR	DEL	AAGG	-	-			TCGA-CJ-4903-01A-01D-1429-08	TCGA-CJ-4903-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:56249399_56249402delAAGG								OR5M3 (11426 upstream) : OR5M8 (8509 downstream)																							gaaacaaagaaaggaaggaaggaa	0.000													2	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	56524183	56524184	+	IGR	DEL	AA	-	-	rs143565690	by1000genomes	TCGA-CJ-4903-01A-01D-1429-08	TCGA-CJ-4903-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:56524183_56524184delAA								OR9G4 (12896 upstream) : OR5AK2 (232205 downstream)																							agaaagaaagaaagagagagag	0.114													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	59066312	59066312	+	IGR	DEL	G	-	-			TCGA-CJ-4903-01A-01D-1429-08	TCGA-CJ-4903-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:59066312delG								MPEG1 (85818 upstream) : OR5AN1 (65620 downstream)																							aggaaagaaaggaaagaaaga	0.000													2	4	---	---	---	---	
PDE2A	5138	broad.mit.edu	37	11	72307526	72307527	+	Intron	INS	-	CACA	CACA	rs72424917		TCGA-CJ-4903-01A-01D-1429-08	TCGA-CJ-4903-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:72307526_72307527insCACA	uc010rrc.1	-						PDE2A_uc001oso.2_Intron|PDE2A_uc010rra.1_Intron|PDE2A_uc001osn.2_Intron|PDE2A_uc010rrb.1_Intron|PDE2A_uc010rrd.1_Intron	NM_002599	NP_002590	O00408	PDE2A_HUMAN	phosphodiesterase 2A isoform 1						platelet activation|signal transduction	cytosol	3',5'-cyclic-AMP phosphodiesterase activity|3',5'-cyclic-GMP phosphodiesterase activity|cGMP binding|cGMP-stimulated cyclic-nucleotide phosphodiesterase activity|metal ion binding			ovary(2)|breast(1)|skin(1)	4			BRCA - Breast invasive adenocarcinoma(5;3.55e-05)		Sildenafil(DB00203)|Sulindac(DB00605)	tctctctctctctcacacacac	0.446													4	2	---	---	---	---	
PPP2R1B	5519	broad.mit.edu	37	11	111625493	111625493	+	Intron	DEL	T	-	-			TCGA-CJ-4903-01A-01D-1429-08	TCGA-CJ-4903-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:111625493delT	uc001plx.1	-						PPP2R1B_uc001plw.1_Intron|PPP2R1B_uc010rwi.1_Intron|PPP2R1B_uc010rwj.1_Intron|PPP2R1B_uc010rwk.1_Intron|PPP2R1B_uc010rwl.1_Intron	NM_002716	NP_002707	P30154	2AAB_HUMAN	beta isoform of regulatory subunit A, protein								protein binding				0		all_cancers(61;2.34e-15)|all_epithelial(67;1.72e-09)|Melanoma(852;1.91e-06)|all_hematologic(158;0.000405)|Acute lymphoblastic leukemia(157;0.000967)|Breast(348;0.0112)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)		BRCA - Breast invasive adenocarcinoma(274;1.13e-06)|Epithelial(105;2.36e-06)|all cancers(92;3.78e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.0761)		CTGAAAGGCATTTTTTTTTTT	0.294													3	3	---	---	---	---	
DLAT	1737	broad.mit.edu	37	11	111897044	111897047	+	Intron	DEL	TTAA	-	-	rs59734230		TCGA-CJ-4903-01A-01D-1429-08	TCGA-CJ-4903-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:111897044_111897047delTTAA	uc001pmo.2	+						DLAT_uc009yyk.1_Intron|DLAT_uc010rwr.1_Intron	NM_001931	NP_001922	P10515	ODP2_HUMAN	dihydrolipoamide S-acetyltransferase precursor						glycolysis|regulation of acetyl-CoA biosynthetic process from pyruvate	mitochondrial pyruvate dehydrogenase complex	dihydrolipoyllysine-residue acetyltransferase activity|protein binding				0		all_cancers(61;4.53e-11)|all_epithelial(67;2.76e-06)|Melanoma(852;9.42e-06)|all_hematologic(158;0.000885)|Acute lymphoblastic leukemia(157;0.000966)|Breast(348;0.0512)|Medulloblastoma(222;0.0523)|all_neural(223;0.0663)		Epithelial(105;4.87e-07)|BRCA - Breast invasive adenocarcinoma(274;6.83e-07)|all cancers(92;9.63e-06)|OV - Ovarian serous cystadenocarcinoma(223;0.0557)	NADH(DB00157)	ttttttttttttaattaatttatt	0.201													10	5	---	---	---	---	
C11orf63	79864	broad.mit.edu	37	11	122805949	122805949	+	Intron	DEL	T	-	-			TCGA-CJ-4903-01A-01D-1429-08	TCGA-CJ-4903-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:122805949delT	uc001pym.2	+							NM_024806	NP_079082	Q6NUN7	CK063_HUMAN	hypothetical protein LOC79864 isoform 1											ovary(3)	3		Breast(109;0.00249)|Lung NSC(97;0.0177)|all_lung(97;0.018)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;5.34e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0311)		AAGAGTCCACttttttttttt	0.244													4	2	---	---	---	---	
ETS1	2113	broad.mit.edu	37	11	128348234	128348235	+	Intron	INS	-	A	A			TCGA-CJ-4903-01A-01D-1429-08	TCGA-CJ-4903-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:128348234_128348235insA	uc010sbs.1	-						ETS1_uc001qej.2_Intron|ETS1_uc009zch.2_Intron|ETS1_uc009zcg.2_Intron	NM_005238	NP_005229	P14921	ETS1_HUMAN	v-ets erythroblastosis virus E26 oncogene						cell motility|immune response|induction of apoptosis|negative regulation of cell cycle|negative regulation of cell cycle|negative regulation of cell proliferation|PML body organization|positive regulation of cellular component movement|positive regulation of erythrocyte differentiation|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription, DNA-dependent|response to antibiotic|transcription from RNA polymerase II promoter	nucleus|nucleus	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|sequence-specific DNA binding transcription factor activity|transcription factor binding			lung(4)|central_nervous_system(1)|pleura(1)	6	all_hematologic(175;0.0537)	Lung NSC(97;0.000542)|all_lung(97;0.000665)|Breast(109;0.00765)|all_neural(223;0.0351)|Medulloblastoma(222;0.0425)		BRCA - Breast invasive adenocarcinoma(274;1.47e-05)|OV - Ovarian serous cystadenocarcinoma(99;0.0174)|LUSC - Lung squamous cell carcinoma(976;0.0815)|Lung(307;0.0833)		aggaaggaaggaggaaggaagg	0.010													4	2	---	---	---	---	
RAPGEF3	10411	broad.mit.edu	37	12	48151827	48151830	+	5'UTR	DEL	CCCA	-	-			TCGA-CJ-4903-01A-01D-1429-08	TCGA-CJ-4903-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:48151827_48151830delCCCA	uc009zkp.2	-	1					RAPGEF3_uc009zkq.2_5'UTR|RAPGEF3_uc001rpz.3_Frame_Shift_Del_p.V13fs|RAPGEF3_uc009zkr.2_RNA|RAPGEF3_uc009zks.2_Frame_Shift_Del_p.V25fs|RAPGEF3_uc001rqb.3_Frame_Shift_Del_p.V13fs	NM_001098532	NP_001092002	A8K2G5	A8K2G5_HUMAN	Rap guanine nucleotide exchange factor 3 isoform						regulation of protein phosphorylation|regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cAMP-dependent protein kinase complex	cAMP-dependent protein kinase regulator activity|guanyl-nucleotide exchange factor activity			lung(2)|skin(1)|pancreas(1)	4	Lung SC(27;0.192)			GBM - Glioblastoma multiforme(48;0.0375)		CACAGCCAGGCCCACCTGCCAGCA	0.657													8	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	76619889	76619890	+	IGR	DEL	TG	-	-	rs3034375		TCGA-CJ-4903-01A-01D-1429-08	TCGA-CJ-4903-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:76619889_76619890delTG								NAP1L1 (141151 upstream) : BBS10 (118376 downstream)																							tacctcacattgtgtgtgtgtg	0.000													4	2	---	---	---	---	
PLEKHG7	440107	broad.mit.edu	37	12	93155419	93155419	+	Intron	DEL	A	-	-	rs145042614	by1000genomes	TCGA-CJ-4903-01A-01D-1429-08	TCGA-CJ-4903-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:93155419delA	uc001tcj.2	+							NM_001004330	NP_001004330	Q6ZR37	PKHG7_HUMAN	pleckstrin homology domain containing, family G						regulation of Rho protein signal transduction	intracellular	Rho guanyl-nucleotide exchange factor activity			ovary(1)	1						agaaagaaagaaagaaagaaa	0.090													6	7	---	---	---	---	
GPC6	10082	broad.mit.edu	37	13	94020591	94020602	+	Intron	DEL	TTCCTTCCTTCC	-	-			TCGA-CJ-4903-01A-01D-1429-08	TCGA-CJ-4903-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:94020591_94020602delTTCCTTCCTTCC	uc001vlt.2	+						GPC6_uc010tig.1_Intron	NM_005708	NP_005699	Q9Y625	GPC6_HUMAN	glypican 6 precursor							anchored to membrane|extracellular space|integral to plasma membrane|proteinaceous extracellular matrix	heparan sulfate proteoglycan binding				0	all_neural(89;0.0684)|Medulloblastoma(90;0.163)	all_cancers(2;5.48e-07)|all_epithelial(2;5.69e-08)|all_lung(2;2.19e-05)|Lung NSC(4;6.09e-05)|Breast(118;0.0395)|Renal(2;0.0568)|Hepatocellular(115;0.217)				cctccctgctttccttccttccttccttcctt	0.042													10	5	---	---	---	---	
ABCC4	10257	broad.mit.edu	37	13	95848985	95848991	+	Intron	DEL	AGAAGGG	-	-	rs113892410		TCGA-CJ-4903-01A-01D-1429-08	TCGA-CJ-4903-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:95848985_95848991delAGAAGGG	uc001vmd.3	-						ABCC4_uc010afk.2_Intron|ABCC4_uc001vme.2_Intron|ABCC4_uc010tih.1_Intron|ABCC4_uc001vmf.2_Intron|ABCC4_uc010afl.1_Intron|ABCC4_uc010afm.1_Intron	NM_005845	NP_005836	O15439	MRP4_HUMAN	ATP-binding cassette, sub-family C, member 4						platelet activation|platelet degranulation	integral to membrane|membrane fraction|plasma membrane|platelet dense granule membrane	15-hydroxyprostaglandin dehydrogenase (NAD+) activity|ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|chloride channel activity			central_nervous_system(3)|skin(1)	4	all_neural(89;0.0878)|Medulloblastoma(90;0.163)				Cefazolin(DB01327)	gaaggaaggaagaagggagggagggaa	0.135													6	3	---	---	---	---	
SLC15A1	6564	broad.mit.edu	37	13	99336799	99336800	+	3'UTR	INS	-	A	A			TCGA-CJ-4903-01A-01D-1429-08	TCGA-CJ-4903-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:99336799_99336800insA	uc001vno.2	-	23						NM_005073	NP_005064	P46059	S15A1_HUMAN	solute carrier family 15 (oligopeptide						digestion|protein transport	integral to plasma membrane|membrane fraction	peptide:hydrogen symporter activity			ovary(1)	1	all_neural(89;0.101)|Medulloblastoma(90;0.18)|Lung SC(71;0.184)				Cefadroxil(DB01140)|Ceftibuten(DB01415)|Cyclacillin(DB01000)	aactctgtctcaaaaaaaaaaa	0.124													5	3	---	---	---	---	
ALKBH1	8846	broad.mit.edu	37	14	78142342	78142342	+	Intron	DEL	T	-	-			TCGA-CJ-4903-01A-01D-1429-08	TCGA-CJ-4903-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:78142342delT	uc001xuc.1	-						ALKBH1_uc001xud.1_Intron	NM_006020	NP_006011	Q13686	ALKB1_HUMAN	alkylated DNA repair protein alkB homolog						DNA dealkylation involved in DNA repair|DNA demethylation|oxidative demethylation|RNA repair	mitochondrion	DNA-(apurinic or apyrimidinic site) lyase activity|ferrous iron binding|methylcytosine dioxygenase activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen			ovary(1)|skin(1)	2			Kidney(204;0.164)	BRCA - Breast invasive adenocarcinoma(234;0.0291)		ttttcttttcttttttttttt	0.104													4	2	---	---	---	---	
POTEB	339010	broad.mit.edu	37	15	22077310	22077310	+	Intron	DEL	A	-	-			TCGA-CJ-4903-01A-01D-1429-08	TCGA-CJ-4903-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:22077310delA	uc010tzr.1	-						POTEB_uc010tzq.1_Intron	NM_207355	NP_997238	Q6S5H4	POTEB_HUMAN	protein expressed in prostate, ovary, testis,												0						TTTTTTTTTTAAAAAGCATTA	0.239													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	23265335	23265336	+	IGR	INS	-	G	G			TCGA-CJ-4903-01A-01D-1429-08	TCGA-CJ-4903-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:23265335_23265336insG								GOLGA9P (2592 upstream) : HERC2P2 (16929 downstream)																							AGGCAGGAAGAGGGGGCTCCCA	0.639													5	4	---	---	---	---	
EXD1	161829	broad.mit.edu	37	15	41487861	41487862	+	Intron	INS	-	A	A	rs33987701		TCGA-CJ-4903-01A-01D-1429-08	TCGA-CJ-4903-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:41487861_41487862insA	uc001znk.2	-						EXD1_uc010ucv.1_Intron	NM_152596	NP_689809	Q8NHP7	EXD1_HUMAN	exonuclease 3'-5' domain containing 1						nucleobase, nucleoside, nucleotide and nucleic acid metabolic process	intracellular	3'-5' exonuclease activity|nucleic acid binding			ovary(1)	1						AATGGAGCACCaaaaaaaaaaa	0.332													5	5	---	---	---	---	
DUOX1	53905	broad.mit.edu	37	15	45434984	45434987	+	Intron	DEL	AGGG	-	-	rs67057268		TCGA-CJ-4903-01A-01D-1429-08	TCGA-CJ-4903-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:45434984_45434987delAGGG	uc001zus.1	+						DUOX1_uc001zut.1_Intron|DUOX1_uc010bee.1_Intron	NM_017434	NP_059130	Q9NRD9	DUOX1_HUMAN	dual oxidase 1 precursor						cuticle development|cytokine-mediated signaling pathway|hormone biosynthetic process|hydrogen peroxide biosynthetic process|hydrogen peroxide catabolic process|response to cAMP|superoxide anion generation	apical plasma membrane|integral to membrane	calcium ion binding|electron carrier activity|flavin adenine dinucleotide binding|heme binding|NAD(P)H oxidase activity|NADP binding|peroxidase activity			ovary(5)|skin(2)|breast(1)	8		all_cancers(109;5.7e-11)|all_epithelial(112;4.65e-09)|Lung NSC(122;3.55e-06)|all_lung(180;2.56e-05)|Melanoma(134;0.027)		all cancers(107;5.77e-18)|GBM - Glioblastoma multiforme(94;5.11e-07)|COAD - Colon adenocarcinoma(120;0.071)|Colorectal(133;0.0717)		gaaggaaggaagggagggaggaag	0.225													4	4	---	---	---	---	
VPS13C	54832	broad.mit.edu	37	15	62257054	62257055	+	Frame_Shift_Del	DEL	AG	-	-			TCGA-CJ-4903-01A-01D-1429-08	TCGA-CJ-4903-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:62257054_62257055delAG	uc002agz.2	-	31	3131_3132	c.3057_3058delCT	c.(3055-3060)GCCTTTfs	p.A1019fs	VPS13C_uc002aha.2_Frame_Shift_Del_p.A976fs|VPS13C_uc002ahb.1_Frame_Shift_Del_p.A1019fs|VPS13C_uc002ahc.1_Frame_Shift_Del_p.A976fs	NM_020821	NP_065872	Q709C8	VP13C_HUMAN	vacuolar protein sorting 13C protein isoform 2A	1019_1020					protein localization					ovary(2)	2						AAAGATGAAAAGGCCACCTAAA	0.376													97	47	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	76039782	76039783	+	IGR	DEL	AA	-	-			TCGA-CJ-4903-01A-01D-1429-08	TCGA-CJ-4903-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:76039782_76039783delAA								DNM1P35 (7280 upstream) : UBE2Q2 (95839 downstream)																							CTAAATAACCaaaaaaaaaaaa	0.342													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	88985952	88985953	+	IGR	DEL	AC	-	-			TCGA-CJ-4903-01A-01D-1429-08	TCGA-CJ-4903-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:88985952_88985953delAC								NTRK3 (186291 upstream) : MRPL46 (16755 downstream)																							AAGTTCATGTacacacacacac	0.366													5	3	---	---	---	---	
PRC1	9055	broad.mit.edu	37	15	91523763	91523764	+	Intron	INS	-	G	G	rs28584391		TCGA-CJ-4903-01A-01D-1429-08	TCGA-CJ-4903-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:91523763_91523764insG	uc002bqm.2	-						PRC1_uc002bqn.2_Intron|PRC1_uc002bqo.2_Intron|PRC1_uc010uqs.1_Intron	NM_003981	NP_003972	O43663	PRC1_HUMAN	protein regulator of cytokinesis 1 isoform 1						cytokinesis|mitotic spindle elongation	cytoplasm|nucleus|spindle microtubule|spindle pole	protein binding			ovary(1)|skin(1)	2	Lung NSC(78;0.0987)|all_lung(78;0.175)					ttttttttttttttgagacagg	0.134													8	8	---	---	---	---	
SOLH	6650	broad.mit.edu	37	16	600733	600734	+	Intron	INS	-	T	T	rs145905062	by1000genomes	TCGA-CJ-4903-01A-01D-1429-08	TCGA-CJ-4903-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:600733_600734insT	uc002chi.2	+						SOLH_uc002chj.2_5'Flank	NM_005632	NP_005623	O75808	CAN15_HUMAN	small optic lobes						proteolysis	intracellular	calcium-dependent cysteine-type endopeptidase activity|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)|breast(1)	2		Hepatocellular(780;0.00335)				TGAGGGTCCCCGTCGGTGAGGG	0.738													4	4	---	---	---	---	
ACACA	31	broad.mit.edu	37	17	35745438	35745439	+	Intron	DEL	CA	-	-	rs141873098		TCGA-CJ-4903-01A-01D-1429-08	TCGA-CJ-4903-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:35745438_35745439delCA	uc002hno.2	-						ACACA_uc002hnn.2_Intron|ACACA_uc002hnq.2_Intron|C17orf78_uc010cva.1_Intron|C17orf78_uc002hns.2_Intron	NM_198834	NP_942131	Q13085	ACACA_HUMAN	acetyl-Coenzyme A carboxylase alpha isoform 1						acetyl-CoA metabolic process|energy reserve metabolic process|fatty acid biosynthetic process|long-chain fatty-acyl-CoA biosynthetic process|positive regulation of cellular metabolic process|protein homotetramerization|triglyceride biosynthetic process	cytosol	acetyl-CoA carboxylase activity|ATP binding|biotin carboxylase activity|metal ion binding|protein binding			large_intestine(1)|ovary(1)	2		Breast(25;0.00157)|Ovarian(249;0.15)			Biotin(DB00121)	AGCTCACCCTCACACCCCCTCC	0.495													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	45879402	45879403	+	IGR	DEL	AC	-	-	rs7214303		TCGA-CJ-4903-01A-01D-1429-08	TCGA-CJ-4903-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:45879402_45879403delAC								TBX21 (55917 upstream) : OSBPL7 (5330 downstream)																							acacacacatacacacacacac	0.436											OREG0024500	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	77876983	77876984	+	IGR	INS	-	CTTC	CTTC	rs12943230	by1000genomes	TCGA-CJ-4903-01A-01D-1429-08	TCGA-CJ-4903-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:77876983_77876984insCTTC								CBX4 (63770 upstream) : TBC1D16 (36837 downstream)																							ttccttccttcctttctttctt	0.000													7	4	---	---	---	---	
MALT1	10892	broad.mit.edu	37	18	56413238	56413240	+	Intron	DEL	ATT	-	-	rs145941401		TCGA-CJ-4903-01A-01D-1429-08	TCGA-CJ-4903-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:56413238_56413240delATT	uc002lhm.1	+						MALT1_uc002lhn.1_Intron	NM_006785	NP_006776	Q9UDY8	MALT1_HUMAN	mucosa associated lymphoid tissue lymphoma						activation of NF-kappaB-inducing kinase activity|anti-apoptosis|nuclear export|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of interleukin-2 production|positive regulation of NF-kappaB transcription factor activity|positive regulation of phosphorylation|positive regulation of protein ubiquitination|positive regulation of T cell cytokine production|protein oligomerization|proteolysis|T cell receptor signaling pathway	CBM complex|cytosol|nucleus|perinuclear region of cytoplasm	cysteine-type endopeptidase activity|protein self-association|signal transducer activity|ubiquitin-protein ligase activity			ovary(2)|lung(1)|central_nervous_system(1)	4						AATTAGTAACATTAGAGTATAtt	0.207			T	BIRC3	MALT								2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	39712586	39712587	+	IGR	DEL	TT	-	-	rs10407372	by1000genomes	TCGA-CJ-4903-01A-01D-1429-08	TCGA-CJ-4903-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:39712586_39712587delTT								SYCN (17680 upstream) : IL28B (21686 downstream)																							tctttctttctttctgtctctc	0.000													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	54279184	54279184	+	IGR	DEL	T	-	-	rs62146188		TCGA-CJ-4903-01A-01D-1429-08	TCGA-CJ-4903-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:54279184delT								MIR519A2 (13500 upstream) : MIR371 (11745 downstream)																							TGAACTTCAATTTAAAAAAAA	0.214													5	3	---	---	---	---	
LILRA5	353514	broad.mit.edu	37	19	54818526	54818526	+	3'UTR	DEL	A	-	-			TCGA-CJ-4903-01A-01D-1429-08	TCGA-CJ-4903-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:54818526delA	uc002qfe.2	-	7						NM_021250	NP_067073	A6NI73	LIRA5_HUMAN	leukocyte immunoglobulin-like receptor subfamily						innate immune response	extracellular region|integral to membrane	receptor activity			upper_aerodigestive_tract(1)	1	Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.105)		actccatctcaaaaaaaaaaa	0.124													5	3	---	---	---	---	
GPCPD1	56261	broad.mit.edu	37	20	5545874	5545874	+	Intron	DEL	T	-	-			TCGA-CJ-4903-01A-01D-1429-08	TCGA-CJ-4903-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:5545874delT	uc002wme.3	-						GPCPD1_uc002wmd.3_Intron	NM_019593	NP_062539	Q9NPB8	GPCP1_HUMAN	hypothetical protein LOC56261						glycerol metabolic process|lipid metabolic process		carbohydrate binding|glycerophosphodiester phosphodiesterase activity				0						CTGAGATCCCttttttttttt	0.219													6	3	---	---	---	---	
XRN2	22803	broad.mit.edu	37	20	21321692	21321693	+	Intron	INS	-	GTA	GTA	rs141054974	by1000genomes	TCGA-CJ-4903-01A-01D-1429-08	TCGA-CJ-4903-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:21321692_21321693insGTA	uc002wsf.1	+						XRN2_uc002wsg.1_Intron|XRN2_uc010zsk.1_Intron	NM_012255	NP_036387	Q9H0D6	XRN2_HUMAN	5'-3' exoribonuclease 2						cell growth|DNA catabolic process, exonucleolytic|mRNA processing|regulation of transcription, DNA-dependent|RNA catabolic process|spermatogenesis|transcription termination, DNA-dependent	nucleolus	5'-3' exoribonuclease activity|nucleic acid binding|protein binding|zinc ion binding			skin(1)	1						AAGAAGAGCACGTAGGATTGTT	0.262													9	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	51455362	51455363	+	IGR	INS	-	CCTT	CCTT			TCGA-CJ-4903-01A-01D-1429-08	TCGA-CJ-4903-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:51455362_51455363insCCTT								ZFP64 (646838 upstream) : TSHZ2 (133514 downstream)																							TTTTCTTTCtcccttccttcct	0.124													4	4	---	---	---	---	
TCFL5	10732	broad.mit.edu	37	20	61491079	61491080	+	Intron	INS	-	T	T			TCGA-CJ-4903-01A-01D-1429-08	TCGA-CJ-4903-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:61491079_61491080insT	uc002ydp.2	-						TCFL5_uc002ydo.2_Intron|TCFL5_uc002ydq.2_Intron	NM_006602	NP_006593	Q9UL49	TCFL5_HUMAN	transcription factor-like 5 protein						cell differentiation|multicellular organismal development|regulation of cell differentiation|regulation of cell proliferation|spermatogenesis|transcription from RNA polymerase II promoter		DNA binding|sequence-specific DNA binding transcription factor activity			large_intestine(1)	1	Breast(26;5.68e-08)					ttgtttttttgttttttttttt	0.124													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	44755923	44755925	+	IGR	DEL	CAT	-	-	rs66544012		TCGA-CJ-4903-01A-01D-1429-08	TCGA-CJ-4903-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:44755923_44755925delCAT								CRYAA (163010 upstream) : SIK1 (78473 downstream)																							tcaccatcaccatcaccaccacc	0.000													4	2	---	---	---	---	
PI4KA	5297	broad.mit.edu	37	22	21147390	21147390	+	Intron	DEL	T	-	-			TCGA-CJ-4903-01A-01D-1429-08	TCGA-CJ-4903-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:21147390delT	uc002zsz.3	-							NM_058004	NP_477352	P42356	PI4KA_HUMAN	phosphatidylinositol 4-kinase type 3 alpha						phosphatidylinositol biosynthetic process|phosphatidylinositol-mediated signaling|synaptic transmission	Golgi-associated vesicle	1-phosphatidylinositol 4-kinase activity|ATP binding|protein binding			lung(2)|upper_aerodigestive_tract(1)|salivary_gland(1)	4	all_cancers(11;7.59e-25)|all_epithelial(7;1.34e-22)|Melanoma(16;0.000465)|Ovarian(15;0.00167)|Colorectal(54;0.0332)|all_neural(72;0.142)	Lung SC(17;0.0262)	LUSC - Lung squamous cell carcinoma(15;0.000536)|Lung(15;0.0108)|Epithelial(17;0.196)			ACACTGCACCTTTCTAAGGAA	0.458													22	10	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	25855682	25855683	+	Intron	INS	-	GTGT	GTGT	rs138963277	by1000genomes	TCGA-CJ-4903-01A-01D-1429-08	TCGA-CJ-4903-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:25855682_25855683insGTGT	uc003abt.2	+						uc003abu.2_Intron|uc003abv.2_Intron					Homo sapiens cDNA clone IMAGE:3542716, partial cds.																		CCTGGCAGCTGgtgtgtgtgtg	0.406													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	31761554	31761555	+	IGR	DEL	GA	-	-			TCGA-CJ-4903-01A-01D-1429-08	TCGA-CJ-4903-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:31761554_31761555delGA								PATZ1 (19305 upstream) : DRG1 (33984 downstream)																							gagagaaagtgagagagagaga	0.015													4	2	---	---	---	---	
PPARA	5465	broad.mit.edu	37	22	46570088	46570089	+	Intron	DEL	AG	-	-			TCGA-CJ-4903-01A-01D-1429-08	TCGA-CJ-4903-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:46570088_46570089delAG	uc003bgw.1	+						PPARA_uc003bgx.1_Intron|PPARA_uc010hab.1_Intron|PPARA_uc003bgy.1_Intron|PPARA_uc003bgz.1_Intron|PPARA_uc003bha.2_5'Flank|PPARA_uc003bhb.1_5'Flank	NM_005036	NP_005027	Q07869	PPARA_HUMAN	peroxisome proliferative activated receptor,						fatty acid metabolic process|fatty acid transport|negative regulation of appetite|negative regulation of cholesterol storage|negative regulation of macrophage derived foam cell differentiation|negative regulation of receptor biosynthetic process|negative regulation of sequestering of triglyceride|negative regulation of transcription from RNA polymerase II promoter|positive regulation of fatty acid beta-oxidation|regulation of cellular ketone metabolic process by positive regulation of transcription from an RNA polymerase II promoter|regulation of glycolysis by positive regulation of transcription from an RNA polymerase II promoter|regulation of lipid transport by positive regulation of transcription from an RNA polymerase II promoter|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor	nucleoplasm	drug binding|ligand-regulated transcription factor activity|lipid binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|steroid hormone receptor activity|ubiquitin conjugating enzyme binding|zinc ion binding			ovary(1)|central_nervous_system(1)	2		Ovarian(80;0.00965)|all_neural(38;0.0416)		UCEC - Uterine corpus endometrioid carcinoma (28;0.00522)	Atorvastatin(DB01076)|Bezafibrate(DB01393)|Clofibrate(DB00636)|Fenofibrate(DB01039)|Gemfibrozil(DB01241)|Simvastatin(DB00641)	gaaggaagaaagagagagagag	0.000													4	2	---	---	---	---	
DHRSX	207063	broad.mit.edu	37	X	2232507	2232510	+	Intron	DEL	GGGA	-	-			TCGA-CJ-4903-01A-01D-1429-08	TCGA-CJ-4903-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:2232507_2232510delGGGA	uc004cqf.3	-							NM_145177	NP_660160	Q8N5I4	DHRSX_HUMAN	dehydrogenase/reductase (SDR family) X-linked								binding|oxidoreductase activity				0		all_cancers(21;9e-05)|all_epithelial(21;6.22e-06)|all_lung(23;0.000597)|Lung NSC(23;0.00901)|Lung SC(21;0.186)				aggaaggaaggggagaaggaagga	0.000													4	3	---	---	---	---	
USP9X	8239	broad.mit.edu	37	X	41064887	41064887	+	Intron	DEL	T	-	-			TCGA-CJ-4903-01A-01D-1429-08	TCGA-CJ-4903-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:41064887delT	uc004dfb.2	+						USP9X_uc004dfc.2_Intron	NM_001039590	NP_001034679	Q93008	USP9X_HUMAN	ubiquitin specific protease 9, X-linked isoform						BMP signaling pathway|cell division|chromosome segregation|female gamete generation|mitosis|protein deubiquitination|transforming growth factor beta receptor signaling pathway|ubiquitin-dependent protein catabolic process	cytoplasm	co-SMAD binding|cysteine-type endopeptidase activity|ubiquitin thiolesterase activity			lung(3)|breast(2)|ovary(1)	6						ATTGGGTGGGTTTTTTTTTTT	0.323													7	4	---	---	---	---	
IL13RA1	3597	broad.mit.edu	37	X	117925585	117925585	+	Intron	DEL	A	-	-	rs11318857		TCGA-CJ-4903-01A-01D-1429-08	TCGA-CJ-4903-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:117925585delA	uc004eqs.2	+						IL13RA1_uc004eqt.1_Intron	NM_001560	NP_001551	P78552	I13R1_HUMAN	interleukin 13 receptor, alpha 1 precursor							interleukin-13 receptor complex	cytokine receptor activity				0						TTCTTAGGTCAAAAAAAAAAA	0.328													6	3	---	---	---	---	
