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
WASH7P	653635	broad.mit.edu	37	1	14930	14930	+	Intron	SNP	A	G	G	rs150145850	by1000genomes	TCGA-AK-3456-01A-02D-1386-10	TCGA-AK-3456-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:14930A>G	uc009vis.2	-						WASH7P_uc009vit.2_Intron|WASH7P_uc001aae.3_Intron|WASH7P_uc009viu.2_Intron|WASH7P_uc001aab.3_Intron|WASH7P_uc001aah.3_Intron|WASH7P_uc009vir.2_Intron|WASH7P_uc009viq.2_Intron|WASH7P_uc001aac.3_Intron|WASH7P_uc009viv.2_RNA|WASH7P_uc009viw.2_RNA					Homo sapiens cDNA FLJ31670 fis, clone NT2RI2004984.												0						ACAGAATTACAAGGTGCTGGC	0.587													17	45	---	---	---	---	PASS
TAS1R3	83756	broad.mit.edu	37	1	1268924	1268924	+	Missense_Mutation	SNP	T	G	G			TCGA-AK-3456-01A-02D-1386-10	TCGA-AK-3456-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:1268924T>G	uc010nyk.1	+	6	1639	c.1639T>G	c.(1639-1641)TCC>GCC	p.S547A		NM_152228	NP_689414	Q7RTX0	TS1R3_HUMAN	taste receptor, type 1, member 3 precursor	547	Extracellular (Potential).				detection of chemical stimulus involved in sensory perception of sweet taste|sensory perception of umami taste	plasma membrane	protein heterodimerization activity|taste receptor activity				0	all_cancers(77;0.00164)|all_epithelial(69;0.000959)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;9.48e-15)|all_lung(118;9.67e-07)|Lung NSC(185;5.59e-05)|Renal(390;0.00571)|Breast(487;0.0183)|Hepatocellular(190;0.0268)|Myeloproliferative disorder(586;0.028)|Ovarian(437;0.127)|Lung SC(97;0.217)		Epithelial(90;3.01e-35)|OV - Ovarian serous cystadenocarcinoma(86;3.88e-21)|Colorectal(212;0.000157)|COAD - Colon adenocarcinoma(227;0.000193)|Kidney(185;0.00229)|BRCA - Breast invasive adenocarcinoma(365;0.00251)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.034)|Lung(427;0.146)	Aspartame(DB00168)	GGATGAGTGGTCCCCGGAGCG	0.647													8	14	---	---	---	---	PASS
NBPF1	55672	broad.mit.edu	37	1	16918693	16918693	+	5'UTR	SNP	A	T	T	rs12134336	by1000genomes	TCGA-AK-3456-01A-02D-1386-10	TCGA-AK-3456-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:16918693A>T	uc009vos.1	-	6					NBPF1_uc010oce.1_5'UTR	NM_017940	NP_060410	Q3BBV0	NBPF1_HUMAN	hypothetical protein LOC55672							cytoplasm					0				UCEC - Uterine corpus endometrioid carcinoma (279;0.00459)|BRCA - Breast invasive adenocarcinoma(304;7.52e-06)|COAD - Colon adenocarcinoma(227;1.05e-05)|Kidney(64;0.00016)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.179)		GCACTTTAGGATCCTTCACCA	0.443													13	108	---	---	---	---	PASS
MPL	4352	broad.mit.edu	37	1	43804224	43804224	+	Missense_Mutation	SNP	G	A	A	rs148276667		TCGA-AK-3456-01A-02D-1386-10	TCGA-AK-3456-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:43804224G>A	uc001ciw.2	+	3	269	c.224G>A	c.(223-225)CGT>CAT	p.R75H	MPL_uc001civ.2_Missense_Mutation_p.R75H|MPL_uc009vwr.2_Missense_Mutation_p.R68H	NM_005373	NP_005364	P40238	TPOR_HUMAN	myeloproliferative leukemia virus oncogene	75	Extracellular (Potential).				cell proliferation|platelet activation	integral to plasma membrane	cytokine receptor activity			haematopoietic_and_lymphoid_tissue(361)|upper_aerodigestive_tract(1)|pancreas(1)	363	all_hematologic(146;0.0958)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0505)				GAGAAGCCCCGTGCTTGCCCC	0.597			Mis		MPD	MPD	congenital amegakaryocytic thrombocytopenia						3	54	---	---	---	---	PASS
FCGR1A	2209	broad.mit.edu	37	1	149763191	149763191	+	3'UTR	SNP	G	A	A			TCGA-AK-3456-01A-02D-1386-10	TCGA-AK-3456-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:149763191G>A	uc001esp.3	+	6					HIST2H2BF_uc010pbj.1_Intron|FCGR1A_uc009wlg.2_RNA	NM_000566	NP_000557	P12314	FCGR1_HUMAN	Fc fragment of IgG, high affinity Ia, receptor						interferon-gamma-mediated signaling pathway|phagocytosis, engulfment	integral to membrane|plasma membrane	IgG binding|receptor activity|receptor signaling protein activity			ovary(1)	1	Breast(34;0.0124)|all_hematologic(923;0.127)				Abciximab(DB00054)|Adalimumab(DB00051)|Alefacept(DB00092)|Alemtuzumab(DB00087)|Basiliximab(DB00074)|Bevacizumab(DB00112)|Cetuximab(DB00002)|Daclizumab(DB00111)|Efalizumab(DB00095)|Etanercept(DB00005)|Gemtuzumab ozogamicin(DB00056)|Ibritumomab(DB00078)|Immune globulin(DB00028)|Methyl aminolevulinate(DB00992)|Muromonab(DB00075)|Natalizumab(DB00108)|Palivizumab(DB00110)|Porfimer(DB00707)|Rituximab(DB00073)|Tositumomab(DB00081)|Trastuzumab(DB00072)	CTCATGGTATGTAACTCTTAA	0.438													6	38	---	---	---	---	PASS
CTSK	1513	broad.mit.edu	37	1	150778608	150778608	+	Nonsense_Mutation	SNP	A	T	T			TCGA-AK-3456-01A-02D-1386-10	TCGA-AK-3456-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:150778608A>T	uc001evp.1	-	3	337	c.213T>A	c.(211-213)TAT>TAA	p.Y71*	CTSK_uc001evq.1_5'UTR|CTSK_uc009wma.1_RNA	NM_000396	NP_000387	P43235	CATK_HUMAN	cathepsin K preproprotein	71					proteolysis	lysosome	cysteine-type endopeptidase activity|protein binding			skin(1)	1	all_cancers(9;2.32e-51)|all_epithelial(9;3.89e-42)|all_lung(15;4.59e-35)|Lung NSC(24;1.7e-31)|Lung SC(34;0.00471)|Ovarian(49;0.0167)|all_hematologic(923;0.0395)|Hepatocellular(266;0.108)|Colorectal(459;0.171)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.0485)|BRCA - Breast invasive adenocarcinoma(12;0.00606)|LUSC - Lung squamous cell carcinoma(543;0.211)			TAGCCAGTTCATATGTATGGA	0.458													77	146	---	---	---	---	PASS
TCHH	7062	broad.mit.edu	37	1	152080550	152080550	+	Missense_Mutation	SNP	G	T	T			TCGA-AK-3456-01A-02D-1386-10	TCGA-AK-3456-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:152080550G>T	uc001ezp.2	-	2	5143	c.5143C>A	c.(5143-5145)CAG>AAG	p.Q1715K	TCHH_uc009wne.1_Missense_Mutation_p.Q1715K	NM_007113	NP_009044	Q07283	TRHY_HUMAN	trichohyalin	1715	23 X 26 AA approximate tandem repeats.				keratinization	cytoskeleton	calcium ion binding			ovary(3)|kidney(1)|central_nervous_system(1)	5	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			CGGCGCAGCTGCTGTTCCTCC	0.577													8	108	---	---	---	---	PASS
SLC9A11	284525	broad.mit.edu	37	1	173474406	173474406	+	Missense_Mutation	SNP	T	C	C			TCGA-AK-3456-01A-02D-1386-10	TCGA-AK-3456-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:173474406T>C	uc001giz.2	-	26	3713	c.3290A>G	c.(3289-3291)AAT>AGT	p.N1097S	SLC9A11_uc009wwe.2_Missense_Mutation_p.N655S	NM_178527	NP_848622	Q5TAH2	S9A11_HUMAN	solute carrier family 9, member 11	1097					sodium ion transport	integral to membrane	ion channel activity|solute:hydrogen antiporter activity			ovary(2)	2						GGTGTTACTATTTCTTTGGGT	0.368													6	479	---	---	---	---	PASS
ETNK2	55224	broad.mit.edu	37	1	204101382	204101382	+	Missense_Mutation	SNP	T	C	C			TCGA-AK-3456-01A-02D-1386-10	TCGA-AK-3456-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:204101382T>C	uc001hao.3	-	8	1418	c.1091A>G	c.(1090-1092)TAC>TGC	p.Y364C	ETNK2_uc010pqr.1_Missense_Mutation_p.Y186C|ETNK2_uc001han.3_3'UTR|ETNK2_uc010pqs.1_Missense_Mutation_p.Y323C|ETNK2_uc010pqt.1_Missense_Mutation_p.Y186C	NM_018208	NP_060678	Q9NVF9	EKI2_HUMAN	ethanolamine kinase 2	364							ATP binding|choline kinase activity|ethanolamine kinase activity			ovary(1)|central_nervous_system(1)	2	all_cancers(21;0.032)|Breast(84;0.116)|all_epithelial(62;0.196)		KIRC - Kidney renal clear cell carcinoma(13;0.0584)|Kidney(21;0.0934)|BRCA - Breast invasive adenocarcinoma(75;0.109)			GATCACTGCGTACCTGTGGGG	0.547													4	177	---	---	---	---	PASS
CTSE	1510	broad.mit.edu	37	1	206331351	206331351	+	3'UTR	SNP	C	T	T			TCGA-AK-3456-01A-02D-1386-10	TCGA-AK-3456-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:206331351C>T	uc001hdu.2	+	9					CTSE_uc001hdv.2_3'UTR|CTSE_uc010prs.1_3'UTR	NM_001910	NP_001901	P14091	CATE_HUMAN	cathepsin E isoform a preproprotein						antigen processing and presentation of exogenous peptide antigen via MHC class II|digestion|proteolysis	endosome	aspartic-type endopeptidase activity			ovary(1)	1			BRCA - Breast invasive adenocarcinoma(75;0.0754)			cacacacacacatatacacac	0.264													3	40	---	---	---	---	PASS
EIF2B4	8890	broad.mit.edu	37	2	27590158	27590158	+	Intron	SNP	C	A	A			TCGA-AK-3456-01A-02D-1386-10	TCGA-AK-3456-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:27590158C>A	uc002rkb.2	-						EIF2B4_uc002rjz.2_Intron|EIF2B4_uc002rka.2_Intron|EIF2B4_uc002rkc.2_Intron|EIF2B4_uc002rkd.2_Intron|EIF2B4_uc002rke.2_Intron|EIF2B4_uc002rkf.1_3'UTR	NM_001034116	NP_001029288	Q9UI10	EI2BD_HUMAN	eukaryotic translation initiation factor 2B,						myelination|negative regulation of translational initiation in response to stress|oligodendrocyte development|ovarian follicle development|response to glucose stimulus|response to heat|response to peptide hormone stimulus	cytosol|eukaryotic translation initiation factor 2B complex	translation initiation factor activity|translation initiation factor binding				0	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					TGTATGATGACAAGCCTATAG	0.448													9	70	---	---	---	---	PASS
THADA	63892	broad.mit.edu	37	2	43801756	43801756	+	Missense_Mutation	SNP	T	C	C			TCGA-AK-3456-01A-02D-1386-10	TCGA-AK-3456-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:43801756T>C	uc002rsw.3	-	11	1800	c.1448A>G	c.(1447-1449)GAG>GGG	p.E483G	THADA_uc002rsx.3_Missense_Mutation_p.E483G|THADA_uc002rsy.3_RNA|THADA_uc010fas.1_RNA|THADA_uc002rsz.2_Missense_Mutation_p.E193G|THADA_uc002rta.2_Missense_Mutation_p.E193G|THADA_uc002rtb.1_Missense_Mutation_p.E483G|THADA_uc002rtc.3_Missense_Mutation_p.E483G|THADA_uc002rtd.2_Missense_Mutation_p.E483G	NM_001083953	NP_001077422	Q6YHU6	THADA_HUMAN	thyroid adenoma associated	483							binding			ovary(2)|skin(1)	3		Acute lymphoblastic leukemia(82;0.00361)|all_hematologic(82;0.00837)				TCCCATCACCTCTAAGATTTG	0.388													5	178	---	---	---	---	PASS
GRB14	2888	broad.mit.edu	37	2	165350992	165350992	+	Silent	SNP	G	A	A	rs138769540	by1000genomes	TCGA-AK-3456-01A-02D-1386-10	TCGA-AK-3456-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:165350992G>A	uc002ucl.2	-	13	1966	c.1425C>T	c.(1423-1425)TTC>TTT	p.F475F	GRB14_uc010zcv.1_Silent_p.F388F|GRB14_uc002ucm.2_RNA	NM_004490	NP_004481	Q14449	GRB14_HUMAN	growth factor receptor-bound protein 14	475	SH2.				blood coagulation|leukocyte migration	cytosol|endosome membrane|Golgi membrane|microsome|plasma membrane	SH3/SH2 adaptor activity			ovary(5)|upper_aerodigestive_tract(1)|lung(1)	7						TTGACAGTACGAAAGTTTTGG	0.328													6	645	---	---	---	---	PASS
COBLL1	22837	broad.mit.edu	37	2	165561492	165561492	+	Missense_Mutation	SNP	G	A	A	rs149060063		TCGA-AK-3456-01A-02D-1386-10	TCGA-AK-3456-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:165561492G>A	uc010zcw.1	-	10	1442	c.1318C>T	c.(1318-1320)CAT>TAT	p.H440Y	COBLL1_uc002ucp.2_Missense_Mutation_p.H374Y|COBLL1_uc002ucq.2_Missense_Mutation_p.H374Y|COBLL1_uc010zcx.1_Missense_Mutation_p.H420Y|COBLL1_uc002ucs.1_RNA|COBLL1_uc002uco.2_Missense_Mutation_p.H143Y	NM_014900	NP_055715	Q53SF7	COBL1_HUMAN	COBL-like 1	412										ovary(2)|pancreas(1)	3						TCACTTTGATGCGGGGGTATT	0.423													62	133	---	---	---	---	PASS
COBLL1	22837	broad.mit.edu	37	2	165561493	165561493	+	Silent	SNP	C	A	A	rs138711091	byFrequency	TCGA-AK-3456-01A-02D-1386-10	TCGA-AK-3456-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:165561493C>A	uc010zcw.1	-	10	1441	c.1317G>T	c.(1315-1317)CCG>CCT	p.P439P	COBLL1_uc002ucp.2_Silent_p.P373P|COBLL1_uc002ucq.2_Silent_p.P373P|COBLL1_uc010zcx.1_Silent_p.P419P|COBLL1_uc002ucs.1_RNA|COBLL1_uc002uco.2_Silent_p.P142P	NM_014900	NP_055715	Q53SF7	COBL1_HUMAN	COBL-like 1	411										ovary(2)|pancreas(1)	3						CACTTTGATGCGGGGGTATTT	0.423													63	135	---	---	---	---	PASS
LASS6	253782	broad.mit.edu	37	2	169622245	169622245	+	Missense_Mutation	SNP	T	C	C			TCGA-AK-3456-01A-02D-1386-10	TCGA-AK-3456-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:169622245T>C	uc002ueb.1	+	9	1113	c.989T>C	c.(988-990)GTT>GCT	p.V330A	LASS6_uc002uec.1_Missense_Mutation_p.V330A	NM_203463	NP_982288	Q6ZMG9	CERS6_HUMAN	longevity assurance homolog 6	330	Cytoplasmic (Potential).|TLC.					endoplasmic reticulum membrane|integral to membrane|nuclear membrane	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|sphingosine N-acyltransferase activity			skin(1)	1						TGCAAAGCTGTTTCAAGAGGC	0.353													5	228	---	---	---	---	PASS
NDUFS1	4719	broad.mit.edu	37	2	207011714	207011714	+	Missense_Mutation	SNP	T	G	G			TCGA-AK-3456-01A-02D-1386-10	TCGA-AK-3456-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:207011714T>G	uc002vbe.2	-	8	777	c.650A>C	c.(649-651)GAA>GCA	p.E217A	NDUFS1_uc010ziq.1_Missense_Mutation_p.E231A|NDUFS1_uc010zir.1_Missense_Mutation_p.E181A|NDUFS1_uc010zis.1_Missense_Mutation_p.E160A|NDUFS1_uc010zit.1_Missense_Mutation_p.E106A|NDUFS1_uc010ziu.1_Missense_Mutation_p.E101A	NM_005006	NP_004997	P28331	NDUS1_HUMAN	NADH dehydrogenase (ubiquinone) Fe-S protein 1,	217					apoptosis|ATP metabolic process|mitochondrial electron transport, NADH to ubiquinone|reactive oxygen species metabolic process|regulation of mitochondrial membrane potential|transport	mitochondrial intermembrane space|mitochondrial respiratory chain complex I	2 iron, 2 sulfur cluster binding|4 iron, 4 sulfur cluster binding|electron carrier activity|metal ion binding|NADH dehydrogenase (ubiquinone) activity|protein binding			ovary(1)	1					NADH(DB00157)	CCCAGACAGTTCAGACATGAA	0.433													70	138	---	---	---	---	PASS
SCN11A	11280	broad.mit.edu	37	3	38888542	38888542	+	Silent	SNP	G	T	T			TCGA-AK-3456-01A-02D-1386-10	TCGA-AK-3456-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:38888542G>T	uc011ays.1	-	26	5218	c.5019C>A	c.(5017-5019)CCC>CCA	p.P1673P		NM_014139	NP_054858	Q9UI33	SCNBA_HUMAN	sodium channel, voltage-gated, type XI, alpha	1673					response to drug	voltage-gated sodium channel complex	voltage-gated sodium channel activity			skin(6)|ovary(1)|haematopoietic_and_lymphoid_tissue(1)|pancreas(1)	9				Kidney(284;0.00202)|KIRC - Kidney renal clear cell carcinoma(284;0.00226)	Cocaine(DB00907)	CACTCACCATGGGCAAGTCCA	0.453													21	67	---	---	---	---	PASS
MUC4	4585	broad.mit.edu	37	3	195505833	195505833	+	Silent	SNP	G	A	A			TCGA-AK-3456-01A-02D-1386-10	TCGA-AK-3456-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:195505833G>A	uc011bto.1	-	3	12694	c.12234C>T	c.(12232-12234)GCC>GCT	p.A4078A	MUC4_uc003fva.2_5'Flank|MUC4_uc003fvb.2_5'Flank|MUC4_uc003fvc.2_5'Flank|MUC4_uc003fvd.2_5'Flank|MUC4_uc003fve.2_5'Flank|MUC4_uc010hzr.2_5'Flank|MUC4_uc011btf.1_Intron|MUC4_uc011btg.1_Intron|MUC4_uc011bth.1_Intron|MUC4_uc011bti.1_Intron|MUC4_uc011btj.1_Intron|MUC4_uc011btk.1_Intron|MUC4_uc011btl.1_Intron|MUC4_uc011btm.1_Intron|MUC4_uc011btn.1_Intron|MUC4_uc003fvo.2_Intron|MUC4_uc003fvp.2_Intron|MUC4_uc010hzu.1_Intron	NM_018406	NP_060876	Q99102	MUC4_HUMAN	mucin 4 isoform a	Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment					cell-matrix adhesion	integral to plasma membrane|proteinaceous extracellular matrix	ErbB-2 class receptor binding|extracellular matrix constituent, lubricant activity				0	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		GAAGAGGGGTGGCGTGACCTG	0.602													4	83	---	---	---	---	PASS
MUC4	4585	broad.mit.edu	37	3	195506373	195506373	+	Silent	SNP	G	A	A			TCGA-AK-3456-01A-02D-1386-10	TCGA-AK-3456-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:195506373G>A	uc011bto.1	-	3	12154	c.11694C>T	c.(11692-11694)TCC>TCT	p.S3898S	MUC4_uc003fva.2_5'Flank|MUC4_uc003fvb.2_5'Flank|MUC4_uc003fvc.2_5'Flank|MUC4_uc003fvd.2_5'Flank|MUC4_uc003fve.2_5'Flank|MUC4_uc010hzr.2_5'Flank|MUC4_uc011btf.1_5'Flank|MUC4_uc011btg.1_5'Flank|MUC4_uc011bth.1_5'Flank|MUC4_uc011bti.1_5'Flank|MUC4_uc011btj.1_5'Flank|MUC4_uc011btk.1_5'Flank|MUC4_uc011btl.1_5'Flank|MUC4_uc011btm.1_5'Flank|MUC4_uc011btn.1_5'Flank|MUC4_uc003fvo.2_Intron|MUC4_uc003fvp.2_Intron|MUC4_uc010hzu.1_Intron	NM_018406	NP_060876	Q99102	MUC4_HUMAN	mucin 4 isoform a	798	Ser-rich.				cell-matrix adhesion	integral to plasma membrane|proteinaceous extracellular matrix	ErbB-2 class receptor binding|extracellular matrix constituent, lubricant activity				0	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		CGTGACCTGTGGATGCTGAGG	0.572													11	95	---	---	---	---	PASS
MUC4	4585	broad.mit.edu	37	3	195506399	195506399	+	Missense_Mutation	SNP	G	T	T			TCGA-AK-3456-01A-02D-1386-10	TCGA-AK-3456-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:195506399G>T	uc011bto.1	-	3	12128	c.11668C>A	c.(11668-11670)CCT>ACT	p.P3890T	MUC4_uc003fva.2_5'Flank|MUC4_uc003fvb.2_5'Flank|MUC4_uc003fvc.2_5'Flank|MUC4_uc003fvd.2_5'Flank|MUC4_uc003fve.2_5'Flank|MUC4_uc010hzr.2_5'Flank|MUC4_uc011btf.1_5'Flank|MUC4_uc011btg.1_5'Flank|MUC4_uc011bth.1_5'Flank|MUC4_uc011bti.1_5'Flank|MUC4_uc011btj.1_5'Flank|MUC4_uc011btk.1_5'Flank|MUC4_uc011btl.1_5'Flank|MUC4_uc011btm.1_5'Flank|MUC4_uc011btn.1_5'Flank|MUC4_uc003fvo.2_Intron|MUC4_uc003fvp.2_Intron|MUC4_uc010hzu.1_Intron	NM_018406	NP_060876	Q99102	MUC4_HUMAN	mucin 4 isoform a	Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment					cell-matrix adhesion	integral to plasma membrane|proteinaceous extracellular matrix	ErbB-2 class receptor binding|extracellular matrix constituent, lubricant activity				0	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		CTGGTGACAGGAAGAGGGGTG	0.587													5	87	---	---	---	---	PASS
MUC4	4585	broad.mit.edu	37	3	195508133	195508133	+	Missense_Mutation	SNP	G	A	A			TCGA-AK-3456-01A-02D-1386-10	TCGA-AK-3456-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:195508133G>A	uc011bto.1	-	3	10394	c.9934C>T	c.(9934-9936)CCT>TCT	p.P3312S	MUC4_uc003fva.2_5'Flank|MUC4_uc003fvb.2_5'Flank|MUC4_uc003fvc.2_5'Flank|MUC4_uc003fvd.2_5'Flank|MUC4_uc003fve.2_5'Flank|MUC4_uc010hzr.2_5'Flank|MUC4_uc011btf.1_5'Flank|MUC4_uc011btg.1_5'Flank|MUC4_uc011bth.1_5'Flank|MUC4_uc011bti.1_5'Flank|MUC4_uc011btj.1_5'Flank|MUC4_uc011btk.1_5'Flank|MUC4_uc011btl.1_5'Flank|MUC4_uc011btm.1_5'Flank|MUC4_uc011btn.1_5'Flank|MUC4_uc003fvo.2_Intron|MUC4_uc003fvp.2_Intron|MUC4_uc010hzu.1_Intron	NM_018406	NP_060876	Q99102	MUC4_HUMAN	mucin 4 isoform a	Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment					cell-matrix adhesion	integral to plasma membrane|proteinaceous extracellular matrix	ErbB-2 class receptor binding|extracellular matrix constituent, lubricant activity				0	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		ACAGGAACAGGGGTGGCGTGA	0.592													6	54	---	---	---	---	PASS
MUC4	4585	broad.mit.edu	37	3	195513685	195513685	+	Missense_Mutation	SNP	T	C	C			TCGA-AK-3456-01A-02D-1386-10	TCGA-AK-3456-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:195513685T>C	uc011bto.1	-	2	5226	c.4766A>G	c.(4765-4767)GAC>GGC	p.D1589G	MUC4_uc003fvo.2_Intron|MUC4_uc003fvp.2_Intron|MUC4_uc010hzu.1_Intron	NM_018406	NP_060876	Q99102	MUC4_HUMAN	mucin 4 isoform a	Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment					cell-matrix adhesion	integral to plasma membrane|proteinaceous extracellular matrix	ErbB-2 class receptor binding|extracellular matrix constituent, lubricant activity				0	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		TGAGGAAGTGTCGGTGACAGG	0.577													6	103	---	---	---	---	PASS
MUC4	4585	broad.mit.edu	37	3	195513686	195513686	+	Missense_Mutation	SNP	C	T	T			TCGA-AK-3456-01A-02D-1386-10	TCGA-AK-3456-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:195513686C>T	uc011bto.1	-	2	5225	c.4765G>A	c.(4765-4767)GAC>AAC	p.D1589N	MUC4_uc003fvo.2_Intron|MUC4_uc003fvp.2_Intron|MUC4_uc010hzu.1_Intron	NM_018406	NP_060876	Q99102	MUC4_HUMAN	mucin 4 isoform a	Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment					cell-matrix adhesion	integral to plasma membrane|proteinaceous extracellular matrix	ErbB-2 class receptor binding|extracellular matrix constituent, lubricant activity				0	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		GAGGAAGTGTCGGTGACAGGA	0.582													7	100	---	---	---	---	PASS
ATP8A1	10396	broad.mit.edu	37	4	42509034	42509034	+	Silent	SNP	G	A	A			TCGA-AK-3456-01A-02D-1386-10	TCGA-AK-3456-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:42509034G>A	uc003gwr.2	-	23	2317	c.2085C>T	c.(2083-2085)ATC>ATT	p.I695I	ATP8A1_uc003gwq.2_5'UTR|ATP8A1_uc003gws.2_Silent_p.I680I	NM_006095	NP_006086	Q9Y2Q0	AT8A1_HUMAN	ATPase, aminophospholipid transporter (APLT),	695	Cytoplasmic (Potential).				ATP biosynthetic process	chromaffin granule membrane|integral to membrane|plasma membrane	aminophospholipid transporter activity|ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|cation-transporting ATPase activity|magnesium ion binding|phospholipid-translocating ATPase activity			skin(2)|central_nervous_system(1)	3					Phosphatidylserine(DB00144)	GTGAATTACCGATGTTAATGG	0.348													81	155	---	---	---	---	PASS
PDCL2	132954	broad.mit.edu	37	4	56448342	56448342	+	Silent	SNP	T	C	C			TCGA-AK-3456-01A-02D-1386-10	TCGA-AK-3456-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:56448342T>C	uc003hbb.2	-	2	172	c.69A>G	c.(67-69)AAA>AAG	p.K23K		NM_152401	NP_689614	Q8N4E4	PDCL2_HUMAN	phosducin-like 2	23											0	Lung NSC(11;0.00256)|Glioma(25;0.08)|all_epithelial(27;0.0863)|all_neural(26;0.101)		LUSC - Lung squamous cell carcinoma(4;1.69e-07)|Lung(4;1.03e-06)|Epithelial(7;0.00669)			TTGACTCTTCTTTAGGAGGAA	0.353													199	354	---	---	---	---	PASS
NHEDC2	133308	broad.mit.edu	37	4	103947531	103947531	+	Missense_Mutation	SNP	A	T	T			TCGA-AK-3456-01A-02D-1386-10	TCGA-AK-3456-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:103947531A>T	uc003hwx.3	-	12	2482	c.1610T>A	c.(1609-1611)GTT>GAT	p.V537D	NHEDC2_uc010iln.1_Intron|NHEDC2_uc003hwy.2_Missense_Mutation_p.V537D|NHEDC2_uc011cew.1_Missense_Mutation_p.V480D|NHEDC2_uc011cex.1_3'UTR	NM_178833	NP_849155	Q86UD5	NHDC2_HUMAN	Na+/H+ exchanger domain containing 2	537					sodium ion transport	integral to membrane|mitochondrial membrane	solute:hydrogen antiporter activity				0				OV - Ovarian serous cystadenocarcinoma(123;2.3e-08)		TCACCTCTAAACTTGCACAGA	0.353													104	194	---	---	---	---	PASS
CARD6	84674	broad.mit.edu	37	5	40843666	40843666	+	Silent	SNP	T	G	G			TCGA-AK-3456-01A-02D-1386-10	TCGA-AK-3456-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:40843666T>G	uc003jmg.2	+	2	771	c.696T>G	c.(694-696)GTT>GTG	p.V232V		NM_032587	NP_115976	Q9BX69	CARD6_HUMAN	caspase recruitment domain family, member 6	232	Asp/Glu-rich.				apoptosis|regulation of apoptosis	intracellular				ovary(2)|skin(2)|lung(1)	5						AAGAGGAGGTTTATGATGACC	0.438													80	122	---	---	---	---	PASS
PLK2	10769	broad.mit.edu	37	5	57753970	57753970	+	Silent	SNP	T	C	C			TCGA-AK-3456-01A-02D-1386-10	TCGA-AK-3456-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:57753970T>C	uc003jrn.2	-	5	781	c.654A>G	c.(652-654)GAA>GAG	p.E218E	PLK2_uc011cql.1_3'UTR	NM_006622	NP_006613	Q9NYY3	PLK2_HUMAN	polo-like kinase 2	218	Protein kinase.				positive regulation of I-kappaB kinase/NF-kappaB cascade		ATP binding|protein binding|protein serine/threonine kinase activity|signal transducer activity			ovary(2)|lung(1)|skin(1)	4		all_cancers(5;1.76e-12)|all_epithelial(5;2.09e-13)|all_lung(5;6.64e-05)|Lung NSC(5;0.000127)|Prostate(74;0.055)|Breast(144;0.0602)|Ovarian(174;0.182)		OV - Ovarian serous cystadenocarcinoma(10;7.03e-37)		CAACTTTTAGTTCCATGGCTT	0.418													5	215	---	---	---	---	PASS
HIVEP1	3096	broad.mit.edu	37	6	12123871	12123871	+	Missense_Mutation	SNP	G	C	C			TCGA-AK-3456-01A-02D-1386-10	TCGA-AK-3456-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:12123871G>C	uc003nac.2	+	4	4022	c.3843G>C	c.(3841-3843)AAG>AAC	p.K1281N	HIVEP1_uc011diq.1_RNA	NM_002114	NP_002105	P15822	ZEP1_HUMAN	human immunodeficiency virus type I enhancer	1281					transcription, DNA-dependent	cytoplasm|nucleus	DNA binding|protein binding|zinc ion binding			ovary(3)|large_intestine(1)|central_nervous_system(1)|skin(1)	6	Breast(50;0.0639)|Ovarian(93;0.0816)	all_hematologic(90;0.117)				CACCCAAAAAGAAAAGGCTCC	0.453													54	77	---	---	---	---	PASS
SLC29A1	2030	broad.mit.edu	37	6	44197391	44197391	+	Silent	SNP	C	T	T			TCGA-AK-3456-01A-02D-1386-10	TCGA-AK-3456-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:44197391C>T	uc003owu.1	+	4	506	c.177C>T	c.(175-177)GAC>GAT	p.D59D	SLC29A1_uc011dvp.1_Silent_p.D78D|SLC29A1_uc003owv.1_Silent_p.D59D|SLC29A1_uc003oww.1_Silent_p.D138D|SLC29A1_uc011dvq.1_Silent_p.D101D|SLC29A1_uc003owx.1_Silent_p.D59D|SLC29A1_uc003owy.1_Silent_p.D59D|SLC29A1_uc003owz.1_Silent_p.D59D	NM_004955	NP_004946	Q99808	S29A1_HUMAN	equilibrative nucleoside transporter 1	59	Extracellular (Potential).				nucleobase, nucleoside and nucleotide metabolic process	apical plasma membrane|basolateral plasma membrane|integral to plasma membrane|membrane fraction	nucleoside transmembrane transporter activity|protein binding			large_intestine(2)|skin(1)	3	all_cancers(18;3.19e-06)|Lung NSC(15;0.00108)|all_lung(25;0.00278)|Hepatocellular(11;0.00908)|Ovarian(13;0.0273)		Colorectal(64;0.00337)|COAD - Colon adenocarcinoma(64;0.00536)		Troglitazone(DB00197)	TGAGCAAGGACGCCCAGGCGT	0.463													69	112	---	---	---	---	PASS
AARS2	57505	broad.mit.edu	37	6	44274036	44274036	+	Silent	SNP	C	A	A			TCGA-AK-3456-01A-02D-1386-10	TCGA-AK-3456-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:44274036C>A	uc010jza.1	-	9	1284	c.1281G>T	c.(1279-1281)GGG>GGT	p.G427G	SPATS1_uc003oxg.2_Intron|TMEM151B_uc003oxf.2_Intron	NM_020745	NP_065796	Q5JTZ9	SYAM_HUMAN	alanyl-tRNA synthetase 2, mitochondrial	427					alanyl-tRNA aminoacylation	mitochondrion	alanine-tRNA ligase activity|ATP binding|metal ion binding|tRNA binding			ovary(1)	1	Hepatocellular(11;0.00908)|all_lung(25;0.0101)|Ovarian(13;0.0273)		Colorectal(64;0.00337)|COAD - Colon adenocarcinoma(64;0.00536)		L-Alanine(DB00160)	TATCTGAAGGCCCCAGGGTCC	0.617													20	50	---	---	---	---	PASS
RPA3	6119	broad.mit.edu	37	7	7676604	7676604	+	3'UTR	SNP	T	C	C			TCGA-AK-3456-01A-02D-1386-10	TCGA-AK-3456-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:7676604T>C	uc003sri.2	-	8					RPA3_uc003srh.2_3'UTR	NM_002947	NP_002938	P35244	RFA3_HUMAN	replication protein A3, 14kDa						cell cycle checkpoint|DNA recombinase assembly|DNA strand elongation involved in DNA replication|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|nucleotide-excision repair, DNA damage removal|nucleotide-excision repair, DNA gap filling|S phase of mitotic cell cycle|telomere maintenance via recombination|telomere maintenance via semi-conservative replication|transcription-coupled nucleotide-excision repair	cytoplasm|DNA replication factor A complex|nucleoplasm	protein binding|single-stranded DNA binding			large_intestine(1)	1		Ovarian(82;0.0607)		UCEC - Uterine corpus endometrioid carcinoma (126;0.202)		TATAGCTCATTTACAATCGTA	0.328								Direct_reversal_of_damage|NER					5	173	---	---	---	---	PASS
VWDE	221806	broad.mit.edu	37	7	12410354	12410354	+	Missense_Mutation	SNP	T	C	C			TCGA-AK-3456-01A-02D-1386-10	TCGA-AK-3456-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:12410354T>C	uc003ssj.2	-	11	2234	c.1724A>G	c.(1723-1725)GAT>GGT	p.D575G	VWDE_uc011jxl.1_RNA|VWDE_uc011jxm.1_Missense_Mutation_p.D29G	NM_001135924	NP_001129396	Q8N2E2	VWDE_HUMAN	von Willebrand factor D and EGF domains	575	VWFD.					extracellular region					0						GTCATGGAAATCATTTTCCGG	0.368													5	180	---	---	---	---	PASS
ABCB5	340273	broad.mit.edu	37	7	20782648	20782648	+	Missense_Mutation	SNP	C	T	T			TCGA-AK-3456-01A-02D-1386-10	TCGA-AK-3456-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:20782648C>T	uc003suw.3	+	16	2384	c.1838C>T	c.(1837-1839)ACT>ATT	p.T613I	ABCB5_uc010kuh.2_Missense_Mutation_p.T1058I	NM_178559	NP_848654	Q2M3G0	ABCB5_HUMAN	ATP-binding cassette, sub-family B, member 5	613	Cytoplasmic (Potential).|ABC transporter 2.				regulation of membrane potential	apical plasma membrane|Golgi membrane|integral to plasma membrane|intercellular canaliculus	ATP binding|ATPase activity, coupled to transmembrane movement of substances|efflux transmembrane transporter activity			skin(2)|large_intestine(1)|haematopoietic_and_lymphoid_tissue(1)|ovary(1)|pancreas(1)	6						GGGAAAAGCACTTCTGTTCAA	0.493													4	293	---	---	---	---	PASS
SPDYE1	285955	broad.mit.edu	37	7	44048299	44048299	+	3'UTR	SNP	C	T	T			TCGA-AK-3456-01A-02D-1386-10	TCGA-AK-3456-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:44048299C>T	uc003tjf.2	+	7					POLR2J4_uc003tjc.2_Intron|POLR2J4_uc003tjd.2_Intron|POLR2J4_uc010kxw.2_Intron|POLR2J4_uc003tje.3_Intron|uc003tjg.1_5'Flank	NM_175064	NP_778234	Q8NFV5	SPDE1_HUMAN	Williams Beuren syndrome chromosome region 19											ovary(1)	1						GGATTTTCAGCAGGAACTTTA	0.483													5	8	---	---	---	---	PASS
PCLO	27445	broad.mit.edu	37	7	82579567	82579567	+	Missense_Mutation	SNP	T	C	C			TCGA-AK-3456-01A-02D-1386-10	TCGA-AK-3456-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:82579567T>C	uc003uhx.2	-	6	10626	c.10337A>G	c.(10336-10338)CAA>CGA	p.Q3446R	PCLO_uc003uhv.2_Missense_Mutation_p.Q3446R|PCLO_uc010lec.2_Missense_Mutation_p.Q411R	NM_033026	NP_149015	Q9Y6V0	PCLO_HUMAN	piccolo isoform 1	3377					cytoskeleton organization|synaptic vesicle exocytosis	cell junction|cytoskeleton|synaptic vesicle	calcium ion binding|calcium-dependent phospholipid binding|profilin binding|transporter activity			ovary(7)	7						GTCATCCGTTTGTACACCACT	0.433													100	227	---	---	---	---	PASS
NPTX2	4885	broad.mit.edu	37	7	98256632	98256632	+	Silent	SNP	C	T	T			TCGA-AK-3456-01A-02D-1386-10	TCGA-AK-3456-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:98256632C>T	uc003upl.2	+	4	1221	c.1044C>T	c.(1042-1044)GGC>GGT	p.G348G		NM_002523	NP_002514	P47972	NPTX2_HUMAN	neuronal pentraxin II precursor	348	Pentaxin.				synaptic transmission	extracellular region	metal ion binding|sugar binding			central_nervous_system(2)|skin(1)	3	all_cancers(62;2.28e-09)|all_epithelial(64;4.86e-10)|Esophageal squamous(72;0.00918)|Lung NSC(181;0.0128)|all_lung(186;0.0142)		STAD - Stomach adenocarcinoma(171;0.215)			AGCCCGGGGGCGTGCTGATCC	0.677													11	25	---	---	---	---	PASS
FAM120A	23196	broad.mit.edu	37	9	96238560	96238560	+	Silent	SNP	A	G	G			TCGA-AK-3456-01A-02D-1386-10	TCGA-AK-3456-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:96238560A>G	uc004atw.2	+	3	769	c.744A>G	c.(742-744)GAA>GAG	p.E248E	FAM120A_uc004atv.2_Silent_p.E248E|FAM120A_uc004atx.2_Silent_p.E30E|FAM120A_uc004aty.2_Silent_p.E30E	NM_014612	NP_055427	Q9NZB2	F120A_HUMAN	oxidative stress-associated Src activator	248						cytoplasm|plasma membrane	RNA binding				0						TGCCTGATGAAGATCTGGCTT	0.348													7	445	---	---	---	---	PASS
SCAI	286205	broad.mit.edu	37	9	127738411	127738411	+	Missense_Mutation	SNP	A	G	G			TCGA-AK-3456-01A-02D-1386-10	TCGA-AK-3456-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:127738411A>G	uc004bpe.2	-	15	1462	c.1381T>C	c.(1381-1383)TAT>CAT	p.Y461H	SCAI_uc004bpd.2_Missense_Mutation_p.Y484H|SCAI_uc010mwu.2_RNA	NM_001144877	NP_001138349	Q8N9R8	SCAI_HUMAN	suppressor of cancer cell invasion isoform 2	461					negative regulation of cell migration|negative regulation of Rho protein signal transduction|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|integral to membrane|nucleus	protein binding|transcription corepressor activity			ovary(2)|breast(2)|central_nervous_system(1)	5						GCTTTTGGATATGCTGTAGGA	0.328													4	92	---	---	---	---	PASS
ANK3	288	broad.mit.edu	37	10	61831542	61831542	+	Missense_Mutation	SNP	C	G	G			TCGA-AK-3456-01A-02D-1386-10	TCGA-AK-3456-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:61831542C>G	uc001jky.2	-	37	9289	c.9097G>C	c.(9097-9099)GGT>CGT	p.G3033R	ANK3_uc001jkw.2_Intron|ANK3_uc009xpa.2_Intron|ANK3_uc001jkx.2_Intron|ANK3_uc010qih.1_Intron|ANK3_uc001jkz.3_Intron|ANK3_uc001jkv.2_Intron|ANK3_uc009xpb.1_Intron	NM_020987	NP_066267	Q12955	ANK3_HUMAN	ankyrin 3 isoform 1	3033					establishment of protein localization|signal transduction	basolateral plasma membrane|cytoplasm|cytoskeleton	protein binding			skin(9)|ovary(6)|pancreas(2)|central_nervous_system(2)	19						GGGCATAAACCTACATAACTC	0.408													42	62	---	---	---	---	PASS
DUPD1	338599	broad.mit.edu	37	10	76797800	76797800	+	Missense_Mutation	SNP	G	A	A	rs148261941	by1000genomes	TCGA-AK-3456-01A-02D-1386-10	TCGA-AK-3456-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:76797800G>A	uc001jwq.1	-	3	457	c.457C>T	c.(457-459)CGG>TGG	p.R153W		NM_001003892	NP_001003892	Q68J44	DUPD1_HUMAN	dual specificity phosphatase and pro isomerase	153	Tyrosine-protein phosphatase.|Substrate binding (Probable).					cytoplasm	protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity			ovary(2)	2	all_cancers(46;0.0207)|all_epithelial(25;0.00126)|Prostate(51;0.0112)|Ovarian(15;0.0348)					GTGGCTGACCGGCTGCGGCCC	0.622													3	22	---	---	---	---	PASS
RRP12	23223	broad.mit.edu	37	10	99145673	99145673	+	Silent	SNP	C	T	T			TCGA-AK-3456-01A-02D-1386-10	TCGA-AK-3456-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:99145673C>T	uc001knf.2	-	9	1234	c.1095G>A	c.(1093-1095)GAG>GAA	p.E365E	RRP12_uc009xvm.2_Silent_p.E83E|RRP12_uc010qou.1_Silent_p.E304E|RRP12_uc009xvn.2_Silent_p.E265E	NM_015179	NP_055994	Q5JTH9	RRP12_HUMAN	ribosomal RNA processing 12 homolog isoform 1	365						integral to membrane|nuclear membrane|nucleolus	protein binding			ovary(2)|central_nervous_system(1)	3		Colorectal(252;0.162)		Epithelial(162;2.72e-09)|all cancers(201;1.76e-07)		GGGCGTTGAGCTCTGCTGACA	0.647													15	26	---	---	---	---	PASS
LOXL4	84171	broad.mit.edu	37	10	100022771	100022771	+	Silent	SNP	C	T	T			TCGA-AK-3456-01A-02D-1386-10	TCGA-AK-3456-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:100022771C>T	uc001kpa.1	-	2	157	c.6G>A	c.(4-6)GCG>GCA	p.A2A		NM_032211	NP_115587	Q96JB6	LOXL4_HUMAN	lysyl oxidase-like 4 precursor	2						extracellular space|membrane	copper ion binding|protein binding|scavenger receptor activity			ovary(3)|breast(1)|skin(1)	5		Colorectal(252;0.234)		Epithelial(162;2.14e-11)|all cancers(201;2.49e-09)		GTGGGGACCACGCCATGGTGA	0.587											OREG0020428	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	8	14	---	---	---	---	PASS
NUP98	4928	broad.mit.edu	37	11	3784174	3784174	+	Silent	SNP	A	G	G			TCGA-AK-3456-01A-02D-1386-10	TCGA-AK-3456-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:3784174A>G	uc001lyh.2	-	9	1335	c.1044T>C	c.(1042-1044)GGT>GGC	p.G348G	NUP98_uc001lyi.2_Silent_p.G348G|NUP98_uc001lyj.1_Silent_p.G348G|NUP98_uc001lyk.1_Silent_p.G348G	NM_016320	NP_057404	P52948	NUP98_HUMAN	nucleoporin 98kD isoform 1	348	Gly/Thr-rich.				carbohydrate metabolic process|DNA replication|glucose transport|interspecies interaction between organisms|mitotic prometaphase|mRNA transport|nuclear pore organization|protein import into nucleus, docking|regulation of glucose transport|transmembrane transport|viral reproduction	cytosol|nuclear membrane|nucleoplasm|Nup107-160 complex	protein binding|structural constituent of nuclear pore|transporter activity			breast(4)|skin(3)|ovary(2)|central_nervous_system(1)|lung(1)|kidney(1)	12		Medulloblastoma(188;0.0025)|Breast(177;0.00328)|all_neural(188;0.0227)		BRCA - Breast invasive adenocarcinoma(625;0.0403)|LUSC - Lung squamous cell carcinoma(625;0.116)|Lung(200;0.199)		GCCCAAAGAGACCTGTTCCTG	0.448			T	HOXA9|NSD1|WHSC1L1|DDX10|TOP1|HOXD13|PMX1|HOXA13|HOXD11|HOXA11|RAP1GDS1|HOXC11	AML								7	365	---	---	---	---	PASS
ZNF215	7762	broad.mit.edu	37	11	6964378	6964378	+	Missense_Mutation	SNP	C	G	G			TCGA-AK-3456-01A-02D-1386-10	TCGA-AK-3456-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:6964378C>G	uc001mey.2	+	5	1136	c.548C>G	c.(547-549)TCT>TGT	p.S183C	ZNF215_uc010raw.1_Intron|ZNF215_uc010rax.1_Intron|ZNF215_uc001mez.1_Missense_Mutation_p.S183C	NM_013250	NP_037382	Q9UL58	ZN215_HUMAN	zinc finger protein 215	183	KRAB.				viral reproduction	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding				0				Epithelial(150;6.33e-08)|BRCA - Breast invasive adenocarcinoma(625;0.134)		CAACTGGACTCTGCTGTAAAG	0.398													93	167	---	---	---	---	PASS
C11orf1	64776	broad.mit.edu	37	11	111750266	111750266	+	5'UTR	SNP	T	A	A			TCGA-AK-3456-01A-02D-1386-10	TCGA-AK-3456-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:111750266T>A	uc001pmd.2	+	1					ALG9_uc010rwo.1_5'Flank|FDXACB1_uc009yyi.2_5'Flank|FDXACB1_uc001pmc.3_5'Flank|C11orf1_uc001pme.2_5'Flank	NM_022761	NP_073598	Q9H5F2	CK001_HUMAN	hypothetical protein LOC64776							nucleus					0		all_cancers(61;1.26e-15)|all_epithelial(67;9.52e-10)|Melanoma(852;1.91e-06)|all_hematologic(158;0.000405)|Acute lymphoblastic leukemia(157;0.000967)|Breast(348;0.0112)|Medulloblastoma(222;0.0228)|all_neural(223;0.0281)		all cancers(92;6.28e-09)|Epithelial(105;4.11e-08)|OV - Ovarian serous cystadenocarcinoma(223;1.52e-07)|BRCA - Breast invasive adenocarcinoma(274;1.1e-06)		GTTTTGAACCTTTTTTCACCT	0.483											OREG0021330	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	75	153	---	---	---	---	PASS
ANKK1	255239	broad.mit.edu	37	11	113264406	113264406	+	Missense_Mutation	SNP	C	T	T			TCGA-AK-3456-01A-02D-1386-10	TCGA-AK-3456-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:113264406C>T	uc001pny.2	+	2	483	c.389C>T	c.(388-390)GCC>GTC	p.A130V		NM_178510	NP_848605	Q8NFD2	ANKK1_HUMAN	ankyrin repeat and kinase domain containing 1	130	Protein kinase.						ATP binding|protein serine/threonine kinase activity			lung(5)|stomach(1)|ovary(1)|breast(1)	8		all_cancers(61;1.53e-11)|all_epithelial(67;3e-06)|Melanoma(852;4.04e-05)|all_hematologic(158;0.000315)|Acute lymphoblastic leukemia(157;0.000966)|Breast(348;0.0461)|Medulloblastoma(222;0.0523)|all_neural(223;0.0663)|Prostate(24;0.194)		BRCA - Breast invasive adenocarcinoma(274;4.82e-06)|Epithelial(105;5.41e-05)|all cancers(92;0.000442)|OV - Ovarian serous cystadenocarcinoma(223;0.238)		ACCAGCTTGGCCATGAACTTC	0.562													4	63	---	---	---	---	PASS
CEP164	22897	broad.mit.edu	37	11	117263760	117263760	+	Missense_Mutation	SNP	G	A	A			TCGA-AK-3456-01A-02D-1386-10	TCGA-AK-3456-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:117263760G>A	uc001prc.2	+	20	2681	c.2534G>A	c.(2533-2535)GGG>GAG	p.G845E	CEP164_uc001prb.2_Missense_Mutation_p.G848E|CEP164_uc010rxk.1_Missense_Mutation_p.G819E|CEP164_uc001prf.2_Intron|CEP164_uc009yzp.1_RNA|CEP164_uc001prg.1_Missense_Mutation_p.G278E	NM_014956	NP_055771	Q9UPV0	CE164_HUMAN	centrosomal protein 164kDa	845	Glu-rich.				cell division|DNA repair|G2/M transition of mitotic cell cycle|mitosis	centriole|cytosol|nucleus				ovary(1)|central_nervous_system(1)	2	all_hematologic(175;0.0487)	Breast(348;0.00908)|Medulloblastoma(222;0.0425)|all_hematologic(192;0.196)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;4e-05)|Epithelial(105;0.0008)		GAAGTGGAAGGGGAGCATGAG	0.592													83	138	---	---	---	---	PASS
HINFP	25988	broad.mit.edu	37	11	119003024	119003024	+	Intron	SNP	G	T	T			TCGA-AK-3456-01A-02D-1386-10	TCGA-AK-3456-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:119003024G>T	uc001pvp.2	+						HINFP_uc001pvq.2_Intron|HINFP_uc001pvr.2_5'UTR	NM_015517	NP_056332	Q9BQA5	HINFP_HUMAN	MBD2 (methyl-CpG-binding protein)-interacting						DNA damage checkpoint|DNA repair|establishment of protein localization|in utero embryonic development|myoblast differentiation|negative regulation of transcription, DNA-dependent|positive regulation of transcription, DNA-dependent|regulation of transcription involved in G1/S phase of mitotic cell cycle	Cajal body	enzyme binding|histone binding|sequence-specific DNA binding transcription factor activity|transcription coactivator activity|transcription regulatory region DNA binding|zinc ion binding			pancreas(2)|ovary(1)|skin(1)	4						ggtgaagctggaattctaact	0.144													6	9	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	12	92109	92109	+	Silent	SNP	C	T	T			TCGA-AK-3456-01A-02D-1386-10	TCGA-AK-3456-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:92109C>T	uc010sdi.1	-	2	229	c.201G>A	c.(199-201)GCG>GCA	p.A67A	uc010sdj.1_RNA					SubName: Full=DEAD/H box polypeptide 11 like 11;																		AAGGGCGCAGCGCCAGGCAGT	0.592													3	11	---	---	---	---	PASS
CACNA1C	775	broad.mit.edu	37	12	2794927	2794927	+	Missense_Mutation	SNP	C	T	T			TCGA-AK-3456-01A-02D-1386-10	TCGA-AK-3456-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:2794927C>T	uc009zdu.1	+	47	6161	c.5848C>T	c.(5848-5850)CGG>TGG	p.R1950W	CACNA1C_uc009zdv.1_Missense_Mutation_p.R1864W|CACNA1C_uc001qkb.2_Missense_Mutation_p.R1867W|CACNA1C_uc001qkc.2_Missense_Mutation_p.R1886W|CACNA1C_uc001qke.2_Missense_Mutation_p.R1856W|CACNA1C_uc001qkf.2_Missense_Mutation_p.R1875W|CACNA1C_uc001qjz.2_Missense_Mutation_p.R1867W|CACNA1C_uc001qkd.2_Missense_Mutation_p.R1886W|CACNA1C_uc001qkg.2_Missense_Mutation_p.R1873W|CACNA1C_uc009zdw.1_Missense_Mutation_p.R1908W|CACNA1C_uc001qkh.2_Missense_Mutation_p.R1875W|CACNA1C_uc001qkl.2_Missense_Mutation_p.R1915W|CACNA1C_uc001qkn.2_Missense_Mutation_p.R1867W|CACNA1C_uc001qko.2_Missense_Mutation_p.R1887W|CACNA1C_uc001qkp.2_Missense_Mutation_p.R1867W|CACNA1C_uc001qkr.2_Missense_Mutation_p.R1884W|CACNA1C_uc001qku.2_Missense_Mutation_p.R1902W|CACNA1C_uc001qkq.2_Missense_Mutation_p.R1895W|CACNA1C_uc001qks.2_Missense_Mutation_p.R1867W|CACNA1C_uc001qkt.2_Missense_Mutation_p.R1886W|CACNA1C_uc001qki.1_Missense_Mutation_p.R1674W|CACNA1C_uc001qkj.1_Missense_Mutation_p.R1638W|CACNA1C_uc001qkk.1_Missense_Mutation_p.R1603W|CACNA1C_uc001qkm.1_Missense_Mutation_p.R1663W|CACNA1C_uc010sea.1_Missense_Mutation_p.R558W|uc001qkx.1_Intron|CACNA1C_uc001qky.1_Missense_Mutation_p.R185W	NM_199460	NP_955630	Q13936	CAC1C_HUMAN	calcium channel, voltage-dependent, L type,	1950	Cytoplasmic (Potential).				axon guidance|calcium ion transport into cytosol|energy reserve metabolic process|regulation of insulin secretion	cytoplasm|postsynaptic density|voltage-gated calcium channel complex	calmodulin binding|voltage-gated calcium channel activity			ovary(10)|central_nervous_system(1)	11			OV - Ovarian serous cystadenocarcinoma(31;0.00256)	LUAD - Lung adenocarcinoma(1;0.134)	Ibutilide(DB00308)|Isradipine(DB00270)|Magnesium Sulfate(DB00653)|Mibefradil(DB01388)|Nicardipine(DB00622)|Verapamil(DB00661)	TGACGAAAATCGGCAACTGAC	0.602													4	68	---	---	---	---	PASS
MCRS1	10445	broad.mit.edu	37	12	49954117	49954117	+	Missense_Mutation	SNP	A	T	T			TCGA-AK-3456-01A-02D-1386-10	TCGA-AK-3456-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:49954117A>T	uc001ruk.1	-	9	1033	c.842T>A	c.(841-843)TTC>TAC	p.F281Y	MCRS1_uc001rui.1_Missense_Mutation_p.F294Y|MCRS1_uc001ruj.1_Missense_Mutation_p.F268Y|MCRS1_uc001rul.1_Missense_Mutation_p.F281Y|MCRS1_uc009zlj.1_Missense_Mutation_p.F90Y|MCRS1_uc001rum.1_Missense_Mutation_p.F268Y	NM_006337	NP_006328	Q96EZ8	MCRS1_HUMAN	microspherule protein 1 isoform 1	281					DNA recombination|DNA repair|protein modification process|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|Ino80 complex|MLL1 complex|nucleolus	protein binding			large_intestine(1)	1						TGCATCAGAGAAGTTCAGCAC	0.562													40	70	---	---	---	---	PASS
CEP290	80184	broad.mit.edu	37	12	88535057	88535057	+	Missense_Mutation	SNP	T	C	C			TCGA-AK-3456-01A-02D-1386-10	TCGA-AK-3456-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:88535057T>C	uc001tar.2	-	2	372	c.28A>G	c.(28-30)ATA>GTA	p.I10V	CEP290_uc009zsl.1_5'Flank|TMTC3_uc009zsm.2_5'Flank|TMTC3_uc001tau.2_5'Flank	NM_025114	NP_079390	O15078	CE290_HUMAN	centrosomal protein 290kDa	10					cilium assembly|eye photoreceptor cell development|G2/M transition of mitotic cell cycle|hindbrain development|otic vesicle formation|positive regulation of transcription, DNA-dependent|pronephros development|protein transport	cell surface|centrosome|cytosol|nucleus|photoreceptor connecting cilium	protein binding			ovary(5)|breast(1)|pancreas(1)	7						ACTTTCATTATTTCTTTCCAG	0.358													6	424	---	---	---	---	PASS
IKBIP	121457	broad.mit.edu	37	12	99007673	99007673	+	Missense_Mutation	SNP	T	C	C			TCGA-AK-3456-01A-02D-1386-10	TCGA-AK-3456-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:99007673T>C	uc001tfv.2	-	3	853	c.743A>G	c.(742-744)GAA>GGA	p.E248G	IKBIP_uc001tfw.2_3'UTR	NM_201612	NP_963906	Q70UQ0	IKIP_HUMAN	IKK interacting protein isoform 2	248					induction of apoptosis|response to X-ray	endoplasmic reticulum membrane|integral to membrane	protein binding				0						ACTCTTTAGTTCGGTTAGCGT	0.383													5	219	---	---	---	---	PASS
LOC284232	284232	broad.mit.edu	37	13	19414116	19414116	+	RNA	SNP	C	T	T			TCGA-AK-3456-01A-02D-1386-10	TCGA-AK-3456-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:19414116C>T	uc010tcj.1	-	1		c.31994G>A				NR_027995				Homo sapiens ankyrin repeat domain 20 family, member A2 pseudogene (LOC284232), non-coding RNA.												0						GATTGATTTACCTGATTTGGA	0.269													7	49	---	---	---	---	PASS
FAM70B	348013	broad.mit.edu	37	13	114469190	114469190	+	Missense_Mutation	SNP	C	T	T			TCGA-AK-3456-01A-02D-1386-10	TCGA-AK-3456-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:114469190C>T	uc001vuh.2	+	2	176	c.149C>T	c.(148-150)ACG>ATG	p.T50M	FAM70B_uc010tkh.1_Missense_Mutation_p.T50M	NM_182614	NP_872420	Q8WV15	FA70B_HUMAN	family with sequence similarity 70, member B	50						integral to membrane					0	Lung NSC(43;0.00976)|all_neural(89;0.0337)|Hepatocellular(20;0.0877)|Medulloblastoma(90;0.163)|Lung SC(71;0.218)	all_lung(25;0.123)|all_epithelial(44;0.133)	all cancers(43;0.181)			ACCACCAGGACGGAGAATGTG	0.652													4	45	---	---	---	---	PASS
UPF3A	65110	broad.mit.edu	37	13	115051721	115051721	+	Intron	SNP	G	A	A			TCGA-AK-3456-01A-02D-1386-10	TCGA-AK-3456-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:115051721G>A	uc001vup.2	+						UPF3A_uc001vuq.2_Intron|UPF3A_uc001vus.2_Intron|UPF3A_uc001vur.2_Intron|UPF3A_uc001vut.2_5'UTR|UPF3A_uc001vuu.2_5'Flank	NM_023011	NP_075387	Q9H1J1	REN3A_HUMAN	UPF3 regulator of nonsense transcripts homolog A						mRNA transport|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay|positive regulation of translation	cytoplasm|nucleus|plasma membrane	nucleocytoplasmic transporter activity|nucleotide binding|protein binding|RNA binding			skin(1)	1	Lung NSC(43;0.00299)|all_neural(89;0.0337)|Medulloblastoma(90;0.163)|Lung SC(71;0.218)	all_cancers(25;0.0191)|all_epithelial(44;0.00716)|all_lung(25;0.0173)|Lung NSC(25;0.0634)|Breast(118;0.238)	BRCA - Breast invasive adenocarcinoma(86;0.0886)	OV - Ovarian serous cystadenocarcinoma(48;0.195)|Epithelial(10;0.2)		ATTATTTTCCGAAATGAATGT	0.333													28	92	---	---	---	---	PASS
NYNRIN	57523	broad.mit.edu	37	14	24886608	24886608	+	Missense_Mutation	SNP	G	A	A			TCGA-AK-3456-01A-02D-1386-10	TCGA-AK-3456-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:24886608G>A	uc001wpf.3	+	9	5971	c.5653G>A	c.(5653-5655)GCC>ACC	p.A1885T		NM_025081	NP_079357	Q9P2P1	NYNRI_HUMAN	hypothetical protein LOC57523	1885					DNA integration	integral to membrane	DNA binding			ovary(2)|central_nervous_system(1)	3						GAAGGCCTTTGCCAAGAGTGG	0.627													8	13	---	---	---	---	PASS
AKAP6	9472	broad.mit.edu	37	14	32902689	32902689	+	5'UTR	SNP	T	A	A			TCGA-AK-3456-01A-02D-1386-10	TCGA-AK-3456-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:32902689T>A	uc001wrq.2	+	2					AKAP6_uc010aml.2_5'UTR	NM_004274	NP_004265	Q13023	AKAP6_HUMAN	A-kinase anchor protein 6						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)		AAGTGAGGTTTAGACTTCTCC	0.448													35	62	---	---	---	---	PASS
PTGDR	5729	broad.mit.edu	37	14	52741643	52741643	+	Silent	SNP	C	T	T			TCGA-AK-3456-01A-02D-1386-10	TCGA-AK-3456-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:52741643C>T	uc001wzq.2	+	2	1143	c.1041C>T	c.(1039-1041)AGC>AGT	p.S347S		NM_000953	NP_000944	Q13258	PD2R_HUMAN	prostaglandin D2 receptor	347	Cytoplasmic (Potential).					integral to membrane|plasma membrane	prostaglandin D receptor activity|protein binding			ovary(1)|lung(1)|central_nervous_system(1)|skin(1)	4	Breast(41;0.0639)|all_epithelial(31;0.0887)				Nedocromil(DB00716)	GGTACAGGAGCCGGTGCAGCA	0.388													124	175	---	---	---	---	PASS
ABCD4	5826	broad.mit.edu	37	14	74763075	74763075	+	Missense_Mutation	SNP	G	C	C			TCGA-AK-3456-01A-02D-1386-10	TCGA-AK-3456-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:74763075G>C	uc001xpr.2	-	5	655	c.503C>G	c.(502-504)CCG>CGG	p.P168R	ABCD4_uc001xps.2_Missense_Mutation_p.P9R|ABCD4_uc001xpt.2_Missense_Mutation_p.P9R|ABCD4_uc010tur.1_Missense_Mutation_p.P81R|ABCD4_uc001xpu.2_5'UTR|ABCD4_uc001xpv.2_RNA	NM_005050	NP_005041	O14678	ABCD4_HUMAN	ATP-binding cassette, sub-family D, member 4	168	ABC transmembrane type-1.					ATP-binding cassette (ABC) transporter complex|integral to membrane|peroxisomal membrane	ATP binding|ATPase activity, coupled to transmembrane movement of substances			upper_aerodigestive_tract(2)|large_intestine(1)|ovary(1)	4				BRCA - Breast invasive adenocarcinoma(234;0.00153)		GAGGGTGAACGGGGAGATGAT	0.602													38	74	---	---	---	---	PASS
DIO2	1734	broad.mit.edu	37	14	80669169	80669169	+	Missense_Mutation	SNP	G	A	A			TCGA-AK-3456-01A-02D-1386-10	TCGA-AK-3456-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:80669169G>A	uc010tvq.1	-	4	1087	c.685C>T	c.(685-687)CGT>TGT	p.R229C	DIO2_uc010tvp.1_Missense_Mutation_p.R265C|DIO2_uc001xut.2_RNA|DIO2_uc010asx.2_3'UTR|DIO2_uc010tvr.1_Missense_Mutation_p.R229C|DIO2_uc010asy.2_3'UTR	NM_000793	NP_000784	Q92813	IOD2_HUMAN	deiodinase, iodothyronine, type II isoform a	229					hormone biosynthetic process|selenocysteine incorporation|thyroid hormone generation	integral to membrane|plasma membrane	thyroxine 5'-deiodinase activity|ubiquitin protein ligase binding			central_nervous_system(1)	1				BRCA - Breast invasive adenocarcinoma(234;0.0281)		ATGCACACACGTTCAAAGGCT	0.527													32	151	---	---	---	---	PASS
SMEK1	55671	broad.mit.edu	37	14	91942217	91942217	+	Missense_Mutation	SNP	G	C	C			TCGA-AK-3456-01A-02D-1386-10	TCGA-AK-3456-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:91942217G>C	uc001xzn.2	-	7	2026	c.1204C>G	c.(1204-1206)CAG>GAG	p.Q402E	SMEK1_uc001xzm.2_Missense_Mutation_p.Q402E|SMEK1_uc001xzo.2_Missense_Mutation_p.Q402E|SMEK1_uc010atz.2_Missense_Mutation_p.Q163E|SMEK1_uc001xzp.1_RNA|SMEK1_uc001xzq.1_Missense_Mutation_p.Q278E	NM_032560	NP_115949	Q6IN85	P4R3A_HUMAN	SMEK homolog 1, suppressor of mek1	402						microtubule organizing center|nucleus	protein binding				0		all_cancers(154;0.0691)|all_epithelial(191;0.219)		COAD - Colon adenocarcinoma(157;0.221)		TGTGCCTCCTGCATGACAAAC	0.363													167	307	---	---	---	---	PASS
SQRDL	58472	broad.mit.edu	37	15	45965852	45965852	+	Missense_Mutation	SNP	T	G	G			TCGA-AK-3456-01A-02D-1386-10	TCGA-AK-3456-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:45965852T>G	uc001zvt.2	+	6	696	c.507T>G	c.(505-507)AAT>AAG	p.N169K	SQRDL_uc001zvu.2_Missense_Mutation_p.N169K|SQRDL_uc001zvv.2_Missense_Mutation_p.N169K	NM_021199	NP_067022	Q9Y6N5	SQRD_HUMAN	sulfide dehydrogenase like precursor	169							oxidoreductase activity			ovary(1)	1		Lung NSC(122;0.000117)|all_lung(180;0.000737)|Melanoma(134;0.0417)		all cancers(107;5.89e-18)|GBM - Glioblastoma multiforme(94;1.21e-06)|COAD - Colon adenocarcinoma(120;0.17)|Colorectal(133;0.188)		TAGGGTCGAATTATTCAGTTA	0.398													141	212	---	---	---	---	PASS
WDR72	256764	broad.mit.edu	37	15	53997254	53997254	+	Missense_Mutation	SNP	T	C	C			TCGA-AK-3456-01A-02D-1386-10	TCGA-AK-3456-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:53997254T>C	uc002acj.2	-	11	1321	c.1279A>G	c.(1279-1281)ACA>GCA	p.T427A	WDR72_uc010bfi.1_Missense_Mutation_p.T427A	NM_182758	NP_877435	Q3MJ13	WDR72_HUMAN	WD repeat domain 72	427	WD 5.									lung(1)|skin(1)	2				all cancers(107;0.0511)		ATGATAATTGTCCCATCTTCA	0.388													6	263	---	---	---	---	PASS
RGMA	56963	broad.mit.edu	37	15	93588747	93588747	+	Silent	SNP	G	T	T			TCGA-AK-3456-01A-02D-1386-10	TCGA-AK-3456-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:93588747G>T	uc002bss.1	-	4	1106	c.834C>A	c.(832-834)GGC>GGA	p.G278G	RGMA_uc002bsq.1_Silent_p.G262G|RGMA_uc010boi.1_Silent_p.G169G|RGMA_uc002bsr.1_Silent_p.G169G|RGMA_uc010urc.1_Silent_p.G286G	NM_020211	NP_064596	Q96B86	RGMA_HUMAN	RGM domain family, member A precursor	278					axon guidance	anchored to membrane|endoplasmic reticulum|plasma membrane					0	Lung NSC(78;0.0542)|all_lung(78;0.0786)		BRCA - Breast invasive adenocarcinoma(143;0.0312)|OV - Ovarian serous cystadenocarcinoma(32;0.108)			CGATGGTGGTGCCGATGTACT	0.612													5	17	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	16	18442362	18442362	+	Missense_Mutation	SNP	G	A	A			TCGA-AK-3456-01A-02D-1386-10	TCGA-AK-3456-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:18442362G>A	uc010bvw.2	-	6	1012	c.356C>T	c.(355-357)CCC>CTC	p.P119L						SubName: Full=cDNA FLJ59085, highly similar to Polycystin-1;																		CTGCGCGGGGGGCCCCGCGGG	0.682													4	11	---	---	---	---	PASS
NLRC5	84166	broad.mit.edu	37	16	57088695	57088695	+	Missense_Mutation	SNP	C	G	G			TCGA-AK-3456-01A-02D-1386-10	TCGA-AK-3456-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:57088695C>G	uc002ekk.1	+	25	3764	c.3539C>G	c.(3538-3540)CCC>CGC	p.P1180R	NLRC5_uc002ekn.2_Missense_Mutation_p.P899R|NLRC5_uc002ekl.2_Missense_Mutation_p.P985R|NLRC5_uc002ekm.2_Missense_Mutation_p.P955R|NLRC5_uc010ccr.1_RNA|NLRC5_uc010ccs.1_RNA|NLRC5_uc002eko.1_RNA|NLRC5_uc002ekp.1_Missense_Mutation_p.P96R|NLRC5_uc002ekq.1_5'UTR|NLRC5_uc002ekr.1_Missense_Mutation_p.P96R	NM_032206	NP_115582	Q86WI3	NLRC5_HUMAN	nucleotide-binding oligomerization domains 27	1180	LRR 12.				defense response to virus|innate immune response|negative regulation of NF-kappaB transcription factor activity|negative regulation of type I interferon production|negative regulation of type I interferon-mediated signaling pathway|positive regulation of interferon-gamma-mediated signaling pathway|positive regulation of MHC class I biosynthetic process|positive regulation of transcription from RNA polymerase II promoter|positive regulation of type I interferon-mediated signaling pathway|regulation of kinase activity	cytosol|nucleus	ATP binding|protein binding|RNA polymerase II core promoter sequence-specific DNA binding			ovary(4)|skin(2)|breast(1)	7		all_neural(199;0.225)				CCGAAAAGCCCCTTCCTGCTG	0.577													25	66	---	---	---	---	PASS
KATNB1	10300	broad.mit.edu	37	16	57775693	57775693	+	Silent	SNP	C	T	T			TCGA-AK-3456-01A-02D-1386-10	TCGA-AK-3456-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:57775693C>T	uc002eml.1	+	3	509	c.135C>T	c.(133-135)GTC>GTT	p.V45V		NM_005886	NP_005877	Q9BVA0	KTNB1_HUMAN	katanin p80 subunit B 1	45	WD 1.|Interaction with centrosomes.|Interaction with dynein (By similarity).				cell division|mitosis|negative regulation of microtubule depolymerization|positive regulation of microtubule depolymerization|protein targeting	katanin complex|microtubule|spindle pole	microtubule binding|protein heterodimerization activity				0		all_neural(199;0.223)				ACTGCCGCGTCAACCTGTGGT	0.652													3	32	---	---	---	---	PASS
RLTPR	146206	broad.mit.edu	37	16	67690372	67690372	+	Missense_Mutation	SNP	C	T	T			TCGA-AK-3456-01A-02D-1386-10	TCGA-AK-3456-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:67690372C>T	uc002etn.2	+	35	3980	c.3860C>T	c.(3859-3861)GCC>GTC	p.A1287V	RLTPR_uc010vjr.1_Missense_Mutation_p.A1251V	NM_001013838	NP_001013860	Q6F5E8	LR16C_HUMAN	RGD motif, leucine rich repeats, tropomodulin	1287										breast(1)	1		Acute lymphoblastic leukemia(13;3.23e-05)|all_hematologic(13;0.00251)|Ovarian(137;0.192)		OV - Ovarian serous cystadenocarcinoma(108;0.0146)|Epithelial(162;0.0481)|all cancers(182;0.232)		CCTGAGTCTGCCACCTGGAAG	0.627													9	36	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	17	21730916	21730916	+	Missense_Mutation	SNP	G	T	T	rs111245273	by1000genomes	TCGA-AK-3456-01A-02D-1386-10	TCGA-AK-3456-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21730916G>T	uc002gyy.3	+	2	343	c.218G>T	c.(217-219)CGG>CTG	p.R73L						SubName: Full=cDNA FLJ51326, highly similar to Homo sapiens ubiquitin B (UBB), mRNA;																		GTCCTGCGTCGGAGAGGTGGT	0.552													5	76	---	---	---	---	PASS
DDX52	11056	broad.mit.edu	37	17	35986131	35986131	+	Missense_Mutation	SNP	C	A	A	rs79312838		TCGA-AK-3456-01A-02D-1386-10	TCGA-AK-3456-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:35986131C>A	uc002hoi.1	-	8	984	c.946G>T	c.(946-948)GTA>TTA	p.V316L	DDX52_uc002hoh.1_Missense_Mutation_p.V208L	NM_007010	NP_008941	Q9Y2R4	DDX52_HUMAN	ATP-dependent RNA helicase ROK1 isoform a	316	Helicase ATP-binding.					nucleolus	ATP binding|ATP-dependent helicase activity|RNA binding			ovary(1)|skin(1)	2		Breast(25;0.00637)|Ovarian(249;0.15)				TCGTCTACTACAAGCCACTCA	0.448													4	81	---	---	---	---	PASS
PRR15L	79170	broad.mit.edu	37	17	46030230	46030230	+	3'UTR	SNP	C	T	T			TCGA-AK-3456-01A-02D-1386-10	TCGA-AK-3456-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:46030230C>T	uc002imp.2	-	2						NM_024320	NP_077296	Q9BU68	PR15L_HUMAN	ATPase family, AAA domain containing 4											ovary(1)	1						TGGCAAGGTCCTGTCTCAGAT	0.527													24	23	---	---	---	---	PASS
AMZ2P1	201283	broad.mit.edu	37	17	62968690	62968690	+	RNA	SNP	A	G	G	rs138671696	by1000genomes	TCGA-AK-3456-01A-02D-1386-10	TCGA-AK-3456-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:62968690A>G	uc002jez.3	-	4		c.641T>C			AMZ2P1_uc002jfa.3_RNA|AMZ2P1_uc002jfb.3_RNA|AMZ2P1_uc010del.2_RNA					Homo sapiens cDNA FLJ32065 fis, clone OCBBF1000086, weakly similar to Archeobacterial metalloproteinase-like protein 2 (EC 3.-.-.-).												0						AAAATTCCACAAGTCTCTTGG	0.373													6	482	---	---	---	---	PASS
ASXL3	80816	broad.mit.edu	37	18	31325636	31325636	+	Missense_Mutation	SNP	A	G	G			TCGA-AK-3456-01A-02D-1386-10	TCGA-AK-3456-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:31325636A>G	uc010dmg.1	+	12	5879	c.5824A>G	c.(5824-5826)ATT>GTT	p.I1942V	ASXL3_uc002kxq.2_Missense_Mutation_p.I1649V	NM_030632	NP_085135	Q9C0F0	ASXL3_HUMAN	additional sex combs like 3	1942					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	metal ion binding			ovary(2)|pancreas(1)	3						CAGGGGCCCCATTCCTACTGC	0.522													4	73	---	---	---	---	PASS
MYO5B	4645	broad.mit.edu	37	18	47363917	47363917	+	Missense_Mutation	SNP	A	G	G	rs138128932	by1000genomes	TCGA-AK-3456-01A-02D-1386-10	TCGA-AK-3456-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:47363917A>G	uc002leb.2	-	37	5396	c.5108T>C	c.(5107-5109)GTC>GCC	p.V1703A	MYO5B_uc002ldz.2_Missense_Mutation_p.V273A|MYO5B_uc002lea.2_Missense_Mutation_p.V818A	NM_001080467	NP_001073936	Q9ULV0	MYO5B_HUMAN	myosin VB	1703	Dilute.				protein transport	myosin complex	actin binding|ATP binding|calmodulin binding|motor activity			ovary(2)|skin(2)|central_nervous_system(1)	5				READ - Rectum adenocarcinoma(32;0.103)		CCAAGAGCAGACGTCCTTCCG	0.527													8	116	---	---	---	---	PASS
ZNF844	284391	broad.mit.edu	37	19	12187458	12187458	+	Missense_Mutation	SNP	A	T	T			TCGA-AK-3456-01A-02D-1386-10	TCGA-AK-3456-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:12187458A>T	uc002mtb.2	+	4	1666	c.1523A>T	c.(1522-1524)AAT>ATT	p.N508I	ZNF844_uc010dym.1_Missense_Mutation_p.N351I	NM_001136501	NP_001129973	Q08AG5	ZN844_HUMAN	zinc finger protein 844	508					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0						AGTGTAAGCAATGTGGGAAAG	0.408													67	127	---	---	---	---	PASS
ITPKC	80271	broad.mit.edu	37	19	41243662	41243662	+	Silent	SNP	C	T	T			TCGA-AK-3456-01A-02D-1386-10	TCGA-AK-3456-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:41243662C>T	uc002oot.2	+	6	1869	c.1836C>T	c.(1834-1836)TTC>TTT	p.F612F		NM_025194	NP_079470	Q96DU7	IP3KC_HUMAN	inositol 1,4,5-trisphosphate 3-kinase C	612						cytoplasm|nucleus	ATP binding|calmodulin binding|inositol trisphosphate 3-kinase activity				0			LUSC - Lung squamous cell carcinoma(20;0.000219)|Lung(22;0.000959)			CCCCCTTCTTCAAGACCCACG	0.532													54	134	---	---	---	---	PASS
NUCB1	4924	broad.mit.edu	37	19	49404186	49404186	+	Missense_Mutation	SNP	C	G	G			TCGA-AK-3456-01A-02D-1386-10	TCGA-AK-3456-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:49404186C>G	uc002plb.3	+	2	205	c.133C>G	c.(133-135)CCC>GCC	p.P45A	NUCB1_uc002pla.2_Missense_Mutation_p.P45A|NUCB1_uc002plc.2_Missense_Mutation_p.P45A|TULP2_uc002pkz.2_5'Flank	NM_006184	NP_006175	Q02818	NUCB1_HUMAN	nucleobindin 1 precursor	45						ER-Golgi intermediate compartment|extracellular space|Golgi apparatus|membrane|microtubule cytoskeleton	calcium ion binding|DNA binding				0		all_lung(116;4.89e-05)|Lung NSC(112;8.3e-05)|all_epithelial(76;8.64e-05)|all_neural(266;0.0506)|Ovarian(192;0.113)		OV - Ovarian serous cystadenocarcinoma(262;0.000171)|all cancers(93;0.000333)|Epithelial(262;0.0174)|GBM - Glioblastoma multiforme(486;0.0244)		GACTGAGAGTCCCGTGAGTGG	0.567													13	23	---	---	---	---	PASS
CEP250	11190	broad.mit.edu	37	20	34065733	34065733	+	Missense_Mutation	SNP	A	G	G			TCGA-AK-3456-01A-02D-1386-10	TCGA-AK-3456-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:34065733A>G	uc002xcm.2	+	18	2572	c.1901A>G	c.(1900-1902)GAG>GGG	p.E634G	CEP250_uc010zve.1_Missense_Mutation_p.E2G|CEP250_uc010zvd.1_RNA	NM_007186	NP_009117	Q9BV73	CP250_HUMAN	centrosomal protein 2	634	Gln/Glu-rich.|Potential.				centriole-centriole cohesion|G2/M transition of mitotic cell cycle|protein localization|regulation of centriole-centriole cohesion	centriole|cilium|cytosol|microtubule basal body|perinuclear region of cytoplasm|protein complex	protein C-terminus binding|protein kinase binding			ovary(4)|central_nervous_system(1)	5	Lung NSC(9;0.00156)|all_lung(11;0.00243)		BRCA - Breast invasive adenocarcinoma(18;0.0106)			AGCAGAATGGAGGCCGCAGAG	0.522													5	176	---	---	---	---	PASS
BRWD1	54014	broad.mit.edu	37	21	40568261	40568261	+	Intron	SNP	C	T	T			TCGA-AK-3456-01A-02D-1386-10	TCGA-AK-3456-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:40568261C>T	uc002yxk.1	-						BRWD1_uc010goc.1_Intron|BRWD1_uc002yxl.2_Missense_Mutation_p.R2245K	NM_018963	NP_061836	Q9NSI6	BRWD1_HUMAN	bromodomain and WD repeat domain containing 1						regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus				skin(3)|ovary(1)	4		Prostate(19;8.44e-08)|all_epithelial(19;0.223)				TCTCACAGTCCTTCTACCCTG	0.383													4	312	---	---	---	---	PASS
C21orf56	84221	broad.mit.edu	37	21	47588323	47588323	+	Missense_Mutation	SNP	G	C	C			TCGA-AK-3456-01A-02D-1386-10	TCGA-AK-3456-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:47588323G>C	uc011afu.1	-	3	1505	c.443C>G	c.(442-444)ACC>AGC	p.T148S	C21orf56_uc002zii.2_5'UTR	NM_001142854	NP_001136326	Q9H0A9	CU056_HUMAN	hypothetical protein LOC84221 isoform 1	148							protein binding			skin(1)	1	Breast(49;0.214)			Colorectal(79;0.241)		CTCCAGCAGGGTCTTGTCCAC	0.622													16	32	---	---	---	---	PASS
FAM9C	171484	broad.mit.edu	37	X	13055631	13055631	+	Intron	SNP	T	A	A			TCGA-AK-3456-01A-02D-1386-10	TCGA-AK-3456-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:13055631T>A	uc004cvh.1	-						FAM9C_uc004cvg.2_3'UTR	NM_174901	NP_777561	Q8IZT9	FAM9C_HUMAN	family with sequence similarity 9, member C							nucleus					0						GTTCTCTACTTGTGACTTCTA	0.303													14	4	---	---	---	---	PASS
CCNB3	85417	broad.mit.edu	37	X	50090691	50090691	+	Missense_Mutation	SNP	T	C	C			TCGA-AK-3456-01A-02D-1386-10	TCGA-AK-3456-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:50090691T>C	uc004dox.3	+	11	4175	c.3877T>C	c.(3877-3879)TAC>CAC	p.Y1293H	CCNB3_uc004doy.2_Missense_Mutation_p.Y1293H|CCNB3_uc004doz.2_Missense_Mutation_p.Y189H|CCNB3_uc010njq.2_Missense_Mutation_p.Y185H|CCNB3_uc004dpa.2_Missense_Mutation_p.Y132H	NM_033031	NP_149020	Q8WWL7	CCNB3_HUMAN	cyclin B3 isoform 3	1293					cell division|meiosis|regulation of cyclin-dependent protein kinase activity|regulation of G2/M transition of mitotic cell cycle	nucleus	protein kinase binding			ovary(4)|lung(3)|large_intestine(1)|pancreas(1)	9	Ovarian(276;0.236)					CCTGCAGGAATACCACTATGT	0.498													4	98	---	---	---	---	PASS
COX7B	1349	broad.mit.edu	37	X	77160816	77160816	+	3'UTR	SNP	A	G	G			TCGA-AK-3456-01A-02D-1386-10	TCGA-AK-3456-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:77160816A>G	uc004ecu.1	+	3						NM_001866	NP_001857	P24311	COX7B_HUMAN	cytochrome c oxidase subunit VIIb precursor						respiratory electron transport chain	integral to membrane|mitochondrial respiratory chain	cytochrome-c oxidase activity				0						TTGATGCCAAATTAAAGCACT	0.343													6	93	---	---	---	---	PASS
CDK11B	984	broad.mit.edu	37	1	1600093	1600093	+	Intron	DEL	G	-	-			TCGA-AK-3456-01A-02D-1386-10	TCGA-AK-3456-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:1600093delG	uc001agv.1	-						CDK11B_uc001ags.1_Intron|CDK11B_uc001agt.1_Intron|CDK11B_uc001aha.1_Intron|CDK11B_uc001agw.1_Intron|CDK11B_uc001agy.1_Intron|CDK11B_uc001agx.1_Intron|CDK11B_uc001agz.1_Intron|SLC35E2B_uc009vkl.1_Intron|SLC35E2B_uc001ahe.3_Intron|SLC35E2B_uc001ahf.3_Intron|SLC35E2B_uc001ahg.3_Intron|SLC35E2B_uc001ahh.3_Intron	NM_033486	NP_277021	P21127	CD11B_HUMAN	cell division cycle 2-like 1 (PITSLRE proteins)						apoptosis|cell proliferation|mitosis|regulation of cell growth|regulation of mRNA processing|regulation of transcription, DNA-dependent	cytoplasm|nucleus	ATP binding|cyclin-dependent protein kinase activity|protein binding			skin(1)	1						TGTTTTTTTTGTTTGTTTGTT	0.313													4	2	---	---	---	---	
CROCCL1	84809	broad.mit.edu	37	1	16956899	16956899	+	Intron	DEL	C	-	-			TCGA-AK-3456-01A-02D-1386-10	TCGA-AK-3456-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:16956899delC	uc009vov.1	-						CROCCL1_uc001aze.2_Intron|CROCCL1_uc001azf.2_Intron|CROCCL1_uc001azg.1_Intron|CROCCL1_uc001azi.1_RNA	NR_026752				Homo sapiens mRNA for FLJ00313 protein.												0						CAGACAAACTCCCAGGCACAC	0.627													4	2	---	---	---	---	
CLSPN	63967	broad.mit.edu	37	1	36231152	36231152	+	Intron	DEL	A	-	-			TCGA-AK-3456-01A-02D-1386-10	TCGA-AK-3456-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:36231152delA	uc001bzi.2	-						CLSPN_uc009vux.2_Intron	NM_022111	NP_071394	Q9HAW4	CLSPN_HUMAN	claspin						activation of protein kinase activity|cell cycle|cellular component disassembly involved in apoptosis|DNA repair|DNA replication|G2/M transition DNA damage checkpoint|mitotic cell cycle DNA replication checkpoint|peptidyl-serine phosphorylation	nucleoplasm	anaphase-promoting complex binding|DNA binding			breast(2)|ovary(2)|central_nervous_system(1)|lung(1)|skin(1)|kidney(1)	8		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0887)				tagtaacggtaaaaaaaaaaa	0.065													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	36665409	36665410	+	IGR	INS	-	A	A	rs72510671		TCGA-AK-3456-01A-02D-1386-10	TCGA-AK-3456-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:36665409_36665410insA								MAP7D1 (18973 upstream) : THRAP3 (24607 downstream)																							CTAGTGTCACCACTCAACAAGT	0.411													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	41882470	41882471	+	IGR	INS	-	T	T			TCGA-AK-3456-01A-02D-1386-10	TCGA-AK-3456-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:41882470_41882471insT								SCMH1 (174682 upstream) : EDN2 (61978 downstream)																							ACACTTGTGGCTTCCCCTGTCT	0.644											OREG0013416	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	4	3	---	---	---	---	
YIPF1	54432	broad.mit.edu	37	1	54327240	54327241	+	Intron	DEL	AG	-	-			TCGA-AK-3456-01A-02D-1386-10	TCGA-AK-3456-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:54327240_54327241delAG	uc001cvu.2	-						YIPF1_uc001cvv.2_Intron|YIPF1_uc001cvw.2_Intron|YIPF1_uc001cvx.2_Intron|YIPF1_uc001cvy.2_Intron	NM_018982	NP_061855	Q9Y548	YIPF1_HUMAN	Yip1 domain family, member 1							integral to membrane|transport vesicle				large_intestine(1)|ovary(1)	2						tggtgactcaagagaGAGAGAG	0.064													4	2	---	---	---	---	
GBP2	2634	broad.mit.edu	37	1	89582466	89582467	+	Intron	INS	-	T	T			TCGA-AK-3456-01A-02D-1386-10	TCGA-AK-3456-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:89582466_89582467insT	uc001dmz.1	-						GBP2_uc001dmy.1_Intron	NM_004120	NP_004111	P32456	GBP2_HUMAN	guanylate binding protein 2,						interferon-gamma-mediated signaling pathway|type I interferon-mediated signaling pathway	plasma membrane	GTP binding|GTPase activity			ovary(1)	1		Lung NSC(277;0.0908)		all cancers(265;0.0151)|Epithelial(280;0.0284)		TAGTTCTTTTCTTTTTTTATTC	0.297													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	110969578	110969579	+	IGR	DEL	GA	-	-	rs67471926		TCGA-AK-3456-01A-02D-1386-10	TCGA-AK-3456-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:110969578_110969579delGA								HBXIP (19032 upstream) : PROK1 (24209 downstream)																							GAGCAAGCAGGAGAGAGAGAGA	0.525													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	143397663	143397664	+	IGR	DEL	AA	-	-			TCGA-AK-3456-01A-02D-1386-10	TCGA-AK-3456-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:143397663_143397664delAA								None (None upstream) : LOC100286793 (249975 downstream)																							TTAGAGAAACAAAGAGAAGTAC	0.248													4	3	---	---	---	---	
NBPF10	100132406	broad.mit.edu	37	1	145753761	145753762	+	Intron	INS	-	A	A			TCGA-AK-3456-01A-02D-1386-10	TCGA-AK-3456-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:145753761_145753762insA	uc001emp.3	+						PDZK1_uc001eon.1_Intron|PDZK1_uc001eoo.1_Intron|PDZK1_uc010oza.1_Intron	NM_017940	NP_060410	A6NDV3	A6NDV3_HUMAN	hypothetical protein LOC55672												0	all_hematologic(923;0.032)			Colorectal(1306;1.36e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.00258)		cactccatctcaaaaaaaaaaa	0.178													5	4	---	---	---	---	
PBX1	5087	broad.mit.edu	37	1	164529470	164529471	+	Intron	DEL	TG	-	-	rs2275559	by1000genomes	TCGA-AK-3456-01A-02D-1386-10	TCGA-AK-3456-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:164529470_164529471delTG	uc001gct.2	+						PBX1_uc010pku.1_Intron|PBX1_uc010pkv.1_Intron|PBX1_uc001gcs.2_Intron	NM_002585	NP_002576	P40424	PBX1_HUMAN	pre-B-cell leukemia homeobox 1						negative regulation of sequence-specific DNA binding transcription factor activity|sex differentiation|steroid biosynthetic process	cytoplasm|nucleus	sequence-specific DNA binding transcription factor activity|transcription factor binding		EWSR1/PBX1(3)	soft_tissue(3)|lung(1)|skin(1)	5						TGTACATATTTGTGTGTGTGTG	0.446			T	TCF3|EWSR1	pre B-ALL|myoepithelioma								4	2	---	---	---	---	
ILDR2	387597	broad.mit.edu	37	1	166944274	166944277	+	Intron	DEL	CACA	-	-	rs67253020		TCGA-AK-3456-01A-02D-1386-10	TCGA-AK-3456-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:166944274_166944277delCACA	uc001gdx.1	-							NM_199351	NP_955383	Q71H61	ILDR2_HUMAN	immunoglobulin-like domain containing receptor							integral to membrane				ovary(1)	1						CTCTCTCTCTcacacacacacaca	0.441													7	6	---	---	---	---	
ESRRG	2104	broad.mit.edu	37	1	217038068	217038069	+	Intron	INS	-	TT	TT	rs141584307	by1000genomes	TCGA-AK-3456-01A-02D-1386-10	TCGA-AK-3456-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:217038068_217038069insTT	uc001hky.1	-						ESRRG_uc009xdp.1_Intron|ESRRG_uc001hkz.1_Intron|ESRRG_uc010puc.1_Intron|ESRRG_uc001hla.1_Intron|ESRRG_uc001hlb.1_Intron|ESRRG_uc010pud.1_Intron|ESRRG_uc001hlc.1_Intron|ESRRG_uc001hld.1_Intron	NM_206595	NP_996318	P62508	ERR3_HUMAN	estrogen-related receptor gamma isoform 2						positive regulation of transcription, DNA-dependent|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor	nucleoplasm	AF-2 domain binding|retinoic acid receptor activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|steroid hormone receptor activity|zinc ion binding			ovary(1)|kidney(1)	2				OV - Ovarian serous cystadenocarcinoma(81;0.0358)|all cancers(67;0.0693)|GBM - Glioblastoma multiforme(131;0.0713)	Diethylstilbestrol(DB00255)	CGTGGAGTAACAGACCAACTTA	0.495													9	5	---	---	---	---	
OR2L13	284521	broad.mit.edu	37	1	248186287	248186288	+	Intron	DEL	AG	-	-			TCGA-AK-3456-01A-02D-1386-10	TCGA-AK-3456-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:248186287_248186288delAG	uc001ids.2	+							NM_175911	NP_787107	Q8N349	OR2LD_HUMAN	olfactory receptor, family 2, subfamily L,						sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity|protein binding			central_nervous_system(2)|ovary(1)|skin(1)	4	all_cancers(71;0.000149)|all_epithelial(71;1.27e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0132)			TATGTCAAACAGAGATTAATCC	0.327													8	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	6561506	6561507	+	IGR	INS	-	AA	AA	rs145479428	by1000genomes	TCGA-AK-3456-01A-02D-1386-10	TCGA-AK-3456-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:6561506_6561507insAA								LOC400940 (433142 upstream) : CMPK2 (418996 downstream)																							GATCACACGGCATTATGACAGA	0.460													5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	20302970	20302970	+	IGR	DEL	A	-	-			TCGA-AK-3456-01A-02D-1386-10	TCGA-AK-3456-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:20302970delA								LAPTM4A (51181 upstream) : SDC1 (97588 downstream)																							tggagcaattaagttctggag	0.000													19	10	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	58479808	58479808	+	IGR	DEL	A	-	-			TCGA-AK-3456-01A-02D-1386-10	TCGA-AK-3456-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:58479808delA								FANCL (11293 upstream) : None (None downstream)																							TTTGtaaattaaaaaaaaaaa	0.234													7	4	---	---	---	---	
XPO1	7514	broad.mit.edu	37	2	61713321	61713321	+	Intron	DEL	T	-	-	rs11438336		TCGA-AK-3456-01A-02D-1386-10	TCGA-AK-3456-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:61713321delT	uc002sbj.2	-						XPO1_uc010fcl.2_Intron|XPO1_uc010ypn.1_Intron|XPO1_uc002sbk.2_Intron|XPO1_uc002sbg.2_5'Flank|XPO1_uc002sbh.2_Intron	NM_003400	NP_003391	O14980	XPO1_HUMAN	exportin 1						intracellular protein transport|mitotic prometaphase|mRNA metabolic process|mRNA transport|viral genome transport in host cell|viral infectious cycle	annulate lamellae|Cajal body|cytosol|kinetochore|nuclear envelope|nucleolus|ribonucleoprotein complex	protein binding|protein transporter activity|RNA binding			ovary(1)|haematopoietic_and_lymphoid_tissue(1)|central_nervous_system(1)|skin(1)	4			LUSC - Lung squamous cell carcinoma(7;5.71e-05)|Epithelial(17;0.0662)|all cancers(80;0.226)			CATTCAAGACttttttttttt	0.199													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	97142988	97142988	+	IGR	DEL	T	-	-			TCGA-AK-3456-01A-02D-1386-10	TCGA-AK-3456-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:97142988delT								NCAPH (101714 upstream) : NEURL3 (20397 downstream)																							aaattgtatcttgttttttat	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	101194688	101194690	+	IGR	DEL	AAA	-	-	rs80004772		TCGA-AK-3456-01A-02D-1386-10	TCGA-AK-3456-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:101194688_101194690delAAA								PDCL3 (1487 upstream) : NPAS2 (241923 downstream)																							ATTTACAAAGAAAAAAAGGTGGT	0.438													3	5	---	---	---	---	
EDAR	10913	broad.mit.edu	37	2	109552102	109552103	+	Intron	INS	-	CA	CA	rs145008294	by1000genomes	TCGA-AK-3456-01A-02D-1386-10	TCGA-AK-3456-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:109552102_109552103insCA	uc002teq.3	-						EDAR_uc010fjn.2_Intron|EDAR_uc010yws.1_Intron	NM_022336	NP_071731	Q9UNE0	EDAR_HUMAN	ectodysplasin A receptor precursor						apoptosis|cell differentiation	integral to membrane	protein binding|transmembrane receptor activity			skin(1)	1						GCACCCCTTTTCACACACACAC	0.391													8	5	---	---	---	---	
COL5A2	1290	broad.mit.edu	37	2	189921602	189921602	+	Intron	DEL	A	-	-			TCGA-AK-3456-01A-02D-1386-10	TCGA-AK-3456-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:189921602delA	uc002uqk.2	-						COL5A2_uc010frx.2_Intron	NM_000393	NP_000384	P05997	CO5A2_HUMAN	alpha 2 type V collagen preproprotein						axon guidance|collagen fibril organization|eye morphogenesis|skin development	collagen type V	extracellular matrix structural constituent			ovary(2)	2			OV - Ovarian serous cystadenocarcinoma(117;0.0106)|Epithelial(96;0.127)			ACTACCAAGGAAACATGACTG	0.373													92	55	---	---	---	---	
ZNF385D	79750	broad.mit.edu	37	3	21474476	21474477	+	Intron	INS	-	AT	AT	rs150173011	by1000genomes	TCGA-AK-3456-01A-02D-1386-10	TCGA-AK-3456-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:21474476_21474477insAT	uc003cce.2	-							NM_024697	NP_078973	Q9H6B1	Z385D_HUMAN	zinc finger protein 385D							nucleus	nucleic acid binding|zinc ion binding			large_intestine(2)|skin(2)|ovary(1)	5						ATCATGACATAATTTGATCCTT	0.327													3	3	---	---	---	---	
MAGI1	9223	broad.mit.edu	37	3	65553048	65553048	+	Intron	DEL	A	-	-			TCGA-AK-3456-01A-02D-1386-10	TCGA-AK-3456-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:65553048delA	uc003dmn.2	-						MAGI1_uc003dmm.2_Intron|MAGI1_uc003dmo.2_Intron|MAGI1_uc003dmp.2_Intron|MAGI1_uc010hny.2_Intron|MAGI1_uc003dmr.2_Intron	NM_001033057	NP_001028229	Q96QZ7	MAGI1_HUMAN	membrane associated guanylate kinase, WW and PDZ						cell adhesion|cell surface receptor linked signaling pathway|protein complex assembly	tight junction	ATP binding|protein C-terminus binding			lung(2)|skin(1)|breast(1)|kidney(1)|pancreas(1)	6		Lung NSC(201;0.0016)		BRCA - Breast invasive adenocarcinoma(55;0.00138)|KIRC - Kidney renal clear cell carcinoma(15;0.0988)|Kidney(15;0.133)		ACTGACCATGAAAAAAAAAAT	0.323													4	3	---	---	---	---	
CADM2	253559	broad.mit.edu	37	3	85757423	85757423	+	Intron	DEL	T	-	-			TCGA-AK-3456-01A-02D-1386-10	TCGA-AK-3456-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:85757423delT	uc003dqj.2	+						CADM2_uc003dqk.2_Intron	NM_153184	NP_694854	Q8N3J6	CADM2_HUMAN	immunoglobulin superfamily, member 4D						adherens junction organization|cell junction assembly	integral to membrane|plasma membrane				ovary(1)|lung(1)|kidney(1)|skin(1)	4		Lung NSC(201;0.0148)		LUSC - Lung squamous cell carcinoma(29;0.000815)|Lung(72;0.00304)|BRCA - Breast invasive adenocarcinoma(55;0.156)|Epithelial(33;0.157)		TATGTTTTTCTTTTTTTTAAT	0.244													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	104436864	104436864	+	IGR	DEL	T	-	-			TCGA-AK-3456-01A-02D-1386-10	TCGA-AK-3456-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:104436864delT								None (None upstream) : ALCAM (648849 downstream)																							gcataccagcttttttttttt	0.000													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	180863907	180863907	+	IGR	DEL	A	-	-			TCGA-AK-3456-01A-02D-1386-10	TCGA-AK-3456-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:180863907delA								DNAJC19 (156377 upstream) : SOX2OT (417602 downstream)																							tagaaaatccaaaaaaaaaaa	0.005													7	5	---	---	---	---	
VPS8	23355	broad.mit.edu	37	3	184766378	184766378	+	Intron	DEL	T	-	-			TCGA-AK-3456-01A-02D-1386-10	TCGA-AK-3456-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:184766378delT	uc003fpb.1	+						VPS8_uc010hyd.1_Intron|VPS8_uc010hye.1_Intron	NM_015303	NP_056118	Q8N3P4	VPS8_HUMAN	vacuolar protein sorting 8 homolog isoform b								zinc ion binding			ovary(1)	1	all_cancers(143;2.51e-11)|Ovarian(172;0.0339)|Breast(254;0.247)		Epithelial(37;1.02e-33)|OV - Ovarian serous cystadenocarcinoma(80;4.81e-22)			TATATTTTTATTTCCCTATTT	0.468													136	68	---	---	---	---	
KNG1	3827	broad.mit.edu	37	3	186440068	186440069	+	Intron	INS	-	A	A			TCGA-AK-3456-01A-02D-1386-10	TCGA-AK-3456-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:186440068_186440069insA	uc011bsa.1	+						KNG1_uc003fqr.2_Intron	NM_001102416	NP_001095886	P01042	KNG1_HUMAN	kininogen 1 isoform 1						blood coagulation, intrinsic pathway|elevation of cytosolic calcium ion concentration|inflammatory response|negative regulation of blood coagulation|negative regulation of cell adhesion|platelet activation|platelet degranulation|positive regulation of apoptosis|positive regulation of renal sodium excretion|positive regulation of urine volume|smooth muscle contraction|vasodilation	extracellular space|plasma membrane|platelet alpha granule lumen	cysteine-type endopeptidase inhibitor activity|heparin binding|receptor binding|zinc ion binding			skin(1)	1	all_cancers(143;8.96e-12)|Ovarian(172;0.0339)		OV - Ovarian serous cystadenocarcinoma(80;4.12e-20)	GBM - Glioblastoma multiforme(93;0.0798)	Ouabain(DB01092)	ATTAGGCTATTAAAAAAATTTA	0.302													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	189991037	189991037	+	IGR	DEL	A	-	-			TCGA-AK-3456-01A-02D-1386-10	TCGA-AK-3456-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:189991037delA								LEPREL1 (150811 upstream) : CLDN1 (32466 downstream)																							TGGATCTTATAAAAAAAATTC	0.358													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	195428679	195428682	+	Intron	DEL	AAAT	-	-	rs112452749		TCGA-AK-3456-01A-02D-1386-10	TCGA-AK-3456-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:195428679_195428682delAAAT	uc011btd.1	+						uc003fux.1_Intron					Homo sapiens cDNA FLJ46488 fis, clone THYMU3026869.																		TTCATTAATCAAATAATTCATGTA	0.368													2	4	---	---	---	---	
TMEM175	84286	broad.mit.edu	37	4	946545	946546	+	Intron	DEL	TG	-	-			TCGA-AK-3456-01A-02D-1386-10	TCGA-AK-3456-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:946545_946546delTG	uc003gbq.2	+						TMEM175_uc010ibl.1_Intron|TMEM175_uc003gbp.1_Intron|TMEM175_uc003gbr.2_Intron|TMEM175_uc003gbu.2_Intron|TMEM175_uc003gbs.2_Intron|TMEM175_uc003gbt.2_Intron|TMEM175_uc003gbv.2_Intron|TMEM175_uc010ibm.2_Intron	NM_032326	NP_115702	Q9BSA9	TM175_HUMAN	transmembrane protein 175							integral to membrane					0			OV - Ovarian serous cystadenocarcinoma(23;0.0158)			GGCCCTGTGCtgtgtgtgtgtg	0.406													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	20017094	20017094	+	IGR	DEL	T	-	-			TCGA-AK-3456-01A-02D-1386-10	TCGA-AK-3456-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:20017094delT								None (None upstream) : SLIT2 (238141 downstream)																							gctcactctctttttaaggcc	0.095													4	2	---	---	---	---	
DCK	1633	broad.mit.edu	37	4	71895356	71895357	+	3'UTR	INS	-	CT	CT			TCGA-AK-3456-01A-02D-1386-10	TCGA-AK-3456-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:71895356_71895357insCT	uc003hfx.2	+	7					DCK_uc011cbb.1_3'UTR	NM_000788	NP_000779	P27707	DCK_HUMAN	deoxycytidine kinase						purine base metabolic process|purine-containing compound salvage|pyrimidine base metabolic process|pyrimidine nucleoside salvage|pyrimidine nucleotide metabolic process	cytosol|nucleus	ATP binding|deoxycytidine kinase activity|drug binding|phosphotransferase activity, alcohol group as acceptor|protein homodimerization activity			ovary(1)	1			Lung(101;0.235)		Cladribine(DB00242)|Clofarabine(DB00631)|Decitabine(DB01262)|Fludarabine(DB01073)|Gemcitabine(DB00441)|Pemetrexed(DB00642)|Zalcitabine(DB00943)	tggttccagtatcagcatagtg	0.109													4	2	---	---	---	---	
PAPSS1	9061	broad.mit.edu	37	4	108608468	108608468	+	Intron	DEL	A	-	-			TCGA-AK-3456-01A-02D-1386-10	TCGA-AK-3456-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:108608468delA	uc003hyk.2	-						PAPSS1_uc011cfh.1_Intron	NM_005443	NP_005434	O43252	PAPS1_HUMAN	3'-phosphoadenosine 5'-phosphosulfate synthase						3'-phosphoadenosine 5'-phosphosulfate biosynthetic process|skeletal system development|sulfate assimilation|xenobiotic metabolic process	cytosol	adenylylsulfate kinase activity|ATP binding|sulfate adenylyltransferase (ATP) activity			ovary(1)	1		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;5.49e-05)		ATATAAACTGAAAAAAAAATC	0.274													5	3	---	---	---	---	
ALPK1	80216	broad.mit.edu	37	4	113310808	113310808	+	Intron	DEL	G	-	-			TCGA-AK-3456-01A-02D-1386-10	TCGA-AK-3456-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:113310808delG	uc003iap.3	+						ALPK1_uc011cfw.1_Intron|ALPK1_uc003ian.3_Intron|ALPK1_uc011cfx.1_Intron|ALPK1_uc003iao.3_Intron|ALPK1_uc003iaq.2_Intron|ALPK1_uc010imo.2_Intron	NM_025144	NP_079420	Q96QP1	ALPK1_HUMAN	alpha-kinase 1								ATP binding|protein serine/threonine kinase activity			ovary(5)	5		Ovarian(17;0.0446)|Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;0.00325)		CAGACGGGGTGGGCACTAAGT	0.478													4	2	---	---	---	---	
ITGA2	3673	broad.mit.edu	37	5	52386613	52386614	+	3'UTR	INS	-	G	G			TCGA-AK-3456-01A-02D-1386-10	TCGA-AK-3456-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:52386613_52386614insG	uc003joy.2	+	30					ITGA2_uc011cqa.1_RNA|ITGA2_uc011cqb.1_RNA|ITGA2_uc011cqc.1_3'UTR|ITGA2_uc011cqd.1_RNA|ITGA2_uc011cqe.1_RNA	NM_002203	NP_002194	P17301	ITA2_HUMAN	integrin alpha 2 precursor						axon guidance|blood coagulation|cell-matrix adhesion|integrin-mediated signaling pathway|interspecies interaction between organisms|organ morphogenesis	integrin complex	collagen binding|identical protein binding|receptor activity			lung(1)	1		Lung NSC(810;3.11e-05)|Breast(144;0.014)|Prostate(461;0.0181)				GGGGGAGGTGCGGGGGGCAGGT	0.391													4	2	---	---	---	---	
HSPA9	3313	broad.mit.edu	37	5	137895942	137895942	+	Intron	DEL	A	-	-			TCGA-AK-3456-01A-02D-1386-10	TCGA-AK-3456-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:137895942delA	uc003ldf.2	-						HSPA9_uc003lde.2_5'Flank|HSPA9_uc011cyw.1_Intron	NM_004134	NP_004125	P38646	GRP75_HUMAN	heat shock 70kDa protein 9 precursor						anti-apoptosis|protein folding	cell surface|mitochondrial nucleoid	ATP binding|unfolded protein binding				0			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00325)			GGTTCCTGCTAATGATCTTCT	0.398													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	153977903	153977904	+	5'Flank	DEL	GG	-	-	rs57660310		TCGA-AK-3456-01A-02D-1386-10	TCGA-AK-3456-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:153977903_153977904delGG	hsa-mir-3141|MI0014165	-																													atggatggatggatggatggat	0.104													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	153977906	153977907	+	5'Flank	DEL	TG	-	-	rs58793078	by1000genomes	TCGA-AK-3456-01A-02D-1386-10	TCGA-AK-3456-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:153977906_153977907delTG	hsa-mir-3141|MI0014165	-																													gatggatggatggatggatgga	0.104													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	180016997	180016997	+	IGR	DEL	G	-	-			TCGA-AK-3456-01A-02D-1386-10	TCGA-AK-3456-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:180016997delG								CNOT6 (11645 upstream) : SCGB3A1 (109 downstream)																							AGACTCTCGCGGCCTCTCTCT	0.547													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	224818	224819	+	IGR	INS	-	A	A	rs150583197	by1000genomes	TCGA-AK-3456-01A-02D-1386-10	TCGA-AK-3456-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:224818_224819insA								None (None upstream) : DUSP22 (67282 downstream)																							accttcgggggctacgaagttc	0.228													5	4	---	---	---	---	
FARS2	10667	broad.mit.edu	37	6	5261686	5261687	+	Intron	INS	-	T	T	rs150913223	by1000genomes	TCGA-AK-3456-01A-02D-1386-10	TCGA-AK-3456-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:5261686_5261687insT	uc010jnv.1	+						LYRM4_uc003mwp.2_5'Flank|LYRM4_uc010jnu.2_5'Flank|LYRM4_uc003mwq.2_5'Flank|FARS2_uc003mwr.2_5'UTR	NM_006567	NP_006558	O95363	SYFM_HUMAN	phenylalanyl-tRNA synthetase 2 precursor						phenylalanyl-tRNA aminoacylation|tRNA processing	mitochondrial matrix|soluble fraction	ATP binding|magnesium ion binding|phenylalanine-tRNA ligase activity|tRNA binding				0	Ovarian(93;0.11)	all_hematologic(90;0.0104)			L-Phenylalanine(DB00120)	AGGTGATGAGCTAGGGGTTCTG	0.644													8	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	14844656	14844657	+	IGR	DEL	TT	-	-			TCGA-AK-3456-01A-02D-1386-10	TCGA-AK-3456-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:14844656_14844657delTT								CD83 (707510 upstream) : JARID2 (401077 downstream)																							TACGGTTGTGTTTTTTTTTTTT	0.396													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	32434431	32434432	+	IGR	DEL	TC	-	-			TCGA-AK-3456-01A-02D-1386-10	TCGA-AK-3456-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:32434431_32434432delTC								HLA-DRA (21610 upstream) : HLA-DRB1 (50731 downstream)																							ctcctgactttctctctctctt	0.000													4	2	---	---	---	---	
CDC5L	988	broad.mit.edu	37	6	44397842	44397842	+	Intron	DEL	T	-	-			TCGA-AK-3456-01A-02D-1386-10	TCGA-AK-3456-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:44397842delT	uc003oxl.2	+							NM_001253	NP_001244	Q99459	CDC5L_HUMAN	CDC5-like						cell cycle|regulation of transcription, DNA-dependent|transcription, DNA-dependent	catalytic step 2 spliceosome|cytoplasm|nuclear speck|nucleolus	DNA binding|RNA binding			lung(3)|ovary(1)|kidney(1)|skin(1)	6	all_lung(25;0.00433)|Ovarian(13;0.0273)|all_hematologic(164;0.208)		Colorectal(64;0.00337)|COAD - Colon adenocarcinoma(64;0.00536)			tttgtttttgttttttttttA	0.353													6	3	---	---	---	---	
EYS	346007	broad.mit.edu	37	6	65987337	65987340	+	Intron	DEL	TTAA	-	-	rs139945760		TCGA-AK-3456-01A-02D-1386-10	TCGA-AK-3456-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:65987337_65987340delTTAA	uc011dxu.1	-							NM_001142800	NP_001136272	Q5T1H1	EYS_HUMAN	eyes shut homolog isoform 1						response to stimulus|visual perception	extracellular region	calcium ion binding			lung(4)|ovary(1)|skin(1)	6						aaaaaaaaagttaattaattaaaa	0.000													3	3	---	---	---	---	
CD109	135228	broad.mit.edu	37	6	74490730	74490731	+	Intron	INS	-	TA	TA	rs145114558		TCGA-AK-3456-01A-02D-1386-10	TCGA-AK-3456-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:74490730_74490731insTA	uc003php.2	+						CD109_uc010kaz.2_Intron|CD109_uc003phq.2_Intron|CD109_uc010kba.2_Intron	NM_133493	NP_598000	Q6YHK3	CD109_HUMAN	CD109 antigen isoform 1 precursor							anchored to membrane|extracellular space|plasma membrane	serine-type endopeptidase inhibitor activity			large_intestine(2)|ovary(2)	4						atgtgtatgcgtgtgtgtgtgt	0.139													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	141380640	141380640	+	IGR	DEL	A	-	-			TCGA-AK-3456-01A-02D-1386-10	TCGA-AK-3456-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:141380640delA								None (None upstream) : None (None downstream)																							AGAAAGCTCTAGGTCTGACTC	0.383													6	4	---	---	---	---	
ARID1B	57492	broad.mit.edu	37	6	157490504	157490505	+	Intron	INS	-	A	A			TCGA-AK-3456-01A-02D-1386-10	TCGA-AK-3456-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:157490504_157490505insA	uc003qqn.2	+						ARID1B_uc003qqo.2_Intron|ARID1B_uc003qqp.2_Intron|ARID1B_uc010kjl.2_Intron	NM_017519	NP_059989	Q8NFD5	ARI1B_HUMAN	AT rich interactive domain 1B (SWI1-like)						chromatin-mediated maintenance of transcription|nervous system development|transcription, DNA-dependent	SWI/SNF complex	DNA binding|protein binding|transcription coactivator activity			ovary(1)|breast(1)	2		Breast(66;0.000162)|Ovarian(120;0.0265)		OV - Ovarian serous cystadenocarcinoma(65;3.19e-17)|BRCA - Breast invasive adenocarcinoma(81;1.01e-05)		TGTACGGGGCCAAAAAAAAATC	0.416													4	2	---	---	---	---	
UNC93A	54346	broad.mit.edu	37	6	167707852	167707852	+	Intron	DEL	A	-	-			TCGA-AK-3456-01A-02D-1386-10	TCGA-AK-3456-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:167707852delA	uc003qvq.2	+						UNC93A_uc003qvr.2_Intron	NM_018974	NP_061847	Q86WB7	UN93A_HUMAN	unc-93 homolog A isoform 1							integral to membrane|plasma membrane					0		Breast(66;7.62e-05)|Ovarian(120;0.105)		OV - Ovarian serous cystadenocarcinoma(33;2.22e-20)|BRCA - Breast invasive adenocarcinoma(81;6.17e-07)|GBM - Glioblastoma multiforme(31;0.00492)		TTCTCCCACCAGCTTCAGAGG	0.622													4	3	---	---	---	---	
UNC93A	54346	broad.mit.edu	37	6	167707855	167707856	+	Intron	INS	-	CC	CC			TCGA-AK-3456-01A-02D-1386-10	TCGA-AK-3456-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:167707855_167707856insCC	uc003qvq.2	+						UNC93A_uc003qvr.2_Intron	NM_018974	NP_061847	Q86WB7	UN93A_HUMAN	unc-93 homolog A isoform 1							integral to membrane|plasma membrane					0		Breast(66;7.62e-05)|Ovarian(120;0.105)		OV - Ovarian serous cystadenocarcinoma(33;2.22e-20)|BRCA - Breast invasive adenocarcinoma(81;6.17e-07)|GBM - Glioblastoma multiforme(31;0.00492)		TCCCACCAGCTTCAGAGGAGGC	0.614													4	3	---	---	---	---	
UNC93A	54346	broad.mit.edu	37	6	167707858	167707859	+	Intron	INS	-	TC	TC			TCGA-AK-3456-01A-02D-1386-10	TCGA-AK-3456-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:167707858_167707859insTC	uc003qvq.2	+						UNC93A_uc003qvr.2_Intron	NM_018974	NP_061847	Q86WB7	UN93A_HUMAN	unc-93 homolog A isoform 1							integral to membrane|plasma membrane					0		Breast(66;7.62e-05)|Ovarian(120;0.105)		OV - Ovarian serous cystadenocarcinoma(33;2.22e-20)|BRCA - Breast invasive adenocarcinoma(81;6.17e-07)|GBM - Glioblastoma multiforme(31;0.00492)		CACCAGCTTCAGAGGAGGCTCC	0.614													5	3	---	---	---	---	
UNC93A	54346	broad.mit.edu	37	6	167707861	167707861	+	Intron	DEL	G	-	-			TCGA-AK-3456-01A-02D-1386-10	TCGA-AK-3456-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:167707861delG	uc003qvq.2	+						UNC93A_uc003qvr.2_Intron	NM_018974	NP_061847	Q86WB7	UN93A_HUMAN	unc-93 homolog A isoform 1							integral to membrane|plasma membrane					0		Breast(66;7.62e-05)|Ovarian(120;0.105)		OV - Ovarian serous cystadenocarcinoma(33;2.22e-20)|BRCA - Breast invasive adenocarcinoma(81;6.17e-07)|GBM - Glioblastoma multiforme(31;0.00492)		CAGCTTCAGAGGAGGCTCCCA	0.607													5	3	---	---	---	---	
PRKAR1B	5575	broad.mit.edu	37	7	632671	632671	+	Intron	DEL	A	-	-			TCGA-AK-3456-01A-02D-1386-10	TCGA-AK-3456-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:632671delA	uc003siu.1	-						PRKAR1B_uc003siv.2_Intron|PRKAR1B_uc003siw.1_Intron|PRKAR1B_uc003six.1_Intron	NM_002735	NP_002726	P31321	KAP1_HUMAN	protein kinase, cAMP-dependent, regulatory, type						activation of phospholipase C activity|activation of protein kinase A activity|blood coagulation|cellular response to glucagon stimulus|energy reserve metabolic process|nerve growth factor receptor signaling pathway|protein phosphorylation|regulation of insulin secretion|transmembrane transport|water transport	cAMP-dependent protein kinase complex|cytosol	cAMP binding|cAMP-dependent protein kinase regulator activity				0		Ovarian(82;0.0779)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0181)|Epithelial(4;5.75e-19)|OV - Ovarian serous cystadenocarcinoma(56;2.01e-18)|all cancers(6;3.96e-16)|BRCA - Breast invasive adenocarcinoma(126;0.152)		acattgtttcaaaaaaattaa	0.234													4	2	---	---	---	---	
BLVRA	644	broad.mit.edu	37	7	43807445	43807445	+	Intron	DEL	A	-	-			TCGA-AK-3456-01A-02D-1386-10	TCGA-AK-3456-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:43807445delA	uc003tir.2	+						BLVRA_uc010kxv.2_Intron	NM_000712	NP_000703	P53004	BIEA_HUMAN	biliverdin reductase A precursor						heme catabolic process	cytosol	biliverdin reductase activity|zinc ion binding			ovary(1)	1					NADH(DB00157)	TGTTAATTACAAAAAAAAAAG	0.318													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	54176641	54176642	+	IGR	INS	-	TTATCTTG	TTATCTTG	rs149734954	by1000genomes	TCGA-AK-3456-01A-02D-1386-10	TCGA-AK-3456-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:54176641_54176642insTTATCTTG								None (None upstream) : HPVC1 (92275 downstream)																							TCTGCCTCCTTTTAACTTTTTT	0.337													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	87943497	87943497	+	IGR	DEL	T	-	-			TCGA-AK-3456-01A-02D-1386-10	TCGA-AK-3456-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:87943497delT								STEAP4 (7288 upstream) : ZNF804B (445256 downstream)																							TCCTAAGCCCTTTTTTTTTGG	0.358													3	3	---	---	---	---	
NPTX2	4885	broad.mit.edu	37	7	98256083	98256084	+	Intron	INS	-	ACAG	ACAG	rs146619878	by1000genomes	TCGA-AK-3456-01A-02D-1386-10	TCGA-AK-3456-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:98256083_98256084insACAG	uc003upl.2	+							NM_002523	NP_002514	P47972	NPTX2_HUMAN	neuronal pentraxin II precursor						synaptic transmission	extracellular region	metal ion binding|sugar binding			central_nervous_system(2)|skin(1)	3	all_cancers(62;2.28e-09)|all_epithelial(64;4.86e-10)|Esophageal squamous(72;0.00918)|Lung NSC(181;0.0128)|all_lung(186;0.0142)		STAD - Stomach adenocarcinoma(171;0.215)			ACCCGCAGCACACAGATCCCTG	0.599													6	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	101278879	101278880	+	IGR	DEL	CT	-	-	rs34435085		TCGA-AK-3456-01A-02D-1386-10	TCGA-AK-3456-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:101278879_101278880delCT								MYL10 (6303 upstream) : CUX1 (180412 downstream)																							CAGGTGGTGACTCTCTGGCTAC	0.584													2	5	---	---	---	---	
KCP	375616	broad.mit.edu	37	7	128527645	128527648	+	Intron	DEL	ACAC	-	-			TCGA-AK-3456-01A-02D-1386-10	TCGA-AK-3456-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:128527645_128527648delACAC	uc011kor.1	-							NM_001135914	NP_001129386	Q6ZWJ8	KCP_HUMAN	cysteine rich BMP regulator 2 isoform 1							extracellular region				central_nervous_system(1)	1						CTCcacacatacacacacagccac	0.211													4	2	---	---	---	---	
KEL	3792	broad.mit.edu	37	7	142654701	142654701	+	Intron	DEL	T	-	-			TCGA-AK-3456-01A-02D-1386-10	TCGA-AK-3456-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:142654701delT	uc003wcb.2	-							NM_000420	NP_000411	P23276	KELL_HUMAN	Kell blood group, metallo-endopeptidase						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)					CCAGGCCTACTTCTGTCTTCC	0.299													8	4	---	---	---	---	
MLL3	58508	broad.mit.edu	37	7	151944708	151944708	+	Intron	DEL	T	-	-	rs113407913		TCGA-AK-3456-01A-02D-1386-10	TCGA-AK-3456-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:151944708delT	uc003wla.2	-							NM_170606	NP_733751	Q8NEZ4	MLL3_HUMAN	myeloid/lymphoid or mixed-lineage leukemia 3						intracellular signal transduction|regulation of transcription, DNA-dependent|transcription, DNA-dependent		DNA binding|protein binding|zinc ion binding			large_intestine(27)|pancreas(13)|ovary(9)|central_nervous_system(8)|breast(3)|upper_aerodigestive_tract(1)|urinary_tract(1)|skin(1)	63	all_neural(206;0.187)	all_hematologic(28;0.0592)|Prostate(32;0.0906)	OV - Ovarian serous cystadenocarcinoma(82;0.00715)	UCEC - Uterine corpus endometrioid carcinoma (81;0.0597)|BRCA - Breast invasive adenocarcinoma(188;0.0462)		ACTAAAAGAATTTTTAAAGTT	0.264			N		medulloblastoma								5	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	1153107	1153110	+	IGR	DEL	TTTG	-	-			TCGA-AK-3456-01A-02D-1386-10	TCGA-AK-3456-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:1153107_1153110delTTTG								ERICH1 (471881 upstream) : DLGAP2 (296459 downstream)																							TCTTAGGGTTtttgtttgtttgtt	0.436													6	3	---	---	---	---	
CSMD1	64478	broad.mit.edu	37	8	2857300	2857301	+	Intron	INS	-	A	A	rs140414939	by1000genomes	TCGA-AK-3456-01A-02D-1386-10	TCGA-AK-3456-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:2857300_2857301insA	uc011kwk.1	-						CSMD1_uc011kwj.1_Intron|CSMD1_uc010lrg.2_Intron	NM_033225	NP_150094	Q96PZ7	CSMD1_HUMAN	CUB and Sushi multiple domains 1 precursor							integral to membrane				breast(20)|large_intestine(5)	25		all_cancers(1;5.7e-41)|all_epithelial(1;2.54e-36)|Lung NSC(1;7.54e-11)|all_lung(1;3.2e-10)|Hepatocellular(1;3.78e-05)|Breast(1;0.000196)|Myeloproliferative disorder(4;0.000374)|Esophageal squamous(1;0.0157)|Ovarian(12;0.091)|Renal(68;0.144)|Colorectal(14;0.234)		all cancers(1;5.03e-41)|Epithelial(1;4.78e-31)|Lung(1;1.14e-14)|LUSC - Lung squamous cell carcinoma(1;2.34e-14)|GBM - Glioblastoma multiforme(1;4.49e-10)|Colorectal(4;1.18e-07)|OV - Ovarian serous cystadenocarcinoma(1;3.2e-07)|BRCA - Breast invasive adenocarcinoma(1;6.17e-07)|COAD - Colon adenocarcinoma(4;0.000539)|READ - Rectum adenocarcinoma(4;0.00896)|Kidney(5;0.00957)|KIRC - Kidney renal clear cell carcinoma(5;0.0689)		GGAAGGAGATCAAAAAAGGAAA	0.396													3	3	---	---	---	---	
SGCZ	137868	broad.mit.edu	37	8	14338102	14338103	+	Intron	INS	-	A	A	rs74439882		TCGA-AK-3456-01A-02D-1386-10	TCGA-AK-3456-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:14338102_14338103insA	uc003wwq.2	-						SGCZ_uc010lss.2_Intron	NM_139167	NP_631906	Q96LD1	SGCZ_HUMAN	sarcoglycan zeta						cytoskeleton organization	cytoplasm|cytoskeleton|integral to membrane|sarcolemma				ovary(2)|central_nervous_system(1)	3				all cancers(2;0.000643)|Colorectal(111;0.00674)|COAD - Colon adenocarcinoma(73;0.0193)|GBM - Glioblastoma multiforme(2;0.026)		TAATCATTCTCATCATGCTGAC	0.243													7	6	---	---	---	---	
SCARA5	286133	broad.mit.edu	37	8	27759367	27759367	+	Intron	DEL	C	-	-			TCGA-AK-3456-01A-02D-1386-10	TCGA-AK-3456-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:27759367delC	uc003xgj.2	-						SCARA5_uc010luz.2_Intron	NM_173833	NP_776194	Q6ZMJ2	SCAR5_HUMAN	scavenger receptor class A, member 5						cellular iron ion homeostasis|endocytosis|iron ion transmembrane transport|protein homotrimerization	integral to plasma membrane	ferritin receptor activity|scavenger receptor activity			central_nervous_system(1)|skin(1)	2		Ovarian(32;0.0218)		UCEC - Uterine corpus endometrioid carcinoma (27;0.023)|KIRC - Kidney renal clear cell carcinoma(542;0.152)|Kidney(114;0.181)|Colorectal(74;0.228)		AAGCCCCCATCCCAGGGTCAG	0.582													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	77159836	77159836	+	IGR	DEL	T	-	-	rs74726863		TCGA-AK-3456-01A-02D-1386-10	TCGA-AK-3456-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:77159836delT								HNF4G (680777 upstream) : LOC100192378 (363279 downstream)																							acttccagaattttttttttt	0.000													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	82501665	82501666	+	IGR	INS	-	A	A	rs138724491	by1000genomes	TCGA-AK-3456-01A-02D-1386-10	TCGA-AK-3456-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:82501665_82501666insA								FABP12 (58115 upstream) : IMPA1 (67485 downstream)																							CTGTCTGCAACATCTCTCCAGC	0.312													6	4	---	---	---	---	
RGS22	26166	broad.mit.edu	37	8	101078720	101078721	+	Intron	INS	-	T	T			TCGA-AK-3456-01A-02D-1386-10	TCGA-AK-3456-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:101078720_101078721insT	uc003yjb.1	-						RGS22_uc003yja.1_Intron|RGS22_uc003yjc.1_Intron|RGS22_uc011lgz.1_Intron|RGS22_uc010mbo.1_Intron	NM_015668	NP_056483	Q8NE09	RGS22_HUMAN	regulator of G-protein signaling 22						negative regulation of signal transduction	cytoplasm|plasma membrane	GTPase activator activity|signal transducer activity			ovary(3)|skin(2)|breast(1)|central_nervous_system(1)	7			Epithelial(11;6.71e-08)|all cancers(13;4.19e-06)|OV - Ovarian serous cystadenocarcinoma(57;0.000469)|STAD - Stomach adenocarcinoma(118;0.169)			TTCAATCCAGATTTTTTTTTCA	0.307													5	3	---	---	---	---	
TOP1MT	116447	broad.mit.edu	37	8	144403652	144403653	+	Intron	DEL	CG	-	-	rs67407424		TCGA-AK-3456-01A-02D-1386-10	TCGA-AK-3456-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:144403652_144403653delCG	uc003yxz.2	-						TOP1MT_uc011lkd.1_Intron|TOP1MT_uc011lke.1_Intron|TOP1MT_uc010mfb.2_Intron|TOP1MT_uc011lkf.1_Intron|TOP1MT_uc010mfd.1_Intron	NM_052963	NP_443195	Q969P6	TOP1M_HUMAN	mitochondrial topoisomerase I precursor						DNA topological change	chromosome|mitochondrial nucleoid	ATP binding|chromatin DNA binding|DNA topoisomerase (ATP-hydrolyzing) activity|DNA topoisomerase type I activity			ovary(1)	1	all_cancers(97;1.01e-10)|all_epithelial(106;4.86e-09)|Lung NSC(106;0.000167)|all_lung(105;0.000459)|Ovarian(258;0.0212)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.156)|Colorectal(110;0.173)		Irinotecan(DB00762)|Topotecan(DB01030)	gcacgccacacgcacgccacac	0.168													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	68419453	68419454	+	IGR	DEL	AA	-	-	rs62545511		TCGA-AK-3456-01A-02D-1386-10	TCGA-AK-3456-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:68419453_68419454delAA								FAM27B (625264 upstream) : MIR1299 (582785 downstream)																							catacacaccaaacacacatac	0.000													6	3	---	---	---	---	
PHF2	5253	broad.mit.edu	37	9	96376037	96376037	+	Intron	DEL	T	-	-			TCGA-AK-3456-01A-02D-1386-10	TCGA-AK-3456-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:96376037delT	uc004aub.2	+						PHF2_uc011lug.1_Intron	NM_005392	NP_005383	O75151	PHF2_HUMAN	PHD finger protein 2						liver development|negative regulation of chromatin silencing at rDNA|transcription, DNA-dependent	nucleolus	histone demethylase activity (H3-K9 specific)|iron ion binding|methylated histone residue binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|zinc ion binding			ovary(1)	1		Myeloproliferative disorder(762;0.0255)		OV - Ovarian serous cystadenocarcinoma(323;9.11e-28)		atattttttgtagagagagtc	0.000													6	3	---	---	---	---	
OBP2A	29991	broad.mit.edu	37	9	138438191	138438216	+	Intron	DEL	AGGCTGGCTTCTGACCCCGTGCTCCC	-	-	rs138953269		TCGA-AK-3456-01A-02D-1386-10	TCGA-AK-3456-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:138438191_138438216delAGGCTGGCTTCTGACCCCGTGCTCCC	uc004cgb.2	+						OBP2A_uc004cgc.2_Intron|OBP2A_uc010nau.2_Intron|OBP2A_uc010nav.2_Intron	NM_014582	NP_055397	Q9NY56	OBP2A_HUMAN	odorant binding protein 2A precursor						response to stimulus|sensory perception of smell	extracellular region	odorant binding|transporter activity				0				OV - Ovarian serous cystadenocarcinoma(145;3.39e-07)|Epithelial(140;1.11e-06)|all cancers(34;2.04e-05)		GTGTCACTGAAGGCTGGCTTCTGACCCCGTGCTCCCAGCCTGGGGT	0.681													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	11929717	11929717	+	Intron	DEL	G	-	-			TCGA-AK-3456-01A-02D-1386-10	TCGA-AK-3456-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:11929717delG	uc001iky.1	-											Homo sapiens cDNA FLJ32141 fis, clone PLACE5000067.																		TGTCAGAGCCGGGGGCAATGG	0.687													4	2	---	---	---	---	
NSUN6	221078	broad.mit.edu	37	10	18931155	18931155	+	Intron	DEL	A	-	-	rs10829067	by1000genomes	TCGA-AK-3456-01A-02D-1386-10	TCGA-AK-3456-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:18931155delA	uc010qcp.1	-							NM_182543	NP_872349	Q8TEA1	NSUN6_HUMAN	NOL1/NOP2/Sun domain family, member 6								methyltransferase activity|RNA binding			ovary(2)	2						TGGGGGGGGGAAAACATCACT	0.343													4	2	---	---	---	---	
ANK3	288	broad.mit.edu	37	10	61815229	61815229	+	Intron	DEL	T	-	-			TCGA-AK-3456-01A-02D-1386-10	TCGA-AK-3456-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:61815229delT	uc001jky.2	-						ANK3_uc001jkw.2_Intron|ANK3_uc009xpa.2_Intron|ANK3_uc001jkx.2_Intron|ANK3_uc010qih.1_Intron|ANK3_uc001jkz.3_Intron|ANK3_uc001jkv.2_Intron	NM_020987	NP_066267	Q12955	ANK3_HUMAN	ankyrin 3 isoform 1						establishment of protein localization|signal transduction	basolateral plasma membrane|cytoplasm|cytoskeleton	protein binding			skin(9)|ovary(6)|pancreas(2)|central_nervous_system(2)	19						TACTTGGAACTTTTTTTTTTA	0.284													8	7	---	---	---	---	
AIFM2	84883	broad.mit.edu	37	10	71873765	71873766	+	Intron	DEL	CT	-	-			TCGA-AK-3456-01A-02D-1386-10	TCGA-AK-3456-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:71873765_71873766delCT	uc010qjg.1	-						AIFM2_uc001jqp.1_3'UTR	NM_032797	NP_116186	Q9BRQ8	AIFM2_HUMAN	apoptosis-inducing factor (AIF)-like						apoptotic mitochondrial changes|chromosome condensation|induction of apoptosis	cytosol|integral to membrane|mitochondrial outer membrane	DNA binding|electron-transferring-flavoprotein dehydrogenase activity|flavin adenine dinucleotide binding			central_nervous_system(1)	1						TGTTTAATACCTCTCTCTCTCC	0.455													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	80049623	80049626	+	Intron	DEL	ACAG	-	-	rs5786331		TCGA-AK-3456-01A-02D-1386-10	TCGA-AK-3456-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:80049623_80049626delACAG	uc010qlp.1	+						uc001jzw.1_Intron					SubName: Full=cDNA FLJ57363;																		CAGGTGGGGTACAGACAGAGACAG	0.529													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	100104312	100104314	+	IGR	DEL	TCT	-	-	rs7081279	by1000genomes	TCGA-AK-3456-01A-02D-1386-10	TCGA-AK-3456-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:100104312_100104314delTCT								LOXL4 (76305 upstream) : PYROXD2 (39009 downstream)																							CTCCTCCTCCTCTGTGGTTGGGA	0.527													4	2	---	---	---	---	
GPAM	57678	broad.mit.edu	37	10	113928063	113928063	+	Intron	DEL	C	-	-			TCGA-AK-3456-01A-02D-1386-10	TCGA-AK-3456-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:113928063delC	uc009xxy.1	-						GPAM_uc001kzp.2_Intron|GPAM_uc001kzq.1_Intron	NM_020918	NP_065969	Q9HCL2	GPAT1_HUMAN	mitochondrial glycerol 3-phosphate						phospholipid biosynthetic process|triglyceride biosynthetic process	integral to membrane|mitochondrial outer membrane	glycerol-3-phosphate O-acyltransferase activity			ovary(1)|skin(1)	2				Epithelial(162;0.0306)|all cancers(201;0.123)		TGTGTAGGTACCCTTACCAGT	0.338													156	104	---	---	---	---	
TRIM68	55128	broad.mit.edu	37	11	4626898	4626898	+	Intron	DEL	C	-	-			TCGA-AK-3456-01A-02D-1386-10	TCGA-AK-3456-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:4626898delC	uc001lzf.1	-						TRIM68_uc001lzg.1_Intron|TRIM68_uc010qyj.1_Intron|TRIM68_uc009yek.1_Intron	NM_018073	NP_060543	Q6AZZ1	TRI68_HUMAN	ring finger protein 137						protein autoubiquitination|regulation of androgen receptor signaling pathway	Golgi apparatus|nucleolus|perinuclear region of cytoplasm	androgen receptor binding|histone acetyltransferase binding|ubiquitin-protein ligase activity|zinc ion binding			ovary(1)	1		Medulloblastoma(188;0.0025)|Breast(177;0.0101)|all_neural(188;0.0227)		Epithelial(150;9.49e-12)|BRCA - Breast invasive adenocarcinoma(625;0.0288)|LUSC - Lung squamous cell carcinoma(625;0.192)		TTCCTTTTGACCCTTTACTGA	0.408													4	2	---	---	---	---	
ELP4	26610	broad.mit.edu	37	11	31541921	31541921	+	Intron	DEL	T	-	-			TCGA-AK-3456-01A-02D-1386-10	TCGA-AK-3456-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:31541921delT	uc001mtb.2	+						ELP4_uc001mta.1_Intron|ELP4_uc001mtc.2_Intron|ELP4_uc010rdz.1_Intron	NM_019040	NP_061913	Q96EB1	ELP4_HUMAN	elongation protein 4 homolog						histone acetylation|regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	cytoplasm|DNA-directed RNA polymerase II, holoenzyme|Elongator holoenzyme complex|transcription elongation factor complex	phosphorylase kinase regulator activity|protein binding			upper_aerodigestive_tract(1)|ovary(1)|prostate(1)	3	Lung SC(675;0.225)					TGTGAATTGATTTTTTTGGAG	0.274													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	41826094	41826094	+	IGR	DEL	T	-	-			TCGA-AK-3456-01A-02D-1386-10	TCGA-AK-3456-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:41826094delT								LRRC4C (344771 upstream) : None (None downstream)																							CCAGTCTTCATTTTTTTACAT	0.164													4	2	---	---	---	---	
CNTN5	53942	broad.mit.edu	37	11	99942834	99942835	+	Intron	INS	-	A	A			TCGA-AK-3456-01A-02D-1386-10	TCGA-AK-3456-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:99942834_99942835insA	uc001pga.2	+						CNTN5_uc009ywv.1_Intron|CNTN5_uc001pfz.2_Intron|CNTN5_uc001pgb.2_Intron	NM_014361	NP_055176	O94779	CNTN5_HUMAN	contactin 5 isoform long						cell adhesion	anchored to membrane|plasma membrane	protein binding			skin(3)|ovary(2)|pancreas(2)|breast(1)	8		all_hematologic(158;1.22e-05)|Acute lymphoblastic leukemia(157;3.81e-05)|Melanoma(852;0.219)		BRCA - Breast invasive adenocarcinoma(274;0.00146)|KIRC - Kidney renal clear cell carcinoma(183;0.156)|Kidney(183;0.196)		CTATAGCACTTAAAAAAATCAT	0.332													4	2	---	---	---	---	
ERC1	23085	broad.mit.edu	37	12	1190172	1190172	+	Intron	DEL	C	-	-			TCGA-AK-3456-01A-02D-1386-10	TCGA-AK-3456-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:1190172delC	uc001qjb.2	+						ERC1_uc001qiz.2_Intron|ERC1_uc001qjc.2_Intron|ERC1_uc001qja.2_Intron|ERC1_uc001qjd.2_Intron|ERC1_uc001qjf.2_Intron|ERC1_uc010sdv.1_5'Flank	NM_178040	NP_829884	Q8IUD2	RB6I2_HUMAN	RAB6-interacting protein 2 isoform epsilon						I-kappaB phosphorylation|multicellular organismal development|positive regulation of anti-apoptosis|positive regulation of NF-kappaB transcription factor activity|protein transport	Golgi membrane|IkappaB kinase complex|presynaptic membrane	leucine zipper domain binding			ovary(2)|lung(2)|breast(1)	5	all_epithelial(11;0.0698)|Ovarian(42;0.107)		OV - Ovarian serous cystadenocarcinoma(31;0.00239)|BRCA - Breast invasive adenocarcinoma(9;0.0567)			ggatctgaaacccagaaagat	0.060													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	4192423	4192424	+	IGR	INS	-	CA	CA			TCGA-AK-3456-01A-02D-1386-10	TCGA-AK-3456-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:4192423_4192424insCA								PARP11 (209815 upstream) : CCND2 (190478 downstream)																							GCTTCCCCCGTCACACACACAC	0.455													4	2	---	---	---	---	
HTR7P1	93164	broad.mit.edu	37	12	13177067	13177070	+	Intron	DEL	GTCT	-	-	rs143221926		TCGA-AK-3456-01A-02D-1386-10	TCGA-AK-3456-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:13177067_13177070delGTCT	uc001rbh.2	+											Homo sapiens cDNA FLJ43688 fis, clone TBAES2003492.												0						acatatttaagtctgtctgttgta	0.020													3	3	---	---	---	---	
SLC2A13	114134	broad.mit.edu	37	12	40223646	40223646	+	Intron	DEL	A	-	-			TCGA-AK-3456-01A-02D-1386-10	TCGA-AK-3456-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:40223646delA	uc010skm.1	-						C12orf40_uc009zjv.1_Intron|SLC2A13_uc001rme.1_3'UTR	NM_052885	NP_443117	Q96QE2	MYCT_HUMAN	solute carrier family 2 (facilitated glucose							integral to membrane|plasma membrane	myo-inositol:hydrogen symporter activity			ovary(1)	1		Lung NSC(34;0.105)|all_lung(34;0.123)				ATAGCTGCCTAAAACTAAAGA	0.378										HNSCC(50;0.14)			4	2	---	---	---	---	
CCDC38	120935	broad.mit.edu	37	12	96334666	96334670	+	Intron	DEL	AAACA	-	-	rs142790641		TCGA-AK-3456-01A-02D-1386-10	TCGA-AK-3456-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:96334666_96334670delAAACA	uc001tek.1	-						AMDHD1_uc001tel.1_5'Flank|AMDHD1_uc009zth.1_5'Flank	NM_182496	NP_872302	Q502W7	CCD38_HUMAN	coiled-coil domain containing 38											skin(1)	1						acaaacaaacaaacaaaaaaaaaaa	0.371													4	2	---	---	---	---	
FBXO21	23014	broad.mit.edu	37	12	117603583	117603583	+	Intron	DEL	A	-	-			TCGA-AK-3456-01A-02D-1386-10	TCGA-AK-3456-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:117603583delA	uc001twk.2	-						FBXO21_uc001twj.2_Intron|FBXO21_uc009zwq.2_Intron|FBXO21_uc001twl.1_Intron	NM_033624	NP_296373	O94952	FBX21_HUMAN	F-box only protein 21 isoform 1						ubiquitin-dependent protein catabolic process	ubiquitin ligase complex	ubiquitin-protein ligase activity			kidney(1)	1	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)			BRCA - Breast invasive adenocarcinoma(302;0.0291)		TGCTCTTAAGAAAAAAAAAAT	0.323													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	128108952	128108955	+	IGR	DEL	AGTT	-	-			TCGA-AK-3456-01A-02D-1386-10	TCGA-AK-3456-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:128108952_128108955delAGTT								None (None upstream) : TMEM132C (790336 downstream)																							CTTCTCTCTCAGTTAGCACATCCT	0.564													7	6	---	---	---	---	
COL4A1	1282	broad.mit.edu	37	13	110921360	110921362	+	Intron	DEL	GGA	-	-	rs72523086		TCGA-AK-3456-01A-02D-1386-10	TCGA-AK-3456-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:110921360_110921362delGGA	uc001vqw.3	-						COL4A1_uc010agl.2_Intron	NM_001845	NP_001836	P02462	CO4A1_HUMAN	alpha 1 type IV collagen preproprotein						angiogenesis|axon guidance		extracellular matrix structural constituent|platelet-derived growth factor binding			ovary(3)|lung(1)|central_nervous_system(1)|pancreas(1)	6	all_cancers(4;9.8e-13)|all_epithelial(4;9.66e-08)|all_lung(23;3.75e-06)|Lung NSC(43;0.000274)|Colorectal(4;0.00178)|all_neural(89;0.00459)|Medulloblastoma(90;0.00596)|Lung SC(71;0.0604)	Breast(118;0.2)	BRCA - Breast invasive adenocarcinoma(86;0.11)|all cancers(43;0.145)			CTTGGCGCACGGAGAACTGATCC	0.581													4	5	---	---	---	---	
SNX6	58533	broad.mit.edu	37	14	35067003	35067003	+	Intron	DEL	T	-	-			TCGA-AK-3456-01A-02D-1386-10	TCGA-AK-3456-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:35067003delT	uc001wsf.1	-						SNX6_uc001wse.1_Intron|SNX6_uc010tpm.1_Intron|SNX6_uc010amm.1_Intron	NM_152233	NP_689419	Q9UNH7	SNX6_HUMAN	sorting nexin 6 isoform b						cell communication|intracellular protein transport|negative regulation of epidermal growth factor receptor activity|negative regulation of transcription, DNA-dependent|negative regulation of transforming growth factor beta receptor signaling pathway|retrograde transport, endosome to Golgi	cytoplasmic vesicle membrane|early endosome membrane|nucleus	phosphatidylinositol binding|protein homodimerization activity				0	Breast(36;0.0473)|Hepatocellular(127;0.158)		LUAD - Lung adenocarcinoma(48;0.00169)|Lung(238;0.00199)|Epithelial(34;0.187)	GBM - Glioblastoma multiforme(112;0.0245)		gattttcaaattttagggcat	0.119													4	4	---	---	---	---	
SAMD4A	23034	broad.mit.edu	37	14	55236554	55236554	+	Intron	DEL	G	-	-			TCGA-AK-3456-01A-02D-1386-10	TCGA-AK-3456-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:55236554delG	uc001xbb.2	+						SAMD4A_uc001xbc.2_Intron|SAMD4A_uc001xbg.2_Intron	NM_015589	NP_056404	Q9UPU9	SMAG1_HUMAN	sterile alpha motif domain containing 4 isoform						positive regulation of translation	cell junction|cytoplasm|dendrite|synapse|synaptosome	translation repressor activity				0						GGGGGAATGTGGATATGGATC	0.423													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	84958045	84958046	+	IGR	INS	-	C	C	rs142437102	by1000genomes	TCGA-AK-3456-01A-02D-1386-10	TCGA-AK-3456-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:84958045_84958046insC								None (None upstream) : None (None downstream)																							ctgccctcagtttatagcttca	0.000													4	9	---	---	---	---	
PACS2	23241	broad.mit.edu	37	14	105848398	105848398	+	Intron	DEL	G	-	-	rs112632153		TCGA-AK-3456-01A-02D-1386-10	TCGA-AK-3456-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:105848398delG	uc001yqt.2	+						PACS2_uc001yqs.2_Intron|PACS2_uc001yqv.2_Intron|PACS2_uc001yqu.2_Intron	NM_015197	NP_056012	Q86VP3	PACS2_HUMAN	phosphofurin acidic cluster sorting protein 2						apoptosis|interspecies interaction between organisms	endoplasmic reticulum lumen|mitochondrion				pancreas(1)	1		all_cancers(154;0.0351)|all_epithelial(191;0.153)|Melanoma(154;0.155)	OV - Ovarian serous cystadenocarcinoma(23;0.0145)|Epithelial(46;0.036)	Epithelial(152;0.138)		AGCTGCAGGTGGGGGTGGAGG	0.692													2	4	---	---	---	---	
SORD	6652	broad.mit.edu	37	15	45323245	45323245	+	Intron	DEL	C	-	-	rs67335344		TCGA-AK-3456-01A-02D-1386-10	TCGA-AK-3456-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:45323245delC	uc001zul.3	+						SORD_uc010uel.1_Intron|SORD_uc001zum.3_Intron|SORD_uc010bdz.2_Intron	NM_003104	NP_003095	Q00796	DHSO_HUMAN	sorbitol dehydrogenase						fructose biosynthetic process|glucose metabolic process|L-xylitol catabolic process|sorbitol catabolic process|sperm motility	cilium|extracellular space|flagellum|membrane fraction|mitochondrial membrane|soluble fraction	L-iditol 2-dehydrogenase activity|NAD binding|sugar binding|zinc ion binding				0		all_cancers(109;3.43e-12)|all_epithelial(112;2.33e-10)|Lung NSC(122;6.01e-07)|all_lung(180;4.38e-06)|Melanoma(134;0.0122)		all cancers(107;1.6e-18)|GBM - Glioblastoma multiforme(94;4.95e-07)|COAD - Colon adenocarcinoma(120;0.0704)|Colorectal(133;0.0706)	NADH(DB00157)	GAGGTCGGGGCAGCCATggtg	0.234													4	2	---	---	---	---	
APH1B	83464	broad.mit.edu	37	15	63598249	63598249	+	3'UTR	DEL	G	-	-			TCGA-AK-3456-01A-02D-1386-10	TCGA-AK-3456-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:63598249delG	uc002ama.2	+	6					APH1B_uc002amb.2_3'UTR|APH1B_uc010bgq.2_3'UTR|APH1B_uc010bgr.2_3'UTR	NM_031301	NP_112591	Q8WW43	APH1B_HUMAN	presenilin stabilization factor-like isoform 1						apoptosis|induction of apoptosis by extracellular signals|membrane protein intracellular domain proteolysis|nerve growth factor receptor signaling pathway|Notch receptor processing|Notch signaling pathway|positive regulation of catalytic activity|protein processing	integral to membrane|plasma membrane|transport vesicle	peptidase activity|protein binding				0						ctgggcacgtggtgagtttta	0.100													4	2	---	---	---	---	
GOLGA6A	342096	broad.mit.edu	37	15	74373249	74373249	+	Intron	DEL	A	-	-			TCGA-AK-3456-01A-02D-1386-10	TCGA-AK-3456-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:74373249delA	uc002axa.1	-							NM_001038640	NP_001033729	Q9NYA3	GOG6A_HUMAN	golgi autoantigen, golgin subfamily a, 6												0						TATTATGGCTAAAAAAAAAAG	0.428													4	4	---	---	---	---	
IGF1R	3480	broad.mit.edu	37	15	99348535	99348535	+	Intron	DEL	T	-	-			TCGA-AK-3456-01A-02D-1386-10	TCGA-AK-3456-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:99348535delT	uc002bul.2	+						IGF1R_uc010urq.1_Intron|IGF1R_uc010bon.2_Intron	NM_000875	NP_000866	P08069	IGF1R_HUMAN	insulin-like growth factor 1 receptor precursor						anti-apoptosis|immune response|insulin receptor signaling pathway|phosphatidylinositol-mediated signaling|positive regulation of cell migration|positive regulation of cell proliferation|positive regulation of DNA replication|protein autophosphorylation|protein tetramerization	microsome	ATP binding|identical protein binding|insulin binding|insulin receptor binding|insulin receptor substrate binding|insulin-like growth factor I binding|insulin-like growth factor receptor activity|metal ion binding|phosphatidylinositol 3-kinase binding			lung(3)|kidney(3)|ovary(1)|central_nervous_system(1)	8	all_cancers(4;4.17e-14)|all_epithelial(3;4.34e-15)|Lung NSC(78;0.00175)|all_lung(78;0.00351)|Melanoma(26;0.00505)|Medulloblastoma(229;0.163)		Epithelial(2;1.94e-12)|all cancers(5;6.83e-11)|BRCA - Breast invasive adenocarcinoma(2;2.88e-09)|OV - Ovarian serous cystadenocarcinoma(32;0.00261)		Insulin Glargine recombinant(DB00047)|Insulin Lyspro recombinant(DB00046)|Insulin recombinant(DB00030)|Insulin, porcine(DB00071)|Mecasermin(DB01277)	CACACGCTGATTTTTTTTTTC	0.388													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	67548407	67548407	+	IGR	DEL	A	-	-	rs72081557		TCGA-AK-3456-01A-02D-1386-10	TCGA-AK-3456-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:67548407delA								AGRP (30691 upstream) : FAM65A (14347 downstream)																							acgctgactcaaaaaaaaaaT	0.204													6	3	---	---	---	---	
CMIP	80790	broad.mit.edu	37	16	81653154	81653155	+	Intron	INS	-	C	C			TCGA-AK-3456-01A-02D-1386-10	TCGA-AK-3456-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:81653154_81653155insC	uc002fgp.2	+						CMIP_uc002fgq.1_Intron|CMIP_uc010vnq.1_Intron	NM_198390	NP_938204	Q8IY22	CMIP_HUMAN	c-Maf-inducing protein isoform C-mip							cytoplasm|nucleus					0						CCTTCGTCAGACCCCCTGAACC	0.589													4	2	---	---	---	---	
RPL13	6137	broad.mit.edu	37	16	89629119	89629119	+	Intron	DEL	T	-	-			TCGA-AK-3456-01A-02D-1386-10	TCGA-AK-3456-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:89629119delT	uc002fnm.1	+						RPL13_uc010vpj.1_Intron|RPL13_uc002fnn.1_Intron|RPL13_uc002fno.1_Intron	NM_000977	NP_000968	P26373	RL13_HUMAN	ribosomal protein L13						endocrine pancreas development|translational elongation|translational termination|viral transcription	cytosolic ribosome	protein binding|RNA binding|structural constituent of ribosome				0		all_hematologic(23;0.0748)		all cancers(4;1.15e-07)|OV - Ovarian serous cystadenocarcinoma(4;7.8e-06)|BRCA - Breast invasive adenocarcinoma(80;0.0139)		AGGGTTTTTCTTTTTTTTTTT	0.478													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	21544829	21544829	+	IGR	DEL	T	-	-			TCGA-AK-3456-01A-02D-1386-10	TCGA-AK-3456-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21544829delT								C17orf51 (67098 upstream) : FAM27L (280541 downstream)																							ctgtttttgattttttttttc	0.000													7	4	---	---	---	---	
FLJ36000	284124	broad.mit.edu	37	17	21906824	21906824	+	Intron	DEL	G	-	-	rs62050046		TCGA-AK-3456-01A-02D-1386-10	TCGA-AK-3456-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21906824delG	uc002gza.2	+							NR_027084				Homo sapiens cDNA FLJ36000 fis, clone TESTI2015180.												0						gtgtgtgtgtgtgtgtgtgtg	0.403													4	3	---	---	---	---	
ACCN1	40	broad.mit.edu	37	17	31574551	31574551	+	Intron	DEL	T	-	-			TCGA-AK-3456-01A-02D-1386-10	TCGA-AK-3456-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:31574551delT	uc002hhu.2	-						ACCN1_uc002hht.2_Intron	NM_001094	NP_001085	Q16515	ACCN1_HUMAN	amiloride-sensitive cation channel 1, neuronal						central nervous system development|peripheral nervous system development|synaptic transmission	integral to plasma membrane	ligand-gated sodium channel activity|protein binding			ovary(2)|large_intestine(1)|central_nervous_system(1)	4		Breast(31;0.042)|Ovarian(249;0.202)		UCEC - Uterine corpus endometrioid carcinoma (308;0.13)|BRCA - Breast invasive adenocarcinoma(366;0.215)	Amiloride(DB00594)	CCTACCAGTATTTTTGGAGGA	0.368													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	36609627	36609630	+	IGR	DEL	TCTC	-	-			TCGA-AK-3456-01A-02D-1386-10	TCGA-AK-3456-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:36609627_36609630delTCTC								SOCS7 (53610 upstream) : ARHGAP23 (4014 downstream)																							TGTGGCTGTTTCTCTGGGTGGATG	0.485													5	4	---	---	---	---	
KIF19	124602	broad.mit.edu	37	17	72349257	72349258	+	Intron	INS	-	T	T			TCGA-AK-3456-01A-02D-1386-10	TCGA-AK-3456-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:72349257_72349258insT	uc002jkm.3	+							NM_153209	NP_694941	Q2TAC6	KIF19_HUMAN	kinesin family member 19						microtubule-based movement	cytoplasm|microtubule	ATP binding|microtubule motor activity				0						ACACCAACAGCTTCTCCCCTGG	0.579													23	12	---	---	---	---	
MGAT5B	146664	broad.mit.edu	37	17	74911549	74911549	+	Intron	DEL	A	-	-			TCGA-AK-3456-01A-02D-1386-10	TCGA-AK-3456-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:74911549delA	uc002jti.2	+						MGAT5B_uc002jth.2_Intron	NM_198955	NP_945193	Q3V5L5	MGT5B_HUMAN	N-acetylglucosaminyltranferase VB isoform 2							Golgi membrane|integral to membrane	alpha-1,6-mannosyl-glycoprotein 6-beta-N-acetylglucosaminyltransferase activity|metal ion binding			ovary(2)|skin(1)	3						gacaagACCGAAAAACAACCC	0.229													4	2	---	---	---	---	
TIMP2	7077	broad.mit.edu	37	17	76866754	76866754	+	Intron	DEL	T	-	-			TCGA-AK-3456-01A-02D-1386-10	TCGA-AK-3456-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:76866754delT	uc002jwf.2	-						TIMP2_uc002jwe.2_Intron|TIMP2_uc010wty.1_Intron	NM_003255	NP_003246	P16035	TIMP2_HUMAN	TIMP metallopeptidase inhibitor 2 precursor								metal ion binding|metalloendopeptidase inhibitor activity			central_nervous_system(2)	2			BRCA - Breast invasive adenocarcinoma(99;0.0101)|OV - Ovarian serous cystadenocarcinoma(97;0.194)			AAATGCTCCCTTTTTTTTGTC	0.517													4	2	---	---	---	---	
C18orf34	374864	broad.mit.edu	37	18	30903296	30903297	+	Intron	INS	-	A	A			TCGA-AK-3456-01A-02D-1386-10	TCGA-AK-3456-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:30903296_30903297insA	uc002kxn.2	-						C18orf34_uc010xbr.1_Intron|C18orf34_uc010dmf.1_Intron|C18orf34_uc002kxo.2_Intron|C18orf34_uc002kxp.2_Intron	NM_001105528	NP_001098998	Q5BJE1	CR034_HUMAN	hypothetical protein LOC374864 isoform 1											ovary(1)	1						AAATATATATCTTTTTATTTAC	0.114													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	47283635	47283636	+	IGR	INS	-	G	G	rs150539338	by1000genomes	TCGA-AK-3456-01A-02D-1386-10	TCGA-AK-3456-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:47283635_47283636insG								LIPG (164359 upstream) : ACAA2 (26239 downstream)																							AAAGTCAGCTTGGGTGTTCTGG	0.401													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	77565540	77565540	+	IGR	DEL	T	-	-			TCGA-AK-3456-01A-02D-1386-10	TCGA-AK-3456-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:77565540delT								CTDP1 (51033 upstream) : KCNG2 (58128 downstream)																							CTCCATTGCCTTTTTTTTTTC	0.448													4	2	---	---	---	---	
BTBD2	55643	broad.mit.edu	37	19	1997185	1997185	+	Intron	DEL	A	-	-			TCGA-AK-3456-01A-02D-1386-10	TCGA-AK-3456-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:1997185delA	uc002lup.1	-							NM_017797	NP_060267	Q9BX70	BTBD2_HUMAN	BTB (POZ) domain containing 2							cytoplasmic mRNA processing body	protein binding			ovary(1)|skin(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)		tctcaaaaagaaaaaaaaaaG	0.254													4	2	---	---	---	---	
SPTBN4	57731	broad.mit.edu	37	19	41071171	41071171	+	Intron	DEL	A	-	-	rs71972087		TCGA-AK-3456-01A-02D-1386-10	TCGA-AK-3456-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:41071171delA	uc002ony.2	+						SPTBN4_uc002onz.2_Intron|SPTBN4_uc010egx.2_Intron	NM_020971	NP_066022	Q9H254	SPTN4_HUMAN	spectrin, beta, non-erythrocytic 4 isoform						actin filament capping|axon guidance|cytoskeletal anchoring at plasma membrane|vesicle-mediated transport	cytosol|nuclear matrix|PML body|spectrin	actin binding|ankyrin binding|structural constituent of cytoskeleton			ovary(3)|central_nervous_system(1)|skin(1)	5			Lung(22;0.000114)|LUSC - Lung squamous cell carcinoma(20;0.000384)			actttatctcaaaaaaaaaaa	0.169													7	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	45132172	45132172	+	Intron	DEL	A	-	-			TCGA-AK-3456-01A-02D-1386-10	TCGA-AK-3456-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:45132172delA	uc002ozk.2	+											SubName: Full=LOC147710 protein; Flags: Fragment;																		cgagtcagggaaggcctccct	0.000													4	2	---	---	---	---	
DDRGK1	65992	broad.mit.edu	37	20	3172771	3172772	+	Intron	INS	-	AT	AT	rs140212933	by1000genomes	TCGA-AK-3456-01A-02D-1386-10	TCGA-AK-3456-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:3172771_3172772insAT	uc002wic.2	-						DDRGK1_uc010gaw.2_Intron	NM_023935	NP_076424	Q96HY6	DDRGK_HUMAN	DDRGK domain containing 1 precursor							endoplasmic reticulum	protein binding				0						CCGAGACACACGAGTGGTAATC	0.530													6	6	---	---	---	---	
SPTLC3	55304	broad.mit.edu	37	20	13054310	13054310	+	Intron	DEL	T	-	-			TCGA-AK-3456-01A-02D-1386-10	TCGA-AK-3456-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:13054310delT	uc002wod.1	+							NM_018327	NP_060797	Q9NUV7	SPTC3_HUMAN	serine palmitoyltransferase, long chain base						sphingoid biosynthetic process	integral to membrane|serine C-palmitoyltransferase complex	pyridoxal phosphate binding|serine C-palmitoyltransferase activity|transferase activity, transferring nitrogenous groups				0					Pyridoxal Phosphate(DB00114)	ATGATTAACATTTTTTTTTAA	0.408													8	5	---	---	---	---	
DSTN	11034	broad.mit.edu	37	20	17585500	17585500	+	Intron	DEL	T	-	-			TCGA-AK-3456-01A-02D-1386-10	TCGA-AK-3456-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:17585500delT	uc002wpr.2	+						DSTN_uc002wpq.2_Intron|DSTN_uc010gck.2_Intron	NM_006870	NP_006861	P60981	DEST_HUMAN	destrin isoform a						actin filament severing|actin polymerization or depolymerization		actin binding			large_intestine(1)|skin(1)	2						AACTATACCCTTGACATTGTC	0.393													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	29600972	29600972	+	IGR	DEL	A	-	-	rs112429825		TCGA-AK-3456-01A-02D-1386-10	TCGA-AK-3456-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:29600972delA								None (None upstream) : FRG1B (10907 downstream)																							aaactatttcaaaaaaatgaa	0.000													2	5	---	---	---	---	
CTSA	5476	broad.mit.edu	37	20	44517116	44517116	+	5'Flank	DEL	G	-	-			TCGA-AK-3456-01A-02D-1386-10	TCGA-AK-3456-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:44517116delG	uc002xqj.3	+						C20orf165_uc002xqf.2_5'Flank|CTSA_uc002xqh.2_5'Flank|CTSA_uc002xqi.2_5'Flank|CTSA_uc010zxi.1_5'Flank	NM_001127695	NP_001121167	P10619	PPGB_HUMAN	cathepsin A isoform b precursor						intracellular protein transport|proteolysis	endoplasmic reticulum|lysosome|nucleus	enzyme activator activity|protein binding|serine-type carboxypeptidase activity			ovary(1)	1		Myeloproliferative disorder(115;0.0122)				ccctagggatgggatgtggga	0.085													4	2	---	---	---	---	
UBASH3A	53347	broad.mit.edu	37	21	43826184	43826185	+	Intron	INS	-	TT	TT	rs117834816	by1000genomes	TCGA-AK-3456-01A-02D-1386-10	TCGA-AK-3456-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:43826184_43826185insTT	uc002zbe.2	+						UBASH3A_uc002zbf.2_Intron|UBASH3A_uc010gpc.2_Intron|UBASH3A_uc010gpd.2_Intron|UBASH3A_uc010gpe.2_Intron	NM_018961	NP_061834	P57075	UBS3A_HUMAN	ubiquitin associated and SH3 domain containing,							cytosol|nucleus				ovary(3)	3						GGGCTGAAGCGGGTAGCCAGGG	0.658													5	3	---	---	---	---	
COL18A1	80781	broad.mit.edu	37	21	46895512	46895512	+	Intron	DEL	G	-	-			TCGA-AK-3456-01A-02D-1386-10	TCGA-AK-3456-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:46895512delG	uc011afs.1	+						COL18A1_uc002zhg.2_Intron|COL18A1_uc002zhi.2_Intron	NM_130444	NP_569711	P39060	COIA1_HUMAN	alpha 1 type XVIII collagen isoform 3 precursor						cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception	collagen|extracellular space	extracellular matrix structural constituent|metal ion binding|protein binding			central_nervous_system(1)	1				Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929)		TCCCAGCAGTGGGGTGACACA	0.677													4	2	---	---	---	---	
LOC91316	91316	broad.mit.edu	37	22	24013007	24013009	+	Intron	DEL	CTT	-	-	rs147809331		TCGA-AK-3456-01A-02D-1386-10	TCGA-AK-3456-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:24013007_24013009delCTT	uc002zxh.3	-						LOC91316_uc002zxi.3_Intron|LOC91316_uc002zxk.3_Intron|LOC91316_uc010gua.2_Intron|LOC91316_uc002zxl.3_Intron|LOC91316_uc011aiz.1_Intron|LOC91316_uc002zxm.3_Intron					Homo sapiens cDNA FLJ32313 fis, clone PROST2003232, weakly similar to BETA-GLUCURONIDASE PRECURSOR (EC 3.2.1.31).												0						TCAGTGTCTCCTTCTCGCCTCCC	0.606													8	5	---	---	---	---	
SRRD	402055	broad.mit.edu	37	22	26883856	26883857	+	Intron	DEL	TC	-	-			TCGA-AK-3456-01A-02D-1386-10	TCGA-AK-3456-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:26883856_26883857delTC	uc010gve.2	+						SRRD_uc003acp.3_Intron	NM_001013694	NP_001013716	Q9UH36	SRR1L_HUMAN	SRR1 domain containing						rhythmic process						0						GCTGGCAGCTTCTCTCTCTCTC	0.470													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	44793220	44793220	+	IGR	DEL	T	-	-			TCGA-AK-3456-01A-02D-1386-10	TCGA-AK-3456-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:44793220delT								KIAA1644 (84489 upstream) : LDOC1L (95230 downstream)																							tgagtctgcctccctgaacct	0.164													4	2	---	---	---	---	
DMD	1756	broad.mit.edu	37	X	31162918	31162918	+	Intron	DEL	A	-	-			TCGA-AK-3456-01A-02D-1386-10	TCGA-AK-3456-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:31162918delA	uc004dda.1	-						DMD_uc004dcq.1_Intron|DMD_uc004dcr.1_Intron|DMD_uc004dcs.1_Intron|DMD_uc004dct.1_Intron|DMD_uc004dcu.1_Intron|DMD_uc004dcv.1_Intron|DMD_uc004dcw.2_Intron|DMD_uc004dcx.2_Intron|DMD_uc004dcz.2_Intron|DMD_uc004dcy.1_Intron|DMD_uc004ddb.1_Intron|DMD_uc004dcm.1_Intron|DMD_uc004dcn.1_Intron|DMD_uc004dco.1_Intron|DMD_uc004dcp.1_Intron|DMD_uc011mkb.1_Intron	NM_004006	NP_003997	P11532	DMD_HUMAN	dystrophin Dp427m isoform						muscle filament sliding|peptide biosynthetic process	cell surface|costamere|cytoskeleton|cytosol|dystrophin-associated glycoprotein complex|sarcolemma	actin binding|dystroglycan binding|nitric-oxide synthase binding|protein binding|structural constituent of cytoskeleton|structural constituent of muscle|zinc ion binding			ovary(3)|pancreas(2)|large_intestine(1)	6		all_cancers(2;1.22e-16)|Acute lymphoblastic leukemia(2;4.65e-06)|all_hematologic(2;0.00108)|all_epithelial(3;0.00626)|all_neural(2;0.0189)|all_lung(315;0.182)|Glioma(3;0.203)				AGAGAAAGAGAAATGAGGAAG	0.468													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	Y	9931514	9931515	+	IGR	DEL	TT	-	-			TCGA-AK-3456-01A-02D-1386-10	TCGA-AK-3456-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:9931514_9931515delTT								TTTY22 (280660 upstream) : None (None downstream)																							tttctttatctttgacttttgg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	Y	27583214	27583215	+	IGR	INS	-	T	T			TCGA-AK-3456-01A-02D-1386-10	TCGA-AK-3456-10A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:27583214_27583215insT								DAZ4 (530034 upstream) : None (None downstream)																							AAAATATTTAGTTTTTTTTTTT	0.337													9	4	---	---	---	---	
